scholarly journals Molecular characterization of partial-open reading frames 1a and 2 of the human astroviruses in South Korea

2010 ◽  
Vol 7 (1) ◽  
Author(s):  
Jae in Lee ◽  
Gyu-Cheol Lee ◽  
Young hee Oh ◽  
Young ki Lee ◽  
Min young Kim ◽  
...  
Keyword(s):  
South Korea ◽  
Molecular Characterization ◽  
Open Reading Frames ◽  
Human Astroviruses ◽  
Reading Frames

scholarly journals Molecular Characterization of a Variant of Bacillus anthracis-Specific Phage AP50 with Improved Bacteriolytic Activity

2008 ◽  
Vol 74 (21) ◽  
pp. 6792-6796 ◽  
Author(s):  
Shanmuga Sozhamannan ◽  
Michael McKinstry ◽  
Shannon M. Lentz ◽  
Matti Jalasvuori ◽  
Farrell McAfee ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Molecular Characterization ◽  
Genome Sequence ◽  
Open Reading Frames ◽  
Genome Architecture ◽  
Wild Type ◽  
Specific Phage ◽  
Mutant Phage ◽  
Reading Frames

ABSTRACT The genome sequence of a Bacillus anthracis-specific clear plaque mutant phage, AP50c, contains 31 open reading frames spanning 14,398 bp, has two mutations compared to wild-type AP50t, and has a colinear genome architecture highly similar to that of gram-positive Tectiviridae phages. Spontaneous AP50c-resistant B. anthracis mutants exhibit a mucoid colony phenotype.

scholarly journals Molecular Characterization of the Complete 23F Capsular Polysaccharide Locus of Streptococcus pneumoniae

1998 ◽  
Vol 180 (19) ◽  
pp. 5273-5278 ◽  
Author(s):  
Mario Ramirez ◽  
Alexander Tomasz
Keyword(s):  
Streptococcus Pneumoniae ◽  
Molecular Characterization ◽  
Dna Sequence ◽  
Capsular Polysaccharide ◽  
Open Reading Frames ◽  
The Other ◽  
Reading Frames

ABSTRACT The complete DNA sequence of the capsular locus 23F ofStreptococcus pneumoniae is presented. The 18.6-kbcps23f locus is composed of 18 open reading frames flanked at the 5′ and 3′ ends by the genes dexB andaliA, an arrangement similar to those of some of the other identified cps loci.

scholarly journals Molecular Characterization of a New Abortive Infection System (AbiU) from Lactococcus lactisLL51-1

2001 ◽  
Vol 67 (11) ◽  
pp. 5225-5232 ◽  
Author(s):  
Gang Dai ◽  
Ping Su ◽  
Gwen E. Allison ◽  
Bruce L. Geller ◽  
Ping Zhu ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Lactococcus Lactis ◽  
Open Reading Frames ◽  
Phage Resistance ◽  
Abortive Infection ◽  
Specific Phage ◽  
Type Phage ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT This study reports on the identification and characterization of a novel abortive infection system, AbiU, from Lactococcus lactis. AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335. The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 × 10−1, 1.0 × 10−2, and 1.0 × 10−1, respectively. abiU involves two open reading frames,abiU1 (1,772 bp) and abiU2 (1,019 bp). Evidence indicates that AbiU1 is responsible for phage resistance and that AbiU2 may downregulate phage resistance against 936 and P335 type phages but not c2 type phage. AbiU appeared to delay transcription of both phage 712 and c2, with the effect being more marked on phage c2.

