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Articles by M Ventura
Total Records ( 3 ) for M Ventura
  G. E Liu , Y Hou , B Zhu , M. F Cardone , L Jiang , A Cellamare , A Mitra , L. J Alexander , L. L Coutinho , M. E Dell'Aquila , L. C Gasbarre , G Lacalandra , R. W Li , L. K Matukumalli , D Nonneman , L. C. d. A Regitano , T. P. L Smith , J Song , T. S Sonstegard , C. P Van Tassell , M Ventura , E. E Eichler , T. G McDaneld and J. W. Keele
 

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.

  F Antonacci , J. M Kidd , T Marques Bonet , M Ventura , P Siswara , Z Jiang and E. E. Eichler
 

The human genome is a highly dynamic structure that shows a wide range of genetic polymorphic variation. Unlike other types of structural variation, little is known about inversion variants within normal individuals because such events are typically balanced and are difficult to detect and analyze by standard molecular approaches. Using sequence-based, cytogenetic and genotyping approaches, we characterized six large inversion polymorphisms that map to regions associated with genomic disorders with complex segmental duplications mapping at the breakpoints. We developed a metaphase FISH-based assay to genotype inversions and analyzed the chromosomes of 27 individuals from three HapMap populations. In this subset, we find that these inversions are less frequent or absent in Asians when compared with European and Yoruban populations. Analyzing multiple individuals from outgroup species of great apes, we show that most of these large inversion polymorphisms are specific to the human lineage with two exceptions, 17q21.31 and 8p23 inversions, which are found to be similarly polymorphic in other great ape species and where the inverted allele represents the ancestral state. Investigating linkage disequilibrium relationships with genotyped SNPs, we provide evidence that most of these inversions appear to have arisen on at least two different haplotype backgrounds. In these cases, discovery and genotyping methods based on SNPs may be confounded and molecular cytogenetics remains the only method to genotype these inversions.

  M Ventura and J. Catalan
 

Amino acids (AAs) are critical biochemical compounds for living organisms. Because of the limited capacity for their de novo synthesis in many animals, the nutritional value of food largely depends on its AA composition relative to the animal's requirements. To improve present knowledge on AA variability in freshwater crustaceans, we studied the inter- and intraspecific variability in three contrasting species from an oligotrophic alpine lake (Daphnia pulicaria, cladocera; Cyclops abyssorum, cyclopoid copepod and Diaptomus cyaneus, calanoid copepod). Inter-species differences were larger than intraspecific variation, confirming a non-strict homeostasis in freshwater crustacean zooplankton. The intraspecific variability differed for each species: in Daphnia, it was mainly related with ontogenetic changes rather than reproduction; in Cyclops, both factors were equally important; and reproduction was the most relevant in Diaptomus. Reproduction changes were associated with serine and phenylalanine in the three species, while the AAs responsible for ontogenetic changes differed in each species. There were no gender differences in AA composition in any of the two copepod species. Free AAs formed a very low percentage of total AA pool (<2.7%). Taking advantage of the fact that Daphnia is the main prey for Cyclops in the lake studied, we further investigated to what extent the AA composition is related with CyclopsDaphnia nitrogen stable isotope fractionation. Only those AAs that are both essential and are not trans-aminated during protein synthesis had a significant correlation with nitrogen stable isotope fractionation, supporting the hypothesis that an AA imbalance can be responsible for a variable nitrogen stable isotope fractionation.

 
 
 
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