Complete sequence plasmids. Medical search. Frequent questions

Genes that confer resistance to antimicrobial drugs used in human or veterinary medicine are often mobilized on plasmids. (cdc.gov)
The ability and frequency with which antimicrobial resistance genes disseminate between bacteria in humans, the environment, and animals is still debated, and the role of plasmids in this movement between ecosystems, including the food chain, is also still contested, despite mounting evidence that it occurs ( 8,9 ). (cdc.gov)
Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. (frontiersin.org)
Some plasmids were also void of par genes and intriguingly, repA gene was also not discovered in these plasmids. (frontiersin.org)
Plasmid stabilization/stability protein-encoding genes were observed in some plasmids but were not established for participating in plasmid segregation. (frontiersin.org)
Conjugation genes were identified portraying the conjugation ability amongst Pandoraea plasmids. (frontiersin.org)
Additionally, we found a shared region amongst some of the plasmids that consists of conjugation genes. (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)
Additionally, genes conferring virulence and antibiotic resistance were identified amongst the plasmids. (frontiersin.org)
Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared with Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. (nih.gov)
blaOXA-163 was located on a 71-kb IncN plasmid with other resistance genes. (ox.ac.uk)
The presence of blaOXA-48-like genes on epidemic plasmids in ST131 is of concern. (ox.ac.uk)
In these plasmids most of the genes have been removed, leaving only genes essential for replication and one or more selectable markers. (wikipedia.org)
David H. Figurski, Robert F. Pohlman, David H. Bechhofer, Alice S. Prince and Christie A. Kelton: "Broad host range plasmid RK2 encodes multiple kil genes potentially lethal to Escherichia coli host cells", Genetics, Volume 79. (wikipedia.org)
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)
Many plasmid-encoded genes could be involved in several functions other than toxin production. (bgu.ac.il)
Some of the most clinically relevant resistance genes, such those encoding carbapenemases (ß-lactamase enzymes able to degrade carbapenem antibiotics), are carried on conjugative plasmids that spread across high-risk bacterial clones 5 , 6 . (nature.com)
We cloned and sequenced a 924-nt fragment that covered part of the 5′UTR and the VP4/VP2 capsid genes. (plos.org)
Compared to the genome of gh-1, the sequence of ϕIBB-PF7A is longer and contains more genes with unassigned function and lacks a few potentially essential and non-essential T7 genes, such as gene1.1, 3.8, and 7. (biomedcentral.com)
Today, phage genome sequencing is commonly performed for classification and characterization purposes and is based on the arrangement of conserved genes and the nucleotide and protein sequence identity [ 5 , 6 ]. (biomedcentral.com)
All these phages, most of which have members of the Enterobacteriaceae as their host, present a highly conserved genome organization and mainly differ at sequence level through the presence or absence of nonessential genes [ 8 ]. (biomedcentral.com)

therefore, dissemination has been attributed to conjugative plasmids rather than to clonal expansion of a bacterial host strain ( 13 ). (cdc.gov)

From this information, PCRs identifying novel features of pCT were designed and applied to isolates from several countries, showing that the plasmid has disseminated worldwide in bacteria from humans and animals. (cdc.gov)
The plasmid spread to unrelated E. coli isolates within an index cattle farm and persisted within the environment. (cdc.gov)
In this study, we report the full sequence and analysis of pCT and demonstrate the spread of pCT-like plasmids in animal and human E. coli isolates from the United Kingdom, Europe, Australia, and Asia. (cdc.gov)
These were all separate isolates, and later found to be identical plasmids. (wikipedia.org)
Complete genome and plasmid sequences of three Canadian isolates of Salmonella enterica subsp. (pacb.com)
In this study, we determined the fitness effects of the major antibiotic resistance plasmid pOXA-48_K8 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. (nature.com)

EXHAUSTIVE SEARCH Most methods of searching nucleotide sequences will only find non-overlapping matches in the input. (cpan.org)
IUPAC SHORT FORMS For DNA and RNA, IUPAC incompletely specified nucleotide sequences can be used. (cpan.org)
Complete nucleotide sequences of plasmids pACK2 and pACK5 from Staphylococcus simulans biovar staphylolyticus. (cdc.gov)

