Computational Analysis of Some Enzymes Involved in Synthesis of Secondary Metabolites in Camellia Sinensis

Tea is one of the most popular beverages worldwide, native to Southeast Asia but currently cultivated in over 35 countries. Studies on its chemical composition reveal that polyphenol metabolites account for 25% to 35% of the total dry weight. Tea has many health benefits owing to secondary metabolites whose level of expression in various tea clones determine tea flavor. The flavor (taste and aroma) and the color of processed tea are used to assess its quality and therefore a detailed analysis of key enzymes involved in the synthesis of secondary metabolites is necessary.  Enzyme PAL (phenylalanine ammonia-lyase) a key enzyme in the phenylpropanoid pathway, playing an important role in the plant development and defense. C4H (cinnamte-4-hydroxylse) an important enzyme in allocating significant amounts of carbon from phenylalanine into the biosynthesis of several metabolites, It maintains activities of the metabolic flux for the operation of the flavanoid pathway. 4CL (4-coumarate: COA ligase) the last enzyme in the general phenylpropanoid pathway that provides precursors for the biosynthesis of a large variety of plant natural products like COA thiol esters of 4-coumarate and other hydroxycinnamate. FLS (flavonol synthase) a key enzyme in flavonol synthesisthat determines the final content of flavonols which play an important role in defense related functions and as potent antioxidants. ANS (anthocyanidin synthase) an enzyme in the biosynthetic pathway to anthocyanin. This study employed a computational approach in the analysis of some of these enzymes to gain insight into the mechanism of synthesis of these bioactive secondary metabolites. Biological databases were used to retrieve amino acid sequences of these key enzymes. Consensus conserved regions in these sequences were identified from highly identical homologs which were useful in modeling the enzymes' three dimensional structures.  A total of 5 key enzymes were analyzed and pockets and cavities in their structures; hence the putative substrate binding sites determined, which gave insight into the enzymes-substrate as well as enzyme cofactor interactions. The preferred orientations of the interactions between substrates and/or co-factors with the enzymes were also simulated through molecular docking.  Analysis of these enzymes revealed unique enzyme structures and very specific substrate and co-factor preference. This analysis offers a platform for optimization of selective expression of these key enzymes through gene expression assays that can potentially alter the quality yield of tea clones. Keywords: camellia sinensis, Secondary metabolites, Conserved regions, Pockets and cavities, Molecular dockin

Computational Design of Novel Candidate Drug Molecules for Schistosomiasis

Schistosomiasis is a parasitic disease that leads to chronic ill-health. Infection is acquired from infested freshwater containing the larval forms (cercariae) of blood flukes, known as schistosomes. The three main species of the parasite that infect humans are Schistosoma haematobium, S.japonicum, and S.mansoni. Schistosomiasis affects at least 230 million people worldwide. The infection is prevalent in tropical and sub-tropical areas, in poor communities without potable water and adequate sanitation. The disease is considered as one of the Neglected Tropical Diseases and so far praziquantel is the only drug used for treatment. Should the parasites develop resistance to praziquantel, treatment would be problematic.  This study incorporated a computational approach to design novel compounds with unprecedented potential as candidate drug compounds for the disease. The Schistosoma mansoni fatty acid binding protein was selected as a suitable drug target for its crucial role in the dependence of the parasite on its host for fatty acids. Screening for potential lead compounds was done using molecular docking software.  Identified lead compounds were analyzed and optimized in silico for their ADMET properties then re-evaluated for suitability of their binding energies. Eight novel compounds with good predicted ADMET properties were designed and found to interact with the S.mansoni fatty acid binding protein with favorable binding energy, showing potential to inhibit this protein. This study opens up new possibilities in antischistosomal drug inquiry and potentiates efficacy studies of such compounds against schistosomiasis. Keywords: computational design, antischistosomal drug inquiry, binding energy, lead optimization, ADMET properties

Epidemiology of Theileria bicornis among black and white rhinoceros metapopulation in Kenya

