ghanaopendata/ghanaian-research-english huggingface dataset:
Genetic polymorphisms in MDR1, CYP3A4 and CYP3A5 genes in a Ghanaian population: a plausible explanation for altered metabolism of ivermectin in humans?

BACKGROUND: Ivermectin, a substrate of multidrug resistance (MDR1) gene and cytochrome P450 (CYP) 3A4, has been used successfully in the treatment of onchocerciasis in Ghana. However, there have been reports of suboptimal response in some patients after repeated treatment. Polymorphisms in host MDR1 and CYP3A genes may explain the observed suboptimal response to ivermectin. We genotyped relevant functional polymorphisms of MDR1 and CYP3A in a random sample of healthy Ghanaians and compared the data with that of ivermectin-treated patients with a view to exploring the relationship between suboptimal response to ivermectin and MDR1 and CYP3A allelic frequencies. METHODS: Using PCR-RFLP, relevant polymorphic alleles of MDR1 and CYP3A4 genes were analysed in 204 randomly selected individuals and in 42 ivermectin treated patients. RESULTS: We recorded significantly higher MDR1 (3435T) variant allele frequency in suboptimal responders (21%) than in patients who responded to treatment (12%) or the random population sample (11%). CYP3A4*1B, CYP3A5*3 and CYP3A5*6 alleles were detected at varied frequencies for the sampled Ghanaian population, responders and suboptimal responders to ivermectin. CYP3A5*1/CYP3A5*1 and CYP3A5*1/CYP3A5*3 genotypes were also found to be significantly different for responders and suboptimal responders. Haplotype (*1/*1/*3/*1) was determined to be significantly different between responders and suboptimal responders indicating a possible role of these haplotypes in treatment response with ivermectin. CONCLUSION: A profile of pharmacogenetically relevant variants for MDR1, CYP3A4 and CYP3A5 genes has been generated for a random population of 204 Ghanaians to address the scarcity of data within indigenous African populations. In 42 patients treated with ivermectin, difference in MDR1 variant allele frequency was observed between suboptimal responders and responders.

Source: UG
Genetic relatedness in carbapenem-resistant isolates from clinical specimens in Ghana using ERIC-PCR technique

Aim Enterobacterial repetitive intergenic consensus (ERIC) sequence analysis is a powerful tool for epidemiological analysis of bacterial species. This study aimed to determine the genetic relatedness or variability in carbapenem-resistant isolates by species using this technique. Methods A total of 111 non-duplicated carbapenem-resistant (CR) Gram-negative bacilli isolates from a three-year collection period (2012–2014) were investigated by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC–PCR) in four selected hospital laboratories in Ghana. The isolates were also screened for carbapenemase and extended spectrum β-lactamase genes by PCR. Results A proportion of 23.4% (26/111) of the genomic DNA extracts were carriers of PCR-positive carbapenemase genes, including 14.4% blaNDM-1, 7.2% blaVIM-1 and 1.8% blaOXA-48. The highest prevalence of carbapenemase genes was from non-fermenters, Acinetobacter baumannii and Pseudomonas aeruginosa. For the ESBL genes tested, 96.4% (107/111) of the CR isolates co-harboured both TEM-1 and SHV-1 genes. The ERIC-PCR gel analysis exhibited 1 to 8 bands ranging from 50 to 800 bp. Band patterns of 93 complex dissimilarities were visually distinguished from the 111 CR isolates studied, while the remaining 18 showed band similarities in pairs. Conclusion Overall, ERIC-PCR fingerprints have shown a high level of diversity among the species of Gram-negative bacterial pathogens and specimen collection sites in this study. ERIC-PCR optimisation assays may serve as a suitable genotyping tool for the assessment of genetic diversity or close relatedness of isolates that are found in clinical settings.

