Molecular phylogeny of Pakistani riverine buffalo based on genetic variability of mitochondrial cytochrome b gene

Mitochondrial cytochrome b gene is considered to be one of the best markers for breed characterization as well as studying the ancestry in the vertebrates due to its exclusive maternal inheritance. DNA fingerprinting by single nucleotide polymorphism is most reliable and widely used molecular technique in modern forensics and is being considered in this study. Partial sequencing of 1,061?bp of aforementioned gene from 14580 to 15643 was conducted in two famous Pakistani buffalo breeds named Nili-Ravi and Kundi. In which we explore seven haplotypes within earlier and none in the latter breed. Nili-Ravi is polymorphic at four codons of this gene, and the protein translation is also different from the reference sample while monomorphic at three codons with no amino acid replacement. Haplotypes frequency distribution of these four haplotypes named NR3, NR4, NR5, NR7 revealed that the prevalence of each haplotype is 0.04?% in the Pakistani buffalo population of this Nili-Ravi breed while complete homoplasmy was observed in the Kundi breed population. Nili-Ravi breed of buffalo is genetically more variable than the Kundi breed as far as the gene in subject is concerned. It means later breed has spent more time to propagate its wild type haplotype which make this breed more ancestral as compare to Nili-Ravi. Secondly both breeds share their common ancestors with regional water buffalo rather than the swamp one.     

Delivering post-abortion care through a community-based reproductive health volunteer programme in pakistan

Summary This qualitative study was conducted in May-June 2010 with women using post-abortion care (PAC) services provided by the Marie Stopes Society in Pakistan during the six month period preceding the study, more than 70% of whom had been referred to the clinics by reproductive health volunteers (RHVs). The aim of the study was to establish the socio-demographic profile of clients, determine their preferred method of treatment, explore their perceptions of the barriers to accessing post-abortion services and to understand the challenges faced by RHVs. The sample women were selected from six randomly selected districts of Sindh and Punjab. Eight focus group discussions were conducted with PAC clients and fifteen in-depth interviews with RHVs. In addition, a quantitative exit interview questionnaire was administered to 76 clients. Medical, rather than surgical, treatment for incomplete and unsafe abortions was preferred because it was perceived to 'cause less pain', was 'easy to employ' and 'having fewer complications'. Household economics influence women's decision-making on seeking post-abortion care. Other restraining factors include objection by husbands and in-laws, restrictions on female mobility, the views of religious clerics and a lack of transport. The involvement of all stakeholders could secure social approval and acceptance of the provision of safe post-abortion care services in Pakistan, and improve the quality of family planning services to the women who want to space their pregnancies.     

Structure based sequence analysis & epitope prediction of gp41 HIV1 envelope glycoprotein isolated in Pakistan

ABSTRACT: BACKGROUND: Gp41 is an envelope glycoprotein of human immune deficiency virus (HIV). HIV viral glycoprotein gp41, present in complex with gp120, assists the viral entry into host cell. Over eighty thousands individuals are HIV infected in Pakistan which makes about 0.2% of 38.6 million infected patients worldwide. Hence, HIV gp41 protein sequences isolated in Pakistan were analyzed for the CD4 and CD8 T cells binding epitopes. RESULTS: Immunoinformatics tools were applied for the study of variant region of HIV gp41envelope protein. The protein nature was analyzed using freely accessible computational software. About 90 gp41 sequences of Pakistani origin were aligned and variable and conserved regions were found. Four segments were found to be conserved in gp41 viral protein. A method was developed, involving the secondary structure, surface accessibility, hydrophobicity, antigenicity and molecular docking for the prediction and location of epitopes in the viral glycoprotein. Some highly conserved CD4 and CD8 binding epitopes were also found using multiple parameters. The predicted continuous epitopes mostly fall in the conserved region of 1-12; 14-22 and 25-46 and can be used as effective vaccine candidates. CONCLUSION: The study revealed potential HIV subtype a derived cytotoxic T cell (CTL) epitopes from viral proteome of Pakistani origin. The conserved epitopes are very useful for the diagnosis of the HIV 1 subtype a. This study will also help scientists to promote research for vaccine development against HIV 1 subtype a, isolated in Pakistan.     

Contrasting views of animal healthcare providers on worm control practices for sheep and goats in an arid environment

A questionnaire survey was conducted to determine the worm control practices and anthelmintic usage of 150 key respondents involved in sheep and goat production in the arid Thal area of Pakistan. The information was collected by visiting farms, and interviewing the key respondents which included veterinary officers (n = 15), veterinary assistants (n = 51), traditional practitioners (n = 24), and small and large scale sheep/goat farm herders and owners (n = 60). Among all interviewed animal healthcare providers, the veterinary officers had the highest level of awareness of parasitic infection and advocated the use of modern available anthelmintics according to the predefined schedule. The farmers on the other hand, had the lowest level of knowledge about parasitic infections. They used modern anthelmintics at low frequencies (every six months) following an unusual practice of diluting the medicine. Veterinary assistants had a medium level of awareness about the parasitic infections using anthelmintic treatments when they deemed necessary rather than following a predefined treatment schedule. Traditional practitioners were also aware of parasitic infections and used traditional anthelmintics or a combination of the traditional and modern anthelmintics. The animal health providers had a different awareness and knowledge of parasitic infections which resulted in contrasting proposals for its' control. The farmers used worm control measures in accordance with their own views and those of animal healthcare advisors, combining modern and traditional treatments. This study provides the first insight into the differing views of those animal healthcare providers who form the basis for effective parasitic control within the sheep and goat industry of an arid region.     

