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Khazaal NM, Alghetaa HF, Al-Shuhaib MBS, Al-Thuwaini TM, Alkhammas AH. A novel deleterious oxytocin variant is associated with the lower twinning ratio in Awassi ewes. Anim Biotechnol 2023; 34:3404-3415. [PMID: 36449364 DOI: 10.1080/10495398.2022.2152038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
This study aimed to assess the possible association of oxytocin (OXT) gene with reproductive traits in two groups of Awassi ewes that differ in their reproductive potentials. Sheep were genotyped using PCR-single-stranded conformation polymorphism approach. Three genotypes were detected in exon 2, CC, CA, and AA, and a novel SNP was identified with a missense effect on oxytocin (c.188C > A → p.Arg55Leu). A significant (p < 0.01) association of p.Arg55Leu with the twinning rate was found as ewes with AA and CA genotypes exhibited, respectively a lower twinning ratio than those with the wild-type CC genotype. The deleterious impact of p.Arg55Leu was demonstrated by all in silico tools that were utilized to assess the effect of this variant on the structure, function, and stability of oxytocin. Molecular docking showed that p.Arg55Leu caused a dramatic alteration in the binding of oxytocin with its receptor and reduced the number of interacted amino acids between them. Our study suggests that ewes with AA and CA genotypes showed a lower reproductive performance due to the presence of p.Arg55Leu, which caused damaging impacts on oxytocin and is binding with the OXT receptor. The utilization of the p.Arg55Leu could be useful for improving Awassi reproductive potential.
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Affiliation(s)
- Neam M Khazaal
- Department of Physiology, Biochemistry and Pharmacology, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Hasan F Alghetaa
- Department of Physiology, Biochemistry and Pharmacology, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | | | - Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Iraq
| | - Ahmed H Alkhammas
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Iraq
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2
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Ahmad SU, Ali Y, Jan Z, Rasheed S, Nazir NUA, Khan A, Rukh Abbas S, Wadood A, Rehman AU. Computational screening and analysis of deleterious nsSNPs in human p14ARF ( CDKN2A gene) protein using molecular dynamic simulation approach. J Biomol Struct Dyn 2023; 41:3964-3975. [PMID: 35446184 DOI: 10.1080/07391102.2022.2059570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
Cyclin-dependent kinase inhibitor 2 A (CDKN2A) gene belongs to the cyclin-dependent kinase family that code for two transcripts (p16INK4A and p14ARF), both work as tumor suppressors proteins. The mutation that occurs in the p14ARF protein can lead to different types of cancers. Single nucleotide polymorphisms (SNPs) are an important type of genetic alteration that can lead to different types of diseases. In this study, we applied the computational strategy on human p14ARF protein to identify the potential deleterious nsSNPs and check their impact on the structure, function, and protein stability. We applied more than ten prediction tools to screen the retrieved 288 nsSNPs, consequently extracting four deleterious nsSNPs i.e., rs139725688 (R10G), rs139725688 (R21W), rs374360796 (F23L) and rs747717236 (L124R). Homology modeling, conservation and conformational analysis of mutant models were performed to examine the divergence of these variants from the native p14ARF structure. All-atom molecular dynamics simulation revealed a significant impact of these mutations on protein stability, compactness, globularity, solvent accessibility and secondary structure elements. Protein-protein interactions indicated that p14ARF operates as a hub linking clusters of different proteins and that changes in p14ARF may result in the disassociation of numerous signal cascades. Our current study is the first survey of computational analysis on p14ARF protein that determines the association of these nsSNPs with the altered function of p14ARF protein and leads to the development of various types of cancers. This research proposes the described functional SNPs as possible targets for proteomic investigations, diagnostic procedures, and treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Syed Umair Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i- Azam University, Islamabad, Pakistan
| | - Zainab Jan
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-i- Azam University, Islamabad, Pakistan
| | - Noor Ul Ain Nazir
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Asif Khan
- Department of Botany, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Shah Rukh Abbas
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
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Chen J, Wang Y, Qi X, Cheng H, Chen N, Ahmed Z, Chen Q, Lei C, Yang X. Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China. Front Genet 2023; 14:1144249. [PMID: 37065480 PMCID: PMC10098193 DOI: 10.3389/fgene.2023.1144249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/17/2023] [Indexed: 04/01/2023] Open
