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Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template

2015-01-19T22:55:40Z

VeronikaJarc:

(Veronika Jarc)

Jeronimo Cello et al. Chemical Synthesis of Poliovirus cDNA: Generation of Infectious virus in the Absence of Natural Template. Science 297, 1016-1018 (2002). URL: http://www.sciencemag.org/content/297/5583/1016.abstract

== Introduction ==

In this article they wanted to synthesis a poliovirus, so that they could see if it interacts with host just like the natural poliovirus. They also wanted to synthesis it by in vitro chemical-biochemical means just by following instructions from a written sequence of the virus itself. Cello and his team have translated and replicated the poliovirus in a cell-free extract and they have done many experiments afterwards. Some experiments were done just so that they could describe biochemical and pathogenic characteristics of the virus. They included experiments in tissue culture with neutralizing antibodies, CD155 receptor-specific antibodies and neurovirulence tests in CD155 transgenic mice.

== Poliovirus ==

Poliovirus is an enterovirus and it belongs to family of Picornaviridae. It is a RNA 7500 nucleotides long non-enveloped virus composed of single-stranded positive-sense RNA genome. The virus is just 30 nm in diameter and has an icosahedral symmetry. It is so small in size and genome length so that it is one of the most characterized viruses. Because of its simplicity it is a model system for understanding the biology of the RNA viruses. (1)
We have 3 different serotypes of poliovirus PV1, PV2 and PV3. The difference between them is a slightly different capsid protein. The capsid proteins are very important for different things, one of them is cellular receptor specificity and virus antigenicity. All of the serotypes are highly infectious, you can get them from fecal-oral contact (2). This means that you can get them from sharing food or drink with a contaminated person. PV1 is the most common poliovirus seen in nature. Today it is most common found in regions of Pakistan, Afghanistan, Nigeria, Niger and Chad. PV2 it is instinct in nature and PV3 was found in parts of Nigeria and Pakistan. (3)

Poliovirus is a virus that infects human cells by binding to CD155, which is an immunoglobulin-like receptor (poliovirus receptor) on the cell surface. When it is attached to the receptor the viral particles enter the cell. Till now it is still not well understood, the whole mechanism, how polioviruses enter the cell.
As said before poliovirus is a positive stranded RNA virus and can be used as a messenger RNA (mRNA) and be immediately translated by the host cell. The poliovirus mRNA has a long 5´ end, which encodes for an internal ribosome entry side (IRES) and is necessary for the translation of the viral RNA. After the translation of the viral RNA it is transcribed into a single polypeptide, polyprotein. It is well processed by two internal proteinases into 10 individual viral proteins. RNA dependent RNA polymerase (3Dpol) is a viral polymerase whose function is to copy and transcribe the whole viral genome. 2Apro and 3Cpro/3CDpro are proteases that use the poliovirus-encoded polyprotein as a substrate. The possibility that these proteinases could degraded cellular proteins is still not explored enough. VPg is a small protein, which is coded as 3B between 3A and 3C. It binds to viral RNA and has a big role in the synthesis of viral positive and negative strand of RNA. 2BC, 2B, 2C, 3AB, 3A, 3B are proteins which are part of a protein complex needed for viral replication. All these elements of the virus above are prat of a non-structural region. The protein VP0 is the only protein, which is part of a structural region and is further cleaved into VP2, VP3, VP1 and VP4 proteins. The role of these proteins is to ensemble the viral capsid. With all this elements that compose a poliovirus we can newly synthesis plus-stranded RNA that represent mRNA for protein synthesis or to encapsidate the virus with the virus proteins. In different mammal tissue culture cells (HeLa) one replication cycle can be complete in 6-8 hours. In each dying cell we can release up from 104 to 105 polio virions per cell. (2)

== Sequence analysis of polioviral RNA ==

The poliovirus RNA was sequenced in three stages. The first was identification of the 3´- terminal poly(A) and the second was the identification of the internal sequences. At the end they characterized the 5´- terminal protein-linked fragment. Kitamura and colleagues used the Sanger´s chain termination method to sequence the poliovirus cDNA. First the poliovirus cDNA was synthesized and chains of 7000-7400 deoxyribonucleotides were selected by centrifugation. Then the poliovirion RNA was digested with RNase A and large oligonucleotides were separated on 2D gel electrophoresis. The large oligonucleotides were eluated from the gel, dephosphorylated on 3´ ends and labelled on 5´ ends with phosphorus-32. Then they prepared four different reaction mixtures with cDNA and 5’-32P-labelled primer was annealed and incubated with E.coli polymerase I in the presence of unlabeled dNTPs and one of the four 2’,3’-dideoxynucleotide triphosphates (ddNTPs). After that the synthesized DNA fragments were separated by gel electrophoresis. The sequence was then determined by reading the four different ladders of bands. The result was a nucleotide sequence of the genome of poliovirus type 1 (Mahoney). The base composition of the genome RNA is 30,2 % of A, 22,8 % of G, 23,1 % of C and 23.9 % of U and with the molecular weight of 2,411 X 106. The chemical structure of poliovirus is C332,652H492,388N98,245O131,196-P7501S2340. This empirical formula was the base for Cello and colleagues de novo chemical-biochemical synthesis of infectious poliovirus. (4)

== Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence ==

Racaniello and Baltimore have synthesized and purified polioviruses RNA and cloned the double-stranded molecules in a plasmid. They inserted the construct into the Pst I site on plasmid pBR322. After that they had made a screening of the tetracycline-resistant clones by colony hybridization using a calf thymus DNA-primed poliovirus cDNA probe. They prepared a restriction fragment form clone pVR103 form bases 149-200 with 5’-end labeled at BamHI site. The fragment was then hybridized to poliovirus RNA and extended with RNA-dependent DNA polymerase (revese transcriptase). Before cloning they chemically determined the sequence of the extension products. Then the extended fragment was given a tail with oligo (dC) and double-stranded with DNA polymerase I in the presence of (dG)12-18. After that it was tailed again with oligo(dC) and inserted into the Pst I site of pBR322. pVR105 contained the sequences from the BamHI site up to the first base of the poliovirus genome. The two plasmids were sequenced by Maxam—Gilbert method. They got the complete sequence of the virus. The nucleotide sequence is 7410 nucleotides long. An open reading frame has a beginning at base 671 and is followed by a methionine codon at 743 and continuous unitil a termination codon 71 bases from the 3’ end. (5)

== Chemical synthesis of poliovirus cDNA ==

As seen above, it is possible to synthesis the poliovirus RNA in a way that it is still functional. In this article Cello and colleagues want to assembly a poliovirus cDNA from scratch. Only with the knowledge of basic chemical building blocks independent of viral components previously formed in vivo and the use of the know sequence which was determined in the articles described above.

They synthesized the genome of poliovirus type 1 (Mahoney) [PV1(M)]. It began with the assembly of a cDNA carrying a phage T7 RNA polymerase promotor on the very end of the 5’ end. This promotor was in the beginning of three large DNA fragments F1, F2 and F3. On the right side of the promotor there was F1 with 3026 bp, then there was F2 with 1895 bp and on the end F3 2682 bp. All of those fragments were overlapping each other (400-600 bp) and they all covered one range of the genome of poliovirus. All of the fragments were synthesized by assembling purified oligonucleotides of plus and minus polarity with overlapping complementary sequences at their termini. The segments were then ligated in different plasmid vectors. (6)

To synthesis the poliovirus cDNA fragments two different approaches were taken. F1 and F3 were synthesized by Integrated DNA Technologies, Inc. they gel-purified oligonucleotides which were 60 nt long and provided complete coverage of each segment with complementary overlaps of 15-30 nt. The oligonucleotides were put in a TE buffer and ligated together with T4 DNA ligase to the size of the segment. The segments were then purified and cut with restriction enzymes (different for F1 and F3 fragment) and ligated into a pUC 18 plasmid vector. Seven clones were sequenced so that they could find the completely correct clone or a clone that could be corrected by standard site mutagenesis. The correct fragments were then ligated and cloned into a pUC 18 vector. This vector was made with 5’ overhanging ends compatible with Sal I and EcoR I restriction sites. These vectors were then sequenced so that the cDNA of the fragment, which was in the plasmid vector, was the correct one. F1 pUC18 had two restricition sites SnaB I and EcoRI and F3 pUC18 had Mlu I and EcoR I. F2 fragment was assembled in a sdifferent way with an asymmetric PCr assay with 8 to 12 gel-purified oligonucleotides. The oligonucleotides were 40 to 93 nt long ans had an overlapping region between two oligonucleotides that was 20 nt long. For the PCR they used Taq and Pwo DNA polymerases which reduce error frequency in PCR products. The PCR products were then ligated into a pGEM-T plasmid vector, which has a 3’T overhangs on the end. Then they checked with sequencing 5 to 10 clones for errors. The right clones were then sequenced for the complete sequence of the F2 gene. In F2 pGEM-T there are two restricition sites SnaB I and EcoR I. (6)

The DNA fragments were assembled step by step with restriction cleavage sites. F1 pUC18 and F2 pGEM-T vectors mixed together so that F2 was inserted into F1 pUC18 trough the restricition sites SnaB I and EcoR I to assembly F 1-2 pUC18. To E. coli cloning vector pBR322, which has restricition sites EcoR I and Sal I, the F 1-2 pUC18 was given. F1 and F2 fragments were inserted through these restricition sites to make a new vector F 1-2 pBR322. This vector has restricition sites EcoR I and Mlu I through which the fragment F3 from vector F3 pUC18 will insert. Now we have the full-length sPV(M) cDNA (F1-2-3 pBR322) as seen in figure 1 in the article. (6)

== sPV1(M) genetic marker ==

For the purpose of distinguishing the synthesized viral genome [sPV1(M)] form the wild type sequence of the PV1(M) [wt PV1(M)] we made nucleotide substitution into the sPV1(M) cDNA in a form of genetic markers. We designed 13 new recognition sites into the sPV1(M) cDNA by changing 20 nt of the wt PV1(M) sequence. They created nt changes in form of creating new restricition sites. The sPV1 (M) cDNA has now new restricition sites for Xma I, BssH II, Sma I, Fsp I, Sac II, Stu I, Xho I, Mlu I, Hpa I, Not I, Pvu II, BbvC I and also PpuM I. They did not just create new restriction sites, but also eliminated one site for the restricition enzyme Pst I. Silent mutations were also made in the ORF by substitution of three nucleotides. One substitution was also created into 2B coding region (creating Stu I site) changed an amino acid IIe to Leu. Another substitution made in the sequence in the 5’NTR separated the cloverleaf from IRES element. (6)

== In vitro transcription and translation ==

sPV1 (M) cDNA and wt poliovirus cDNA were put in a pT7PVM and linearized with EcoR I. after the transcription the results were put on a gel electrophoresis. The RNA transcript from the synthetic and wild type poliovirus were purified by phenol-chloroform extraction and ethanol precipitation and translated in the presence of [35S] Translabel. This mixture was then processed in HeLa cell-free extracts for 15 hours. The samples were then analyzed on SDS polyacrylamide gels. The gel was treated with En3Hamce and exposed to x-ray. With this experiment they wanted to see if the results will be the same for the synthetic as for the wild type poliovirus. The length of the transcripts from the wild type and the synthetic were the same as the virion RNA. (6)

== De novo synthesis of poliovirus in a HeLa cell-free system and plaque assay ==

De novo synthesis is an experiment capable of translating RNA of poliovirus type 1 (Mahoney) with good accuracy. The viral proteins in poliovirus are visible except VP2 in VP4. VP2 can be detected by imunnoprecipitation with antibodies to VP2. The most difficult to detect is VP4 even in [35S] methionine-labeled extracts of infected cells, because it contains only one methionine. RNA was taken from the synthetic or wild type poliovirus and was incubated with HeLa cell-free extracts. After 15 hours the plagues appeared and the morphology of them was characteristic to poliovirus. To avoid problems such as transfection of monolayer cells with mRNA used for translation they added a mixture of ribonuclease A and RNase T1 before added to the cells. After 30 min they incubated the mixture with HeLa cell monolayers for 1 hour, so that they could test the presence of infectious virus particles in the cell-free incubating mixture. The monolayers were then washed and after 48 hours the cells were stained with 1% crystal violet. (6)

In the results for the proteolytic processing of poliovirus RNA in HeLa cell-free extract (seen in figure 2 in the article) we see that the transcript RNA from the synthetic poliovirus and the virion RNA from the wild type poliovirus were the same. As seen in figure 3 in article the synthetic RNA was translated and replicated in the cell-free extract and that newly synthesized RNA was encapsidated into coat proteins which lead to de novo synthesis of the infectious poliovirus. The expression of the proteins in the synthetic poliovirus and the wild type poliovirus are the same. (6)

== Detection of engineered genetic markers ==

Then they carried out experiments to confirm, that the infectious material from the cell-free extract was sPV1(M). They isolated viruses from the spinal cord of paralyzed mice. RNA was isolated from the infected cells with TRIZOL. Then they carried out RT-PCR using downstream and upstream primers for the amplification of the region. They tested all of the RNA samples by PCR without reverse transcription to exclude the possibility that some signals were residual DNA template. There was no band seen in the absence of cDNA synthesis, which indicates that the signals that were seen were poliovirus RNA. The products were then analyzed with restriction enzymes. (6)

== Biological characterization of sPV1(M) ==

They tested the effects of the poliovirus receptor-specific monoclonal antibody (Mab) D171 and type-specific hyperimmune sera on plaque formation by sPV1(M). With this test they wanted to see if de novo poliovirus particles synthesized in the cell-free extract were serotype 1. They grown HeLa cells in monolayers and incubated them with MAb D171. After 1 hour they added 100 PFU of sPV1(M) or wt PV1(M) to the cells and incubated. After that they mixed anti-poliovirus serum with 100 PFU of sPV1(M) or wt PV1(M). They added the antibody-virus mixture to the HeLa monolayers. And then they washed and stained the plates. Mab D171 is shown to block infection of all three serotypes by binding to the CD155 (as seen in table 1 in the article). No plaques were observed when sPV1(M) was treated with poliovirus type 1 serum. Nevertheless synthetic virus was type-specific because hyperimmune serum to poliovirus type 2 did not inhibit plaque formation. The results were very similar also in the wild type poliovirus. (6)

== Neurovirulence assay ==

Tis assay was made to determine whether synthetic poliovirus expresses a neurovirulent phenotype in mice transgenic for the human poliovirus receptor (CD155). Four tg CD155 mice were given poliovirus the synthetic one and the wild type one. Mice were then examined for 21 days for paralysis or death. After the 21 days the mice were taken the spinal cord and tested for the presence of the two viruses. The virus that induced paralysis or death in 50 % of the mice (PLD50) was calculated. The animals developed paralysis or death in animals injected with the wild type or synthetic poliovirus. The difference was in the inoculum between the polioviruses (as seen in table 1 in the article). There was an increase in the magnitude of attenuation in the mice treated with sPV1(M) which was the cause of silent mutations in the ORF. The mechanism of how silent mutations effect pathogenesis is not known. (6)

The region that had the engineered marker Not I was located in the region between 5260 and 6016 nt. The fragment (757 bp long) was treated with Not I in order to identify the restriction site in sPV1(M). The position of the RT-PCR product is in 561 bp and 196 bp. After the RT-PCR they put the products on 1,2 % agarose gel. The results showed that synthetic poliovirus treated with Not I had presence of 2 bands (561 and 196 nt). When it was not treated with Not I it was no band observed at all, indicating that the virus contained the engineered marker. In wild type poliovirus we see only a single band at 757 nt when digested with Not I or without. (6)

== Conclusion ==

The synthesis of the synthetic poliovirus is plausible with the right knowledge and experimental tools. In the article they showed that you can make a synthetic poliovirus from scratch and that it is functional. This article will be the basis of lots of new researches in developing new vaccination and treatments. It can be also used as an example how to synthesis other RNA viruses which are more complex.

== References ==

1. Hogle J. Poliovirus cell entry: common structural themes in viral cell entry pathways. Annu Rev Microbiol 56: 677–702 (2002).

2. Racaniello and Baltimore, D. Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proc. Natl. Acad. Sci. U.S.A. 78 (8): 4887–91 (1981)

3. Transmission of wild poliovirus type 2—apparent global interruption. Wkly. Epidemiol. Rec. 76 (13): 95–7 (2001).

4. Kitamura N. et al. Primary structure, gene organization and polypeptide expression of poliovirus RNA. Nature 291, 547 (1981).

5. V. R. Racaniello, D. Baltimore. Molecular cloning of poliovirus cDNA and the determination of the complete nucleotide sequence of the viral genome. Proc. Natl. Acad. Sci. U.S.A. 78, 4887 (1981).

6. Jeronimo Cello et al. Chemical Synthesis of Poliovirus cDNA: Generation of Infectious virus in the Absence of Natural Template. Science 297, 1016-1018 (2002).

Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template

2015-01-19T22:53:37Z

VeronikaJarc:

(Veronika Jarc)

Jeronimo Cello et al. Chemical Synthesis of Poliovirus cDNA: Generation of Infectious virus in the Absence of Natural Template. Science 297, 1016-1018 (2002). URL:

== Introduction ==

In this article they wanted to synthesis a poliovirus, so that they could see if it interacts with host just like the natural poliovirus. They also wanted to synthesis it by in vitro chemical-biochemical means just by following instructions from a written sequence of the virus itself. Cello and his team have translated and replicated the poliovirus in a cell-free extract and they have done many experiments afterwards. Some experiments were done just so that they could describe biochemical and pathogenic characteristics of the virus. They included experiments in tissue culture with neutralizing antibodies, CD155 receptor-specific antibodies and neurovirulence tests in CD155 transgenic mice.

== Poliovirus ==

Poliovirus is an enterovirus and it belongs to family of Picornaviridae. It is a RNA 7500 nucleotides long non-enveloped virus composed of single-stranded positive-sense RNA genome. The virus is just 30 nm in diameter and has an icosahedral symmetry. It is so small in size and genome length so that it is one of the most characterized viruses. Because of its simplicity it is a model system for understanding the biology of the RNA viruses. (1)
We have 3 different serotypes of poliovirus PV1, PV2 and PV3. The difference between them is a slightly different capsid protein. The capsid proteins are very important for different things, one of them is cellular receptor specificity and virus antigenicity. All of the serotypes are highly infectious, you can get them from fecal-oral contact (2). This means that you can get them from sharing food or drink with a contaminated person. PV1 is the most common poliovirus seen in nature. Today it is most common found in regions of Pakistan, Afghanistan, Nigeria, Niger and Chad. PV2 it is instinct in nature and PV3 was found in parts of Nigeria and Pakistan. (3)

Poliovirus is a virus that infects human cells by binding to CD155, which is an immunoglobulin-like receptor (poliovirus receptor) on the cell surface. When it is attached to the receptor the viral particles enter the cell. Till now it is still not well understood, the whole mechanism, how polioviruses enter the cell.
As said before poliovirus is a positive stranded RNA virus and can be used as a messenger RNA (mRNA) and be immediately translated by the host cell. The poliovirus mRNA has a long 5´ end, which encodes for an internal ribosome entry side (IRES) and is necessary for the translation of the viral RNA. After the translation of the viral RNA it is transcribed into a single polypeptide, polyprotein. It is well processed by two internal proteinases into 10 individual viral proteins. RNA dependent RNA polymerase (3Dpol) is a viral polymerase whose function is to copy and transcribe the whole viral genome. 2Apro and 3Cpro/3CDpro are proteases that use the poliovirus-encoded polyprotein as a substrate. The possibility that these proteinases could degraded cellular proteins is still not explored enough. VPg is a small protein, which is coded as 3B between 3A and 3C. It binds to viral RNA and has a big role in the synthesis of viral positive and negative strand of RNA. 2BC, 2B, 2C, 3AB, 3A, 3B are proteins which are part of a protein complex needed for viral replication. All these elements of the virus above are prat of a non-structural region. The protein VP0 is the only protein, which is part of a structural region and is further cleaved into VP2, VP3, VP1 and VP4 proteins. The role of these proteins is to ensemble the viral capsid. With all this elements that compose a poliovirus we can newly synthesis plus-stranded RNA that represent mRNA for protein synthesis or to encapsidate the virus with the virus proteins. In different mammal tissue culture cells (HeLa) one replication cycle can be complete in 6-8 hours. In each dying cell we can release up from 104 to 105 polio virions per cell. (2)

== Sequence analysis of polioviral RNA ==

The poliovirus RNA was sequenced in three stages. The first was identification of the 3´- terminal poly(A) and the second was the identification of the internal sequences. At the end they characterized the 5´- terminal protein-linked fragment. Kitamura and colleagues used the Sanger´s chain termination method to sequence the poliovirus cDNA. First the poliovirus cDNA was synthesized and chains of 7000-7400 deoxyribonucleotides were selected by centrifugation. Then the poliovirion RNA was digested with RNase A and large oligonucleotides were separated on 2D gel electrophoresis. The large oligonucleotides were eluated from the gel, dephosphorylated on 3´ ends and labelled on 5´ ends with phosphorus-32. Then they prepared four different reaction mixtures with cDNA and 5’-32P-labelled primer was annealed and incubated with E.coli polymerase I in the presence of unlabeled dNTPs and one of the four 2’,3’-dideoxynucleotide triphosphates (ddNTPs). After that the synthesized DNA fragments were separated by gel electrophoresis. The sequence was then determined by reading the four different ladders of bands. The result was a nucleotide sequence of the genome of poliovirus type 1 (Mahoney). The base composition of the genome RNA is 30,2 % of A, 22,8 % of G, 23,1 % of C and 23.9 % of U and with the molecular weight of 2,411 X 106. The chemical structure of poliovirus is C332,652H492,388N98,245O131,196-P7501S2340. This empirical formula was the base for Cello and colleagues de novo chemical-biochemical synthesis of infectious poliovirus. (4)

== Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence ==

Racaniello and Baltimore have synthesized and purified polioviruses RNA and cloned the double-stranded molecules in a plasmid. They inserted the construct into the Pst I site on plasmid pBR322. After that they had made a screening of the tetracycline-resistant clones by colony hybridization using a calf thymus DNA-primed poliovirus cDNA probe. They prepared a restriction fragment form clone pVR103 form bases 149-200 with 5’-end labeled at BamHI site. The fragment was then hybridized to poliovirus RNA and extended with RNA-dependent DNA polymerase (revese transcriptase). Before cloning they chemically determined the sequence of the extension products. Then the extended fragment was given a tail with oligo (dC) and double-stranded with DNA polymerase I in the presence of (dG)12-18. After that it was tailed again with oligo(dC) and inserted into the Pst I site of pBR322. pVR105 contained the sequences from the BamHI site up to the first base of the poliovirus genome. The two plasmids were sequenced by Maxam—Gilbert method. They got the complete sequence of the virus. The nucleotide sequence is 7410 nucleotides long. An open reading frame has a beginning at base 671 and is followed by a methionine codon at 743 and continuous unitil a termination codon 71 bases from the 3’ end. (5)

== Chemical synthesis of poliovirus cDNA ==

As seen above, it is possible to synthesis the poliovirus RNA in a way that it is still functional. In this article Cello and colleagues want to assembly a poliovirus cDNA from scratch. Only with the knowledge of basic chemical building blocks independent of viral components previously formed in vivo and the use of the know sequence which was determined in the articles described above.

