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Affiliations
1 Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN

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Current Science, Vol 111, No 1 (2016), Pagination: 184-191

Abstract

The present study applies metagenomics to characterize the diversity and relative abundance of protozoa residing in the rumen of Indian Surti buffalo (Bubalus bubalis). To increase protozoa representation in the metagenome, protozoa enrichment was performed by density sedimentation and confirmed by quantitative real time PCR. The highly enriched metagenome sample was subjected to shotgun sequencing by Ion Torrent PGM which resulted in 10,303,375 reads total-ling 1.6 gigabases. The taxonomic profile obtained by comparison with SILVA SSU database showed pre-dominance of the class Litostomatea (99.78%) fol-lowed by Coccidia (0.10%) and Aconoidasida (0.06%). At the genus level Isotricha (48.06%) followed by Polyplastron (9.90%), Dasytricha (9.87%) and Eudiplodinium (7.47%) were predominant. The taxo-nomic assignment based on protein coding regions showed discrepancy with the SSU-based assignments, possibly due to the absence of most eukaryotic ge-nomes in public databases. According to the SEED subsystems annotation database, genes for protein me-tabolism were the most abundant followed by genes for RNA metabolism, regulation and cell signalling. The present study offers a preliminary snapshot of di-versity, functional potential and relative abundance of protozoa within the Indian Surti buffalo rumen and al-so expands our knowledge of these unicellular eukary-otes present in the rumen ecosystem.

Keywords

Buffalo Rumen, Metagenome, Protozoa Enrichment, Quantitative Real Time PCR, Shotgun Sequencing.

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Identification of Genetic Variants in PDC, RHO, PDE6A and PDE6B in Dogs with Progressive Retinal Atrophy

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Authors

Dipal Y. Pandya ¹, Divyesh N. Kelawala ², Namrata V. Patel ¹, Tejas M. Shah ¹, Anand B. Patel ¹, Nidhi R. Parmar ¹, Bhaskar Reddy ¹, Deepak B. Patil ², Chaitanya G. Joshi ¹

Affiliations
1 Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
2 Department of Veterinary Surgery and Radiology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN

Source

Current Science, Vol 111, No 10 (2016), Pagination: 1640-1648

Abstract

The progressive retinal atrophy (PRA) is an inherited eye disease and characterized by progressive retinal degeneration which leads to impaired vision in dogs. Using targeted next generation sequencing of nine PRA cases and six controls, we have identified SNPs in PDC, PDE6A and PDE6B, which were not previously associated with PRA. The gene in which the highest mutations found was PDE6A (113 and 104 SNPs), followed by PDE6B, PDC and RHO in all dog breeds and Spitz-only respectively. Five SNPs identified in PDC gene of Spitz-only breed showed significant association with PRA. However, no pathogenetically relevant mutations were found in RHO gene for PRA. The SNP in PDE6B chr3: 91763017 (G/A) in Spitz-only breed, and PDE6A chr4: 5912574 (T/C) and PDC chr7: 19511750 (T/A) were associated with PRA in the breeds of dog studied. Our results show that PRA is genetically heterogeneous and is caused by multiple, distinct mutations.

Keywords

Genome-Wide Association, Next Generation Sequencing, Progressive Retinal Atrophy, Single Nucleotide Polymorphisms.

Full Text

References

Petersen-Jones, S., Advances in the molecular understanding of canine retinal diseases. J. Small Anim. Pract., 2005, 46(8), 371–380.

Downs, L. M., Wallin-Hakansson, B. and Boursnell, M., A frameshift mutation in golden retriever dogs with progressive reti-nal atrophy endorses SLC4A3 as a candidate gene for human reti-nal degenerations. PLoS ONE, 2011, 6(6), e21452.

Parry, H. B., Degenerations of the dog retina. II. Generalized pro-gressive atrophy of hereditary origin. Br. J. Ophthalmol., 1953, 37(8), 487–502.

