https://wiki.fkkt.uni-lj.si/api.php?action=feedcontributions&feedformat=atom&user=NfrauskokWiki FKKT - User contributions [en]2026-04-04T13:49:40ZUser contributionsMediaWiki 1.39.3https://wiki.fkkt.uni-lj.si/index.php?title=Dispersing_biofilms_with_engineered_enzymatic_bacteriophage&diff=15902Dispersing biofilms with engineered enzymatic bacteriophage2019-07-24T11:22:51Z<p>Nfrauskok: </p>
<hr />
<div>Izvorni članek: Lu, T., et al, Dispersing biofilms with engineered enzymatic bacteriophage, PNAS, 2007.<ref>[http://www.pnas.org/content/104/27/11197]</ref><br />
<br />
== Introduction ==<br />
<br />
When faced with certain challenges in various living habitats, bacteria have the ability to form biofilms, or organized aggregates of microorganisms living within an extracellular polymeric matrix (EPM) <ref name="jamal">https://www.ncbi.nlm.nih.gov/pubmed/29042186</ref>. The complex EPM is formed by heterogeneous extracellular polymeric substances (EPS), which is occupied mostly by water (97%) and other macromolecules in lower concentrations (proteins (~2%), polysaccharides (1-2%); nucleic acids (<1%) and ions (bound and free)) <ref name="jamal" />. This organized communities are formed on either biological or non-biological surfaces, and allow bacterium to surpass harsh environmental conditions, such as UV exposure, metal toxicity, acid exposure, dehydration and salinity, phagocytosis and several antibiotics and antimicrobial agents <ref name="dva">https://www.ncbi.nlm.nih.gov/pubmed/15040259</ref>. The ability to surpass latter conditions represent a challenge in the medical, industrial and food branches, as biofilm formation accounts for over 65% of microbial infections, and over 80% of chronic infections based on the statistics from the National Institutes of Health <ref name="dva" />. Due to the concerning numbers, and the rise of antibiotic resistance, a novel and effective treatment for bacterial biofilms is necessary. The main target in biofilm degradation is disruption of the EPM, more precisely to target the EPS and mechanism involved in EPS production and secretion (DNase, exopolysaccharides, protein components, cGMP/cAMP levels, signal and secretion pathways) <ref>[https://www.ncbi.nlm.nih.gov/pubmed/28944770]</ref>. In the following paper, we will show a potential treatment with synthetically engineered bacteriophages that possess the enzymatic ability to disperse bacterial biofilms.<br />
<br />
== Bacteriophages and biofilms ==<br />
<br />
The use of bacteriophages against bacterial infections is not a novelty method, as it is dates from the early 20th century. With the growing knowledge of engineering and manipulating biological organisms, and the highly annotated phage genome, makes bacteriophages prime candidates for targeting biofilms. Bacteriophages are viruses that infect and replicate within bacteria, and in comparison with antibiotics and other antimicrobial agents, possess the ability to penetrate biofilms, and disperse biofilms by various proposed mechanisms <ref>[https://www.ncbi.nlm.nih.gov/pubmed/23306440]</ref> <ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790368/]</ref>. As mentioned above, enzymatic targeting exopolysaccharides with EPS-degrading is one of the possible strategies for targeting biofilms <ref name="tri" />. The challenge lies in isolating a natural phage that is both specific for the bacteria to be targeted and expresses a relevant EPS-degrading enzyme. The solution lies in designing an artificial biofilm-degrading bacteriophage that express a specific EPS-degrading enzyme. <br />
<br />
== Dispersin B==<br />
<br />
While studying the strain A. actinomycetemcomitans which causes periodontal disease in adolescents and its biofilm formation and degradation properties for disease spreading, researchers have come upon a novel specific biofilm-releasing glycoside hydrolase <ref name="tri">https://www.ncbi.nlm.nih.gov/pubmed/15878175</ref>. This novel protein disperin B or DspB has the ability to degrade an important EPS polysaccharide adhesin known as β-1,6-N-acetyl-D-glucosamine <ref name="tri" />. N-acetyl-D-glucosamine residues form various polymeric structures with their linear β-1,6-linkages, such as PIA and PNAG (abbreviations)<ref name="tri" />. By hydrolyzing polymers, the protein disrupts the formation of the biofilm matrix and allows adherent cells to be released <ref name="tri" />. From a structural point of view, disperin B consist of a single domain with intertwining α/β structures <ref name="tri" />. The protein is a member of the 20 β-hexosaminidases family (GH-20), and has a highly conserved acidic active site (D183, E184, E332) which cleaves terminal monosaccharide residues from the non-reducing end of the polymers <ref name="tri" />.<br />
<br />
== Design of enzymatically active bacteriophage ==<br />
<br />
Once a suitable protein for biofilm removal that covers a wide specter was found, the design of engineered bacteriophages could commence. The idea is based on exploiting the lytic phage life cycle, which is based on hijacking the cell machinery, and synthesizing components of the phage genome <ref name="cet">https://www.ncbi.nlm.nih.gov/pubmed/12776216</ref>. Once all sufficient components are available, the phages reassembles inside the cell, causing the cell to burst and releasing its component in to the local environment <ref name="cet" />. This two-pronged attack strategy, would exploit the enzyme to remove bacterial biofilm, and the phage infections to lyse cells, while achieving high concentrations of the enzyme and lytic phage. The backbone of the design is based on using an E.coli specific lytic T7 phage, which was modified in a way that it had a few of nonessential gene deletions. The T7 phage had one of the first completely sequenced genomes (40-kb) that codes for 55 proteins <ref name="pet">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525648/</ref>. The T7 is widely used in molecular biology and has various traits that make this strain suitable for phage experiments <ref name="pet" />. The biofilm removing T7 phage was design to express DspB under the strong control of T7 ϕ10 promoter intracellularly during the infection, so that it could be released in to the environment upon cell lysis. The experiment was focused on strains that possess the F-plasmid, as it enhances biofilm maturation, and forms more thick biofilms, making them a more appealing group. Bacterial strains that contain the F-plasmid can disrupt efficient T7 replication. To tackle this problem, they inserted a 1.2 gene from T3 phage so the phage would not be limited only to strains that lack the F-plasmid, but to widen the spectrum of target <ref name="set">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208987/</ref>. Gene 1.2 is an inhibitor of the host dGTPase, which is involved in the process of DNA replication <ref name="set" />. A control was designed by cloning an S-tag into the T7 genome, to assure quality results. The phages were named T7DspB and T7Control respectively.<br />
<br />
== Characterization of enzymatically active bacteriophage ==<br />
<br />
The first task was to determine if T7DspB was more effective against biofilms than T7Control. Effectiveness of modified phages was also compared to wild-type T3 and T7 phages to determine if modified phages possess an edge over natural occurring ones. To measure effectiveness, crystal violet (CV) methods was used, which is based on staining attached cells (in our case bacterial cells/biofilms) with crystal violet dye, which binds to proteins and DNA <ref name="ket">https://www.ncbi.nlm.nih.gov/pubmed/27037069/</ref>. Those cells that undergo cell death lose their adherence, which shows as reducing amount of CV staining in a culture <ref name="ket" />. Absorbance (A600) measurement after a 24 h treatment period had shown that T7DspB phage removes biofilms with more efficiency than wild-type and especially T7Control. To confirm primary results, additional test such as sonication were ran, to obtain viable cell counts (CFU per peg) for bacteria surviving in biofilms after treatment. The results show consistency with CV, and confirm that T7DspB shows much more promising signs of biofilm removal than other tested phages, especially in comparison with T7Control. As mentioned above, the idea is based on a two-pronged attack strategy. Promising results were obtained for enzymatic activity of DspB, but also we have to ensure that phages sustain sufficient replication. PFU counts from microtiter plate wells and biofilms (after sonication) show that PFU counts were significantly higher in plates than biofilms, and that overall PFU surpassed initial 10<sup>3</sup> PFU by a few orders of magnitude which confirms efficient phage multiplication. <br />
<br />
== Time courses and dose-response for enzymatically active bacteriophage treatment ==<br />
<br />
Experiments to optimize the time-course and dose-response for both enzymatic activity and phage replication were carried out. Time-course results shown that after a 24h period of treatment, T7DspB had biofilms cell densities of two magnitudes lower than T7Control and 99,9% in comparison with untreated biofilms. Further on, time dependence on phage replication was tested, and showed that both T7Control and T7DspB began to multiply rapidly after inoculation in a similar fashion. Dosage response showed that T7DspB had lower cell densities at starting inoculation levels (PFU 10<sup>2</sup>) than T7Control, while higher inoculation concentrations showed even more efficiency against removing biofilms. Phage dosage tested exhibited phage multiplication within the biofilm.<br />
<br />
== Discussion ==<br />
<br />
The following experiments have shown that enzymatically modified phage shows greater efficiency in biofilm removal than natural accruing phages. Future improvements to this design may include directed evolution for optimal enzyme activity, delaying cell lysis or using multiple phage promoters to allow for increased enzyme production, targeting multiple biofilm EPS components with different proteins as well as targeting multi-species biofilm with a mixture of different species-specific engineered enzymatically active phage, and combination therapy with antibiotics and phage to improve the efficacy of both types of treatment. This strategy allows opens a possibility of establishing a library of biofilm dispersing phage. The upside of this method is that it does not need to deliver, express and purify large enzyme concentrations to the site of infection. This type of phage therapy should be looked into as additional therapy for treating bacterial biofilms in various industries, but not before several challenges are overcome. Firstly, a properly designed clinical trial is needed, which will tackle the problems such as phage development resistance, immunogenicity in humans, body clearance, release of toxins after cell lysis and phage specificity. Once all the challenges are overcome, phage therapy against biofilms will be considered as our first line of defense.<br />
<br />
== References ==<br />
[1]. Lu, T., et al., Dispersing biofilms with engineered enzymatic bacteriophage, ''PNAS'', 2007.<br />
<br />
[2]. Jamal, M., et al., Bacterial biofilm and associated infections, ''Journal of the Chinese Medical Association'', 2017.<br />
<br />
[3]. Hall-Stoodley, L., et al., Bacterial biofilms: From the natural environment to infectious disease, ''Nature Reviews'', 2004.<br />
<br />
[4]. Koo, H., et al., Targeting microbial biofilms: current and prospective therapeutic strategies, ''Nature Reviews'', 2017.<br />
<br />
[5]. Hu, B., et al., The bacteriophage t7 virion undergoes extensive structural remodeling during infection, ''Science'', 2013.<br />
<br />
[6]. Harper, D., et al., Bacteriophages and Biofilms, ''Antibiotics'', 2014.<br />
<br />
[7]. Ramasubbu, N., et al., Structural Analysis of Dispersin B, a Biofilm-releasing Glycoside Hydrolase from the Periodontopathogen Actinobacillus actinomycetemcomitans, ''Journal of Molecular Biology'', 2005.<br />
<br />
[8]. Campbell, A., The future of bacteriophage biology, ''Nature Reviews'', 2003.<br />
<br />
[9]. Serwer, P., et al., Evidence for bacteriophage T7 tail extension during DNA injection, ''BMC Research Notes'', 2008.<br />
<br />
[10]. Schmitt, C.K., et al., Genes 1.2 and 10 of bacteriophages T3 and T7 determine the permeability lesions observed in infected cells of Escherichia coli expressing the F plasmid gene pifA, ''Journal of Bacteriology'', 1991. <br />
<br />
[11]. Feoktistova, M., et al., Crystal Violet Assay for Determining Viability of Cultured Cells, ''Cold Spring Harbor Protocols'', 2018.<br />
<br />
=Abbreviation=<br />
<br />
extracellular polymeric matrix (EPM)<br />
<br />
extracellular polymeric substances (EPS)<br />
<br />
partially deacetylated Poly-β-1,6-N-Acetyl-glucosamine(PIA) <br />
<br />
Poly-β-1,6-N-Acetyl-glucosamine (PNAG)<br />
<br />
crystal violet (CV)</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Dispersing_biofilms_with_engineered_enzymatic_bacteriophage&diff=15901Dispersing biofilms with engineered enzymatic bacteriophage2019-07-23T16:50:42Z<p>Nfrauskok: /* References */</p>
<hr />
<div>Izvorni članek: Lu, T., et al, Dispersing biofilms with engineered enzymatic bacteriophage, PNAS, 2007.<ref>[http://www.pnas.org/content/104/27/11197]</ref><br />
<br />
== Introduction ==<br />
<br />
When faced with certain challenges in various living habitats, bacteria have the ability to form biofilms, or organized aggregates of microorganisms living within an extracellular polymeric matrix (EPM) <ref name="jamal">https://www.ncbi.nlm.nih.gov/pubmed/29042186</ref>. The complex EPM is formed by heterogeneous extracellular polymeric substances (EPS), which is occupied mostly by water (97%) and other macromolecules in lower concentrations (proteins (~2%), polysaccharides (1-2%); nucleic acids (<1%) and ions (bound and free)) <ref name="jamal" />. This organized communities are formed on either biological or non-biological surfaces, and allow bacterium to surpass harsh environmental conditions, such as UV exposure, metal toxicity, acid exposure, dehydration and salinity, phagocytosis and several antibiotics and antimicrobial agents <ref name="dva">https://www.ncbi.nlm.nih.gov/pubmed/15040259</ref>. The ability to surpass latter conditions represent a challenge in the medical, industrial and food branches, as biofilm formation accounts for over 65% of microbial infections, and over 80% of chronic infections based on the statistics from the National Institutes of Health <ref name="dva" />. Due to the concerning numbers, and the rise of antibiotic resistance, a novel and effective treatment for bacterial biofilms is necessary. The main target in biofilm degradation is disruption of the EPM, more precisely to target the EPS and mechanism involved in EPS production and secretion (DNase, exopolysaccharides, protein components, cGMP/cAMP levels, signal and secretion pathways) <ref>[https://www.ncbi.nlm.nih.gov/pubmed/28944770]</ref>. In the following paper, we will show a potential treatment with synthetically engineered bacteriophages that possess the enzymatic ability to disperse bacterial biofilms.<br />
<br />
== Bacteriophages and biofilms ==<br />
<br />
The use of bacteriophages against bacterial infections is not a novelty method, as it is dates from the early 20th century. With the growing knowledge of engineering and manipulating biological organisms, and the highly annotated phage genome, makes bacteriophages prime candidates for targeting biofilms. Bacteriophages are viruses that infect and replicate within bacteria, and in comparison with antibiotics and other antimicrobial agents, possess the ability to penetrate biofilms, and disperse biofilms by various proposed mechanisms <ref>[https://www.ncbi.nlm.nih.gov/pubmed/23306440]</ref> <ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790368/]</ref>. As mentioned above, enzymatic targeting exopolysaccharides with EPS-degrading is one of the possible strategies for targeting biofilms <ref name="tri" />. The challenge lies in isolating a natural phage that is both specific for the bacteria to be targeted and expresses a relevant EPS-degrading enzyme. The solution lies in designing an artificial biofilm-degrading bacteriophage that express a specific EPS-degrading enzyme. <br />
<br />
== Dispersin B==<br />
<br />
While studying the strain A. actinomycetemcomitans which causes periodontal disease in adolescents and its biofilm formation and degradation properties for disease spreading, researchers have come upon a novel specific biofilm-releasing glycoside hydrolase <ref name="tri">https://www.ncbi.nlm.nih.gov/pubmed/15878175</ref>. This novel protein disperin B or DspB has the ability to degrade an important EPS polysaccharide adhesin known as β-1,6-N-acetyl-D-glucosamine <ref name="tri" />. N-acetyl-D-glucosamine residues form various polymeric structures with their linear β-1,6-linkages, such as PIA, PNAG, PGA (abbreviations)<ref name="tri" />. By hydrolyzing polymers, the protein disrupts the formation of the biofilm matrix and allows adherent cells to be released <ref name="tri" />. From a structural point of view, disperin B consist of a single domain with intertwining α/β structures <ref name="tri" />. The protein is a member of the 20 β-hexosaminidases family (GH-20), and has a highly conserved acidic active site (D183, E184, E332) which cleaves terminal monosaccharide residues from the non-reducing end of the polymers <ref name="tri" />.<br />
<br />
== Design of enzymatically active bacteriophage ==<br />
<br />
Once a suitable protein for biofilm removal that covers a wide specter was found, the design of engineered bacteriophages could commence. The idea is based on exploiting the lytic phage life cycle, which is based on hijacking the cell machinery, and synthesizing components of the phage genome <ref name="cet">https://www.ncbi.nlm.nih.gov/pubmed/12776216</ref>. Once all sufficient components are available, the phages reassembles inside the cell, causing the cell to burst and releasing its component in to the local environment <ref name="cet" />. This two-pronged attack strategy, would exploit the enzyme to remove bacterial biofilm, and the phage infections to lyse cells, while achieving high concentrations of the enzyme and lytic phage. The backbone of the design is based on using an E.coli specific lytic T7 phage, which was modified in a way that it had a few of nonessential gene deletions. The T7 phage had one of the first completely sequenced genomes (40-kb) that codes for 55 proteins <ref name="pet">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525648/</ref>. The T7 is widely used in molecular biology and has various traits that make this strain suitable for phage experiments <ref name="pet" />. The biofilm removing T7 phage was design to express DspB under the strong control of T7 ϕ10 promoter intracellularly during the infection, so that it could be released in to the environment upon cell lysis. The experiment was focused on strains that possess the F-plasmid, as it enhances biofilm maturation, and forms more thick biofilms, making them a more appealing group. Bacterial strains that contain the F-plasmid can disrupt efficient T7 replication. To tackle this problem, they inserted a 1.2 gene from T3 phage so the phage would not be limited only to strains that lack the F-plasmid, but to widen the spectrum of target <ref name="set">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208987/</ref>. Gene 1.2 is an inhibitor of the host dGTPase, which is involved in the process of DNA replication <ref name="set" />. A control was designed by cloning an S-tag into the T7 genome, to assure quality results. The phages were named T7DspB and T7Control respectively.<br />
<br />
== Characterization of enzymatically active bacteriophage ==<br />
<br />
The first task was to determine if T7DspB was more effective against biofilms than T7Control. Effectiveness of modified phages was also compared to wild-type T3 and T7 phages to determine if modified phages possess an edge over natural occurring ones. To measure effectiveness, crystal violet (CV) methods was used, which is based on staining attached cells (in our case bacterial cells/biofilms) with crystal violet dye, which binds to proteins and DNA <ref name="ket">https://www.ncbi.nlm.nih.gov/pubmed/27037069/</ref>. Those cells that undergo cell death lose their adherence, which shows as reducing amount of CV staining in a culture <ref name="ket" />. Absorbance (A600) measurement after a 24 h treatment period had shown that T7DspB phage removes biofilms with more efficiency than wild-type and especially T7Control. To confirm primary results, additional test such as sonication were ran, to obtain viable cell counts (CFU per peg) for bacteria surviving in biofilms after treatment. The results show consistency with CV, and confirm that T7DspB shows much more promising signs of biofilm removal than other tested phages, especially in comparison with T7Control. As mentioned above, the idea is based on a two-pronged attack strategy. Promising results were obtained for enzymatic activity of DspB, but also we have to ensure that phages sustain sufficient replication. PFU counts from microtiter plate wells and biofilms (after sonication) show that PFU counts were significantly higher in plates than biofilms, and that overall PFU surpassed initial 10<sup>3</sup> PFU by a few orders of magnitude which confirms efficient phage multiplication. <br />
<br />
== Time courses and dose-response for enzymatically active bacteriophage treatment ==<br />
<br />
Experiments to optimize the time-course and dose-response for both enzymatic activity and phage replication were carried out. Time-course results shown that after a 24h period of treatment, T7DspB had biofilms cell densities of two magnitudes lower than T7Control and 99,9% in comparison with untreated biofilms. Further on, time dependence on phage replication was tested, and showed that both T7Control and T7DspB began to multiply rapidly after inoculation in a similar fashion. Dosage response showed that T7DspB had lower cell densities at starting inoculation levels (PFU 10<sup>2</sup>) than T7Control, while higher inoculation concentrations showed even more efficiency against removing biofilms. Phage dosage tested exhibited phage multiplication within the biofilm.<br />
<br />
== Discussion ==<br />
<br />
The following experiments have shown that enzymatically modified phage shows greater efficiency in biofilm removal than natural accruing phages. Future improvements to this design may include directed evolution for optimal enzyme activity, delaying cell lysis or using multiple phage promoters to allow for increased enzyme production, targeting multiple biofilm EPS components with different proteins as well as targeting multi-species biofilm with a mixture of different species-specific engineered enzymatically active phage, and combination therapy with antibiotics and phage to improve the efficacy of both types of treatment. This strategy allows opens a possibility of establishing a library of biofilm dispersing phage. The upside of this method is that it does not need to deliver, express and purify large enzyme concentrations to the site of infection. This type of phage therapy should be looked into as additional therapy for treating bacterial biofilms in various industries, but not before several challenges are overcome. Firstly, a properly designed clinical trial is needed, which will tackle the problems such as phage development resistance, immunogenicity in humans, body clearance, release of toxins after cell lysis and phage specificity. Once all the challenges are overcome, phage therapy against biofilms will be considered as our first line of defense.<br />
<br />
== References ==<br />
[1]. Lu, T., et al., Dispersing biofilms with engineered enzymatic bacteriophage, ''PNAS'', 2007.<br />
<br />
[2]. Jamal, M., et al., Bacterial biofilm and associated infections, ''Journal of the Chinese Medical Association'', 2017.<br />
<br />
[3]. Hall-Stoodley, L., et al., Bacterial biofilms: From the natural environment to infectious disease, ''Nature Reviews'', 2004.<br />
<br />
[4]. Koo, H., et al., Targeting microbial biofilms: current and prospective therapeutic strategies, ''Nature Reviews'', 2017.<br />
<br />
[5]. Hu, B., et al., The bacteriophage t7 virion undergoes extensive structural remodeling during infection, ''Science'', 2013.<br />
<br />
[6]. Harper, D., et al., Bacteriophages and Biofilms, ''Antibiotics'', 2014.<br />
<br />
[7]. Ramasubbu, N., et al., Structural Analysis of Dispersin B, a Biofilm-releasing Glycoside Hydrolase from the Periodontopathogen Actinobacillus actinomycetemcomitans, ''Journal of Molecular Biology'', 2005.<br />
<br />
[8]. Campbell, A., The future of bacteriophage biology, ''Nature Reviews'', 2003.<br />
<br />
[9]. Serwer, P., et al., Evidence for bacteriophage T7 tail extension during DNA injection, ''BMC Research Notes'', 2008.<br />
<br />
[10]. Schmitt, C.K., et al., Genes 1.2 and 10 of bacteriophages T3 and T7 determine the permeability lesions observed in infected cells of Escherichia coli expressing the F plasmid gene pifA, ''Journal of Bacteriology'', 1991. <br />
<br />
[11]. Feoktistova, M., et al., Crystal Violet Assay for Determining Viability of Cultured Cells, ''Cold Spring Harbor Protocols'', 2018.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Dispersing_biofilms_with_engineered_enzymatic_bacteriophage&diff=15900Dispersing biofilms with engineered enzymatic bacteriophage2019-07-23T16:48:02Z<p>Nfrauskok: </p>
<hr />
<div>Izvorni članek: Lu, T., et al, Dispersing biofilms with engineered enzymatic bacteriophage, PNAS, 2007.<ref>[http://www.pnas.org/content/104/27/11197]</ref><br />
<br />
== Introduction ==<br />
<br />
When faced with certain challenges in various living habitats, bacteria have the ability to form biofilms, or organized aggregates of microorganisms living within an extracellular polymeric matrix (EPM) <ref name="jamal">https://www.ncbi.nlm.nih.gov/pubmed/29042186</ref>. The complex EPM is formed by heterogeneous extracellular polymeric substances (EPS), which is occupied mostly by water (97%) and other macromolecules in lower concentrations (proteins (~2%), polysaccharides (1-2%); nucleic acids (<1%) and ions (bound and free)) <ref name="jamal" />. This organized communities are formed on either biological or non-biological surfaces, and allow bacterium to surpass harsh environmental conditions, such as UV exposure, metal toxicity, acid exposure, dehydration and salinity, phagocytosis and several antibiotics and antimicrobial agents <ref name="dva">https://www.ncbi.nlm.nih.gov/pubmed/15040259</ref>. The ability to surpass latter conditions represent a challenge in the medical, industrial and food branches, as biofilm formation accounts for over 65% of microbial infections, and over 80% of chronic infections based on the statistics from the National Institutes of Health <ref name="dva" />. Due to the concerning numbers, and the rise of antibiotic resistance, a novel and effective treatment for bacterial biofilms is necessary. The main target in biofilm degradation is disruption of the EPM, more precisely to target the EPS and mechanism involved in EPS production and secretion (DNase, exopolysaccharides, protein components, cGMP/cAMP levels, signal and secretion pathways) <ref>[https://www.ncbi.nlm.nih.gov/pubmed/28944770]</ref>. In the following paper, we will show a potential treatment with synthetically engineered bacteriophages that possess the enzymatic ability to disperse bacterial biofilms.<br />
<br />
== Bacteriophages and biofilms ==<br />
<br />
The use of bacteriophages against bacterial infections is not a novelty method, as it is dates from the early 20th century. With the growing knowledge of engineering and manipulating biological organisms, and the highly annotated phage genome, makes bacteriophages prime candidates for targeting biofilms. Bacteriophages are viruses that infect and replicate within bacteria, and in comparison with antibiotics and other antimicrobial agents, possess the ability to penetrate biofilms, and disperse biofilms by various proposed mechanisms <ref>[https://www.ncbi.nlm.nih.gov/pubmed/23306440]</ref> <ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790368/]</ref>. As mentioned above, enzymatic targeting exopolysaccharides with EPS-degrading is one of the possible strategies for targeting biofilms <ref name="tri" />. The challenge lies in isolating a natural phage that is both specific for the bacteria to be targeted and expresses a relevant EPS-degrading enzyme. The solution lies in designing an artificial biofilm-degrading bacteriophage that express a specific EPS-degrading enzyme. <br />
<br />
== Dispersin B==<br />
<br />
While studying the strain A. actinomycetemcomitans which causes periodontal disease in adolescents and its biofilm formation and degradation properties for disease spreading, researchers have come upon a novel specific biofilm-releasing glycoside hydrolase <ref name="tri">https://www.ncbi.nlm.nih.gov/pubmed/15878175</ref>. This novel protein disperin B or DspB has the ability to degrade an important EPS polysaccharide adhesin known as β-1,6-N-acetyl-D-glucosamine <ref name="tri" />. N-acetyl-D-glucosamine residues form various polymeric structures with their linear β-1,6-linkages, such as PIA, PNAG, PGA (abbreviations)<ref name="tri" />. By hydrolyzing polymers, the protein disrupts the formation of the biofilm matrix and allows adherent cells to be released <ref name="tri" />. From a structural point of view, disperin B consist of a single domain with intertwining α/β structures <ref name="tri" />. The protein is a member of the 20 β-hexosaminidases family (GH-20), and has a highly conserved acidic active site (D183, E184, E332) which cleaves terminal monosaccharide residues from the non-reducing end of the polymers <ref name="tri" />.<br />
<br />
== Design of enzymatically active bacteriophage ==<br />
<br />
Once a suitable protein for biofilm removal that covers a wide specter was found, the design of engineered bacteriophages could commence. The idea is based on exploiting the lytic phage life cycle, which is based on hijacking the cell machinery, and synthesizing components of the phage genome <ref name="cet">https://www.ncbi.nlm.nih.gov/pubmed/12776216</ref>. Once all sufficient components are available, the phages reassembles inside the cell, causing the cell to burst and releasing its component in to the local environment <ref name="cet" />. This two-pronged attack strategy, would exploit the enzyme to remove bacterial biofilm, and the phage infections to lyse cells, while achieving high concentrations of the enzyme and lytic phage. The backbone of the design is based on using an E.coli specific lytic T7 phage, which was modified in a way that it had a few of nonessential gene deletions. The T7 phage had one of the first completely sequenced genomes (40-kb) that codes for 55 proteins <ref name="pet">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525648/</ref>. The T7 is widely used in molecular biology and has various traits that make this strain suitable for phage experiments <ref name="pet" />. The biofilm removing T7 phage was design to express DspB under the strong control of T7 ϕ10 promoter intracellularly during the infection, so that it could be released in to the environment upon cell lysis. The experiment was focused on strains that possess the F-plasmid, as it enhances biofilm maturation, and forms more thick biofilms, making them a more appealing group. Bacterial strains that contain the F-plasmid can disrupt efficient T7 replication. To tackle this problem, they inserted a 1.2 gene from T3 phage so the phage would not be limited only to strains that lack the F-plasmid, but to widen the spectrum of target <ref name="set">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208987/</ref>. Gene 1.2 is an inhibitor of the host dGTPase, which is involved in the process of DNA replication <ref name="set" />. A control was designed by cloning an S-tag into the T7 genome, to assure quality results. The phages were named T7DspB and T7Control respectively.<br />
<br />
== Characterization of enzymatically active bacteriophage ==<br />
<br />
The first task was to determine if T7DspB was more effective against biofilms than T7Control. Effectiveness of modified phages was also compared to wild-type T3 and T7 phages to determine if modified phages possess an edge over natural occurring ones. To measure effectiveness, crystal violet (CV) methods was used, which is based on staining attached cells (in our case bacterial cells/biofilms) with crystal violet dye, which binds to proteins and DNA <ref name="ket">https://www.ncbi.nlm.nih.gov/pubmed/27037069/</ref>. Those cells that undergo cell death lose their adherence, which shows as reducing amount of CV staining in a culture <ref name="ket" />. Absorbance (A600) measurement after a 24 h treatment period had shown that T7DspB phage removes biofilms with more efficiency than wild-type and especially T7Control. To confirm primary results, additional test such as sonication were ran, to obtain viable cell counts (CFU per peg) for bacteria surviving in biofilms after treatment. The results show consistency with CV, and confirm that T7DspB shows much more promising signs of biofilm removal than other tested phages, especially in comparison with T7Control. As mentioned above, the idea is based on a two-pronged attack strategy. Promising results were obtained for enzymatic activity of DspB, but also we have to ensure that phages sustain sufficient replication. PFU counts from microtiter plate wells and biofilms (after sonication) show that PFU counts were significantly higher in plates than biofilms, and that overall PFU surpassed initial 10<sup>3</sup> PFU by a few orders of magnitude which confirms efficient phage multiplication. <br />
<br />
== Time courses and dose-response for enzymatically active bacteriophage treatment ==<br />
<br />
Experiments to optimize the time-course and dose-response for both enzymatic activity and phage replication were carried out. Time-course results shown that after a 24h period of treatment, T7DspB had biofilms cell densities of two magnitudes lower than T7Control and 99,9% in comparison with untreated biofilms. Further on, time dependence on phage replication was tested, and showed that both T7Control and T7DspB began to multiply rapidly after inoculation in a similar fashion. Dosage response showed that T7DspB had lower cell densities at starting inoculation levels (PFU 10<sup>2</sup>) than T7Control, while higher inoculation concentrations showed even more efficiency against removing biofilms. Phage dosage tested exhibited phage multiplication within the biofilm.<br />
<br />
== Discussion ==<br />
<br />
The following experiments have shown that enzymatically modified phage shows greater efficiency in biofilm removal than natural accruing phages. Future improvements to this design may include directed evolution for optimal enzyme activity, delaying cell lysis or using multiple phage promoters to allow for increased enzyme production, targeting multiple biofilm EPS components with different proteins as well as targeting multi-species biofilm with a mixture of different species-specific engineered enzymatically active phage, and combination therapy with antibiotics and phage to improve the efficacy of both types of treatment. This strategy allows opens a possibility of establishing a library of biofilm dispersing phage. The upside of this method is that it does not need to deliver, express and purify large enzyme concentrations to the site of infection. This type of phage therapy should be looked into as additional therapy for treating bacterial biofilms in various industries, but not before several challenges are overcome. Firstly, a properly designed clinical trial is needed, which will tackle the problems such as phage development resistance, immunogenicity in humans, body clearance, release of toxins after cell lysis and phage specificity. Once all the challenges are overcome, phage therapy against biofilms will be considered as our first line of defense.<br />
<br />
== References ==<br />
[2]. Jamal, M., et al., Bacterial biofilm and associated infections, ''Journal of the Chinese Medical Association'', 2017.<br />
<br />
[3]. Hall-Stoodley, L., et al., Bacterial biofilms: From the natural environment to infectious disease, ''Nature Reviews'', 2004.<br />
<br />
[4]. Koo, H., et al., Targeting microbial biofilms: current and prospective therapeutic strategies, ''Nature Reviews'', 2017.<br />
<br />
[5]. Hu, B., et al., The bacteriophage t7 virion undergoes extensive structural remodeling during infection, ''Science'', 2013.<br />
<br />
[6]. Harper, D., et al., Bacteriophages and Biofilms, ''Antibiotics'', 2014.<br />
<br />
[7]. Ramasubbu, N., et al., Structural Analysis of Dispersin B, a Biofilm-releasing Glycoside Hydrolase from the Periodontopathogen Actinobacillus actinomycetemcomitans, ''Journal of Molecular Biology'', 2005.<br />
<br />
[8]. Campbell, A., The future of bacteriophage biology, ''Nature Reviews'', 2003.<br />
<br />
