SEARCH · PubMed Health

Results for “genome segmentation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources

PubMed1984

A transcriptionally active monkey genomic segment homologous to the regulatory region of simian virus 40 is associated with DNase I-hypersensitive sites.

Segments of monkey genomic DNA that are homologous to the control region around the origin of replication of simian virus 40 were previously cloned and characterized (Queen et al., Mol. Cell Biol. 1:1061-1068, 1981). We describe here two DNase I-hypersensitive sites that map in the region of monkey chromatin around one such ori-like segment. One of these sites lies within the simian virus 40 homologous segment which is also a site from which transcription initiates bidirectionally (J. Saffer and M. Singer, submitted for publication).

Animals↗

PubMed1990

Expression in Escherichia coli of the large genomic segment of infectious pancreatic necrosis virus.

A complete cDNA clone of the larger A segment of the genome of infectious pancreatic necrosis virus (IPNV) was expressed in Escherichia coli in an effort to develop a vaccine for IPNV in fish. When the cDNA insert was positioned in the correct orientation to the pUC19 lacZ promoter, the viral proteins VP2, NS, and VP3 were synthesized and processed as observed in infected cells. When the insert was placed in the opposite orientation, VP3 and a 38-kDa virus-specific polypeptide were also synthesized. In addition, specific deletions made from the 3' end into the NS gene of the cloned A segment led to inactivation of the NS proteolytic activity and subsequently, the synthesis of an unprocessed VP2-NS polyprotein precursor. Antiserum to this polyprotein distinguished NS (28.5 kDa) from VP3 (31 kDa) and led to the identification of a previously undescribed 38-kDa virus-specific polypeptide in infected cells. Thus, both internal translational initiation and proteolytic cleavage could lead to the synthesis of VP2, NS, and VP3 from a single mRNA with a single open reading frame. A trpE expression vector, pATH2, was used to synthesize large quantities of the A-segment-encoded proteins in bacteria. The resulting bacterial lysate was very effective in inducing protective immunity in rainbow trout fry.

Animals↗

PubMed2001

Nucleotide sequence of genome segment 5 from Bombyx mori cypovirus 1.

The complete nucleotide sequences of the double-stranded RNA genome segments 5 (S5) from Bombyx mori cypovirus 1 (BmCPV-1) strains I and H were determined. The segments consisted of 2,852 nucleotides encoding putative proteins of 881 amino acids with molecular masses of approximately 101 kDa (p101). A homology search showed that p101 has high similarity (93%) to foot-and-mouth disease virus (FMDV) 2A protease (2Apro) at amino acid position 219 to 235. These findings suggest the possibility that p101 encoded by BmCPV-1 S5 might be cleaved into two non-structural proteins by post-translational autocleavage involving a 2Apro-like protease.

Amino Acid Sequence↗

PubMed1996

Genome segment 5 of rice ragged stunt virus encodes a virion protein.

The complete nucleotide sequence of the genome segment 5 (S5) of a Thai isolate of rice ragged stunt virus (RRSV) was determined. The 2682 nucleotide sequence contains a single long open reading frame capable of encoding a polypeptide with a molecular mass of approximately 91 kDa. Polypeptides encoded by various truncated cDNAs of S5 were expressed using the pGEX fusion protein vector and the highest level of fusion protein was obtained from a construct encoding a hydrophilic region of S5 protein. Antibodies raised against this fusion protein recognized a minor polypeptide, with a molecular mass of approximately 91 kDa, that was present in purified preparations of RRSV particles, infected insect vectors and infected rice plants. This indicates that RRSV S5 encodes a minor structural protein. Comparing the RRSV S5 sequence with sequences of other reoviruses did not reveal any significant sequence similarities.

Amino Acid Sequence↗

PubMed1988

Sequence of the small double-stranded RNA genomic segment of infectious bursal disease virus and its deduced 90-kDa product.

