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Hoda A, Bixheku X, Lika Çekani M. Computational analysis of non-synonymous single nucleotide polymorphism in the bovine PKLR geneComputational analysis of bovine PKLR gene. J Biomol Struct Dyn 2024; 42:4155-4168. [PMID: 37278385 DOI: 10.1080/07391102.2023.2219315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
Pyruvate kinase (PKLR) is a potential candidate gene for milk production traits in cows. The main aim of this work is to investigate the potentially deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the PKLR gene by using several computational tools. In silico tools including SIFT, Polyphen-2, SNAP2 and Panther indicated only 18 nsSNPs out of 170 were considered deleterious. The analysis of proteins' stability change due to amino acid substitution performed by the use of the I-mutant, MUpro, CUPSTAT, SDM and Dynamut confirmed that 9 nsSNPs decreased protein stability. ConSurf analysis predicted that all 18 nsSNPs were evolutionary moderately or highly conserved. Two different domains of PKLR protein were revealed by the InterPro tool with 12 nsSNPs positioned in the Pyruvate Kinase barrel domain and 6 nsSNP present in the Pyruvate Kinase C Terminal. The PKLR 3D model was predicted by MODELLER software and validated via Ramachandran plot and Prosa which indicated a good quality model. The analysis of energy minimizations for the native and mutated structures was performed by SWISS PDB viewer with GROMOS 96 program and showed that 3 structural and 4 functional residues had total energy higher than the native model. These findings indicate that these mutant structures (rs441424814, rs449326723, rs476805413, rs472263384, rs474320860, rs475521477, rs441633284) were less stable than the native model. Molecular Dynamics simulations were performed to confirm the impact of nsSNPs on the protein structure and function. The present study provides useful information about functional SNPs that have an impact on PKLR protein in cattle.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anila Hoda
- Agricultural University of Tirana, Tirana, Albania
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Kwak MJ, Ha DJ, Park MY, Eor JY, Whang KY, Kim Y. Comparison study between single enzyme and multienzyme complex in distiller's dred grains with soluble supplemented diet in broiler chicken. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:398-411. [PMID: 38628689 PMCID: PMC11016744 DOI: 10.5187/jast.2023.e90] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 04/19/2024]
Abstract
Upregulation of the nutritional value of feed is the major target of various studies in the livestock industry, and dietary enzyme supplementation could aid in digesting the nondegrading nutrients of grains in feed ingredients. Dried distillers' grains with solubles (DDGS) is a byproduct of the fermentation process in the beverage industry and can be used as a large supply source of fiber in feed. Therefore, we conducted an experiment with male broiler chickens to investigate the effect of various types of enzymes on DDGS and compare the efficacy of single enzyme and multienzyme complexes on growth performance and gut environments in broiler chickens. We used 420 1-day-old broiler chickens (Ross 308), and they were allotted into 4 dietary treatments with seven replications (CON, corn-soybean meal [SBM] diet; NC, DDGS supplemented diet; SE, 0.05 % of mannanase supplemented DDGS-based diet; MC, 0.10% of multienzyme complex (mannanase and xylanase, glucanase) supplemented DDGS-based diet. The dietary exogenous enzyme in the DDGS-supplemented diet could improve growth performance as much as the growth of the control group, and digestibility of dry matter, crude protein, and gross energy were significantly increased by enzyme addition in groups of chicks fed DDGS-supplementation diet. Moreover, the populations of pathogenic bacteria, coliforms, and Bacteroidetes were significantly decreased by enzyme supplementation, which might lead to improved gut mucus-secreting cells and inflammatory cytokines in the jejunum. Collectively, dietary single enzyme and multienzyme complexes could improve gut environments, including intestinal immune responses and gut microbial population, and lead to improvement of growth performance in broiler chickens.