Abstract
Altay white-headed cattle have not received enough attention for several reasons. Due to irrational breeding and selection practices, the number of pure Altay white-headed cattle has decreased significantly and the breed is now on the eve of extinction. The genomic characterization will be a crucial step towards understanding the genetic basis of productivity and adaptability to survival under native Chinese agropastoral systems; nevertheless, no attempt has been made in Altay white-headed cattle. In the current study, we compared the genomes of 20 Altay white-headed cattle to the genomes of 144 individuals in representative breeds. Population genetic diversity revealed that the nucleotide diversity of Altay white-headed cattle was less than that of indicine breeds and comparable to that of Chinese taurus cattle. Using population structure analysis, we also found that Altay white-headed cattle carried the ancestry of the European and East Asian cattle lineage. In addition, we used three different methods (FST, θπ ratio and XP-EHH) to investigate the adaptability and white-headed phenotype of Altay white-headed cattle and compared it with Bohai black cattle. We found EPB41L5, SCG5 and KIT genes on the list of the top one percent genes, these genes might have an association with environmental adaptability and the white-headed phenotype for this breed. Our research reveals the distinctive genomic features of Altay white-headed cattle at the genome-wide level.
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Affiliation(s)
- Jialei Chen
- Life Science College, Luoyang Normal University, Luoyang, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yushu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xingshan Qi
- Biyang Xianan Cattle Technology and Development Company Ltd., Biyang, China
| | - Haijian Cheng
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zulfiqar Ahmed
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, and Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Shabestar, Pakistan
| | - Qiuming Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- *Correspondence: Chuzhao Lei, ; Xueyi Yang,
| | - Xueyi Yang
- Life Science College, Luoyang Normal University, Luoyang, China
- *Correspondence: Chuzhao Lei, ; Xueyi Yang,
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Sensitivity and applications of the PCR Single-Strand Conformation Polymorphism method. Mol Biol Rep 2021; 48:3629-3635. [PMID: 33893925 PMCID: PMC8065318 DOI: 10.1007/s11033-021-06349-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/08/2021] [Indexed: 12/14/2022]
Abstract
PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.
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Preiss J, Almansouri Z. Validation through a comparison of physical examination and DNA test results: OLFML3 case study. Meta Gene 2021. [DOI: 10.1016/j.mgene.2020.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Al-Thuwaini TM, Al-Shuhaib MBS, Lepretre F, Dawud HH. Two co-inherited novel SNPs in the MC4R gene related to live body weight and hormonal assays in Awassi and Arabi sheep breeds of Iraq. Vet Med Sci 2020; 7:897-907. [PMID: 33369226 PMCID: PMC8136946 DOI: 10.1002/vms3.421] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 11/10/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022] Open
Abstract
Melanocortin‐4 receptor (MC4R) gene plays a key role in the regulation of body weight and energy homeostasis. This study aims to evaluate the association of single nucleotide polymorphisms (SNPs) of the MC4R gene with live body weight and hormonal assays in two breeds of sheep that differ in productive performance, Awassi and Arabi. All known coding sequences of the MC4R gene were covered in this study. DNA samples from 150 animals (Awassi and Arabi breed) were genotyped by PCR‐single‐strand conformation polymorphism (PCR‐SSCP) to assess their pattern of genetic variation. Concerning exon 1, clear heterogeneity was detected with three different SSCP‐banding patterns. The sequencing reactions confirmed these variations by detecting the presence of the two novel SNPs, 107G/C and 138A/C, and three genotypes, GC, AC and AA. The 107G/C SNP was detected in GC genotype, while the 138A/C was detected on both GC and AC genotypes. The other SSCP‐banding pattern (AA genotype) did not show any detectable unique variation. Both SNPs were closely and strongly linked in both breeds (D' and r2 values were 1.00), which signifies that both loci were co‐inherited as one unit. Association analysis indicated that both breeds with GC/AC haplotype showed higher live body weight (37.250 ± 0.790) relative to the GG/AA (30.244 ± 0.968) and CC/CC (47.231 ± 1.230) haplotypes (p < .05). Concerning the genotyping of exon 2, only 362 bp showed heterogeneity with a missense mutation, with no significant association (p > .05) with the measured traits. In conclusion, the two novel SNPs (107G/C and 138 A/C) were highly associated with live body weight in both breeds. Haplotype analysis confirmed that these two novel SNPs were in strong linkage disequilibrium (LD) and could be used as genetic markers for sheep phenotypic trait improvement.