They synthesized the genome of poliovirus type 1 (Mahoney) [PV1(M)]. It began with the assembly of a cDNA carrying a phage T7 RNA polymerase promotor on the very end of the 5’ end. This promotor was in the beginning of three large DNA fragments F1, F2 and F3. On the right side of the promotor there was F1 with 3026 bp, then there was F2 with 1895 bp and on the end F3 2682 bp. All of those fragments were overlapping each other (400-600 bp) and they all covered one range of the genome of poliovirus. All of the fragments were synthesized by assembling purified oligonucleotides of plus and minus polarity with overlapping complementary sequences at their termini. The segments were then ligated in different plasmid vectors. (6)

To synthesis the poliovirus cDNA fragments two different approaches were taken. F1 and F3 were synthesized by Integrated DNA Technologies, Inc. they gel-purified oligonucleotides which were 60 nt long and provided complete coverage of each segment with complementary overlaps of 15-30 nt. The oligonucleotides were put in a TE buffer and ligated together with T4 DNA ligase to the size of the segment. The segments were then purified and cut with restriction enzymes (different for F1 and F3 fragment) and ligated into a pUC 18 plasmid vector. Seven clones were sequenced so that they could find the completely correct clone or a clone that could be corrected by standard site mutagenesis. The correct fragments were then ligated and cloned into a pUC 18 vector. This vector was made with 5’ overhanging ends compatible with Sal I and EcoR I restriction sites. These vectors were then sequenced so that the cDNA of the fragment, which was in the plasmid vector, was the correct one. F1 pUC18 had two restricition sites SnaB I and EcoRI and F3 pUC18 had Mlu I and EcoR I. F2 fragment was assembled in a sdifferent way with an asymmetric PCr assay with 8 to 12 gel-purified oligonucleotides. The oligonucleotides were 40 to 93 nt long ans had an overlapping region between two oligonucleotides that was 20 nt long. For the PCR they used Taq and Pwo DNA polymerases which reduce error frequency in PCR products. The PCR products were then ligated into a pGEM-T plasmid vector, which has a 3’T overhangs on the end. Then they checked with sequencing 5 to 10 clones for errors. The right clones were then sequenced for the complete sequence of the F2 gene. In F2 pGEM-T there are two restricition sites SnaB I and EcoR I. (6)

The DNA fragments were assembled step by step with restriction cleavage sites. F1 pUC18 and F2 pGEM-T vectors mixed together so that F2 was inserted into F1 pUC18 trough the restricition sites SnaB I and EcoR I to assembly F 1-2 pUC18. To E. coli cloning vector pBR322, which has restricition sites EcoR I and Sal I, the F 1-2 pUC18 was given. F1 and F2 fragments were inserted through these restricition sites to make a new vector F 1-2 pBR322. This vector has restricition sites EcoR I and Mlu I through which the fragment F3 from vector F3 pUC18 will insert. Now we have the full-length sPV(M) cDNA (F1-2-3 pBR322) as seen in figure 1 in the article. (6)

== sPV1(M) genetic marker ==

For the purpose of distinguishing the synthesized viral genome [sPV1(M)] form the wild type sequence of the PV1(M) [wt PV1(M)] we made nucleotide substitution into the sPV1(M) cDNA in a form of genetic markers. We designed 13 new recognition sites into the sPV1(M) cDNA by changing 20 nt of the wt PV1(M) sequence. They created nt changes in form of creating new restricition sites. The sPV1 (M) cDNA has now new restricition sites for Xma I, BssH II, Sma I, Fsp I, Sac II, Stu I, Xho I, Mlu I, Hpa I, Not I, Pvu II, BbvC I and also PpuM I. They did not just create new restriction sites, but also eliminated one site for the restricition enzyme Pst I. Silent mutations were also made in the ORF by substitution of three nucleotides. One substitution was also created into 2B coding region (creating Stu I site) changed an amino acid IIe to Leu. Another substitution made in the sequence in the 5’NTR separated the cloverleaf from IRES element. (6)

== In vitro transcription and translation ==

sPV1 (M) cDNA and wt poliovirus cDNA were put in a pT7PVM and linearized with EcoR I. after the transcription the results were put on a gel electrophoresis. The RNA transcript from the synthetic and wild type poliovirus were purified by phenol-chloroform extraction and ethanol precipitation and translated in the presence of [35S] Translabel. This mixture was then processed in HeLa cell-free extracts for 15 hours. The samples were then analyzed on SDS polyacrylamide gels. The gel was treated with En3Hamce and exposed to x-ray. With this experiment they wanted to see if the results will be the same for the synthetic as for the wild type poliovirus. The length of the transcripts from the wild type and the synthetic were the same as the virion RNA. (6)

De novo synthesis of poliovirus in a HeLa cell-free system and plaque assay

De novo synthesis is an experiment capable of translating RNA of poliovirus type 1 (Mahoney) with good accuracy. The viral proteins in poliovirus are visible except VP2 in VP4. VP2 can be detected by imunnoprecipitation with antibodies to VP2. The most difficult to detect is VP4 even in [35S] methionine-labeled extracts of infected cells, because it contains only one methionine. RNA was taken from the synthetic or wild type poliovirus and was incubated with HeLa cell-free extracts. After 15 hours the plagues appeared and the morphology of them was characteristic to poliovirus. To avoid problems such as transfection of monolayer cells with mRNA used for translation they added a mixture of ribonuclease A and RNase T1 before added to the cells. After 30 min they incubated the mixture with HeLa cell monolayers for 1 hour, so that they could test the presence of infectious virus particles in the cell-free incubating mixture. The monolayers were then washed and after 48 hours the cells were stained with 1% crystal violet. (6)

In the results for the proteolytic processing of poliovirus RNA in HeLa cell-free extract (seen in figure 2 in the article) we see that the transcript RNA from the synthetic poliovirus and the virion RNA from the wild type poliovirus were the same. As seen in figure 3 in article the synthetic RNA was translated and replicated in the cell-free extract and that newly synthesized RNA was encapsidated into coat proteins which lead to de novo synthesis of the infectious poliovirus. The expression of the proteins in the synthetic poliovirus and the wild type poliovirus are the same. (6)

Detection of engineered genetic markers

Then they carried out experiments to confirm, that the infectious material from the cell-free extract was sPV1(M). They isolated viruses from the spinal cord of paralyzed mice. RNA was isolated from the infected cells with TRIZOL. Then they carried out RT-PCR using downstream and upstream primers for the amplification of the region. They tested all of the RNA samples by PCR without reverse transcription to exclude the possibility that some signals were residual DNA template. There was no band seen in the absence of cDNA synthesis, which indicates that the signals that were seen were poliovirus RNA. The products were then analyzed with restriction enzymes. (6)

Biological characterization of sPV1(M)

They tested the effects of the poliovirus receptor-specific monoclonal antibody (Mab) D171 and type-specific hyperimmune sera on plaque formation by sPV1(M). With this test they wanted to see if de novo poliovirus particles synthesized in the cell-free extract were serotype 1. They grown HeLa cells in monolayers and incubated them with MAb D171. After 1 hour they added 100 PFU of sPV1(M) or wt PV1(M) to the cells and incubated. After that they mixed anti-poliovirus serum with 100 PFU of sPV1(M) or wt PV1(M). They added the antibody-virus mixture to the HeLa monolayers. And then they washed and stained the plates. Mab D171 is shown to block infection of all three serotypes by binding to the CD155 (as seen in table 1 in the article). No plaques were observed when sPV1(M) was treated with poliovirus type 1 serum. Nevertheless synthetic virus was type-specific because hyperimmune serum to poliovirus type 2 did not inhibit plaque formation. The results were very similar also in the wild type poliovirus. (6)

Neurovirulence assay

Tis assay was made to determine whether synthetic poliovirus expresses a neurovirulent phenotype in mice transgenic for the human poliovirus receptor (CD155). Four tg CD155 mice were given poliovirus the synthetic one and the wild type one. Mice were then examined for 21 days for paralysis or death. After the 21 days the mice were taken the spinal cord and tested for the presence of the two viruses. The virus that induced paralysis or death in 50 % of the mice (PLD50) was calculated. The animals developed paralysis or death in animals injected with the wild type or synthetic poliovirus. The difference was in the inoculum between the polioviruses (as seen in table 1 in the article). There was an increase in the magnitude of attenuation in the mice treated with sPV1(M) which was the cause of silent mutations in the ORF. The mechanism of how silent mutations effect pathogenesis is not known. (6)

The region that had the engineered marker Not I was located in the region between 5260 and 6016 nt. The fragment (757 bp long) was treated with Not I in order to identify the restriction site in sPV1(M). The position of the RT-PCR product is in 561 bp and 196 bp. After the RT-PCR they put the products on 1,2 % agarose gel. The results showed that synthetic poliovirus treated with Not I had presence of 2 bands (561 and 196 nt). When it was not treated with Not I it was no band observed at all, indicating that the virus contained the engineered marker. In wild type poliovirus we see only a single band at 757 nt when digested with Not I or without. (6)

Conclusion

The synthesis of the synthetic poliovirus is plausible with the right knowledge and experimental tools. In the article they showed that you can make a synthetic poliovirus from scratch and that it is functional. This article will be the basis of lots of new researches in developing new vaccination and treatments. It can be also used as an example how to synthesis other RNA viruses which are more complex.

References

1. Hogle J. Poliovirus cell entry: common structural themes in viral cell entry pathways. Annu Rev Microbiol 56: 677–702 (2002).

2. Racaniello and Baltimore, D. Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proc. Natl. Acad. Sci. U.S.A. 78 (8): 4887–91 (1981)

3. Transmission of wild poliovirus type 2—apparent global interruption. Wkly. Epidemiol. Rec. 76 (13): 95–7 (2001).

4. Kitamura N. et al. Primary structure, gene organization and polypeptide expression of poliovirus RNA. Nature 291, 547 (1981).

5. V. R. Racaniello, D. Baltimore. Molecular cloning of poliovirus cDNA and the determination of the complete nucleotide sequence of the viral genome. Proc. Natl. Acad. Sci. U.S.A. 78, 4887 (1981).

6. Jeronimo Cello et al. Chemical Synthesis of Poliovirus cDNA: Generation of Infectious virus in the Absence of Natural Template. Science 297, 1016-1018 (2002).

Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template

2015-01-19T22:51:34Z

VeronikaJarc: New page: (Veronika Jarc) Jeronimo Cello et al. Chemical Synthesis of Poliovirus cDNA: Generation of Infectious virus in the Absence of Natural Template. Science 297, 1016-1018 (2002). URL: Intro...

(Veronika Jarc)

Jeronimo Cello et al. Chemical Synthesis of Poliovirus cDNA: Generation of Infectious virus in the Absence of Natural Template. Science 297, 1016-1018 (2002). URL:

Introduction

In this article they wanted to synthesis a poliovirus, so that they could see if it interacts with host just like the natural poliovirus. They also wanted to synthesis it by in vitro chemical-biochemical means just by following instructions from a written sequence of the virus itself. Cello and his team have translated and replicated the poliovirus in a cell-free extract and they have done many experiments afterwards. Some experiments were done just so that they could describe biochemical and pathogenic characteristics of the virus. They included experiments in tissue culture with neutralizing antibodies, CD155 receptor-specific antibodies and neurovirulence tests in CD155 transgenic mice.

Poliovirus

Poliovirus is an enterovirus and it belongs to family of Picornaviridae. It is a RNA 7500 nucleotides long non-enveloped virus composed of single-stranded positive-sense RNA genome. The virus is just 30 nm in diameter and has an icosahedral symmetry. It is so small in size and genome length so that it is one of the most characterized viruses. Because of its simplicity it is a model system for understanding the biology of the RNA viruses. (1)
We have 3 different serotypes of poliovirus PV1, PV2 and PV3. The difference between them is a slightly different capsid protein. The capsid proteins are very important for different things, one of them is cellular receptor specificity and virus antigenicity. All of the serotypes are highly infectious, you can get them from fecal-oral contact (2). This means that you can get them from sharing food or drink with a contaminated person. PV1 is the most common poliovirus seen in nature. Today it is most common found in regions of Pakistan, Afghanistan, Nigeria, Niger and Chad. PV2 it is instinct in nature and PV3 was found in parts of Nigeria and Pakistan. (3)

Poliovirus is a virus that infects human cells by binding to CD155, which is an immunoglobulin-like receptor (poliovirus receptor) on the cell surface. When it is attached to the receptor the viral particles enter the cell. Till now it is still not well understood, the whole mechanism, how polioviruses enter the cell.
As said before poliovirus is a positive stranded RNA virus and can be used as a messenger RNA (mRNA) and be immediately translated by the host cell. The poliovirus mRNA has a long 5´ end, which encodes for an internal ribosome entry side (IRES) and is necessary for the translation of the viral RNA. After the translation of the viral RNA it is transcribed into a single polypeptide, polyprotein. It is well processed by two internal proteinases into 10 individual viral proteins. RNA dependent RNA polymerase (3Dpol) is a viral polymerase whose function is to copy and transcribe the whole viral genome. 2Apro and 3Cpro/3CDpro are proteases that use the poliovirus-encoded polyprotein as a substrate. The possibility that these proteinases could degraded cellular proteins is still not explored enough. VPg is a small protein, which is coded as 3B between 3A and 3C. It binds to viral RNA and has a big role in the synthesis of viral positive and negative strand of RNA. 2BC, 2B, 2C, 3AB, 3A, 3B are proteins which are part of a protein complex needed for viral replication. All these elements of the virus above are prat of a non-structural region. The protein VP0 is the only protein, which is part of a structural region and is further cleaved into VP2, VP3, VP1 and VP4 proteins. The role of these proteins is to ensemble the viral capsid. With all this elements that compose a poliovirus we can newly synthesis plus-stranded RNA that represent mRNA for protein synthesis or to encapsidate the virus with the virus proteins. In different mammal tissue culture cells (HeLa) one replication cycle can be complete in 6-8 hours. In each dying cell we can release up from 104 to 105 polio virions per cell. (2)

Sequence analysis of polioviral RNA

The poliovirus RNA was sequenced in three stages. The first was identification of the 3´- terminal poly(A) and the second was the identification of the internal sequences. At the end they characterized the 5´- terminal protein-linked fragment. Kitamura and colleagues used the Sanger´s chain termination method to sequence the poliovirus cDNA. First the poliovirus cDNA was synthesized and chains of 7000-7400 deoxyribonucleotides were selected by centrifugation. Then the poliovirion RNA was digested with RNase A and large oligonucleotides were separated on 2D gel electrophoresis. The large oligonucleotides were eluated from the gel, dephosphorylated on 3´ ends and labelled on 5´ ends with phosphorus-32. Then they prepared four different reaction mixtures with cDNA and 5’-32P-labelled primer was annealed and incubated with E.coli polymerase I in the presence of unlabeled dNTPs and one of the four 2’,3’-dideoxynucleotide triphosphates (ddNTPs). After that the synthesized DNA fragments were separated by gel electrophoresis. The sequence was then determined by reading the four different ladders of bands. The result was a nucleotide sequence of the genome of poliovirus type 1 (Mahoney). The base composition of the genome RNA is 30,2 % of A, 22,8 % of G, 23,1 % of C and 23.9 % of U and with the molecular weight of 2,411 X 106. The chemical structure of poliovirus is C332,652H492,388N98,245O131,196-P7501S2340. This empirical formula was the base for Cello and colleagues de novo chemical-biochemical synthesis of infectious poliovirus. (4)

Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence

Racaniello and Baltimore have synthesized and purified polioviruses RNA and cloned the double-stranded molecules in a plasmid. They inserted the construct into the Pst I site on plasmid pBR322. After that they had made a screening of the tetracycline-resistant clones by colony hybridization using a calf thymus DNA-primed poliovirus cDNA probe. They prepared a restriction fragment form clone pVR103 form bases 149-200 with 5’-end labeled at BamHI site. The fragment was then hybridized to poliovirus RNA and extended with RNA-dependent DNA polymerase (revese transcriptase). Before cloning they chemically determined the sequence of the extension products. Then the extended fragment was given a tail with oligo (dC) and double-stranded with DNA polymerase I in the presence of (dG)12-18. After that it was tailed again with oligo(dC) and inserted into the Pst I site of pBR322. pVR105 contained the sequences from the BamHI site up to the first base of the poliovirus genome. The two plasmids were sequenced by Maxam—Gilbert method. They got the complete sequence of the virus. The nucleotide sequence is 7410 nucleotides long. An open reading frame has a beginning at base 671 and is followed by a methionine codon at 743 and continuous unitil a termination codon 71 bases from the 3’ end. (5)

Chemical synthesis of poliovirus cDNA

As seen above, it is possible to synthesis the poliovirus RNA in a way that it is still functional. In this article Cello and colleagues want to assembly a poliovirus cDNA from scratch. Only with the knowledge of basic chemical building blocks independent of viral components previously formed in vivo and the use of the know sequence which was determined in the articles described above.

They synthesized the genome of poliovirus type 1 (Mahoney) [PV1(M)]. It began with the assembly of a cDNA carrying a phage T7 RNA polymerase promotor on the very end of the 5’ end. This promotor was in the beginning of three large DNA fragments F1, F2 and F3. On the right side of the promotor there was F1 with 3026 bp, then there was F2 with 1895 bp and on the end F3 2682 bp. All of those fragments were overlapping each other (400-600 bp) and they all covered one range of the genome of poliovirus. All of the fragments were synthesized by assembling purified oligonucleotides of plus and minus polarity with overlapping complementary sequences at their termini. The segments were then ligated in different plasmid vectors. (6)

To synthesis the poliovirus cDNA fragments two different approaches were taken. F1 and F3 were synthesized by Integrated DNA Technologies, Inc. they gel-purified oligonucleotides which were 60 nt long and provided complete coverage of each segment with complementary overlaps of 15-30 nt. The oligonucleotides were put in a TE buffer and ligated together with T4 DNA ligase to the size of the segment. The segments were then purified and cut with restriction enzymes (different for F1 and F3 fragment) and ligated into a pUC 18 plasmid vector. Seven clones were sequenced so that they could find the completely correct clone or a clone that could be corrected by standard site mutagenesis. The correct fragments were then ligated and cloned into a pUC 18 vector. This vector was made with 5’ overhanging ends compatible with Sal I and EcoR I restriction sites. These vectors were then sequenced so that the cDNA of the fragment, which was in the plasmid vector, was the correct one. F1 pUC18 had two restricition sites SnaB I and EcoRI and F3 pUC18 had Mlu I and EcoR I. F2 fragment was assembled in a sdifferent way with an asymmetric PCr assay with 8 to 12 gel-purified oligonucleotides. The oligonucleotides were 40 to 93 nt long ans had an overlapping region between two oligonucleotides that was 20 nt long. For the PCR they used Taq and Pwo DNA polymerases which reduce error frequency in PCR products. The PCR products were then ligated into a pGEM-T plasmid vector, which has a 3’T overhangs on the end. Then they checked with sequencing 5 to 10 clones for errors. The right clones were then sequenced for the complete sequence of the F2 gene. In F2 pGEM-T there are two restricition sites SnaB I and EcoR I. (6)

The DNA fragments were assembled step by step with restriction cleavage sites. F1 pUC18 and F2 pGEM-T vectors mixed together so that F2 was inserted into F1 pUC18 trough the restricition sites SnaB I and EcoR I to assembly F 1-2 pUC18. To E. coli cloning vector pBR322, which has restricition sites EcoR I and Sal I, the F 1-2 pUC18 was given. F1 and F2 fragments were inserted through these restricition sites to make a new vector F 1-2 pBR322. This vector has restricition sites EcoR I and Mlu I through which the fragment F3 from vector F3 pUC18 will insert. Now we have the full-length sPV(M) cDNA (F1-2-3 pBR322) as seen in figure 1 in the article. (6)

sPV1(M) genetic marker

For the purpose of distinguishing the synthesized viral genome [sPV1(M)] form the wild type sequence of the PV1(M) [wt PV1(M)] we made nucleotide substitution into the sPV1(M) cDNA in a form of genetic markers. We designed 13 new recognition sites into the sPV1(M) cDNA by changing 20 nt of the wt PV1(M) sequence. They created nt changes in form of creating new restricition sites. The sPV1 (M) cDNA has now new restricition sites for Xma I, BssH II, Sma I, Fsp I, Sac II, Stu I, Xho I, Mlu I, Hpa I, Not I, Pvu II, BbvC I and also PpuM I. They did not just create new restriction sites, but also eliminated one site for the restricition enzyme Pst I. Silent mutations were also made in the ORF by substitution of three nucleotides. One substitution was also created into 2B coding region (creating Stu I site) changed an amino acid IIe to Leu. Another substitution made in the sequence in the 5’NTR separated the cloverleaf from IRES element. (6)

In vitro transcription and translation

sPV1 (M) cDNA and wt poliovirus cDNA were put in a pT7PVM and linearized with EcoR I. after the transcription the results were put on a gel electrophoresis. The RNA transcript from the synthetic and wild type poliovirus were purified by phenol-chloroform extraction and ethanol precipitation and translated in the presence of [35S] Translabel. This mixture was then processed in HeLa cell-free extracts for 15 hours. The samples were then analyzed on SDS polyacrylamide gels. The gel was treated with En3Hamce and exposed to x-ray. With this experiment they wanted to see if the results will be the same for the synthetic as for the wild type poliovirus. The length of the transcripts from the wild type and the synthetic were the same as the virion RNA. (6)

De novo synthesis of poliovirus in a HeLa cell-free system and plaque assay

De novo synthesis is an experiment capable of translating RNA of poliovirus type 1 (Mahoney) with good accuracy. The viral proteins in poliovirus are visible except VP2 in VP4. VP2 can be detected by imunnoprecipitation with antibodies to VP2. The most difficult to detect is VP4 even in [35S] methionine-labeled extracts of infected cells, because it contains only one methionine. RNA was taken from the synthetic or wild type poliovirus and was incubated with HeLa cell-free extracts. After 15 hours the plagues appeared and the morphology of them was characteristic to poliovirus. To avoid problems such as transfection of monolayer cells with mRNA used for translation they added a mixture of ribonuclease A and RNase T1 before added to the cells. After 30 min they incubated the mixture with HeLa cell monolayers for 1 hour, so that they could test the presence of infectious virus particles in the cell-free incubating mixture. The monolayers were then washed and after 48 hours the cells were stained with 1% crystal violet. (6)

In the results for the proteolytic processing of poliovirus RNA in HeLa cell-free extract (seen in figure 2 in the article) we see that the transcript RNA from the synthetic poliovirus and the virion RNA from the wild type poliovirus were the same. As seen in figure 3 in article the synthetic RNA was translated and replicated in the cell-free extract and that newly synthesized RNA was encapsidated into coat proteins which lead to de novo synthesis of the infectious poliovirus. The expression of the proteins in the synthetic poliovirus and the wild type poliovirus are the same. (6)

Detection of engineered genetic markers

Then they carried out experiments to confirm, that the infectious material from the cell-free extract was sPV1(M). They isolated viruses from the spinal cord of paralyzed mice. RNA was isolated from the infected cells with TRIZOL. Then they carried out RT-PCR using downstream and upstream primers for the amplification of the region. They tested all of the RNA samples by PCR without reverse transcription to exclude the possibility that some signals were residual DNA template. There was no band seen in the absence of cDNA synthesis, which indicates that the signals that were seen were poliovirus RNA. The products were then analyzed with restriction enzymes. (6)

Biological characterization of sPV1(M)

They tested the effects of the poliovirus receptor-specific monoclonal antibody (Mab) D171 and type-specific hyperimmune sera on plaque formation by sPV1(M). With this test they wanted to see if de novo poliovirus particles synthesized in the cell-free extract were serotype 1. They grown HeLa cells in monolayers and incubated them with MAb D171. After 1 hour they added 100 PFU of sPV1(M) or wt PV1(M) to the cells and incubated. After that they mixed anti-poliovirus serum with 100 PFU of sPV1(M) or wt PV1(M). They added the antibody-virus mixture to the HeLa monolayers. And then they washed and stained the plates. Mab D171 is shown to block infection of all three serotypes by binding to the CD155 (as seen in table 1 in the article). No plaques were observed when sPV1(M) was treated with poliovirus type 1 serum. Nevertheless synthetic virus was type-specific because hyperimmune serum to poliovirus type 2 did not inhibit plaque formation. The results were very similar also in the wild type poliovirus. (6)

Neurovirulence assay

Tis assay was made to determine whether synthetic poliovirus expresses a neurovirulent phenotype in mice transgenic for the human poliovirus receptor (CD155). Four tg CD155 mice were given poliovirus the synthetic one and the wild type one. Mice were then examined for 21 days for paralysis or death. After the 21 days the mice were taken the spinal cord and tested for the presence of the two viruses. The virus that induced paralysis or death in 50 % of the mice (PLD50) was calculated. The animals developed paralysis or death in animals injected with the wild type or synthetic poliovirus. The difference was in the inoculum between the polioviruses (as seen in table 1 in the article). There was an increase in the magnitude of attenuation in the mice treated with sPV1(M) which was the cause of silent mutations in the ORF. The mechanism of how silent mutations effect pathogenesis is not known. (6)

The region that had the engineered marker Not I was located in the region between 5260 and 6016 nt. The fragment (757 bp long) was treated with Not I in order to identify the restriction site in sPV1(M). The position of the RT-PCR product is in 561 bp and 196 bp. After the RT-PCR they put the products on 1,2 % agarose gel. The results showed that synthetic poliovirus treated with Not I had presence of 2 bands (561 and 196 nt). When it was not treated with Not I it was no band observed at all, indicating that the virus contained the engineered marker. In wild type poliovirus we see only a single band at 757 nt when digested with Not I or without. (6)

Conclusion

The synthesis of the synthetic poliovirus is plausible with the right knowledge and experimental tools. In the article they showed that you can make a synthetic poliovirus from scratch and that it is functional. This article will be the basis of lots of new researches in developing new vaccination and treatments. It can be also used as an example how to synthesis other RNA viruses which are more complex.

