Sulfated homologues of heparin inhibit hepatitis C virus entry into mammalian cells

The mechanism of entry of hepatitis C virus (HCV) through interactions between the envelope glycoproteins and specific cell surface receptors remains unclear at this time. We have previously shown with the vesicular stomatitis virus (VSV)/HCV pseudotype model that the hypervariable region 1 of the HCV E2 envelope glycoprotein helps in binding with glycosaminoglycans present on the cell surface. In this study, we have examined the binding of HCV envelope glycoproteins with chemically modified derivatives of heparin. Furthermore, we have determined the functional relevance of the interaction of heparin derivatives with HCV envelope glycoproteins for infectivity by using a human immunodeficiency virus (HIV)/HCV pseudotype, a VSV/HCV pseudotype, and cell culture-grown HCV genotype 1a. Taken together, our results suggest that the HCV envelope glycoproteins rely upon O-sulfated esters of a heparin homologue to facilitate entry into mammalian cells.     

Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs

One of the most important applications of genomic selection in maize breeding is to predict and identify the best untested lines from biparental populations, when the training and validation sets are derived from the same cross. Nineteen tropical maize biparental populations evaluated in multienvironment trials were used in this study to assess prediction accuracy of different quantitative traits using low-density (~200 markers) and genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs), respectively. An extension of the Genomic Best Linear Unbiased Predictor that incorporates genotype × environment (GE) interaction was used to predict genotypic values; cross-validation methods were applied to quantify prediction accuracy. Our results showed that: (1) low-density SNPs (~200 markers) were largely sufficient to get good prediction in biparental maize populations for simple traits with moderate-to-high heritability, but GBS outperformed low-density SNPs for complex traits and simple traits evaluated under stress conditions with low-to-moderate heritability; (2) heritability and genetic architecture of target traits affected prediction performance, prediction accuracy of complex traits (grain yield) were consistently lower than those of simple traits (anthesis date and plant height) and prediction accuracy under stress conditions was consistently lower and more variable than under well-watered conditions for all the target traits because of their poor heritability under stress conditions; and (3) the prediction accuracy of GE models was found to be superior to that of non-GE models for complex traits and marginal for simple traits.     

Epilithic diatoms as indicators in tropical African rivers (Lake Victoria catchment)

We investigated epilithic diatoms in rivers draining to the Nyanza Bay in Lake Victoria (Kenya) with the aim of determining environmental gradients in the assemblages and testing the usefulness of diatom metrics from temperate regions. Spatial and temporal variations of assemblages were studied in 12 sites of three rivers. Kibos, Nyando, and Kisat rivers contained 224 diatom taxa collected on seven sampling occasions over 4 years. Species richness showed a marginal decrease downstream and was the lowest at sites with high conductivity and ammonia–nitrogen levels. Two-Way Indicator Species Analysis and Canonical Correspondence Analysis revealed two major groups of river sites. Conductivity, alkalinity, turbidity, dissolved oxygen, and silicate were the most important variables influencing species distribution. Ecological diatom metrics of temperate regions and the Specific Pollution sensitivity Index showed good relationships with environmental variables. Both diatom assemblages and averaged indicator values were strong in predicting sites of ecological deterioration and in differentiating an upstream site of better quality (drinking water supply of Kisumu), thereby confirming epilithic diatoms as suitable water quality indicators in equatorial rivers. The use of metrics initially designed for temperate rivers, however, appears less valuable in good quality tropical rivers because potential indicators are not considered.     

