Lidstrom:Journal Club

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(Journal Club Schedule)
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{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Date'''
| align="center" style="background:#f0f0f0;"|'''Date'''
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| align="center" style="background:#f0f0f0;"|'''Host'''
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| align="center" style="background:#f0f0f0;"|'''Presenter'''
| align="center" style="background:#f0f0f0;"|'''Paper'''
| align="center" style="background:#f0f0f0;"|'''Paper'''
| align="center" style="background:#f0f0f0;"|'''Snack Provider'''
| align="center" style="background:#f0f0f0;"|'''Snack Provider'''
|-
|-
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| 2013/08/09 || Nate || ?? || ??
+
| 2014/08/08 || Amanda|| [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003483#pcbi-1003483-g004 Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism] || ???
|-
|-
-
| 2013/08/02 || ?? || ?? || ??
+
| 2014/08/01 || Aaron|| [http://www.ncbi.nlm.nih.gov/pubmed/20868748 Rozova ON et al. Characterization of recombinant pyrophosphate-dependent 6-phosphofructokinase from halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. ''Res Microbiol'' (2010).] || Janet
|-
|-
-
| 2013/07/26 || Alexey || [http://www.ncbi.nlm.nih.gov/pubmed/20929806 Ajikumar et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. ''Science'' (2010)] || ??
+
| 2014/07/18 || Alexey|| [http://pubs.acs.org/doi/pdf/10.1021/ie202914s Ramezani M et al. Improved Modeling of Bubble Column Reactors by Considering the Bubble Size Distribution. ''I&EC Research'' (2012)] || :(
 +
|-
 +
| 2014/07/11 || Frances ||  [http://www.ncbi.nlm.nih.gov/pubmed/22484247 Chen KH et al. Bacteriohemerythrin bolsters the activity of the pMMO in Methylococcus capsulatus (Bath). ''J Inorg Biochem'' (2012).] || Amanda
 +
|-
 +
| 2014/06/27 || Amanda, Janet, & Aaron ||  Metabolic Engineering X Conference Recap || :(
 +
|-
 +
| 2014/06/13 || Bo ||  [http://www.ncbi.nlm.nih.gov/pubmed/23575629 Paddon CJ et al. High-level semi-synthetic production of the potent antimalarial artemisinin. ''Nature'' (2013).] || Maria
 +
|-
 +
| 2014/05/30 || Mila || [http://www.ncbi.nlm.nih.gov/pubmed/5965346 Kemp MB & Quayle JR. Microbial growth on C1 compounds. Incorporation of C1 units into allulose phosphate by extracts of Pseudomonas methanica. ''Biochem J'' (1966).] || Mila
 +
|-
 +
| 2014/05/23 || Aaron ||  [http://www.ncbi.nlm.nih.gov/pubmed/24776799 Crombie AT & Murrell JC. Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris. ''Nature'' (2014).] || Mila
 +
|-
 +
| 2014/05/16 || Maria ||  [http://www.ncbi.nlm.nih.gov/pubmed/22544346 Chauhan A et al. Composition of methane-oxidizing bacterial communities as a function of nutrient loading in the Florida everglades. ''Microb Ecol'' (2012).] || Mila
 +
|-
 +
| 2014/05/09 || Amanda ||  [http://www.ncbi.nlm.nih.gov/pubmed/24131951 Chou H & Keasling JD. Programming adaptive control to evolve increased metabolite production. ''Nat Comm'' (2013).] || Janet
 +
|-
 +
| 2014/05/02 || Sascha ||  [http://www.ncbi.nlm.nih.gov/pubmed/24304674 Andrade-Domínguez A et al. Eco-evolutionary feedbacks drive species interactions. ''ISME J'' (2014).] || Mila
 +
|-
 +
