scholarly journals Phylogenetic relationships among sandfly fever group viruses (Phlebovirus: Bunyaviridae) based on the small genome segment

2007 ◽  
Vol 88 (8) ◽  
pp. 2312-2319 ◽  
Author(s):  
Fangling Xu ◽  
Hongli Chen ◽  
Amelia P. A. Travassos da Rosa ◽  
Robert B. Tesh ◽  
Shu-Yuan Xiao
Keyword(s):  
Genetic Divergence ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Genome Segment ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Small Genome ◽  
Sequence Identity ◽  
Nucleoprotein N ◽  
Antigenic Relationships

The phleboviruses are more diverse in terms of arthropod vectors and antigenic relationships than most other genera of arthropod-borne viruses. In this study, 30 sandfly fever group viruses from the Naples, Sicilian, Punta Toro, Icoaraci and Frijoles serocomplexes were sequenced. Phylogenetic analyses were performed based on the sequence of the open reading frame for the nucleoprotein (N) and non-structural (NSs) protein genes of the small (S) segment. The five resultant genotypic lineages correlated with the serological grouping and were similar to analysis of M segment sequences. The sequence identity for N and NSs genes within the Sicilian, Naples, Punta Toro, Icoaraci and Frijoles serocomplexes was determined. The results indicated that genetic divergence for the S segment is lower than that for the M segment, suggesting that the S segment is more stable during evolution.

scholarly journals Open reading frame structure analysis as a novel genotyping tool for hepatitis E virus and the subsequent discovery of an inter-genotype recombinant

2009 ◽  
Vol 90 (6) ◽  
pp. 1353-1358 ◽  
Author(s):  
Jun Fan
Keyword(s):  
Structure Analysis ◽  
Hepatitis E Virus ◽  
Phylogenetic Analyses ◽  
Hepatitis E ◽  
Open Reading Frame ◽  
Frame Structure ◽  
Reading Frame ◽  
Good Criterion ◽  
Genotype 2 ◽  
Statistical Support

Accurate viral genotyping is important. Here I investigate genotypes in hepatitis E virus (HEV) and find that the open reading frame (ORF) structure (the lengths of three ORFs and the overlapping relationships among the ORFs) can be a good criterion for genotyping HEV. An inter-genotype recombinant (GenBank accession no. DQ450072) was revealed by analysing the ORF structure and confirmed by phylogenetic analyses. This discovery of the inter-genotype recombinant indicates that genotyping in HEV should be based on full-length sequences. The Mexican strain which is currently classified as a genotype 2 strain also exhibited the mosaic sequence pattern, although without statistical support.

scholarly journals Glutathione S-transferase class Kappa: characterization by the cloning of rat mitochondrial GST and identification of a human homologue

1996 ◽  
Vol 319 (3) ◽  
pp. 749-754 ◽  
Author(s):  
Sally E PEMBLE ◽  
Anthony F WARDLE ◽  
John B TAYLOR
Keyword(s):  
Dna Sequences ◽  
Protein Sequence ◽  
Sequence Similarity ◽  
Open Reading Frame ◽  
Glutathione S Transferase ◽  
Reading Frame ◽  
Sequence Identity ◽  
Methionine Residue ◽  
N Terminus ◽  
Related Proteins

We have isolated a cDNA clone that encodes rat glutathione S-transferase (GST) subunit 13, a GST originally isolated from rat liver mitochondrial matrix by Harris, Meyer, Coles and Ketterer [(1991) Biochem. J. 278, 137–141]. The 896 bp cDNA contains an open reading frame of 678 bp encoding a deduced protein sequence of which the first 33 residues (excluding the initiation methionine residue) correspond to the N-terminal sequence reported by Harris et al. Hence like many other nuclear-encoded, mitochondrially located proteins, there is no cleavable mitochondrial presequence at the N-terminus. GST subunit 13 was originally placed into the Theta class of GSTs on the basis of sequence identity at the N-terminus; however, this is the only identity with the Theta class and in fact GST subunit 13 shows little sequence similarity to any of the known GST classes. Most importantly it lacks the SNAIL/TRAIL motif that has so far been a characteristic of soluble GSTs, although it does possess a second motif (FGXXXXVXXVDGXXXXXF) reported for GST-related proteins (Koonin, Mushegian, Tatusov, Altschul, Bryant, Bork and Valencia [(1994) Protein Sci. 3, 2045–2054]. Southern and Northern blot analyses of rat DNA and mRNA are consistent with GST subunit 13's being the product of a single hybridizing gene locus. Searches of EST databases identified numerous similar human DNA sequences and a single pig sequence. We have derived a human cDNA sequence from these EST sequences which shows a high nucleotide similarity (77%) to rat GST subunit 13. The largest open reading frame is identical in length with subunit 13 and yields a deduced protein sequence identity of 70%. Most unusually the 3´ non-coding nucleotide sequence identity is also 77%. We conclude that these cDNAs belong to a novel GST class hereby designated Kappa, with the rat GST subunit 13 gene designated rGSTK1 and the human gene being called hGSTK1.

