Reads sequences plasmids. Medical search. Frequent questions

MDR plasmid transfer from Salmonella to commensal Escherichia coli was demonstrated by PCR and whole-genome sequencing of isolates purified from agar plates containing cefotaxime. (nih.gov)
To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
Complete genome and plasmid sequences of three Canadian isolates of Salmonella enterica subsp. (pacb.com)

Some plasmids were also void of par genes and intriguingly, repA gene was also not discovered in these plasmids. (frontiersin.org)
We offer comprehensive upstream and downstream services, including template DNA sequencing , de novo gene synthesis , Express Cloning into free expression vectors, customized vector construction , and protein expression and purification . (genscript.com)
The complete sequence of the template including the target gene and its vector. (genscript.com)
Due to optimizing the crRNA sequence, the information rewriting tool became highly adaptable to complex information, thus resulting in rewriting reliability of up to 94%, which is comparable to existing gene-editing systems. (phys.org)
Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)
Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)
or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)
Apparently a gene is a segment of the DNA strand and it can be a very long segment, even of thousands of paired chemicals, and there is some kind of chemical sequence that is different from the body of the gene that tells you where it begins and ends. (evcforum.net)
Whereas heterozogosity is the pairing of different alleles or different forms of the same gene, meaning a different chemical sequence on both sides of the pair? (evcforum.net)
Two plasmids were identified containing part of the axhD3 gene. (megazyme.com)
This open forum co-hosted by Sarepta Therapeutics , a company at the forefront of genetic medicine, served as a platform to disseminate knowledge as well as experiences implementing Next-Generation Sequencing (NGS) for gene therapy development. (genedata.com)
To kickstart the event, co-host, Mehmet Karaca, and Associate Director of Molecular Biology - Sequencing and Analytical Development at Sarepta Therapeutics provided insights on the use of NGS in gene therapy product characterization. (genedata.com)
An annotated genomic sequence of the corn anthracnose fungus Colletotrichum graminicola has been published previously, but correct identification of gene models by means of automated gene annotation remains a challenge. (biomedcentral.com)
Based on the nucleotide sequence information of transcripts, we identified 819 novel transcriptionally active regions (nTARs) and revised 906 incorrectly predicted gene models, including revisions of exon-intron structure, gene orientation and sequencing errors. (biomedcentral.com)
We successfully employed deep sequencing RNA-Seq data in combination with an elaborate bioinformatics strategy in order to identify novel genes, incorrect gene models and mechanisms of transcript processing in the corn anthracnose fungus C. graminicola . (biomedcentral.com)
Sequence data of the revised genome annotation including several hundreds of novel transcripts, improved gene models and candidate genes for alternative splicing have been made accessible in a comprehensive database. (biomedcentral.com)
The Neisseria gonorrhoeae assay uses LCR TM (ligase chain reaction) amplification technology in the LCx Probe System for the direct, qualitative detection of a specific target nucleic acid sequence in the Opa gene of Neisseria gonorrhoeae . (cdc.gov)
The four oligonucleotide probes in the LCx assay recognize and hybridize to a specific target sequence within the Opa gene of Neisseria gonorrhoeae DNA. (cdc.gov)
The bla NDM-1 gene was encoded on plasmids that were easily transferable. (who.int)
KPCs) are Ambler class A plasmid- gene by polymerase chain reaction cin, imipenem, ertapenem, meropenem, encoded enzymes that are capable of (PCR) assay provides laboratories trimethoprim/sulfamethoxazole, piper- hydrolyzing all beta-lactam antibiotics, with a means to quickly identify the acillin, piperacillin/tazobactam and including monobactams, extended- presence of this important resistance tobramycin (Oxoid). (who.int)

Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. (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)
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)
We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase bla CTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity. (nih.gov)
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)
Moreover, 5′- and 3′-UTR sequences of 4378 genes have been retrieved and alternatively spliced variants of 69 genes have been identified. (biomedcentral.com)
lactamase encoding genes ( bla ) including bla NDM-1 and plasmid-mediated quinolone and aminoglycoside resistance determinants. (who.int)
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)