The smaller dsRNA segment of the genome of infectious bursal disease virus (IBDV) encodes a single polypeptide of approximately 90 kDa (VP1). The consensus nucleotide sequence, derived from independent and overlapping cDNA clones, contains a single open reading frame which begins with an exact Kozak sequence and could encode a polypeptide of 878 amino acid residues. It has been suggested that VP1 could be the viral RNA-dependent RNA polymerase. A comparison of the predicted amino acid sequence of this protein with those of other DNA-dependent and ssRNA-dependent RNA polymerases has failed to reveal any homology between VP1 and the conserved regions in these enzymes. It is possible that the polypeptide encoded by the IBDV virus may represent a new class of polymerases which are involved in the replication of double-stranded RNA genomes.

Amino Acid Sequence↗

PubMed2003

Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical SLA class I gene clusters.

Genome analysis of the swine leukocyte antigen ( SLA) region is needed to obtain information on the MHC genomic sequence similarities and differences between the swine and human, given the possible use of swine organs for xenotransplantation. Here, the genomic sequences of a 433-kb segment located between the non-classical and classical SLA class I gene clusters were determined and analyzed for gene organization and contents of repetitive sequences. The genomic organization and diversity of this swine non-class I gene region was compared with the orthologous region of the human leukocyte antigen ( HLA) complex. The length of the fully sequenced SLA genomic segment was 433 kb compared with 595 kb in the corresponding HLA class I region. This 162-kb difference in size between the swine and human genomic segments can be explained by indel activity, and the greater variety and density of repetitive sequences within the human MHC. Twenty-one swine genes with strong sequence similarity to the corresponding human genes were identified, with the gene order from the centromere to telomere of HCR - SPR1 - SEEK1 - CDSN - STG - DPCR1 - KIAA1885 - TFIIH - DDR - IER3 - FLOT1 - TUBB - KIAA0170 - NRM - KIAA1949 - DDX16 - FLJ13158 - MRPS18B - FB19 - ABCFI - CAT56. The human SEEK1 and DPCR1 genes are pseudogenes in swine. We conclude that the swine non-class I gene region that we have sequenced is highly conserved and therefore homologous to the corresponding region located between the HLA-C and HLA-E genes in the human.

Animals↗

PubMed1995

Rice ragged stunt Oryzavirus genome segment 9 encodes a 38 600 Mr structural protein.

The complete nucleotide sequence of rice ragged stunt virus genome segment 9 (S9) was determined. The S9 segment is 1132 nucleotides long and has a long open reading frame starting from the first AUG codon at nucleotide position 14-16 and terminating at a UAG codon located at 1028-1030, which could encode a polypeptide with an Mr of 38 600 (P9). The encoded polypeptide has no sequence homology to polypeptides of any other plant reoviruses published previously. An immunological study demonstrated that P9 was the smallest of the structural proteins. The P9 polypeptide was expressed as a fusion protein with maltose binding protein in Escherichia coli. Antisera to purified virions and to the fusion protein reacted with both the bacterially expressed polypeptide and the smallest polypeptide of the purified virus in immunoblotting analyses.

Amino Acid Sequence↗

PubMed1984

Nucleotide sequence of human rotavirus genome segment 10, an RNA encoding a glycosylated virus protein.

The complete nucleotide sequence of human rotavirus (Wa strain) genome segment 10 was determined by using a cloned DNA copy. The sequence data indicated that segment 10 is A + T rich (65%) and consists of 750 base pairs. The positive strand of segment 10 contains a single open reading frame that extends 175 codons from the first AUG triplet (residues 42 through 44). The amino acid sequence of the segment 10 product was deduced from the nucleotide sequence. There are two distinct glycosylation sites at the N-terminal hydrophobic region, consistent with previous findings that this protein exists in a glycosylated form. The apparent molecular weight (20,000) of the unglycosylated, precursor polypeptide is in good agreement with the one calculated from the predicted amino acid sequence. Structural analysis of the positive strand (mRNA from segment 10) showed that it could form, like mRNA from segment 11, a stable panhandle structure involving the 5' and 3'-terminal regions. The nucleotide sequence of segment 10 from simian rotavirus, recently determined by Both et al. (J. Virol. 48:335-339, 1983) was found to be highly homologous to, and to share several important features with, segment 10 of human rotavirus.

