Sequences extrachromosomal. Medical search. Frequent questions

A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. (wikipedia.org)
The resulting avatars are unique in that they behave like a grade 4 glioma-a fast-growing type of tumor that starts in the glial cells of the brain-in their level of pathology, transcriptome signatures, engineered genetic alterations and evolution of genetic mutations, such as the emergence of extrachromosomal DNA and chromosomal rearrangements. (reachmd.com)
ALT is a recombination-based mechanism where one telomere uses other chromosomal, or extrachromosomal, telomeric DNA sequences as a template for telomere elongation. (oncotarget.com)
In order to isolate a particular gene from human chromosomal DNA, it would be necessary to isolate a sequence of a few hundred or few thousand basepairs from the entire human genome. (addgene.org)
They serve as guardians of genome stability but they also have dynamic features playing important role in cell aging and immortalization, both as chromosomal components or as extrachromosomal DNA. (irb.hr)
However, it can be difficult to identify plasmid sequences from chromosomal sequences in genomic and metagenomic data. (iit.edu)

Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. (wikipedia.org)
To address the gap of knowledge on this, the complete sequences of eight plasmids from Pandoraea spp. (frontiersin.org)
Plasmids are one of the primary sources for extrachromosomal DNA in bacteria and are capable of self-transmission. (frontiersin.org)
Typically plasmids contain the minimum essential DNA sequences for this purpose, which includes a DNA replication origin, an antibiotic-resistance gene, and a region in which exogenous DNA fragments can be inserted. (addgene.org)
Plasmids are extrachromosomal DNA found in microorganisms. (iit.edu)
Additionally, tRNA loci are often found on extrachromosomal elements, such as plasmids and bacteriophages. (springeropen.com)

It is a tool for detecting viral integration and fusion mRNA sequences from Next Generation Sequencing data. (biomedcentral.com)
Here, using Next Generation Sequencing we identified a novel gene fusion event between DAXX and the kinesin motor protein, KIFC3, leading to the translation of a chimeric DAXX-KIFC3 fusion protein. (oncotarget.com)
Advancements in embryo culture, blastocyst biopsy techniques, 24-chromosome aneuploidy screening platforms, and improved genomic coverage of new sequencing platforms, such as next-generation sequencing, have made PGT safe and accessible for all patients who undergo in vitro fertilization. (medscape.com)
[ 2 ] This technique has evolved throughout the years and is now largely performed by biopsy of the blastocyst trophectoderm cells with analysis using techniques such as next-generation sequencing (NGS) and comparative genomic hybridization (CGH) to test for aneuploidy. (medscape.com)

The most commonly used molecular approach for exploring microbial diversity is based on the PCR amplification and sequencing of genes encoding small subunit ribosomal RNA (16S rRNA) directly from environmental sources [ 16 ]. (biomedcentral.com)
The production of Wolbachia genomic DNA free of contamination from host DNA, as required for Wolbachia-targeted sequencing, was then only possible after the amplification and extraction of a large amount of clonal Wolbachia DNA. (bvsalud.org)

In the new study, researchers identified a mechanism by which cells develop the genetic changes, known as extrachromosomal DNAs (ecDNAs) and complex genomic rearrangements, needed to acquire resistance to targeted drugs. (cancer.gov)
Nowadays, the production of full Wolbachia genomes does not require the physical isolation of the bacterial strains from their respective hosts, and the bacterium is often sequenced as a by-catch of host genomic projects. (bvsalud.org)
They combined advanced sequencing techniques with pioneering bioinformatics algorithms to construct a detailed genomic map of the circular DNA. (mskcc.org)
Here, we demonstrate the power of machine learning in classifying plasmid sequences from genomic data. (iit.edu)
RESULTS: Whole genome shotgun sequencing (WGS) and mapping of reads from both glyphosate-resistant and sensitive (R and S) plants to the reference cassette was performed to compare genomic representation and variation across the EPSPS cassette. (usda.gov)
To determine any genomic differences that may occur between S. citri populations, the bacterium was isolated and cultured from different times and hosts, and S. citri DNA purified and subjected to PacBio sequencing. (biomedcentral.com)

Even so, the team's follow-up analyses - including RNA sequencing experiments - indicated that rearrangements stemming from extrachromosomal circular DNA from MYCN and other genes may be a recurrent and ongoing source of new mutations through a multi-hit model in neuroblastoma. (genomeweb.com)
Researchers tracked down a handful of previously unappreciated susceptibility genes using exome sequences for more than 244,000 European women with or without breast cancer. (genomeweb.com)
For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. (bvsalud.org)

Later in 1968, it was decided that the term plasmid should be adopted as the term for extrachromosomal genetic element, and to distinguish it from viruses, the definition was narrowed to genetic elements that exist exclusively or predominantly outside of the chromosome and can replicate autonomously. (wikipedia.org)
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)
Using a combination of bioinformatic, genetic and molecular approaches, we cloned and sequenced a series of different inserts, including one full-length virus sequence. (reading.ac.uk)
High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. (biomedcentral.com)
High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. (biomedcentral.com)
Electron microscopic research on the extrachromosomal genetic elements of Escherichia coli. (org.ua)

Together, these approaches uncovered almost 5,700 small extrachromosomal circular DNAs per tumor, on average, and an average of 0.82 large, copy number-amplified extrachromosomal circular DNA sequences, the authors reported, noting that "DNA circularization is not restricted to proto-oncogenes, but also affects various coding and non-coding regions with yet unknown functional consequences. (genomeweb.com)

The first "complete" human genome sequence was actually complete only in terms of what researchers could achieve with the technology available at that time. (jax.org)
The original reference genome sequence, as well as my own, was generated using short read sequencing technology. (jax.org)
The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes. (pacb.com)
Here we describe the features of the S. mucosus strain DSM 16094 T together with its genome sequence and annotation. (ncl.ac.uk)
The 5,689,389-bp genome sequence consists of one chromosome and several extrachromosomal elements. (ncl.ac.uk)
The whole genome sequence of five strains of S. citri are described herein. (biomedcentral.com)

Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)
Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. (bvsalud.org)
Ebola virus Nanopore sequencing resources (project)ARTICnetwork, Wellcome Trust. (cdc.gov)

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)
The rapid development of new sequencing platforms, such as Roche 454 sequencing system (Roche Diagnostics) and Illumina sequencing platforms (Illumina, Inc.) offered 1000-fold increase in throughput over the Sanger sequencing technology and supported the progressive publication of more helminth genomes [ 11 ]. (biomedcentral.com)
To investigate the biology of resistance, Dr. Lo and his colleagues sequenced the genomes of the melanoma tumors immediately after the cells were exposed to a targeted therapy combination for tumors with BRAF V600 mutations. (cancer.gov)
To see how the genomes continued to change over time, the researchers repeated the sequencing after the tumors had stopped responding to the drugs. (cancer.gov)

Nearly 10 percent of the genome, including highly repetitive sequences at the ends (telomeres) and middles (centromeres) of chromosomes, remained inaccessible. (jax.org)
Telomeres are among most important repetitive sequences, located at the end of linear chromosomes. (irb.hr)
[11] Riabowol K, Shmookler Reis RJ, Goldstein S. Interspersed repetitive and tandemly repetitive sequences are differentially represented in extrachromosomal covalently closed circular DNA of human diploid fibroblasts. (org.ua)

It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. (pacb.com)
Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. (shengsci.com)
Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. (shengsci.com)
[1] Flavell AJ, Ish-Horowicz D. The origin of extrachromosomal circular copia elements. (org.ua)
[4] Fujimoto S, Tsuda T, Toda M, Yamagishi H. Transposon-like sequences in extrachromosomal circular DNA from mouse thymocytes. (org.ua)
L1 sequences in HeLa extrachromosomal circular DNA: evidence for circularization by homologous recombination. (org.ua)

That finding prompted the team to take a closer look at these sequences using a modified version of circle sequencing (Circle-seq) in 21 of the neuroblastoma tumors, making it possible to enrich for circularized DNA. (genomeweb.com)

The information on plasmid sequences in Pandoraea spp. (frontiersin.org)
We have developed a new tool called PlasmidHunter, which uses machine learning to predict plasmid sequences based on gene content profile. (iit.edu)

