• Scientists at the J. Craig Venter Institute (JCVI), a genomics research facility, transplanted a bacterial chromosome from one type of bacteria into another, and have completely replaced an entire bacterial genome and its expression. (medgadget.com)
  • Genome transplantation is an essential enabling step in the field of synthetic genomics as it is a key mechanism by which chemically synthesized chromosomes can be activated into viable living cells. (medgadget.com)
  • A team led by Steven L. Salzberg of TIGR and including Eisen of UC Berkeley s Center for Integrative Genomics published their discovery in the most recent issue of the open access journal Genome Biology, published this week. (innovations-report.com)
  • Boris Vinatzer, assistant professor of plant pathology, physiology, and weed science in the College of Agriculture and Life Sciences, has received a $1 million, five-year Faculty Early Career Development (CAREER) award from the National Science Foundation (NSF) to investigate the pathogen that causes bacterial speck disease of tomatoes and to develop a new undergraduate course in microbial genomics. (bio-medicine.org)
  • The value and power of comparative genomics and proteomics, bioinformatics, microarrays, and knockout animal models in analyzing genomes, bacteria-host interactions and disease are demonstrated. (springer.com)
  • At this early stage in comparative genomics, the main generalizations that are emerging concerning rearrangements in bacterial genome organization are as follows. (biomedcentral.com)
  • This chapter summarizes the recent findings of bacterial genomics and comments on the themes and trends which are emerging. (asmscience.org)
  • A comprehensive understanding of the metabolic network at the system level is particularly important for both biotechnological and biomedical research and is now made possible by rapid advances in genome sequencing and functional genomics. (biomedcentral.com)
  • Several applications of single-cell genomics to the infectious disease field are developing, such as tracking pathogen persistence and transmission, targeted and untargeted pathogen-genome recovery, and the identification of novel bacteria that have pathogenic potential from the human microbiome. (biomedcentral.com)
  • In this application of single-cell genomics, roughly 400 amplified genomes of interest from 25 different genera from the indoor environment of a health care facility were captured using an automated process. (biomedcentral.com)
  • It is anticipated that this situation will change rapidly in the next few years as the results of bacterial genomics are successfully translated into new antibiotic drug discovery targets. (europeanmedical.info)
  • The automated and excellent bacterial whole genome resequencing platform at CD Genomics enables high-effective and affordable microbial whole genome resequencing. (cd-genomics.com)
  • 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)
  • The feasibility to introduce targeted mutations into the BAC cloned virus genome was shown by mutation of the immediate-early 1 gene and generation of a mutant virus. (pnas.org)
  • Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous recombination-based procedures, including gene knockout (disruption), knock-in (insertion), and allelic exchange. (mdpi.com)
  • Apart from these methods, which directly modify the genomic structure, an alternative approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. (mdpi.com)
  • 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)
  • Gene acquisition is an ongoing process in many bacterial genomes, contributing to adaptation and ecological diversification. (sciencemag.org)
  • We measured the extent of phylogenetic conflict and alien-gene acquisition within quartets of sequenced genomes. (sciencemag.org)
  • In all but the most reduced bacterial genomes, there is a substantial fraction of genes whose distributions and compositional features indicate that they originated by lateral gene transfer (LGT) ( 1 ). (sciencemag.org)
  • It "is a landmark in biological engineering taking us from moving one gene or a set of genes to the ability to move an intact genome," said Barbara Jasny, deputy editor of the journal Science, which first reported the experiment in this week's issue. (bio-medicine.org)
  • We study the mechanisms responsible of the bacterial genome variability, with a special interest for those involved in exogenous gene acquisition - the horizontal gene transfer. (pasteur.fr)
  • In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. (mdpi.com)
  • Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent. (biomedcentral.com)
  • 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)
  • The genome has a high coding density (97%) with many overlapping genes and reduced gene length. (semanticscholar.org)
  • Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. (biomedcentral.com)
  • The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes. (biomedcentral.com)
  • In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation. (biomedcentral.com)
  • ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) is a new bioinformatic tool that was created to detect existing and putative new antibiotic resistance (AR) genes in bacterial genomes. (asm.org)
  • Finally, the analysis of 178 Acinetobacter baumannii and 20 Staphylococcus aureus genomes allowed the detection of a significantly higher number of AR genes than the Resfinder gene analyzer and 11 point mutations in target genes known to be associated with AR. (asm.org)
  • This tenet of bacterial genome evolution generally does not extend to obligate intracellular bacteria owing to their reduced contact with other microbes and a predominance of gene deletion over gene transfer. (oup.com)
  • Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. (dtic.mil)
  • While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. (openrepository.com)
  • Published Dec. 18, 2017 in Nature Genetics, a team led by researchers at Joint Genome Institute (JGI) and the Howard Hughes Medical Institute at the University of North Carolina at Chapel Hill (UNC) have exploited a catalog of bacterial genomes to identify and characterize candidate genes that aid bacteria in adapting to plant environments, specifically genes involved in bacterial root colonization. (eurekalert.org)
  • Such a task was previously seen as a true tour de force: The chemically synthesised bacterial genome presented eleven years ago by the American genetics pioneer Craig Venter was the result of ten years of work by 20 scientists, according to media reports. (teknoscienze.com)
  • The task is regarded as a true tour de force: The bacterial genome presented by the genetics pioneer Craig Venter was the result of 10 years of work according to media reports. (biotecnika.org)
  • Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. (nih.gov)
  • The general trends of bacterial evolution indicate that bacteria started as free-living organisms. (wikipedia.org)
  • Genome transplantation (GT) allows the installation of purified chromosomes into recipient cells, causing the resulting organisms to adopt the genotype and the phenotype conferred by the donor cells. (jcvi.org)
  • These findings might help shed light on the evolution of bacterial endosymbionts and on the mechanisms these organisms use to alter the cell cycle of the host in order to reproduce. (innovations-report.com)
  • Deoxyribonucleic acid (DNA) double‐strand breaks, which are caused by many factors such as chemical treatments, radiations and, often, biological factors, are lethal events in organisms carrying DNA as their genome, which include bacteria. (els.net)
  • However, genomes harbor two very different categories of genes: those genes present in a majority of organisms - persistent genes - and those present in very few organisms - rare genes. (biomedcentral.com)
  • In addition to discovering an evolutionary recent and large-scale horizontal phage transfer between coinfecting obligate intracellular bacteria, we demonstrate that "targeted genome capture" can enrich target DNA to alleviate the problem of isolating symbiotic microbes that are difficult to culture or purify from the conglomerate of organisms inside eukaryotes. (oup.com)
  • The researchers found that while only 63.5 percent of TCGA samples analyzed were from tumors, the tumor samples contained 99.9 percent of reads supporting bacterial integration. (nsf.gov)
  • 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)
  • 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)
  • Researchers have developed several theories to explain the patterns of genome size evolution amongst bacteria. (wikipedia.org)
  • This enables researchers to choose the optimal strategy for completely decoding even the genomes of bacteria with very complex DNA. (admin.ch)
  • Replacing a Genome Boosts Race to Develop Designer Bugs: Study ( Researchers transformed one bacterial s. (bio-medicine.org)
  • The researchers took the genome of a simple, one-celled organism called Mycoplasma mycoides and transplanted it into a close relative, M. capricolum. (bio-medicine.org)
  • The researchers acknowledged that they were not sure how the one genome displaced the other. (bio-medicine.org)
  • To better understand this balance, National Institutes of Health researchers have set out to explore the skin's microbiome, which is all of the DNA, or genomes, of all of the microbes that inhabit human skin. (genome.gov)
  • While Venter's team made an exact copy of a natural genome, the researchers at ETH Zurich radically altered their genome using a computer algorithm. (teknoscienze.com)
  • The researchers screened 2,739 ancient human remains in total, eventually reconstructing eight Salmonella genomes up to 6,500 years old-the oldest reconstructed bacterial genomes to date. (phys.org)
  • The researchers were able to determine that all six Salmonella genomes recovered from herders and farmers are progenitors to a strain that specifically infects humans but is rare today, Paratyphi C. Those ancient Salmonella, however, were probably not yet adapted to humans, and instead infected humans and animals alike, which suggests the cultural practices uniquely associated with the Neolithization process facilitated the emergence of those progenitors and subsequently human-specific disease. (phys.org)