Source: UG
Genetic relationship between bacteria isolated from intraoperative air samples and surgical site infections at a major teaching hospital in Ghana

Background: In low- and middle-income countries (LMICs) the rate of surgical site infections (SSI) is high, leading to negative patient outcomes and excess healthcare costs. A causal relationship between airborne bacteria in the operating room and SSI has not been established, at a molecular or genetic level. We studied the relationship between intraoperative airborne bacteria and bacteria causing SSI in an LMIC. Methods: Active air sampling using a portable impactor was performed during clean or clean-contaminated elective surgical procedures. Active patient follow-up consisting of phone calls and clinical examinations was performed 3, 14 and 30 days after surgery. Bacterial isolates recovered from SSI and air samples were compared by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) identification, ribotyping, whole genome sequencing (WGS), and metagenomic analysis. Results: Of 128 included patients, 116 (91%) completed follow-up and 11 (9%) developed SSI. Known pathogenic bacteria were isolated from intraoperative air samples in all cases with SSI. A match between air and SSI isolates was found by MALDI-TOF in eight cases. Matching ribotypes were found in six cases and in one case both WGS and metagenomic analysis showed identity between air- and SSI-isolates. Conclusion: The study showed high levels of intraoperative airborne bacteria, an SSIrate of 9% and a genetic link between intraoperative airborne bacteria and bacteria

Source: UG
Genetic relationships among improved cassava accessions and landraces for resistance to the cassava mosaic disease

This study was conducted to determine the genetic relationships among 21 accessions of cassava (Manihot esculenta), with varying levels of resistance to cassava mosaic disease (CMD), based on their phenotypic response to the disease. The accessions were ranked according to their area under the disease progress curve (AUDPC). Hierarchical cluster analysis based on Ward's linkage method separated the accessions into three major groups and the susceptible clones were distinct from the resistant accessions. Further analysis using K-means defined four groups which were similar to the groupings by the hierarchical method, but the susceptible landrace TME 117 was distinct from the other susceptible accessions. Principal component analysis showed that there was considerable amount of variation and the first three components accounted for 78.87% of the total variation in the accessions. A scatter-plot of the scores of the first and second principal components for responses to CMD showed that, generally, the resistant accessions were different from the susceptible accessions and the most susceptible landrace TME 117 formed a single member group distinct from the other susceptible groups. The large amount of variation implies that using any combination of resistant accessions to recombine different favorable alleles will not reduce the overall diversity of the breeding population.

Source: UG
Genetic Selection for Thermotolerance in Ruminants

Variations in climatic variables (temperature, humidity and solar radiation) negatively impact livestock growth, reproduction, and production. Heat stress, for instance, is a source of huge financial loss to livestock production globally. There have been significant advances in physical modifications of animal environment and nutritional interventions as tools of heat stress mitigation. Unfortunately, these are short-term solutions and may be unsustainable, costly, and not applicable to all production systems. Accordingly, there is a need for innovative, practical, and sustainable approaches to overcome the challenges posed by global warming and climate change-induced heat stress. This review highlights attempts to genetically select and breed ruminants for thermotolerance and thereby sustain production in the face of changing climates. One e ective way is to incorporate sustainable heat abatement strategies in ruminant production. Improved knowledge of the physiology of ruminant acclimation to harsh environments, the opportunities and tools available for selecting and breeding thermotolerant ruminants, and the matching of animals to appropriate environments should help to minimise the e ect of heat stress on sustainable animal genetic resource growth, production, and reproduction to ensure protein food security.

Source: UG
The genetic significance of carbon and oxygen isotopic variations in Mn-bearing carbonates from the Palaeo-Proterozoic (∼2.2 GA) Nsuta deposit in the Birimian of Ghana