Amino Acid Sequence↗

PubMed1999

Identity by descent genome segmentation based on single nucleotide polymorphism distributions.

In the course of our efforts to build extended regions of human genomic sequence by assembling individual BAC sequences, we have encountered several instances where a region of the genome has been sequenced independently using reagents derived from two different individuals. Comparing these sequences allows us to analyze the frequency and distribution of single nucleotide polymorphisms (SNPs) in the human genome. The observed transition/transversion frequencies are consistent with a biological origin for the sequence discrepancies, and this suggests that the data produced by large sequencing centers are accurate enough to be used as the basis for SNP analysis. The observed distribution of single nucleotide polymorphisms in the human genome is not uniform. An apparent duplication in the human genome extending over more than 130 kb between chromosomes 1p34 and 16p13 is reported. Independently derived sequences covering these regions are more than 99.9% identical, indicating that this duplication event must have occurred quite recently. FISH mapping results reported by the relevant laboratories indicate that the human population may be polymorphic for this duplication. We present a population genetic theory for the expected distribution of SNPs and derive an algorithm for probabilistically segmenting genomic sequence into regions that are identical by descent (IBD) between two individuals based on this theory and the observed locations of polymorphisms. Based on these methods and a random mating model for the human population, estimates are made for the mutation rate in the human genome.

Algorithms↗

PubMed1994

Nucleotide sequence of RNA 1, the largest genomic segment of rice stripe virus, the prototype of the tenuiviruses.

The complete nucleotide sequence of RNA 1, the largest genomic segment of rice stripe virus (RSV), was determined using two sets of overlapping cDNA clones. RNA segment 1 comprises 8970 nucleotides and on the viral complementary sequence has a single long open reading frame coding for a protein of 2919 amino acids with an estimated M(r) of 336860. Amino acid sequence comparisons of the putative protein indicated strong homology (30% amino acid identity over about 1500 residues) with the L protein of the genus Phlebovirus of the Bunyaviridae, but no detectable similarity with other members of the Bunyaviridae. However, weak similarity was detected with the L protein of Tacaribe arenavirus. The highly homologous sequence domain includes the conserved motifs of the putative RNA-dependent RNA polymerase. The data presented here, along with previous work clearly show significant similarities in genome organization, structure and expression between RSV and members of the genus Phlebovirus of the Bunyaviridae. Taken together, we propose that tenuiviruses should be included in the Bunyaviridae under the genus Tenuivirus.

Amino Acid Sequence↗

PubMed2003

Molecular diversity of RNA-2 genome segments in pecluviruses causing peanut clump disease in West Africa and India.

The complete nucleotide sequence of RNA-2 genome segments of four isolates of Peanut clump virus (PCV) and two isolates of Indian peanut clump virus (IPCV) were determined. Comparisons among the complete RNA-2 sequences of six isolates from this study and two published earlier, revealed a high degree of variability in size (between 4290 and 4652 nucleotides) and nucleotide sequence identities (between 58 % and 79 %). Amino acid sequence alignments of the five open reading frames (ORF) showed that ORF 4, which encodes the second of the triple gene block proteins, is highly conserved (90 to 98 % identical) whereas the protein encoded by ORF 2, whose function is unknown, is less conserved (25 to 60 % identical). The coat protein of the eight isolates showed amino acid identities between 37 % and 89 % and contained several conserved residues. Phylogenetic comparisons, based on complete RNA-2 sequences, revealed that the eight isolates grouped into two distinct clusters with no geographical distinction between PCV and IPCV isolates. Phylogenetic tree topologies for individual ORFs showed an overall similarity with that obtained from entire RNA-2 sequences, although the relative positions of individual isolates vary within each cluster. The results indicate that there is substantial divergence among the RNA-2 genomes of pecluviruses and suggest that different proteins have evolved differently, possibly due to different selection pressures.

Africa, Western↗

PubMed2003

DNA vaccination with plasmids containing various fragments of large segment genome of infectious bursal disease virus.

