scholarly journals Structural and functional effects of single nucleotide polymorphism on canine cytochrome b 5 reductase - in silico

2021 ◽  
Vol 2 (3) ◽  
pp. 73-76
Author(s):  
MUSA, S. Ibrahim
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Web Application ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Cytochrome B5 ◽  
Nucleotide Polymorphism ◽  
3D Protein Structure ◽  
Single Nucleotide ◽  
Cytochrome B5 Reductase

The objectives of this study were to investigate the effects of single nucleotide polymorphism in Canine cytochrome b5 reductase using computational methods. Data was obtained from database of National Centre for Biotechnology Information (db SNP) and computational software was used for the analysis. The 3D protein structure was predicted using phyre 2 server. PANTHER analysis predicted the effect of single nucleotide polymorphism (substitution of Isoleucine for Leucine at position 194) as damaging. Analysis using the Mutpred 2 web application also indicated deleterious effects of the amino acid substitution. Molecular mechanisms of structural changes in the amino acid were determined using Mutpred 2 to be altered ordered interface, gain of allosteric sites and altered metal binding. The study indicated that the substitution of Isoleucine by Leucine at position 194 of the amino acid sequence (Ile 194 Leu) resulted in the destabilization of the amino acid structure leading to functional deviation in canine cytochrome b5 reductase.

scholarly journals Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Abinaya Manivannan ◽  
Jin-Hee Kim ◽  
Eun-Young Yang ◽  
Yul-Kyun Ahn ◽  
Eun-Su Lee ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Disease Resistance ◽  
Next Generation Sequencing ◽  
Molecular Mechanisms ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
The Impact ◽  
Generation Sequencing

Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP) indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.

scholarly journals Single Nucleotide Polymorphism in the Cytolethal Distending Toxin B Gene Confers Heterogeneity in the Cytotoxicity of Actinobacillus actinomycetemcomitans

2006 ◽  
Vol 74 (12) ◽  
pp. 7014-7020 ◽  
Author(s):  
Shuichi Nishikubo ◽  
Masaru Ohara ◽  
Masae Ikura ◽  
Katsuo Katayanagi ◽  
Tamaki Fujiwara ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Actinobacillus Actinomycetemcomitans ◽  
Single Amino Acid ◽  
Polymorphism Analysis ◽  
Cytolethal Distending Toxin ◽  
Single Nucleotide Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Toxin B

ABSTRACT Clinical Actinobacillus actinomycetemcomitans produces cytolethal distending toxin (CDT) with titers ranging from 102 to 108 U/mg. Single nucleotide polymorphism analysis of the cdt gene in clinical isolates identified a variation of a single amino acid at residue 281 of CdtB, which significantly affected CDT toxicity by modulating the chromatin-degrading activity of CdtB.

scholarly journals Các biến thể gene OsTZF1 liên quan đến khả năng chịu mặn ở giống lúa Đốc Phụng bằng phương pháp giải trình tự bộ gene

2021 ◽  
Vol 57 (4) ◽  
pp. 159-168
Author(s):  
Huỳnh Kỳ ◽  
Đặng Thành Phát Trần ◽  
Thị Kim Phụng Nguyễn ◽  
Văn Quốc Giang ◽  
Văn Mạnh Nguyễn ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Next Generation Sequencing ◽  
Amino Acid ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Generation Sequencing

