ghanaopendata/ghanaian-research-english huggingface dataset:
Identification of fluorinases from streptomyces sp MA37, norcardia brasiliensis, and actinoplanes sp N902-109 by genome mining

The fluorinase is an enzyme that catalyses the combination of S-adenosyl-L-methionine (SAM) and a fluoride ion to generate 5′-fluorodeoxy adenosine (FDA) and L-methionine through a nucleophilic substitution reaction with a fluoride ion as the nucleophile. It is the only native fluorination enzyme that has been characterised. The fluorinase was isolated in 2002 from Streptomyces cattleya, and, to date, this has been the only source of the fluorinase enzyme. Herein, we report three new fluorinase isolates that have been identified by genome mining. The novel fluorinases from Streptomyces sp. MA37, Nocardia brasiliensis, and an Actinoplanes sp. have high homology (80-87 % identity) to the original S. cattleya enzyme. They all possess a characteristic 21-residue loop. The three newly identified genes were overexpressed in E. coli and shown to be fluorination enzymes. An X-ray crystallographic study of the Streptomyces sp. MA37 enzyme demonstrated that it is almost identical in structure to the original fluorinase. Culturing of the Streptomyces sp. MA37 strain demonstrated that it not only also elaborates the fluorometabolites, fluoroacetate and 4-fluorothreonine, similar to S. cattleya, but this strain also produces a range of unidentified fluorometabolites. These are the first new fluorinases to be reported since the first isolate, over a decade ago, and their identification extends the range of fluorination genes available for fluorination biotechnology. Get on the fluor! The fluorinase enzyme from Streptomyces cattleya was identified in 2002 as the only fluorination enzyme known in biochemistry. Three additional fluorinases expressed through bacterial genome mining are now reported. These new fluorinases extend the range of genes available for developing fluorination biotechnology. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Source: UG
Identification of Fluorinases from Streptomyces sp MA37,Norcardia brasiliensis, and Actinoplanes sp N902-109 by Genome Mining

The fluorinase is an enzyme that catalyses the combination of S-adenosyl-l-methionine (SAM) and a fluoride ion to generate 5’-fluorodeoxy adenosine (FDA) and l-methionine through a nucleophilic substitution reaction with a fluoride ion as the nucleophile. It is the only native fluorination enzyme that has been characterised. The fluorinase was isolated in 2002 from Streptomyces cattleya, and, to date, this has been the only source of the fluorinase enzyme. Herein, we report three new fluorinase isolates that have been identified by genome mining. The novel fluorinases from Streptomyces sp. MA37, Nocardia brasiliensis, and an Actinoplanes sp. have high homology (80–87% identity) to the original S. cattleya enzyme. They all possess a characteristic 21-residue loop. The three newly identified genes were overexpressed in E. coli and shown to be fluorination enzymes. An X-ray crystallographic study of the Streptomyces sp. MA37 enzyme demonstrated that it is almost identical in structure to the original fluorinase. Culturing of the Streptomyces sp. MA37 strain demonstrated that it not only also elaborates the fluorometabolites, fluoroacetate and 4-fluorothreonine, similar to S. cattleya, but this strain also produces a range of unidentified fluorometabolites. These are the first new fluorinases to be reported since the first isolate, over a decade ago, and their identification extends the range of fluorination genes available for fluorination biotechnology.

Source: UG
Identification of Genomic Regions Associated with Agronomic and Disease Resistance Traits in a Large Set of Multiple DH Populations