| 2014/04/25 || Bo ||  [http://www.ncbi.nlm.nih.gov/pubmed/22474341 Lan EL & Liao JC. ATP drives direct photosynthetic production of 1-butanol in cyanobacteria. ''Proc Natl Acad Sci'' (2012).] || Mila
 +
|-
 +
| 2014/04/18 || Frances ||  [http://www.ncbi.nlm.nih.gov/pubmed/18004300 Dunfield PF et al. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. ''Nature'' (2007).] || Bo
 +
|-
 +
| 2014/04/11 || Amanda ||  [http://www.ncbi.nlm.nih.gov/pubmed/24142050 Dahl RH et al. Engineering dynamic pathway regulation using stress-response promoters. ''Nat Biotechnol'' (2013).] || Frances
 +
|-
 +
| 2014/03/21 || Maria ||  [http://www.ncbi.nlm.nih.gov/pubmed/21385187 Wieczorek AS et al. Organic acids and ethanol inhibit the oxidation of methane by mire methanotrophs. ''FEMS Microbiol Ecol'' (2011).] || Aaron
 +
|-
 +
| 2014/03/14 || Sascha ||  [http://www.ncbi.nlm.nih.gov/pubmed/24373058 Dam B et al. Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2. ''Environ Microbiol'' (2013).] || Amanda
 +
|-
 +
| 2014/02/28 || Aaron ||  [http://www.ncbi.nlm.nih.gov/pubmed/24077099 Bogorad IW et al. Synthetic non-oxidative glycolysis enables complete carbon conservation. ''Nature'' (2013).] || Maria
 +
|-
 +
| 2014/02/21 || Janet ||  [http://www.ncbi.nlm.nih.gov/pubmed/23360965 Jiang W et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. ''Nat Biotechnol'' (2013).] || Igor
 +
|-
 +
| 2014/02/14 || Dave || [http://www.ncbi.nlm.nih.gov/pubmed/24473129 Gomaa AA et al. Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems. ''mBio'' (2014).] || Sascha
 +
|-
 +
| 2014/02/07 || Bo || [http://www.ncbi.nlm.nih.gov/pubmed/23334451 Na D et al. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. ''Nat Biotechnol'' (2013).] || Janet
 +
|-
 +
| 2014/01/31 || Alexey || [http://www.ncbi.nlm.nih.gov/pubmed/21832992 Dellomonaco C et al. Engineered reversal of the b-oxidation cycle for the synthesis of fuels and chemicals. ''Nature'' (2011).]  || Amanda
 +
|-
 +
| 2014/01/24 || Amanda || [http://www.ncbi.nlm.nih.gov/pubmed/19359587 Kudla G et al. Coding-Sequence Determinants of Gene Expression in Escherichia coli. ''Science'' (2009).]  || Frances
 +
|-
 +
| 2014/01/17 || Frances || [http://www.ncbi.nlm.nih.gov/pubmed/19748469 Goodman AL et al. Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat. ''Cell Host Microbe'' (2009).] || Aaron
 +
|-
 +
| 2014/01/10 || Aaron || [http://www.ncbi.nlm.nih.gov/pubmed/23985741 Tamas I et al. The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis. ''ISME J'' (2013).] || Mila
 +
|-
 +
| colspan="4" style="text-align: center;" align="center" | 2013
 +
|-
 +
| 2013/12/06 || Alexey || [http://www.ncbi.nlm.nih.gov/pubmed/23659832 Wen M et al. Production of advanced biofuels in engineered E. Coli. ''Curr Opin Chem Biol'' (2013).] || Amanda
 +
|-
 +
| 2013/11/22 || Mila || [http://www.ncbi.nlm.nih.gov/pubmed/24302011 Kalyuzhnaya MG et al. Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. ''Nat Commun'' (2013).] || Mila
 +
|-
 +
| 2013/11/15 || Dave || [http://www.ncbi.nlm.nih.gov/pubmed/23395959 Lee SJ et al. Control of substrate access to the active site in methane monooxygenase. ''Nature'' (2013).] || Aaron
 +
|-
 +
| 2013/11/08 || Amanda || [http://www.ncbi.nlm.nih.gov/pubmed/22992527 Blount ZD et al. Genomic analysis of a key innovation in an experimental Escherichia coli population. ''Nature'' (2012).] || Yanfen
 +
|-
 +