References

1. Hogle J. Poliovirus cell entry: common structural themes in viral cell entry pathways. Annu Rev Microbiol 56: 677–702 (2002).

2. Racaniello and Baltimore, D. Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proc. Natl. Acad. Sci. U.S.A. 78 (8): 4887–91 (1981)

3. Transmission of wild poliovirus type 2—apparent global interruption. Wkly. Epidemiol. Rec. 76 (13): 95–7 (2001).

4. Kitamura N. et al. Primary structure, gene organization and polypeptide expression of poliovirus RNA. Nature 291, 547 (1981).

5. V. R. Racaniello, D. Baltimore. Molecular cloning of poliovirus cDNA and the determination of the complete nucleotide sequence of the viral genome. Proc. Natl. Acad. Sci. U.S.A. 78, 4887 (1981).

6. Jeronimo Cello et al. Chemical Synthesis of Poliovirus cDNA: Generation of Infectious virus in the Absence of Natural Template. Science 297, 1016-1018 (2002).

SB students resources

2015-01-19T22:27:30Z

VeronikaJarc: /* List of articles for presentation */

===Introduction to our students resources in Synthetic Biology===
(Marko Dolinar)

Synthetic biology made a vast progress in good 10 years since it established itself as an interdisciplinary field of research on the interface of molecular biology and engineering. University of Ljubljana Faculty of Chemistry and Chemical Technology has introduced a Synthetic Biology course as a part od Biochemistry MSc programme only in 2013/14. This is relatively late, considering a great success of Slovenian students at iGEM competitions since their first attendance in 2006. On the other hand, the field is still in its first stages if development and a complete textbook for a MSc level course is still missing. This is the reason why our students collaborated on the preparation of a Synthetic Biology textbook with the working title Synthetic Biology - A Students Textbook. It exists as a draft that is not publicly available and is actually part 1 of a (to be) 2-volumes title. Part I is subtitled Engineering Biology, while Part II (that currently doesn't exisist yet) will be subtitled Synthetic Biology Applications.

As in all highly competitive fields of science and technology, students should be following recent progress by reading articles in high quality journals. However, this is often a very difficult task, especially at the BSc level. Specificities of the scientific and technical language, push of publishers towards very short methodological chapters and limited knowledge studens might have about advanced techniques make understanding papers a very challenging task. Therefore, I decided to face MSc students with the challenge to explain selected SB articles in a manner that would make the content of these articles understandable to BSc level students and non-experts.

In 2014/15, seminars in Synthetic Biology include explanations and presentations of some of the top-cited articles from the field of Synthetic Biology. I compiled a list of 95 articles published between 2000 and 2014 having the highest number of citations according to the Web of Science database. The list ended with the paper just exceeding the 100 citations limit. Not included in the list were reviews. With 20 students enrolled in the course, the list has been further reduced to top 40 papers in the field. Students have been asked to check for content (they further eliminated 3 papers which proved to be reviews) and availabitly (they all seemed to be available as full texts with our university subscriptions). My suggestion was to avoid selecting for presentation papers with very similar content. Especially in the field of genome editing there has been a very rapid progress in the past few years resulting in a number of highly-cited articles which could appear very similar in content for a non-specialist. From the shortlist of 37 articles, students selected a topic they believed would be most interesting or easiest to explain. Presentations will be both written (in English, which is not the mother tongue of my students) and oral (in Slovenian, to establish and maintain Slovenian terminology in the field).

===List of articles for presentation===

This is the list of top-cited papers from the broader field of Synthetic Biology that students chose for explanation in 2014/15 (sorted by year of publication):

#[[A synthetic oscillatory network of transcriptional regulators]], Michael B. Elowitz & Stanislas Leibler, Letters to Nature, 2000 - Valter Bergant
#[[Construction of a genetic toggle switch in Escherichia coli]]. Gardner ''et al''., Nature, 2000 - Urban Bezeljak
#[[Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion]]. Becskei ''et al''., EMBO J, 2001 - Andreja Bratovš
#[[Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template]]. Jeronimo Cello ''et al''., Science,2002 - Veronika Jarc
#[[Combinatorial synthesis of genetic networks]]. Guet C.C. ''et al'', Science, 2002 - Maja Remškar
#Engineering a mevalonate pathway in Escherichia coli for production of terpenoids (2003) - Ana Kapraljević
#Programmed population control by cell-cell communication and regulated killing. You et al, Nature (2004)[http://wiki.fkkt.uni-lj.si/index.php/7.Programmed_population_control_by_cell-cell_communication_and_regulated_killing] - Alja Zottel
#Gene regulation at the single-cell level (2005) - Katarina Uršič
#[[A synthetic multicellular system for programmed pattern formation]]. (2005) - Mitja Crček
#[[Long-term monitoring of bacteria undergoing programmed population control in a microchemostat]]. Balagadde ''et al.'', ''Science'', 2005 - Jana Verbančič
#[[Tuning genetic control through promoter engineering]], Hal Alper ''et al''., PNAS, 2005 - Špela Pohleven
#[[Production of the antimalarial drug precursor artemisinic acid in engineered yeast ]]. Ro ''et al''., ''Nature''., 2006- Živa Marsetič
#[[An improved zinc-finger nuclease architecture for highly specific genome editing]], Miller ''et al''., ''Nature Biotechnol''., 2007 - Eva Knapič
#[[Establishment of HIV-1 resistance in CD4(+) T cells by genome editing using zinc-finger nucleases]] (2008) - Tamara Marić
#[[Synthetic protein scaffolds provide modular control over metabolic flux]]. Dueber ''et al''., Nature Biotechnology, 2009. - Ana Dolinar
#[[Creation of a bacterial cell controlled by a chemically synthesized genome]]. Gibson, D. G. ''et al.'', Science, 2010 - Eva Lucija Kozak
#[[A TALE nuclease architecture for efficient genome editing]], Miller ''et al'', ''Nature Biotechnol''., 2011 - Jernej Mustar
#Multiplex genome engineering using CRISPR/Cas systems (2013) - Uroš Stupar
#[[RNA-guided human genome engineering via Cas9]]. Mali ''et al''., Science, 2013 - Luka Smole
#[[One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering (2013)]] - Andrej Vrankar

''Please link the title of each paper with your written seminar wiki page. Expand the citation according to the following example:
''
#Emergent bistability by a growth-modulating positive feedback circuit. Tan et al., Nature Chem. Biol., 2009

Proizvodnja fuzijskega proteina iz domene 3 zunajceličnega proteina virusa denge in liganda M-celic v transgenem rižu kali

2014-05-25T19:39:31Z

VeronikaJarc: /* Uvod */

== '''Uvod''' ==

Virus denge je RNA virus in spada med flaviviruse . Na ljudi se prenaša s pomočjo več vrst komarjev iz rodu Aedes in sicer predvsem A. aegypti. Obstajajo štirje serotipi virusa denge (DEN 1-4). Virusni genom je sestavljen iz 11000 bp, ki kodira tri strukturne proteine (protein kapside C, membranski protein prM in ovojnični protein E), sedem ne strukturnih proteinov (NS1, NS2a, NS2b, NS3, NS4a, NS4b in NS5) ter kratki nekodirajoči regiji na 5' in 3' koncu.
Protein E je pomemben ovojnični protein s pomočjo katerega se virus pritrdi na gostiteljevo celico. Za razvoj cepiva je protein E primerna tarča, saj vsebuje domeno III (EDIII), ki ima ključno vlogo pri vezavi na gostiteljsko celico. Zaradi več serotipov virusa denge je velik problem razviti cepivo, saj infekcija samo z enim serotipom lahko vodi do celega spektra simptomov denge(vročina, denga hemoragična mrzlica ali šok sindrom denge po zaporednih okužbah). Zato so tetravalentne vrste cepiv narejena tako, da so zmožne zagotoviti zaščito proti vsem serotipom brez reaktivacije samega virusa. Za razvoj cepiva so naredili konsenzno zaporedje z primerjavo aminokislinske sekvence EDIII različnih izolatov vseh štirih serotipov. Miške so nato imunizirali z rekombinantno konsenzno domeno III (cEDIII), te pa so razvile nevtralizirana protitelesa proti vsem štirim serotipom virusa denge.
Sistem proizvodnje s pomočjo rastlin nam nudi varno,poceni in oralno cepivo. Vendar je pri oralenem privzemu cepiva lahko problem, zaradi nizke proizvodnje antigenov in s tem povezanim nizkim imunskim odzivom. En način zvišanja imunskega odziva v mukozalnem imunskem sistemu je fuzija antigenskih proteinov z ligandi, ki imajo možnost da prenesejo fuzijski proteinski antigen v mukozalni imunski sistem za povečanje antigenskega privzema v mukozalne imunske celice. Eden od teh ligandov je M celično tarčni peptidni ligand Co1. Ta je pri oralni vakcinaciji mišk povečal privzem fuzijskega antigena v efektivno mesto mukozalnega imunskega sistema in imunskega odziva proti fuzijskem antigenu v primerjavi z samim antigenom. V tej študiji so naredili fuzijo med peptidnim ligandom Co1 in konsenznim genom domene III virusnega proteina E (scEDIII), da bi povečali mukozalni imunski odziv.

'''cEDIII- Co1'''

cEDIII- Co1 fuzijski protein je bil pod kontrolo riževo amilazega 3D promotorja (močen inducibilen promotor) v pogojih sladkornega stradanja v riževem ekspresijskem sistemu. Biološka funkcija fuzijskega proteina pa je bila gledana v mišjem modelu.

'''NAČRTOVANJE EKSPRESIJSKIH RASTLINSKIH VEKTORJEV IN GENOMSKA PCR AMPLIFIKACIJA:'''
Najprej so naredili konstrukt oz fuzijo obeh genov v pMY657. Sledila je amplifikacija z specifičnimi oligonukleotidi. PCR produkt so nato klonirali v pGEM-T Easy vektor, sekvenco pa potrdili z analizo DNA sekvence. Nato so potrjeno DNA sekvenco klonirali na ista mesta v nov vektor pMYV685, ki ima promotor za signalni peptid in 3'UTR regijo rižno amilaznega gena 3D. Transformacijo v riž kali so opravili z bombandiranjem z vektorjem pMYV685. Po transformaciji vektorjev v riž so naredil selekcijo transgenih rižev s pomočjo higromicina (antibiotik). 10 vzorcev transgenega riža kali z fuzijskim genom smo dobili 2-4 tedne po transformaciji. Fuzijski gen ustreza velikosti 400 bp. Tega so opazili le pri transgenih rižih in ne pri ne transgenih.

'''NORTHERN BLOT:'''
Izolirali so totalno RNA iz ne transgenih in transgenih rižev kali 5 dni po indukciji, ki so jo kontrolirali s sladkornim stradanjem. Pri 8/10 je prišlo do pozitivnih signalov za fuzijski protein pri transgenih rižih.

'''WESTERN BLOT IN KVANTIFIKACIJA LIGANDA FUZIJSKEGA PROTEINA:'''
Transgenega in ne transgenega riža so analizirali za detekcijo fuzijskega proteina. Linije transgenega riža, ki so kazale na visoko ekspresijo fuzijskega proteina so nato aplicirali v suspenzijsko kulturo. Za western blot so analizirali 6 transgenih rižev, ki so imeli najmočnejše signale pri northern blotu. Fuzijski protein je bil najden kot 3 lise na gelu pri 17kDA z anti-denge virusnimi protitelesi. Kvantificirali so fuzijske proteine št. 5,6 in 9 kažejo visoko ekspresijo fuzijskega proteina pri western blotu. Te so nato vzpostavili pogojem sladkornega stradanja in jih nato kvantificirali z ELISO. Največ proteina je proizvajal transgeni riž št. 6 ki je bil nato izbran za selekcijo in vitro in in vivo z privzemom antigena.

'''TEST ''IN VITRO'' IN ''IN VIVO'' PRIVZEMA ANTIGENA:'''
Za ''in vitro'' so uporabljali črevesno zanko, ki vsebuje agregatne limfoidne nodule (Peyers Patches) iz moške BALB/C miške. Proteinske ekstrakte iz ne transgenega riža in transgenega riža, ki so ekspresirali cEDIII ali cEDIII-Co1 fuzijski protein so dodali nodulom in zraven še protitelesa z fluorescentnimi označevalci.
Za opazovanje ''in vivo'' antigenskega privzema so opazovali tako da so tem miškam dali proteinske ekstrakte ne transgenega riža in transgenega riža z fuzijskim proteinom. Nato so jih žrtvovali in spirali nato dodali protitelesa z fluorescentnim označevalcem in nato opazovali dalje.

=='''Zaključek'''==

Uporaba ligandov se je izkazala za dobro metodo, ki povzroči prenos fuzijskega proteina v mukozalni imunski sistem za izboljšanje antigenskega privzema in antigenske predstavitve na antigen predstavljajočimi celicami. Tu smo potrdili vezavo cDEIII-Co1 fuzijskega proteina na Preyers Patches s testom M-celične vezave pri miših.

'''VIR:''' T.G. Kim, M.Y. Kim, N.X. Huy, S.H. Kim, M.S. Yang (2013). M-Cell targeting ligand and consensus dengue virus envelope protein domain III fusion protein production ans transgenic rice calli. ''Mol. Biotechnol'', 54, 880-887.

Proizvodnja fuzijskega proteina iz domene 3 zunajceličnega proteina virusa denge in liganda M-celic v transgenem rižu kali

2014-05-25T19:38:12Z

VeronikaJarc: /* Uvod */

== '''Uvod''' ==

Virus denge je RNA virus in spada med flaviviruse . Na ljudi se prenaša s pomočjo več vrst komarjev iz rodu Aedes in sicer predvsem A. aegypti. Obstajajo štirje serotipi virusa denge (DEN 1-4). Virusni genom je sestavljen iz 11000 bp, ki kodira tri strukturne proteine (protein kapside C, membranski protein prM in ovojnični protein E), sedem ne strukturnih proteinov (NS1, NS2a, NS2b, NS3, NS4a, NS4b in NS5) ter kratki nekodirajoči regiji na 5' in 3' koncu.
Protein E je pomemben ovojnični protein s pomočjo katerega se virus pritrdi na gostiteljevo celico. Za razvoj cepiva je protein E primerna tarča, saj vsebuje domeno III (EDIII), ki ima ključno vlogo pri vezavi na gostiteljsko celico. Zaradi več serotipov virusa denge je velik problem razviti cepivo, saj infekcija samo z enim serotipom lahko vodi do celega spektra simptomov denge(vročina, denga hemoragična mrzlica ali šok sindrom denge po zaporednih okužbah). Zato so tetravalentne vrste cepiv narejena tako, da so zmožne zagotoviti zaščito proti vsem serotipom brez reaktivacije samega virusa. Za razvoj cepiva so naredili konsenzno zaporedje z primerjavo aminokislinske sekvence EDIII različnih izolatov vseh štirih serotipov. Miške so nato imunizirali z rekombinantno konsenzno domeno III (cEDIII), te pa so razvile nevtralizirana protitelesa proti vsem štirim serotipom virusa denge.
Sistem proizvodnje s pomočjo rastlin nam nudi varno,poceni in oralno cepivo. Vendar je pri oralenem privzemu cepiva lahko problem, zaradi nizke proizvodnje antigenov in s tem povezanim nizkim imunskim odzivom. En način zvišanja imunskega odziva v mukozalnem imunskem sistemu je fuzija antigenskih proteinov z ligandi, ki imajo možnost da prenesejo fuzijski proteinski antigen v mukozalni imunski sistem za povečanje antigenskega privzema v mukozalne imunske celice. Eden od teh ligandov je M celično tarčni peptidni ligand Co1. Ta je pri oralni vakcinaciji mišk povečal privzem fuzijskega antigena v efektivno mesto mukozalnega imunskega sistema in imunskega odziva proti fuzijskem antigenu v primerjavi z samim antigenom. V tej študiji so naredili fuzijo med peptidnim ligandom Co1 in konsenznim genom domene III virusnega proteina E (scEDIII), da bi povečali mukozalni imunski odziv.

'''cEDIII- Co1'''

cEDIII- Co1 fuzijski protein je bil pod kontrolo riževo amilazega 3D promotorja (močen inducibilen promotor) v pogojih sladkornega stradanja v riževem ekspresijskem sistemu. Biološka funkcija fuzijskega proteina pa je bila gledana v mišjem modelu.

'''NAČRTOVANJE EKSPRESIJSKIH RASTLINSKIH VEKTORJEV IN GENOMSKA PCR AMPLIFIKACIJA:'''
Najprej so naredili konstrukt oz fuzijo obeh genov v pMY657. Sledila je amplifikacija z specifičnimi oligonukleotidi. PCR produkt so nato klonirali v pGEM-T Easy vektor, sekvenco pa potrdili z analizo DNA sekvence. Nato so potrjeno DNA sekvenco klonirali na ista mesta v nov vektor pMYV685, ki ima promotor za signalni peptid in 3'UTR regijo rižno amilaznega gena 3D. Transformacijo v riž kali so opravili z bombandiranjem z vektorjem pMYV685. Po transformaciji vektorjev v riž so naredil selekcijo transgenih rižev s pomočjo higromicina (antibiotik). 10 vzorcev transgenega riža kali z fuzijskim genom smo dobili 2-4 tedne po transformaciji. Fuzijski gen ustreza velikosti 400 bp. Tega so opazili le pri transgenih rižih in ne pri ne transgenih.

'''NORTHERN BLOT:'''
Izolirali so totalno RNA iz ne transgenih in transgenih rižev kali 5 dni po indukciji, ki so jo kontrolirali s sladkornim stradanjem. Pri 8/10 je prišlo do pozitivnih signalov za fuzijski protein pri transgenih rižih.

'''WESTERN BLOT IN KVANTIFIKACIJA LIGANDA FUZIJSKEGA PROTEINA:'''
Transgenega in ne transgenega riža so analizirali za detekcijo fuzijskega proteina. Linije transgenega riža, ki so kazale na visoko ekspresijo fuzijskega proteina so nato aplicirali v suspenzijsko kulturo. Za western blot so analizirali 6 transgenih rižev, ki so imeli najmočnejše signale pri northern blotu. Fuzijski protein je bil najden kot 3 lise na gelu pri 17kDA z anti-denge virusnimi protitelesi. Kvantificirali so fuzijske proteine št. 5,6 in 9 kažejo visoko ekspresijo fuzijskega proteina pri western blotu. Te so nato vzpostavili pogojem sladkornega stradanja in jih nato kvantificirali z ELISO. Največ proteina je proizvajal transgeni riž št. 6 ki je bil nato izbran za selekcijo in vitro in in vivo z privzemom antigena.

'''TEST IN VITRO IN IN VIVO PRIVZEMA ANTIGENA:'''
Za in vitro so uporabljali črevesno zanko, ki vsebuje agregatne limfoidne nodule (Peyers Patches) iz moške BALB/C miške. Proteinske ekstrakte iz ne transgenega riža in transgenega riža, ki so ekspresirali cEDIII ali cEDIII-Co1 fuzijski protein so dodali nodulom in zraven še protitelesa z fluorescentnimi označevalci.
Za opazovanje in vivo antigenskega privzema so opazovali tako da so tem miškam dali proteinske ekstrakte ne transgenega riža in transgenega riža z fuzijskim proteinom. Nato so jih žrtvovali in spirali nato dodali protitelesa z fluorescentnim označevalcem in nato opazovali dalje.

=='''Zaključek'''==

Uporaba ligandov se je izkazala za dobro metodo, ki povzroči prenos fuzijskega proteina v mukozalni imunski sistem za izboljšanje antigenskega privzema in antigenske predstavitve na antigen predstavljajočimi celicami. Tu smo potrdili vezavo cDEIII-Co1 fuzijskega proteina na Preyers Patches s testom M-celične vezave pri miših.

'''VIR:''' T.G. Kim, M.Y. Kim, N.X. Huy, S.H. Kim, M.S. Yang (2013). M-Cell targeting ligand and consensus dengue virus envelope protein domain III fusion protein production ans transgenic rice calli. ''Mol. Biotechnol'', 54, 880-887.

Proizvodnja fuzijskega proteina iz domene 3 zunajceličnega proteina virusa denge in liganda M-celic v transgenem rižu kali

2014-05-23T21:12:57Z

VeronikaJarc: New page: == '''Uvod''' == Virus denge je RNA virus in spada med flaviviruse . Na ljudi se prenaša s pomočjo več vrst komarjev iz rodu Aedes in sicer predvsem A. aegypti. Obstajajo štirje sero...

