ghanaopendata/ghanaian-research-english huggingface dataset:
Genotype By Environment Interaction Effect And Fresh Root Yield Stability Of Cassava Genotypes Under Contrasting Nitrogen Regimes.

Nitrogen (N) is an important nutrient element needed by cassava for optimum yield and it is a vital component of nucleotides (nucleic acids), enzymes, amino acids (proteins), chlorophyll molecules and hormones, among other essential compounds required for growth and development of cassava. Nitrogen stress is a major cassava production constraint. the study aimed to examine genotype by environment interaction (GEI) effects and fresh root yield stability of 203 diverse cassava clones to identify genotypes with stable performance under low and optimum nitrogen regimes across environments using AMMI and GGE biplot analysis. Experiments were conducted using an augmented block design with three replications for two years in three locations in Nigeria. There were significant differences (p< 0.001) in the genotype’s mean performances as well as significant differences (p< 0.001) in the environment’s mean performances for all the traits measured in both nitrogen regimes. The AMMI analysis of variance showed significant effects (p< 0.001) for genotypes, environments and the interactions for fresh root yield in both nitrogen regimes. The biplot analysis showed that for fresh root yield in the optimum nitrogen regime, the principal component accounted for 81.54% of the G+GE (Genotype plus and Genotype by Environment) variation. The G+GE for fresh root yield in the low nitrogen regime accounted for a total of 71.64% of the variation. Ten genotypes were identified as the best genotypes under the optimum nitrogen regime, while eleven genotypes were the best under the low nitrogen regime. Three genotypes under optimum nitrogen regimes were high-yielding. Still, they were unstable in their fresh root yield performance across the environments and can be recommended as specifically adapted to the environments they performed best. Three other genotypes were high-yielding genotypes under low nitrogen but were highly unstable in their fresh root yield mean performance across the environments. The environments Otobi_YR1, Igbariam_ YR2, and Umudike_YR1 were identified as the most discriminatory among the test environments. The environments Umudike_YR2 and Igbariam_YR1 were identified as the most representative of the test environments and can represent a mega-environment. The best 21 genotypes that performed above the grand mean for fresh root yield in both nitrogen regimes can be further evaluated on the farmer’s field for possible advancement.

Source: UG
Genotype diversity of group A rotavirus strains in children with acute diarrhea in urban Burkina Faso, 2008-2010

Most research activities involve the use of molecular methods such as regular PCR (PCR), quantitative PCR (Q-PCR), genomic sequence and analysis using different software, genetic engineering, probe hybridization techniques, biological and molecular cloning, evaluation of immune markers for laboratory diagnosis of infections, serological assays involving the use of rapid tests, ELISA-based evaluations and immunofluorescent assay techniques.

Source: UG
Genotype‑by‑environment interaction and stability of root mealiness and other organoleptic properties of boiled cassava roots

Genetic enhancement of cassava aimed at improving cooking and eating quality traits is a major goal for cassava breeders to address the demand for varieties that are desirable for the fresh consumption market segment. Adoption of such cassava genotypes by consumers will largely rely not only on their agronomic performance, but also on end-user culinary qualities such as root mealiness. The study aimed to examine genotype× environment interaction (GEI) efects for root mealiness and other culinary qualities in 150 cassava genotypes and detect genotypes combining stable performance with desirable mealiness values across environments using GGE biplot analysis. Experiments were conducted using an alpha-lattice design with three replications for two years in three locations in Nigeria. The analysis of variance revealed a signifcant infuence of genotype, environment, and GEI on the performance of genotypes. Mealiness scores showed no signifcant relationship with frmness values of boiled roots assessed by a penetration test, implying that large-scale rapid and accurate phenotyping of mealiness of boiled cassava roots remains a major limitation for the efective development of varieties with adequate mealiness, a good quality trait for direct consumption (boil-and-eat) as well as for pounding into ‘fufu’. The moderate broad-sense heritability estimate and relatively high genetic advance observed for root mealiness suggest that signifcant genetic gains can be achieved in a future hybridization program. The genotype main efects plus genotype× environment interaction (GGE) biplot analysis showed that the diferent test environments discriminated among the genotypes. Genotypes G80 (NR100265) and G120 (NR110512) emerged as the best performers for root mealiness in Umudike, whereas G13 (B1-50) and the check, G128 (TMEB693) performed best in Igbariam and Otobi. Based on the results of this study, fve genotypes, G13 (B1-50), G34 (COB6-4), G46 (NR010161), the check, G128 (TMEB693), and G112 (NR110376), which were found to combine stability with desirable mealiness values, were the most suitable candidates to recommend for use as parents to improve existing cassava germplasm for root mealiness

