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 ...
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 ...
... 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. ...
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 ...
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 ...
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…
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. ...
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
This Application Note shows how the Dual luciferase assay can help to assess the Replication of the Hepatitis C Virus subgenomic replicon. Read more.
Kaposis sarcoma-associated herpesvirus (KSHV) is thought to be an oncogenic member of the γ-herpesvirus subfamily. The virus usually establishes latency upon infection as a default infection pattern. The viral genome replicates according to the host cell cycle by recruiting the host cellular replication machinery. Among the latently expressing viral factors, LANA seems to play pivotal roles in viral genome replication, partitioning, and maintenance. LANA binds with two LANA-binding sites (LBS1/2) within a terminal repeat sequence and is indispensable for viral genome replication in latency. The nuclear matrix region seems to be important as a replication site, since LANA as well as cellular replication factors accumulate there and recruit the viral replication origin in latency (ori-P) by its binding activity to LBS. KSHV ori-P consists of LBS followed by a 32 bp GC-rich segment (32GC). Although it has been reported that LANA recruits cellular pre-replication complexes (pre-RC) such as origin
Several metagenomic projects have been accomplished or are in progress. However, in most cases, it is not feasible to generate complete genomic assemblies of species from the metagenomic sequencing of a complex environment. Only a few studies have reported the reconstruction of bacterial genomes from complex metagenomes. 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. A total 1156 bacterial genomes belonging to 219 bacterial families and, 279 viral genomes belonging to 84 viral families could be identified. More than 80% complete draft genome sequences could be reconstructed for a total of 126 bacterial and 11 viral genomes. Selected draft assembled genomes could be validated with 99.8% accuracy using their ORFs. The study provides useful information on the assembly expected for a species given its number of reads and abundance. This approach along with spiking was also ...
We aim to determine how cells faithfully complete genome replication. Accurate and complete genome replication is essential for all life. A single DNA replication error in a single cell division can give rise to a genomic disorder. However, almost all experimental data are ensemble; collected from millions of cells. We used a combination of high-resolution, genomic-wide DNA replication data, mathematical modelling and single cell experiments to demonstrate that ensemble data mask the significant heterogeneity present within a cell population; see [1-4]. Therefore, the pattern of replication origin usage and dynamics of genome replication in individual cells remains largely unknown. We are now developing cutting-edge single molecule methods and allied mathematical models to determine the dynamics of genome replication at the DNA sequence level in normal and perturbed human cells.. [1] de Moura et al., 2010, Nucleic Acids Research, 38: 5623-5633. [2] Retkute et al, 2011, PRL, 107:068103. [3] ...
In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (Bacteriophage MS2). The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs.[7] The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research.. The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of ...
Chikungunya (CHIK-un-goon-ya) virus (also known as CHIKV) is a mosquito-transmitted alphavirus that has spread around the world and is currently infecting people in about 60 countries globally. CHIKV is rarely fatal, but causes severe joint pain for months to years that can debilitate affected patients for long periods of time. There are currently no known drugs to treat CHIKV infection, primarily due to a lack of understanding of the structure of CHIKV proteins involved in viral genome replication. The Geiss lab has worked on developing drug targeting the membrane bound CHIKV nsP1 protein, which is the anchor for the viral genome replication complex on cellular membranes and a multifunctional enzyme that forms a 5 RNA cap structure on the end of the CHIKV RNA genome. Solving the structure of the CHIKV nsP1 protein would provide critical information for designing drugs that inhibit nsP1 function and abort viral genome replication ...
The C11-13 strain from the Siberian subtype of tick-borne encephalitis virus (TBEV) was isolated from human brain using pig embryo kidney (PEK), 293, and Neuro-2a cells. Analysis of the complete viral genome of the C11-13 variants during six passages in these cells revealed that the cell-adapted C11-13 variants had multiple amino acid substitutions as compared to TBEV from human brain. Seven out of eight amino acids substitutions in the high-replicating C11-13(PEK) variant mapped to non-structural proteins; 13 out of 14 substitutions in the well-replicating C11-13(293) variant, and all four substitutions in the low-replicating C11-13(Neuro-2a) variant were also localized in non-structural proteins, predominantly in the NS2a (2), NS3 (6) and NS5 (3) proteins ...
The UAB investigators went on to molecularly clone and sequence the complete viral genomes from four individual chimpanzees. According to UAB post-doctoral researcher Brandon Keele, Ph.D., lead author of the report, this allowed for unprecedented genetic comparisons to be done between HIV-1 and its closest simian virus counterpart. He went on to say that finding this cluster of naturally infected chimpanzees will allow us to explore the natural history and behavior of SIVcpz in its natural host and help us begin to unravel how and why SIVcpz made the jump to humans ...
