Computational analysis of non-synonymous single nucleotide polymorphism in the bovine cattle kappa-casein (CSN3) gene

Computational analysis of non-synonymous single nucleotide polymorphism in the bovine PKLR geneComputational analysis of bovine PKLR gene

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.

Novel lncRNA regulatory elements in milk somatic cells of Holstein dairy cows associated with mastitis

Despite regulatory elements such as long non - coding RNAs representing most of the transcriptome, the functional understanding of long non - coding RNAs in relation to major health conditions including bovine mastitis is limited. This study examined the milk somatic cell transcriptome from udder quarters of 6 Holstein dairy cows to identify differentially expressed long non - coding RNAs using RNA - Sequencing. Ninety - four differentially expressed long non - coding RNAs are identified, 5 of which are previously annotated for gene name and length, 11 are annotated for gene name and 78 are novel, having no gene name or length previously annotated. Significant inflammatory response and regulation of immune response pathways (false discovery rate < 0.05) are associated with the differentially expressed long non - coding RNAs. QTL annotation analysis revealed 31 QTL previously annotated in the genomic regions of the 94 differentially expressed long non - coding RNAs, and the majority are associated with milk traits. This research provides a better understanding of long non - coding RNAs regulatory elements in milk somatic cells, which may enhance current breeding strategies for more adaptable or high mastitis resistant cattle.

Exploring genome-wide differentiation and signatures of selection in Italian and North American Holstein populations

Among Italian dairy cattle, the Holstein is the most reared breed for the production of Parmigiano Reggiano protected designation of origin cheese, which represents one of the most renowned products in the entire Italian dairy industry. In this work, we used a medium-density genome-wide data set consisting of 79,464 imputed SNPs to study the genetic structure of Italian Holstein breed, including the population reared in the area of Parmigiano Reggiano cheese production, and assessing its distinctiveness from the North American population. Multidimensional scaling and ADMIXTURE approaches were used to explore the genetic structure among populations. We also investigated putative genomic regions under selection among these 3 populations by combining 4 different statistical methods based either on allele frequencies (single marker and window-based) or extended haplotype homozygosity (EHH; standardized log-ratio of integrated EHH and cross-population EHH). The genetic structure results allowed us to clearly distinguish the 3 Holstein populations; however, the most remarkable difference was observed between Italian and North American stock. Selection signature analyses identified several significant SNPs falling within or closer to genes with known roles in several traits such as milk quality, resistance to disease, and fertility. In particular, a total of 22 genes related to milk production have been identified using the 2 allele frequency approaches. Among these, a convergent signal has been found in the VPS8 gene which resulted to be involved in milk traits, whereas other genes (CYP7B1, KSR2, C4A, LIPE, DCDC1, GPR20, and ST3GAL1) resulted to be associated with quantitative trait loci related to milk yield and composition in terms of fat and protein percentage. In contrast, a total of 7 genomic regions were identified combining the results of standardized log-ratio of integrated EHH and cross-population EHH. In these regions candidate genes for milk traits were also identified. Moreover, this was also confirmed by the enrichment analyses in which we found that the majority of the significantly enriched quantitative trait loci were linked to milk traits, whereas the gene ontology and pathway enrichment analysis pointed to molecular functions and biological processes involved in AA transmembrane transport and methane metabolism pathway. This study provides information on the genetic structure of the examined populations, showing that they are distinguishable from each other. Furthermore, the selection signature analyses can be considered as a starting point for future studies in the identification of causal mutations and consequent implementation of more practical application.