[9]. Serwer, P., et al., Evidence for bacteriophage T7 tail extension during DNA injection, ''BMC Research Notes'', 2008.<br />
<br />
[10]. Schmitt, C.K., et al., Genes 1.2 and 10 of bacteriophages T3 and T7 determine the permeability lesions observed in infected cells of Escherichia coli expressing the F plasmid gene pifA, ''Journal of Bacteriology'', 1991. <br />
<br />
[11]. Feoktistova, M., et al., Crystal Violet Assay for Determining Viability of Cultured Cells, ''Cold Spring Harbor Protocols'', 2018.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Seminarji_SB_2018/19&diff=14533Seminarji SB 2018/192018-12-02T16:55:45Z<p>Nfrauskok: </p>
<hr />
<div>V študijskem letu 2018/19 študentje predstavljajo naslednje teme: <br />
<br />
RAZISKOVALNI ČLANKI<br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do izhodiščnega članka na spletu.) <br><br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/MoClo:_modularni_klonirni_sistem_za_standardizirano_sestavljanje_ve%C4%8Dgenskih_konstruktov MoClo: modularni klonirni sistem za standardizirano sestavljanje večgenskih konstruktov] (Valentina Levak)<br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/RNA-stikala_tipa_%C2%BBToehold%C2%AB:_de_novo_oblikovani_regulatorji_izra%C5%BEanja_genov RNA-stikala tipa Toehold: de novo oblikovani regulatorji izražanja genov] (Špela Malenšek)<br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/Raznoliko_in_modelno_zasnovana_priprava_sinteti%C4%8Dnih_genskih_vezij_s_predvidenimi_lastnostmi Raznoliko in modelno zasnovana priprava sintetičnih genskih vezij s predvidenimi lastnostmi] (Matej Kolarič)<br />
<br />
[[Dispersing biofilms with engineered enzymatic bacteriophage]] (Fran Krstanović)<br />
<br />
<br />
NAGRAJENI ŠTUDENTSKI PROJEKTI <br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do wiki strani študentske ekipe, katere projekt opisujete.) <br><br />
<br />
<br />
<br />
<br />
Povzetki v slovenščini naj imajo 1200-1500 besed (viri v to vsoto ne štejejo). Predstavitev seminarja naj bo dolga 15 minut (13-17). Sledila bo razprava, ki praviloma ne bo daljša od 5 minut. <br />
<br />
----<br />
<br />
<br />
Razpored po datumih predstavitev (pri vsakem terminu je navedeno število možnih seminarjev; vpišite ime in priimek pri dnevu, ko želite predstaviti seminar ter dopišite naslov seminarja, ki naj bo povezan s povzetkom): <br />
<br />
22.11.<br> <br />
1 <br><br />
2 Valentina Levak <br><br />
<br />
27.11.<br><br />
1 <br><br />
2 <br><br />
3 <br><br />
4 <br><br />
<br />
29.11.<br><br />
1 Matej Kolarič<br><br />
2 Špela Malenšek<br><br />
3 <br><br />
4 <br><br />
<br />
<br />
4.12.<br><br />
1 Gašper Žun<br><br />
2 Fran Krstanovic<br><br />
3 <br><br />
4 <br><br />
<br />
6.12.<br><br />
1 Urška Jelenovec<br><br />
2 Ernest Šprager<br><br />
3 Rok Miklavčič <br><br />
4 <br><br />
<br />
11.12.<br><br />
1 Jerneja Ovčar<br><br />
2 Neža Koritnik<br><br />
3 Gašper Virant<br><br />
4 Gašper Marinšek<br><br />
<br />
18.12.<br><br />
1 Tina Požun<br><br />
2 Anamarija Habič<br><br />
3 Roberta Mulac<br><br />
4 Kity Požek<br><br />
<br />
3.1.<br><br />
1 Urška Kašnik<br><br />
2 Nina Mavec<br><br />
3 Primož Tič<br><br />
4 Milena Stojkovska<br><br />
<br />
8.1.<br><br />
1 Marija Atanasova<br><br />
2 Bine Tršavec<br><br />
3 Peter Pečan<br><br />
4 Tjaša Sorčan<br><br />
<br />
10.1.<br><br />
1 Špela Koren<br><br />
2 Natalija Pucihar<br><br />
3 Karmen Žbogar<br><br />
4 Uroš Zavrtanik<br><br />
<br />
15.1.<br><br />
1 Jerneja Kocutar<br><br />
2 Blaž Lebar<br><br />
3 Tadej Satler<br><br />
4 Miha Koprivnikar Krajnc<br></div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Dispersing_biofilms_with_engineered_enzymatic_bacteriophage&diff=14532Dispersing biofilms with engineered enzymatic bacteriophage2018-12-02T16:54:37Z<p>Nfrauskok: New page: Izvorni članek: Lu, T., et al, Dispersing biofilms with engineered enzymatic bacteriophage, PNAS, 2007.<ref>[http://www.pnas.org/content/104/27/11197]</ref> == Introduction == When face...</p>
<hr />
<div>Izvorni članek: Lu, T., et al, Dispersing biofilms with engineered enzymatic bacteriophage, PNAS, 2007.<ref>[http://www.pnas.org/content/104/27/11197]</ref><br />
<br />
== Introduction ==<br />
<br />
When faced with certain challenges in various living habitats, bacteria have the ability to form biofilms, or organized aggregates of microorganisms living within an extracellular polymeric matrix (EPM) <ref name="jamal">https://www.ncbi.nlm.nih.gov/pubmed/29042186</ref>. The complex EPM is formed by heterogeneous extracellular polymeric substances (EPS), which is occupied mostly by water (97%) and other macromolecules in lower concentrations (proteins (~2%), polysaccharides (1-2%); nucleic acids (<1%) and ions (bound and free)) <ref name="jamal" />. This organized communities are formed on either biological or non-biological surfaces, and allow bacterium to surpass harsh environmental conditions, such as UV exposure, metal toxicity, acid exposure, dehydration and salinity, phagocytosis and several antibiotics and antimicrobial agents <ref name="dva">https://www.ncbi.nlm.nih.gov/pubmed/15040259</ref>. The ability to surpass latter conditions represent a challenge in the medical, industrial and food branches, as biofilm formation accounts for over 65% of microbial infections, and over 80% of chronic infections based on the statistics from the National Institutes of Health <ref name="dva" />. Due to the concerning numbers, and the rise of antibiotic resistance, a novel and effective treatment for bacterial biofilms is necessary. The main target in biofilm degradation is disruption of the EPM, more precisely to target the EPS and mechanism involved in EPS production and secretion (DNase, exopolysaccharides, protein components, cGMP/cAMP levels, signal and secretion pathways) <ref>[https://www.ncbi.nlm.nih.gov/pubmed/28944770]</ref>. In the following paper, we will show a potential treatment with synthetically engineered bacteriophages that possess the enzymatic ability to disperse bacterial biofilms. <br />
<br />
== Bacteriophages and biofilms ==<br />
<br />
The use of bacteriophages against bacterial infections is not a novelty method, as it is dates from the early 20th century. With the growing knowledge of engineering and manipulating biological organisms, and the highly annotated phage genome, makes bacteriophages prime candidates for targeting biofilms. Bacteriophages are viruses that infect and replicate within bacteria, and in comparison with antibiotics and other antimicrobial agents, possess the ability to penetrate biofilms, and disperse biofilms by various proposed mechanisms <ref>[https://www.ncbi.nlm.nih.gov/pubmed/23306440]</ref> <ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790368/]</ref>. As mentioned above, enzymatic targeting exopolysaccharides with EPS-degrading is one of the possible strategies for targeting biofilms <ref name="tri" />. The challenge lies in isolating a natural phage that is both specific for the bacteria to be targeted and expresses a relevant EPS-degrading enzyme. The solution lies in designing an artificial biofilm-degrading bacteriophage that express a specific EPS-degrading enzyme. <br />
<br />
== Dispersin B==<br />
<br />
While studying the strain A. actinomycetemcomitans which causes periodontal disease in adolescents and its biofilm formation and degradation properties for disease spreading, researchers have come upon a novel specific biofilm-releasing glycoside hydrolase <ref name="tri">https://www.ncbi.nlm.nih.gov/pubmed/15878175</ref>. This novel protein disperin B or DspB has the ability to degrade an important EPS polysaccharide adhesin known as β-1,6-N-acetyl-D-glucosamine <ref name="tri" />. N-acetyl-D-glucosamine residues form various polymeric structures with their linear β-1,6-linkages, such as PIA, PNAG, PGA (abbreviations)<ref name="tri" />. By hydrolyzing polymers, the protein disrupts the formation of the biofilm matrix and allows adherent cells to be released <ref name="tri" />. From a structural point of view, disperin B consist of a single domain with intertwining α/β structures <ref name="tri" />. The protein is a member of the 20 β-hexosaminidases family (GH-20), and has a highly conserved acidic active site (D183, E184, E332) which cleaves terminal monosaccharide residues from the non-reducing end of the polymers <ref name="tri" />.<br />
<br />
== Design of enzymatically active bacteriophage ==<br />
<br />
Once a suitable protein for biofilm removal that covers a wide specter was found, the design of engineered bacteriophages could commence. The idea is based on exploiting the lytic phage life cycle, which is based on hijacking the cell machinery, and synthesizing components of the phage genome <ref name="cet">https://www.ncbi.nlm.nih.gov/pubmed/12776216</ref>. Once all sufficient components are available, the phages reassembles inside the cell, causing the cell to burst and releasing its component in to the local environment <ref name="cet" />. This two-pronged attack strategy, would exploit the enzyme to remove bacterial biofilm, and the phage infections to lyse cells, while achieving high concentrations of the enzyme and lytic phage. The backbone of the design is based on using an E.coli specific lytic T7 phage, which was modified in a way that it had a few of nonessential gene deletions. The T7 phage had one of the first completely sequenced genomes (40-kb) that codes for 55 proteins <ref name="pet">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525648/</ref>. The T7 is widely used in molecular biology and has various traits that make this strain suitable for phage experiments <ref name="pet" />. The biofilm removing T7 phage was design to express DspB under the strong control of T7 ϕ10 promoter intracellularly during the infection, so that it could be released in to the environment upon cell lysis. The experiment was focused on strains that possess the F-plasmid, as it enhances biofilm maturation, and forms more thick biofilms, making them a more appealing group. Bacterial strains that contain the F-plasmid can disrupt efficient T7 replication. To tackle this problem, they inserted a 1.2 gene from T3 phage so the phage would not be limited only to strains that lack the F-plasmid, but to widen the spectrum of target <ref name="set">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208987/</ref>. Gene 1.2 is an inhibitor of the host dGTPase, which is involved in the process of DNA replication <ref name="set" />. A control was designed by cloning an S-tag into the T7 genome, to assure quality results. The phages were named T7DspB and T7Control respectively.<br />
<br />
== Characterization of enzymatically active bacteriophage ==<br />
<br />
The first task was to determine if T7DspB was more effective against biofilms than T7Control. Effectiveness of modified phages was also compared to wild-type T3 and T7 phages to determine if modified phages possess an edge over natural occurring ones. To measure effectiveness, crystal violet (CV) methods was used, which is based on staining attached cells (in our case bacterial cells/biofilms) with crystal violet dye, which binds to proteins and DNA <ref name="ket">https://www.ncbi.nlm.nih.gov/pubmed/27037069/</ref>. Those cells that undergo cell death lose their adherence, which shows as reducing amount of CV staining in a culture <ref name="ket" />. Absorbance (A600) measurement after a 24 h treatment period had shown that T7DspB phage removes biofilms with more efficiency than wild-type and especially T7Control. To confirm primary results, additional test such as sonication were ran, to obtain viable cell counts (CFU per peg) for bacteria surviving in biofilms after treatment. The results show consistency with CV, and confirm that T7DspB shows much more promising signs of biofilm removal than other tested phages, especially in comparison with T7Control. As mentioned above, the idea is based on a two-pronged attack strategy. Promising results were obtained for enzymatic activity of DspB, but also we have to ensure that phages sustain sufficient replication. PFU counts from microtiter plate wells and biofilms (after sonication) show that PFU counts were significantly higher in plates than biofilms, and that overall PFU surpassed initial 10<sup>3</sup> PFU by a few orders of magnitude which confirms efficient phage multiplication. <br />
<br />
== Time courses and dose-response for enzymatically active bacteriophage treatment ==<br />
<br />
Experiments to optimize the time-course and dose-response for both enzymatic activity and phage replication were carried out. Time-course results shown that after a 24h period of treatment, T7DspB had biofilms cell densities of two magnitudes lower than T7Control and 99,9% in comparison with untreated biofilms. Further on, time dependence on phage replication was tested, and showed that both T7Control and T7DspB began to multiply rapidly after inoculation in a similar fashion. Dosage response showed that T7DspB had lower cell densities at starting inoculation levels (PFU 10<sup>2</sup>) than T7Control, while higher inoculation concentrations showed even more efficiency against removing biofilms. Phage dosage tested exhibited phage multiplication within the biofilm.<br />
<br />
== Discussion ==<br />
<br />
The following experiments have shown that enzymatically modified phage shows greater efficiency in biofilm removal than natural accruing phages. Future improvements to this design may include directed evolution for optimal enzyme activity, delaying cell lysis or using multiple phage promoters to allow for increased enzyme production, targeting multiple biofilm EPS components with different proteins as well as targeting multi-species biofilm with a mixture of different species-specific engineered enzymatically active phage, and combination therapy with antibiotics and phage to improve the efficacy of both types of treatment. This strategy allows opens a possibility of establishing a library of biofilm dispersing phage. The upside of this method is that it does not need to deliver, express and purify large enzyme concentrations to the site of infection. This type of phage therapy should be looked into as additional therapy for treating bacterial biofilms in various industries, but not before several challenges are overcome. Firstly, a properly designed clinical trial is needed, which will tackle the problems such as phage development resistance, immunogenicity in humans, body clearance, release of toxins after cell lysis and phage specificity. Once all the challenges are overcome, phage therapy against biofilms will be considered as our first line of defense.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Seminarji_SB_2018/19&diff=14531Seminarji SB 2018/192018-12-02T16:54:13Z<p>Nfrauskok: </p>
<hr />
<div>V študijskem letu 2018/19 študentje predstavljajo naslednje teme: <br />
<br />
RAZISKOVALNI ČLANKI<br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do izhodiščnega članka na spletu.) <br><br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/MoClo:_modularni_klonirni_sistem_za_standardizirano_sestavljanje_ve%C4%8Dgenskih_konstruktov MoClo: modularni klonirni sistem za standardizirano sestavljanje večgenskih konstruktov] (Valentina Levak)<br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/RNA-stikala_tipa_%C2%BBToehold%C2%AB:_de_novo_oblikovani_regulatorji_izra%C5%BEanja_genov RNA-stikala tipa Toehold: de novo oblikovani regulatorji izražanja genov] (Špela Malenšek)<br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/Raznoliko_in_modelno_zasnovana_priprava_sinteti%C4%8Dnih_genskih_vezij_s_predvidenimi_lastnostmi Raznoliko in modelno zasnovana priprava sintetičnih genskih vezij s predvidenimi lastnostmi] (Matej Kolarič)<br />
<br />
[[Dispersing biofilms with engineered enzymatic bacteriophage]]<br />
<br />
<br />
NAGRAJENI ŠTUDENTSKI PROJEKTI <br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do wiki strani študentske ekipe, katere projekt opisujete.) <br><br />
<br />
<br />
<br />
<br />
Povzetki v slovenščini naj imajo 1200-1500 besed (viri v to vsoto ne štejejo). Predstavitev seminarja naj bo dolga 15 minut (13-17). Sledila bo razprava, ki praviloma ne bo daljša od 5 minut. <br />
<br />
----<br />
<br />
<br />
Razpored po datumih predstavitev (pri vsakem terminu je navedeno število možnih seminarjev; vpišite ime in priimek pri dnevu, ko želite predstaviti seminar ter dopišite naslov seminarja, ki naj bo povezan s povzetkom): <br />
<br />
22.11.<br> <br />
1 <br><br />
2 Valentina Levak <br><br />
<br />
27.11.<br><br />
1 <br><br />
2 <br><br />
3 <br><br />
4 <br><br />
<br />
29.11.<br><br />
1 Matej Kolarič<br><br />
2 Špela Malenšek<br><br />
3 <br><br />
4 <br><br />
<br />
<br />
4.12.<br><br />
1 Gašper Žun<br><br />
2 Fran Krstanovic<br><br />
3 <br><br />
4 <br><br />
<br />
6.12.<br><br />
1 Urška Jelenovec<br><br />
2 Ernest Šprager<br><br />
3 Rok Miklavčič <br><br />
4 <br><br />
<br />
11.12.<br><br />
1 Jerneja Ovčar<br><br />
2 Neža Koritnik<br><br />
3 Gašper Virant<br><br />
4 Gašper Marinšek<br><br />
<br />
18.12.<br><br />
1 Tina Požun<br><br />
2 Anamarija Habič<br><br />
3 Roberta Mulac<br><br />
4 Kity Požek<br><br />
<br />
3.1.<br><br />
1 Urška Kašnik<br><br />
2 Nina Mavec<br><br />
3 Primož Tič<br><br />
4 Milena Stojkovska<br><br />
<br />
8.1.<br><br />
1 Marija Atanasova<br><br />
2 Bine Tršavec<br><br />
3 Peter Pečan<br><br />
4 Tjaša Sorčan<br><br />
<br />
10.1.<br><br />
1 Špela Koren<br><br />
2 Natalija Pucihar<br><br />
3 Karmen Žbogar<br><br />
4 Uroš Zavrtanik<br><br />
<br />
15.1.<br><br />
1 Jerneja Kocutar<br><br />
2 Blaž Lebar<br><br />
3 Tadej Satler<br><br />
4 Miha Koprivnikar Krajnc<br></div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Seminarji_SB_2018/19&diff=14530Seminarji SB 2018/192018-12-02T16:51:19Z<p>Nfrauskok: </p>
<hr />
<div>V študijskem letu 2018/19 študentje predstavljajo naslednje teme: <br />
<br />
RAZISKOVALNI ČLANKI<br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do izhodiščnega članka na spletu.) <br><br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/MoClo:_modularni_klonirni_sistem_za_standardizirano_sestavljanje_ve%C4%8Dgenskih_konstruktov MoClo: modularni klonirni sistem za standardizirano sestavljanje večgenskih konstruktov] (Valentina Levak)<br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/RNA-stikala_tipa_%C2%BBToehold%C2%AB:_de_novo_oblikovani_regulatorji_izra%C5%BEanja_genov RNA-stikala tipa Toehold: de novo oblikovani regulatorji izražanja genov] (Špela Malenšek)<br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/Raznoliko_in_modelno_zasnovana_priprava_sinteti%C4%8Dnih_genskih_vezij_s_predvidenimi_lastnostmi Raznoliko in modelno zasnovana priprava sintetičnih genskih vezij s predvidenimi lastnostmi] (Matej Kolarič)<br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/Talk:Main_Page]<br />
<br />
<br />
NAGRAJENI ŠTUDENTSKI PROJEKTI <br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do wiki strani študentske ekipe, katere projekt opisujete.) <br><br />
<br />
<br />
<br />
<br />
Povzetki v slovenščini naj imajo 1200-1500 besed (viri v to vsoto ne štejejo). Predstavitev seminarja naj bo dolga 15 minut (13-17). Sledila bo razprava, ki praviloma ne bo daljša od 5 minut. <br />
<br />
----<br />
<br />
<br />
Razpored po datumih predstavitev (pri vsakem terminu je navedeno število možnih seminarjev; vpišite ime in priimek pri dnevu, ko želite predstaviti seminar ter dopišite naslov seminarja, ki naj bo povezan s povzetkom): <br />
<br />
22.11.<br> <br />
1 <br><br />
2 Valentina Levak <br><br />
<br />
27.11.<br><br />
1 <br><br />
2 <br><br />
3 <br><br />
4 <br><br />
<br />
29.11.<br><br />
1 Matej Kolarič<br><br />
2 Špela Malenšek<br><br />
3 <br><br />
4 <br><br />
<br />
<br />
4.12.<br><br />
1 Gašper Žun<br><br />
2 Fran Krstanovic<br><br />
3 <br><br />
4 <br><br />
<br />
6.12.<br><br />
1 Urška Jelenovec<br><br />
2 Ernest Šprager<br><br />
3 Rok Miklavčič <br><br />
4 <br><br />
<br />
11.12.<br><br />
1 Jerneja Ovčar<br><br />
2 Neža Koritnik<br><br />
3 Gašper Virant<br><br />
4 Gašper Marinšek<br><br />
<br />
18.12.<br><br />
1 Tina Požun<br><br />
2 Anamarija Habič<br><br />
3 Roberta Mulac<br><br />
4 Kity Požek<br><br />
<br />
3.1.<br><br />
1 Urška Kašnik<br><br />
2 Nina Mavec<br><br />
3 Primož Tič<br><br />
4 Milena Stojkovska<br><br />
<br />
8.1.<br><br />
1 Marija Atanasova<br><br />
2 Bine Tršavec<br><br />
3 Peter Pečan<br><br />
4 Tjaša Sorčan<br><br />
<br />
10.1.<br><br />
1 Špela Koren<br><br />
2 Natalija Pucihar<br><br />
3 Karmen Žbogar<br><br />
4 Uroš Zavrtanik<br><br />
<br />
15.1.<br><br />
1 Jerneja Kocutar<br><br />
2 Blaž Lebar<br><br />
3 Tadej Satler<br><br />
4 Miha Koprivnikar Krajnc<br></div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Seminarji_SB_2018/19&diff=14529Seminarji SB 2018/192018-12-02T16:44:25Z<p>Nfrauskok: </p>
<hr />
<div>V študijskem letu 2018/19 študentje predstavljajo naslednje teme: <br />
<br />
RAZISKOVALNI ČLANKI<br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do izhodiščnega članka na spletu.) <br><br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/MoClo:_modularni_klonirni_sistem_za_standardizirano_sestavljanje_ve%C4%8Dgenskih_konstruktov MoClo: modularni klonirni sistem za standardizirano sestavljanje večgenskih konstruktov] (Valentina Levak)<br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/RNA-stikala_tipa_%C2%BBToehold%C2%AB:_de_novo_oblikovani_regulatorji_izra%C5%BEanja_genov RNA-stikala tipa Toehold: de novo oblikovani regulatorji izražanja genov] (Špela Malenšek)<br />
<br />
[http://wiki.fkkt.uni-lj.si/index.php/Raznoliko_in_modelno_zasnovana_priprava_sinteti%C4%8Dnih_genskih_vezij_s_predvidenimi_lastnostmi Raznoliko in modelno zasnovana priprava sintetičnih genskih vezij s predvidenimi lastnostmi] (Matej Kolarič)<br />
<br />
<br />
<br />
<br />
NAGRAJENI ŠTUDENTSKI PROJEKTI <br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do wiki strani študentske ekipe, katere projekt opisujete.) <br><br />
<br />
<br />
<br />
<br />
Povzetki v slovenščini naj imajo 1200-1500 besed (viri v to vsoto ne štejejo). Predstavitev seminarja naj bo dolga 15 minut (13-17). Sledila bo razprava, ki praviloma ne bo daljša od 5 minut. <br />
<br />
----<br />
<br />
<br />
Razpored po datumih predstavitev (pri vsakem terminu je navedeno število možnih seminarjev; vpišite ime in priimek pri dnevu, ko želite predstaviti seminar ter dopišite naslov seminarja, ki naj bo povezan s povzetkom): <br />
<br />
22.11.<br> <br />
1 <br><br />
2 Valentina Levak <br><br />
<br />
27.11.<br><br />
1 <br><br />
2 <br><br />
3 <br><br />
4 <br><br />
<br />
29.11.<br><br />
1 Matej Kolarič<br><br />
2 Špela Malenšek<br><br />
3 <br><br />
4 <br><br />
<br />
<br />
4.12.<br><br />
1 Gašper Žun<br><br />
2 Fran Krstanovic<br><br />
3 <br><br />
4 <br><br />
<br />
6.12.<br><br />
1 Urška Jelenovec<br><br />
2 Ernest Šprager<br><br />
3 Rok Miklavčič <br><br />
4 <br><br />
<br />
11.12.<br><br />
1 Jerneja Ovčar<br><br />
2 Neža Koritnik<br><br />
3 Gašper Virant<br><br />
4 Gašper Marinšek<br><br />
<br />
18.12.<br><br />
1 Tina Požun<br><br />
2 Anamarija Habič<br><br />
3 Roberta Mulac<br><br />
4 Kity Požek<br><br />
<br />
3.1.<br><br />
1 Urška Kašnik<br><br />
2 Nina Mavec<br><br />
3 Primož Tič<br><br />
4 Milena Stojkovska<br><br />
<br />
8.1.<br><br />
1 Marija Atanasova<br><br />
2 Bine Tršavec<br><br />
3 Peter Pečan<br><br />
4 Tjaša Sorčan<br><br />
<br />
10.1.<br><br />
1 Špela Koren<br><br />
2 Natalija Pucihar<br><br />
3 Karmen Žbogar<br><br />
4 Uroš Zavrtanik<br><br />
<br />
15.1.<br><br />
1 Jerneja Kocutar<br><br />
2 Blaž Lebar<br><br />
3 Tadej Satler<br><br />
4 Miha Koprivnikar Krajnc<br></div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Talk:Main_Page&diff=14528Talk:Main Page2018-12-02T16:43:16Z<p>Nfrauskok: </p>
<hr />
<div>Izvorni članek: Lu, T., et al, Dispersing biofilms with engineered enzymatic bacteriophage, PNAS, 2007.<ref>[http://www.pnas.org/content/104/27/11197]</ref><br />
<br />
== Introduction ==<br />
<br />
When faced with certain challenges in various living habitats, bacteria have the ability to form biofilms, or organized aggregates of microorganisms living within an extracellular polymeric matrix (EPM) <ref name="jamal">https://www.ncbi.nlm.nih.gov/pubmed/29042186</ref>. The complex EPM is formed by heterogeneous extracellular polymeric substances (EPS), which is occupied mostly by water (97%) and other macromolecules in lower concentrations (proteins (~2%), polysaccharides (1-2%); nucleic acids (<1%) and ions (bound and free)) <ref name="jamal" />. This organized communities are formed on either biological or non-biological surfaces, and allow bacterium to surpass harsh environmental conditions, such as UV exposure, metal toxicity, acid exposure, dehydration and salinity, phagocytosis and several antibiotics and antimicrobial agents <ref name="dva">https://www.ncbi.nlm.nih.gov/pubmed/15040259</ref>. The ability to surpass latter conditions represent a challenge in the medical, industrial and food branches, as biofilm formation accounts for over 65% of microbial infections, and over 80% of chronic infections based on the statistics from the National Institutes of Health <ref name="dva" />. Due to the concerning numbers, and the rise of antibiotic resistance, a novel and effective treatment for bacterial biofilms is necessary. The main target in biofilm degradation is disruption of the EPM, more precisely to target the EPS and mechanism involved in EPS production and secretion (DNase, exopolysaccharides, protein components, cGMP/cAMP levels, signal and secretion pathways) <ref>[https://www.ncbi.nlm.nih.gov/pubmed/28944770]</ref>. In the following paper, we will show a potential treatment with synthetically engineered bacteriophages that possess the enzymatic ability to disperse bacterial biofilms. <br />
<br />
== Bacteriophages and biofilms ==<br />
<br />
The use of bacteriophages against bacterial infections is not a novelty method, as it is dates from the early 20th century. With the growing knowledge of engineering and manipulating biological organisms, and the highly annotated phage genome, makes bacteriophages prime candidates for targeting biofilms. Bacteriophages are viruses that infect and replicate within bacteria, and in comparison with antibiotics and other antimicrobial agents, possess the ability to penetrate biofilms, and disperse biofilms by various proposed mechanisms <ref>[https://www.ncbi.nlm.nih.gov/pubmed/23306440]</ref> <ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790368/]</ref>. As mentioned above, enzymatic targeting exopolysaccharides with EPS-degrading is one of the possible strategies for targeting biofilms <ref name="tri" />. The challenge lies in isolating a natural phage that is both specific for the bacteria to be targeted and expresses a relevant EPS-degrading enzyme. The solution lies in designing an artificial biofilm-degrading bacteriophage that express a specific EPS-degrading enzyme. <br />
<br />
== Dispersin B==<br />
<br />
While studying the strain A. actinomycetemcomitans which causes periodontal disease in adolescents and its biofilm formation and degradation properties for disease spreading, researchers have come upon a novel specific biofilm-releasing glycoside hydrolase <ref name="tri">https://www.ncbi.nlm.nih.gov/pubmed/15878175</ref>. This novel protein disperin B or DspB has the ability to degrade an important EPS polysaccharide adhesin known as β-1,6-N-acetyl-D-glucosamine <ref name="tri" />. N-acetyl-D-glucosamine residues form various polymeric structures with their linear β-1,6-linkages, such as PIA, PNAG, PGA (abbreviations)<ref name="tri" />. By hydrolyzing polymers, the protein disrupts the formation of the biofilm matrix and allows adherent cells to be released <ref name="tri" />. From a structural point of view, disperin B consist of a single domain with intertwining α/β structures <ref name="tri" />. The protein is a member of the 20 β-hexosaminidases family (GH-20), and has a highly conserved acidic active site (D183, E184, E332) which cleaves terminal monosaccharide residues from the non-reducing end of the polymers <ref name="tri" />.<br />
<br />
== Design of enzymatically active bacteriophage ==<br />
<br />
Once a suitable protein for biofilm removal that covers a wide specter was found, the design of engineered bacteriophages could commence. The idea is based on exploiting the lytic phage life cycle, which is based on hijacking the cell machinery, and synthesizing components of the phage genome <ref name="cet">https://www.ncbi.nlm.nih.gov/pubmed/12776216</ref>. Once all sufficient components are available, the phages reassembles inside the cell, causing the cell to burst and releasing its component in to the local environment <ref name="cet" />. This two-pronged attack strategy, would exploit the enzyme to remove bacterial biofilm, and the phage infections to lyse cells, while achieving high concentrations of the enzyme and lytic phage. The backbone of the design is based on using an E.coli specific lytic T7 phage, which was modified in a way that it had a few of nonessential gene deletions. The T7 phage had one of the first completely sequenced genomes (40-kb) that codes for 55 proteins <ref name="pet">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525648/</ref>. The T7 is widely used in molecular biology and has various traits that make this strain suitable for phage experiments <ref name="pet" />. The biofilm removing T7 phage was design to express DspB under the strong control of T7 ϕ10 promoter intracellularly during the infection, so that it could be released in to the environment upon cell lysis. The experiment was focused on strains that possess the F-plasmid, as it enhances biofilm maturation, and forms more thick biofilms, making them a more appealing group. Bacterial strains that contain the F-plasmid can disrupt efficient T7 replication. To tackle this problem, they inserted a 1.2 gene from T3 phage so the phage would not be limited only to strains that lack the F-plasmid, but to widen the spectrum of target <ref name="set">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208987/</ref>. Gene 1.2 is an inhibitor of the host dGTPase, which is involved in the process of DNA replication <ref name="set" />. A control was designed by cloning an S-tag into the T7 genome, to assure quality results. The phages were named T7DspB and T7Control respectively.<br />
<br />
== Characterization of enzymatically active bacteriophage ==<br />
<br />
The first task was to determine if T7DspB was more effective against biofilms than T7Control. Effectiveness of modified phages was also compared to wild-type T3 and T7 phages to determine if modified phages possess an edge over natural occurring ones. To measure effectiveness, crystal violet (CV) methods was used, which is based on staining attached cells (in our case bacterial cells/biofilms) with crystal violet dye, which binds to proteins and DNA <ref name="ket">https://www.ncbi.nlm.nih.gov/pubmed/27037069/</ref>. Those cells that undergo cell death lose their adherence, which shows as reducing amount of CV staining in a culture <ref name="ket" />. Absorbance (A600) measurement after a 24 h treatment period had shown that T7DspB phage removes biofilms with more efficiency than wild-type and especially T7Control. To confirm primary results, additional test such as sonication were ran, to obtain viable cell counts (CFU per peg) for bacteria surviving in biofilms after treatment. The results show consistency with CV, and confirm that T7DspB shows much more promising signs of biofilm removal than other tested phages, especially in comparison with T7Control. As mentioned above, the idea is based on a two-pronged attack strategy. Promising results were obtained for enzymatic activity of DspB, but also we have to ensure that phages sustain sufficient replication. PFU counts from microtiter plate wells and biofilms (after sonication) show that PFU counts were significantly higher in plates than biofilms, and that overall PFU surpassed initial 10<sup>3</sup> PFU by a few orders of magnitude which confirms efficient phage multiplication. <br />
<br />
== Time courses and dose-response for enzymatically active bacteriophage treatment ==<br />
<br />
Experiments to optimize the time-course and dose-response for both enzymatic activity and phage replication were carried out. Time-course results shown that after a 24h period of treatment, T7DspB had biofilms cell densities of two magnitudes lower than T7Control and 99,9% in comparison with untreated biofilms. Further on, time dependence on phage replication was tested, and showed that both T7Control and T7DspB began to multiply rapidly after inoculation in a similar fashion. Dosage response showed that T7DspB had lower cell densities at starting inoculation levels (PFU 10<sup>2</sup>) than T7Control, while higher inoculation concentrations showed even more efficiency against removing biofilms. Phage dosage tested exhibited phage multiplication within the biofilm.<br />
<br />
== Discussion ==<br />
<br />
The following experiments have shown that enzymatically modified phage shows greater efficiency in biofilm removal than natural accruing phages. Future improvements to this design may include directed evolution for optimal enzyme activity, delaying cell lysis or using multiple phage promoters to allow for increased enzyme production, targeting multiple biofilm EPS components with different proteins as well as targeting multi-species biofilm with a mixture of different species-specific engineered enzymatically active phage, and combination therapy with antibiotics and phage to improve the efficacy of both types of treatment. This strategy allows opens a possibility of establishing a library of biofilm dispersing phage. The upside of this method is that it does not need to deliver, express and purify large enzyme concentrations to the site of infection. This type of phage therapy should be looked into as additional therapy for treating bacterial biofilms in various industries, but not before several challenges are overcome. Firstly, a properly designed clinical trial is needed, which will tackle the problems such as phage development resistance, immunogenicity in humans, body clearance, release of toxins after cell lysis and phage specificity. Once all the challenges are overcome, phage therapy against biofilms will be considered as our first line of defense.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Talk:Main_Page&diff=14527Talk:Main Page2018-12-02T16:25:15Z<p>Nfrauskok: </p>
<hr />
<div>Izvorni članek: Lu, T., et al, Dispersing biofilms with engineered enzymatic bacteriophage, PNAS, 2007.<ref>[http://www.pnas.org/content/104/27/11197]</ref><br />
<br />
== Introduction ==<br />
<br />
When faced with certain challenges in various living habitats, bacteria have the ability to form biofilms, or organized aggregates of microorganisms living within an extracellular polymeric matrix (EPM) <ref>[https://www.ncbi.nlm.nih.gov/pubmed/29042186]</ref>. The complex EPM is formed by heterogeneous extracellular polymeric substances (EPS), which is occupied mostly by water (97%) and other macromolecules in lower concentrations (proteins (~2%), polysaccharides (1-2%); nucleic acids (<1%) and ions (bound and free)) <ref>[https://www.ncbi.nlm.nih.gov/pubmed/29042186]</ref>. This organized communities are formed on either biological or non-biological surfaces, and allow bacterium to surpass harsh environmental conditions, such as UV exposure, metal toxicity, acid exposure, dehydration and salinity, phagocytosis and several antibiotics and antimicrobial agents <ref>[https://www.ncbi.nlm.nih.gov/pubmed/15040259]</ref>. The ability to surpass latter conditions represent a challenge in the medical, industrial and food branches, as biofilm formation accounts for over 65% of microbial infections, and over 80% of chronic infections based on the statistics from the National Institutes of Health <ref>[https://www.ncbi.nlm.nih.gov/pubmed/15040259]</ref>. Due to the concerning numbers, and the rise of antibiotic resistance, a novel and effective treatment for bacterial biofilms is necessary. The main target in biofilm degradation is disruption of the EPM, more precisely to target the EPS and mechanism involved in EPS production and secretion (DNase, exopolysaccharides, protein components, cGMP/cAMP levels, signal and secretion pathways) <ref>[https://www.ncbi.nlm.nih.gov/pubmed/28944770]</ref>. In the following paper, we will show a potential treatment with synthetically engineered bacteriophages that possess the enzymatic ability to disperse bacterial biofilms. <br />
<br />
<br />
== Bacteriophages and biofilms ==<br />
<br />
The use of bacteriophages against bacterial infections is not a novelty method, as it is dates from the early 20th century. With the growing knowledge of engineering and manipulating biological organisms, and the highly annotated phage genome, makes bacteriophages prime candidates for targeting biofilms. Bacteriophages are viruses that infect and replicate within bacteria, and in comparison with antibiotics and other antimicrobial agents, possess the ability to penetrate biofilms, and disperse biofilms by various proposed mechanisms <ref>[https://www.ncbi.nlm.nih.gov/pubmed/23306440][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790368/]</ref>. As mentioned above, enzymatic targeting exopolysaccharides with EPS-degrading is one of the possible strategies for targeting biofilms <ref>[https://www.ncbi.nlm.nih.gov/pubmed/15878175]</ref>. The challenge lies in isolating a natural phage that is both specific for the bacteria to be targeted and expresses a relevant EPS-degrading enzyme. The solution lies in designing an artificial biofilm-degrading bacteriophage that express a specific EPS-degrading enzyme. <br />