Influence of aqueous leaf extract of common lambsquarters and NaCl salinity on the germination, growth, and nutrient content of wheat

Aqueous leaf extract of common lambsquarters (Chenopodium album L.) was evaluated alone or in combination with NaCl salinity for its influence on germination, seedling growth and contents of Na, K, and Ca by shoots and roots of wheat. The leaf extract and NaCl alone or in combination did not have any significant effect on germination, but the shoot and root lengths of seedlings and their dry weight decreased significantly by the treatments. Root growth was affected more than the shoot. The combination of leaf extract and NaCl drastically reduced the growth more than the separate effects of these stress treatments. The incorporation of leaf extract in the growth media decreased the content of Na by shoot, whereas the contents of K and Ca increased. NaCl treatments in combination with leaf extract increased the content of Na. Similar increases were observed for K and Ca in shoot, while these nutrients were increased in roots compared to control.     

The root growth of wheat plants,the water conservation and fertility status of sandy soils influenced by plant growth promoting rhizobacteria

Plant growth promoting rhizobacteria were isolated and characterized from sandy soils in Pakistan. The role of the rhizobacteria, in association with plant growth regulators, was studied on the roots of wheat grown under water stressed conditions. The plant growth promoting rhizobacteria were characterized on the basis of colony morphology, biochemical traits and identified on the basis of 16S-rRNA gene sequencing which identified the selected isolates Planomicrobium chinense, Bacillus cereus and Pseudomonas fluorescens. Antibacterial and antifungal activities were determined. The fresh cultures (24 h old) of isolates were used to soak the seeds for 2–3 h prior to sowing. The growth regulators salicylic acid and putrescine were applied to the plant as foliar spray at three leaf stage. The plant growth promoting rhizobacteria produced exopolysaccharides that formed soil aggregation around roots of the plants and significantly enhanced water holding capacity of sandy soil. The relative water content (80%) of leaves and root fresh (80%) and dry weight (68%) were higher in plant growth promoting rhizobacteria inoculated plants. The nutrient content of rhizosphere soil of treated plants was also enhanced (Ca 35%, K 34%, Mg 52% and Na 42%) over stressed controls. Integrative use of effective plant growth promoting rhizobacteria in combination with salicylic acid appears to be an effective eco-friendly approach to increase drought tolerance in wheat plants to combat desertification.     

Measurement of phosphorylated phospholamban levels in cardiomyocytes (HL-1) by immunoprecipitation

Phospholamban (PLN) is a key regulatory protein involved in cardiac calcium signaling through the pumping of cytoplasmic Ca²⁺ into the sarcoplasmic reticulum (SR). Recent systems-level studies have focused on integrating quantitative data (e.g. protein expression levels) for a better understanding of cardiac systems biology. In this view, we developed a capillary electrophoresis (CE) based immunoprecipitation method for the measurement of phospho-PLN (ser 16) in cardiomyocytes (HL-1 cell line). Dose-dependent isoproterenol (Iso) treated cells were analyzed using CE, and the phospho-PLN levels were quantified using specific polyclonal antibodies. The CE method employed was accurate, quick and easier compare to other techniques and the results are useful for the subsequent computational systems biology research.     

Solution structure of ERK2 binding domain of MAPK phosphatase MKP-3: structural insights into MKP-3 activation by ERK2

MAP kinases (MAPKs), which control mitogenic signal transduction in all eukaryotic organisms, are inactivated by dual specificity MAPK phosphatases (MKPs). MKP-3, a prototypical MKP, achieves substrate specificity through its N-terminal domain binding to the MAPK ERK2, resulting in the activation of its C-terminal phosphatase domain. The solution structure and biochemical analysis of the ERK2 binding (EB) domain of MKP-3 show that regions that are essential for ERK2 binding partly overlap with its sites that interact with the C-terminal catalytic domain, and that these interactions are functionally coupled to the active site residues of MKP-3. Our findings suggest a novel mechanism by which the EB domain binding to ERK2 is transduced to cause a conformational change of the C-terminal catalytic domain, resulting in the enzymatic activation of MKP-3.     

FRS2 PTB domain conformation regulates interactions with divergent neurotrophic receptors

Membrane-anchored adaptor proteins FRS2alpha/beta (also known as SNT-1/2) mediate signaling of fibroblast growth factor receptors (FGFRs) and neurotrophin receptors (TRKs) through their N-terminal phosphotyrosine binding (PTB) domains. The FRS2 PTB domain recognizes tyrosine-phosphorylated TRKs at an NPXpY (where pY is phosphotyrosine) motif, whereas its constitutive association with FGFR involves a receptor juxtamembrane region lacking Tyr and Asn residues. Here we show by isothermal titration calorimetry that the FRS2alpha PTB domain binding to peptides derived from TRKs or FGFR is thermodynamically different. TRK binding is largely enthalpy-driven, whereas the FGFR interaction is governed by a favorable entropic contribution to the free energy of binding. Furthermore, our NMR spectral analysis suggests that disruption of an unstructured region C-terminal to the PTB domain alters local conformation and dynamics of the residues at the ligand-binding site, and that structural disruption of the beta8-strand directly weakens the PTB domain association with the FGFR ligand. Together, our new findings support a molecular mechanism by which conformational dynamics of the FRS2alpha PTB domain dictates its association with either fibroblast growth factor or neurotrophin receptors in neuronal development.