TY - BOOK. T1 - Viral genome replication. AU - Cameron, Craig Eugene. AU - Raney, Kevin D.. AU - Götte, Matthias. PY - 2009/1/1. Y1 - 2009/1/1. N2 - Provides the first comprehensive review of viral genome replication strategies, emphasizing not only pathways and regulation but also the structure-function, mechanism, and inhibition of proteins and enzymes required for this process Currently, there is no single source that permits comparison of the factors, elements, enzymes and/or mechanisms employed by different classes of viruses for genome replication. As a result, we (and our students) often restrict our focus to our particular system, missing out on the opportunity to define unifying themes in viral genome replication or benefit from the advances in other systems. For example, extraordinary biological and experimental paradigms that have been established over the past five years for the DNA replication systems of bacteriophage T4 and T7 will likely be of great value to anyone interested in ...
Read Analysis of the full-length genome sequence of papaya lethal yellowing virus (PLYV), determined by deep sequencing, confirms its classification in the genus Sobemovirus, Archives of Virology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
There was a thread on this less than a month ago on the bioperl list. CHeck their archives around Feb 14th for a thread titled: [Bioperl-l] Fetching genomic sequences based on HUGO names or GeneIDs There are example scripts and docs available for this kind of activity now via their wiki. hjm On Thursday 02 March 2006 10:45, Ryan Golhar wrote: , Thanks for all your responses, but maybe I need to clarify what Im , trying to do. I have a list of accession #s for genes. I want to get , the full-length genomic sequences (including exons and introns). , , I can get the chromosome and genomic coordinates using NCBIs eutils , efetch method, however Im not sure how to retrieve part of a sequence. , I dont see information on NCBIs eutils documentation and was wondering , if anyone here knew. , , In other words, say I have a gene that occurs on human chromosome 1. , The accession # of chr1 is NC_000001, and I have the genomic , coordinates, say 100 to 5000 on the positive strand. Without retrieving , ...
Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental
When viruses cross species, serial transmission may lead to the selection for mutations that confer improved replication or transmission in the new host. Identifying such mutations in human viruses is extremely difficult: we cannot conduct the appropriate experiments in humans, and often do not have viral isolates spanning the time from spillover through prolonged circulation. The 2013-2016 outbreak of Ebola virus in West Africa is unique because viral genome sequences were obtained early and throughout the epidemic. The results of two new studies (link to paper one, link to paper two) suggest that some of the observed mutations increase infectivity for human cells. The impact of these mutations on infection of humans, and their role in the West African outbreak, remain unknown.. Many mutations have been identified among the many hundreds of genome sequences obtained during the recent Ebola virus epidemic. One stands out: a mutation that leads to a single amino acid change in the viral ...
The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.
The role and relative importance of intrinsic and extrinsic factors in the development of complex diseases such as cancer still remains a controversial issue. Determining the amount of variation explained by these factors needs experimental data and statistical models. These models are nevertheless based on the occurrence and accumulation of random mutational events during stem cell division, thus rendering cancer development a stochastic outcome. We demonstrate that not only individual genome sequencing is uninformative in determining cancer risk, but also assigning a unique genome sequence to any given individual (healthy or affected) is not meaningful. Current whole-genome sequencing approaches are therefore unlikely to realize the promise of personalized medicine. In conclusion, since genome sequence differs from cell to cell and changes over time, it seems that determining the risk factor of complex diseases based on genome sequence is somewhat unrealistic, and therefore, the resulting data ...
Clearly, its time to develop a sophisticated global system to catalog viruses and detect emerging diseases throughout the world. One such system, now being proposed, would routinely screen human blood to identify every human virus and monitor any new viruses that may appear in humans. The viral genomes would be collected in a database called the human virome.. The proposal goes something like this: Scientists would collect blood from hospitals and labs weekly. Then they would extract viruses from it and sequence the viral genomes. Once a database of viruses is constructed, researchers could use it to screen for new viruses as they appear in the population.. Having a database of genome sequences could speed the characterization of emerging viruses. For instance, genomic information about coronaviruses, collected over many years, helped researchers identify the SARS genome in a matter of weeks. We want to know whats actually going around, and that is something that nobody knows, says ...
Landmarks of the HIV genome shows a graphical map of the genes and proteins of HIV-1, including the breakpoints on reference strain HXB2.