Carbon and oxygen isotope analyses of manganese-bearing carbonates from the Palaeo-Proterozoic Nsuta manganese deposit, Ghana, suggest important relationships between isotopic composition of the Mn-bearing carbonates and lithology, locality and carbonate microfacies. Lithologically, δ13C and δ18O PDB values obtained from manganese carbonate ore exhibit greater variation than similar values from host Mn bearing phyllite. In terms of locality, quite a restricted range in isotope values is observed in carbonates from various parts of the deposit both stratigraphically and along strike. The greatest spread, however, occurs in samples from an economically important portion of the deposit where δ13C and δ 18O PDB vary from -1.5 to -20.9 and -10.9 to -18.2‰, respectively. With respect to carbonate microfacies, coarser grained carbonates vary greatly in isotopic distribution than carbonates of microcrystalline and microconcretionary texture. Mineralogically, carbonate rocks or ore consisting dominantly of rhodochrosite vary greatly in 13C and 18O than dolomite- and/or complex type carbonates such as kutnahorite, dolomite and solid solutions of magnesite-rhodochrosite. Together with detailed petrographic observations, isotope values obtained from fine-grained Mn carbonate ore and immediate host Mn bearing phyllite are interpreted to be primary, having possibly been only slightly affected by the pervasive but low-grade greenschist facies metamorphism that affected Birimian rocks. On the contrary, isotope values in coarse grained carbonates typical of restricted but economically the most important part of the deposit are interpreted to be secondary in origin, most likely the result of post-metamorphic (hydrothermal?) overprinting on primary carbonate signatures. These genetic interpretations seem to contradict, or are rather opposite to, interpretations of the carbon and oxygen isotopic composition of carbonates reported by earlier workers on the deposit.

Source: UG
Genetic structure of olive ridley sea turtles (Lepidochelys olivacea) in Ghana, West Africa

Sea turtles migrate across ocean basins to reach foraging and breeding areas but still exhibit significant population structure across nesting beaches. Although five species of sea turtles nest in West Africa, the genetic structure of many species in this region has not been adequately explored. We investigated the diversity of mitochondrial and nuclear DNA for nesting olive ridley (Lepidochelys olivacea) turtles in two coastal communities (Mankoadze and Ada Foah) in Ghana that are approximately 160 km apart. Samples were collected during four nesting seasons: 2006, 2014, 2015 and 2016. Analysis of the control region of mtDNA (n = 45) revealed six variable positions defining five haplotypes, of which one was previously undescribed (Lo91). These findings are indicative of population expansion from a small ancestral population and support the scenario of colonization of the Atlantic via founder effect. Eleven microsatellite loci were used to analyze two years (2015 and 2016) from Mankoadze. We determined these nesting cohorts were not genetically distinct (FST = 0.025, P = 0.286) and can therefore be considered a single population. This population was compared to six females from Ada Foah across seven loci. Individuals from the two locations were less related than expected under a model of random chance, and showed signs of outbreeding, and reflected moderate variation between the two (FIS = -0.160, P = 1.00; FST = 0.104, P = 0.002). The structuring between locations indicate nesting individuals may utilize different migration routes, foraging grounds, or breeding grounds and that Ghana may serve as a transitional area between central and west African rookeries.

Source: UG
Genetic structure of seventy cocoyam (Xanthosoma sagittifolium, Linn, Schott) accessions in Ghana based on RAPD

Seventy cocoyam accessions collected from the eastern and Volta regions of Ghana were studied using RAPD technique. Ten primers were used to study the genetic diversity and structure of the experimental material and a total of 120 different bands were detected. Levels of polymorphic fragments detected by the ten primers ranged from 69.2% to 100%. In the accessions from the eastern region, the mean observed and effective number of alleles per individual per population and mean Nei's gene diversity were 1.99±0.01, 1.53±0.12 and 0.312±0.05, respectively. Mean observed and effective number of alleles per individual per population and Nei's gene diversity were 1.76± 0.17, 1.44±0.16 and 0.264±0.08, respectively for the accessions from the Volta region. Considering the entire collections, the mean observed and effective number of alleles per individual per population and Nei's gene diversity for primers were 1.99±0.02, 1.54±0.12 and 0.319±0.05, respectively. In terms of Nei's F-statistics in the subdivided populations for all primers, the overall gene diversity (Ht) ranged from 0.230 to 0.396 with a mean of 0.313+0.06, within sample gene diversity (Hs) ranged from 0.214 to 0.372 with a mean of 0.286+0.06, gene differentiation (Gst) ranged between 0.005 and 0.178 with a mean of 0.086. Geneflow estimate ranged between 2.309 and 99.500 with a mean of 5.314. The accessions grouped into three main clusters. Accession BD96/183 was the most diverse and may be incorporated into cocoyam breeding programs. The 70 accessions did not cluster into their distinct geographical regions suggesting that there may have been movement of germplasm across the two regions.