The sequence was a 93,629- bp plasmid encoding a single antimicrobial drug resistance gene, bla CTX-M-14. (cdc.gov)
Bacterial plasmids are key vectors of horizontal gene transfer, mediating the mobilization of genetic material from 1 bacterium to another. (cdc.gov)
A protein consists of one or more chains of amino acids (called polypeptides) whose sequence is encoded in a gene. (genome.gov)
BLAST can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families. (nih.gov)
Entrez is NCBI's primary text search and retrieval system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. (nih.gov)
cDNAs from the Mammalian Gene Collection, cloned into pCMV-Sprot 6 plasmid, were collected from three 384-well plates (total of human 1062 transcripts) as follows: 10 µl sterile dH2O was added to each well and incubated at 37oC for 10 min to resuspend plasmid DNA in water. (nih.gov)
Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. (genomeweb.com)
Quantification of cytosolic plasmid DNA degradation using high-throughput sequencing: implications for gene delivery. (genomeweb.com)
The experts at Bionexus (over 9 years experience), will construct your gene and sequence both strands to ensure that you get no mutants. (bionexus.net)
Synthetic gene sequence guaranteed to be the same sequence as submitted by research group. (bionexus.net)
The experienced staff at Bionexus's Gene Sysnthesis Services department will construct your gene in 2 weeks (1kb) and provide you with the sequencing documentation and the lyophilized gene in a standard vector. (bionexus.net)
A sequence of interest gene email it to us. (bionexus.net)
Clone the synthetic gene in the standard plasmid. (bionexus.net)
Sequence both strands to verify the integrity of the synthetic gene sequence. (bionexus.net)
20 ug of lyophilized plasmid DNA containing the synthetic gene. (bionexus.net)
M ake sure the final gene sequence optimized and modified to your own specifications. (bionexus.net)
The genome sequence contains many of the canonical P. multocida virulence factors associated with a range of human and animal diseases, including the pmHAS gene for hyaluronidase associated with bovine haemorrhagic septicaemia. (bvsalud.org)

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 genome contains a circular chromosome and two circular plasmids. (pacb.com)

Comparison of the complete genome sequences of Pseudomonas syringae pv. (nih.gov)
Here, we sequenced 43 H. cinaedi- or H. canicola -like strains isolated from humans, hamsters, rats and dogs and collected 81 genome sequences of H. cinaedi , H. canicola and other enterohepatic Helicobacter strains from public databases. (microbiologyresearch.org)
Genome Sequences of Penicillin-Resistant Bacillus anthracis Strains. (cdc.gov)

5 , 6 ), plasmids with the ability to spread efficiently, or epidemic plasmids, also are believed to be responsible for disseminating CTX-M ESBLs ( 7 ). (cdc.gov)

Hence, the spread of virulence factors and antibiotic resistance properties caused by plasmids is possible, leading to a threat in public health. (frontiersin.org)

A collection of consolidated records describing proteins identified in annotated coding regions in GenBank and RefSeq, as well as SwissProt and PDB protein sequences. (nih.gov)

Find regions of similarity between this sequence and other sequences using BLAST. (nih.gov)
By sequence similarity analysis and functional assays from the species Streptomyces lividans TK23, S. coelicolor A3(2) and S. glaucescens GLA.O, first hints for a widespread lack of MalP and presence of AmlE in the class Actinobacteria were given. (frontiersin.org)
Finds regions of local similarity between biological sequences. (nih.gov)
COBALT is a protein multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. (nih.gov)
Twenty eight (46.7%) of the proteins encoded by this virus exhibit sequence similarity to coliphage T7 proteins while 34 (81.0%) are similar to proteins of Pseudomonas phage gh-1. (biomedcentral.com)

The IncP-1 plasmid group (IncP plasmids in Escherichia coli) of which RK2 is a part has been described as "highly potent, self-transmissible, selfish DNA molecules with a complicated regulatory circuit" RK2 was first isolated in connection with an outbreak of antibiotic-resistant Pseudomonas aeruginosa and Klebsiella aerogenes in Birmingham in 1969, as one of a family of plasmids implicated in transfer of Ampicillin resistance between bacterial strains. (wikipedia.org)

The RK2 Plasmid is a broad-host-range plasmid belonging to the incP incompatibility group It is notable for its ability to replicate in a wide variety of single-celled organisms, which makes it suitable as a genetic engineering tool. (wikipedia.org)