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Affiliation(s)
- Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Babil, Iraq
| | | | - Frederic Lepretre
- University of Lille, Plateau de Genomique Fonctionnelle et Structurale, Lille, France
| | - Halla Hassan Dawud
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Babil, Iraq
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Albakri AH, Al-Shuhaib MBS, Alwan SL, AbdulAzeez S, Borgio JF. Deleterious missense variants in the aflatoxin biosynthesis genes explain the low toxicity of Aspergillus flavus from infected rice. Microb Pathog 2020; 152:104605. [PMID: 33166617 DOI: 10.1016/j.micpath.2020.104605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/23/2020] [Accepted: 11/02/2020] [Indexed: 01/10/2023]
Abstract
Aspergillus flavus is one of the most natural contaminants of the improperly stored rice grains. It produces several secondary metabolites, like aflatoxins, which are well known hepatotoxic, hepatocarcinogenic and mutagenic agents. This study describes the in silico consequences of the missense mutations identified in several genes of aflatoxins biosynthesis in rice-contaminating A. flavus isolates. In the in vitro portion of the study, aflatoxins production profile was measured, and PCR-single strand-conformation polymorphism (SSCP)-sequencing method was used to genotype the studied genetic loci: aflP, aflM, aflR, PEP, and cob. Results showed aflatoxigenic potential in 79 out of 109 A. flavus isolates. Twenty-two missense and fifty-five synonymous mutations were found to be distributed variably on the studied loci. In the in silico portion of this study, several computations were utilized to predict the effect of each observed missense mutation on proteins structure, function, and stability. Seven mutations (O-methyl transferase: p.G256C; ver-1 dehydrogenase: p.K179 N and p.V183L; aspergillopepsin-1: p.P137L, p.S138F, p.G154C, and p.S158C) were found to be highly deleterious among the missense variants with damaging effects on their proteins' structure and function. In contrast to these detected variations in the aflatoxigenic loci, all missense mutations in the control non-aflatoxigenic cob gene were found to be neutral. These findings indicated that the observed mutations may reduce the concomitant biohazard of their biosynthesized aflatoxins. The current findings suggest that the naturally available variants may reduce or eliminates the dangerous consequences of aflatoxins upon ingesting the rice infected with A. flavus. To the best of our knowledge, this study is the first comprehensive report to analyze the missense mutations on the aflatoxin biosynthesis genes using in vitro and the state-of-art bio-computational tools.
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Affiliation(s)
- Ali H Albakri
- Department of Plant Protection, College of Agriculture, University of Kufa, Al-Kufa, Najaf, 54001, Iraq.
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq.
| | - Sabah L Alwan
- Department of Plant Protection, College of Agriculture, University of Kufa, Al-Kufa, Najaf, 54001, Iraq.