== '''Uvod''' ==

Virus denge je RNA virus in spada med flaviviruse . Na ljudi se prenaša s pomočjo več vrst komarjev iz rodu Aedes in sicer predvsem A. aegypti. Obstajajo štirje serotipi virusa denge (DEN 1-4). Virusni genom je sestavljen iz 11000 bp, ki kodira tri strukturne proteine (protein kapside C, membranski protein prM in ovojnični protein E), sedem ne strukturnih proteinov (NS1, NS2a, NS2b, NS3, NS4a, NS4b in NS5) ter kratki nekodirajoči regiji na 5' in 3' koncu.
Protein E je pomemben ovojnični protein s pomočjo katerega se virus pritrdi na gostiteljevo celico. Za razvoj cepiva je protein E primerna tarča, saj vsebuje domeno III (EDIII), ki ima ključno vlogo pri vezavi na gostiteljsko celico. Zaradi več serotipov virusa denge je velik problem razviti cepivo, saj infekcija samo z enim serotipom lahko vodi do celega spektra simptomov denge(vročina, denga hemoragična mrzlica ali šok sindrom denge po zaporednih okužbah). Zato so tetravalentne vrste cepiv narejena tako, da so zmožne zagotoviti zaščito proti vsem serotipom brez reaktivacije samega virusa. Za razvoj cepiva so naredili konsenzno zaporedje z primerjavo aminokislinske sekvence EDIII različnih izolatov vseh štirih serotipov. Miške so nato imunizirali z rekombinantno konsenzno domeno III (cEDIII), te pa so razvile nevtralizirana protitelesa proti vsem štirim serotipom virusa denge.
Sistem proizvodnje s pomočjo rastlin nam nudi varno,poceni in oralno cepivo. Vendar je pri oralenem privzemu cepiva lahko problem, zaradi nizke proizvodnje antigenov povezanih in s tem povezanim nizkim imunskim odzivom. En način zvišanja imunskega odziva v mukozalnem imunskem sistemu je fuzija antigenskih proteinov z ligandi, ki imajo možnost da prenesejo fuzijski proteinski antigen v mukozalni imunski sistem za povečanje antigenskega privzema v mukozalne imunske celice. Eden od teh ligandov je M celično tarčni peptidni ligand Co1. Ta je pri oralni vakcinaciji miškah povečal privzem fuzijskega antigena v efektivno mesto mukozalnega imunskega sistema in imunskega odziva proti fuzijskem antigenu v primerjavi z samim antigenom. V tej študiji so naredili fuzijo med peptidnim ligandom Co1 in konsenznim genom domene III virusnega proteina E (scEDIII), da bi povečali mukozalni imunski odziv.

'''cDEIII- Co1'''

cDEIII- Co1 fuzijski protein je bil pod kontrolo riževo amilazega 3D promotorja (močen inducibilen promotor) v pogojih sladkornega stradanja v riževem ekspresijskem sistemu. Biološka funkcija fuzijskega proteina pa je bila gledana v mišjem modelu.

'''NAČRTOVANJE EKSPRESIJSKIH RASTLINSKIH VEKTORJEV IN GENOMSKA PCR AMPLIFIKACIJA:'''
Najprej so naredili konstrukt oz fuzijo obeh genov v pMY657. Sledila je amplifikacija z specifičnimi oligonukleotidi. PCR produkt so nato klonirali v pGEM-T Easy vektor, sekvenco pa potrdili z analizo DNA sekvence. Nato so potrjeno DNA sekvenco klonirali na ista mesta v nov vektor pMYV685, ki ima promotor za signalni peptid in 3'UTR regijo rižno amilaznega gena 3D. Transformacijo v riž kali so opravili z bombandiranjem z vektorjem pMYV685. Po transformaciji vektorjev v riž so naredil selekcijo transgenih rižev s pomočjo higromicina (antibiotik). 10 vzorcev transgenega riža kali z fuzijskim genom smo dobili 2-4 tedne po transformaciji. Fuzijski gen ustreza velikosti 400 bp. Tega so opazili le pri transgenih rižih in ne pri ne transgenih.

'''NORTHERN BLOT:'''
Izolirali so totalno RNA iz ne transgenih in transgenih rižev kali 5 dni po indukciji, ki so jo kontrolirali s sladkornim stradanjem. Pri 8/10 je prišlo do pozitivnih signalov za fuzijski protein pri transgenih rižih.

'''WESTERN BLOT IN KVANTIFIKACIJA LIGANDA FUZIJSKEGA PROTEINA:'''
Transgenega in ne transgenga riža so analizirali za detekcijo fuzijskega proteina. Linije transgenega riža, ki so kazale na visoko ekspresijo fuzijskega proteina so nato aplicirali v suspenzijsko kulturo. Za western blot so analizirali 6 transgenih rižev, ki so imeli najmočnejše signale pri northern blotu. Fuzijski protein je bil najden kot 3 lise na gelu pri 17kDA z anti-denge virusnimi protitelesi. Kvantificirali so fuzijske proteine št. 5,6 in 9 kažejo visoko ekspresijo fuzijskega proteina pri western blotu. Te so nato vzpostavili pogojem sladkornega stradanja in jih nato kvantificirali z ELISO. Največ proteina je proizvajal transgeni riž št. 6 ki je bil nato izbran za selekcijo in vitro in in vivo z privzemom antigena.

'''TEST IN VITRO IN IN VIVO PRIVZEMA ANTIGENA:'''
Za in vitro so uporabljali črevesno zanko, ki vsebuje agregatne limfoidne nodule (Peyers Patches) iz moške BALB/C miške. Proteinske ekstrakte iz ne transgenega riža in transgenega riža, ki so ekspresirali cEDIII ali cEDIII-Co1 fuzijski protein so dodali nodulom in zraven še protitelesa z fluorescentnimi označevalci.
Za opazovanje in vivo antigenskega privzema so opazovali tako da so tem miškam dali proteinske ekstrakte ne transgenega riža in transgenega riža z fuzijskim proteinom. Nato so jih žrtvovali in spirali nato dodali protitelesa z fluorescentnim označevalcem in nato opazovali dalje.

=='''Zaključek'''==

Uporaba ligandov se je izkazala za dobro metodo, ki povzroči prenos fuzijskega proteina v mukozalni imunski sistem za izboljšanje antigenskega privzema in antigenske predstavitve na antigen predstavljajočimi celicami. Tu smo potrdili vezavo cDEIII-Co1 fuzijskega proteina na Preyers Patches s testom M-celične vezave pri miših.

'''VIR:''' T.G. Kim, M.Y. Kim, N.X. Huy, S.H. Kim, M.S. Yang (2013). M-Cell targeting ligand and consensus dengue virus envelope protein domain III fusion protein production ans transgenic rice calli. ''Mol. Biotechnol'', 54, 880-887.

MBT seminarji 2014

2014-05-23T21:02:49Z

VeronikaJarc:

'''Seznam seminarjev iz Molekularne biotehnologije v študijskem letu 2013/14'''

V študijskem letu 13/14 izvajamo predmet Molekularna biotehnologija (in s tem tudi seminarje) prvič.
Tabela za razpored po tednih bo objavljena v spletni učilnici, vanjo pa se vpišite tudi za kratke predstavitve novic (5 min). Na tej strani bo samo seznam odobrenih člankov za seminar in povezave do člankov in do povzetkov, ki jih morate objaviti najkasneje tri dni pred predstavitvijo (petek).

Način vnosa:

# The importance of ''Arabidopsis'' glutathione peroxidase 8 for protecting ''Arabidopsis'' plant and ''E. coli'' cells against oxidative stress (A. Gaber; GM Crops & Food 5(1), 2014; http://dx.doi.org/10.4161/gmcr.26979) Pomen glutation peroksidaze 8 iz repnjakovca za zaščito rastline ''Arabidopsis thaliana'' in bakterije ''Escherichia coli'' pred oksidativnim stresom. Janez Novak, 15. marca 2014
(slovenski naslov povežete z novo stranjo, na kateri bo povzetek)

Naslovi odobrenih člankov:

# A plant factory for moth pheromone production (B-J. Ding ''et al''.; Nature Communications 5, 3353, 2014; http://www.nature.com/ncomms/2014/140225/ncomms4353/full/ncomms4353.html) [[Proizvodnja feremonov vešče v rastlinah]]. Filip Kolenc, 24. marca 2014
# Introduction of the rd29A:AtDREB2A CA gene into soybean (Glycine max L. Merril) and its molecular characterization in leaves and roots during dehydration (C. Engels ''et al''.; Genetics and Molecular Biology 36(4): 556–565, 2013; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873188/) [[Vstavitev gena rd29A:AtDREB2A CA v sojo in njegova molekulska karakterizacija v listih in koreninah med dehidracijo]]. Aleksander Krajnc, 24. marca 2014
# Enantioselective lactic acid production by an Enterococcus faecium strain showing potential in agro-industrial waste bioconversion: Physiological and proteomic studies (A. Pessione ''et al''.; Journal of Biotechnology 173, 31–40, 2014; http://dx.doi.org/10.1016/j.jbiotec.2014.01.014) [[Produkcija optično čiste mlečne kisline v sevu enterococcus faecium kaže potencial v biopretvorbi odpadkov kmetijske industrije: fiziološka in proteomska študija]]. Žan Železnik, 31. marca
# Isolation and characterization of formaldehyde-degrading fungi and its formaldehyde metabolism (D. Yu ''et al''.; Environmental Science and Pollution Research 2014 - v tisku; http://dx.doi.org/10.1007/s11356-014-2543-2) [[Glive, sposobne razgradnje formaldehida: izolacija, karakterizacija in njihov metabolizem formaldehida.]] Sara Sajko, 31. marca
# Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface (S. M. Lewis et al.; Nature Biotechnology 32, 191–198, 2014; http://www.nature.com/nbt/journal/v32/n2/full/nbt.2797.html) [[Priprava bispecifičnih IgG protiteles s pomočjo ustvarjanja strukturno baziranega ortogonalnega Fab vmesnika.]] Vito Frančič, 7. aprila
# Generation of protective immune response against anthrax by oral immunization with protective antigen plant-based vaccine (J. Gorantala, ''et al''; Journal of Biotechnology, 176, 2014, str. 1-10.; http://www.sciencedirect.com/science/article/pii/S0168165614000571) - [[Pridobitev zaščitnega imunskega odziva proti antraksu preko oralne imunizacije z zaščitnim antigenom kot cepivom, pridobljenim na osnovi rastlin]]. Sabina Kolar, 7. aprila
# Development of influenza H7N9 virus like particle (VLP) vaccine: Homologous A/Anhui/1/2013 (H7N9) protection and heterologous A/chicken/Jalisco/CPA1/2012 (H7N3) cross-protection in vaccinated mice challenged with H7N9 virus (G. E. Smith ''et al''.; Vaccine 31, 4305-4313, 2013; http://www.sciencedirect.com/science/article/pii/S0264410X13009870). [[Razvoj cepiva za virus gripe H7N9 na osnovi virusu podobnih delcev]]. Ana Dolinar, 14. aprila
# Generation of tumor-targeted human T lymphocytes from induced pluripotent stem cells for cancer therapy (M. Themeli ''et al.''; Nature Biotechnology 31, 928–933, 2013; http://www.nature.com/nbt/journal/v31/n10/full/nbt.2678.html). [[Iz induciranih pluripotentnih izvornih celic pripravljeni človeški limfociti T za terapijo raka]]. Urban Bezeljak, 14. aprila
# Engineering ''Escherichia coli'' for selective geraniol production with minimized endogenous dehydrogenation (J. Zhou; Journal of Biotechnology 169, 2014; http://www.sciencedirect.com/science/article/pii/S016816561300494X) [[Inženiring Escherichie coli za selektivno produkcijo geraniola z minimalno endogeno dehidrogenacijo]]. Maja Remškar, 5. maja
# Identifying producers of antibacterial compounds by screening for antibiotic resistance. (M. N. Thaker et al.; Nature Biotechnology 31, 922-927; 2013). [[Identifikacija proizvajalcev antibakterijskih spojin z iskanjem odpornosti proti antibiotikom]]. Špela Podjed, 5. maja
# Consolidated conversion of protein waste into biofuels and ammonia using Bacillus subtilis (K-Y. Choi ''et al''.; Metabolic Engineering 2014 - v tisku; http://dx.doi.org/10.1016/j.ymben.2014.02.007). [[Pretvorba proteinskih odpadkov v biogoriva in amonijak z bakterijo B. subtilis]] Elmina Handanović, 12. maja 2014
# Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose (J. Li ''et al''.; Biotechnology for Biofuels 7:31, 2014; http://www.biotechnologyforbiofuels.com/content/7/1/31/abstract). [[Primerjava transkriptoma filamentoznih gliv Neurospora crassa pri rasti na treh različnih vrstah monosaharidov: D-glukoze, D-ksiloze in L-arabinoze]] Luka Bevc, 12. maja
# Influence of valine and other amino acids on total diacetyl and 2,3-pentanedione levels during fermentation of brewer’s wort. (K. Krogerus, et al., Microbiol Biotechnol. 2013 Aug; http://link.springer.com/article/10.1007%2Fs00253-013-4955-1). [[Vpliv valina in drugih aminokislin na vsebnost diacetila in 2,3-pentadiona v pivini]] Jernej Mustar, 19. maja
# Xylanase and cellulase systems of Clostridium sp.: An insight on molecular approaches for strain improvement (L. Thomas ''et al''.; Bioresource Technology 2014 - v tisku; http://dx.doi.org/10.1016/j.biortech.2014.01.140)[[Ksilanazni ter celulosomski sistemi klostridij:vpogled v molekularni pristoti za izboljšavo sevov]] Luka Grm, 19. maja
# M Cell-Targeting Ligand and Consensus Dengue Virus Envelope Protein Domain III Fusion Protein Production in Transgenic Rice Calli (Tae-Geum K.''et al''.; Molecular Biotechnology 54, 880-887, 2013; http://link.springer.com/article/10.1007%2Fs12033-012-9637-1 ) [[Proizvodnja fuzijskega proteina iz domene 3 zunajceličnega proteina virusa denge in liganda M-celic v transgenem rižu kali]] Veronika Jarc, 26. maja
# Negative selection and stringency modulation in phage-assisted continuous evolution (Jacob C. Carlson, Ahmed H. Badran, Drago A. Guggiana-Nilo & David R. Liu; Nature chemical biology 10, 216–222, 2014; http://www.nature.com/nchembio/journal/v10/n3/full/nchembio.1453.html) [[Negativna selekcija in spreminjanje striktnosti pri zvezni evoluciji s pomočjo fagov.]] Valter Bergant, 26. maja

MBT seminarji 2014

2014-03-07T18:42:15Z

VeronikaJarc:

'''Seznam seminarjev iz Molekularne biotehnologije v študijskem letu 2013/14'''

V študijskem letu 13/14 izvajamo predmet Molekularna biotehnologija (in s tem tudi seminarje) prvič.
Tabela za razpored po tednih bo objavljena v spletni učilnici, vanjo pa se vpišite tudi za kratke predstavitve novic (5 min). Na tej strani bo samo seznam odobrenih člankov za seminar in povezave do člankov in do povzetkov, ki jih morate objaviti najkasneje tri dni pred predstavitvijo (petek).

Način vnosa:

# The importance of ''Arabidopsis'' glutathione peroxidase 8 for protecting ''Arabidopsis'' plant and ''E. coli'' cells against oxidative stress (A. Gaber; GM Crops & Food 5(1), 2014; http://dx.doi.org/10.4161/gmcr.26979) Pomen glutation peroksidaze 8 iz repnjakovca za zaščito rastline ''Arabidopsis thaliana'' in bakterije ''Escherichia coli'' pred oksidativnim stresom. Janez Novak, 15. marca 2014
(slovenski naslov povežete z novo stranjo, na kateri bo povzetek)

Naslovi odobrenih člankov:

# A plant factory for moth pheromone production (B-J. Ding ''et al''.; Nature Communications 5, 3353, 2014; http://www.nature.com/ncomms/2014/140225/ncomms4353/full/ncomms4353.html). Filip Kolenc, 24. marca 2014
# Introduction of the rd29A:AtDREB2A CA gene into soybean (Glycine max L. Merril) and its molecular characterization in leaves and roots during dehydration (C. Engels ''et al''.; Genetics and Molecular Biology 36(4): 556–565, 2013; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873188/) Aleksander Krajnc, 24. marca 2014
# Generation of protective immune response against anthrax by oral immunization with protective antigen plant-based vaccine. Sabina Kolar
# Influence of valine and other amino acids on total diacetyl and 2,3-pentanedione levels during fermentation of brewer’s wort. Jernej Mustar
# Development of influenza H7N9 virus like particle (VLP) vaccine: Homologous A/Anhui/1/2013 (H7N9) protection and heterologous A/chicken/Jalisco/CPA1/2012 (H7N3) cross-protection in vaccinated mice challenged with H7N9 virus (G. E. Smith ''et al''.; Vaccine 31, 4305-4313, 2013; http://www.sciencedirect.com/science/article/pii/S0264410X13009870). Razvoj cepiva za virus gripe H7N9 na osnovi virusu podobnih delcev ter primer uporabe cepiva pri miših. Ana Dolinar
# Generation of tumor-targeted human T lymphocytes from induced pluripotent stem cells for cancer therapy (M. Themeli ''et al.''; Nature Biotechnology 31, 928–933, 2013; http://www.nature.com/nbt/journal/v31/n10/full/nbt.2678.html). [[Iz induciranih pluripotentnih izvornih celic pripravljeni človeški limfociti T za terapijo raka]]. Urban Bezeljak
# Negative selection and stringency modulation in phage-assisted continuous evolution (Jacob C. Carlson, Ahmed H. Badran, Drago A. Guggiana-Nilo & David R. Liu; Nature chemical biology 10, 216–222, 2014; http://www.nature.com/nchembio/journal/v10/n3/full/nchembio.1453.html) Negativna selekcija in spreminjanje striktnosti pri zvezni evoluciji s pomočjo fagov. Valter Bergant
# ... Vito Frančič
# Engineering ''Escherichia coli'' for selective geraniol production with minimized endogenous dehydrogenation (J. Zhou; Journal of Biotechnology 169, 2014; http://www.sciencedirect.com/science/article/pii/S016816561300494X) Inženiring ''Escherichie coli'' za selektivno produkcijo geraniola z minimalno endogeno dehidrogenacijo. Maja Remškar
# M Cell-Targeting Ligand and Consensus Dengue Virus Envelope Protein Domain III Fusion Protein Production in Transgenic Rice Calli (Tae-Geum K.''et al''.; Molecular Biotechnology 54, 880-887, 2013; http://link.springer.com/article/10.1007%2Fs12033-012-9637-1 ) Veronika Jarc
# ... Špela Podjed
# Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose (J. Li ''et al''.; Biotechnology for Biofuels 7:31, 2014; http://www.biotechnologyforbiofuels.com/content/7/1/31/abstract). Luka Bevc
# Xylanase and cellulase systems of Clostridium sp.: An insight on molecular approaches for strain improvement (L. Thomas ''et al''.; Bioresource Technology 2014 - v tisku; http://dx.doi.org/10.1016/j.biortech.2014.01.140) Luka Grm
# Consolidated conversion of protein waste into biofuels and ammonia using Bacillus subtilis (K-Y. Choi ''et al''.; Metabolic Engineering 2014 - v tisku; http://dx.doi.org/10.1016/j.ymben.2014.02.007). Elmina Handanović
# Isolation and characterization of formaldehyde-degrading fungi and its formaldehyde metabolism (D. Yu ''et al''.; Environmental Science and Pollution Research 2014 - v tisku; http://dx.doi.org/10.1007/s11356-014-2543-2) Sara Sajko
# Enantioselective lactic acid production by an Enterococcus faecium strain showing potential in agro-industrial waste bioconversion: Physiological and proteomic studies (A. Pessione ''et al''.; Journal of Biotechnology 173, 31–40, 2014; http://dx.doi.org/10.1016/j.jbiotec.2014.01.014) Žan Železnik

Identification and mapping of clone-specific chromosomal abnormalities

2013-12-06T17:42:21Z

VeronikaJarc: New page: == METODA ZA DOLOČEVANJE NOVIH MOLEKULSKIH MARKERJEV ZA DOLOČANJE MINIMALNIH PREOSTANKOV BOLEZNI PRI PACIENTIH Z AKUTNO LEVKEMIJO == '''UVOD''' Akutna levkemija je vrsta levkemije, ki...

== METODA ZA DOLOČEVANJE NOVIH MOLEKULSKIH MARKERJEV ZA DOLOČANJE MINIMALNIH PREOSTANKOV BOLEZNI PRI PACIENTIH Z AKUTNO LEVKEMIJO ==

'''UVOD'''

Akutna levkemija je vrsta levkemije, ki prizadene nezrele in slabo diferencirane celice. Posledice bolezni so huda anemija, krvavitve ter povečana vranica in bezgavke. Prav tako pacienti z akutno levkemijo umrejo v nekaj mesecih. Poznamo 2 tipa akutne levkemije: limfocitno levkemijo (ALL) in mieloidno levkemijo (AML).
Vse te kromosomske mutacije, aberacije in genske preurejenosti lahko senzitivno in kvantitativno detektiramo s pomočjo opazovanja minimalnih preostankov bolezni (MRD) celic, ki jih je prizadela levkemija. Ta način opazovanja z levkemijo prizadetih celic se je izkazal za zelo pomembnega, saj lahko napovemo kakšna bo kakovost odziva na zdravljenje, čas popolne remisije in napoved individualnega tveganja za ponovitev bolezni. V zadnjem času se je PCR v realnem času izkazal kot občutljiv in specifičen ter s tem najbolj primeren za diagnosticiranje akutne levkemije in ocenjevanja minimalnih preostankov bolezni. Vendar se je ta metoda izkazala za neprimerno v primeru, da pacientu ne dokažemo nobene od prej naštetih kromosomskih aberacij. Zato je pomembno, da identificiramo nove klonsko specifične markerje pri celicah prizadetih z levkemijo, ki bi jih lahko spremljali z opazovanjem MRD.

'''METODE IN REZULTATI'''

MOLEKULARNA CITOGENETSKA ANALIZA, KROMOSOMSKO MIKROSICIRANJE IN DOP-PCR
Analizirali so celično linijo K562 in kostni mozeg ter periferno kri iz štirih pacientov. Kariotip celične linije kot tudi kostnega mozga in krvi na prelomih kromosomov je bil izveden z multipleksno fluorescenco in situ hibridizacijo in metodami barvanja kromosomov (mFISH in mBAND). Ti metodi barvanja kromosomov pobarvata različne predele posameznega kromosoma z različnimi barvami in tako omogočata boljše nadaljnje analize posameznih predelov kromosomov, ki so jih Jancuskova in sodelavci potrebovali.
Kromosome so mikrosicirali na regijah v bližini njihovih prelomov. Tako so dobili fragmente kromosomov, ki so vsebovali prelomni del kromosoma. Nato so tem fragmentom dodali izbrano raztopino in jih pripravili za pomnoževanje z DOP PCR (angl. degenerate oligonucleotide-pirmed PCR).

SEKVENCIRANJE NASLEDNJE GENERACIJE IN LR-PCR
Nukleotidno zaporedje so določali z GS Junior sistemom. Katerega so nato primerjali med seboj z referenčnim zaporedjem in nato sestavili nove oligonukleotide za LR-PCR (PCR z velikim območjem). Na podlagi tega so naredili oligonukleotide primerne za PCR v realnem času za opazovanje minimalnih preostankov bolezni celic, okuženih z levkemijo.

'''REZULTATI'''

CELIČNA LINIJA K562
Po mikrosiciranju so dobili 11 fragmentov, ki so jih pomnožili z DOP-PCR. Po določanju nukleotidnega zaporedja z GS Juniorjem so dobili 80798 rezultatov, ki so jih analizirali, kjer jim je za referenčno sekvenco služil kromosom 3 in 10. Ker nukleotidno zaporedje ob prelomu v kromosomu 3 in 10 ni dokončno znano so na koncu dobili malo primernih zaporedij na podlagi katerih so nato naredili LR-PCR. Po zadnjemu PCR so dobili 4,5 kb dolg produkt. Ta produkt so bili geni CDC25A na kromosomu 3 in GRID1 na kromosomu 10.

PACIENT 1
Prišlo je do fuzije genov MLL-AF4. To je bilo potrjeno s strani PCR v realnem času kot tudi s strani sekvenciranja. Prav tako so naredili vse analize, ki so bile prikazane na celični liniji. Po sekvenciranju so dobili 122279 rezultatov za kromosom 4 in 120209 rezultatov za kromosom 11. Rezultat LR-PCR sta bila 0,5 kb (kromosom 4) in 3 kb (kromosom 11) dolg produkt. Pri tem pacientu je derivat kromosoma 4 vseboval zlitje psevdogena LOC392539 iz kromosoma X in AF4 gena iz 4q21.

