Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably ...access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge "Introduction to Bioinformatics" course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery-mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online "question and discussion" forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic ...bioinformatics support to researchers through an online ticketing platform. The following article reports on the H3ABioNet HD (H3A-HD)'s development, outlining its design, management, usage and evaluation framework, as well as the lessons learned through implementation.
The H3A-HD evaluated using automatically generated usage logs, user feedback and qualitative ticket evaluation. Evaluation revealed that communication methods, ticketing strategies and the technical platforms used are some of the primary factors which may influence the effectivity of HD.
To continuously improve the H3A-HD services, the resource should be regularly monitored and evaluated. The H3A-HD design, implementation and evaluation framework could be easily adapted for use by interested stakeholders within the Bioinformatics community and beyond.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background: Diversity in
poses a major threat to malaria control and elimination interventions. This study utilized 12 polymorphic microsatellite (MS) markers and the Msp2 marker to examine ...diversity, multiplicity of infection (MOI) as well as the population structure of parasites circulating in two sites separated by about 92 km and with varying malaria transmission intensities within the Greater Accra Region of Ghana.
The diversity and MOI of
parasites in 160 non-symptomatic volunteers living in Obom (high malaria transmission intensity) and Asutsuare (low malaria transmission intensity) aged between 8 and 60 years was determined using Msp2 genotyping and microsatellite analysis.
The prevalence of asymptomatic
carriers as well as the parasite density of infections was significantly higher in Obom than in Asutsuare. Samples from Asutsuare and Obom were 100% and 65% clonal, respectively, by Msp2 genotyping but decreased to 50% and 5%, respectively, when determined by MS analysis. The genetic composition of parasites from Obom and Asutsuare were highly distinct, with parasites from Obom being more diverse than those from Asutsuare.
parasites circulating in Obom are genetically more diverse and distinct from those circulating in Asutsuare. The MOI in samples from both Obom and Asutsuare increased when assessed by MS analysis relative to MSP2 genotyping. The TA40 and TA87 loci are useful markers for estimating MOI in high and low parasite prevalence settings.
A surge in pro-inflammatory markers, Il-6 and TNF-α, has been associated with type 2 diabetes mellitus (T2DM). However, there is no data on the dynamics of these markers in T2DM Ghanaian populations. ...The aim of this study was to determine variations in the levels of IL-6 and TNF-α in T2DM patients. This study also examined the associations of IL-6 and TNF-α with anthropometric measurement and the effect of co-morbidity with hypertension using rural and urban dwellers in the Ashanti region, Ghana.
A nested case-control design using participants aged 25-70 years consisting of 77 T2DM ± hypertension patients and 112 controls were selected from a larger study on Research on Obesity and Diabetes among African Migrants (RODAM). Anthropometric measurements, blood pressure and body fat percentage were measured. Fasting blood samples were analyzed for glucose, IL-6 and TNF-α levels.
The median level of IL-6 was significantly higher (p < 0.0001) among rural dwellers compared to urban dwellers. Inversely, urban dwellers had significantly higher (p = 0.0424) median level of TNF-α compared to rural cases. No significant differences were observed in IL-6 (p = 0.3571) and TNF-α (p = 0.2581) among T2DM patients compared with T2DM ± hypertension patients. A weak negative correlation was found between IL-6 and BMI in urban T2DM.
The average level of IL-6 was higher in rural T2DM participants compared with those in urban setting. However, higher levels of TNF-α was observed among the study participants with T2DM in urban settings compared to those of rural. In this study, we observed that co-morbidity of hypertension had no significant effect on the levels of IL-6 and TNF-α. We are of the opinion that higher physical activity levels among rural particpants and high obesity levels in urabn participants explain the observation but needs more numbers to validate.
This study revealed that IL-6 levels were higher among rural dwellers than urban while TNF-α levels were higher in urban dwellers than rural in patients with T2DM. There was no association of body fat percentage and body mass index with IL-6 and TNF-α levels. Co-morbidity of hypertension with T2DM had no effect on IL-6 and TNF-α levels.