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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Imran FS, Al-Thuwaini TM, Al-Shuhaib MBS, Lepretre F. A Novel Missense Single Nucleotide Polymorphism in the GREM1 Gene is Highly Associated with Higher Reproductive Traits in Awassi Sheep. Biochem Genet 2020; 59:422-436. [PMID: 33048279 DOI: 10.1007/s10528-020-10006-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/29/2020] [Indexed: 11/24/2022]
Abstract
GREM1 (gremlin1) is a known inhibitor for BMP15 (bone morphogenetic protein 15) family, but its genetic diversity in sheep is unknown. The present study was conducted to analyze the polymorphism of GREM1 gene using PCR- single-strand conformation polymorphism (SSCP) and DNA sequencing methods and to assess the possible association of GREM1 gene polymorphism with reproductive traits in Awassi ewes. A total of 224 ewes, 124 producing singles and 100 producing twins, were included in the study. Two SSCP patterns were detected in two amplified loci within the exon 2. Two exonic novel single nucleotide polymorphism (SNP)s were identified, c.74 T > G (the silent SNP p.Met123 =) and c.30 T > A with (the missense SNP p.Ile237Phe). Statistical analyses indicated a non-significant (P > 0.05) association of p.Met123 = with the analyzed reproductive traits of fecundity, prolificacy, litter size, and twinning rate. Meanwhile, p.Ile237Phe SNP exhibited a highly significant (P < 0.01) association with the measured reproductive traits, in which ewes with TA genotype (with p.Ile237Phe SNP) exhibited higher litter size, twinning ratio, fecundity, and prolificacy than those with TT genotype (without p.Ile237Phe SNP). The deleterious impact of p.Ile237Phe SNP was observed by the means of ten different state-of-the-art in silico tools that predicted a highly damaging effect of p.Ile237Phe SNP on the structure, function, and stability of gremlin1. In conclusion, the results of our study suggest that p.Ile237Phe SNP has a remarkable negative impact on the gremlin1 structure, function, and stability. Since gremlin1 is a known inhibitor of reproductive performance, a consequent higher reproductive performance was observed in ewes with damaged gremlin1 (with p.Ile237Phe SNP) than those with non-damaged gremlin1 (without p.Ile237Phe SNP). Therefore, it can be stated that the implementation of the novel p.Ile237Phe SNP in the GREM1 gene could be a useful marker in marker-assisted selection. This manuscript is the first one to describe GREM1 gene variations in sheep.
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Affiliation(s)
- Faris S Imran
- Branch of Physiology, College of Veterinary Medicine, University of Kerbala, Fraiha, Kerbala, 56001, Iraq
| | - Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq.
| | - Frederic Lepretre
- Univ. Lille, Plateau de Genomique Fonctionnelle Et Structurale, CHU Lille, Lille, France
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Al-Thuwaini TM, Al-Shuhaib MBS, Lepretre F, Mahdi ZA. Co-inherited novel SNPs of the LIPE gene associated with increased carcass dressing and decreased fat-tail weight in Awassi breed. Trop Anim Health Prod 2020; 52:3631-3638. [PMID: 32939705 DOI: 10.1007/s11250-020-02400-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022]
Abstract
The lipase E hormone-sensitive (LIPE) enzyme is one of the lipolytic enzymes, and it plays a key role in the regulation of adipose tissue deposition. This study was conducted to investigate the possible association between the LIPE gene variations and the main body weight measurements in Awassi sheep. A total of 160 of sexually mature Awassi rams (Ovis aries) that aged between 2 and 3 years were included in the present study. Genomic DNA was extracted and two specific PCR amplicons were designed to amplify two coding regions within the LIPE gene. Genotyping experiments were performed using polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP). Two different SSCP banding patterns were identified, CC and CD in exon 2, and AA and AT in exon 9. Five novel single-nucleotide polymorphisms (SNPs) were detected by sequencing, namely g.151C > A and g.198C > T in exon 2, and g.213G > C, g.226G > T, and g.232A > C in exon 9. Haplotype block analysis showed strong linkage disequilibrium values between the two SNPs in exon 2 and the three SNPs in exon 9. Association analysis of haplotypes with carcass traits demonstrated a significantly higher dressing percentage (P < 0.05) and lower fat tail weight (FTW) in CACT and GCGTAC haplotypes made these haplotypes more favorable for human consumption. The current research is the first one to report a tight association between the LIPE genetic polymorphism and the dressing percentage and FTW traits, suggesting a pivotal role played by these co-inherited SNPs in the metabolism of carcass traits in sheep.
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Affiliation(s)
- Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq.
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Frederic Lepretre
- Plateau de genomique fonctionnelle et structurale, CHU Lille, University of Lille, Lille, France
| | - Zainab A Mahdi
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
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Association between polymorphism in BMP15 and GDF9 genes and impairing female fecundity in diabetes type 2. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2020. [DOI: 10.1186/s43043-020-00032-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Background
A shortened reproductive period and earlier menopause have been associated with type 2 diabetes. Growth differentiation factor 9(GDF9) and bone morphogenetic protein 15 (BMP15) gene mutations have been associated with earlier menopause. Therefore, this study aimed to evaluate the association between BMP15 and GDF9 mutations with impairing female fecundity in diabetic patients. The study subjects comprised 90 female diabetic patients and 60 female healthy controls. The physio-biochemical analysis was measured using enzymatic determination. A single-strand conformation polymorphism (SSCP) protocol was utilized to assess the pattern of genetic variations.