The present study was undertaken to determine the effectiveness in including VP2 gene of the large segment genome of infectious bursal disease virus (IBDV) in the DNA vaccine for protection of chickens against infectious bursal disease (IBD). Different fragments of the large segment gene of IBDV standard challenge (STC) strain were successfully amplified by reverse transcription-polymerase chain reaction (RT-PCR) followed by cloning into a eukaryotic expression plasmid vector (pCR3.1) as DNA vaccines. Transient expression of the encoded genes from various constructed plasmids was characterized in COS-7 cells by positive immunofluorescent staining with polyclonal or monoclonal antibody to IBDV. Chickens (1-day old) were intramuscularly injected with the individual plasmid three times at weekly intervals, challenged with IBDV strain STC at 21-day old, and observed for 10 days. Chickens receiving the plasmids containing VP2 genes, including VP243, VP24, or VP2 fragment, did not have clinical signs, mortality, and bursal atrophy and were effectively protected against IBDV infection. On the contrary, chickens receiving plasmids without containing VP2 genes, including VP4, VP3, or VP43 fragment, had marked bursal atrophy and were not protected against IBD. Antigen detection was correlated with protection; chickens protected from IBDV infection had undetectable IBDV antigen in bursae. Enzyme-linked immunosorbent assay (ELISA) antibody titer to IBDV was low or undetectable prior to or after challenge with IBDV in protected chickens receiving the plasmids containing the VP2 gene. The results indicate that inclusion of VP2 gene in the plasmid DNA is essential in achieving effective protection mediated by DNA vaccination against IBDV infection in chickens.

Animals↗

PubMed1995

The genome segments of DpRV, a commensal reovirus of the wasp Diadromus pulchellus (Hymenoptera).

The complete nucleotide sequences of the five double-stranded RNA genome segments of the Diadromus pulchellus reovirus (DpRV) have been determined. They consist of 985, 1240, 1318, 1652, and 4230 bp. Each segment contains at least one putative open reading frame encoding 33-, 40-, 45-, 49-, and 148-kDa proteins, respectively. The proteins have no significant similarities with sequences in data banks. Analysis of these segments and of two other previously published segments revealed the presence of degenerate consensus inverted repeats at both ends (5'-rCAAUUUUnnACU...AGUAAAAAAAUnrG-3'). The biological, structural, and genomic features of DpRV suggest that this virus is related to members of the Orthoreovirus genus.

Amino Acid Sequence↗

PubMed1993

In vitro translation of rice dwarf phytoreovirus genome segments S4 to S10.

The individual synthetic plus-strand transcripts from full-length cDNAs of rice dwarf phytoreovirus genome segments S4 to S10 directed the in vitro synthesis of predominant polypeptides, whose migration positions in SDS-polyacrylamide gel indicated molecular masses of 83 k (P4), 89 k (P5), 56 k (P6), 58 k (P7), 43 k (P8), 49 k (P9), and 35 k (P10), respectively. P7 and P8 had the same mobilities as those of the structural proteins, supporting the previous observations. The other proteins (P4, P6, P10) as well as P9, which had been considered an outer capsid protein, are probably nonstructural proteins, since no polypeptides with similar migration behavior were found in a purified RDV preparation. It remains to be confirmed biochemically whether S5 encodes the outer layer protein.

Base Sequence↗

PubMed1998

Rice ragged stunt oryzavirus genome segment S4 could encode an RNA dependent RNA polymerase and a second protein of unknown function.

The complete nucleotide sequence of genome segment S4 of rice ragged stunt oryzavirus (RRSV, Thai-isolate) was determined. The 3823 bp sequence contains two large open reading frames (ORFs). ORF1, spanning nucleotides 12 to 3776, is capable of encoding a protein of M(r) 141,380 (P4a). The P4a amino acid sequence predicted from the nucleotide sequence contains sequence motifs conserved in RNA-dependent RNA polymerases (RDRPs). When compared for evolutionary relationships with RDRPs of other reoviruses using the amino acid sequences around the conserved GDD motif, P4a was shown to be more related to Nilaparvata lugens reovirus and reovirus serotype 3 than to rice dwarf phytoreovirus, bovine rotavirus or bluetongue virus. The ORF2, spanning nucleotides 491 to 1468, is out of frame with ORF1 and is capable of encoding a protein of 36,920 (P4b). Coupled in vitro transcription-translation from cloned ORF2 in wheat germ extract confirmed the existence of ORF2 but in vivo production and possible function of P4b is yet to be determined.