<br />
<br />
== Dispersin B==<br />
<br />
While studying the strain A. actinomycetemcomitans which causes periodontal disease in adolescents and its biofilm formation and degradation properties for disease spreading, researchers have come upon a novel specific biofilm-releasing glycoside hydrolase <ref>[https://www.ncbi.nlm.nih.gov/pubmed/15878175]</ref>. This novel protein disperin B or DspB has the ability to degrade an important EPS polysaccharide adhesin known as β-1,6-N-acetyl-D-glucosamine <ref>[https://www.ncbi.nlm.nih.gov/pubmed/15878175]</ref>. N-acetyl-D-glucosamine residues form various polymeric structures with their linear β-1,6-linkages, such as PIA, PNAG, PGA (abbreviations) <ref>[https://www.ncbi.nlm.nih.gov/pubmed/15878175]</ref>. By hydrolyzing polymers, the protein disrupts the formation of the biofilm matrix and allows adherent cells to be released <ref>[https://www.ncbi.nlm.nih.gov/pubmed/15878175]</ref>. From a structural point of view, disperin B consist of a single domain with intertwining α/β structures <ref>[https://www.ncbi.nlm.nih.gov/pubmed/15878175]</ref>. The protein is a member of the 20 β-hexosaminidases family (GH-20), and has a highly conserved acidic active site (D183, E184, E332) which cleaves terminal monosaccharide residues from the non-reducing end of the polymers <ref>[https://www.ncbi.nlm.nih.gov/pubmed/15878175]</ref>.<br />
<br />
== Design of enzymatically active bacteriophage ==<br />
<br />
Once a suitable protein for biofilm removal that covers a wide specter was found, the design of engineered bacteriophages could commence. The idea is based on exploiting the lytic phage life cycle, which is based on hijacking the cell machinery, and synthesizing components of the phage genome <ref>[https://www.ncbi.nlm.nih.gov/pubmed/12776216]</ref>. Once all sufficient components are available, the phages reassembles inside the cell, causing the cell to burst and releasing its component in to the local environment <ref>[https://www.ncbi.nlm.nih.gov/pubmed/12776216]</ref>. This two-pronged attack strategy, would exploit the enzyme to remove bacterial biofilm, and the phage infections to lyse cells, while achieving high concentrations of the enzyme and lytic phage. The backbone of the design is based on using an E.coli specific lytic T7 phage, which was modified in a way that it had a few of nonessential gene deletions. The T7 phage had one of the first completely sequenced genomes (40-kb) that codes for 55 proteins <ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525648/]</ref>. The T7 is widely used in molecular biology and has various traits that make this strain suitable for phage experiments <ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525648/]</ref>. The biofilm removing T7 phage was design to express DspB under the strong control of T7 ϕ10 promoter intracellularly during the infection, so that it could be released in to the environment upon cell lysis. The experiment was focused on strains that possess the F-plasmid, as it enhances biofilm maturation, and forms more thick biofilms, making them a more appealing group. Bacterial strains that contain the F-plasmid can disrupt efficient T7 replication. To tackle this problem, they inserted a 1.2 gene from T3 phage so the phage would not be limited only to strains that lack the F-plasmid, but to widen the spectrum of target <ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208987/]</ref>. Gene 1.2 is an inhibitor of the host dGTPase, which is involved in the process of DNA replication <ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208987/]</ref>. A control was designed by cloning an S-tag into the T7 genome, to assure quality results. The phages were named T7DspB and T7Control respectively.<br />
<br />
<br />
== Characterization of enzymatically active bacteriophage ==<br />
<br />
The first task was to determine if T7DspB was more effective against biofilms than T7Control. Effectiveness of modified phages was also compared to wild-type T3 and T7 phages to determine if modified phages possess an edge over natural occurring ones. To measure effectiveness, crystal violet (CV) methods was used, which is based on staining attached cells (in our case bacterial cells/biofilms) with crystal violet dye, which binds to proteins and DNA <ref>[https://www.ncbi.nlm.nih.gov/pubmed/27037069]</ref>. Those cells that undergo cell death lose their adherence, which shows as reducing amount of CV staining in a culture <ref>[https://www.ncbi.nlm.nih.gov/pubmed/27037069]</ref>. Absorbance (A600) measurement after a 24 h treatment period had shown that T7DspB phage removes biofilms with more efficiency than wild-type and especially T7Control. To confirm primary results, additional test such as sonication were ran, to obtain viable cell counts (CFU per peg) for bacteria surviving in biofilms after treatment. The results show consistency with CV, and confirm that T7DspB shows much more promising signs of biofilm removal than other tested phages, especially in comparison with T7Control. As mentioned above, the idea is based on a two-pronged attack strategy. Promising results were obtained for enzymatic activity of DspB, but also we have to ensure that phages sustain sufficient replication. PFU counts from microtiter plate wells and biofilms (after sonication) show that PFU counts were significantly higher in plates than biofilms, and that overall PFU surpassed initial 10<sup>3</sup> PFU by a few orders of magnitude which confirms efficient phage multiplication. <br />
<br />
== Time courses and dose-response for enzymatically active bacteriophage treatment ==<br />
<br />
Experiments to optimize the time-course and dose-response for both enzymatic activity and phage replication were carried out. Time-course results shown that after a 24h period of treatment, T7DspB had biofilms cell densities of two magnitudes lower than T7Control and 99,9% in comparison with untreated biofilms. Further on, time dependence on phage replication was tested, and showed that both T7Control and T7DspB began to multiply rapidly after inoculation in a similar fashion. Dosage response showed that T7DspB had lower cell densities at starting inoculation levels (PFU 10<sup>2</sup>) than T7Control, while higher inoculation concentrations showed even more efficiency against removing biofilms. Phage dosage tested exhibited phage multiplication within the biofilm.<br />
<br />
== Discussion ==<br />
<br />
The following experiments have shown that enzymatically modified phage shows greater efficiency in biofilm removal than natural accruing phages. Future improvements to this design may include directed evolution for optimal enzyme activity, delaying cell lysis or using multiple phage promoters to allow for increased enzyme production, targeting multiple biofilm EPS components with different proteins as well as targeting multi-species biofilm with a mixture of different species-specific engineered enzymatically active phage, and combination therapy with antibiotics and phage to improve the efficacy of both types of treatment. This strategy allows opens a possibility of establishing a library of biofilm dispersing phage. The upside of this method is that it does not need to deliver, express and purify large enzyme concentrations to the site of infection. This type of phage therapy should be looked into as additional therapy for treating bacterial biofilms in various industries, but not before several challenges are overcome. Firstly, a properly designed clinical trial is needed, which will tackle the problems such as phage development resistance, immunogenicity in humans, body clearance, release of toxins after cell lysis and phage specificity. Once all the challenges are overcome, phage therapy against biofilms will be considered as our first line of defense.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Talk:Main_Page&diff=14526Talk:Main Page2018-12-02T16:13:48Z<p>Nfrauskok: New page: Izvorni članek: Lu, T., et al, Dispersing biofilms with engineered enzymatic bacteriophage, PNAS, 2007.[http://www.pnas.org/content/104/27/11197] == Introduction == When faced with cert...</p>
<hr />
<div>Izvorni članek: Lu, T., et al, Dispersing biofilms with engineered enzymatic bacteriophage, PNAS, 2007.[http://www.pnas.org/content/104/27/11197]<br />
<br />
== Introduction ==<br />
<br />
When faced with certain challenges in various living habitats, bacteria have the ability to form biofilms, or organized aggregates of microorganisms living within an extracellular polymeric matrix (EPM) [https://www.ncbi.nlm.nih.gov/pubmed/29042186]. The complex EPM is formed by heterogeneous extracellular polymeric substances (EPS), which is occupied mostly by water (97%) and other macromolecules in lower concentrations (proteins (~2%), polysaccharides (1-2%); nucleic acids (<1%) and ions (bound and free)) [https://www.ncbi.nlm.nih.gov/pubmed/29042186]. This organized communities are formed on either biological or non-biological surfaces, and allow bacterium to surpass harsh environmental conditions, such as UV exposure, metal toxicity, acid exposure, dehydration and salinity, phagocytosis and several antibiotics and antimicrobial agents [https://www.ncbi.nlm.nih.gov/pubmed/15040259]. The ability to surpass latter conditions represent a challenge in the medical, industrial and food branches, as biofilm formation accounts for over 65% of microbial infections, and over 80% of chronic infections based on the statistics from the National Institutes of Health [https://www.ncbi.nlm.nih.gov/pubmed/15040259]. Due to the concerning numbers, and the rise of antibiotic resistance, a novel and effective treatment for bacterial biofilms is necessary. The main target in biofilm degradation is disruption of the EPM, more precisely to target the EPS and mechanism involved in EPS production and secretion (DNase, exopolysaccharides, protein components, cGMP/cAMP levels, signal and secretion pathways) [https://www.ncbi.nlm.nih.gov/pubmed/28944770]. In the following paper, we will show a potential treatment with synthetically engineered bacteriophages that possess the enzymatic ability to disperse bacterial biofilms. <br />
<br />
<br />
== Bacteriophages and biofilms ==<br />
<br />
The use of bacteriophages against bacterial infections is not a novelty method, as it is dates from the early 20th century. With the growing knowledge of engineering and manipulating biological organisms, and the highly annotated phage genome, makes bacteriophages prime candidates for targeting biofilms. Bacteriophages are viruses that infect and replicate within bacteria, and in comparison with antibiotics and other antimicrobial agents, possess the ability to penetrate biofilms, and disperse biofilms by various proposed mechanisms [https://www.ncbi.nlm.nih.gov/pubmed/23306440][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790368/]. As mentioned above, enzymatic targeting exopolysaccharides with EPS-degrading is one of the possible strategies for targeting biofilms [https://www.ncbi.nlm.nih.gov/pubmed/15878175]. The challenge lies in isolating a natural phage that is both specific for the bacteria to be targeted and expresses a relevant EPS-degrading enzyme. The solution lies in designing an artificial biofilm-degrading bacteriophage that express a specific EPS-degrading enzyme. <br />
<br />
<br />
== Dispersin B==<br />
<br />
While studying the strain A. actinomycetemcomitans which causes periodontal disease in adolescents and its biofilm formation and degradation properties for disease spreading, researchers have come upon a novel specific biofilm-releasing glycoside hydrolase [https://www.ncbi.nlm.nih.gov/pubmed/15878175]. This novel protein disperin B or DspB has the ability to degrade an important EPS polysaccharide adhesin known as β-1,6-N-acetyl-D-glucosamine [https://www.ncbi.nlm.nih.gov/pubmed/15878175]. N-acetyl-D-glucosamine residues form various polymeric structures with their linear β-1,6-linkages, such as PIA, PNAG, PGA (abbreviations) [https://www.ncbi.nlm.nih.gov/pubmed/15878175]. By hydrolyzing polymers, the protein disrupts the formation of the biofilm matrix and allows adherent cells to be released [https://www.ncbi.nlm.nih.gov/pubmed/15878175]. From a structural point of view, disperin B consist of a single domain with intertwining α/β structures [https://www.ncbi.nlm.nih.gov/pubmed/15878175]. The protein is a member of the 20 β-hexosaminidases family (GH-20), and has a highly conserved acidic active site (D183, E184, E332) which cleaves terminal monosaccharide residues from the non-reducing end of the polymers [https://www.ncbi.nlm.nih.gov/pubmed/15878175].<br />
<br />
== Design of enzymatically active bacteriophage ==<br />
<br />
Once a suitable protein for biofilm removal that covers a wide specter was found, the design of engineered bacteriophages could commence. The idea is based on exploiting the lytic phage life cycle, which is based on hijacking the cell machinery, and synthesizing components of the phage genome [https://www.ncbi.nlm.nih.gov/pubmed/12776216]. Once all sufficient components are available, the phages reassembles inside the cell, causing the cell to burst and releasing its component in to the local environment [https://www.ncbi.nlm.nih.gov/pubmed/12776216]. This two-pronged attack strategy, would exploit the enzyme to remove bacterial biofilm, and the phage infections to lyse cells, while achieving high concentrations of the enzyme and lytic phage. The backbone of the design is based on using an E.coli specific lytic T7 phage, which was modified in a way that it had a few of nonessential gene deletions. The T7 phage had one of the first completely sequenced genomes (40-kb) that codes for 55 proteins [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525648/]. The T7 is widely used in molecular biology and has various traits that make this strain suitable for phage experiments [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525648/]. The biofilm removing T7 phage was design to express DspB under the strong control of T7 ϕ10 promoter intracellularly during the infection, so that it could be released in to the environment upon cell lysis. The experiment was focused on strains that possess the F-plasmid, as it enhances biofilm maturation, and forms more thick biofilms, making them a more appealing group. Bacterial strains that contain the F-plasmid can disrupt efficient T7 replication. To tackle this problem, they inserted a 1.2 gene from T3 phage so the phage would not be limited only to strains that lack the F-plasmid, but to widen the spectrum of target [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208987/]. Gene 1.2 is an inhibitor of the host dGTPase, which is involved in the process of DNA replication [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208987/]. A control was designed by cloning an S-tag into the T7 genome, to assure quality results. The phages were named T7DspB and T7Control respectively.<br />
<br />
<br />
== Characterization of enzymatically active bacteriophage ==<br />
<br />
The first task was to determine if T7DspB was more effective against biofilms than T7Control. Effectiveness of modified phages was also compared to wild-type T3 and T7 phages to determine if modified phages possess an edge over natural occurring ones. To measure effectiveness, crystal violet (CV) methods was used, which is based on staining attached cells (in our case bacterial cells/biofilms) with crystal violet dye, which binds to proteins and DNA [https://www.ncbi.nlm.nih.gov/pubmed/27037069]. Those cells that undergo cell death lose their adherence, which shows as reducing amount of CV staining in a culture [10]. Absorbance (A600) measurement after a 24 h treatment period had shown that T7DspB phage removes biofilms with more efficiency than wild-type and especially T7Control. To confirm primary results, additional test such as sonication were ran, to obtain viable cell counts (CFU per peg) for bacteria surviving in biofilms after treatment. The results show consistency with CV, and confirm that T7DspB shows much more promising signs of biofilm removal than other tested phages, especially in comparison with T7Control. As mentioned above, the idea is based on a two-pronged attack strategy. Promising results were obtained for enzymatic activity of DspB, but also we have to ensure that phages sustain sufficient replication. PFU counts from microtiter plate wells and biofilms (after sonication) show that PFU counts were significantly higher in plates than biofilms, and that overall PFU surpassed initial 103 PFU by a few orders of magnitude which confirms efficient phage multiplication. <br />
<br />
== Time courses and dose-response for enzymatically active bacteriophage treatment ==<br />
<br />
Experiments to optimize the time-course and dose-response for both enzymatic activity and phage replication were carried out. Time-course results shown that after a 24h period of treatment, T7DspB had biofilms cell densities of two magnitudes lower than T7Control and 99,9% in comparison with untreated biofilms. Further on, time dependence on phage replication was tested, and showed that both T7Control and T7DspB began to multiply rapidly after inoculation in a similar fashion. Dosage response showed that T7DspB had lower cell densities at starting inoculation levels (PFU 10<sup>2</sup>) than T7Control, while higher inoculation concentrations showed even more efficiency against removing biofilms. Phage dosage tested exhibited phage multiplication within the biofilm.<br />
<br />
== Discussion ==<br />
<br />
The following experiments have shown that enzymatically modified phage shows greater efficiency in biofilm removal than natural accruing phages. Future improvements to this design may include directed evolution for optimal enzyme activity, delaying cell lysis or using multiple phage promoters to allow for increased enzyme production, targeting multiple biofilm EPS components with different proteins as well as targeting multi-species biofilm with a mixture of different species-specific engineered enzymatically active phage, and combination therapy with antibiotics and phage to improve the efficacy of both types of treatment. This strategy allows opens a possibility of establishing a library of biofilm dispersing phage. The upside of this method is that it does not need to deliver, express and purify large enzyme concentrations to the site of infection. This type of phage therapy should be looked into as additional therapy for treating bacterial biofilms in various industries, but not before several challenges are overcome. Firstly, a properly designed clinical trial is needed, which will tackle the problems such as phage development resistance, immunogenicity in humans, body clearance, release of toxins after cell lysis and phage specificity. Once all the challenges are overcome, phage therapy against biofilms will be considered as our first line of defense.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Seminarji_SB_2018/19&diff=14424Seminarji SB 2018/192018-11-15T09:02:55Z<p>Nfrauskok: </p>
<hr />
<div>V študijskem letu 2018/19 študentje predstavljajo naslednje teme: <br />
<br />
RAZISKOVALNI ČLANKI<br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do izhodiščnega članka na spletu.) <br><br />
<br />
<br />
<br />
<br />
NAGRAJENI ŠTUDENTSKI PROJEKTI <br />
<br />
(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do wiki strani študentske ekipe, katere projekt opisujete.) <br><br />
<br />
<br />
<br />
<br />
Povzetki v slovenščini naj imajo 1200-1500 besed (viri v to vsoto ne štejejo). Predstavitev seminarja naj bo dolga 15 minut (13-17). Sledila bo razprava, ki praviloma ne bo daljša od 5 minut. <br />
<br />
----<br />
<br />
<br />
Razpored po datumih predstavitev (pri vsakem terminu je navedeno število možnih seminarjev; vpišite ime in priimek pri dnevu, ko želite predstaviti seminar ter dopišite naslov seminarja, ki naj bo povezan s povzetkom): <br />
<br />
22.11.<br> <br />
1 <br><br />
2 Valentina Levak <br><br />
<br />
27.11.<br><br />
1 <br><br />
2 <br><br />
3 <br><br />
4 <br><br />
<br />
29.11.<br><br />
1 Rok Miklavčič <br><br />
2 Špela Malenšek<br />
<br />
4.12.<br><br />
1 <br><br />
2 Fran Krstanovic<br />
3 <br><br />
4 <br><br />
<br />
6.12.<br><br />
1 <br><br />
2 <br><br />
<br />
11.12.<br><br />
1 Jerneja Ovčar<br><br />
2 <br><br />
3 <br><br />
4 <br><br />
<br />
18.12.<br><br />
1 <br><br />
2 <br><br />
3 <br><br />
4 <br><br />
<br />
3.1.<br><br />
1 <br><br />
2 <br><br />
3 <br><br />
4 Milena Stojkovska<br><br />
<br />
8.1.<br><br />
1 Peter Pečan<br><br />
2 Tjaša Sorčan<br><br />
3 Marija Atanasova<br><br />
4 <br><br />
<br />
10.1.<br><br />
1 Natalija Pucihar<br><br />
2 <br><br />
<br />
15.1.<br><br />
1 <br><br />
2 <br><br />
3 <br><br />
4 <br></div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Mehanizmi_izjemne_odpornosti_proti_radioaktivnemu_sevanju_pri_prokariontih&diff=11639Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih2016-06-05T14:17:10Z<p>Nfrauskok: /* Introduction */</p>
<hr />
<div>== '''Introduction''' ==<br />
Extremophiles are organisms that live, metabolize and reproduce to human extreme conditions. We define a variety of extreme conditions such as high or low temperatures, pH, salinity, pressure and radiation. Scientists find this organisms extraordinary, especially their metabolism, mechanisms of DNA repair and protein antioxidants. The most impressive extremophile organisms are those resistant to high levels of ionizing radiation. Bacterium Deinococcus radiodurans can survive exposures as high as 15 kGy (Gray is an SI unit for absorbed radiation dose), while for humans a lethal dose is around 10 Gy and average bacterium around 200 Gy. Ionizing radiation causes severe damage on living cells such as formation of ROS, DNA single and double strand brakes, DNA extensive base modifications. Evidently some bacterium have mechanism that fight radiation damage. Due to lack of radioprotectors this bacterium ability rises high interest as a potential suppressor of radiation effects. Suppressing side effect on healthy cells in cancer radiations treatments would have enormous benefit as higher radiation doses would be allowed with better anticancer effect.<br />
<br />
== '''Analysis''' ==<br />
This highly complex mechanism can’t be a single standing one. Because of its complicity a series of mechanism need to interact to repair and resist radiation. The mechanism would have to consist of a more efficient DNA repair mechanism (In comparison with radiation intolerant species), nucleotide condensation, DNA and protein antioxidant system, protein recovery and lipid dynamics. It’s important to mention that radiotolerant strains are not phylogenetically related and that a universal mechanism doesn’t exist. Because of their diversity it is believed that radiotoleration was acquired by different strains during evolution. We can’t study just D. radiodurans and conclude that the mechanism is broad for resistant bacterium. There is a bunch of different genes and proteins that have roles in their domains. We focus mostly on D. radiodurans because it is the most resistant and studied bacterium (Research led by Croatian scientist Miroslav Radman, fully sequenced genome) and with sequence analysis find correspondence with other resistant bacterium. D. radiodurans can be found in organic-rich environments and harsh environments like deserts and rocks. It is believed that D. radiodurans resistance to radiation stress was as a byproduct to dehydration adaptation. Other studies state that D. radiodurans could be Martian descendant, as the earth lacks radiation levels that could explain D. radiodurans high resistance. It is interesting to mention that radioresistance was developed under laboratory conditions on sensitive E.coli. Cycles of radiation lead to genetic mutations in key mechanisms such as recA protein and higher ratio of Mn/Fe intercellular ions. This alteration are similar to that of D. radiodurans which we will explain in the following paragraph. <br />
<br />
== '''Protein antioxidant system''' ==<br />
Protein oxidation causes covalent modifications on proteins leading to changes in protein physical and chemical properties (conformation, structure, solubility, proteolysis, activity,) which can lead to cell death and mutations. Carbonylation (introduction of carbon monoxide) is the most common oxidative modification, used as a biomarker for protein oxidation. Protein oxidation stress caused by oxygen species: hydroxyl radicals (OH•), superoxide radicals (O2-•), and hydrogen peroxide (H2O2). Deinococcus radiodurans is resistant to all three oxygen species by an enzymatic and nonenzymatic antioxidant system. Enzymatic system is based on higher levels of catalases (H2O2), superoxide dismutases (O2-•) and peroxidases (H2O2) than in radiosensitive species. Apart from the primary enzymes, D. radiodurans has more oxidative defense proteins in the form of: glutaredoxin, thioredoxin, thioredoxin reductase and alkyl hydroperoxide reductase. Dps proteins (Ferritin-like protein, iron releasing/storage) protect from oxidative damage by binding DNA and reducing H2O2. Nonenzymatic defense is based on carotenoids and manganese complexes. Carotenoids play an important role in oxidative stress protection, but their presence isn’t necessarily needed as they don’t contribute on radiation stress. D. radiodurans has a high intracellular manganese concentration. Manganese forms complexes with cellular metabolites, which is a very effective defense. It has the ability to replace Fe in proteins protecting from fenton (H2O2 iron catalyzed oxidation reaction) driven protein oxidation. It was found that the high ratio of intercellular Mn/Fe is linked to low protein oxidation and high radiation resistance. Mn mostly forms complexes with orthophosphate (O2-•) and peptidase. Mn defense system is effective in protecting DNA repair proteins, protein recovery and oxidation, but ineffective against DSBs. <br />
<br />
== '''DNA repair mechanism''' ==<br />
Precise and accurate DNA repair mechanism is of great importance for bacterial genome repairs caused by radiation stress. Sequence analysis in DNA repair hasn’t found a single protein conserved in all species. Protein recA is detected the highest percentage in the sequence analysis. RecA has a pivotal role in D. radiodurans DNA repair. RecA-mediated homologous recombination is crucial for DSB. RecA also interacts with Holliday junction resolvasome RuvABC. Apart from recA pathways, bacterium have a recA independent mechanism, non-homologous end joining (NHEJ). One third of the mechanism doesn’t require recA. The mechanism is based on proteins like DdrA, DdrB, SSB and RadA. RecA dependent/independent mechanisms are believed to interact with one another<br />
<br />
== '''Nucleotide condensation''' ==<br />
D. radiodurans has a more condensed genomic DNA to maintain DNA linearity and protection of free radicals formed in the cytoplasm. The ability of DNA linearity in the presence of DNA breaks highly increase repair possibility by not allowing DNA fragments to diffuse to higher distances. <br />
<br />
== '''Histone like proteins''' ==<br />
Histone like proteins (HU) are bacterial proteins that share a similar role as eukaryotic histones, the ability of DNA binding. HU can control gene expression and nucleotide organization. The bacteria constantly have high concentrations of HU present, so higher levels are not needed during radiation stress. HU doesn’t have the ability to bind on DNA fragments so it had to adapt a particular structure during evolution that would enable DNA fragment binding. HU binds to a four way DNA junction, and stabilizes recombination intermediates. <br />
<br />
== '''Lipid dynamics''' ==<br />
Bacterial membranes have modified lipid, protein and carbohydrate compositions to survive in rough environments that were mentioned above. The membrane is the first line of defense from radiation. Although there isn’t a lipid structure that can’t block radiation, its ability to sustain radiation damage, adapt and integrate with other mechanisms separates them from radio intolerant organisms. Radiation can cause oxidation of membranes proteins and puncture. Although the mechanism isn’t still known it is believed that the protein antioxidant system protects membrane proteins which is of great importance because of the signal pathways, transportation and defense roles that the proteins have. Some changes in the fatty acid composition were found leading to change in membrane fluidity which is believed to have a signal role. Another possible resistance advantage is the presence of the S-layer D. radiodurans membrane. The loss of the S-layer lead to higher stress damage.<br />
<br />
=='''References''' ==<br />
1. Pavlopoulou A., et all., Mutation Research / Reviews in Mutation Research Unraveling the mechanisms of extreme radioresistance in prokaryotes:Lessons from nature, ''Mutation Research-Reviews in Mutation Research'',2015.,Vol. 767.<br />
<br />
2. Slade D., et all., Oxidative Stress Resistance in Deinococcus radiodurans, ''Microbiology and molecular biology reviews'', 2011., Vol. 75.<br />
<br />
3. Munteanu A., et all., Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria, ''Extremophiles'', 2015., Vol. 19.<br />
<br />
4. Tian B., et all., Proteomic analysis of membrane proteins from a radioresistant and moderate thermophilic bacterium Deinococcus geothermalis, ''Molecular BioSystems'', 2010., Vol. 10.<br />
<br />
[[Category:SEM]] [[Category:BMB]]</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Mehanizmi_izjemne_odpornosti_proti_radioaktivnemu_sevanju_pri_prokariontih&diff=11638Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih2016-06-05T13:43:38Z<p>Nfrauskok: </p>
<hr />
<div>== '''Introduction''' ==<br />
Extremophiles are organism that live, metabolize and reproduce to human extreme conditions. We define a variety of extreme conditions such as high or low temperatures, pH, salinity, pressure and radiation. Scientists find this organisms extraordinary, especially their metabolism, mechanisms of DNA repair and protein antioxidants. The most impressive extremophile organisms are those resistant to high levels of ionizing radiation. Bacterium Deinococcus radiodurans can survive exposures as high as 15 kGy (Gray is an SI unit for absorbed radiation dose), while for humans a lethal dose is around 10 Gy and average bacterium around 200 Gy. Ionizing radiation causes severe damage on living cells such as formation of ROS, DNA single and double strand brakes, DNA extensive base modifications. Evidently some bacterium have mechanism that fight radiation damage. Due to lack of radioprotectors this bacterium ability rises high interest as a potential suppressor of radiation effects. Suppressing side effect on healthy cells in cancer radiations treatments would have enormous benefit as higher radiation doses would be allowed with better anticancer effect.<br />
<br />
== '''Analysis''' ==<br />
This highly complex mechanism can’t be a single standing one. Because of its complicity a series of mechanism need to interact to repair and resist radiation. The mechanism would have to consist of a more efficient DNA repair mechanism (In comparison with radiation intolerant species), nucleotide condensation, DNA and protein antioxidant system, protein recovery and lipid dynamics. It’s important to mention that radiotolerant strains are not phylogenetically related and that a universal mechanism doesn’t exist. Because of their diversity it is believed that radiotoleration was acquired by different strains during evolution. We can’t study just D. radiodurans and conclude that the mechanism is broad for resistant bacterium. There is a bunch of different genes and proteins that have roles in their domains. We focus mostly on D. radiodurans because it is the most resistant and studied bacterium (Research led by Croatian scientist Miroslav Radman, fully sequenced genome) and with sequence analysis find correspondence with other resistant bacterium. D. radiodurans can be found in organic-rich environments and harsh environments like deserts and rocks. It is believed that D. radiodurans resistance to radiation stress was as a byproduct to dehydration adaptation. Other studies state that D. radiodurans could be Martian descendant, as the earth lacks radiation levels that could explain D. radiodurans high resistance. It is interesting to mention that radioresistance was developed under laboratory conditions on sensitive E.coli. Cycles of radiation lead to genetic mutations in key mechanisms such as recA protein and higher ratio of Mn/Fe intercellular ions. This alteration are similar to that of D. radiodurans which we will explain in the following paragraph. <br />
<br />
== '''Protein antioxidant system''' ==<br />
Protein oxidation causes covalent modifications on proteins leading to changes in protein physical and chemical properties (conformation, structure, solubility, proteolysis, activity,) which can lead to cell death and mutations. Carbonylation (introduction of carbon monoxide) is the most common oxidative modification, used as a biomarker for protein oxidation. Protein oxidation stress caused by oxygen species: hydroxyl radicals (OH•), superoxide radicals (O2-•), and hydrogen peroxide (H2O2). Deinococcus radiodurans is resistant to all three oxygen species by an enzymatic and nonenzymatic antioxidant system. Enzymatic system is based on higher levels of catalases (H2O2), superoxide dismutases (O2-•) and peroxidases (H2O2) than in radiosensitive species. Apart from the primary enzymes, D. radiodurans has more oxidative defense proteins in the form of: glutaredoxin, thioredoxin, thioredoxin reductase and alkyl hydroperoxide reductase. Dps proteins (Ferritin-like protein, iron releasing/storage) protect from oxidative damage by binding DNA and reducing H2O2. Nonenzymatic defense is based on carotenoids and manganese complexes. Carotenoids play an important role in oxidative stress protection, but their presence isn’t necessarily needed as they don’t contribute on radiation stress. D. radiodurans has a high intracellular manganese concentration. Manganese forms complexes with cellular metabolites, which is a very effective defense. It has the ability to replace Fe in proteins protecting from fenton (H2O2 iron catalyzed oxidation reaction) driven protein oxidation. It was found that the high ratio of intercellular Mn/Fe is linked to low protein oxidation and high radiation resistance. Mn mostly forms complexes with orthophosphate (O2-•) and peptidase. Mn defense system is effective in protecting DNA repair proteins, protein recovery and oxidation, but ineffective against DSBs. <br />
<br />
== '''DNA repair mechanism''' ==<br />
Precise and accurate DNA repair mechanism is of great importance for bacterial genome repairs caused by radiation stress. Sequence analysis in DNA repair hasn’t found a single protein conserved in all species. Protein recA is detected the highest percentage in the sequence analysis. RecA has a pivotal role in D. radiodurans DNA repair. RecA-mediated homologous recombination is crucial for DSB. RecA also interacts with Holliday junction resolvasome RuvABC. Apart from recA pathways, bacterium have a recA independent mechanism, non-homologous end joining (NHEJ). One third of the mechanism doesn’t require recA. The mechanism is based on proteins like DdrA, DdrB, SSB and RadA. RecA dependent/independent mechanisms are believed to interact with one another<br />
<br />
== '''Nucleotide condensation''' ==<br />
D. radiodurans has a more condensed genomic DNA to maintain DNA linearity and protection of free radicals formed in the cytoplasm. The ability of DNA linearity in the presence of DNA breaks highly increase repair possibility by not allowing DNA fragments to diffuse to higher distances. <br />
<br />
== '''Histone like proteins''' ==<br />
Histone like proteins (HU) are bacterial proteins that share a similar role as eukaryotic histones, the ability of DNA binding. HU can control gene expression and nucleotide organization. The bacteria constantly have high concentrations of HU present, so higher levels are not needed during radiation stress. HU doesn’t have the ability to bind on DNA fragments so it had to adapt a particular structure during evolution that would enable DNA fragment binding. HU binds to a four way DNA junction, and stabilizes recombination intermediates. <br />
<br />
== '''Lipid dynamics''' ==<br />