Petersen-Jones, S. M., Animal models of human retinal dystro-phies. Eye (London), 1998, 12(Pt 3b), 566–570.

Vilboux., T., Chaudieu, G. and Jeannin, P., Progressive retinal atro-phy in the Border Collie: a new XLPRA. BMC Vet. Res., 2008, 4, 10.

Zangerl, B., Goldstein, O. and Philp, A. R., Identical mutation in a novel retinal gene causes progressive rod-cone degeneration in dogs and retinitis pigmentosa in humans. Genomics, 2006, 88(5), 551–563.

Miyadera, K., Acland, G. M. and Aguirre, G. D., Genetic and phe-notypic variations of inherited retinal diseases in dogs: the power of within- and across-breed studies. Mamm. Genome, 2012, 23(1–2), 40–61.

Ahonen, S. J., Arumilli, M. and Lohi, H. A., CNGB1 frameshift mutation in papillon and phalene dogs with progressive retinal at-rophy. PLoS ONE, 2013, 8(8), e72122.

Grondahl, J., Estimation of prognosis and prevalence of retinitis pigmentosa and Usher syndrome in Norway. Clin. Genet., 1987, 31(4), 255–264.

Haim, M., Holm, N. V. and Rosenberg, T., Prevalence of retinitis pigmentosa and allied disorders in Denmark. I. Main results. Acta Ophthalmol., 1992, 70(2), 178–186.

Pagon, R. A., Retinitis pigmentosa. Surv. Ophthalmol., 1988, 33(3), 137–177.

Patterson, D. F., Pexieder, T., Schnarr, W. R., Navratil, T. and Alaili, R. A., Single major-gene defect underlying cardiac cono-truncal malformations interferes with myocardial growth during embryonic development: studies in the CTD line of keeshond dogs. Am. J. Hum. Genet., 1993, 52(2), 388–397.

Beggs, A. H., Bohm, J. and Snead, E., MTM1 mutation associated with X-linked myotubular myopathy in Labrador Retrievers. Proc. Natl. Acad. Sci. USA, 2010, 107(33), 14697–14702.

Sidjanin, D. J., Lowe, J. K. and McElwee, J. L., Canine CNGB3 mutations establish cone degeneration as orthologous to the human achromatopsia locus ACHM3. Hum. Mol. Genet. 2002, 11(16), 1823–1833.

Mellersh, C. S., Boursnell, M. E. and Pettitt, L., Canine RPGRIP1 mutation establishes cone-rod dystrophy in miniature longhaired dachshunds as a homologue of human Leber congenital amaurosis. Genomics, 2006, 88(3), 293–301.

McC. Howell, J., Fletcher, S., Kakulas, B. A., O’Hara, M., Lochmuller, H. and Karpati, G., Use of the dog model for Du-chenne muscular dystrophy in gene therapy trials. Neuromusc. Disord., 1997, 7(5), 325–328.

Acland, G. M., Aguirre, G. D. and Ray, J., Gene therapy restores vision in a canine model of childhood blindness. Nat. Genet., 2001, 28(1), 92–95.

Ponder, K. P., Melniczek, J. R. and Xu, L., Therapeutic neonatal hepatic gene therapy in mucopolysaccharidosis VII dogs. Proc. Natl. Acad. Sci. USA, 2002, 99(20), 13102–13107.

Bainbridge, J. W., Smith, A. J. and Barker, S. S., Effect of gene therapy on visual function in Leber’s congenital amaurosis. New Engl. J. Med., 2008, 358(21), 2231–2239.

Narfstrom, K., Jeong, M., Hyman, J., Madsen, R. W. and Berg-strom, T. F., Assessment of hereditary retinal degeneration in the English springer spaniel dog and disease relationship to an RPGRIP1 mutation. Stem Cells Int., 2012, 2012, 685901.

