• Since Cas9 has no DNA recognition specificity except for the PAM sequence, simple multiplication of gRNAs along with a common Cas9 protein results in multiplex genome engineering. (nature.com)
  • To introduce the sequence of a hammerhead ribozyme in between the T promoter and viral genome, PCR reactions with pTPVSplI as template and the antisense primer SPL and sense primers Rib and BHTRib (Table), containing partial ribozyme sequence, have been performed to generate a fragment spanning among BamHI (inside the pBR sequence) and SplI (in the viral sequence) containing the T promoter, ribozyme, and 'terminal poliovirus nt. (dna-alkylating.com)
  • To generate plasmids encoding viral genomes with novel mutations, pairs of oligonucleotide primers containing a particular mutagenic sequence (muts) or its complement (muta) (Table) at 1 end and either SPLI or Rib, in the other, have been used in PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/3439027 separate PCRs with pTPVRibMS as template. (dna-alkylating.com)
  • is useful as the sequences did not match any known plasmid sequence deposited in public databases. (frontiersin.org)
  • Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates. (kegg.jp)
  • Complete genome sequence of the universal killer Salmonella enterica Serovar Typhimurium UK-1 (ATCC 68169). (kegg.jp)
  • It is important to sequence the genome of Mycoplasma hyopneumoniae in order to analyze how much the bacteria is involved in respiratory diseases in pigs and to also detect antibodies against the bacteria. (kenyon.edu)
  • PlasClass improves plasmid sequence classification. (cdc.gov)
  • oryzae CIX2779 Includes the First Sequence of a Plasmid for an African Representative of This Rice Pathogen. (bvsalud.org)
  • Genome sequence of Xanthomonas fuscans subsp. (bvsalud.org)
  • If the sequence result was of low quality, the amplicon was cloned into a plasmid vector using a TOPO TA cloning kit (Invitrogen, Carlsbad, California) and then sequenced using the primers provided with the kit. (who.int)
  • KEGG GENOME: Salmonella enterica subsp. (kegg.jp)
  • Like other badnaviruses, BSV sequences integrate into the genome of Musa spp. (nature.com)
  • The eBSV sequences are mainly integrated in the B genome derived from M. balbisiana 5 . (nature.com)
  • Multiple copies of eBSV viral sequences have become integrated as direct and inverted tandem repeats at a single locus in the B genome of the host during viral infection 5 . (nature.com)
  • In this study, CRISPR/Cas9-based genome-editing technology was applied to inactivate eBSV sequences in the host plantain genome. (nature.com)
  • The genome-edited events of plantain Gonja Manjaya were generated with mutations in the targeted sites of integrated eBSV sequences in the host genome. (nature.com)
  • To address the gap of knowledge on this, the complete sequences of eight plasmids from Pandoraea spp. (frontiersin.org)
  • The information on plasmid sequences in Pandoraea spp. (frontiersin.org)
  • Complete genome and plasmid sequences of three Canadian isolates of Salmonella enterica subsp. (pacb.com)
  • Here, we report the fully assembled genome and plasmid sequences of three S. Heidelberg strains with phage types 9, 29, and 41. (pacb.com)
  • Comparison of the complete genome sequences of Pseudomonas syringae pv. (nih.gov)
  • Over 375 repetitive extragenic palindromic sequences unique to Pss B728a when compared with Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. (nih.gov)
  • Researchers can perform restriction enzyme analyses, edit sequences, create plasmid maps, cut and ligate "in silico," analyze GC content, make homology plots, and select primer sites from a user-specified database. (the-scientist.com)
  • MTase methylates specific DNA sequences (recognition sites) in the host genome. (biomedcentral.com)
  • Whole genome sequencing (WGS) performed at CDC on isolates from 15 patients* confirmed that the recent isolates did not share common strains or plasmids with the 2012 outbreak. (cdc.gov)
  • Rising fluoroquinolone MIC values among Shigella isolates may be related to the emergence of plasmid-mediated quinolone resistance (PMQR) genes in Shigella species in the United States. (cdc.gov)
  • Shigella strains harboring PMQR genes were identified earlier this year following whole genome sequencing of isolates from a multistate outbreak of multidrug-resistant Shigella flexneri infections predominantly affecting adult men, many of whom identify as men who have sex with men, according to epidemiologic data collected by CDC's Shigella program as part of outbreak response. (cdc.gov)
  • Methods: We sequenced the genomes of 175 isolates longitudinally collected from 30 patients with MABC lung infection. (cdc.gov)
  • The Pss B728a genome (6.1 Mb) contains a circular chromosome and no plasmid, whereas the Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. (nih.gov)