Results
Genotyping analysis of the BMP15 gene showed a heterogeneous pattern with the presence of two genotypes: AA and AC genotypes. Five novel missense single nucleotide polymorphisms (SNPs) were identified in the BMP15 gene: four SNPs detected in both genotypes, and Met4Leu, a specific SNP, was detected only in the AC genotype. Cumulative in silico tools indicated a highly deleterious effect for the Met4Leu on the mutant protein structure, function, and stability. Diabetes patients showed a significantly higher frequency of genotype AC. The physio-biochemical analysis of fasting plasma glucose (FBG), glycosylated hemoglobin (HbA1c), and luteinizing hormone (LH) were significantly higher (P < 0.05) in AC genotype than AA genotype.
Conclusions
The current research provides the first indication regarding the tight association of BMP15 polymorphism with the impairing female fecundity in the diabetic. A pivotal role is played by the novel (Met4Leu) SNP that can be used as a predictor for the impairing female fecundity of diabetes, while no polymorphism was found in exon 4 of the GDF9 gene.
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Al-Thuwaini TM, Al-Shuhaib MBS, Hussein ZM. A novel T177P missense variant in the HSPA8 gene associated with the low tolerance of Awassi sheep to heat stress. Trop Anim Health Prod 2020; 52:2405-2416. [PMID: 32277322 DOI: 10.1007/s11250-020-02267-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/30/2020] [Indexed: 01/19/2023]
Abstract
This study was conducted to identify the association of coding variations in the HSPA8 gene with heat stress in two different breeds of sheep. All the coding regions of the HSPA8 gene of Awassi and Arabi sheep were covered by amplifying nine exons. A single-strand conformation polymorphism (SSCP) was utilized to assess the genetic variations in both breeds. The possible association of the observed genotypes with rectal temperature (RT), respiratory rate (RR), and heat tolerance coefficient (HTC) was analyzed in different seasons. While all the coding regions of both sheep were monomorphous, a remarkable heterogeneity was observed in exon 4, of which two SSCP patterns, a normal TT and a mutant TG, were detected. The TG genotype was characterized by a missense variant of T177P with frequencies of 77% in Awassi and 54% in Arabi. Cumulative in silico tools indicated extremely deleterious consequences for T177P on protein structure, function, and stability. Results indicated that sheep with the TT genotype had significantly (P < 0.05) lower RT, RR, and HTC values than sheep with the TG genotype. Therefore, a significant association of T177P with a lower tolerance of Awassi to higher temperature conditions was revealed. In conclusion, the identified T177P may have damaging effects in the HSPA8, which affects the ability of Awassi sheep to cope up with elevated temperatures compared with Arabi sheep. This manuscript describes a novel description of a highly deleterious missense variant in the HSPA8 gene that may reduce the ability of sheep to withstand high-temperature conditions.
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Affiliation(s)
- Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq.