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Affiliation(s)
- Min-Jin Kwak
- Department of Agricultural Biotechnology
and Research Institute of Agriculture and Life Science, Seoul National
University, Seoul 08826, Korea
| | - Dong-Jin Ha
- Division of Biotechnology, College of Life
Science and Biotechnology, Korea University, Seoul 02841,
Korea
| | - Min Young Park
- Department of Basic Science and
Craniofacial Biology, New York University College of
Dentistry, New York 10012, USA
| | - Ju Young Eor
- Department of Agricultural Biotechnology
and Research Institute of Agriculture and Life Science, Seoul National
University, Seoul 08826, Korea
| | - Kwang-Youn Whang
- Division of Biotechnology, College of Life
Science and Biotechnology, Korea University, Seoul 02841,
Korea
| | - Younghoon Kim
- Department of Agricultural Biotechnology
and Research Institute of Agriculture and Life Science, Seoul National
University, Seoul 08826, Korea
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Huang J, Yin H, Zhang Y, Qiao H, Su L, Wang J. Expression of TGF-β/Smads in Cecum and Spleen of Chicken Infected with E. Tenella. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2022. [DOI: 10.1590/1806-9061-2021-1446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- J Huang
- Henan University of Technology, China; State Administration of Grain, China
| | - H Yin
- Henan University of Technology, China; State Administration of Grain, China
| | - Y Zhang
- Henan University of Technology, China
| | - H Qiao
- Henan University of Technology, China
| | - L Su
- Henan University of Technology, China
| | - J Wang
- Henan University of Technology, China
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Juárez OE, Lafarga-De la Cruz F, Lazo JP, Delgado-Vega R, Chávez-García D, López-Landavery E, Tovar-Ramírez D, Galindo-Sánchez CE. Transcriptomic assessment of dietary fishmeal partial replacement by soybean meal and prebiotics inclusion in the liver of juvenile Pacific yellowtail (Seriola lalandi). Mol Biol Rep 2021; 48:7127-7140. [PMID: 34515920 DOI: 10.1007/s11033-021-06703-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/07/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Seriola lalandi is an important species for aquaculture, due to its rapid growth, adaptation to captivity and formulated diets, and high commercial value. Due to the rise in fishmeal (FM) price, efforts have been and still are made to replace it partially or entirely with vegetable meals in diets for carnivorous fish. The use of prebiotics when feeding vegetable meals has improved fish health. METHODS Four experimental diets were assessed in juveniles, the control diet consisted of FM as the main protein source, the second diet included 2% of GroBiotic®-A (FM-P), in the third diet FM was partially replaced (25%) by soybean meal (SM25), and the fourth consisted of SM25 with 2% of GroBiotic®-A (SM25-P). Growth was evaluated and RNA-seq of the liver tissue was performed, including differential expression analysis and functional annotation to identify genes affected by the diets. RESULTS Growth was not affected by this level of FM replacement, but it was improved by prebiotics. Annotation was achieved for 59,027 transcripts. Gene expression was affected by the factors: 225 transcripts due to FM replacement, 242 due to prebiotics inclusion, and 62 due to the interaction of factors. The SM25-P diet showed the least amount of differentially expressed genes against the control diet. CONCLUSION The replacement of FM (25%) by soybean meal combined with prebiotics (2%) represents a good cost-benefit balance for S. lalandi juveniles since the fish growth increased and important metabolic and immune system genes in the liver were upregulated with this diet.
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Affiliation(s)
- Oscar E Juárez
- Department of Marine Biotechnology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana #3918, Zona Playitas, 22860, Ensenada, Baja California, México
| | - Fabiola Lafarga-De la Cruz
- Department of Aquaculture, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana #3918, Zona Playitas, 22860, Ensenada, Baja California, México
| | - Juan Pablo Lazo
- Department of Aquaculture, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana #3918, Zona Playitas, 22860, Ensenada, Baja California, México
| | - Rigoberto Delgado-Vega
- Department of Aquaculture, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana #3918, Zona Playitas, 22860, Ensenada, Baja California, México
| | - Denisse Chávez-García
- Department of Aquaculture, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana #3918, Zona Playitas, 22860, Ensenada, Baja California, México
| | - Edgar López-Landavery
- Department of Marine Biotechnology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana #3918, Zona Playitas, 22860, Ensenada, Baja California, México
| | - Dariel Tovar-Ramírez
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional #195, Playa Palo de Santa Rita Sur, 23096, La Paz, Baja California Sur, México
| | - Clara Elizabeth Galindo-Sánchez
- Department of Marine Biotechnology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana #3918, Zona Playitas, 22860, Ensenada, Baja California, México.
