Genomic Segment

2020 ◽  
Author(s):  
Keyword(s):  
Genomic Segment

Comparative sequence analysis of rotavirus genomic segment 6--the gene specifying viral subgroups 1 and 2.

1984 ◽  
Vol 51 (1) ◽  
pp. 97-101 ◽  
Author(s):  
G W Both ◽  
L J Siegman ◽  
A R Bellamy ◽  
N Ikegami ◽  
A J Shatkin ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Comparative Sequence Analysis ◽  
Genomic Segment ◽  
Comparative Sequence

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

Repetitive Dictyostelium heat-shock promotor functions in Saccharomyces cerevisiae

1984 ◽  
Vol 4 (4) ◽  
pp. 591-598
Author(s):  
J Cappello ◽  
C Zuker ◽  
H F Lodish
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Shock ◽  
Nucleotide Sequence ◽  
Dna Sequence ◽  
Base Pair ◽  
Shock Treatment ◽  
Yeast Cells ◽  
Genomic Segment ◽  
Heat Shock Treatment ◽  
Shock Response

The Dictyostelium genome contains 40 copies of a 4.7-kilobase repetitive and apparently transposable DNA sequence (DIRS-1) and about 250 smaller elements that appear to be deletions or rearrangements of DIRS-1. Transcripts of these sequences are induced during differentiation and also by heat shock treatment of growing cells. We showed that one such cloned element, pB41.6 (2.5 kilobases) contains a nucleotide sequence identical to the Drosophila consensus heat shock promotor. To test whether this sequence might indeed control the expression of DIRS-1-related RNAs, we have cloned this genomic segment into yeast cells. In yeast cells, 41.6 directs synthesis of a 1.7-kilobase RNA that is induced at least 10-fold by heat shock. Transcription initiates at about 124 bases 3' of the putative promotor sequence and terminates within the 41.6 insert. A 381-base-pair subclone that contains the putative promotor sequence is sufficient to induce the heat shock response of 41.6 in yeast cells.

scholarly journals Repetitive Dictyostelium heat-shock promotor functions in Saccharomyces cerevisiae.

1984 ◽  
Vol 4 (4) ◽  
pp. 591-598 ◽  
Author(s):  
J Cappello ◽  
C Zuker ◽  
H F Lodish
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Shock ◽  
Nucleotide Sequence ◽  
Dna Sequence ◽  
Base Pair ◽  
Shock Treatment ◽  
Yeast Cells ◽  
Genomic Segment ◽  
Heat Shock Treatment ◽  
Shock Response

The Dictyostelium genome contains 40 copies of a 4.7-kilobase repetitive and apparently transposable DNA sequence (DIRS-1) and about 250 smaller elements that appear to be deletions or rearrangements of DIRS-1. Transcripts of these sequences are induced during differentiation and also by heat shock treatment of growing cells. We showed that one such cloned element, pB41.6 (2.5 kilobases) contains a nucleotide sequence identical to the Drosophila consensus heat shock promotor. To test whether this sequence might indeed control the expression of DIRS-1-related RNAs, we have cloned this genomic segment into yeast cells. In yeast cells, 41.6 directs synthesis of a 1.7-kilobase RNA that is induced at least 10-fold by heat shock. Transcription initiates at about 124 bases 3' of the putative promotor sequence and terminates within the 41.6 insert. A 381-base-pair subclone that contains the putative promotor sequence is sufficient to induce the heat shock response of 41.6 in yeast cells.

