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) ?
2017/12/29 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) ?
2016/12/15 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) ?
2015/010/26 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
2014/12/19 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
2013/12/06 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