Evolution of the hepatitis E virus hypervariable region. (ox.ac.uk)
The presence of a hypervariable (HVR) region within the genome of hepatitis E virus (HEV) remains unexplained. (ox.ac.uk)
HVR16
HVR1 is considered a "low resolution" region and HVR2 is considered a "high resolution" region. (wikipedia.org)
5'-untranslated region (5'UTR), the hypervariable region 1 (HVR1), non-structural gene 5a (NS5a) and non-structural gene 5b (NS5b). (cdc.gov)
Analysis of 2179 clonal sequences derived from hypervariable region 1 (HVR1) of the HCV genome in samples obtained from patients with acute (n = 49) and chronic (n = 102) HCV infection showed that intra-host HVR1 diversity was 1.8 times higher in patients with chronic than acute infection. (iospress.com)
This is accomplished in humans by sequencing one or more of the hypervariable control regions (HVR1 or HVR2) of the mitochondrial DNA. (dadamo.com)
Comparison of the hexon gene sequences of simian adenovirus types identified in this study with human and simian adenovirus sequences from GenBank revealed 9 previously reported hypervariable regions (HVRs): HVR1-HVR9 ( 5 , 7 ). (cdc.gov)
Using a series of diverse virology and computational methods, as well as molecular dynamics simulations for conformational mobility, the researchers showed that hypervariable region 1 (HVR1) acts as a "safety catch" that regulates entry. (who.int)
RRNA gene3
Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. (frontiersin.org)
For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. (asm.org)
Unlike previous studies that have reported shared microbes between mothers and infants, the new work includes a full-length analysis of all 9 hypervariable regions in the 16s rRNA gene. (eurekalert.org)
Sequences10
Others have proposed that the region has no function, that it reflects a hypermutable region of the virus genome, that it is derived from the insertion and evolution of host sequences or that it is subject to positive selection. (ox.ac.uk)
Through an analysis of published sequences, we conclude that the range of HVR diversity observed within virus genotypes can be explained by the accumulation of substitutions and, to a much lesser extent, through deletions or duplications of this region. (ox.ac.uk)
What you can do now, is align all of your sequences and the rCRS together and see if you can infer where the hypervariable regions fall in your target sequences. (stackexchange.com)
Since, presumably, the rest of the sequence will be more conserved since it isn't hypervariable, you should be able to identify the syntenic blocks and locate the hypervariable regions in your sequences. (stackexchange.com)
I would expect to see a very high level of sequence identity in the non-hypervariable regions across all of your sequences (since they're all human mitochondria), so you should be able to find the hypervariable ones as the regions of low sequence similarity which also coincide with the known coordinates of the rCRS. (stackexchange.com)
Whereas virus sequences in the infectious source were relatively homogeneous, distinct HVR variants were observed in each anti-D recipient, indicating that this region can evolve in multiple directions from the same point. (ox.ac.uk)
Where HVR variants with dissimilar sequences were present in a single individual, the frequency of synonymous substitution in the flanking regions suggested that the lineages diverged more than a decade previously. (ox.ac.uk)
Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. (frontiersin.org)
These regions, termed hypervariable, are typically based on repeat sequences in the DNA. (wikisummaries.org)
Short sequences of amino acids found on the antibody variable region that collectively form the paratope. (stratech.co.uk)
Antibodies6
In antibodies, hypervariable regions form the antigen-binding site and are found on both light and heavy chains. (wikipedia.org)
Antibodies are remarkably specific, thanks to hypervariable regions in both light and heavy chains. (wikipedia.org)
Further defining the functional significance of these regions may have important implications for genotype 3a E2 virus-receptor interactions and for vaccine studies that aim to induce cross-reactive anti-E2 antibodies. (lonelyjoeparker.com)
The hypervariable region (HVR) of the VP2 protein [VP2(HVR)] elicits neutralising antibodies. (upm.edu.my)
Antibodies are heavy (~150 k Da ) proteins of about 10 nm in size, [7] arranged in three globular regions that roughly form a Y shape. (wikipedia.org)
The antigenic determinant created by the hypervariable regions (paratope) of the individual antibodies. (stratech.co.uk)
Mitochondrial DNA6
A hypervariable region (HVR) is a location within nuclear DNA or the D-loop of mitochondrial DNA in which base pairs of nucleotides repeat (in the case of nuclear DNA) or have substitutions (in the case of mitochondrial DNA). (wikipedia.org)