  • The sites of orthodox R-M systems that are encoded in host genomes for a long time are avoided more often (up to 100 % in certain cohorts) than the sites of recently acquired ones. (biomedcentral.com)
  • A purified plasmid can be used for many standard applications, such as sequencing and transfections into cells. (wikipedia.org)
  • Similarly, if the plasmid is to be used for sequencing or PCR, a purification method that results in high yield and minimal contaminants is desirable. (wikipedia.org)
  • See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)
  • Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
  • When the banana plants are stressed, the eBSV recombines to produce a functional episomal viral genome and infectious viral particles and as a result the plant develops disease symptoms. (nature.com)
  • The plasmid pTPVSplI containing the fulllength viral genome was assembled by the fragment ligation applying the above fragment at the same time as the ntlong KpnIBglII and ntlong ScaIBglII fragments in the pBRbased plasmid pTPV. (dna-alkylating.com)
  • Unique restriction web-sites, MluI and SacI within a region encoding the viral protein C at positions and in the viral genome, respectively, were introduced within this plasmid by fusion PCR reactions (facts of this process are out there upon request) to generate the basal plasmid pTPVRibMS. (dna-alkylating.com)
  • encoding the fulllength viral genome, as described within the preceding paragraph. (dna-alkylating.com)
  • The goods obtained in every pair of these reactions have been fused collectively in an further PCR with Rib and SPL primers, digested with ApaI and SplI, and employed to generated plasmids encoding the fulllength viral genome as above. (dna-alkylating.com)
  • During the purification procedure, the plasmid DNA is often separated from contaminating proteins and genomic DNA. (wikipedia.org)
  • In Cas9 nuclease-mediated genome editing, we constructed an all-in-one vector expressing Cas9 nuclease and seven gRNAs and targeted seven genomic loci. (nature.com)
  • Hello, everyone: Does any one know how to recover one copy yeast plasmid using competent E. coli cell, or how to separate the plasmid DNA from yeast genomic DNA? (bio.net)
  • Content of the genomic islands varies, with one containing a prophage and another the plasmid pKLC102 of Pseudomonas aeruginosa PAO1. (nih.gov)
  • As in other mycoplasmas, it contains the minimum amount of organelles needed to survive along with a small genome and tightly coiled chromosomes. (kenyon.edu)
  • AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. (mdpi.com)
  • These methods invariably involve three steps: growth of the bacterial culture, harvesting and lysis of the bacteria, and purification of the plasmid DNA. (wikipedia.org)
  • Plasmids are almost always purified from liquid bacteria cultures, usually E. coli, which have been transformed and isolated. (wikipedia.org)
  • Virtually all plasmid vectors in common use encode one or more antibiotic resistance genes as a selectable marker, for example a gene encoding ampicillin or kanamycin resistance, which allows bacteria that have been successfully transformed to multiply uninhibited. (wikipedia.org)
  • Bacteria that have not taken up the plasmid vector are assumed to lack the resistance gene, and thus only colonies representing successful transformations are expected to grow. (wikipedia.org)
  • Minipreparation of plasmid DNA is a rapid, small-scale isolation of plasmid DNA from bacteria. (wikipedia.org)
  • Plasmids are one of the primary sources for extrachromosomal DNA in bacteria and are capable of self-transmission. (frontiersin.org)
  • Mycoplasma hyopneumoniae is a type of bacteria that has a small genome and does not contain a cell wall. (kenyon.edu)
  • Plasmid-mediated resistance genes are of particular concern because of their ability to spread between bacteria and their ability to promote chromosomal mutations conferring quinolone resistance, potentially resulting in rapid spread of fluoroquinolone resistance within or between populations of bacteria. (cdc.gov)
  • After ingestion of infected blood, the bacteria survive in the midgut of the flea owing to a plasmid-encoded phospholipase D that protects them from digestive juices. (medscape.com)
  • CRISPR/Cas9 editing of endogenous banana streak virus in the B genome of Musa spp. (nature.com)
  • CRISPR/Cas9-mediated genome editing is a next-generation strategy for genetic modifications, not only for single gene targeting, but also for multiple targeted mutagenesis. (nature.com)
  • Genome editing using clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9 is an easy and efficient strategy for the generation of gene-modified cells and organisms 1 , 2 . (nature.com)
  • In addition, the plasmids for the second-step reaction retained the structure of a CRISPR/Cas9 expression vector harboring single gRNA and Cas9 expression cassettes and can therefore be used separately for single gene targeting. (nature.com)