Breeding maize lines with the improved level of desired agronomic traits under optimum and drought conditions as well as increased levels of resistance to several diseases such as maize lethal necrosis (MLN) is one of the most sustainable approaches for the sub-Saharan African region. In this study, 879 doubled haploid (DH) lines derived from 26 biparental populations were evaluated under artificial inoculation of MLN, as well as under well-watered (WW) and water-stressed (WS) conditions for grain yield and other agronomic traits. All DH lines were used for analyses of genotypic variability, association studies, and genomic predictions for the grain yield and other yield-related traits. Genome-wide association study (GWAS) using a mixed linear FarmCPU model identified SNPs associated with the studied traits i.e., about seven and eight SNPs for the grain yield; 16 and 12 for anthesis date; seven and eight for anthesis silking interval; 14 and 5 for both ear and plant height; and 15 and 5 for moisture under both WW and WS environments, respectively. Similarly, about 13 and 11 SNPs associated with gray leaf spot and turcicum leaf blight were identified. Eleven SNPs associated with senescence under WS management that had depicted drought-stress-tolerant QTLs were identified. Under MLN artificial inoculation, a total of 12 and 10 SNPs associated with MLN disease severity and AUDPC traits, respectively, were identified. Genomic prediction under WW, WS, and MLN disease artificial inoculation revealed moderate-to-high prediction accuracy. The findings of this study provide useful information on understanding the genetic basis for the MLN resistance, grain yield, and other agronomic traits under MLN artificial inoculation, WW, and WS conditions. Therefore, the obtained information can be used for further validation and developing functional molecular markers for marker-assisted selection and for implementing genomic prediction to develop superior elite lines.

Source: UG
Identification of Hepatitis B Virus Genotype A/E Recombinants in Ghana

Hepatitis B virus (HBV) exhibits a high degree of heterogeneity with at least 10 genotypes (A-J) identified to date. Intergenotypic recombination is relatively common. Previously, we investigated HBV drug resistance in HIV/HBV co-infected individuals in Ghana. After identifying multiple circulating genotypes and a novel D/E recombinant, we sought to determine if additional individuals were also infected with recombinant HBV. Partial genome sequences from three individuals were initially identified as genotype A4. Full-length HBV genomes were obtained using rolling circle amplification followed by PCR and shown to cluster with known A/E recombinant viruses. Similar recombination breakpoints were observed in these three individuals suggesting local spread of this novel recombinant HBV in Ghana.

Source: UG
Identification of historic shifts in daily rainfall regime, Wenchi, Ghana

The characteristics of rainfall regime and its variability in the sub-humid region of mid-Ghana is analyzed using daily rainfall data from the Wenchi, 1950–2000. Prior research in the area, suggests that climatic variability occurs at lower frequencies than the typical ENSO signal and may be more closely related to noted shifts in global climatic patterns. Fifty-six possible starting dates encompassing the traditional growing season, extending from late January to early November, at five day increments, are used to define temporal units of varying lengths, variable temporal units (VTUs). Rainfall characteristics in each unit are described by two variables: total rainfall and number of rainy days. Given the widely noted global climatic shift in the 1970s and the results of regional analyses, the 50 year record is sub-divided into two 20 year periods, 1950–1969 (period 1) and 1980–2000 (period 2). The means and variances of the two variables in each VTU are compared to identify any times when the changes in rainfall characteristics are most noticeable within the rainfall regime between periods. Both variables yield results consistent with the main rainy season and the long dry season being relatively unchanged, however the short dry spell is becoming wetter and the minor rainy season (September/October) has become significantly drier and shorter. The observations are consistent with the general north-south erosion of the bi-modal regime in West African which is associated with the southward shift of the ITCZ and the monsoonal system. This phenomenon is believed to be ongoing for the last 10,000 years in step with the hypothesized shift of the perihelion into the boreal winter. The use of independent arbitrary starting dates and durations (VTU) advances the understanding of temporal variability of rainfall, at a scale appropriate to agricultural practices in the study area.

Source: UG
Identification of lactic acid bacteria isolated during traditional fura processing in Ghana