scholarly journals Identification of a Divergent Isolate of Ryegrass Mosaic Virus in Ohio Wheat

2020 ◽  
Vol 9 (23) ◽  
Author(s):  
B. A. Hodge ◽  
P. A. Paul ◽  
L. R. Stewart
Keyword(s):  
Nucleotide Sequence ◽  
Mosaic Virus ◽  
Complete Genome ◽  
Nucleotide Sequence Identity ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Sequence Identity ◽  
Virus Sequence

ABSTRACT A divergent isolate of ryegrass mosaic virus (RGMV) has been identified that is associated with wheat samples collected in Ohio. The complete genome of the virus is 9,570 nucleotides, with a polyprotein open reading frame that shares 77.2% nucleotide sequence identity with the reference ryegrass mosaic virus sequence.

scholarly journals Complete Nucleotide Sequence Analysis of the Norovirus GII.4 Sydney Variant in South Korea

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Ji-Sun Park ◽  
Sung-Geun Lee ◽  
Ji-Young Jin ◽  
Han-Gil Cho ◽  
Weon-Hwa Jheong ◽  
...  
Keyword(s):  
South Korea ◽  
Recombinant Strain ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Complete Sequence ◽  
Open Reading Frame ◽  
Nucleotide Sequence Analysis ◽  
Reading Frame ◽  
The World ◽  
Norovirus Gii

Norovirus is the primary cause of acute gastroenteritis in individuals of all ages. In Australia, a new strain of norovirus (GII.4) was identified in March 2012, and this strain has spread rapidly around the world. In August 2012, this new GII.4 strain was identified in patients in South Korea. Therefore, to examine the characteristics of the epidemic norovirus GII.4 2012 variant in South Korea, we conducted KM272334 full-length genomic analysis. The genome of the gg-12-08-04 strain consisted of 7,558 bp and contained three open reading frame (ORF) composites throughout the whole genome: ORF1 (5,100 bp), ORF2 (1,623 bp), and ORF3 (807 bp). Phylogenetic analyses showed that gg-12-08-04 belonged to the GII.4 Sydney 2012 variant, sharing 98.92% nucleotide similarity with this variant strain. According to SimPlot analysis, the gg-12-08-04 strain was a recombinant strain with breakpoint at the ORF1/2 junction between Osaka 2007 and Apeldoorn 2008 strains. This study is the first report of the complete sequence of the GII.4 Sydney 2012 strain in South Korea. Therefore, this may represent the standard sequence of the norovirus GII.4 2012 variant in South Korea and could therefore be useful for the development of norovirus vaccines.

scholarly journals Correlation of Rhs elements with Escherichia coli population structure.

Genetics ◽  
1995 ◽  
Vol 141 (1) ◽  
pp. 15-24
Author(s):  
C W Hill ◽  
G Feulner ◽  
M S Brody ◽  
S Zhao ◽  
A B Sadosky ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Open Reading Frame ◽  
Clonal Structure ◽  
Reading Frame ◽  
E Coli ◽  
Sequence Identity ◽  
Reference Collection ◽  
K 12 ◽  
Recent Variation ◽  
Fourth Member

Abstract The Rhs family of composite genetic elements was assessed for variation among independent Escherichia coli strains of the ECOR reference collection. The location and content of the RhsA-B-C-F subfamily correlates highly with the clonal structure of the ECOR collection. This correlation exists at several levels: the presence of Rhs core homology in the strain, the location of the Rhs elements present, and the identity of the Rhs core-extensions associated with each element. A provocative finding was that an identical 1518-bp segment, covering core-extension-b1 and its associated downstream open reading frame, is present in two distinct clonal groups, but in association with different Rhs elements. The sequence identity of this segment when contrasted with the divergence of other chromosomal segments suggests that shuffling of Rhs core extensions has been a relatively recent variation. Nevertheless the copies of core-extension-b1 were placed within the respective Rhs elements before the emergence of the clonal groups. In the course of this analysis, two new Rhs elements absent from E. coli K-12 were discovered: RhsF, a fourth member of the RhsA-B-C-F subfamily, and RhsG, the prototype of a third Rhs subfamily.