  • But if the mcr-1 gene is transferred and ends up on a resistance plasmid that contained genes encoding carbapenemases or 16s methylation , for example, it could be dire. (genomeweb.com)
  • The glossary features nearly 250 terms explained in an easy-to-understand way by leading scientists and professionals at the National Human Genome Research Institute. (genome.gov)
  • The E. coli was found to contain the mcr-1 gene on a transmissible plasmid as well as genes conferring other types of antibiotic resistance. (genomeweb.com)
  • The E. coli in question wound up having two plasmids with different complements of other antibiotic resistance genes, including extended-spectrum beta-lactamase genes, but Snesrud emphasized that it was not a pan-resistant strain. (genomeweb.com)
  • The Standardized Genome Architecture (SEGA) platform allows fast and simple genome engineering of E. coli. (belspo.be)
  • The gene is flanked by β-lactam regulatory genes similar to mecR , mecI , and blaZ and is part of an 84.6-kb multidrug-resistance plasmid that harbors genes encoding additional resistances to aminoglycosides ( aacA-aphD , aphA , and aadK ) as well as macrolides ( ermB ) and tetracyclines ( tetS ). (cdc.gov)
  • Here, we report both a plasmid-encoded, and thereby transferable, methicillin resistance encoded by mecB and the occurrence of this gene in an isolate of the genus Staphylococcus . (cdc.gov)
  • While thousands of bacterial genomes are available to date, there is no software that facilitates comparisons of individual gene loci for a large number of genomes. (chalmers.se)
  • Some plasmids were also void of par genes and intriguingly, repA gene was also not discovered in these plasmids. (frontiersin.org)
  • High transformation efficiency of citrus is of great importance for large scale characterization of gene functions and also cultivar development via transgenic and genome editing technologies. (springer.com)
  • Resistant strains have existed for a long time, Snesrud said, but previously these were due to genetic mutations on the genome that could only be passed on to daughter cells. (genomeweb.com)
  • The mcr-1 on transferrable plasmids can instead be passed on to "other strains and other species that they come in contact with in the environment," he said. (genomeweb.com)
  • Comparative Genome Analysis of Two Bacillus pumilus Strains Producing High Level of Extracellular Hydrolases. (uibk.ac.at)
  • The regenerated genome-edited events of Gonja Manjaya showed mutations in the targeted sites with the potential to prevent proper transcription or/and translational into functional viral proteins. (nature.com)
  • BHQ black hole quencher .bConstruction of viruses with the preferred mutations Since the viruses generated by the SELEX process (see beneath) not infrequently contained mutations outside the apex of domain d, certain analogous genomes lacking these undesired mutations had been constructed. (dna-alkylating.com)
  • The most frequent target of resistance mutations was the plasmid-encoded SpCas9 that was inactivated by bacterial genome rearrangements involving translocation of mobile genetic elements such as insertion elements. (dtu.dk)
  • In contrast to frequent interstrain and interspecies transmission of resistance plasmids by conjugation or transduction, only a relatively low rate of spontaneous horizontal transfer of SCC mec elements is assumed, resulting in still-manageable and controllable MRSA rates if prevention measures are adequate ( 20 - 24 ). (cdc.gov)
  • The particular plasmid type that contains the resistance elements is important to the epidemiology. (genomeweb.com)
  • Additionally, genes conferring virulence and antibiotic resistance were identified amongst the plasmids. (frontiersin.org)
  • Hence, the spread of virulence factors and antibiotic resistance properties caused by plasmids is possible, leading to a threat in public health. (frontiersin.org)
  • Carbapenemases, enzymes that confer resistance to the carbapenem class of antibiotics, are believed to contribute to increasing transmission and regional spread of CRE because the genes encoding these enzymes can reside on mobile plasmids and can be transferred among bacterial species. (cdc.gov)
  • Finally, we highlighted a 23-kb mercury -resistance plasmid whose loss during chronic infection conferred phenotypic susceptibility to organic and nonorganic mercury compounds. (cdc.gov)
  • Plasmid stabilization/stability protein-encoding genes were observed in some plasmids but were not established for participating in plasmid segregation. (frontiersin.org)
  • The identification of genes involved in replication, segregation, toxin-antitoxin systems and conjugation, would aid the design of drugs to prevent the survival or transmission of plasmids carrying pathogenic properties. (frontiersin.org)