Fura is a millet-based spontaneously fermented dumpling produced and consumed in parts of West Africa, particularly Nigeria, Burkina Faso and Ghana. From eight traditional fura production sites in northern Ghana, 862 lactic acid bacteria were isolated and identified to species level using a combination of genotypic and phenotypic methods including (GTG)5-based PCR fingerprinting and 16S rRNA gene sequencing, multiplex PCR by means of recA gene sequence comparison, conventional morphological characteristics and carbohydrate fermentation profiling. During millet dough fermentation, pH decreased from 5.6-6.4 to 4.1-3.7 and total lactic acid bacteria (LAB) counts increased from 4.4-5.3 to 7.9-9.2 log10 (cfu/g). The initial stages of the fermentation were characterized by co-dominance of homo- and heterofermentative species of Pediococcus acidilactici, Weisella confusa, Lactobacillus fermentum, Lactobacillus reuteri, Lactobacillus salivarius, and Lactobacillus paraplantarum whereas L. fermentum was dominating at the end of the fermentation. L. fermentum was predominant in all fermentations (p &lt; 0.05) and a high uniformity was observed among production sites regarding the dominance of L. fermentum. L. fermentum and W. confusa were isolated in all production sites and almost at all fermentation stages indicating that they are indigenous to traditional fura processing. The other LAB bacteria species which comprised a minor proportion of the total LAB occurred occasionally and in an irregular pattern among the production sites. © 2012 Elsevier Ltd.

Source: UG
Identification of new sources of resistance for pearl millet downy mildew disease under field conditions

Pearl millet is an important cereal crop for smallholder farmers’ food security in Africa and India. However, its production has stagnated due to several factors such as downy mildew (DM). Thus, a study was conducted to identify new sources of resistance from pearl millet inbred lines derived from a collection of landraces originated from West and Central African countries. A set of 101 lines, including 99 inbred lines from West and Central Africa along with a 7042S and SOSAT C 88 as susceptible and resistant checks, respectively, were evaluated under field conditions with infector rows in Bambey and Nioro research stations during the rainy season of 2016. Data on DM incidence and severity, plant height, flowering time, panicle length and productive tillers were recorded. The results showed highly significant differences among lines for all observed traits. Among the tested lines, 55 including SOSAT C 88 were resistant, 16 moderately resistant and 30 including 7042S were susceptible to the disease. Out of the 55 resistant lines, 20 were disease free. Hierarchical ascendant cluster analysis grouped the lines into three clusters with the DM parameters and plant height as the most discriminant factors. Cluster II contains the susceptible lines, while cluster III comprises the moderately resistant lines. The lines which belongs to cluster I were characterized by their resistance to the disease. Further use of these available new sources of resistance will be very useful for improvement of pearl millet for DM resistance and other agronomic traits.

Source: UG
Identification of novel Atg3-Atg8 inhibitors using virtual screening for autophagy modulation

A collection of 9050 natural products, their derivatives, and mimetics, was virtually screened against the human Atg3-Atg8 (Atg - autophagy) binding scaffold. By blocking this interaction, the lipidation of Atg8 does not occur and the formation of autophagosomes is inhibited. Forty-three (43) potential ligands were tested using enhanced Green Fluorescent Protein (eGFP) tagged LC3, the human ortholog of Atg8, in MCF7 breast cancer cells. Three hits showed single digit μM IC50 values with AT110, an isoflavone derivative, being the best at 1.2 ± 0.6 μM. Molecular modelling against Atg8 in conjunction with structural activity relationship (SAR) strongly supports the binding to this target. Testing in a panel of cancer cell lines showed little cytotoxic effect as compared to chloroquine. However, same concentration of AT110 was shown to be toxic to young zebrafish embryos. This can be explained in terms of the autophagy process being very active in the zebrafish embryos rendering them susceptible to AT110 whereas in the cancer cells tested the autophagy is not usually active. Nevertheless, AT110 blocks autophagy flux in the zebrafish confirming that the ligand is modulating autophagy. A small molecule non-cytotoxic autophagy inhibitor would open the door for adjunct therapies to bolster many established anticancer drugs, reducing their efficacious concentration thus limiting undesirable site effects. In addition, since many cancer types rely on the autophagy mechanism to survive a therapeutic regime, recurrence can potentially be reduced. The discovery of AT110 is an important step in establishing such an adjunct therapy.

Source: UG
Identification of novel Ghanaian G8P[6] human-bovine reassortant rotavirus strain by next generation sequencing

The main research focus of the Electron Microscopy and Histopathology Department in the past 20 years has been in the areas of enteric diarrhoeas with special emphasis on rotavirus. Through its diarrhoea surveillance studies, the Department has helped to firmly establish rotaviruses as a major cause of diarrhoea in children, and document the circulation of unusual rotavirus genotypes in Ghana. The Department has also recently expanded its diagnostic repertoire to include the identification and characterization of noroviruses, astroviruses, and other enteric viruses.

