• 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)
  • 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)
  • 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)
  • The availability of a rapidly increasing number of completely sequenced bacterial genomes makes it possible to explore gene order conservation in related and distant species. (biomedcentral.com)
  • 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)
  • Since retrons are not mobile, their appearance in diverse bacterial species is not a "selfish DNA" phenomenon. (wikipedia.org)
  • 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)
  • 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)
  • This chapter summarizes the recent findings of bacterial genomics and comments on the themes and trends which are emerging. (asmscience.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
  • A reader at Nick's blog came up with an improved list- one that reflects the genomes for which we actually have data (depending on who is doing the sequencing, a project will be registered with NCBI, often months before any sequencing is done). (scienceblogs.com)
  • 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)
  • GenBank
  • Thereby generating private databases and sending model genomes to global nucleotide databases such as GenBank of the NCBI or the nucleotide database of the EMBL. (wikipedia.org)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • demonstration
  • 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)
  • 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)
  • main
  • capricolum (Mcap), and the main factors driving the compatibility between a donor genome and a recipient cell are poorly understood. (jcvi.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)