Trong nghiên cứu này, kỹ thuật giải trình tự thế hệ mới (next generation sequencing) được ứng dụng để giải trình tự của bộ gene 2 giống lúa Đốc Phụng (giống chống chịu mặn) và giống Nếp Mỡ (giống mẫn cảm với mặn), nhằm tìm các chỉ thị phân tử là gene chức năng mà các gene này liên quan đến cơ chế chống chịu mặn có trong giống lúa Đốc Phụng. Kết quả so sánh với bộ gene tham chiếu, bộ gene của giống lúa Đốc Phụng có khoảng 1.918.726 biến thể dạng thay đổi một nucleotide (Single Nucleotide Polymorphism) và và chèn vào khoảng 81.435, mất đi khoảng 81.974. Trong khi đó ở giống Nếp Mỡ, có khoảng 1.931.380 SNP và chèn vào khoảng 88.473, mất đi khoảng 83.190 vùng DNA. Đa số các biến thể xuất hiện ở các vùng không mang chức năng như trước sau và giữa các gene chiếm tỉ lệ trên 75%. Kết quả khảo sát biến thể xuất hiện trong vùng gene OsTZF1 (LOC_Os05g10670.1), có chức năng điều hòa các nhóm gene liên quan đến các yếu tố stress sinh học và phi sinh học, cho thấy ở giống Đốc Phụng có 7 biến thể SNP và có chèn thêm 9 nucleotide mã hóa 3 amino acid arginine khi so với giống Nếp Mỡ dựa trên bộ gene tham chiếu. Thông tin này giúp cho các nhà chọn giống sử dụng nó như chi thị phân tử, chọn tạo giống chống chịu...

scholarly journals Identification of two duplicate etiolation genes (py1, py2) in pakchoi (Brassica rapa L. ssp. chinensis)

2019 ◽  
Author(s):  
Kun Zhang ◽  
Yu Mu ◽  
Weijia Li ◽  
Xiaofei Shan ◽  
Nan Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Molecular Mechanisms ◽  
Microspore Culture ◽  
Differentially Expressed Gene ◽  
Growth Period ◽  
Segregation Ratio ◽  
Single Amino Acid ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Leaf Mutant

Abstract We identified a stably inherited yellow leaf mutant derived from ‘Huaguan’ pakchoi variety via isolated microspore culture and designated as pylm . This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Two recessive nuclear genes named py1 and py2 had a duplicate effect on etiolation. BSR-Seq revealed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F 3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1,520 F 3:4 yellow-colored individuals co-segregated with py1 . For py2 , 1,860 recessive homozygous F 3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One single-nucleotide polymorphism of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to qRT-PCR, BraA07001774 was downregulated in pylm. Thus, BraA09004189 and BraA07001774 are candidate genes for py1 and py2 . These findings will elucidate the molecular mechanisms of the gene interactions controlling pakchoi etiolation.

scholarly journals Computational Analysis of Gly482Ser Single-Nucleotide Polymorphism in PPARGC1A Gene Associated with CAD, NAFLD, T2DM, Obesity, Hypertension, and Metabolic Diseases

PPAR Research ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Somayye Taghvaei ◽  
Leila Saremi ◽  
Sepideh Babaniamansour
Keyword(s):  
Molecular Dynamics ◽  
Single Nucleotide Polymorphism ◽  
Molecular Dynamics Simulation ◽  
Structural Changes ◽  
Metabolic Diseases ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Structural Conformation

Peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PPARGC1A) regulates the expression of energy metabolism’s genes and mitochondrial biogenesis. The essential roles of PPARGC1A encouraged the researchers to assess the relation between metabolism-related diseases and its variants. To study Gly482Ser (+1564G/A) single-nucleotide polymorphism (SNP) after PPARGC1A modeling, we substitute Gly482 for Ser482. Stability prediction tools showed that this substitution decreases the stability of PPARGC1A or has a destabilizing effect on this protein. We then utilized molecular dynamics simulation of both the Gly482Ser variant and wild type of the PPARGC1A protein to analyze the structural changes and to reveal the conformational flexibility of the PPARGC1A protein. We observed loss flexibility in the RMSD plot of the Gly482Ser variant, which was further supported by a decrease in the SASA value in the Gly482Ser variant structure of PPARGC1A and an increase of H-bond with the increase of β-sheet and coil and decrease of turn in the DSSP plot of the Gly482Ser variant. Such alterations may significantly impact the structural conformation of the PPARGC1A protein, and it might also affect its function. It showed that the Gly482Ser variant affects the PPARGC1A structure and makes the backbone less flexible to move. In general, molecular dynamics simulation (MDS) showed more flexibility in the native PPARGC1A structure. Essential dynamics (ED) also revealed that the range of eigenvectors in the conformational space has lower extension of motion in the Gly482Ser variant compared with WT. The Gly482Ser variant also disrupts PPARGC1A interaction. Due to this single-nucleotide polymorphism in PPARGC1A, it became more rigid and might disarray the structural conformation and catalytic function of the protein and might also induce type 2 diabetes mellitus (T2DM), coronary artery disease (CAD), and nonalcoholic fatty liver disease (NAFLD). The results obtained from this study will assist wet lab research in expanding potent treatment on T2DM.

