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P SS, Chennuru S, Krovvidi S, Chitichoti J. Status of tick-borne haemoprotozoan infection in south Indian sheep in association with variation in Ovar-DRB1 gene. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Differential regulation of mRNAs and lncRNAs related to lipid metabolism in Duolang and Small Tail Han sheep. Sci Rep 2022; 12:11157. [PMID: 35778462 PMCID: PMC9249921 DOI: 10.1038/s41598-022-15318-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/22/2022] [Indexed: 11/21/2022] Open
Abstract
The function of long non-coding RNA (lncRNA) can be achieved through the regulation of target genes, and the deposition of fat is regulated by lncRNA. Fat has an important effect on meat quality. However, there are relatively few studies on lncRNAs in the subcutaneous adipose tissue of Duolang sheep and Small Tail Han sheep. In this study, RNA-Seq technology and bioinformatics methods were used to identify and analyze the lncRNA and mRNA in the subcutaneous adipose tissue of the two breeds of sheep. The results showed that 107 lnRNAs and 1329 mRNAs were differentially expressed. The differentially expressed genes and lncRNA target genes were significantly enriched in the biosynthesis of unsaturated fatty acids signaling pathway, fatty acid metabolism, adipocyte differentiation and other processes related to fat deposition. Among them, LOC105616076, LOC114118103, LOC105607837, LOC101116622, and LOC105603235 target FADS1, SCD, ELOVL6, HSD17B12 and HACD2, respectively. They play a key regulatory role in the biosynthesis of unsaturated fatty acids. This study lays a foundation for the study of the molecular mechanism of lncRNA on fat development, and has reference value for studying the differences in fat deposition between Duolang sheep and Small Tail Han sheep.
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Li X, Jiang S, Wang X, Jia B. Intestinal transcriptomes in Kazakh sheep with different haplotypes after experimental Echinococcus granulosus infection. Parasite 2021; 28:14. [PMID: 33666549 PMCID: PMC7934610 DOI: 10.1051/parasite/2021011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/04/2021] [Indexed: 11/20/2022] Open
Abstract
Cystic echinococcosis (CE) is a chronic zoonosis caused by infection with the larval stage of the cestode Echinococcus granulosus. As the intermediate host, sheep are highly susceptible to this disease. Our previous studies have shown that sheep with haplotype MHC Mva Ibc-Sac IIab-Hin1I ab were resistant to CE infection, while their counterparts without this haplotype were not. In order to reveal the molecular mechanism of resistance in Kazakh sheep, after selecting the differential miRNA in our previous study, herein, transcriptome analyses were conducted to detect the differential expression genes in the intestinal tissue of Kazakh sheep with resistant and non-resistant MHC haplotypes, after peroral infection with E. granulosus eggs. A total of 3835 differentially expressed genes were identified between the two groups, with 2229 upregulated and 1606 downregulated. Further function analysis showed that the most significant genes were related to both innate immune response and adaptive response participating in the defense against E. granulosus infection and the metabolic changes associated with it. The results suggest that genes related to lectin receptors, NK cells activation, chemokines, and tumor necrosis factor, may play important roles in the response of intestinal tissue to E. granulosus.
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Affiliation(s)
- Xin Li
- College of Life Sciences, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China - College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Song Jiang
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Xuhai Wang
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Bin Jia
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
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MHC-DRB1 exon 2 polymorphism and its association with mycoplasma ovipneumonia resistance or susceptibility genotypes in sheep. J Genet 2020. [DOI: 10.1007/s12041-020-1175-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Pourseif MM, Moghaddam G, Naghili B, Saeedi N, Parvizpour S, Nematollahi A, Omidi Y. A novel in silico minigene vaccine based on CD4 + T-helper and B-cell epitopes of EG95 isolates for vaccination against cystic echinococcosis. Comput Biol Chem 2017; 72:150-163. [PMID: 29195784 DOI: 10.1016/j.compbiolchem.2017.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 01/03/2023]
Abstract
EG95 oncospheral antigen plays a crucial role in Echinococcus granulosus pathogenicity. Considering the diversity of antigen among different EG95 isolates, it seems to be an ideal antigen for designing a universal multivalent minigene vaccine, so-called multi-epitope vaccine. This is the first in silico study to design a construct for the development of global EG95-based hydatid vaccine against E. granulosus in intermediate hosts. After antigen sequence selection, the three-dimensional structure of EG95 was modeled and multilaterally validated. The preliminary parameters for B-cell epitope prediction were implemented such as the possible transmembrane helix, signal peptide, post-translational modifications and allergenicity. The high ranked linear and conformational B-cell epitopes derived from several online web-servers (e.g., ElliPro, BepiPred v1.0, BcePred, ABCpred, SVMTrip, IEDB algorithms, SEPPA v2.0 and Discotope v2.0) were utilized for multiple sequence alignment and then for engineering the vaccine construct. T-helper based epitopes were predicted by molecular docking between the high frequent ovar class II allele (Ovar-DRB1*1202) and hexadecamer fragments of the EG95 protein. Having used the immune-informatics tools, we formulated the first EG95-based minigene vaccine based on T-helper epitope with high-binding affinity to the ovar MHC allele. This designed construct was analyzed for different physicochemical properties. It was also codon-optimized for high-level expression in Escherichia coli k12. Taken all, we propose the present in silico vaccine constructs as a promising platform for the generation of broadly protective vaccines for species and genus-specific immunization of the natural hosts of the parasite.