Suber, M. L., Pittler, S. J. and Qin, N., Irish setter dogs affected with rod/cone dysplasia contain a nonsense mutation in the rod cGMP phosphodiesterase beta-subunit gene. Proc. Natl. Acad. Sci., USA, 1993, 90(9), 3968–3972.

Dekomien, G., Runte, M., Godde, R. and Epplen, J. T., General-ized progressive retinal atrophy of Sloughi dogs is due to an 8-bp insertion in exon 21 of the PDE6B gene. Cytogenet. Genome Res., 2000, 90(3–4), 261–267.

Petersen-Jones, S. M., Entz, D. D. and Sargan, D. R., cGMP phos-phodiesterase-alpha mutation causes progressive retinal atrophy in the Cardigan Welsh corgi dog. Invest. Ophth. Vis. Sci., 1999, 40(8), 1637–1644.

Zhang, Q., Acland, G. M., Parshall, C. J., Haskell, J., Ray, K. and Aguirre, G. D., Characterization of canine photoreceptor phosducin cDNA and identification of a sequence variant in dogs with photoreceptor dysplasia. Gene, 1998, 215(2), 231–239.

Kijas, J. W., Cideciyan, A. V. and Aleman, T. S., Naturally occur-ring rhodopsin mutation in the dog causes retinal dysfunction and degeneration mimicking human dominant retinitis pigmentosa. Proc. Natl. Acad. Sci. USA, 2002, 99(9), 6328–6333.

Kijas, J. W., Miller, B. J., Pearce-Kelling, S. E., Aguirre, G. D. and Acland, G. M., Canine models of ocular disease: outcross breedings define a dominant disorder present in the English mas-tiff and bull mastiff dog breeds. J. Hered., 2003, 94(1), 27–30.

McKenna, A., Hanna, M. and Banks, E., The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 2010, 20(9), 1297–1303.

Abe, T., Kikuchi, T. and Shinohara, T., The sequence of the human phosducin gene (PDC) and its 5-flanking region. Ge-nomics, 1994, 19(2), 369–372.

Lee, R. H., Fowler, A., McGinnis, J. F., Lolley, R. N. and Craft, C. M., Amino acid and cDNA sequence of bovine phosducin, a soluble phosphoprotein from photoreceptor cells. J. Biol. Chem., 1990, 265(26), 15867–15873.

Lee, R. H., Lieberman, B. S. and Lolley, R. N., Retinal accumula-tion of the phosducin/T beta gamma and transducin complexes in developing normal mice and in mice and dogs with inherited retinal degeneration. Exp. Eye Res., 1990, 51(3), 325–333.

Lin, C. T., Petersen-Jones, S. M. and Sargan, D. R., Isolation and investigation of canine phosducin as a candidate for canine gener-alized progressive retinal atrophies. Exp. Eye Res., 1998, 67(4), 473–480.

Palczewski, K., Kumasaka, T. and Hori, T., Crystal structure of rhodopsin: A G protein-coupled receptor. Science, 2000, 289(5480), 739–745.

Rattner, A., Sun, H. and Nathans, J., Molecular genetics of human retinal disease. Annu. Rev. Genet., 1999, 33, 89–131.

Yuan, L., Kawada, M., Havlioglu, N., Tang, H. and Wu, J. Y., Mutations in PRPF31 inhibit pre-mRNA splicing of rhodopsin gene and cause apoptosis of retinal cells. J. Neurosci., 2005, 25(3), 748–757.

Danciger, M., Blaney, J. and Gao, Y. Q., Mutations in the PDE6B gene in autosomal recessive retinitis pigmentosa. Genomics, 1995, 30(1), 1–7.

Huang, S. H., Pittler, S. J., Huang, X., Oliveira, L., Berson, E. L. and Dryja, T. P., Autosomal recessive retinitis pigmentosa caused by mutations in the alpha subunit of rod cGMP phosphodiesterase. Nat. Genet., 1995, 11(4), 468–471.