Our virulent BAC cloned MDV genome that generates a fully virulent virus will be passed in cell culture, which is known to attenuate the virus. At every 10 passages, the viral population will be used to challenge chickens to determine the amount of MD incidence. This will continue until the viral population is completely avirulent. Preceeding populations will have their viral genome purified and sequenced using next generation sequencers (e.g., Illumina GA or ABI SOLiD) to identify polymorphisms in the genome as well as the allele frequency. In addition, RNAs from the same sequenced populations will be sequenced, which when combined with the genomic sequence information, will confirm polymorphisms and reveal changes in viral gene transcription pattern. Following analysis, key genetic changes will be introduced into the virulent viral genome to address whether the polymorphisms do promote attenuation. ...
One of the more futuristic-sounding ideas for curing HIV involves removing the genome of the virus from the genome of the cells into which it has ...
TORONTO, June 15, 2015- Researchers sequence and assemble first full genome of a living organism using technology the size of smartphone.
Sequence analysis of the 3′ termini of RSV antigenome and genome RNA isolated from RSV infected cells.(A) Putative structures formed by the terminal sequences
The more we get to know about the past, the more obvious it becomes that old Darwinian assumptions have to be discarded. Many species seem to have resisted change for far longer than was thought. A good illustration of this is in a paper recently published in the journal Nature that reports on the full genome sequence of an ancient horse ...
Does anyone have any informations on the positive and negative regulation of HIV genome? I would greatly appreciate any informations send to ptran at po-box.mcgill.ca thank ...
The construct was inserted on the minus strand of the genome. The gene in which ... The construct was inserted on the minus strand of the genome. The gene in which the insertion occurred is also on the minus strand. ...
Kaposi sarcoma is a tumor caused by Kaposi sarcoma herpesvirus (KSHV) infection and is thought to originate from lymphatic endothelial cells (LEC). While KSHV establishes latency in virtually all susceptible cell types, LECs support spontaneous expression of oncogenic lytic genes, high viral genome copies, and release of infectious virus. It remains unknown the contribution of spontaneous virus production to the expansion of KSHV-infected tumor cells and the cellular factors that render the lymphatic environment unique to KSHV life cycle. We show here that expansion of the infected cell population, observed in LECs, but not in blood endothelial cells, is dependent on the spontaneous virus production from infected LECs. The drivers of lymphatic endothelium development, SOX18 and PROX1, regulated different steps of the KSHV life cycle. SOX18 enhanced the number of intracellular viral genome copies and bound to the viral origins of replication. Genetic depletion or chemical inhibition of SOX18 ...
In this communication, we report a novel strategy for the genetic manipulation of large viral DNA genomes. In a single step we cloned an infectious cytomegalovirus DNA as a bacterial artificial chromosome in E. coli and reconstituted virus progeny after transfection of the BAC plasmid into eukaryotic cells. This approach makes the CMV genome accessible to the genetic techniques established for E. coli. As an example for the power of the mutagenesis procedures, we performed a targeted insertion of four nucleotides into the 230-kb MCMV genome. In principle, any mutation (point mutations, insertions, and deletions) in any region of the genome can now be introduced using the described mutagenesis procedure. Moreover, other procedures, for example a random transposon mutagenesis of the CMV genome are conceivable. Multiple mutations can be introduced in consecutive rounds of mutagenesis without the need to reconstitute infectious viral intermediates. Construction of revertant genomes can be easily ...
387440791 - EP 0832191 A4 2000-11-15 - RECOMBINANT VIRAL NUCLEIC ACIDS - [origin: WO9640867A1] The present invention relates to a recombinant viral nucleic acid selected from a (+) sense, single stranded RNA virus possessing a native subgenomic promoter encoding for a first viral subgenomic promoter, a nucleic acid sequence that codes for a viral coat protein whose transcription is regulated by the first viral subgenomic promoter, a second viral subgenomic promoter and a second nucleic acid sequence whose transcription is regulated by the second viral subgenomic promoter. The first and second viral subgenomic promoters of the recombinant viral nucleic acid do not have homologous sequences relative to each other. The recombinant viral nucleic acid provides the particular advantage that it systematically transcribes the second nucleic acid in the host. Host organisms encompassed by the present invention include procaryotes and eucaryotes, particularly animals and plants. The present invention also relates
The construction of cDNA clones encoding large-size RNA molecules of biological interest, like coronavirus genomes, which are among the largest mature RNA molecules known to biology, has been hampered by the instability of those cDNAs in bacteria. Herein, we show that the application of two strategi …
Given a recent increase in the number of bacteriophage genome sequenced- Nathan ( @NathanMB3) has updated the all-v-all comparison with more genomes (~5500 in total).Image at bottom of page. After reading the recent paper MASH:fast genome and metagenome distance and estimation using MinHash and meeting Nathan Brown at the University of Leicester, we discussed using MASH for identification of phage genomes and comparison thereof. The authors of the genome biology paper had included viruses in the microbial comparison in Figure 3 . Here we just focused on bacteriophage genomes.. For rapid identification of phage genomes we first constructed a database of phage genomes that were public. This included all phage genomes from the NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/all.fna.tar.gz) , which were then filtered to remove eukaryotic viruses. In addition phage genomes were collected from the phagesdb.org website. A sketch was made for all of these phages and collated, the mash database of ...