While past research has pointed to a role for circularized, extrachromosomal MYCN oncogene sequences in neuroblastoma, the team explained, the full suite and the frequency of somatic mutations involving small or large stretches of circularized extrachromosomal DNA amplifications had not been fully explored. (genomeweb.com)

This indicates that the most likely mechanism for extrachromosomal element insertion is homologous recombination between the extrachromosomal element tRNA and PAI flanking tRNA loci (Hacker and Kaper 2000 ). (springeropen.com)

The term plasmid was introduced in 1952 by the American molecular biologist Joshua Lederberg to refer to "any extrachromosomal hereditary determinant. (wikipedia.org)
In 1952, Joshua Lederberg coined the term plasmid, in reference to any extrachromosomal heritable determinant. (addgene.org)

Single-molecule reads that span the entire genome can capture species without an existing reference sequence as well as detect variants within a particular species. (jax.org)
Here, we provide a step-by-step protocol to (1) identify whether host genome projects contain reads from associated Wolbachia and (2) isolate/retrieve the Wolbachia reads from the rest of the sequenced material. (bvsalud.org)
Sampling of R and S biotypes from multiple states revealed complete assembly and deep representation with sequences from R plants, but lack of contiguity and breaks in coverage were observed with reads from S plants. (usda.gov)

Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)
Somatic hypermutation alters variable region sequence, and switch recombination joins a new constant region (Cγ1) to the expressed variable region, producing an extrachromosomal DNA circle (bottom), which contains the deleted region. (biomedcentral.com)
It mostly consists of non-coding DNA of various repeats, often prone to recombination including creation of extrachromosomal DNA which can be re-integrated into distant parts of the genome, often in different chromosome. (irb.hr)

In somatic hypermutation, targeted and rampant mutagenesis alters the sequences of the expressed heavy and light chain variable (VDJ) regions. (biomedcentral.com)

He takes advantage of state-of-the-art technologies in microbial genomics studies, such as third generation sequencing (e.g. (iit.edu)
The genome sequences reported here will be used for comparative genomics and to better understand the etiology, relationships and evolution among the spiroplasmas. (biomedcentral.com)

The circularized sequences were mapped back to their original sites in the genome using additional long-read and single-molecule real-time sequences, the investigators explained, and they validated candidate DNA circles with PCR and Sanger sequencing. (genomeweb.com)

Long read sequencing technologies haven't pushed aside short read sequencing or Illumina, the largest company in the field, as some predicted back then, but they are now being applied to a wider range of research applications. (jax.org)

Three nt (G-G) and a substitution of 1 nt (C to T), when com- different SSUrRNA sequences (Pov 1-3) were found in each variant-type isolate, and two different SSUrRNA pared with the classic type, the Nigerian I/CDC strain (6). (cdc.gov)
In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. (pacb.com)
According to Multilocus Sequence Typing (MLST) analysis this strain belongs to ST21. (bvsalud.org)
The phylogenomic analysis of E. faecalis 6805 was performed with ST21 representatives from the PubMLST database, including the E. faecalis IE81 strain from clinical sample in Brazil, which had its genome sequenced in this study. (bvsalud.org)
Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF. (cdc.gov)

With that in mind, Henssen and colleagues from Germany, the US, and Spain profiled matched tumor and normal blood samples from 93 neuroblastoma patients using whole-genome sequencing and an algorithm that uncovers circularized DNA based on paired read orientation, uncovering preliminary evidence for complex and relatively frequent ecDNAs in neuroblastoma. (genomeweb.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)

The sequencing revealed the process by which specific DNA sections separate from a chromosome to form the circles before reintegrating into the chromosome at a different location. (mskcc.org)

She then continued with her Ph.D. studies in molecular biology at the University of Cambridge, England, where she used DNA sequencing to study the nucleic acid composition of a specific bacteriophage. (frontiersin.org)
For this purpose, the whole-genome sequencing (WGS) was carried out aiming to elucidate its molecular mechanisms of antimicrobial resistance and its phylogenetic relationships amongst strains from other sources and countries. (bvsalud.org)
This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology. (biomedcentral.com)

The variant isolates we ana- only source of available sequence for the cytochrome b lyzed were ST243 (Rakhine State) and MC53 (Tanintharyi ( cyt b ) gene (16). (cdc.gov)
or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)
We have determined the nucleotide sequence of the C gene. (shengsci.com)
The amplified unit, a 399-kb extrachromosomal DNA, the EPSPS cassette, was unique to glyphosate-resistant plants and contained 1 copy of the 10-kb EPSPS gene. (usda.gov)

The T2T (telomere-to-telomere) consortium announced in late March 2022 that it had generated the first complete, gapless sequence of a human genome. (jax.org)

Here, to better understand the development of ecDNA, we analysed whole-genome sequencing (WGS) data from patients with oesophageal adenocarcinoma (EAC) or Barrett's oesophagus. (nature.com)
All sequence data has been deposited in DDBJ/ENA/GenBank under the accession numbers CP046368-CP046373 and CP047426-CP047446. (biomedcentral.com)
Adapter screening and quality filtering of raw sequencing data were performed using SMRT Analysis (PacBio) with default settings. (biomedcentral.com)

Genome-wide identification of endogenous viral sequences in alfalfa (Medicago sativa L.). Virol. (reading.ac.uk)

The team, led by MSK computational biologist Richard Koche and Anton Henssen of Charité University Hospital Berlin, made this discovery by studying extrachromosomal DNA in neuroblastoma cells. (mskcc.org)

Using whole-genome sequencing on drug-exposed cell lines, researchers saw high mutation rates in control cell lines intermittently treated with a compound called CX-5461. (genomeweb.com)
It's therefore fitting that researchers leading the long read innovation charge at institutions around the country came to JAX for its recent long read sequencing workshop , including some of the leaders of the T2T effort. (jax.org)

Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements. (cdc.gov)

CONCLUSIONS: High sequence conservation of the EPSPS cassette from R populations widely separated across the USA indicated that glyphosate resistance most likely originated from a single population. (usda.gov)

sequences (Poc 1-2) in each classic-type isolate. (cdc.gov)

Cameroon and MAL/MAI isolates, whereas Poc 1-2 were probe used by the commercially available microtiter-plate closer to sequences previously found in two clones of the hybridization (MPH) method for malaria diagnosis (4). (cdc.gov)

The DNA sequences of ospA , ospB , rrs-rrlA , and ospC ideal for deer and the small mammals that maintain the I. were determined for use in our phylogenetic analysis. (cdc.gov)

The Jackson Laboratory (JAX) has considerable expertise in long read sequencing, and many faculty members rely on it for their research. (jax.org)
Long read sequencing has long been important for sequencing microbes. (jax.org)

partial sequences are also primary infection (3). (cdc.gov)
Significantly, KSHV LANA mutants lacking the acidic domain reader sequence are deficient for establishment of latency and persistent infection. (ucp.pt)

Extrachromosomal DNA provides great impact in the evolution of bacteria in adapting to their surroundings. (frontiersin.org)
DNA from cultures were sequenced and genome assembled to expand the database to improve detection assays and better understand its genetics and evolution. (biomedcentral.com)

Anatomy17

Organisms31

Diseases3

Chemicals and Drugs53

Analytical, Diagnostic and Therapeutic Techniques and Equipment26

Phenomena and Processes83

Disciplines and Occupations1

Technology, Industry, Agriculture1

Information Science4

Chromosomal6

Plasmids6

Next Generation Sequencing4

Amplification2

Genomic6

Genes3

Genetic6

DNAs1

Genome sequence6

Nanopore3

Genomes4

Repetitive sequences3

Circular6

Tumors1

Plasmid sequences2

Oncogene1

Homologous recombination1

Determinant2

Reads3

Recombination3

Somatic1

Genomics2

Sanger1

Illumina1

Strain5

Samples from 931

5,0001

Chromosome1

Molecular3

Gene4

20221

Data3

Viral1

Neuroblastoma1

Researchers2

Strains1

Conclusions1

Isolate1

Closer1

Small1

Long-read2

Infection2

Evolution2