McLaughlin, M. E., Ehrhart, T. L., Berson, E. L. and Dryja, T. P., Mutation spectrum of the gene encoding the beta subunit of rod phosphodiesterase among patients with autosomal recessive retini-tis pigmentosa. Natl. Acad. Sci. USA, 1995, 92(8), 3249–3253.

Bowes, C., Li, T., Danciger, M., Baxter, L. C., Applebury, M. L. and Farber, D. B., Retinal degeneration in the rd mouse is caused by a defect in the beta subunit of rod cGMP-phosphodiesterase. Nature, 1990, 347(6294), 677–680.

Pittler, S. J. and Baehr, W., Identification of a nonsense mutation in the rod photoreceptor cGMP phosphodiesterase beta-subunit gene of the rd mouse. Proc. Natl. Acad. Sci. USA, 1991, 88(19), 8322–8326.

Clements, P. J., Gregory, C. Y., Peterson-Jones, S. M., Sargan, D. R. and Bhattacharya, S. S., Confirmation of the rod cGMP phos-phodiesterase beta subunit (PDE beta) nonsense mutation in affected rcd-1 Irish setters in the UK and development of a diag-nostic test. Curr. Eye Res., 1993, 12(9), 861–866.

Ray, K., Baldwin, V. J., Acland, G. M., Blanton, S. H. and Aguir-re, G. D., Cosegregation of codon 807 mutation of the canine rod cGMP phosphodiesterase beta gene and rcd1. Invest. Ophth. Vis. Sci., 1994, 35(13), 4291–4299.

Genome-Wide Analysis of a Potent Functional Dairy Starter Bacterium Streptococcus thermophilus MTCC 5460:A Comprehensive Study of its Dairy Niche Adaptive Features

Abstract Views :279 | PDF Views:92

Authors

Jashbhai B. Prajapati ¹, Hemaxi P. Zala ¹, Neelam M. Nathani ², Manisha Sajnani ², Chaitanya G. Joshi ²

Affiliations
1 Department of Dairy Microbiology, Sheth MC College of Dairy Science, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
2 Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN

Source

Current Science, Vol 113, No 12 (2017), Pagination: 2292-2297

Abstract

Genomic analysis of Streptococcus thermophilus strain MTCC 5460, an isolate from market dahi (curd), revealed particular gene features that contributed towards its adaptation to a dairy-specific niche. The genome comprising 1.6 Mb, encoding 1809 genes, revealed the presence of genes involved in lactose/galactose utilization; well-developed proteolytic system including cell envelop proteinases and several transporters; and bacteriocin synthesis and competence proteins involved in defence mechanism, which help prevent food spoilage. The genome comprised genes for stress resistance property of the strain, contributing to its gut endurance and gene encoding formation of aroma compounds. Unlike pathogenic streptococci, genes for virulence property were absent in the genome. Overall, the study revealed features within the genome that enabled the organism to survive in a gastric environment and assisted in its interaction with the host microbiota and mucosa, thus, validating the strain as a potent functional dairy starter and a promising candidate for potential probiotic applications.

Keywords

Dairy Starter, Genome, MTCC 5460, Probiotics.

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References

Goh, Y. J., Goin, C., O’Flaherty, S., Altermann, E. and Hutkins, R., Specialized adaptation of a lactic acid bacterium to the milk environment: The comparative genomics of streptococcus thermophilus lmd-9. Microb. Cell Fact., 2011, 10(Suppl 1), S22.

Settachaimongkon, S. et al., Influence of different proteolytic strains of streptococcus thermophilus in co-culture with lactobacillus delbrueckii subsp. Bulgaricus on the metabolite profile of set-yoghurt. Int. J. Food Microbiol., 2014, 177, 29–36.

Hols, P. et al., New insights in the molecular biology and physiology of streptococcus thermophilus revealed by comparative genomics. FEMS Microbiol. Rev., 2005, 29, 435–463.