Efect of emergency oral contraceptive use on condom utilization and sexual risk taking behaviours among university students, Northwest Ethiopia: a cross-sectional study

ABSTRACT: BACKGROUND: Young people between the ages of 15 and 24 years are both the most at risk of HIV and the greatest hope for turning the tide against HIV/AIDS. Although various surveys have been done on sexual behaviour of youth in Ethiopia, studies assessing the effect of emergency oral contraceptives on condom utilization of university students are lacking. METHODS: A cross-sectional study was conducted in two major universities of Ethiopia from January to May 2011 using structured self administered questionnaire with the aim to assess the effect of introducing oral emergency contraceptive pills on condom utilization and sexual risk taking behaviours among female university students. Study participants were selected by simple random sampling using the list from the associate registrars of each University. Data were entered, cleaned and analyzed using SPSS version 17.0. Bivariate and multiple logistic regression analyses were used to determine factors associated with condom utilization. RESULTS: a total of 623 students out of 660 were included giving response rate of 94.4%. A total of 103(16.5%) had history of sexual intercourse and nearly half (45.6%) of them had sex before the age of 20 years. Forty (6.4%) students had history of sexually transmitted infections (STI). Sixty seven percent of students had heard about emergency oral contraceptives. One hundred and ninety one (45.7%) of students believe that EOC is effective in preventing pregnancy. Believing that EOC is effective in preventing pregnancy (adjusted Odds ratio, AOR = 0.22 95% CI 0.06, 0.87), condom prevents STI (AOR = 10.37, 95%CI 1.73, 62.24) and younger age below 20 years (AOR = 11.68 95% CI 1.25, 109.19) were statistically significantly associated with condom use. CONCLUSION: a significant number of students had history of sexual intercourse and used emergency contraception. The belief in the effectiveness of EOC negatively affects condom use. The preference for the pill may make teenagers less prepared to practice STI protective behaviours in specific situations. Therefore, there is an urgent need to educate young people in universities about reproductive health and family planning and skills on how to prevent HIV/STIs including unwanted pregnancy.     

Vapor Phase Deposition, Structure, and Plasmonic Properties of Polymer-Based Composites Containing Ag–Cu Bimetallic Nanoparticles

Nanocomposite (NC) thin films with noble metal nanoparticles embedded in a dielectric material show very attractive plasmonic properties due to dielectric and quantum confinement effects. For single component nanoparticles (NPs), the plasmon resonance frequency can only be tuned in a narrow range. Much interest aroused in bimetallic nanoparticles (BNPs), however many wet chemical approaches do not allow large variation of the NP alloy composition and filling factor. Here, we report a vapor phase co-deposition method to produce polymer–metal NCs with embedded Ag_1 − x Cu _x alloy particles. The method allows production of NPs with controlled alloy composition (x), metal filling (f) and nanostructure in a protecting Teflon AF matrix. The nanostructure size and shape were characterized by transmission electron microscope. Energy dispersive X-ray spectroscopy was used to determine x and f. The optical properties and the position of surface plasmon resonances were studied by UV–Vis spectroscopy. The plasmon resonances can be tuned over a large range of the visible spectrum associated with the change in x, f, and nanostructure. For low filling factors and small particle sizes, only one resonance peak was observed. This is attributed to enhanced miscibility at the nanoscale. Double plasmon resonances were seen for larger particle sizes in accord with phase separation expected from the bulk phase diagram and were explained in terms of the formation of core-shell structures with Cu core and Ag shell. Changes upon annealing at 200 °C are also reported.     

Nucleotide-Dependent Isomerization of Glutamate Dehydrogenase in Relation to Total RNA Contents of Peanut

