The Effect of a Single Nucleotide Substitution in the Splicing Silencer in thetat/revIntron on HIV Type 1 Envelope Expression

2006 ◽  
Vol 22 (1) ◽  
pp. 76-82 ◽  
Author(s):  
Saowakon Paca-Uccaralertkun ◽  
Christian Kroun Damgaard ◽  
Prasert Auewarakul ◽  
Arunee Thitithanyanont ◽  
Pirada Suphaphiphat ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Single Nucleotide Substitution ◽  
Single Nucleotide ◽  
Splicing Silencer ◽  
Hiv Type 1

scholarly journals Thirty two novel nsSNPs May effect on HEXA protein Leading to Tay-Sachs disease (TSD) Using a Computational Approach

2019 ◽  
Author(s):  
Tebyan A. Abdelhameed ◽  
Mohamed Mustafa Osman Fadul ◽  
Dina Nasereldin Abdelrahman Mohamed ◽  
Amal Mohamed Mudawi ◽  
Sayaf Kamal Khalifa Fadul Allah ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Neurodegenerative Disorder ◽  
Structure And Function ◽  
Single Nucleotide Substitution ◽  
Single Nucleotide ◽  
Bioinformatics Tools ◽  
Tay Sachs Disease ◽  
Hexosaminidase A ◽  
And Function

ABSTRACTBackgroundGenetic polymorphisms in the HEXA gene are associated with a neurodegenerative disorder called Tay-Sachs disease (TSD) (GM2 gangliosidosis type 1). This study aimed to predict the possible pathogenic SNPs of this gene and their impact on the protein using different bioinformatics tools.MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms collectively predicted the effect of single nucleotide substitution on both structure and function of the hexosaminidase A protein.ResultsFifty nine mutations were found to be highly damaging to the structure and function of the HEXA gene protein.ConclusionAccording to this study, thirty two novel nsSNP in HEXA are predicted to have possible role in Tay-Saches Disease using different bioinformatics tools. Our findings could help in genetic study and diagnosis of Tay-Saches Disease.

scholarly journals A single nucleotide substitution in the coding region of Ogura male sterile gene, orf138, determines effectiveness of a fertility restorer gene, Rfo, in radish

2021 ◽  
Author(s):  
Hiroshi Yamagishi ◽  
Megumi Jikuya ◽  
Kanako Okushiro ◽  
Ayako Hashimoto ◽  
Asumi Fukunaga ◽  
...  
Keyword(s):  
Male Sterility ◽  
Nucleotide Substitution ◽  
Fertility Restoration ◽  
Type A ◽  
Restorer Gene ◽  
Single Nucleotide Substitution ◽  
Coding Region ◽  
Fertility Restorer ◽  
Single Nucleotide ◽  
Fertility Restorer Gene

AbstractCytoplasmic male sterility (CMS) observed in many plants leads defect in the production of functional pollen, while the expression of CMS is suppressed by a fertility restorer gene in the nuclear genome. Ogura CMS of radish is induced by a mitochondrial orf138, and a fertility restorer gene, Rfo, encodes a P-type PPR protein, ORF687, acting at the translational level. But, the exact function of ORF687 is still unclear. We found a Japanese variety showing male sterility even in the presence of Rfo. We examined the pollen fertility, Rfo expression, and orf138 mRNA in progenies of this variety. The progeny with Type H orf138 and Rfo showed male sterility when their orf138 mRNA was unprocessed within the coding region. By contrast, all progeny with Type A orf138 were fertile though orf138 mRNA remained unprocessed in the coding region, demonstrating that ORF687 functions on Type A but not on Type H. In silico analysis suggested a specific binding site of ORF687 in the coding region, not the 5′ untranslated region estimated previously, of Type A. A single nucleotide substitution in the putative binding site diminishes affinity of ORF687 in Type H and is most likely the cause of the ineffectiveness of ORF687. Furthermore, fertility restoration by RNA processing at a novel site in some progeny plants indicated a new and the third fertility restorer gene, Rfs, for orf138. This study clarified that direct ORF687 binding to the coding region of orf138 is essential for fertility restoration by Rfo.

A novel single‐nucleotide substitution in the proximal ABO promoter gives rise to the B 3 phenotype

Transfusion ◽  
2019 ◽  
Vol 59 (10) ◽  
Author(s):  
åsa Hellberg ◽  
Annika K. Hult ◽  
Ines Moser ◽  
Beatriz Tomaz ◽  
Maria Rodrigues ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Single Nucleotide Substitution ◽  
Single Nucleotide

scholarly journals Expanded insecticide catabolic activity gained by a single nucleotide substitution in a bacterial carbamate hydrolase gene