Amino Acid Sequence↗

PubMed2002

The S4 genome segment of baboon reovirus is bicistronic and encodes a novel fusion-associated small transmembrane protein.

We demonstrate that the S4 genome segment of baboon reovirus (BRV) contains two sequential partially overlapping open reading frames (ORFs), both of which are functional in vitro and in virus-infected cells. The 15-kDa gene product (p15) of the 5"-proximal ORF induces efficient cell-cell fusion when expressed by itself in transfected cells, suggesting that p15 is the only viral protein required for induction of syncytium formation by BRV. The p15 protein is a small, hydrophobic, basic, integral membrane protein, properties shared with the p10 fusion-associated small transmembrane (FAST) proteins encoded by avian reovirus and Nelson Bay reovirus. As with p10, the BRV p15 protein is also a nonstructural protein and, therefore, is not involved in virus entry. Sequence analysis indicates that p15 shares no significant sequence similarity with the p10 FAST proteins and contains a unique repertoire and arrangement of sequence-predicted structural and functional motifs. These motifs include a functional N-terminal myristylation consensus sequence, an N-proximal proline-rich motif, two potential transmembrane domains, and an intervening polybasic region. The unique structural properties of p15 suggest that this protein is a novel member of the new family of FAST proteins.

Amino Acid Sequence↗

PubMed1988

Expression of the Hantaan virus M genome segment by using a vaccinia virus recombinant.

A cDNA containing the complete open reading frame of the Hantaan virus (HTN) M genome segment has been cloned into vaccinia virus. This recombinant virus expresses two glycoproteins which are similar to the HTN structural glycoproteins, G1 and G2, in molecular weight, cleavage pattern, and cellular distribution. Both HTN and recombinant vaccinia virus glycoproteins are exclusively associated with the Golgi apparatus of the cell. Despite this intracellular restriction, mice inoculated with the recombinant vaccinia virus raised neutralizing antibodies against HTN. The specificity of virus neutralization appears to reside in the HTN glycoproteins, since a vaccinia virus recombinant expressing the HTN nucleocapsid protein was unable to elicit a neutralizing antibody response.

Animals↗

PubMed2006

Microplitis demolitor bracovirus genome segments vary in abundance and are individually packaged in virions.

Polydnaviruses (PDVs) are distinguished by their unique association with parasitoid wasps and their segmented, double-stranded (ds) DNA genomes that are non-equimolar in abundance. Relatively little is actually known, however, about genome packaging or segment abundance of these viruses. Here, we conducted electron microscopy (EM) and real-time polymerase chain reaction (PCR) studies to characterize packaging and segment abundance of Microplitis demolitor bracovirus (MdBV). Like other PDVs, MdBV replicates in the ovaries of females where virions accumulate to form a suspension called calyx fluid. Wasps then inject a quantity of calyx fluid when ovipositing into hosts. The MdBV genome consists of 15 segments that range from 3.6 (segment A) to 34.3 kb (segment O). EM analysis indicated that MdBV virions contain a single nucleocapsid that encapsidates one circular DNA of variable size. We developed a semi-quantitative real-time PCR assay using SYBR Green I. This assay indicated that five (J, O, H, N and B) segments of the MdBV genome accounted for more than 60% of the viral DNAs in calyx fluid. Estimates of relative segment abundance using our real-time PCR assay were also very similar to DNA size distributions determined from micrographs. Analysis of parasitized Pseudoplusia includens larvae indicated that copy number of MdBV segments C, B and J varied between hosts but their relative abundance within a host was virtually identical to their abundance in calyx fluid. Among-tissue assays indicated that each viral segment was most abundant in hemocytes and least abundant in salivary glands. However, the relative abundance of each segment to one another was similar in all tissues. We also found no clear relationship between MdBV segment and transcript abundance in hemocytes and fat body.

Animals↗