Genetska raznolikost Mareecha i Barela pasmina jednogrbih deva iz Pakistana na temelju mikrosatelitskih markera

The genetic diversity of Pakistani dromedary camels is poorly documented. The present study evaluated the genetic variations of two well-known Pakistani camel breeds, Mareecha and Barela, that are well-adapted to the Cholistan desert climate. Camel can serve as a beneficial participant in the food supply chain by providing milk, meat and other food products for the livelihood of pastoral peoples. To explore a new world of resources, greater attention to needed to create standard procedures to genetically characterize, classify and identify camel breeds in the country. For this purpose, 66 unrelated animals of the Mareecha (n=35) and Barela (n=31) breeds were genotyped using a set of 12 labelled microsatellite loci. DNA fragment sizes were determined in an ABI 3130 Genetic Analyzer. All microsatellite markers were successfully amplified and exhibited a polymorphic nature, with an average Polymorphic Information Content (PIC) of 0.72 and 0.70 in Mareecha and Barela, respectively. A total of 107 alleles with an average of 8.91 alleles per locus were identified by these markers in both breeds. CMS15 was highly polymorphic with 13 alleles, while VOLP-032 was the lowest with two loci. The Fit and Fis values were low but high population differentiation (17%) was observed in both breeds, due to the migrations of pastoral people to different remote areas during climate fluctuations.Genetska raznolikost pakistanskih jednogrbih deva slabo je dokumentirana. Ova studija procijenila je genetske varijacije dviju dobro poznatih pasmina pakistanskih deva - mareecha i barela - koje su vrlo dobro prilagođene klimi pustinje Cholistan. Deva može poslužiti kao koristan sudionik u lancu opskrbe hranom, osiguravajući mlijeko, meso i druge prehrambene proizvode za život pastira. Da bi se istražio novi svijet resursa, potrebno je više pozornosti za obavljanje standardnih postupaka za genetsku karakterizaciju, razvrstavanje i identifikaciju pasmina deva u zemlji. U tu svrhu, ukupno 66 životinja koje nisu u srodstvu pasmine mareecha (n=35) i barela (n=31) genotipizirane su uporabom 12 označenih mikrosatelitskih lokusa. Veličine fragmenata DNK određene su u ABI 3130 genetskom analizatoru. Svi mikrosatelitski markeri uspješno su pojačani i pokazali su polimorfnu narav s prosječnim sadržajem polimorfnih informacija (PIC) od 0,72 i 0,70 za mareecha, odnosno barela pasminu. Ukupno 107 alela s prosječno 8,91 alelom po lokusu u obje pasmine identificirano je tim markerima. CMS15 bio je vrlo polimorfan s 13 alela dok je VOLP-032 bio najniži s 2 lokusa. Fit i Fis vrijednosti bile su niske, ali je uočena velika diferencijacija populacije (17 %) za obje pasmine koje su posljedica migracije pastira u različite udaljene krajeve tijekom promjena klime

Microsatellite marker based genetic diversity among four varieties of Pakistani Aseel chicken

Indian Aseel chicken (Gallus gallus) is traditionally used as a favorite game bird all over the world. Bird fighting communities of Pakistan are the major source of its conservation and there are at least four distinctively recognized varieties of Aseel chicken based upon selective breeding, geographical location and color patterns. A pioneering study on genetic diversity of these varieties namely Lakha (n=17), Mushki (n=19), Mianwali (n=19) and Peshawari (n=13) was undertaken using FAO recommended 10 microsatellite loci. A total of 91 alleles were observed in 4 varieties of Aseel chicken with an average of 9.1 alleles per locus. Number of alleles varied between 4 to 8 in Lakha, 4 to 9 in Mushki, 3 to 10 in Mianwali and 3 to 7 in Pashawari. Mean polymorphic information content values were 0.67, 0.69, 0.71 and 0.65 in individual varieties, respectively. Mean observed and expected heterozygosity index values of 0.3941 and 0.7376 were recorded in Lakha, 0.4105 and 0.7468 for Mushki, 0.4105 and 0.7718 Mianwali and 0.3692 and 0.7191 for Peshawari. Mean Fixation index (Fst) value was calculated as 0.1264. Highest Nei's standard genetic distance (Ds) value of 1.0735 was observed between Mushki and Peshawari, whereas its value was minimum (0.3533) between Lakha and Mushki. This report describes genetic diversity of Aseel chicken in Pakistan and provides foundation data to initiate extensive and more comprehensive studies on indigenous chicken genetic resource conservation and its future utilization in commercial breeding programs. (C) 2011 PVJ. All rights reserve

