Lidstrom:Journal Club

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The Lidstrom Lab journal club is held from 10-11 AM every other Friday in the 4th floor conference room.

Journal Club Schedule

Date	Presenter	Paper	Snack Provider
2018/11/2	Jue	Yishai et al. In Vivo Assimilation of One-Carbon via a Synthetic Reductive Glycine Pathway in Escherichia coli. ACS Synth. Biol. (2018)	?
2018/10/12	Mitch	Feng Y et al. Coexistence of two blaNDM-5 genes on an IncF plasmid as revealed by nano pore sequencing. Antimicrob Agents Chemother (2018)	?
2018/09/28	Lian	?	?
2018/09/14	Mila	Research Update	Mila
2018/08/31	Joseph	Deng YW et al. Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C J Biol Inorg Chem (2018)	?
2018/08/17	Aaron	Helfrich EJN et al. Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome. Nat Microbiol (2018)	?
2018/07/06	Mitch	Maddamsetti R & Lenski RE. Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection. PLoS Genetics (2018)	?
2018/05/04	Jue	Bar-Even A. Daring metabolic designs for enhanced plant carbon fixation. Plant Science (2018)	?
2018/03/23	Lian	Akberdin IR et al. Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach. Sci Rep (2018)	?
2018/02/23	Aaron	Calatrava V et al. Ok, thanks! A new mutualism between Chlamydomonas and Methylobacteria facilitates growth on amino acids and peptides. FEMS Microbiol Lett (2018)	?
2018/02/09	Joseph	Mota CS et al. Effects of molybdate and tungstate on expression levels and biochemical characteristics of formate dehydrogenases produced by Desulfovibrio alaskensis NCIMB 13491. J Bacteriol (2011)	?
2017
2017/12/29	Mitch	Wei XM et al. Responses of methanotrophic activity, community and EPS production to CH4 and O2 concentrations in waste biocover soils. Waste Manag (2015)	?
2017/12/01	Lian	Ghosh A et al. A peptide-based method for 13C Metabolic Flux Analysis in microbial communities. PLoS Comput Biol (2014)	?
2017/11/17	Aaron	Ueoka R et al. Toblerols, Cyclopropanol-Containing Modulators of Methylobacterial Antibiosis Generated by an Unusual Polyketide Synthase. Angew Chem Int Ed Engl (2017)	?
2017/11/03	Mitch	Haft DH et al. Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC Biol (2006)	?
2017/10/20	Joseph	Czarnecki J et al. Lifestyle-determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685. Environ Microbiol (2017)	?
2017/10/06	Zheng	Leinweber A et al. Cheating fosters species co-existence in well-mixed bacterial communities. ISME J (2017)	?
2017/09/22	Yanfen	Basler G et al. Control of fluxes in metabolic networks. Genome Res (2016)	?
2017/09/01	Lian	Kochanowski K et al. Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli. Mol Syst Biol (2017)	?
2017/08/18	Yue	McAnulty MJ et al. Electricity from methane by reversing methanogenesis. Nat Commun (2017)	?
2017/08/04	Mitch	Casjens SR et al. Plasmid diversity and phylogenetic consistency in the Lyme disease agent Borrelia burgdorferi. BMC Genomics (2017)	?
2017/06/16	Aaron	Dassama LM et al. Methanobactin transport machinery. PNAS (2016)	?
2017/06/02	Lian	Henard CA et al. Phosphoketolase overexpression increases biomass and lipid yield from methane in an obligate methanotrophic biocatalyst. Metab Eng (2017)	?
2017/05/19	Jing	Price JV et al. Scaffoldless engineered enzyme assembly for enhanced methanol utilization. PNAS (2016)	?
2017/04/27	Yanfen	Hackett SR et al. Systems-level analysis of mechanisms regulating yeast metabolic flux. Science (2016)	?
2017/04/07	Sascha	Bellenger JP et al. Uptake of molybdenum and vanadium by a nitrogen-fixing soil bacterium using siderophores. Nat Geoscience (2008)	?
2017/03/24	Aaron	Schwander T et al. A synthetic pathway for the fixation of carbon dioxide in vitro. Science (2016)	?
2017/02/23	Mitch	Dziewit L et al. Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686. Front Microbiol. (2015)	?
2017/02/09	Nejc	Louca S et al. High taxonomic variability despite stable functional structure across microbial communities. Nature Ecology & Evolution (2016)	Nejc
2017/01/12	Yue	Wegener G et al. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria. Nature (2015)	?
2016
2016/12/15	Jing	Zetsche B et al. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol (2016)	?
2016/12/01	Mitch	Gifford SM et al. Quantitative Transcriptomics Reveals the Growth- and Nutrient-Dependent Response of a Streamlined Marine Methylotroph to Methanol and Naturally Occurring Dissolved Organic Matter. MBio (2016)	?
2016/11/10	Alexey	Bacteriohemerythrin review including Chen KH et al. Bacteriohemerythrin bolsters the activity of the particulate methane monooxygenase (pMMO) in Methylococcus capsulatus (Bath). J Inorg Biochem (2012)	Mitch
2016/10/28	Aaron	Price MN et al. Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes. bioRxiv (2016)	?
2016/10/14	Zheng	Hatzenpichler R et al. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. PNAS (2016)	?