Alanine racemase activity was investigated in Bacillus subtilis. A putative second alanine racemase gene (yncD) was cloned in parallel with the previously identified alanine racemase gene, dal. Each ...of the B. subtilis genes, dal and yncD complemented the Escherichia coli Alr⁻ DadX⁻ double mutant alanine auxotrophic strain MB2159 in vivo, restoring the prototrophic phenotype. Alanine racemase activity was also detected in vitro in cell-free extracts prepared from cultures of E. coli MB2159 harboring plasmids expressing either of the cloned B. subtilis genes and preliminary characterization of enzyme activity is presented.
Summary
We report on the characterization and genomic analysis of bacteriophage E3 isolated from soil and propagating in Rhodococcus equi strains. Phage E3 has a circular genome of 142 563 bp and is ...the first Myoviridae reported for the genus Rhodococcus and for a non‐mycobacterial actinomycete. Phylogenetic analyses placed E3 in a distinct Myoviridae clade together with Mycobacterium phages Bxz1 and Myrna. The highly syntenic genomes of this myoviridal group comprise vertically evolving core phage modules flanked by hyperplastic regions specific to each phage and rich in horizontally acquired DNA. The hyperplastic regions contain numerous tRNA genes in the mycobacteriophages which are absent in E3, possibly reflecting bacterial host‐specific translation‐related phage fitness constraints associated with rate‐limiting tRNAs. A structural proteome analysis identified 28 E3 polypeptides, including 15 not previously known to be virion‐associated proteins. The E3 genome and comparative analysis provide insight into short‐term genome evolution and adaptive plasticity in tailed phages from the environmental microbiome.
Most sexually transmitted infection (STI) management efforts focus on the syndromic approach to diagnose and treat patients. However, most women with STIs have been shown to be entirely asymptomatic, ...or if symptoms exist, are often missed when either clinical or conventional bacteriologic diagnostic tools are employed.
We assessed the performance of a multiplex real time PCR assay to describe other potential pathogens that could be missed by conventional bacteriological techniques in 200 women attending a routine STI clinic in Kumasi, Ghana.
Although a total 78.00% of the women were asymptomatic, 77.1% of them tested positive for at least one bacterial STI pathogen.
was the most commonly detectable pathogen present in 67.5% of all women. Of those testing positive, 25.0% had single infections, while 38.0% and 19.5% had double and triple infections respectively. Altogether, 86.54% and 90.91% of the symptomatic and asymptomatic women respectively tested positive for at least one pathogen (p<0.05). There were no significant associations (p<0.05) between the clinical manifestations of the symptomatic women and the pathogens detected in their samples.
Our study confirmed the importance of complementing the syndromic approach to STI management with pathogen detection and most importantly recognise that STIs in women are asymptomatic and regular empirical testing even for both symptomatic and asymptomatic patients is critical for complete clinical treatment.
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Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Objectives
The objective of this study is to describe the burden of human papillomavirus (HPV) infection among women living with HIV and non‐infected women in Ghana.
Methods
A case–control study was ...conducted involving 107 women living with HIV aged between 18 and 59 years (cases) and 100 non‐HIV‐infected apparently healthy women (controls) who were recruited from the Kumasi South Hospital, from July to December, 2014. Cervicovaginal swabs were taken from study participants to characterise 28 high‐ and low‐risk HPV genotypes using a multiplex real‐time PCR.
Results
The overall mean age for the participants was 40.10 ± 9.76 years. The prevalence of high‐risk (hr)‐HPV genotypes was significantly higher among the cases than the controls (77.4% vs. 41.6%, P < 0.0001). Overall, HPV 58 and 54 were the most predominant high‐risk (18.8%) and low‐risk (15.0%) genotypes detected. The two most common hr‐HPV genotype isolates were 58 (18.8%) and 35 (15.9%) with 58 being the most prevalent among age group 35–44 years compared with hr‐HPV 16, 18, 35 and 45, found predominantly among 18–34 age group.
Conclusions
Significant variations exist in HPV genotypes among HIV‐infected and uninfected women.
Objectifs
Décrire la charge de l'infection par le VPH chez les femmes infectées et non infectées par le VIH au Ghana.
Méthodes
Une étude cas‐témoins portant sur 107 femmes vivant avec le VIH, âgées de 18 à 59 ans (les cas) et 100 femmes non infectées par le VIH, apparemment en bonne santé (les témoins), inscrites dans l'hôpital de Kumasi South, de juillet à décembre 2014. Des échantillons d’écouvillonnage cervicovaginal ont été prélevés chez les participantes pour caractériser 28 génotypes du VPH de risque élevé et faible, en utilisant une PCR multiplex en temps réel.
