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MBT seminarji 2021

2021-05-19T21:24:20Z

Zeljkae:

Seminarji iz Molekularne biotehnologije so letos organizirani tako, da vsak študent (praviloma v paru, lahko pa tudi samostojno) obdela temo s področja cepiv proti virusu SARS-CoV-2 in o tem pripravi kratek poljudno napisan povzetek. Ta del seminarjev je predstavljen na [[protikovidna cepiva|ločeni strani]].
V drugem delu vsak študent predstavi nek raziskovalni dosežek s širšega področja molekularne biotehnologije. Seznam tem in predstavitev za študijsko leto 2020/21 je predstavljen tu.

Povzetke morate objaviti do torka do polnoči v tednu, ko imate seminar (v četrtek). Angleški naslov prevedite tudi v slovenščino - to bo naslov povzetka, ki ga objavite na posebni strani, tako kot so to naredili kolegi pred vami (oz. predlani).

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 (28.2.) 
(slovenski naslov povežite z novo stranjo, na kateri bo povzetek)

----

Naslovi odobrenih člankov po temah:

'''Farmacevtsko pomembni proteini''' 
# Development of Antibody-Fragment-Producing Rice for Neutralization of Human Norovirus (A. Sasou ''et. al''; Frontiers in Plant Science 12, 2021; https://doi.org/10.3389/fpls.2021.639953). [[Proizvodnja riža za sintezo fragmentov protiteles proti humanemu norovirusu.]] Mateja Žvipelj (11.3.)
# A New Plant Expression System for Producing Pharmaceutical Proteins (N. Abd-Aziz ''et. al''; Molecular Biotechnology 62, 2020; https://doi.org/10.1007/s12033-020-00242-2). [[Razvoj ekspresijskega sistema za proizvodnjo farmacevtskih proteinov v rastlini Mucuna bracteata]]. Jernej Imperl (18.3.)
# Development of a Recombinant Monospecific Anti-PLGF Bivalent Nanobody and Evaluation of it in Angiogenesis Modulation (A. Nikooharf "et all"; Molecular Biotechnology 62, 2020; https://link.springer.com/article/10.1007/s12033-020-00275-7#additional-information) [[Razvoj rekombinantnih monospecifičnih bivalentnih nanoteles proti PLGF-u]]. Nika Zaveršek (18.3.)

'''Cepiva''' 
# Development of a DNA Vaccine for Melanoma Metastasis by Inhalation Based on an Analysis of Transgene Expression Characteristics of Naked pDNA and a Ternary Complex in Mouse Lung Tissues (Kodama ''et.al'';Pharmaceutics 12,2020; https://www.mdpi.com/1999-4923/12/6/540#framed_div_cited_count) [[ Razvoj DNA cepiva proti metastazam melanoma z vdihavanjem na podlagi analize značilnosti transgene ekspresije gole pDNA in trojni kompleks v mišjem pljučnem tkivu]]. Paula Horvat (25.3.) 
# An AMA1/MSP119 Adjuvanted Malaria Transplastomic Plant‑Based Vaccine Induces Immune Responses in Test Animals (Evelia M. Milán‑Noris ''et. al''; Molecular Biotechnology 62, 2020; https://doi.org/10.1007/s12033-020-00271-x) [[V rastlinah proizvedeno transplastomsko antimalarijsko cepivo z AMA1/MSP119 in dodanim adjuvansom inducira imunski odziv v testnih živalih]]. Neža Pavko (25.3.) 

'''Gensko spremenjene rastline''' 
# A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch (C. Saintenac ''et al.''; Nat. Commun. 12, 2021, https://doi.org/10.1038/s41467-020-20685-0). [[Receptorju podobna kinaza bogata s cisteini, pšenici daje odpornost proti širokemu spektru pegavosti Septoria tritici]]. Andrej Race (7.4.)
# RNAi silenced ζ-carotene desaturase developed variegated tomato transformants with increased phytoene content (M. A. Babu ''et. al''; Plant Growth Regul. 93, 2021; https://doi.org/10.1007/s10725-020-00678-1). [[Vpliv utišanja ζ-karoten desaturaze na vsebnost karotenoidov v gensko spremenjenih paradižnikih]]. Peter Škrinjar (7.4.)

'''Gensko spremenjene živali in celične linije''' 
# Engineering carotenoid production in mammalian cells for nutritionally enhanced cell-cultured foods (A. J. Stout "et. al"; Metabolic Engineering 62, 2020; https://doi.org/10.1016/j.ymben.2020.07.011). [[Razvoj proizvodnje karotenoidov v sesalskih celicah za prehransko izboljšano celično pridobljeno meso]]. Urša Lovše (8.4.)
# Efficient photoactivatable Dre recombinase for cell type-specific spatiotemporal control of genome engineering in the mouse (H. Li ''et. al''; Proc. Natl. Acad. Sci. U. S. A. 117(52), 2021; https://doi.org/10.1073/pnas.2003991117). [[Priprava fotoinducibilne rekombinaze Dre kot orodje za prostorsko in časovno odvisno urejanje genoma v specifičnih mišjih celicah.]] Matija Ruparčič (8.4.)

'''Nizkomolekularni biotehnološki produkti''' 
# Fermentative N-Methylanthranilate Production by Engineered ''Corynebacterium glutamicum''. (T. Walter ''et. al.''; Microorganisms 8(6), 2020; https://doi.org/10.3390/microorganisms8060866). [[Fermentativna proizvodnja N-metilantranilata z inženirsko spremenjeno Corynebacterium glutamicum]]. Saša Slabe (14.4.)
# Efficient Biosynthesis of Vanillin from Isoeugenol by Recombinant Isoeugenol Monooxygenase from ''Pseudomonas nitroreducens'' Jin1. (Wang Q, Wu X, Lu X, He Y, Ma B, Xu Y. Efficient Biosynthesis of Vanillin from Isoeugenol by Recombinant Isoeugenol Monooxygenase from Pseudomonas nitroreducens Jin1. Appl Biochem Biotechnol. 2021:1116-1128. doi:10.1007/s12010-020-03478-5). [[Učinkovita biosinteza vanilina iz izoevgenola z uporabo rekombinantne izoevgenol monooksigenaze Jin1 iz bakterije Pseudomonas nitroreducens]]. Luka Gnidovec (15.4.)
# One-pot production of butyl butyrate from glucose using a cognate “diamond-shaped” ''E. coli'' consortium (J. P. Sinumvayo "et. al"; Bioresources and Bioprocessing 8, 2021; https://bioresourcesbioprocessing.springeropen.com/articles/10.1186/s40643-021-00372-8#Sec9). [[Proizvodnja butil butirata iz glukoze z uporabo "diamantnega" konzorcija E. coli]] Liza Ulčakar (15.4.)

'''Biotehnološki polimeri''' 
# Biotechnologically produced fucosylated oligosaccharides inhibit the binding of human noroviruses to their natural receptors (S. M. Derya et al., “Biotechnologically produced fucosylated oligosaccharides inhibit the binding of human noroviruses to their natural receptors,” ''J. Biotechnol.'', vol. 318, no. April, pp. 31–38, 2020, doi: 10.1016/j.jbiotec.2020.05.001). [[Inhibicija vezave humanega norovirusa na naravni receptor z biotehnološko proizvedenimi fukoziliranimi oligosaharidi]] Anže Karlek (21.4.)
# Complete biosynthesis of a sulfated chondroitin in ''Escherichia coli'' (Badri, A., ''et al''; Nature communications 12 (2021); https://doi.org/10.1038/s41467-021-21692-5). [[Popolna biosinteza hondroitin sulfata v E. coli]] Ana Maklin (22.4.)
# Optimization of cultivation medium and cyclic fed-batch fermentation strategy for enhanced polyhydroxyalkanoate production by Bacillus thuringiensis using a glucose-rich hydrolyzate (Singh et al. Bioresour. Bioprocess. (2021) 8:11, https://doi.org/10.1186/s40643-021-00361-x) [[Optimizacija fermentacijske proizvodnje PHA-bioplastike z b. thuringiensis in z glukozo bogatimi hidrolizati]] Urban Hribar (22.4.)

'''Biotehnološko pridobljeni encimi''' 
# Engineering a carboxypeptidase from ''Aspergillus niger'' M00988 by mutation to increase its ability in high Fischer ratio oligopeptide preparation (Xiong K., Liu J., Wang X., Sun B., Zhang Y., Zhao Z., Pei P., & Li X.; Journal of Biotechnology, 330, 1–8, 2021, https://doi.org/10.1016/j.jbiotec.2021.02.015). [[Priprava karboksipeptidaze iz glive Aspergillus niger M00988 za izboljšanje priprave oligopeptidov z visokim Fischerjevim razmerjem]] Urška Fajdiga (5.5.)
# Cell-Based High-Throughput Screening Protocol for Discovering Antiviral Inhibitors Against SARS-COV-2 Main Protease (3CLpro) (Rothan, H.A., Teoh, T.C; Mol Biotechnol 63, 240–248 (2021); https://doi.org/10.1007/s12033-021-00299-7) [[Visoko zmogljiv presejalni protokol na osnovi celic za raziskovanje antivirusnih inhibitorjev proti Sars-Cov-2 glavni proteazi (3CLpro)]] Mirsad Mešić (6.5.)
# A novel cold-active type I pullulanase from a hot-spring metagenome for effective debranching and production of resistant starch (M. Thakur ''et al''.; Bioresource Technology 320, 2021; https://doi.org/10.1016/j.biortech.2020.124288). [[Pri nizkih temperaturah aktivna pululanaza tipa I iz metagenoma vročih vrelcev omogoča učinkovito klestenje in proizvodnjo odpornega škroba]] Martina Lokar (6.5.)

'''Metabolno inženirstvo v biotehnologiji''' 
# Production of Tyrian purple indigoid dye from tryptophan in ''Escherichia coli'' (J. Lee ''et al.''; Nat. Chem. Biol. 17, 2021; https://doi.org/10.1038/s41589-020-00684-4). [http://wiki.fkkt.uni-lj.si/index.php/Proizvodnja_%C5%A1krlatnega_indigoidnega_barvila_iz_triptofana_v_bakteriji_Escherichia_coli Proizvodnja škrlatnega indigoidnega barvila iz triptofana v bakteriji ''Escherichia coli''] Jerneja Nimac (12.5.)
# Development of ''Pseudomonas asiatica'' as a host for the production of 3-hydroxypropionic acid from glycerol (T. Thi Nguyen et al., Bioresource Technology, vol. 329, 2021; https://doi.org/10.1016/j.biortech.2021.124867). [[Razvoj gostiteljskega organizma Pseudomonas asiatica za proizvodnjo 3-hidroksipropionske kisline iz glicerola]] Urška Pečarič Strnad (12.5.)
# Generation of an engineered food-grade ''Lactococcus lactis'' strain for production of an antimicrobial peptide: ''in vitro'' and ''in silico'' evaluation (A. Tanhaeian ''et. al''; BMC Biotechnol. 20(1), 2020; https://doi.org/10.1186/s12896-020-00612-3). [[Priprava in ovrednotenje novega seva bakterij Lactococcus lactis za proizvodnjo protimikrobnega peptida]]. Klementina Polanec (13.5.)
# Metabolic engineering of ''E. coli'' for producing phloroglucinol from acetate (S. Yu et. al; Applied Microbiology and Biotechnology. 2020; https://doi.org/10.1007/s00253-020-10591-2). [[Metabolno inženirstvo bakterije Escherichia coli za pridobivanje floroglucinola iz acetata]]. Ernestina Lavrih (13.5.)

'''Biomasa in biogoriva''' 
# Green Deep Eutectic Solvents for ''Microwave-Assisted Biomass'' Delignification and Valorisation (Grillo G. ''et al.''; Molecules 2021; https://www.mdpi.com/1420-3049/26/4/798/htm) [[Zelena globoka evtektična topila za delignifikacijo in valorizacijo biomase s pomočjo mikrovalov]]. Željka Erić (19.5.)
# Incorporating a molecular antenna in diatom microalgae cells enhances photosynthesis (Leone, G., De la Cruz Valbuena, G., Cicco, S.R. ''et al.''; Sci Rep 11, 2021; https://www.nature.com/articles/s41598-021-84690-z#Sec10) [[Vključevanje molekularne antene v celice mikroskopsko majhnih kremenastih alg (diatomej) za izboljšanje fotosintetske učinkovitosti]]. Karin Dobravc Škof (20.5.)
# Integrated cascade biorefinery processes for the production of single cell oil by ''Lipomyces starkeyi'' from ''Arundo donax L.'' hydrolysates (Di Fidio N ''et al.''; ''Bioresour. Tecnhol.'', vol.325, p.124635, Apr. 2021.; https://doi.org/10.1016/j.biortech.2020.124635). [[Integrirana procesa biorafinerijske proizvodnje znotrajceličnih založnih lipidov iz Arundo donax L. v Lipomyces starkeyi]] . Katja Doberšek (20.5.)

'''Okoljski vidiki biotehnologije in bioremediacija''' 
# Almina Tahirović (26.5.)
# Eva Keber (27.5.)
# Nina Lukančič (27.5.)

MBT seminarji 2021

2021-05-19T21:22:53Z

Zeljkae:

Seminarji iz Molekularne biotehnologije so letos organizirani tako, da vsak študent (praviloma v paru, lahko pa tudi samostojno) obdela temo s področja cepiv proti virusu SARS-CoV-2 in o tem pripravi kratek poljudno napisan povzetek. Ta del seminarjev je predstavljen na [[protikovidna cepiva|ločeni strani]].
V drugem delu vsak študent predstavi nek raziskovalni dosežek s širšega področja molekularne biotehnologije. Seznam tem in predstavitev za študijsko leto 2020/21 je predstavljen tu.

Povzetke morate objaviti do torka do polnoči v tednu, ko imate seminar (v četrtek). Angleški naslov prevedite tudi v slovenščino - to bo naslov povzetka, ki ga objavite na posebni strani, tako kot so to naredili kolegi pred vami (oz. predlani).

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 (28.2.) 
(slovenski naslov povežite z novo stranjo, na kateri bo povzetek)

----

Naslovi odobrenih člankov po temah:

'''Farmacevtsko pomembni proteini''' 
# Development of Antibody-Fragment-Producing Rice for Neutralization of Human Norovirus (A. Sasou ''et. al''; Frontiers in Plant Science 12, 2021; https://doi.org/10.3389/fpls.2021.639953). [[Proizvodnja riža za sintezo fragmentov protiteles proti humanemu norovirusu.]] Mateja Žvipelj (11.3.)
# A New Plant Expression System for Producing Pharmaceutical Proteins (N. Abd-Aziz ''et. al''; Molecular Biotechnology 62, 2020; https://doi.org/10.1007/s12033-020-00242-2). [[Razvoj ekspresijskega sistema za proizvodnjo farmacevtskih proteinov v rastlini Mucuna bracteata]]. Jernej Imperl (18.3.)
# Development of a Recombinant Monospecific Anti-PLGF Bivalent Nanobody and Evaluation of it in Angiogenesis Modulation (A. Nikooharf "et all"; Molecular Biotechnology 62, 2020; https://link.springer.com/article/10.1007/s12033-020-00275-7#additional-information) [[Razvoj rekombinantnih monospecifičnih bivalentnih nanoteles proti PLGF-u]]. Nika Zaveršek (18.3.)

'''Cepiva''' 
# Development of a DNA Vaccine for Melanoma Metastasis by Inhalation Based on an Analysis of Transgene Expression Characteristics of Naked pDNA and a Ternary Complex in Mouse Lung Tissues (Kodama ''et.al'';Pharmaceutics 12,2020; https://www.mdpi.com/1999-4923/12/6/540#framed_div_cited_count) [[ Razvoj DNA cepiva proti metastazam melanoma z vdihavanjem na podlagi analize značilnosti transgene ekspresije gole pDNA in trojni kompleks v mišjem pljučnem tkivu]]. Paula Horvat (25.3.) 
# An AMA1/MSP119 Adjuvanted Malaria Transplastomic Plant‑Based Vaccine Induces Immune Responses in Test Animals (Evelia M. Milán‑Noris ''et. al''; Molecular Biotechnology 62, 2020; https://doi.org/10.1007/s12033-020-00271-x) [[V rastlinah proizvedeno transplastomsko antimalarijsko cepivo z AMA1/MSP119 in dodanim adjuvansom inducira imunski odziv v testnih živalih]]. Neža Pavko (25.3.) 

'''Gensko spremenjene rastline''' 
# A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch (C. Saintenac ''et al.''; Nat. Commun. 12, 2021, https://doi.org/10.1038/s41467-020-20685-0). [[Receptorju podobna kinaza bogata s cisteini, pšenici daje odpornost proti širokemu spektru pegavosti Septoria tritici]]. Andrej Race (7.4.)
# RNAi silenced ζ-carotene desaturase developed variegated tomato transformants with increased phytoene content (M. A. Babu ''et. al''; Plant Growth Regul. 93, 2021; https://doi.org/10.1007/s10725-020-00678-1). [[Vpliv utišanja ζ-karoten desaturaze na vsebnost karotenoidov v gensko spremenjenih paradižnikih]]. Peter Škrinjar (7.4.)

'''Gensko spremenjene živali in celične linije''' 
# Engineering carotenoid production in mammalian cells for nutritionally enhanced cell-cultured foods (A. J. Stout "et. al"; Metabolic Engineering 62, 2020; https://doi.org/10.1016/j.ymben.2020.07.011). [[Razvoj proizvodnje karotenoidov v sesalskih celicah za prehransko izboljšano celično pridobljeno meso]]. Urša Lovše (8.4.)
# Efficient photoactivatable Dre recombinase for cell type-specific spatiotemporal control of genome engineering in the mouse (H. Li ''et. al''; Proc. Natl. Acad. Sci. U. S. A. 117(52), 2021; https://doi.org/10.1073/pnas.2003991117). [[Priprava fotoinducibilne rekombinaze Dre kot orodje za prostorsko in časovno odvisno urejanje genoma v specifičnih mišjih celicah.]] Matija Ruparčič (8.4.)