Insight of Tp53 Mutations and their effect on Protein in Different Feline and Canine Neoplasms

Background: Mutations in the Tp53 gene, a tumor suppressor gene, may cause dysfunction in growing cells and hinder the phenomenon of apoptosis, an alleged cause of tumorigenesis. It is involved in conservation of the genome and DNA repair, mutations of this gene may cause the damaged cells to grow continuously.Methods: The type of molecular changes in Tp53 gene and their effects on physiochemical and structural properties of this protein in various Canine and Feline cancers were observed in this study by using online bioinformatics tools.Results: Our results indicated that lymphomas and perianal adenocarcinomas (PAC) have the same mutation at c. 104, while mammary tumors and canine transmissible venereal tumor (CTVT) contain different mutations. Referring to changes in protein, synonymous mutations in granulomas were observed while certain mutations in squamous cell carcinoma (SCC) and head & neck tumors were detected in Canis familiaris. In Felis catus, the mutant protein was similar to wild type protein with exception of mutant 5 of mammary tumor, which had a deletion at the 287 amino acid position.Conclusion: The insight gathered on the p53 mutant proteins in both species aided our understanding of the in-vivo fate of the p53 protein and its isoforms and the effects that morphological changes can have on the fate of cells. Furthermore, isolation of this protein may augment our understanding about the structural biology of these proteins

Različitost interferona-α-A (IFN-α-A) u jaka (Bos grunniens) iz Pakistana

Among the various species of livestock, the domestic yak (Bos grunniens) belongs to the class Bovidae and is specially adapted for survival at high altitudes under extreme climatic conditions. Yak is a very useful species due to the multiple products it provides, such as meat, hide, milk and other dairy products. Like other livestock species, domestic yak is also in danger of infection by microbial infections. However, multiple immunity genes encode special protein products to fight infection. One of these immunity genes is interferon-α-A (IFN-α-A), which encodes proteins that belongs to cytokines and fights viral infections. The current study analysed the genetic variation and phylogenetic analysis of the IFN-α-A gene in domestic yak, with comparisons to other mammalian species to investigate immune diversity level, with the aim of designing molecular selection strategies for better disease resistant animals.Među različitim vrstama stoke, jedna je vrsta i jak (Bos grunniens). Ova životinja pripada obitelji Bovidae. Ova je vrsta prilagođena je preživljavanju na velikim visinama i u ekstremnim klimatskim uvjetima. Jak je vrlo korisna životinja zbog brojnih proizvoda koje od njega dobivamo, poput mesa, kože, mlijeka i mliječnih proizvoda. Kao i druge vrste stoke i jak je u opasnosti od infekcije brojnim mikrobnim infekcijama. Međutim, mnogo je imunogena koji kodiraju posebne proteinske proizvode za borbu protiv infekcija. Jedan od tih imunogena je interferon-α-A (IFN-α-A) koji kodira proteine koji pripadaju citokinima i bori se protiv virusnih infekcija. Ova studija osmišljena je za analizu genetske varijacije i filogenetsku analizu IFN-α –A gena u jaka (Bos grunniens) te njegovu usporedbu s drugim vrstama sisavaca u svrhu istraživanja razine različitosti imunosti za osmišljenja strategija molekularnog odabira za veću otpornost životinja na bolesti

The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths andweaknesses that need to be highlighted.We compared and presented results of six most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate

Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds 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 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 are shown to be of Iberian, and not African, decent. 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.Comment: 38 pages, 15 figures. Various changes made to respond to peer reviews. Mostly, arguments were clarified and additional f-statistics were adde

