Elements in genomes. Medical search. Frequent questions

While many CTCF binding sites fall within transposable elements (TEs), their contribution to 3D chromatin structural evolution is unknown. (nature.com)
Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi. (nature.com)
Compared to other species of the species complex, the species best adapted to oilseed rape, L. maculans "brassicae", causing important losses in the crop, has a genome that was submitted to a recent and massive burst of transposition by a few families of transposable elements (TEs). (pasteur.fr)
Transposable elements will provide invaluable tools for manipulating the frog genome. (biomedcentral.com)
A genetic toolbox of 'cut-and-paste' DNA transposable elements is now available for use in vertebrates and includes Tol2 and piggyBac . (biomedcentral.com)
Here, we review the application of transposable elements to modification of the frog genome. (biomedcentral.com)
In this work we review the state-of-the-art of chromosome organisation and so-called "transposable elements" (TEs), pieces of DNA that have the tendency to copy themselves and "jump" to other parts of the genome. (unitn.eu)
Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA. (blogspot.com)
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. (inrae.fr)
Raquel Garza Gómez defends her Ph.D. thesis "Transposable elements in the healthy and diseased human brain ' on Friday, January 19th. (lu.se)
With a background in computational biology, Raquel's research focuses on studying the role of transposable elements in the human brain. (lu.se)
Transposable elements refer to DNA sequences capable of moving from one part of the genome to another. (lu.se)
During my Ph.D. studies, my focus has been analyzing sequencing data in relation to transposable elements. (lu.se)
My research questions have explored different aspects of transposable elements, including their transcription and epigenetic regulation. (lu.se)
This is important for the understanding of human brain evolution as well as diseases with complex networks where transposable elements may play a regulatory role. (lu.se)
Thanks to technological advances in recent decades, more researchers like us have been able to dig deeper into the role of transposable elements in disease contexts and answer big questions about evolution and brain development. (lu.se)
During my Ph.D., my research has primarily focused on studying transposable elements in the human brain in various contexts such as development, healthy adulthood, and certain disease contexts. (lu.se)
My focus has been on the data analysis side of things, employing different computational methods to deal with mapping ambiguity and adapting new technologies such as single-cell RNA sequencing to better understand three families of transposable elements. (lu.se)
Transposable elements (TEs) are mobile genetic sequences that comprise around 50% of our genomic DNA. (lu.se)

The regions upstream to all genes were first isolated from the yeast genome database MIPS using the information in the annotation files of the database. (aaai.org)
Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) and bind to RA response elements (RAREs) in the regulatory regions of their target genes. (nih.gov)
Although previous studies on limited sets of RA-regulated genes have defined canonical RAREs as direct repeats of the consensus RGKTCA separated by 1, 2, or 5 nucleotides (DR1, DR2, DR5), we show that in mouse embryoid bodies or F9 embryonal carcinoma cells, RARs occupy a large repertoire of sites with DR0, DR8, and IR0 (inverted repeat 0) elements. (nih.gov)
The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. (nature.com)
In addition, the location of effector genes within genome regions enriched in TEs has direct consequences on adaptation to plant resistance and favours a multiplicity of mutation events allowing "breakdown" of resistance. (pasteur.fr)
These data are substantiated by other examples in the literature showing that fungi tend to have a "two-speed" genome, in which a plastic compartment enriched in TE host genes is involved in pathogenicity and adaptation to host. (pasteur.fr)
1 It turns out that the bacterial genome has a few high-level instructions that control a few middle-level processes, that in turn control a massive number of protein-coding genes. (creation.com)
In terms of clinical utility, next-gen sequencing will significantly improve the positive detection rate of tests, because many genes are tested simultaneously, as in the case of gene panel-based test, or all genes are interrogated in the case of whole exome or whole genome sequencing. (aacc.org)
By understanding the cephalopod genome, we can gain insight into the genes that are important in setting up the nervous system, as well as into neuronal function. (scitechdaily.com)
Chromosomal-level assemblies allowed us to better refine what genes are there and what their order is, because the genome is less fragmented," Albertin said. (scitechdaily.com)
So now we can start to study the regulatory elements that may be driving expression of these genes. (scitechdaily.com)
This presents an interesting situation: genes are put into new locations in the genome, with new regulatory elements driving the genes' expression. (scitechdaily.com)
TEs can be repurposed by incorporation into new genes, new regulatory elements, or telomeres. (plantae.org)
The team's analyses of the 816 million base genome assembly uncovered 26,046 predicted protein-coding genes. (genomeweb.com)
How many genes are in the human genome? (cshlpress.com)
How Many Protein-coding Genes Are Present in the Genome? (cshlpress.com)
Which Genes Are Present in the Mitochondrial Genome? (cshlpress.com)
How Are Genes Organized in the Mitochondrial Genome? (cshlpress.com)
How Are microRNA Genes Distributed in the Genome? (cshlpress.com)
What Is the Size Distribution of snRNA Genes and Related Sequences in the Genome? (cshlpress.com)
You're listening to Nice Genes where we peek into the world of genomics, sponsored by Genome British Columbia. (genomebc.ca)
The vast majority of these, however, lie outside of known genes, as 98.5% of our genome doesn't code for proteins. (nih.gov)
To gain insights into these non-coding regions, a team of scientists partly supported by NIH's National Human Genome Research Institute (NHGRI) carried out a genome-wide survey of epigenetic marks - factors that change the way genes are read, or expressed, without changing the DNA sequence itself. (nih.gov)
This problem is primarily caused by antimicrobial resistance (AMR), which disseminates by clonal spread of resistant organisms and horizontal transmission of mobile genetic elements with AMR genes. (cdc.gov)