[Background] A huge effort in rhinoceros conservation has focused on poaching and habitat loss as factors leading to the dramatic declines in the endangered eastern black rhinoceros (Diceros bicornis michaeli) and the southern white rhinoceros (Ceratotherium simum simum). Nevertheless, the role disease and parasite infections play in the mortality of protected populations has largely received limited attention. Infections with piroplasmosis caused by Babesia bicornis and Theileria bicornis has been shown to be fatal especially in small and isolated populations in Tanzania and South Africa. However, the occurrence and epidemiology of these parasites in Kenyan rhinoceros is not known.[Results] Utilizing 18S rRNA gene as genetic marker to detect rhinoceros infection with Babesia and Theileria, we examined blood samples collected from seven rhinoceros populations consisting of 114 individuals of black and white rhinoceros. The goal was to determine the prevalence in Kenyan populations, and to assess the association of Babesia and Theileria infection with host species, age, sex, location, season and population mix (only black rhinoceros comparing to black and white rhinoceros populations). We did not detect any infection with Babesia in the sequenced samples, while the prevalence of T. bicornis in the Kenyan rhinoceros population was 49.12% (56/114). White rhinoceros had significantly higher prevalence of infection (66%) compared to black rhinoceros (43%). The infection of rhinoceros with Theileria was not associated with animal age, sex or location. The risk of infection with Theileria was not higher in mixed species populations compared to populations of pure black rhinoceros.[Conclusion] In the rhinoceros studied, we did not detect the presence of Babesia bicornis, while Theileria bicornis was found to have a 49.12% prevalence with white rhinoceros showing a higher prevalence (66%) comparing with black rhinoceros (43%). Other factors such as age, sex, location, and population mix were not found to play a significant role.We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI)Peer reviewe

The Potential for DPPIV/CD26 usage as a surrogate marker for Antiretroviral Therapy Efficacy in HIV Infected populations

Background: Human Immunodeficiency Virus (HIV) viral load and CD4+ cell counts are the most commonly used markers for monitoring efficacy of anti-retroviral therapy (ART) in HIV infected individuals. The high cost of viral load monitoring limits its usage in resource limited countries, often leaving the use of CD4+ T cell counts as the only alternative. Though cheaper and more readily available, CD4+ cell counts as a measure of detecting treatment failure, is an unreliable predictor of disease progression. Hence, there is a need for more sensitive alternative, but less costly techniques for detecting treatment failure which can be used in resource limited settings. Objective: To evaluate the feasibility of using plasma CD26/Dipeptidyl peptidase IV (DPPIV) as a novel marker for clinical evaluation of treatment efficacy in HIV infected children. Method: Blood samples collected from HIV+ children (n=76) before and after initiation on ART, were assessed for HIV RNA (viral load), CD4+ T-cell count and DPPIV/CD26 levels. Viral load levels were analyzed using Roche Amplicor HIV-1 Monitor Test kit; CD4+ T-Cell Counts were analyzed using BD FACS Calibur flow cytometer while DPPIV/CD 26 levels were analyzed using Human DPPIV/CD26 Quantikine ELISA kit (R&D Systems, Minneapolis MN). Results: The plasma DPPIV/CD26 levels increased significantly in children after ART initiation (p = 0.017), while the viral load levels declined after ART initiation with subsequent CD4+ cell counts increase. The DPPIV/CD 26 increase positively correlated with viral load decrease while negatively correlating to the CD4+ cell count increase. Conclusion: These findings demonstrate an inverse relationship between DPPIV/CD26 levels and HIV viral load and the direct proportionality of CD4+ Cell counts and DPPIV/CD26 levels, suggesting potential for use of DPPIV/CD26 as a surrogate marker for evaluating HIV disease progression in children receiving anti-retroviral therapy. Key words: CD26/Dipeptidyl peptidase IV (DPPIV), ELISA, Surrogate marker, Viral Load, CD4 Count, antiretroviral

Current conservation status of the Blue Swallow Hirundo atrocaerulea Sundevall 1850 in Africa

The global Blue Swallow Hirundo atrocaerulea was classified as Vulnerable in 2010 on account of its small and rapidly declining population estimated at less than 1 500 pairs. We undertook this study to gain a better understanding of the current status and threats facing this migratory species. Three previously unknown areas that might be part of the species’ non-breeding range were identified in Kenya and northern Tanzania. Within its breeding range we identified three previously unknown areas of potentially suitable habitat, one in Tanzania and two in Malawi, which require further exploration. Population viability assessment predicted that the Blue Swallow population will decline by 8% in 10 years. The overall probability of extinction of the species in the wild is 3%. Minimum viable population size analysis suggests that a goal for the long-term conservation of the Blue Swallow should be to mitigate current threats that are driving declines such that the population increases to a minimum of 3 600 individuals. This should consist of at least 900 individuals in each of the four clusters identified, along with a minimum of 500 individuals in at least one of the meta-populations per cluster. The four clusters are located in (1) the southeasten Democratic Republic of the Congo, (2) highlands of southern Tanzania and northern Malawi, (3) eastern highlands of Zimbabwe and (4) South Africa and Swaziland. The current proportions of the Blue Swallow population in strictly protected and unprotected areas on their breeding grounds are 53% and 47%, respectively, whereas on their non-breeding grounds the corresponding percentages are 25% and 75%, respectively. Our reassessment of the Blue Swallow’s risk of extinction indicates that it continues to qualify as Vulnerable according to the IUCN/SSC criteria C2a(i).http://www.tandfonline.com/loi/tost202016-09-30hb2016Zoology and Entomolog