  • Hidden Giants in Forest Soils In Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. (doe.gov)
  • Our bacterial whole genome resequencing platform enables researchers to conduct research on disease outbreaks and treatments, as well as drug development and microbial control in many fields. (cd-genomics.com)
  • Shown are the annotation progress monitor for two genome annotation projects ( E.coli and C.trachomatis ) in various states of completion, a full-scale and expanded graphical genome map for E.coli and a sample annotation report. (nih.gov)
  • The approach allows mutagenesis of the MCMV genome as one entity in E. coli using standard procedures, and the highly efficient generation of viral mutants. (pnas.org)
  • Utilize the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing in real cases of other bacterial and pathogen genomes. (coursera.org)
  • Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in ~60h using 16 processors. (peerj.com)
  • In a sample of 50 E. coli genome assemblies it has identified from zero to three plasmids ranging in size from 1,549 to 133,843 bp and present in 42% of the assemblies examined. (cdc.gov)
  • The biological effects of these rearrangements are far-reaching and impact on bacterial virulence, antibiotic resistance and the ability of bacteria to avoid the attentions of the host immune system (e.g. antigenic variation). (ecampus.com)
  • Dr. Segre had been working with the Clinical Center's Clinical Microbiology Department to study the evolution of bacterial antibiotic resistance when she heard about the outbreak. (eurekalert.org)
  • 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)
  • It has also become evident that subinhibitory concentrations of antibiotics, which pollute all kind of terrestrial and aquatic environments, have a non-negligible effect on the evolution of antibiotic resistance in bacterial populations. (mdpi.com)
  • The enhanced Mycoplasma mycoides genome was added to a test-tube of M. capricolum, and the contents of the tube were exposed to an antibiotic. (bio-medicine.org)
  • 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)
  • One way to approach this is to build a minimal genome that includes only the genes essential for life. (sciencemag.org)
  • Bacteria with this minimal genome are viable under laboratory conditions. (teknoscienze.com)
  • As a result, the scientists seeded many small modifications into the minimal genome, which in their entirety are, however, impressive: more than a sixth of all of the 800,000 DNA letters in the artificial genome were replaced, compared to the "natural" minimal genome. (teknoscienze.com)
  • As a result, the scientists seeded many small alterations into the minimum genome, which in their entirety are, however, impressive: more than a sixth of all of the 800,000 DNA letters from the artificial genome were substituted, compared to "natural" minimal genome. (biotecnika.org)
  • In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods. (mdpi.com)
  • This book imparts fundamental knowledge on the structure, organization, and evolution of bacterial genomes. (springer.com)
  • 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)
  • This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. (nature.com)
  • A representative physical map with a high density of marker genes was developed in which 64 aligned BAC clones covered almost the entire genome. (uni-bielefeld.de)
  • 2000) A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. (els.net)
  • Correct reconstitution of the viral genome can only be verified after growth and isolation of the mutant virus. (pnas.org)
  • Construction of the mutant genome is completely independent of the biological fitness of the mutant virus and the recombinant genome can be characterized and controlled prior to reconstitution of viral progeny. (pnas.org)
  • In the earlier HCMV BACs, portions of the viral genome, Us2 to Us6 ( 3 ) or Us1 to Us12 ( 14 ), were deleted to accommodate insertion of the BAC vector. (asm.org)
  • CGMs are preidentified by making comparisons among a relatively small number of completely or nearly completely sequenced genomes and then applied to analyze larger bacterial populations by targeted identification techniques. (asm.org)
  • The origin of replication in each genome is approximately at coordinate 1 and the terminus dif sites are approximately midway through each genome, as marked by grey vertical bars. (nih.gov)
  • There is a lack of CMV mutants because due to the large genome size and slow replication kinetics construction of CMV recombinants turned out to be difficult. (pnas.org)
  • It is our working model of a minimal cell, the result of a compromise between small genome size and an experimentally useful replication rate. (geoset.info)
  • Bacterial origins regulate orisome assembly, a nuclei-protein complex assembled on the origin responsible for unwinding the origin and loading all the replication machinery. (wikipedia.org)