Browsing by Author "Marx, Christopher J"
Now showing items 1-20 of 33
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The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum
Harcombe, William R.; Delaney, Nigel F.; Leiby, Nicholas; Klitgord, Niels; Marx, Christopher J. (Public Library of Science, 2013)The most powerful genome-scale framework to model metabolism, flux balance analysis (FBA), is an evolutionary optimality model. It hypothesizes selection upon a proposed optimality criterion in order to predict the set of ... -
Adaptation and Specialization in the Evolution of Bacterial Metabolism
Leiby, Nicholas (2014-06-06)Specialization is a balance of evolutionary adaptation and its accompanying costs. Here we focus on the Lenski Long-Term Evolution Experiment, which has maintained cultures of Escherichia coli in the same, defined seasonal ... -
Burkholderia Xenovorans LB400 Harbors a Multi-Replicon, 9.73-Mbp Genome Shaped for Versatility
Konstantinidis, Konstantinos T.; Seeger, Michael; Vergez, Lisa M.; Chain, Patrick S. G.; Malfatti, Stephanie A.; Denef, Vincent J.; Zhulin, Igor B.; Mahenthiralingam, Eshwar; LiPuma, John J.; Lao, Victoria; Larimer, Frank; Cordova, Macarena; Sul, Woo Jun; Tiedje, James M.; Spilker, Theodore; Land, Miriam; Tsoi, Tamara V.; Ulrich, Luke E.; Reyes, Valeria Latorre; Agullo, Loreine; Smith, Daryl; Parnell, J. Jacob; Ramette, Alban; Hauser, Loren; Richardson, Paul; Marx, Christopher; Gonzalez, Myriam; Gomez, Luis (National Academy of Sciences, 2006)<i>Burkholderia xenovorans</i> LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic <i>Burkholderia</i> isolate ... -
Can You Sequence Ecology? Metagenomics of Adaptive Diversification
Marx, Christopher J (Public Library of Science, 2013)Few areas of science have benefited more from the expansion in sequencing capability than the study of microbial communities. Can sequence data, besides providing hypotheses of the functions the members possess, detect the ... -
Development of a Broad-Host-Range SacB-Based Vector for Unmarked Allelic Exchange
Marx, Christopher J (BioMed Central, 2008)Background: Although genome sequences are available for an ever-increasing number of bacterial species, the availability of facile genetic tools for physiological analysis have generally lagged substantially behind traditional ... -
Development of an Insertional Expression Vector System for Methylobacterium Extorquens AM1 and Generation of Null Mutants Lacking mtdA and/or fch
Marx, Christopher; Lidstrom, Mary E. (Society for General Microbiology, 2004)Over the past few years, the genetic 'toolkit' available for use with <i>Methylobacterium extorquens</i> AM1 has expanded significantly. Here a further advance is presented and demonstrated, an insertional expression system ... -
Development of an Optimized Medium, Strain and High-Throughput Culturing Methods for Methylobacterium extorquens
Delaney, Nigel Francis; Kaczmarek, Maria E.; Ward, Lewis M.; Swanson, Paige Kathleen; Lee, Ming-Chun; Marx, Christopher J (Public Library of Science, 2013)Methylobacterium extorquens strains are the best-studied methylotrophic model system, and their metabolism of single carbon compounds has been studied for over 50 years. Here we develop a new system for high-throughput ... -
Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation
Chou, H.-H.; Chiu, H.-C.; Delaney, N. F.; Segre, D.; Marx, Christopher J (American Association for the Advancement of Science (AAAS), 2011)Epistasis has substantial impacts on evolution, in particular, the rate of adaptation. We generated combinations of beneficial mutations that arose in a lineage during rapid adaptation of a bacterium whose growth depended ... -
The Enigmatic Planctomycetes May Hold a Key to the Origins of Methanogenesis and Methylotrophy
Staley, James T.; Kalyuzhnaya, Marina G.; Lidstrom, Mazy E.; Jenkins, Cheryl; Lapidus, Alla; Vorholt, Julia A.; Chistoserdova, Ludmila; Marx, Christopher (Oxford University Press, 2004)Methanogenesis and methane oxidation are the major biological processes affecting the global cycling of the powerful greenhouse gas methane. To carry out the two alternative bioconversions, Nature has cleverly recycled key ... -
Epistasis from functional dependence of fitness on underlying traits
Chiu, Hsuan-Chao; Marx, Christopher J; Segrè, Daniel (The Royal Society, 2012)Epistasis between mutations in two genes is thought to reflect an interdependence of their functions. While sometimes epistasis is predictable using mechanistic models, its roots seem, in general, hidden in the complex ... -
Evolution after Introduction of a Novel Metabolic Pathway Consistently Leads to Restoration of Wild-Type Physiology
Carroll, Sean; Marx, Christopher J (Public Library of Science, 2013)Organisms cope with physiological stressors through acclimatizing mechanisms in the short-term and adaptive mechanisms over evolutionary timescales. During adaptation to an environmental or genetic perturbation, beneficial ... -
Evolution as an experimental tool in microbiology: 'Bacterium, improve thyself!'