From the viral genome, researchers have deduced the sequences and structures of the viral proteins, hoping to use this information to develop treatments and vaccines for SARS. (sciencedaily.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)
Introns sequences account for about 30% of the genome. (blogspot.com)
By scanning the available genome sequences, Demuth et al. (blogspot.com)
For modeling and analysis - such as in cancer research, for example, which is what we do here - by far the most important parts of the human genome assembly are the parts that code for protein ( transcribed regions and their ORFs ), along with their adjacent regulatory sequences . (bcgsc.ca)
Almost 35 percent of the existing genome assembly is made up of sequences representing repetitive elements from thousands of families, researchers reported. (genomeweb.com)
Even so, they explained that repeats may actually make up a somewhat larger proportion of the overall lamprey genome, since some repetitive element sequences are unwittingly collapsed by genome assembly software. (genomeweb.com)
The two lineages also shared sequences from hundreds of conserved non-coding elements. (genomeweb.com)
While homologous to conserved non-coding sequences in the jawed vertebrate genomes, though, the lamprey versions of these elements shared sequence identity over around half of each element, on average. (genomeweb.com)
Spoligotyping: Identifies the M. tuberculosis genotype based on presence or absence of spacer sequences found in a direct-repeat region of the M. tuberculosis genome where 43 identical sequences and 36 base pairs are interspersed by spacer sequences. (cdc.gov)

The sea urchin genome is 814,000 kb or about 1/4 the size of a typical mammalian genome. (blogspot.com)
Like mammalian genomes, the sea urchin genome contains a lot of junk DNA, especially repetitive DNA. (blogspot.com)
Dr. Lisa Dailey FIREWACH: A Functional approach for elucidating transcriptional regulatory elements within mammalian genomes. (cuny.edu)
FIREWACH: A Functional approach for elucidating transcriptional regulatory elements within mammalian genomes. (cuny.edu)

Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
In this paper, we evaluate the link between genome plasticity and adaptive potential using genomics and comparative genomics approaches. (pasteur.fr)
These results reveal a new dimension of comparative genomics such that a comparison of two genomes needs to be comprehensive over all levels of genome organization. (ucsd.edu)
By establishing the order of A's, C's, G's, and T's in the human genome, the HGP essentially set the stage for functional genomics research and clinical translation. (genengnews.com)
Today, the human genome, genomics (a rarely used word 15 years ago), and sequencing inform virtually all of biology. (genengnews.com)
Biologists at the University of Rochester, including Amanda Larracuente, an associate professor of biology, and Daven Presgraves , a University Dean's Professor of Biology, have for the first time used population genomics to shed light on the evolution and consequences of a selfish genetic element known as Segregation Distorter ( SD ). (eurekalert.org)
But this is the first time they have used what is known as population genomics-examining genome-wide patterns of DNA sequence variations among individuals in a population-to study the dynamics, evolution, and long-term effects of SD on a genome's evolution. (eurekalert.org)
After lecturing on genomics at Caltech in 2004, his efforts have centered on writing about the human genome. (cshlpress.com)
Genome structure, comparative genomics, and bioinformatics. (lu.se)

The sequence of the human genome. (nih.gov)

The 2000s witnessed an explosion of genome sequencing and mapping in evolutionarily diverse species. (wikipedia.org)
While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosomal regions from more than a few species is not yet possible. (wikipedia.org)
Genome-wide transcription start site (TSS) profiles of the enterobacteria Escherichia coli and Klebsiella pneumoniae were experimentally determined through modified 5' RACE followed by deep sequencing of intact primary mRNA. (ucsd.edu)
In a Perspective article published in the November 2012 issue of Clinical Chemistry , Dr. Yiping Shen and his colleagues in Boston and Shanghai explored a whole exome and whole genome sequencing as clinical tests. (aacc.org)
Dr. Shen, in your Perspective article you discuss the transformative effect of next-gen sequencing-based genetic testing, particularly exome and whole genome-based test on the molecular diagnostic practice. (aacc.org)
Now, Doctor, you mentioned there were panels of test and whole exome and whole genome-based next-gen sequencing tests. (aacc.org)
Not only did the HGP achieve its stated goal-sequencing the human genome-it has also had consequences that continue to ripple outward, changing the way we think about biology, changing the way we pursue medicine, and unleashing a host of technological and commercial initiatives. (genengnews.com)
It reached this goal ahead of schedule, having completed sequencing for 700 patients (accumulating 1,400 whole genomes) to date. (genengnews.com)
Sequencing these three cephalopod genomes, never mind comparing them, was a tour de force effort funded by the Grass Foundation that took place over several years in labs around the world. (scitechdaily.com)
All for one, and one for all: Denmark's new technological and institutional infrastructure allows for genome sequencing at scale, opening doors for clinicians and researchers. (mckinsey.com)
Other countries are moving ahead with their own efforts on a national-genome-sequencing program. (mckinsey.com)
For the new study, members of the team from Washington University's Genome Institute tackled the lamprey genome with whole-genome shotgun sequencing, fosmid sequencing, and BAC library sequencing, using genomic DNA from a female sea lamprey caught wild in the Great Lakes. (genomeweb.com)
Genome Sequencing in the Clinic - The question is not whether the glass is half-full or half-empty but whether or not the glass is the right tool. (cdc.gov)
A decade ago, sequencing and interpreting even the small portion of the human genome that the exome represents would have been cost-prohibitive. (cdc.gov)
Low-cost exome and genome sequencing technologies, as a group, represent disruptive technologies that in time could supplant- existing molecular diagnostic approaches. (cdc.gov)
The analytic validity and capacity to reliably identify disease-associated variant varies across the genome and are dependent on the effective use of the sequencing instrumentation and subsequent analysis. (cdc.gov)
In contrast, a negative result from sequencing is less informative in the context of rare, undiagnosed conditions and in most instances will not rule out the presence of a disease-associated variant In 2011, the CDC convened a national workgroup to establish elements of a quality management system to assure the analytical validity and compliance of next generation sequencing tests with existing regulatory and professional quality standards. (cdc.gov)
This study examined the added value of whole genome sequencing (WGS) for investigating a non-point source outbreak of Salmonella ser. (who.int)
2 Whole genome England and Central Coast local health districts of sequencing (WGS) is a high-resolution typing method NSW. (who.int)

Background: Repetitive elements make up significant proportions of genomes. (syr.edu)
To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. (syr.edu)
Results: The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. (syr.edu)
Conclusions: The enriched association of specific categories of repetitive elements with fish habitats suggests the importance of repetitive elements in genome evolution and their potential roles in fish adaptation to their living environments. (syr.edu)

It turns out that the size of the nucleus is related to the size of the cell, such that large genomes give rise to large nuclei and large cells. (blogspot.com)

This is the first time anyone has sequenced the whole genomes of SD chromosomes and therefore been able to make inferences about both the history and the genomic consequences of being a supergene," Presgraves says. (eurekalert.org)

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)
Together with Senior Graphics Editor Jen Christiansen, we've looked at everything from the evolution of the genomes of SARS-Cov-2 strains to how pets contribute to the bacterial flora in your home . (bcgsc.ca)
Specific sections of the M. tuberculosis genome form distinct genetic patterns that help distinguish different strains of M. tuberculosis . (cdc.gov)
VNTR-MIRU: Distinguishes the M. tuberculosis strains by the difference in the number of copies of tandem repeats at specific regions, or loci, of the M. tuberculosis genome. (cdc.gov)
Here, we show that the nuclear genomes of three strains of Anaeramoeba encode between 45 and 103 inteins, in stark contrast to four found in the most intein-rich eukaryotic genome described previously. (lu.se)

Since leaving Minnesota, he has focused on bioinformatics, both in industry and in the analysis of the Candida albicans genome. (cshlpress.com)

b Comparison of 2275 gene pairs from the terminal 150 Mb of short chromosome arms from A and B genomes. (biomedcentral.com)
Comparative chromosome painting and related techniques are very powerful approaches in comparative genome studies. (wikipedia.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 beginning of the human Y chromosome as seen with the Skittle Genome Visualization Tool. (creation.com)
Its genome contains one genome copy from the S. uvarum parental genome and two heterozygous copies of the S. cerevisiae parental genome, with the exception of a monosomic S. cerevisiae chromosome III, where the sex-determining MAT locus is located. (frontiersin.org)

By May 2003, a coronavirus had been identified as the cause of SARS, and the full genome sequence of this new human pathogen, which may have jumped from civet cats to people, had been published. (sciencedaily.com)
This and other putative roles need to be tested experimentally, but given that the s2m element is absent in the human genome, its unusual structural features could be an attractive target for the design of antiviral therapeutic agents. (sciencedaily.com)
The first step of the Human Genome Project took place when Tjio and Levan, in 1956, reported the accurate diploid number of human chromosomes as 2n = 46. (wikipedia.org)
The human genome is the most complex computer operating system anywhere in the known universe. (creation.com)
The human genome operates in four dimensions. (creation.com)
The genome, though, runs a hyper-complex machine called the human body. (creation.com)
The large black area is a repeat that the human genome project skipped over (they did not yet have the technology to sequence highly repetitive DNA). (creation.com)
The human genome is about 1.8m long. (creation.com)
Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. (researchgate.net)
However, a comprehensive genome-wide map of human S/MARs is yet not available. (researchgate.net)
Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. (researchgate.net)
Ten years after its "official" completion, what can be said about the Human Genome Project (HGP)? (genengnews.com)
GEN asked four questions of the panel: Why should completing the human genome project be considered such a historical accomplishment? (genengnews.com)
What were the main surprises that have come from studying the human genome? (genengnews.com)
What next needs to be done to advance our knowledge and to capitalize on our understanding of the human genome? (genengnews.com)
Toward a complete human genome sequence. (nih.gov)
The Doryteuthis genome is 1.5 times larger than the human genome, and the octopus genome is 90% the size of a human's. (scitechdaily.com)
The information graphic showing the history of the human genome assembly is part of my series of designs created for the Scientific American Graphic Science page. (bcgsc.ca)
In March 2022, a flurry of publications announced the first ever complete assembly of a human genome. (bcgsc.ca)
Because the human genome - a human genome - is complete. (bcgsc.ca)
You've probably already heard - and have been hearing for the last 15 years - that the human genome has been sequenced. (bcgsc.ca)
92% of the human genome is euchromatic. (bcgsc.ca)
Understanding human DNA structures is an essential element of medical and life sciences. (ibm.com)
The human genome is littered with "selfish genetic elements," which do not seem to benefit their hosts, but instead seek only to propagate themselves. (eurekalert.org)
Although the human genome has been sequenced, it often can be surprisingly difficult to find answers to seemingly simple questions about its characteristics. (cshlpress.com)
This convenient handbook, written in question-and-answer format, allows researchers and teachers alike access to basic facts about the human genome. (cshlpress.com)
Using a recent assembly of the human genome sequence, Stewart Scherer has compiled answers to a broad range of questions about the structure and function of the human genome. (cshlpress.com)
While at Minnesota, he spent time working at the LBL Human Genome Center. (cshlpress.com)
Which Types of Proteases Are Found in the Human Genome? (cshlpress.com)
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. (bvsalud.org)
Genome, Human. (who.int)
Toxic substances to understand and analyze the such as heavy metals--for example, arsenic and nickel-- human genome. (medlineplus.gov)
The second phase focuses on characterizing epigenetic sequence and apply it to better understand human biology changes caused by environmental exposures in different and improve health, and thanks to a new understanding of types of cell tissues such as the brain, lung, liver, skin, and how people's genomes and epigenomes work, ENCODE's blood. (medlineplus.gov)