Source: UG
Genotype-by-Environment Interaction and Yield Stability of Maize Single Cross Hybrids Developed from Tropical Inbred Lines

Nitrogen (N) is one of the most important nutrients required for high productivity of the maize plant. In most farmers’ fields in Sub-Saharan Africa (SSA), there is low availability of N in the soil mainly due to continuous cultivation of the land, crop residues removal, little or no application of fertilizers and rapid leaching. There is a need to develop low N tolerant and adapted maize genotypes. Evaluation of maize genotypes under different nitrogen conditions would therefore be useful in identifying genotypes that combine stability with high yield potential for both stress and non-stress environment. Eighty maize hybrids were evaluated at Mbalmayo and Nkolbisson in Cameroon, during 2012 and 2013 minor and major cropping seasons across 11 environments under low and high N conditions. The objectives of the study were: (i) to determine the effect of genotype x environment interaction (G × E) on grain yield and yield stability of single cross maize hybrids across low N and optimum N environments and (ii) to identify genotypes to recommend for further use in the breeding program. Yield data of 80 hybrids were analyzed initially and the analysis of 20 best performing genotypes was further performed for a better visualization and interpretation of the results. Combined analysis of variance showed highly significant G × E effects for grain yield. The GGE biplot analysis divided the study area into three mega environments: one related to the major cropping season while the two others were related to the minor cropping season. The grain yield of the 20 highest yielding hybrids ranged from 4484.7 to 5198.3 kg ha−1. Hybrid 1368 × 87036 was the highest yielding in the minor season while the most outstanding hybrid, TL-11-A-1642-5 × 87036 was the best for the major season. The latter hybrid showed the potential for production across environments and should therefore be further tested in multiple environments to confirm consistency of its high yield performance and stability, and to facilitate its release as a commercial hybrid. High yielding but not stable hybrids across environments could be recommended for the specific environments where they performed well.

Source: UG
Genotypic analysis of β-tubulin in Onchocerca volvulus from communities and individuals showing poor parasitological response to ivermectin treatment

Ivermectin (IVM) has been in operational use for the control of onchocerciasis for two decades and remains the only drug of choice. To investigate the parasitological responses and genetic profile of Onchocerca volvulus, we carried out a 21. month epidemiological study to determine the response of the parasite to IVM in 10 Ghanaian endemic communities. Onchocerca nodules were surgically removed from patients in three IVM response categories (good, intermediate and poor) and one IVM naïve community. DNA from adult worms was analyzed to determine any association between genotype and IVM response phenotypic. Embryogramme analysis showed significantly higher reproductive activity in worms from poor response communities, which had up to 41% of females with live stretched microfilaria (mf) in utero, despite IVM treatment, compared with good response communities, which had no intra-uterine stretched mf.?-tubulin isotype 1 gene has been shown to be linked to IVM selection in O. volvulus and also known to be associated with IVM resistance in veterinary nematodes. We have genotyped the full length genomic DNA sequence of the ?-tubulin gene from 127 adult worms obtained from the four community categories. We found SNPs at 24 sites over the entire 3696. bp. Eight of the SNPs occurred at significantly higher (. p<. 0.05) frequencies in the poor response communities compared with the good response communities and the IVM naïve community. Phenotypic and genotypic analyses show that IVM resistance has been selected and the genotype (1183GG/1188CC/1308TT/1545GG) was strongly associated with the resistance phenotype. Since the region in the ?-tubulin gene where these four SNPs occur is within 362. bp, it is feasible to develop a genetic marker for the early detection of IVM resistance. © 2012 Australian Society for Parasitology.

Source: UG
Genotypic And Phenotypic Characterisation Of Three Local Chicken Ecotypes Of Ghana Based On Principal Component Analysis And Body Measurements.

This study aimed to characterise three Ghanaian local chicken ecotypes, namely, Interior Savannah, Forest, and Coastal Savannah, based on morphological data and single nucleo tide polymorphism (SNP) genotypes. Morphological data including body weight, shank length, body girth, back length, thigh length, beak length, comb length, and wattle length were collected from 250 local chickens. DNA isolated from blood of 1,440 local chickens was used for SNP genotyping with the Affymetrix chicken 600k SNP chip. Principal compo nent analysis showed that Forest and Coastal Savannah birds were closely related. Gener ally, all three ecotypes exhibited high genetic diversity, especially birds from the Interior Savannah zone. Morphological characterisation showed that ecotype (p = 0.016) and sex (p = 0.000) had significant effects on body weight. Birds of the Interior Savannah ecotype were the heaviest (p = 0.004), with mean weights of 1.23 kg for females and 1.40 kg for males. Sex also had a strong significant effect on most of the morphological measurements, but the sex * ecotype interaction effect was not significant. Very few of the feather phenotypes pre viously reported to be associated with heat resistance–frizzle (2%) and naked neck (1.6%)– were found in the studied populations. It is concluded that the three local ecotypes are genetically diverse but with similar morphological features and the information provided would be useful for future selection decisions.