'''Nizkomolekularni biotehnološki produkti''' 
# Fermentative N-Methylanthranilate Production by Engineered ''Corynebacterium glutamicum''. (T. Walter ''et. al.''; Microorganisms 8(6), 2020; https://doi.org/10.3390/microorganisms8060866). [[Fermentativna proizvodnja N-metilantranilata z inženirsko spremenjeno Corynebacterium glutamicum]]. Saša Slabe (14.4.)
# Efficient Biosynthesis of Vanillin from Isoeugenol by Recombinant Isoeugenol Monooxygenase from ''Pseudomonas nitroreducens'' Jin1. (Wang Q, Wu X, Lu X, He Y, Ma B, Xu Y. Efficient Biosynthesis of Vanillin from Isoeugenol by Recombinant Isoeugenol Monooxygenase from Pseudomonas nitroreducens Jin1. Appl Biochem Biotechnol. 2021:1116-1128. doi:10.1007/s12010-020-03478-5). [[Učinkovita biosinteza vanilina iz izoevgenola z uporabo rekombinantne izoevgenol monooksigenaze Jin1 iz bakterije Pseudomonas nitroreducens]]. Luka Gnidovec (15.4.)
# One-pot production of butyl butyrate from glucose using a cognate “diamond-shaped” ''E. coli'' consortium (J. P. Sinumvayo "et. al"; Bioresources and Bioprocessing 8, 2021; https://bioresourcesbioprocessing.springeropen.com/articles/10.1186/s40643-021-00372-8#Sec9). [[Proizvodnja butil butirata iz glukoze z uporabo "diamantnega" konzorcija E. coli]] Liza Ulčakar (15.4.)

'''Biotehnološki polimeri''' 
# Biotechnologically produced fucosylated oligosaccharides inhibit the binding of human noroviruses to their natural receptors (S. M. Derya et al., “Biotechnologically produced fucosylated oligosaccharides inhibit the binding of human noroviruses to their natural receptors,” ''J. Biotechnol.'', vol. 318, no. April, pp. 31–38, 2020, doi: 10.1016/j.jbiotec.2020.05.001). [[Inhibicija vezave humanega norovirusa na naravni receptor z biotehnološko proizvedenimi fukoziliranimi oligosaharidi]] Anže Karlek (21.4.)
# Complete biosynthesis of a sulfated chondroitin in ''Escherichia coli'' (Badri, A., ''et al''; Nature communications 12 (2021); https://doi.org/10.1038/s41467-021-21692-5). [[Popolna biosinteza hondroitin sulfata v E. coli]] Ana Maklin (22.4.)
# Optimization of cultivation medium and cyclic fed-batch fermentation strategy for enhanced polyhydroxyalkanoate production by Bacillus thuringiensis using a glucose-rich hydrolyzate (Singh et al. Bioresour. Bioprocess. (2021) 8:11, https://doi.org/10.1186/s40643-021-00361-x) [[Optimizacija fermentacijske proizvodnje PHA-bioplastike z b. thuringiensis in z glukozo bogatimi hidrolizati]] Urban Hribar (22.4.)

'''Biotehnološko pridobljeni encimi''' 
# Engineering a carboxypeptidase from ''Aspergillus niger'' M00988 by mutation to increase its ability in high Fischer ratio oligopeptide preparation (Xiong K., Liu J., Wang X., Sun B., Zhang Y., Zhao Z., Pei P., & Li X.; Journal of Biotechnology, 330, 1–8, 2021, https://doi.org/10.1016/j.jbiotec.2021.02.015). [[Priprava karboksipeptidaze iz glive Aspergillus niger M00988 za izboljšanje priprave oligopeptidov z visokim Fischerjevim razmerjem]] Urška Fajdiga (5.5.)
# Cell-Based High-Throughput Screening Protocol for Discovering Antiviral Inhibitors Against SARS-COV-2 Main Protease (3CLpro) (Rothan, H.A., Teoh, T.C; Mol Biotechnol 63, 240–248 (2021); https://doi.org/10.1007/s12033-021-00299-7) [[Visoko zmogljiv presejalni protokol na osnovi celic za raziskovanje antivirusnih inhibitorjev proti Sars-Cov-2 glavni proteazi (3CLpro)]] Mirsad Mešić (6.5.)
# A novel cold-active type I pullulanase from a hot-spring metagenome for effective debranching and production of resistant starch (M. Thakur ''et al''.; Bioresource Technology 320, 2021; https://doi.org/10.1016/j.biortech.2020.124288). [[Pri nizkih temperaturah aktivna pululanaza tipa I iz metagenoma vročih vrelcev omogoča učinkovito klestenje in proizvodnjo odpornega škroba]] Martina Lokar (6.5.)

'''Metabolno inženirstvo v biotehnologiji''' 
# Production of Tyrian purple indigoid dye from tryptophan in ''Escherichia coli'' (J. Lee ''et al.''; Nat. Chem. Biol. 17, 2021; https://doi.org/10.1038/s41589-020-00684-4). [http://wiki.fkkt.uni-lj.si/index.php/Proizvodnja_%C5%A1krlatnega_indigoidnega_barvila_iz_triptofana_v_bakteriji_Escherichia_coli Proizvodnja škrlatnega indigoidnega barvila iz triptofana v bakteriji ''Escherichia coli''] Jerneja Nimac (12.5.)
# Development of ''Pseudomonas asiatica'' as a host for the production of 3-hydroxypropionic acid from glycerol (T. Thi Nguyen et al., Bioresource Technology, vol. 329, 2021; https://doi.org/10.1016/j.biortech.2021.124867). [[Razvoj gostiteljskega organizma Pseudomonas asiatica za proizvodnjo 3-hidroksipropionske kisline iz glicerola]] Urška Pečarič Strnad (12.5.)
# Generation of an engineered food-grade ''Lactococcus lactis'' strain for production of an antimicrobial peptide: ''in vitro'' and ''in silico'' evaluation (A. Tanhaeian ''et. al''; BMC Biotechnol. 20(1), 2020; https://doi.org/10.1186/s12896-020-00612-3). [[Priprava in ovrednotenje novega seva bakterij Lactococcus lactis za proizvodnjo protimikrobnega peptida]]. Klementina Polanec (13.5.)
# Metabolic engineering of ''E. coli'' for producing phloroglucinol from acetate (S. Yu et. al; Applied Microbiology and Biotechnology. 2020; https://doi.org/10.1007/s00253-020-10591-2). [[Metabolno inženirstvo bakterije Escherichia coli za pridobivanje floroglucinola iz acetata]]. Ernestina Lavrih (13.5.)

'''Biomasa in biogoriva''' 
# Green Deep Eutectic Solvents for ''Microwave-Assisted Biomass'' Delignification and Valorisation (Grillo G. ''et al.''; Molecules 2021, 26(4), 798; https://www.mdpi.com/1420-3049/26/4/798/htm) [[Zelena globoka evtektična topila za delignifikacijo in valorizacijo biomase s pomočjo mikrovalov]]. Željka Erić (19.5.)
# Incorporating a molecular antenna in diatom microalgae cells enhances photosynthesis (Leone, G., De la Cruz Valbuena, G., Cicco, S.R. ''et al.''; Sci Rep 11, 2021; https://www.nature.com/articles/s41598-021-84690-z#Sec10) [[Vključevanje molekularne antene v celice mikroskopsko majhnih kremenastih alg (diatomej) za izboljšanje fotosintetske učinkovitosti]]. Karin Dobravc Škof (20.5.)
# Integrated cascade biorefinery processes for the production of single cell oil by ''Lipomyces starkeyi'' from ''Arundo donax L.'' hydrolysates (Di Fidio N ''et al.''; ''Bioresour. Tecnhol.'', vol.325, p.124635, Apr. 2021.; https://doi.org/10.1016/j.biortech.2020.124635). [[Integrirana procesa biorafinerijske proizvodnje znotrajceličnih založnih lipidov iz Arundo donax L. v Lipomyces starkeyi]] . Katja Doberšek (20.5.)

'''Okoljski vidiki biotehnologije in bioremediacija''' 
# Almina Tahirović (26.5.)
# Eva Keber (27.5.)
# Nina Lukančič (27.5.)

MBT seminarji 2021

2021-05-19T21:21:38Z

Zeljkae:

Seminarji iz Molekularne biotehnologije so letos organizirani tako, da vsak študent (praviloma v paru, lahko pa tudi samostojno) obdela temo s področja cepiv proti virusu SARS-CoV-2 in o tem pripravi kratek poljudno napisan povzetek. Ta del seminarjev je predstavljen na [[protikovidna cepiva|ločeni strani]].
V drugem delu vsak študent predstavi nek raziskovalni dosežek s širšega področja molekularne biotehnologije. Seznam tem in predstavitev za študijsko leto 2020/21 je predstavljen tu.

Povzetke morate objaviti do torka do polnoči v tednu, ko imate seminar (v četrtek). Angleški naslov prevedite tudi v slovenščino - to bo naslov povzetka, ki ga objavite na posebni strani, tako kot so to naredili kolegi pred vami (oz. predlani).

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 (28.2.) 
(slovenski naslov povežite z novo stranjo, na kateri bo povzetek)

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Naslovi odobrenih člankov po temah:

'''Farmacevtsko pomembni proteini''' 
# Development of Antibody-Fragment-Producing Rice for Neutralization of Human Norovirus (A. Sasou ''et. al''; Frontiers in Plant Science 12, 2021; https://doi.org/10.3389/fpls.2021.639953). [[Proizvodnja riža za sintezo fragmentov protiteles proti humanemu norovirusu.]] Mateja Žvipelj (11.3.)
# A New Plant Expression System for Producing Pharmaceutical Proteins (N. Abd-Aziz ''et. al''; Molecular Biotechnology 62, 2020; https://doi.org/10.1007/s12033-020-00242-2). [[Razvoj ekspresijskega sistema za proizvodnjo farmacevtskih proteinov v rastlini Mucuna bracteata]]. Jernej Imperl (18.3.)
# Development of a Recombinant Monospecific Anti-PLGF Bivalent Nanobody and Evaluation of it in Angiogenesis Modulation (A. Nikooharf "et all"; Molecular Biotechnology 62, 2020; https://link.springer.com/article/10.1007/s12033-020-00275-7#additional-information) [[Razvoj rekombinantnih monospecifičnih bivalentnih nanoteles proti PLGF-u]]. Nika Zaveršek (18.3.)

'''Cepiva''' 
# Development of a DNA Vaccine for Melanoma Metastasis by Inhalation Based on an Analysis of Transgene Expression Characteristics of Naked pDNA and a Ternary Complex in Mouse Lung Tissues (Kodama ''et.al'';Pharmaceutics 12,2020; https://www.mdpi.com/1999-4923/12/6/540#framed_div_cited_count) [[ Razvoj DNA cepiva proti metastazam melanoma z vdihavanjem na podlagi analize značilnosti transgene ekspresije gole pDNA in trojni kompleks v mišjem pljučnem tkivu]]. Paula Horvat (25.3.) 
# An AMA1/MSP119 Adjuvanted Malaria Transplastomic Plant‑Based Vaccine Induces Immune Responses in Test Animals (Evelia M. Milán‑Noris ''et. al''; Molecular Biotechnology 62, 2020; https://doi.org/10.1007/s12033-020-00271-x) [[V rastlinah proizvedeno transplastomsko antimalarijsko cepivo z AMA1/MSP119 in dodanim adjuvansom inducira imunski odziv v testnih živalih]]. Neža Pavko (25.3.) 

'''Gensko spremenjene rastline''' 
# A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch (C. Saintenac ''et al.''; Nat. Commun. 12, 2021, https://doi.org/10.1038/s41467-020-20685-0). [[Receptorju podobna kinaza bogata s cisteini, pšenici daje odpornost proti širokemu spektru pegavosti Septoria tritici]]. Andrej Race (7.4.)
# RNAi silenced ζ-carotene desaturase developed variegated tomato transformants with increased phytoene content (M. A. Babu ''et. al''; Plant Growth Regul. 93, 2021; https://doi.org/10.1007/s10725-020-00678-1). [[Vpliv utišanja ζ-karoten desaturaze na vsebnost karotenoidov v gensko spremenjenih paradižnikih]]. Peter Škrinjar (7.4.)

'''Gensko spremenjene živali in celične linije''' 
# Engineering carotenoid production in mammalian cells for nutritionally enhanced cell-cultured foods (A. J. Stout "et. al"; Metabolic Engineering 62, 2020; https://doi.org/10.1016/j.ymben.2020.07.011). [[Razvoj proizvodnje karotenoidov v sesalskih celicah za prehransko izboljšano celično pridobljeno meso]]. Urša Lovše (8.4.)
# Efficient photoactivatable Dre recombinase for cell type-specific spatiotemporal control of genome engineering in the mouse (H. Li ''et. al''; Proc. Natl. Acad. Sci. U. S. A. 117(52), 2021; https://doi.org/10.1073/pnas.2003991117). [[Priprava fotoinducibilne rekombinaze Dre kot orodje za prostorsko in časovno odvisno urejanje genoma v specifičnih mišjih celicah.]] Matija Ruparčič (8.4.)

'''Nizkomolekularni biotehnološki produkti''' 
# Fermentative N-Methylanthranilate Production by Engineered ''Corynebacterium glutamicum''. (T. Walter ''et. al.''; Microorganisms 8(6), 2020; https://doi.org/10.3390/microorganisms8060866). [[Fermentativna proizvodnja N-metilantranilata z inženirsko spremenjeno Corynebacterium glutamicum]]. Saša Slabe (14.4.)
# Efficient Biosynthesis of Vanillin from Isoeugenol by Recombinant Isoeugenol Monooxygenase from ''Pseudomonas nitroreducens'' Jin1. (Wang Q, Wu X, Lu X, He Y, Ma B, Xu Y. Efficient Biosynthesis of Vanillin from Isoeugenol by Recombinant Isoeugenol Monooxygenase from Pseudomonas nitroreducens Jin1. Appl Biochem Biotechnol. 2021:1116-1128. doi:10.1007/s12010-020-03478-5). [[Učinkovita biosinteza vanilina iz izoevgenola z uporabo rekombinantne izoevgenol monooksigenaze Jin1 iz bakterije Pseudomonas nitroreducens]]. Luka Gnidovec (15.4.)
# One-pot production of butyl butyrate from glucose using a cognate “diamond-shaped” ''E. coli'' consortium (J. P. Sinumvayo "et. al"; Bioresources and Bioprocessing 8, 2021; https://bioresourcesbioprocessing.springeropen.com/articles/10.1186/s40643-021-00372-8#Sec9). [[Proizvodnja butil butirata iz glukoze z uporabo "diamantnega" konzorcija E. coli]] Liza Ulčakar (15.4.)

'''Biotehnološki polimeri''' 
# Biotechnologically produced fucosylated oligosaccharides inhibit the binding of human noroviruses to their natural receptors (S. M. Derya et al., “Biotechnologically produced fucosylated oligosaccharides inhibit the binding of human noroviruses to their natural receptors,” ''J. Biotechnol.'', vol. 318, no. April, pp. 31–38, 2020, doi: 10.1016/j.jbiotec.2020.05.001). [[Inhibicija vezave humanega norovirusa na naravni receptor z biotehnološko proizvedenimi fukoziliranimi oligosaharidi]] Anže Karlek (21.4.)
# Complete biosynthesis of a sulfated chondroitin in ''Escherichia coli'' (Badri, A., ''et al''; Nature communications 12 (2021); https://doi.org/10.1038/s41467-021-21692-5). [[Popolna biosinteza hondroitin sulfata v E. coli]] Ana Maklin (22.4.)
# Optimization of cultivation medium and cyclic fed-batch fermentation strategy for enhanced polyhydroxyalkanoate production by Bacillus thuringiensis using a glucose-rich hydrolyzate (Singh et al. Bioresour. Bioprocess. (2021) 8:11, https://doi.org/10.1186/s40643-021-00361-x) [[Optimizacija fermentacijske proizvodnje PHA-bioplastike z b. thuringiensis in z glukozo bogatimi hidrolizati]] Urban Hribar (22.4.)

'''Biotehnološko pridobljeni encimi''' 
# Engineering a carboxypeptidase from ''Aspergillus niger'' M00988 by mutation to increase its ability in high Fischer ratio oligopeptide preparation (Xiong K., Liu J., Wang X., Sun B., Zhang Y., Zhao Z., Pei P., & Li X.; Journal of Biotechnology, 330, 1–8, 2021, https://doi.org/10.1016/j.jbiotec.2021.02.015). [[Priprava karboksipeptidaze iz glive Aspergillus niger M00988 za izboljšanje priprave oligopeptidov z visokim Fischerjevim razmerjem]] Urška Fajdiga (5.5.)
# Cell-Based High-Throughput Screening Protocol for Discovering Antiviral Inhibitors Against SARS-COV-2 Main Protease (3CLpro) (Rothan, H.A., Teoh, T.C; Mol Biotechnol 63, 240–248 (2021); https://doi.org/10.1007/s12033-021-00299-7) [[Visoko zmogljiv presejalni protokol na osnovi celic za raziskovanje antivirusnih inhibitorjev proti Sars-Cov-2 glavni proteazi (3CLpro)]] Mirsad Mešić (6.5.)
# A novel cold-active type I pullulanase from a hot-spring metagenome for effective debranching and production of resistant starch (M. Thakur ''et al''.; Bioresource Technology 320, 2021; https://doi.org/10.1016/j.biortech.2020.124288). [[Pri nizkih temperaturah aktivna pululanaza tipa I iz metagenoma vročih vrelcev omogoča učinkovito klestenje in proizvodnjo odpornega škroba]] Martina Lokar (6.5.)