The project was divided between the Washington University Genome Sequencing Center (WUGSC) and the Sanger Institute, and was supported by the National Human Genome Research Institute (NHGRI) and The Wellcome Trust. (genome.gov)
As with C. elegans , that project is supported by the NHGRI and The Welcome Trust and is being carried out in collaboration between the Washington University Genome Sequencing Center and the Sanger Institute. (genome.gov)
Azenta Life Sciences, formerly GENEWIZ's Direct Colony Sequencing services utilizes rolling circle amplification (RCA) to enable the Sanger sequencing of bacterial clone or phage sample templates without the need for plasmid preparation. (genewiz.com)
Using RCA for DNA amplification expedites the Sanger sequencing process and allows your data to be delivered within 24 hours** of sample receipt at Azenta. (genewiz.com)
Upon completion the sample is ready for Sanger sequencing. (genewiz.com)
linear templates will not be amplified sufficiently for direct Sanger sequencing. (genewiz.com)
He began his talk by sharing an overview of the AAV vector manufacturing workflow highlighting the different steps (upstream, downstream, and formulation) at which NGS can be implemented in replacement of Sanger sequencing providing crucial information and a clearer picture to support data-informed decision-making. (genedata.com)
How does whole plasmid sequencing compare to Sanger sequencing? (eurofinsgenomics.com)
Sanger sequencing and Oxford Nanopore sequencing (ONT) are both methods for determining the sequence of nucleotides in a piece of DNA. (eurofinsgenomics.com)
Typically Sanger is consider the most accurate method for short-read sequencing and NGS is better for long-read sequencing. (eurofinsgenomics.com)
Overall, the choice between Sanger sequencing and ONT will depend on the specific needs of the application. (eurofinsgenomics.com)

Azenta RCA protocols can handle sequencing projects of any size, and are optimized to produce high quality reads from both bacterial colonies and glycerol stocks as well as phage plaques and supernatants. (genewiz.com)
Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification. (genewiz.com)
Antibody phage display library validation: Direct phage sequencing for faster screening and validation. (genewiz.com)
This work describes the complete genome sequence of this phage. (biomedcentral.com)
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)
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)
Here, we report the fully assembled genome and plasmid sequences of three S. Heidelberg strains with phage types 9, 29, and 41. (pacb.com)

Transfer occurred to seven E. coli sequence types at high rates, even in the absence of cefotaxime, with resistant strains isolated within 3 days. (nih.gov)
Bacterial strains and plasmids are described in Table 1 . (hindawi.com)
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)

Recently, genome sequences revealed that in addition to rpoS , an rpoS -like sigma factor was found in V. alginolyticus 12G01. (hindawi.com)

Visionnement en ligne- The quiet epidemic 20 novembre 2023 et le 4 décembre 2023. (canlyme.com)

PCR amplification and sequencing confirmed that this organism contained VIM-2 carbapenemase. (cdc.gov)
The Chlamydia trachomatis assay uses LCR TM (ligase chain reaction) amplification technology in the LCx Probe System for the direct, qualitative detection of plasmid DNA of Chlamydia trachomatis . (cdc.gov)
They can then be enzymatically joined to form the amplification product, which subsequently serves as an additional target sequence during further rounds of amplication. (cdc.gov)

We have several standard primers for the most common vectors and for bacterial 16S rDNA sequencing. (helsinki.fi)
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. (nordiag.com)
It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. (nih.gov)
Here we use the chicken gut microbiota as an exemplar to model the effects of bacterial infection, antibiotic administration, and plasmid transfer. (nih.gov)
DNA methylation analysis: Save time & obtain high-quality reads by cloning PCR products directly and sequencing the bacterial colonies. (genewiz.com)

Sigma factors are a class of proteins constituting essential dissociable subunits that confer sequence-specific DNA binding properties to RNA polymerase (RNAP). (hindawi.com)

We show that transfer of a multidrug-resistant plasmid from the zoonotic pathogen Salmonella to commensal Escherichia coli occurs at a high rate, even in the absence of antibiotic administration. (nih.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)
Transfer of antimicrobial resistance via plasmid exchange is of particular concern as it enables unrelated bacteria to acquire resistance. (nih.gov)
There is an urgent need for expanded resistance surveillance for carbapenemase-producing organisms and their resistance plasmids in food products that are not captured under current programs. (cdc.gov)

This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)
We developed permissR, an R package to identify permissive sites for chromosomal integration, which can be used in conjunction with pSelAct-Express, a non-replicating integrative plasmid that enables recombination into a permissive genomic location. (biorxiv.org)

The National Human Genome Research Institute (NHGRI) has supported a number of sequencing projects aimed at producing draft assemblies of roundworm (Caenorhabditis) genomes. (genome.gov)
The sequencing of the genomes of three additional roundworm species -- C. remanei, C. japonica, and C. sp. (genome.gov)
The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. (asm.org)
We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis . (asm.org)
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)