'''ZAKLJUČEK'''
Kombinacija citogenetskih in molekularnih metod, naj bi bila najboljše orodje za identifikacijo novih markerjev. S pomočjo citogenetskih metod se namreč poišče lokacijo kjer se nahaja mutacija, z molekularnimi tehnikami pa pridobimo njihovo sekvenco in kvantifikacijo MRD. Metoda PCR v realnem času z kvantificiranjem MRD bi se lahko uporabljala direkten in hiter prikaz kromosomskih aberacij pri pacientih. V primerjavi z mapiranjem s pomočjo FISH, nam naša tehnika omogoča vpogled v nukleotidno zaporedje preiskovane regije in s tem določitev genov, ki se tu nahajajo. Celoten postopek od odvzema vzorca do PCR v realnem času s pomočjo MRD testa ne traja dolgo (6 tednov), zato bi to v klinični praksi lahko uporabljali kot orodje personalizirane medicine.

VIR: Jancuskova T., Plachy R., Stika J., Zemankova L., W. Hardekopf D., Liehr T., Kosyakova N., Cmejla R., Zejskova L., Kozak T., Zak P., Zavrelova A., Havlikova P., Karas M., Junge A., Ramel C., Pekova S. (2013). A method to identify new molecular markers for assessing minimal residual disease in acute leukemia patients. Leukemia Research. 37, 1363-1373

Seminarji TehDNA

2013-10-08T17:39:27Z

VeronikaJarc:

Seminarje iz Tehnologije DNA bo v študijskem letu 2013/14 vodila asist. dr. Helena Čelešnik.

Seznam tem za seminarje:

# Mutageneza (16.10.) (povzetek in porocilo lahko oddate v pon., 14.10), 3 seminarji:
# Izražanje na površini (23.10.), 3 seminarji:
# Dvohibridni sistemi (30.10.), 3 seminarji:
# Mutageneza, izražanje na površini ali dvohibridni sistemi (6.11.), 3 seminarji: 1. Valter Bergant
# GSO v agronomiji (13.11.), 3 seminarji: 1. Niki Bursič, 2. Petra Malavašič, 3. Jernej Mustar
# Transgenske živali (27.11.), 3 seminarji: 1. Andrea Grof, 2. Eva Lucija Kozak, 3. Špela Pohleven
# Izvorne celice (4.12.), 4 seminarji: 1. Sara Primec, 2. Alja Zottel, 3. Tjaša Goričan, 4. Rok Štemberger
# DNA-diagnostika (11.12.), 4 seminarji: 1. Tina Gregorič , 2. Eva Knapič, 3. Veronika Jarc, 4. Jana Verbančič
# Forenzika, arheologija, sistematika (18.12.), 3 seminarji: 1. Matja Zalar, 2. Andreja Bratovš, 3. Maja Remškar
# Mikromreže, genomike (8.1.), 3 seminarji: 1. Andrej Vrankar, 2. Filip Kolenc
# Gensko zdravljenje s. lat. (15.1.), 3 seminarji: 1. Ana Dolinar

Seminarji TehDNA

2013-10-08T14:00:04Z

VeronikaJarc:

Seminarje iz Tehnologije DNA bo v študijskem letu 2013/14 vodila asist. dr. Helena Čelešnik.

Seznam tem za seminarje:

# Mutageneza (16.10.)
# Izražanje na površini (23.10.)
# Dvohibridni sistemi (30.10.)
# Mikromrežne tehnologije (6.11.)
# GSO v agronomiji (13.11.)
# Transgenske živali (27.11.) Andrea Grof
# Izvorne celice (4.12.) Sara Primec, Alja Zottel
# DNA-diagnostika (11.12.) Tina Gregorič , Eva Knapič, Veronika Jarc
# Forenzika, arheologija, sistematika (18.12.)
# Mikromreže, genomike (8.1.)
# Gensko zdravljenje s. lat. (15.1.)

RNA-interferenca

2012-02-29T14:13:41Z

VeronikaJarc: /* Predstavitev seminarja 2011/12 */

== Predstavitev seminarja 2011/12 ==
Seminarska tema pri predmetu Molekularna biologija (Biokemija, 2. letnik) v študijskem letu 2011/12 je utišanje izražanja genov z RNA-interferenco.
Študenti se bodo razporedili v več skupin (po 3 študente) in obdelali isto temo z več vidikov. Pripravili bodo kratka predavanja znotraj letnika in napisali povzetek v obliki wiki-strani. Naslovi poglavij so:

# Raziskave, ki so privedle do odkritja RNA-interference (1995-1998)
# Odkritje kratke interferenčne RNA (siRNA) (2000-2001)
# Odkritje encima 'dicer' (2000-2001)
# Odkritje mikro-RNA (miRNA) (2001)
# Odkritje kratke lasnične RNA (shRNA) (2003)
# Odkritje in delovanje nukleaze Drosha (2003-)
# Prvi poskusi zdravljenja z RNAi (2003-2004)
# Odkritje aktivacije genov z malo RNA (RNAa) (2006)
# Evolucijski pomen RNAi (2006-)
# Odkritje in delovanje kompleksa RISC
# Pomen RNAi kot obramba pred virusi in transpozoni
# Posebnosti in primeri RNAi pri rastlinah
# Klinični preizkusi z učinkovinami na osnovi RNAi
# Biotehnološka uporaba RNAi
# Možni pristopi k zdravljenju raka z RNAi

Povezave do nekaterih ključnih člankov najdete na strani [http://www.rnaiweb.com/RNAi/RNAi_Timeline/ RNAi Web].

Vsako temo obdelajo 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 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. (več o tem v nadaljevanju).

Vse skupine morajo objaviti povzetek seminarja na wikiju najkasneje 2.4. opolnoči. Predstavitve seminarjev 1 - 4 bodo 4.4., 5 - 8 6.4., 9 - 12 11.4 in 13 - 15 13.4. Vsaka skupina ima torej za predstavitev 14-18 minut časa, 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').

=== Skupine ===

''Skupine za projektno nalogo - po trije za vsako poglavje (imena in priimke vpišite v oklepaj za naslovom teme):''

# Raziskave, ki so privedle do odkritja RNA-interference
# Odkritje kratke interferenčne RNA (siRNA)
# Odkritje encima 'dicer' (Iza Ogris, Maja Grdadolnik, Karmen Hrovat)
# Odkritje m
ikro-RNA (miRNA)
# Odkritje kratke lasnične RNA (shRNA) (Alja Zottel, Eva Knapič, Taja Karner)
# Odkritje in delovanje nukleaze Drosha (Ines Kerin, Petra Malavasic)
# Prvi poskusi zdravljenja z RNAi (Mirjam Kmetič, Ana Dolinar)
# Odkritje aktivacije genov z malo RNA (RNAa)
# Evolucijski pomen RNAi (Špela Pohleven, Rok Vene, Jana Verbančič)
# Odkritje in delovanje kompleksa RISC
# Pomen RNAi kot obramba pred virusi in transpozoni(Veronika Jarc, Tjaša Goričan, Kaja Javoršek)
# Posebnosti in primeri RNAi pri rastlinah(Tina G., Sara D., Teja B.)
# Klinični preizkusi z učinkovinami na osnovi RNAi
# Biotehnološka uporaba RNAi
# Možni pristopi k zdravljenju raka z RNAi (Andreja Bratovš, Matja Zalar, Tamara Marić)

Naslov teme povežite z novo wiki-stranjo, na katero napišite povzetek. Na koncu besedila (pod viri) v novo vrstico dodajte naslednji oznaki:<nowiki>
[[Category:SEM]] [[Category:BMB]]</nowiki>

Kako so bili urejeni seminarji lani, si lahko ogledate na strani [[Epigenetsko uravnavanje izražanja genov]], kjer boste našli tudi dodatne informacije za bolj poglobljeno učenje Molekularne biologije na to temo.

BIO2 Povzetki seminarjev 2011

2011-10-21T16:54:57Z

VeronikaJarc:

== Sara Draščič: On the spur of a whim ==

Serotonin ali 5-hidroksitriptamin (5-HT) spada v skupino heterogenih biokemičnih snovi, ki prenašajo informacije po živčnem sistemu in ki jim rečemo nevrotransmiterji. Ima pomembno vlogo pri veliko najrazličnejših reakcijah v telesu. Njegovo nepravilno delovanje vpliva na počutje, apetit, slabost, spanje, telesno temperaturo, staranje, bolečino, anksioznost, agresijo, spomin, migrene in na številne druge procese v organizmu. Večina serotonina se sintetizira v prebavnem traktu, preostali del pa v centralnem živčnem sistemu in trombocitih. Kljub temu, da se sintetizira le v določenih delih telesa, je prisoten povsod. Dokaz za njegovo prisotnost pa so serotoninski receptorji. Serotonin ima veliko receptorjev, ki so jih organizirali v sedem skupin glede na njihove fiziološke in strukturne razlike. Ravno zaradi tako velikega števila raznoraznih receptorjev, je serotonin pomemben pri tolikih različnih procesih, saj je njegovo delovanje, v veliki meri, odvisno od tega, na kateri receptor se bo vezal. Veliki pomen pri delovanju serotonina ima tudi njegov transporter. To je protein, katerega struktura še ni znana, vendar vemo kje in na katerem kromosomu se nahaja. Transporter je tudi glavna tarča raznih antidepresivov in drog kot so ecstasy, kokain in LSD.

== Ula Štok: Neuregulin 1 ==

Neuregulin-1 je član proteinov iz družine neuregulinov in je kodiran s strani gena NRG1. Obstaja veliko tipov Neuregulina-1, ki se razlikujejo po funkcionalnosti ter mestu v telesu na katerem delujejo. Najpogosteje delujejo v živčnem sistemu, kjer lahko z nepravilnim delovanjem med drugimi povzročajo tudi zelo razširjeno bolezen - shizofrenijo. Delujejo pa tudi na ostalih tkivih in organih (na primer: srce, pljuča, oprsje in želodec). Generalno obstajata dve poti signaliziranja Neuregulina-1, in sicer: Običajna ter neobičajna pot. Pri običajni poti je ErbB receptor aktiviran direktno, v enem koraku z vezavo Neuregulina-1. To najpogosteje povzroči dimerizacijo ali heterodimerizacijo ErbB receptorja. Dimerizacija ali heterodimerizacija sicer nista nujno potrebni, a vendar do njiju pride na skoraj vseh receptorjih ErbB. Ta združitev povzroči avto- in trans-fosforilacijo intracelularnih domen tega receptorja, kar aktivira vse nadaljnje poti signaliziranja. V končni fazi pa NRG1/ErbB signaliziranje vpliva direktno na transkripcijo. Pri neobičajni poti je postopek podoben, a vendar poteka začetna stopnja malo drugače. Na začetku namreč sodeluje JMa oblika receptorja ErbB4, ki se pod vplivom TACE cepi. Del receptorja (ErbB4-CTF) se odcepi v notranjost celice. Ta peptid je velik približno 80 kD in ima specifično izoblikovano vezavno mesto za Neuregulin-1. Nadaljnji procesi pa potekajo zelo podobno kot pri običajni signalni poti. Neuregulin-1 lahko povzroča shizofrenijo na različne načine, saj sodeluje pri zelo pomembnih procesih, kot so: tvorba sinaps, mielinizacija aksonov, razvoj oligodendrocit itd. Shizofrenija je zelo razširjena bolezen in nihče še ni odkril direktnega postopka k popolni odpravi te bolezni. A vendar, v letu 2009 se je zgodila neke vrste prelomnica v študiju shizofrenije. Odkrili so namreč, da posamezniki, ki so imeli gen za shizofrenijo niso zboleli. Še več! Napaka se jim je odrazila kot zvišanje kreativnih sposobnosti na znanstvenem ali umetniškem področju, odvisno od posameznika. Ob tem se je pojavilo mnogo vprašanj, saj bi na ta način mogoče lahko poiskali pot, da bi shizofrenija postala popolnoma ozdravljiva. A vendar, je to področje še raziskano, saj znanstveniki ne vedo po kakšnih poteh pride do tega, da te mutacije na NRG1 genu ne izrazijo v bolezenskem stanju.

== Maša Mirković: Proteinski produkti genov za disleksijo in z disleksijo povezane motnje ==

Disleksija je motnja, ki se kaže v nesposobnosti branja oziroma razumevanja prebranega, ter napakah in težavah pri izgovarjanju besed. Disleksiki,kot imenujemo posameznike, ki trpijo za disleksijo, imajo kljub normalnim intelektualnim sposobnostim, znanjem in izobrazbo, moteni veščini pisanja in branja s tendenco, da pomešajo med seboj črke ali besede med branjem ali pisanjem. V zadnjih letih, so uspeli ugotoviti mesta na kromosomih, povezana z dovzetnostjo za disleksijo. DYX1C1,KIAA0319,DCDC2 in ROBO1, so bili označeni kot kandidati, z dovzetnostjo za disleksijo. Najbolj obetaven je protein KIAA0319. Je transmembranski protein iz desetih transmembranskih vijačnic, najden v plazemski membrani nevronov. Njegov C-terminalni konec gleda v ekstracelularni matriks, manjši N-terminalni konec pa prehaja v citoplazmo nevrona. C-terminalni konec je visoko glikoziliran in nosi 5 PKD(polycystyc kidney desease) domene in eno MANEC(motif at the N terminus with eight cysteines) domeno. KIAA0319 igra vlogo pri rasti možganov in njihovi migraciji med razvojem možganov-iz tega je razvidno, da je disleksija problem v razvoju nevronov že v zgodnjih letih. Posamezniki z disleksijo nosijo izoobliko tega proteina, ki povzroči nižjo izraženost le tega. Spremembe so v 5'-regiji, ki kodira izoobliko proteina. Najopaznejše povezave z disleksijo se kažejo v 2,3 kb regiji, ki zavzema promotor, prvi nepreveden ekson in del prvega introna – odprti kromatin. Te ugotovitve vodijo, da je 5'-regija KIAA0319 gena tista lokacija alelov, ki največ prispeva k motnji branja.

== Katra Koman: INZULIN ==

Inzulin je peptidni hormon, ki sodeluje v uravnavanju ravni glukoze v krvi. Sintetizira in skladišči se v β-celicah Langerhansovih otočkov trebušne slinavke. Sinteza poteka od prekurzorske molekule preproinzulina preko proinzulina do dokončne zrele molekule inzulina, ki se shrani v skladiščnih veziklih. Ob povišanju ravni glukoze v krvi, na primer po obroku, glukoza, ki je tudi glavni stimulator sekrecije inzulina, iz krvi preide v β-celice skozi GLUT2 transporter. Tam se fosforilira v glukozo-6-fosfat, saj tako fosforilirana ne more več iz celice, lahko pa vstopi v proces glikolize, ki mu sledita še Krebsov cikel in oksidativna fosforilacija, ki povzroči pretvorbo ADP v ATP molekule. ATP molekula stimulira zaprtje kalijevih kanalčkov, kar privede do depolarizacije celične membrane, to pa sproži na odprtje kalcijevih kanalčkov in vdor Ca2+ ionov. Povišana koncentracija kalcijevih Ca2+ ionov v celici stimulira prenos in zlitje skladiščnih veziklov z inzulinom z membrano. Inzulin se tako sprosti v krvni obtok in potuje do tarčnih celic, ki imajo na površini izražene inzulinske receptorje. Ko se veže nanj, prenese signal o povišanju ravni glukoze v krvi v celico. To povzroči kaskado reakcij znotraj celice, ki pa na koncu privedejo do translokacije veziklov z GLUT4 transporterjev na površino celice. Število teh transporterjev za glukozo se na površini celične membrane poveča in glukoza lahko prehaja v celico, posledično pa pade raven glukoze v krvi. Razgradnja inzulina poteka v jetrih in ledvicah. Okvare na katerikoli stopnji poti inzulina se odražajo v diabetesu ali drugih boleznih.

== Rok Štemberger: Protein GABAA (gama aminomaslena kislina A) - zgradba, vloga in zanimivosti ==

V svoji seminarski nalogi sem raziskoval vlogo, pomen in zanimivosti proteina GABAA (gama-aminomaslena kislina A). To je receptor, ki se nahaja predvsem v centralnem živčnem sistemu in je zadolžen zato, da opravlja funkcijo inhibitorja. Lociran je na površini nevrotičnih sinaps in prekinja elektrokemični signal, tako da omogoči prehod kloridnih ionov znotraj celice. To se zgodi takrat ko se ustrezen ligand Gama veže na aktivno mesto tega receptorja. Konformacija podenot se spremeni in to omogoči aktivacijo receptorja. Znanstveniki so ugotovili, da obstaja več vrst GABAA receptorjev, kar pa je odvisno od sestave podenot. Najbolj pogoste podenote so alfa beta in gama v razmerju 2:2:1. V primeru da do prekinitve ne pride se lahko pojavijo epileptični napadi, psihiatrične motnje itd. Stres lahko v dobi odraščanja močno vpliva na GABAA receptorje in jih tudi permanentno strukturno spremeni, kar pa lahko kasneje v našem življenju vpliva predvsem na naš spanec in njegovo kvaliteto. Absint je bila v preteklosti prepovedana pijača, saj je povzročala razna obolenja zaradi substance imenovane tujon. Le ta se je vezala na GABAA receptorje in tako onemogočila njegovo delovanje, zato ker je preprečevala prehod kloridnih ionov v membrano. Sedaj potekajo raziskave teh receptorjev, saj je ključnega pomena čim boljša ozdravitev bolezni, ki nastanejo zaradi nepravilnega delovanja GABAA receptorja.

== Veronika Jarc: Perforin ==

Perforin je protein, ki nastane iz citotoksičnih limfocitov T. S pomočjo grancimov napade tarčno celico in jo uniči. Rečemo lahko, da je pomemben člen pri imunskem odzivu in sodeluje s NK celicami. Sestavljen je iz 555 aminokislin, njegova molekulska masa pa je 62-67 kD. Sestavljen je iz dveh pomembnih domen, domene MACPF in domene C2. Za domeno C2 je značilno, da ima afiniteto do Ca2+ ionov. Saj se na lipidni dvosloj veže le ob prisotnosti kalcija. Drugače obstajata dva različna tipa C2 domene, ki sta bila izolirana iz različnih organizmov. Lahko rečemo, da sta oba tipa zelo podobna v tem, da sta pri tipu 1 N-konec in C-konec obrnjena na vrh domene, kar je nasprotno kot pri tipu 2. Poznamo tri MACPF domene: Plu-MACPF, C8a MACPF in lipokalin C8g. Vse te domene primerjamo z skupino proteinov citolizinov in ugotovimo nekaj podobnosti in nekaj razlik. Na splošno, pa lahko rečemo, da je evolucija poskrbela tako, da so sta si domena MACPF in citolizini raszlični le v nekaj aminokislinah. Poznamo tri mehanizme kako perforin preide v tarčno celico in pri tem pomaga gramcimom B uničit to celico. Prvi mehanizem je prehajanje preko perforinske pore in sicer s pomočjo veziklov preide v celico. Naslednji mehanizem je endosomolitični model, pri katerem je pomemben kompleks s pomočjo katerega prehaja v celico. Kot zadnji mehanizem pa je model prehodne perforinske pore, ki pove, da perforin tvori kanalčke s pomočjo katerih grancimi B preidejo direktno v celico. Grancimi B so serinske proteaze, ki se sintetizirajo v citotoksičnih limfocitih T in NK celicah.

BIO2 Seminar 2011

2011-10-09T14:22:34Z

VeronikaJarc: /* Seznam seminarjev - datumi še niso dokončni, listka na katerem imam napisano kdaj kdo ne more nimam doma in bom to popravil v ponedeljek */

= Biokemijski seminar =

Seminarje vodi doc. dr. Gregor Gunčar in so na urniku vsako sredo in petek po eni uri predavanj iz Biokemije.

Ocena seminarjev predstavlja 30% končne ocene in vsebuje vse točke, ki jih študent/ka lahko zbere pri seminarju in ostalih dejavnostih, ki niso del pisnega izpita.

== Seznam seminarjev - datumi še niso dokončni, listka na katerem imam napisano kdaj kdo ne more nimam doma in bom to popravil v ponedeljek==
Vpišite svoj izbrani naslov!!!
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Ime in priimek'''
| align="center" style="background:#f0f0f0;"|'''Naslov seminarja'''
| align="center" style="background:#f0f0f0;"|'''Rok za oddajo'''
| align="center" style="background:#f0f0f0;"|'''Rok za recenzijo'''
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''
| align="center" style="background:#f0f0f0;"|'''Recenzent1'''
| align="center" style="background:#f0f0f0;"|'''Recenzent2'''
|-
| Ula Štok||Tipping the mind||17.10.11||19.10.11||21.10.11||||
|-
| Maša Mirković||Naslov seminarja||17.10.11||19.10.11||21.10.11||||
|-
| Sara Draščič||On the spur of a whim||17.10.11||19.10.11||21.10.11||||
|-
| Katra Koman||Naslov seminarja||18.10.11||23.10.11||26.10.11||||
|-
| Iza Ogris||Naslov seminarja||21.10.11||25.10.11||28.10.11||||
|-
| Ana Remžgar||Naslov seminarja||21.10.11||25.10.11||28.10.11||||
|-
| Urška Rauter||Naslov seminarja||21.10.11||25.10.11||28.10.11||||
|-
| Taja Karner||Throb||21.10.11||26.10.11||02.11.11||||
|-
| Rok Štemberger||Naslov seminarja||21.10.11||28.10.11||04.11.11||||
|-
| Maša Mohar||Naslov seminarja||21.10.11||28.10.11||04.11.11||||
|-
| Veronika Jarc||Our hollow architecture||21.10.11||28.10.11||04.11.11||||
|-
| Mirjam Kmetič||Naslov seminarja||26.10.11||02.11.11||09.11.11||||
|-
| Janez Meden||Naslov seminarja||28.10.11||04.11.11||11.11.11||||
|-
| Tjaša Flis||Naslov seminarja||28.10.11||04.11.11||11.11.11||||
|-
| Sandi Botonjić||Naslov seminarja||28.10.11||04.11.11||11.11.11||||
|-
| Kaja Javoršek||Naslov seminarja||02.11.11||09.11.11||16.11.11||||
|-
| Rok Vene||Naslov seminarja||04.11.11||11.11.11||18.11.11||||
|-
| Ines Šterbal||Naslov seminarja||04.11.11||11.11.11||18.11.11||||
|-
| Andreja Bratovš||Naslov seminarja||04.11.11||11.11.11||18.11.11||||
|-
| Matevž Ambrožič||Naslov seminarja||09.11.11||16.11.11||23.11.11||||
|-
| Matevž Merljak||Naslov seminarja||11.11.11||18.11.11||25.11.11||||
|-
| Mitja Crček||Naslov seminarja||11.11.11||18.11.11||25.11.11||||
|-
| Dominik Kert||Naslov seminarja||11.11.11||18.11.11||25.11.11||||
|-
| Petra Malavašič||Going unnoticed||16.11.11||23.11.11||30.11.11||||
|-
| Eva Knapič||Life's first breath||18.11.11||25.11.11||02.12.11||||
|-
| Marko Radojković||Naslov seminarja||18.11.11||25.11.11||02.12.11||||
|-
| Tjaša Goričan||Naslov seminarja||18.11.11||25.11.11||02.12.11||||
|-
| Tina Gregorič||Naslov seminarja||23.11.11||30.11.11||07.12.11||||
|-
| Tamara Marić||Naslov seminarja||25.11.11||02.12.11||09.12.11||||
|-
| Ana Dolinar||The juice of life||25.11.11||02.12.11||09.12.11||||
|-
| Maja Remškar||Naslov seminarja||25.11.11||02.12.11||09.12.11||||
|-
| Matja Zalar||Naslov seminarja||30.11.11||07.12.11||14.12.11||||
|-
| Urška Navodnik||Naslov seminarja||02.12.11||09.12.11||16.12.11||||
|-
| Jernej Mustar||Silent pain||02.12.11||09.12.11||16.12.11||||
|-
| Ines Kerin||Naslov seminarja||02.12.11||09.12.11||16.12.11||||
|-
| Alja Zottel||Sleepless nights||07.12.11||14.12.11||21.12.11||||
|-
| Alenka Mikuž||Molecular chastity||09.12.11||16.12.11||23.12.11||||
|-
| Maja Grdadolnik||Ear of Stone||09.12.11||16.12.11||23.12.11||||
|-
| Jana Verbančič||Hidden power||09.12.11||16.12.11||23.12.11||||
|-
| Petra Gorečan||Naslov seminarja||14.12.11||21.12.11||04.01.12||||
|-
| Karmen Hrovat||Naslov seminarja||16.12.11||23.12.11||06.01.12||||
|-
| Andrej Vrankar||The things we forget||16.12.11||23.12.11||06.01.12||||
|-
| Teja Banič||Cool news||16.12.11||23.12.11||06.01.12||||
|-
| Špela Pohleven||Naslov seminarja||21.12.11||04.01.12||11.01.12||||
|-
| Sabina Mavretič ||Naslov seminarja||23.12.11||06.01.12||13.01.12||||
|-
| Karmen Belšak ||Another dark horse||23.12.11||06.01.12||13.01.12||||
|-
| Ime in priimek ||Naslov seminarja||23.12.11||06.01.12||13.01.12||||
|-
| Ime in priimek ||Naslov seminarja||04.01.12||11.01.12||18.01.12||||
|-
| Ime in priimek ||Naslov seminarja||06.01.12||13.01.12||20.01.12||||
|-
| Ime in priimek ||Naslov seminarja||06.01.12||13.01.12||20.01.12||||
|-
| Ime in priimek ||Naslov seminarja||06.01.12||13.01.12||20.01.12||||
|}

== Gradivo za seminarje ==
Gradivo za predavanja in seminarje najdete na http://bio.ijs.si/~zajec/bio2/
username: bio2
password: samozame

==Naloga==
'''Vaša naloga za seminar je: '''
Samostojno pripraviti seminar o enem od proteinov opisanih v [http://web.expasy.org/spotlight/back_issues/2011/ ProteinSpotlight] Poiskati morate vsaj še tri znanstvene članke, ki se nanašajo na opisano temo in jih uporabiti kot podlago za seminarsko nalogo!
V seminarsko nalogo mora biti vključeno:
* sekvenca proteina in SwissProt oznaka proteina
* slika strukture proteina (če je le-ta znana), ki jo naredite sami s programom Pymol. Če struktura še ni znana, vključite sliko proteina, ki je vašemu najbolj podoben po sekvenci in katerega struktura je znana
* poiskati morate, na katerem kromosomu se v človeškem genu nahaja ta protein in narisati shematsko sliko gena (eksonov in intronov) tega proteina. Če protein ni človeškega izvora, poiščite protein, ki je vašemu najbolj podoben in vse navedeno opišite za ta protein.