  • In this study, we constructed plasmids to create all-in-one vectors expressing two to seven gRNAs with Cas9 nuclease or nickase ( Figure 1 ). (nature.com)
  • bacterial genome editing using of 'suicide' vectors for allelic exchange. (uibk.ac.at)
  • 2023). First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale . (uibk.ac.at)
  • The virulence of this bacterium results from the 32 Y pestis chromosomal genes and two Y pestis -specific plasmids, constituting the only new genetic material acquired since its evolution from its predecessor. (medscape.com)
  • In resolution WHA52.10 the Health Assembly mandated that only the two WHO- approved repositories may hold stocks of variola virus, but this approach needs review as it no longer ensures that full-length variola genomes exist in the two repositories only. (who.int)
  • Title : A Human Papillomavirus Whole Genome Plasmid Repository: A Resource for HPV DNA Quality Control Reagents Personal Author(s) : Thapa, Hem R.;Unger, Elizabeth R.;Querec, Troy D. (cdc.gov)
  • Addgene is a nonprofit plasmid repository. (addgene.org)
  • From the 178 plasmids sent, 167 were able to grow in bacterial culture and 92 of the ASFV proteins were expressed individually in mammalian cells. (intvetvaccnet.co.uk)
  • Lysozyme is usually added to the bacterial culture, followed by heating and/or shaking the culture to release the plasmid DNA. (wikipedia.org)
  • Enzymatic lysis, also called Lysozyme lysis, involves the use of enzymes to digest the cell wall and release the plasmid DNA. (wikipedia.org)
  • A plasmid preparation is a method of DNA extraction and purification for plasmid DNA, it is an important step in many molecular biology experiments and is essential for the successful use of plasmids in research and biotechnology. (wikipedia.org)
  • Purification of plasmids is central to molecular cloning. (wikipedia.org)
  • It is important to consider the downstream applications of the plasmid DNA when choosing a purification method. (wikipedia.org)
  • For example, if the plasmid is to be used for transfection or electroporation, a purification method that results in high purity and low endotoxin levels is desirable. (wikipedia.org)
  • However, cotransfection of multiple plasmids can cause low targeting efficiency in cells that are inefficient in DNA transfection. (nature.com)
  • The GenElute Endotoxin-free Plasmid Kit offers a simple, rapid, cost effective method for purifying plasmid DNA with ≤0.1 EU/μg DNA for high efficiency transfection. (sigmaaldrich.com)
  • Endotoxins (also known as lipopolysaccharides or LPS) are often co-purified with plasmid DNA and significantly reduce transfection efficiencies in endotoxin-sensitive cell lines. (sigmaaldrich.com)
  • In this project we propose a comprehensive approach where we will compare the pattern of antibody recognition of domestic pig and wild pig sera using a DNA library encoding the complete ASFV Kenya 1033 genome individually and test their neutralizing capacity. (intvetvaccnet.co.uk)
  • Mycoplasma hyopneumoniae 232 has a complete genome. (kenyon.edu)
  • The Complete Genome Resource of Xanthomonas oryzae pv. (bvsalud.org)
  • To this end, RNA had been isolated from preparations of your relevant viruses as well as a segment encompassing the finish from the genome as much as position was generated by PCR using the Rib and SPLI primers. (dna-alkylating.com)
  • The avoidance of orthodox Type II R-M system recognition sites in prokaryotic genomes is a widespread phenomenon. (biomedcentral.com)
  • It also restricts germplasm movement of genotypes with the B genome worldwide due to this potential activation of eBSV into the episomal infectious form of virus. (nature.com)
  • Currently, two or more kinds of plasmids or DNA fragments are generally used for multiple targeting in cultured cells 7 . (nature.com)
  • This fragment was made use of in the fragment ligation with each other with all the BamHIEcoRI and EcoRISplI fragments of pTPVSpl to produce the plasmid pTPVRib. (dna-alkylating.com)
  • The plasmids containing individual EcoRI-fragments of the M. pneumoniae genome. (uni-heidelberg.de)
  • Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. (biomedcentral.com)
  • Banana cultivars are polyploid clones derived from Musa accuminata (A genome) or/and Musa balbisiana (B genome). (nature.com)
  • After assembling the plasmids, we were able to easily screen for correctly-assembled clones by colony PCR, as shown in Supplementary Fig. S1 . (nature.com)
  • Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. (frontiersin.org)
  • To date, information on plasmid analysis in Pandoraea spp. (frontiersin.org)
  • gplas: a comprehensive tool for plasmid analysis using short-read graphs. (cdc.gov)
  • The plasmid DNA yield will vary depending on the plasmid copy number, type and size, the bacterial strain, the growth conditions, and the kit. (wikipedia.org)
  • A typical plasmid DNA yield of a miniprep is 5 to 50 µg depending on the cell strain. (wikipedia.org)