| 2013/11/01 || Frances || [http://www.ncbi.nlm.nih.gov/pubmed/23682956 Semrau JD et al. Methanobactin and MmoD work in concert to act as the 'copper-switch' in methanotrophs. ''Environmental Microbiology'' (2013).]  || Janet
 +
|-
 +
| 2013/10/25 || Bo || [http://www.ncbi.nlm.nih.gov/pubmed/23656325 Dietrich JA et al. Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ''ACS Synth Biol'' (2013).] || Frances
 +
|-
 +
| 2013/10/18 || Aaron || [http://www.ncbi.nlm.nih.gov/pubmed/21984248 Iguchi H et al. Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia. ''Appl Environ Microbiol'' (2011).]  || Amanda
 +
|-
 +
| 2013/10/11 || Mila || [http://www.ncbi.nlm.nih.gov/pubmed/24012541 Stock M et al. Exploration and prediction of interactions between methanotrophs and heterotrophs. ''Res Microbiol'' (2013).] || Mila
 +
|-
 +
| 2013/10/04 || Alexey || [http://www.ncbi.nlm.nih.gov/pubmed/16612385 Ro DK et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. ''Nature'' (2006).] || Igor
 +
|-
 +
| 2013/09/20 || Amanda || [http://www.ncbi.nlm.nih.gov/pubmed/19838166 Barrick JE et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. ''Nature'' (2009).] || Janet
 +
|-
 +
| 2013/09/13 || Frances || [http://www.ncbi.nlm.nih.gov/pubmed/23209751 Nakagawa T et al. A catalytic role of XoxF1 as La3+-dependent methanol dehydrogenase in Methylobacterium extorquens strain AM1. ''PLoS One'' (2012).] || Bo
 +
|-
 +
| 2013/09/06 || Igor || [http://www.ncbi.nlm.nih.gov/pubmed/19833965 Dekas AE et al. Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. ''Science'' (2009).] || Frances
 +
|-
 +
| 2013/08/30 || Mila || [http://www.ncbi.nlm.nih.gov/pubmed/23892779 Haroon MF et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. ''Nature'' (2013).]|| Mila
 +
|-
 +
| 2013/08/23 || Amanda || [http://www.ncbi.nlm.nih.gov/pubmed/18524956 Blount ZD et al. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. ''Proc Natl Acad Sci'' (2008).]|| Dave
 +
|-
 +
| 2013/08/16 || Yanfen || [http://www.ncbi.nlm.nih.gov/pubmed/22556256 Schuetz R et al. Multidimensional optimality of microbial metabolism. ''Science'' (2012).]  || Mila
 +
|-
 +
| 2013/08/09 || Nate || [http://www.ncbi.nlm.nih.gov/pubmed/20118267 Okubo Y et al. Alternative route for glyoxylate consumption during growth on two-carbon compounds by Methylobacterium extorquens AM1. ''J Bacteriol'' (2010).] || Janet
 +
|-
 +
| 2013/08/02 || Aaron || [http://www.ncbi.nlm.nih.gov/pubmed/20336137 Ettwig KF et al. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. ''Nature'' (2010).] || Amanda
 +
|-
 +
| 2013/07/26 || Alexey || [http://www.ncbi.nlm.nih.gov/pubmed/20929806 Ajikumar PK et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. ''Science'' (2010).] || Aaron
|-
|-
| 2013/07/19 || Bo || [http://www.ncbi.nlm.nih.gov/pubmed/17548827 Erb TJ et al. Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway. ''Proc Natl Acad Sci'' (2007).] || :(
| 2013/07/19 || Bo || [http://www.ncbi.nlm.nih.gov/pubmed/17548827 Erb TJ et al. Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway. ''Proc Natl Acad Sci'' (2007).] || :(

Current revision

Back to Lidstrom

The Lidstrom Lab journal club is held from 9:30-10:30 AM on Fridays in the 4th floor conference room.

Journal Club Schedule

Date Presenter Paper Snack Provider
2014/08/08 Amanda Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism  ???