Field measures of strengthen plant-microbial remediation of PAHs-FQs compound pollution

In this study, five PAHs (benzo [b] fluoranthene (BbF), phenanthrene (Phe), fluoranthene (Flu), fluorene (Fl), benzo [A] pyrene (Bap)), and five FQs (ofloxacin (OFL), enrofloxacin (ENR), ciprofloxacin (CIP), norfloxacin (NOR), lomefloxacin (LOM)) were selected as ligands; peroxidase (1NML) was selected as receptor degrading protein. In the plant-microbial degradation, the factors with significant inhibitory effects are NOR, Bap, CIP, ENR, OFL, Flu, LOM, Phe, Fl, and BbF by the fractional factorial design experiment and molecular docking-assisted molecular dynamics methods. Using Taguchi experiment and molecular dynamics simulation methods, the main external field measures were designed and screened to effectively promote the degradation of PAHs-FQs under the combined pollution scenarios of Bap-CIP and BbF-NOR, respectively. The peroxidase mutation design plans with enhanced substrate affinity were then designed and screened using the DS software by predicting the virtual key amino acid of peroxidase. The novel biodegradable enzymes 2YCD-1, 2YCD-4, 2YCD-5, 2YCD-7, and 2YCD-9 had better structures and showed excellent degradability for PAHs and FQs. This study explored the degradation rules of the composite pollutants in the coexistence systems of multiple PAHs and FQs, providing the best external field measures for the control and treatment of the combined pollution effects of different PAHs and FQs. Overall, the current study has important practical significance for promoting the plant-microbial joint remediation of PAHs-FQs pollution and for reducing the combined pollution of PAHs and FQs in farmland systems.

Genetic Variants and Their Putative Effects on microRNA-Seed Sites: Characterization of the 3' Untranslated Region of Genes Associated with Temperament

The 3' untranslated region has an important role in gene regulation through microRNAs, and it has been estimated that microRNAs regulate up to 50% of coding genes in mammals. With the aim of allelic variant identification of 3' untranslated region microRNA seed sites, the 3' untranslated region was searched for seed sites of four temperament-associated genes (CACNG4, EXOC4, NRXN3, and SLC9A4). The microRNA seed sites were predicted in the four genes, and the CACNG4 gene had the greatest number with 12 predictions. To search for variants affecting the predicted microRNA seed sites, the four 3' untranslated regions were re-sequenced in a Brahman cattle population. Eleven single nucleotide polymorphisms were identified in the CACNG4, and eleven in the SLC9A4. Rs522648682:T>G of the CACNG4 gene was located at the predicted seed site for bta-miR-191. Rs522648682:T>G evidenced an association with both exit velocity (p = 0.0054) and temperament score (p = 0.0097). The genotype TT had a lower mean exit velocity (2.93 ± 0.4 m/s) compared with the TG and GG genotypes (3.91 ± 0.46 m/s and 3.67 ± 0.46 m/s, respectively). The allele associated with the temperamental phenotype antagonizes the seed site, disrupting the bta-miR-191 recognition. The G allele of CACNG4-rs522648682 has the potential to influence bovine temperament through a mechanism associated with unspecific recognition of bta-miR-191.

A Simulation Analysis and Screening of Deleterious Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) in Sheep LEP Gene

Leptin is a polypeptide hormone produced in the adipose tissue and governs many processes in the body. Recently, polymorphisms in the LEP gene revealed a significant change in body weight regulation, energy balance, food intake, and reproductive hormone secretion. This study considers its crucial role in the regulation of the economically important traits of sheep. Several computational tools, including SIFT, Predict SNP2, SNAP2, and PROVEAN, have been used to screen out the deleterious nsSNPs. Following the screening of 11 nsSNPs in the sheep genome, 5 nsSNPs, T86M (C → T), D98N (G → A), N136T (A → C), R142Q (G → A), and P157Q (C → A), were predicted to have a significant deleterious effect on the LEP protein function, leading to phenotypic difference. The analysis of proteins’ stability change due to amino acid substitution using the I-stable, SDM, and DynaMut consistently confirmed that three nsSNPs (T86M (C → T), D98N (G → A), and P157Q (C → A)) increased protein stability. It is suggested that these three nsSNPs may enhance the evolvability of LEP protein, which is vital for the evolutionary adaptation of sheep. Our findings demonstrate that the five nsSNPs reported in this study might be responsible for sheep’s structural and functional modifications of LEP protein. This is the first comprehensive report on the sheep LEP gene. It narrow downs the candidate nsSNPs for in vitro experiments to facilitate the development of reliable molecular markers for associated traits.