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Affiliation(s)
- Mohammad M Pourseif
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran; Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamali Moghaddam
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Behrouz Naghili
- Research Center for Infectious and Tropical Diseases, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazli Saeedi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Nematollahi
- Department of Pathobiology, Veterinary College, University of Tabriz, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; School of Advanced Biomedical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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Yakubu A, Salako AE, De Donato M, Peters SO, Takeet MI, Wheto M, Okpeku M, Imumorin IG. Association of SNP variants of MHC Class II DRB gene with thermo-physiological traits in tropical goats. Trop Anim Health Prod 2016; 49:323-336. [PMID: 27909914 DOI: 10.1007/s11250-016-1196-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/24/2016] [Indexed: 11/30/2022]
Abstract
Host defense in vertebrates depend on many secreted regulatory proteins such as major histocompatibility complex (MHC) class II which provide important regulatory and effector functions of T cells. Gene polymorphism in the second exon of Capra-DRB gene in three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS), and Sahel (SH)] was analyzed by restriction fragment length polymorphisms (RFLP). Four restriction enzymes, BsaHI, AluI, HaeIII, and SacII, were utilized. The association between the polymorphic sites and some heat tolerance traits were also investigated in a total of 70 WAD, 90 RS, and 50 SH goats. Fourteen different types of alleles identified in the Nigerian goats, four of which were found in the peptide coding region (A57G, Q89R, G104D, and T112I), indicate a high degree of polymorphism at the DRB locus in this species. An obvious excess (P < 0.01) of non-synonymous substitutions than synonymous (dN/dS) in this locus is a reflection of adaptive evolution and positive selection. The phylogenetic trees revealed largely species-wise clustering in DRB gene. BsaHI, AluI, HaeIII, and SacII genotype frequencies were in Hardy-Weinberg equilibrium (P > 0.05), except AluI in RS goats and HaeIII in WAD goats (P < 0.05). The expected heterozygosity (H), which is a measure of gene diversity in the goat populations, ranged from 0.16 to 0.50. Genotypes AA (BsaHI), GG, GC and CC (AluI) and GG, GA, AA (HaeIII) appeared better in terms of heat tolerance. The heat-tolerant ability of SH and RS goats to the hot and humid tropical environment of Nigeria seemed better than that of the WAD goats. Sex effect (P < 0.05) was mainly on pulse rate and heat stress index, while there were varying interaction effects on heat tolerance. Variation at the DRB locus may prove to be important in possible selection and breeding for genetic resistance to heat stress in the tropics.
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Affiliation(s)
- Abdulmojeed Yakubu
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA. .,Department of Animal Science, Nasarawa State University, Lafia, Nigeria. .,Department of Animal Science, University of Ibadan, Ibadan, Nigeria.
| | | | - Marcos De Donato
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Laboratorio Genetica Molecular, IBB, Universidad de Oriente, Cumana, Venezuela
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mt Berry, GA, 30249, USA
| | - Michael I Takeet
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Department of Veterinary Microbiology and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Mathew Wheto
- Department of Animal Breeding and Genetics, University of Agriculture, Abeokuta, Nigeria
| | - Moses Okpeku
- Department of Livestock Production, Niger Delta University, Amassoma, Nigeria.,State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Science (CAS), Kunming Institute of Zoology, Kunming, Yunnan Province, China
| | - Ikhide G Imumorin
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.
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Jiang S, Li X, Wang X, Ban Q, Hui W, Jia B. MicroRNA profiling of the intestinal tissue of Kazakh sheep after experimental Echinococcus granulosus infection, using a high-throughput approach. ACTA ACUST UNITED AC 2016; 23:23. [PMID: 27235195 PMCID: PMC4884269 DOI: 10.1051/parasite/2016023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/30/2016] [Indexed: 12/15/2022]
Abstract
Cystic echinococcosis (CE), caused by infection with the larval stage of the cestode Echinococcus granulosus, is a chronic zoonosis, to which sheep are highly susceptible. Previously, we found that Kazakh sheep with different MHC haplotypes differed in CE infection. Sheep with haplotype MHCMvaIbc-SacIIab-Hin1Iab were resistant to CE infection, while their counterparts without this haplotype were not. MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at the post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. To identify microRNA controlling resistance to CE in the early stage of infection, microRNA profiling was conducted in the intestinal tissue of sheep with resistant and non-resistant MHC haplotypes after peroral infection with E. granulosus eggs. A total of 351 known and 186 novel miRNAs were detected in the resistant group, against 353 known and 129 novel miRNAs in the non-resistant group. Among these miRNAs, 83 known miRNAs were significantly differentially expressed, including 75 up-regulated and 8 down-regulated miRNAs. Among these known microRNAs, miR-21-3p, miR-542-5p, miR-671, miR-134-5p, miR-26b, and miR-27a showed a significantly higher expression in CE-resistant sheep compared to the CE-non-resistant library, with the FC > 3. Functional analysis showed that they were NF-kB pathway-responsive miRNAs, which are involved in the inflammation process. The results suggest that these microRNAs may play important roles in the response of intestinal tissue to E. granulosus.