When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. (plos.org)
Complete genome sequence of Enterococcus durans KLDS6.0930, a strain with probiotic properties. (pacb.com)
strain RB-44 complete genome sequence using PacBio single-molecule real-time sequencing technology. (genomeweb.com)
The mtDNA of each strain formed a single 80-90kbp band but the mF + strains yielded a 14-16kbp mF plasmid band in addition to this main band. (go.jp)
Using this method, we successfully identified multiple HCCM complex-containing human faecal metagenome samples and obtained the sequence information covering almost the entire genome of each strain. (microbiologyresearch.org)

The complete genomic sequence 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)
Content of the genomic islands varies, with one containing a prophage and another the plasmid pKLC102 of Pseudomonas aeruginosa PAO1. (nih.gov)
Moreover, genomic results showed a link between pOXA-48_K8 fitness effects and bacterial phylogeny, helping to explain plasmid epidemiology. (nature.com)
An allele is one of two or more versions of DNA sequence (a single base or a segment of bases) at a given genomic location. (genome.gov)
This tool compares nucleotide or protein sequences to genomic sequence databases and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST) algorithm. (nih.gov)
The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns. (tau.ac.il)

Restriction analysis and hybridization demonstrated that this plasmid was identical in at least 13 strains. (udg.edu)
Southern hybridization using labeled plasmid DNA as the probe allowed the mF - strains to be classified into two categories: simple mF - having only an mID sequence and ΔmF having some part of the mF plasmid integrated into the mtDNA. (go.jp)
In Situ Hybridization FBL1 In situ hybridization was completed seeing that described [20] previously. (mingsheng88.org)

It is rarely found that plasmid encode the DNA polymerase. (elsevierpure.com)
The IL-33 cDNA sequences encode 270 and 266 amino acid polypeptides for human and mouse, respectively, corresponding to full-length proteins with calculated masses of 30 and 29.9 kDa [ 2 ]. (hindawi.com)

Incorporating our fitness results into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. (nature.com)

The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. (nih.gov)

Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131. (ox.ac.uk)
OXA-48-like enzymes have emerged as important extended-spectrum β-lactamases/carbapenemases in Escherichia coli sequence type 131 (ST131). (ox.ac.uk)

Given the particulars of a sequence (DNA/RNA/protein, linear molecule/circular plasmid, single/double stranded) it attempts to figure out all of the possible matches without any false-positive or duplicated matches. (cpan.org)
For efficiency, none of the input sequence data is copied at all except to extract matches (but this can be disabled with "no_substr") and to implement circular searches (though the amount copied is usually very small). (cpan.org)

Genome sequencing information provides the genetic basis for bioinformatics analysis of bile salt and acid tolerance, cell adhesion, and molecular mechanisms responsible for lipid metabolism. (pacb.com)

Complete DNA sequences can be used as a platform to develop rapid epidemiologic tools to identify and trace the spread of plasmids in clinically relevant pathogens, thus facilitating a better understanding of their distribution and ability to transfer between bacteria of humans and animals. (cdc.gov)
Plasmids are one of the primary sources for extrachromosomal DNA in bacteria and are capable of self-transmission. (frontiersin.org)
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)
Plasmids are extra-chromosomal mobile genetic elements able to transfer between bacteria through conjugation 1 . (nature.com)
Comparative sequence analysis of pPATH pathogenicity plasmids in Pantoea agglomerans gall-forming bacteria. (tau.ac.il)

A duplex PCR assay was developed to survey the prevalence of plasmid pEI70 and also that of pEA29, which had previously been described in several E. amylovora strains. (udg.edu)
These results help to explain the high prevalence of plasmids in the greatly diverse natural microbial communities. (nature.com)
Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. (plos.org)

A collection of sequence alignments and profiles representing protein domains conserved in molecular evolution. (nih.gov)
Conserved Domains is a database of protein domains represented by sequence alignments and profiles for protein domains conserved in molecular evolution. (nih.gov)

Plasmid DNAs were collected and combined in 1.5 mL tube with aid of multichannel pipette and concentrated by ethanol precipitation. (nih.gov)

A collection of related protein sequences (clusters), consisting of Reference Sequence proteins encoded by complete prokaryotic and organelle plasmids and genomes. (nih.gov)