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). The students break open the cups (simulating viral uncoating in the host cell) and decide how host and/or viral enzymes will convert the genome into viral proteins and new genomes. The sequences provided describe a double-stranded DNA virus, single-stranded RNA viruses (+ or - strand), a retrovirus, and a double-stranded RNA virus. Templates for photocopying the genomes, sample worksheets, and an instructors answer key are included.
Sequencing RNA genomes was difficult in the 1980s, and cDNA cloning was just emerging. The first complete genome sequence of a coronavirus was for infectious bronchitis virus in 1987 (Boursnell et al., 1987) and a few years later it was completed for MHV (Lee et al., 1991). These genomes were assembled from many short cDNA clones and, when completed, indicated that the genome was ∼30 kb, significantly longer than had been estimated previously by sucrose gradient centrifugation, and that it was the longest of any known RNA virus. These sequences revealed two long open reading frames, ORF1a and 1b encoding 16 nonstructural proteins. It was also shown that both ORF1a and ORF1ab proteins were translated from genome RNA, and ORF1b via a translational frame shift at the end of ORF1a revealing new mechanisms of translational control (Bredenbeek et al., 1990). Alexander Gorbalenyas insightful analyses of the proteins encoded in ORFs1a and 1b revealed several protease and other enzymatic domains (for ...
Background New sequencing technologies possess opened up the true method towards the discovery as well as the characterization of pathogenic infections in scientific samples. in 1337532-29-2 supplier all full cases, our pre-processed technique improved genome set up, just its combination by using SPAdes allowed us to get the full-length from the viral genomes examined in a single contig. Conclusions The suggested pipeline can overcome drawbacks because of the era of chimeric reads through the amplification of viral RNA which significantly boosts the assembling of full-length viral genomes. Electronic supplementary materials The online edition of this content (doi:10.1186/s40659-016-0099-y) contains supplementary materials, which is open to certified users. and in 1983 from sp, a types owned by rodents (Gerbilinae), respectively, had been amplified by serial passing in the mind of new-born mice. After many passages, the brains were centrifuged and homogenized before a lyophilisation of every ...
Background New sequencing technologies possess opened up the true method towards the discovery as well as the characterization of pathogenic infections in scientific samples. in 1337532-29-2 supplier all full cases, our pre-processed technique improved genome set up, just its combination by using SPAdes allowed us to get the full-length from the viral genomes examined in a single contig. Conclusions The suggested pipeline can overcome drawbacks because of the era of chimeric reads through the amplification of viral RNA which significantly boosts the assembling of full-length viral genomes. Electronic supplementary materials The online edition of this content (doi:10.1186/s40659-016-0099-y) contains supplementary materials, which is open to certified users. and in 1983 from sp, a types owned by rodents (Gerbilinae), respectively, had been amplified by serial passing in the mind of new-born mice. After many passages, the brains were centrifuged and homogenized before a lyophilisation of every ...
Common plasmids are simple DNA molecules which contain a few genes and regulatory elements. Most viral genomes are more complex. For example, the genome of phage lambda contains approximately 50 genes. About 4,000 genes are present in the E. coli genome while there is approximately 1,000 times more DNA in the genome of a mammal. This progression in genome complexity is the topic of this exercise. Here, students compare the electrophoretic patterns of restriction digests of a plasmid, phage lambda DNA, and cow DNA from thymus and kidney as shown in the figure below. The exercise serves as a good introduction for determining the size of DNA molecules and provides an appreciation for the complexity of genomes from different organisms.. ...
The genes encoding the two major structural proteins and a putative NTPase belong to a cluster of five genes/ORFs (genes 3, 4 and 8; ORFs 6 and 7 of Halorubrum pleomorphic virus 1) that are collinear and conserved among members of the family Pleolipoviridae (Figure 2.Pleolipoviridae; (Senčilo et al., 2012). Pleolipoviruses have non-lytic life cycles. Although there is no direct evidence for the entry mechanism, it has been proposed that the entry of pleolipoviral genomes occurs by membrane fusion of the viral envelope with the host cell cytoplasmic membrane (Pietilä et al., 2009). Viruses are predicted to employ different genome replication strategies, including rolling circle replication (RCR; circular genomes) and protein-primed replication carried out by family B-type polymerase (linear genomes), although direct experimental evidence is missing (Pietilä et al., 2009, Roine et al., 2010, Bath et al., 2006). Viruses exit the cells continuously starting 3-4 hours post infection (Pietilä et ...
View Notes - Lecture 2 from PLB 40175 at UC Davis. PLB 113 Lecture 2 II. Genome Organization and Gene Expression A. Plants have big (and small genomes) B. Genomes consist of single (LOW) copy and