2016 ◽  
Vol 18 (12) ◽  
pp. 4878-4887 ◽  
Author(s):  
Başak Öztürk ◽  
Maarten Ghequire ◽  
Thi Phi Oanh Nguyen ◽  
René De Mot ◽  
Ruddy Wattiez ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Single Nucleotide Substitution ◽  
Single Nucleotide ◽  
Catabolic Activity

scholarly journals Codon Substitution Mutations at Two Positions in the L Polymerase Protein of Human Parainfluenza Virus Type 1 Yield Viruses with a Spectrum of Attenuation In Vivo and Increased Phenotypic Stability In Vitro

2004 ◽  
Vol 78 (4) ◽  
pp. 2029-2036 ◽  
Author(s):  
Josephine M. McAuliffe ◽  
Sonja R. Surman ◽  
Jason T. Newman ◽  
Jeffrey M. Riggs ◽  
Peter L. Collins ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nucleotide Substitution ◽  
Wild Type ◽  
Phenotypic Stability ◽  
Single Nucleotide ◽  
Codon Substitution ◽  
Substitution Mutations ◽  
Human Parainfluenza Virus

ABSTRACT The Y942H and L992F temperature-sensitive (ts) and attenuating amino acid substitution mutations, previously identified in the L polymerase of the HPIV3cp45 vaccine candidate, were introduced into homologous positions of the L polymerase of recombinant human parainfluenza virus type 1 (rHPIV1). In rHPIV1, the Y942H mutation specified the ts phenotype in vitro and the attenuation (att) phenotype in hamsters, whereas the L992F mutation specified neither phenotype. Each of these codon mutations was generated by a single nucleotide substitution and therefore had the potential to readily revert to a codon specifying the wild-type amino acid residue. We introduced alternative amino acid assignments at codon 942 or 992 as a strategy to increase genetic stability and to generate mutants that exhibit a range of attenuation. Twenty-three recombinants with codon substitutions at position 942 or 992 of the L protein were viable. One highly ts and att mutant, the Y942A virus, which had a difference of three nucleotides from the codon encoding a wild-type tyrosine, also possessed a high level of genetic and phenotypic stability upon serial passage in vitro at restrictive temperatures compared to that of the parent Y942H virus, which possessed a single nucleotide substitution. We obtained mutants with substitutions at position 992 that, in contrast to the L992F virus, possessed the ts and att phenotypes. These findings identify the use of alternative codon substitution mutations as a method that can be used to generate candidate vaccine viruses with increased genetic stability and/or a modified level of attenuation.

A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

Phytotaxa ◽  
2021 ◽  
Vol 484 (1) ◽  
pp. 44-74
Author(s):  
OLGA V. YURTSEVA ◽  
N.K. BADMAEVA ◽  
EVGENY V. MAVRODIEV
Keyword(s):  
Maximum Likelihood ◽  
Nucleotide Substitution ◽  
Single Nucleotide Substitution ◽  
Sem Images ◽  
Single Nucleotide ◽  
Bayesian Analyses ◽  
Dune Sands ◽  
F Region ◽  
Specific Morphology ◽  
Length Width

Maximum Likelihood (ML) and Bayesian analyses (BI) applied for 3-plastid loci (cpDNA trnL(UAA) intron, trnL–trnF IGS, and rpl32–trnL(UAG) IGS regions) / 55 tips of Atraphaxis revealed a subclade of two endemics from Transbaikalia (Dahuria) which are often mistaken for A. pungens and A. frutescens but phylogenetically distant from both. Atraphaxis selengensis is a species new to science which inhabits dune sands along the Selenga and Chikoy rivers and has specific morphology of perianth, fruits, ochreas, leaf blades, and pollen. Atraphaxis davurica inhabits stony mountain steppe in Buryatia and Chita region and differs from A. pungens and A. frutescens by longer ochreas, fruits, styles and stigmas extended to ends. Two varieties recognized by Ledebour in plants from Russian Transbaikalia have no clear morphological and molecular distinctions, but the plants from Khentei-Chikoy Highlands subtly differ in leaf ratio (length/width), bark colour, and a single-nucleotide substitution in trnL–F region. These plants are described as A. davurica var. chikoensis var. nov. Morphological descriptions of A. selengensis and A. davurica are supplied with LM and SEM images and a distributional map. Atraphaxis frutescens and A. pungens are absent from Russian Transbaikalia but distributed in Altai, Tuva, Khakassia, Mongolia and China.

A novel primary KIT exon 9 single nucleotide substitution c.1427G>T (p.Ser476Ile) in a gastrointestinal stromal tumor

2010 ◽  
Vol 457 (5) ◽  
pp. 623-625
Author(s):  
Florian Grabellus ◽  
Sien-Yi Sheu ◽  
Sebastian Bauer ◽  
Norbert Speich ◽  
Kurt W. Schmid ◽  
...  
Keyword(s):  
Gastrointestinal Stromal Tumor ◽  
Nucleotide Substitution ◽  
Stromal Tumor ◽  
Single Nucleotide Substitution ◽  
Single Nucleotide ◽  
Exon 9
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