Genome-wide profiling of uncapped mRNA

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale

Spotting the Critical Service Quality Determinants in the Ghanaian Retail Banking: Importance and Effects

Critical of the areas in customer-centered marketing paradigms and philosophies, is ensuring that existing customers are satisfied to enable you maintain their loyalty, repurchase and to woo in new clientele. The study examined the critical influences of customer satisfaction in the retail banking of Ghana and its effects on customers’ purchasing behavior. The study included 791 clienteles drawn from the sampling population. A cross-sectional survey was used to examine the experience of benefiting from service quality elements, perceived service quality and customers purchasing behavior based on a customized 18 dimensions of SERVQUAL. By means of frequency and mediation analysis, estimates for the direct and indirect effects of benefiting from the service quality influences on perceived service quality and consumer purchasing behavior was assessed. The impacts of evidence of service quality factors on customers purchasing behavior, was partially-mediated by perceived service quality with statistically-significant indirect effect. The results prompted that the banks’ aesthetics, cleanliness, communication skills, competence, availability, access and security of their clienteles be prioritized areas they can’t afford to fail. Keywords: Service Quality, Determinants, Retail Banking, Customer Satisfaction, Behavioral intentions. DOI: 10.7176/EJBM/11-27-08 Publication date:September 30th 201

SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants

In plants, microRNAs (miRNAs) regulate their mRNA targets by precisely guiding cleavages between the 10th and 11th nucleotides in the complementary regions. High-throughput sequencing-based methods, such as PARE or degradome profiling coupled with a computational analysis of the sequencing data, have recently been developed for identifying miRNA targets on a genome-wide scale. The existing algorithms limit the number of mismatches between a miRNA and its targets and strictly do not allow a mismatch or G:U Wobble pair at the position 10 or 11. However, evidences from recent studies suggest that cleavable targets with more mismatches exist indicating that a relaxed criterion can find additional miRNA targets. In order to identify targets including the ones with weak complementarities from degradome data, we developed a computational method called SeqTar that allows more mismatches and critically mismatch or G:U pair at the position 10 or 11. Precisely, two statistics were introduced in SeqTar, one to measure the alignment between miRNA and its target and the other to quantify the abundance of reads at the center of the miRNA complementary site. By applying SeqTar to publicly available degradome data sets from Arabidopsis and rice, we identified a substantial number of novel targets for conserved and non-conserved miRNAs in addition to the reported ones. Furthermore, using RLM 5′-RACE assay, we experimentally verified 12 of the novel miRNA targets (6 each in Arabidopsis and rice), of which some have more than 4 mismatches and have mismatches or G:U pairs at the position 10 or 11 in the miRNA complementary sites. Thus, SeqTar is an effective method for identifying miRNA targets in plants using degradome data sets

The CORONIS Trial. International study of caesarean section surgical techniques: A randomised fractional, factorial trial

Background: Caesarean section is one of the most commonly performed operations on women throughout the world. Rates have increased in recent years – about 20–25% in many developed countries. Rates in other parts of the world vary widely. A variety of surgical techniques for all elements of the caesarean section operation are in use. Many have not yet been rigorously evaluated in randomised controlled trials, and it is not known whether any are associated with better outcomes for women and babies. Because huge numbers of women undergo caesarean section, even small differences in post-operative morbidity rates between techniques could translate into improved health for substantial numbers of women, and significant cost savings. Design: CORONIS is a multicentre, fractional, factorial randomised controlled trial and will be conducted in centres in Argentina, Ghana, India, Kenya, Pakistan and Sudan. Women are eligible if they are undergoing their first or second caesarean section through a transverse abdominal incision. Five comparisons will be carried out in one trial, using a 2 × 2 × 2 × 2 × 2 fractional factorial design. This design has rarely been used, but is appropriate for the evaluation of several procedures which will be used together in clinical practice. The interventions are: • Blunt versus sharp abdominal entry • Exteriorisation of the uterus for repair versus intra-abdominal repair • Single versus double layer closure of the uterus • Closure versus non-closure of the peritoneum (pelvic and parietal) • Chromic catgut versus Polyglactin-910 for uterine repair The primary outcome is death or maternal infectious morbidity (one or more of the following: antibiotic use for maternal febrile morbidity during postnatal hospital stay, antibiotic use for endometritis, wound infection or peritonitis) or further operative procedures; or blood transfusion. The sample size required is 15,000 women in total; at least 7,586 women in each comparison. Discussion: Improvements in health from optimising caesarean section techniques are likely to be more significant in developing countries, because the rates of postoperative morbidity in these countries tend to be higher. More women could therefore benefit from improvements in techniques. Trial registration: The CORONIS Trial is registered in the Current Controlled Trials registry. ISCRTN31089967

Awareness and practice of emergency contraception at a private university in Nigeria.