Za pripravo seminarja velja naslednje: 
* [[BIO2 Povzetki seminarjev 2011|Povzetek seminarja]] opišete na wikiju v približno 200 besedah, besedilo naj vsebuje sliko strukture proteina, ki jo sami narišete s programom PyMol - najkasneje do dne ko morate oddati seminar recenzentom.
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.
* Seminar pripravite v obliki seminarske naloge na ~5-9 straneh A4 (pisava 12, enojni razmak, 2,5 cm robovi; važno je, da je obseg od 2700 do 3000 besed), vsebovati mora najmanj tri slike. Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko.
* Natisnjen seminar oddajte dva tedna pred predstavitvijo vsakemu od recenzentov (docentu ga pošljite po e-pošti v formatu .doc ali .docx).
* Recenzenti do dneva določenega v tabeli določijo popravke in podajo oceno pisnega dela.
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 20-30 minut. Recenzenti morajo biti na predstavitvi prisotni.
* Predstavitvi sledi razprava. Recenzenti podajo oceno predstavitve in postavijo najmanj dve vprašanji.
* Na dan predstavitve morate docentu oddati končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu.
* Seminarska naloga in povzetek morajo biti v slovenskem jeziku!

==Ocenjevanje seminarjev==
Recenzenti ocenijo seminar tako, da izpolnijo [[https://spreadsheets.google.com/viewform?hl=en&formkey=dE1aOFU1aE1iMlBrNEJzLTRGeTdWZXc6MQ#gid=0 recenzentsko poročilo]] na spletu.

== Mnenje o predstavitvi ==
Vsak posameznik '''mora''' oceniti seminar, tako da odda svoje [https://spreadsheets.google.com/viewform?hl=en&formkey=dDlsbDlnclNrc3dIS2otRFdxUEFTNnc6MQ#gid=0 mnenje] najkasneje v treh dneh po predstavitvi. Kdor na seminarju ni bil prisoten, mnenja '''ne sme''' oddati.

==Urejanje spletnih strani na wikiju==
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'.''

==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.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. 
'''Citiranje knjig:''' 
Priimek, I. ''Naslov''. Kraj: Založba, letnica. 
Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN. 

Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005. 
Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4. 
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:''' 
Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani. 
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: 
Priimek, I. (letnica, številka). Naslov. Naslov revije, strani. 
Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.

Revija Science uporablja skrajšani zapis: 
C. Lartigue ''et al''. Science 317, 632 (2007) 

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:''' 
Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov 
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 
Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.

BIO1 Povzetki seminarjev 2011

2011-03-13T21:21:49Z

VeronikaJarc: /* Veronika Jarc: Hepatitis C */

== Veronika Jarc: Hepatitis C ==
Hepatitis C(HCV) je nalezljiva bolezen, ki napade ljudi, šimpanze ter nekatere majhne modelne živali. HCV spada med RNA viruse z ovojnico.Razvrščen pa je v rod hepacivirus ter družino flaviviridae. Sestavljen je iz 6 genotipov (1-6), ki se razlikujejo v nukleotidni sekvenci od 30-35%, sedmega pa so odkrili leta 2008 (Gottwein et al., 2008). HCV vsebuje pozitiven trak gena (9,6 kb), ki je sestavljen iz 5´-NCR( non-coding region), 3´- NCR in IRES( internal ribosome entry side). IRES vsebuje odprto bralno ogrodje, ki šifrira strukturne in ne strukturne proteine. Med strukturne proteine spadajo proteinsko jedro, virusna RNA ter dva glikoproteina E1 in E2. Sestavni deli ne strukturnih proteinov pa so hidrofoben protein p7, NS2-3 proteaza, NS3 serin proteaza, NS4A polipeptid, NS4B protein, NS5A protein in NS5B RNA odvisna RNA polimeraza (RdRp).
S pomočjo različnih odkritij, kot so HCVpp(sestavljen iz lipidne ovojnice z E1-E2 proteini, na retrovirusni nukleokapsidi), izoliranje kloniranega gena 2a ter s pomočjo tega gena HCVcc( cell-culture produced HCV), so znanstveniki začeli preučevati življenski cikel in celično strukturo hepatitisa C. To so dosegli z preučevanjem različnih eksperimentalnih modelov kot so imunski odzivi, NK celice in dendritske celice.
Poznamo tudi proteine, ki jih HCv sreča v hepatocitski celici in ti so in tegrin RGE/RGD, LDL receptor, HDL receptor, klaudin okludin in tetraspanin CD81.

== Matja Zalar: Protein p53 ==
Protein p53, včasih imenovan tudi varuh genoma, kodira gen TP53 na sedemnajstem kromosomu. Je eden izmed tako imenovanih tumor-supresorskih proteinov, ki, kot to sporoča že samo ime, zavirajo nastanek in rast tumorjev. Na področju razumevanja delovanja, vloge in strukture proteina p53 in njegovih mutantov se izvaja veliko raziskav. Trenutno je p53 najbolj raziskan tumor-supresorski protein, še zdaleč pa ni edini. Gre za protein, ki se kopiči v jedru in z vezavo na DNA v obliki teramera nadzoruje in regulira procese kot so apoptoza, zaustavitev celičnega cikla in popravljanje poškodovane DNA. Za raziskovalce je še posebno zanimiv zaradi dejstva, da v nemutirani obliki zavira nastanek in rast tumojev, njegove GOF mutirane oblike pa pripomorejo k nenadzorovani delitvi celic in nastanku rakastih tkiv. Veliko raziskav se ukvarjaja z iskanjem snovi, ki bi obnovile osnovno obliko p53, oziroma uničile mutantske oblike p53 v rakastih celicah ter s tem uničile tumor. To pa bi lahko bistveno izboljšalo tehnike zdravljenja rakavih obolenj in odziv človeškega organizma na ta zdravljenja. Odkrili so že kar nekaj takšnih snovi (RITA, PRIMA, nutlin3), ki pa jih še vedno testirajo in še niso v redni uporabi pri zdravljenju rakavih obolenj.

== Andrej Vrankar: Androgena alopecija ==
Na podlagi raziskav, ki so jih znanstveniki izvedli na celičnih vzorcih posameznikov z androgeno alopecijo, so ugotovili, da je bila domneva, da je za nastanek AGA kriv propad matičnih celic v lasnem mešičku oziroma, propad samega lasnega mešička napačna. Raziskave so pokazale ravno nasprotno in sicer, da se matične celice tudi v plešastem lasišču posameznika z AGA ohranjajo in da lasni mešički ne propadejo, vendar se le zelo skrčijo. So pa ugotovili, da se število celic imenovanih predniške celice v plešastem lasišču močno zmanjša, kar je eden od glavnih vzrokov za nastanek AGA, saj so prav predniške celice tiste, ki so zaslužene za rast las. Čeprav se dednost smatra kot glavni vzrok za nastanek AGA, pa tudi hormoni igrajo pomembno vlogo. Pri moških je to moški hormon testosteron, ki se s pomočjo encima 5-α-reduktaze v lasno mešičnih celicah pretvarja v svojo bolj aktivno obliko dihidrotestosteron (DHT). Ta se se nato s posebno vezjo veže na androgene receptorje v lasnih mešičkih, kar sproži posebne procese, ki skrajšajo anageno fazo celičnega cikla. Zaradi skrajšanja te faze las prej prestopi v telogeno fazo in izpade. Kako občutljivi so lasni mešički na androgene pa je seveda gensko pogojeno.

== Sandi Botonjić: Tioredoksinu podoben protein (TXNL2) ščiti kancerogene celice pred oksidativnim stresom ==
Kisikovi radikali, ki povzročajo oksidativni stres lahko v skrajnem primeru poškodujejo DNA in tako povzročijo nenadzorovano delitev celic, kar pomeni nastanek raka v organizmu. Hkrati pa je raven kisikovih radikalov v rakastih celicah višja, kot v zdravih, in sicer zaradi onkogenih stimulacij, povečane presnovne aktivnosti ter okvare mitohondrijev. Toda rakave celice imajo, kot protiutež tudi močan antioksidantni mehanizem s katerim zavirajo programirano celično smrt.

Raziskovalci so tekom analiziranja večih tkiv, ki so obolela z različnimi vrstami raka ugotovili, da je pri vseh povečana raven [http://www.thesgc.org/structures/structure_images/2WZ9_400x400.png tioredoksinu podobnega proteina - TXNL2]. Zatem so izvajali poskuse na miših tako, da so jim vbrizgali kancerogene eritrocite in ko so se pojavili simptomi tumorja – so jim vbrizgali še protein TXNL2. Ugotovili so, da protein TXNL2 zavira rast rakavih celic. Proučevali so tudi vpliv proteina TXNL2 v mišjih zarodkih. Prišli so do zaključka, da protein TXNL2 regulira raven kisikovih radikalov tako pri živečih organizmih, kot med embriogenezo.

Znanstveniki so prepričani, da je protein TXNL2 potencialna tarča bioloških zdravil v prihodnosti. Namreč monoklonska protitelesa (med katere spade tudi TXNL2) za zdravljenje raka z vezavo na receptorje za rastne dejavnike blokirajo celično rast in diferenciacijo ter tako zaustavijo rast tumorja. Zaustavijo lahko tudi rast tumorskega ožilja in s tem posredno onemogočajo rast tumorjev in metastaziranje. Med mehanizme delovanja monoklonskih protiteles, spada tudi ciljanje drugih efektorskih molekul na mesta delovanja - kot so npr. kisikovi radikali. Raziskave so potrdile, da to velja tudi za protein TXNL2.

== Ana Dolinar: Prilagojena ali prilagodljiva imunost? Primer naravnih celic ubijalk ==
Naravne celice ubijalke (NK celice) so vrsta levkocitov. V človeškem telesu so zadolžene za uničevanje patogenih organizmov s pomočjo za celice strupenih snovi. Na površini imajo pet skupin receptorjev: aktivacijske, inhibitorne, kemotaksične in citokine ter adhezijske receptorje.

Njihova aktivacija je odvisna od vezave ligandov na površinske receptorje NK celice. Če je vezanih več inhibitornih ligandov kot aktivacijskih, potem se NK celica ne aktivira, ker inhibitorni ligandi zavrejo delovanje NK celice. V primeru, da se veže več aktivacijskih kot inhibitornih ligandov ali pa se slednji sploh ne vežejo, se NK celica aktivira ([http://www.georg-speyer-haus.de/agkoch/research/subframe_en.htm aktivirana NK celica-rumeno, tarčna celica-rdeče]). Vezava kemotaksičnih ligandov vpliva na gibanje molekule zaradi kemičnih signalov, vezava citokinov spodbuja rast celic ali sintezo snovi, ki jih potrebuje imunski sistem, vezava adhezijskih ligandov pa omogoča pritrjanje NK celice na tarčno celico.

Raziskovalci se trudijo, da bi našli optimalno imunoterapijo, pri kateri bi sodelovale NK celice. Te terapije bi bile uporabne predvsem pri rakavih obolenjih, vendar so možnosti tudi pri obolenjih z virusom HIV ali z virusom hepatitisa C. Ta način imunoterapije je mogoč, ker večina tumorskih celic in virusov ne izraža MHC tipa 1, pomembnega inhibitorskega liganda za NK celice. [http://media.wiley.com/CurrentProtocols/IM/ima01n/ima01n-fig-0004-1-full.gif Zgradba MHC-1 molekule, prikazana z Ribbonovim diagramom in vezanim peptidom (A) ter površinska struktura molekule z vezanim peptidom (C). Slika B prikazuje molekulo MHC-2 z vezanim peptidom.]

== Urška Rauter: Razvojne vloge Srf, kortikalnega citoskeleta in celične oblike pri orientaciji epidermalnega vretena ==
Mehanizem nastajanja polariziranega epidermalnega sloja, ki s procesoma stratifikacije in diferenciacije tvori kožo, regulira več različnih med seboj v komplekse povezanih bioloških molekul. Trije najbolj osnovni procesi so delovanje proteinov aktina, orientacija vretena in sistem celične signalizacije. Znanstveniki pa so v obširni raziskavi potrdili tudi pomembno vlogo t. i. Srf proteina (serum response factor protein), transkripcijskega dejavnika, katerega pomembna vloga je regulacija celične diferenciacije.

Srf je transkripcijski dejavnik, ki se veže na določen, njemu ustrezen receptorski element; Sre (serum response element), to so predvsem geni v zgodnjem razvoju, geni za razvoj nevronov in mišična gena (proteina) aktin in miozin. Ker je njegova primarna funkcija regulacija ekspresije naštetih genov, odločilno vpliva na celično rast in diferenciacijo, prenos med nevroni in razvoj mišic.

Namen raziskave je obširen. Rezultati obetajoči. Dokazali so pomembno vlogo Srf proteina pri marsikaterem mehanizmu/procesu v embrionalnem razvoju. Tako recimo Srf odločilno vpliva na diferenciacijo celic, saj izguba le-tega povzroči kaotično deljenje in diferenciacijo celic med več plastmi epidermisa. Nadalje vpliva tudi na pravilno vzpostavitev polarnosti bazalne lamine in še najbolj ključno na tvorbo aktinsko-miozinskega skeleta, ki je nujen za pravilno mitozo, posledično za obliko in trdnost celice. Orientacija vretena in asimetrično dedovanje sta po zadnjih raziskavah osrednja mehanizma, ki omogočata matičnim celicam samostojno obnovi in diferenciacijo v pravilni smeri. Rezultati kažejo, da lahko takšne signale pošiljamo preko Srf proteina in aktinsko-miozinskega skeleta, za pravilno tvorbo in nadzirano regulacijo orientacije vretena, asimetrične celične delitve in nasploh usodo posamezne celice. Rezultati razkrivajo nove pojasnitve bioloških procesov, ki sodelujejo pri tvorbi morfologije epidermisa.

== Špela Pohleven: Prioni ==

Prioni so patogeni proteini, ki se od svojih nepatogenih, normalnih, v zaporedju aminokislin enakih dvojnikov, razlikujejo v 3D strukturi – imajo večji del β ploskev. Poznamo več vrst prionov, toda običajno govorimo le o proteinu PrP, ki je prisoten pri ljudeh in živalih. Ostali so namreč značilni za glive, ki so tako primerne za razne raziskave.
Za prione je značilno povezovanje v nitaste polimere, ki jih imenjujemo amiloidi. Znanstveniki domnevajo, da je prav njihova urejena struktura tista, zaradi katere so slabo topni v detergentih in odporni na proteaze.
Najbolj nenavadna lastnost prionov pa je njihova zmožnost širjenja brez potrebe po DNA in RNA. V zvezi s tem potekajo številne raziskave, saj prioni povzročajo številne smrtne bolezni, kot so Creutzfeldt-Jakobova bolezen, smrtonosna družinska nespečnost in druge. Z informacijami, ki jih tako pridobivajo, je možnost za odkritje zdravila večja.
Pri eni od nedavnih raziskav so tako ugotovili, da obstajata dve prionski obliki proteina PrP – infektivna in toksična. Za raziskave so uporabili miši z različnim izražanjem gena PRNP za PrP protein. Vse so okužili s prioni praskavca (ena od prionskih bolezni). Vse so dosegle enak prag infektivnosti, toda smrt ni nastopila istočasno. Iz meritev so znanstveniki prišli do zaključka, da morata obstajati dve različni obliki. To pa je le izhodišče za nove raziskave.

== Maša Mohar: Sladkorna bolezen, kot bolezen imunskega sistema ==

Diabetes mellitus je kronična motnja metabolizma beljakovin, lipidov in ogljikovih hidratov. Nastane zaradi zmanjšane funkcije proizvajanja insulina v telesu. Njen vzrok pa je lahko studi zmanjšana sposobnost telesnih celic za pravilno izkoriščanje insulina. Tip 2 je od insulina neodvisen diabetes (NIDDM). Ta tip ima 80-90% vseh pacientov in se pojavi v odraslem obdobju življenja, spodbudijo ga lahko različni mehanizmi, in za nekatere se še ne ve točno kako pride do tega, je pa res da k temu veliko pripomore nezdrav način življenja in seveda dednost. Prav tako se diabetes tipa 2 deli v dve skupini in sicer na debeli tip, ki ga ima približno 80% vse populacije in na ne debeli tip.
Da je T2D bolezen imunskega sistema pa ugotovimo s tem ko vidimo kako se telo odzovena določene mehanizme, ki sprožijo to bolezen. To so oksidativni stres, stres ER( endoplazemski retikel), lipotoksičnost in glukotoksičnost. Prav tako je potrebno poudariti, da ima diabetes tipa 2 svoje metabolne karakteristike in skupaj s temi patogenimi mehanizmi tvori formulo za nastanek bolezni. Seveda lahko pri T2D pride tudi do dolgoročnih komplikacij, kot so makro in mikro- vaskularne bolezni, problemi z ledvicami, očmi in živci. Te pa so glavni dejavniki za povzročitev hujšega bolezenskega stanja in ne nazadnje tudi smrti zaradi diabetesa.

BIO1-seminar 2011

2011-03-12T12:56:04Z

VeronikaJarc: /* Seznam seminarjev */

= Temelji biokemije- seminar =

Seminarje vodi doc. dr. Gregor Gunčar in so na urniku vsak ponedeljek od 10:00 do 11:30.

Ocena seminarjev predstavlja ??% končne ocene in vsebuje vse točke, ki jih študent/ka lahko zbere pri seminarju in ostalih dejavnostih, ki niso del pisnega izpita.