In E. coli, multiple plasmid copies appear to cluster together, creating a few multiplasmid clusters in each cell. (wikipedia.org)
Two such mutants, PFF1cop254D and PFF1cop271C, increase the copy number of PFF1 in E. coli from approximately 39-40 to about 501 and 113 plasmids per cell, respectively. (wikipedia.org)
To amplify the library 10 ng of plasmid library was transferred into E.coli DH5α (Invitrogen catalog no. 18258-012) with heat shock method. (nih.gov)
The plasmid pSP65 which has cloned the complete HBV sequence, was amplified by transformation of coli (DH5). (bvsalud.org)

Minimal plasmids such as PFF1 are useful for studying the basic mechanisms of plasmid replication and copy number regulation, as there are less superfluous genetic elements which might affect the processes being studied. (wikipedia.org)
A codon is a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genetic information encoding a particular amino acid. (genome.gov)

To date, information on plasmid analysis in Pandoraea spp. (frontiersin.org)
Complete this form to request this certificate of analysis. (atcc.org)
PRADA: Pipeline for RNA sequencing Data Analysis. (genomeweb.com)
To investigate the origin of the mF plasmid, we collected many Physarum laboratory strains as are available at present throughout the world, and classified their origin on the basis of the results of mating-type analysis and restriction endonuclease analysis of their mtDNA. (go.jp)
Sequence Analysis Protein sequence alignment was performed by DNASIS Maximum Version 3.0 (MiraiBio, San Francisco, CA). Domain name architectures for BmSlit had been determined by Wise [18]. (mingsheng88.org)
You can send it and we can sequence it, but we cannot predict or promise the analysis outcome. (eurofinsgenomics.com)

Third, most mathematical models of plasmid population biology study clonal or near-clonal populations. (nature.com)

The purified plasmid (1 µg) is used in EcoRI digestion, and checked by electrophoresis. (primelabmed.com)
The complete digestion of plasmid DNA was assessed by DNA gel electrophoresis. (nih.gov)

Complete sequence and organization of pBtoxis, the toxin-coding plasmid of Bacillus thuringiensis subsp. (bgu.ac.il)
The entire 127,923-bp sequence of the toxin-encoding plasmid pBtoxis from Bacillus thuringiensis subsp. (bgu.ac.il)
Dive into the research topics of 'Complete sequence and organization of pBtoxis, the toxin-coding plasmid of Bacillus thuringiensis subsp. (bgu.ac.il)

The mID sequence is almost identical to a 475-bp sequence (pID) of the mF plasmid. (go.jp)

The sequence of the four nucleotide bases encodes DNA's information. (genome.gov)

An anticodon is a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule, which is complementary to a corresponding codon in a messenger RNA (mRNA) sequence. (genome.gov)

We report the structures of the first fully sequenced blaOXA-163 plasmid and of two other blaOXA-48 plasmids in this lineage. (ox.ac.uk)
Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing. (genomeweb.com)

Furthermore, the conclusion of silkworm genome sequencing facilitates research on molecular biology [17]. (mingsheng88.org)

A 570 bp DNA fragment of probe was produced by digesting the recombinant plasmid with RNA disturbance. (mingsheng88.org)
The primer and probe sequences are listed in the appended table. (cdc.gov)
The HBV sequence was then labeled for its utilization as a probe in the HBV DNA detection in serum of patients with HBsAg positive, with no evident physical symptoms of the disease. (bvsalud.org)

Clinically, she completed training in Pediatrics and Pediatric Infectious Diseases at Boston Children's Hospital and now sees patients on the Pediatric Infectious Diseases service at Lucille Packard Children's Hospital. (stanford.edu)

Sanger sequencing and Oxford Nanopore sequencing (ONT) are both methods for determining the sequence of nucleotides in a piece of DNA. (eurofinsgenomics.com)

For IVT RNA: Plasmids were linearized by NotI-HF enzyme so that the SP6 polymerase promoter site will be upstream of the sequences to be transcribed. (nih.gov)
Reaction composed of 1 µg of library plasmid, 1X transcription buffer, 0.5 mM of NTPs (GTP,ATP, CTP, and UTP), 40 U of SP6 RNA polymerase and 10 µl of RNase-free water. (nih.gov)

feed matrix to subsequently perform a whole-genome-sequencing. (pulsus.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)
The observed features in the plasmids shed light on the Pandoraea spp. (frontiersin.org)

Design and test primers for this sequence using Primer-BLAST. (nih.gov)
To confirm this finding, we designed PCR primers for amplifying certain parts of the mF plasmid. (go.jp)