Source: UG
Genetic variability among wheat (Triticum aestivum L.) germplasm for resistance to spot blotch disease

Spot blotch caused by Bipolaris sorokiniana (Sacc.) Shoem. is the most devastating disease limiting wheat productivity in warm and humid environments. One hundred and fifty wheat genotypes were evaluated under field conditions in 2013 and 2014 in six different locations in Zambia. The genotypes showed different levels of resistance to spot blotch. Genotypes 19HRWSN6 (Kenya Heroe), 19HRWSN7 (Prontia Federal) and 19HRWSN15 (BRBT2/METSO) were resistant lines across environments. The genotype plus genotype by environment (GGE) biplot grouped the six environments (E) into three mega-environments (ME) with respect to spot blotch severity. ME I contained Golden Valley Agricultural Research Trust (GART) (E6) only. Mpongwe (E4), Mt. Makulu (E5 and E2) and GART (E3) formed ME II, while ME III contained only Mutanda (E1). Genotypes 16HRWYT5, SB50 and 20HRWSN33 were the most susceptible genotypes in ME I, II and III, respectively. Genotype 19HRWSN7 was the most resistant across test locations. The locations in ME III were highly correlated indicating that they provided similar information on genotypes. This suggests that one location could be chosen among the locations in ME III for screening spot blotch resistance each year if the pattern repeats across years. This could aid in reducing the cost of genotype evaluation and improve efficiency as genotypes would be handled in fewer environments. © 2018, Kassel University Press GmbH. All rights reserved.

Source: UG
Genetic Variability and Its Implications on Early Generation Sorghum Lines Selection for Yield, Yield Contributing Traits, and Resistance to Sorghum Midge

Sorghum is the second most important cereal crop in Niger. The crop is grown in a wide range of ecological environments in the country. However, sorghum grain yield in Niger is limited by both abiotic and biotic constraints. Recombinant inbred lines derived from the cross of a local variety with a midge resistant variety and two local checks were evaluated during the 2015 rainy season across two planting dates in two environments in Niger. The objective was to investigate genetic variability for yield, yield related traits, and resistance to sorghum midge. High phenotypic coefficient of variation (PCV) versus genotypic coefficient of variation (GCV) was observed in both sites and planting dates. Across planting dates at both Konni and Maradi, grain yield, plant height, panicle weight, and midge damage had high heritability coupled with high estimates of genetic advance. At Konni, high genetic advance coupled with high heritability was detected for grain yield, plant height, panicle weight, and resistance to midge. There were similar results at Maradi for grain yield, plant height, and panicle weight. Therefore, selection might be successful for the above characters in their respective environments.

Source: UG
Genetic Variability in Micronutrients Composition of Orchardgrass (Dactylis glomerata L.)

