Department of Molecular Biosciences
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Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host.
PloS one Jan, 2011 | Pubmed ID: 21283682
Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture.
Microbiology (Reading, England) Sep, 2011 | Pubmed ID: 21700661
Nanostructured hybrid transparent conductive films with antibacterial properties.
ACS nano Jun, 2012 | Pubmed ID: 22519712
Draft genome sequences of two Campylobacter jejuni clinical isolates, NW and D2600.
Journal of bacteriology Oct, 2012 | Pubmed ID: 23012285
Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load.
Proceedings of the National Academy of Sciences of the United States of America Jan, 2013 | Pubmed ID: 23248287
Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system.
Physical biology Apr, 2013 | Pubmed ID: 23492852
Decaffeination and measurement of caffeine content by addicted Escherichia coli with a refactored N-demethylation operon from Pseudomonas putida CBB5.
ACS synthetic biology Jun, 2013 | Pubmed ID: 23654268
Caffeine junkie: an unprecedented glutathione S-transferase-dependent oxygenase required for caffeine degradation by Pseudomonas putida CBB5.
Journal of bacteriology Sep, 2013 | Pubmed ID: 23813729
Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli.
Proceedings of the National Academy of Sciences of the United States of America Feb, 2014 | Pubmed ID: 24379390
Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness.
Nature chemical biology Mar, 2014 | Pubmed ID: 24487692
Engineering reduced evolutionary potential for synthetic biology.
Molecular bioSystems Jul, 2014 | Pubmed ID: 24556867
Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.
Methods in molecular biology (Clifton, N.J.) , 2014 | Pubmed ID: 24838886
Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli.
mBio Sep, 2014 | Pubmed ID: 25205090
Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.
BMC genomics Nov, 2014 | Pubmed ID: 25432719
Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli.
PloS one , 2014 | Pubmed ID: 25502413
Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution.
Journal of bacteriology Mar, 2015 | Pubmed ID: 25512307
The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts.
Journal of biological engineering , 2014 | Pubmed ID: 25525459
Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq.
Frontiers in genetics , 2014 | Pubmed ID: 25653667
Rapid evolution of silver nanoparticle resistance in Escherichia coli.
Frontiers in genetics , 2015 | Pubmed ID: 25741363
Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli.
Genetics Jun, 2015 | Pubmed ID: 25911659
Draft Genome Sequence of the Bacterium Pseudomonas putida CBB5, Which Can Utilize Caffeine as a Sole Carbon and Nitrogen Source.
Genome announcements Jun, 2015 | Pubmed ID: 26067973
Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator.
ACS synthetic biology Aug, 2015 | Pubmed ID: 26096262
The Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm.
PloS one , 2015 | Pubmed ID: 26114300
Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.
Molecular biology and evolution Nov, 2015 | Pubmed ID: 26199375
Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.
PLoS computational biology Aug, 2015 | Pubmed ID: 26275208
Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment.
eLife Oct, 2015 | Pubmed ID: 26465114
Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli.
Molecular biology and evolution Aug, 2016 | Pubmed ID: 27189550
Tempo and mode of genome evolution in a 50,000-generation experiment.
Nature Aug, 2016 | Pubmed ID: 27479321
Emergence of a Competence-Reducing Filamentous Phage from the Genome of Acinetobacter baylyi ADP1.
Journal of bacteriology Dec, 2016 | Pubmed ID: 27645387
Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli.
ACS synthetic biology Jan, 2017 | Pubmed ID: 27648665
Specificity of genome evolution in experimental populations of evolved at different temperatures.
Proceedings of the National Academy of Sciences of the United States of America Mar, 2017 | Pubmed ID: 28202733
Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions.
BMC genomics Apr, 2017 | Pubmed ID: 28412930
The E. coli molecular phenotype under different growth conditions.
Scientific reports Apr, 2017 | Pubmed ID: 28417974
Reduced Mutation Rate and Increased Transformability of Transposon-Free Acinetobacter baylyi ADP1-ISx.
Applied and environmental microbiology Sep, 2017 | Pubmed ID: 28667117
Arresting Evolution.