The organisation and evolution of the eukaryotic genomes. (lu.se)

Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling. (ucsd.edu)
Comparative analysis of these regulatory elements revealed the use of multiple TSSs, identical sequence motifs of promoter and Shine-Dalgarno sequence, reflecting conserved gene expression apparatuses between the two species. (ucsd.edu)
662 conserved promoters having TSSs in both species resulted in the same number of comparable 5' UTR pairs, and that regulatory element was found to be the most variant region in sequence among promoter, 5' UTR, and ORF. (ucsd.edu)
For instance, the team saw signs suggesting that the so-called Shh appendage-specific regulatory element, or ShARE, - crucial for limb development in jawed vertebrates - likely appeared within that lineage after the split with the lamprey lineage. (genomeweb.com)
For example, sequence alone does not determine multi-functionality of regulatory elements (e.g. enhancers, insulators). (pitt.edu)
This suggests that these DNA changes are disrupting important regulatory elements and thus play a role in disease biology. (nih.gov)

Transposons have widely been used in plant and invertebrate model species to integrate foreign DNA into the host genome. (biomedcentral.com)
Once integrated into the frog genome, the 'cut-and-paste' DNA transposons are targets for remobilization by re-expression of the appropriate transposase enzyme. (biomedcentral.com)

These elements are involved in control of gene expression which governs the phenotype and also plays role in disease biology. (researchgate.net)
Probably the greatest advance in this new work is providing chromosomal-level assemblies of no less than three cephalopod genomes, all of which are available for study at the MBL," said co-author Clifton Ragsdale, professor of Neurobiology and of Biology and Anatomy at the University of Chicago. (scitechdaily.com)
And going forward, the study's authors said, the lamprey genome offers opportunities to explore evolutionary questions, both within the lamprey lineage and across vertebrates as a whole, while at once uncovering new features of lamprey biology. (genomeweb.com)

Furthermore, genome data from non-pathogen lineages are necessary to provide a more robust comparative genomic framework to help place the rice blast fungus in an evolutionary context and to understand the evolution of pathogenesis and other characters of these important organisms. (nature.com)
The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms," senior author Weiming Li, with MSU's Department of Fisheries and Wildlife, and colleagues explained. (genomeweb.com)
image: Rochester researchers used fruit flies as model organisms to study Segregator Distorter (SD), a selfish genetic element that skews the rules of fair genetic transmission. (eurekalert.org)

We have examined methods and developed a general software tool for finding and analyzing combinations of transcription factor binding sites that occur relatively often in gene upstream regions (putative promoter regions) in the yeast genome. (aaai.org)
Next, all occurrences of the yeast transcription factor binding sites, as given in the IMD database, were located in the genome and in the selected regions in particular. (aaai.org)
Two types of NER exist: global genome (GG-NER) and transcription coupled (TC-NER). (medscape.com)

The genome of the SARS virus is a single strand of RNA that folds into regular repeating patterns to form secondary structures such as helices. (sciencedaily.com)
Together with data from existing genomes, patterns in the lamprey genome point to at least two whole-genome duplication events prior to the split between the lamprey lineage and the lineage leading to the jawed vertebrates, researchers noted. (genomeweb.com)
Patterns of activity for enhancer elements, they found, correlated strongly with patterns of expression for the nearest gene. (nih.gov)

The scientists assessed chromatin states across 9 different cell types by mapping the locations across the genome of several epigenetic modifications to DNA, such as methylation and acetylation. (nih.gov)

This element sits at one end of the viral genome, and, as the researchers show, its sequence is highly conserved in related coronaviruses. (sciencedaily.com)
This strong sequence conservation indicates that the tertiary structure of s2m could be important for viral function, and when the researchers solved the three-dimensional crystal structure of the element, they found that it had a unique tertiary structure. (sciencedaily.com)
Finding a similar 90° kink in a region of ribosomal RNA that binds factors necessary for the initiation of protein synthesis, the researchers speculate that the SARS virus may use the s2m element to hijack its host cell's protein synthesis machinery. (sciencedaily.com)
Genome Insider: Methane Makers in Yosemite's Lakes Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work. (doe.gov)
But with two projects, communities are forming to generate high quality genomes to benefit researchers. (doe.gov)
The Materials Genome Initiative invested $63 million into such efforts this year, fostering collaboration and data sharing among academic and private-sector materials science researchers, MIT said. (cleanenergyauthority.com)

Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. (mdpi.com)
Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of this species. (biomedcentral.com)
Two features of X. laevis that have hindered genetic studies are the long generation time (1 to 2 years) and the tetraploid genome of this species. (biomedcentral.com)
Barbara McClintock was awarded the Nobel prize for the discovery and study of these elements, which are now recognised as key contributors of genome evolution but also causing cancer and other genetic diseases if they proliferate uncontrolled. (unitn.eu)
Selfish genetic elements can wreak havoc by, for instance, distorting sex ratios, impairing fertility, causing harmful mutations, and even potentially causing population extinction. (eurekalert.org)
Males, however, transmit SD chromosomes to nearly 100 percent of their offspring, because SD kills any sperm that do not carry the selfish genetic element. (eurekalert.org)
The selfish genetic element gains a short-term transmission advantage by shutting down recombination to ensure it gets passed on to all of its offspring. (eurekalert.org)
The total genetic content is referred to as the genome. (cdc.gov)

With this new work, we now know that the evolution of soft-bodied cephalopods involved similarly massive genome changes, but the changes are not whole-genome duplications but rather immense genome rearrangements, as if the ancestral genomes were put in a blender. (scitechdaily.com)
Given the critical phylogenetic position of the lamprey as an outgroup to the gnathostomes," Li and colleagues explained, "comparing the lamprey genome to gnathostome genomes holds the promise of providing insights into the structure and gene content of the ancestral vertebrate genome. (genomeweb.com)

In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. (nature.com)
In many animals, gene order within the genome has been preserved over evolutionary time," Albertin said. (scitechdaily.com)

However, 3D genome evolution and its relationship with natural selection remains largely unexplored. (nature.com)
Tracing the Evolution of Shiitake Mushrooms Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. (doe.gov)
Key events in vertebrate evolution, leading to humans, include two rounds of whole-genome duplication," Ragsdale said. (scitechdaily.com)
NEW YORK (GenomeWeb News) - An international team led by investigators at the Michigan State University and the University of Kentucky have sequenced and assembled the genome of sea lamprey , Petromyzon marinus , using the sequence to begin refining their understanding of vertebrate evolution. (genomeweb.com)
Despite its potential for providing insights into vertebrate evolution, though, the lamprey genome had previously proven tough to sequence, authors of the current study explained, owing to the its extensive repetitive element content and the lack of a related reference sequence. (genomeweb.com)
Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. (inrae.fr)

S/MARs identified in present study and their subsequent analysis also suggests that these elements act as hotspots for integration of retroviruses. (researchgate.net)
The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome. (unitn.eu)
Cloud reduces the cost of genome analysis. (ibm.com)
This blog post focuses on GATK, a popular genome analysis toolkit with essential utilities and command lines for genome analysis. (ibm.com)
Users can write a WDL file consisting of multiple GATK commands so that they can reproduce or reuse genome analysis using Cromwell. (ibm.com)
From the perspective of computing infrastructure, a challenge of genome analysis is its data scale and required computation power. (ibm.com)
Another problematic scenario is that you may also need to run genome analysis on your "private" cloud to meet constraints of data location and privacy. (ibm.com)
Genome-Based Epidemiologic Analysis of VIM/IMP Carbapenemase-Producing Enterobacter spp. (cdc.gov)

A single genome file is generated as a 100 GB dataset, including errors and redundancy. (ibm.com)

Importantly, we present emerging approaches toward surveillance of pathogens and their resistance elements as well as promising treatment strategies that can circumvent common resistance mechanisms. (cdc.gov)

In functional assays, DR8 and IR0 elements act as independent RAREs, whereas DR0 does not. (nih.gov)
Scaffold/matrix attachment regions (S/MARs) are DNA elements that serve to compartmentalize the chromatin into structural and functional domains. (researchgate.net)
functional chromosomal elements and chromatin structure. (lu.se)

Many TEs proliferate through replicative mechanisms that enable exponential amplification and dispersal to new locations throughout their host genome. (nature.com)

