Core Gene Expression and Association of Genotypes with Viral Load in Hepatitis C Virus (HCV) - Infected Patients in Punjab, Pakistan

Purpose: To determine genotypic distribution, ribonucleic acid (RNA) RNA viral load and express core gene from Hepatitis C Virus (HCV) infected patients in Punjab, Pakistan.Methods: A total of 1690 HCV RNA positive patients were included in the study. HCV genotyping was tested by type-specific genotyping assay, viral load, by real time polymerase chain reaction (PCR) and HCV core protein was expressed in E. coli. Antigenicity of core protein was confirmed by enzyme-linked immunosorbant assay (ELISA).Results: Out of total 1690 serum samples, type-specific PCR fragments were observed in 1482 (87.69 %) of the samples. In both genders, genotype 3a (55.44 %) was most prevalent followed by 3b (15.03 %), 1a (6.98 %) and 1b (3.14 %). Regionally, genotype 3a occurred most frequently in Jaranwala (59.72 %). Patients infected with genotype 3 had pre-treatment viral load values of 52.56, 15.79 and 31.65 %, while patients infected by other genotypes showed viral load values of 13.43, 35.27 and 51.3 % for low, intermediate and high categories of viral load, respectively. ELISA showed that core protein possessed greater antigenicity.Conclusion: HCV genotype 3a is the most prevalent genotype in Punjab, although the distribution of HCV genotypes in eight cities of Punjab was not uniform. HCV core protein used to develop local screening assays may be more effective than current commercial assays.Keywords: Hepatitis C, Antigenicity, Genotyping, Viral load, Core gen

Comparison of transgenic plant production for bacterial blight resistance in Pakistani local rice (Oryza sativa L.) cultivars

The study was carried out to improve bacterial leaf blight resistance in three rice cultivars (Basmati - 370, DR - 82 and IR - 6) by Agrobacterium mediated transformation system. Three week-old scutellum derived calli were infected with Agrobacterium strain EHA101, containing binary vector pTCL5 which has Xa 21 gene. Different levels of acetosyringone were tested to enhance transformation efficiency. Acetosyringone at 300 ìM showed 56.6% GUS expression with 100 and 200 ìM acetosyringone showing 13.3 and 30.0% GUS expression, respectively. Maximum transformation efficiency was obtained using DR - 82 with calli exposed to 300 ìM acetosyringone for 2 min. Direct hygromycin selection with 48 h ofco-cultivation was superior to pre-selection in all three cultivars. Transient GUS expression was 51.4% while stable GUS expression in calli was 18.8%. PCR analysis confirmed the presence of the Xa 21 gene in transformed regenerated plants. Stable varietal transformation efficiency was DR - 82 > Basmati-370 > IR - 6. Resistance of transgenic plants against Xanthomonas oryzae pathovar oryzae was evaluated with various strains/isolates at the seedling stage. All PCR positive transgenic plants of DR - 82 and Basmati - 370 were resistant with lesion areas less than 5% of the inoculated leaf area. The tested transgenic plants were resistant to all the indigenous and exotic strains tested due to the broad spectrum protection provided by the Xa 21 gene

Ethnicity and socioeconomic status are related to dietary patterns at age 5 in the Amsterdam born children and their development (ABCD) cohort

Background: Health inequalities are already present at young age and tend to vary with ethnicity and socioeconomic status (SES). Diet is a major determinant of overweight, and studying dietary patterns as a whole in relation to overweight rather than single nutrients or foods has been suggested. We derived dietary patterns at age 5 and determined whether ethnicity and SES were both related to these dietary patterns. Methods: We analysed 2769 validated Food Frequency Questionnaires filled in by mothers of children (5.7 ± 0.5y) in the Amsterdam Born Children and their Development (ABCD) cohort. Food items were reduced to 41 food groups. Energy adjusted intake per food group (g/d) was used to derive dietary patterns using Principal Component Analysis and children were given a pattern score for each dietary pattern. We defined 5 ethnic groups (Dutch, Surinamese, Turkish, Moroccan, other ethnicities) and 3 SES groups (low, middle, high, based on maternal education). Multivariate ANOVA, with adjustment for age, gender and maternal age, was used to test potential associations between ethnicity or SES and dietary pattern scores. Post-hoc analyses with Bonferroni adjustment were used to examine differences between groups. Results: Principal Component Analysis identified 4 dietary patterns: a snacking, full-fat, meat and healthy dietary pattern, explaining 21% of the variation in dietary intake. Ethnicity was related to the dietary pattern scores (p < 0.01): non-Dutch children scored high on snacking and healthy pattern, whereas Turkish children scored high on full-fat and Surinamese children on the meat pattern. SES was related to the snacking, full-fat and meat patterns (p < 0.01): low SES children scored high on the snacking and meat pattern and low on the full-fat pattern. Conclusions: This study indicates that both ethnicity and SES are relevant for dietary patterns at age 5 and may enable more specific nutrition education to specific ethnic and low socioeconomic status target groups

Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data

Genome-wide association studies (GWASs) identify single nucleotide polymorphisms (SNPs) that are enriched in individuals suffering from a given disease. Most disease-associated SNPs fall into non-coding regions, so that it is not straightforward to infer phenotype or function; moreover, many SNPs are in tight genetic linkage, so that a SNP identified as associated with a particular disease may not itself be causal, but rather signify the presence of a linked SNP that is functionally relevant to disease pathogenesis. Here, we present an analysis method that takes advantage of the recent rapid accumulation of epigenomics data to address these problems for some SNPs. Using asthma as a prototypic example; we show that non-coding disease-associated SNPs are enriched in genomic regions that function as regulators of transcription, such as enhancers and promoters. Identifying enhancers based on the presence of the histone modification marks such as H3K4me1 in different cell types, we show that the location of enhancers is highly cell-type specific. We use these findings to predict which SNPs are likely to be directly contributing to disease based on their presence in regulatory regions, and in which cell types their effect is expected to be detectable. Moreover, we can also predict which cell types contribute to a disease based on overlap of the disease-associated SNPs with the locations of enhancers present in a given cell type. Finally, we suggest that it will be possible to re-analyze GWAS studies with much higher power by limiting the SNPs considered to those in coding or regulatory regions of cell types relevant to a given disease

Inhibition of activin/nodal signalling is necessary for pancreatic differentiation of human pluripotent stem cells

Peer reviewedPublisher PD

Stratigraphic correlation and paleoenvironmental analysis of the hydrocarbon-bearing Early Miocene Euphrates and Jeribe formations in the Zagros folded-thrust belt

The Lower Miocene Euphrates and Jeribe formations are considered as the main targets of the Tertiary petroleum system in the western part of the Zagros Basin. The formations consist of carbonates with some evaporate intercalations of the Dhiban Formation. This study utilized data from a field investigation including newly described outcrop sections and newly discovered productive oil fields within the Kirkuk embayment zone of the Zagros fold and thrust belt such as Sarqala and Kurdamir wells. This work is the first to show a stratigraphic correlation and paleoenvironmental interpretation by investigating both well data and new outcrop data. Three depositional environments were identified, (1) an inner and outer ramp belts environment, (2) shoal environment, and (3) restricted lagoon environment. Within these 3 environments, 12 microfacies were identified, based on the distribution of fauna mainly benthonic foraminifera, rock textures, and sedimentary structures. The inferred shallow water depths and variable salinities in both the Euphrates Formation and Jeribe Formation carbonates are consistent with deposition on the inner ramp (restricted lagoon and shoal) environments. Those found in the Euphrates Formation constrained the depositional environment to the restricted lagoon and shoal environment, while the microfacies in the Jeribe Formation provided evidence for an inner ramp and middle to outer ramp belt environments. This study represents the first detailed research that focuses on the stratigraphic correlation and changes in carbonate facies with the main aim to provide a wider understanding of stratigraphy of these carbonate reservoirs throughout the northern part of Iraq

Marginal increase of sunitinib exposure by grapefruit juice

Clinical Oncolog

DNA hypermethylation in the normal colonic mucosa of patients with colorectal cancer