The physiological function of glutamate dehydrogenase (GDH) was investigated by treating germinating peanut (Arachis hypogaea L.) seeds with nucleoside triphosphate (NTP) solutions in order to alter the isoenzyme distribution patterns. The free nucleosides and nucleotides of the GTP-treated peanut were the highest [8.7 μmol g⁻¹(f.m.)], and they decreased through the ATP-treated peanut [5.8 μmol g⁻¹(f.m.)], and CTP-treated peanut [5.5 μmol g⁻¹(f.m.)], to the UTP-treated peanut [4.1 μmol g⁻¹(f.m.)]. The combination of 4 NTPs induced 20 % higher content of Pi [173 nmol g⁻¹(f.m.)] than in the control, but the combined ATP+UTP treatment induced the lowest (93.0 nmol g⁻¹(f.m.)] Pi. The 4 NTP treatment also induced the highest number of GDH isoenzymes (28) followed by the purine NTP treatments (15 to 20), but the pyrimidine NTP treatments and the combined purine + pyrimidine NTP treatments induced the lowest numbers (<15) of isoenzymes. The deamination/amination ratios were generally higher in the UTP (0.11), and CTP (0.06) treated peanuts than in the GTP (0.04), and ATP (0.07) treated peanuts. There were mutual relationships between higher numbers of GDH isoenzymes present in the GTP-, and ATP-treated peanuts and higher RNA (236.5 and 239.4 μg g⁻¹, respectively) contents on one hand, and between the lower numbers of isoenzymes in the CTP-, and UTP-treated peanuts and lower RNA (162.0 and 152.5 μg g⁻¹, respectively) contents. The recurrent relationships of the effects of the NTP treatments of peanut were UTP > ATP > CTP > GTP. This revised version was published online in July 2006 with corrections to the Cover Date.     

Ethnobotanical study of medicinal plants in Ganta Afeshum District,Eastern Zone of Tigray,Northern Ethiopia

Background

Starting from the ancient time, the people of Ethiopia use medicinal plants as traditional medicine to heal different human and livestock ailments. This ethnobotanical study of medicinal plants was carried out in Ganta Afeshum District, Eastern Zone of Tigray, Northern Ethiopia, to identify medicinal plant species used by the local community to treat various human and livestock ailments.

Methods

A total of 78 informants (54 men and 24 women) were selected to collect ethnobotanical information from four study sites. Among the 78 informants, 20 key informants were selected purposefully; the other 58 informants were selected randomly by lottery method. Ethnobotanical data were collected using semi-structured interviews, field observations, guided field walks, and group discussions and were analyzed by preference ranking, paired comparison, direct matrix ranking, informant consensus factor, fidelity level (FL), use-value, independent samples t test, and Pearson correlation coefficients.

Results

A total of 173 medicinal plants were collected and identified that were distributed across 77 families and 156 genera. The family Fabaceae stood first by contributing 17 (9.8%) species followed by Lamiaceae and Solanaceae with 9 (5.2%) species each. Rhamnus prinoides was reported for the treatment of many of the described diseases. One hundred sixteen (67.1%) medicinal plant species were collected from natural vegetation, 34 (19.7) were from home gardens, 13 (7.5%) from farmland, and 10 (5.8%) were from natural vegetation and home gardens. The most widely used life form was herbs (69 species, 39.9%) followed by shrubs (58 species, 33.5%). The most commonly used part of the medicinal plants was the leaves followed by roots. The plants were prepared by grinding, powdering, squeezing, roasting, and burning and were administered through oral, dermal, nasal, anal, ocular, and vaginal, and on the surface of the teeth. The most commonly used applications were by drinking, smearing, eating, fumigation, and chewing. There was no difference between men and women informants, showing that the two sexes had similar knowledge in the use of traditional medicinal plants. Educational level and medicinal plant knowledge of informants were negatively correlated; whereas age and medicinal plant knowledge of informants were positively correlated.

Conclusions

Ganta Afeshum District is relatively rich in diversity of medicinal plant resources accompanied with a rich indigenous knowledge within the local communities to harvest and effectively use to prevent different human and livestock ailments. However, nowadays, deforestation, agricultural expansion, overgrazing, drought, and overexploitation are threatening these properties. Therefore, people of the study area should apply complementary conservation approaches (in situ and ex situ) for sustainable use of these resources and to prevent species extinction.