Maternal Malaria and Malnutrition (M3) initiative, a pooled birth cohort of 13 pregnancy studies in Africa and the Western Pacific.

PURPOSE: The Maternal Malaria and Malnutrition (M3) initiative has pooled together 13 studies with the hope of improving understanding of malaria-nutrition interactions during pregnancy and to foster collaboration between nutritionists and malariologists. PARTICIPANTS: Data were pooled on 14 635 singleton, live birth pregnancies from women who had participated in 1 of 13 pregnancy studies. The 13 studies cover 8 countries in Africa and Papua New Guinea in the Western Pacific conducted from 1996 to 2015. FINDINGS TO DATE: Data are available at the time of antenatal enrolment of women into their respective parent study and at delivery. The data set comprises essential data such as malaria infection status, anthropometric assessments of maternal nutritional status, presence of anaemia and birth weight, as well as additional variables such gestational age at delivery for a subset of women. Participating studies are described in detail with regard to setting and primary outcome measures, and summarised data are available from each contributing cohort. FUTURE PLANS: This pooled birth cohort is the largest pregnancy data set to date to permit a more definite evaluation of the impact of plausible interactions between poor nutritional status and malaria infection in pregnant women on fetal growth and gestational length. Given the current comparative lack of large pregnancy cohorts in malaria-endemic settings, compilation of suitable pregnancy cohorts is likely to provide adequate statistical power to assess malaria-nutrition interactions, and could point towards settings where such interactions are most relevant. The M3 cohort may thus help to identify pregnant women at high risk of adverse outcomes who may benefit from tailored intensive antenatal care including nutritional supplements and alternative or intensified malaria prevention regimens, and the settings in which these interventions would be most effective

Development and validation of a diagnostic aid for convulsive epilepsy in sub-Saharan Africa: a retrospective case-control study

Background: Identification of convulsive epilepsy in sub-Saharan Africa relies on access to resources that are often unavailable. Infrastructure and resource requirements can further complicate case verification. Using machine-learning techniques, we have developed and tested a region-specific questionnaire panel and predictive model to identify people who have had a convulsive seizure. These findings have been implemented into a free app for health-care workers in Kenya, Uganda, Ghana, Tanzania, and South Africa. Methods: In this retrospective case-control study, we used data from the Studies of the Epidemiology of Epilepsy in Demographic Sites in Kenya, Uganda, Ghana, Tanzania, and South Africa. We randomly split these individuals using a 7:3 ratio into a training dataset and a validation dataset. We used information gain and correlation-based feature selection to identify eight binary features to predict convulsive seizures. We then assessed several machine-learning algorithms to create a multivariate prediction model. We validated the best-performing model with the internal dataset and a prospectively collected external-validation dataset. We additionally evaluated a leave-one-site-out model (LOSO), in which the model was trained on data from all sites except one that, in turn, formed the validation dataset. We used these features to develop a questionnaire-based predictive panel that we implemented into a multilingual app (the Epilepsy Diagnostic Companion) for health-care workers in each geographical region. Findings: We analysed epilepsy-specific data from 4097 people, of whom 1985 (48·5%) had convulsive epilepsy, and 2112 were controls. From 170 clinical variables, we initially identified 20 candidate predictor features. Eight features were removed, six because of negligible information gain and two following review by a panel of qualified neurologists. Correlation-based feature selection identified eight variables that demonstrated predictive value; all were associated with an increased risk of an epileptic convulsion except one. The logistic regression, support vector, and naive Bayes models performed similarly, outperforming the decision-tree model. We chose the logistic regression model for its interpretability and implementability. The area under the receiver operator curve (AUC) was 0·92 (95% CI 0·91–0·94, sensitivity 85·0%, specificity 93·7%) in the internal-validation dataset and 0·95 (0·92–0·98, sensitivity 97·5%, specificity 82·4%) in the external-validation dataset. Similar results were observed for the LOSO model (AUC 0·94, 0·93–0·96, sensitivity 88·2%, specificity 95·3%). Interpretation: On the basis of these findings, we developed the Epilepsy Diagnostic Companion as a predictive model and app offering a validated culture-specific and region-specific solution to confirm the diagnosis of a convulsive epileptic seizure in people with suspected epilepsy. The questionnaire panel is simple and accessible for health-care workers without specialist knowledge to administer. This tool can be iteratively updated and could lead to earlier, more accurate diagnosis of seizures and improve care for people with epilepsy

