The epidemic of HIV/AIDS in developing countries; the current scenario in Pakistan

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

Distribution of Common Coot (Fulica atra) Collected from Wet Lands of Punjab, Pakistan

Population survey was conducted to evaluate the population of common coot (Fulicaatra) and ten years population trend at Chashma Barrage (29883±6458), Taunsa Barrage (4198±515), Ucchali Lake (7253±1466), Head Qadirabad (2789±785), Head Marala (3226±984), Head Rasool (3261±84)), Khabbeki Lack (1486±230), Head Sulaimanki (1809±180), Jhalar Lake (526±206) and Head Islam (1779±257). The population atChashma barrage was statistically highly significant as compared to other wetlands. The overall year wise abundance and relative abundance of different wet lands were recorded. To evaluate the food preference, total weight of gut (63.98±3.946), total weight of gizzard (26.99 ± 1.325), weight of food material (3.59±0.187), gizzard weight without food material (23.39± 1.244), weight of seed (1.24± 0.075), weight of vegetation (1.65±0.103) and weight of other material (0.69±0.067) were calculated. The comparison between male and femalegave results that the total weight of gut, total weight of gizzard, weight of food material, Gizzard weight without food material and weight of other material was statistically highly significant and weight of seed, weight of vegetation was statistically significant.The richness, abundance, Shannon’s variety list, Simpson’s variety record and evenness for gizzard contents were calculated. Among the 40 samples, 19 samples were found infected in by parasites of seven types of Gastro-intestinal parasites were distinguished and recorded as Amidostomum anseris, Capillaria contorta, Strongyloides avium, Echinoparyphium recurvatum, Notocotylus attenuatus, and Giardia sp. D. balacea was recorded among the six wetlands. S. avium and N. attenuates wererecorded among the four wetlands, A. anseris, E. recurvatum and Giardia sp. wererecorded among the three wetlands, and C.contortawererecorded among the two wetlands.The current study provides the information for the management planning, conservation and improvement of habitat of common coot. The knowledge of parasites can be helpful to grasp the host-parasite interactions and give important standard data to the assessment of fitness and wellbeing status of this species

Detection of Four Novel Polymorphisms in PrP gene of Pakistani sheep (Damani and Hashtnagri) and goats (Kamori and Local Hairy) breeds

Scrapie is a fatal neurodegenerative disorder of sheep and goats caused by post-translational conformational change in the host-encoded prion protein (PrPC). Susceptibility or resistance to scrapie has been associated with the presence of polymorphisms in the prion protein (PrP) gene. In the present study, we analyzed the PrP gene sequence to determine the frequency of polymorphisms in 56 sheep (28 each from Damani and Hashtnagri breeds) and 56 goats (28 each from Kamori and Local Hairy breeds). A total of 7 amino acid polymorphisms were detected in the PrP gene for sheep and 4 for goats. These amino acid polymorphisms were combined in 13 alleles and 15 genotypes in sheep and 5 alleles and 6 genotypes in goats. The overall frequency of the most sheep scrapie-resistant polymorphism (Q171R) was calculated to be 0.107. The most scrapie-susceptible polymorphism (A136V) was not detected in any of the studied sheep. The overall frequency of scrapie-associated polymorphism (H143R) in goats was found to be 0.152. Along with already known amino acid polymorphisms, two novel polymorphisms were also detected for each of sheep (Q171N and T191I) and goats (G22C and P63L). However, the overall frequency of these polymorphisms was extremely low

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

Molekularna istraživanja na rajanpuri soju pasmine beetal koza iz Pakistana potpunim područjem pomaka mtDNK i mikrosatelitnim markerima

