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MSphere 2018Experimental evolution is a method in which populations of organisms, often microbes, are founded by one or more ancestors of known genotype and then propagated under...
Experimental evolution is a method in which populations of organisms, often microbes, are founded by one or more ancestors of known genotype and then propagated under controlled conditions to study the evolutionary process. These evolving populations are influenced by all population genetic forces, including selection, mutation, drift, and recombination, and the relative contributions of these forces may be seen as mysterious. Here, I describe why the outcomes of experimental evolution should be viewed with greater certainty because the force of selection typically dominates. Importantly, any mutant rising rapidly to high frequency in large populations must have acquired adaptive traits in the selective environment. Sequencing the genomes of these mutants can identify genes or pathways that contribute to an adaptation. I review the logic and simple mathematics why this evolve-and-resequence approach is a powerful way to find the mutations or mutation combinations that best increase fitness in any new environment.
Topics: Adaptation, Biological; Evolution, Molecular; Genetics, Microbial; Genetics, Population; Models, Biological; Selection, Genetic
PubMed: 29743200
DOI: 10.1128/mSphere.00121-18 -
Microbiology Spectrum Oct 2014This chapter revisits the historical development and outcome of studies focused on the transmissible, extrachromosomal genetic elements called plasmids. Early work on... (Review)
Review
This chapter revisits the historical development and outcome of studies focused on the transmissible, extrachromosomal genetic elements called plasmids. Early work on plasmids involved structural and genetic mapping of these molecules, followed by the development of an understanding of how plasmids replicate and segregate during cell division. The intriguing property of plasmid transmission between bacteria and between bacteria and higher cells has received considerable attention. The utilitarian aspects of plasmids are described, including examples of various plasmid vector systems. This chapter also discusses the functional attributes of plasmids needed for their persistence and survival in nature and in man-made environments. The term plasmid biology was first conceived at the Fallen Leaf Lake Conference on Promiscuous Plasmids, 1990, Lake Tahoe, California. The International Society for Plasmid Biology was established in 2004 (www.ISPB.org).
Topics: Adaptation, Biological; Biology; Evolution, Molecular; Extrachromosomal Inheritance; Gene Transfer, Horizontal; Genetics, Microbial; History, 20th Century; History, 21st Century; Molecular Biology; Plasmids; Selection, Genetic
PubMed: 26104369
DOI: 10.1128/microbiolspec.PLAS-0019-2013 -
Trends in Biotechnology Nov 2005As the global threat of drug-resistant pathogens continues to rise, new strategies and resources are required to accelerate and advance the drug discovery process. We... (Review)
Review
As the global threat of drug-resistant pathogens continues to rise, new strategies and resources are required to accelerate and advance the drug discovery process. We believe that rapid progress in metagenomics has opened up a new era in the study of marine microbial diversity that enables direct access to the genomes of numerous uncultivable microorganisms. This review outlines recent developments and future trends in metagenomics-based drug discovery in marine microbial communities and their associated chemical prosperity.
Topics: Chromosome Mapping; Drug Design; Genetic Variation; Genetics, Microbial; Genomics; Marine Biology; Pharmaceutical Preparations; Water Microbiology
PubMed: 16154653
DOI: 10.1016/j.tibtech.2005.08.006 -
Journal of General Microbiology Jan 1968
Topics: Alleles; Extrachromosomal Inheritance; Genes; Genetics, Microbial; Mutation; Terminology as Topic
PubMed: 5635521
DOI: 10.1099/00221287-50-1-1 -
Research in Microbiology Jun 2014
Topics: Gene Expression Regulation, Bacterial; Genetics, Microbial; History, 20th Century; Molecular Biology; Operon
PubMed: 24873987
DOI: 10.1016/j.resmic.2014.05.006 -
Molecular Biology and Evolution May 2021DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are...
DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple individuals or "haplotypes." However, current next-generation sequencing instruments, in conjunction with single-molecule barcoded linked-reads, cannot distinguish long haplotypes directly. Computational reconstruction of haplotypes from pooled sequencing has been attempted in virology, bacterial genomics, metagenomics, and human genetics, using algorithms based on either cross-host genetic sharing or within-host genomic reads. Here, we describe PoolHapX, a flexible computational approach that integrates information from both genetic sharing and genomic sequencing. We demonstrated that PoolHapX outperforms state-of-the-art tools tailored to specific organismal systems, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from 50 pools each containing 12 different haplotypes. By analyzing real data, we uncovered dynamic variations in the evolutionary processes of within-patient HIV populations previously unobserved in single position-based analysis.
Topics: Algorithms; Biological Evolution; Genetic Techniques; Genetics, Microbial; HIV; Haplotypes; Humans; Plasmodium vivax; Software
PubMed: 33547786
DOI: 10.1093/molbev/msab037 -
Rivista Di Biologia 1988
Topics: Biotechnology; Genetics, Microbial; Molecular Biology
PubMed: 3375742
DOI: No ID Found -
Nature Genetics Dec 1999
Topics: Computer Systems; Education, Continuing; Equipment Design; Genes, Fungal; Genetics, Microbial; Oligonucleotide Array Sequence Analysis; Robotics; Saccharomyces cerevisiae
PubMed: 10581012
DOI: 10.1038/70468 -
Nature Sep 1972
Topics: Escherichia coli; Genetics, Microbial; Neurospora; Streptococcus pneumoniae; Transformation, Genetic
PubMed: 4404144
DOI: 10.1038/239234a0 -
Nature Medicine Jan 2002
Topics: Academies and Institutes; Anthrax; Biological Warfare; Genetics, Microbial; Genome, Bacterial; United States
PubMed: 11786887
DOI: 10.1038/nm0102-8b