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Computational analysis of missense variants in MMP2 gene linked with Winchester syndrome and Nodulosis-Arthropathy-Osteolysis reveals structural shift in protein-protein and protein-ligand complexes. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Pang M, Luo W, Fu B, Yu X, Zhou Y, Tong J. Transcriptomic Profiles of Brain Provide Insights into Molecular Mechanism of Feed Conversion Efficiency in Crucian Carp (Carassius auratus). Int J Mol Sci 2018. [PMID: 29538345 PMCID: PMC5877719 DOI: 10.3390/ijms19030858] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Feed efficiency is an economically crucial trait for cultured animals, however, progress has been scarcely made in the genetic analyses of feed conversion efficiency (FCE) in fish because of the difficulties in measurement of trait phenotypes. In the present investigation, we present the first application of RNA sequencing (RNA-Seq) combined with differentially expressed genes (DEGs) analysis for identification of functional determinants related to FCE at the gene level in an aquaculture fish, crucian carp (Carassius auratus). Brain tissues of six crucian carp with extreme FCE performances were subjected to transcriptome analysis. A total of 544,612 unigenes with a mean size of 644.38 bp were obtained from Low- and High-FCE groups, and 246 DEGs that may be involved in FCE traits were identified in these two groups. qPCR confirmed that genes previously identified as up- or down-regulated by RNA-Seq were effectively up- or down-regulated under the studied conditions. Thirteen key genes, whose functions are associated with metabolism (Dgkk, Mgst3 and Guk1b), signal transduction (Vdnccsa1b, Tgfα, Nr4a1 and Tacr2) and growth (Endog, Crebrtc2, Myh7, Myh1,Myh14 and Igfbp7) were identified according to GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations. Our novel findings provide useful pathway information and candidate genes for future studies of genetic mechanisms underlying FCE in crucian carp.
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Affiliation(s)
- Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Weiwei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
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Patel JB, Chauhan JB. Computational analysis of non-synonymous single nucleotide polymorphism in the bovine cattle kappa-casein (CSN3) gene. Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Pang M, Fu B, Yu X, Liu H, Wang X, Yin Z, Xie S, Tong J. Quantitative trait loci mapping for feed conversion efficiency in crucian carp (Carassius auratus). Sci Rep 2017; 7:16971. [PMID: 29209087 PMCID: PMC5717303 DOI: 10.1038/s41598-017-17269-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/21/2017] [Indexed: 11/29/2022] Open
Abstract
QTL is a chromosomal region including single gene or gene clusters that determine a quantitative trait. While feed efficiency is highly important in aquaculture fish, little genetic and genomic progresses have been made for this trait. In this study, we constructed a high-resolution genetic linkage map in a full-sib F1 family of crucian carp (Carassius auratus) consisting of 113 progenies with 8,460 SNP markers assigning onto 50 linkage groups (LGs). This genetic map spanned 4,047.824 cM (0.478 cM/marker) and covered 98.76% of the crucian carp genome. 35 chromosome-wide QTL affecting feed conversion efficiency (FCE, 8 QTL), relative growth rate (RGR, 9 QTL), average daily gain (ADG, 13 QTL) and average daily feed intake (ADFI, 5 QTL) were detected on 14 LGs, explaining 14.0–20.9% of the phenotypic variations. In LGs of LG16, LG25, LG36 and LG49, several QTL affecting different traits clustered together at the identical or close regions of the same linkage group. Seven candidate genes, whose biological functions may involve in the energy metabolism, digestion, biosynthesis and signal transduction, were identified from these QTL intervals by comparative genomics analysis. These results provide a basis for elucidating genetic mechanism of feed efficiency and potential marker-assisted selection in crucian carp.