'''Metabolno inženirstvo v biotehnologiji''' 
# Production of Tyrian purple indigoid dye from tryptophan in ''Escherichia coli'' (J. Lee ''et al.''; Nat. Chem. Biol. 17, 2021; https://doi.org/10.1038/s41589-020-00684-4). [http://wiki.fkkt.uni-lj.si/index.php/Proizvodnja_%C5%A1krlatnega_indigoidnega_barvila_iz_triptofana_v_bakteriji_Escherichia_coli Proizvodnja škrlatnega indigoidnega barvila iz triptofana v bakteriji ''Escherichia coli''] Jerneja Nimac (12.5.)
# Development of ''Pseudomonas asiatica'' as a host for the production of 3-hydroxypropionic acid from glycerol (T. Thi Nguyen et al., Bioresource Technology, vol. 329, 2021; https://doi.org/10.1016/j.biortech.2021.124867). [[Razvoj gostiteljskega organizma Pseudomonas asiatica za proizvodnjo 3-hidroksipropionske kisline iz glicerola]] Urška Pečarič Strnad (12.5.)
# Generation of an engineered food-grade ''Lactococcus lactis'' strain for production of an antimicrobial peptide: ''in vitro'' and ''in silico'' evaluation (A. Tanhaeian ''et. al''; BMC Biotechnol. 20(1), 2020; https://doi.org/10.1186/s12896-020-00612-3). [[Priprava in ovrednotenje novega seva bakterij Lactococcus lactis za proizvodnjo protimikrobnega peptida]]. Klementina Polanec (13.5.)
# Metabolic engineering of ''E. coli'' for producing phloroglucinol from acetate (S. Yu et. al; Applied Microbiology and Biotechnology. 2020; https://doi.org/10.1007/s00253-020-10591-2). [[Metabolno inženirstvo bakterije Escherichia coli za pridobivanje floroglucinola iz acetata]]. Ernestina Lavrih (13.5.)

'''Biomasa in biogoriva''' 
# Green Deep Eutectic Solvents for ''Microwave-Assisted Biomass'' Delignification and Valorisation (Grillo G
''et al.'';Molecules 2021, 26(4), 798; https://www.mdpi.com/1420-3049/26/4/798/htm) [[Zelena globoka evtektična topila za delignifikacijo in valorizacijo biomase s pomočjo mikrovalov]]. Željka Erić (19.5.)
# Incorporating a molecular antenna in diatom microalgae cells enhances photosynthesis (Leone, G., De la Cruz Valbuena, G., Cicco, S.R. ''et al.''; Sci Rep 11, 2021; https://www.nature.com/articles/s41598-021-84690-z#Sec10) [[Vključevanje molekularne antene v celice mikroskopsko majhnih kremenastih alg (diatomej) za izboljšanje fotosintetske učinkovitosti]]. Karin Dobravc Škof (20.5.)
# Integrated cascade biorefinery processes for the production of single cell oil by ''Lipomyces starkeyi'' from ''Arundo donax L.'' hydrolysates (Di Fidio N ''et al.''; ''Bioresour. Tecnhol.'', vol.325, p.124635, Apr. 2021.; https://doi.org/10.1016/j.biortech.2020.124635). [[Integrirana procesa biorafinerijske proizvodnje znotrajceličnih založnih lipidov iz Arundo donax L. v Lipomyces starkeyi]] . Katja Doberšek (20.5.)

'''Okoljski vidiki biotehnologije in bioremediacija''' 
# Almina Tahirović (26.5.)
# Eva Keber (27.5.)
# Nina Lukančič (27.5.)

Zelena globoka evtektična topila za delignifikacijo in valorizacijo biomase s pomočjo mikrovalov

2021-05-15T15:01:37Z

Zeljkae:

==Uvod==

V zadnjem desetletju je naraščajoča zavest o vplivu topil na onesnaževanje okolja povzročila iskanje bolj zelenih in bolj trajnostnih možnosti. Lignocelulozna biomasa je lahko dostopen, poceni in obnovljiv vir, sestavljen predvsem iz treh biopolimerov, in sicer: 1) celuloze, 2) hemiceluloze in 3) lignina.
Najobetavnejša komercialno izvedljiva pot za valorizacijo lignocelulozne biomase je fermentacija celuloznega in hemiceluloznega sladkorja v etanol. Postopek pretvorbe lignoceluloze v etanol je dražji kot cena omenjenega izdelka, etanola. Obetavna strategija za znižanje proizvodnih stroškov celuloznega etanola je razvoj biorafinerije, ki vključuje valorizacijo vseh komponent biomase s proizvodnjo kemikalij poleg etanola. Zaradi interakcij celuloza-lignin pa so za pridobitev ostankov, bogatih s celulozo, potrebni ostri pogoji predobdelave (močne kisline, visoka temperatura, dolg čas postopka itd.). Mikrovalovi (MW) opozarjajo na vse večjo pozornost zaradi njegovega potenciala za selektivno aktivacijo podlage in manjšega povpraševanja po energiji.

==Diskusija==

Topila, pridobljena iz biomase (zlasti hemiceluloze in lignina), vključno z γ-valerolaktonom (GVL), 2-metiltetrahidrofuranom, tetrahidrofuranom (THF), ionskimi tekočinami (Ils) in globokimi evtektičnimi topili (DES), se uspešno uporabljajo pri predobdelavi in pretvorbi biomase. Ionske tekočine so postale pozorne kot alternativna topila za predobdelavo biomase, ker je sposobnost nekaterih izmed njih, da raztopijo celulozo ali jo naredijo amorfno. S fizikalnimi in kemijskimi lastnostmi, primerljivimi z IL, so se globoka evtektična topila (DES) nedavno pojavila kot potencialna bolj zelena alternativa za več kemičnih in bioloških aplikacij. Poleg tega je postala priljubljena nova vrsta globokih evtektičnih topil, znana kot naravna globoka evtektična topila (NADES). So bolj zelena in učinkovita alternativa običajnim organskim topilom za postopke predobdelave biomase. NADES so običajno sestavljeni iz dveh ali več nestrupenih in poceni spojin, ki so vezane na vodikovo vez. Razvit je bil nov razred obnovljivih NADES iz lignina (LigDES), ki združuje uporabo ChCl (kot HBA) z nekaterimi fenoli, pridobljenimi iz lignina (kot HBD), kot so 4-hidroksibenzil alkohol (ChCl: HBA), katehol (ChCl: CAT ), vanilin (ChCl: VAN) in p-kumarna kislina (ChCl: PCA), da dobimo novo evtektično mešanico, primerno za razločitev beljakovine. Zato bodo v tem prispevku nekateri NADES, vključno s tistimi iz lignina, testirani v kombinaciji s tehnologijo MW, da bi izboljšali razločitev pšenične slame za nadaljnjo encimsko pretvorbo.

==Rezultati==
'''1. Naravna globoka evtektična topila (NaDES) in globoko evtektična topila, pridobljena iz lignina (LigDES)'''
Izbrani so bili štirje različni NaDES, da bi ocenili vpliv teh topil na WS delignifikacijo pri obsevanju z MW. Dokazano je, da lahko dodajanje zelo majhnih količin vode povzroči dramatično zmanjšanje viskoznosti večine NaDES.

'''2. Dielektrične lastnosti globokih evtektičnih topil (NaDES in LigDES)'''
Sinergija med ogrevanjem NaDES in MW bi lahko zelo učinkovito prispevala k razločitvi biomase zaradi interakcije obsevanja MW z elektrolitskimi topili. Izmerili so dielektrične lastnosti vseh NaDES-ov in LigDES-ov, saj je dobro znano, da je ogrevanje MW strogo povezano z dielektričnimi značilnostmi vzorcev.

'''3. Delignifikacija pšenične slame s pomočjo mikrovalov - NaDES in LigDES'''
Predhodno pripravljeni in karakterizirani NaDES in LigDES so bili uporabljeni kot topila za dekonstrukcijo pšenične slame (WS) s pomočjo MW za pridobivanje celuloze bogate snovi in lignina.

'''4. Antioksidativna aktivnost obnovljene tekoče frakcije - precipitacije pred in po ligninu'''
Po obdelavi s pomočjo MW so bili pridobljeni ekstrakti testirani na njihovo antioksidativno aktivnost z metodo 2,2-difenil-1-pikrilhidrazil (DPPH). NaDES-i so pokazali popolno odsotnost aktivnosti, LigDES-i imajo zelo nizke vrednosti EC50, kar izraža močno antioksidativno moč.

'''5. Encimska hidroliza (EH)'''
Po obdelavi WS s pomočjo MW smo izpeljano trdno frakcijo izkoristili za encimsko hidrolizo (EH). Rezultati so pokazali, da se je s povečevanjem časa encimske reakcije koncentracija sproščenih reducirajočih sladkorjev nekoliko povečala.

==Zaključek==

Cilj za premagovanje težav sedanjega koraka predhodne obdelave biomase, zelenih topil in tehnologije MW so bili povezani za doseganje trajnostne lignitocelulozne biomase. Študija kaže, da so DES-ji učinkoviti pri selektivnem raztapljanju lignina pri frakcioniranju biomase. Ogrevanje z MW ta postopek izboljša s hitrejšim ogrevanjem. Nadaljnja podrobna preiskava teh raziskovalnih področij bo zagotovila vsestransko uporabo NaDES za bistveno nižje stroške in okolju prijazne procese. Nov NaDES, pridobljen iz lignina, ChPPh, kaže odlične dielektrične lastnosti in bi lahko bil obetavno topilo za široko paleto aplikacij s pomočjo MW.

==Viri==

1. Grillo, Giorgio; Calcio Gaudino, Emanuela; Rosa, Robert; Leonelli, Cristina; Timonina, Ana; Grygiškis, Saulius; Tabasso, Silvia and Cravotto, Giancarlo 2021. „Green Deep Eutectic Solvents for Microwave-Assisted Biomass Delignification and Valorisation“, Bio-based and Safer Solvents.

2. 3,5-Dinitrosalicilna kislina, Wikipedia; https://en.wikipedia.org/wiki/3,5-Dinitrosalicylic_acid (pridobljeno: 10.5.2021)

3. Waste Valorization Techniques, GreenChemistry; https://greenchemistry.chemistryconferences.org/events-list/waste-valorization-techniques#:~:text=Waste%20valorization%20is%20the%20procedure%20of%20getting%20waste,recycling%2C%20composting%20from%20wastes%2C%20and%20sources%20of%20energy. (pridobljeno: 11.5.2021)

4. DPPH (2,2-Diphenyl-1-(2,4,6-trinitrophenyl)hydrazin-1-yl), Wikipedia; https://en.wikipedia.org/wiki/DPPH (pridobljeno: 14.5.2021)

Zelena globoka evtektična topila za delignifikacijo in valorizacijo biomase s pomočjo mikrovalov

2021-05-15T14:58:28Z

Zeljkae: New page: ==Uvod== V zadnjem desetletju je naraščajoča zavest o vplivu topil na onesnaževanje okolja povzročila iskanje bolj zelenih in bolj trajnostnih možnosti. Lignocelulozna biomasa je la...

==Uvod==

V zadnjem desetletju je naraščajoča zavest o vplivu topil na onesnaževanje okolja povzročila iskanje bolj zelenih in bolj trajnostnih možnosti. Lignocelulozna biomasa je lahko dostopen, poceni in obnovljiv vir, sestavljen predvsem iz treh biopolimerov, in sicer: 1) celuloze, 2) hemiceluloze in 3) lignina.
Najobetavnejša komercialno izvedljiva pot za valorizacijo lignocelulozne biomase je fermentacija celuloznega in hemiceluloznega sladkorja v etanol. Postopek pretvorbe lignoceluloze v etanol je dražji kot cena omenjenega izdelka, etanola. Obetavna strategija za znižanje proizvodnih stroškov celuloznega etanola je razvoj biorafinerije, ki vključuje valorizacijo vseh komponent biomase s proizvodnjo kemikalij poleg etanola. Zaradi interakcij celuloza-lignin pa so za pridobitev ostankov, bogatih s celulozo, potrebni ostri pogoji predobdelave (močne kisline, visoka temperatura, dolg čas postopka itd.). Mikrovalovi (MW) opozarjajo na vse večjo pozornost zaradi njegovega potenciala za selektivno aktivacijo podlage in manjšega povpraševanja po energiji.

==Diskusija==

Topila, pridobljena iz biomase (zlasti hemiceluloze in lignina), vključno z γ-valerolaktonom (GVL), 2-metiltetrahidrofuranom, tetrahidrofuranom (THF), ionskimi tekočinami (Ils) in globokimi evtektičnimi topili (DES), se uspešno uporabljajo pri predobdelavi in pretvorbi biomase . Ionske tekočine so postale pozorne kot alternativna topila za predobdelavo biomase, ker je sposobnost nekaterih izmed njih, da raztopijo celulozo ali jo naredijo amorfno. S fizikalnimi in kemijskimi lastnostmi, primerljivimi z IL, so se globoka evtektična topila (DES) nedavno pojavila kot potencialna bolj zelena alternativa za več kemičnih in bioloških aplikacij. Poleg tega je postala priljubljena nova vrsta globokih evtektičnih topil, znana kot naravna globoka evtektična topila (NADES). So bolj zelena in učinkovita alternativa običajnim organskim topilom za postopke predobdelave biomase. NADES so običajno sestavljeni iz dveh ali več nestrupenih in poceni spojin, ki so vezane na vodikovo vez. Razvit je bil nov razred obnovljivih NADES iz lignina (LigDES), ki združuje uporabo ChCl (kot HBA) z nekaterimi fenoli, pridobljenimi iz lignina (kot HBD), kot so 4-hidroksibenzil alkohol (ChCl: HBA), katehol (ChCl: CAT ), vanilin (ChCl: VAN) in p-kumarna kislina (ChCl: PCA), da dobimo novo evtektično mešanico, primerno za razločitev beljakovine. Zato bodo v tem prispevku nekateri NADES, vključno s tistimi iz lignina, testirani v kombinaciji s tehnologijo MW, da bi izboljšali razločitev pšenične slame za nadaljnjo encimsko pretvorbo.

==Rezultati==
'''1. Naravna globoka evtektična topila (NaDES) in globoko evtektična topila, pridobljena iz lignina (LigDES)'''
Izbrani so bili štirje različni NaDES, da bi ocenili vpliv teh topil na WS delignifikacijo pri obsevanju z MW. Dokazano je, da lahko dodajanje zelo majhnih količin vode povzroči dramatično zmanjšanje viskoznosti večine NaDES.

'''2. Dielektrične lastnosti globokih evtektičnih topil (NaDES in LigDES)'''
Sinergija med ogrevanjem NaDES in MW bi lahko zelo učinkovito prispevala k razločitvi biomase zaradi interakcije obsevanja MW z elektrolitskimi topili. Izmerili so dielektrične lastnosti vseh NaDES-ov in LigDES-ov, saj je dobro znano, da je ogrevanje MW strogo povezano z dielektričnimi značilnostmi vzorcev.

'''3. Delignifikacija pšenične slame s pomočjo mikrovalov - NaDES in LigDES'''
Predhodno pripravljeni in karakterizirani NaDES in LigDES so bili uporabljeni kot topila za dekonstrukcijo pšenične slame (WS) s pomočjo MW za pridobivanje celuloze bogate snovi in lignina.

'''4. Antioksidativna aktivnost obnovljene tekoče frakcije - precipitacije pred in po ligninu'''
Po obdelavi s pomočjo MW so bili pridobljeni ekstrakti testirani na njihovo antioksidativno aktivnost z metodo 2,2-difenil-1-pikrilhidrazil (DPPH). NaDES-i so pokazali popolno odsotnost aktivnosti, LigDES-i imajo zelo nizke vrednosti EC50, kar izraža močno antioksidativno moč.

'''5. Encimska hidroliza (EH)'''
Po obdelavi WS s pomočjo MW smo izpeljano trdno frakcijo izkoristili za encimsko hidrolizo (EH). Rezultati so pokazali, da se je s povečevanjem časa encimske reakcije koncentracija sproščenih reducirajočih sladkorjev nekoliko povečala.

==Zaključek==

Cilj za premagovanje težav sedanjega koraka predhodne obdelave biomase, zelenih topil in tehnologije MW so bili povezani za doseganje trajnostne lignitocelulozne biomase. Študija kaže, da so DES-ji učinkoviti pri selektivnem raztapljanju lignina pri frakcioniranju biomase. Ogrevanje z MW ta postopek izboljša s hitrejšim ogrevanjem. Nadaljnja podrobna preiskava teh raziskovalnih področij bo zagotovila vsestransko uporabo NaDES za bistveno nižje stroške in okolju prijazne procese. Nov NaDES, pridobljen iz lignina, ChPPh, kaže odlične dielektrične lastnosti in bi lahko bil obetavno topilo za široko paleto aplikacij s pomočjo MW.

==Viri==

1. Grillo, Giorgio; Calcio Gaudino, Emanuela; Rosa, Robert; Leonelli, Cristina; Timonina, Ana; Grygiškis, Saulius; Tabasso, Silvia and Cravotto, Giancarlo 2021. „Green Deep Eutectic Solvents for Microwave-Assisted Biomass Delignification and Valorisation“, Bio-based and Safer Solvents.