Source: UG
Identification of novel potential inhibitors of varicella-zoster virus thymidine kinase from ethnopharmacologic relevant plants through an in-silico approach

Although Varicella or chickenpox infection which is caused by the varicella-zoster virus (VZV) has sig nificantly been managed through vaccination, it remains an infection that poses threats to the nearest future due to therapeutic drawbacks. The focus of this research was geared towards in silico screening for the identification of novel compounds in plants of ethnopharmacological relevance in the treat ment of chicken pox in West Africa. The work evaluated 65 compounds reported to be present in Achillea millefolium, Psidium guajava and Vitex doniana sweet to identify potential inhibitors of thymi dine kinase, the primary drug target of varicella zoster virus. Out of the 65 compounds docked, 42 of these compounds were observed to possess binding energies lower than 7.0 kcal/mol, however only 20 were observed to form hydrogen bond interactions with the protein. These interactions were eluci dated using LigPlotþ and MM-PBSA analysis with residue Ala134 predicted as critical for binding. Pharmacological profiling predicted three potential lead compounds comprising myricetin, apigenin- 4’ -glucoside and Abyssinone V to possess good pharmacodynamics properties and negligibly toxic. The molecules were predicted as antivirals including anti-herpes and involved in mechanisms comprising inhibition of polymerase, ATPase and membrane integrity, which were corroborated previously in other viruses. These drug-like compounds are plausible biotherapeutic moieties for further biochemical and cell-based assaying to discover their potential for use against chickenpox.

Source: UG
Identification of Plasmodium falciparum circumsporozoite protein-specific CD8+ T cell epitopes in a malaria exposed population

The Department of Immunology conducts research in the field of immunology of infectious and non-infectious diseases. The Department has the overall goal of contributing knowledge to better diagnosis, management, control and prevention of infectious and non-infectious diseases in Ghana and worldwide. This is consistent with the overall strategy of the Noguchi Memorial Institute for Medical Research (NMIMR) and in line with the strategy of the College of Health Sciences of the University of Ghana.

Source: UG
Identification of poor households for premium exemptions in Ghana's National Health Insurance Scheme: Empirical analysis of three strategies

Summary: Objectives To evaluate the effectiveness of three alternative strategies to identify poor households: means testing (MT), proxy means testing (PMT) and participatory wealth ranking (PWR) in urban, rural and semi-urban settings in Ghana. The primary motivation was to inform implementation of the National Health Insurance policy of premium exemptions for the poorest households.Methods Survey of 145-147 households per setting to collect data on consumption expenditure to estimate MT measures and of household assets to estimate PMT measures. We organized focus group discussions to derive PWR measures. We compared errors of inclusion and exclusion of PMT and PWR relative to MT, the latter being considered the gold standard measure to identify poor households.Results Compared to MT, the errors of exclusion and inclusion of PMT ranged between 0.46-0.63 and 0.21-0.36, respectively, and of PWR between 0.03-0.73 and 0.17-0.60, respectively, depending on the setting.Conclusion Proxy means testing and PWR have considerable errors of exclusion and inclusion in comparison with MT. PWR is a subjective measure of poverty and has appeal because it reflects community's perceptions on poverty. However, as its definition of the poor varies across settings, its acceptability as a uniform strategy to identify the poor in Ghana may be questionable. PMT and MT are potential strategies to identify the poor, and their relative societal attractiveness should be judged in a broader economic analysis. This study also holds relevance to other programmes that require identification of the poor in low-income countries. © 2010 Blackwell Publishing Ltd.