Meyer, A. L., Elmadfa, I., Herbacek, I. and Micksche, M., Probiotic, as well as conventional yogurt, can enhance the stimulated production of proinflammatory cytokines. J. Hum. Nutr. Diet., 2007, 20, 590–598.

Rodriguez, C., Medici, M., Rodriguez, A. V., Mozzi, F. and Font de Valdez, G., Prevention of chronic gastritis by fermented milks made with exopolysaccharide-producing streptococcus thermophilus strains. J. Dairy Sci., 2009, 92, 2423–2434.

Burton, J. P., Chilcott, C. N., Moore, C. J., Speiser, G. and Tagg, J. R., A preliminary study of the effect of probiotic streptococcus salivarius k12 on oral malodour parameters. J. Appl. Microbiol., 2006, 100, 754–764.

Bolotin, A. et al., Complete sequence and comparative genome analysis of the dairy bacterium streptococcus thermophilus. Nat. Biotechnol., 2004, 22, 1554–1558.

Salminen, S., Nurmi, J. and Gueimonde, M., The genomics of probiotic intestinal microorganisms. Genome Biol., 2005, 6, 225.

Prajapati, J. B. et al., Whole-genome shotgun sequencing of an indian-origin lactobacillus helveticus strain, mtcc 5463, with probiotic potential. J. Bacteriol., 2011, 193, 4282–4283.

Prajapati, J. B. et al., Whole-genome shotgun sequencing of lactobacillus rhamnosus mtcc 5462, a strain with probiotic potential. J. Bacteriol., 2012, 194, 1264–1265.

Broadbent, J. R., McMahon, D. J., Welker, D. L., Oberg, C. J. and Moineau, S., Biochemistry, genetics, and applications of exopolysaccharide production in streptococcus thermophilus: a review. J. Dairy Sci., 2003, 86, 407–423.

Mills, S., Griffin, C., Coffey, A., Meijer, W. C., Hafkamp, B. and Ross, R. P., Crispr analysis of bacteriophage-insensitive mutants (bims) of industrial streptococcus thermophilus – implications for starter design. J. Appl. Microbiol., 2010, 108, 945–955.

Abendon, S. T., Bacterial ‘immunity’ against bacteriophages. Bacteriophage, 2012, 2, 50–54.

Horvath, P. et al., Diversity, activity, and evolution of crispr loci in streptococcus thermophilus. J. Bacteriol., 2008, 190, 1401–1412.

Prajapati, J. B., Nathani, N. M., Patel, A. K., Senan, S. and Joshi, C. G., Genomic analysis of dairy starter culture streptococcus thermophilus mtcc 5461. J. Microbiol. Biotechnol., 2013, 23, 459–466.

Miyoshi, A. et al., Controlled production of stable heterologous proteins in lactococcus lactis. Appl. Environ. Microbiol., 2002, 68, 3141–3146.

Poquet, I., Saint, V., Seznec, E., Simoes, N., Bolotin, A. and Gruss, A., Htra is the unique surface housekeeping protease in lactococcus lactis and is required for natural protein processing. Mol. Microbiol., 2000, 35, 1042–1050.

Garault, P., Le Bars, D., Besset, C. and Monnet, V., Three oligopeptide-binding proteins are involved in the oligopeptide transport of streptococcus thermophilus. J. Biol. Chem., 2002, 277, 32–39.

Monnet, V., Bacterial oligopeptide-binding proteins. Cell. Mol. Life Sci.: CMLS, 2003, 60, 2100–2114.

Broadbent, J. R., Barnes, M., Brennand, C., Strickland, M., Houck, K., Johnson, M. E. and Steele, J. L., Contribution of lactococcus lactis cell envelope proteinase specificity to peptide accumulation and bitterness in reduced-fat cheddar cheese. Appl. Environ. Microbiol., 2002, 68, 1778–1785.