2. 3,5-Dinitrosalicilna kislina, Wikipedia; https://en.wikipedia.org/wiki/3,5-Dinitrosalicylic_acid (pridobljeno: 10.5.2021)

3. Waste Valorization Techniques, GreenChemistry; https://greenchemistry.chemistryconferences.org/events-list/waste-valorization-techniques#:~:text=Waste%20valorization%20is%20the%20procedure%20of%20getting%20waste,recycling%2C%20composting%20from%20wastes%2C%20and%20sources%20of%20energy. (pridobljeno: 11.5.2021)

4. DPPH (2,2-Diphenyl-1-(2,4,6-trinitrophenyl)hydrazin-1-yl), Wikipedia; https://en.wikipedia.org/wiki/DPPH (pridobljeno: 14.5.2021)

MBT seminarji 2021

2021-05-15T13:19:20Z

Zeljkae:

Seminarji iz Molekularne biotehnologije so letos organizirani tako, da vsak študent (praviloma v paru, lahko pa tudi samostojno) obdela temo s področja cepiv proti virusu SARS-CoV-2 in o tem pripravi kratek poljudno napisan povzetek. Ta del seminarjev je predstavljen na [[protikovidna cepiva|ločeni strani]].
V drugem delu vsak študent predstavi nek raziskovalni dosežek s širšega področja molekularne biotehnologije. Seznam tem in predstavitev za študijsko leto 2020/21 je predstavljen tu.

Povzetke morate objaviti do torka do polnoči v tednu, ko imate seminar (v četrtek). Angleški naslov prevedite tudi v slovenščino - to bo naslov povzetka, ki ga objavite na posebni strani, tako kot so to naredili kolegi pred vami (oz. predlani).

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 (28.2.) 
(slovenski naslov povežite z novo stranjo, na kateri bo povzetek)

----

Naslovi odobrenih člankov po temah:

'''Farmacevtsko pomembni proteini''' 
# Development of Antibody-Fragment-Producing Rice for Neutralization of Human Norovirus (A. Sasou ''et. al''; Frontiers in Plant Science 12, 2021; https://doi.org/10.3389/fpls.2021.639953). [[Proizvodnja riža za sintezo fragmentov protiteles proti humanemu norovirusu.]] Mateja Žvipelj (11.3.)
# A New Plant Expression System for Producing Pharmaceutical Proteins (N. Abd-Aziz ''et. al''; Molecular Biotechnology 62, 2020; https://doi.org/10.1007/s12033-020-00242-2). [[Razvoj ekspresijskega sistema za proizvodnjo farmacevtskih proteinov v rastlini Mucuna bracteata]]. Jernej Imperl (18.3.)
# Development of a Recombinant Monospecific Anti-PLGF Bivalent Nanobody and Evaluation of it in Angiogenesis Modulation (A. Nikooharf "et all"; Molecular Biotechnology 62, 2020; https://link.springer.com/article/10.1007/s12033-020-00275-7#additional-information) [[Razvoj rekombinantnih monospecifičnih bivalentnih nanoteles proti PLGF-u]]. Nika Zaveršek (18.3.)

'''Cepiva''' 
# Development of a DNA Vaccine for Melanoma Metastasis by Inhalation Based on an Analysis of Transgene Expression Characteristics of Naked pDNA and a Ternary Complex in Mouse Lung Tissues (Kodama ''et.al'';Pharmaceutics 12,2020; https://www.mdpi.com/1999-4923/12/6/540#framed_div_cited_count) [[ Razvoj DNA cepiva proti metastazam melanoma z vdihavanjem na podlagi analize značilnosti transgene ekspresije gole pDNA in trojni kompleks v mišjem pljučnem tkivu]]. Paula Horvat (25.3.) 
# An AMA1/MSP119 Adjuvanted Malaria Transplastomic Plant‑Based Vaccine Induces Immune Responses in Test Animals (Evelia M. Milán‑Noris ''et. al''; Molecular Biotechnology 62, 2020; https://doi.org/10.1007/s12033-020-00271-x) [[V rastlinah proizvedeno transplastomsko antimalarijsko cepivo z AMA1/MSP119 in dodanim adjuvansom inducira imunski odziv v testnih živalih]]. Neža Pavko (25.3.) 

'''Gensko spremenjene rastline''' 
# A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch (C. Saintenac ''et al.''; Nat. Commun. 12, 2021, https://doi.org/10.1038/s41467-020-20685-0). [[Receptorju podobna kinaza bogata s cisteini, pšenici daje odpornost proti širokemu spektru pegavosti Septoria tritici]]. Andrej Race (7.4.)
# RNAi silenced ζ-carotene desaturase developed variegated tomato transformants with increased phytoene content (M. A. Babu ''et. al''; Plant Growth Regul. 93, 2021; https://doi.org/10.1007/s10725-020-00678-1). [[Vpliv utišanja ζ-karoten desaturaze na vsebnost karotenoidov v gensko spremenjenih paradižnikih]]. Peter Škrinjar (7.4.)

'''Gensko spremenjene živali in celične linije''' 
# Engineering carotenoid production in mammalian cells for nutritionally enhanced cell-cultured foods (A. J. Stout "et. al"; Metabolic Engineering 62, 2020; https://doi.org/10.1016/j.ymben.2020.07.011). [[Razvoj proizvodnje karotenoidov v sesalskih celicah za prehransko izboljšano celično pridobljeno meso]]. Urša Lovše (8.4.)
# Efficient photoactivatable Dre recombinase for cell type-specific spatiotemporal control of genome engineering in the mouse (H. Li ''et. al''; Proc. Natl. Acad. Sci. U. S. A. 117(52), 2021; https://doi.org/10.1073/pnas.2003991117). [[Priprava fotoinducibilne rekombinaze Dre kot orodje za prostorsko in časovno odvisno urejanje genoma v specifičnih mišjih celicah.]] Matija Ruparčič (8.4.)

'''Nizkomolekularni biotehnološki produkti''' 
# Fermentative N-Methylanthranilate Production by Engineered ''Corynebacterium glutamicum''. (T. Walter ''et. al.''; Microorganisms 8(6), 2020; https://doi.org/10.3390/microorganisms8060866). [[Fermentativna proizvodnja N-metilantranilata z inženirsko spremenjeno Corynebacterium glutamicum]]. Saša Slabe (14.4.)
# Efficient Biosynthesis of Vanillin from Isoeugenol by Recombinant Isoeugenol Monooxygenase from ''Pseudomonas nitroreducens'' Jin1. (Wang Q, Wu X, Lu X, He Y, Ma B, Xu Y. Efficient Biosynthesis of Vanillin from Isoeugenol by Recombinant Isoeugenol Monooxygenase from Pseudomonas nitroreducens Jin1. Appl Biochem Biotechnol. 2021:1116-1128. doi:10.1007/s12010-020-03478-5). [[Učinkovita biosinteza vanilina iz izoevgenola z uporabo rekombinantne izoevgenol monooksigenaze Jin1 iz bakterije Pseudomonas nitroreducens]]. Luka Gnidovec (15.4.)
# One-pot production of butyl butyrate from glucose using a cognate “diamond-shaped” ''E. coli'' consortium (J. P. Sinumvayo "et. al"; Bioresources and Bioprocessing 8, 2021; https://bioresourcesbioprocessing.springeropen.com/articles/10.1186/s40643-021-00372-8#Sec9). [[Proizvodnja butil butirata iz glukoze z uporabo "diamantnega" konzorcija E. coli]] Liza Ulčakar (15.4.)

'''Biotehnološki polimeri''' 
# Biotechnologically produced fucosylated oligosaccharides inhibit the binding of human noroviruses to their natural receptors (S. M. Derya et al., “Biotechnologically produced fucosylated oligosaccharides inhibit the binding of human noroviruses to their natural receptors,” ''J. Biotechnol.'', vol. 318, no. April, pp. 31–38, 2020, doi: 10.1016/j.jbiotec.2020.05.001). [[Inhibicija vezave humanega norovirusa na naravni receptor z biotehnološko proizvedenimi fukoziliranimi oligosaharidi]] Anže Karlek (21.4.)
# Complete biosynthesis of a sulfated chondroitin in ''Escherichia coli'' (Badri, A., ''et al''; Nature communications 12 (2021); https://doi.org/10.1038/s41467-021-21692-5). [[Popolna biosinteza hondroitin sulfata v E. coli]] Ana Maklin (22.4.)
# Optimization of cultivation medium and cyclic fed-batch fermentation strategy for enhanced polyhydroxyalkanoate production by Bacillus thuringiensis using a glucose-rich hydrolyzate (Singh et al. Bioresour. Bioprocess. (2021) 8:11, https://doi.org/10.1186/s40643-021-00361-x) [[Optimizacija fermentacijske proizvodnje PHA-bioplastike z b. thuringiensis in z glukozo bogatimi hidrolizati]] Urban Hribar (22.4.)

'''Biotehnološko pridobljeni encimi''' 
# Engineering a carboxypeptidase from ''Aspergillus niger'' M00988 by mutation to increase its ability in high Fischer ratio oligopeptide preparation (Xiong K., Liu J., Wang X., Sun B., Zhang Y., Zhao Z., Pei P., & Li X.; Journal of Biotechnology, 330, 1–8, 2021, https://doi.org/10.1016/j.jbiotec.2021.02.015). [[Priprava karboksipeptidaze iz glive Aspergillus niger M00988 za izboljšanje priprave oligopeptidov z visokim Fischerjevim razmerjem]] Urška Fajdiga (5.5.)
# Cell-Based High-Throughput Screening Protocol for Discovering Antiviral Inhibitors Against SARS-COV-2 Main Protease (3CLpro) (Rothan, H.A., Teoh, T.C; Mol Biotechnol 63, 240–248 (2021); https://doi.org/10.1007/s12033-021-00299-7) [[Visoko zmogljiv presejalni protokol na osnovi celic za raziskovanje antivirusnih inhibitorjev proti Sars-Cov-2 glavni proteazi (3CLpro)]] Mirsad Mešić (6.5.)
# A novel cold-active type I pullulanase from a hot-spring metagenome for effective debranching and production of resistant starch (M. Thakur ''et al''.; Bioresource Technology 320, 2021; https://doi.org/10.1016/j.biortech.2020.124288). [[Pri nizkih temperaturah aktivna pululanaza tipa I iz metagenoma vročih vrelcev omogoča učinkovito klestenje in proizvodnjo odpornega škroba]] Martina Lokar (6.5.)

'''Metabolno inženirstvo v biotehnologiji''' 
# Production of Tyrian purple indigoid dye from tryptophan in ''Escherichia coli'' (J. Lee ''et al.''; Nat. Chem. Biol. 17, 2021; https://doi.org/10.1038/s41589-020-00684-4). [http://wiki.fkkt.uni-lj.si/index.php/Proizvodnja_%C5%A1krlatnega_indigoidnega_barvila_iz_triptofana_v_bakteriji_Escherichia_coli Proizvodnja škrlatnega indigoidnega barvila iz triptofana v bakteriji ''Escherichia coli''] Jerneja Nimac (12.5.)
# Development of ''Pseudomonas asiatica'' as a host for the production of 3-hydroxypropionic acid from glycerol (T. Thi Nguyen et al., Bioresource Technology, vol. 329, 2021; https://doi.org/10.1016/j.biortech.2021.124867). [[Razvoj gostiteljskega organizma Pseudomonas asiatica za proizvodnjo 3-hidroksipropionske kisline iz glicerola]] Urška Pečarič Strnad (12.5.)
# Generation of an engineered food-grade ''Lactococcus lactis'' strain for production of an antimicrobial peptide: ''in vitro'' and ''in silico'' evaluation (A. Tanhaeian ''et. al''; BMC Biotechnol. 20(1), 2020; https://doi.org/10.1186/s12896-020-00612-3). [[Priprava in ovrednotenje novega seva bakterij Lactococcus lactis za proizvodnjo protimikrobnega peptida]]. Klementina Polanec (13.5.)
# Metabolic engineering of ''E. coli'' for producing phloroglucinol from acetate (S. Yu et. al; Applied Microbiology and Biotechnology. 2020; https://doi.org/10.1007/s00253-020-10591-2). [[Metabolno inženirstvo bakterije Escherichia coli za pridobivanje floroglucinola iz acetata]]. Ernestina Lavrih (13.5.)

'''Biomasa in biogoriva''' 
# Green Deep Eutectic Solvents for ''Microwave-Assisted Biomass'' Delignification and Valorisation (Department of Chemi., University of Turin, 4.2.2021; https://www.mdpi.com/1420-3049/26/4/798/htm) [[Zelena globoka evtektična topila za delignifikacijo in valorizacijo biomase s pomočjo mikrovalov]]. Željka Erić (19.5.)
# Karin Dobravc Škof (20.5.)
# Katja Doberšek (20.5.)

'''Okoljski vidiki biotehnologije in bioremediacija''' 
# Almina Tahirović (26.5.)
# Eva Keber (27.5.)
# Nina Lukančič (27.5.)

Značilnosti cepiva VBI-2902a (virusom podobni delci)

2021-05-07T09:46:55Z

Zeljkae: New page: =UVOD= VBI Vaccines Inc. je biofarmacevtsko podjetje, ki ga poganja imunologija in si prizadeva za močno preprečevanje in zdravljenje bolezni. S svojim inovativnim pristopom k virusom po...

=UVOD=
VBI Vaccines Inc. je biofarmacevtsko podjetje, ki ga poganja imunologija in si prizadeva za močno preprečevanje in zdravljenje bolezni. S svojim inovativnim pristopom k virusom podobnim delcem ("VLP"), vključno s tehnologijo platforme VLP ("eVLP"), VBI razvija kandidate za cepiva, ki posnemajo naravno predstavitev virusov, namenjene izvabljanju prirojene moči človeškega imunskega sistema.

=KAJ JE VBI-2902a CEPIVO=
VBI-2902a je kandidat za preskusno cepivo, ki uporablja ekspresijo virusnih podobnih delcev modificirano verzijo glikoproteina spike SARS-CoV-2 in je zasnovan tako, da inducira nevtralizirajoča protitelesa in imunski odziv, ki ga povzročajo celice, proti SARS-CoV-2 spike proteinu. VBI-2902a z vsebnostjo do 10 μg proteinov in dodatkom aluminijevega fosfata se daje z intramuskularno injekcijo.

=KLINIČNE ŠTUDIJE=
Študija faze 1/2 bo ovrednotila varnost, prenašanje in imunogenost zdravila VBI-2902a v režimu enega in dveh odmerkov ter dve ravni odmerka (5 μg in 10 μg spike proteina) v primerjavi s placebom (fiziološka raztopina) pri zdravih odrasli, stari 18 let ali več. Število udeležencev je 780.

Začetna študija faze 1/2 VBI-2902a, se je začela 15. marca 2021 in naj bi bila končana junija 2022.

=LITERATURA=
[1] Jeff Baxter, CEO; David E. Anderson, CSO Preclinical Coronavirus Program Data (https://1o976r1jw2eculmeoxz46ig6-wpengine.netdna-ssl.com/wp-content/uploads/2020/08/August-2020-VBI-2900-Preclinical-Data-Announcement_Final.pdf)

[2] Anne-Catherine Fluckiger, Barthelemy Ontsouka, Jasminka Bozic, Abebaw Diress, Tanvir Ahmed, Tamara Berthoud, Anh Tran, Diane Duque, Mingmin Liao, Michael McCluskie, Francisco Diaz-Mitoma, David E. Anderson, Catalina Soare, “An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose” bioRxiv, 28.4.2021 (https://www.biorxiv.org/content/10.1101/2021.04.28.441832v1.full)

[3] VBI-2902 – Wikipedia https://en.wikipedia.org/wiki/VBI-2902 (pridobljeno 5. 5. 2021)

[4] VBIVACCINE – VBI Vaccines Announces Publication of Preclinical and Challenge Study Data of its eVLP Vaccine Candidate Against COVID-19 (VBI-2902)
April 28, 2021 https://www.vbivaccines.com/press-releases/vbi-2902-preclinical-and-challenge-study-data/ (pridobljeno 6. 5. 2021)

[5] VBIVACCINE - VBI Vaccines Announces Preclinical Coronavirus Program Data and Selection of Clinical Candidates with Potential as One-Dose Vaccines https://www.vbivaccines.com/press-releases/preclinical-coronavirus-data-candidate-selection/ (pridobljeno: 7. 5. 2021)

[6] VBI-2902a - ClinicalTrials.gov, Safety, Tolerability, and Immunogenicity of the COVID-19 Vaccine Candidate (VBI-2902a) https://clinicaltrials.gov/ct2/show/NCT04773665 (pridobljeno: 7. 5. 2021)

Protikovidna cepiva

2021-05-07T09:46:33Z

Zeljkae:

Študentski seminar pri predmetu Molekularna biotehnologija 2020/21 
Univerza v Ljubljani, Fakulteta za kemijo in kemijsko tehnologijo 
Magistrski študij Biokemija 

Seminar pripravljajo študentje 1. in 2. letnika magistrskega študija. Kratki povzetki morajo biti napisani na taki ravni zahtevnosti, da so razumljivi širši javnosti. Predstavitve seminarjev (6 oz. 12 minut) imajo splošen uvod in strokovno nadaljevanje. Vsebina temelji na javno dostopnih podatkih v času priprave seminarja. Po zadnji seminarski predstavitvi bomo predvidoma izdali zbornih povzetkov, ki bo vključeval tudi slikovne razlage. Poleg tega seminarja morajo študentje pripraviti tudi daljšo predstavitev teme iz znanstvene literature.