Reaction was incubated at 37oC for 2 h to achieve complete digestion. (nih.gov)

For example, when searching for the sequence "AA" in the input "AAAA", perl's "m/AA/g" searches will only return 2 matches: AAAA -- -- With this module you get all three matches: AAAA -- -- -- For DNA data this can be useful for finding the comprehensive set of possible molecules that could exist after a restriction enzyme cleaving. (cpan.org)

However, sequence data alone provides minimal insights to identify and prepare for future prepandemic viruses. (nature.com)
A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
Multi-perspective quality control of Illumina exome sequencing data using QC3. (genomeweb.com)
We also developed a method to systematically search for H. cinaedi sequences in large metagenome data sets based on the results of genome comparison. (microbiologyresearch.org)
Send the hard copies of sequencing data including the chromatograms. (bionexus.net)
Data were reported after all laboratory testing was complete. (cdc.gov)

Here, we report the fully assembled genome and plasmid sequences of three S. Heidelberg strains with phage types 9, 29, and 41. (pacb.com)
This work describes the complete genome sequence of this phage. (biomedcentral.com)
This work focuses on the determination of the complete genome sequence of the P. fluorescens phage ϕIBB-PF7A. (biomedcentral.com)
The DNA sequence of phage ϕIBB-PF7A was determined and it consists of linear double-stranded DNA of 40,973 bp. (biomedcentral.com)

The purified plasmid DNA is suitable for transfection, sequencing reactions, PCR, and in-vitro transcription. (primelabmed.com)

In DNA a sequence of three bases, which is called a codon, is responsible for the encoding of a single amino acid. (wikibooks.org)

IMP-84) and were char- acterized as multilocus sequence type 235 (ST235). (cdc.gov)
Recommended prevention and control measures the isolate as multilocus sequence type 235 (ST235). (cdc.gov)

Plasmid pEI70 was found widely dispersed across Europe with frequencies of 5-92%, but it was absent in E. amylovora analyzed populations from outside of Europe. (udg.edu)
In addition to the four known Cry and two known Cyt toxins, a third Cyt-type sequence was found with an additional C-terminal domain previously unseen in such proteins. (bgu.ac.il)
The mitochondrial-fusion promoting (mF) plasmid first found in the slime mold Physarum polycephalum is a parasitic, selfish mitochondrial plasmid, and is capable of manipulating mitochondria behavior as indicated by its name. (go.jp)
The sequence to be found is specified by a restricted version of regular expressions. (cpan.org)

Comparative genomics of several strains of Erwinia amylovora, a plant pathogenic bacterium causal agent of fire blight disease, revealed that its diversity is primarily attributable to the flexible genome comprised of plasmids. (udg.edu)

Difficult to sequence repetitive regions without gaps and resolve large variations. (eurofinsgenomics.com)
A 188-bp DNA fragment obtained by PCR amplification using an oligonucleotide primer pair which anneal to the ends of a highly repetitive 155-bp Trypanosoma cruzi nuclear DNA was cloned in pUC18 and its sequences determined. (bvsalud.org)

Anatomy8

Organisms39

Diseases1

Chemicals and Drugs75

Analytical, Diagnostic and Therapeutic Techniques and Equipment33

Phenomena and Processes104

Disciplines and Occupations2

Technology, Industry, Agriculture2

Information Science6

Health Care1

Genes21

Conjugative plasmids1

Isolates6

Nucleotide Sequences3

Gene17

Contains a circular chromosome2

Genome sequences3

Epidemic plasmids1

Antibiotic resistance1

GenBank1

Similarity5

Bacterial strains1

Incompatibility group1

Strain5

Genomic7

Hybridization3

Encode2

Stability1

Annotation1

Escherichia2

Circular2

Bioinformatics analysis1

Bacteria5

Prevalence3

Alignments and profiles2

DNAs1

Prokaryotic1

Coli4

Genetic2

Analysis6

Clonal1

Electrophoresis2

Bacillus3

Identical1

Encodes1

Molecule1

Structures2

Molecular Biology1

Probe3

Clinically1

Nucleotides1

Polymerase2

Subsequently1

Pandoraea3

Primers2

Digestion1

Restriction1

Data6

Phage4

Reactions1

Amino acid1

Multilocus2

Found4

Comparative1

Repetitive2