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Ali A, Rehman MU, Ahmad SM, Mehraj T, Hussain I, Nadeem A, Mir MUR, Ganie SA. In Silico Tools for Analysis of Single-Nucleotide Polymorphisms in the Bovine Transferrin Gene. Animals (Basel) 2022; 12:ani12060693. [PMID: 35327090 PMCID: PMC8944579 DOI: 10.3390/ani12060693] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023] Open
Abstract
Dairy cattle with a high milk yield are susceptible to many infectious diseases, such as mastitis. Subclinical mastitis (SCM) is the most prevalent form of mastitis that predominantly affects animal health, and causes adverse effects on the quality and quantity of milk. In dairy animals, subclinical mastitis often remains undetected, as no gross changes in udder characteristics are visible. In the present study, 135 Holstein Friesian dairy animals were selected and screened as healthy (n = 25) and mastitic (n = 110) based on diagnostic tests such as the California mastitis test, pH, electrical conductivity, and somatic cell count. In this study, the somatic cell count was used as a gold-standard test in differentiating subclinical mastitis animals from healthy ones. The present study was carried out to study polymorphisms in the bovine transferrin gene in cows (with subclinical mastitis and healthy). For the early detection of resistant/or susceptible animals, a useful marker could be provided by the detection of single-nucleotide polymorphisms (SNPs) in the transferrin gene, which are often associated with mammary innate immune response. The sequencing results revealed three nucleotide substitutions: two transversions (230 A > C, 231 C > A) and one transition (294 A > G) in susceptible cows as compared to disease-free subjects. The nucleotide variations at position 230 (GAC > GCA) and 231 (GAC > GCA) were nonsynonymous, and corresponded to an amino acid change from aspartic acid to alanine; whereas at position 294 (GAA > GAG), the mutation was synonymous. In the present study, many in silico tools were taken into consideration to determine the effect of SNPs on protein structure and function. The PROVEAN tool found the amino acid substitution to be neutral and deleterious. PolyPhen-2 revealed the amino acid variations at positions 320 and 321 to most likely be damaging; and at the 341 position, the variations were benign. The I-Mutant and MUpro tools found that the protein stability decreased for nonsynonymous variations. The SIFT tool revealed the protein function was likely to be affected in nonsynonymous variations, with no change in the case of synonymous ones. Phylogenetic analysis of the bovine transferrin gene revealed a close relation of the CA allele with the Bos taurus transferrin, while the G allele was closely related to a cross of Bos indicus × Bos taurus serotransferrins, followed by the Bison bison transferrin. The least relation was shown by both alleles to Capra hircus, Ovis aries, and Bubalus bubalis.
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Affiliation(s)
- Aarif Ali
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India;
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India; (I.H.); (M.U.R.M.)
| | - Muneeb U. Rehman
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: (M.U.R.); (S.A.G.)
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India;
| | - Tabish Mehraj
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA;
| | - Ishraq Hussain
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India; (I.H.); (M.U.R.M.)
| | - Ahmed Nadeem
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Manzoor Ur Rahman Mir
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India; (I.H.); (M.U.R.M.)
| | - Showkat Ahmad Ganie
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India;
- Correspondence: (M.U.R.); (S.A.G.)
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Hill PB, Imai A. The immunopathogenesis of staphylococcal skin infections - A review. Comp Immunol Microbiol Infect Dis 2016; 49:8-28. [PMID: 27865269 DOI: 10.1016/j.cimid.2016.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 07/22/2016] [Accepted: 08/10/2016] [Indexed: 12/20/2022]
Abstract
Staphylococcus aureus and S. pseudintermedius are the major causes of bacterial skin disease in humans and dogs. These organisms can exist as commensals on the skin, but they can also cause severe or even devastating infections. The immune system has evolved mechanisms to deal with pathogenic microorganisms and has strategies to combat bacteria of this type. What emerges is a delicate "peace" between the opposing sides, but this balance can be disrupted leading to a full blown "war". In the ferocious battle that ensues, both sides attempt to get the upper hand, using strategies that are comparable to those used by modern day armies. In this review article, the complex interactions between the immune system and the organisms are described using such military analogies. The process is described in a sequential manner, starting with the invasion itself, and progressing to the eventual battlezone in which there are heavy casualties on both sides. By the end, the appearance of a simple pustule on the skin surface will take on a whole new meaning.
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Affiliation(s)
- P B Hill
- Companion Animal Health Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy Campus, Roseworthy SA 5371, Australia.
| | - A Imai
- Dermatology resident, Synergy Animal General Hospital, 815 Kishigami Kawaguchi, Saitama, 333-0823, Japan
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Ju ZH, Li QL, Huang JM, Hou MH, Li RL, Li JB, Zhong JF, Wang CF. Three novel SNPs of the bovine Tf gene in Chinese native cattle and their associations with milk production traits. GENETICS AND MOLECULAR RESEARCH 2011; 10:340-52. [PMID: 21365550 DOI: 10.4238/vol10-1gmr1038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Transferrin (Tf) is a β-globulin protein that transports iron ions in mammalian cells. It contributes to innate immunity to microbial pathogens, primarily by limiting microbial access to iron. Thus, polymorphisms present in bovine Tf could potentially underlie inherited differences in mastitis resistance and milk production traits. We detected three novel single-nucleotide polymorphisms of the Tf gene in Chinese native cattle by screening for genetic variation of Tf in 751 individuals of three Chinese cattle breeds, namely China Holstein, Luxi Yellow and Bohai Black, using PCR-RFLP and DNA sequencing techniques. The three new SNPs, g.-1748G>A ss250608649, g.13942T>C ss250608650, and g.14037A>G ss250608651, had allele frequencies of 85.9, 86.3 and 92.5%, 64.5, 73.3 and 65.0%, and 67.6, 73.7 and 60.0%, respectively. SNP g.-1748G>A was located in the 5' flanking region of Tf. SNP g.14037A>G was located in intron 8 of Tf. SNP g.13942T>C, located in exon 8 of Tf, was a synonymous mutation (TTA > CTA), encoding a leucine (326 aa) in the Tf protein. Associations of the Tf SNPs with milk traits were also analyzed. Significant (P < 0.05) relationships among the Tf polymorphisms, somatic cell scores (SCS), and milk productive traits were observed. Cows with genotypes TT (g.13942T>C), GG (g.-1748G>A) and AG (g.14037A>G) had a lower SCS and higher protein levels and 305-day milk yield. Nineteen combinations of different haplotypes from the three SNPs were identified in Chinese Holstein cattle. The haplotype combination ATA/GCA, GCA/GCA and GCG/ GTA was dominant in cows with a lower SCS, a higher protein level and a higher 305-day milk yield, respectively. Moreover, the gene expression level of Tf was higher in mastitis-affected mammary tissues than in normal mammary tissues. These results suggest that the Tf gene affects milk production, as well as mastitis-resistance traits, in Chinese Holsteins.
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Affiliation(s)
- Z H Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong Province, China
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