Bacterial membranes have modified lipid, protein and carbohydrate compositions to survive in rough environments that were mentioned above. The membrane is the first line of defense from radiation. Although there isn’t a lipid structure that can’t block radiation, its ability to sustain radiation damage, adapt and integrate with other mechanisms separates them from radio intolerant organisms. Radiation can cause oxidation of membranes proteins and puncture. Although the mechanism isn’t still known it is believed that the protein antioxidant system protects membrane proteins which is of great importance because of the signal pathways, transportation and defense roles that the proteins have. Some changes in the fatty acid composition were found leading to change in membrane fluidity which is believed to have a signal role. Another possible resistance advantage is the presence of the S-layer D. radiodurans membrane. The loss of the S-layer lead to higher stress damage.<br />
<br />
=='''References''' ==<br />
1. Pavlopoulou A., et all., Mutation Research / Reviews in Mutation Research Unraveling the mechanisms of extreme radioresistance in prokaryotes:Lessons from nature, ''Mutation Research-Reviews in Mutation Research'',2015.,Vol. 767.<br />
<br />
2. Slade D., et all., Oxidative Stress Resistance in Deinococcus radiodurans, ''Microbiology and molecular biology reviews'', 2011., Vol. 75.<br />
<br />
3. Munteanu A., et all., Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria, ''Extremophiles'', 2015., Vol. 19.<br />
<br />
4. Tian B., et all., Proteomic analysis of membrane proteins from a radioresistant and moderate thermophilic bacterium Deinococcus geothermalis, ''Molecular BioSystems'', 2010., Vol. 10.<br />
<br />
[[Category:SEM]] [[Category:BMB]]</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Popravljanje_mutacij_in_rekombinacijski_procesi&diff=11637Popravljanje mutacij in rekombinacijski procesi2016-06-05T13:41:24Z<p>Nfrauskok: </p>
<hr />
<div>V študijskem letu 2015/16 bodo seminarji obsegali dve med seboj povezani temi: Popravljanje okvar in mutacij ter mehanizme rekombinacije genetskega materiala. Tema je razdeljena na 18 poglavij, pri čemer zadnja poglavja zajemajo posebne primere in mehanizme popravljanja, ki niso vezani na DNA, pač pa na proces translacije pri poškodovani RNA, zadnji dve temi pa sta dodani kasneje in bosta predstavljeni v angleščini kot individualna seminarja. Kot izhodišče za pripravo si najprej preberite ustrezna poglavja v učbeniku, kjer so ta navedena na spodnjem seznamu. Naslove lahko v okviru danih izhodišč prilagodite, ne smete pa se odmakniti od osnovne teme seminarja. <br />
<br />
Vsako temo obdelajo praviloma dva ali trije študenti. Predlagate lahko tudi dodatne teme ali spremembe naslovov, če se vam to zdi smiselno. Vsaka skupina pripravi povzetek seminarja z vsaj 1000 besedami in ne več kot 1500 besedami in ga objavi na tem wikiju. Povzetek ne vsebuje slikovnega gradiva, lahko pa vključuje povezave do slik in videov na spletu. Navedite do 5 ključnih virov (ti ne štejejo v vsoto 1000 besed), ki ste jih uporabili. Osredotočite se na osnovno temo, ki ste si jo izbrali in vključite čim manj splošnega uvoda. Pripravite tudi predstavitev, dolgo pribl. 15 min. Razširjenega seminarja ni treba pripraviti v pisni obliki; napišete samo povzetek na wikiju in predstavite seminar v predavalnici. <br />
<br />
Vsaka skupina mora objaviti povzetek seminarja na wikiju najkasneje en dan pred predstavitvijo (do polnoči), torej najkasneje v nedeljo ali v torek za ponedeljkove oziroma sredine seminarje. Predstavitve seminarjev 1-4 bodo 23. maja, 5-8 25. maja, 9-12 30. maja, 13-16 1. junija 2016, 17-18 pa sta kratka seminarja in bosta na vrsti 6. junija. Za vsak seminar imate na voljo 14-18 minut časa, da ga predstavite, sledi pa razprava (~5 min.). Vsak član skupine mora predstaviti en del seminarja, pri čemer mora biti delo enakomerno razdeljeno med vse. V povzetku navedite, kdo je napisal kateri del (na wiki strani uporabite zavihek 'discussion').<br />
<br />
Vsebina seminarjev je izpitna snov, razen seminarjev št. 4 ter 13-18. <br />
<br />
<br />
Poglavja za seminarje so:<br />
<br />
# Direktno popravljanje mutacij (Principles of Molecular Biology: 9.7)<br />
# Popravljanje z izcepom baze (9.8)<br />
# Popravljanje z izcepom nukleotida (9.9)<br />
# Xeroderma pigmentosum<br />
# Popravljanje neujemanja (9.10)<br />
# SOS-popravljanje (9.11)<br />
# Popravljanje kolapsa replikacijskih vilic (10.1)<br />
# Mitozna rekombinacija (10.2)<br />
# Nehomologno povezovanje koncev (10.4)<br />
# Mejozna rekombinacija (10.5)<br />
# Razreševanje Hollidayevega križišča (Lewin's Essential Genes: 15.6)<br />
# Popravljanje DNA v kontekstu kromatina (Lewin's Essential Genes: 16.9)<br />
# Menjava spola pri kvasovki (Lewin's Essential Genes: 15.9)<br />
# Vloga p53 pri ohranjanju genoma (Lewin's Essential Genes: str. 400)<br />
# Trans-translacija (translacija pri poškodovani mRNA)<br />
# Od RNA neodvisna elongacija (Science 347, 75 (2015))<br />
# Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih<br />
# Kompleksne preureditve kromosomov<br />
<br />
<br />
----<br />
<br />
Vpišite se v oklepaj za naslovom seminarja:<br />
<br />
<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Neposredno_popravljanje_mutacij Direktno popravljanje mutacij] (Matej Hvalec)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/POPRAVLJANJE_Z_IZCEPOM_BAZE_%28BER%29 Popravljanje z izcepom baze (BER)] (Urša Čerček, Urša Kopač, Ema Gašperšič)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Popravljanje_z_izcepom_nukleotida#Sklopitev_GG-NER_in_TC-NER Popravljanje z izcepom nukleotida] (Petra Hruševar, Gašper Žun, Uroš Zavrtanik)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Xeroderma_pigmentosum Xeroderma pigmentosum] (Maja Zupanc, Elvira Boršič)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Popravljanje_neujemanja Popravljanje neujemanja] Popravljanje neujemanja (Kristjan Stibilj, Rok Miklavčič, Sara Tekavec)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/SOS-popravljanje SOS-popravljanje] (Tadej Satler, Gašper Virant)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Popravljanje_kolapsa_replikacijskih_vilic Popravljanje kolapsa replikacijskih vilic] (Klara Lenart, Tilen Tršelič)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Mitozna_rekombinacija Mitozna rekombinacija] (Peter Pečan, Valentina Levak, Janja Krapež)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Nehomologno_povezovanje_koncev Nehomologno povezovanje koncev] (Klara Kuret, Blaž Lebar, Neža Koritnik)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Mejozna_rekombinacija Mejozna rekombinacija] (Eva Rajh, Katja Čop)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Razreševanje_Hollidayevega_križišča#Viri Razreševanje Hollidayevega križišča] (Nejc Kejžar, Lovro Kotnik)<br />
# [[Popravljanje DNA v kontekstu kromatina|Popravljanje DNA v kontekstu kromatina]] (Špela Malenšek, Tjaša Lukšič)<br />
# Menjava spola pri kvasovki <br />
# [http://wiki.fkkt.uni-lj.si/index.php/Vloga_p53_pri_ohranjanju_genoma Vloga p53 pri ohranjanju genoma] (Miha Koprivnikar Krajnc, Katja Brezovar)<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Trans-translacija ''Trans''-translacija] (Lara Jerman, Aleksandra Uzar, Simon Aleksič)<br />
# Od RNA neodvisna elongacija<br />
# [http://wiki.fkkt.uni-lj.si/index.php/Mehanizmi_izjemne_odpornosti_proti_radioaktivnemu_sevanju_pri_prokariontih] (Fran Krstanović)<br />
# "Mechanisms of origin, phenotypic effects and diagnostic implications of complex chromosome rearrangements" (Javier Fraguas)<br />
<br />
<br />
<br />
Naslov teme povežite z novo wiki-stranjo, na katero napišite povzetek. Na koncu besedila (pod viri) v novo vrstico dodajte oznaki: <br />
<nowiki>[[Category:SEM]] [[Category:BMB]]</nowiki> <br />
<br />
Primer, kako so bili urejeni seminarji v prejšnjih letih, si lahko ogledate na strani [[Reprogramiranje celic]].</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Mehanizmi_izjemne_odpornosti_proti_radioaktivnemu_sevanju_pri_prokariontih&diff=11636Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih2016-06-05T13:39:34Z<p>Nfrauskok: /* References */</p>
<hr />
<div>== '''Introduction''' ==<br />
Extremophiles are organism that live, metabolize and reproduce to human extreme conditions. We define a variety of extreme conditions such as high or low temperatures, pH, salinity, pressure and radiation. Scientists find this organisms extraordinary, especially their metabolism, mechanisms of DNA repair and protein antioxidants. The most impressive extremophile organisms are those resistant to high levels of ionizing radiation. Bacterium Deinococcus radiodurans can survive exposures as high as 15 kGy (Gray is an SI unit for absorbed radiation dose), while for humans a lethal dose is around 10 Gy and average bacterium around 200 Gy. Ionizing radiation causes severe damage on living cells such as formation of ROS, DNA single and double strand brakes, DNA extensive base modifications. Evidently some bacterium have mechanism that fight radiation damage. Due to lack of radioprotectors this bacterium ability rises high interest as a potential suppressor of radiation effects. Suppressing side effect on healthy cells in cancer radiations treatments would have enormous benefit as higher radiation doses would be allowed with better anticancer effect.<br />
<br />
== '''Analysis''' ==<br />
This highly complex mechanism can’t be a single standing one. Because of its complicity a series of mechanism need to interact to repair and resist radiation. The mechanism would have to consist of a more efficient DNA repair mechanism (In comparison with radiation intolerant species), nucleotide condensation, DNA and protein antioxidant system, protein recovery and lipid dynamics. It’s important to mention that radiotolerant strains are not phylogenetically related and that a universal mechanism doesn’t exist. Because of their diversity it is believed that radiotoleration was acquired by different strains during evolution. We can’t study just D. radiodurans and conclude that the mechanism is broad for resistant bacterium. There is a bunch of different genes and proteins that have roles in their domains. We focus mostly on D. radiodurans because it is the most resistant and studied bacterium (Research led by Croatian scientist Miroslav Radman, fully sequenced genome) and with sequence analysis find correspondence with other resistant bacterium. D. radiodurans can be found in organic-rich environments and harsh environments like deserts and rocks. It is believed that D. radiodurans resistance to radiation stress was as a byproduct to dehydration adaptation. Other studies state that D. radiodurans could be Martian descendant, as the earth lacks radiation levels that could explain D. radiodurans high resistance. It is interesting to mention that radioresistance was developed under laboratory conditions on sensitive E.coli. Cycles of radiation lead to genetic mutations in key mechanisms such as recA protein and higher ratio of Mn/Fe intercellular ions. This alteration are similar to that of D. radiodurans which we will explain in the following paragraph. <br />
<br />
== '''Protein antioxidant system''' ==<br />
Protein oxidation causes covalent modifications on proteins leading to changes in protein physical and chemical properties (conformation, structure, solubility, proteolysis, activity,) which can lead to cell death and mutations. Carbonylation (introduction of carbon monoxide) is the most common oxidative modification, used as a biomarker for protein oxidation. Protein oxidation stress caused by oxygen species: hydroxyl radicals (OH•), superoxide radicals (O2-•), and hydrogen peroxide (H2O2). Deinococcus radiodurans is resistant to all three oxygen species by an enzymatic and nonenzymatic antioxidant system. Enzymatic system is based on higher levels of catalases (H2O2), superoxide dismutases (O2-•) and peroxidases (H2O2) than in radiosensitive species. Apart from the primary enzymes, D. radiodurans has more oxidative defense proteins in the form of: glutaredoxin, thioredoxin, thioredoxin reductase and alkyl hydroperoxide reductase. Dps proteins (Ferritin-like protein, iron releasing/storage) protect from oxidative damage by binding DNA and reducing H2O2. Nonenzymatic defense is based on carotenoids and manganese complexes. Carotenoids play an important role in oxidative stress protection, but their presence isn’t necessarily needed as they don’t contribute on radiation stress. D. radiodurans has a high intracellular manganese concentration. Manganese forms complexes with cellular metabolites, which is a very effective defense. It has the ability to replace Fe in proteins protecting from fenton (H2O2 iron catalyzed oxidation reaction) driven protein oxidation. It was found that the high ratio of intercellular Mn/Fe is linked to low protein oxidation and high radiation resistance. Mn mostly forms complexes with orthophosphate (O2-•) and peptidase. Mn defense system is effective in protecting DNA repair proteins, protein recovery and oxidation, but ineffective against DSBs. <br />
<br />
== '''DNA repair mechanism''' ==<br />
Precise and accurate DNA repair mechanism is of great importance for bacterial genome repairs caused by radiation stress. Sequence analysis in DNA repair hasn’t found a single protein conserved in all species. Protein recA is detected the highest percentage in the sequence analysis. RecA has a pivotal role in D. radiodurans DNA repair. RecA-mediated homologous recombination is crucial for DSB. RecA also interacts with Holliday junction resolvasome RuvABC. Apart from recA pathways, bacterium have a recA independent mechanism, non-homologous end joining (NHEJ). One third of the mechanism doesn’t require recA. The mechanism is based on proteins like DdrA, DdrB, SSB and RadA. RecA dependent/independent mechanisms are believed to interact with one another<br />
<br />
== '''Nucleotide condensation''' ==<br />
D. radiodurans has a more condensed genomic DNA to maintain DNA linearity and protection of free radicals formed in the cytoplasm. The ability of DNA linearity in the presence of DNA breaks highly increase repair possibility by not allowing DNA fragments to diffuse to higher distances. <br />
<br />
== '''Histone like proteins''' ==<br />
Histone like proteins (HU) are bacterial proteins that share a similar role as eukaryotic histones, the ability of DNA binding. HU can control gene expression and nucleotide organization. The bacteria constantly have high concentrations of HU present, so higher levels are not needed during radiation stress. HU doesn’t have the ability to bind on DNA fragments so it had to adapt a particular structure during evolution that would enable DNA fragment binding. HU binds to a four way DNA junction, and stabilizes recombination intermediates. <br />
<br />
== '''Lipid dynamics''' ==<br />
Bacterial membranes have modified lipid, protein and carbohydrate compositions to survive in rough environments that were mentioned above. The membrane is the first line of defense from radiation. Although there isn’t a lipid structure that can’t block radiation, its ability to sustain radiation damage, adapt and integrate with other mechanisms separates them from radio intolerant organisms. Radiation can cause oxidation of membranes proteins and puncture. Although the mechanism isn’t still known it is believed that the protein antioxidant system protects membrane proteins which is of great importance because of the signal pathways, transportation and defense roles that the proteins have. Some changes in the fatty acid composition were found leading to change in membrane fluidity which is believed to have a signal role. Another possible resistance advantage is the presence of the S-layer D. radiodurans membrane. The loss of the S-layer lead to higher stress damage.<br />
<br />
=='''References''' ==<br />
1. Pavlopoulou A., et all., Mutation Research / Reviews in Mutation Research Unraveling the mechanisms of extreme radioresistance in prokaryotes:Lessons from nature, ''Mutation Research-Reviews in Mutation Research'',2015.,Vol. 767.<br />
<br />
2. Slade D., et all., Oxidative Stress Resistance in Deinococcus radiodurans, ''Microbiology and molecular biology reviews'', 2011., Vol. 75.<br />
<br />
3. Munteanu A., et all., Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria, ''Extremophiles'', 2015., Vol. 19.<br />
<br />
4. Tian B., et all., Proteomic analysis of membrane proteins from a radioresistant and moderate thermophilic bacterium Deinococcus geothermalis, ''Molecular BioSystems'', 2010., Vol. 10.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Mehanizmi_izjemne_odpornosti_proti_radioaktivnemu_sevanju_pri_prokariontih&diff=11635Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih2016-06-05T13:39:03Z<p>Nfrauskok: /* References */</p>
<hr />
<div>== '''Introduction''' ==<br />
Extremophiles are organism that live, metabolize and reproduce to human extreme conditions. We define a variety of extreme conditions such as high or low temperatures, pH, salinity, pressure and radiation. Scientists find this organisms extraordinary, especially their metabolism, mechanisms of DNA repair and protein antioxidants. The most impressive extremophile organisms are those resistant to high levels of ionizing radiation. Bacterium Deinococcus radiodurans can survive exposures as high as 15 kGy (Gray is an SI unit for absorbed radiation dose), while for humans a lethal dose is around 10 Gy and average bacterium around 200 Gy. Ionizing radiation causes severe damage on living cells such as formation of ROS, DNA single and double strand brakes, DNA extensive base modifications. Evidently some bacterium have mechanism that fight radiation damage. Due to lack of radioprotectors this bacterium ability rises high interest as a potential suppressor of radiation effects. Suppressing side effect on healthy cells in cancer radiations treatments would have enormous benefit as higher radiation doses would be allowed with better anticancer effect.<br />
<br />
== '''Analysis''' ==<br />
This highly complex mechanism can’t be a single standing one. Because of its complicity a series of mechanism need to interact to repair and resist radiation. The mechanism would have to consist of a more efficient DNA repair mechanism (In comparison with radiation intolerant species), nucleotide condensation, DNA and protein antioxidant system, protein recovery and lipid dynamics. It’s important to mention that radiotolerant strains are not phylogenetically related and that a universal mechanism doesn’t exist. Because of their diversity it is believed that radiotoleration was acquired by different strains during evolution. We can’t study just D. radiodurans and conclude that the mechanism is broad for resistant bacterium. There is a bunch of different genes and proteins that have roles in their domains. We focus mostly on D. radiodurans because it is the most resistant and studied bacterium (Research led by Croatian scientist Miroslav Radman, fully sequenced genome) and with sequence analysis find correspondence with other resistant bacterium. D. radiodurans can be found in organic-rich environments and harsh environments like deserts and rocks. It is believed that D. radiodurans resistance to radiation stress was as a byproduct to dehydration adaptation. Other studies state that D. radiodurans could be Martian descendant, as the earth lacks radiation levels that could explain D. radiodurans high resistance. It is interesting to mention that radioresistance was developed under laboratory conditions on sensitive E.coli. Cycles of radiation lead to genetic mutations in key mechanisms such as recA protein and higher ratio of Mn/Fe intercellular ions. This alteration are similar to that of D. radiodurans which we will explain in the following paragraph. <br />
<br />
== '''Protein antioxidant system''' ==<br />
Protein oxidation causes covalent modifications on proteins leading to changes in protein physical and chemical properties (conformation, structure, solubility, proteolysis, activity,) which can lead to cell death and mutations. Carbonylation (introduction of carbon monoxide) is the most common oxidative modification, used as a biomarker for protein oxidation. Protein oxidation stress caused by oxygen species: hydroxyl radicals (OH•), superoxide radicals (O2-•), and hydrogen peroxide (H2O2). Deinococcus radiodurans is resistant to all three oxygen species by an enzymatic and nonenzymatic antioxidant system. Enzymatic system is based on higher levels of catalases (H2O2), superoxide dismutases (O2-•) and peroxidases (H2O2) than in radiosensitive species. Apart from the primary enzymes, D. radiodurans has more oxidative defense proteins in the form of: glutaredoxin, thioredoxin, thioredoxin reductase and alkyl hydroperoxide reductase. Dps proteins (Ferritin-like protein, iron releasing/storage) protect from oxidative damage by binding DNA and reducing H2O2. Nonenzymatic defense is based on carotenoids and manganese complexes. Carotenoids play an important role in oxidative stress protection, but their presence isn’t necessarily needed as they don’t contribute on radiation stress. D. radiodurans has a high intracellular manganese concentration. Manganese forms complexes with cellular metabolites, which is a very effective defense. It has the ability to replace Fe in proteins protecting from fenton (H2O2 iron catalyzed oxidation reaction) driven protein oxidation. It was found that the high ratio of intercellular Mn/Fe is linked to low protein oxidation and high radiation resistance. Mn mostly forms complexes with orthophosphate (O2-•) and peptidase. Mn defense system is effective in protecting DNA repair proteins, protein recovery and oxidation, but ineffective against DSBs. <br />
<br />
== '''DNA repair mechanism''' ==<br />
Precise and accurate DNA repair mechanism is of great importance for bacterial genome repairs caused by radiation stress. Sequence analysis in DNA repair hasn’t found a single protein conserved in all species. Protein recA is detected the highest percentage in the sequence analysis. RecA has a pivotal role in D. radiodurans DNA repair. RecA-mediated homologous recombination is crucial for DSB. RecA also interacts with Holliday junction resolvasome RuvABC. Apart from recA pathways, bacterium have a recA independent mechanism, non-homologous end joining (NHEJ). One third of the mechanism doesn’t require recA. The mechanism is based on proteins like DdrA, DdrB, SSB and RadA. RecA dependent/independent mechanisms are believed to interact with one another<br />
<br />
== '''Nucleotide condensation''' ==<br />
D. radiodurans has a more condensed genomic DNA to maintain DNA linearity and protection of free radicals formed in the cytoplasm. The ability of DNA linearity in the presence of DNA breaks highly increase repair possibility by not allowing DNA fragments to diffuse to higher distances. <br />
<br />
== '''Histone like proteins''' ==<br />
Histone like proteins (HU) are bacterial proteins that share a similar role as eukaryotic histones, the ability of DNA binding. HU can control gene expression and nucleotide organization. The bacteria constantly have high concentrations of HU present, so higher levels are not needed during radiation stress. HU doesn’t have the ability to bind on DNA fragments so it had to adapt a particular structure during evolution that would enable DNA fragment binding. HU binds to a four way DNA junction, and stabilizes recombination intermediates. <br />
<br />
== '''Lipid dynamics''' ==<br />
Bacterial membranes have modified lipid, protein and carbohydrate compositions to survive in rough environments that were mentioned above. The membrane is the first line of defense from radiation. Although there isn’t a lipid structure that can’t block radiation, its ability to sustain radiation damage, adapt and integrate with other mechanisms separates them from radio intolerant organisms. Radiation can cause oxidation of membranes proteins and puncture. Although the mechanism isn’t still known it is believed that the protein antioxidant system protects membrane proteins which is of great importance because of the signal pathways, transportation and defense roles that the proteins have. Some changes in the fatty acid composition were found leading to change in membrane fluidity which is believed to have a signal role. Another possible resistance advantage is the presence of the S-layer D. radiodurans membrane. The loss of the S-layer lead to higher stress damage.<br />
<br />
=='''References''' ==<br />
1. Pavlopoulou A., et all., Mutation Research / Reviews in Mutation Research Unraveling the mechanisms of extreme radioresistance in prokaryotes:Lessons from nature, ''Mutation Research-Reviews in Mutation Research'',2015.,Vol. 767<br />
<br />
2. Slade D., et all., Oxidative Stress Resistance in Deinococcus radiodurans,''Microbiology and molecular biology reviews'', 2011., Vol. 75<br />
<br />
3. Munteanu A., et all., Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria, ''Extremophiles'', 2015., Vol. 19<br />
<br />
4. Tian B., et all., Proteomic analysis of membrane proteins from a radioresistant and moderate thermophilic bacterium Deinococcus geothermalis, ''Molecular BioSystems'', 2010., Vol. 10</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Mehanizmi_izjemne_odpornosti_proti_radioaktivnemu_sevanju_pri_prokariontih&diff=11634Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih2016-06-05T13:38:49Z<p>Nfrauskok: /* References */</p>
<hr />
<div>== '''Introduction''' ==<br />
Extremophiles are organism that live, metabolize and reproduce to human extreme conditions. We define a variety of extreme conditions such as high or low temperatures, pH, salinity, pressure and radiation. Scientists find this organisms extraordinary, especially their metabolism, mechanisms of DNA repair and protein antioxidants. The most impressive extremophile organisms are those resistant to high levels of ionizing radiation. Bacterium Deinococcus radiodurans can survive exposures as high as 15 kGy (Gray is an SI unit for absorbed radiation dose), while for humans a lethal dose is around 10 Gy and average bacterium around 200 Gy. Ionizing radiation causes severe damage on living cells such as formation of ROS, DNA single and double strand brakes, DNA extensive base modifications. Evidently some bacterium have mechanism that fight radiation damage. Due to lack of radioprotectors this bacterium ability rises high interest as a potential suppressor of radiation effects. Suppressing side effect on healthy cells in cancer radiations treatments would have enormous benefit as higher radiation doses would be allowed with better anticancer effect.<br />
<br />
== '''Analysis''' ==<br />
This highly complex mechanism can’t be a single standing one. Because of its complicity a series of mechanism need to interact to repair and resist radiation. The mechanism would have to consist of a more efficient DNA repair mechanism (In comparison with radiation intolerant species), nucleotide condensation, DNA and protein antioxidant system, protein recovery and lipid dynamics. It’s important to mention that radiotolerant strains are not phylogenetically related and that a universal mechanism doesn’t exist. Because of their diversity it is believed that radiotoleration was acquired by different strains during evolution. We can’t study just D. radiodurans and conclude that the mechanism is broad for resistant bacterium. There is a bunch of different genes and proteins that have roles in their domains. We focus mostly on D. radiodurans because it is the most resistant and studied bacterium (Research led by Croatian scientist Miroslav Radman, fully sequenced genome) and with sequence analysis find correspondence with other resistant bacterium. D. radiodurans can be found in organic-rich environments and harsh environments like deserts and rocks. It is believed that D. radiodurans resistance to radiation stress was as a byproduct to dehydration adaptation. Other studies state that D. radiodurans could be Martian descendant, as the earth lacks radiation levels that could explain D. radiodurans high resistance. It is interesting to mention that radioresistance was developed under laboratory conditions on sensitive E.coli. Cycles of radiation lead to genetic mutations in key mechanisms such as recA protein and higher ratio of Mn/Fe intercellular ions. This alteration are similar to that of D. radiodurans which we will explain in the following paragraph. <br />
<br />
== '''Protein antioxidant system''' ==<br />
Protein oxidation causes covalent modifications on proteins leading to changes in protein physical and chemical properties (conformation, structure, solubility, proteolysis, activity,) which can lead to cell death and mutations. Carbonylation (introduction of carbon monoxide) is the most common oxidative modification, used as a biomarker for protein oxidation. Protein oxidation stress caused by oxygen species: hydroxyl radicals (OH•), superoxide radicals (O2-•), and hydrogen peroxide (H2O2). Deinococcus radiodurans is resistant to all three oxygen species by an enzymatic and nonenzymatic antioxidant system. Enzymatic system is based on higher levels of catalases (H2O2), superoxide dismutases (O2-•) and peroxidases (H2O2) than in radiosensitive species. Apart from the primary enzymes, D. radiodurans has more oxidative defense proteins in the form of: glutaredoxin, thioredoxin, thioredoxin reductase and alkyl hydroperoxide reductase. Dps proteins (Ferritin-like protein, iron releasing/storage) protect from oxidative damage by binding DNA and reducing H2O2. Nonenzymatic defense is based on carotenoids and manganese complexes. Carotenoids play an important role in oxidative stress protection, but their presence isn’t necessarily needed as they don’t contribute on radiation stress. D. radiodurans has a high intracellular manganese concentration. Manganese forms complexes with cellular metabolites, which is a very effective defense. It has the ability to replace Fe in proteins protecting from fenton (H2O2 iron catalyzed oxidation reaction) driven protein oxidation. It was found that the high ratio of intercellular Mn/Fe is linked to low protein oxidation and high radiation resistance. Mn mostly forms complexes with orthophosphate (O2-•) and peptidase. Mn defense system is effective in protecting DNA repair proteins, protein recovery and oxidation, but ineffective against DSBs. <br />
<br />
== '''DNA repair mechanism''' ==<br />
Precise and accurate DNA repair mechanism is of great importance for bacterial genome repairs caused by radiation stress. Sequence analysis in DNA repair hasn’t found a single protein conserved in all species. Protein recA is detected the highest percentage in the sequence analysis. RecA has a pivotal role in D. radiodurans DNA repair. RecA-mediated homologous recombination is crucial for DSB. RecA also interacts with Holliday junction resolvasome RuvABC. Apart from recA pathways, bacterium have a recA independent mechanism, non-homologous end joining (NHEJ). One third of the mechanism doesn’t require recA. The mechanism is based on proteins like DdrA, DdrB, SSB and RadA. RecA dependent/independent mechanisms are believed to interact with one another<br />
<br />
== '''Nucleotide condensation''' ==<br />
D. radiodurans has a more condensed genomic DNA to maintain DNA linearity and protection of free radicals formed in the cytoplasm. The ability of DNA linearity in the presence of DNA breaks highly increase repair possibility by not allowing DNA fragments to diffuse to higher distances. <br />
<br />
== '''Histone like proteins''' ==<br />
Histone like proteins (HU) are bacterial proteins that share a similar role as eukaryotic histones, the ability of DNA binding. HU can control gene expression and nucleotide organization. The bacteria constantly have high concentrations of HU present, so higher levels are not needed during radiation stress. HU doesn’t have the ability to bind on DNA fragments so it had to adapt a particular structure during evolution that would enable DNA fragment binding. HU binds to a four way DNA junction, and stabilizes recombination intermediates. <br />
<br />
== '''Lipid dynamics''' ==<br />
Bacterial membranes have modified lipid, protein and carbohydrate compositions to survive in rough environments that were mentioned above. The membrane is the first line of defense from radiation. Although there isn’t a lipid structure that can’t block radiation, its ability to sustain radiation damage, adapt and integrate with other mechanisms separates them from radio intolerant organisms. Radiation can cause oxidation of membranes proteins and puncture. Although the mechanism isn’t still known it is believed that the protein antioxidant system protects membrane proteins which is of great importance because of the signal pathways, transportation and defense roles that the proteins have. Some changes in the fatty acid composition were found leading to change in membrane fluidity which is believed to have a signal role. Another possible resistance advantage is the presence of the S-layer D. radiodurans membrane. The loss of the S-layer lead to higher stress damage.<br />
<br />
=='''References''' ==<br />
1. Pavlopoulou A., et all., Mutation Research / Reviews in Mutation Research Unraveling the mechanisms of extreme radioresistance in prokaryotes:Lessons from nature, ''Mutation Research-Reviews in Mutation Research'',2015.,Vol. 767<br />
<br />
2. Slade D., et all., Oxidative Stress Resistance in Deinococcus radiodurans,''Microbiology and molecular biology reviews'', 2011., Vol. 75<br />
<br />
3. Munteanu A.,Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria, ''Extremophiles'', 2015., Vol. 19<br />
<br />
4. Tian B., et all., Proteomic analysis of membrane proteins from a radioresistant and moderate thermophilic bacterium Deinococcus geothermalis, ''Molecular BioSystems'', 2010., Vol. 10</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Mehanizmi_izjemne_odpornosti_proti_radioaktivnemu_sevanju_pri_prokariontih&diff=11633Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih2016-06-05T13:35:51Z<p>Nfrauskok: </p>
<hr />
<div>== '''Introduction''' ==<br />
Extremophiles are organism that live, metabolize and reproduce to human extreme conditions. We define a variety of extreme conditions such as high or low temperatures, pH, salinity, pressure and radiation. Scientists find this organisms extraordinary, especially their metabolism, mechanisms of DNA repair and protein antioxidants. The most impressive extremophile organisms are those resistant to high levels of ionizing radiation. Bacterium Deinococcus radiodurans can survive exposures as high as 15 kGy (Gray is an SI unit for absorbed radiation dose), while for humans a lethal dose is around 10 Gy and average bacterium around 200 Gy. Ionizing radiation causes severe damage on living cells such as formation of ROS, DNA single and double strand brakes, DNA extensive base modifications. Evidently some bacterium have mechanism that fight radiation damage. Due to lack of radioprotectors this bacterium ability rises high interest as a potential suppressor of radiation effects. Suppressing side effect on healthy cells in cancer radiations treatments would have enormous benefit as higher radiation doses would be allowed with better anticancer effect.<br />
<br />
== '''Analysis''' ==<br />
This highly complex mechanism can’t be a single standing one. Because of its complicity a series of mechanism need to interact to repair and resist radiation. The mechanism would have to consist of a more efficient DNA repair mechanism (In comparison with radiation intolerant species), nucleotide condensation, DNA and protein antioxidant system, protein recovery and lipid dynamics. It’s important to mention that radiotolerant strains are not phylogenetically related and that a universal mechanism doesn’t exist. Because of their diversity it is believed that radiotoleration was acquired by different strains during evolution. We can’t study just D. radiodurans and conclude that the mechanism is broad for resistant bacterium. There is a bunch of different genes and proteins that have roles in their domains. We focus mostly on D. radiodurans because it is the most resistant and studied bacterium (Research led by Croatian scientist Miroslav Radman, fully sequenced genome) and with sequence analysis find correspondence with other resistant bacterium. D. radiodurans can be found in organic-rich environments and harsh environments like deserts and rocks. It is believed that D. radiodurans resistance to radiation stress was as a byproduct to dehydration adaptation. Other studies state that D. radiodurans could be Martian descendant, as the earth lacks radiation levels that could explain D. radiodurans high resistance. It is interesting to mention that radioresistance was developed under laboratory conditions on sensitive E.coli. Cycles of radiation lead to genetic mutations in key mechanisms such as recA protein and higher ratio of Mn/Fe intercellular ions. This alteration are similar to that of D. radiodurans which we will explain in the following paragraph. <br />
<br />
== '''Protein antioxidant system''' ==<br />