Liu, M., Bayjanov, J. R., Renckens, B., Nauta, A. and Siezen, R. J., The proteolytic system of lactic acid bacteria revisited: a genomic comparison. BMC Genomics, 2010, 11, 36.

Cotter, P. D. and Hill, C., Surviving the acid test: responses of gram-positive bacteria to low ph. Microbiol. Mol. Biol. Rev., 2003, 67, 429–453.

Zotta, T., Ricciardi, A., Rossano, R. and Parente, E., Urease production by streptococcus thermophilus. Food Microbiol., 2008, 25, 113–119.

Senan, S., Prajapati, J. B. and Joshi, C. G., Comparative genome-scale analysis of niche-based stress-responsive genes in lactobacillus helveticus strains. Genome, 2014, 57, 185–192.

Krastel, K., Senadheera, D. B., Mair, R., Downey, J. S., Goodman, S. D. and Cvitkovitch, D. G., Characterization of a glutamate transporter operon, glnqhmp, in streptococcus mutans and its role in acid tolerance. J. Bacteriol., 2010, 192, 984–993.

DeVuyst, L. and Leroy, F., Bacteriocins from lactic acid bacteria: Production, purification and food applications. J. Mol. Microbiol. Biotechnol., 2007, 13, 194–199.

Leroy, F. and DeVuyst, L., Lactic acid bacteria as functional starter cultures for the food fermentation industry. Trends Food Sci. Technol., 2004, 15, 67–78.

Claverys, J. P. and Martin, B., Bacterial 'competence' genes: signatures of active transformation, or only remnants? Trends Microbiol., 2003, 11, 161–165.

Letort, C. and Juillard, V., Development of a minimal chemically-defined medium for the exponential growth of streptococcus thermophilus. J. Appl. Microbiol., 2001, 91, 1023–1029.

Neviani, E., Giraffa, G., Brizzi, A. and Carminati, D., Amino acid requirements and peptidase activities of streptococcus salivarius subsp. Thermophilus. J. Appl. Bacteriol., 1995, 79, 302–307.

Altermann, E. et al., Complete genome sequence of the probiotic lactic acid bacterium lactobacillus acidophilus ncfm. Proc. Natl. Acad. Sci. USA, 2005, 102, 3906–3912.

Tanous, C., Kieronczyk, A., Helinck, S., Chambellon, E. and Yvon, M., Glutamate dehydrogenase activity: a major criterion for the selection of flavour-producing lactic acid bacteria strains. Antonie van Leeuwenhoek, 2002, 82, 271–278.

Wu, Q., Tun, H. M., Leung, F. C. C. and Shah, N. P., Genomic insights into high exopolysaccharide-producing dairy starter bacterium streptococcus thermophilus ascc 1275. Sci. Rep., 2014, 4, 4974.

Ott, A., Germond, J. E. and Chaintreau, A., Origin of acetaldehyde during milk fermentation using (13)c-labeled precursors. J. Agric. Food Chem., 2000, 48, 1512–1517.

Teraguchi, S., Ono, J., Kiyosawa, I. and Okonogi, S., Oxygen uptake activity and aerobic metabolism of streptococcus thermophilus sth450. J. Dairy Sci., 1987, 70, 514–523.

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Joshi, Chaitanya G.

Rumen Virome:An Assessment of Viral Communities and their Functions in the Rumen of an Indian Buffalo

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Analysis of Community Structure and Species Richness of Protozoa-Enriched Rumen Metagenome from Indian Surti by Shotgun Sequencing

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Identification of Genetic Variants in PDC, RHO, PDE6A and PDE6B in Dogs with Progressive Retinal Atrophy

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Genome-Wide Analysis of a Potent Functional Dairy Starter Bacterium Streptococcus thermophilus MTCC 5460:A Comprehensive Study of its Dairy Niche Adaptive Features

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References