2014/08/01 Aaron Rozova ON et al. Characterization of recombinant pyrophosphate-dependent 6-phosphofructokinase from halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Res Microbiol (2010). Janet
2014/07/18 Alexey Ramezani M et al. Improved Modeling of Bubble Column Reactors by Considering the Bubble Size Distribution. I&EC Research (2012)  :(
2014/07/11 Frances Chen KH et al. Bacteriohemerythrin bolsters the activity of the pMMO in Methylococcus capsulatus (Bath). J Inorg Biochem (2012). Amanda
2014/06/27 Amanda, Janet, & Aaron Metabolic Engineering X Conference Recap  :(
2014/06/13 Bo Paddon CJ et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature (2013). Maria
2014/05/30 Mila Kemp MB & Quayle JR. Microbial growth on C1 compounds. Incorporation of C1 units into allulose phosphate by extracts of Pseudomonas methanica. Biochem J (1966). Mila
2014/05/23 Aaron Crombie AT & Murrell JC. Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris. Nature (2014). Mila
2014/05/16 Maria Chauhan A et al. Composition of methane-oxidizing bacterial communities as a function of nutrient loading in the Florida everglades. Microb Ecol (2012). Mila
2014/05/09 Amanda Chou H & Keasling JD. Programming adaptive control to evolve increased metabolite production. Nat Comm (2013). Janet
2014/05/02 Sascha Andrade-Domínguez A et al. Eco-evolutionary feedbacks drive species interactions. ISME J (2014). Mila
2014/04/25 Bo Lan EL & Liao JC. ATP drives direct photosynthetic production of 1-butanol in cyanobacteria. Proc Natl Acad Sci (2012). Mila
2014/04/18 Frances Dunfield PF et al. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature (2007). Bo
2014/04/11 Amanda Dahl RH et al. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol (2013). Frances
2014/03/21 Maria Wieczorek AS et al. Organic acids and ethanol inhibit the oxidation of methane by mire methanotrophs. FEMS Microbiol Ecol (2011). Aaron
2014/03/14 Sascha Dam B et al. Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2. Environ Microbiol (2013). Amanda
2014/02/28 Aaron Bogorad IW et al. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature (2013). Maria
2014/02/21 Janet Jiang W et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol (2013). Igor
2014/02/14 Dave Gomaa AA et al. Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems. mBio (2014). Sascha
2014/02/07 Bo Na D et al. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol (2013). Janet
2014/01/31 Alexey Dellomonaco C et al. Engineered reversal of the b-oxidation cycle for the synthesis of fuels and chemicals. Nature (2011). Amanda
2014/01/24 Amanda Kudla G et al. Coding-Sequence Determinants of Gene Expression in Escherichia coli. Science (2009). Frances
2014/01/17 Frances Goodman AL et al. Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat. Cell Host Microbe (2009). Aaron
2014/01/10 Aaron Tamas I et al. The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis. ISME J (2013). Mila
2013
2013/12/06 Alexey Wen M et al. Production of advanced biofuels in engineered E. Coli. Curr Opin Chem Biol (2013). Amanda
2013/11/22 Mila Kalyuzhnaya MG et al. Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat Commun (2013). Mila
2013/11/15 Dave Lee SJ et al. Control of substrate access to the active site in methane monooxygenase. Nature (2013). Aaron
2013/11/08 Amanda Blount ZD et al. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature (2012). Yanfen
2013/11/01 Frances Semrau JD et al. Methanobactin and MmoD work in concert to act as the 'copper-switch' in methanotrophs. Environmental Microbiology (2013). Janet
2013/10/25 Bo Dietrich JA et al. Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ACS Synth Biol (2013). Frances
2013/10/18 Aaron Iguchi H et al. Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia. Appl Environ Microbiol (2011). Amanda
2013/10/11 Mila Stock M et al. Exploration and prediction of interactions between methanotrophs and heterotrophs. Res Microbiol (2013). Mila
2013/10/04 Alexey Ro DK et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature (2006). Igor
2013/09/20 Amanda Barrick JE et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature (2009). Janet
2013/09/13 Frances Nakagawa T et al. A catalytic role of XoxF1 as La3+-dependent methanol dehydrogenase in Methylobacterium extorquens strain AM1. PLoS One (2012). Bo
2013/09/06 Igor Dekas AE et al. Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science (2009). Frances
2013/08/30 Mila Haroon MF et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature (2013). Mila
2013/08/23 Amanda Blount ZD et al. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci (2008). Dave
2013/08/16 Yanfen Schuetz R et al. Multidimensional optimality of microbial metabolism. Science (2012). Mila
2013/08/09 Nate Okubo Y et al. Alternative route for glyoxylate consumption during growth on two-carbon compounds by Methylobacterium extorquens AM1. J Bacteriol (2010). Janet
2013/08/02 Aaron Ettwig KF et al. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature (2010). Amanda
2013/07/26 Alexey Ajikumar PK et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science (2010). Aaron
2013/07/19 Bo Erb TJ et al. Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway. Proc Natl Acad Sci (2007).  :(
2013/07/12 Frances Balasubramanian R et al. Oxidation of methane by a biological dicopper centre. Nature (2010). Amanda
2013/06/28 Aaron Chistoserdova L et al. C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic Archaea. Science (1998). Frances
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