| | - Zainab Manji Hussein
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
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Sarhan SR, Hashim HO, Al-Shuhaib MBS. The Gly152Val mutation possibly confers resistance to beta-lactam antibiotics in ovine Staphylococcus aureus isolates. Open Vet J 2019; 9:339-348. [PMID: 32042657 PMCID: PMC6971359 DOI: 10.4314/ovj.v9i4.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/21/2019] [Indexed: 12/30/2022] Open
Abstract
Background: The mecA gene is a key factor that allows bacterial cells to resist several antibiotics. Aim: This study was conducted to detect the mecA gene polymorphism in ovine wounds and its possible association with the structure and function of penicillin binding protein A2 (PBP2A). Methods: One genetic locus of 1,967 bp that covered the majority of the coding regions of the mecA gene within methicillin-resistant Staphylococcus aureus (MRSA) DNA sequences was designed. Results: In addition to standard microbiological tests, PCR-sequencing reactions and phylogenetic analyses confirmed the identity of the targeted MRSA bacteria. Seven novel missense SNPs, including N57T, N115Y, D120N, D139N, G152V, E189K, and F211V, were observed in the mecA amplicons. Multiple state-of-the-art in silico tools were utilized to assess the consequences of each observed SNP in terms of its effect on the corresponding PBP2A protein structure and function. It was shown that some MRSA isolates exhibited a highly PBP2A-damaging SNP, G152V, which showed an entirely deleterious effect on the PBP2A. Furthermore, G152V induced an alteration in the PBP2A interaction with its receptor, which presumably reduced its affinity to bind with the beta-lactams. Conclusion: The present report indicated a possible role for the observed deleterious G152V SNP in the reduction of PBP2A binding with beta-lactams, which has led to a remarkable increase in MRSA’s resistance to antibiotics.
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Affiliation(s)
- Sarhan R Sarhan
- Department of Pharmacology and Physiology, College of Veterinary Medicine, Wasit University, Wasit, Iraq
| | - Hayder O Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Iraq
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil 51001, Iraq
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Deleterious amino acid substitutions with a series of putative damaging effects on egg components are revealed in the ovalbumin gene family; an in silico approach. NOVA BIOTECHNOLOGICA ET CHIMICA 2019. [DOI: 10.2478/nbec-2019-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
This study was conducted to identify the most deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) in the ovalbumin gene family, including OVALX, OVALY, and OVAL genes, which are involved in the synthesis of the most important components in the chickens’ eggs using a comprehensive in silico approach. Ten different computational servers were utilized to prioritize the possible deleterious effects of the retrieved nsSNPs in terms of structure, function, and stability. Results indicated entirely damaging effects of H365P in OVALX, I167T in OVALY, and V209G, L231P, F307C, and S317P in OVAL proteins. Further prediction tools showed that all of these deleterious nsSNPs were positioned in variable locations within several α-helix motifs in all studied ovalbumin proteins. Furthermore, all witnessed nsSNPs were predicted to be resided in the receptors binding sites, signifying remarkable involvement of such nsSNPs in damaging of the altered proteins. In conclusion, the present study provides the first inclusive data with regard to the most deleterious nsSNPs in OVALX, OVALY and OVAL genes in chickens. The present bioinformatics data may be useful for breeders who intend to raise chickens for egg production, in such a way the presence of any of these deleterious nsSNPs in any selected breed may possess several damaging effects on the egg components, which may impair egg production. Therefore, it can be stated that breeders have to confirm the absence of any of these deleterious nsSNPs before being proceeded further for large-scale egg-production purposes.
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Al-Shuhaib MBS. D76V, L161R, and C117S are the most pathogenic amino acid substitutions with several dangerous consequences on leptin structure, function, and stability. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2019. [DOI: 10.1186/s43042-019-0033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Leptin is a versatile hormone with a variety of functions, including regulation of food intake by inhibiting hunger. Any deleterious mutation in this protein can lead to serious consequences for the body. This study was conducted to identify the most deleterious non-synonymous single-nucleotide polymorphisms (nsSNPs) of human LEP gene and their impact on its encoded protein.
Methods
To predict the possible impact of nsSNPs on leptin, a total of 90 nsSNPs were retrieved from dbSNP and investigated using many in silico tools which specially designed to analyze nsSNPs’ consequences on the protein structure, function, and stability.
Results
Three nsSNPs, namely D76V, L161R, and C117S, were found to be completely deleterious by all utilized nsSNPs prediction tools, thus affecting leptin protein structure, biological activity, and stability. Evolutionary information indicated L161R and C117S mutations to be located in extremely high conserved positions. Furthermore, several deleterious mechanisms controlled by both L161R and C117S mutations which alter several motifs in the secondary structure of leptin were detected. However, all D76V, L161R, and C117S mutations exhibited alteration in polar interactions in their representative positions. Further in-depth analyses proved several harmful structural effects of the three nsSNPs on leptin, which may lead to multiple intrinsic disorders in the altered protein forms.