A computational in silico approach to predict high-risk coding and non-coding SNPs of human PLCG1 gene

PLCG1 gene is responsible for many T-cell lymphoma subtypes, including peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL), cutaneous T-cell lymphoma (CTCL), adult T-cell leukemia/lymphoma along with other diseases. Missense mutations of this gene have already been found in patients of CTCL and AITL. The non-synonymous single nucleotide polymorphisms (nsSNPs) can alter the protein structure as well as its functions. In this study, probable deleterious and disease-related nsSNPs in PLCG1 were identified using SIFT, PROVEAN, PolyPhen-2, PhD-SNP, Pmut, and SNPS&GO tools. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-mutant 2.0, MUpro, Consurf, and Netsurf 2.0 server. Some SNPs were finalized for structural analysis with PyMol and BIOVIA discovery studio visualizer. Out of the 16 nsSNPs which were found to be deleterious, ten nsSNPs had an effect on protein stability, and six mutations (L411P, R355C, G493D, R1158H, A401V and L455F) were predicted to be highly conserved. Among the six highly conserved mutations, four nsSNPs (R355C, A401V, L411P and L455F) were part of the catalytic domain. L411P, L455F and G493D made significant structural change in the protein structure. Two mutations-Y210C and R1158H had post-translational modification. In the 5' and 3' untranslated region, three SNPs, rs139043247, rs543804707, and rs62621919 showed possible miRNA target sites and DNA binding sites. This in silico analysis has provided a structured dataset of PLCG1 gene for further in vivo researches. With the limitation of computational study, it can still prove to be an asset for the identification and treatment of multiple diseases associated with the target gene.

Characteristics of kappa-casein gene polymorphism in cows of Swiss breed and their productive qualities at a large dairy

Kappa-casein is a fraction of the main milk protein, which determines the technological properties of milk and the quality of dairy products, especially cheese and fermented milk products. The study tested the distribution of kappa-casein gene genotype polymorphism (CSN3) in mothers and daughters of the Swiss breed cows, taking into account their milk productivity qualities. The study was performed on 111 cows of the Swiss breed on a large dairy. The observation group I included 51 cow-mothers of the Swiss breed; group II – 60 cow-daughters of the Swiss breed. In a study of the polymorphism of the kappa-casein gene in cow-mothers and cow-daughters of the Swiss breed, the dominance of allele B (0.73 and 0.70) was found, which was registered more than two times more often than allele A. The incidence of genotypes AA – AB – BB in cow-mothers of the Swiss breed was as follows: 5.9% – 43.1% – 51.0% with indicators of observed heterozygosity 0.43 and expected heterozygosity 0.40. In cow-daughters of the Swiss breed the frequency of the BB genotype was the same, but, genotype АА was registered almost twice as often, with lower indicators of observed heterozygosity and smaller increases of indicators of expected heterozygosity than in cow-mothers. Cow-mothers of the Swiss breed with the AA genotype, in comparison with the AB genotypes, had higher milk yields during lactation (by 43%), fat production (by 86.9%), ratio of fat to protein (by 40.5%). Also note, the cow-mothers of the Swiss breed with the AA genotype, in comparison with the BB genotypes, had reliably high rates of fat to protein (by 35.8%) and only a trend to higher fat production; fat and protein. The production of fat in dairy cows-daughters with the BB genotype was higher than with the AA genotype, but only at the level of tendency. The correlation analysis showed that the AA genotype of the kappa-casein gene in cow-mothers of the Swiss breed was associated with the duration of lactation, indicators of milk yield during lactation, fat production, fat content and protein in milk with registration of reliable and positive coefficients of correlation. The genotypes in cow-daughters did not have a reliable correlation with the duration of lactation and fat or protein content in milk. The results of the kappa-casein gene polymorphism study indicated that the AA genotype of cow-mothers of the Swiss breed was associated with higher productive milk qualities which should be taken into account when forming a highly productive herd of cattle of the Swiss breed under intensiveoperative technology at a large-scale dairy unit.