Protein oxidation causes covalent modifications on proteins leading to changes in protein physical and chemical properties (conformation, structure, solubility, proteolysis, activity,) which can lead to cell death and mutations. Carbonylation (introduction of carbon monoxide) is the most common oxidative modification, used as a biomarker for protein oxidation. Protein oxidation stress caused by oxygen species: hydroxyl radicals (OH•), superoxide radicals (O2-•), and hydrogen peroxide (H2O2). Deinococcus radiodurans is resistant to all three oxygen species by an enzymatic and nonenzymatic antioxidant system. Enzymatic system is based on higher levels of catalases (H2O2), superoxide dismutases (O2-•) and peroxidases (H2O2) than in radiosensitive species. Apart from the primary enzymes, D. radiodurans has more oxidative defense proteins in the form of: glutaredoxin, thioredoxin, thioredoxin reductase and alkyl hydroperoxide reductase. Dps proteins (Ferritin-like protein, iron releasing/storage) protect from oxidative damage by binding DNA and reducing H2O2. Nonenzymatic defense is based on carotenoids and manganese complexes. Carotenoids play an important role in oxidative stress protection, but their presence isn’t necessarily needed as they don’t contribute on radiation stress. D. radiodurans has a high intracellular manganese concentration. Manganese forms complexes with cellular metabolites, which is a very effective defense. It has the ability to replace Fe in proteins protecting from fenton (H2O2 iron catalyzed oxidation reaction) driven protein oxidation. It was found that the high ratio of intercellular Mn/Fe is linked to low protein oxidation and high radiation resistance. Mn mostly forms complexes with orthophosphate (O2-•) and peptidase. Mn defense system is effective in protecting DNA repair proteins, protein recovery and oxidation, but ineffective against DSBs. <br />
<br />
== '''DNA repair mechanism''' ==<br />
Precise and accurate DNA repair mechanism is of great importance for bacterial genome repairs caused by radiation stress. Sequence analysis in DNA repair hasn’t found a single protein conserved in all species. Protein recA is detected the highest percentage in the sequence analysis. RecA has a pivotal role in D. radiodurans DNA repair. RecA-mediated homologous recombination is crucial for DSB. RecA also interacts with Holliday junction resolvasome RuvABC. Apart from recA pathways, bacterium have a recA independent mechanism, non-homologous end joining (NHEJ). One third of the mechanism doesn’t require recA. The mechanism is based on proteins like DdrA, DdrB, SSB and RadA. RecA dependent/independent mechanisms are believed to interact with one another<br />
<br />
== '''Nucleotide condensation''' ==<br />
D. radiodurans has a more condensed genomic DNA to maintain DNA linearity and protection of free radicals formed in the cytoplasm. The ability of DNA linearity in the presence of DNA breaks highly increase repair possibility by not allowing DNA fragments to diffuse to higher distances. <br />
<br />
== '''Histone like proteins''' ==<br />
Histone like proteins (HU) are bacterial proteins that share a similar role as eukaryotic histones, the ability of DNA binding. HU can control gene expression and nucleotide organization. The bacteria constantly have high concentrations of HU present, so higher levels are not needed during radiation stress. HU doesn’t have the ability to bind on DNA fragments so it had to adapt a particular structure during evolution that would enable DNA fragment binding. HU binds to a four way DNA junction, and stabilizes recombination intermediates. <br />
<br />
== '''Lipid dynamics''' ==<br />
Bacterial membranes have modified lipid, protein and carbohydrate compositions to survive in rough environments that were mentioned above. The membrane is the first line of defense from radiation. Although there isn’t a lipid structure that can’t block radiation, its ability to sustain radiation damage, adapt and integrate with other mechanisms separates them from radio intolerant organisms. Radiation can cause oxidation of membranes proteins and puncture. Although the mechanism isn’t still known it is believed that the protein antioxidant system protects membrane proteins which is of great importance because of the signal pathways, transportation and defense roles that the proteins have. Some changes in the fatty acid composition were found leading to change in membrane fluidity which is believed to have a signal role. Another possible resistance advantage is the presence of the S-layer D. radiodurans membrane. The loss of the S-layer lead to higher stress damage.<br />
<br />
=='''References''' ==<br />
1. Pavlopoulou A., et all., Mutation Research / Reviews in Mutation Research Unraveling the mechanisms of extreme radioresistance in prokaryotes:Lessons from nature, ''Mutation Research-Reviews in Mutation Research'',2015.,Vol. 767<br />
<br />
2. Slade D., et all., Oxidative Stress Resistance in Deinococcus radiodurans,''Microbiology and molecular biology reviews'', 2011., Vol. 75<br />
<br />
3. Munteanu A.,Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria, ''Extremophiles'', 2015., Vol. 19</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Mehanizmi_izjemne_odpornosti_proti_radioaktivnemu_sevanju_pri_prokariontih&diff=11632Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih2016-06-05T13:19:10Z<p>Nfrauskok: </p>
<hr />
<div>== '''Introduction''' ==<br />
Extremophiles are organism that live, metabolize and reproduce to human extreme conditions. We define a variety of extreme conditions such as high or low temperatures, pH, salinity, pressure and radiation. Scientists find this organisms extraordinary, especially their metabolism, mechanisms of DNA repair and protein antioxidants. The most impressive extremophile organisms are those resistant to high levels of ionizing radiation. Bacterium Deinococcus radiodurans can survive exposures as high as 15 kGy (Gray is an SI unit for absorbed radiation dose), while for humans a lethal dose is around 10 Gy and average bacterium around 200 Gy. Ionizing radiation causes severe damage on living cells such as formation of ROS, DNA single and double strand brakes, DNA extensive base modifications. Evidently some bacterium have mechanism that fight radiation damage. Due to lack of radioprotectors this bacterium ability rises high interest as a potential suppressor of radiation effects. Suppressing side effect on healthy cells in cancer radiations treatments would have enormous benefit as higher radiation doses would be allowed with better anticancer effect.<br />
<br />
== '''Analysis''' ==<br />
This highly complex mechanism can’t be a single standing one. Because of its complicity a series of mechanism need to interact to repair and resist radiation. The mechanism would have to consist of a more efficient DNA repair mechanism (In comparison with radiation intolerant species), nucleotide condensation, DNA and protein antioxidant system, protein recovery and lipid dynamics. It’s important to mention that radiotolerant strains are not phylogenetically related and that a universal mechanism doesn’t exist. Because of their diversity it is believed that radiotoleration was acquired by different strains during evolution. We can’t study just D. radiodurans and conclude that the mechanism is broad for resistant bacterium. There is a bunch of different genes and proteins that have roles in their domains. We focus mostly on D. radiodurans because it is the most resistant and studied bacterium (Research led by Croatian scientist Miroslav Radman, fully sequenced genome) and with sequence analysis find correspondence with other resistant bacterium. D. radiodurans can be found in organic-rich environments and harsh environments like deserts and rocks. It is believed that D. radiodurans resistance to radiation stress was as a byproduct to dehydration adaptation. Other studies state that D. radiodurans could be Martian descendant, as the earth lacks radiation levels that could explain D. radiodurans high resistance. It is interesting to mention that radioresistance was developed under laboratory conditions on sensitive E.coli. Cycles of radiation lead to genetic mutations in key mechanisms such as recA protein and higher ratio of Mn/Fe intercellular ions. This alteration are similar to that of D. radiodurans which we will explain in the following paragraph. <br />
<br />
== Protein antioxidant system ==<br />
Protein oxidation causes covalent modifications on proteins leading to changes in protein physical and chemical properties (conformation, structure, solubility, proteolysis, activity,) which can lead to cell death and mutations. Carbonylation (introduction of carbon monoxide) is the most common oxidative modification, used as a biomarker for protein oxidation. Protein oxidation stress caused by oxygen species: hydroxyl radicals (OH•), superoxide radicals (O2-•), and hydrogen peroxide (H2O2). Deinococcus radiodurans is resistant to all three oxygen species by an enzymatic and nonenzymatic antioxidant system. Enzymatic system is based on higher levels of catalases (H2O2), superoxide dismutases (O2-•) and peroxidases (H2O2) than in radiosensitive species. Apart from the primary enzymes, D. radiodurans has more oxidative defense proteins in the form of: glutaredoxin, thioredoxin, thioredoxin reductase and alkyl hydroperoxide reductase. Dps proteins (Ferritin-like protein, iron releasing/storage) protect from oxidative damage by binding DNA and reducing H2O2. Nonenzymatic defense is based on carotenoids and manganese complexes. Carotenoids play an important role in oxidative stress protection, but their presence isn’t necessarily needed as they don’t contribute on radiation stress. D. radiodurans has a high intracellular manganese concentration. Manganese forms complexes with cellular metabolites, which is a very effective defense. It has the ability to replace Fe in proteins protecting from fenton (H2O2 iron catalyzed oxidation reaction) driven protein oxidation. It was found that the high ratio of intercellular Mn/Fe is linked to low protein oxidation and high radiation resistance. Mn mostly forms complexes with orthophosphate (O2-•) and peptidase. Mn defense system is effective in protecting DNA repair proteins, protein recovery and oxidation, but ineffective against DSBs. <br />
<br />
== '''DNA repair mechanism''' ==<br />
Precise and accurate DNA repair mechanism is of great importance for bacterial genome repairs caused by radiation stress. Sequence analysis in DNA repair hasn’t found a single protein conserved in all species. Protein recA is detected the highest percentage in the sequence analysis. RecA has a pivotal role in D. radiodurans DNA repair. RecA-mediated homologous recombination is crucial for DSB. RecA also interacts with Holliday junction resolvasome RuvABC. Apart from recA pathways, bacterium have a recA independent mechanism, non-homologous end joining (NHEJ). One third of the mechanism doesn’t require recA. The mechanism is based on proteins like DdrA, DdrB, SSB and RadA. RecA dependent/independent mechanisms are believed to interact with one another<br />
<br />
== '''Nucleotide condensation''' ==<br />
D. radiodurans has a more condensed genomic DNA to maintain DNA linearity and protection of free radicals formed in the cytoplasm. The ability of DNA linearity in the presence of DNA breaks highly increase repair possibility by not allowing DNA fragments to diffuse to higher distances. <br />
<br />
== '''Histone like proteins''' ==<br />
Histone like proteins (HU) are bacterial proteins that share a similar role as eukaryotic histones, the ability of DNA binding. HU can control gene expression and nucleotide organization. The bacteria constantly have high concentrations of HU present, so higher levels are not needed during radiation stress. HU doesn’t have the ability to bind on DNA fragments so it had to adapt a particular structure during evolution that would enable DNA fragment binding. HU binds to a four way DNA junction, and stabilizes recombination intermediates. <br />
<br />
= '''Lipid dynamics''' =<br />
Bacterial membranes have modified lipid, protein and carbohydrate compositions to survive in rough environments that were mentioned above. The membrane is the first line of defense from radiation. Although there isn’t a lipid structure that can’t block radiation, its ability to sustain radiation damage, adapt and integrate with other mechanisms separates them from radio intolerant organisms. Radiation can cause oxidation of membranes proteins and puncture. Although the mechanism isn’t still known it is believed that the protein antioxidant system protects membrane proteins which is of great importance because of the signal pathways, transportation and defense roles that the proteins have. Some changes in the fatty acid composition were found leading to change in membrane fluidity which is believed to have a signal role. Another possible resistance advantage is the presence of the S-layer D. radiodurans membrane. The loss of the S-layer lead to higher stress damage.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Mehanizmi_izjemne_odpornosti_proti_radioaktivnemu_sevanju_pri_prokariontih&diff=11631Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih2016-06-05T13:09:03Z<p>Nfrauskok: New page: Introduction Extremophiles are organism that live, metabolize and reproduce to human extreme conditions. We define a variety of extreme conditions such as high or low temperatures, pH, sa...</p>
<hr />
<div>Introduction <br />
Extremophiles are organism that live, metabolize and reproduce to human extreme conditions. We define a variety of extreme conditions such as high or low temperatures, pH, salinity, pressure and radiation. Scientists find this organisms extraordinary, especially their metabolism, mechanisms of DNA repair and protein antioxidants. The most impressive extremophile organisms are those resistant to high levels of ionizing radiation. Bacterium Deinococcus radiodurans can survive exposures as high as 15 kGy (Gray is an SI unit for absorbed radiation dose), while for humans a lethal dose is around 10 Gy and average bacterium around 200 Gy. Ionizing radiation causes severe damage on living cells such as formation of ROS, DNA single and double strand brakes, DNA extensive base modifications. Evidently some bacterium have mechanism that fight radiation damage. Due to lack of radioprotectors this bacterium ability rises high interest as a potential suppressor of radiation effects. Suppressing side effect on healthy cells in cancer radiations treatments would have enormous benefit as higher radiation doses would be allowed with better anticancer effect.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Popravljanje_mutacij_in_rekombinacijski_procesi&diff=11360Popravljanje mutacij in rekombinacijski procesi2016-04-18T17:24:50Z<p>Nfrauskok: </p>
<hr />
<div>V študijskem letu 2015/16 bodo seminarji obsegali dve med seboj povezani temi: Popravljanje okvar in mutacij ter mehanizme rekombinacije genetskega materiala. Tema je razdeljena na 18 poglavij, pri čemer zadnja poglavja zajemajo posebne primere in mehanizme popravljanja, ki niso vezani na DNA, pač pa na proces translacije pri poškodovani RNA, zadnji dve temi pa sta dodani kasneje in bosta predstavljeni v angleščini kot individualna seminarja. Kot izhodišče za pripravo si najprej preberite ustrezna poglavja v učbeniku, kjer so ta navedena na spodnjem seznamu. Naslove lahko v okviru danih izhodišč prilagodite, ne smete pa se odmakniti od osnovne teme seminarja. <br />
<br />
Vsako temo obdelajo praviloma dva ali trije študenti. Predlagate lahko tudi dodatne teme ali spremembe naslovov, če se vam to zdi smiselno. Vsaka skupina pripravi povzetek seminarja z vsaj 1000 besedami in ne več kot 1500 besedami in ga objavi na tem wikiju. Povzetek ne vsebuje slikovnega gradiva, lahko pa vključuje povezave do slik in videov na spletu. Navedite do 5 ključnih virov (ti ne štejejo v vsoto 1000 besed), ki ste jih uporabili. Osredotočite se na osnovno temo, ki ste si jo izbrali in vključite čim manj splošnega uvoda. Pripravite tudi predstavitev, dolgo pribl. 15 min. Razširjenega seminarja ni treba pripraviti v pisni obliki; napišete samo povzetek na wikiju in predstavite seminar v predavalnici. <br />
<br />
Vsaka skupina mora objaviti povzetek seminarja na wikiju najkasneje en dan pred predstavitvijo (do polnoči), torej najkasneje v nedeljo ali v torek za ponedeljkove oziroma sredine seminarje. Predstavitve seminarjev 1-4 bodo 23. maja, 5-8 25. maja, 9-12 30. maja, 13-16 1. junija 2016, 17-18 pa sta kratka seminarja in bosta na vrsti 6. junija. Za vsak seminar imate na voljo 14-18 minut časa, da ga predstavite, sledi pa razprava (~5 min.). Vsak član skupine mora predstaviti en del seminarja, pri čemer mora biti delo enakomerno razdeljeno med vse. V povzetku navedite, kdo je napisal kateri del (na wiki strani uporabite zavihek 'discussion').<br />
<br />
Vsebina seminarjev je izpitna snov, razen seminarjev št. 4 ter 13-18. <br />
<br />
<br />
Poglavja za seminarje so:<br />
<br />
# Direktno popravljanje mutacij (9.7)<br />
# Popravljanje z izcepom baze (9.8)<br />
# Popravljanjem z izcepom nukleotida (9.9)<br />
# Xeroderma pigmentosum<br />
# Popravljanje neujemanja (9.10)<br />
# SOS-popravljanje (9.11)<br />
# Popravljanje kolapsa replikacijskih vilic (10.1)<br />
# Mitozna rekombinacija (10.2)<br />
# Nehomologno povezovanje koncev (10.4)<br />
# Mejozna rekombinacija (10.5)<br />
# Razreševanje Hollidayevega križišča (15.6)<br />
# Popravljanje DNA v kontekstu kromatina (16.9)<br />
# Menjava spola pri kvasovki (15.9.)<br />
# Vloga p53 pri ohranjanju genoma (str. 400)<br />
# Trans-translacija (translacija pri poškodovani mRNA)<br />
# Od RNA neodvisna elongacija (Science 347, 75 (2015)<br />
# Mehanizmi izjemne odpornosti proti radioaktivnemu sevanju pri prokariontih<br />
# Kompleksne preureditve kromosomov<br />
<br />
<br />
----<br />
<br />
Vpišite se v oklepaj za naslovom seminarja:<br />
<br />
<br />
# Direktno popravljanje mutacij<br />
# Popravljanje z izcepom baze (Urša Čerček, Urša Kopač, Ema Gašperšič)<br />
# Popravljanjem z izcepom nukleotida (Petra Hruševar, Gašper Žun, Uroš Zavrtanik)<br />
# Xeroderma pigmentosum (Maja Zupanc, Elvira Boršič)<br />
# Popravljanje neujemanja (Kristjan Stibilj, Rok Miklavčič, Sara Tekavec)<br />
# SOS-popravljanje (Tadej Satler, Gašper Virant)<br />
# Popravljanje kolapsa replikacijskih vilic (Tilen Tršelič, Klara Lenart)<br />
# Mitozna rekombinacija (Peter Pečan, Valentina Levak, Janja Krapež)<br />
# Nehomologno povezovanje koncev (Klara Kuret, Blaž Lebar, Neža Koritnik)<br />
# Mejozna rekombinacija (Eva Rajh, Katja Čop)<br />
# Razreševanje Hollidayevega križišča (Nejc Kejžar, Lovro Kotnik)<br />
# Popravljanje DNA v kontekstu kromatina (Špela Malenšek, Tjaša Lukšič)<br />
# Menjava spola pri kvasovki <br />
# Vloga p53 pri ohranjanju genoma (Miha Koprivnikar Krajnc, Katja Brezovar)<br />
# Trans-translacija (Lara Jerman, Aleksandra Uzar, Simon Aleksič)<br />
# Od RNA neodvisna elongacija<br />
# "Unraveling the mechanisms of extreme radioresistance in prokaryotes: Lessons from nature"(Fran Krstanović)<br />
# "Mechanisms of origin, phenotypic effects and diagnostic implications of complex chromosome rearrangements" (Javier Fraguas)<br />
<br />
<br />
<br />
Naslov teme povežite z novo wiki-stranjo, na katero napišite povzetek. Na koncu besedila (pod viri) v novo vrstico dodajte oznaki: <br />
<nowiki>[[Category:SEM]] [[Category:BMB]]</nowiki> <br />
<br />
Primer, kako so bili urejeni seminarji v prejšnjih letih, si lahko ogledate na strani [[Reprogramiranje celic]].</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=Popravljanje_mutacij_in_rekombinacijski_procesi&diff=11343Popravljanje mutacij in rekombinacijski procesi2016-04-05T21:44:20Z<p>Nfrauskok: </p>
<hr />
<div>V študijskem letu 2015/16 bodo seminarji obsegali dve med seboj povezani temi: Popravljanje okvar in mutacij ter mehanizme rekombinacije genetskega materiala. Tema je razdeljena na 16 poglavij, pri čemer zadnja poglavja zajemajo posebne primere in mehanizme popravljanja, ki niso vezani na DNA, pač pa na proces translacije pri poškodovani RNA. Kot izhodišče za pripravo si najprej preberite ustrezna poglavja v učbeniku, kjer so ta navedena na spodnjem seznamu. Naslove lahko v okviru danih izhodišč prilagodite, ne smete pa se odmakniti od osnovne teme seminarja. <br />
<br />
Vsako temo obdelajo praviloma dva ali trije študenti. Predlagate lahko tudi dodatne teme ali spremembe naslovov, če se vam to zdi smiselno. Vsaka skupina pripravi povzetek seminarja z vsaj 1000 besedami in ne več kot 1500 besedami in ga objavi na tem wikiju. Povzetek ne vsebuje slikovnega gradiva, lahko pa vključuje povezave do slik in videov na spletu. Navedite do 5 ključnih virov (ti ne štejejo v vsoto 1000 besed), ki ste jih uporabili. Osredotočite se na osnovno temo, ki ste si jo izbrali in vključite čim manj splošnega uvoda. Pripravite tudi predstavitev, dolgo pribl. 15 min. Razširjenega seminarja ni treba pripraviti v pisni obliki; napišete samo povzetek na wikiju in predstavite seminar v predavalnici. <br />
<br />
Vsaka skupina mora objaviti povzetek seminarja na wikiju najkasneje en dan pred predstavitvijo (do polnoči), torej najkasneje v nedeljo ali v torek za ponedeljkove oziroma sredine seminarje. Predstavitve seminarjev 1-4 bodo 23. maja, 5-8 25. maja, 9-12 30. maja, 13-16 pa 1. junija 2016. Za vsak seminar imate na voljo 14-18 minut časa, da ga predstavite, sledi pa razprava (~5 min.). Vsak član skupine mora predstaviti en del seminarja, pri čemer mora biti delo enakomerno razdeljeno med vse. V povzetku navedite, kdo je napisal kateri del (na wiki strani uporabite zavihek 'discussion').<br />
<br />
Vsebina seminarjev je izpitna snov, razen seminarjev št. 4 ter 13-16. <br />
<br />
<br />
Poglavja za seminarje so:<br />
<br />
# Direktno popravljanje mutacij (9.7)<br />
# Popravljanje z izcepom baze (9.8)<br />
# Popravljanjem z izcepom nukleotida (9.9)<br />
# Xeroderma pigmentosum<br />
# Popravljanje neujemanja (9.10)<br />
# SOS-popravljanje (9.11)<br />
# Popravljanje kolapsa replikacijskih vilic (10.1)<br />
# Mitozna rekombinacija (10.2)<br />
# Nehomologno povezovanje koncev (10.4)<br />
# Mejozna rekombinacija (10.5)<br />
# Razreševanje Hollidayevega križišča (15.6)<br />
# Popravljanje DNA v kontekstu kromatina (16.9)<br />
# Menjava spola pri kvasovki (15.9.)<br />
# Vloga p53 pri ohranjanju genoma (str. 400)<br />
# Trans-translacija (translacija pri poškodovani mRNA)<br />
# Od RNA neodvisna elongacija (Science 347, 75 (2015)<br />
<br />
<br />
----<br />
<br />
Vpišite se v oklepaj za naslovom seminarja:<br />
<br />
<br />
# Direktno popravljanje mutacij<br />
# Popravljanje z izcepom baze (Urša Čerček, Urša Kopač, Ema Gašperšič)<br />
# Popravljanjem z izcepom nukleotida (Petra Hruševar, Gašper Žun, Uroš Zavrtanik)<br />
# Xeroderma pigmentosum (Maja Zupanc, Elvira Boršič)<br />
# Popravljanje neujemanja<br />
# SOS-popravljanje (Tadej Satler, Gašper Virant)<br />
# Popravljanje kolapsa replikacijskih vilic (Tilen Tršelič, Klara Lenart)<br />
# Mitozna rekombinacija (Peter Pečan, Valentina Levak)<br />
# Nehomologno povezovanje koncev (Klara Kuret, Blaž Lebar, Neža Koritnik)<br />
# Mejozna rekombinacija (Eva Rajh, Katja Čop)<br />
# Razreševanje Hollidayevega križišča (Nejc Kejžar, Lovro Kotnik)<br />
# Popravljanje DNA v kontekstu kromatina (Špela Malenšek, Tjaša Lukšič)<br />
# Menjava spola pri kvasovki (Kristjan Stibilj, Rok Miklavčič, Sara Tekavec)<br />
# Vloga p53 pri ohranjanju genoma (Miha Koprivnikar Krajnc, Katja Brezovar)<br />
# Trans-translacija (Lara Jerman, Aleksandra Uzar)<br />
# Od RNA neodvisna elongacija<br />
# "Unraveling the mechanisms of extreme radioresistance in prokaryotes: Lessons from nature"(Fran Krstanović)<br />
<br />
<br />
<br />
Naslov teme povežite z novo wiki-stranjo, na katero napišite povzetek. Na koncu besedila (pod viri) v novo vrstico dodajte oznaki: <br />
<nowiki>[[Category:SEM]] [[Category:BMB]]</nowiki> <br />
<br />
Primer, kako so bili urejeni seminarji v prejšnjih letih, si lahko ogledate na strani [[Reprogramiranje celic]].</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=BIO2_Seminar_2015&diff=10844BIO2 Seminar 20152015-11-17T16:54:05Z<p>Nfrauskok: /* Seznam seminarjev */</p>
<hr />
<div>= Biokemijski seminar =<br />
doc. dr. Gregor Gunčar, K2.022<br />
<br />
== Seznam seminarjev ==<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Ime Priimek'''<br />
| align="center" style="background:#f0f0f0;"|'''poglavje'''<br />
| align="center" style="background:#f0f0f0;"|'''Naslov seminarja'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 1'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 2'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum oddaje'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum recenzije'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''<br />
|-<br />
| Kristjan Stibilj||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Kristjan_Stibilj:_Inhibicija PI3k/AKT/mTOR signalne poti kot orožje proti raku||Lovro Kotnik||Blaž Lebar]||21/10/15||23/10/15||28/10/15<br />
|-<br />
| Tjaša Lukšič||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tjasa_Luksic: Alternativno izrezovanje GPCR-jev s poudarkom na sekretinski družini]||Karmen Žbogar||Aleksandra Uzar||21/10/15||23/10/15||28/10/15<br />
|-<br />
| Klara Kuret||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Klara_Kuret: Vpliv bakterijskih efektorjev na celični ubikvitinacijski sistem in rastlinski imunski odziv]||Klara Lenart||Petra Hruševar||21/10/15||23/10/15||28/10/15<br />
|-<br />
| Rok Miklavčič||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Rok_Miklavčič: Preusmeritve signalnih poti preko TNFR1 v boju s patogeni]||Katja Čop||Lovro Kotnik||28/10/15||30/10/15||04/11/15<br />
|-<br />
| Ema Gašperšič||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Ema_Gaspersic: PKC in njihov vpliv na raka ter Alzheimerjevo bolezen]||Nejc Kejžar||Karmen Žbogar||28/10/15||30/10/15||04/11/15<br />
|-<br />
| Tadej Satler||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tadej_Satler: PD-1 limfocitov in melanomskih celic]||Neža Brezovar||Klara Lenart||28/10/15||30/10/15||04/11/15<br />
|-<br />
| Tina Šimunović||14-15||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tina_Simunovic: Pentoza-fosfatna pot, njena regulacija in povezava z rakom]||Kristjan Stibilj||Katja Čop||04/11/15||06/11/15||11/11/15<br />
|-<br />
| Maja Zupanc||14-15||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Maja_Zupanc: Kako dolge nekodirajoče RNA vplivajo na metabolizem]||Tjaša Lukšič||Nejc Kejžar||04/11/15||06/11/15||11/11/15<br />
|-<br />
| Tilen Tršelič||14-15||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tilen_Trselic: PKM2 in njegova vloga pri razvoju rakavih celic]||Klara Kuret||Dorotea Borković||04/11/15||06/11/15||11/11/15<br />
|-<br />
| Lara Jerman||16||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Lara_Jerman: Warburgov učinek: od raka do avtoimunosti]||Rok Miklavčič||Neža Brezovar||11/11/15||13/11/15||18/11/15<br />
|-<br />
| Eva Rajh||16||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Eva_Rajh: Vpliv intermediatov Krebsovega cikla na modifikacije DNK in histonov ter vpliv na staranje]||Ema Gašperšič||Kristjan Stibilj||11/11/15||13/11/15||18/11/15<br />
|-<br />
| Sara Tekavec||16||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Sara_Tekavec: Mutacije encimov Krebsovega cikla in vpliv na razvoj ter rast tumorjev]||Tadej Satler||Tjaša Lukšič||11/11/15||13/11/15||18/11/15<br />
|-<br />
| Fran Krstanović||17||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Fran_Krstanovic: L-Carnitine enhances exercise endurance capacity]||Tina Šimunović||Klara Kuret||18/11/15||20/11/15||25/11/15<br />
|-<br />
| Elvira Boršić||17||Posledice spremenjenega metabolizma maščobnih kislin v kardiomiocitih||Maja Zupanc||Rok Miklavčič||18/11/15||20/11/15||25/11/15<br />
|-<br />
| Janja Krapež||17||||Tilen Tršelič||Ema Gašperšič||18/11/15||20/11/15||25/11/15<br />
|-<br />
| Janez Javornik||18||||Lara Jerman||Tadej Satler||25/11/15||27/11/15||02/12/15<br />
|-<br />
| Miha Koprivnikar Krajnc||18||||Eva Rajh||Tina Šimunović||25/11/15||27/11/15||02/12/15<br />
|-<br />
| Špela Malenšek||18|| Aminokislinska regulacija mTORC1||Sara Tekavec||Maja Zupanc||25/11/15||27/11/15||02/12/15<br />
|-<br />
| Urša Kopač||19||||Fran Krstanović||Tilen Tršelič||02/12/15||04/12/15||09/12/15<br />
|-<br />
| Neža Koritnik||19||Uravnavanje koncentracije ROS v mitohondriju z glutationilacijo||Dorotea Borković||Lara Jerman||02/12/15||04/12/15||09/12/15<br />
|-<br />
| Gašper Virant||19||||Elvira Boršić||Eva Rajh||02/12/15||04/12/15||09/12/15<br />
|-<br />
| Uroš Zavrtanik||20||||Janja Krapež||Sara Tekavec||09/12/15||11/12/15||16/12/15<br />
|-<br />
| Simon Aleksič||20||||Janez Javornik||Fran Krstanović||09/12/15||11/12/15||16/12/15<br />
|-<br />
| Matej Hvalec||20||||Miha Koprivnikar Krajnc||Elvira Boršić||09/12/15||11/12/15||16/12/15<br />
|-<br />
| Urša Čerček||21||||Špela Malenšek||Janja Krapež||16/12/15||18/12/15||23/12/15<br />
|-<br />
| Katja Brezovar||21||Vloga sfingolipidov pri fagocitozi ''Candide albicans''||Urša Kopač||Janez Javornik||16/12/15||18/12/15||23/12/15<br />
|-<br />
| Gašper Žun||21||||Neža Koritnik||Miha Koprivnikar Krajnc||16/12/15||18/12/15||23/12/15<br />
|-<br />
| Blaž Lebar||22||||Gašper Virant||Špela Malenšek||23/12/15||03/01/16||06/01/16<br />
|-<br />
| Aleksandra Uzar||22||||Uroš Zavrtanik||Urša Kopač||23/12/15||03/01/16||06/01/16<br />
|-<br />
| Petra Hruševar||22||||Simon Aleksič||Neža Koritnik||23/12/15||03/01/16||06/01/16<br />
|-<br />
| Dorotea Borković||23||||Matej Hvalec||Gašper Virant||06/01/16||08/01/16||12/01/16<br />
|-<br />
| Karmen Žbogar||23||||Katja Brezovar||Simon Aleksič||06/01/16||08/01/16||13/01/16<br />
|-<br />
| Klara Lenart||23||||Gašper Žun||Matej Hvalec||06/01/16||08/01/16||13/01/16<br />
|-<br />
| Lovro Kotnik||23||||Urša Čerček||Uroš Zavrtanik||06/01/16||08/01/16||13/01/16<br />
|-<br />
| Katja Čop||23||||Blaž Lebar||Urša Čerček||13/01/16||15/01/16||20/01/16<br />
|-<br />
| Nejc Kejžar||23||Hormonska regulacija razvoja T-celic||Aleksandra Uzar||Katja Brezovar||13/01/16||15/01/16||20/01/16<br />
|-<br />
| Neža Brezovar||23||||Petra Hruševar||Gašper Žun||13/01/16||15/01/16||20/01/16<br />
|}<br />
<br />
*številka v okencu za temo pomeni poglavje v Lehningerju, v katerega naj izbrana tema spada<br />
<br />
== Gradivo za predavanja ==<br />
Gradivo za predavanja in seminarje najdete na http://bio.ijs.si/~zajec/bio2/<br />
username: bio2<br />
password: samozame<br />
<br />
==Naloga==<br />
'''Vaša naloga za seminar je:<br>'''<br />
Samostojno pripraviti seminar o seminarski temi, ki vam je bila dodeljena. Za osnovo morate vzeti pregledni članek iz revije, ki ima faktor vpliva nad 5 (npr. [http://www.sciencedirect.com/science/journal/09680004/ TIBS]. Poiskati morate še vsaj tri znanstvene članke, ki se nanašajo na opisano temo in jih uporabiti kot podlago za seminarsko nalogo! Članki so dostopni [http://93.174.95.27/scimag/ tukaj].<br />
<br />
Za pripravo seminarja velja naslednje:<br><br />
* [[BIO2 Povzetki seminarjev 2015|Povzetek seminarja]] opišete na wikiju '''v 200 besedah''' (+- dvajset besed) - najkasneje do dne ko morate oddati seminar recenzentom. <br />
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.<br />
* Seminar pripravite v obliki seminarske naloge na ~5-12 straneh A4 (pisava 12, enojni razmak, 2,5 cm robovi). Zelo pomembno je, da je obseg od <font color=red>2700 do 3000 besed </font>, a ne več kot 3500 besed. Seminarska naloga mora vsebovati najmanj tri slike. <font color=red>Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko. </font><br />
* Seminar oddajte do datuma oddaje, ki je naveden v tabeli v elektronski obliki z uporabo [http://bio.ijs.si/~zajec/poslji/ tega obrazca].<br />
* Vsi seminarji so v elektronski obliki dostopni [http://bio.ijs.si/~zajec/poslji/bioseminar/ tukaj].<br />
* Recenzenti do dneva določenega v tabeli določijo popravke (v elektronski obliki) in podajo oceno pisnega dela. Popravljen seminar oddajte z uporabo [http://bio.ijs.si/~zajec/poslji/ tega obrazca].<br />
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 20 minut. Recenzenti morajo biti na predstavitvi prisotni.<br />
* Predstavitvi sledi razprava. Recenzenti podajo oceno predstavitve in postavijo najmanj dve vprašanji.Vsi ostali morajo postaviti še dve dodatni vprašanji v toku celega seminarskega obdobja.<br />
* Na dan predstavitve morate docentu še pred predstavitvijo oddati končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu, elektronsko verzijo seminarja in predstavitev pa oddati na strežnik na dan predstavitve do polnoči.<br />
* Seminarska naloga in povzetek morajo biti v slovenskem jeziku, razen za študente, katerih materni jezik ni slovenščina. Ti lahko oddajo seminar v angleškem jeziku.<br />
<br />
==<font color=green>Imena datotek</font>==<br />
Prosim vas, da vse datoteke, ki mi jih pošiljate poimenujete po naslednjem receptu:<br />
* 312_BIO_Priimek_Ime.doc(x) za seminar, npr. 312_BIO_Guncar_Gregor.docx<br />
* 312_BIO_Priimek_ime_final.doc(x) za končno verzijo seminarja<br />
* 312_BIO_Priimek_Ime_rec_Priimek2.doc(x) za recenzijo, kjer je Priimek2 priimek recenzenta, npr. 312_BIO_Guncar_Gregor_rec_Scott.docx (če se pišete Scott in odajate recenzijo za seminar, ki ga je napisal Gunčar)<br />
* 312_BIO_Priimek_Ime.ppt(x) za prezentacijo, npr 312_BIO_Guncar_Gregor.pptx<br />
* <font color=green>312_BIO_Priimek_ime_poprava.doc(x) za popravljeno končno verzijo seminarja, če so popravki manjši<br />
* 116_BIO_Priimek_Ime.doc(x) za seminar, ki je napisan na novo in je bil prijavljen v shemo 50%</font><br />
<br />
==Ocenjevanje seminarjev==<br />
Recenzenti ocenijo seminar tako, da izpolnijo [https://docs.google.com/forms/d/1EQDYwFO-DEzZ2R7jf8DhLqIeV4FFxRd3-ScceEASpt4/viewform recenzentsko poročilo] na spletu. Recenzentsko poročilo morate oddati najkasneje do 21:00, en dan pred predstavitvijo seminarja.<br />
<br />
== Mnenje o predstavitvi ==<br />
Vsak posameznik odda svoje mnenje o predstavitvi takoj po predstavitvi z online glasovanjem.<br />
<br />
==Urejanje spletnih strani na wikiju==<br />
Wiki so razvili zato, da lahko spletne vsebine ureja vsakdo. Ukazi so preprosti, dokler si ne zamislite česa prav posebnega. Vseeno pa je Word v primerjavi z wikijem pravo čudežno orodje... Če imate težave z oblikovanjem besedila, si preberite poglavje o urejanju wiki-strani na Wikipediji ([http://en.wikipedia.org/wiki/Help:Editing tule] v angleščini in [http://sl.wikipedia.org/wiki/Wikipedija:Urejanje_strani tu] v slovenščini). Pomaga tudi, če pogledate, kako je zapisana kakšna stran, ki se vam zdi v redu: kliknite na zavihek 'Uredite stran' in si poglejte, kako so vpisane povezave, kako nov odstavek in podobno. ''Na koncu seveda pod oknom za urejanje kliknite na 'Prekliči'.''<br />
<br />
==Citiranje virov==<br />
Citiranje je možno po več shemah, važno je, da se držite ene same. V seminarskih nalogah in diplomskih nalogah FKKT uprabljajte shemo citiranja, ki je pobarvana <font color=green>zeleno</font>.<br />
Temeljno načelo je, da je treba vir navesti na tak način, da ga je mogoče nedvoumno poiskati.<br />
Za citate v naravoslovju je najpogostejše citiranje po pravilniku ISO 690. [http://www.zveza-zotks.si/gzm/dokumenti/literatura.html Pravila], ki upoštevajo omenjeni standard, so pripravili pri ZTKS. Sicer pa ima vsaka revija lahko svoj način citiranja, ki ga je treba pri pisanju članka upoštevati.<br><br />
'''Citiranje knjig:'''<br><br />
Priimek, I. ''Naslov''. Kraj: Založba, letnica.<br><br />
Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN.<br><br />
<br />
Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005.<br><br />
Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4.<br><br />
Če so avtorji trije, je beseda in med drugim in tretjim avtorjem. Če so avtorji več kot trije, napišemo samo prvega in dopišemo ''et al''. (in drugi, po latinsko). Vse, kar je latinsko, pišemo poševno (npr. tudi imena rastlin in živali, pojme ''in vivo'', ''in vitro'' ipd.). <br />
<br />
'''Citiranje člankov:'''<br><br />
Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani.<br><br />
<font color=green>Lartigue, C., Glass, J. I., Alperovich, N., Pieper, R., Parmar, P. P., Hutchison III, C. A., Smith, H. O. in Venter, J. C.<br />
Genome transplantation in bacteria: changing one species to another. ''Science'', 2007, 317, str. 632-638.</font><br />
<br />
Alternativni način citiranja (predvsem v družboslovju) je po pravilih APA, kjer članke citirajo takole:<br><br />
Priimek, I. (letnica, številka). Naslov. Naslov revije, strani.<br><br />
Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.<br />
<br />
Revija Science uporablja skrajšani zapis:<br><br />
C. Lartigue ''et al''. Science 317, 632 (2007)<br><br />
<br />
V diplomah na FKKT je treba navesti vire tako, da izpišete tudi naslov citiranega dela in strani od-do (ne samo začetne). Navesti morate tudi vse avtorje dela, razen v primeru, ko jih je 10 ali več. Takrat navedite le prvih devet, za ostale pa uporabite okrajšavo in sod. (in sodelavci). Pred zadnjim avtorjem naj bo vedno besedica "in". <br />
<br />
<br />
'''Citiranje spletnih virov:'''<br><br />
Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov<br><br />
strangeguitars. ''On the brink of artificial life''. 6. 10. 2007. [citirano 13. 11. 2007] http://www.metafilter.com/65331/On-the-brink-of-artificial-life<br><br />
Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=BIO2_Seminar_2015&diff=10843BIO2 Seminar 20152015-11-17T16:50:53Z<p>Nfrauskok: /* Seznam seminarjev */</p>
<hr />