scholarly journals Automated Construction of an Open Reading Frame Library from Sinorhizobium meliloti

2003 ◽  
Vol 8 (3) ◽  
pp. 44-49
Author(s):  
Todd C. Edwards ◽  
Amber Marsh ◽  
Christina Sanders ◽  
Joanna S. Albala ◽  
Christa K. Prange ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
High Throughput ◽  
Genomic Dna ◽  
Sinorhizobium Meliloti ◽  
Open Reading Frame ◽  
Construction Process ◽  
Reading Frame ◽  
Library Construction ◽  
E Coli ◽  
Sequence Identity

An automated, high-throughput, open reading frame (ORF) library construction process has been developed. ORFs from genomic DNA of the microbe Sinorhizobium meliloti were amplified by PCR and cloned into the library vector by homologous recombination instead of traditional ligation. From 960 targets, we successfully generated 723 (75.3%) ORFs from the initial PCR. After cloning the successful samples into the library vector, transforming into E. coli and PCR colony screening, 371 (38.6% overall) ORFs were placed into the new library and sequenced. Our prototype library contained 314 (32.7% overall) clones with sequence identity to the Sinorhizobium meliloti genome.

scholarly journals Identification of an Efflux Pump Gene,pmrA, Associated with Fluoroquinolone Resistance inStreptococcus pneumoniae

1999 ◽  
Vol 43 (1) ◽  
pp. 187-189 ◽  
Author(s):  
Martin J. Gill ◽  
Nigel P. Brenwald ◽  
Richard Wise
Keyword(s):  
Drug Sensitivity ◽  
Amino Acid Sequence Identity ◽  
Efflux Pump ◽  
Open Reading Frame ◽  
Fluoroquinolone Resistance ◽  
Transmembrane Segment ◽  
Reading Frame ◽  
Sequence Identity ◽  
Major Facilitator ◽  
Resistant Pneumococcus

ABSTRACT An open reading frame (ORF) homologous to norA was insertionally inactivated with cat in a fluoroquinolone-resistant pneumococcus with an efflux phenotype; this inactivation caused reversion to drug sensitivity. The ORF product has 24% amino acid sequence identity each to NorA and Bmr, which suggests that it is a major facilitator system pump of the 12-transmembrane-segment class.

scholarly journals Molecular cloning, chromosomal assignment and tissue-specific expression of a murine α(1,2)fucosyltransferase expressed in thymic and epididymal epithelial cells

1997 ◽  
Vol 327 (1) ◽  
pp. 105-115 ◽  
Author(s):  
Steven E. DOMINO ◽  
Nozomu HIRAIWA ◽  
John B. LOWE
Keyword(s):  
Epithelial Cells ◽  
Blood Group ◽  
Single Copy ◽  
Interspecific Backcross ◽  
Open Reading Frame ◽  
Chromosomal Assignment ◽  
Specific Expression ◽  
Reading Frame ◽  
Sequence Identity ◽  
Group Locus

Terminal Fucα(1-2)Galβ epitopes have been proposed to play significant roles in cell–cell interactions in development, cell adhesion, and malignant transformation. To begin to investigate the regulation and function of α(1-2)fucosylated epitopes in an animal model, we have isolated and characterized a mouse genomic DNA segment encoding a protein orthologous to the human H blood group locus α(1,2)fucosyltransferase (FUT1). This segment maintains an open reading frame encoding 376 amino acids sharing 75% sequence identity with the enzyme encoded by human FUT1, and 55% sequence identity with the enzyme encoded by the human Secretor blood group locus (FUT2). Expression of the open reading frame in COS-7 cells yields an α(1,2)fucosyltransferase activity with a Km of 7.6 mM for phenyl-β-d-galactoside. Southern blotting and interspecific backcross analyses indicate that this murine locus represents a single copy sequence mapping to a novel locus 2.1 centimorgans from the Klk1 locus, in a region of homology between mouse chromosome 7 and the human FUT1 locus on the long arm of chromosome 19. Mouse FUT1 yields a 2.8 kb mRNA transcript identifiable in many organs, including thymus, lung, stomach, pancreas, small intestine, colon, uterus and epididymis. Hybridization analyses in situ localize expression of FUT1 transcripts to thymic medullary and epididymal epithelial cells, implying that this gene determines the expression of cell surface Fucα(1-2)Galβ epitopes in these tissues.

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