Source: UG
Identification of Potential Drought Areas in West Africa Under Climate Change and Variability

The study investigates how the rising global temperature will affect the spatial pattern of rainfall and consequently drought in West Africa. The precipitation and potential evapotranspiration variables that are obtained from the Rossby Centre regional atmospheric model (RCA4) and driven by ten (10) global climate models under the RCP8.5 scenario were used. The model data were obtained from the Coordinated Regional Climate Downscaling Experiment (CORDEX) and analyzed at four specific global warming levels (GWLs) (i.e., 1.5 °C, 2.0 °C, 2.5 °C, and 3.0 °C) above the pre-industrial level. This study utilized four (4) indices: the standardized precipitation index, the precipitation concentration index, the precipitation concentration degree, and the precipitation concentration period over West Africa to explore the spatiotemporal variations in the characteristics of precipitation concentrations. Additionally, studying the impact of the four GWLs on consecutive dry days, consecutive wet days, and frequency of the intense rainfall events led to a better understanding of the spatiotemporal pattern of extreme precipitation. The results show that, at each GWL studied, the onset of rainfall comes 1 month earlier in the Gulf of Guinea compared to the historical period (1971–2000) with increasing rainfall intensity in the whole study domain, and the northeastern part of the study area becomes wetter. The rainfall concentration is uniformly distributed over the Gulf of Guinea and the Savanna zone for both the historical period and RCP8.5 scenario, while the Sahel zone which has shown an irregular concentration of rainfall for the historical period shows a uniform concentration of rainfall under all four GWLs.

Source: UG
Identification of Pro-vitamin A Cassava (Manihot esculenta Crantz) Varieties for Adaptation and Adoption through Participatory Research

In spite of diligent efforts by National Root Crops Research Institute (NRCRI) Umudike and International Institute of Tropical Agriculture (IITA) to make Nigeria the largest producer of cassava in the world, the adoption rate of elite cultivars by farmers is about 40% and that is unacceptable. In addition, all cassava cultivars presently grown in Nigeria are low in essential minerals, vitamins, and protein content, and high in cyanogenic content. Cassava with yellow roots contains elevated levels of β-carotene (pro-vitamin A), an essential nutrient, but they are not commonly grown in Nigeria. Because farmers select cultivars based on multiple criteria, participatory rural appraisal and selection are essential for a successful adoption of new improved varieties. A participatory rural appraisal (PRA) and sensory evaluation were conducted in Abia, Imo, and Ebonyi states of Nigeria to assess farmers' preferences for pro-vitamin A cassava. Some of the farmer-preferred traits included high yield, early maturity, tolerance to pests and diseases, sweetness, high amount of dry matter (DM) content, easy peeling, marketable roots, and roots that keep long in the ground without decaying. High pro-vitamin A cassava cultivars TMS 01-1368, TMS 05-1636, and TMS 05-0473 were better than farmers' cultivar NR 8082, because of their color, high premium price, nutritional value, texture, among others, and were selected for adoption. © Taylor & Francis Group, LLC.

Source: UG
Identification of Quantitative Trait Loci for Grain Yield and Other Traits in Tropical Maize Under High and Low Soil-Nitrogen Environments

Low soil Nitrogen (low-N) is one of the most important abiotic stressors responsible for significant yield losses in maize (Zea mays L.). The development and commercialization of low-N-tolerant genotypes can contribute to improved food security in developing countries. However, selection for low-N tolerance is difficult because it is a complex trait with strong interaction between genotypes and environments. Marker-assisted breeding holds great promise for improving such complex traits more efficiently and in less time, but requires markers associated with the trait of interest. In this study, 150 BC2F1 families of CML 444 × CML 494 were evaluated at two locations for two consecutive seasons to identify SNP markers associated with quantitative trait loci (QTL) for yield and other agronomic traits under low- and high-N environments. A total of 13 QTL were identified with 158 SNP markers, of which nine and four QTL were detected under low- and high-N environments, respectively. Five QTL one each for grain yield (qgy-1), days to silking (qdts-1) and anthesis- silking interval (qasi-6), and two for stay green characteristic (qsg-1 and qsg-4) were close to their adjacent markers, with an interval of 0.7 to 5.2 cM between them and explained phenotypic variance of 9 to 21%. These QTL would be invaluable for rapid introgression of genomic regions into maize populations using marker-assisted selection (MAS) approaches. However, further validation of these QTL is needed before use in MAS.

Source: UG