Razpored predstavitev:

# [[Molekularnobiološke značilnosti SARS-CoV-2 in aktualni mutanti (južnoafriški, britanski, nigerijski,...)]] - 11.3. (12 min) 
# [[Interakcija SARS-CoV-2 s tarčno celico]] - 11.3. (6 min) 
# [[Značilnosti cepiva proizvajalca Moderna (mRNA)]] - 18.3. (12 min) 
# [[Rezultati kliničnih testiranj cepiva proizvajalca Moderna (mRNA) ]] - 18.3.(6 min) 
# [[Značilnosti cepiva proizvajalca AstraZeneca / Oxford University (ChAdOx1)]] - 25.3. (12 min) 
# [[Rezultati kliničnih testiranj proizvajalca AstraZeneca / Oxford University (ChAdOx1)]] - 25.3. (6 min) 
# [[Značilnosti cepiva proizvajalca Pfizer / BioNTech (mRNA)]] - 1.4. (12 min) 
# [[Rezultati kliničnih testiranj cepiva proizvajalca Pfizer / BioNTech (mRNA)]] - 1.4. (12 min) 
# [[Značilnosti cepiva proizvajalca Johnson&Johnson / Jennsen (Ad26)]] - 8.4. (6 min) 
# [[Opuščena cepiva: Merck (IAVI, Themix), Imperial College London, Univ. of Queensland]] - 8.4. (12 min) 
# [[Značilnosti cepiva Sputnik V (Gamaleya) (Ad26, Ad5)]] - 15.4. (12 min) 
# [[Značilnosti cepiva CanSino (Ad5)]] - 15.4. (12 min) 
# [[Značilnosti cepiv Sinopharm in Sinovac (inaktivirano)]] - 22.4. (12 min) 
# [[Značilnosti cepiva Bharat Biotech (inaktivirano)]] - 22.4. (12 min) 
# [[Značilnosti cepiva Novavax (proteinsko)]] - 6.5. (12 min) 
# [[Značilnosti cepiva EpiVacCorona (peptidno)]] - 6.5. (6 min) 
# [[Značilnosti cepiva VBI-2902a (virusom podobni delci)]] - 13.5. (6 min) 
nerazporejeno:
# Značilnosti cepiva Zydus Cadila (DNA) 
# Značilnosti cepiva COVAXX / UBI (peptidno) 
 
----
Povezava do [https://www.youtube.com/watch?v=K3odScka55A videa z razlago] o načinu določanja učinkovitosti cepiv in o (ne)smislu primerjanja teh vrednosti (Vox).

User talk:Zeljkae

2021-05-07T09:44:59Z

Zeljkae:

User talk:Zeljkae

2021-05-07T09:44:03Z

Zeljkae:

=UVOD=
VBI Vaccines Inc. je biofarmacevtsko podjetje, ki ga poganja imunologija in si prizadeva za močno preprečevanje in zdravljenje bolezni. S svojim inovativnim pristopom k virusom podobnim delcem ("VLP"), vključno s tehnologijo platforme VLP ("eVLP"), VBI razvija kandidate za cepiva, ki posnemajo naravno predstavitev virusov, namenjene izvabljanju prirojene moči človeškega imunskega sistema.

=KAJ JE VBI-2902a CEPIVO=
VBI-2902a je kandidat za preskusno cepivo, ki uporablja ekspresijo virusnih podobnih delcev modificirano verzijo glikoproteina spike SARS-CoV-2 in je zasnovan tako, da inducira nevtralizirajoča protitelesa in imunski odziv, ki ga povzročajo celice, proti SARS-CoV-2 spike proteinu. VBI-2902a z vsebnostjo do 10 μg proteinov in dodatkom aluminijevega fosfata se daje z intramuskularno injekcijo.

=KLINIČNE ŠTUDIJE=
Študija faze 1/2 bo ovrednotila varnost, prenašanje in imunogenost zdravila VBI-2902a v režimu enega in dveh odmerkov ter dve ravni odmerka (5 μg in 10 μg spike proteina) v primerjavi s placebom (fiziološka raztopina) pri zdravih odrasli, stari 18 let ali več. Število udeležencev je 780.

Začetna študija faze 1/2 VBI-2902a, se je začela 15. marca 2021 in naj bi bila končana junija 2022.

=LITERATURA=
[1] Jeff Baxter, CEO; David E. Anderson, CSO Preclinical Coronavirus Program Data (https://1o976r1jw2eculmeoxz46ig6-wpengine.netdna-ssl.com/wp-content/uploads/2020/08/August-2020-VBI-2900-Preclinical-Data-Announcement_Final.pdf)

[2] Anne-Catherine Fluckiger, Barthelemy Ontsouka, Jasminka Bozic, Abebaw Diress, Tanvir Ahmed, Tamara Berthoud, Anh Tran, Diane Duque, Mingmin Liao, Michael McCluskie, Francisco Diaz-Mitoma, David E. Anderson, Catalina Soare, “An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose” bioRxiv, 28.4.2021 (https://www.biorxiv.org/content/10.1101/2021.04.28.441832v1.full)

[3] A. B. Ryzhikov et al., “Immunogenicity and protectivity of the peptide candidate vaccine against SARS-CoV-2,” Ann. Russ. Acad. Med. Sci., vol. 76, no. 1, pp. 5–19, 2021.

[4] VBI-2902 – Wikipedia https://en.wikipedia.org/wiki/VBI-2902 (pridobljeno 5. 5. 2021)

[5] VBIVACCINE – VBI Vaccines Announces Publication of Preclinical and Challenge Study Data of its eVLP Vaccine Candidate Against COVID-19 (VBI-2902)
April 28, 2021 https://www.vbivaccines.com/press-releases/vbi-2902-preclinical-and-challenge-study-data/ (pridobljeno 6. 5. 2021)

[6] VBIVACCINE - VBI Vaccines Announces Preclinical Coronavirus Program Data and Selection of Clinical Candidates with Potential as One-Dose Vaccines https://www.vbivaccines.com/press-releases/preclinical-coronavirus-data-candidate-selection/ (pridobljeno: 7. 5. 2021)

[7] VBI-2902a - ClinicalTrials.gov, Safety, Tolerability, and Immunogenicity of the COVID-19 Vaccine Candidate (VBI-2902a) https://clinicaltrials.gov/ct2/show/NCT04773665 (pridobljeno: 7. 5. 2021)

User talk:Zeljkae

2021-05-07T09:43:19Z

Zeljkae:

=UVOD=
VBI Vaccines Inc. je biofarmacevtsko podjetje, ki ga poganja imunologija in si prizadeva za močno preprečevanje in zdravljenje bolezni. S svojim inovativnim pristopom k virusom podobnim delcem ("VLP"), vključno s tehnologijo platforme VLP ("eVLP"), VBI razvija kandidate za cepiva, ki posnemajo naravno predstavitev virusov, namenjene izvabljanju prirojene moči človeškega imunskega sistema.

=KAJ JE VBI-2902a CEPIVO=
VBI-2902a je kandidat za preskusno cepivo, ki uporablja ekspresijo virusnih podobnih delcev modificirano verzijo glikoproteina spike SARS-CoV-2 in je zasnovan tako, da inducira nevtralizirajoča protitelesa in imunski odziv, ki ga povzročajo celice, proti SARS-CoV-2 spike proteinu. VBI-2902a z vsebnostjo do 10 μg proteinov in dodatkom aluminijevega fosfata se daje z intramuskularno injekcijo.

=KLINIČNE ŠTUDIJE=
Študija faze 1/2 bo ovrednotila varnost, prenašanje in imunogenost zdravila VBI-2902a v režimu enega in dveh odmerkov ter dve ravni odmerka (5 μg in 10 μg spike proteina) v primerjavi s placebom (fiziološka raztopina) pri zdravih odrasli, stari 18 let ali več. Število udeležencev je 780.

Začetna študija faze 1/2 VBI-2902a, se je začela 15. marca 2021 in naj bi bila končana junija 2022.

=LITERATURA=
[1] Jeff Baxter, CEO; David E. Anderson, CSO Preclinical Coronavirus Program Data (https://1o976r1jw2eculmeoxz46ig6-wpengine.netdna-ssl.com/wp-content/uploads/2020/08/August-2020-VBI-2900-Preclinical-Data-Announcement_Final.pdf)

[2] View ORCID ProfileAnne-Catherine Fluckiger, View ORCID ProfileBarthelemy Ontsouka, Jasminka Bozic, Abebaw Diress, Tanvir Ahmed, Tamara Berthoud, Anh Tran, Diane Duque, Mingmin Liao, Michael McCluskie, View ORCID ProfileFrancisco Diaz-Mitoma, David E. Anderson, Catalina Soare, “An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose” bioRxiv, 28.4.2021 (https://www.biorxiv.org/content/10.1101/2021.04.28.441832v1.full)

[3] A. B. Ryzhikov et al., “Immunogenicity and protectivity of the peptide candidate vaccine against SARS-CoV-2,” Ann. Russ. Acad. Med. Sci., vol. 76, no. 1, pp. 5–19, 2021.

[4] VBI-2902 – Wikipedia https://en.wikipedia.org/wiki/VBI-2902 (pridobljeno 5. 5. 2021)

[5] VBIVACCINE – VBI Vaccines Announces Publication of Preclinical and Challenge Study Data of its eVLP Vaccine Candidate Against COVID-19 (VBI-2902)
April 28, 2021 https://www.vbivaccines.com/press-releases/vbi-2902-preclinical-and-challenge-study-data/ (pridobljeno 6. 5. 2021)

[6] VBIVACCINE - VBI Vaccines Announces Preclinical Coronavirus Program Data and Selection of Clinical Candidates with Potential as One-Dose Vaccines https://www.vbivaccines.com/press-releases/preclinical-coronavirus-data-candidate-selection/ (pridobljeno: 7. 5. 2021)

[7] VBI-2902a - ClinicalTrials.gov, Safety, Tolerability, and Immunogenicity of the COVID-19 Vaccine Candidate (VBI-2902a) https://clinicaltrials.gov/ct2/show/NCT04773665 (pridobljeno: 7. 5. 2021)

User talk:Zeljkae

2021-05-07T09:41:56Z

Zeljkae:

='''UVOD'''=
VBI Vaccines Inc. je biofarmacevtsko podjetje, ki ga poganja imunologija in si prizadeva za močno preprečevanje in zdravljenje bolezni. S svojim inovativnim pristopom k virusom podobnim delcem ("VLP"), vključno s tehnologijo platforme VLP ("eVLP"), VBI razvija kandidate za cepiva, ki posnemajo naravno predstavitev virusov, namenjene izvabljanju prirojene moči človeškega imunskega sistema.

='''KAJ JE VBI-2902a CEPIVO'''=
VBI-2902a je kandidat za preskusno cepivo, ki uporablja ekspresijo virusnih podobnih delcev modificirano verzijo glikoproteina spike SARS-CoV-2 in je zasnovan tako, da inducira nevtralizirajoča protitelesa in imunski odziv, ki ga povzročajo celice, proti SARS-CoV-2 spike proteinu. VBI-2902a z vsebnostjo do 10 μg proteinov in dodatkom aluminijevega fosfata se daje z intramuskularno injekcijo.

='''KLINIČNE ŠTUDIJE'''=
Študija faze 1/2 bo ovrednotila varnost, prenašanje in imunogenost zdravila VBI-2902a v režimu enega in dveh odmerkov ter dve ravni odmerka (5 μg in 10 μg spike proteina) v primerjavi s placebom (fiziološka raztopina) pri zdravih odrasli, stari 18 let ali več. Število udeležencev je 780.

Začetna študija faze 1/2 VBI-2902a, se je začela 15. marca 2021 in naj bi bila končana junija 2022.

='''LITERATURA'''=
[1] Jeff Baxter, CEO; David E. Anderson, CSO Preclinical Coronavirus Program Data (https://1o976r1jw2eculmeoxz46ig6-wpengine.netdna-ssl.com/wp-content/uploads/2020/08/August-2020-VBI-2900-Preclinical-Data-Announcement_Final.pdf)

[2] View ORCID ProfileAnne-Catherine Fluckiger, View ORCID ProfileBarthelemy Ontsouka, Jasminka Bozic, Abebaw Diress, Tanvir Ahmed, Tamara Berthoud, Anh Tran, Diane Duque, Mingmin Liao, Michael McCluskie, View ORCID ProfileFrancisco Diaz-Mitoma, David E. Anderson, Catalina Soare, “An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose” bioRxiv, 28.4.2021 (https://www.biorxiv.org/content/10.1101/2021.04.28.441832v1.full)

[3] A. B. Ryzhikov et al., “Immunogenicity and protectivity of the peptide candidate vaccine against SARS-CoV-2,” Ann. Russ. Acad. Med. Sci., vol. 76, no. 1, pp. 5–19, 2021.

[4] VBI-2902 – Wikipedia https://en.wikipedia.org/wiki/VBI-2902 (pridobljeno 5. 5. 2021)

[5] VBIVACCINE – VBI Vaccines Announces Publication of Preclinical and Challenge Study Data of its eVLP Vaccine Candidate Against COVID-19 (VBI-2902)
April 28, 2021 https://www.vbivaccines.com/press-releases/vbi-2902-preclinical-and-challenge-study-data/ (pridobljeno 6. 5. 2021)

[6] VBIVACCINE - VBI Vaccines Announces Preclinical Coronavirus Program Data and Selection of Clinical Candidates with Potential as One-Dose Vaccines https://www.vbivaccines.com/press-releases/preclinical-coronavirus-data-candidate-selection/ (pridobljeno: 7. 5. 2021)

[7] VBI-2902a - ClinicalTrials.gov, Safety, Tolerability, and Immunogenicity of the COVID-19 Vaccine Candidate (VBI-2902a) https://clinicaltrials.gov/ct2/show/NCT04773665 (pridobljeno: 7. 5. 2021)

User talk:Zeljkae

2021-05-07T09:41:08Z

Zeljkae:

='''Uvod'''=
VBI Vaccines Inc. je biofarmacevtsko podjetje, ki ga poganja imunologija in si prizadeva za močno preprečevanje in zdravljenje bolezni. S svojim inovativnim pristopom k virusom podobnim delcem ("VLP"), vključno s tehnologijo platforme VLP ("eVLP"), VBI razvija kandidate za cepiva, ki posnemajo naravno predstavitev virusov, namenjene izvabljanju prirojene moči človeškega imunskega sistema.

='''Kaj je VBI-2902a cepivo'''=
VBI-2902a je kandidat za preskusno cepivo, ki uporablja ekspresijo virusnih podobnih delcev modificirano verzijo glikoproteina spike SARS-CoV-2 in je zasnovan tako, da inducira nevtralizirajoča protitelesa in imunski odziv, ki ga povzročajo celice, proti SARS-CoV-2 spike proteinu. VBI-2902a z vsebnostjo do 10 μg proteinov in dodatkom aluminijevega fosfata se daje z intramuskularno injekcijo.

='''Klinične študije'''=
Študija faze 1/2 bo ovrednotila varnost, prenašanje in imunogenost zdravila VBI-2902a v režimu enega in dveh odmerkov ter dve ravni odmerka (5 μg in 10 μg spike proteina) v primerjavi s placebom (fiziološka raztopina) pri zdravih odrasli, stari 18 let ali več. Število udeležencev je 780.

Začetna študija faze 1/2 VBI-2902a, se je začela 15. marca 2021 in naj bi bila končana junija 2022.

=Literatura=
[1] Jeff Baxter, CEO; David E. Anderson, CSO Preclinical Coronavirus Program Data (https://1o976r1jw2eculmeoxz46ig6-wpengine.netdna-ssl.com/wp-content/uploads/2020/08/August-2020-VBI-2900-Preclinical-Data-Announcement_Final.pdf)

[2] View ORCID ProfileAnne-Catherine Fluckiger, View ORCID ProfileBarthelemy Ontsouka, Jasminka Bozic, Abebaw Diress, Tanvir Ahmed, Tamara Berthoud, Anh Tran, Diane Duque, Mingmin Liao, Michael McCluskie, View ORCID ProfileFrancisco Diaz-Mitoma, David E. Anderson, Catalina Soare, “An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose” bioRxiv, 28.4.2021 (https://www.biorxiv.org/content/10.1101/2021.04.28.441832v1.full)

[3] A. B. Ryzhikov et al., “Immunogenicity and protectivity of the peptide candidate vaccine against SARS-CoV-2,” Ann. Russ. Acad. Med. Sci., vol. 76, no. 1, pp. 5–19, 2021.

[4] VBI-2902 – Wikipedia https://en.wikipedia.org/wiki/VBI-2902 (pridobljeno 5. 5. 2021)

[5] VBIVACCINE – VBI Vaccines Announces Publication of Preclinical and Challenge Study Data of its eVLP Vaccine Candidate Against COVID-19 (VBI-2902)
April 28, 2021 https://www.vbivaccines.com/press-releases/vbi-2902-preclinical-and-challenge-study-data/ (pridobljeno 6. 5. 2021)

[6] VBIVACCINE - VBI Vaccines Announces Preclinical Coronavirus Program Data and Selection of Clinical Candidates with Potential as One-Dose Vaccines https://www.vbivaccines.com/press-releases/preclinical-coronavirus-data-candidate-selection/ (pridobljeno: 7. 5. 2021)

[7] VBI-2902a - ClinicalTrials.gov, Safety, Tolerability, and Immunogenicity of the COVID-19 Vaccine Candidate (VBI-2902a) https://clinicaltrials.gov/ct2/show/NCT04773665 (pridobljeno: 7. 5. 2021)

User talk:Zeljkae

2021-05-07T09:38:31Z

Zeljkae:

=Uvod=
VBI Vaccines Inc. je biofarmacevtsko podjetje, ki ga poganja imunologija in si prizadeva za močno preprečevanje in zdravljenje bolezni. S svojim inovativnim pristopom k virusom podobnim delcem ("VLP"), vključno s tehnologijo platforme VLP ("eVLP"), VBI razvija kandidate za cepiva, ki posnemajo naravno predstavitev virusov, namenjene izvabljanju prirojene moči človeškega imunskega sistema.

=Kaj je VBI-2902a cepivo=
VBI-2902a je kandidat za preskusno cepivo, ki uporablja ekspresijo virusnih podobnih delcev modificirano verzijo glikoproteina spike SARS-CoV-2 in je zasnovan tako, da inducira nevtralizirajoča protitelesa in imunski odziv, ki ga povzročajo celice, proti SARS-CoV-2 spike proteinu. VBI-2902a z vsebnostjo do 10 μg proteinov in dodatkom aluminijevega fosfata se daje z intramuskularno injekcijo.

=Klinične študije=
Študija faze 1/2 bo ovrednotila varnost, prenašanje in imunogenost zdravila VBI-2902a v režimu enega in dveh odmerkov ter dve ravni odmerka (5 μg in 10 μg spike proteina) v primerjavi s placebom (fiziološka raztopina) pri zdravih odrasli, stari 18 let ali več. Število udeležencev je 780.