Résultats
L’âge moyen global pour les participantes était de 40,10 ± 9,76 ans. La prévalence des génotypes de risque élevé du VPH était significativement plus élevée chez les cas que chez les témoins (77,4% versus 41,6%; p <0,0001). Globalement, les génotypes HPV 58 et 54 étaient les plus prédominants de risque élevé (18,8%) et de risque faible (15,0%) détectés. Les deux génotypes HPV les plus couramment retrouvés dans les isolats étaient 58 (18,8%) et 35 (15,9%), 58 étant le plus prévalent dans le groupe d’âge 35‐44 ans par rapport à HR‐HPV 16, 18, 35 et 45, retrouvés principalement dans le groupe d’âge 18‐34.
Conclusions
Des variations importantes existent dans les génotypes du VPH chez les femmes infectées et non infectées par le VIH.
Objetivos
Describir la carga de infección por VPH entre mujeres viviendo con VIH y mujeres no infectadas en Ghana.
Métodos
Estudio caso control con 107 mujeres viviendo con VIH y edades entre 18‐59 años (casos) y 100 mujeres no infectadas con VIH y aparentemente sanas (controles), reclutadas del Hospital de Kumasi Sur, entre Julio y Diciembre del 2014. Se tomaron frotis cervico‐vaginales de las participantes del estudio para caracterizar 28 genotipos de VPH de alto y bajo riesgo, utilizando la PCR multiplex a tiempo real.
Resultados
La edad media de los participantes era de 40.10±9.76 años. La prevalencia de genotipos de alto riesgo (ar)‐VPH era significativamente mayor entre los casos que los controles (77.4% versus 41.6%, p< 0.0001). En general, los genotipos más predominantemente detectados de alto (18.8%) y bajo (15.0%) riesgo eran VPH 58 y 54. Los dos genotipos de ar‐VPH aislados eran 58 (18.8%) y 35 (15.9%), siendo el 58 el más prevalente entre los grupos de edad 35‐44 años, comparado con ar‐VPH 16, 18, 35 y 45, encontradas de forma predominante entre el grupo de edad de 18‐34 años.
Conclusiones
Existen variaciones significativas en los genotipos del VPH en mujeres infectadas con VIH y sin infectar.
Background A surge in pro-inflammatory markers, Il-6 and TNF-alpha, has been associated with type 2 diabetes mellitus (T2DM). However, there is no data on the dynamics of these markers in T2DM ...Ghanaian populations. The aim of this study was to determine variations in the levels of IL-6 and TNF-alpha in T2DM patients. This study also examined the associations of IL-6 and TNF-alpha with anthropometric measurement and the effect of co-morbidity with hypertension using rural and urban dwellers in the Ashanti region, Ghana. Methods A nested case-control design using participants aged 25-70 years consisting of 77 T2DM + or - hypertension patients and 112 controls were selected from a larger study on Research on Obesity and Diabetes among African Migrants (RODAM). Anthropometric measurements, blood pressure and body fat percentage were measured. Fasting blood samples were analyzed for glucose, IL-6 and TNF-alpha levels. Results The median level of IL-6 was significantly higher (p < 0.0001) among rural dwellers compared to urban dwellers. Inversely, urban dwellers had significantly higher (p = 0.0424) median level of TNF-alpha compared to rural cases. No significant differences were observed in IL-6 (p = 0.3571) and TNF-alpha (p = 0.2581) among T2DM patients compared with T2DM + or - hypertension patients. A weak negative correlation was found between IL-6 and BMI in urban T2DM. Discussion The average level of IL-6 was higher in rural T2DM participants compared with those in urban setting. However, higher levels of TNF-alpha was observed among the study participants with T2DM in urban settings compared to those of rural. In this study, we observed that co-morbidity of hypertension had no significant effect on the levels of IL-6 and TNF-alpha. We are of the opinion that higher physical activity levels among rural particpants and high obesity levels in urabn participants explain the observation but needs more numbers to validate. Conclusion This study revealed that IL-6 levels were higher among rural dwellers than urban while TNF-alpha levels were higher in urban dwellers than rural in patients with T2DM. There was no association of body fat percentage and body mass index with IL-6 and TNF-alpha levels. Co-morbidity of hypertension with T2DM had no effect on IL-6 and TNF-alpha levels.
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