In this study, it is hypothesized that plants selected and/or bred for improved desired characteristics (e.g., macronutrients) may affect other characteristics (e.g., micronutrients) negatively. To test the hypothesis, we evaluated the metal micronutrient concentrations of four experimental strains viz., HighMgE, HighMgM, LowEq and LowMg and two commercial cultivars viz., Okamidori and Akimidori of orchardgrass. There were no genetic differences among the experimental strains/cultivars of orchardgrass for dry matter accumulation. The concentration of micronutrients varied with genetic differences among the four strains and the two commercial cultivars of orchardgrass. The amounts of Mn, Fe, Zn, Cu, Mo, Co, Ni, Se and I in the shoot, irrespective of strain or cultivars used, were 76.36, 74.83, 14.03, 9.36, 2.19, 5.00, 5.17, 2.00 and 19.33 μg g-1 at first harvest and 85.89, 74.56, 15.06, 12.30, 3.84, 6.14, 4.99, 2.54 and 19.53 μg g-1 at second harvest, respectively. The average amounts at the third harvest were 119.97, 90.36, 17.67, 13.39, 3.36, 4.56, 4.89, 2.36 and 20.06 μg g-1, respectively, whereas the corresponding amounts at the fourth harvest were 128.22, 156.00, 21.92, 10.31, 4.25, 4.53, 4.54, 1.47 and 28.72 μg g-1, respectively. Apart from few exceptions, Mn, Fe, Zn, Mo and I levels were highest in the fourth harvest, whereas the levels of Co and Se were highest in the second harvest. The level of Cu was the highest in the third harvest. The levels of Mn, Fe, Ni, Se and Mo were higher in low Mg containing plants irrespective of strain or cultivar. On the other hand, Co, Cu and I tended to peak in plants containing higher amounts of Mg. The Cu/Mo ratio was highest in the first harvest followed by the third, second and fourth harvests. The amounts of Mn, Fe, Ni, Co, Zn and Mo were within the optimum levels required for maintaining forage quality.

Source: UG
Genetic variances and heritabilities of early yellow maize population following cycles of improvement for Striga resistance and drought tolerance

Drought and Striga are principal constraints to maize production in sub-Saharan Africa. An early yellow maize population, TZE-Y Pop DT STR that had undergone five cycles of selection for resistance to Striga, followed by three cycles of improvement for drought tolerance was investigated for yield gains, changes in genetic variances and interrelationships among traits under drought-stress and optimum environments. Two hundred and forty S1 lines comprising 60 each from the base population and subsequent populations from three selection-cycles improved for grain yield and drought tolerance, were assessed under drought and optimal environments in Nigeria, 2010 – 2012. Genetic improvements in grain yield of 423 and 518 kg ha-1 cycle-1 were achieved under drought-stress and optimum environments. Predicted improvements in selection for yield were 348 and 377 kg ha-1 cycle-1 under drought-stress and optimum environments, respectively. The highest yield observed in C3 was accompanied by reduced days to silking, anthesis-silking interval, improved plant aspect, ear aspect, and increased plant height and ears per plant across research environments as well as improved stay green characteristic under drought. The level of genetic variability for yield and some few other traits were maintained under drought and optimal environments in the population. Presence of residual genetic variability for yield and other assayed traits in C3 indicated that progress could be made from future selection in the population depending on the ability of breeders to identify outstanding genotypes and precision level of experimentation. Substantial improvement has been made in yield and drought tolerance in C3 of population.

Source: UG
Genetics of anther indehiscence with exerted stigmas and its application in hybrid rice breeding

Complete indehiscence of anthers accompanied with exerted stigmas outside the hull could be useful in hybrid rice breeding if the genetics and possible environmental effects are well understood. Studies were undertaken to identify the sources, confirm the mode of inheritance, and examine the possible environmental effects and potential application of anther indehiscence with exerted stigmas in hybrid rice breeding. Direct and reciprocal crosses were made between Jasmine 85, selected interspecific and intersubspecific lines and two wide compatibility varieties. The resulting F1 progenies were evaluated for their expression of anther indehiscence and exerted stigmas. Expression of anther indehiscence with exerted stigmas by both direct and reciprocal crosses suggested no effect of cytoplasmic factors on the expression of the trait. Segregation analysis supported the 7:1 (indehiscence:dehiscence) mode of inheritance. Temperature and relative humidity could not modulate the fertility/sterility status of anther indehiscent plants. Utilization of anther indehiscence with exerted stigmas in hybrid rice breeding was hindered by trait fixation and propagation. © 2018 Informa UK Limited, trading as Taylor & Francis Group.

Source: UG