The mitochondrial DNA sequences of DNA-D loops (mtDNA) from 105 individuals (11 Beetal goat Rajanpuri strains and 94 sequences extracted from GenBank) from 19 geographically and phenotypically defined domestic goat breeds in Pakistan were analysed in this experiment. In this study, we examined variability and molecular phylogeny of breeds. A total of 81 haplotypes were observed in 105 individuals, with a haplotype diversity of 0.984±0.006 and nucleotide diversity of 0.03953±0.00843. Phylogenetic analysis based on the mtDNA hyper variable segment (HVI) of the control region (481 bp), showed four mtDNA haplogroups (A, B1, C, and D) identified in Pakistani domestic goats, in which haplogroup A (84.11%) was dominant and widely distributed among all investigated breeds. The study revealed that all Rajanpuri strain haplotypes belonged to haplogroup A. The Rajanpuri is a rare local strain of Beetal goat breed located in western Punjab province of Pakistan. The results of genetic diversity based on 11 microsatellite loci revealed allelic diversity (3.6363) and high genetic diversity (0.8342) in the examined Rajanpuri goat breeds. The analysis for signature bottleneck events, using three models, revealed significant deviation of Rajanpuri goats from mutation drift equilibrium. The qualitative test of mode shift analysis also supported the results obtained under three models, indicating the presence of a recent genetic bottleneck in the Rajanpuri strain. This study provides the first information on the mtDNA architecture, genetic diversity and bottleneck analysis, which will be useful in the conservation and management of the highly valued Rajanpuri goat.Mitohondrijske DNK sekvence DNK-D petlji (mtDNK) 105 jedinki (11 ratalpuri sojeva beetal koze i 94 sekvence iz GenBank) od 19 geografskih i fenotipičnih domaćih pasmina koza u Pakistanu rabljeno je u ovom eksperimentu. U ovoj smo studiji istražili varijabilnost i njezinu molekularnu filogeniju. Zamijećen je ukupno 81 različit haplotip u 105 jedinki s raznolikošću haplotipova 0,984±0,006 i nukleotidnom raznolikošću 0,03953±0,00843. Filogenetskom analizom ustvrđen iz mtDNK hipervarijabilni segment (HVI) kontrolnog područja (481 bp) i pokazala je četiri haploskupine mtDNK (A, B1, C i D) identificirane u pakistanskih domaćih koza, u kojima se haploskupina A (84,11 %) pokazala dominantnom i široko rasprostranjenom među svim istraživanim pasminama. Studija je otkrila da svi haplotipovi rajanpuri soja pripadaju haploskupini A. Rajanpuri je rijedak lokalni soj beetal pasmine koza smješten u zapadnoj regiji provincije Punjab u Pakistanu. Rezultati genetske raznolikosti na temelju 11 mikrosatelitnih lokusa otkrili su alelnu raznolikost (3,6363) i visoku genetsku raznolikost (0,8342) istraživane rajanpuri pasmine koza. Rezultati analize za potpis za događaje uskog grla uporabom tri modela otkrili su značajno odstupanje rajanpuri koza od ravnoteže mutacija i pomaka. Kvalitativni test analize modalnog pomaka podržao je i rezultate dobivene trima modelima, ukazujući na prisutnost genetskog uskog grla u rajanpuri soja u nedavnoj prošlosti. Ova studija po prvi put pruža informacije o arhitekturi mtDNK, genetskoj raznolikosti, analizi uskog grla koje će biti korisne u donošenju odluke o očuvanju i upravljanju cijenjenom i skupocjenom rajanpuri kozom

Frequency and Outcome of Carotid Atheromatous Disease in Patients With Stroke in Pakistan

Background And Purpose: Limited data exist on the frequency and outcome of carotid artery disease in Pakistan. Such information would help guide the usefulness of screening for the condition in this low-middle income health care setting. Methods: A prospective, descriptive study was conducted among 3 large teaching hospitals in Karachi, Pakistan. Patients referred for carotid Doppler ultrasound examination were included if they had experienced a stroke or TIA within the previous month. The severity and morphology of carotid disease were characterized by trained technicians using standardized criteria. Demographic and risk factor data were collected at baseline, and the outcome of Patients was assessed at least 6 months later. Results: A total of 672 Patients underwent bilateral carotid Doppler ultrasound (1344 carotid examinations). The findings revealed 0% to 50% stenosis in 526 (78%), 51% to 69% stenosis in 57 (8%), 70% to 99% stenosis in 82 (12%), and total occlusion in 7 Patients (1%). Potentially surgically correctable disease, defined as 70% to 99% carotid artery stenosis, was present in only 79 (12%) Patients, of whom 47 (60%) were ipsilateral symptomatic, 15 (20%) asymptomatic, and 17 (20%) had status unknown. Outcome information at \u3e= 6 months follow-up was available for 36 of the 47 (76%) surgically correctable and only 4 of these Patients (12%) had undergone surgical or radiological intervention (carotid endarterectomy in 3 Patients and carotid stenting in 1 Patient). Conclusion: The frequency of carotid artery disease of at least moderate severity is very low in Patients with recent stroke or TIA and there is low utilization of high-cost, carotid intervention procedures in Pakistan. These data raise questions regarding the applicability and cost-effectiveness of routine carotid ultrasound screening in our country and similar population in Asia. The local socio-economic and clinical data do not support routine carotid Doppler ultrasound in every Patient with stroke and TIA in Pakistan. Studies are warranted to determine predictors of significant carotid artery stenosis in stroke/TIA Patients of our country to develop reliable stroke guidelines appropriate for local population

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