BACKGROUND: The pursuit of formal education now causes many people in developing countries to marry later in life, thereby leading to increased premarital sex and unintended pregnancies. Efforts have been made to characterize awareness and use of emergency contraception (EC) among undergraduate students in public universities in Nigeria; however, it is not known if students in private tertiary institutions adopt different practices or if having an affluent family background plays a role. This pilot study therefore aimed to assess the awareness and use of EC among students at a private Nigerian university toward assisting education planners in developing strategies in improving students' reproductive well-being. RESULTS: Out of 94 female students, 42 (44.7%) had sexual experience, but only 32 (34.0%) were currently sexually active. Six students (6.4%) had had unwanted pregnancies, of which all but one were terminated. Fifty-seven respondents (60.6%) were aware of EC, though only 10 (10.6%) ever practiced it. The greatest source of EC information was from health workers and peers; the lowest source was family or relatives. Most respondents desired orientation and availability of EC on campus. EC awareness among the students was predicted by upper social class background (adjusted odds ratio [OR], 2.73; 95% confidence interval [CI], 1.06-7.45) and upbringing in the Federal Capital Territory (adjusted OR, 4.45; 95% CI, 1.56-14.22). CONCLUSIONS: Though awareness of EC was higher among the private university students in this study than at most public universities, there was no difference in EC usage. A high pregnancy termination rate was observed; dilatation and curettage were mainly adopted. In Nigeria, youth-friendly reproductive health information and access should not be limited to government-owned tertiary institutions but also extended to private ones

Comparative analysis of miRNAs and their targets across four plant species

BACKGROUND: MicroRNA (miRNA) mediated regulation of gene expression has been recognized as a major posttranscriptional regulatory mechanism also in plants. We performed a comparative analysis of miRNAs and their respective gene targets across four plant species: Arabidopsis thaliana (Ath), Medicago truncatula(Mtr), Brassica napus (Bna), and Chlamydomonas reinhardtii (Cre). RESULTS: miRNAs were obtained from mirBase with 218 miRNAs for Ath, 375 for Mtr, 46 for Bna, and 73 for Cre, annotated for each species respectively. miRNA targets were obtained from available database annotations, bioinformatic predictions using RNAhybrid as well as predicted from an analysis of mRNA degradation products (degradome sequencing) aimed at identifying miRNA cleavage products. On average, and considering both experimental and bioinformatic predictions together, every miRNA was associated with about 46 unique gene transcripts with considerably variation across species. We observed a positive and linear correlation between the number miRNAs and the total number of transcripts across different plant species suggesting that the repertoire of miRNAs correlates with the size of the transcriptome of an organism. Conserved miRNA-target pairs were found to be associated with developmental processes and transcriptional regulation, while species-specific (in particular, Ath) pairs are involved in signal transduction and response to stress processes. Conserved miRNAs have more targets and higher expression values than non-conserved miRNAs. We found evidence for a conservation of not only the sequence of miRNAs, but their expression levels as well. CONCLUSIONS: Our results support the notion of a high birth and death rate of miRNAs and that miRNAs serve many species specific functions, while conserved miRNA are related mainly to developmental processes and transcriptional regulation with conservation operating at both the sequence and expression level

Hybrid off-river augmentation system as an alternative raw water resource: the hydrogeochemistry of abandoned mining ponds

The use of water from abandoned mining ponds under a hybrid off-river augmentation system (HORAS) has been initiated as an alternative water resource for raw water. However, it raises the questions over the safety of the use of such waters. In this study, the hydrogeochemical analysis of the waters is presented to assess the degree to which the water has been contaminated. Comparisons were made between sampling sites, i.e. abandoned mining ponds, active sand mining ponds and the receiving streams within Bestari Jaya, Selangor River basin. The aqueous geochemistry analysis showed different hydrochemical signatures of major elements between sites, indicating different sources of minerals in the water. Discharges from the sand mining ponds were found to contain elevated availability of dissolved concentrations of iron, manganese, lead, copper and zinc, among others. However, the quality of the water (from the main river) that is supplied for potable water consumption is at a satisfactory level despite being partly sourced from the abandoned mining ponds. In fact, all the metal concentrations detected were well below the Malaysia Ministry of Health guideline limits for untreated raw water. In addition, the results of the geochemical index analysis (i.e. geoaccumulation index, enrichment factor and modified contamination factor) showed that the rivers and abandoned mining ponds were generally unpolluted with respect to the metals found in sediments

Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations

We lack the understanding of why HIV-infected individuals in South Africa progress to AIDS. We hypothesised that in end-stage disease there is a shifting dynamic between T cell imposed immunity and viral immune escape, which, through both compensatory and reverting viral mutations, results in increased viral fitness, elevated plasma viral loads and disease progression. We explored how T cell responses, viral adaptation and viral fitness inter-relate in South African cohorts recruited from Bloemfontein, the Free State (n = 278) and Durban, KwaZulu-Natal (n = 775). Immune responses were measured by γ-interferon ELISPOT assays. HLA-associated viral polymorphisms were determined using phylogenetically corrected techniques, and viral replication capacity (VRC) was measured by comparing the growth rate of gag-protease recombinant viruses against recombinant NL4-3 viruses. We report that in advanced disease (CD4 counts <100 cells/µl), T cell responses narrow, with a relative decline in Gag-directed responses (p<0.0001). This is associated with preserved selection pressure at specific viral amino acids (e.g., the T242N polymorphism within the HLA-B*57/5801 restricted TW10 epitope), but with reversion at other sites (e.g., the T186S polymorphism within the HLA-B*8101 restricted TL9 epitope), most notably in Gag and suggestive of “immune relaxation”. The median VRC from patients with CD4 counts <100 cells/µl was higher than from patients with CD4 counts ≥500 cells/µl (91.15% versus 85.19%, p = 0.0004), potentially explaining the rise in viral load associated with disease progression. Mutations at HIV Gag T186S and T242N reduced VRC, however, in advanced disease only the T242N mutants demonstrated increasing VRC, and were associated with compensatory mutations (p = 0.013). These data provide novel insights into the mechanisms of HIV disease progression in South Africa. Restoration of fitness correlates with loss of viral control in late disease, with evidence for both preserved and relaxed selection pressure across the HIV genome. Interventions that maintain viral fitness costs could potentially slow progression