<div>= Biokemijski seminar =<br />
doc. dr. Gregor Gunčar, K2.022<br />
<br />
== Seznam seminarjev ==<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Ime Priimek'''<br />
| align="center" style="background:#f0f0f0;"|'''poglavje'''<br />
| align="center" style="background:#f0f0f0;"|'''Naslov seminarja'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 1'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 2'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum oddaje'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum recenzije'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''<br />
|-<br />
| Kristjan Stibilj||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Kristjan_Stibilj:_Inhibicija PI3k/AKT/mTOR signalne poti kot orožje proti raku||Lovro Kotnik||Blaž Lebar]||21/10/15||23/10/15||28/10/15<br />
|-<br />
| Tjaša Lukšič||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tjasa_Luksic: Alternativno izrezovanje GPCR-jev s poudarkom na sekretinski družini]||Karmen Žbogar||Aleksandra Uzar||21/10/15||23/10/15||28/10/15<br />
|-<br />
| Klara Kuret||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Klara_Kuret: Vpliv bakterijskih efektorjev na celični ubikvitinacijski sistem in rastlinski imunski odziv]||Klara Lenart||Petra Hruševar||21/10/15||23/10/15||28/10/15<br />
|-<br />
| Rok Miklavčič||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Rok_Miklavčič: Preusmeritve signalnih poti preko TNFR1 v boju s patogeni]||Katja Čop||Lovro Kotnik||28/10/15||30/10/15||04/11/15<br />
|-<br />
| Ema Gašperšič||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Ema_Gaspersic: PKC in njihov vpliv na raka ter Alzheimerjevo bolezen]||Nejc Kejžar||Karmen Žbogar||28/10/15||30/10/15||04/11/15<br />
|-<br />
| Tadej Satler||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tadej_Satler: PD-1 limfocitov in melanomskih celic]||Neža Brezovar||Klara Lenart||28/10/15||30/10/15||04/11/15<br />
|-<br />
| Tina Šimunović||14-15||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tina_Simunovic: Pentoza-fosfatna pot, njena regulacija in povezava z rakom]||Kristjan Stibilj||Katja Čop||04/11/15||06/11/15||11/11/15<br />
|-<br />
| Maja Zupanc||14-15||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Maja_Zupanc: Kako dolge nekodirajoče RNA vplivajo na metabolizem]||Tjaša Lukšič||Nejc Kejžar||04/11/15||06/11/15||11/11/15<br />
|-<br />
| Tilen Tršelič||14-15||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tilen_Trselic: PKM2 in njegova vloga pri razvoju rakavih celic]||Klara Kuret||Dorotea Borković||04/11/15||06/11/15||11/11/15<br />
|-<br />
| Lara Jerman||16||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Lara_Jerman: Warburgov učinek: od raka do avtoimunosti]||Rok Miklavčič||Neža Brezovar||11/11/15||13/11/15||18/11/15<br />
|-<br />
| Eva Rajh||16||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Eva_Rajh: Vpliv intermediatov Krebsovega cikla na modifikacije DNK in histonov ter vpliv na staranje]||Ema Gašperšič||Kristjan Stibilj||11/11/15||13/11/15||18/11/15<br />
|-<br />
| Sara Tekavec||16||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Sara_Tekavec: Mutacije encimov Krebsovega cikla in vpliv na razvoj ter rast tumorjev]||Tadej Satler||Tjaša Lukšič||11/11/15||13/11/15||18/11/15<br />
|-<br />
| Fran Krstanović||17||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Fran Krstanovic: L-Carnitine enhances exercise endurance capacity]||L-Carnitine enhances exercise endurance capacity||Tina Šimunović||Klara Kuret||18/11/15||20/11/15||25/11/15<br />
|-<br />
| Elvira Boršić||17||Posledice spremenjenega metabolizma maščobnih kislin v kardiomiocitih||Maja Zupanc||Rok Miklavčič||18/11/15||20/11/15||25/11/15<br />
|-<br />
| Janja Krapež||17||||Tilen Tršelič||Ema Gašperšič||18/11/15||20/11/15||25/11/15<br />
|-<br />
| Janez Javornik||18||||Lara Jerman||Tadej Satler||25/11/15||27/11/15||02/12/15<br />
|-<br />
| Miha Koprivnikar Krajnc||18||||Eva Rajh||Tina Šimunović||25/11/15||27/11/15||02/12/15<br />
|-<br />
| Špela Malenšek||18|| Aminokislinska regulacija mTORC1||Sara Tekavec||Maja Zupanc||25/11/15||27/11/15||02/12/15<br />
|-<br />
| Urša Kopač||19||||Fran Krstanović||Tilen Tršelič||02/12/15||04/12/15||09/12/15<br />
|-<br />
| Neža Koritnik||19||Uravnavanje koncentracije ROS v mitohondriju z glutationilacijo||Dorotea Borković||Lara Jerman||02/12/15||04/12/15||09/12/15<br />
|-<br />
| Gašper Virant||19||||Elvira Boršić||Eva Rajh||02/12/15||04/12/15||09/12/15<br />
|-<br />
| Uroš Zavrtanik||20||||Janja Krapež||Sara Tekavec||09/12/15||11/12/15||16/12/15<br />
|-<br />
| Simon Aleksič||20||||Janez Javornik||Fran Krstanović||09/12/15||11/12/15||16/12/15<br />
|-<br />
| Matej Hvalec||20||||Miha Koprivnikar Krajnc||Elvira Boršić||09/12/15||11/12/15||16/12/15<br />
|-<br />
| Urša Čerček||21||||Špela Malenšek||Janja Krapež||16/12/15||18/12/15||23/12/15<br />
|-<br />
| Katja Brezovar||21||Vloga sfingolipidov pri fagocitozi ''Candide albicans''||Urša Kopač||Janez Javornik||16/12/15||18/12/15||23/12/15<br />
|-<br />
| Gašper Žun||21||||Neža Koritnik||Miha Koprivnikar Krajnc||16/12/15||18/12/15||23/12/15<br />
|-<br />
| Blaž Lebar||22||||Gašper Virant||Špela Malenšek||23/12/15||03/01/16||06/01/16<br />
|-<br />
| Aleksandra Uzar||22||||Uroš Zavrtanik||Urša Kopač||23/12/15||03/01/16||06/01/16<br />
|-<br />
| Petra Hruševar||22||||Simon Aleksič||Neža Koritnik||23/12/15||03/01/16||06/01/16<br />
|-<br />
| Dorotea Borković||23||||Matej Hvalec||Gašper Virant||06/01/16||08/01/16||12/01/16<br />
|-<br />
| Karmen Žbogar||23||||Katja Brezovar||Simon Aleksič||06/01/16||08/01/16||13/01/16<br />
|-<br />
| Klara Lenart||23||||Gašper Žun||Matej Hvalec||06/01/16||08/01/16||13/01/16<br />
|-<br />
| Lovro Kotnik||23||||Urša Čerček||Uroš Zavrtanik||06/01/16||08/01/16||13/01/16<br />
|-<br />
| Katja Čop||23||||Blaž Lebar||Urša Čerček||13/01/16||15/01/16||20/01/16<br />
|-<br />
| Nejc Kejžar||23||Hormonska regulacija razvoja T-celic||Aleksandra Uzar||Katja Brezovar||13/01/16||15/01/16||20/01/16<br />
|-<br />
| Neža Brezovar||23||||Petra Hruševar||Gašper Žun||13/01/16||15/01/16||20/01/16<br />
|}<br />
<br />
*številka v okencu za temo pomeni poglavje v Lehningerju, v katerega naj izbrana tema spada<br />
<br />
== Gradivo za predavanja ==<br />
Gradivo za predavanja in seminarje najdete na http://bio.ijs.si/~zajec/bio2/<br />
username: bio2<br />
password: samozame<br />
<br />
==Naloga==<br />
'''Vaša naloga za seminar je:<br>'''<br />
Samostojno pripraviti seminar o seminarski temi, ki vam je bila dodeljena. Za osnovo morate vzeti pregledni članek iz revije, ki ima faktor vpliva nad 5 (npr. [http://www.sciencedirect.com/science/journal/09680004/ TIBS]. Poiskati morate še vsaj tri znanstvene članke, ki se nanašajo na opisano temo in jih uporabiti kot podlago za seminarsko nalogo! Članki so dostopni [http://93.174.95.27/scimag/ tukaj].<br />
<br />
Za pripravo seminarja velja naslednje:<br><br />
* [[BIO2 Povzetki seminarjev 2015|Povzetek seminarja]] opišete na wikiju '''v 200 besedah''' (+- dvajset besed) - najkasneje do dne ko morate oddati seminar recenzentom. <br />
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.<br />
* Seminar pripravite v obliki seminarske naloge na ~5-12 straneh A4 (pisava 12, enojni razmak, 2,5 cm robovi). Zelo pomembno je, da je obseg od <font color=red>2700 do 3000 besed </font>, a ne več kot 3500 besed. Seminarska naloga mora vsebovati najmanj tri slike. <font color=red>Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko. </font><br />
* Seminar oddajte do datuma oddaje, ki je naveden v tabeli v elektronski obliki z uporabo [http://bio.ijs.si/~zajec/poslji/ tega obrazca].<br />
* Vsi seminarji so v elektronski obliki dostopni [http://bio.ijs.si/~zajec/poslji/bioseminar/ tukaj].<br />
* Recenzenti do dneva določenega v tabeli določijo popravke (v elektronski obliki) in podajo oceno pisnega dela. Popravljen seminar oddajte z uporabo [http://bio.ijs.si/~zajec/poslji/ tega obrazca].<br />
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 20 minut. Recenzenti morajo biti na predstavitvi prisotni.<br />
* Predstavitvi sledi razprava. Recenzenti podajo oceno predstavitve in postavijo najmanj dve vprašanji.Vsi ostali morajo postaviti še dve dodatni vprašanji v toku celega seminarskega obdobja.<br />
* Na dan predstavitve morate docentu še pred predstavitvijo oddati končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu, elektronsko verzijo seminarja in predstavitev pa oddati na strežnik na dan predstavitve do polnoči.<br />
* Seminarska naloga in povzetek morajo biti v slovenskem jeziku, razen za študente, katerih materni jezik ni slovenščina. Ti lahko oddajo seminar v angleškem jeziku.<br />
<br />
==<font color=green>Imena datotek</font>==<br />
Prosim vas, da vse datoteke, ki mi jih pošiljate poimenujete po naslednjem receptu:<br />
* 312_BIO_Priimek_Ime.doc(x) za seminar, npr. 312_BIO_Guncar_Gregor.docx<br />
* 312_BIO_Priimek_ime_final.doc(x) za končno verzijo seminarja<br />
* 312_BIO_Priimek_Ime_rec_Priimek2.doc(x) za recenzijo, kjer je Priimek2 priimek recenzenta, npr. 312_BIO_Guncar_Gregor_rec_Scott.docx (če se pišete Scott in odajate recenzijo za seminar, ki ga je napisal Gunčar)<br />
* 312_BIO_Priimek_Ime.ppt(x) za prezentacijo, npr 312_BIO_Guncar_Gregor.pptx<br />
* <font color=green>312_BIO_Priimek_ime_poprava.doc(x) za popravljeno končno verzijo seminarja, če so popravki manjši<br />
* 116_BIO_Priimek_Ime.doc(x) za seminar, ki je napisan na novo in je bil prijavljen v shemo 50%</font><br />
<br />
==Ocenjevanje seminarjev==<br />
Recenzenti ocenijo seminar tako, da izpolnijo [https://docs.google.com/forms/d/1EQDYwFO-DEzZ2R7jf8DhLqIeV4FFxRd3-ScceEASpt4/viewform recenzentsko poročilo] na spletu. Recenzentsko poročilo morate oddati najkasneje do 21:00, en dan pred predstavitvijo seminarja.<br />
<br />
== Mnenje o predstavitvi ==<br />
Vsak posameznik odda svoje mnenje o predstavitvi takoj po predstavitvi z online glasovanjem.<br />
<br />
==Urejanje spletnih strani na wikiju==<br />
Wiki so razvili zato, da lahko spletne vsebine ureja vsakdo. Ukazi so preprosti, dokler si ne zamislite česa prav posebnega. Vseeno pa je Word v primerjavi z wikijem pravo čudežno orodje... Če imate težave z oblikovanjem besedila, si preberite poglavje o urejanju wiki-strani na Wikipediji ([http://en.wikipedia.org/wiki/Help:Editing tule] v angleščini in [http://sl.wikipedia.org/wiki/Wikipedija:Urejanje_strani tu] v slovenščini). Pomaga tudi, če pogledate, kako je zapisana kakšna stran, ki se vam zdi v redu: kliknite na zavihek 'Uredite stran' in si poglejte, kako so vpisane povezave, kako nov odstavek in podobno. ''Na koncu seveda pod oknom za urejanje kliknite na 'Prekliči'.''<br />
<br />
==Citiranje virov==<br />
Citiranje je možno po več shemah, važno je, da se držite ene same. V seminarskih nalogah in diplomskih nalogah FKKT uprabljajte shemo citiranja, ki je pobarvana <font color=green>zeleno</font>.<br />
Temeljno načelo je, da je treba vir navesti na tak način, da ga je mogoče nedvoumno poiskati.<br />
Za citate v naravoslovju je najpogostejše citiranje po pravilniku ISO 690. [http://www.zveza-zotks.si/gzm/dokumenti/literatura.html Pravila], ki upoštevajo omenjeni standard, so pripravili pri ZTKS. Sicer pa ima vsaka revija lahko svoj način citiranja, ki ga je treba pri pisanju članka upoštevati.<br><br />
'''Citiranje knjig:'''<br><br />
Priimek, I. ''Naslov''. Kraj: Založba, letnica.<br><br />
Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN.<br><br />
<br />
Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005.<br><br />
Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4.<br><br />
Če so avtorji trije, je beseda in med drugim in tretjim avtorjem. Če so avtorji več kot trije, napišemo samo prvega in dopišemo ''et al''. (in drugi, po latinsko). Vse, kar je latinsko, pišemo poševno (npr. tudi imena rastlin in živali, pojme ''in vivo'', ''in vitro'' ipd.). <br />
<br />
'''Citiranje člankov:'''<br><br />
Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani.<br><br />
<font color=green>Lartigue, C., Glass, J. I., Alperovich, N., Pieper, R., Parmar, P. P., Hutchison III, C. A., Smith, H. O. in Venter, J. C.<br />
Genome transplantation in bacteria: changing one species to another. ''Science'', 2007, 317, str. 632-638.</font><br />
<br />
Alternativni način citiranja (predvsem v družboslovju) je po pravilih APA, kjer članke citirajo takole:<br><br />
Priimek, I. (letnica, številka). Naslov. Naslov revije, strani.<br><br />
Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.<br />
<br />
Revija Science uporablja skrajšani zapis:<br><br />
C. Lartigue ''et al''. Science 317, 632 (2007)<br><br />
<br />
V diplomah na FKKT je treba navesti vire tako, da izpišete tudi naslov citiranega dela in strani od-do (ne samo začetne). Navesti morate tudi vse avtorje dela, razen v primeru, ko jih je 10 ali več. Takrat navedite le prvih devet, za ostale pa uporabite okrajšavo in sod. (in sodelavci). Pred zadnjim avtorjem naj bo vedno besedica "in". <br />
<br />
<br />
'''Citiranje spletnih virov:'''<br><br />
Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov<br><br />
strangeguitars. ''On the brink of artificial life''. 6. 10. 2007. [citirano 13. 11. 2007] http://www.metafilter.com/65331/On-the-brink-of-artificial-life<br><br />
Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=BIO2_Povzetki_seminarjev_2015&diff=10842BIO2 Povzetki seminarjev 20152015-11-17T16:46:27Z<p>Nfrauskok: /* Biokemija- Povzetki seminarjev 2015/2016 */</p>
<hr />
<div>== Biokemija- Povzetki seminarjev 2015/2016 ==<br />
Nazaj na osnovno [http://wiki.fkkt.uni-lj.si/index.php/BIO2_Seminar_2015 stran]<br />
<br />
=== Kristjan Stibilj: PI3K kaskada in njihova vloga pri rakavih obolenjih ===<br />
Dandanes je zdravljenje rakavih obolenj poglavitna točka v razvoju farmacevtskih zdravil. Velike multinacionalke vlagajo ogromno denarja v razvoj zdravila, ki bi ozdravil tumorje oz. omilil njihovo delovanje. Za nastanek rakavih obolenj so v veliki meri krivi receptorji tirozin kinaze (RTK) in njihova PI3K/AKT/mTOR signalna pot. Ta namreč nadzoruje celično proliferacijo, metabolizem, premikanje in preživetje. Mutacije ključnih proteinov v PI3K kaskadi vodijo do nenadzorovane rasti in delitve celic, kar privede do nastanka tumorjev. Glavni princip zdravljenja oz. iskanje zdravila za rakava obolenja je torej poiskati takšno molekulo, ki bi uspešno inhibirala mutiran protein in s tem ustavila njegovo hiperaktivacjo. Znanstveniki so v zadnjih letih odkrili precej inhibitorjev, ki so bolj ali majn specifični in so sedaj v preiskavah kot morebitno zdravilo. Za inhibiranje PI3K molekule sta se v predkličninih študijah pokazala kot uspešna pictilisib in buparlisib, ki se vežeta na ATP-vezavno mesto. Na enak način deluje tudi večina AKT inhibitorjev, kamor spada tudi dobro raziskan Inhibitor VIII. mTOR, zadnja molekula v PI3K kaskadi, pa ima prav tako kar nekaj sintetičnih inhibitorjev, ki so analogni naravni molekuli rapamcin. Vsi našteti inhibitorji pa žal še niso zdravila za raka, saj so interakcije z ostalimi encimi v celici še vedno nepoznane.<br />
<br />
=== Klara Kuret: Vpliv bakterijskih efektorjev na celični ubikvitinacijski sistem in rastlinski imunski odziv ===<br />
Patogene bakterije uporabljajo efektorje za zatiranje imunskega odziva gostitelja. Tarča mnogih efektorskih proteinov je celični ubikvitinacijski sistem (UBS), ki je pomemben regulator imunskega odgovora. Ubikvitinska signalizacija poteka preko treh encimskih kompleksov, ki na proteinske substrate vežejo molekule ubikvitina. Dolžina in oblika ubikvitinske verige narekujeta, kakšen bo biološki odgovor celice na ubikvitinacijo oz. kaj se bo s substratom zgodilo. Ker prokarionti nimajo lastnega ubikvitinacijskega sistema, so morali razviti drugačne mehanizme, ki jim omogočajo interakcijo z evkariontskimi proteini, kateri nastopajo pri ubikvitinaciji. Efektorji lahko gostiteljski UBS izkoriščajo tako, da strukturno ali funkcijsko posnemajo evkariontske komponente UBS, ali pa so homologi evkariontskih proteinov. Lahko tudi pospešujejo ali inhibirajo delovanje 26S proteasoma. Efektorski proteini torej izkoriščajo evkariontske strategije za nadzor in manipulacijo gostiteljevih celičnih procesov, v smeri, ki patogenu omogoča čim boljšo možnost razvoja in množitve. Efektorji AvrPtoB, HopM1 ter VirF so nastali z različnim evolucijskim razvojem, zato se tudi mehanizmi njihovega delovanja na UBS razlikujejo. Patogeni efektorji lahko preko ubikvitinacije pomembnih signalnih proteinov v imunskih kaskadah povzročijo nezmožnost celice, da aktivira PAMP ter ETI imunost. Razgradnja gostiteljevih proteinov vodi lahko do motenj v izražanju genov, motenj v vezikularnem transportu in številnih drugih nepravilnosti v celičnih procesih, ki pripeljejo do večje dovzetnosti celice za okužbo.<br />
<br />
=== Tjaša Lukšič: Alternativno izrezovanje GPCR-jev s poudarkom na sekretinski družini ===<br />
Alternativno izrezovanje GPCR-jev je pogost pojav, še posebej pri sekretinski in nekaterih sorodnih družinah. Receptorji sekretinske družine se pojavljajo v zanimivih izooblikah, ki odstirajo nove poglede na regulacijo celične signalizacije. V sedmi transmembranski vijačnici sekretinskih GPCR-jev je dobro ohranjen ekson 12 oz. zaporedje 14 aminokislin, ki je tarča izrezovalno-povezovalnega kompleksa pri nekaterih receptorjih. Delecija eksona 12 nima izrazitega vpliva na vezavo primarnih sporočevalcev, ima pa zato toliko večje posledice pri prenosu signalov. Povezovanje z G-proteini je onemogočeno, ker skrajšana TMD7 ne omogoča normalne konformacijske spremembe. Le-ta se v običajnih izooblikah zgodi zaradi premika TMD6 in TMD7 proti statični TMD3, kar razkrije intracelularno vezavno domeno za navzdolnje efektorje. Poleg omenjene funkcije lažnega receptorja, se oslabi tudi membranska ekspresija kratkih-TMD7 receptorjev, saj je izbrisan transportni motiv v eksonu 12 in zmanjšana hidrofobnost C konca. Najbolj fascinantna posledica je zagotovo dominantno negativna regulacija membranske ekspresije ostalih izooblik. Za transport GPCR-jev iz kontrolnega sistema endoplazmatskega retikuluma je potrebna oligomerizacija. Hetero-oligomeri določenih kombinacij s kratkim-TMD7 receptorjem ne uspejo zapustiti ER, število delujočih receptorjev v membrani se zmanjšuje in celica je slabše odzivna na njihove primarne sporočevalce. Med tem pa nekateri receptorji nimajo težav pri transportu skupaj s skrajšanimi izooblikami. Številna bolezenska stanja so povezana s patološkimi izooblikami ali z neuspešnim transportom proteinov iz ER, za kar obstaja potencialna rešitev v farmakoloških šaperonih.<br />
<br />
=== Rok Miklavčič: Preusmeritve signalnih poti preko TNFR1 v boju s patogeni ===<br />
Celice so se skozi čas prilagodile na življenje v okolju, polnem potencialno škodljivih patogenov. Razvilo se je mnogo mehanizmov celičnega odgovora, ki so prilagojeni tako, da lahko ustrezen odgovor na patogene pripravijo v različnih situacijah. En takih mehanizmov predstavlja tudi signalna kaskada preko TNFR1, receptorja za citokin TNFα. TNFα sprostijo celice imunskega sistema, ko zaznajo prisotnost patogena. Osnovni celični odgovor pri stimulaciji TNFR1 je kaskada, ki preko zaporedja ubikvitinacij sodelujočih proteinov, privede do translokacije transkripcijskega faktorja NF-κB v jedro. NF-κB tam sproži prepisovanje genov za vnetne citokine, ki ob kasnejšem sproščanju v okolico celice povzročijo vnetni odziv sosednjih celic ter s tem omejitev okužbe. Nekateri patogeni pa so na ta odziv prilagojeni tako, da inhibirajo ključne proteine v začetni kaskadi in s tem zmanjšajo vnetje, vendar pa imajo na to prilagoditev odgovor tudi gostiteljske celice. Pri taki inhibiciji pride do prenosa signala po drugi poti, ki privede do apoptoze napadene celice, kar ubije tudi patogene v njej, in tako omeji okužbo. Patogeni lahko inhibirajo tudi samo apoptozo, zaradi česar obstaja tudi zasilni celični mehanizem odgovora nanje. V primeru inhibicije apoptoze se kaskada konča z aktivacijo psevdokinaze MLKL, ki je glavni efektor za mehanizem programirane nekroze z imenom nekroptoza. Pri nekroptozi pride kot pri nekrozi do celične lize, pri čemer se v okolico sprostijo DAMP-i, ki sprožijo vnetni odziv okoliškega tkiva.<br />
<br />
=== Ema Gašperšič: PKC in njihov vpliv na raka ter Alzheimerjevo bolezen ===<br />
Protein kinaze C (PKC) so družina encimov, ki sodelujejo v številnih signalnih poteh v celici. S fosforilacijo serina ali treonina nekega drugega proteina regulira njegovo aktivnost. Vplivajo na proliferacijo in diferenciacijo celice, apoptozo, oblikovanje sinaps, učenje ter shranjevanje spominov, nevrološke motnje in mnogo drugih procesov v celici. Za aktivacijo PKC sta ključni povečani koncentraciji diacilglicerola (DAG) in kalcijevih ionov Ca2+, ki z vezavo na PKC povzročita prehod iz neaktivne v aktivno obliko. Aktivacija PKC vpliva na spodbujanje oziroma inhibiranje razvoja raznih bolezni, kot so rak, ishemična možganska kap ali Alzheimerjeva bolezen in druge nevrodegenerativne bolezni. Problem je v tem, da je pri zdravljenju raka potrebno rast celic čim prej zaustaviti, med tem ko morajo pri nevrodegenerativnih boleznih nevroni ostajati živi. Poleg tega je zanimivo, da naj bi nekateri aktivatorji protein kinaz C rast rakavih celic spodbujali, drugi pa zavirali. Običajen mehanizem delovanja PKC je težko opisati, saj obstaja več oblik PKC izoencimov, ki so po različnih tkivih različno razporejeni, v celici imajo različne funkcije, poleg tega pa obstaja več signalnih poti, ki vodijo do aktivacije PKC. Vse to so razlogi za oteženo delo raziskovalcev, ki želijo odkriti načine zdravljenja prej omenjenih boleznih, zato torej to področje zahteva še precej raziskav, ki bi posledično lahko olajšale njihovo zdravljenje.<br />
<br />
=== Tadej Satler: PD-1 limfocitov in melanomskih celic ===<br />
Melanom je najnevarnejša oblika kožnega raka in znanstveniki že desetletja borijo izboljšali rezultate zdravljenja. Vzpodbuditi želijo proti-tumorski odziv imunskega sistema, vendar so zaradi kontrolnih točk neuspešni. Kontrolne točke so ključne za ohranjanje imunske homeostaze, saj bi brez njih bili žrtev številnim avtoimunskim boleznim in poškodbam tkiva ob prevelikem odzivu sistema na patogene vnetje. Med imunske kontrolne točke spada tudi receptor PD-1. Je monomer sestavljen iz imunoglobulinske in citoplazemske domene. Zanj sta značilna tudi dva liganda (PD-L1 in PD-L2), ki sta potrebna za njegovo aktivacijo. Najdemo ga predvsem pri limfocitih T in nekaterih melanomskih celicah. Izražanje PD-1 je raziskano predvsem pri limfocitih T, kjer ob interakciji z ligandoma inhibira delovanje in funkcije limfocitov ter povzroča njihovo apoptozo. To doseže s pomočjo zaviranja številnih ključnih procesov znotraj celice, ki so potrebni za njeno normalno delovanje. Pri melanomskih celicah je pa delovanje PD-1 še dokaj neraziskano. Do zdaj njegova prisotnost ni bila znana, vendar so nedavne raziskave pokazale njegovo izražanje na nekaterih celicah limfocitov. Obnašanje PD-1 melanomskih celic je drugačno kot pa pri limfocitih, saj njegovo izražanje spodbuja rast tumorja. S pomočjo boljšega poznavanja delovanja PD-1 v limfocitih T in melanomskih celicah, bo lažje razviti učinkovitejše metode boja proti raku.<br />
<br />
=== Tilen Tršelič: PKM2 in njegova vloga pri razvoju rakavih celic ===<br />
Piruvat kinaza (PK) je pomemben glikolitski encim, ki se pojavlja v štirih različnih oblikah. Oblika M2 je posebno zanimiva, saj poleg svoje glikolitske funkcije opravlja še mnoge druge, nemetabolične funkcije. Poleg tega je PKM2 prevladujoča oblika encima v rakavih celicah. Razlog za povečano izražanje le-tega verjeno izhaja iz dejstva, da lahko PKM2 zavzema aktivno tetramerno obliko ali skoraj neaktivno dimerno obliko. Možnost menjavanja svojih oblik celicam, bodisi zdravim ali rakavim, omogoča prilagajanje delovanja njihovim potrebam. Če celici primanjkuje energije, lahko encim zavzema pretežno aktivno tetramerno obliko in tako spodbuja proizvodnjo ATP. Če celica potrebuje nove makromolekule za proliferacijo, tu encim lahko zavzame pretežno neaktivno dimerno obliko in spodbuja kopičenje intermediatov glikolize. Te so ključni za sintezo novih snovi, saj služijo kot njihovi prekurzorji. <br />
Aktivnost encima PKM2 se regulira na več načinov. Vlogo regulatorjev po navadi opravljajo post-translacijske modifikacije encima, lahko pa tudi nekatere druge spremembe v celičnem okolju. <br />
PKM2 v svoji manj aktivni dimerni obliki prav tako lahko regulira druge procese. Predvsem pospešuje celično rast in razvoj prek reakcij z pomembnimi transkripcijskimi faktorji v jedru. Izkazalo se je, da delovanje encima PKM2 močno koristi rakavim celicam.<br />
Ker je encim PKM2 zelo pomemben za razvoj takšnih celic, predstavlja dobro potencialno tarčo za zdravljenje. Raziskave potrjujejo, da bi bilo slednje možno, ne ponujajo pa konkretnega odgovora na vprašanje, kako bi takšno zdravljenje potekalo.<br />
<br />
=== Tina Šimunović: Pentoza-fosfatna pot, njena regulacija in povezava z rakom ===<br />
Pod imenom rak razumemo bolezen, za katero je značilna nenadzorovana rast in celična delitev. Rakave celice imajo tako večjo potrebo po biosintezi pomembnih makromolekul, ki jo zadostijo s prilagoditvijo in spremembo svojih metaboličnih poti. Ena izmed prilagoditev je lahko sprememba pentoza-fosfatne poti (PPP). To je ena izmed metaboličnih poti glukoze, katere glavna produkta sta riboza-5-fosfat in NADPH. Prva se naprej uporablja pri sintezi nukleinskih kislin, NADPH pa je pomemben za sintezo makromolekul in za detoksikacijo. Regulacija PPP poteka preko njenih metabolnih encimov. V rakavih celicah je predvsem izražena povišana aktivnost glukoza-6-fosfat dehidrogenaze in s tem aktivnost PPP. Pri tem encimu sta, poleg mnogih drugih, najpomembnejša regulatorja NADPH in tumorski supresor p53. Aktivnost PPP lahko poveča tudi acetilacija 6-fosfoglukonat dehidrogenaze ali pa povečano izražanje transketolaze. Na pospešeno proliferacijo rakavih celic vplivajo tudi inaktivirani tumorski supresorji in aktivirani onkoproteini, npr. p53, TIGAR, ATM, Ras, mTORC1 in Nrf2. Največji pomen PPP pri rakavih celicah, je v zaščiti pred celično smrtjo, saj se s povečano aktivnostjo PPP pospeši tvorba njenih produktov, ki so ključni pri preživetju celice. Z inhibicijo te poti, bi lahko tudi inhibirali rast tumorjev. PPP je tako postala potenciala tarča za zdravljenje raka, vendar je za to potrebnih še veliko raziskav in boljše razumevanje metabolizma rakavih celic. <br />
<br />
=== Maja Zupanc: Kako dolge nekodirajoče RNA vplivajo na regulacijo metabolizma ===<br />
Ena najbolj fascinantnih lastnosti metabolizma je njegova regulacija. Za homeostazo metabolizma hranil in energije v telesu je nujna specializirana regulacija centralnega živčnega sistema, Langerhansovih otočkov trebušne slinavke in glavnih metabolnih tkiv (maščobno tkivo, skeletne mišice in jetra). Dolge nekodirajoče molekule RNA (lncRNA) so RNA molekule dolge več kot 200 nukleotidov, ki ne kodirajo proteinov. Njihov spekter delovanja je izredno širok, na metabolizem vplivajo prek regulacije procesov adipogeneze in hepatičnega metabolizma, nadzora funkcionalnosti Langerhansovih otočkastih celic, regulacije razvoja skeletnih mišic, in energijske homeostaze. Do sedaj je bilo odkritih že več kot 60000 dolgih nekodirajočih RNA molekul in repetuar njihovih funkcij se z vsako novo raziskavo širi. Vloga lncRNA je še pred desetimi leti bila neznanka, od takrat pa nam je že postalo jasno, da so pomembni regulatorji izražanja DNA, diferenciacije in razvoja celic, razvoja tkiva in tumorogeneze. V resnici pa vemo zelo malo, oziroma smo šele na začetku razumevanja lncRNA. Ker se zaradi tega z vsakim novim odkritjem pojavlja še več vprašanj (o podrobnih principih delovanja lncRNA in njihovega sodelovanja z drugimi molekulami, o še nepoznanih funkcijah, vpletenosti v bolezni in možnosti razvoja novih tehnik zdravljenja…), so raziskave na tem področju zelo aktualne.<br />
<br />
=== Lara Jerman: Warburgov učinek: od raka do avtoimunosti ===<br />
V dvajsetih letih prejšnjega stoletja je Otto Warburg s svojimi sodelavci meril porabo kisika in sintezo laktata v rakastem tkivu. Pri tem je prišel do zelo pomembnega opažanja, ki ostaja zelo aktualno – da celice rakastega tkiva tudi ob normoksičnih pogojih vztrajajo pri močno povečani glikolizi. Danes vemo, da se Warburgov učinek v rakastih tkivi pojavlja skoraj univerzalno. Večina Warburgovih opažanj in meritev je bila kvantitativno pravilna. Njegova razlaga vzroka pojava pa se je izkazala za napačno, saj povečano stopnjo glikolize zasledimo v mnogih rakastih tkivih brez določljivih mitohondrijskih mutacij ali motenj oksidativno-fosforilacijske metabolne poti. V takih tkivih sinteza ATP v mitohondrijih poteka nemoteno in enako učinkovito kot pri normalnih tkivih z enako koncentracijo kisika. Raziskave zadnjih let kažejo na to, da je povečana glikoliza strateška poteza rakastih celic, ki zadovoljuje predvsem njihove potrebe po sintezi biomase. V skoraj stoletju od Warburgovega prvotnega odkritja je postalo jasno, da metabolična stikala omogočajo celici, da se prilagaja svojim bioenergetskim in biosintetskim potrebam. Zmožnost hitrega prilagajanje potrebam je še posebej pomembna pri imunskih celicah, ki morajo ob imunskem odzivu hitro preiti iz mirujočega stanja. Zato ni presenetljivo, da so si rakaste in imunske celice glede zagotavljanja metabolnih tokov in bionenergetike za rast in širjenje v marsičem podobne.<br />
<br />
=== Sara Tekavec: Mutacije encimov Krebsovega cikla in vpliv na razvoj ter rast tumorjev ===<br />
Encimi izocitrat dehidrogenaza (IDH), sukcinat dehidrogenaza (SDH) in fumarat hidrataza (FH) sodelujejo v Krebsovem ciklu. Prvi omogoča pretvorbo izocitrata v α-ketoglutarat (α-KG), drugi pretvorbo sukcinata v fumarat, tretji pa pretvorbo fumarata v malat. Za gene, ki kodirajo te encime, so značilne mutacije, ki vodijo v nastanek in rast tumorjev. Mutacije so lahko onkogen-aktivirajoče (mutacija IDH) ali tumor-supresor deaktivirajoče (mutacije SDH in FH). Mutacija IDH tako v encimu vzpodbudi novo funkcijo, in sicer pretvorbo α-ketoglutarata ob prisotnosti NADPH v onkometabolit 2-hidroksiglutarat (2-HG). Pri drugih dveh mutacijah pa gre za to, da je aktivnost encima zmanjšana oz. je sploh ni, kar ima za posledico kopičenje sukcinata ali fumarata. To ugodno vpliva na rast tumorja, saj lahko te tri omenjene molekule na različne načine inducirajo izražanje genov, pomembnih za celično rast in preživetje. Vse tri na primer stabilizirajo hipoksični inducibilni faktor (HIF), ki nato sproži transkripcijo in angiogenezo (rast krvnih žil). Z zmanjšano koncentracijo dveh antioksidantov NADPH in α-ketoglutarata se poveča tudi tveganje za nove mutacije, povzročene s strani reaktivnih kisikovih zvrsti. Poleg tega lahko α-KG sam deluje kot mutagen ali pa tudi inhibira metilacijo DNA in histonov, zaradi česar je izražanje onkogenov povečano. Kljub temu, da je ta metabolična pot pri tumorjih precej kompleksna, nam bodo nove metode detekcije tumorjev kmalu omogočile tudi boljše razumevanje samih mutacij in mehanizma nastanka tumorjev, ki tiči v ozadju.<br />
<br />
=== Fran Krstanović: L-Carnitine enhances exercise endurance capacity ===<br />
Our energy metabolism is working constantly to cover energy need of our body. ATP represents the first line of action. With cellular ATP concentration low, our body needs other sources of energy as fuel. Fats carbs and proteins play that part. To get energy from fats they need to be oxidase. The process of fat oxidation is situated in the mitochondria. Fats need a special transporter to get into the cell, l-carnitine.<br />
Apart from fat transportation l-carnitine has many other roles; enhancing exercise endurance capacity is believed to be one of them. Mice fed with L-carnitine showed great promise to confirm this theory. Glycogen concentrations were higher, all important parameters for fatty acid intake and mitochondria biogenesis were higher and do additional AMPK was activated. The most important parameter was higher endurance capacity was reached. The problem lies in implicating the theory on humans; consuming concentrations are unknown (high can lead to problems, low won’t have affect). Further experiments will surely be held as carnitine provides great attention from sports industries as a supplement for fat burning or maybe for greater athletes’ fatigue.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=BIO2_Seminar_2015&diff=10819BIO2 Seminar 20152015-11-07T08:59:17Z<p>Nfrauskok: /* Seznam seminarjev */</p>
<hr />
<div>= Biokemijski seminar =<br />
doc. dr. Gregor Gunčar, K2.022<br />
<br />
== Seznam seminarjev ==<br />
{| {{table}}<br />
| align="center" style="background:#f0f0f0;"|'''Ime Priimek'''<br />
| align="center" style="background:#f0f0f0;"|'''poglavje'''<br />
| align="center" style="background:#f0f0f0;"|'''Naslov seminarja'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 1'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 2'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum oddaje'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum recenzije'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''<br />
|-<br />
| Kristjan Stibilj||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Kristjan_Stibilj:_Inhibicija PI3k/AKT/mTOR signalne poti kot orožje proti raku||Lovro Kotnik||Blaž Lebar]||21/10/15||23/10/15||28/10/15<br />
|-<br />
| Tjaša Lukšič||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tjasa_Luksic: Alternativno izrezovanje GPCR-jev s poudarkom na sekretinski družini]||Karmen Žbogar||Aleksandra Uzar||21/10/15||23/10/15||28/10/15<br />
|-<br />
| Klara Kuret||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Klara_Kuret: Vpliv bakterijskih efektorjev na celični ubikvitinacijski sistem in rastlinski imunski odziv]||Klara Lenart||Petra Hruševar||21/10/15||23/10/15||28/10/15<br />
|-<br />
| Rok Miklavčič||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Rok_Miklavčič: Preusmeritve signalnih poti preko TNFR1 v boju s patogeni]||Katja Čop||Lovro Kotnik||28/10/15||30/10/15||04/11/15<br />
|-<br />
| Ema Gašperšič||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Ema_Gaspersic: PKC in njihov vpliv na raka ter Alzheimerjevo bolezen]||Nejc Kejžar||Karmen Žbogar||28/10/15||30/10/15||04/11/15<br />
|-<br />
| Tadej Satler||12||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tadej_Satler: PD-1 limfocitov in melanomskih celic]||Neža Brezovar||Klara Lenart||28/10/15||30/10/15||04/11/15<br />
|-<br />
| Tina Šimunović||14-15||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Tina_Simunovic: Pentoza-fosfatna pot, njena regulacija in povezava z rakom]||Kristjan Stibilj||Katja Čop||04/11/15||06/11/15||11/11/15<br />
|-<br />
| Maja Zupanc||14-15||[http://wiki.fkkt.uni-lj.si/index.php/BIO2_Povzetki_seminarjev_2015#Maja_Zupanc: Kako dolge nekodirajoče RNA vplivajo na metabolizem]||Tjaša Lukšič||Nejc Kejžar||04/11/15||06/11/15||11/11/15<br />
|-<br />
| Tilen Tršelič||14-15||PKM2 in njegova vloga pri razvoju rakavih celic||Klara Kuret||Dorotea Borković||04/11/15||06/11/15||11/11/15<br />
|-<br />
| Lara Jerman||16||||Rok Miklavčič||Neža Brezovar||11/11/15||13/11/15||18/11/15<br />
|-<br />
| Eva Rajh||16||Vpliv intermediatov Krebsovega cikla na posttranslacijske modifikacije in DNA metilacijo ||Ema Gašperšič||Kristjan Stibilj||11/11/15||13/11/15||18/11/15<br />
|-<br />
| Sara Tekavec||16||Mutacije encimov Krebsovega cikla in nastanek tumorja||Tadej Satler||Tjaša Lukšič||11/11/15||13/11/15||18/11/15<br />
|-<br />
| Fran Krstanović||17||L-Carnitine enhances exercise endurance capacity||Tina Šimunović||Klara Kuret||18/11/15||20/11/15||25/11/15<br />
|-<br />
| Elvira Boršić||17||Posledice spremenjenega metabolizma maščobnih kislin pri srčnem popuščanju||Maja Zupanc||Rok Miklavčič||18/11/15||20/11/15||25/11/15<br />
|-<br />
| Janja Krapež||17||||Tilen Tršelič||Ema Gašperšič||18/11/15||20/11/15||25/11/15<br />
|-<br />
| Janez Javornik||18||||Lara Jerman||Tadej Satler||25/11/15||27/11/15||02/12/15<br />
|-<br />
| Miha Koprivnikar Krajnc||18||||Eva Rajh||Tina Šimunović||25/11/15||27/11/15||02/12/15<br />
|-<br />
| Špela Malenšek||18|| Aminokislinska regulacija mTORC1||Sara Tekavec||Maja Zupanc||25/11/15||27/11/15||02/12/15<br />
|-<br />
| Urša Kopač||19||||Fran Krstanović||Tilen Tršelič||02/12/15||04/12/15||09/12/15<br />
|-<br />
| Neža Koritnik||19||Uravnavanje koncentracije ROS v mitohondriju z glutationilacijo||Dorotea Borković||Lara Jerman||02/12/15||04/12/15||09/12/15<br />
|-<br />
| Gašper Virant||19||||Elvira Boršić||Eva Rajh||02/12/15||04/12/15||09/12/15<br />
|-<br />
| Uroš Zavrtanik||20||||Janja Krapež||Sara Tekavec||09/12/15||11/12/15||16/12/15<br />
|-<br />
| Simon Aleksič||20||||Janez Javornik||Fran Krstanović||09/12/15||11/12/15||16/12/15<br />
|-<br />
| Matej Hvalec||20||||Miha Koprivnikar Krajnc||Elvira Boršić||09/12/15||11/12/15||16/12/15<br />
|-<br />
| Urša Čerček||21||||Špela Malenšek||Janja Krapež||16/12/15||18/12/15||23/12/15<br />
|-<br />
| Katja Brezovar||21||Vloga sfingolipidov pri fagocitozi ''Candide albicans''||Urša Kopač||Janez Javornik||16/12/15||18/12/15||23/12/15<br />
|-<br />
| Gašper Žun||21||||Neža Koritnik||Miha Koprivnikar Krajnc||16/12/15||18/12/15||23/12/15<br />
|-<br />
| Blaž Lebar||22||||Gašper Virant||Špela Malenšek||23/12/15||03/01/16||06/01/16<br />
|-<br />
| Aleksandra Uzar||22||||Uroš Zavrtanik||Urša Kopač||23/12/15||03/01/16||06/01/16<br />
|-<br />