Generation of wt genomes by excision of the BAC vector from the MCMV BAC genome.After transfection of the MCMV BAC plasmid into eukaryotic cells we expected homologous recombination via the duplicated sequences leading to excision of the vector sequences and generation of a wt genome (see Fig. 2 and Fig. 3A, maps 4 and 5). During construction of the original MCMV BAC plasmid pSM3 we had observed that overlength genomes are not stable in cells (22), suggesting that overlength genomes are poorly packaged into viral capsids. Similar observations have been made for other DNA viruses. An overlength of more than 5% over the adenovirus wt genome leads to unstable genomes (2), and Epstein-Barr virus preferentially packages genomes within a very narrow size range (3). Thus, we expected that even when rare recombination events occur at the created target site, preferential packaging of unit length genomes should lead to an accumulation of viruses with the wt genome.. For reconstitution of virus progeny ...
Adeno-associated virus 2 ATCC ® 37215™ Designation: pAV1 TypeStrain=False Application: Contains the complete viral genome for use in site-specific mutagenesis.
Adeno-associated virus 2 ATCC ® 37215™ Designation: pAV1 TypeStrain=False Application: Contains the complete viral genome for use in site-specific mutagenesis.
Read Complete genomic sequence of a Tobacco rattle virus isolate from Michigan-grown potatoes, Archives of Virology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Hi all, I am looking for a way or a tool to map all the GC rich (of given percentage say, 60% or 70% GC) short stretches of nucleotides anywhere between 20-80 base pairs in Bacteriophage T4 and other Phage genomes.I could not find such a tool at NCBI website. I highly appreciate your help. Thank you so much Kiran ...
The study analysed data from the first wave of the pandemic at Addenbrookes, between March and June 2020.. Researchers identified five wards where multiple individuals, including patients and healthcare workers, tested positive for Covid-19 within a short space of time, suggesting a local outbreak.. Using new statistical methods that combines viral genome sequence with clinical information about the locations of individuals, researchers identified cases where the data was consistent with transmission between people in the hospital. Looking in detail at these transmission events revealed patterns in the data.. The results of the study showed that patients who were infected in the hospital were mostly infected by other patients, rather than by hospital staff. Out of 22 cases where patients were infected in hospital, 20 of these were the result of the virus spreading from patients to other patients. ...
Plays a role in viral genome replication by driving entry of quiescent cells into the cell cycle. Stimulation of progression from G1 to S phase allows the virus to efficiently use the cellular DNA replicating machinery to achieve viral genome replication. E7 protein has both transforming and trans-activating activities. Induces the disassembly of the E2F1 transcription factor from RB1, with subsequent transcriptional activation of E2F1-regulated S-phase genes. Interferes with host histone deacetylation mediated by HDAC1 and HDAC2, leading to transcription activation. Plays also a role in the inhibition of both antiviral and antiproliferative functions of host interferon alpha. Interaction with host TMEM173/STING impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta ...
VIROME: Goal is to characterize the whole viral population. (Lambda control gave quantitative recovery.) 10^10 phage per gram of stool! Circular contigs (genomes?) all about 5-6 kb. Linear ones very diverse lengths. 7000 new virus genomes! 19-785 per individual sample. Lots of unknown! No contigs of eukaryotic viruses at all, but bits of eukaryotic viral genomes in phage genomes. He thinks there has been lots of misidentification - what appears to be DNA indicating presence of a eukaryotic virus is really jsut a bit of phage genome. See CRISPR system used to compete with other phage (I forget what CRISPR does ...
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. (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. As I and several other creationist researchers have proposed, its far more likely that ERVs were part of Gods 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 mans sin. This began a process of degeneration and corruption, yet His amazing handiwork is still seen in fully functional genomes ...
The basic concepts central to understanding virus reverse genetics and molecular clones are summarized in Figures 1 and 2. The central idea is that the virion is an extracellular vehicle that transfers the viral genome (e.g., RNA or DNA genomes) between susceptible cells and protects the nucleic acid genome from degradation in the environment (Figure 2, Part A). Following entry, the viral genome is programmed to initiate a series of events that result in the production of a replicase complex that transcribes mRNA and replicates the genome. As discussed in the previous section, nucleic acid structure and organization determines the pathway of events needed to express mRNA and initiate virus gene expression and infection. Not all viruses, however, require virion attachment and entry to mediate a productive infection. In these cases, viral genomes can be isolated from virions and transfected directly into susceptible hosts cells. If the genome is infectious, viral RNAs and proteins will be ...
