Computational analysis for the determination of deleterious nsSNPs in human MTHFR gene.

Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme involved in folate metabolism and plays a central role in DNA methylation and biosynthesis. MTHFR mutations may alter the cellular folate supply which in turn affects nucleic acid synthesis, DNA methylation and chromosomal damage. The identification of number of SNPs in the human genome growing nowadays and hence, the evaluation of functional & structural consequences of these SNPs is very laborious by means of experimental analysis. Therefore, in the present study, recently developed various computational algorithms have been used which can predict the functional and structural consequences of the SNPs. Various computational tools like SIFT, PolyPhen2, PROVEAN, SNAP2, nsSNPAnalyzer, SNPs&GO, PhD-SNP, PMut, I-Mutant, iPTREE-STAB and MUpro were used to predict most deleterious SNPs. Additionally, ConSurf was used to find amino acids conservation and NCBI conserved domain search tool to find conserved domains in MTHFR. Post translational modification sites were predicted using ModPred. SPARKS-X was used to generate 3D structure of the native and mutant MTHFR protein, ModRefiner for further refinement, Varify3D and RAMPAGE to validate structure. Ligand binding sites were predicted using FTsite, RaptorX binding and COACH. Three SNPs i.e. R157Q, L323P and W500C predicted the most deleterious in all the tools used for functional and stability analysis. Moreover, both residues R157, L323 and W500 were predicted highly conserved, buried and structural residues by ConSurf. Post translational modification sites were also predicted at R157 and W500. The ligand binding sites were predicted at R157, L323 and W500.

Computational analysis for the determination of deleterious nsSNPs in human MTHFD1 gene.

Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol. Out of 327 nsSNPs form human MTHFD1 gene, total 45 SNPs were predicted as functionally most significant SNPs, among which 17 were highly conserved and functional, 17 were highly conserved and structural residues. Among 45 most significant SNPs, 15 were predicted to be involved in post translational modifications. The p.Gly165Arg may interfere in homodimer interface formation. The p.Asn439Lys and p.Asp445Asn may interfere in binding interactions of MTHFD1 protein with cesium cation and potassium. The two SNPs (p.Asp562Gly and p.Gly637Cys) might interfere in interactions of MTHFD1 with ligand.

Novel cytogenetic finding: an unusual X;X-translocation in Mehsana buffalo (Bubalus bubalis).

Cytogenetic investigations of a phenotypically normal Mehsana river buffalo calf (Bubalusbubalis) revealed an XXY chromosome complement due to X;X-translocation in all screened metaphase plates. The chromosomal anomaly was identified by GTG-banding while CBG- and RBG-banding revealed two heterochromatin blocks and that one of the two X chromosomes was late replicating, respectively. The normal cytogenetic profiles of sire, dam and relatives of the calf suggest that the anomaly could have arisen spontaneously during oogenesis. This is the first report on a male river buffalo calf having an XXY chromosome complement with translocation between the two X chromosomes.

The nematode-trapping efficacy of two chlamydospore-forming fungi against Haemonchus contortus in sheep.

An in vitro study was carried out to determine efficacy of Indian isolates of the nematode-trapping fungi Arthrobotrys musiformis and Duddingtonia flagrans to capture infective larvae of Haemonchus contortus. These fungi have previously been screened and selected for their survival in the gastrointestinal tract of sheep without losing growth and nematode capturing potential. Following the feeding of chlamydospores of these two fungi alone or in combination in sheep experimentally infected with Haemonchus contortus, coprocultures were set up to enumerate the infective third stage larvae. The number of larvae captured from faeces of fungus-fed sheep was significantly higher compared with fungus-unfed controls irrespective of the fungus used. The fungal combination produced no antagonistic effect and thus can be used as efficiently as the fungi alone in the biological control of animal parasitic nematodes.

Implications of fungicidal effects of benzimidazole compounds on Duddingtonia flagrans in integrated nematode parasite management in livestock.

An in vitro trial with carbendazim fungicide on the growth profile of the predatory fungus Duddingtonia flagrans was undertaken and in vivo trials in sheep and buffaloes, fed on chlamydospores of D. flagrans and administered albendazole anthelmintic, were conducted. Although no growth inhibition was detected at a carbendazim concentration of 0.05 ppm, growth inhibition was recorded of 50% and above at concentrations of 0.25 and 1.00 ppm (p < 0.001) and of around 90% at concentrations of 2.00 to 5.00 ppm (p <0.0001). Scanty recovery of the fungus was made from faecal culture 48 h following a single dose of albendazole both in sheep and buffaloes. However, profuse fungal recovery was made from 96 h post dosing onwards. When the drug was used as an intraruminal slow-release capsule, no faecal fungal recovery could be made from day 3 after administration of the capsule, when the albendazole sulphoxide concentration was around 1.0 microg/ml. However, profuse and scanty fungal recovery could be made on days 1 and 2, respectively, after administration of the capsule, when the plasma albendazole sulphoxide concentration was around 0.4 and 0.9 microg/ml, respectively. The implications for use of a combination of anthelmintics and biological control in sustainable parasite control programmes are discussed.