Malaria, malnutrition, and birthweight: A meta-analysis using individual participant data.

BACKGROUND: Four studies previously indicated that the effect of malaria infection during pregnancy on the risk of low birthweight (LBW; <2,500 g) may depend upon maternal nutritional status. We investigated this dependence further using a large, diverse study population. METHODS AND FINDINGS: We evaluated the interaction between maternal malaria infection and maternal anthropometric status on the risk of LBW using pooled data from 14,633 pregnancies from 13 studies (6 cohort studies and 7 randomized controlled trials) conducted in Africa and the Western Pacific from 1996-2015. Studies were identified by the Maternal Malaria and Malnutrition (M3) initiative using a convenience sampling approach and were eligible for pooling given adequate ethical approval and availability of essential variables. Study-specific adjusted effect estimates were calculated using inverse probability of treatment-weighted linear and log-binomial regression models and pooled using a random-effects model. The adjusted risk of delivering a baby with LBW was 8.8% among women with malaria infection at antenatal enrollment compared to 7.7% among uninfected women (adjusted risk ratio [aRR] 1.14 [95% confidence interval (CI): 0.91, 1.42]; N = 13,613), 10.5% among women with malaria infection at delivery compared to 7.9% among uninfected women (aRR 1.32 [95% CI: 1.08, 1.62]; N = 11,826), and 15.3% among women with low mid-upper arm circumference (MUAC <23 cm) at enrollment compared to 9.5% among women with MUAC ≥ 23 cm (aRR 1.60 [95% CI: 1.36, 1.87]; N = 9,008). The risk of delivering a baby with LBW was 17.8% among women with both malaria infection and low MUAC at enrollment compared to 8.4% among uninfected women with MUAC ≥ 23 cm (joint aRR 2.13 [95% CI: 1.21, 3.73]; N = 8,152). There was no evidence of synergism (i.e., excess risk due to interaction) between malaria infection and MUAC on the multiplicative (p = 0.5) or additive scale (p = 0.9). Results were similar using body mass index (BMI) as an anthropometric indicator of nutritional status. Meta-regression results indicated that there may be multiplicative interaction between malaria infection at enrollment and low MUAC within studies conducted in Africa; however, this finding was not consistent on the additive scale, when accounting for multiple comparisons, or when using other definitions of malaria and malnutrition. The major limitations of the study included availability of only 2 cross-sectional measurements of malaria and the limited availability of ultrasound-based pregnancy dating to assess impacts on preterm birth and fetal growth in all studies. CONCLUSIONS: Pregnant women with malnutrition and malaria infection are at increased risk of LBW compared to women with only 1 risk factor or none, but malaria and malnutrition do not act synergistically

Clinical Forms of Chikungunya in Gabon, 2010

Chikungunya fever (CHIK) is a disease caused by a virus transmitted to humans by infected mosquitos. The virus is responsible for multiple outbreaks in tropical and temperate areas worldwide, and is now a global concern. Clinical and biological features of the disease are poorly described, especially in Africa, where the disease is neglected because it is considered benign. During a recent CHIK outbreak that occurred in southeast Gabon, we prospectively studied clinical and biological features of 270 virologically confirmed cases. Fever and arthralgias were the predominant symptoms. Furthermore, variable and distinct clinical pictures including pure febrile, pure arthralgic and unusual forms (neither fever nor arthralgias) were detected. No severe forms or deaths were reported. These findings suggest that, during CHIK epidemics, some patients may not have classical symptoms (fever and arthralgias). Local surveillance is needed to detect any changes in the pathogenicity of this virus