The CpG-island methylator phenotype (CIMP+) in colorectal cancer (CRC) is characterised by frequent hypermethylation of promoter regions in tumour suppressor genes. Low level methylation of some CpG islands is also seen in the normal colonic mucosa and increases with age; however, it is still unclear what other factors regulate this phenomenon. The first aim of our study was to determine whether the level of promoter methylation is elevated in the normal colonic mucosa of patients with CIMP+ tumours. The second aim was to investigate whether common, functional polymorphisms in genes involved in methyl group metabolism are associated with the level of methylation in this tissue. CpG islands within the ERα, MYOD, P16(INK4A), MLH1, APC, P14(ARF), DAPK and TIMP3 genes were quantitatively evaluated for methylation in normal colonic mucosa from a large series of CRC patients using the MethyLight assay. Genotyping was carried out for polymorphisms in the MTHFR, TS, MS, MTHFD1 and DNMT3b genes. Methylation of ERα and MYOD in normal colonic mucosa increased with age and was higher in female subjects. Methylation of P16(INK4A), MLH1, TIMP3 and DAPK in normal mucosa occurred at a lower level than ERα and MYOD but also increased with age and was significantly higher in patients with CIMP+ tumours. The DNMT3b C46359T polymorphism was associated with significantly less methylation of MYOD and MLH1 and with trends for lower methylation in each of the other CpG islands examined. Our results demonstrate that age, gender and genetic factors can influence the methylation level of CpG islands in gene promoter regions of normal colonic mucosa. Further work is required to determine whether such methylation is associated with the development of CIMP+ CRC

Hemoglobin E syndromes in Pakistani population

<p>Abstract</p> <p>Background</p> <p>Hemoglobin E is an important hemoglobin variant with a worldwide distribution. A number of hemoglobinopathies have been reported from Pakistan. However a comprehensive description of hemoglobin E syndromes for the country was never made. This study aimed to describe various hemoglobin E disorders based on hematological parameters and chromatography. The sub-aim was to characterize hemoglobin E at molecular level.</p> <p>Methods</p> <p>This was a hospital based study conducted prospectively for a period of one year extending from January 1 to December 31, 2008. EDTA blood samples were analyzed for completed blood counts and hemoglobin variants through automated hematology analyzer and Bio-Rad beta thalassaemia short program respectively. Six samples were randomly selected to characterize HbE at molecular level through RFLP-PCR utilizing <it>Mnl</it>I restriction enzyme.</p> <p>Results</p> <p>During the study period, 11403 chromatograms were analyzed and Hb E was detected in 41 (or 0.36%) samples. Different hemoglobin E syndromes identified were HbEA (n = 20 or 49%), HbE/β-thalassemia (n = 14 or 34%), HbEE (n = 6 or 15%) and HbE/HbS (n = 1 or 2%). Compound heterozygosity for HbE and beta thalassaemia was found to be the most severely affected phenotype. RFLP-PCR utilizing <it>Mnl</it>I successfully characterized HbE at molecular level in six randomly selected samples.</p> <p>Conclusions</p> <p>Various HbE phenotypes are prevalent in Pakistan with HbEA and HbE/β thalassaemia representing the most common syndromes. Chromatography cannot only successfully identify hemoglobin E but also assist in further characterization into its phenotype including compound heterozygosity. Definitive diagnosis of HbE can easily be achieved through RFLP-PCR.</p

Are we failing to protect threatened mangroves in the Sundarbans world heritage ecosystem?

The Sundarbans, the largest mangrove ecosystem in the world, is under threat from historical and future human exploitation and sea level rise. Limited scientific knowledge on the spatial ecology of the mangroves in this world heritage ecosystem has been a major impediment to conservation efforts. Here, for the first time, we report on habitat suitability analyses and spatial density maps for the four most prominent mangrove species - Heritiera fomes, Excoecaria agallocha, Ceriops decandra and Xylocarpus mekongensis. Globally endangered H. fomes abundances declined as salinity increased. Responses to nutrients, elevation, and stem density varied between species. H. fomes and X. mekongensis preferred upstream habitats. E. agallocha and C. decandra preferred down-stream and mid-stream habitats. Historical harvesting had negative influences on H. fomes, C. decandra and X. mekongensis abundances. The established protected area network does not support the most suitable habitats of these threatened species. We therefore recommend a reconfiguration of the network to include these suitable habitats and ensure their immediate protection. These novel habitat insights and spatial predictions can form the basis for future forest studies and spatial conservation planning, and have implications for more effective conservation of the Sundarbans mangroves and the many other species that rely on them