Rapid detection of SARS-CoV-2 viral nucleic acids based on surface enhanced infrared absorption spectroscopy

Nanoscale ◽  
2021 ◽  
Author(s):  
Zhiqi Yao ◽  
Qiongdi Zhang ◽  
Wenting Zhu ◽  
Massimiliano Galluzzi ◽  
Wenhua Zhou ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Absorption Spectroscopy ◽  
Infrared Absorption ◽  
Rapid Detection ◽  
Infrared Absorption Spectroscopy ◽  
Genomic Segment ◽  
Surface Enhanced

A rapid and sensitive SEIRA-based method for SARS-CoV-2 detection is proposed and analyzed. The proposed method can effectively detect as low as 2.98 copies per μL (∼5 aM) SARS-CoV-2 viral genomic segment within 30 minutes.

scholarly journals A Reverse Genetics System for Cypovirus Based on a Bacmid Expressing T7 RNA Polymerase

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 314 ◽  
Author(s):  
Gaobo Zhang ◽  
Jian Yang ◽  
Fujun Qin ◽  
Congrui Xu ◽  
Jia Wang ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Reverse Genetics ◽  
T7 Rna Polymerase ◽  
Sf9 Cells ◽  
Genomic Segment ◽  
Egfp Gene ◽  
A Genome ◽  
Typical Morphology ◽  
Occlusion Bodies ◽  
Rescue System

Dendrolimus punctatus cypovirus (DpCPV), belonging to the genus Cypovirus within the family Reoviridae, is considered the most destructive pest of pine forests worldwide. DpCPV has a genome consisting of 10 linear double-stranded RNA segments. To establish a reverse genetics system, we cloned cDNAs encoding the 10 genomic segments of DpCPV into three reverse genetics vectors in which each segment was transcribed under the control of a T7 RNA polymerase promoter and terminator tagged with a hepatitis delta virus ribozyme sequence. We also constructed a vp80-knockout Autographa californica multiple nucleopolyhedrovirus bacmid to express a T7 RNA polymerase codon-optimized for Sf9 cells. Following transfection of Sf9 cells with the three vectors and the bacmid, occlusion bodies (OBs) with the typical morphology of cypovirus polyhedra were observed by optical microscopy. The rescue system was verified by incorporation of a HindIII restriction enzyme site null mutant of the 9th genomic segment. Furthermore, when we co-transfected Sf9 cells with the reverse genetics vectors, the bacmid, and an additional vector bearing an egfp gene flanked with the 5′ and 3′ untranslated regions of the 10th genomic segment, aggregated green fluorescence co-localizing with the OBs was observed. The rescued OBs were able to infect Spodopetra exigua larvae, although their infectivity was significantly lower than that of wild-type DpCPV. This reverse genetics system for DpCPV could be used to explore viral replication and pathogenesis and to facilitate the development of novel bio-insecticides and expression systems for exogenous proteins.

scholarly journals Identification of regions of positive selection using Shared Genomic Segment analysis

2011 ◽  
Vol 19 (6) ◽  
pp. 667-671 ◽  
Author(s):  
Zheng Cai ◽  
Nicola J Camp ◽  
Lisa Cannon-Albright ◽  
Alun Thomas
Keyword(s):  
Positive Selection ◽  
Genomic Segment

scholarly journals Mal de Río Cuarto virus (MRCV) genomic segment S3 codes for the major core capsid protein

Virus Genes ◽  
2009 ◽  
Vol 38 (3) ◽  
pp. 455-460 ◽  
Author(s):  
Ana J. Distéfano ◽  
Sara Maldonado ◽  
H. Esteban Hopp ◽  
Mariana del Vas
Keyword(s):  
Capsid Protein ◽  
Genomic Segment

scholarly journals First Complete Squash leaf curl China virus Genomic Segment DNA-A Sequence from East Timor

2017 ◽  
Vol 5 (24) ◽  
Author(s):  
Solomon Maina ◽  
Owain R. Edwards ◽  
Luis de Almeida ◽  
Abel Ximenes ◽  
Roger A. C. Jones
Keyword(s):  
East Timor ◽  
Genomic Segment ◽  
Genome Sequences ◽  
World Regions ◽  
A Genome ◽  
Other World ◽  
Leaf Curl

ABSTRACT We present here the first complete Squash leaf curl China virus (SLCCV) genomic segment DNA-A sequence from East Timor. It was isolated from a pumpkin plant. When compared with 15 complete SLCCV DNA-A genome sequences from other world regions, it most resembled the Malaysian isolate MC1 sequence.

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