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  • Sequence
  • The study was published as "Genome Sequence of the Mercury Methylating Strain Desulfovibrio desulfuricans ND132. (redorbit.com)
  • and almost every other known insertion sequence ( Mahillon and Chandler 1998 ), RAYTs presumably transpose REPINs by cutting them out of the genome and pasting them into another part of the genome. (genetics.org)
  • Also, the list contains only de novo genomes: we start from DNA and wind up with a new sequence. (scienceblogs.com)
  • Mykrobe Predictor streamlines this process by automating genome analysis, cross-checking the bacterium's DNA sequence with previous strains to look for resistance-causing mutations and presenting information about the bug in an easy-to-understand format. (ox.ac.uk)
  • Wolbachia made headlines a year ago with the publication of the genome sequence of the species Wolbachia pipientis, which lives inside the reproductive cells of the laboratory fruit fly Drosophila melanogaster. (innovations-report.com)
  • Every sequence of the genome that shares homology or identity with the plasmid may thus appear to be bound by the protein of interest. (wikipedia.org)
  • species
  • Few bacterial species are capable of this conversion, and exactly how the transformation takes place has been a matter of debate for decades. (redorbit.com)
  • This key process remains a bottleneck in synthetic biology, especially for genome engineering strategies of intractable and economically important microbial species. (jcvi.org)
  • All Vibrio species have genome constituted of two circular chromosomes with distinct dynamic characteristics, and we aim at understanding both the selective benefit of this organization as well as the specific machinery in charge of their maintenance. (pasteur.fr)
  • Apply the tools for species identification, MLST typing and resistance gene detection in real cases of other bacterial and pathogen genomes. (coursera.org)
  • The existence of these bacterial species inside the fruit fly genome database is an artifact of the way the fly was sequenced, Eisen said. (innovations-report.com)
  • They were able to reconstruct 95 percent (1,440,650 base pairs) of the genome of one new species from D. ananassae, which they called Wolbachia wAna. (innovations-report.com)
  • The group chose to work with these species of mycoplasmas for several reasons - the small genomes of these organisms which make them easier to work with, their lack of cell walls, and the team's experience and expertise with mycoplasmas. (medgadget.com)
  • The ability to transfer the naked DNA isolated from one species into a second microbial species paves the way for next experiments to transplant a fully synthetic bacterial chromosome into a living organism and if successful, "boot up" the new entity. (medgadget.com)
  • For example, the genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. (ualberta.ca)
  • Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. (ualberta.ca)
  • Bacterial genomes are generally smaller and less variant in size among species when compared with genomes of animals and single cell eukaryotes. (wikipedia.org)
  • Genome size is of little relevance when considering the number of functional genes in eukaryotic species. (wikipedia.org)
  • The process of genome instability often leads to a situation of aneuploidy, in which the cells present a chromosomic number that is either higher or lower than the normal complement for the species. (wikipedia.org)
  • Since nearly all RT genes function in retrovirus replication and/or the movement of transposable elements, it is reasonable to imagine that retrons might be mobile genetic elements, but there has been little supporting evidence for such a hypothesis, save for the observed fact that msDNA is widely yet sporadically dispersed among bacterial species in a manner suggestive of both horizontal and vertical transfer. (wikipedia.org)
  • Chlamydia species have genomes around 1.0 to 1.3 megabases in length. (wikipedia.org)
  • Some species also contain a DNA plasmids or phage genomes (see Table). (wikipedia.org)
  • Genome features of selected Chlamydia species and strains. (wikipedia.org)
  • Since retrons are not mobile, their appearance in diverse bacterial species is not a "selfish DNA" phenomenon. (wikipedia.org)
  • genes
  • The estimates also suggest that many truncated genes are in the process of being eliminated from the genome. (genetics.org)
  • For instance, in plant mitochondrial genomes, which have an α-proteobacterial ancestry, most, if not all, of the laterally transferred genes are pseudogenes ( R ichardson and P almer 2007 ). (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)
  • But Eisen, a geneticist who mines the fruit fly and other genomes for clues to how genes shape the organism, had an inkling they were there, and in a quick search of the genome database late last year, turned up a slew of bacterial genes. (innovations-report.com)
  • A study that included, but was not limited to, 478 bacterial genomes, concluded that as genome size increases, the number of genes increases at a disproportionately slower rate in eukaryotes than in non-eukaryotes. (wikipedia.org)
  • Another source of genome instability may be epigenetic or mutational reductions in expression of DNA repair genes. (wikipedia.org)
  • The genomic epidemiological database for global identification of microorganisms or global microbial identifier (GMI) is a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect and track-and-trace infectious disease outbreaks and emerging pathogens. (wikipedia.org)
  • coli