Marx, Christopher J (Society for Applied Microbiology, 2011) -
Flux Analysis Uncovers Key Role of Functional Redundancy in Formaldehyde Metabolism
Marx, Christopher; Van Dien, Stephen J.; Lidstrom, Mary E. (Public Library of Science, 2005)Genome-scale analysis of predicted metabolic pathways has revealed the common occurrence of apparent redundancy for specific functional units, or metabolic modules. In many cases, mutation analysis does not resolve function, ... -
FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations
Chubiz, Lon M; Lee, Ming-Chun; Delaney, Nigel Francis; Marx, Christopher J (Public Library of Science, 2012)Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq) that leverages Illumina ... -
Genetic and Phenotypic Comparison of Facultative Methylotrophy between Methylobacterium extorquens Strains PA1 and AM1
Nayak, Dipti D.; Marx, Christopher J. (Public Library of Science, 2014)Methylobacterium extorquens AM1, a strain serendipitously isolated half a century ago, has become the best-characterized model system for the study of aerobic methylotrophy (the ability to grow on reduced single-carbon ... -
Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness Arising from Synonymous Mutations in a Key Enzyme
Agashe, Deepa; Martinez-Gomez, N. Cecilia; Drummond, D. Allan; Marx, Christopher J (Oxford University Press, 2012)Biased codon usage in protein-coding genes is pervasive, whereby amino acids are largely encoded by a specific subset of possible codons. Within individual genes, codon bias is stronger at evolutionarily conserved residues, ... -
An Integrative Approach to Understanding Microbial Diversity: From Intracellular Mechanisms to Community Structure
Gudelj, Ivana; Weitz, Joshua S; Ferenci, Tom; Claire Horner-Devine, M; Marx, Christopher J; Meyer, Justin R; Forde, Samantha E (Blackwell Publishing Ltd., 2010)Trade-offs have been put forward as essential to the generation and maintenance of diversity. However, variation in trade-offs is often determined at the molecular level, outside the scope of conventional ecological inquiry. ... -
Introduction to Focus Issue: Genetic Interactions
Segrè, Daniel; Marx, Christopher J (AIP Publishing, 2010)The perturbation of a gene in an organism’s genome often causes changes in the organism’s observable properties or phenotypes. It is not obvious a priori whether the simultaneous perturbation of two genes produces a ... -
Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance
Carroll, Sean Michael; Xue, Katherine S; Marx, Christopher J (BioMed Central, 2014)Background: A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutations ... -
Mapping the Fitness Landscape of Gene Expression Uncovers the Cause of Antagonism and Sign Epistasis between Adaptive Mutations
Chou, Hsin-Hung; Delaney, Nigel F.; Draghi, Jeremy A.; Marx, Christopher J. (Public Library of Science, 2014)How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial ...