The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.

The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve, and 11 of the 15 possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used a high-throughput assay with 54,693 SNP loci developed for Bos taurus taurus to rapidly genotype 678 individuals representing 61 Pecoran species. We produced a highly resolved phylogeny for this diverse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a method to amplify and screen genomic information from extinct species, and place Bison priscus within the Bovidae. The quality of genotype calls and the placement of samples within a wellsupported phylogeny may provide an important test for validating the fidelity and integrity of ancient samples. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.ancient DNA ͉ Pecorans ͉ domestication

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A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were generated to study the effect of sequence length, indel size, deletion rate, and insertion rate. Results showed that alignment quality was highly dependent on the number of deletions and insertions in the sequences and that the sequence length and indel size had a weaker effect. Overall, ProbCons was consistently on the top of list of the evaluated MSA tools. SATe, being little less accurate, was 529.10% faster than ProbCons and 236.72% faster than MAFFT(L-INS-i). Among other tools, Kalign and MUSCLE achieved the highest sum of pairs. We also considered BALiBASE benchmark datasets and the results relative to BAliBASE- and indel-Seq-Gen-generated alignments were consistent in the most cases.

In this study, mRNA-Seq was used to characterize and compare the leukocyte transcriptomes from two taurine breeds (Holstein and Jersey), and one indicine breed (Cholistani). At the genomic level, we identified breed-specific base changes in protein coding regions. Among 7,793,425 coding bases, only 165 differed between Holstein and Jersey, and 3,383 (0.04%) differed between Holstein and Cholistani, 817 (25%) of which resulted in amino acid changes in 627 genes. At the transcriptional level, we assembled transcripts and estimated their abundances including those from more than 3,000 unannotated intergeneic regions. Differential gene expression analysis showed a high similarity between Holstein and Jersey, and a much greater difference between the taurine breeds and the indicine breed. We identified gene ontology pathways that were systematically altered, including the electron transport chain and immune response pathways that may contribute to different levels of heat tolerance and disease resistance in taurine and indicine breeds. At the post-transcriptional level, sequencing mRNA allowed us to identify a number of genes undergoing differential alternative splicing among different breeds. This study provided a high-resolution survey of the variation between bovine transcriptomes at different levels and may provide important biological insights into the phenotypic differentiation among cattle breeds.

A molecular study was conducted to investigate the prevalence of Hepatitis C virus genotypes in HCV infected population of Balochistan. Forty HCV seropositive samples belonging to seven different locations of Balochistan were collected from different health care centres. Qualitative analysis of these samples using PCR resulted in 28 positive samples. The PCR positive samples were subjected to genotyping using the method described by Ohno et al (J Clin Microbiol 35:201-202, 1997) with minor modifications. Genotyping of 28 samples revealed three different genotypes including 3a, 3b and 1a. The most prevalent genotype was 3a with rate of 50% followed by genotype 3b and 1a, respectively. Nine samples remained untyped, suggesting the need of further investigation of genotypes in this region. It has been proposed that sequencing of these samples may be helpful to unreveal these genotypes and further epidemiology of HCV genotypes. Further more, extensive and large scale studies are needed to understand the epidemiology of HCV genotypes, as no such study has been carried in this province.

HIV (Human Immunodeficiency virus) causes (acquired immunodeficiency syndrome) AIDS, in which the immune system of body totally fails to develop any defense against the foreign invaders. Infection with HIV occurs by transfer of blood, semen, and breast milk. HIV/AIDS is a global problem and it results nearly 25 million deaths worldwide. Developing countries like Pakistan have issues regarding Public Health. Currently, epidemic of HIV/AIDS is established in Pakistan and there is a threat of an expanded HIV/AIDS outbreak in the country. The major reason is that population is engaging in high-risk practices, low awareness about HIV/AIDS, and treacherous blood transfusion practices. A supplementary threat to Pakistan is India because both sharing a border and India is facing a rapidly growing HIV/AIDS epidemic. Local NGOs, National and International organizations are warning that in near future Pakistan may experiences bad situation regarding HIV/AIDS.In the present article we focused current situation of surveillance of HIV/AIDS, its virology, genotype, diagnostics, high-risk groups, reasons of vulnerability in Pakistani population, and the role of different national and international organizations in this situation.

Background:Current advancements in next-generation sequencing technology have made possible to sequence whole genome but assembling a large number of short sequence reads is still a big challenge. In this article, we present the comparative study of seven assemblers, namely, ABySS, Velvet, Edena, SGA, Ray, SSAKE, and Perga, using prokaryotic and eukaryotic paired-end as well as single-end data sets from Illumina platform.Results:Results showed that in case of single-end data sets, Velvet and ABySS outperformed in all the seven assemblers with comparatively low assembling time and high genome fraction. Velvet consumed the least amount of memory than any other assembler. In case of paired-end data sets, Velvet consumed least amount of time and produced high genome fraction after ABySS and Ray. In terms of low memory usage, SGA and Edena outperformed in all the assemblers. Ray also showed good genome fraction; however, extremely high assembling time consumed by the Ray might make it prohibitively slow on larger data sets of single and paired-end data.Conclusions:Our comparison study will provide assistance to the scientists for selecting the suitable assembler according to their data sets and will also assist the developers to upgrade or develop a new assembler for de novo assembling.