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Affiliation(s)
- Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xinhua Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Shouqi Xie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Yoshida GM, Lhorente JP, Carvalheiro R, Yáñez JM. Bayesian genome-wide association analysis for body weight in farmed Atlantic salmon (Salmo salar L.). Anim Genet 2017; 48:698-703. [PMID: 29044715 DOI: 10.1111/age.12621] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2017] [Indexed: 12/15/2022]
Abstract
We performed a genome-wide association study to detect markers associated with growth traits in Atlantic salmon. The analyzed traits included body weight at tagging (BWT) and body weight at 25 months (BW25M). Genotypes of 4662 animals were imputed from the 50K SNP chip to the 200K SNP chip using fimpute software. The markers were simultaneously modeled using Bayes C to identify genomic regions associated with the traits. We identified windows explaining a maximum of 3.71% and 3.61% of the genetic variance for BWT and BW25M respectively. We found potential candidate genes located within the top ten 1-Mb windows for BWT and BW25M. For instance, the vitronectin (VTN) gene, which has been previously reported to be associated with cell growth, was found within one of the top ten 1-Mb windows for BWT. In addition, the WNT1-inducible-signaling pathway protein 3, melanocortin 2 receptor accessory protein 2, myosin light chain kinase, transforming growth factor beta receptor type 3 and myosin light chain 1 genes, which have been reported to be associated with skeletal growth in humans, growth stimulation during the larval stage in zebrafish, body weight in pigs, feed conversion in chickens and growth rate of sheep skeletal muscle respectively, were found within some of the top ten 1-Mb windows for BW25M. These results indicate that growth traits are most likely controlled by many variants with relatively small effects in Atlantic salmon. The genomic regions associated with the traits studied here may provide further insight into the functional regions underlying growth traits in this species.
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Affiliation(s)
- G M Yoshida
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, La Pintana, Santiago, 8820808, Chile.,Animal Science Department, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Campus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, 14884-900, Jaboticabal, Brazil
| | | | - R Carvalheiro
- Animal Science Department, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Campus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, 14884-900, Jaboticabal, Brazil
| | - J M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, La Pintana, Santiago, 8820808, Chile.,Aquainnovo, Cardonal S/N, Puerto Montt, Chile
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Computational Analysis of High Risk Missense Variant in Human UTY Gene: A Candidate Gene of AZFa Sub-region. J Reprod Infertil 2017; 18:298-306. [PMID: 29062794 PMCID: PMC5641439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The human Ubiquitously transcribed tetratricopeptide repeat gene, Y-linked (UTY) gene encodes histone demethylase involved in protein-protein interactions. UTY protein evidence at protein level predicted intracellular and secreted protein. UTY is also involved in spermatogenesis process. METHODS The high-risk non-synonymous single nucleotide polymorphism in the coding region of the UTY gene was screened by SNP database and identified missense variants were subjected to computational analysis to understand the effect on protein function, stability and structure by SIFT, PolyPhen 2, PANTHER, PROVEAN, I-Mutant 2, iPTREE-STAB, ConSurf, ModPred, SPARKS-X, QMEAN, PROCHECK, project HOPE and STRING. RESULTS A total of 151 nsSNPs variants were retrieved in UTY gene out of which one missense variant (E18D) was predicted to be damaging or deleterious using SIFT, PolyPhen 2, PANTHER and PROVEAN. Additionally, E18D variant showed less stability, high conservation and having role in post translation modification using i-Mutant 2 and iPTREE-STAB, ConSurf and ModPred, respectively. The predicted 3D model of UTY using SPARKS-X with z-score of 15.16 was generated and validated via QMEAN (Z-score of 0.472) and PROCHECK which plots Ramachandran plot (85.3% residues in most favored regions, 12.3% in additionally allowed regions, 2.0% in generously allowed regions and 4.0% were in disallowed regions) and it indicates a good quality model. STRING showed that UTY interacts with ten different proteins. CONCLUSION This study revealed that SNP data available on database was deduced to find out the most damaging nsSNPs i.e. rs3212293 (E18D). Therefore, it provides useful information about functional SNPs for future prospects concerning infertility in men.
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Bhardwaj A, Dhar YV, Asif MH, Bag SK. In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations. Sci Rep 2016; 6:38715. [PMID: 27929054 PMCID: PMC5144076 DOI: 10.1038/srep38715] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022] Open
Abstract
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases. Out of these, 1838 SNPs were non-synonymous and distributed in 988 protein coding genes. Among these, 23 genes containing 96 SNPs were involved in traits markedly different between the two species. Furthermore, there were 28 deleterious SNPs distributed in 27 genes and a few of these genes were involved in plant pathogen interaction and plant hormone pathways. Molecular docking and simulations of several selected proteins showed the effect of SNPs in terms of compactness, conformation and interaction ability. Observed SNPs exhibited various types of motif binding effects due to nucleotide changes. SNPs that provide the evidence of differential motif binding and interaction behaviour could be effectively used for the crop improvement program.