scholarly journals Identification of two recessive etiolation genes (py1, py2) in pakchoi (Brassica rapa L. ssp. chinensis)

2019 ◽  
Author(s):  
Kun Zhang ◽  
Yu Mu ◽  
Weijia Li ◽  
Xiaofei Shan ◽  
Nan Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Molecular Mechanisms ◽  
Microspore Culture ◽  
Differentially Expressed Gene ◽  
Growth Period ◽  
Segregation Ratio ◽  
Single Amino Acid ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Leaf Mutant

Abstract We identified a stably inherited yellow leaf mutant derived from ‘Huaguan’ pakchoi variety via isolated microspore culture and designated as pylm . This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Two recessive nuclear genes named py1 and py2 had a duplicate effect on etiolation. BSR-Seq revealed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F 3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1,520 F 3:4 yellow-colored individuals co-segregated with py1 . For py2 , 1,860 recessive homozygous F 3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One single-nucleotide polymorphism of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to qRT-PCR, BraA07001774 was downregulated in pylm. Thus, BraA09004189 and BraA07001774 are candidate genes for py1 and py2 . These findings will elucidate the molecular mechanisms of the gene interactions controlling pakchoi etiolation.

scholarly journals Pyrosequencing Using the Single-Nucleotide Polymorphism Protocol for Rapid Determination of TEM- and SHV-Type Extended-Spectrum β-Lactamases in Clinical Isolates and Identification of the Novel β-Lactamase Genes blaSHV-48, blaSHV-105, and blaTEM-155

2008 ◽  
Vol 53 (3) ◽  
pp. 977-986 ◽  
Author(s):  
C. Hal Jones ◽  
Alexey Ruzin ◽  
Margareta Tuckman ◽  
Melissa A. Visalli ◽  
Peter J. Petersen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Sequence Data ◽  
Rapid Determination ◽  
The United States ◽  
Amino Acid Substitutions ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Extended Spectrum ◽  
Rapid Sequence

ABSTRACT TEM- and SHV-type extended-spectrum β-lactamases (ESBLs) are the most common ESBLs found in the United States and are prevalent throughout the world. Amino acid substitutions at a number of positions in TEM-1 lead to the ESBL phenotype, although substitutions at residues 104 (E to K), 164 (R to S or H), 238 (G to S), and 240 (E to K) appear to be particularly important in modifying the spectrum of activity of the enzyme. The SHV-1-derived ESBLs are a less diverse collection of enzymes; however, the majority of amino acid substitutions resulting in an ESBL mirror those seen in the TEM-1-derived enzymes. Pyrosequencing by use of the single-nucleotide polymorphism (SNP) protocol was applied to provide sequence data at positions critical for the ESBL phenotype spanning the bla TEM and bla SHV genes. Three novel β-lactamases are described: the ESBLs TEM-155 (Q39K, R164S, E240K) and SHV-105 (I8F, R43S, G156D, G238S, E240K) and a non-ESBL, SHV-48 (V119I). The ceftazidime, ceftriaxone, and aztreonam MICs for an Escherichia coli isolate expressing bla SHV-105 were >128, 128, and >128 μg/ml, respectively. Likewise, the ceftazidime, ceftriaxone, and aztreonam MICs for an E. coli isolate expressing bla TEM-155 were >128, 64, and > 128 μg/ml, respectively. Pyrosequence analysis determined the true identity of the β-lactamase on plasmid R1010 to be SHV-11 rather than SHV-1, as previously reported. Pyrosequencing is a real-time sequencing-by-synthesis approach that was applied to SNP detection for TEM- and SHV-type ESBL identification and represents a robust tool for rapid sequence determination that may have a place in the clinical setting.