citation needed] Cambridge Reference Sequence Genealogical DNA test Human mitochondrial DNA haplogroup mtDNA control region van Oven M, Kayser M (February 2009). (wikipedia.org)
Iguchi, Kei-ichiro & Nishida, Mutsumi (2005): Unexpected Ceiling of Genetic Differentiation in the Control Region of the Mitochondrial DNA between Different Subspecies of the Ayu Plecoglossus altivelis. (wikipedia.org)
How to extract hypervariable region of mitochondrial dna from its fasta file? (stackexchange.com)
Recently I've done some analysis on human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed are linked to only hypervariable regions. (stackexchange.com)
A visual of the mitochondrial DNA molecule shows where the DNA gets analyzed by forensic geneticists, the hypervariable regions 1 and 2. (bartleby.com)
Genes5
In this study, V1-V3 hyper variable regions from 16S rRNA genes of some known bacteria is taken from the work of A. Cosic. (edu.ba)
However, functional annotation of population-differentiating genomic regions revealed numerous genes involved in host invasion, toxin production, and secondary metabolism, and implicated plant hosts, microbial competitors, and temperature and light as major drivers of adaptive divergence. (usda.gov)
Human chromosome 15q11-q13 is a critical region for Prader-Willi syndrome (PWS) and Angelman syndrome (AS) and most of the genes are under the condition of imprinting mechanism. (researchgate.net)
However, there was no real evidence for this link other than some genetic association studies with genes in this hypervariable region of chromosome 6. (medscape.com)
Gene3
Selected positive samples underwent sequencing analysis targeting the second hypervariable region of the G gene using next-generation sequencing. (who.int)
However, we did not find the 72-nucleotide duplication in the second hypervariable region of the G gene, a characteristic of genotype ON1, in any RSV-A samples. (who.int)
They described a large, genome-wide association (GWA) study of a huge number of subjects in whom they found a strong association between schizophrenia and a gene on the HLA region of chromosome 6 that codes for complement 4 (C4) protein. (medscape.com)
Amplification1
Hepatitis C RNA: Testing for HCV RNA by reverse-transcriptase ¬polymerase-chain reaction (RT-PCR) amplification of the 5' noncoding region was performed on anti-HCV positive samples. (cdc.gov)
RDNA1
The next-generation sequencing technology was used to determine the V2-V4 hypervariable regions of 16S rDNA to investigate the microbiome on the tongue coating. (spandidos-publications.com)
HVR21
Another variable region of E2 centered on codon 60 shows similar constraints, while HVR2 was relatively unconstrained. (ox.ac.uk)
Repeats2
Changes or repeats in the hypervariable region are highly polymorphic. (wikipedia.org)
For example, one copy of a specific short tandem repeat (STR) region might have 10 repeats, while the other copy might have 11 repeats. (ojp.gov)
MtDNA2
In addition, certain regions of the mtDNA are useful for ancestry research. (easydna.co.uk)
Currently, an "mtDNA type" refers to the sequence within hypervariable regions I and II (HV1/HV2) of the control region, approximately 610 bp. (nih.gov)
Antigenic1
Within each antigenic site, the variable region of the antibody "arm" interacts through weak noncovalent forces with antigen at numerous sites. (sigmaaldrich.com)
Segment1
We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. (nih.gov)
Enzyme1
Non-coding regions of DNA containing a restriction site for the enzyme Alu 1. (ojp.gov)
Sequence2
In the Ayu (Plecoglossus altivelis), an East Asian protacanthopterygian, control region mutation rate is not markedly lowered, but sequence differences between subspecies are far lower in the control region than elsewhere. (wikipedia.org)
You can use Mitomap to get the coordinates of the hypervariable regions in the rCRS mitochondrial sequence (the standard MT sequence in the field). (stackexchange.com)
Molecule6
Part of the antibody molecule produced using papain to cleave above the hinge region, comprising one constant domain and one variable domain of each of a heavy and light chain. (stratech.co.uk)
Part of the antibody molecule produced using pepsin to cleave below the hinge region, comprising two Fab Fragments joined by disulfide bonds. (stratech.co.uk)
Figure 3: F(ab')2 Fragments are produced by pepsin digestion which cleaves the Fragment from the Fc region retaining a bridging disulfide bond interconnecting two Fab arms making the molecule bivalent. (stratech.co.uk)
Part of the antibody molecule produced using papain to cleave above the hinge region, comprising the CH2 and CH3 domains in the case of IgG. (stratech.co.uk)
The larger of the two types of polypeptide chain that make up an antibody molecule, comprising a constant region with three (IgA, IgG, and IgD) or four (IgM and IgE) constant domains and a variable region. (stratech.co.uk)