Source: UG
Genotypic and phenotypic diversity of Mycobacterium tuberculosis complex genotypes prevalent in West Africa

Findings from previous comparative genomics studies of the Mycobacterium tuberculosis complex (MTBC) suggest genomic variation among the genotypes may have phenotypic implications. We investigated the diversity in the phenotypic profiles of the main prevalent MTBC genotypes in West Africa. Thirty-six whole genome sequenced drug susceptible MTBC isolates belonging to lineages 4, 5 and 6 were included in this study. The isolates were phenotypically characterized for urease activity, tween hydrolysis, Thiophen-2- Carboxylic Acid Hydrazide (TCH) susceptibility, nitric oxide production, and growth rate in both liquid (7H9) and solid media (7H11 and Lo¨wenstein–Jensen (L-J)). Lineage 4 isolates showed the highest growth rate in both liquid (p = 0.0003) and on solid (L-J) media supplemented with glycerol (p<0.001) or pyruvate (p = 0.005). L6 isolates optimally utilized pyruvate compared to glycerol (p<0.001), whereas L5 isolates grew similarly on both media (p = 0.05). Lineage 4 isolates showed the lowest average time to positivity (TTP) (p = 0.01; Average TTP: L4 = 15days, L5 = 16.7days, L6 = 29.7days) and the highest logCFU/mL (p = 0.04; average logCFU/mL L4 = 5.9, L5 = 5.0, L6 = 4.4) on 7H11 supplemented with glycerol, but there was no significant difference in growth on 7H11 supplemented with pyruvate (p = 0.23). The highest release of nitrite was recorded for L5 isolates, followed by L4 and L6 isolates. However, the reverse was observed in the urease activity for the lineages. All isolates tested were resistant to TCH except for one L6 isolate. Comparative genomic analyses revealed several mutations that might explain the diverse phenotypic profiles of these isolates. Our findings showed significant phenotypic diversity among the MTBC lineages used for this study.

Source: UG
Genotypic characterization of extended-spectrum β-lactamase producing urinary isolates among pregnant women in Ho municipality, Ghana

Objective: The case of antibiotic resistance has become a major global concern and Extended Spectrum β-lactamase (ESBL) producing organisms have so far remained the biggest culprit. The consequences of urinary tract infection (UTI) and antibiotic resistance among pregnant women cannot be underestimated. We investigated UTI and ESBL production among urinary pathogens isolated from pregnant women. Method: We obtained non-repeat, clean catch midstream urine samples from 1345 pregnant women suspected of having UTI for bacterial identification at the Ho Teaching Hospital Laboratory between June 2013 and March 2015. The isolates were taken through relevant biochemical testing for identification and then subjected to antimicrobial agents for susceptibility testing using the disc diffusion method. We tested for ESBL production by the combined disc method and ESBL positive (þESBL) phenotype isolates were genotyped for BlaTEM, BlaSHV, and BlaCTX-M using polymerase chain reaction (PCR). Data were analyzed using SPSS v24 and p-values < 0.05 were considered statistically significant. Results: Of the 1345 urine samples tested, 230 (17.1%, 95% CI: 15.1%–19.1%) yielded significant bacteriuria. The most common bacterium isolated was Staphylococcus aureus (29.6%) followed closely by Escherichia coli (28.7%) both of which were highest during the second trimester of gestation. We isolated 152 gram-negative isolates with 41.4% (63/230) being þ ESBL. Of the 63 þ ESBL, 45 (71.4%) possessed blaTEM, 42 (66.7%) had blaCTX-M and 2 (3.2%) possessed blaSHV genes; 38 possessed multiple ESBL genes comprising 2 with both SHV and TEM genes and 36 with both CTX-M and TEM genes. Conclusion: High prevalence of UTI and persistent transmission of ESBLs among pregnant women in the Ho Municipality is worrying and a course for public health concern. We recommend urine culture during pregnancy as a routine laboratory investigation to avoid birth-related complications.