== Seznam seminarjev ==
{| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"
| align="center" style="background:#f0f0f0;"|'''Ime in priimek'''
| align="center" style="background:#f0f0f0;"|'''Slovenski naslov članka'''
| align="center" style="background:#f0f0f0;"|'''Faktor vpliva revije'''
| align="center" style="background:#f0f0f0;"|'''Rok za oddajo'''
| align="center" style="background:#f0f0f0;"|'''Rok za recenzijo'''
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 1'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 2'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 3'''
|-
| BOTONJIĆ SANDI||[http://wiki.fkkt.uni-lj.si/index.php/BIO1_Povzetki_seminarjev#Sandi_Botonji.C4.87:_Tioredoksinu_podoben_protein_.28TXNL2.29_.C5.A1.C4.8Diti_kancerogene_celice_pred_oksidativnim_stresom Tioredoksinu podoben protein (TXNL2) ščiti kancerogene celice pred oksidativnim stresom]
||15.387||28.02.||03.03.||07.03.||RODE URŠKA||KERIN INES||OGRIS IZA
|-
| VRANKAR ANDREJ||Število lasno-mešičnih matičnih celic se v plešastem lasišču moških z androgeno alopecijo ohranja za razliko od števila CD200-rich in CD34-positive lasno-mešičnih predniških celic||||28.02.||03.03.||07.03.||HROVAT KARMEN||BOHNEC IVO||JAVORŠEK KAJA
|-
| ZALAR MATJA||Protein p53||||28.02.||03.03.||07.03.||OGRIS IZA||CRČEK MITJA||ZOTTEL ALJA
|-
| ZOTTEL ALJA||Vloga imunskega sistema pri aterosklerozi||31.434||07.03.||10.03.||14.03.||RADOJKOVIĆ MARKO||KERT DOMINIK||HROVAT KARMEN
|-
| DOLINAR ANA||[http://wiki.fkkt.uni-lj.si/index.php/BIO1_Povzetki_seminarjev#Ana_Dolinar:_Prilagojena_ali_prilagodljiva_imunost.3F_Primer_naravnih_celic_ubijalk Prirojena ali prilagodljiva imunost? Primer naravnih celic ubijalk]||28||07.03.||10.03.||14.03.||RAUTER URŠKA||MOHAR MAŠA||VERBANČIČ JANA
|-
| RAUTER URŠKA||Razvojna vloga Srf, kortikalnega citoskeleta in celične oblike v orientaciji epidermalnega vretena||19.527||07.03.||10.03.||14.03.||MUSTAR JERNEJ||JAVORŠEK KAJA||MOHAR MAŠA
|-
| MOHAR MAŠA||Sladkorna bolezen tipa 2 kot bolezen imunskega sistema||30,006||14.03.||17.03.||21.03.||VENE ROK||RAUTER URŠKA||GORIČAN TJAŠA
|-
| POHLEVEN ŠPELA||Prioni||34||14.03.||17.03.||21.03.||KEPIC LEA||RADOJKOVIĆ MARKO||DOLINAR ANA
|-
| KEPIC LEA||Agonisti adrenoreceptorjev β2||34.48||14.03.||17.03.||21.03.||VRANKAR ANDREJ||BRATOVŠ ANDREJA||MUSTAR JERNEJ
|-
| KMETIČ MIRJAM||Celična regulacija metabolizma železa||5,371||14.03.||17.03.||21.03.||MARIĆ TAMARA||REMŠKAR MAJA||KOMAN KATRA
|-
| JARC VERONIKA||Eksperimentalni modeli za študijo imunobiologije hepatitisa C||3.26||14.03.||21.03.||28.03.||REMŠKAR MAJA||MUSTAR JERNEJ||KEPIC LEA
|-
| KOMAN KATRA||naslov||||14.03.||21.03.||28.03.||ČUPOVIĆ VANA||KARNER TAJA||KMETIČ MIRJAM
|-
| OGRIS IZA||Zakaj imajo možgani glikogen?||||14.03.||21.03.||28.03.||KNAPIČ EVA||BRGLEZ ŽIVA||VRANKAR ANDREJ
|-
| KERIN INES||Kanabinoidi za zdravljenje shizofrenije? Uravnotežena nevrokemična sestava za škodljive in terapevtske učinke uživanja konoplje||4.458||14.03.||21.03.||28.03.||ŠTOK ULA||ŠTEMBERGER ROK||KERT DOMINIK
|-
| VERBANČIČ JANA||Apoptozi podobna smrt v bakterijah, ki ji povzroča HAMLET, človeški mlečni lipidno-proteinski kompleks||4.351||21.03.||28.03.||04.04.||KARNER TAJA||ZOTTEL ALJA||KNAPIČ EVA
|-
| KNAPIČ EVA||Kako virusi vodijo delovanje celice.||14.101||21.03.||28.03.||04.04.||ZALAR MATJA||POHLEVEN ŠPELA||LORBEK SARA
|-
| REMŽGAR ANA||naslov||||21.03.||28.03.||04.04.||BOTONJIĆ SANDI||LORBEK SARA||ČUPOVIĆ VANA
|-
| GRDADOLNIK MAJA||naslov||||21.03.||28.03.||04.04.||MOHAR MAŠA||REMŽGAR ANA||FRANKO NIK
|-
| JAVORŠEK KAJA||Potencial matične celice pri Parkinsonovi bolezni in molekularni faktorji za tvorbo dopaminergičnih nevronov||4.139||28.03.||04.04.||11.04.||GEC KARMEN||MARIĆ TAMARA||RADOJKOVIĆ MARKO
|-
| BRATOVŠ ANDREJA||Vloga GPCR v patologiji Alzheimerjeve bolezni||26||28.03.||04.04.||11.04.||ZOTTEL ALJA||ČUPOVIĆ VANA||GRDADOLNIK MAJA
|-
| CRČEK MITJA||naslov||||28.03.||04.04.||11.04.||BOHNEC IVO||KMETIČ MIRJAM||BRATOVŠ ANDREJA
|-
| MARIĆ TAMARA||ciljanje kemokinskih receptorjev ob alergijskih obolenjih||5.155||28.03.||04.04.||11.04.||NAVODNIK URŠKA||GEC KARMEN||REMŠKAR MAJA
|-
| ŠTEMBERGER ROK||naslov||||04.04.||11.04.||18.04.||JAVORŠEK KAJA||VRANKAR ANDREJ||BOTONJIĆ SANDI
|-
| LORBEK SARA||naslov||||04.04.||11.04.||18.04.||POHLEVEN ŠPELA||KNAPIČ EVA||VENE ROK
|-
| REMŠKAR MAJA||naslov||||04.04.||11.04.||18.04.||KERIN INES||POVŠE KATJA||CRČEK MITJA
|-
| ČUPOVIĆ VANA||naslov||||04.04.||11.04.||18.04.||REMŽGAR ANA||VERBANČIČ JANA||RODE URŠKA
|-
| RODE URŠKA||naslov||||24.04.||03.05.||09.05.||GRDADOLNIK MAJA||FRANKO NIK||MARIĆ TAMARA
|-
| RADOJKOVIĆ MARKO||naslov||||24.04.||03.05.||09.05.||FRANKO NIK||VENE ROK||POVŠE KATJA
|-
| VENE ROK||naslov||||24.04.||03.05.||09.05.||VERBANČIČ JANA||NAVODNIK URŠKA||ZALAR MATJA
|-
| FRANKO NIK||naslov||||24.04.||03.05.||09.05.||ŠTEMBERGER ROK||HROVAT KARMEN||BOHNEC IVO
|-
| HROVAT KARMEN||naslov||||04.05.||09.05.||16.05.||KERT DOMINIK||JARC VERONIKA||KARNER TAJA
|-
| AMBROŽIČ MATEVŽ||naslov||||04.05.||09.05.||16.05.||LORBEK SARA||KEPIC LEA||REMŽGAR ANA
|-
| NAVODNIK URŠKA||naslov||||04.05.||09.05.||16.05.||AMBROŽIČ MATEVŽ||ŠTOK ULA||ŠTEMBERGER ROK
|-
| BRGLEZ ŽIVA||naslov||||09.05.||16.05.||23.05.||DOLINAR ANA||BOTONJIĆ SANDI||JARC VERONIKA
|-
| KARNER TAJA||naslov||||09.05.||16.05.||23.05.||KOMAN KATRA||OGRIS IZA||NAVODNIK URŠKA
|-
| KERT DOMINIK||naslov||||09.05.||16.05.||23.05.||GORIČAN TJAŠA||GRDADOLNIK MAJA||RAUTER URŠKA
|-
| MUSTAR JERNEJ||naslov||||16.05.||23.05.||30.05.||JARC VERONIKA||AMBROŽIČ MATEVŽ||BRGLEZ ŽIVA
|-
| GEC KARMEN||naslov||||16.05.||23.05.||30.05.||POVŠE KATJA||ZALAR MATJA||AMBROŽIČ MATEVŽ
|-
| GORIČAN TJAŠA||naslov||||16.05.||23.05.||30.05.||KMETIČ MIRJAM||RODE URŠKA||POHLEVEN ŠPELA
|-
| BOHNEC IVO||naslov||||23.05.||30.05.||06.06.||CRČEK MITJA||GORIČAN TJAŠA||ŠTOK ULA
|-
| ŠTOK ULA||naslov||||23.05.||30.05.||06.06.||BRGLEZ ŽIVA||DOLINAR ANA||KERIN INES
|-
| nihce ||naslov||||23.05.||30.05.||06.06.||BRATOVŠ ANDREJA||KOMAN KATRA||GEC KARMEN
|}

==Naloga==
* samostojno pripraviti seminar, katerega osnova je znanstveni članek s področja biokemije, ki ga po želji izberete v reviji s področja biokemije, ki ima faktor vpliva večji kot 3 in je bil objavljen v letu 2011. Poleg tega članka morate za seminar uporabiti še najmanj pet drugih virov! http://www.cobiss.si/scripts/cobiss?command=CONNECT&base=JCR
* osnovni članek in naslov pošljete meni, najkasneje pet dni pred rokom za oddajo (rok-5), da ocenim, če je primeren za predstavitev. Naslov vpišete v tabelo, takoj ko ste si ga izbrali!
* [[BIO1 Povzetki seminarjev|Povzetek seminarja]] opišete na wikiju v približno 200 besedah - najkasneje do dne ko morate oddati seminar recenzentom. Povezave do slik so dobrodošle, niso pa nujne.
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.
* Seminar pripravite v obliki seminarske naloge (pisava 12, enojni razmak, 2,5 cm robovi; važno je, da je obseg od 1800 do 2000 besed), vsebovati mora najmanj eno sliko. Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko.
* Natisnjen seminar oddajte do roka vsakemu od recenzentov (docentu ga pošljite po e-pošti v formatu .doc ali .docx).
* Recenzenti do dneva določenega v tabeli določijo popravke in podajo oceno pisnega dela, v predpisanem formatu elektronskega obrazca na internetu.
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 15 minut. Recenzenti morajo biti na predstavitvi prisotni.
* Predstavitvi sledi razprava- 5 minut. Recenzenti podajo oceno predstavitve in postavijo vsak vsaj dve vprašanji.
* Na dan predstavitve morate docentu oddati končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu.
* Seminarska naloga in povzetek na wikiju morajo biti v slovenskem jeziku!

==Ocenjevanje seminarjev==
Recenzenti ocenijo seminar tako, da izpolnijo [[https://spreadsheets.google.com/viewform?formkey=dFM2SktfM3Q4VU1wNUQzdU45OTlWVXc6MA recenzentsko poročilo]] na spletu.

== Mnenje o predstavitvi ==
Vsak posameznik '''mora''' oceniti seminar, tako da odda svoje [https://spreadsheets.google.com/viewform?formkey=dFd3TGhLV3ZSa2xsLVlmMVVUaEFURWc6MA mnenje] najkasneje v treh dneh po predstavitvi. Kdor na seminarju ni bil prisoten, mnenja '''ne sme''' oddati.

==Urejanje spletnih strani na wikiju==
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'.''

==Faktor vpliva==
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.

==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. 
'''Citiranje knjig:''' 
Priimek, I. ''Naslov''. Kraj: Založba, letnica. 
Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN. 

Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005. 
Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4. 
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:''' 
Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani. 
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: 
Priimek, I. (letnica, številka). Naslov. Naslov revije, strani. 
Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.

Revija Science uporablja skrajšani zapis: 
C. Lartigue ''et al''. Science 317, 632 (2007) 

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:''' 
Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov 
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 
Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.

BIO1-seminar 2011

2011-03-11T19:32:12Z

VeronikaJarc: /* Seznam seminarjev */

= Temelji biokemije- seminar =

Seminarje vodi doc. dr. Gregor Gunčar in so na urniku vsak ponedeljek od 10:00 do 11:30.

Ocena seminarjev predstavlja ??% končne ocene in vsebuje vse točke, ki jih študent/ka lahko zbere pri seminarju in ostalih dejavnostih, ki niso del pisnega izpita.

== Seznam seminarjev ==
{| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"
| align="center" style="background:#f0f0f0;"|'''Ime in priimek'''
| align="center" style="background:#f0f0f0;"|'''Slovenski naslov članka'''
| align="center" style="background:#f0f0f0;"|'''Faktor vpliva revije'''
| align="center" style="background:#f0f0f0;"|'''Rok za oddajo'''
| align="center" style="background:#f0f0f0;"|'''Rok za recenzijo'''
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 1'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 2'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 3'''
|-
| BOTONJIĆ SANDI||[http://wiki.fkkt.uni-lj.si/index.php/BIO1_Povzetki_seminarjev#Sandi_Botonji.C4.87:_Tioredoksinu_podoben_protein_.28TXNL2.29_.C5.A1.C4.8Diti_kancerogene_celice_pred_oksidativnim_stresom Tioredoksinu podoben protein (TXNL2) ščiti kancerogene celice pred oksidativnim stresom]
||15.387||28.02.||03.03.||07.03.||RODE URŠKA||KERIN INES||OGRIS IZA
|-
| VRANKAR ANDREJ||Število lasno-mešičnih matičnih celic se v plešastem lasišču moških z androgeno alopecijo ohranja za razliko od števila CD200-rich in CD34-positive lasno-mešičnih predniških celic||||28.02.||03.03.||07.03.||HROVAT KARMEN||BOHNEC IVO||JAVORŠEK KAJA
|-
| ZALAR MATJA||Protein p53||||28.02.||03.03.||07.03.||OGRIS IZA||CRČEK MITJA||ZOTTEL ALJA
|-
| ZOTTEL ALJA||Vloga imunskega sistema pri aterosklerozi||31.434||07.03.||10.03.||14.03.||RADOJKOVIĆ MARKO||KERT DOMINIK||HROVAT KARMEN
|-
| DOLINAR ANA||[http://wiki.fkkt.uni-lj.si/index.php/BIO1_Povzetki_seminarjev#Ana_Dolinar:_Prilagojena_ali_prilagodljiva_imunost.3F_Primer_naravnih_celic_ubijalk Prirojena ali prilagodljiva imunost? Primer naravnih celic ubijalk]||28||07.03.||10.03.||14.03.||RAUTER URŠKA||MOHAR MAŠA||VERBANČIČ JANA
|-
| RAUTER URŠKA||Razvojna vloga Srf, kortikalnega citoskeleta in celične oblike v orientaciji epidermalnega vretena||19.527||07.03.||10.03.||14.03.||MUSTAR JERNEJ||JAVORŠEK KAJA||MOHAR MAŠA
|-
| MOHAR MAŠA||Sladkorna bolezen tipa 2 kot bolezen imunskega sistema||30,006||14.03.||17.03.||21.03.||VENE ROK||RAUTER URŠKA||GORIČAN TJAŠA
|-
| POHLEVEN ŠPELA||Prioni||34||14.03.||17.03.||21.03.||KEPIC LEA||RADOJKOVIĆ MARKO||DOLINAR ANA
|-
| KEPIC LEA||Agonisti adrenoreceptorjev β2||34.48||14.03.||17.03.||21.03.||VRANKAR ANDREJ||BRATOVŠ ANDREJA||MUSTAR JERNEJ
|-
| KMETIČ MIRJAM||Celična regulacija metabolizma železa||5,371||14.03.||17.03.||21.03.||MARIĆ TAMARA||REMŠKAR MAJA||KOMAN KATRA
|-
| JARC VERONIKA||Eksperimentalne metode za študijo imunobiologije hepatitisa C||3.26||14.03.||21.03.||28.03.||REMŠKAR MAJA||MUSTAR JERNEJ||KEPIC LEA
|-
| KOMAN KATRA||naslov||||14.03.||21.03.||28.03.||ČUPOVIĆ VANA||KARNER TAJA||KMETIČ MIRJAM
|-
| OGRIS IZA||Zakaj imajo možgani glikogen?||||14.03.||21.03.||28.03.||KNAPIČ EVA||BRGLEZ ŽIVA||VRANKAR ANDREJ
|-
| KERIN INES||naslov||||14.03.||21.03.||28.03.||ŠTOK ULA||ŠTEMBERGER ROK||KERT DOMINIK
|-
| VERBANČIČ JANA||naslov||||21.03.||28.03.||04.04.||KARNER TAJA||ZOTTEL ALJA||KNAPIČ EVA
|-
| KNAPIČ EVA||Kako virusi vodijo delovanje celice.||14.101||21.03.||28.03.||04.04.||ZALAR MATJA||POHLEVEN ŠPELA||LORBEK SARA
|-
| REMŽGAR ANA||naslov||||21.03.||28.03.||04.04.||BOTONJIĆ SANDI||LORBEK SARA||ČUPOVIĆ VANA
|-
| GRDADOLNIK MAJA||naslov||||21.03.||28.03.||04.04.||MOHAR MAŠA||REMŽGAR ANA||FRANKO NIK
|-
| JAVORŠEK KAJA||Potencial matične celice pri Parkinsonovi bolezni in molekularni faktorji za tvorbo dopaminergičnih nevronov||4.139||28.03.||04.04.||11.04.||GEC KARMEN||MARIĆ TAMARA||RADOJKOVIĆ MARKO
|-
| BRATOVŠ ANDREJA||Vloga GPCR v patologiji Alzheimerjeve bolezni||26||28.03.||04.04.||11.04.||ZOTTEL ALJA||ČUPOVIĆ VANA||GRDADOLNIK MAJA
|-
| CRČEK MITJA||naslov||||28.03.||04.04.||11.04.||BOHNEC IVO||KMETIČ MIRJAM||BRATOVŠ ANDREJA
|-
| MARIĆ TAMARA||ciljanje kemokinskih receptorjev ob alergijskih obolenjih||5.155||28.03.||04.04.||11.04.||NAVODNIK URŠKA||GEC KARMEN||REMŠKAR MAJA
|-
| ŠTEMBERGER ROK||naslov||||04.04.||11.04.||18.04.||JAVORŠEK KAJA||VRANKAR ANDREJ||BOTONJIĆ SANDI
|-
| LORBEK SARA||naslov||||04.04.||11.04.||18.04.||POHLEVEN ŠPELA||KNAPIČ EVA||VENE ROK
|-
| REMŠKAR MAJA||naslov||||04.04.||11.04.||18.04.||KERIN INES||POVŠE KATJA||CRČEK MITJA
|-
| ČUPOVIĆ VANA||naslov||||04.04.||11.04.||18.04.||REMŽGAR ANA||VERBANČIČ JANA||RODE URŠKA
|-
| RODE URŠKA||naslov||||24.04.||03.05.||09.05.||GRDADOLNIK MAJA||FRANKO NIK||MARIĆ TAMARA
|-
| RADOJKOVIĆ MARKO||naslov||||24.04.||03.05.||09.05.||FRANKO NIK||VENE ROK||POVŠE KATJA
|-
| VENE ROK||naslov||||24.04.||03.05.||09.05.||VERBANČIČ JANA||NAVODNIK URŠKA||ZALAR MATJA
|-
| FRANKO NIK||naslov||||24.04.||03.05.||09.05.||ŠTEMBERGER ROK||HROVAT KARMEN||BOHNEC IVO
|-
| HROVAT KARMEN||naslov||||04.05.||09.05.||16.05.||KERT DOMINIK||JARC VERONIKA||KARNER TAJA
|-
| AMBROŽIČ MATEVŽ||naslov||||04.05.||09.05.||16.05.||LORBEK SARA||KEPIC LEA||REMŽGAR ANA
|-
| NAVODNIK URŠKA||naslov||||04.05.||09.05.||16.05.||AMBROŽIČ MATEVŽ||ŠTOK ULA||ŠTEMBERGER ROK
|-
| BRGLEZ ŽIVA||naslov||||09.05.||16.05.||23.05.||DOLINAR ANA||BOTONJIĆ SANDI||JARC VERONIKA
|-
| KARNER TAJA||naslov||||09.05.||16.05.||23.05.||KOMAN KATRA||OGRIS IZA||NAVODNIK URŠKA
|-
| KERT DOMINIK||naslov||||09.05.||16.05.||23.05.||GORIČAN TJAŠA||GRDADOLNIK MAJA||RAUTER URŠKA
|-
| MUSTAR JERNEJ||naslov||||16.05.||23.05.||30.05.||JARC VERONIKA||AMBROŽIČ MATEVŽ||BRGLEZ ŽIVA
|-
| GEC KARMEN||naslov||||16.05.||23.05.||30.05.||POVŠE KATJA||ZALAR MATJA||AMBROŽIČ MATEVŽ
|-
| GORIČAN TJAŠA||naslov||||16.05.||23.05.||30.05.||KMETIČ MIRJAM||RODE URŠKA||POHLEVEN ŠPELA
|-
| BOHNEC IVO||naslov||||23.05.||30.05.||06.06.||CRČEK MITJA||GORIČAN TJAŠA||ŠTOK ULA
|-
| ŠTOK ULA||naslov||||23.05.||30.05.||06.06.||BRGLEZ ŽIVA||DOLINAR ANA||KERIN INES
|-
| nihce ||naslov||||23.05.||30.05.||06.06.||BRATOVŠ ANDREJA||KOMAN KATRA||GEC KARMEN
|}

==Naloga==
* samostojno pripraviti seminar, katerega osnova je znanstveni članek s področja biokemije, ki ga po želji izberete v reviji s področja biokemije, ki ima faktor vpliva večji kot 3 in je bil objavljen v letu 2011. Poleg tega članka morate za seminar uporabiti še najmanj pet drugih virov! http://www.cobiss.si/scripts/cobiss?command=CONNECT&base=JCR
* osnovni članek in naslov pošljete meni, najkasneje pet dni pred rokom za oddajo (rok-5), da ocenim, če je primeren za predstavitev. Naslov vpišete v tabelo, takoj ko ste si ga izbrali!
* [[BIO1 Povzetki seminarjev|Povzetek seminarja]] opišete na wikiju v približno 200 besedah - najkasneje do dne ko morate oddati seminar recenzentom. Povezave do slik so dobrodošle, niso pa nujne.
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.
* Seminar pripravite v obliki seminarske naloge (pisava 12, enojni razmak, 2,5 cm robovi; važno je, da je obseg od 1800 do 2000 besed), vsebovati mora najmanj eno sliko. Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko.
* Natisnjen seminar oddajte do roka vsakemu od recenzentov (docentu ga pošljite po e-pošti v formatu .doc ali .docx).
* Recenzenti do dneva določenega v tabeli določijo popravke in podajo oceno pisnega dela, v predpisanem formatu elektronskega obrazca na internetu.
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 15 minut. Recenzenti morajo biti na predstavitvi prisotni.
* Predstavitvi sledi razprava- 5 minut. Recenzenti podajo oceno predstavitve in postavijo vsak vsaj dve vprašanji.
* Na dan predstavitve morate docentu oddati končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu.
* Seminarska naloga in povzetek na wikiju morajo biti v slovenskem jeziku!

==Ocenjevanje seminarjev==
Recenzenti ocenijo seminar tako, da izpolnijo [[https://spreadsheets.google.com/viewform?formkey=dFM2SktfM3Q4VU1wNUQzdU45OTlWVXc6MA recenzentsko poročilo]] na spletu.

== Mnenje o predstavitvi ==
Vsak posameznik '''mora''' oceniti seminar, tako da odda svoje [https://spreadsheets.google.com/viewform?formkey=dFd3TGhLV3ZSa2xsLVlmMVVUaEFURWc6MA mnenje] najkasneje v treh dneh po predstavitvi. Kdor na seminarju ni bil prisoten, mnenja '''ne sme''' oddati.

==Urejanje spletnih strani na wikiju==
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'.''

==Faktor vpliva==
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.

==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. 
'''Citiranje knjig:''' 
Priimek, I. ''Naslov''. Kraj: Založba, letnica. 
Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN. 

Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005. 
Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4. 
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:''' 
Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani. 
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: 
Priimek, I. (letnica, številka). Naslov. Naslov revije, strani. 
Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.

Revija Science uporablja skrajšani zapis: 
C. Lartigue ''et al''. Science 317, 632 (2007) 

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:''' 
Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov 
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 
Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.

BIO1-seminar 2011

2011-03-06T20:27:31Z

VeronikaJarc: /* Seznam seminarjev */

= Temelji biokemije- seminar =

Seminarje vodi doc. dr. Gregor Gunčar in so na urniku vsak ponedeljek od 10:00 do 11:30.

Ocena seminarjev predstavlja ??% končne ocene in vsebuje vse točke, ki jih študent/ka lahko zbere pri seminarju in ostalih dejavnostih, ki niso del pisnega izpita.