The combining site of an antibody is located in the F(ab) portion of the antibody molecule and is assembled from the hypervariable regions of the heavy and light chains. (sigmaaldrich.com)
Antibody3
The constant region at the trunk of the antibody includes sites involved in interactions with other components of the immune system. (wikipedia.org)
Distinct sections of the antibody constant region. (stratech.co.uk)
The region on an antigen that is recognized by an antibody. (stratech.co.uk)
Microbiome1
In a previous article, the accuracy of the program is also tested when it is applied to common PCR products of the 16S rRNA variable regions, which are the only product of laboratories in microbiome projects. (edu.ba)
Analysis1
R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies. (nih.gov)
Membrane2
The map showed regions in the membrane where the Ras molecules had stopped and possibly clustered together. (elifesciences.org)
Mechanistically, intracellular mature IL-37 directly bound to the CAAX motif in the C-terminal hypervariable region of Rac1, and then inhibited Rac1 membrane translocation and subsequent downstream signaling. (nature.com)
Amino acid1
In a preferred embodiment, a GEF-H1 polypeptide is provided that lacks the amino acid region between residues 162 and 354 of SEQ ID NO. 2. (justia.com)
Chains1
The heavy and light chains are divided into a variable (V) region and a constant (C) region. (msdmanuals.com)
Mutations1
Furthermore, we developed a targeted ultra-deep sequencing approach to assess the dynamics of clinically relevant mutations in the RdRp-region and to detect insertions in the HVR-domain in the HEV genomes. (nature.com)
Genetic1
In addition, each population had unique genetic signatures of adaptive selection that were largely focused in hypervariable regions of chromosomes. (usda.gov)
Genome2
It is a hepatotropic, approximately 7.2 kb single-stranded positive-sense RNA virus whose genome contains three open reading frames (ORF1, ORF2, and ORF3), 5′ and 3′ untranslated regions (UTRs), and a poly(A) tract at the 3′ end. (nature.com)
The initial PCR reaction amplifies a region of the HCV genome (External primers). (cdc.gov)
Evolution3
Long-term evolution of the hypervariable region of hepatitis C virus in a common-source-infected cohort. (ox.ac.uk)
The long-term evolution of the hepatitis C virus hypervariable region (HVR) and flanking regions of the E1 and E2 envelope proteins have been studied in a cohort of women infected from a common source of anti-D immunoglobulin. (ox.ac.uk)
This hypervariable region may have arisen through accelerated evolution as a result of selective pressures from host enzymes on parasite inhibitors. (usda.gov)
Found2
actually, I read about it and found out that hypervariable regions(HVR) 1,2, 3 have target coordinates and I suppose they will differ in each of my files downloaded from GenBank and when I checked, there was no such information in GenBank regarding that. (stackexchange.com)
Structural components of the variable domain, found between the complementary determining regions (CDRs). (stratech.co.uk)
Determine2
These 440 base pairs are then compared to the control regions of other individuals (either specific people or subjects in a database) to determine maternal lineage. (dadamo.com)
Within the V regions, hypervariable regions determine the specificity of the immunoglobulin (Ig). (msdmanuals.com)
Individuals1
The solution to this problem is to focus only on the small regions of the DNA which are known to vary widely among individuals. (wikisummaries.org)
Human4
There are two mitochondrial hypervariable regions used in human mitochondrial genealogical DNA testing. (wikipedia.org)
Using this new approach, we not only identified several insertions of human (AHNAK, RPL18) and viral origin (RdRp-derived) in the HVR-region isolated from an exemplary sample but detected a variant containing two different insertions simultaneously (AHNAK- and RdRp-derived). (nature.com)
This algorithm works on both human oral/nasal and non-oral/non-nasal samples and are independent of sequenced regions (Al-Hebshi et al, 2015). (forsyth.org)
2014 ) Sequencing human mitochondrial hypervariable region II as a molecular fingerprint for environmental waters. (academictree.org)
The hyperbariable regions for the antigen-binding site. (wikipedia.org)
A hypervariable region exists within the reactive site of the three isoforms, which accounts for most of the lack of complete identity. (usda.gov)
High1
METHODS: Golestan Cohort Study (GCS) has been conducted since 2004 in a region with high rates of esophageal squamous cell carcinoma (ESCC). (cdc.gov)
Major1
The mtDNAs belonging to R0 (approximately 57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. (nih.gov)
Frequency1
When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. (nih.gov)