Začetna študija faze 1/2 VBI-2902a, se je začela 15. marca 2021 in naj bi bila končana junija 2022.

=Literatura=
[1] Jeff Baxter, CEO; David E. Anderson, CSO Preclinical Coronavirus Program Data (https://1o976r1jw2eculmeoxz46ig6-wpengine.netdna-ssl.com/wp-content/uploads/2020/08/August-2020-VBI-2900-Preclinical-Data-Announcement_Final.pdf)

[2] View ORCID ProfileAnne-Catherine Fluckiger, View ORCID ProfileBarthelemy Ontsouka, Jasminka Bozic, Abebaw Diress, Tanvir Ahmed, Tamara Berthoud, Anh Tran, Diane Duque, Mingmin Liao, Michael McCluskie, View ORCID ProfileFrancisco Diaz-Mitoma, David E. Anderson, Catalina Soare, “An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose” bioRxiv, 28.4.2021 (https://www.biorxiv.org/content/10.1101/2021.04.28.441832v1.full)

[3] A. B. Ryzhikov et al., “Immunogenicity and protectivity of the peptide candidate vaccine against SARS-CoV-2,” Ann. Russ. Acad. Med. Sci., vol. 76, no. 1, pp. 5–19, 2021.

[4] VBI-2902 – Wikipedia https://en.wikipedia.org/wiki/VBI-2902 (pridobljeno 5. 5. 2021)

[5] VBIVACCINE – VBI Vaccines Announces Publication of Preclinical and Challenge Study Data of its eVLP Vaccine Candidate Against COVID-19 (VBI-2902)
April 28, 2021 https://www.vbivaccines.com/press-releases/vbi-2902-preclinical-and-challenge-study-data/ (pridobljeno 6. 5. 2021)

[6] VBIVACCINE - VBI Vaccines Announces Preclinical Coronavirus Program Data and Selection of Clinical Candidates with Potential as One-Dose Vaccines https://www.vbivaccines.com/press-releases/preclinical-coronavirus-data-candidate-selection/ (pridobljeno: 7. 5. 2021)

[7] VBI-2902a - ClinicalTrials.gov, Safety, Tolerability, and Immunogenicity of the COVID-19 Vaccine Candidate (VBI-2902a) https://clinicaltrials.gov/ct2/show/NCT04773665 (pridobljeno: 7. 5. 2021)

A synthetic biology approach to transform Yarrowia Lypolytica into a competitive biotechnological producer of β-carotene:

2020-05-11T12:50:39Z

Zeljkae:

I based my assignment on this research: [https://www.researchgate.net/publication/320270906_A_synthetic_biology_approach_to_transform_Yarrowia_lipolytica_into_a_competitive_biotechnological_producer_of_b-carotene_Production_of_b-carotene_in_Y_lipolytica]

'''A SYNTHETIC BIOLOGY APPROACH TO TRANSFORM YARROWIA LYPOLYTICA INTO A COMPETITIVE BIOTECHNOLOGICAL PRODUCER OF β-CAROTENE'''

'''1.''' [[INTRODUCTION]]
β-carotene is an orange pigment and a well-known precursor of vitamin A. It is a biochemical synthesized terpenoid and is added to the group of carotenoids- β-carotene can be produced either chemically or biotechnologically, extracting it from the natural producer of microorganisms such as Blakeslea trispora. Yarrowia lipolytica is an oleaginous yeast greatly investigated and modified, for the sake of production of biotechnologically relevant compounds.

'''2.''' [[THEORETICAL FRAMEWORK]]
'''2.1''' ''MATERIALS AND METHODS – STRAINS AND MEDIA''
The materials and methods are divided into a series of steps, intended to create a producer of β-carotene out of the aforementioned yeast, Yarrowia lipolytica. The needed steps are: 1) strain construction, 2) construction of the DNA, 3) β-carotene measurement, 4) developing microscopy images, 5) lipid content quantification, 6) biomass, sugar and acid quantification and lastly come the 7) bioreactor procedures.

'''3.''' [[RESULTS AND DISCUSSION]]
''' 3.1''' ''Lipid over-producer strain synthesizes higher amount of β-carotene''
Previous set of reports documented that the over-expression of three genes (geranylgeranyl diphosphate synthase (GGS1), pytoene synthase/lycopene cyclase and phytoene dehydrogenase) promote and increase the production of β-carotene in Y. lipolytica. The reseachers used an expression cassette (a car-cassette), where the expression of the GGS1 is controlled by the promoter PGMp. The sole expression, within the cassette itself (in the parental strain) allows a production of a substantial amount of β-carotene.

''' 3.2''' ''Continuous metabolic engineering magnifies carotene content''
In order to enhance the production of caroteonids, the over-expression of HMG1 (hydroxymethylglutaryl-CoA reductase) is well known. In order to enhance the production of β-carotene, they over-expressed the gene YALI0E04807. It was done under the control of the constitutive TEF promoter in the strain of ob-C. The generated strain (ob-CH) enhanced the production β-carotene by a substantial amount.
A study was conducted, to analyze if the production β-carotene is rather limited by the levels of expression of the over-expressed genes, a second copy of the car-cassette was introduced in the genome of ob-CH, which resulted in the creation of ob-CHC. The conclusion stated that the generated and produced amount of the desired product increased, more than by using the parental strain ob-CH. The results indicated that the expression of some of the gene encoded in the car-cassette is limiting the production of β-carotene. In order to overcome such a sudden obstacle, they combined the optimization of the promoter strength and the copy number for each gene.

'''3.3''' ''Identifying the best promoter set for the production of β-carotene''
The increase in promoter strength can enhance the transcription level more than five times. They use the Closing Gate cloning system in promoter shuffling. This strategy consists in a digestion-ligation reaction guided by Bsal defined sites where the three promoters can be introduced and guided within the promoter positions in the car-cassettes. The pool of cassettes were then set for transformation, the wild type parental strains enable the screening of different color intensity. Once they finished the transformation, they obtained 387 colonies. By analyzing the overall combination of promoters, the presence of a strong TEF promoter is favored as it stood in the second position of the car-cassette.

'''3.4''' ''The construction of the β-carotene over-producer strain''
Seeing as how an extra copy of the car-cassette in the strain ob-CH increased the production of β-carotene greatly, the cassette was optimized by a set of promoters and as a result there became: carTEF-cassette. By expressing the carTEF-cassette in the strain ob-CH, the production of β-carotene was increased. Moreover, an extra copy of the carTEF-cassette was brought to construct the strain ob-CHCTEFCTEF . Said strain was able to also enhance the production of β-carotene.

'''3.5''' ''A trade off between production titer and yield''
Two different kinds of media were tested, rich media (YPD) and synthetic media (YNB). A higher concentration of the carbon/nitrogen ratio is known to increase lipid production and by that, it enhances the production of carotenoids. Glucose and glycerol were tested as the first carbon source. The selected media were YPD10, YPD60, YNB20, YNB30, YNB60, and YNBGLY60. They concluded that there wasn't much of an influence on the carbon source since glucose and glycerol showed similar between both titer and yields. The best β-carotene titer so far was found in YPD60, whilst the winning yield is YPD10.

''' 3.6''' ''Boosting β-carotene production by the engineered strain ob-CHCTEFCTEF''
With the perforation of fed-batch fermentation using a rich media (Y10P20D), they added glucose. The glucose concentration began to rise due to the lack of consumption. The strain led to a production of β-carotene and citric acid. Designing a culture media with the double amount of yeast extract and peptone (Y20P40D), they optimized bioreactor conditions. The results show that Y. lipolytica engineered using synthetic biology and metabolic engineering is a potential industrial producer of β-carotene.

'''4.''' [[CONCLUSION]]
With the combination of traditional metabolic engineering strategies and synthetic biology tools, it's been proven that Y. lipolytica serve as a valid production source for β-carotene. The increase of gene copy numbers and lipogenesis with the use of favourable promoters massively enhanced the production of β-carotene and also, the fed-batch fermentation was proven as the best pathway in generating β-carotene.
The process can also be further improved not only by engineering strains and bioreactor condition optimization but also by the use of low cost carbon sources. The selection of suitable microorganism and strains plays a great role in electing a more successful source of production of β-carotene. The rapid development of synthetic biology tools for genome editing and DNA assembly is alleviating the manipulation of non-conventional organisms, growing the range of biotechnological „vehicles“ for metabolic engineering.

'''5.''' [[RELATED LITERATURE]]
''1.'' Larroude, M., Celinska, E., Back, A., Thomas, S., Nicaud, J-M., Amaro, R. N., Wiley, Biotechnology and bioengineering, A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnologist, October 11th, 2017 (data obtained and approved by ResearchGate on March 12th)

''2.'' CSH Protocols (2017) Yeast Extract-Peptone-Dextrose, taken from: http://cshprotocols.cshlp.org/content/2017/8/pdb.rec090563.full?text_only=true (data found on March 18th)

''3.'' Microbial food.org (2014), Microbe guide: Yarrowia lipolytica, taken from: http://microbialfoods.org/microbe-guide-yarrowia-lipolytica/, (data found on March 17th)

A synthetic biology approach to transform Yarrowia Lypolytica into a competitive biotechnological producer of β-carotene:

2020-05-11T12:49:32Z

Zeljkae:

I based my assignment on this research: [https://www.researchgate.net/publication/320270906_A_synthetic_biology_approach_to_transform_Yarrowia_lipolytica_into_a_competitive_biotechnological_producer_of_b-carotene_Production_of_b-carotene_in_Y_lipolytica]

'''A SYNTHETIC BIOLOGY APPROACH TO TRANSFORM YARROWIA LYPOLYTICA INTO A COMPETITIVE BIOTECHNOLOGICAL PRODUCER OF β-CAROTENE'''

'''1.''' [[INTRODUCTION]]
β-carotene is an orange pigment and a well-known precursor of vitamin A. It is a biochemical synthesized terpenoid and is added to the group of carotenoids- β-carotene can be produced either chemically or biotechnologically, extracting it from the natural producer of microorganisms such as Blakeslea trispora. Yarrowia lipolytica is an oleaginous yeast greatly investigated and modified, for the sake of production of biotechnologically relevant compounds.

'''2.''' [[THEORETICAL FRAMEWORK]]
'''2.1''' ''MATERIALS AND METHODS – STRAINS AND MEDIA''
The materials and methods are divided into a series of steps, intended to create a producer of β-carotene out of the aforementioned yeast, Yarrowia lipolytica. The needed steps are: 1) strain construction, 2) construction of the DNA, 3) β-carotene measurement, 4) developing microscopy images, 5) lipid content quantification, 6) biomass, sugar and acid quantification and lastly come the 7) bioreactor procedures.

'''3.''' [[RESULTS AND DISCUSSION]]
''' 3.1''' ''Lipid over-producer strain synthesizes higher amount of β-carotene''
Previous set of reports documented that the over-expression of three genes (geranylgeranyl diphosphate synthase (GGS1), pytoene synthase/lycopene cyclase and phytoene dehydrogenase) promote and increase the production of β-carotene in Y. lipolytica. The reseachers used an expression cassette (a car-cassette), where the expression of the GGS1 is controlled by the promoter PGMp. The sole expression, within the cassette itself (in the parental strain) allows a production of a substantial amount of β-carotene.

''' 3.2''' ''Continuous metabolic engineering magnifies carotene content''
In order to enhance the production of caroteonids, the over-expression of HMG1 (hydroxymethylglutaryl-CoA reductase) is well known. In order to enhance the production of β-carotene, they over-expressed the gene YALI0E04807. It was done under the control of the constitutive TEF promoter in the strain of ob-C. The generated strain (ob-CH) enhanced the production β-carotene by a substantial amount.
A study was conducted, to analyze if the production β-carotene is rather limited by the levels of expression of the over-expressed genes, a second copy of the car-cassette was introduced in the genome of ob-CH, which resulted in the creation of ob-CHC. The conclusion stated that the generated and produced amount of the desired product increased, more than by using the parental strain ob-CH. The results indicated that the expression of some of the gene encoded in the car-cassette is limiting the production of β-carotene. In order to overcome such a sudden obstacle, they combined the optimization of the promoter strength and the copy number for each gene.

'''3.3''' ''Identifying the best promoter set for the production of β-carotene''
The increase in promoter strength can enhance the transcription level more than five times. They use the Closing Gate cloning system in promoter shuffling. This strategy consists in a digestion-ligation reaction guided by Bsal defined sites where the three promoters can be introduced and guided within the promoter positions in the car-cassettes. The pool of cassettes were then set for transformation, the wild type parental strains enable the screening of different color intensity. Once they finished the transformation, they obtained 387 colonies. By analyzing the overall combination of promoters, the presence of a strong TEF promoter is favored as it stood in the second position of the car-cassette.

'''3.4''' ''The construction of the β-carotene over-producer strain''
Seeing as how an extra copy of the car-cassette in the strain ob-CH increased the production of β-carotene greatly, the cassette was optimized by a set of promoters and as a result there became: carTEF-cassette. By expressing the carTEF-cassette in the strain ob-CH, the production of β-carotene was increased. Moreover, an extra copy of the carTEF-cassette was brought to construct the strain ob-CHCTEFCTEF . Said strain was able to also enhance the production of β-carotene.

'''3.5''' ''A trade off between production titer and yield''
Two different kinds of media were tested, rich media (YPD) and synthetic media (YNB). A higher concentration of the carbon/nitrogen ratio is known to increase lipid production and by that, it enhances the production of carotenoids. Glucose and glycerol were tested as the first carbon source. The selected media were YPD10, YPD60, YNB20, YNB30, YNB60, and YNBGLY60. They concluded that there wasn't much of an influence on the carbon source since glucose and glycerol showed similar between both titer and yields. The best β-carotene titer so far was found in YPD60, whilst the winning yield is YPD10.

''' 3.6''' ''Boosting β-carotene production by the engineered strain ob-CHCTEFCTEF''
With the perforation of fed-batch fermentation using a rich media (Y10P20D), they added glucose. The glucose concentration began to rise due to the lack of consumption. The strain led to a production of β-carotene and citric acid. Designing a culture media with the double amount of yeast extract and peptone (Y20P40D), they optimized bioreactor conditions. The results show that Y. lipolytica engineered using synthetic biology and metabolic engineering is a potential industrial producer of β-carotene.

'''4.''' [[CONCLUSION]]
With the combination of traditional metabolic engineering strategies and synthetic biology tools, it's been proven that Y. lipolytica serve as a valid production source for β-carotene. The increase of gene copy numbers and lipogenesis with the use of favourable promoters massively enhanced the production of β-carotene and also, the fed-batch fermentation was proven as the best pathway in generating β-carotene.
The process can also be further improved not only by engineering strains and bioreactor condition optimization but also by the use of low cost carbon sources. The selection of suitable microorganism and strains plays a great role in electing a more successful source of production of β-carotene. The rapid development of synthetic biology tools for genome editing and DNA assembly is alleviating the manipulation of non-conventional organisms, growing the range of biotechnological „vehicles“ for metabolic engineering.

'''5.''' [[RELATED LITERATURE]]
'''1.''' Larroude, M., Celinska, E., Back, A., Thomas, S., Nicaud, J-M., Amaro, R. N., Wiley, Biotechnology and bioengineering, A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnologist, October 11th, 2017 (data obtained and approved by ResearchGate on March 12th)
'''2.''' CSH Protocols (2017) Yeast Extract-Peptone-Dextrose, taken from: http://cshprotocols.cshlp.org/content/2017/8/pdb.rec090563.full?text_only=true (data found on March 18th)
'''3.''' Microbial food.org (2014), Microbe guide: Yarrowia lipolytica, taken from: http://microbialfoods.org/microbe-guide-yarrowia-lipolytica/, (data found on March 17th)

A synthetic biology approach to transform Yarrowia Lypolytica into a competitive biotechnological producer of β-carotene:

2020-05-11T12:46:52Z

Zeljkae: New page: I based my assignment on this research: [https://www.researchgate.net/publication/320270906_A_synthetic_biology_approach_to_transform_Yarrowia_lipolytica_into_a_competitive_biotechnologica...

Seminarji SB 2019/20

2020-05-11T12:46:01Z

Zeljkae:

V študijskem letu 2019/20 študentje 1. letnika predstavljajo naslednje teme:

RAZISKOVALNI ČLANKI

(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do izhodiščnega članka na spletu.) 

Primer: 
1 [http://wiki.fkkt.uni-lj.si/index.php/MoClo:_modularni_klonirni_sistem_za_standardizirano_sestavljanje_ve%C4%8Dgenskih_konstruktov MoClo: modularni klonirni sistem za standardizirano sestavljanje večgenskih konstruktov] (Valentina Levak)

NAGRAJENI ŠTUDENTSKI PROJEKTI

(Vpišite naslov seminarja v slovenščini in ga povežite z novo stranjo, kjer bo povzetek. Na tej novi strani naj bo pod naslovom povezava do wiki strani študentske ekipe, katere projekt opisujete.) 
Primer: 
1 [http://wiki.fkkt.uni-lj.si/index.php/Phactory:_proizvodnja_bakteriofagov_za_precizno_zdravljenje Phactory: proizvodnja bakteriofagov za precizno zdravljenje] (Rok Miklavčič)

Povzetki v slovenščini naj imajo 1200-1500 besed (viri v to vsoto ne štejejo). Povzetek je treba objaviti dva dni pred predstavitvijo do polnoči (za seminarje v sredo torej v ponedeljek). Predstavitev seminarja naj bo dolga 15 minut (13-17). Sledila bo razprava, ki praviloma ne bo daljša od 5 minut.