Two-step genomic sequence comparison strategy to design Trichoderma strain-specific primers for quantitative PCR. (redasoft.com)

To deselect, click back on the nucleotide sequence. (addgene.org)
Displays a graphical map based on nucleotide sequence data labeled with restriction enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)
List of restriction enzymes that can cut a given nucleotide sequence. (addgene.org)
List of common features detected in a given nucleotide sequence. (addgene.org)
List of commonly used primers detected in a given nucleotide sequence. (addgene.org)

The nucleotide sequences were combined and three open reading frames (ORFs) were found. (megazyme.com)
Displays both strands of base paired nucleotide sequences with annotated enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)
Bioinformatic analysis of the junctions of the inserted sequences and the maize genomic DNA, identified eleven open reading frames (ORFs). (cogem.net)

If you want to use your own primers, take good care that you design them suitable for sequencing. (helsinki.fi)

RCA was identified in natural systems as a DNA replication mechanism frequently employed in plasmid and viral propagation. (genewiz.com)

Understanding the genetic makeup of plasmids is crucial in molecular biology and genetic research. (prmac.com)
Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. (nordiag.com)
Here, we present a suite of tools for genetic manipulation in the tomato pathogen C. michiganensis including a markerless deletion system, an integrative plasmid, and an R package for identification of permissive sites for plasmid integration. (biorxiv.org)
The use of genetic engineering and modern techniques such as transcriptomics, proteomics and sequence analysis are included in the course. (lu.se)

The ease of NDM-1 plasmid transmissibility may help their dissemination among the Enterobacteriaceae. (who.int)

The gastrointestinal tract is replete with bacteria and provides an environment for plasmid transfer between commensals and pathogens. (nih.gov)

Plasmids encoding PE1, PE2 (same as PE3), and pegRNA expression vectors are available from Addgene. (nature.com)
Previously described plasmids expressing sgRNAs are also available from Addgene, such as Addgene plasmid no. 65777. (nature.com)

BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. (addgene.org)

Because of the high specificity between complementary pairs of nucleic acid molecules, the information-encoded DNA sequences were accurately reconstructed by recombinase to encode new information. (phys.org)
These 'guide' crRNAs are incorporated into a ribonucleoprotein interference complex that can recognize and cleave its complementary target sequence, thus destroying the invading nucleic acid. (elifesciences.org)
The LCx Chlamydia trachomatis assay uses the nucleic acid amplication method LCR to detect the presence of C. trachomatis plasmid DNA directly in clinical specimens. (cdc.gov)

PlasClass improves plasmid sequence classification. (cdc.gov)

We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. (nordiag.com)
The oligonuleotides are designed to be complementary to the target sequence so that in the presence of target, the probes will bind adjacent to one another. (cdc.gov)

To solve the rewriting problem, Prof. Liu Kai from the Department of Chemistry, Tsinghua University, Prof. LI Jingjing from the Changchun Institute of Applied Chemistry (CIAC) of the Chinese Academy of Sciences, and Prof. Chen Dong from Zhejiang University led a research team that recently developed a dual-plasmid editing system for accurately processing digital information in a microbial vector. (phys.org)
At the event, discussions were centered on the evolution of sequencing technology, AAV vector manufacturing, GxP validation, and the assessment of critical quality attributes such as identity, potency, and safety. (genedata.com)

Quantification errors will not usually make the reaction fail completely, but they will seriously affect read lengths. (helsinki.fi)

Properties such as GC-content, repeats such as poly(A)-tails and loop structures affect sequencing reactions, so any information you can provide will help us select suitable reaction protocol. (helsinki.fi)
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)

The genome of C. elegans was the first of any multicellular organism to be sequenced in its entirety. (genome.gov)
An organism with 95.5 percent sequence identity to Pseudomonas fluorescens was isolated on Mueller-Hinton agar. (cdc.gov)

The applicant showed by Southern blot analyses that maize line 4114 contains one copy of the insert at a single integration locus and that the backbone of the plasmid used for transformation is absent. (cogem.net)