The genome can be understood as the mapping of identity-functions to elements along the DNA molecule. (pitt.edu)

Furthermore, unlike the rest of the SARS genome, which changes rapidly, the s2m element is absolutely conserved in SARS variants obtained from patients during the SARS epidemic. (sciencedaily.com)
Those variants were predominantly Pseudomonas aeruginosa -derived In238-like elements, present with IncHI2+HI2A, IncFII+FIA, IncFIB, or IncN3 plasmids, or chromosomal genomic islands in 30 Enterobacter STs. (cdc.gov)

Our results reveal an unexpected diversity in the spacing and topology of binding elements for the RAR-RXR heterodimer. (nih.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)

More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. (syr.edu)

We need to pay carefull attention to such contaminations in genome data bases. (go.jp)
Therefore, these data will help toward better understanding of genome functioning and designing effective anti-viral therapeutics. (researchgate.net)
The Genome Center hopes to use large amounts of heterogeneous biological data to profile individuals much more closely and prescribe for each one a targeted and more personal treatment. (mckinsey.com)
Collaborators at the MSU Genomic Core sequenced lamprey RNA, meanwhile, generated transcriptome data that helped in annotating the newly sequenced genome. (genomeweb.com)

This DNA was identified as E. coli insertion element 5. (go.jp)
IS 6110 -based RFLP: This method detects variations in a specific section of the M. tuberculosis genome called insertion element IS 6110 . (cdc.gov)

Scott and colleagues used this approach to hypothesize that the function of the s2m element involves interaction with a conserved host factor during the SARS life cycle. (sciencedaily.com)
In general, herpesviruses do not have the ability to integrate into the host genomes since they do not have a chromosomal integration step in their life cycles. (pieronline.jp)
The M. phaseolina genome provides a framework of the infection process at the cytological and molecular level which uses a diverse arsenal of enzymatic and toxin tools to destroy the host plants. (biomedcentral.com)

Once the amount of heterochromatin is subtracted from total genome content, all mammals have very similar genome sizes. (wikipedia.org)
There is a lot of information packed into the four letters used to spell out the first dimension of the genome, but this is not even the tip of the iceberg of the total information content in the genome. (creation.com)

In this work we propose new computational and experimental strategies based on the physical principle of "perturb and measure" to understand the interplay of 3D genome organisation and dynamics TE integration. (unitn.eu)
Mobile DNA elements and the dynamics of genomes. (lu.se)

Further understanding of the M. phaseolina genome-based plant-pathogen interactions will be instrumental in designing rational strategies for disease control, essential to ensuring global agricultural crop production and security. (biomedcentral.com)

How the DNA encoding these selfish elements spreads within and between genomes is poorly understood, particularly in eukaryotes where inteins are scarce. (lu.se)

Each technology has strengths and limitations in its ability to detect different variations in the genome. (cdc.gov)
Other studies have examined variations across the entire genomes of many people (an approach called genome-wide association studies or GWAS) to determine whether any specific areas of the genome are associated with IQ. (medlineplus.gov)

In a related study (Schmidbaur et a l .), published last week, the team explored how the highly reorganized genome in Euprymna scolopes affects gene expression. (scitechdaily.com)

These elements take up a large part of plants genomes (up to 70% in maize) and also in humans. (unitn.eu)

Anatomy13

Organisms17

Diseases4

Chemicals and Drugs55

Analytical, Diagnostic and Therapeutic Techniques and Equipment33

Phenomena and Processes145

Disciplines and Occupations3

Technology, Industry, Agriculture3

Information Science13

Health Care1

Transposable19

Genes24

Sequences11

Mammalian4

Genomics9

Sequence of the human genome1

Sequencing19

Repetitive elements4

Large genomes1

Whole genomes1

Strains5

Bioinformatics1

Chromosome5

Human33

Eukaryotic1

Regulatory6

Transposons2

Biology3

Organisms3

Transcription3

Patterns3

Epigenetic1

Researchers6

Genetic8

Ancestral2

Evolutionary2

Evolution6

Analysis8

Dataset1

Approaches1

Functional3

Amplification1

Molecule1

Variants2

Diversity1

Encode1

Importantly1

Data4

Insertion element2

Host3

Content2

Dynamics2

Pathogen1

Understood1

Variations2

Gene expression1

Humans1