----

Razpored po datumih predstavitev (pri vsakem terminu so možni največ 4 seminarji; vpišite ime in priimek pri dnevu, ko želite predstaviti seminar):

15.4. 
1 [[Robustno večcelično računanje z uporabo gensko kodiranih vrat NE-ALI in kemičnih 'žic']] (Tanja Zupan) 
2 [http://wiki.fkkt.uni-lj.si/index.php/PETEXE_-_sistem_za_filtracijo_mikroplastike_v_pralnih_strojih PETEXE - sistem za filtracijo mikroplastike v pralnih strojih]
(Lana Vogrinec) 
3 [http://wiki.fkkt.uni-lj.si/index.php/Magi.Coli:_sinteza_psilocibina_s_pomo%C4%8Djo_E.coli Magi.Coli: sinteza psilocibina s pomočjo ''E.coli''] (Luka Lavrič) 
4 [http://wiki.fkkt.uni-lj.si/index.php/SONOBE_-_proteinski_sistem_za_agregacijo_mikroplastike SONOBE - proteinski sistem za agregacijo mikroplastike] (Vesna Podgrajšek) 

21.4. 
1 [http://wiki.fkkt.uni-lj.si/index.php/The_real_MVP:_ekspresijski_sistem_za_pripravo_modularnih_virusom_podobnih_delcev The real MVP: ekspresijski sistem za pripravo modularnih virusom podobnih delcev] (Žiga Vičič) 
2 [http://wiki.fkkt.uni-lj.si/index.php/Proizvodnja_%C5%A1inorina%2C_naravne_za%C5%A1%C4%8Dite_pred_soncem%2C_z_uporabo_cianobakterije Proizvodnja šinorina, naravne zaščite pred soncem, z uporabo cianobakterije] (Tina Turel) 
3 [http://wiki.fkkt.uni-lj.si/index.php/Prenos_informacije_med_bakterijami_v_sesalskem_%C4%8Drevesju_z_uporabo_sistema_zaznavanja_gostote_populacije Prenos informacije med bakterijami v sesalskem črevesju z uporabo sistema zaznavanja gostote populacije] (Anže Jenko) 
4 [http://wiki.fkkt.uni-lj.si/index.php/BI%28OIL%29OGICAL_FACTORY_-_sistem_za_proizvodnjo_sestavin_palmovega_olja_v_mikroalgi BI(OIL)OGICAL FACTORY - sistem za proizvodnjo sestavin palmovega olja v mikroalgi](Dunia Sahir) 

22.4. 
1 [http://wiki.fkkt.uni-lj.si/index.php/Sinhronizirani_cikli_lize_bakterijskih_celic_za_in_vivo_dostavo_terapevtikov Sinhronizirani cikli lize bakterijskih celic za ''in vivo'' dostavo terapevtikov](Milica Janković) 
2 [http://wiki.fkkt.uni-lj.si/index.php/Antihipertenzivni_probiotik_-_nov_pristop_zni%C5%BEevanja_krvnega_tlaka Antihipertenzivni probiotik - nov pristop zniževanja krvnega tlaka] (Nika Testen) 
3 [http://wiki.fkkt.uni-lj.si/index.php/Sintezna_pot_fiksacije_ogljikovega_dioksida Sintezna pot fiksacije ogljikovega dioksida] (Ana Obaha) 
4 [http://wiki.fkkt.uni-lj.si/index.php/ProQuorum:_probiotik_kot_zdravilo_proti_okužbi_s_C._difficile ProQuorum: probiotik kot zdravilo proti okužbi s ''C. difficile''] (Ana Maklin) 

5.5. 
1 [http://wiki.fkkt.uni-lj.si/index.php/Sistem_za_brezcelično_sintezno_biologijo_na_osnovi_E.coli Sistem za brezcelično sintezno biologijo na osnovi ''E.coli''] (Ajda Lenardič) 
2 [http://wiki.fkkt.uni-lj.si/index.php/Engineering_Customized_Cell_Sensing_and_Response_Behaviors_Using_Synthetic_Notch_Receptors Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors] (Jelena Štrbac) 
3 [http://wiki.fkkt.uni-lj.si/index.php/Programabilni_enocelični_sesalski_bioračunalniki Programabilni enocelični sesalski bioračunalniki] (Andreja Habič) 
4 [http://wiki.fkkt.uni-lj.si/index.php/Priprava_sistema_s_proteinskimi_logi%C4%8Dnimi_vrati_na_povr%C5%A1ini_lipidnih_membran Priprava sistema s proteinskimi logičnimi vrati na površini lipidnih membran] (Uroš Prešern) 

6.5. 
1 [http://wiki.fkkt.uni-lj.si/index.php/ALiVE_%E2%80%93_analiza_%C5%BEivih_celic_z_vezikularnim_izvozom ALiVE – analiza živih celic z vezikularnim izvozom] (Sara Korošec) 
2 [http://wiki.fkkt.uni-lj.si/index.php/Kompleksno_celi%C4%8Dno_logi%C4%8Dno_ra%C4%8Dunanje_z_RNA-napravami Kompleksno celično logično računanje z RNA-napravami] (Peter Škrinjar) 
3 [http://wiki.fkkt.uni-lj.si/index.php/Daljinsko_upravljanje_s_sesalskimi_celicami%2C_na_podlagi_temperaturno_reguliranih_genetskih_stikal_s_svetlobno-toplotnimi_utripi Daljinsko upravljanje s sesalskimi celicami, na podlagi temperaturno reguliranih genetskih stikal s svetlobno-toplotnimi utripi] (Luka Gregorič) 
4 [http://wiki.fkkt.uni-lj.si/index.php/Komunikacija_na_osnovi_DNA_v_populacijah_sinteticnih_protocelic Komunikacija na osnovi DNA v populacijah sintetičnih protocelic] (Urban Hribar) 

12.5. 
1 [http://wiki.fkkt.uni-lj.si/index.php/Na%C4%8Drtovanje_mikrobnih_konzorcijev_z_dolo%C4%8Denimi_dru%C5%BEbenimi_interakcijami Načrtovanje mikrobnih konzorcijev z določenimi družbenimi interakcijami] (Jerneja Nimac) 
2 [http://wiki.fkkt.uni-lj.si/index.php/Orodje_za_modularno_sestavljanje_večgenskih_konstruktov_v_kvasovki: Sistem za modularno sestavljanje večgenskih konstruktov v kvasovki] (Katja Doberšek) 
3 [http://wiki.fkkt.uni-lj.si/index.php/Genetski_programi_zgrajeni_iz_več_plasti_logičnih_vrat_v_posameznih_celicah Genetski programi zgrajeni iz več plasti logičnih vrat v posameznih celicah] (Daria Latysheva) 
4 [http://wiki.fkkt.uni-lj.si/index.php/Modularni_klonirni_sistem_MoClo_za_biološko_sintezo_v_mikroalgi_C._reinhardtii Modularni klonirni sistem MoClo za biološko sintezo v mikroalgi ''C. reinhardtii''] (Veronika Razpotnik) 

13.5. 
1 [http://wiki.fkkt.uni-lj.si/index.php/Vpliv_sinteznih_metabolnih_poti_glikolata_na_produktivnost_rastlin Vpliv sinteznih metabolnih poti glikolata na produktivnost rastlin] Ines Medved 
2 [http://wiki.fkkt.uni-lj.si/index.php/A_synthetic_biology_approach_to_transform_Yarrowia_Lypolytica_into_a_competitive_biotechnological_producer_of_%CE%B2-carotene: A synthetic biology approach to transform Yarrowia Lypolytica into a competitive biotechnological producer of β-carotene] (Željka Erić) 
3 [http://wiki.fkkt.uni-lj.si/index.php/NoTox_%E2%80%93_sistem_za_prepre%C4%8Devanje_botulinskih_izbruhov NoToX-sistem za preprečevanje botulinskih izbruhov] Patricija Miklavc 
4 [http://wiki.fkkt.uni-lj.si/index.php/In%C5%BEenirsko_pripravljeni_promotorji%2C_ki_omogo%C4%8Dajo_izra%C5%BEanje_ne_glede_na_%C5%A1tevilo_kopij Inženirsko pripravljeni promotorji, ki omogočajo izražanje ne glede na število kopij] (Benjamin Malovrh) 

19.5. 
1 Samo Purič 
2 Sara Jereb 
3 Primož Bembič 
4 Andrej Race 

20.5. 
1 Katja Malenšek 
2 Vid Modic 
3 Andrej Ivanovski 
4 Maja Globočnik 

26.5. 
1 Nika Zaveršek 
2 Janina Gea Cvikl 
3 
4 

27.5. Rezervni termin 
1 
2 
3 
4

A synthetic biology approach to transform Yarrowia Lypolytica into a competitive biotechnological producer of β-carotene

2020-05-11T12:44:17Z

Pojdi na

2020-05-11T12:39:14Z

Zeljkae: Removing all content from page

Pojdi na

2020-05-11T12:38:55Z

I based my assignment on this research: [https://www.researchgate.net/publication/320270906_A_synthetic_biology_approach_to_transform_Yarrowia_lipolytica_into_a_competitive_biotechnological_producer_of_b-carotene_Production_of_b-carotene_in_Y_lipolytica]

'''A SYNTHETIC BIOLOGY APPROACH TO TRANSFORM YARROWIA LYPOLYTICA INTO A COMPETITIVE BIOTECHNOLOGICAL PRODUCER OF β-CAROTENE'''

'''1.''' [[INTRODUCTION]]
β-carotene is an orange pigment and a well-known precursor of vitamin A. It is a biochemical synthesized terpenoid and is added to the group of carotenoids- β-carotene can be produced either chemically or biotechnologically, extracting it from the natural producer of microorganisms such as Blakeslea trispora. Yarrowia lipolytica is an oleaginous yeast greatly investigated and modified, for the sake of production of biotechnologically relevant compounds.

'''2.''' [[THEORETICAL FRAMEWORK]]
'''2.1''' ''MATERIALS AND METHODS – STRAINS AND MEDIA''
The materials and methods are divided into a series of steps, intended to create a producer of β-carotene out of the aforementioned yeast, Yarrowia lipolytica. The needest steps are: 1) strain construction, 2) construction of the DNA, 3) β-carotene measurement, 4) developing microscopy images, 5) lipid content quantification, 6) biomass, sugar and acid quantification and lastly come the 7) bioreactor procedures.

'''3.''' [[RESULTS AND DISCUSSION]]
''' 3.1''' ''Lipid overproducer strain synthesizes higher amount of β-carotene''
Previous set of reports documented that the overexpression of three genes (geranylgeranyl diphosphate synthase (GGS1), pytoene synthase/lycopene cyclase and phytoene dehydrogenase) promote and increase the production of β-carotene in Y. lipolytica. The reseachers used an expression cassette (a car-cassette), where the expression of the GGS1 is controlled by the promoter PGMp. The sole expression, within the cassette itself (in the parental strain) allows a production of a substantial amount of β-carotene.

''' 3.2''' ''Continuous metabolic engineering magnifies carotene content''
In order to enhance the production of caroteonids, the overexpression of HMG1 (hydroxymethylglutaryl-CoA reductase) is well known. In order to enhance the production of β-carotene, they overexpressed the gene YALI0E04807. It was done under the control of the constitutive TEF promoter in the strain of ob-C. The generated strain (ob-CH) enhanced the production β-carotene by a substantial amount.

'''3.3''' ''Identifying the best promoter set for the production of β-carotene''
The increase in promoter strength can enchance the transcription level more than five times. They use the Closing Gate cloning system in promoter shuffling. This strategy consists in a digestion-ligation reaction guided by Bsal defined sites where the three promotors can be introduced and guided within the promotor positions in the car-cassettes. The pool of cassettes were then set for transformation, the wild type parental strains enable the screening of different colour intensity. Once they finished the transformation, they obtained 387 colonies. By analyzing the overall combination of promoters, the presence of a strong TEF promoter is favoured as it stood in the second position of the car-cassette.

'''3.4''' ''The construction of the β-carotene overproducer strain''
Seeing as how an extra copy of the car-cassette in the strain ob-CH increased the production of β-carotene greatly, the cassette was optimized by a set of promoters and as a result there became: carTEF-cassette. By expressing the carTEF-cassette in the strain ob-CH, the production of β-carotene was increased. Moreover, an extra copy of the carTEF-cassette was brought to construct the strain ob-CHCTEFCTEF . Said strain was able to also enhance the production of β-carotene.

'''3.5''' ''A trade off between production titer and yield''
Two different kinds of media were tested, rich media (YPD) and synthetic media (YNB). A higher concentration of the carbon/nitrogen ratio is known to increase lipid production and by that, it enhances the production of carotenoids. Glucose and glycerol were tested as the first carbon source. The selected media were YPD10, YPD60, YNB20, YNB30, YNB60, and YNBGLY60. They concluded that there wasn't much of an influence on the carbon source since glucose and glycerol showed similar between both titer and yields. The best β-carotene titer so far was found in YPD60, whilst the winning yield is YPD10.

''' 3.6''' ''Boosting β-carotene production by the engineered strain ob-CHCTEFCTEF''
With the performation of fed-batch fermantation using a rich media (Y10P20D), they added glucose. The glucose concentration began to rise due to the lack of consumption. The strain led to a production of β-carotene and citric acid. Designing a culture media with the double amount of yeast extract and peptone (Y20P40D), they optimized bioreactor conditions. The results show that Y. lipolytica engineered using synthetic biology and metabolic engineering is a potential industrial producer of β-carotene.

'''4.''' [[CONCLUSION]]
With the combination of traditional metabollic engineering strategies and synthetic biology tools, it's been proven that Y. lipolytica serve as a valid production source for β-carotene. The increase of gene copy numbers and lipogenesis with the use of favourable promoters massively enhanced the production of β-carotene and also, the fed-batch fermentation was proven as the best pathway in generating β-carotene.
The process can also be further improved not only by engineering strains and bioreactor condition optimization but also by the use of low cost carbon sources. The selection of suitable microorganism and strains plays a great role in electing a more successful source of production of β-carotene. The rapid development of synthetic biology tools for genome editing and DNA assembly is alleviating the manipulation of non-conventional organisms, growing the range of biotechnological „vehicles“ for metabolic engineering.

User talk:Zeljkae

2020-05-11T12:37:36Z

Zeljkae: Removing all content from page

User talk:Zeljkae

2020-05-11T12:37:22Z

I based my assignment on this research: [https://www.researchgate.net/publication/320270906_A_synthetic_biology_approach_to_transform_Yarrowia_lipolytica_into_a_competitive_biotechnological_producer_of_b-carotene_Production_of_b-carotene_in_Y_lipolytica]

'''A SYNTHETIC BIOLOGY APPROACH TO TRANSFORM YARROWIA LYPOLYTICA INTO A COMPETITIVE BIOTECHNOLOGICAL PRODUCER OF β-CAROTENE'''

'''1.''' [[INTRODUCTION]]
β-carotene is an orange pigment and a well-known precursor of vitamin A. It is a biochemical synthesized terpenoid and is added to the group of carotenoids- β-carotene can be produced either chemically or biotechnologically, extracting it from the natural producer of microorganisms such as Blakeslea trispora. Yarrowia lipolytica is an oleaginous yeast greatly investigated and modified, for the sake of production of biotechnologically relevant compounds.

'''2.''' [[THEORETICAL FRAMEWORK]]
'''2.1''' ''MATERIALS AND METHODS – STRAINS AND MEDIA''
The materials and methods are divided into a series of steps, intended to create a producer of β-carotene out of the aforementioned yeast, Yarrowia lipolytica. The needest steps are: 1) strain construction, 2) construction of the DNA, 3) β-carotene measurement, 4) developing microscopy images, 5) lipid content quantification, 6) biomass, sugar and acid quantification and lastly come the 7) bioreactor procedures.

'''3.''' [[RESULTS AND DISCUSSION]]
''' 3.1''' ''Lipid overproducer strain synthesizes higher amount of β-carotene''
Previous set of reports documented that the overexpression of three genes (geranylgeranyl diphosphate synthase (GGS1), pytoene synthase/lycopene cyclase and phytoene dehydrogenase) promote and increase the production of β-carotene in Y. lipolytica. The reseachers used an expression cassette (a car-cassette), where the expression of the GGS1 is controlled by the promoter PGMp. The sole expression, within the cassette itself (in the parental strain) allows a production of a substantial amount of β-carotene.

''' 3.2''' ''Continuous metabolic engineering magnifies carotene content''
In order to enhance the production of caroteonids, the overexpression of HMG1 (hydroxymethylglutaryl-CoA reductase) is well known. In order to enhance the production of β-carotene, they overexpressed the gene YALI0E04807. It was done under the control of the constitutive TEF promoter in the strain of ob-C. The generated strain (ob-CH) enhanced the production β-carotene by a substantial amount.

'''3.3''' ''Identifying the best promoter set for the production of β-carotene''
The increase in promoter strength can enchance the transcription level more than five times. They use the Closing Gate cloning system in promoter shuffling. This strategy consists in a digestion-ligation reaction guided by Bsal defined sites where the three promotors can be introduced and guided within the promotor positions in the car-cassettes. The pool of cassettes were then set for transformation, the wild type parental strains enable the screening of different colour intensity. Once they finished the transformation, they obtained 387 colonies. By analyzing the overall combination of promoters, the presence of a strong TEF promoter is favoured as it stood in the second position of the car-cassette.

'''3.4''' ''The construction of the β-carotene overproducer strain''
Seeing as how an extra copy of the car-cassette in the strain ob-CH increased the production of β-carotene greatly, the cassette was optimized by a set of promoters and as a result there became: carTEF-cassette. By expressing the carTEF-cassette in the strain ob-CH, the production of β-carotene was increased. Moreover, an extra copy of the carTEF-cassette was brought to construct the strain ob-CHCTEFCTEF . Said strain was able to also enhance the production of β-carotene.