This is an application for renewal of a grant to study picornavirus genome replication. All positive-strand RNA viruses hijack and/or remodel host membranes to...
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Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
Zalckvar, E., C. Paulus, D. Tillo, A. Asbach-Nitzsche, Y. Lubling, iv, C. Winterling, N. Strieder, K. Mücke, F. Goodrum, E. Segal, et al., Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein., Proc Natl Acad Sci U S A, vol. 110, issue 32, pp. 13126-31, 2013 Aug 6. PMCID: PMC3740854 PMID: 23878222 ...
Using Beagle, one of the fastest supercomputers devoted to life sciences, the complete genome analysis can be radically accelerated, a new study reveals.
Two newly discovered giant viruses are bigger than many bacteria and carry massive and largely unique genomes that hint at new branches of life.
Replication in P2P architectures No proactive replication (Gnutella) - Hosts store and serve only what they requested - A copy can be found only by probing a host with a copy Proactive replication of
Today I was looking at ScienceDaily.com and found 3 really exciting developments. Bound to change medicine and our lives forever. Cancer detection, full genome sequencing on a small budget and fixing the broken Fixer responsible for the bad effects of Aging. Cancer Detection In the early 70s President Nixon launched the War On Cancer. While…
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Putative novel papillomavirus genome with complete genome sequence data available and that is ,70% related to papillomaviruses within the genus.. ...
One view of evolution is that it is a process by which simple organisms become more complex. The simplicity of many viruses lead to their placement at the origin of life. This long-standing hypothesis ignores the fact that viral genomes are subject to selective pressure to maintain minimal size to ensure rapid replication rates. The authors conclude that viral simplicity is a consequence of parasitism, not antiquity.. Even though viruses are not living and should not be included in the tree of life, they play an important role in evolution of their cellular hosts by regulating population and biodiversity.. Are you convinced by these arguments? Post a comment and let us know whether you think viruses or living or not.. Moreira, D., & López-García, P. (2009). Ten reasons to exclude viruses from the tree of life Nature Reviews Microbiology, 7 (4), 306-311 DOI: 10.1038/nrmicro2108. ...
We each begin life with a unique genome. As we grow and develop, we are each subjected to a range of factors that influence the way development proceeds. Most of those factors are common to us all, the intracellular and intercellular signals, hormones, birth, milk. But the precise combination and the range and duration of those factors varies between individuals, such as the duration of gestation or the composition and quantity of a mothers milk, for example. In addition we each undergo diff ...
We each begin life with a unique genome. As we grow and develop, we are each subjected to a range of factors that influence the way development proceeds. Most of those factors are common to us all, the intracellular and intercellular signals, hormones, birth, milk. But the precise combination and the range and duration of those factors varies between individuals, such as the duration of gestation or the composition and quantity of a mothers milk, for example. In addition we each undergo diff ...
In a breakthrough that experts say will help feed the growing global population in the coming decades, scientists Thursday revealed they have cracked the f
When DNA is used as the starting template, nanogram amounts of cloned template, up to microgram amounts of genomic DNA, or up to 20,000 target copies can be a good starting point for optimization. However, even very low levels of sample (i.e., mRNA from tens of cells, DNA from single cells or individual viral genomes) may be sufficient for PCR amplification ...
Flagship action for the treatment of SARS-COV-2 virus. Epidemiological study in Greece through extensive testing for virus and antibodies for viral genome sequencing and genetic analysis of patients - Εμβληματική δράση για την αντιμετώπιση του ιού SARS-COV-2. Επιδημιολογική μελέτη στην Ελλάδα μέσω εκτεταμένων εξετάσεων ανίχνευσης ιού και αντισωμάτων αλληλούχισης ιικών γονιδιωμάτων και γενετικής ανάλυσης ασθενών - SarsCOV2 ...
There is a lot we still have to learn about SARS-CoV-2 and the disease it causes in humans. One aspect of the virus that we do know a lot about is its underlying molecular blueprint. We have the core viral genome, and broadly speaking we know the parts list of proteins that are translated and…
Hanta Virus- Structure, Genome, Epidemiology, Transmission, Replication, Pathogenesis, Clinical Manifestation, Lab Diagnosis, Treatment, Prevention, Control
Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells. . ...