     

Multi-generation genomic prediction of maize yield using parametric and non-parametric sparse selection indices

Genomic prediction models are often calibrated using multi-generation data. Over time, as data accumulates, training data sets become increasingly heterogeneous. Differences in allele frequency and linkage disequilibrium patterns between the training and prediction genotypes may limit prediction accuracy. This leads to the question of whether all available data or a subset of it should be used to calibrate genomic prediction models. Previous research on training set optimization has focused on identifying a subset of the available data that is optimal for a given prediction set. However, this approach does not contemplate the possibility that different training sets may be optimal for different prediction genotypes. To address this problem, we recently introduced a sparse selection index (SSI) that identifies an optimal training set for each individual in a prediction set. Using additive genomic relationships, the SSI can provide increased accuracy relative to genomic-BLUP (GBLUP). Non-parametric genomic models using Gaussian kernels (KBLUP) have, in some cases, yielded higher prediction accuracies than standard additive models. Therefore, here we studied whether combining SSIs and kernel methods could further improve prediction accuracy when training genomic models using multi-generation data. Using four years of doubled haploid maize data from the International Maize and Wheat Improvement Center (CIMMYT), we found that when predicting grain yield the KBLUP outperformed the GBLUP, and that using SSI with additive relationships (GSSI) lead to 5–17% increases in accuracy, relative to the GBLUP. However, differences in prediction accuracy between the KBLUP and the kernel-based SSI were smaller and not always significant.Subject terms: Quantitative trait, Genetic models     

The implementation and impact of a pilot hydrocele surgery camp for LF-endemic communities in Ethiopia

BackgroundEthiopia aims to eliminate lymphatic filariasis by 2020, through a dual approach of mass drug administration to interrupt transmission and morbidity control which includes making hydrocele surgery available in all endemic areas. Locating patients requiring surgery, providing high quality surgeries, and following up patients are all formidable challenges for many resource-challenged or difficult-to-reach communities. To date, hydrocele surgery in Ethiopia has only occurred when a patient has the knowledge, time and resources to travel to regional hospitals. Ethiopia tested the novel approach of using a surgical camp, defined as mobilizing, transporting, providing surgery at a static site, and following up of a large cohort of hydrocele patients within a hospital’s catchment area, to address delays in seeking and receiving care.Methodology and resultsHealth extension workers mobilized 252 patients with scrotal swelling from a list of 385 suspected hydrocele cases from seven endemic districts in the region of Beneshangul-Gumuz. Clinical health workers and surgeons confirmed 119 as eligible for surgery. Of 70 additional patients who self-referred, 56 were eligible for surgery. Over a two-week period at a regional hospital, 175 hydrocele excision surgeries were conducted. After discharge three days after surgery, trained clinical health workers followed up with the patients on Day 5, Day 8, Day 14 and 1st-month benchmarks with a randomized follow-up of a selection of patients conducted at 9–12 months. There were no post-operative complications upon discharge at Day 3 and 22, while minor complications occurred (12.6%) between Day 3 and one month. The 9–12 month follow-up found patients self-reported an improvement in quality of life, health and economic status.ConclusionA hydrocele surgery camp was effective at providing a large number of quality surgeries in a short time. Using peripheral health workers to mobilize and follow up patients helped address delays in seeking and receiving quality care. Mainstreaming patient mobilization and follow-up into a community health system could be effective in other countries. The camp’s results also influenced two regions in Ethiopia to change their policies in order to offer free hydrocele surgery (including patient transport, consultation, surgery, diagnostic tests and necessary medications).     

Estimating number of clusters based on a general similarity matrix with application to microarray data

Many clustering methods require that the number of clusters believed present in a given data set be specified a priori, and a number of methods for estimating the number of clusters have been developed. However, the selection of the number of clusters is well recognized as a difficult and open problem and there is a need for methods which can shed light on specific aspects of the data. This paper adopts a model for clustering based on a specific structure for a similarity matrix. Publicly available gene expression data sets are analyzed to illustrate the method and the performance of our method is assessed by simulation.