== Seznam seminarjev ==
{| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"
| align="center" style="background:#f0f0f0;"|'''Ime in priimek'''
| align="center" style="background:#f0f0f0;"|'''Slovenski naslov članka'''
| align="center" style="background:#f0f0f0;"|'''Faktor vpliva revije'''
| align="center" style="background:#f0f0f0;"|'''Rok za oddajo'''
| align="center" style="background:#f0f0f0;"|'''Rok za recenzijo'''
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 1'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 2'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 3'''
|-
| BOTONJIĆ SANDI||[http://wiki.fkkt.uni-lj.si/index.php/BIO1_Povzetki_seminarjev Tioredoksinu podoben protein (TXNL2) ščiti kancerogene celice pred oksidativnim stresom]
||||28.02.||03.03.||07.03.||RODE URŠKA||KERIN INES||OGRIS IZA
|-
| VRANKAR ANDREJ||Število lasno-mešičnih matičnih celic se v plešastem lasišču moških z androgeno alopecijo ohranja za razliko od števila CD200-rich in CD34-positive lasno-mešičnih predniških celic||||28.02.||03.03.||07.03.||HROVAT KARMEN||BOHNEC IVO||JAVORŠEK KAJA
|-
| ZALAR MATJA||Protein p53||||28.02.||03.03.||07.03.||OGRIS IZA||CRČEK MITJA||ZOTTEL ALJA
|-
| ZOTTEL ALJA||Vloga imunskega sistema pri aterosklerozi||31.434||07.03.||10.03.||14.03.||RADOJKOVIĆ MARKO||KERT DOMINIK||HROVAT KARMEN
|-
| DOLINAR ANA||[http://wiki.fkkt.uni-lj.si/index.php/BIO1_Povzetki_seminarjev#Ana_Dolinar:_Prilagojena_ali_prilagodljiva_imunost.3F_Primer_naravnih_celic_ubijalk Prirojena ali prilagodljiva imunost? Primer naravnih celic ubijalk]||28||07.03.||10.03.||14.03.||RAUTER URŠKA||MOHAR MAŠA||VERBANČIČ JANA
|-
| RAUTER URŠKA||Razvojna vloga Srf, kortikalnega citoskeleta in celične oblike v orientaciji epidermalnega vretena||19.527||07.03.||10.03.||14.03.||MUSTAR JERNEJ||JAVORŠEK KAJA||MOHAR MAŠA
|-
| MOHAR MAŠA||Sladkorna bolezen tipa 2 kot bolezen imunskega sistema||30,006||14.03.||17.03.||21.03.||VENE ROK||RAUTER URŠKA||GORIČAN TJAŠA
|-
| POHLEVEN ŠPELA||jhfjsdf sdh fjhds v||12||14.03.||17.03.||21.03.||KEPIC LEA||RADOJKOVIĆ MARKO||DOLINAR ANA
|-
| KEPIC LEA||naslov||||14.03.||17.03.||21.03.||VRANKAR ANDREJ||BRATOVŠ ANDREJA||MUSTAR JERNEJ
|-
| KMETIČ MIRJAM||Celična regulacija metabolizma železa||5,371||14.03.||17.03.||21.03.||MARIĆ TAMARA||REMŠKAR MAJA||KOMAN KATRA
|-
| JARC VERONIKA||Hepatitis C||3.26||14.03.||21.03.||28.03.||REMŠKAR MAJA||MUSTAR JERNEJ||KEPIC LEA
|-
| KOMAN KATRA||naslov||||14.03.||21.03.||28.03.||ČUPOVIĆ VANA||KARNER TAJA||KMETIČ MIRJAM
|-
| OGRIS IZA||Zakaj imajo možgani glikogen?||||14.03.||21.03.||28.03.||KNAPIČ EVA||BRGLEZ ŽIVA||VRANKAR ANDREJ
|-
| KERIN INES||naslov||||14.03.||21.03.||28.03.||ŠTOK ULA||ŠTEMBERGER ROK||KERT DOMINIK
|-
| VERBANČIČ JANA||naslov||||21.03.||28.03.||04.04.||KARNER TAJA||ZOTTEL ALJA||KNAPIČ EVA
|-
| KNAPIČ EVA||naslov||||21.03.||28.03.||04.04.||ZALAR MATJA||POHLEVEN ŠPELA||LORBEK SARA
|-
| REMŽGAR ANA||naslov||||21.03.||28.03.||04.04.||BOTONJIĆ SANDI||LORBEK SARA||ČUPOVIĆ VANA
|-
| POVŠE KATJA||naslov||||21.03.||28.03.||04.04.||MOHAR MAŠA||REMŽGAR ANA||FRANKO NIK
|-
| JAVORŠEK KAJA||naslov||||28.03.||04.04.||11.04.||GEC KARMEN||MARIĆ TAMARA||RADOJKOVIĆ MARKO
|-
| BRATOVŠ ANDREJA||naslov||||28.03.||04.04.||11.04.||ZOTTEL ALJA||ČUPOVIĆ VANA||GRDADOLNIK MAJA
|-
| CRČEK MITJA||naslov||||28.03.||04.04.||11.04.||BOHNEC IVO||KMETIČ MIRJAM||BRATOVŠ ANDREJA
|-
| MARIĆ TAMARA||ciljanje kemokinskih receptorjev ob alergijskih obolenjih||5.155||28.03.||04.04.||11.04.||NAVODNIK URŠKA||GEC KARMEN||REMŠKAR MAJA
|-
| ŠTEMBERGER ROK||naslov||||04.04.||11.04.||18.04.||JAVORŠEK KAJA||VRANKAR ANDREJ||BOTONJIĆ SANDI
|-
| LORBEK SARA||naslov||||04.04.||11.04.||18.04.||POHLEVEN ŠPELA||KNAPIČ EVA||VENE ROK
|-
| REMŠKAR MAJA||naslov||||04.04.||11.04.||18.04.||KERIN INES||POVŠE KATJA||CRČEK MITJA
|-
| ČUPOVIĆ VANA||naslov||||04.04.||11.04.||18.04.||REMŽGAR ANA||VERBANČIČ JANA||RODE URŠKA
|-
| RODE URŠKA||naslov||||24.04.||03.05.||09.05.||GRDADOLNIK MAJA||FRANKO NIK||MARIĆ TAMARA
|-
| RADOJKOVIĆ MARKO||naslov||||24.04.||03.05.||09.05.||FRANKO NIK||VENE ROK||POVŠE KATJA
|-
| VENE ROK||naslov||||24.04.||03.05.||09.05.||VERBANČIČ JANA||NAVODNIK URŠKA||ZALAR MATJA
|-
| FRANKO NIK||naslov||||24.04.||03.05.||09.05.||ŠTEMBERGER ROK||HROVAT KARMEN||BOHNEC IVO
|-
| HROVAT KARMEN||naslov||||04.05.||09.05.||16.05.||KERT DOMINIK||JARC VERONIKA||KARNER TAJA
|-
| AMBROŽIČ MATEVŽ||naslov||||04.05.||09.05.||16.05.||LORBEK SARA||KEPIC LEA||REMŽGAR ANA
|-
| NAVODNIK URŠKA||naslov||||04.05.||09.05.||16.05.||AMBROŽIČ MATEVŽ||ŠTOK ULA||ŠTEMBERGER ROK
|-
| BRGLEZ ŽIVA||naslov||||09.05.||16.05.||23.05.||DOLINAR ANA||BOTONJIĆ SANDI||JARC VERONIKA
|-
| KARNER TAJA||naslov||||09.05.||16.05.||23.05.||KOMAN KATRA||OGRIS IZA||NAVODNIK URŠKA
|-
| KERT DOMINIK||naslov||||09.05.||16.05.||23.05.||GORIČAN TJAŠA||GRDADOLNIK MAJA||RAUTER URŠKA
|-
| GRDADOLNIK MAJA||naslov||||16.05.||23.05.||30.05.||JARC VERONIKA||AMBROŽIČ MATEVŽ||BRGLEZ ŽIVA
|-
| GEC KARMEN||naslov||||16.05.||23.05.||30.05.||POVŠE KATJA||ZALAR MATJA||AMBROŽIČ MATEVŽ
|-
| GORIČAN TJAŠA||naslov||||16.05.||23.05.||30.05.||KMETIČ MIRJAM||RODE URŠKA||POHLEVEN ŠPELA
|-
| BOHNEC IVO||naslov||||23.05.||30.05.||06.06.||CRČEK MITJA||GORIČAN TJAŠA||ŠTOK ULA
|-
| ŠTOK ULA||naslov||||23.05.||30.05.||06.06.||BRGLEZ ŽIVA||DOLINAR ANA||KERIN INES
|-
| MUSTAR JERNEJ||naslov||||23.05.||30.05.||06.06.||BRATOVŠ ANDREJA||KOMAN KATRA||GEC KARMEN
|}

==Naloga==
* samostojno pripraviti seminar, katerega osnova je znanstveni članek s področja biokemije, ki ga po želji izberete v reviji s področja biokemije, ki ima faktor vpliva večji kot 3 in je bil objavljen v letu 2011. Poleg tega članka morate za seminar uporabiti še najmanj pet drugih virov! http://www.cobiss.si/scripts/cobiss?command=CONNECT&base=JCR
* osnovni članek in naslov pošljete meni, najkasneje pet dni pred rokom za oddajo (rok-5), da ocenim, če je primeren za predstavitev. Naslov vpišete v tabelo, takoj ko ste si ga izbrali!
* [[BIO1 Povzetki seminarjev|Povzetek seminarja]] opišete na wikiju v približno 200 besedah - najkasneje do dne ko morate oddati seminar recenzentom. Povezave do slik so dobrodošle, niso pa nujne.
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.
* Seminar pripravite v obliki seminarske naloge (pisava 12, enojni razmak, 2,5 cm robovi; važno je, da je obseg od 1800 do 2000 besed), vsebovati mora najmanj eno sliko. Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko.
* Natisnjen seminar oddajte do roka vsakemu od recenzentov (docentu ga pošljite po e-pošti v formatu .doc ali .docx).
* Recenzenti do dneva določenega v tabeli določijo popravke in podajo oceno pisnega dela, v predpisanem formatu elektronskega obrazca na internetu.
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 15 minut. Recenzenti morajo biti na predstavitvi prisotni.
* Predstavitvi sledi razprava- 5 minut. Recenzenti podajo oceno predstavitve in postavijo vsak vsaj dve vprašanji.
* Na dan predstavitve morate docentu oddati končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu.
* Seminarska naloga in povzetek na wikiju morajo biti v slovenskem jeziku!

==Ocenjevanje seminarjev==
Recenzenti ocenijo seminar tako, da izpolnijo [[https://spreadsheets.google.com/viewform?formkey=dFM2SktfM3Q4VU1wNUQzdU45OTlWVXc6MA recenzentsko poročilo]] na spletu.

== Mnenje o predstavitvi ==
Vsak posameznik '''mora''' oceniti seminar, tako da odda svoje [https://spreadsheets.google.com/viewform?formkey=dFd3TGhLV3ZSa2xsLVlmMVVUaEFURWc6MA mnenje] najkasneje v treh dneh po predstavitvi. Kdor na seminarju ni bil prisoten, mnenja '''ne sme''' oddati.

==Urejanje spletnih strani na wikiju==
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'.''

==Faktor vpliva==
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.

==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. 
'''Citiranje knjig:''' 
Priimek, I. ''Naslov''. Kraj: Založba, letnica. 
Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN. 

Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005. 
Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4. 
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:''' 
Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani. 
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: 
Priimek, I. (letnica, številka). Naslov. Naslov revije, strani. 
Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.

Revija Science uporablja skrajšani zapis: 
C. Lartigue ''et al''. Science 317, 632 (2007) 

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:''' 
Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov 
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 
Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.

BIO1-seminar 2011

2011-03-01T18:08:43Z

VeronikaJarc: /* Seznam seminarjev */

= Temelji biokemije- seminar =

Seminarje vodi doc. dr. Gregor Gunčar in so na urniku vsak ponedeljek od 10:00 do 11:30.

Ocena seminarjev predstavlja ??% končne ocene in vsebuje vse točke, ki jih študent/ka lahko zbere pri seminarju in ostalih dejavnostih, ki niso del pisnega izpita.

== Seznam seminarjev ==
{| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"
| align="center" style="background:#f0f0f0;"|'''Ime in priimek'''
| align="center" style="background:#f0f0f0;"|'''Slovenski naslov članka'''
| align="center" style="background:#f0f0f0;"|'''Faktor vpliva revije'''
| align="center" style="background:#f0f0f0;"|'''Rok za oddajo'''
| align="center" style="background:#f0f0f0;"|'''Rok za recenzijo'''
| align="center" style="background:#f0f0f0;"|'''Datum predstavitve'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 1'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 2'''
| align="center" style="background:#f0f0f0;"|'''Recenzent 3'''
|-
| BOTONJIĆ SANDI||Tioredoksinu podoben protein (TXNL2) ščiti kancerogene celice pred oksidativnim stresom.||||28.02.||03.03.||07.03.||RODE URŠKA||KERIN INES||OGRIS IZA
|-
| VRANKAR ANDREJ||Število lasno-mešičnih matičnih celic se v plešastem lasišču moških z androgeno alopecijo ohranja za razliko od števila CD200-rich in CD34-positive lasno-mešičnih predniških celic||||28.02.||03.03.||07.03.||HROVAT KARMEN||BOHNEC IVO||JAVORŠEK KAJA
|-
| ZALAR MATJA||Protein p53||||28.02.||03.03.||07.03.||OGRIS IZA||CRČEK MITJA||ZOTTEL ALJA
|-
| ZOTTEL ALJA||Vloga imunskega sistema pri aterosklerozi||||07.03.||10.03.||14.03.||RADOJKOVIĆ MARKO||KERT DOMINIK||HROVAT KARMEN
|-
| DOLINAR ANA||Prirojena ali prilagodljiva imunost? Primer naravnih celic ubijalk||28||07.03.||10.03.||14.03.||RAUTER URŠKA||MOHAR MAŠA||VERBANČIČ JANA
|-
| RAUTER URŠKA||Razvojna vloga Srf, kortikalnega citoskeleta in celične oblike v orientaciji epidermalnega vretena||19.527||07.03.||10.03.||14.03.||MUSTAR JERNEJ||JAVORŠEK KAJA||MOHAR MAŠA
|-
| MOHAR MAŠA||naslov||||14.03.||17.03.||21.03.||VENE ROK||RAUTER URŠKA||GORIČAN TJAŠA
|-
| POHLEVEN ŠPELA||jhfjsdf sdh fjhds v||12||14.03.||17.03.||21.03.||KEPIC LEA||RADOJKOVIĆ MARKO||DOLINAR ANA
|-
| KEPIC LEA||naslov||||14.03.||17.03.||21.03.||VRANKAR ANDREJ||BRATOVŠ ANDREJA||MUSTAR JERNEJ
|-
| KMETIČ MIRJAM||naslov||||14.03.||17.03.||21.03.||MARIĆ TAMARA||REMŠKAR MAJA||KOMAN KATRA
|-
| JARC VERONIKA||Hepatitis C||||14.03.||21.03.||28.03.||REMŠKAR MAJA||MUSTAR JERNEJ||KEPIC LEA
|-
| KOMAN KATRA||naslov||||14.03.||21.03.||28.03.||ČUPOVIĆ VANA||KARNER TAJA||KMETIČ MIRJAM
|-
| OGRIS IZA||naslov||||14.03.||21.03.||28.03.||KNAPIČ EVA||BRGLEZ ŽIVA||VRANKAR ANDREJ
|-
| KERIN INES||naslov||||14.03.||21.03.||28.03.||KARNER TAJA||ŠTEMBERGER ROK||KERT DOMINIK
|-
| VERBANČIČ JANA||naslov||||21.03.||28.03.||04.04.||ŠTOK ULA||ZOTTEL ALJA||KNAPIČ EVA
|-
| KNAPIČ EVA||naslov||||21.03.||28.03.||04.04.||ZALAR MATJA||POHLEVEN ŠPELA||LORBEK SARA
|-
| REMŽGAR ANA||naslov||||21.03.||28.03.||04.04.||BOTONJIĆ SANDI||LORBEK SARA||ČUPOVIĆ VANA
|-
| GRDADOLNIK MAJA||naslov||||21.03.||28.03.||04.04.||MOHAR MAŠA||REMŽGAR ANA||FRANKO NIK
|-
| JAVORŠEK KAJA||naslov||||28.03.||04.04.||11.04.||GEC KARMEN||MARIĆ TAMARA||RADOJKOVIĆ MARKO
|-
| BRATOVŠ ANDREJA||naslov||||28.03.||04.04.||11.04.||ZOTTEL ALJA||ČUPOVIĆ VANA||GRDADOLNIK MAJA
|-
| CRČEK MITJA||naslov||||28.03.||04.04.||11.04.||BOHNEC IVO||KMETIČ MIRJAM||BRATOVŠ ANDREJA
|-
| MARIĆ TAMARA||naslov||||28.03.||04.04.||11.04.||NAVODNIK URŠKA||GEC KARMEN||REMŠKAR MAJA
|-
| ŠTEMBERGER ROK||naslov||||04.04.||11.04.||18.04.||JAVORŠEK KAJA||VRANKAR ANDREJ||BOTONJIĆ SANDI
|-
| LORBEK SARA||naslov||||04.04.||11.04.||18.04.||POHLEVEN ŠPELA||KNAPIČ EVA||VENE ROK
|-
| REMŠKAR MAJA||naslov||||04.04.||11.04.||18.04.||KERIN INES||POVŠE KATJA||CRČEK MITJA
|-
| KARNER TAJA||naslov||||04.04.||11.04.||18.04.||REMŽGAR ANA||VERBANČIČ JANA||RODE URŠKA
|-
| RODE URŠKA||naslov||||24.04.||03.05.||09.05.||GRDADOLNIK MAJA||FRANKO NIK||MARIĆ TAMARA
|-
| RADOJKOVIĆ MARKO||naslov||||24.04.||03.05.||09.05.||FRANKO NIK||VENE ROK||POVŠE KATJA
|-
| VENE ROK||naslov||||24.04.||03.05.||09.05.||VERBANČIČ JANA||NAVODNIK URŠKA||ZALAR MATJA
|-
| AMBROŽIČ MATEVŽ||naslov||||24.04.||03.05.||09.05.||ŠTEMBERGER ROK||HROVAT KARMEN||BOHNEC IVO
|-
| HROVAT KARMEN||naslov||||04.05.||09.05.||16.05.||KERT DOMINIK||JARC VERONIKA||KARNER TAJA
|-
| FRANKO NIK||naslov||||04.05.||09.05.||16.05.||LORBEK SARA||KEPIC LEA||REMŽGAR ANA
|-
| NAVODNIK URŠKA||naslov||||04.05.||09.05.||16.05.||AMBROŽIČ MATEVŽ||ŠTOK ULA||ŠTEMBERGER ROK
|-
| BRGLEZ ŽIVA||naslov||||09.05.||16.05.||23.05.||DOLINAR ANA||BOTONJIĆ SANDI||JARC VERONIKA
|-
| ČUPOVIĆ VANA||naslov||||09.05.||16.05.||23.05.||KOMAN KATRA||OGRIS IZA||NAVODNIK URŠKA
|-
| KERT DOMINIK||naslov||||09.05.||16.05.||23.05.||GORIČAN TJAŠA||GRDADOLNIK MAJA||RAUTER URŠKA
|-
| POVŠE KATJA||naslov||||16.05.||23.05.||30.05.||JARC VERONIKA||AMBROŽIČ MATEVŽ||BRGLEZ ŽIVA
|-
| GEC KARMEN||naslov||||16.05.||23.05.||30.05.||POVŠE KATJA||ZALAR MATJA||AMBROŽIČ MATEVŽ
|-
| GORIČAN TJAŠA||naslov||||16.05.||23.05.||30.05.||KMETIČ MIRJAM||RODE URŠKA||POHLEVEN ŠPELA
|-
| BOHNEC IVO||naslov||||23.05.||30.05.||06.06.||CRČEK MITJA||GORIČAN TJAŠA||ŠTOK ULA
|-
| ŠTOK ULA||naslov||||23.05.||30.05.||06.06.||BRGLEZ ŽIVA||DOLINAR ANA||KERIN INES
|-
| MUSTAR JERNEJ||naslov||||23.05.||30.05.||06.06.||BRATOVŠ ANDREJA||KOMAN KATRA||GEC KARMEN
|}

==Naloga==
* samostojno pripraviti seminar, katerega osnova je znanstveni članek s področja biokemije, ki ga po želji izberete v reviji s področja biokemije, ki ima faktor vpliva večji kot 3 in je bil objavljen v letu 2011. Poleg tega članka morate za seminar uporabiti še najmanj pet drugih virov! http://www.cobiss.si/scripts/cobiss?command=CONNECT&base=JCR
* osnovni članek in naslov pošljete meni, najkasneje pet dni pred rokom za oddajo (rok-5), da ocenim, če je primeren za predstavitev. Naslov vpišete v tabelo, takoj ko ste si ga izbrali!
* [[BIO1 Povzetki seminarjev|Povzetek seminarja]] opišete na wikiju v približno 200 besedah - najkasneje do dne ko morate oddati seminar recenzentom. Povezave do slik so dobrodošle, niso pa nujne.
* Povezavo do povzetka vnesete v tabelo seminarjev tekočega letnika.
* Seminar pripravite v obliki seminarske naloge (pisava 12, enojni razmak, 2,5 cm robovi; važno je, da je obseg od 1800 do 2000 besed), vsebovati mora najmanj eno sliko. Slika mora imeti legendo in v besedilu mora biti na ustreznem mestu sklic na sliko.
* Natisnjen seminar oddajte do roka vsakemu od recenzentov (docentu ga pošljite po e-pošti v formatu .doc ali .docx).
* Recenzenti do dneva določenega v tabeli določijo popravke in podajo oceno pisnega dela, v predpisanem formatu elektronskega obrazca na internetu.
* Ustna predstavitev sledi na dan, ki je vpisan v tabeli. Za predstavitev je na voljo 15 minut. Recenzenti morajo biti na predstavitvi prisotni.
* Predstavitvi sledi razprava- 5 minut. Recenzenti podajo oceno predstavitve in postavijo vsak vsaj dve vprašanji.
* Na dan predstavitve morate docentu oddati končno (popravljeno) in natisnjeno verzijo seminarja v enem izvodu.
* Seminarska naloga in povzetek na wikiju morajo biti v slovenskem jeziku!

==Ocenjevanje seminarjev==
Recenzenti ocenijo seminar tako, da izpolnijo [[https://spreadsheets.google.com/viewform?formkey=dFM2SktfM3Q4VU1wNUQzdU45OTlWVXc6MA recenzentsko poročilo]] na spletu.

== Mnenje o predstavitvi ==
Vsak posameznik '''mora''' oceniti seminar, tako da odda svoje [https://spreadsheets.google.com/viewform?formkey=dFd3TGhLV3ZSa2xsLVlmMVVUaEFURWc6MA mnenje] najkasneje v treh dneh po predstavitvi. Kdor na seminarju ni bil prisoten, mnenja '''ne sme''' oddati.

==Urejanje spletnih strani na wikiju==
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'.''

==Faktor vpliva==
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.

==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. 
'''Citiranje knjig:''' 
Priimek, I. ''Naslov''. Kraj: Založba, letnica. 
Priimek, I. ''Naslov: podnaslov''. Izdaja. Kraj: Založba, letnica. Zbirka, številka. ISBN. 

Boyer, R. ''Temelji biokemije''. Ljubljana: Študentska založba, 2005. 
Glick BR in Pasternak JJ. ''Molecular biotechnology: principles and applications of recombinant DNA''. 3. izdaja. Washington: ASM Press, 2003. ISBN 1-55581-269-4. 
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:''' 
Priimek, I. Naslov. ''Naslov revije'', letnica, letnik, številka, strani. 
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: 
Priimek, I. (letnica, številka). Naslov. Naslov revije, strani. 
Lartigue C. ''et al.'' (2007, 317) Genome transplantation in bacteria: changing one species to another. ''Science'', 632-638.

Revija Science uporablja skrajšani zapis: 
C. Lartigue ''et al''. Science 317, 632 (2007) 

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:''' 
Priimek, I. ''Naslov dokumenta''. Izdaja. Kraj: Založnik, letnica. Datum zadnjega popravljanja. [Datum citiranja.] spletni naslov 
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 
Navedemo čim več podatkov; pogosto vseh iz pravila ne boste našli.

BIO1-seminar 2011

2011-02-22T16:02:40Z

VeronikaJarc: /* Seznam seminarjev */