'''3.5''' ''A trade off between production titer and yield''
Two different kinds of media were tested, rich media (YPD) and synthetic media (YNB). A higher concentration of the carbon/nitrogen ratio is known to increase lipid production and by that, it enhances the production of carotenoids. Glucose and glycerol were tested as the first carbon source. The selected media were YPD10, YPD60, YNB20, YNB30, YNB60, and YNBGLY60. They concluded that there wasn't much of an influence on the carbon source since glucose and glycerol showed similar between both titer and yields. The best β-carotene titer so far was found in YPD60, whilst the winning yield is YPD10.

''' 3.6''' ''Boosting β-carotene production by the engineered strain ob-CHCTEFCTEF''
With the performation of fed-batch fermantation using a rich media (Y10P20D), they added glucose. The glucose concentration began to rise due to the lack of consumption. The strain led to a production of β-carotene and citric acid. Designing a culture media with the double amount of yeast extract and peptone (Y20P40D), they optimized bioreactor conditions. The results show that Y. lipolytica engineered using synthetic biology and metabolic engineering is a potential industrial producer of β-carotene.

'''4.''' [[CONCLUSION]]
With the combination of traditional metabollic engineering strategies and synthetic biology tools, it's been proven that Y. lipolytica serve as a valid production source for β-carotene. The increase of gene copy numbers and lipogenesis with the use of favourable promoters massively enhanced the production of β-carotene and also, the fed-batch fermentation was proven as the best pathway in generating β-carotene.
The process can also be further improved not only by engineering strains and bioreactor condition optimization but also by the use of low cost carbon sources. The selection of suitable microorganism and strains plays a great role in electing a more successful source of production of β-carotene. The rapid development of synthetic biology tools for genome editing and DNA assembly is alleviating the manipulation of non-conventional organisms, growing the range of biotechnological „vehicles“ for metabolic engineering.

User:Zeljkae

2020-05-11T12:33:53Z

Zeljkae:

I based my assignment on this research: [https://www.researchgate.net/publication/320270906_A_synthetic_biology_approach_to_transform_Yarrowia_lipolytica_into_a_competitive_biotechnological_producer_of_b-carotene_Production_of_b-carotene_in_Y_lipolytica]

'''A SYNTHETIC BIOLOGY APPROACH TO TRANSFORM YARROWIA LYPOLYTICA INTO A COMPETITIVE BIOTECHNOLOGICAL PRODUCER OF β-CAROTENE'''

'''1.''' [[INTRODUCTION]]
β-carotene is an orange pigment and a well-known precursor of vitamin A. It is a biochemical synthesized terpenoid and is added to the group of carotenoids- β-carotene can be produced either chemically or biotechnologically, extracting it from the natural producer of microorganisms such as Blakeslea trispora. Yarrowia lipolytica is an oleaginous yeast greatly investigated and modified, for the sake of production of biotechnologically relevant compounds.

'''2.''' [[THEORETICAL FRAMEWORK]]
'''2.1''' ''MATERIALS AND METHODS – STRAINS AND MEDIA''
The materials and methods are divided into a series of steps, intended to create a producer of β-carotene out of the aforementioned yeast, Yarrowia lipolytica. The needest steps are: 1) strain construction, 2) construction of the DNA, 3) β-carotene measurement, 4) developing microscopy images, 5) lipid content quantification, 6) biomass, sugar and acid quantification and lastly come the 7) bioreactor procedures.

'''3.''' [[RESULTS AND DISCUSSION]]
''' 3.1''' ''Lipid overproducer strain synthesizes higher amount of β-carotene''
Previous set of reports documented that the overexpression of three genes (geranylgeranyl diphosphate synthase (GGS1), pytoene synthase/lycopene cyclase and phytoene dehydrogenase) promote and increase the production of β-carotene in Y. lipolytica. The reseachers used an expression cassette (a car-cassette), where the expression of the GGS1 is controlled by the promoter PGMp. The sole expression, within the cassette itself (in the parental strain) allows a production of a substantial amount of β-carotene.

''' 3.2''' ''Continuous metabolic engineering magnifies carotene content''
In order to enhance the production of caroteonids, the overexpression of HMG1 (hydroxymethylglutaryl-CoA reductase) is well known. In order to enhance the production of β-carotene, they overexpressed the gene YALI0E04807. It was done under the control of the constitutive TEF promoter in the strain of ob-C. The generated strain (ob-CH) enhanced the production β-carotene by a substantial amount.

'''3.3''' ''Identifying the best promoter set for the production of β-carotene''
The increase in promoter strength can enchance the transcription level more than five times. They use the Closing Gate cloning system in promoter shuffling. This strategy consists in a digestion-ligation reaction guided by Bsal defined sites where the three promotors can be introduced and guided within the promotor positions in the car-cassettes. The pool of cassettes were then set for transformation, the wild type parental strains enable the screening of different colour intensity. Once they finished the transformation, they obtained 387 colonies. By analyzing the overall combination of promoters, the presence of a strong TEF promoter is favoured as it stood in the second position of the car-cassette.

'''3.4''' ''The construction of the β-carotene overproducer strain''
Seeing as how an extra copy of the car-cassette in the strain ob-CH increased the production of β-carotene greatly, the cassette was optimized by a set of promoters and as a result there became: carTEF-cassette. By expressing the carTEF-cassette in the strain ob-CH, the production of β-carotene was increased. Moreover, an extra copy of the carTEF-cassette was brought to construct the strain ob-CHCTEFCTEF . Said strain was able to also enhance the production of β-carotene.

'''3.5''' ''A trade off between production titer and yield''
Two different kinds of media were tested, rich media (YPD) and synthetic media (YNB). A higher concentration of the carbon/nitrogen ratio is known to increase lipid production and by that, it enhances the production of carotenoids. Glucose and glycerol were tested as the first carbon source. The selected media were YPD10, YPD60, YNB20, YNB30, YNB60, and YNBGLY60. They concluded that there wasn't much of an influence on the carbon source since glucose and glycerol showed similar between both titer and yields. The best β-carotene titer so far was found in YPD60, whilst the winning yield is YPD10.

''' 3.6''' ''Boosting β-carotene production by the engineered strain ob-CHCTEFCTEF''
With the performation of fed-batch fermantation using a rich media (Y10P20D), they added glucose. The glucose concentration began to rise due to the lack of consumption. The strain led to a production of β-carotene and citric acid. Designing a culture media with the double amount of yeast extract and peptone (Y20P40D), they optimized bioreactor conditions. The results show that Y. lipolytica engineered using synthetic biology and metabolic engineering is a potential industrial producer of β-carotene.

'''4.''' [[CONCLUSION]]
With the combination of traditional metabollic engineering strategies and synthetic biology tools, it's been proven that Y. lipolytica serve as a valid production source for β-carotene. The increase of gene copy numbers and lipogenesis with the use of favourable promoters massively enhanced the production of β-carotene and also, the fed-batch fermentation was proven as the best pathway in generating β-carotene.
The process can also be further improved not only by engineering strains and bioreactor condition optimization but also by the use of low cost carbon sources. The selection of suitable microorganism and strains plays a great role in electing a more successful source of production of β-carotene. The rapid development of synthetic biology tools for genome editing and DNA assembly is alleviating the manipulation of non-conventional organisms, growing the range of biotechnological „vehicles“ for metabolic engineering.

User:Zeljkae

2020-05-11T12:32:37Z

Zeljkae: A synthetic biology approach to transform Yarrowia Lypolytica into a competitive biotechnological producer of β-carotene

I based my assignment on this research: [https://www.researchgate.net/publication/320270906_A_synthetic_biology_approach_to_transform_Yarrowia_lipolytica_into_a_competitive_biotechnological_producer_of_b-carotene_Production_of_b-carotene_in_Y_lipolytica]
'''A SYNTHETIC BIOLOGY APPROACH TO TRANSFORM YARROWIA LYPOLYTICA INTO A COMPETITIVE BIOTECHNOLOGICAL PRODUCER OF β-CAROTENE'''

'''1.''' [[INTRODUCTION]]
β-carotene is an orange pigment and a well-known precursor of vitamin A. It is a biochemical synthesized terpenoid and is added to the group of carotenoids- β-carotene can be produced either chemically or biotechnologically, extracting it from the natural producer of microorganisms such as Blakeslea trispora. Yarrowia lipolytica is an oleaginous yeast greatly investigated and modified, for the sake of production of biotechnologically relevant compounds.

'''2.''' [[THEORETICAL FRAMEWORK]]
'''2.1''' ''MATERIALS AND METHODS – STRAINS AND MEDIA''
The materials and methods are divided into a series of steps, intended to create a producer of β-carotene out of the aforementioned yeast, Yarrowia lipolytica. The needest steps are: 1) strain construction, 2) construction of the DNA, 3) β-carotene measurement, 4) developing microscopy images, 5) lipid content quantification, 6) biomass, sugar and acid quantification and lastly come the 7) bioreactor procedures.

'''3.''' [[RESULTS AND DISCUSSION]]
''' 3.1''' ''Lipid overproducer strain synthesizes higher amount of β-carotene''
Previous set of reports documented that the overexpression of three genes (geranylgeranyl diphosphate synthase (GGS1), pytoene synthase/lycopene cyclase and phytoene dehydrogenase) promote and increase the production of β-carotene in Y. lipolytica. The reseachers used an expression cassette (a car-cassette), where the expression of the GGS1 is controlled by the promoter PGMp. The sole expression, within the cassette itself (in the parental strain) allows a production of a substantial amount of β-carotene.

''' 3.2''' ''Continuous metabolic engineering magnifies carotene content''
In order to enhance the production of caroteonids, the overexpression of HMG1 (hydroxymethylglutaryl-CoA reductase) is well known. In order to enhance the production of β-carotene, they overexpressed the gene YALI0E04807. It was done under the control of the constitutive TEF promoter in the strain of ob-C. The generated strain (ob-CH) enhanced the production β-carotene by a substantial amount.

'''3.3''' ''Identifying the best promoter set for the production of β-carotene''
The increase in promoter strength can enchance the transcription level more than five times. They use the Closing Gate cloning system in promoter shuffling. This strategy consists in a digestion-ligation reaction guided by Bsal defined sites where the three promotors can be introduced and guided within the promotor positions in the car-cassettes. The pool of cassettes were then set for transformation, the wild type parental strains enable the screening of different colour intensity. Once they finished the transformation, they obtained 387 colonies. By analyzing the overall combination of promoters, the presence of a strong TEF promoter is favoured as it stood in the second position of the car-cassette.

'''3.4''' ''The construction of the β-carotene overproducer strain''
Seeing as how an extra copy of the car-cassette in the strain ob-CH increased the production of β-carotene greatly, the cassette was optimized by a set of promoters and as a result there became: carTEF-cassette. By expressing the carTEF-cassette in the strain ob-CH, the production of β-carotene was increased. Moreover, an extra copy of the carTEF-cassette was brought to construct the strain ob-CHCTEFCTEF . Said strain was able to also enhance the production of β-carotene.

'''3.5''' ''A trade off between production titer and yield''
Two different kinds of media were tested, rich media (YPD) and synthetic media (YNB). A higher concentration of the carbon/nitrogen ratio is known to increase lipid production and by that, it enhances the production of carotenoids. Glucose and glycerol were tested as the first carbon source. The selected media were YPD10, YPD60, YNB20, YNB30, YNB60, and YNBGLY60. They concluded that there wasn't much of an influence on the carbon source since glucose and glycerol showed similar between both titer and yields. The best β-carotene titer so far was found in YPD60, whilst the winning yield is YPD10.

''' 3.6''' ''Boosting β-carotene production by the engineered strain ob-CHCTEFCTEF''
With the performation of fed-batch fermantation using a rich media (Y10P20D), they added glucose. The glucose concentration began to rise due to the lack of consumption. The strain led to a production of β-carotene and citric acid. Designing a culture media with the double amount of yeast extract and peptone (Y20P40D), they optimized bioreactor conditions. The results show that Y. lipolytica engineered using synthetic biology and metabolic engineering is a potential industrial producer of β-carotene.

'''4.''' [[CONCLUSION]]
With the combination of traditional metabollic engineering strategies and synthetic biology tools, it's been proven that Y. lipolytica serve as a valid production source for β-carotene. The increase of gene copy numbers and lipogenesis with the use of favourable promoters massively enhanced the production of β-carotene and also, the fed-batch fermentation was proven as the best pathway in generating β-carotene.
The process can also be further improved not only by engineering strains and bioreactor condition optimization but also by the use of low cost carbon sources. The selection of suitable microorganism and strains plays a great role in electing a more successful source of production of β-carotene. The rapid development of synthetic biology tools for genome editing and DNA assembly is alleviating the manipulation of non-conventional organisms, growing the range of biotechnological „vehicles“ for metabolic engineering.

User:Zeljkae

2020-05-11T12:25:37Z

Zeljkae: A synthetic biology approach to transform Yarrowia Lypolytica into a competitive biotechnological producer of β-carotene

'''A SYNTHETIC BIOLOGY APPROACH TO TRANSFORM YARROWIA LYPOLYTICA INTO A COMPETITIVE BIOTECHNOLOGICAL PRODUCER OF β-CAROTENE'''

'''1.''' [[INTRODUCTION]]
β-carotene is an orange pigment and a well-known precursor of vitamin A. It is a biochemical synthesized terpenoid and is added to the group of carotenoids- β-carotene can be produced either chemically or biotechnologically, extracting it from the natural producer of microorganisms such as Blakeslea trispora. Yarrowia lipolytica is an oleaginous yeast greatly investigated and modified, for the sake of production of biotechnologically relevant compounds.

'''2.''' [[THEORETICAL FRAMEWORK]]
'''2.1''' ''MATERIALS AND METHODS – STRAINS AND MEDIA''
The materials and methods are divided into a series of steps, intended to create a producer of β-carotene out of the aforementioned yeast, Yarrowia lipolytica. The needest steps are: 1) strain construction, 2) construction of the DNA, 3) β-carotene measurement, 4) developing microscopy images, 5) lipid content quantification, 6) biomass, sugar and acid quantification and lastly come the 7) bioreactor procedures.

'''3.''' [[RESULTS AND DISCUSSION]]
''' 3.1''' ''Lipid overproducer strain synthesizes higher amount of β-carotene''
Previous set of reports documented that the overexpression of three genes (geranylgeranyl diphosphate synthase (GGS1), pytoene synthase/lycopene cyclase and phytoene dehydrogenase) promote and increase the production of β-carotene in Y. lipolytica. The reseachers used an expression cassette (a car-cassette), where the expression of the GGS1 is controlled by the promoter PGMp. The sole expression, within the cassette itself (in the parental strain) allows a production of a substantial amount of β-carotene.

''' 3.2''' ''Continuous metabolic engineering magnifies carotene content''
In order to enhance the production of caroteonids, the overexpression of HMG1 (hydroxymethylglutaryl-CoA reductase) is well known. In order to enhance the production of β-carotene, they overexpressed the gene YALI0E04807. It was done under the control of the constitutive TEF promoter in the strain of ob-C. The generated strain (ob-CH) enhanced the production β-carotene by a substantial amount.

'''3.3''' ''Identifying the best promoter set for the production of β-carotene''
The increase in promoter strength can enchance the transcription level more than five times. They use the Closing Gate cloning system in promoter shuffling. This strategy consists in a digestion-ligation reaction guided by Bsal defined sites where the three promotors can be introduced and guided within the promotor positions in the car-cassettes. The pool of cassettes were then set for transformation, the wild type parental strains enable the screening of different colour intensity. Once they finished the transformation, they obtained 387 colonies. By analyzing the overall combination of promoters, the presence of a strong TEF promoter is favoured as it stood in the second position of the car-cassette.

'''3.4''' ''The construction of the β-carotene overproducer strain''
Seeing as how an extra copy of the car-cassette in the strain ob-CH increased the production of β-carotene greatly, the cassette was optimized by a set of promoters and as a result there became: carTEF-cassette. By expressing the carTEF-cassette in the strain ob-CH, the production of β-carotene was increased. Moreover, an extra copy of the carTEF-cassette was brought to construct the strain ob-CHCTEFCTEF . Said strain was able to also enhance the production of β-carotene.

'''3.5''' ''A trade off between production titer and yield''
Two different kinds of media were tested, rich media (YPD) and synthetic media (YNB). A higher concentration of the carbon/nitrogen ratio is known to increase lipid production and by that, it enhances the production of carotenoids. Glucose and glycerol were tested as the first carbon source. The selected media were YPD10, YPD60, YNB20, YNB30, YNB60, and YNBGLY60. They concluded that there wasn't much of an influence on the carbon source since glucose and glycerol showed similar between both titer and yields. The best β-carotene titer so far was found in YPD60, whilst the winning yield is YPD10.

''' 3.6''' ''Boosting β-carotene production by the engineered strain ob-CHCTEFCTEF''
With the performation of fed-batch fermantation using a rich media (Y10P20D), they added glucose. The glucose concentration began to rise due to the lack of consumption. The strain led to a production of β-carotene and citric acid. Designing a culture media with the double amount of yeast extract and peptone (Y20P40D), they optimized bioreactor conditions. The results show that Y. lipolytica engineered using synthetic biology and metabolic engineering is a potential industrial producer of β-carotene.

'''4.''' [[CONCLUSION]]
With the combination of traditional metabollic engineering strategies and synthetic biology tools, it's been proven that Y. lipolytica serve as a valid production source for β-carotene. The increase of gene copy numbers and lipogenesis with the use of favourable promoters massively enhanced the production of β-carotene and also, the fed-batch fermentation was proven as the best pathway in generating β-carotene.
The process can also be further improved not only by engineering strains and bioreactor condition optimization but also by the use of low cost carbon sources. The selection of suitable microorganism and strains plays a great role in electing a more successful source of production of β-carotene. The rapid development of synthetic biology tools for genome editing and DNA assembly is alleviating the manipulation of non-conventional organisms, growing the range of biotechnological „vehicles“ for metabolic engineering.

User:Zeljkae

2020-05-11T12:24:03Z

Zeljkae: A synthetic biology approach to transform Yarrowia Lypolytica into a competitive biotechnological producer of β-carotene