Trends in genetics : TIG Dec, 2017 | Pubmed ID: 29029851
Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids.
ACS synthetic biology May, 2018 | Pubmed ID: 29608282
Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides.
PLoS genetics Apr, 2018 | Pubmed ID: 29649242
Bacterial Production of Gellan Gum as a Do-It-Yourself Alternative to Agar.
Journal of microbiology & biology education , 2018 | Pubmed ID: 29983852
Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates.
Nucleic acids research Sep, 2018 | Pubmed ID: 30137492
Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure.
ACS synthetic biology Mar, 2019 | Pubmed ID: 30703321
Bioassay for Determining the Concentrations of Caffeine and Individual Methylxanthines in Complex Samples.
Applied and environmental microbiology Dec, 2019 | Pubmed ID: 31540989
Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria.
Nature communications Dec, 2019 | Pubmed ID: 31863068
Engineered symbionts activate honey bee immunity and limit pathogens.
Science (New York, N.Y.) Jan, 2020 | Pubmed ID: 32001655
Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining.
Nucleic acids research May, 2020 | Pubmed ID: 32232367
Experimental Evolution of Leads to Loss of Motility, N (σ54) Deletion and Genome Reduction.
Frontiers in microbiology , 2020 | Pubmed ID: 33240235
Engineering a Culturable Strain for Aphid Paratransgenesis.
Applied and environmental microbiology Mar, 2021 | Pubmed ID: 33277267
Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with .
Proceedings of the National Academy of Sciences of the United States of America Feb, 2021 | Pubmed ID: 33441451
Global Transcriptional Response of to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition.
Microorganisms Feb, 2021 | Pubmed ID: 33578755
Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria.
Nature communications Feb, 2021 | Pubmed ID: 33579917
Rates of gene conversions between Escherichia coli ribosomal operons.
G3 (Bethesda, Md.) Feb, 2021 | Pubmed ID: 33585862
pLannotate: engineered plasmid annotation.
Nucleic acids research Jul, 2021 | Pubmed ID: 34019636
Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance.
Proceedings of the National Academy of Sciences of the United States of America Jun, 2021 | Pubmed ID: 34083444
Engineering insects from the endosymbiont out.
Trends in microbiology Jan, 2022 | Pubmed ID: 34103228
High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing.
Cell systems Dec, 2021 | Pubmed ID: 34536379
The Genomic Basis of Evolutionary Novelties in a Leafhopper.
Molecular biology and evolution Sep, 2022 | Pubmed ID: 36026509
Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection.
Artificial life 13 : proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems. International Conference on the Simulation and Synthesis of Living Systems (13th : 2012 : East Lansing, Mich.) , 2013 | Pubmed ID: 36129423
OSTIR: open source translation initiation rate prediction.
Journal of open source software , 2021 | Pubmed ID: 36177308
Honey bee functional genomics using symbiont-mediated RNAi.
Nature protocols Mar, 2023 | Pubmed ID: 36460809
Electron Tomography and Machine Learning for Understanding the Highly Ordered Structure of Leafhopper Brochosomes.
Biomacromolecules Jan, 2023 | Pubmed ID: 36516996
Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals.
BMC biology Dec, 2022 | Pubmed ID: 36575413
The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of -colonizing .
bioRxiv : the preprint server for biology Feb, 2023 | Pubmed ID: 36824770
Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences.
bioRxiv : the preprint server for biology Apr, 2023 | Pubmed ID: 37090600
The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae.
ISME communications May, 2023 | Pubmed ID: 37225918
Jeffrey E. Barrick1,2,
Zachary D. Blount2,3,
Devin M. Lake2,4,
Jack H. Dwenger1,
Jesus E. Chavarria-Palma1,
Minako Izutsu2,3,
Michael J. Wiser2,5
1Department of Molecular Biosciences, The University of Texas at Austin,
2BEACON Center for the Study of Evolution in Action, Michigan State University,
3Department of Microbiology and Molecular Genetics, Michigan State University,
4Department of Integrative Biology, Michigan State University,
5Biological Sciences Program, Michigan State University
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