• sequences
  • DNA sequences called endogenous retroviruses (ERVs) are abundant in mammalian genomes. (icr.org)
  • Currently, reverse transcription followed by polymerase chain reaction (RT-PCR) with primers designed to amplify specific viral RNA sequences is the most common method for amplifying RNA viruses prior to sequencing and other downstream applications. (pubmedcentralcanada.ca)
  • The hearts were examined histologically and analyzed for the presence of viral sequences by polymerase chain reaction (PCR) or reverse transcription-PCR. (onlinejacc.org)
  • More than 80% complete draft genome sequences could be reconstructed for a total of 126 bacterial and 11 viral genomes. (blogspot.com)
  • The new features allow users to 1) add primer annotations or other data sets in batch mode, 2) export differences between sequences to other genome browsers, 3) compare multiple genomes at a single nucleotide level of detail, 4) create new alignments from subsets/subsequences of a very large master alignment and 5) allow display of summaries of deep RNA sequencing data sets on a genome sequence. (biomedcentral.com)
  • BBB-v2 significantly improves the ability of virologists to work with genome sequences and provides a platform with which they can use a multiple sequence alignment as the basis for their own editable documents. (biomedcentral.com)
  • The study provides definitive proof of a theory that was first proposed in the 1950s by Nobel Laureate in physiology and medicine, Barbara McClintock, who hypothesized that transposable elements, mobile pieces of the genetic material (DNA), such as viral sequences, could be "control elements" that affect gene regulation once inserted in the genome. (redorbit.com)
  • This by itself would be very surprising, but the investigators go further and demonstrate that many of the sites are imbedded within a class of DNA sequences called "transposable" elements because of their ability to move to new places in the genome. (redorbit.com)
  • Although they do not regularly integrate into the host genome, sequences from certain caulimoviruses, such as Petunia vein clearing virus and Banana streak virus have been found in host genomes. (wikipedia.org)
  • viruses
  • Evolutionists have long claimed that human chromosomes were infected with many different viruses over millions of years, which then multiplied in the genome. (icr.org)
  • Then evolutionists proclaimed the animal genomes evolved to their present state, in part by repeated infection with viruses initially deemed part of an organism's 'junk' DNA. (icr.org)
  • In particular, it was discovered that specific types of viruses that inserted themselves in the human genomes millions of years ago have dramatically changed the gene regulatory network in human stem cells. (redorbit.com)
  • This family contains all plant viruses that consist of a double-stranded DNA genome that has a reverse transcribing phase in its lifecycle. (wikipedia.org)
  • The genomes of viruses from this family contain monopartite, double-stranded DNA in either an open circular or linear structure. (wikipedia.org)
  • Viral Ecology and Disturbances: Impact of Environmental Disruption on the Viruses of Microorganisms. (wikipedia.org)
  • Quantitative Viral Ecology: Dynamics of Viruses and Their Microbial Hosts. (wikipedia.org)
  • Viruses that establish lifelong latent infections must ensure that the viral genome is maintained within the latently infected cell throughout the life of the host, yet at the same time must also be capable of avoiding elimination by the immune surveillance system especially must avoid being detected by host CD8+ cytotoxic T lymphocytes (CTLs). (wikipedia.org)
  • sequence
  • Students working in pairs or small groups receive a simulated virus: two paper cups taped together, enclosing a strip of paper listing an RNA or DNA sequence (an abbreviated viral genome). (asmscience.org)
  • However, traditional viral detection methods rely on prior sequence or antigen knowledge. (pubmedcentralcanada.ca)
  • In this study, we describe sequence-independent amplification for samples containing ultra-low amounts of viral RNA coupled with Illumina sequencing and de novo assembly optimized for viral genomes. (pubmedcentralcanada.ca)