To date, information on plasmid analysis in Pandoraea spp. (frontiersin.org)
Sequence-Analysis Beerware DNA sequence analysis software needn't be expensive. (the-scientist.com)
For a decade, molecular biologist Kjeld Olesen has spent much of his spare time developing pDRAW32, a free sequence-analysis software package for Windows PCs. (the-scientist.com)
DNA sequence analysis software needn't be expensive. (the-scientist.com)
Comparative analysis of RNA-Seq data and the genome sequence did not provide evidence for RNA editing in C. graminicola . (biomedcentral.com)
Sequence analysis revealed that the cDNA of long neurotoxin has an open reading frame encoding 94 amino acids, including a signal peptide of 21 amino acids. (eurekaselect.com)
You can send it and we can sequence it, but we cannot predict or promise the analysis outcome. (eurofinsgenomics.com)
gplas: a comprehensive tool for plasmid analysis using short-read graphs. (cdc.gov)

When designing the primer, remember that the readable sequence will not start right after the primer and the sequence quality might be poor during the first 10-20 bases. (helsinki.fi)

In the last few years, a large number of T7-like phages have been sequenced most of which have been gathered in a new viral subfamily within the family Podoviridae . (biomedcentral.com)
Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies: A mini-review. (cdc.gov)

The chromosome encodes 5,674 potential protein-coding open reading frames. (wikipedia.org)

Array colonies in a grid on the agar plate and circle the colonies requiring sequencing. (genewiz.com)

A sequenced strain, IFM 10152, is also known to contain two plasmids, pNF1 pNF2. (wikipedia.org)
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)

DNA* has problems printing non-horizontal text (ie labels on circ plasmid maps) on LJIIP, color output for Tektronics Phaser II is limited. (bio.net)

Isolate relatedness was determined by multilocus sequence typing (MLST). (who.int)

High-throughput sequencing data have been deposited to the NCBI Sequence Read Archive database under accession PRJNA565979 . (nature.com)
The primary output is automatically interpreted by a program that gives text data, in other words the sequence output in letters (ACGT and IUPAC ambiguity codes). (helsinki.fi)
A framework for variation discovery and genotyping using next-generation DNA sequencing data. (nordiag.com)
The dual-plasmid system can serve as a universal platform for DNA-based information rewriting in vivo, thus offering a new strategy for information processing and target-specific rewriting of large and complicated data on a molecular level. (phys.org)
Use with SnapGene software or the free Viewer to visualize additional data and align other sequences. (addgene.org)
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)
(OPTIONAL) .fastq file - raw data on reads. (eurofinsgenomics.com)
Read the LABDOC file for detailed data processing and editing protocols. (cdc.gov)

This dual-plasmid system is suitable for storing, reading and rewriting various types of information, including text, codebooks and images. (phys.org)

We require 5 µl of plasmid DNA for a single reaction in concentration of 100ng/µl. (helsinki.fi)

The mature peptide encoding sequence was inserted into plasmid pET-28 (a+), and then which was expressed in the E. coli BL21 (DE3). (eurekaselect.com)

There are 52 open reading frames which occupy 94.6% of the genome ranging from 137 to 3995 nucleotides. (biomedcentral.com)

Direct Colony Sequencing is also extremely effective when low amounts of DNA starting material are available (e.g. low copy plasmids). (genewiz.com)

To achieve high efficiency as well as reliability in rewriting complex information stored in exogenous DNA sequences in vivo, a variety of CRISPR-associated proteins (Cas) and recombinase were used. (phys.org)

The tools were guided by their corresponding CRISPR RNA (crRNA) to cleave a target locus in a DNA sequence so that the specific information could be addressed and rewritten. (phys.org)

In fact, as reported by Drancourt et al (2004), genotyping performed on bacteria derived from the remains of plague victims of the first two epidemics revealed sequences similar to that of Orientalis. (medscape.com)

Anatomy2

Organisms12

Diseases1

Chemicals and Drugs32

Analytical, Diagnostic and Therapeutic Techniques and Equipment26

Phenomena and Processes70

Disciplines and Occupations3

Information Science9

Health Care2

Isolates3

Gene20

Genes14

Sanger11

Phage8

Strains3

Genome sequences1

20231

Amplification3

Bacterial5

Polymerase1

Multidrug-Resistant1

Resistance3

Recombination2

Genomes5

Genomic sequence1

Nucleotide sequence5

ORFs3

Primers1

Replication1

Genetic4

Dissemination1

Pathogens1

Addgene2

Similarity1

Nucleic acid3

Improves1

Complementary2

Vector2

Lengths1

Content2

Organism2

Analyses1

Analysis8

Primer1

Viral2

Protein1

Agar1

Strain2

Horizontal1

Multilocus1

Data8

Suitable1

Concentration1

Peptide1

Open readin1

Colony1

Proteins1

CrRNA1

Plague1