  • It's kinda very cool to realize that half of the E. coli genomes are, in part, my fault (obviously lots of people are involved with the project). (scienceblogs.com)
  • 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)
  • Sequencing
  • This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more relevant for the medical sector. (coursera.org)
  • This course is for you if you are interested in getting to know more about Whole genome sequencing applied to bacterial characterization and surveillance. (coursera.org)
  • This webinar will discuss an optimized protocol for methyl-CpG binding domain sequencing (MBD-seq), which enables comprehensive, adequately powered, and cost-effective large-scale methylome-wide association studies (MWAS) of almost all 28 million CpG sites in the genome. (genomeweb.com)
  • One of the barriers to making whole genome sequencing a routine part of NHS care is the need for powerful computers and expertise to interpret the masses of complex data. (ox.ac.uk)
  • The software is now being evaluated in hospitals in Oxford, Brighton and Leeds in a project led by Professor Derrick Crook, which in collaboration with parallel programmes at UCL and Cambridge University aims to develop whole genome sequencing as a routine tool for the diagnosis and control of infections within the NHS. (ox.ac.uk)
  • third-generation sequencing might eventually yield a complete genome in a few hours. (wikipedia.org)
  • A significant achievement in the second decade of bacterial genome sequencing was the production of metagenomic data, which covers all DNA present in a sample. (wikipedia.org)
  • Starting the second millennium, many microbiological laboratories, as well as national health institutes, started genome sequencing projects for sequencing the infectious agents collections they had in their biobanks. (wikipedia.org)
  • Biologist
  • Computational biologist Sergei Maslov of Brookhaven National Laboratory worked with graduate student Tin Yau Pang from Stony Brook University to compare the frequency with which components "survive" in two complex systems: bacterial genomes and operating systems on Linux computers. (itwire.com)
  • 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)
  • genomics
  • 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)
  • 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)
  • 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)
  • Plasmid
  • In particular, this is true of the open reading frame of the protein of interest, which is present in both the plasmid and the genome. (wikipedia.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)
  • 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)
  • amino acid
  • 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)
  • introns
  • the other two families of known bacterial retroelements are group II introns and diversity-generating retroelements (DGRs). (wikipedia.org)
  • 2016
  • 2012 - 2016: Development of a robust IT-backbone for the database, and development of novel genome analysis algorithms and software. (wikipedia.org)
  • Researchers
  • 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)
  • 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)
  • Design and synthesis of a minimal bacterial genome. (wikipedia.org)
  • proteins
  • The DNA genome, proteins, and ribosomes are retained in the reticulate body. (wikipedia.org)
  • The reticular body is basically the structure in which the chlamydial genome is transcribed into RNA, proteins are synthesized, and the DNA is replicated. (wikipedia.org)
  • mutations
  • These are not resequenced genomes (SNP calling) where we map a strain's mutations back to a previously sequenced genome (there was some confusion about that over at Nick's place). (scienceblogs.com)
  • 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)
  • isolation
  • Outer ring denotes the taxonomic group, central ring denotes the isolation source, and inner ring denotes the root-associated genomes within plant-associated genomes. (eurekalert.org)
  • novel
  • However, the lack of evidence for novel REPIN insertions probably means that duplication rates are low, despite the presence of hundreds of REPINs in some genomes ( Bertels and Rainey 2011b ). (genetics.org)
  • fungi
  • The genome sizes of thousands of eukaryotes have been analyzed over the past 50 years, and these data are available in online databases for animals, plants, and fungi (see external links). (wikipedia.org)
  • nuclear
  • Nuclear genome size is typically measured in eukaryotes using either densitometric measurements of Feulgen-stained nuclei (previously using specialized densitometers, now more commonly using computerized image analysis) or flow cytometry. (wikipedia.org)
  • cellular
  • Synthetic biology marries biology and engineering and scientist with mad skills in engineering genomes, building cellular circuits and understanding cellular systems would likely be in demand in years to come. (wordpress.com)
  • evolution
  • As the first CAM eudicot to have its genome sequenced, Kalanchoë offers researchers a reference to trace the evolution of CAM photosynthesis in this group. (doe.gov)
  • cells
  • For instance, Dr. Stephen Meyer of Discovery Institute says that "bacterial cells are propelled by rotary engines called flagellar motors that rotate at 100,000 rpm," which is powerful evidence for design by an intelligent cause. (blogspot.fi)
  • often
  • The term "genome size" is often erroneously attributed to Hinegardner, even in discussions dealing specifically with terminology in this area of research (e.g. (wikipedia.org)
  • vary
  • Protist genomes have been reported to vary more than 300,000-fold in size, but the high end of this range (Amoeba) has been called into question. (wikipedia.org)