Characterization Of A Novel Hydrolytic Enzyme Producing Thermophilic Bacterium Isolated From The Hot Spring Of Azad Kashmir-Pakistan

ABSTRACT A thermophilic bacterium (TP-2) was isolated from the Tatta Pani hot spring in Azad Kashmir and was characterized using phenotypic and genotypic characters. The strain developed cream colored, round, smooth, flat and slimy colonies while the cells were Gram positive rods that ranged in size from about 2.1-3.6 μm to 0.2-0.3 μm in width. Sequence analysis of its 16S rRNA gene showed that isolate TP-2 had 89% homology with Geobacillus debilis. It grew within pH range of 5.5 to 8.5 with optimum growth at pH 7.0. The isolate showed optimum growth at 65ºC and gave positive results for gelatin hydrolysis (GEL), ortho nitrophenyl-β-D-galactopyranosidase (ONPG), and nitrate production and produced acid from sucrose, glucose and maltose. It utilized glucose, fructose, maltose, lactose, sucrose, xylan, starch, filter paper and carboxymethylcellulose as sole carbon source. Isolate TP-2 produced significant amount of industrially important enzymes i.e. extracellular α-amylase, CMCase, FPase, Xylanase, Protease and Lipase and intracellular CMCase and FPase

Double-Stranded Break Repair in Mammalian Cells and Precise Genome Editing

In mammalian cells, double-strand breaks (DSBs) are repaired predominantly by error-prone non-homologous end joining (NHEJ), but less prevalently by error-free template-dependent homologous recombination (HR). DSB repair pathway selection is the bedrock for genome editing. NHEJ results in random mutations when repairing DSB, while HR induces high-fidelity sequence-specific variations, but with an undesirable low efficiency. In this review, we first discuss the latest insights into the action mode of NHEJ and HR in a panoramic view. We then propose the future direction of genome editing by virtue of these advancements. We suggest that by switching NHEJ to HR, full fidelity genome editing and robust gene knock-in could be enabled. We also envision that RNA molecules could be repurposed by RNA-templated DSB repair to mediate precise genetic editing

The study of gene GJB2/DFNB1 causing deafness in humans by linkage analysis from district Peshawar

Families with at least 2 or more individuals having hereditary hearing loss were enrolled from different areas of Khyber Pakhtoonkhwa, mainly from district Peshawar. Detailed history was taken from each family to minimize the presence of other abnormalities and environmental causes for deafness. Families were questioned about skin pigmentation, hair pigmentation, and problems relating to balance, vision, night blindness, thyroid, kidneys, heart, and infectious diseases like meningitis, antibiotic usage, injury, and typhoid. The pedigree structures were based upon interviews with multiple family members, and pedigrees of the enrolled families were drawn using Cyrillic program (version 2.1). All families showed recessive mode of inheritance. I studied 8 families of these 10. For linkage analyses, studies for DFNB1 locus, 3 STR markers (D13S175, D13S292, and D13S787) were genotyped using polyacrylamide gel electrophoresis (PAGE) and haplotypes were constructed to determined, linkage with DFNB1 locus. From a total of 8 families, a single family-10 showed linkage to DFNB1 locus

SAliBASE: A Database of Simulated Protein Alignments

Simulated alignments are alternatives to manually constructed multiple sequence alignments for evaluating performance of multiple sequence alignment tools. The importance of simulated sequences is recognized because their true evolutionary history is known, which is very helpful for reconstructing accurate phylogenetic trees and alignments. However, generating simulated alignments require expertise to use bioinformatics tools and consume several hours for reconstructing even a few hundreds of simulated sequences. It becomes a tedious job for an end user who needs a few datasets of variety of simulated sequences. Currently, there is no databank available which may help researchers to download simulated sequences/alignments for their study. Major focus of our study was to develop a database of simulated protein sequences (SAliBASE) based on different varying parameters such as insertion rate, deletion rate, sequence length, number of sequences, and indel size. Each dataset has corresponding alignment as well. This repository is very useful for evaluating multiple alignment methods