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Cell Mar 2018
Topics: Bacillus Phages; Bacillus subtilis; DNA, Viral; Genetics, Microbial; Sigma Factor; Templates, Genetic
PubMed: 29522732
DOI: 10.1016/j.cell.2018.02.041 -
Current Protocols in Microbiology May 2012Agrobacterium species are plant-associated relatives of the rhizobia. Several species cause plant diseases such as crown gall and hairy root, although there are also...
Agrobacterium species are plant-associated relatives of the rhizobia. Several species cause plant diseases such as crown gall and hairy root, although there are also avirulent species. A. tumefaciens is the most intensively studied species and causes crown gall, a neoplastic disease that occurs on a variety of plants. Virulence is specified by large plasmids, and in the case of A. tumefaciens, this is called the Ti (tumor-inducing) plasmid. During pathogenesis virulent agrobacteria copy a segment of the Ti plasmid and transfer it to the plant, where it subsequently integrates into the plant genome, and expresses genes that result in the disease symptoms. A. tumefaciens has been used extensively as a plant genetic engineering tool and is also a model microorganism that has been well studied for host-microbe associations, horizontal gene transfer, cell-cell communication, and biofilm formation. This unit describes standard protocols for genetic manipulation of A. tumefaciens.
Topics: Agrobacterium tumefaciens; Gene Transfer Techniques; Genetic Engineering; Genetic Vectors; Genetics, Microbial; Host-Pathogen Interactions; Plant Diseases; Plant Tumor-Inducing Plasmids; Plants; Plants, Genetically Modified; Virulence
PubMed: 22549163
DOI: 10.1002/9780471729259.mc03d02s25 -
Medical Principles and Practice :... 2005The diagnosis and management of bacterial diseases has been done by traditional methods for a century or more. With the advent of molecular methods, however, these... (Review)
Review
The diagnosis and management of bacterial diseases has been done by traditional methods for a century or more. With the advent of molecular methods, however, these traditional approaches are being challenged. This review examines the pros and cons of traditional versus modern methods and tries to answer the question: when are molecular methods useful or essential? The following topics are addressed with appropriate examples: diagnosis; identification, typing and fingerprinting; pathogenesis; patient management; susceptibility to disease, and resistance to antimicrobial agents. It was concluded that there is still a place for both traditional and modern molecular methods, and training of staff must include both methodologies. Innovation is encouraged--but new technologies must be thoroughly tested before introduction into the routine lab. Liaison between laboratory scientist and physician is important, but above all experience is paramount.
Topics: Bacteriology; Communicable Diseases; Drug Resistance, Microbial; Genetic Predisposition to Disease; Genetics, Microbial; Humans; Molecular Diagnostic Techniques; Polymerase Chain Reaction; Polymorphism, Genetic
PubMed: 16103710
DOI: 10.1159/000086181 -
Microbial Biotechnology Sep 2019For over seven decades, bacteria served as a valuable source of bioactive natural products some of which were eventually developed into drugs to treat infections, cancer... (Review)
Review
For over seven decades, bacteria served as a valuable source of bioactive natural products some of which were eventually developed into drugs to treat infections, cancer and immune system-related diseases. Traditionally, novel compounds produced by bacteria were discovered via conventional bioprospecting based on isolation of potential producers and screening their extracts in a variety of bioassays. Over time, most of the natural products identifiable by this approach were discovered, and the pipeline for new drugs based on bacterially produced metabolites started to run dry. This mini-review highlights recent developments in bacterial bioprospecting for novel compounds that are based on several out-of-the-box approaches, including the following: (i) targeting bacterial species previously unknown to produce any bioactive natural products, (ii) exploring non-traditional environmental niches and methods for isolation of bacteria and (iii) various types of 'genome mining' aimed at unravelling genetic potential of bacteria to produce secondary metabolites. All these approaches have already yielded a number of novel bioactive compounds and, if used wisely, will soon revitalize drug discovery pipeline based on bacterial natural products.