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Affiliation(s)
- Song Jiang
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Xin Li
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Xuhai Wang
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Qian Ban
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Road Jiulong, Hefei 230000, Anhui, PR China
| | - Wenqiao Hui
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China - Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Sciences, Road Nongkenan, Hefei 230031, Anhui, PR China
| | - Bin Jia
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
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Shrivastava K, Kumar P, Sahoo NR, Kumar A, Khan MF, Kumar A, Prasad A, Patel BHM, Nasir A, Bhushan B, Sharma D. Genotyping of major histocompatibility complex Class II DRB gene in Rohilkhandi goats by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing. Vet World 2015; 8:1183-8. [PMID: 27047015 PMCID: PMC4774653 DOI: 10.14202/vetworld.2015.1183-1188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/26/2015] [Accepted: 09/05/2015] [Indexed: 11/16/2022] Open
Abstract
Aim: To study the major histocompatibility complex (MHC) Class II DRB1 gene polymorphism in Rohilkhandi goat using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and nucleotide sequencing techniques. Materials and Methods: DNA was isolated from 127 Rohilkhandi goats maintained at sheep and goat farm, Indian Veterinary Research Institute, Izatnagar, Bareilly. A 284 bp fragment of exon 2 of DRB1 gene was amplified and digested using BsaI and TaqI restriction enzymes. Population genetic parameters were calculated using Popgene v 1.32 and SAS 9.0. The genotypes were then sequenced using Sanger dideoxy chain termination method and were compared with related breeds/species using MEGA 6.0 and Megalign (DNASTAR) software. Results: TaqI locus showed three and BsaI locus showed two genotypes. Both the loci were found to be in Hardy–Weinberg equilibrium (HWE), however, population genetic parameters suggest that heterozygosity is still maintained in the population at both loci. Percent diversity and divergence matrix, as well as phylogenetic analysis revealed that the MHC Class II DRB1 gene of Rohilkhandi goats was found to be in close cluster with Garole and Scottish blackface sheep breeds as compared to other goat breeds included in the sequence comparison. Conclusion: The PCR-RFLP patterns showed population to be in HWE and absence of one genotype at one locus (BsaI), both the loci showed excess of one or the other homozygote genotype, however, effective number of alleles showed that allelic diversity is present in the population. Sequence comparison of DRB1 gene of Rohilkhandi goat with other sheep and goat breed assigned Rohilkhandi goat in divergence with Jamanupari and Angora goats.
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Affiliation(s)
- Kush Shrivastava
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Pushpendra Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Nihar Ranjan Sahoo
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Amod Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Mohd Faheem Khan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Amit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Arvind Prasad
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - B H M Patel
- LPM Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - A Nasir
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Deepak Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
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Polat M, Aida Y, Takeshima SN, Aniwashi J, Halik M. The diversity of major histocompatibility complex class II DRB1 gene in sheep breeds from Xinjiang, China. ACTA ACUST UNITED AC 2014; 85:50-7. [PMID: 25430475 DOI: 10.1111/tan.12480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 10/14/2014] [Accepted: 10/28/2014] [Indexed: 11/24/2022]
Abstract
Exon 2 of the ovine leukocyte antigen OLA-DRB1 locus was examined in sheep from the Xinjiang Karakul Ram and Bashibai populations, and three generations of hybrids were derived from a cross between Bashibai and Altai Argali wild sheep. This identified 12 novel alleles and 30 previously reported alleles. A neighbor-joining tree of the amino acid sequences of these 42 alleles revealed allelic clusters shared across the study populations. There were significant differences in allelic frequency between Karakul Ram and Bashibai sheep. DRB1*K18cC was the most frequent allele in Kararul Ram with a frequency of 21.2%, while DRB1*2F10c8 (13.2%) and DRB1*0803 (13.2%) were the most frequent alleles found in Bashibai sheep; the alleles DRB1*2F16c2, DRB1*1601, and DRB1*0803 occurred most frequently in F1, F2, and F3 populations, with frequencies of 17.6%, 14.3%, and 20%, respectively. Although many alleles were shared by Bashibai and hybrid sheep, some alleles differed between them, especially in the F1 generation of the Bashibai × Altai Argali cross. The hybrid-specific alleles indicated the introgression of Altai Argali alleles into hybrid flocks. A population tree based on the OLA-DRB1 allelic frequency in each population indicated that the Bashibai sheep and three hybrid populations were similar, with Karakul Ram being genetically distinct.
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Affiliation(s)
- M Polat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, China; Viral Infectious Diseases Unit, RIKEN, Wako, Japan; Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Wako, Japan
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