| Petra Hruševar||22||||Simon Aleksič||Neža Koritnik||23/12/15||03/01/16||06/01/16<br />
|-<br />
| Lovro Kotnik||23||||Urša Čerček||Uroš Zavrtanik||06/01/16||08/01/16||13/01/16<br />
|-<br />
| Karmen Žbogar||23||||Katja Brezovar||Simon Aleksič||06/01/16||08/01/16||13/01/16<br />
|-<br />
| Klara Lenart||23||||Gašper Žun||Matej Hvalec||06/01/16||08/01/16||13/01/16<br />
|-<br />
| Dorotea Borković||23||||Matej Hvalec||Gašper Virant||06/01/16||08/01/16||14/01/16<br />
|-<br />
| Katja Čop||23||||Blaž Lebar||Urša Čerček||13/01/16||15/01/16||20/01/16<br />
|-<br />
| Nejc Kejžar||23||Hormonska regulacija razvoja T-celic||Aleksandra Uzar||Katja Brezovar||13/01/16||15/01/16||20/01/16<br />
|-<br />
| Neža Brezovar||23||||Petra Hruševar||Gašper Žun||13/01/16||15/01/16||20/01/16<br />
|}<br />
<br />
*številka v okencu za temo pomeni poglavje v Lehningerju, v katerega naj izbrana tema spada<br />
<br />
== Gradivo za predavanja ==<br />
Gradivo za predavanja in seminarje najdete na http://bio.ijs.si/~zajec/bio2/<br />
username: bio2<br />
password: samozame<br />
<br />
==Naloga==<br />
'''Vaša naloga za seminar je:<br>'''<br />
Samostojno pripraviti seminar o seminarski temi, ki vam je bila dodeljena. Za osnovo morate vzeti pregledni članek iz revije, ki ima faktor vpliva nad 5 (npr. [http://www.sciencedirect.com/science/journal/09680004/ TIBS]. Poiskati morate še vsaj tri znanstvene članke, ki se nanašajo na opisano temo in jih uporabiti kot podlago za seminarsko nalogo! <br />
<br />
Za pripravo seminarja velja naslednje:<br><br />
* [[BIO2 Povzetki seminarjev 2015|Povzetek seminarja]] opišete na wikiju '''v 200 besedah''' (+- dvajset besed) - najkasneje do dne ko morate oddati seminar recenzentom. <br />
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.<br />
* Seminar pripravite v obliki seminarske naloge na ~5-12 straneh A4 (pisava 12, enojni razmak, 2,5 cm robovi). Zelo pomembno je, da je obseg od <font color=red>2700 do 3000 besed </font>, a ne več kot 3500 besed. Seminarska naloga mora vsebovati najmanj tri slike. <font color=red>Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko. </font><br />
* Seminar oddajte do datuma oddaje, ki je naveden v tabeli v elektronski obliki z uporabo [http://bio.ijs.si/~zajec/poslji/ tega obrazca].<br />
* Vsi seminarji so v elektronski obliki dostopni [http://bio.ijs.si/~zajec/poslji/bioseminar/ tukaj].<br />
* Recenzenti do dneva določenega v tabeli določijo popravke (v elektronski obliki) in podajo oceno pisnega dela. Popravljen seminar oddajte z uporabo [http://bio.ijs.si/~zajec/poslji/ tega obrazca].<br />
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 20 minut. Recenzenti morajo biti na predstavitvi prisotni.<br />
* Predstavitvi sledi razprava. Recenzenti podajo oceno predstavitve in postavijo najmanj dve vprašanji.Vsi ostali morajo postaviti še dve dodatni vprašanji v toku celega seminarskega obdobja.<br />
* Na dan predstavitve morate docentu še pred predstavitvijo oddati končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu, elektronsko verzijo seminarja in predstavitev pa oddati na strežnik na dan predstavitve do polnoči.<br />
* Seminarska naloga in povzetek morajo biti v slovenskem jeziku, razen za študente, katerih materni jezik ni slovenščina. Ti lahko oddajo seminar v angleškem jeziku.<br />
<br />
==<font color=green>Imena datotek</font>==<br />
Prosim vas, da vse datoteke, ki mi jih pošiljate poimenujete po naslednjem receptu:<br />
* 312_BIO_Priimek_Ime.doc(x) za seminar, npr. 312_BIO_Guncar_Gregor.docx<br />
* 312_BIO_Priimek_ime_final.doc(x) za končno verzijo seminarja<br />
* 312_BIO_Priimek_Ime_rec_Priimek2.doc(x) za recenzijo, kjer je Priimek2 priimek recenzenta, npr. 312_BIO_Guncar_Gregor_rec_Scott.docx (če se pišete Scott in odajate recenzijo za seminar, ki ga je napisal Gunčar)<br />
* 312_BIO_Priimek_Ime.ppt(x) za prezentacijo, npr 312_BIO_Guncar_Gregor.pptx<br />
* <font color=green>312_BIO_Priimek_ime_poprava.doc(x) za popravljeno končno verzijo seminarja, če so popravki manjši<br />
* 116_BIO_Priimek_Ime.doc(x) za seminar, ki je napisan na novo in je bil prijavljen v shemo 50%</font><br />
<br />
==Ocenjevanje seminarjev==<br />
Recenzenti ocenijo seminar tako, da izpolnijo [https://docs.google.com/forms/d/1EQDYwFO-DEzZ2R7jf8DhLqIeV4FFxRd3-ScceEASpt4/viewform recenzentsko poročilo] na spletu. Recenzentsko poročilo morate oddati najkasneje do 21:00, en dan pred predstavitvijo seminarja.<br />
<br />
== Mnenje o predstavitvi ==<br />
Vsak posameznik '''mora''' oceniti seminar, tako da odda svoje [https://docs.google.com/forms/d/19bnx0Yh4RIuC2Kzkdaa8t8WqRTBgXYNTV_IWfjrO0W4/viewform?usp=send_form mnenje] najkasneje v sedmih dneh po predstavitvi. Kdor na seminarju ni bil prisoten, mnenja '''ne sme''' oddati.<br />
<br />
==Urejanje spletnih strani na wikiju==<br />
Wiki so razvili zato, da lahko spletne vsebine ureja vsakdo. Ukazi so preprosti, dokler si ne zamislite česa prav posebnega. Vseeno pa je Word v primerjavi z wikijem pravo čudežno orodje... Če imate težave z oblikovanjem besedila, si preberite poglavje o urejanju wiki-strani na Wikipediji ([http://en.wikipedia.org/wiki/Help:Editing tule] v angleščini in [http://sl.wikipedia.org/wiki/Wikipedija:Urejanje_strani tu] v slovenščini). Pomaga tudi, če pogledate, kako je zapisana kakšna stran, ki se vam zdi v redu: kliknite na zavihek 'Uredite stran' in si poglejte, kako so vpisane povezave, kako nov odstavek in podobno. ''Na koncu seveda pod oknom za urejanje kliknite na 'Prekliči'.''<br />
<br />
==Citiranje virov==<br />
Citiranje je možno po več shemah, važno je, da se držite ene same. V seminarskih nalogah in diplomskih nalogah FKKT uprabljajte shemo citiranja, ki je pobarvana <font color=green>zeleno</font>.<br />
Temeljno načelo je, da je treba vir navesti na tak način, da ga je mogoče nedvoumno poiskati.<br />
Za citate v naravoslovju je najpogostejše citiranje po pravilniku ISO 690. [http://www.zveza-zotks.si/gzm/dokumenti/literatura.html Pravila], ki upoštevajo omenjeni standard, so pripravili pri ZTKS. Sicer pa ima vsaka revija lahko svoj način citiranja, ki ga je treba pri pisanju članka upoštevati.<br><br />
'''Citiranje knjig:'''<br><br />
Priimek, I. ''Naslov''. Kraj: Založba, letnica.<br><br />
Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN.<br><br />
<br />
Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005.<br><br />
Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4.<br><br />
Če so avtorji trije, je beseda in med drugim in tretjim avtorjem. Če so avtorji več kot trije, napišemo samo prvega in dopišemo ''et al''. (in drugi, po latinsko). Vse, kar je latinsko, pišemo poševno (npr. tudi imena rastlin in živali, pojme ''in vivo'', ''in vitro'' ipd.). <br />
<br />
'''Citiranje člankov:'''<br><br />
Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani.<br><br />
<font color=green>Lartigue, C., Glass, J. I., Alperovich, N., Pieper, R., Parmar, P. P., Hutchison III, C. A., Smith, H. O. in Venter, J. C.<br />
Genome transplantation in bacteria: changing one species to another. ''Science'', 2007, 317, str. 632-638.</font><br />
<br />
Alternativni način citiranja (predvsem v družboslovju) je po pravilih APA, kjer članke citirajo takole:<br><br />
Priimek, I. (letnica, številka). Naslov. Naslov revije, strani.<br><br />
Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.<br />
<br />
Revija Science uporablja skrajšani zapis:<br><br />
C. Lartigue ''et al''. Science 317, 632 (2007)<br><br />
<br />
V diplomah na FKKT je treba navesti vire tako, da izpišete tudi naslov citiranega dela in strani od-do (ne samo začetne). Navesti morate tudi vse avtorje dela, razen v primeru, ko jih je 10 ali več. Takrat navedite le prvih devet, za ostale pa uporabite okrajšavo in sod. (in sodelavci). Pred zadnjim avtorjem naj bo vedno besedica "in". <br />
<br />
<br />
'''Citiranje spletnih virov:'''<br><br />
Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov<br><br />
strangeguitars. ''On the brink of artificial life''. 6. 10. 2007. [citirano 13. 11. 2007] http://www.metafilter.com/65331/On-the-brink-of-artificial-life<br><br />
Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=TBK2014-seminar&diff=9389TBK2014-seminar2014-05-01T09:38:19Z<p>Nfrauskok: /* Seznam seminarjev */</p>
<hr />
<div>= Temelji biokemije- seminar =<br />
<br />
Seminarje vodi prof. dr. Brigita Lenarčič in so na urniku vsak ponedeljek od 11:00 do 12:30. Seminarji so obvezni.<br />
<br />
Ocena seminarjev (6-10) predstavlja enako število odstotkov, ki se prištejeh končnipisni oceni izpita. <br />
Stran na strežniku s seminarskimi nalogami je zaščitena.<br />
Uporabniško ime je: tbk, password pa: samozame## "##" sta dve številki, ki ju izveste na predavanjih.<br />
<br />
== Seznam seminarjev ==<br />
{| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" <br />
| align="center" style="background:#f0f0f0;"|'''Ime in priimek'''<br />
| align="center" style="background:#f0f0f0;"|'''Naslov seminarja'''<br />
| align="center" style="background:#f0f0f0;"|'''Povezava'''<br />
| align="center" style="background:#f0f0f0;"|'''Rok za oddajo'''<br />
| align="center" style="background:#f0f0f0;"|'''Rok za recenzijo'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 1'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 2'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 3'''<br />
|-<br />
| Črt Kovač||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#.C4.8Crt_Kova.C4.8D:_Naslov_v_sloven.C5.A1.C4.8Dini Naslov]||[http://www.sciencedaily.com/releases/2013/06/130627142551.htm link]||03.03.||06.03.||10.03.||Liza Otorepec||Marija Srnko||Luka Dejanović<br />
|-<br />
| Bine Tršavec||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Bine_Tršavec:_Stikalo,_ki_pove,_da_je_čas_za_spanje Stikalo, ki pove, da je čas za spanje]||[http://www.sciencedaily.com/releases/2014/02/140219124730.htm Povezava]||03.03.||06.03.||10.03.||Naida Hajdarević||Eva Škrjanec||Katja Malovrh<br />
|-<br />
| Jernej Vidmar||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Jernej_Vidmar:_Boljša_slikovna_obdelava_z_nanozamrzovanjem Boljša slikovna obdelava z nanozamrzovanjem]||[http://www.sciencedaily.com/releases/2014/02/140226133000.htm Povezava]||03.03.||06.03.||10.03.||Nuša Kelhar||Vesna Podgrajšek||Nina Mavec<br />
|-<br />
| Ernest Šprager||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Ernest_Sprager:_ Doslej najuspešnejše utišanje genov v jetrih z RNA interferenco po zaslugi novih nanodelcev]||[http://www.pnas.org/content/early/2014/02/06/1322937111.full.pdf+html Povezava]||03.03.||06.03.||10.03.||Tamara Božič||Nives Mikešić||Ana Kompan<br />
|-<br />
| Andrej Žulič|| [http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Andrej_.C5.BDuli.C4.8D:_Prva_umetna_celica_z_delujo.C4.8Dimi_organeli Prva umetna celica z delujočimi organeli] || [http://www.sciencedaily.com/releases/2014/01/140114091707.htm Povezava] ||10.03.||13.03.||17.03.||Črt Kovač||Liza Otorepec||Marija Srnko<br />
|-<br />
| Urška Černe||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Ur.C5.A1ka_.C4.8Cerne:_Boj_imunskega_sistema_proti_malariji Boj imunskega sistema proti malariji]||[http://www.sciencedaily.com/releases/2014/01/140113154225.htm Povezava]||10.03.||13.03.||17.03.||Bine Tršavec||Naida Hajdarević||Eva Škrjanec<br />
|-<br />
| Tadej Ulčnik||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Tadej_Ul.C4.8Dnik:_Prisotnost_proteinov_UCP_dolo.C4.8Da_metabolizem_celice Prisotnost proteinov UCP določa metabolizem celice] ||[http://www.sciencedaily.com/releases/2014/03/140304071208.htm Povezava]||10.03.||13.03.||17.03.||Jernej Vidmar||Nuša Kelhar||Vesna Podgrajšek<br />
|-<br />
| Jerneja Kocutar||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Jerneja_Kocutar:_Odziv_celic_na_stresne_situacije Odziv celic na stresne situacije]||[http://www.sciencedaily.com/releases/2014/02/140228103435.htm Povezava]||10.03.||13.03.||17.03.||Ernest Šprager||Tamara Božič||Nives Mikešić<br />
|-<br />
| Hrvoje Malkoč||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Hrvoje_Malkoč:_Adsorbcija_mielinskega_bazičnega_proteina_na_membrane_mielinskih_lipidnih_dvoslojev Adsorbcija mielinskega bazičnega proteina na membrane mielinskih lipidnih dvoslojev]||[http://www.sciencedaily.com/releases/2014/02/140225143937.htm Povezava]||17.03.||20.03.||24.03.||Andrej Žulič||Črt Kovač||Liza Otorepec<br />
|-<br />
| Janja Krapež||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Janja_Krape.C5.BE:_Nanopore_omogo.C4.8Dajo_transport_DNA_skozi_membrane Nanopore omogočajo transport DNA skozi membrane]||[http://www.sciencedaily.com/releases/2013/10/131023090540.htm Povezava]||17.03.||20.03.||24.03.||Urška Černe||Bine Tršavec||Naida Hajdarević<br />
|-<br />
| Inge Sotlar||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Inge_Sotlar:_CPEB_proteini_oblikujejo_dolgoročni_spomin CPEB proteini oblikujejo dolgoročni spomin]||[http://www.sciencedaily.com/releases/2014/02/140211174613.htm Povezava]||24.03.||27.03.||31.03.||Tadej Ulčnik||Jernej Vidmar||Nuša Kelhar<br />
|-<br />
| Monika Pepelnjak||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Monika_Pepelnjak:_Odpornost_tumorjev_na_kemoterapijo Odpornost tumorjev na kemoterapijo]||[http://www.sciencedaily.com/releases/2013/12/131202094320.htm Povezava]||24.03.||27.03.||31.03.||Jerneja Kocutar||Ernest Šprager||Tamara Božič<br />
|-<br />
| Jerneja Ovčar||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Jerneja_Ov.C4.8Dar:_Vztrajno_zavezujo.C4.8D_mehanizem_za_vizualni_nadzor_gibanja Vztrajno zavezujoč mehanizem za vizualni nadzor gibanja]||[http://www.sciencedaily.com/releases/2014/03/140313123139.htm Povezava]||24.03.||27.03.||31.03.||Hrvoje Malkoč||Andrej Žulič||Črt Kovač<br />
|-<br />
| Anja Tanšek||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Anja_Tan.C5.A1ek:_Potrditev_klju.C4.8Dne_beljakovine_odgovorne_za_razre.C5.A1itev_skrivnosti_mitoze Potrditev ključne beljakovine odgovorne za razrešitev skrivnosti mitoze]||[http://www.sciencedaily.com/releases/2014/02/140218101018.htm Povezava]||24.03.||27.03.||31.03.||Janja Krapež||Urška Černe||Bine Tršavec<br />
|-<br />
| ||||||24.03.||27.03.||31.03.||Inge Sotlar||Tadej Ulčnik||Jernej Vidmar<br />
|-<br />
| Angela Mihajloska||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Angela_Mihajloska:_Proteine.2Cki_so_odkriti_v_gonoreje_lahko_ponudijo_novi_pristop_k_zdravljenju Proteine ki so odkriti v gonoreje lahko ponudijo novi pristop k zdravljenju]||[http://www.sciencedaily.com/releases/2014/03/140331131010.htm Povezava]||31.03.||03.04.||07.04.||Monika Pepelnjak||Jerneja Kocutar||Ernest Šprager<br />
|-<br />
| Božin Krstanoski||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Božin_Krstanoski:_Uporaba_bakterij_pri_naftnih_razlitjih Uporaba bakterij pri naftnih razlitjih]||[http://www.sciencedaily.com/releases/2014/03/140310090615.htm Povezava]||31.03.||03.04.||07.04.||Jerneja Ovčar||Hrvoje Malkoč||Andrej Žulič<br />
|-<br />
| Domagoj Majić||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Domagoj_Maji.C4.87:_Low_vitamin_D_levels_raise_anemia_risk_in_children Low vitamin D levels raise anemia risk in children]||[http://www.sciencedaily.com/releases/2013/10/131021155625.htm Povezava]||31.03.||03.04.||07.04.||Anja Tanšek||Janja Krapež||Urška Černe<br />
|-<br />
| Amadeja Lapornik||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Amadeja_Lapornik:_Nanodelci,_ki_omogočajo_zgodnje_odkrivanje_krvnih_strdkov Nanodelci, ki omogočajo zgodnje odkrivanje krvnih strdkov]||[http://www.sciencedaily.com/releases/2013/10/131016123038.htm Povezava]||31.03.||03.04.||07.04.||Anja Šantl||Inge Sotlar||Tadej Ulčnik<br />
|-<br />
| Peter Pečan|| [http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Peter_Pe.C4.8Dan:_Reprogramiranje_ko.C5.BEnih_celic_v_sr.C4.8Dne, Reprogramiranje kožnih celic v srčne]||[http://www.sciencedaily.com/releases/2014/02/140220132202.htm Povezava]||07.04.||10.04.||14.04.||Angela Mihajloska||Monika Pepelnjak||Jerneja Kocutar<br />
|-<br />
| Živa Moravec|| [http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#.C5.BDiva_Moravec:_Klju.C4.8Den_korak_naprej_pri_tiskanju_3D_tkiv, Ključen korak naprej pri tiskanju 3D tkiv]||[http://www.sciencedaily.com/releases/2014/02/140219095501.htm Povezava]||07.04.||10.04.||14.04.||Božin Krstanoski||Jerneja Ovčar||Hrvoje Malkoč<br />
|-<br />
| Tjaša Sorčan||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Tja.C5.A1a_Sor.C4.8Dan:_Posamezni_Iks_kanali_na_povr.C5.A1ini_sr.C4.8Dnih_celic_sesalcev_vsebujejo_dve_KCNE1_podenoti, Posamezni Iks kanali na površini celic sesalcev vsebujejo dve KCNE1 podenoti]||[http://www.sciencedaily.com/releases/2014/03/140304141740.htm Povezava]||21.04.||24.04.||05.05.||Domagoj Majić||Anja Tanšek||Janja Krapež<br />
|-<br />
| Tomaž Žagar|| [http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Toma.C5.BE_.C5.BDagar:_Klju.C4.8Dna_proteina_pri_uravnavanju_celi.C4.8Dne_smrti Ključna proteina pri uravnavanju celične smrti]||[http://www.sciencedaily.com/releases/2014/03/140327140059.htm Povezava]||21.04.||24.04.||05.05.||Amadeja Lapornik||Anja Šantl||Inge Sotlar<br />
|-<br />
| Fran Krstanović|| [http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Fran_Krstanovi.C4.87:_Breast_milk_protein_may_be_key_to_protecting_babies_from_HIV Breast milk protein may be key to protecting babies from HIV] ||[http://www.sciencedaily.com/releases/2013/10/131021153200.htm Povezava]||21.04.||24.04.||05.05.||Peter Pečan||Angela Mihajloska||Monika Pepelnjak<br />
|-<br />
| Jure Zadravec|| [http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Jure_Zadravec:_Vloga_tumorskih_ozna.C4.8Devalcev_CA19-9.2C_CA125_in_CA72-4_pri_diagnozi_raka_trebu.C5.A1ne_slinavke Vloga tumorskih označevalcev CA19-9, CA125 in CA72-4 pri diagnozi raka trebušne slinavke]||[http://www.sciencedaily.com/releases/2014/01/140121164754.htm Povezava]||21.04.||24.04.||05.05.||Živa Moravec||Božin Krstanoski||Jerneja Ovčar<br />
|-<br />
| Primož Tič||||[http://www.sciencedaily.com/releases/2014/04/140408115610.htm Povezava]||05.05.||08.05.||12.05.||Tjaša Sorčan||Domagoj Majić||Anja Tanšek<br />
|-<br />
| Valentina Levak||||||05.05.||08.05.||12.05.||Tomaž Žagar||Amadeja Lapornik||Anja Šantl<br />
|-<br />
| Enja Kokalj||||||05.05.||08.05.||12.05.||Fran Krstanović||Peter Pečan||Angela Mihajloska<br />
|-<br />
| Hasiba Kamenjaković||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Hasiba_Kamenjaković:_Podobnosti_med_HIV./.AIDS.opioidne_odvisnosti_epidemije Podobnosti med HIV / AIDS, opioidne odvisnosti epidemije] ||[http://www.sciencedaily.com/releases/2014/04/140401162205.htm Povezava]|| 05.05.||08.05.||12.05.||Jure Zadravec||Živa Moravec||Božin Krstanoski<br />
|-<br />
| Luka Dejanović||||||12.05.||15.05.||19.05.||Primož Tič||Tjaša Sorčan||Domagoj Majić<br />
|-<br />
| Katja Malovrh||||||12.05.||15.05.||19.05.||Valentina Levak||Tomaž Žagar||Amadeja Lapornik<br />
|-<br />
| Nina Mavec||||||12.05.||15.05.||19.05.||Enja Kokalj||Fran Krstanović||Peter Pečan<br />
|-<br />
| Anja Šantl||||||12.05.||15.05.||19.05.||Hasiba Kamenjaković||Jure Zadravec||Živa Moravec<br />
|-<br />
| Marija Srnko||||||19.05.||22.05.||26.05.||Luka Dejanović||Primož Tič||Tjaša Sorčan<br />
|-<br />
| Eva Škrjanec||||||19.05.||22.05.||26.05.||Katja Malovrh||Valentina Levak||Tomaž Žagar<br />
|-<br />
| Vesna Podgrajšek||||[http://www.sciencedaily.com/releases/2014/01/140130210734.htm Povezava]||19.05.||22.05.||26.05.||Nina Mavec||Enja Kokalj||Fran Krstanović<br />
|-<br />
| Nives Mikešić||||||19.05.||22.05.||26.05.||Ana Kompan||Hasiba Kamenjaković||Jure Zadravec<br />
|-<br />
| Liza Otorepec||||||26.05.||29.05.||02.06.||Marija Srnko||Luka Dejanović||Primož Tič<br />
|-<br />
| Naida Hajdarević||||||26.05.||29.05.||02.06.||Eva Škrjanec||Katja Malovrh||Valentina Levak<br />
|-<br />
| Nuša Kelhar||||||26.05.||29.05.||02.06.||Vesna Podgrajšek||Nina Mavec||Enja Kokalj<br />
|-<br />
| Tamara Božič||||||26.05.||29.05.||02.06.||Nives Mikešić||Ana Kompan||Hasiba Kamenjaković<br />
|}<br />
<br />
==Naloga==<br />
* samostojno pripraviti seminar, katerega tema je novica iz področja biokemije na portalu [http://www.sciencedaily.com ScienceDaily], ki je bila objavljena kasneje kot 1. avgusta 2013. Osnova za seminar naj bo znanstveni članek, ki je podlaga za to novico. Poleg tega članka za seminar uporabite še najmanj pet drugih virov, od teh vsaj še dva druga znanstvena članka, ki se navezujeta na to vsebino. <br />
* članke na temo lahko iščete v PubMed povezavi [http://www.ncbi.nlm.nih.gov/pubmed/ tukaj]<br />
* naslov izbrane teme in povezavo do novice vpišite v tabelo seminarjev takoj ko ste si izbrali temo, najkasneje pa en teden pred rokom za oddajo <br />
* [[TBK2014 Povzetki seminarjev|Povzetek seminarja]] opišete na wikiju v približno 200 besedah - najkasneje do dne ko morate oddati seminar recenzentom. <br />
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.<br />
* Seminar pripravite v obliki seminarske naloge (pisava Cambria, font 11, enojni razmak, 2,5 cm robovi; tekst naj obsega okoli 1000 besed), vsebuje naj 1-2 sliki. Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko. Vse uporabljene vire citirajte v tekstu, kot npr. (Nobel, 2010), na koncu pa navedite točen seznam literature, kot je opisano spodaj!<br />
*Celotni seminar naj obsega 2 strani A4 formata (po možnosti dvostransko tiskanje).<br />
* Seminar oddajte do datuma oddaje, ki je naveden v tabeli v elektronski obliki z uporabo [http://bio.ijs.si/~zajec/tbk/poslji/ tega obrazca].<br />
* vsi seminarji so v elektronski obliki dostopni [http://bio.ijs.si/~zajec/tbk/poslji//bioseminar/ tukaj].<br />
* Recenzenti do dneva določenega v tabeli določijo popravke in podajo oceno pisnega dela, v predpisanem formatu elektronskega obrazca na internetu.<br />
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 12 minut. Recenzenti morajo biti na predstavitvi prisotni. Prvi recenzent vodi predstavitve in razpravo ter skrbi za to, da vse poteka v zastavljenih časovnih okvirih.<br />
* Predstavitvi sledi razprava do 8 minut. Sledijo vprašanja prisotnih, recenzenti postavijo vsak vsaj dve vprašanji in na koncu podajo oceno predstavitve.<br />
* En dan pred predstavitvijo na strežnik oddajte tudi končno verzijo. Na dan predstavitve morate oddati tudi končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu.<br />
* Seminarska naloga in povzetek na wikiju morajo biti v slovenskem jeziku!<br />
<br />
==<font color=green>Imena datotek</font>==<br />
Prosim vas, da vse datoteke, ki jih pošiljate poimenujete po spodnjih pravilih. Ne uporabljajte ČŽŠčžš!<br />
* TBK_2014_Priimek_Ime.doc(x) za seminar, npr. TBK_2014_Guncar_Gregor.docx<br />
* TBK_2014_Priimek_ime_final.doc(x) za končno verzijo seminarja<br />
* TBK_2014_Priimek_Ime_rec_Priimek2.doc(x) za recenzijo, kjer je Priimek2 priimek recenzenta, npr. TBK_2014_Guncar_Gregor_rec_Scott.docx (če se pišete Scott in odajate recenzijo za seminar, ki ga je napisal Gunčar)<br />
* TBK_2014_Priimek_Ime.ppt(x) za prezentacijo, npr TBK_2014_Guncar_Gregor.pptx<br />
<br />
==Ocenjevanje seminarjev==<br />
Recenzenti ocenijo seminar tako, da izpolnijo [[https://docs.google.com/forms/d/1oW_38CbGfOhTcS8zqMEFvdAOS66yRtDMd_e52uoUYLw/viewform recenzentsko poročilo]] na spletu.<br />
<br />
== Mnenje o predstavitvi ==<br />
Vsak posameznik '''mora''' oceniti seminar tako, da odda svoje [https://docs.google.com/forms/d/1XbEJ2iXlXsT3b7-jpM3pCGQazdIwskieL07-vBmRU8k/viewform mnenje] najkasneje v enem tednu po predstavitvi. Kdor na seminarju ni bil prisoten, mnenja '''ne sme''' oddati.<br />
<br />
==Urejanje spletnih strani na wikiju==<br />
Wiki so razvili zato, da lahko spletne vsebine ureja vsakdo. Ukazi so preprosti, dokler si ne zamislite česa prav posebnega. Vseeno pa je Word v primerjavi z wikijem pravo čudežno orodje... Če imate težave z oblikovanjem besedila, si preberite poglavje o urejanju wiki-strani na Wikipediji ([http://en.wikipedia.org/wiki/Help:Editing tule] v angleščini in [http://sl.wikipedia.org/wiki/Wikipedija:Urejanje_strani tu] v slovenščini). Pomaga tudi, če pogledate, kako je zapisana kakšna stran, ki se vam zdi v redu: kliknite na zavihek 'Uredite stran' in si poglejte, kako so vpisane povezave, kako nov odstavek in podobno. ''Na koncu seveda pod oknom za urejanje kliknite na 'Prekliči'.''<br />
<br />
<br />
==Faktor vpliva==<br />
Faktor vpliva (angl. impact factor) neke revije pove, kolikokrat so bili v poprečju citirani članki v tej reviji v dveh letih skupaj pred objavo tega faktorja. Faktorje vpliva za posamezno revijo lahko najdete v [http://www.cobiss.si/scripts/cobiss?command=CONNECT&base=JCR COBISS-u]. V polje "Naslov revije" vnesite ime revije za katero želite izvedeti faktor vpliva in pritisnite na gumb POIŠČI. V skrajnem desnem stolpcu se bodo izpisali faktorji vpliva za revije, ki ustrezajo vašim iskalnim kriterijem. Zadetkov za posamezno revijo je več zato, ker so navedeni faktorji vpliva za posamezno leto. Za leto 2011 faktorji vpliva še niso objavljeni, zato se orientirajte po faktorjih vpliva zadnjih par let. Če faktorja vpliva za vašo izbrano revijo ne najdete v bazi COBISS, potem izberite članek iz kakšne druge revije.<br />
<br />
==Citiranje virov==Citiranje je možno po več shemah, važno je, da se v seminarju držite ene same.Temeljno načelo je, da je treba vir navesti na tak način, da ga je mogoče nedvoumno poiskati.Za citate v naravoslovju je najpogostejše citiranje po pravilniku ISO 690. [http://www.google.com/url?sa=t&source=web&cd=6&sqi=2&ved=0CEUQFjAF&url=http%3A%2F%2Fwww.tre.sik.si%2Fmain%2Fpomoc%2Ffiles%2Fcitiranje_in_navajanje_virov.pdf&rct=j&q=citiranje%20po%20pravilniku%20ISO%20690&ei=jPBqTe6FC9DKswaWk-TmDA&usg=AFQjCNF8r6X9Y781sanDObaXNdCew4suUg&sig2=cTqKObSJsTicekWGRGa72g&cad=rja Pravila], ki upoštevajo omenjeni standard, so pripravili pri ZTKS. Sicer pa ima vsaka revija lahko svoj način citiranja, ki ga je treba pri pisanju članka upoštevati.<br>'''Citiranje knjig:'''<br>Priimek, I. ''Naslov''. Kraj: Založba, letnica.<br>Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN.<br>Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005.<br>Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4.<br>Če so avtorji trije, je beseda in med drugim in tretjim avtorjem. Če so avtorji več kot trije, napišemo samo prvega in dopišemo ''et al''. (in drugi, po latinsko). Vse, kar je latinsko, pišemo poševno (npr. tudi imena rastlin in živali, pojme ''in vivo'', ''in vitro'' ipd.). '''Citiranje člankov:'''<br>Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani.<br>Lartigue C. ''et al''. Genome transplantation in bacteria: changing one species to another. ''Science'', 2007, letn. 317, str. 632-638.Alternativni način citiranja (predvsem v družboslovju) je po pravilih APA, kjer članke citirajo takole:<br>Priimek, I. (letnica, številka). Naslov. Naslov revije, strani.<br>Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.Revija Science uporablja skrajšani zapis:<br>C. Lartigue ''et al''. Science 317, 632 (2007)<br>V diplomah na FKKT je treba navesti vire tako, da izpišete tudi naslov citiranega dela in strani od-do (ne samo začetne).'''Citiranje spletnih virov:'''<br>Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov<br>strangeguitars. ''On the brink of artificial life''. 6. 10. 2007. [citirano 13. 11. 2007] http://www.metafilter.com/65331/On-the-brink-of-artificial-life<br>Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=TBK2014_Povzetki_seminarjev&diff=9388TBK2014 Povzetki seminarjev2014-05-01T09:30:38Z<p>Nfrauskok: /* 5.5 */</p>
<hr />
<div>[[TBK2014-seminar|Nazaj na osnovno stran]]<br />
<br />
<br />
<br />
== 17.3. ==<br />
<br />
=== Andrej Žulič: Prva umetna celica z delujočimi organeli ===<br />
<br />
Prvič v zgodovini je znanstvenikom na nizozemski univerzu Radboud v Nijmegenu uspelo ustvariti umetno celico z delujočimi organeli, ki lahko v večih korakih, kemičnih reakcijah, reagent preko raznih vmesnih stopenj privedejo do končnega produkta, rezorufina, ki je fluorescenten in se ga zato na koncu reakcije lažje opazi. Te organele so ustvarili tako, da so majhne polimerosome narejene iz PS-b-PIAT polprepustnega polimera napolnili z encimi in jih potem vnesli v miniskulno kapljico vode, ki je vsebovala še proste encime in substrate, in to kapljico še enkrat obdali s lipidnim slojem – celično steno narejeno iz PB-b-PEO hidrofobnega polimera. Zaradi fluorescence produkta so lahko preverili, da se predvidene reakcije resnično dogajajo po korakih v polimerosomnih nanoreaktorjih ali organelih. Produkti posameznih organelov lahko prestopijo steno organela v celično plazmo od koder najdejo pot v druge celične organele, kjer se izvršujejo posledični koraki te ''kaskadne'' reakcije. Obstaja več načinov kako zgraditi strukture podobne celicam. Poleg opisanega, ki kombinira več pristopov, se lahko umetne celice gradi iz majhnih kapljic tekočine podobne citoplazmi, iz polimerov ali maščobnih kislin. Naslednjih korak je nedvomno narediti umetno celico, ki lahko sama proizvaja svojo energijo. S preučevanjem tega področja lahko biokemiki vedno bolje razumemo kaj se dogaja na celičnem nivoju in kako to uporabiti v nadaljnih raziskavah.<br />
<br />
=== Urška Černe: Boj imunskega sistema proti malariji ===<br />
Malarijo povzroča infekcija z parazitom, vrste Plasmodium falciparum, ki se prenese na človeka z pikom okuženega komarja mrzličarja. Ko piči človeka, se trosi prenesejo v njegovo kri in se začnejo množiti v jetrih. Nastanejo merozoiti, ki vstopajo v rdeča krvna telesca (eritrocite), kjer se nadalje delijo, dokler eritrocit ne poči. P. falciparum je specifični gostitelj, kar predstavlja težavo pri izvedbi človeške infekcije na laboratorijskih živalih kot so miši. Za premagovanje tega izziva so raziskovalci razvili miš z človeškimi eritrociti in jim dodali človeške imunske celice (miš RICH). Imunski sistem ima pri obvladovanju okužbe ključno vlogo. Študije na miših z uporabo človeških sevov Plasmodium so pokazale, da imunske celice (naravne celice ubijalke = celice NK, T celice in celice B) prispevajo k antiparazitski imunosti, pri čemer so bistvenega pomena celice NK. Te reagirajo z okuženimi eritrociti in jih tudi eliminirajo. Okuženi eritrociti postanejo sploščeni, kar kaže na uhajanje celične vsebine in izgubo volumna celice. Celični receptor LFA-1 je vključen v interakcijo celic NK z okuženimi eritrociti in njihov pomor. Pojasnitev molekularne narave vseh teh interakcij je bistveno za razumevanje mehanizma odzivanja naravnih celic ubijalk na infekcijo s P. falciparum.<br />
<br />
<br />
<br />
=== Jerneja Kocutar: Odziv celic na stresne situacije ===<br />
Kadar so celice izpostavljene stresnim pogojem, ki ogrozajo njihovo prezivetje se v njih aktivira stresni odziv, da bi čimprej spet vzpostavile homeostazo. Tak odziv je univerzalen in ga lahko najdemo v vseh organizmih in v vseh vrstah celic. Celice proizvajajo stresne proteine, ki izpolnjujejo razlicne naloge npr. preprečujejo tvorbo agregatov in neaktivnih intermediatov, odstranjujejo že poškodovane proteine, varujejo celične strukture, reorganizirajo celično oskrbo z energijo...Preden pa celica začne tvoriti proteine se aktivirajo transkripcijski receptrorji, od katerih je najpomembnejši HSF1. Aktivni HSF1 je trimer in ima dolčcene skupine fosolizirane. Regulacija stresnega odziva je odvisna od več celičnih procesov in organelov, najpomembnejši pa so procesi v jedru. Za uravnavanje stresnega odziva imamo 55 pozitivnih in 14 negativnih modulatorjev, ki so locirani v jedru, citoplazmi ali organelih. Pozitivni stresni odziv podaljšujejo in preprečujejo agregacijo proteinov, negativni pa odziv zavirajo. Vsi modulatorji so zelo tesno povezani med seboj, saj opazimo veliko več povezav kot med nakljičnim proteini. Kot najpomembnejši modulator je bila spoznana acetiltransferaza EP300, ki z acetiliranjem lizinov uravnava delovanje HSF1. V prihodnosti bi stresni odziv lahko uporabili tudi za zdravljenje bolezni pri katerih je problem obsežno propadanje celic. S tarčno aktivacijo stresnega odziva bi lahko reducirali poškodbe na celicah.<br />
<br />
<br />
<br />
=== Tadej Ulčnik: Prisotnost proteinov UCP določa metabolizem celice ===<br />
Vzorec izražanja razklopnih proteinov med diferenciacijo matičnih celic daje nov namig o njihovii vlogi. Izmed družine petih razklopnih proteinov je znana le vloga razklopnega proteina UCP1, funkcija ostalih štirih pa še vedno ni znana. Znanstveniki so na podlagi rezultatov več analiz domnevali, da vzorec izražanja UPC proteinov sovpada s specifičnimi celicami, ki imajo podoben metabolizem, in se spremeni, če se celice same spremenijo. Analizirali so izražanje UCP2 v mišjih embrionalnih matičnih celicah pred in po diferenciaciji v nevrone. Dokazali so, da je samo UCP2 prisoten v nediferenciranih matičnih celicah in izgine takoj, ko se te začnejo diferencirati v nevrone. Nasprotno od tega se istočasno poviša raven izražanja UCP4 in tipičnih nevralnih označevalnih proteinov. Prisotnost proteina UCP2 v matičnih, rakavih in imunskih celicah, kaže na to, da je UCP2 prisoten v celicah z veliko zmožnostjo razmnoževanja, za katere je tudi značilen metabolizem, ki temelji na glikolizi. Protein UCP4 pa je prisoten samo v diferenciranih živčnih celicah, ki se niso sposobne deliti. Odkrili so da se UCP2 izraža tudi v nevroblastomih, katerih metabolizem je podoben rakavim celicam, ne izraža pa se UCP4. Te ugotovitve bi lahko pripomogle k hitrejšem odkrivanju rakavih celic, ki se od ostalih razlikujejo v metabolizmu in nekaterih proteinih.<br />
<br />
== 24.3. ==<br />
<br />
=== Hrvoje Malkoč: Adsorbcija mielinskega bazičnega proteina na membrane mielinskih lipidnih dvoslojev ===<br />
<br />
Da bi razumeli demielizacijske bolezni moramo najprej vedeti, kako pride do njih. Zato so znanstveniki iz Kalifornijske univerze Santa Barbara izvedli poskus s katerim so preverjali sestavo in lastnosti mielinskih dvoslojev. Mielin je več lipidnih dvoslojev skupaj, ki morajo biti kompaktni in med seboj vsebovati čim manjše količine vode. Že majhna sprememba v zgradbi mielinske ovojnice lahko povzroči težave pri izolaciji aksona in s tem povzroči različne motnje ali celo to, da impulz ne prispe na cilj. Posledice so lahko bolezni, kot je multipla skleroza, vzroki pa so lahko avtoimunski odzivi, infekcije, izpostavljenost določenim kemikalijam, pa tudi genetika. Opravljene so bile raziskave o adsorbciji mielinskega bazičnega proteina (MBP) na membrane mielinskih lipidnih dvoslojev in njihov vpliv na strukturo, ravnovesni razmik in adhezijske sile med njima. Znanstveniki so na obe strani aparata površinskih sil postavili lipidni dvosloj, ga dali v pufersko raztopino z MBP-jem in jih približali da so se zlepili. Nato so jih dali narazen in merili adhezijo in debelino filma. Ugotovili so, da je zdrav mielin veliko bolj kompakten in vsebuje manj vode med membranami, pa tudi ima močnejšo adhezijo, in se bolj prijema na nasprotnega. Ta raziskava se razlikuje od drugih po tem, da ima molekularen pristop za razliko od drugih in bi zato lahko omogočila napredek v raziskavi demielizacijskih bolezni.<br />
<br />
=== Janja Krapež: Nanopore omogočajo transport DNA skozi membrane ===<br />
<br />
Celice obdaja lipidni dvosloj, ki je polprepusten in loči zunanjost celice od notranjosti (vse snovi torej ne morejo v celico). Prehod molekul je v veliki meri odvisen od transmebranskih proteinov, ki omogočajo transport snovi, ki ne morejo direktno skozi lipidni dvosloj, to so ioni in druge večje molekule. Nekateri proteini pa v neki drugi celici povzročijo majhne pore – nanopore. Pri tem ioni in molekule prosto prehajajo, kar privede do celične smrti, ker prehod snovi ni več nadzorovan. Raziskovalci želijo skozi take nanopore spraviti tudi DNA ali proteine. Težava je le v tem, da je težko nadzorovati prehode molekul skozi nanopore. Raziskovalci namreč ne želijo, da bi skozi nanopre lahko v celico vstopale vse molekule. Vstopale naj bi le tiste molekule, ki imajo za to pravo gensko informacijo. Profesorju Maglia in njegovi ekipi je uspelo sestaviti nanoporo, ki deluje kot cikel in prepušča DNA. Točno določeni deli DNA v raztopini hibridizirajo in se transportirajo skozi DNA poro. Na nasprotni strani pore pa je druga DNA, ki izpusti iskano genetsko zaporedje iz pore v celico. Ta prenos se zgodi vsakokrat, ko ima DNA, ki želi skozi membrano, pravilno zaporedje. Ta prehod poteka spontano in deluje kot tekoči trak. DNA vijačnico so združili z vrhom proteinske nanopore. Tako so dobili membranski sistem, ki je omogočil transport specifične DNA molekule skozi nanoporo.<br />
<br />
== 31.3. ==<br />
<br />
=== Monika Pepelnjak: Odpornost tumorjev na kemoterapijo ===<br />
<br />
Rak debelega črevesja in danke je drugi najpogostejši rak v Sloveniji. Kadar bolezen ni odkrita dovolj hitro, je za zdravljenje poleg kirurške odstranitve malignega tumorja potrebno tudi zdravljenje s citostatiki (kemoterapija). Najpogosteje uporabljen citostatik pri kolorektalnem raku je oksaliplatin, ki poškoduje DNA zaporedje in tako prepreči delovanje in hitro delitev celic. Velik problem pri zdravljenju pa povzročata primarna in pridobljena odpornost na oksaliplatin. Odpornost je lahko posledica več različnih dejavnikov, eden izmed njih so tudi epigenetske spremembe. Raziskovalci so odkrivali razloge za odpornost z epigenetskega vidika in primerjali metilacije različnih genov v odpornih in odzivnih celicah. Ugotovili do, da se največje razlike pojavljajo v metilaciji SRBC gena, ki je znan kot interaktor s produktom gena BRCA1. Dokazali so, da je metilacija tega gena, in s tem njegovo utišanje, resnično odgovorna za zmanjšano odzivnost celic na oksaliplatin. Epigenetska inaktivacija SRBC gena se je pojavila pri 29.8% pacientov, povezali pa so tudi utišanje tega gena in krajše obdobje preživetja brez nadaljevanja bolezni pri pacientih, ki so se zdravili z oksaliplatinom, vendar jim metastaz kirurško niso mogli odstraniti. Rezultati postavljajo osnovo za nadaljne študije, kjer bi lahko metilacijo gena SRBC uporabili kot predhodnji pokazatelj odpornosti na oksaliplatin.<br />