2016/09/30	Yanfen	Link H et al. Real-time metabolome profiling of the metabolic switch between starvation and growth. Nat Methods (2015)	?
2016/09/16	Nejc	Roller BR et al. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. Nat Microbiol (2016)	?
2016/09/02	Amanda	Xiao Y et al. Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis. Nat Chem Biol (2016)	?
2016/08/12	Sascha	Biller SJ et al. Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus. ISME J (2016)	?
2016/07/25	Mitch	Lee HH et al. Vibrio natriegens, a new genomic powerhouse. bioRxiv (2016)	Amanda (peach crisp)
2016/07/15	Aaron	Lau JT et al. Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling. Genome Med. (2016)	?
2016/04/25	Mitch	Hug LA et al. A New View of the Tree of Life. Nat Microbiol (2016)	?
2016/04/08	Nejc	Price M et al. A Comparison of the Costs and Benefits of Bacterial Gene Expression. bioRxiv (2016)	?
2016/01/22	Alexey	McGlynn SE et al. Single cell activity reveals direct electron transfer in methanotrophic consortia. Nature (2015)
2016/01/08	Aaron	Peter DM et al. Screening and Engineering the Synthetic Potential of Carboxylating Reductases from Central Metabolism and Polyketide Biosynthesis. Angew Chem (2015)	?
2015
2015/010/26	Melissa	Oberhardt et al. Harnessing the landscape of microbial culture media to predict new organism–media pairings Nat Commun (2015)	Frances
2015/08/14	Alexey	Farzadfard F & Lu TK. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations Science (2014)	?
2015/08/07	Frances	Liu J et al. Metabolic co-dependence gives rise to collective oscillations within biofilms Nature (2015)	?
2015/07/31	Mitch	Raman S et al. Evolution-guided optimization of biosynthetic pathways. PNAS (2014)	?
2015/07/24	Aaron	Raggi L et al. Bacterial symbionts of Bathymodiolus mussels and Escarpia tubeworms from Chapopote, an asphalt seep in the Southern Gulf of Mexico. Environ Microbiol (2013)	?
2015/07/10	Melissa	Sundstrom ER & Criddle CS. Optimization of Methanotrophic Growth and Production of Poly(3-Hydroxybutyrate) in a High-Throughput Microbioreactor System. AEM (2015)	Frances
2015/06/12	Frances	Kits et al. Methane oxidation coupled to nitrate reduction under hypoxia by Gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1. Environ Microbiol (2015)	?
2015/05/15	Melissa	Zhou K et al. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat Biotechnol (2015)	Frances
2015/05/01	Aaron	Methylotrophy Lecture Practice	?
2015/04/17	Frances	Degnan et al. Human gut microbes use multiple transporters to distinguish vitamin B12 analogs and compete in the gut. Cell Host & Microbe (2014)	?
2015/04/10	Mila	JGI meeting roundup	?
2015/03/20	Aaron	Fitzgerald JT et al. Analysis and refactoring of the A-74528 biosynthetic pathway. JACS (2013)	Janet
2015/03/13	Roundtable	Banerjee R et al. Structure of the key species in the enzymatic oxidation of methane to methanol. Nature (2015)	Amanda
2015/03/06	Melissa	Wang M et al. Quorum sensing and policing of Pseudomonas aeruginosa social cheaters. PNAS (2015)	Frances
2015/02/20	Frances	Ecuador recap	Melissa/Yanfen
2015/02/06	Alexey	Chang et al. Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nat Chem Biol. (2011)	Aaron/Amanda
2015/01/30	Amanda	Muller et al. Engineering Escherichia coli for methanol conversion. Metab Eng (2015)	Melissa
2015/01/23	Melissa	Tsai SQ et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol (2014)	Amanda
2015/01/16	Frances	Ling LL et al. A new antibiotic kills pathogens without detectable resistance. Nature (2015)	Mila
2015/01/09	Aaron	Michener JK et al. Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement. Elife (2014)	Janet
2014
2014/12/19	Sascha	Deutzmann JS et al. Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake. PNAS (2014)	Mila
2014/12/04	Mila	Nyak DD & Marx CJ. Methylamine Utilization via the N-Methylglutamate Pathway in Methylobacterium extorquens PA1 Involves a Novel Flow of Carbon through C1 Assimilation and Dissimilation Pathways. J Bacteriol (2014).	Mila
2014/11/14	Amanda	Bogorad et al. Building carbon-carbon bonds using a biocatalytic methanol condensation cycle.	Frances
2014/11/07	Frances	Wang BL et al. Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol (2014).	Sascha
2014/10/31	Aaron	Ye RW et al. Construction of the astaxanthin biosynthetic pathway in a methanotrophic bacterium Methylomonas sp. strain 16a. J Ind Microbiol Biotechnol (2007).	Amanda
2014/10/03	Melissa	Lin MT et al. A faster Rubisco with potential to increase photosynthesis in crops. Nature (2014).	Janet
2014/09/26	Alexey	Tips and tricks for being a good lab human	Mila
2014/08/08	Amanda	Noor E et al. Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism PLoS Comput Biol (2014).	:(
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