  • The methods presented here are scalable to large numbers of samples and capable of generating full or near full length viral genomes from clone and clinical samples with low amounts of viral RNA, without prior sequence information and in the presence of substantial host contamination. (pubmedcentralcanada.ca)
  • Obtaining genomic sequence from such samples can provide valuable insights into viral attenuation, response to host immune pressure and drug treatment during infection, disease severity, transmission and epidemic spread. (pubmedcentralcanada.ca)
  • The original version of Base-By-Base (BBB) [ 1 ] was developed by the Virus Bioinformatics Resource Center primarily because of a need for a customizable, platform-independent (Java), multiple sequence alignment (MSA) editor that could be used for the comparison, annotation and analysis of viral genomes, and also integrated directly with our MySQL database. (biomedcentral.com)
  • We have endeavoured to make the tool intuitive and to add features that are useful to molecular biologists working daily with large viral genomes (up to 300 kb) that contain approximately 1 gene/kb of sequence. (biomedcentral.com)
  • This sequencing method and equipment were used to sequence the genome of the M13 bacteriophage. (wikipedia.org)
  • hepatitis C vir
  • An expanded taxonomy of hepatitis C virus genotype 6: Characterization of 22 new full-length viral genomes. (ox.ac.uk)
  • We characterized the full-length genomes of 22 hepatitis C virus genotype 6 (HCV-6) isolates: 10 from Vietnam (classified into subtypes 6e, 6h, 6p, 6r, 6s, and 6u), one from China (confirmed as a new subtype 6xd), and 11 from the Lao PDR (representing a new subtype 6xe plus eight novel variants). (ox.ac.uk)
  • Capsid
  • Some studies attribute this observation to selective pressure toward small genome sizes mediated by the physical constraints of packaging the genome in a viral capsid, particularly one of icosahedral geometry. (wikipedia.org)
  • genomic
  • 4 In brief, these elements are clearly part of the original created genomic blueprint for each creature and not the result of numerous viral infestations over eons of time. (icr.org)
  • As I and several other creationist researchers have proposed, it's far more likely that ERVs were part of God's original genomic blueprint for different kinds of animals and humans, and that external viral genomes were derived from human and animal ERVs only after God cursed the creation for man's sin. (icr.org)
  • double-stranded
  • Such DNA hairpin setup can be made in two ways: 1) In the case of double-stranded DNA molecules (for whole genome sequencing, or targeted sequencing), the DNA fragment is ligated to a DNA loop at one end and a DNA fork structure, labeled with biotin and digoxigenin at the two ends. (wikipedia.org)
  • gene
  • By comparing the genomes of mouse with human, the scientists were able to show that the binding sites for gene regulatory factors are very often not in the same place between the two species. (redorbit.com)
  • in most cases the overprinted gene is more phylogenetically restricted and is less likely to match the codon usage distribution found in the genome overall. (wikipedia.org)
  • antigens
  • The gamma-herpesviruses are characteristically latent in lymphocytes and drive the proliferation that requires the expression of latent viral antigens. (wikipedia.org)
  • evolutionary
  • In a recent article, I go into more detail about ERVs and why the evolutionary story is completely backwards when it comes to explaining their presence in the genome. (icr.org)
  • There are a number of such elements believed to be the evolutionary remnants of viral genomes, but it was very surprising to learn that they were carrying binding sites for regulatory elements to new locations. (redorbit.com)
  • bacterial
  • Only a few studies have reported the reconstruction of bacterial genomes from complex metagenomes. (blogspot.com)
  • In this work, Binning-Assembly approach has been proposed and demonstrated for the reconstruction of bacterial and viral genomes from 72 human gut metagenomic datasets. (blogspot.com)
  • A total 1156 bacterial genomes belonging to 219 bacterial families and, 279 viral genomes belonging to 84 viral families could be identified. (blogspot.com)
  • This approach along with spiking was also demonstrated to be useful in improving the draft assembly of a bacterial genome. (blogspot.com)
