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  • gene
  • Bacterial gene content variation during the course of evolution has been widely acknowledged and its pattern has been actively modeled in recent years. (genetics.org)
  • Gene truncation or gene pseudogenization also plays an important role in shaping bacterial genome content. (genetics.org)
  • Analysis using the new model not only provides more accurate estimates on gene gains/losses (or insertions/deletions), but also reduces any concern of a systematic bias from applying simplified models to bacterial genome evolution. (genetics.org)
  • reported that genomes with truncated homologs might erroneously lead to false inferences of "gene gain" rather than multiple instances of "gene loss. (genetics.org)
  • This will not only yield more accurate estimates of the rates of gene insertions/deletions, but also provide a quantitative view of the effect of truncated genes on rate estimation, which has been understudied in bacterial genome evolution. (genetics.org)
  • Analysis of over 2000 Escherichia coli genomes reveals an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. (wikipedia.org)
  • As single-gene comparisons have largely given way to genome comparisons, phylogeny of bacterial genomes have improved in accuracy. (wikipedia.org)
  • Models proposed to explain clustering did not take into account the function of the gene products nor the likely presence or absence of a given gene in a genome. (biomedcentral.com)
  • We propose a model accounting specifically for such clustering, and show that indispensability in a genome with frequent gene deletion and insertion leads to the transient clustering of these genes. (biomedcentral.com)
  • Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. (wikipedia.org)
  • genomic
  • 10. Explain the concept and be able to use the integrated bacterial analysis pipeline for batch analysis and typing of genomic data 11. (coursera.org)
  • The discovery of these three new genomes demonstrates how powerful the public release of raw sequencing data can be," wrote the authors, who have deposited their findings in Genbank, an open repository of genomic sequences. (innovations-report.com)
  • Genome instability (also genetic instability or genomic instability) refers to a high frequency of mutations within the genome of a cellular lineage. (wikipedia.org)
  • For straight forward diagnostic identification the WGS information of a microbiological sample is fed into a global genomic database and compared using BLAST procedures to the genomes already present in the database. (wikipedia.org)
  • This created a wealth of genomic information and independent databases for eukaryotic as well as prokaryotic genomes. (wikipedia.org)
  • antibiotic
  • A study on more than 4,500 retrospective patient samples, published today in Nature Communications, shows that Mykrobe Predictor accurately detects antibiotic resistance in two life-threatening bacterial infections: Staphylococcus aureus (one form of which causes MRSA) and tuberculosis (TB). (ox.ac.uk)
  • By comparing the genomes of S. pneumoniae samples known to be resistant to beta lactam antibiotics with those that responded to treatment, they identified 50 regions of the genome in which mutations appeared to confer antibiotic resistance. (phgfoundation.org)
  • Nucleotide
  • This modified nucleotide is absent from the vast majority of eukaryotes, but is widespread in bacterial genomes, as part of the restriction modification or DNA repair systems. (wikipedia.org)
  • Synthesis
  • A high frequency of externally caused DNA damage can be one source of genome instability since DNA damages can cause inaccurate translesion synthesis past the damages or errors in repair, leading to mutation. (wikipedia.org)
  • There are hotspots in the genome where DNA sequences are prone to gaps and breaks after inhibition of DNA synthesis such as in the aforementioned checkpoint arrest. (wikipedia.org)
  • Design and synthesis of a minimal bacterial genome. (wikipedia.org)
  • Researchers
  • Over the years, researchers have proposed several theories to explain the general trend of bacterial genome decay and the relatively small size of bacterial genomes. (wikipedia.org)
  • NEW YORK (GenomeWeb) - In a proof-of-principle demonstration that genomes can be assembled from long, noisy nanopore reads alone, researchers at the Ontario Institute for Cancer Research in Toronto and the University of Birmingham in the UK have used data from the Oxford Nanopore MinIon to assemble a bacterial genome into a single contig. (genomeweb.com)
  • transplantation
  • JCVI: Impact of Donor-recipient Phylogenetic Distance on Bacterial Genome Transplantation. (jcvi.org)
  • The JCVI team devised several key steps to enable the genome transplantation. (medgadget.com)
  • When installed by transplantation, the resulting cell, JCVI-syn2.0, grows continuously in independent culture and has a genome smaller than that of any such cell found in nature. (geoset.info)
  • mutational
  • The small range and the low level of the REPIN duplication rates suggest a universal trade-off between the survival of the REPIN population and the reduction of the mutational load for the host genome. (genetics.org)
  • In order to study the optimization of the pressure, we compared mutational transition probability matrices from bacterial genomes with artificial matrices fulfilling the same general features as the real ones, e.g., the stationary distribution and the speed of convergence to the stationarity. (sigmaaldrich.com)
  • We observed no substantial differences between the effects of mutational matrices on protein-coding sequences in genomes under study in respect of differently replicated DNA strands, mutational cost types and properties of the referenced artificial matrices. (sigmaaldrich.com)
  • Another source of genome instability may be epigenetic or mutational reductions in expression of DNA repair genes. (wikipedia.org)
  • mutations
  • In humans, mutations that would change an amino acid within the protein coding region of the genome occur at an average of only 0.35 per generation (less than one mutated protein per generation). (wikipedia.org)
  • These sites are called fragile sites, and can occur commonly as naturally present in most mammalian genomes or occur rarely as a result of mutations, such as DNA-repeat expansion. (wikipedia.org)
  • decay
  • Bacterial RNA would hardly be detectable in human RNA-seq library - if you do poly-A selection, bacterial reads won't be there since there's almost no poly-A tails, and total RNA would still not capture bacterial RNA since they decay too fast (you need a special protocol for bacterial RNA-seq). (biostars.org)
  • Wolbachia
  • Given the Wolbachia genome and the likelihood that W. pipientis had been sequenced along with the fruit fly genome, Eisen performed a quick look for Wolbachia in the Trace Archive, an open source for raw genome data. (innovations-report.com)
  • Wolbachia, a bacterial endosymbiont of diverse arthropods, affects its host's reproduction and so is consequential for its host's fitness. (ualberta.ca)
  • introns
  • the other two families of known bacterial retroelements are group II introns and diversity-generating retroelements (DGRs). (wikipedia.org)