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Affiliation(s)
- Archana Bhardwaj
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Yogeshwar Vikram Dhar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Mehar Hasan Asif
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Sumit K Bag
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
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Liu J, Sun Y, Yang C, Zhang Y, Jiang Q, Huang J, Ju Z, Wang X, Zhong J, Wang C. Functional SNPs of INCENP Affect Semen Quality by Alternative Splicing Mode and Binding Affinity with the Target Bta-miR-378 in Chinese Holstein Bulls. PLoS One 2016; 11:e0162730. [PMID: 27669152 PMCID: PMC5036895 DOI: 10.1371/journal.pone.0162730] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/26/2016] [Indexed: 12/22/2022] Open
Abstract
Inner centromere protein (INCENP) plays an important role in mitosis and meiosis as the main member of chromosomal passenger protein complex (CPC). To investigate the functional markers of the INCENP gene associated with semen quality, the single nucleotide polymorphisms (SNPs) g.19970 A>G and g.34078 T>G were identified and analyzed. The new splice variant INCENP-TV is characterized by the deletion of exon 12. The g.19970 A>G in the exonic splicing enhancer (ESE) motif region results in an aberrant splice variant by constructing two minigene expression vectors using the pSPL3 exon capturing vector and transfecting vectors into MLTC-1 cells. INCENP-TV was more highly expressed than INCENP-reference in adult bull testes. The g.34078 T>G located in the binding region of bta-miR-378 could affect the expression of INCENP, which was verified by luciferase assay. To analyze comprehensively the correlation of SNPs with sperm quality, haplotype combinations constructed by g.19970 A>G and g.34078 T>G, as well as g.-692 C>T and g.-556 G>T reported in our previous studies, were analyzed. The bulls with H1H12 and H2H2 exhibited a higher ejaculate volume than those with H2H10 and H9H12, respectively (P < 0.05). Bulls with H11H11 and H2H10 exhibited higher initial sperm motility than those with H2H2 (P < 0.05). The expression levels of INCENP in bulls with H1H12 and H11H11 were significantly higher than those in bulls with H9H12 (P < 0.05), as determined by qRT-PCR. Findings suggest that g.19970 A>G and g.34078 T>G in INCENP both of which appear to change the molecular and biological characteristics of the mRNA transcribed from the locus may serve as a biomarkers of male bovine fertility by affecting alternative splicing mode and binding affinity with the target bta-miR-378.
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Affiliation(s)
- Juan Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
- College of Agronomic Sciences in Shandong Agricultural University, Taian, China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
- * E-mail:
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Identification of Deleterious Mutations in Myostatin Gene of Rohu Carp (Labeo rohita) Using Modeling and Molecular Dynamic Simulation Approaches. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7562368. [PMID: 27019850 PMCID: PMC4785247 DOI: 10.1155/2016/7562368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/13/2016] [Accepted: 01/27/2016] [Indexed: 11/18/2022]
Abstract
The myostatin (MSTN) is a known negative growth regulator of skeletal muscle. The mutated myostatin showed a double-muscular phenotype having a positive significance for the farmed animals. Consequently, adequate information is not available in the teleosts, including farmed rohu carp, Labeo rohita. In the absence of experimental evidence, computational algorithms were utilized in predicting the impact of point mutation of rohu myostatin, especially its structural and functional relationships. The four mutations were generated at different positions (p.D76A, p.Q204P, p.C312Y, and p.D313A) of MSTN protein of rohu. The impacts of each mutant were analyzed using SIFT, I-Mutant 2.0, PANTHER, and PROVEAN, wherein two substitutions (p.D76A and p.Q204P) were predicted as deleterious. The comparative structural analysis of each mutant protein with the native was explored using 3D modeling as well as molecular-dynamic simulation techniques. The simulation showed altered dynamic behaviors concerning RMSD and RMSF, for either p.D76A or p.Q204P substitution, when compared with the native counterpart. Interestingly, incorporated two mutations imposed a significant negative impact on protein structure and stability. The present study provided the first-hand information in identifying possible amino acids, where mutations could be incorporated into MSTN gene of rohu carp including other carps for undertaking further in vivo studies.
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