Molecular Characterization of a Novel Partitivirus and a Fusarivirus Co-infected in the Nigrospora Sphaerica Fungus

2021 ◽  
Author(s):  
Jie Zhong ◽  
Ze Zhong Yang ◽  
Xin Yang ◽  
Zhao Jiang Guo ◽  
Wen Xie ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Pathogenic Fungus ◽  
Rna Replication ◽  
Open Reading Frames ◽  
Helicase Domain ◽  
Polya Tail ◽  
Viral Rdrp ◽  
The Family ◽  
Reading Frames

Abstract Here we reported the molecular characterization of two novel mycoviruses co-infected in a plant pathogenic fungus, Nigrospora sphaerica that were designated as Nigrospora sphaerica fusarivirus 1 (NsFV1) and Nigrospora sphaerica partitivirus 1 (NsPV1), respectively. NsFV1 has an undivided genome of 6,147 bp, excluding the polyA tail, and was predicted to contain two nonoverlapping open reading frames (ORF1 and 2). The larger ORF1 encoded a polyprotein containing a conserved RNA-dependent RNA polymerase (RdRp) and a helicase domain that have functions for RNA replication, and the smaller ORF2 encoded a putative protein with an unknown function. The NsPV1 was consists of two genome segments, which were in lengths of 1,796 bp and 1,455 bp, respectively. Each of the two dsRNAs had a single ORF and were deduced to encode proteins with homology to viral RdRp and coat protein (CP), respectively, in the family Partitiviridae. Phylogenetic analysis showed that NsFV1 was placed within the newly proposed family Fusariviridae, while NsPV1 was belonging to the genus Gammapartitivirus in the family Partitiviridae. This was the first description of mycovirses infected the fungus N. sphaerica.

MOLECULAR CHARACTERIZATION OF A NOVEL RAT PARVOVIRUS IN TAIWAN

2014 ◽  
Vol 40 (01) ◽  
pp. 11-19 ◽  
Author(s):  
Yi-Chun Liao ◽  
Ming-Hseng Wang ◽  
Cho-Hua Wan
Keyword(s):  
Molecular Characterization ◽  
Open Reading Frames ◽  
Infectious Agents ◽  
Sequence Comparisons ◽  
Laboratory Rats ◽  
Laboratory Rodents ◽  
Reading Frames

Rodent parvoviruses are among the most prevalent infectious agents in laboratory rodents and have been shown to interfere with in vivo and in vitro research. A newly recognized rat parvovirus (RPV) that is distinct from the prototypic RPV was recently identified in naturally infected laboratory rats in Taiwan. Nucleotide and amino acid sequence comparisons showed that this newly identified variant of RPV is most closely related to rat parvovirus type 1a (RPV-1a) and type 1b (RPV-1b) and is distinctly different from type UT (RPV/UT) and other rodent parvoviruses. This variant was designated rat parvovirus type National Taiwan University 1 (RPV-NTU1). Phylogenetic and sequence analyses revealed that RPV-NTU1 contains conserved open reading frames with an overall genome organization similar to known RPV-1. RPV-NTU1 is the second RPV-1 variant whose full-length molecular characterization has been performed.

scholarly journals Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 27
Author(s):  
Jun Kwon ◽  
Sang Guen Kim ◽  
Hyoun Joong Kim ◽  
Sib Sankar Giri ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Open Reading Frames ◽  
Genome Comparison ◽  
The Novel ◽  
Promising Alternative ◽  
Isolation And Characterization ◽  
Global Issue ◽  
Reading Frames ◽  
Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

scholarly journals Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Chaitanya Erady ◽  
Adam Boxall ◽  
Shraddha Puntambekar ◽  
N. Suhas Jagannathan ◽  
Ruchi Chauhan ◽  
...  
Keyword(s):  
Transcript Level ◽  
Open Reading Frames ◽  
The Cancer Genome Atlas ◽  
Small Subset ◽  
Cancer Tissue ◽  
Post Translational Modifications ◽  
Cancer Genome Atlas ◽  
Systematic Identification ◽  
Reading Frames

AbstractUncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.

scholarly journals Characterization of Chlamydia trachomatis Plasmid-Encoded Open Reading Frames

2013 ◽  
Vol 195 (17) ◽  
pp. 3819-3826 ◽  
Author(s):  
S. Gong ◽  
Z. Yang ◽  
L. Lei ◽  
L. Shen ◽  
G. Zhong
Keyword(s):  
Chlamydia Trachomatis ◽  
Open Reading Frames ◽  
Reading Frames
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