Conclusions
This study provides the first comprehensive computation of the effect of the most damaging nsSNPs on leptin. The exploration of these missense mutations may present novel perspectives for various deleterious consequences originated from such amino acids substitutions. The dynamics of leptin performance, therefore, in many biological pathways, may be changed to create a variety of disorders, such as obesity and diabetes. These findings will help in detecting the most harmful variations needed to be screened for clinically diagnosed patients with leptin disorders.
Trial registration
ISRCTN73824458
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Al-Shuhaib MBS, Al-Kafajy FR, Al-Jashami GS. A computational approach for explaining the effect of the prl gene polymorphism on prolactin structure and biological activity in Japanese quails. Anim Biotechnol 2019; 32:273-281. [PMID: 31661660 DOI: 10.1080/10495398.2019.1683568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Prolactin is a versatile hormone with multiple activities, including a negative control on egg production. This study was conducted to genotype all the coding portions of the prl gene using PCR-SSCP-sequencing, and to investigate the effects of amino acid substitutions of the prl gene on the structure and function of prolactin in quails using in silico approach. Though all genotyped exons exerted homogenous PCR-SSCP patterns, a total of 12 novel SNPs were detected in the investigated exons, including three SNPs in exon-1, 8 SNPs in exon-2, and one SNP in exon-4. Three adjacent missense SNPs were detected in exon-2, namely H69P, T70P, and S71F. Computational tools indicated obvious deleterious effects of T70P, with less extent to H69P and S71F on prolactin functions and activity, which may lead to limited participation of this hormone in the negative control of egg production. In conclusion, the introduction of in silico prediction has suggested an alternative solution for the breeders to evaluate the effect of each witnessed nsSNP in protein structure and function. The current study suggests three nsSNPs, T70P, T70P, and S71F as strong candidates for the negative effect on prolactin biological activity with a consequent reversal positive effect on egg productivity traits.
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Affiliation(s)
| | - Fadhil R Al-Kafajy
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, Iraq
| | - Ghadeer S Al-Jashami
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, Iraq
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Al-Shuhaib MBS, Al-Thuwaini TM, Fadhil IA, Aljubouri TRS. GHRL gene-based genotyping of ovine and caprine breeds reveals highly polymorphic intronic sequences in Awassi sheep with several RNA motifs. J Genet Eng Biotechnol 2019; 17:3. [PMID: 31659533 PMCID: PMC6821144 DOI: 10.1186/s43141-019-0004-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/20/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND The current study was conducted to identify the genetic polymorphism of ghrelin (GHRL) gene of sheep and goats, as well as to determine whether these polymorphisms were associated with the evolutionary genetic differences in the involved species. This study was performed on 233 sheep and 91 goats. Two genetic loci of 113 bp and 262 bp partially spanning over exon 2/intron 2 and intron 4/exon 5 of GHRL gene respectively were amplified and genotyped using polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and DNA sequencing methods. RESULTS The SSCP banding pattern of 262-bp locus indicated the presence of four diplotypes (BC, BB, AC, and AB) in Awassi sheep, three diplotypes (BC, BB, and AB) in Karadi sheep, and only two diplotypes (BC and BB) in all goats' samples. The current study detected several novel SNPs in the ovine-caprine populations as well as two SNPs that are observed only in sheep, including intron4:119 C>A and intron4:123 T>G. The phylogenetic analysis revealed that the observed diplotypes resided within ovine sequences and were closely related to caprine counterparts. Computational analyses indicated the presence of various intronic RNA motifs. However, all these motifs were gathered in Awassi breed. CONCLUSION It is stated that the intron 4 is highly diverse amongst goats and sheep as well as within sheep with a particular emphasis on Awassi. This genetic peculiarity may in turn suggest a high polymorphic pattern of this breed in comparison with other related counterparts.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, 8-Al-Qasim, Hillah, Babil, 51001, Iraq.
| | - Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, 8-Al-Qasim, Hillah, Babil, 51001, Iraq
| | - Israa A Fadhil
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, 8-Al-Qasim, Hillah, Babil, 51001, Iraq
| | - Thamer R S Aljubouri
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, 8-Al-Qasim, Hillah, Babil, 51001, Iraq
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