Topics: Bacteria; Biological Products; Bioprospecting; Data Mining; Genetics, Microbial; Genome, Bacterial; Metabolic Engineering
PubMed: 30834674
DOI: 10.1111/1751-7915.13398 -
Nature Reviews. Genetics Oct 2015Evolve and resequence (E&R) experiments use experimental evolution to adapt populations to a novel environment, then next-generation sequencing to analyse genetic... (Review)
Review
Evolve and resequence (E&R) experiments use experimental evolution to adapt populations to a novel environment, then next-generation sequencing to analyse genetic changes. They enable molecular evolution to be monitored in real time on a genome-wide scale. Here, we review the field of E&R experiments across diverse systems, ranging from simple non-living RNA to bacteria, yeast and the complex multicellular organism Drosophila melanogaster. We explore how different evolutionary outcomes in these systems are largely consistent with common population genetics principles. Differences in outcomes across systems are largely explained by different starting population sizes, levels of pre-existing genetic variation, recombination rates and adaptive landscapes. We highlight emerging themes and inconsistencies that future experiments must address.
Topics: Adaptation, Physiological; Animals; Bacteria; Biological Evolution; Drosophila melanogaster; Epistasis, Genetic; Evolution, Molecular; Genetics, Microbial; Genetics, Population; High-Throughput Nucleotide Sequencing; Mutation; RNA Folding; Selection, Genetic
PubMed: 26347030
DOI: 10.1038/nrg3937 -
Virulence Apr 2014Antibiotic resistance is a major threat to human health and well-being. To effectively combat this problem we need to understand the range of different resistance genes... (Review)
Review
Antibiotic resistance is a major threat to human health and well-being. To effectively combat this problem we need to understand the range of different resistance genes that allow bacteria to resist antibiotics. To do this the whole microbiota needs to be investigated. As most bacteria cannot be cultivated in the laboratory, the reservoir of antibiotic resistance genes in the non-cultivatable majority remains relatively unexplored. Currently the only way to study antibiotic resistance in these organisms is to use metagenomic approaches. Furthermore, the only method that does not require any prior knowledge about the resistance genes is functional metagenomics, which involves expressing genes from metagenomic clones in surrogate hosts. In this review the methods and limitations of functional metagenomics to isolate new antibiotic resistance genes and the mobile genetic elements that mediate their spread are explored.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Bacterial; Ecosystem; Gene Expression; Genetics, Microbial; Humans; Interspersed Repetitive Sequences; Metagenomics
PubMed: 24556726
DOI: 10.4161/viru.28196 -
British Medical Journal Mar 1968
Topics: Anti-Bacterial Agents; Drug Resistance, Microbial; Enterobacteriaceae; Genetics, Microbial
PubMed: 5644167
DOI: 10.1136/bmj.1.5591.574-a -
FEMS Yeast Research Aug 2017The methods based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system have quickly gained popularity for genome... (Review)
Review
The methods based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system have quickly gained popularity for genome editing and transcriptional regulation in many organisms, including yeast. This review aims to provide a comprehensive overview of CRISPR application for different yeast species: from basic principles and genetic design to applications.
Topics: CRISPR-Cas Systems; Gene Editing; Genetics, Microbial; Metabolic Engineering; Saccharomyces cerevisiae
PubMed: 28505256
DOI: 10.1093/femsyr/fox030 -
Nature Reviews. Genetics Nov 2005Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms... (Review)
Review
Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent only a fraction of the living or once-living organisms of interest. Many species are difficult to study in isolation because they fail to grow in laboratory culture, depend on other organisms for critical processes, or have become extinct. Methods that are based on DNA sequencing circumvent these obstacles, as DNA can be isolated directly from living or dead cells in various contexts. Such methods have led to the emergence of a new field, which is referred to as metagenomics.
Topics: Animals; Base Sequence; Environmental Microbiology; Genetics, Microbial; Genomics; Humans; Sequence Analysis, DNA
PubMed: 16304596
DOI: 10.1038/nrg1709 -
Genome Biology 2005More than 99% of prokaryotes in the environment cannot be cultured in the laboratory, a phenomenon that limits our understanding of microbial physiology, genetics, and... (Review)
Review
More than 99% of prokaryotes in the environment cannot be cultured in the laboratory, a phenomenon that limits our understanding of microbial physiology, genetics, and community ecology. One way around this problem is metagenomics, the culture-independent cloning and analysis of microbial DNA extracted directly from an environmental sample. Recent advances in shotgun sequencing and computational methods for genome assembly have advanced the field of metagenomics to provide glimpses into the life of uncultured microorganisms.
Topics: Genetics, Microbial; Genomics; Oceans and Seas; Sequence Analysis, DNA
PubMed: 16086859
DOI: 10.1186/gb-2005-6-8-229