Base excision repair of N4,5-dimethylcytosine in DNA

Master's thesis in Biological chemistry5-Methylcytosine (m5C) replaces cytosine (C) in DNA in prokaryotic and eukaryotic cells to execute a number of important cellular functions, but damage to m5C have received little attention. For instance, almost no studies exist on erroneous methylation of m5C by alkylating agents to double and triple methylated bases. Due to chemical evidence, and because many prokaryotes express methylases able to convert m5C into the double methylated N4,5-dimethylcytosine (mN4,5C) in DNA, this base lesion is likely to be present in cellular DNA. In this study, we used DNA with one mN4,5C residue incorporated at a specific site where mN4,5C was placed opposite G, A, C or T (called mN4,5C:G-DNA, mN4,5C:A-DNA, mN4,5C:C-DNA and mN4,5C:T-DNA, respectively. We set up several experiments to find putative repair activity for mN4,5C using different E. coli and human glycosylases, major initiators of the base excision repair (BER) pathway. We found the highest repair activity for mN4,5C:C-DNA and mN4,5C:G-DNA by the two Escherichia coli DNA glycosylases Fpg and Nei, respectively. To confirm this repair activity, endonuclease IV and T4-polynucleotide kinase were employed to define and process the 3´-end products following Fpg and Nei-mediated incision of mN4,5C:C-DNA and mN4,5C:G-DNA, respectively. In contrast, several other E. coli DNA glycosylases like Ung and Mug and the human enzyme hUNG did not show repair activity at employed conditions. To our knowledge, this is the first report describing a repair activity for a further methylated m5C in DNA as well as the first alkylated base allocated to Fpg and Nei as substrate

Comparing risk factors of HIV among hijra sex workers in Larkana and other cities of Pakistan: an analytical cross sectional study

Background In 2005, Pakistan was first labeled as a country with concentrated epidemic of Human Immunodeficiency Virus (HIV). This was revealed through second generation surveillance conducted by HIV/AIDS Surveillance Project (HASP). While injection drug users (IDUs) were driving the epidemic, subsequent surveys showed that Hijra (transgender) sex workers (HSWs) were emerging as the second most vulnerable group with an average national prevalence of 6.4%. An exceptionally high prevalence (27.6%) was found in Larkana, which is a small town on the right bank of river Indus near the ruins of Mohenjo-Daro in the province of Sindh. This paper presents the risk factors associated with high prevalence of HIV among HSWs in Larkana as compared to other cities of the country. Methods Data were extracted for secondary analysis from 2008 Integrated behavioral and biological survey (IBBS) to compare HSWs living in Larkana with those living in other cities including Karachi and Hyderabad in Sindh; Lahore and Faisalabad in Punjab; and Peshawar in Khyber Pakhtunkhwa provinces. After descriptive analysis, univariate and multivariate analyses were performed to identify risk factors. P value of 0.25 or less was used to include factors in multivariate analysis. Results We compared 199 HSWs from Larkana with 420 HSWs from other cities. The average age of HSWs in Larkana was 26.42 (±5.4) years. Majority were Sindhi speaking (80%), uneducated (68%) and unmarried (97%). In univariate analysis, factors associated with higher prevalence of HIV in Larkana included younger age i.e. 20–24 years (OR: 5.8, CI: 2.809–12.15), being unmarried (OR: 2.4, CI: 1.0–5.7), sex work as the only mode of income (OR: 5.5, CI: 3.70–8.2) and longer duration of being involved in sex work 5–10 years (OR: 3.3, CI: 1.7–6.12). In multivariate logistic regression the HSWs from Larkana were more likely to lack knowledge regarding preventive measures against HIV (OR 11.9, CI: 3.4–41.08) and were more prone to use of alcohol during anal intercourse (OR: 6.3, CI: 2.77–17.797). Conclusion Outreach programs focusing on safer sexual practices and VCT are urgently needed to address the upsurge of HIV among HSWs in Larkana