  • The Binning-Assembly approach can be successfully used to reconstruct bacterial and viral genomes from multiple metagenomic datasets obtained from similar environments. (blogspot.com)
  • humans
  • Very rare cases which require further investigation have been reported of paternal mitochondrial inheritance in humans, in which the father's mitochondrial genome is found in offspring. (wikipedia.org)
  • polymerase
  • The genome is detectable by reverse transcriptase-polymerase chain reaction in the head, thorax, abdomen and wings of infected bees. (wikipedia.org)
  • insight
  • Massively parallel sequencing allows for rapid and low-cost deep sequencing of viral genomes and provides an opportunity to gain greater insight into viral evolution, fitness, emergence and transmission. (pubmedcentralcanada.ca)
  • functional
  • This began a process of degeneration and corruption, yet His amazing handiwork is still seen in fully functional genomes. (icr.org)
  • Structure
  • With these 22 new genomes, HCV-6 now has a diverse and extended taxonomic structure, comprised of 28 assigned subtypes (denoted 6a-6xe) and 27 unassigned lineages, all of which have been represented by full-length genomes. (ox.ac.uk)
  • Instead, it appears that the main way that expression of viral transcripts is maintained at a lower level during latency is through chromatin structure. (wikipedia.org)
  • The 3' end of the TCV genome contains the hairpin H4, a T-shaped structure (TSS), which contains hairpins 4a, 4b and hairpin 5 and a promoter hairpin. (wikipedia.org)
  • detection
  • The aim of this study was to investigate the frequency of viral nucleic acid detection in the myocardium of human immunodeficiency virus (HIV)-infected children to determine whether an association exists with the development of heart disease. (onlinejacc.org)
  • promoter
  • Now if you drop a promoter anywhere in the genome, it has a good chance of promoting the transcription of some native DNA. (blogspot.fr)
  • Templates
  • Templates for photocopying the genomes, sample worksheets, and an instructor's answer key are included. (asmscience.org)
  • However, standard RT-PCR methods are not adequate for the generation of templates suitable for sequencing low-copy viral RNA samples, where labor-intensive methods such as nested PCR ( 15 ) or single-genome amplification (SGA) ( 16 , 17 ) are typically required. (pubmedcentralcanada.ca)
  • found
  • In molecular biology, Turnip crinkle virus (TCV) hairpin H4 is an RNA hairpin found at the 3' end of the Turnip crinkle virus (TCV) genome. (wikipedia.org)
  • cells
  • Dr Eddy Rubin, Director of the U.S. Department of Energy Joint Genome Institute and Director of the Genomics Division at Lawrence Berkeley National Laboratory in Berkeley added, "This study using a comparative genomics strategy discovered important human specific properties of the regulatory network in human ES cells. (redorbit.com)
  • Examples
  • Examples of low-copy viral RNA samples include the following: HIV controllers (capable of controlling the virus in the absence of antiretroviral therapy) ( 18 ), dengue virus (DENV) clinical samples collected after peak viremia ( 19 ), and West Nile virus (WNV) surveillance samples ( 20 ). (pubmedcentralcanada.ca)
  • inflammation
  • Early growth response-1 (EGR1) is a multifunctional transcription factor that regulates diverse biological functions, including inflammation, apoptosis, differentiation, tumorigenesis, and even viral infection. (sigmaaldrich.com)
  • Myocardial samples were obtained from the postmortem hearts of 32 HIV-infected children and from 32 age-matched controls consisting of patients with structural congenital heart disease and no myocardial inflammation and no cardiac or systemic viral infection. (onlinejacc.org)
  • immune
  • Now a new study shows many other ERVs across the genome play key roles in controlling immune responses, another important process necessary for the survival of mammals. (icr.org)
  • common
  • These data suggest that the presence of viral nucleic acid in the myocardium is common in HIV-infected children, and may relate to the development of myocarditis, DCM or CHF and may contribute to the rapid progression of HIV disease. (onlinejacc.org)
  • They are especially common in viral genomes. (wikipedia.org)