<br />
=== Anja Tanšek: Potrditev ključne beljakovine odgovorne za razrešitev skrivnosti mitoze ===<br />
<br />
V celicah sesalcev je endocitoza, posredovana s klatrinom (CME), glavna pot za vstop večjih molekul skozi membrano preko različnih receptorjev. Mehanizem CME se zaustavi kmalu po tem, ko celica vstopi v profazo in začne ponovno delovati v pozni anafazi, kjer je potreben za membransko dinamiko pri citokinezi. Predlagana sta bila dva glavna mehanizma, ki bi lahko povzročila inhibicijo CME. Prva hipoteza pravi, da direktna mitotska fosforilacija CME sistema zmanjša njegovo aktivnost. V podporo tej predpostavki so številni endocitozni proteini, ki so fosforilirani med mitozo, vendar vpliv teh modifikacij na CME ni jasen, niti dokazan. Druga hipoteza pravi, da povečana membranska napetost mitotskih celic prepreči nastanek jamice in izoblikovanje v vezikel med CME. Celicam, ki so v fazi mitoze, se membranska napetost poveča. Posledično se poveča tudi potreba po aktinskem citoskeletu, ker se formira celični korteks. Zato aktinski citoskelet ni na voljo mehanizmu CME za premagovanje povečane obremenitve zaradi membranske napetosti in se endocitoza v celici ustavi. V tej študiji so raziskovalci dokazali, da je za zaviranje CME v času mitoze odgovorno pomanjkanje aktina. Dokazali so, da lahko CME poteka tudi v mitotskih celicah, kljub visoki membranski napetosti, tako da so omogočili delovanje aktina pri CME. Mitotska fosforilacija endocitoznih proteinov je bila prisotna tudi v celicah s ponovno vzpostavljeno CME, kar kaže, da direktna fosforilacija CME mehanizma ni odgovorna za njegovo inhibicijo.<br />
<br />
=== Jerneja Ovčar: Vztrajno zavezujoč mehanizem za vizualni nadzor gibanja ===<br />
<br />
Človeški motorični sistem je izjemno napreden pri nadzoru vizualno vodenih premikov, saj se zelo hitro prilagaja spremembam. To doseže skozi niz visoko avtomatičnih procesov, ki prevajajo vizualne informacije v predstavitve. Motorični sistem je del osrednjega živčnega sistema in se ukvarja z gibanjem. Sestoji iz piramidalnega in ekstrapiramidalnega sistema. Da pa se lahko doseže takšen niz visoko avtomatičnih procesov za oblikovanje predstavitev, ki so primerne za vklop motoričnega nadzora, potrebuje motorični nadzor vizualne informacije, ki se nanašajo na cilj. V ta namen je bila raziskana vloga pozornosti v vizualno povratnem nadzoru, tako da je bil motorični sistem izzvan z več poskusi. Rezultati so pokazali, da vizualna pozornost spreminja obdelavo ciljne informacije. Ugotovili so, da je učinek spremembe pozornosti večji pri premikih ciljev (nek predmet) kot pa pri premikih kurzorjev (npr. rok). Zato sklepamo na obstoj ločenega vizualno-motoričnega zavezujočega mehanizma, ki daje prednost vizualnim podatkom, ki predstavljajo gibanje premikajočega uda. Vizualno-motoričen mehanizem pojasnjuje učinkovitost in hitrost, s katero lahko človek hkrati izvaja več ciljno usmerjenih gibanj. Njegova prednost je, da loči med ciljem in motečimi predmeti na poti. Zaznavanje vizualnih dražljajev, ki se nanašajo na naše gibanje, je temeljni proces pri nadzoru segajočih gibanj. Vizualno-motorični mehanizem je skupen vsem vrstam, ki se pri usmerjanju gibanja opirajo na vid.<br />
<br />
=== Inge Sotlar: CPEB proteini oblikujejo dolgoročni spomin ===<br />
,<br />
Dolgoročni spomin hrani vse, kar se v življenju naučimo. Spomin z leti slabi, motnje spomina pa se pojavijo tudi pri nevrodegenerativnih boleznih, kot sta npr. Alzheimerjeva in Parkinsonova bolezen. Znanstveniki so poskušali odkriti proteine, odgovorne za ohranjanje dolgoročnega spomina. Za pomembne regulatorje sinteze proteinov v sinaptičnih membranah so se izkazali CPEB proteini, ki največkrat delujejo kot aktivatorji translacije mRNA v različnih tipih celic, tudi v nevronih. Pri raziskavi na vinskih mušicah so našli protein iz družine CPEB, Orb2, ki je s svojimi oligomeri, podobnim amiloidom, potreben za shranjevanje informacij v dolgoročni spomin. Njegov monomer, Orb2A, je v živčnem sistemu prisoten v zelo majhnih količinah, a tvori pomemben kompleks s proteinom Tob, regulatorjem celičnega cikla. Da povezavo Tob-Orb2A uravnava fosforilacija, so dokazali z dodatkom kalikulina, inhibitorjem, ki blokira proteinsko fosfatazo 2 (PP2A). Dodatek je povzročil, da se je število povezav Tob-2A zmanjšalo. Pri iskanju kinaz, ki fosforilirajo protein Tob, so se osredotočili na kinazo LimK, saj se sintetizira le v sinapsah in je potrebna za njihovo oblikovanje. Dokazali so, da gre pri nastanku oligomerov Orb2 za součinkovanje med proteinom Tob, kinazo LimK in fosfatazo PP2A. Kako se podatki shranjujejo v spomin je zapleten proces, vendar raziskovanje biokemijskih reakcij nudi možnosti za zdravljenje neozdravljivih bolezni živčevja.<br />
<br />
== 7.4. ==<br />
<br />
=== Božin Krstanoski: Uporaba bakterij pri naftnih razlitjih ===<br />
<br />
Kljub sodobni tehnologiji so razlitja nafte še vedno pogosta težava za oceane. Zaradi kompleksne strukture molekule nafte lahko čiščenje razlitja traja tudi mesece ali leta, kar pa je zelo škodljivo za morsko okolje. Znanstveniki so ugotovili, da si je narava sposobna sama pomagati ob nesrečah kot so razlitja nafte - z morskimi bakterijami. Poznamo tri vrste bakterij, ki pripomorejo k bioremediaciji - bakterije, ki proizvajajo kislino in so anaerobne, bakterije, ki zmanjšujejo sulfate ter splošne aerobne bakterije. Najnovejše raziskave pa kažejo, da je mogoče s pravo mero vzpodbude povzročiti, da so te bakterije pri bioremediaciji še bolj učinkovite. Ugotovili so, da so bakterije pri poskusih, ko so imele dovolj zalog nutrientov kot so fosfati in dušik dosegle večjo in bolj učinkovito razgradnjo nafte. Najpomembnejša morska bakterija, ki je sposobna razgradnje nafte je Alcanivorax borkumensis. A. borkumensis primarno uporablja alkane kot vir energije, vendar lahko prebavi tudi nekatere druge organske spojine. Ko uporablja alkane za vir energije, vsaka celica A. borkumensis tvori biosurfaktant na svoji površini, ki je dodatna plast, ki nastane ob celični membrani. Snovi, ki sestavljajo biosurfaktant znižajo površinsko napetost vode, kar pripomore k boljši razgradnji nafte. Druga pomembna morska bakterija, ki je pomembna ob razlitjih nafte, je Oleispira antarctica. Ker je ta bakterija psihrofil, je sposobna preživeti ekstremne pogoje, kot so nizke temperature in je zato zelo učinkovita pri bioremediaciji v polarnih morjih. Odkritje Oleispire antarctice je zelo pomembno, saj nam je njihova ekološka tekmovalnost v hladnih okoljih odprla nove poti za iskanje biotehnoloških rešitev za zmanjšanje onesnaževanja v polarnih morjih.<br />
<br />
=== Amadeja Lapornik: Nanodelci, ki omogočajo zgodnje odkrivanje krvnih strdkov ===<br />
<br />
Koagulacija je proces pri katerem v krvi nastajajo strdki. Strjevanje krvi je pomemben mehanizem odziva na poškodbe, saj strdki ob raztrganju stene žil preprečijo uhajanje krvi. Tromboza je nastanek krvnega strdka (trombusa) v žili, kar onemogoča normalen pretok krvi po krvožilnem sistemu. Najpogostejši vzroki za nastanek venske tromboze so poškodbe žilnih sten in upočasnitve toka krvi na mestu poškodbe, dolgotrajna nepremičnost, rakava in internistična obolenja. Najpomembnejši encim, ki je regulator hemostaze (proces, zaustavljanja krvavitve) je trombin. Je encim, ki se nahaja v krvni plazmi, spada v skupino serin proteaz. V članku so predvidevali, da je možno odkrivanje krvnih strdkov (in s tem nevarnost tromboze) s posebnimi nanodelci. Kot pomoč za zgodnje odkrivanje nevarnih bolezni so znanstveniki razvili beljakovinske substrate, ki so občutljivi na proteaze in jih poimenovali sintezni biomarkerji. Predpostavili so, da so sintezni biomarkerji oblikovani za preiskovanje notranjosti žil, zaznavanje aktivnosti proteaze in posledično odkrivanja zasnov akutne tromboze. V raziskavi so znanstveniki uporabili fluorescenčno spektroskopijo in encimskoimunski test (ELISA), ki se uporablja za detekcijo protiteles ali antigenov v vzorcu. Takšen način testiranj lahko odkriva zgodnje nevarnosti bolezni, ki se nahajajo globoko v telesu, kot so pljuča. Testiranja omogočajo analizo urina za kvantitativno oceno količine krvnih strdkov, ki bremenijo žilo.<br />
<br />
<br />
=== Angela Mihajloska: Proteine,ki so odkriti v gonoreje lahko ponudijo novi pristop k zdravljenju ===<br />
Gonoreja (lat. gonorrhoea) ali kapavica je močno razširjena spolno prenosljiva bolezen, ki se večinoma prenaša s spolnim stikom in jo povzroča gonokok, kateri nastane na sluznicah spolovil gnojno vnetje z gnojnim izločkom. Bacterija Neisseria gonorrhoeae (GC) najpogoste se prenese iz enega partnerja na drugega med spolnim odnosom preko semenske oziroma vaginalne tekočine pri nezaščitenih spolnih odnosih in večinoma prizadane spolne organe.Znanstveniki so odkrili nove proteine v ali na površini bakterije, ki povzroča gonorejo. Ti ponujajo obetavne novi pogled za napada proti spolne bolezne, ki imajo se večjo odpornost na antibiotike. Samo tretja generacija cefalosporinskih antibiotih še vedno povejo dobro učinkovitost proti gonoreji, ustvarjajo teki s časom, da bi našli nekaj alternativni način za zdravljenje te bolezni, ki imajo resne posledice za zdravje.So odkrili skupno 22 različite proteinov. Med temi proteinov ki so prikazani podobno obilje v štirih GC sevov, 32 so bili ugotovljeni v obeh celične ovojnice in membranske mehurčke frakciji.<br />
Osredotočiti na eno od njih, in homolog protein zunajne membrane LptD, smo dokazali da je njena izčrpavanje povzrčil izgubo GC.<br />
<br />
<br />
=== Domagoj Majić: Low vitamin D levels raise anemia risk in children ===<br />
Low levels of the “sunshine” vitamin D appear to increase a child’s risk of anemia, according to new research. The study is believed to be the first one to extensively explore the link between the two conditions in children.<br />
<br />
== 14.4. ==<br />
<br />
=== Peter Pečan: Reprogramiranje kožnih celic v srčne ===<br />
Srčni zastoj, ki je v razvitem svetu med glavnimi razlogi za smrt, povzroči pri osebah, ki ga preživijo, izgubo ali okvaro srčnega tkiva. Kljub napredkom na področju biomedicine, je vračanje funkcionalnosti poškodovanemu srčnemu tkivu precejšen izziv. Napredki na področju induciranih pluripotentnih matičnih celic (angl. »induced pluripotent stem cell«) so vzpodbudili raziskovanje možnosti reprogramiranja enga tipa celice v drugega, ne da bi pri tem šle skozi pluripotentno stanje; ta proces se imenuje transdiferenciacija. Postopek obeta možnost popravkov poškodovanih srčnih celic brez povečanega tveganja za nastanek tumorjev, povezanega s pluripotentnimi celicami pri terapiji z zamenjavo celic in/ali pri in vivo regeneraciji s pomočjo reprogramiranja. Čeprav do zdaj znani načini, ki uporabljajo več genskih faktorjev (med 4 in 7), dokazujejo možnost reprogramiranja, takšne genske manipulacije prinašajo številne težave, predvsem na področju varnosti in učinkovitosti. Poleg tega bi bilo za učinkovitejšo uporabo transdiferencialne terapije potrebno zmanjšati ali pa povsem odstraniti potrebo po genski manipulaciji. To bi lahko dosegli z zamenjavo transkripcijskih faktorjev s tako imenovanimi majhnimi molekulami (angl. »small molecules«), ki bi lahko ustvarile pogoje za reprogramiranje z enim samim transkripcijskim faktorjem.<br />
<br />
=== Živa Moravec: Ključen korak naprej pri tiskanju 3D tkiv ===<br />
Znanstveniki se že leta trudijo ustvariti umetna tkiva, ki bi bila čim bolj podobna pravim. Če želijo to doseči, morajo biti umetno ustvarjeni tkivni konstrukti sestavljeni iz treh glavnih komponent – celic, zunajceličnega matriksa in žil, ki morajo biti urejene v pravilne geometrijske vzorce. Verjetno najpomembnejše je ožiljenje tkiva. Če žilno omrežje manjka, bo slej ko prej prišlo do razvoja nekrotičnega jedra zaradi odsotnosti učinkovitega dotoka hranil, rastnih in signalnih faktorjev ter odvajanja odvečnih produktov. V študiji, predstavljeni v članku, so razvili novo metodo 3D biotiskanja, ki omogoča izdelovanje tkiv, opremljenih z žilami, več tipi celic naenkrat in zunajceličnim matriksom. Za te potrebe so razvili tiskalnik s štirimi neodvisnimi tiskalnimi šobami in več črnil, glede na različne lastnosti posameznih glavnih komponent: za izdelavo ožilja so razvili začasno podporno črnilo na osnovi praška Pluronic F127, za izdelavo zunajceličnega matriksa in črnila, ki so ga uporabili kot nosilec celic, pa so sintetizirali gelatin metakrilat. Z uporabo teh črnil so najprej natisnili več vzorčnih 1D, 2D in 3D omrežij, s katerimi so posnemali osnovne strukture v tkivih, nato so se osredotočili na endotelizacijo žilnih sten, pri čemer so v vzorec tkiva injicirali raztopino človeških endotelnih celic. Kot zadnjo in najbolj kompleksno strukturo so natisnili model tkiva iz štirih plasti, v katerega so vključili dva tipa celic (človeške in mišje). Taka tridimenzionalna okolja odpirajo nove možnosti testiranja zdravil in raziskave na več medicinskih področjih, z nadaljnjimi izboljšavami pa bi lahko ta tehnika vodila tudi do proizvodnje funkcionalnih tridimenzionalnih tkiv, morda tudi organov.<br />
<br />
== 5.5 ==<br />
<br />
=== Jure Zadravec: Vloga tumorskih označevalcev CA19-9, CA125 in CA72-4 pri diagnozi raka trebušne slinavke ===<br />
<br />
CA125 in CA72-4 spadata v družino glikoliziranih proteinov z visoko molekulsko maso in se pogosto uporabljata kot tumorska označevalca pri diagnozi raka jajčnikov ter raka želodca. Zadnje raziskave pa so pokazale, da omenjena označevalca igrata pomembno vlogo tudi pri diagnosticiranju raka trebušne slinavke. Ker je pri tem raku razpoložljivost podatkov o tumorskih označevalcih omejena, je bil cilj te raziskave ugotoviti klinično vlogo CA19-9 (specifičen za raka trebušne slinavke), CA125 in CA72-4 ter povezavo z mednarodno klasifikacijo tumorjev - TNM (Tumor Node Metastasis). Z imunoradiometrično metodo so merili koncentracijo tumorskih označevalec pri pacientih z rakom ter pri pacientih z benignimi spremembami na trebušni slinavki. Rezultati so pokazali občutno višje koncentracije označevalcev pri pacientih z rakom v primerjavi s tistimi z benignimi spremembami. Raziskavo so zaključili z ugotovitvijo, da odkrivanje s kombinacijo označevalcev CA19-9 in CA72-4 močno izboljša specifičnost diagnoze, kombiniranje CA125 in CA19-9 pa je povezano s histološkim tipom tumorja.<br />
<br />
=== Tomaž Žagar: Ključna proteina pri uravnavanju celične smrti ===<br />
<br />
Za normalno delovanje večceličnega organizma je potrebno, da se celice delijo in rastejo kontrolirano, ker drugače lahko to privede razvoja raka. Celice pa so tekom evolucije razvile nekatere mehanizme, s katerimi lahko samo sebe pokončajo/razgradijo, če prejmejo signal, da je čas da propadejo. Ta mehanizma sta avtofagija in apoptoza. Signali pa lahko pridejo od zunaj ali od znotraj. Če pridejo od znotraj, se vežejo na mitohondrijsko membrano in začnejo proces celične smrti. Ključna proteina, ki uravnavata celično smrt sta protein Bcl-2 in protein NAF-1. Prvi protein ima med drugim na svoji površini dve domeni. Ena inhibira, druga pa inducira apoptozo. Protein NAP-1 se lahko veže na katerokoli izmed dome, res pa je, da se močneje veže na dome, ki inhibira apoptozo. Kljub temu, da natančen mehanizem še ni poznan, so se raziskovalci odločili raziskati kje se proteina vežeta in kakšne so posledice vezave na aktivnost proteinov. S tem so hoteli ustvariti temelje za bodoče raziskave na področju odkrivanja zdravila proti raku, saj se je izkazalo, da je pri rakastih celicah povečano število NAF-1 proteinov.<br />
<br />
=== Tjaša Sorčan: Posamezni Iks kanali na površini srčnih celic sesalcev vsebujejo dve KCNE1 podenoti ===<br />
<br />
Da se naše srce lahko krči in razteza, potrebujemo posebne IKS kanale, ki se nahajajo na površini srčnih celic. Sestavljata jih dva proteina: E1, katerega število je bilo do nedavnega neznano, in Q1, za katerega vemo da tvori poro s štirimi podenotami. Kljub temu da Q1 lahko sam tvori napetostno odvisni kalijev kanal, pa je nujno potreben tudi E1, ker nadzira kinetiko prehoda, površinsko izražanje, kako so celice regulirane z zdravili, napetostno odvisnost, enotno prevodnost in farmakologijo nastalih kompleksov. Njuno razmerje se ne spreminja, tudi če povečamo ali znižamo raven le enega proteina. V članku sta opisani dve nasprotujoči raziskavi. Prva pripada Morinu in Kobertzu, ki sta s pomočjo škorpijonovega strupa CTX in njegove povezave s E1 določila dve podenoti. Nasprotovala pa jima je raziskava Nakajo et al. , ki je zagovarjala spreminjajočo stehiometrijo med dvema in štirimi E1 podenotami. Vendar naj bi bile njegove domneve napačne, kar so tudi dokazali z fotobeljenjem z enim fluorescenčnim delčkom na površini žive celice sesalca. Demonstrirali so tri spektroskopske metode štetja in za oceno rezultatov uporabili dva statistična pristopa. Te so dokazale, da posamezni IKS kanali na površini celic sesalca res vsebujejo le in samo dve E1 podenoti.<br />
<br />
=== Fran Krstanović: Breast milk protein may be key to protecting babies from HIV ===<br />
<br />
HIV is an incurable disease that attacks our immune system leaving it shattered. One of the many ways of transmission is with breastfeeding from a HIV-1 positive mother,but not all of the children get effected. Breast milk is full of healthy benefits such as antibodies that help babies build their own immune system. A study at Duke Medical Science has found a protein(TNC) that is responsible for repression of HIV-1 and the explanation why a higher rate of children are not effected via breastfeeding.Further studies will show if TNC neutralizing characteristics could be used as a breakthrough in HIV-prevention therapy if given orally to infants prior to breastfeeding.<br />
<br />
== 12.5. ==<br />
<br />
=== Hasiba Kamenjaković: Podobnosti med HIV / AIDS, opioidne odvisnosti epidemije ===<br />
Bolezni uporabe opioidov so najhitreje rastoča vrsta težav z drogami . Po mnenju raziskovalcev , veliko od trenutne izpostavljenosti opioidov je povezana z eksplozijo široko dostopna , močnih protibolečinskih zdravil na recept , ki imajo enak učinek v možganih kot heroin . Čeprav je veliko koristi od znatnega lajšanje bolečin in izboljšanje kakovosti življenja , opioidi na recept, zdaj ubil več ljudi kot heroin in kokain skupaj. Raziskovalci so ugotovili , da medtem ko razširjena, je zasvojenost marginalizirana kot ga določa ločeno od drugih bolezni, socialni problem , z ovirami za zdravljenje , od strogih meril za vstop v omejene razpoložljivosti zdravljenja.<br />
<br />
Tudi so opisal potrebo po celovitem preprečevanju, diagnostiko in zdravljenje kampanjo za boj proti prevelik odmerek , skupaj s standardno -of- nego modele zdravljenja , ki temeljijo na obstoječih dokazov . Predlagajo, več izobraževanja za medicinske stroke in da izobraževalni viri za zasvojenost v medicinsko usposabljanje se na par z drugih kroničnih bolezni . Prav tako, kot s HIV / AIDS , bolniki , ki trpijo zaradi odvisnosti bi morali biti vključeni v oblikovanje in izvajanje programov in izdelkov , namenjenih , da jim služi .</div>Nfrauskokhttps://wiki.fkkt.uni-lj.si/index.php?title=TBK2014-seminar&diff=9350TBK2014-seminar2014-04-21T08:39:08Z<p>Nfrauskok: /* Temelji biokemije- seminar */</p>
<hr />
<div>= Temelji biokemije- seminar =<br />
<br />
Seminarje vodi prof. dr. Brigita Lenarčič in so na urniku vsak ponedeljek od 11:00 do 12:30. Seminarji so obvezni.<br />
<br />
Ocena seminarjev (6-10) predstavlja enako število odstotkov, ki se prištejeh končnipisni oceni izpita. <br />
Stran na strežniku s seminarskimi nalogami je zaščitena.<br />
Uporabniško ime je: tbk, password pa: samozame## "##" sta dve številki, ki ju izveste na predavanjih.<br />
<br />
== Seznam seminarjev =={| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" <br />
| align="center" style="background:#f0f0f0;"|'''Ime in priimek'''<br />
| align="center" style="background:#f0f0f0;"|'''Naslov seminarja'''<br />
| align="center" style="background:#f0f0f0;"|'''Povezava'''<br />
| align="center" style="background:#f0f0f0;"|'''Rok za oddajo'''<br />
| align="center" style="background:#f0f0f0;"|'''Rok za recenzijo'''<br />
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 1'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 2'''<br />
| align="center" style="background:#f0f0f0;"|'''Recenzent 3'''<br />
|-<br />
| Črt Kovač||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#.C4.8Crt_Kova.C4.8D:_Naslov_v_sloven.C5.A1.C4.8Dini Naslov]||[http://www.sciencedaily.com/releases/2013/06/130627142551.htm link]||03.03.||06.03.||10.03.||Liza Otorepec||Marija Srnko||Luka Dejanović<br />
|-<br />
| Bine Tršavec||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Bine_Tršavec:_Stikalo,_ki_pove,_da_je_čas_za_spanje Stikalo, ki pove, da je čas za spanje]||[http://www.sciencedaily.com/releases/2014/02/140219124730.htm Povezava]||03.03.||06.03.||10.03.||Naida Hajdarević||Eva Škrjanec||Katja Malovrh<br />
|-<br />
| Jernej Vidmar||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Jernej_Vidmar:_Boljša_slikovna_obdelava_z_nanozamrzovanjem Boljša slikovna obdelava z nanozamrzovanjem]||[http://www.sciencedaily.com/releases/2014/02/140226133000.htm Povezava]||03.03.||06.03.||10.03.||Nuša Kelhar||Vesna Podgrajšek||Nina Mavec<br />
|-<br />
| Ernest Šprager||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Ernest_Sprager:_ Doslej najuspešnejše utišanje genov v jetrih z RNA interferenco po zaslugi novih nanodelcev]||[http://www.pnas.org/content/early/2014/02/06/1322937111.full.pdf+html Povezava]||03.03.||06.03.||10.03.||Tamara Božič||Nives Mikešić||Ana Kompan<br />
|-<br />
| Andrej Žulič|| [http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Andrej_.C5.BDuli.C4.8D:_Prva_umetna_celica_z_delujo.C4.8Dimi_organeli Prva umetna celica z delujočimi organeli] || [http://www.sciencedaily.com/releases/2014/01/140114091707.htm Povezava] ||10.03.||13.03.||17.03.||Črt Kovač||Liza Otorepec||Marija Srnko<br />
|-<br />
| Urška Černe||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Ur.C5.A1ka_.C4.8Cerne:_Boj_imunskega_sistema_proti_malariji Boj imunskega sistema proti malariji]||[http://www.sciencedaily.com/releases/2014/01/140113154225.htm Povezava]||10.03.||13.03.||17.03.||Bine Tršavec||Naida Hajdarević||Eva Škrjanec<br />
|-<br />
| Tadej Ulčnik||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Tadej_Ul.C4.8Dnik:_Prisotnost_proteinov_UCP_dolo.C4.8Da_metabolizem_celice Prisotnost proteinov UCP določa metabolizem celice] ||[http://www.sciencedaily.com/releases/2014/03/140304071208.htm Povezava]||10.03.||13.03.||17.03.||Jernej Vidmar||Nuša Kelhar||Vesna Podgrajšek<br />
|-<br />
| Jerneja Kocutar||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Jerneja_Kocutar:_Odziv_celic_na_stresne_situacije Odziv celic na stresne situacije]||[http://www.sciencedaily.com/releases/2014/02/140228103435.htm Povezava]||10.03.||13.03.||17.03.||Ernest Šprager||Tamara Božič||Nives Mikešić<br />
|-<br />
| Hrvoje Malkoč||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Hrvoje_Malkoč:_Adsorbcija_mielinskega_bazičnega_proteina_na_membrane_mielinskih_lipidnih_dvoslojev Adsorbcija mielinskega bazičnega proteina na membrane mielinskih lipidnih dvoslojev]||[http://www.sciencedaily.com/releases/2014/02/140225143937.htm Povezava]||17.03.||20.03.||24.03.||Andrej Žulič||Črt Kovač||Liza Otorepec<br />
|-<br />
| Janja Krapež||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Janja_Krape.C5.BE:_Nanopore_omogo.C4.8Dajo_transport_DNA_skozi_membrane Nanopore omogočajo transport DNA skozi membrane]||[http://www.sciencedaily.com/releases/2013/10/131023090540.htm Povezava]||17.03.||20.03.||24.03.||Urška Černe||Bine Tršavec||Naida Hajdarević<br />
|-<br />
| Inge Sotlar||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Inge_Sotlar:_CPEB_proteini_oblikujejo_dolgoročni_spomin CPEB proteini oblikujejo dolgoročni spomin]||[http://www.sciencedaily.com/releases/2014/02/140211174613.htm Povezava]||24.03.||27.03.||31.03.||Tadej Ulčnik||Jernej Vidmar||Nuša Kelhar<br />
|-<br />
| Monika Pepelnjak||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Monika_Pepelnjak:_Odpornost_tumorjev_na_kemoterapijo Odpornost tumorjev na kemoterapijo]||[http://www.sciencedaily.com/releases/2013/12/131202094320.htm Povezava]||24.03.||27.03.||31.03.||Jerneja Kocutar||Ernest Šprager||Tamara Božič<br />
|-<br />
| Jerneja Ovčar||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Jerneja_Ov.C4.8Dar:_Vztrajno_zavezujo.C4.8D_mehanizem_za_vizualni_nadzor_gibanja Vztrajno zavezujoč mehanizem za vizualni nadzor gibanja]||[http://www.sciencedaily.com/releases/2014/03/140313123139.htm Povezava]||24.03.||27.03.||31.03.||Hrvoje Malkoč||Andrej Žulič||Črt Kovač<br />
|-<br />
| Anja Tanšek||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Anja_Tan.C5.A1ek:_Potrditev_klju.C4.8Dne_beljakovine_odgovorne_za_razre.C5.A1itev_skrivnosti_mitoze Potrditev ključne beljakovine odgovorne za razrešitev skrivnosti mitoze]||[http://www.sciencedaily.com/releases/2014/02/140218101018.htm Povezava]||24.03.||27.03.||31.03.||Janja Krapež||Urška Černe||Bine Tršavec<br />
|-<br />
| ||||||24.03.||27.03.||31.03.||Inge Sotlar||Tadej Ulčnik||Jernej Vidmar<br />
|-<br />
| Angela Mihajloska||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Angela_Mihajloska:_Proteine.2Cki_so_odkriti_v_gonoreje_lahko_ponudijo_novi_pristop_k_zdravljenju Proteine ki so odkriti v gonoreje lahko ponudijo novi pristop k zdravljenju]||[http://www.sciencedaily.com/releases/2014/03/140331131010.htm Povezava]||31.03.||03.04.||07.04.||Monika Pepelnjak||Jerneja Kocutar||Ernest Šprager<br />
<br />
| Božin Krstanoski||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Božin_Krstanoski:_Uporaba_bakterij_pri_naftnih_razlitjih Uporaba bakterij pri naftnih razlitjih]||[http://www.sciencedaily.com/releases/2014/03/140310090615.htm Povezava]||31.03.||03.04.||07.04.||Jerneja Ovčar||Hrvoje Malkoč||Andrej Žulič<br />
|-<br />
| Domagoj Majić||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Domagoj_Maji.C4.87:_Low_vitamin_D_levels_raise_anemia_risk_in_children Low vitamin D levels raise anemia risk in children]||[http://www.sciencedaily.com/releases/2013/10/131021155625.htm Povezava]||31.03.||03.04.||07.04.||Anja Tanšek||Janja Krapež||Urška Černe<br />
|-<br />
| Amadeja Lapornik||[http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Amadeja_Lapornik:_Nanodelci,_ki_omogočajo_zgodnje_odkrivanje_krvnih_strdkov Nanodelci, ki omogočajo zgodnje odkrivanje krvnih strdkov]||[http://www.sciencedaily.com/releases/2013/10/131016123038.htm Povezava]||31.03.||03.04.||07.04.||Anja Šantl||Inge Sotlar||Tadej Ulčnik<br />
|-<br />
| Peter Pečan|| [http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#Peter_Pe.C4.8Dan:_Reprogramiranje_ko.C5.BEnih_celic_v_sr.C4.8Dne, Reprogramiranje kožnih celic v srčne]||[http://www.sciencedaily.com/releases/2014/02/140220132202.htm Povezava]||07.04.||10.04.||14.04.||Angela Mihajloska||Monika Pepelnjak||Jerneja Kocutar<br />
|-<br />
| Živa Moravec|| [http://wiki.fkkt.uni-lj.si/index.php/TBK2014_Povzetki_seminarjev#.C5.BDiva_Moravec:_Klju.C4.8Den_korak_naprej_pri_tiskanju_3D_tkiv, Ključen korak naprej pri tiskanju 3D tkiv]||[http://www.sciencedaily.com/releases/2014/02/140219095501.htm Povezava]||07.04.||10.04.||14.04.||Božin Krstanoski||Jerneja Ovčar||Hrvoje Malkoč<br />
|-<br />
| Tjaša Sorčan||||[http://www.sciencedaily.com/releases/2014/03/140304141740.htm Povezava]||21.04.||24.04.||05.05.||Domagoj Majić||Anja Tanšek||Janja Krapež<br />
|-<br />
| Tomaž Žagar|||| [http://www.sciencedaily.com/releases/2014/03/140303154011.htm Povezava]||21.04.||24.04.||05.05.||Amadeja Lapornik||Anja Šantl||Inge Sotlar<br />
|-<br />
| Fran Krstanović||||[http://www.sciencedaily.com/releases/2013/10/131021153200.htm Povezava]||21.04.||24.04.||05.05.||Peter Pečan||Angela Mihajloska||Monika Pepelnjak<br />
|-<br />
| Jure Zadravec||||||21.04.||24.04.||05.05.||Živa Moravec||Božin Krstanoski||Jerneja Ovčar<br />
|-<br />
| Primož Tič||||||05.05.||08.05.||12.05.||Tjaša Sorčan||Domagoj Majić||Anja Tanšek<br />
|-<br />
| Valentina Levak||||||05.05.||08.05.||12.05.||Tomaž Žagar||Amadeja Lapornik||Anja Šantl<br />
|-<br />
| Enja Kokalj||||||05.05.||08.05.||12.05.||Fran Krstanović||Peter Pečan||Angela Mihajloska<br />
|-<br />
| Hasiba Kamenjaković||||||05.05.||08.05.||12.05.||Jure Zadravec||Živa Moravec||Božin Krstanoski<br />
|-<br />
| Luka Dejanović||||||12.05.||15.05.||19.05.||Primož Tič||Tjaša Sorčan||Domagoj Majić<br />
|-<br />
| Katja Malovrh||||||12.05.||15.05.||19.05.||Valentina Levak||Tomaž Žagar||Amadeja Lapornik<br />
|-<br />
| Nina Mavec||||||12.05.||15.05.||19.05.||Enja Kokalj||Fran Krstanović||Peter Pečan<br />
|-<br />
| Anja Šantl||||||12.05.||15.05.||19.05.||Hasiba Kamenjaković||Jure Zadravec||Živa Moravec<br />
|-<br />
| Marija Srnko||||||19.05.||22.05.||26.05.||Luka Dejanović||Primož Tič||Tjaša Sorčan<br />
|-<br />
| Eva Škrjanec||||||19.05.||22.05.||26.05.||Katja Malovrh||Valentina Levak||Tomaž Žagar<br />
|-<br />
| Vesna Podgrajšek||||[http://www.sciencedaily.com/releases/2014/01/140130210734.htm Povezava]||19.05.||22.05.||26.05.||Nina Mavec||Enja Kokalj||Fran Krstanović<br />
|-<br />
| Nives Mikešić||||||19.05.||22.05.||26.05.||Ana Kompan||Hasiba Kamenjaković||Jure Zadravec<br />
|-<br />
| Liza Otorepec||||||26.05.||29.05.||02.06.||Marija Srnko||Luka Dejanović||Primož Tič<br />
|-<br />
| Naida Hajdarević||||||26.05.||29.05.||02.06.||Eva Škrjanec||Katja Malovrh||Valentina Levak<br />
|-<br />
| Nuša Kelhar||||||26.05.||29.05.||02.06.||Vesna Podgrajšek||Nina Mavec||Enja Kokalj<br />
|-<br />
| Tamara Božič||||||26.05.||29.05.||02.06.||Nives Mikešić||Ana Kompan||Hasiba Kamenjaković<br />
|}<br />
<br />
==Naloga==<br />
* samostojno pripraviti seminar, katerega tema je novica iz področja biokemije na portalu [http://www.sciencedaily.com ScienceDaily], ki je bila objavljena kasneje kot 1. avgusta 2013. Osnova za seminar naj bo znanstveni članek, ki je podlaga za to novico. Poleg tega članka za seminar uporabite še najmanj pet drugih virov, od teh vsaj še dva druga znanstvena članka, ki se navezujeta na to vsebino. <br />
* članke na temo lahko iščete v PubMed povezavi [http://www.ncbi.nlm.nih.gov/pubmed/ tukaj]<br />
* naslov izbrane teme in povezavo do novice vpišite v tabelo seminarjev takoj ko ste si izbrali temo, najkasneje pa en teden pred rokom za oddajo <br />
* [[TBK2014 Povzetki seminarjev|Povzetek seminarja]] opišete na wikiju v približno 200 besedah - najkasneje do dne ko morate oddati seminar recenzentom. <br />
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.<br />
* Seminar pripravite v obliki seminarske naloge (pisava Cambria, font 11, enojni razmak, 2,5 cm robovi; tekst naj obsega okoli 1000 besed), vsebuje naj 1-2 sliki. Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko. Vse uporabljene vire citirajte v tekstu, kot npr. (Nobel, 2010), na koncu pa navedite točen seznam literature, kot je opisano spodaj!<br />
*Celotni seminar naj obsega 2 strani A4 formata (po možnosti dvostransko tiskanje).<br />
* Seminar oddajte do datuma oddaje, ki je naveden v tabeli v elektronski obliki z uporabo [http://bio.ijs.si/~zajec/tbk/poslji/ tega obrazca].<br />
* vsi seminarji so v elektronski obliki dostopni [http://bio.ijs.si/~zajec/tbk/poslji//bioseminar/ tukaj].<br />
* Recenzenti do dneva določenega v tabeli določijo popravke in podajo oceno pisnega dela, v predpisanem formatu elektronskega obrazca na internetu.<br />
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 12 minut. Recenzenti morajo biti na predstavitvi prisotni. Prvi recenzent vodi predstavitve in razpravo ter skrbi za to, da vse poteka v zastavljenih časovnih okvirih.<br />
* Predstavitvi sledi razprava do 8 minut. Sledijo vprašanja prisotnih, recenzenti postavijo vsak vsaj dve vprašanji in na koncu podajo oceno predstavitve.<br />
* En dan pred predstavitvijo na strežnik oddajte tudi končno verzijo. Na dan predstavitve morate oddati tudi končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu.<br />
* Seminarska naloga in povzetek na wikiju morajo biti v slovenskem jeziku!<br />
<br />
==<font color=green>Imena datotek</font>==<br />
Prosim vas, da vse datoteke, ki jih pošiljate poimenujete po spodnjih pravilih. Ne uporabljajte ČŽŠčžš!<br />
* TBK_2014_Priimek_Ime.doc(x) za seminar, npr. TBK_2014_Guncar_Gregor.docx<br />
* TBK_2014_Priimek_ime_final.doc(x) za končno verzijo seminarja<br />
* TBK_2014_Priimek_Ime_rec_Priimek2.doc(x) za recenzijo, kjer je Priimek2 priimek recenzenta, npr. TBK_2014_Guncar_Gregor_rec_Scott.docx (če se pišete Scott in odajate recenzijo za seminar, ki ga je napisal Gunčar)<br />
* TBK_2014_Priimek_Ime.ppt(x) za prezentacijo, npr TBK_2014_Guncar_Gregor.pptx<br />
<br />
==Ocenjevanje seminarjev==<br />
Recenzenti ocenijo seminar tako, da izpolnijo [[https://docs.google.com/forms/d/1oW_38CbGfOhTcS8zqMEFvdAOS66yRtDMd_e52uoUYLw/viewform recenzentsko poročilo]] na spletu.<br />
<br />
== Mnenje o predstavitvi ==<br />
Vsak posameznik '''mora''' oceniti seminar tako, da odda svoje [https://docs.google.com/forms/d/1XbEJ2iXlXsT3b7-jpM3pCGQazdIwskieL07-vBmRU8k/viewform mnenje] najkasneje v enem tednu po predstavitvi. Kdor na seminarju ni bil prisoten, mnenja '''ne sme''' oddati.<br />
<br />
==Urejanje spletnih strani na wikiju==<br />
Wiki so razvili zato, da lahko spletne vsebine ureja vsakdo. Ukazi so preprosti, dokler si ne zamislite česa prav posebnega. Vseeno pa je Word v primerjavi z wikijem pravo čudežno orodje... Če imate težave z oblikovanjem besedila, si preberite poglavje o urejanju wiki-strani na Wikipediji ([http://en.wikipedia.org/wiki/Help:Editing tule] v angleščini in [http://sl.wikipedia.org/wiki/Wikipedija:Urejanje_strani tu] v slovenščini). Pomaga tudi, če pogledate, kako je zapisana kakšna stran, ki se vam zdi v redu: kliknite na zavihek 'Uredite stran' in si poglejte, kako so vpisane povezave, kako nov odstavek in podobno. ''Na koncu seveda pod oknom za urejanje kliknite na 'Prekliči'.''<br />
<br />
<br />
==Faktor vpliva==<br />
Faktor vpliva (angl. impact factor) neke revije pove, kolikokrat so bili v poprečju citirani članki v tej reviji v dveh letih skupaj pred objavo tega faktorja. Faktorje vpliva za posamezno revijo lahko najdete v [http://www.cobiss.si/scripts/cobiss?command=CONNECT&base=JCR COBISS-u]. V polje "Naslov revije" vnesite ime revije za katero želite izvedeti faktor vpliva in pritisnite na gumb POIŠČI. V skrajnem desnem stolpcu se bodo izpisali faktorji vpliva za revije, ki ustrezajo vašim iskalnim kriterijem. Zadetkov za posamezno revijo je več zato, ker so navedeni faktorji vpliva za posamezno leto. Za leto 2011 faktorji vpliva še niso objavljeni, zato se orientirajte po faktorjih vpliva zadnjih par let. Če faktorja vpliva za vašo izbrano revijo ne najdete v bazi COBISS, potem izberite članek iz kakšne druge revije.<br />
<br />
==Citiranje virov==Citiranje je možno po več shemah, važno je, da se v seminarju držite ene same.Temeljno načelo je, da je treba vir navesti na tak način, da ga je mogoče nedvoumno poiskati.Za citate v naravoslovju je najpogostejše citiranje po pravilniku ISO 690. [http://www.google.com/url?sa=t&source=web&cd=6&sqi=2&ved=0CEUQFjAF&url=http%3A%2F%2Fwww.tre.sik.si%2Fmain%2Fpomoc%2Ffiles%2Fcitiranje_in_navajanje_virov.pdf&rct=j&q=citiranje%20po%20pravilniku%20ISO%20690&ei=jPBqTe6FC9DKswaWk-TmDA&usg=AFQjCNF8r6X9Y781sanDObaXNdCew4suUg&sig2=cTqKObSJsTicekWGRGa72g&cad=rja Pravila], ki upoštevajo omenjeni standard, so pripravili pri ZTKS. Sicer pa ima vsaka revija lahko svoj način citiranja, ki ga je treba pri pisanju članka upoštevati.<br>'''Citiranje knjig:'''<br>Priimek, I. ''Naslov''. Kraj: Založba, letnica.<br>Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN.<br>Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005.<br>Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4.<br>Če so avtorji trije, je beseda in med drugim in tretjim avtorjem. Če so avtorji več kot trije, napišemo samo prvega in dopišemo ''et al''. (in drugi, po latinsko). Vse, kar je latinsko, pišemo poševno (npr. tudi imena rastlin in živali, pojme ''in vivo'', ''in vitro'' ipd.). '''Citiranje člankov:'''<br>Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani.<br>Lartigue C. ''et al''. Genome transplantation in bacteria: changing one species to another. ''Science'', 2007, letn. 317, str. 632-638.Alternativni način citiranja (predvsem v družboslovju) je po pravilih APA, kjer članke citirajo takole:<br>Priimek, I. (letnica, številka). Naslov. Naslov revije, strani.<br>Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.Revija Science uporablja skrajšani zapis:<br>C. Lartigue ''et al''. Science 317, 632 (2007)<br>V diplomah na FKKT je treba navesti vire tako, da izpišete tudi naslov citiranega dela in strani od-do (ne samo začetne).'''Citiranje spletnih virov:'''<br>Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov<br>strangeguitars. ''On the brink of artificial life''. 6. 10. 2007. [citirano 13. 11. 2007] http://www.metafilter.com/65331/On-the-brink-of-artificial-life<br>Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.</div>Nfrauskok