Research fatigue among injecting drug users in Karachi, Pakistan

Background Karachi is the largest metropolis of Pakistan and its economic hub attracting domestic migrants for economic opportunities. It is also the epicenter of HIV epidemic in the country. Since 2004, one pilot study and four behavioral and biological surveillance rounds have been conducted in Karachi. In addition many student research projects have also focused on key risk groups including injection drug users (IDUs). As a result of this extra ordinary exposure of same kind of questions, IDUs know how to respond to high value questions related to sharing of needles or unsafe sexual practices. The purpose of the study was to explore the element of research fatigue among IDUs in Karachi, Pakistan. Methods The study was conducted on 32 spots in Karachi, selected on the basis of estimate of IDUs at each spot. A trained field worker (recovered IDU) visited each spot; observed sharing behavior of IDUs and asked questions related to practices in January 2009. Verbal consent was obtained from each respondent before asking questions. Results On average 14 IDUs were present at each spot and out of 32 selected spots, 81% were active while more than two groups were present at 69% spots. In each group three to four IDUs were present and everyone in the group was sharing. One dose of injecting narcotics was observed. Sharing of syringes, needles and distilled water was observed at 63% spots while professional injector/street doctor was present at 60% spots. Conclusion There is a need to check internal consistency in surveillance research. It is highly likely that IDUs and other risk groups know how to respond to key questions but their responses do not match with the practices

Metastatic Hepatic Epithelioid Hemangioendothelioma In 10 Years Old Boy; A Rare Case Report

OBJECTIVES Epithelioid Hemangioendothelioma is an infrequent vascular neoplasm of intermediate malignant potential oddly affecting children. It is primarily noted in soft tissues, the stomach, breast, spleen, brain, and liver. No definite risk factor is identified in children. However, following WWTR1-CAMTA1 and YAP1-TFE3 gene fusions are frequently seen in these tumours. We present a case of very rare childhood Epithelioid Hemangioendothelioma of the liver in a ten-year-old boy. A 10-year-old boy presented with abdominal pain, mild weight loss, and abnormal liver function tests. Radiologically, hepatic, pulmonary, and bony lesions are noted. The biopsy report showed Epithelioid Hemangioendothelioma confirmed by an Immunohistochemical panel. Due to the lack of facilities in our centre, palliative treatment was given to the patient. Surgical resection, liver transplant, and radiofrequency ablation were impossible due to widespread hepatic and pulmonary disease. The patient was resistant to any medical treatment. The patient died at the seventh-month follow-up. HEHE is a scarcely seen tumour with no definite management protocol. Surgical resection is the preferred treatment for resectable tumours. In non-resectable extensive bifocal tumours, like in our case, the preferred treatment is radio-frequency ablation and hepatic transplant. The overall survival is trivial due to the non-compliant nature of the disease

Wheat in the Era of Genomics and Transgenics

Wheat, as one of the most important cereal crops in the world and second major caloric source in the world after rice, is the major staple food in South Asia and many other countries of the world. Prior to onset of “Green Revolution,” South Asian countries were facing the threat of severe famine. Green Revolution wheat genotypes brought out these countries from the crisis they were facing and has helped them to sustain their productions for more than half a century. With the emergence of molecular biology and biotechnology, another window of opportunity is opened to sustain wheat yields by using modern techniques of genes identification and utilization. Through this chapter, we have tried to gather information that was generated for wheat improvement in last 3 decades. These afforest included the development of molecular markers, mapping of genes, sequencing of markers genes, and their utilization through marker-assisted selection. The other part recorded various efforts to genetically transform wheat for traits improvements and/or to study their molecular control

Heat transport investigation of engine oil based rotating nanomaterial liquid flow in the existence of partial slip effect

In this study, rotational nano liquid movement above a linearly stretching surface has been formulated. A two-phase model is used for this analysis. Base fluid engine oil and two distinct types of nanoparticles are used as nanoparticles, i.e. copper and aluminum oxide (Cu & Al2O3). This study is aimed to describe the changed possessions on velocity and temperature for rotational nanofluid flow above a linear enlarging surface in the existence of the slip effect. The leading structure of PDEs is converted into ODEs with a similarity transformation. Numerical findings are gained utilizing a sophisticated numerical approach. For both nanofluids, the results for rotational flow and heat transmission characteristics are emphasized with the help of graphs. At the linear extending surface, the influence of physical concentrations like heat flow rates and skin friction coefficients is investigated and visually clarified. Cunanoparticles proved to be better heat carriers than Al2O3 nanoparticles