scholarly journals The effect of a single nucleotide polymorphism on human α2-antiplasmin activity

Blood ◽  
2007 ◽  
Vol 109 (12) ◽  
pp. 5286-5292 ◽  
Author(s):  
Victoria J. Christiansen ◽  
Kenneth W. Jackson ◽  
Kyung N. Lee ◽  
Patrick A. McKee
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Amino Terminus ◽  
Healthy Population ◽  
Plasma Samples ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Polymorphic Forms

Abstract The primary inhibitor of plasmin, α2-antiplasmin (α2AP), is secreted by the liver into plasma with Met as the amino-terminus. During circulation, Met-α2AP is cleaved by antiplasmin-cleaving enzyme (APCE), yielding Asn-α2AP, which is crosslinked into fibrin approximately 13 times faster than Met-α2AP. The Met-α2AP gene codes for either Arg or Trp as the sixth amino acid, with both polymorphic forms found in human plasma samples. We determined the Arg6Trp genotype frequency in a healthy population and its effects on Met-α2AP cleavage and fibrinolysis. Genotype frequencies were RR 62.5%, RW 34.0%, and WW 3.5%. The polymorphism related to the percentage of Met-α2AP in plasma was WW (56.4%), RW (40.6%), and RR (23.6%). WW plasma tended to have shorter lysis times than RR and RW plasmas. APCE cleaved purified Met-α2AP(Arg6) approximately 8-fold faster than Met-α2AP(Trp6), which is reflected in Asn-α2AP/Met-α2AP ratios with time in RR, RW, and WW plasmas. Removal of APCE from plasma abrogated cleavage of Met-α2AP. We conclude that the Arg6Trp polymorphism is functionally significant, as it clearly affects conversion of Met-α2AP to Asn-α2AP, and thereby, the rate of α2AP incorporation into fibrin. Therefore, the Arg6Trp polymorphism may play a significant role in governing the long-term deposition/removal of intravascular fibrin.

scholarly journals A Single Nucleotide Polymorphism Affects the Binding Affinity of H2A.X and Regulates Latexin Transcription and Hematopoietic Stem Cell Function

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2914-2914
Author(s):  
Ying Liang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Stem Cell ◽  
Natural Variation ◽  
Molecular Mechanisms ◽  
Luciferase Assay ◽  
Regulatory Sequence ◽  
Nucleotide Polymorphism ◽  
Self Renewal ◽  
Single Nucleotide ◽  
Hematopoietic Stem

Hematopoietic stem cells (HSCs) provide life-long production of blood cells and undergo self-renewal division in order to sustain the stem cell pool. Precisely regulated HSC pool maintenance and blood cell production is vital for organismal survival. We have identified a protein, latexin (Lxn), as a novel regulator of HSCs in mice, whose natural variation in the expression is inversely correlated with HSC population size. However, the molecular mechanisms involved in transcriptional regulation of Lxn in HSCs have not been clearly defined, and the genetic factors contributing to its natural variation are unknown. Here we report that an upstream regulatory sequence of the Lxn gene controls the promoter activity, and histone protein H2A.X interacts with the promoter and acts as a transcriptional activator. We identify a functional single nucleotide polymorphism (SNP), rs31528793, in the Lxn promoter that is associated with the differential binding of H2A.X, as identified by mass spectrometry. SNP rs31528793 attenuates the ability of H2A.X to bind and activate the Lxn promoter, as shown by chromatin immunoprecipitation and promoter luciferase assay. Moreover, overexpression of H2A.X increases the endogenous Lxn level and decreases HSC number and self-renewal. Concomitant blockage of Lxn activation significantly reverses these phenotypic changes, suggesting Lxn is one of the downstream targets and functional mediators of H2A.X. This study, for the first time, reveal the regulatory mechanism involved in Lxn transcription and uncover the functional role of naturally occurring genetic variants in determining differential gene expression and phenotypic diversity in HSC population. Disclosures No relevant conflicts of interest to declare.

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