Source: UG
Genotypic diversity and drug susceptibility patterns among M. tuberculosis complex isolates from South-Western Ghana

The Bacteriology Department aims to improve the quality of life first for Ghanaians and the world at large by conducting research into bacterial diseases of public health importance to Ghana and globally. In addition to working on enteric pathogens and sexually transmitted diseases, the department’s current main focus is on the two most important mycobacterial diseases of public health importance to Ghana, namely Buruli ulcer (BU) and tuberculosis (TB).

Source: UG
Genotypic glucose-6-phosphate dehydrogenase (G6PD) deficiency protects against Plasmodium falciparum infection in individuals living in Ghana

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
Genotyping and Drug Susceptibility Testing Of Mycobacterial Isolates from Population-Based Tuberculosis Prevalence Survey in Ghana.

The Bacteriology Department aims to improve the quality of life first for Ghanaians and the world at large by conducting research into bacterial diseases of public health importance to Ghana and globally. In addition to working on enteric pathogens and sexually transmitted diseases, the department’s current main focus is on the two most important mycobacterial diseases of public health importance to Ghana, namely Buruli ulcer (BU) and tuberculosis (TB).

Source: UG
Gentamicin nephrotoxicity: Animal experimental correlate with human pharmacovigilance outcome

Background: National Agency for Food and Drugs Administration and Control (NAFDAC), which is responsible for pharmacovigilance activity in Nigeria, recently withdrew injection gentamicin 280 mg, used in the management of life-threatening and multidrug-resistant infections from circulation, due to reported toxicity. Thus, this study aimed to investigate the toxicity profile of the commonly used strengths (80 mg and 280 mg) of gentamicin on kidney using animal models. Methods: Animals were divided into five groups of 16 rats each. For rats of groups 1 and 2, gentamicin (1.14 mg/kg each group) was administered intramuscularly twice daily for 7 and 14 days, respectively, after which eight of them were sacrificed by cervical dislocation. Blood was collected via cardiac puncture and the kidneys were carefully removed and weighed immediately. The remaining eight animals were kept for reversibility study for another 7 and 14 days, respectively. For groups 3 and 4, gentamicin (4 mg/kg each group) was administered as a single daily dose for 7 and 14 days, respectively, and eight animals from the groups were subjected to reversibility study for 7 and 14 days, respectively. Group 5, the control group animals, were given 10 ml/kg distilled water for 14 days. Histopathology of the kidneys, serum creatinine levels, and antioxidant enzyme activities were investigated. Results: Significant increase (p ≤ 0.001) in the level of creatinine of rats administered 4.0 mg/kg for 14 days was observed compared with all other groups. Significant (p ≤ 0.001) elevations in the lipid peroxidation in all gentamicin-administered animals and acute tubular necrosis in most of the gentamicin-administered animals were observed. Conclusion: Toxicity profile of gentamicin on the kidneys is dependent on both dose and duration of administration.The findings justify the decision made by NAFDAC to ban the use of high-dose inj. gentamicin 280 mg in Nigeria. © 2015, Chang Gung Medical Journal. All rights reserved.

Source: UG
Geochemical and Sm-Nd isotopic evidence for the composition of the Palaeoproterozoic crust of the West African Craton in Ghana

The metasedimentary rocks of the Sefwi and Lawra volcanic belts in Ghana respectively were analysed for their major and trace elements and Sr‐Nd isotopic compositions to constrain the provenance, palaeo‐weathering conditions, and tectonic setting of the rocks. Geochemical characteristics of the metasedimentary rocks show low to moderate chemical weathering in their source regions and the rocks are interpreted to have been derived from mixture of mafic and felsic rock components. The LREE show much enrichment in relation to the HREE (LaN/LuN, 4.67‐11.66). The εNd (2.1 Ga) values of −0.12 to +3.72 strongly suggest that the source of the sedimentary rocks was derived from a depleted mantle source and that they were most likely produced in an almost entirely oceanic environment with minor influence from the continental crust. The Nd model ages ranging from +2.05 to 2.41 Ga suggest possible contributions of a pre‐Birimian crustal material (or Archaean?) in the source material of the volcanic rocks. The rock types that contributed as detritus to the Birimian metasedimentary rocks were mainly pyroclastics and basalts, and their REE patterns suggest that the contribution to the phyllites can be modelled after 20% basalt, 13% andesite, and 67% dacite. Similarly, the schists can be modelled as a mixture of 16% basalt, 34% andesite, and 50% dacite. The Nd isotopic modeling implies that the bulk of the sedimentary detritus was supplied by the Palaeoproterozoic volcanic arc with contributions of less than 10% from the pre‐Birimian crust (Archaean?).

Source: UG
Geochemical and Sr‐Nd isotopic records of Paleoproterozoic metavolcanics and mafic intrusive rocks from the West African Craton: Evidence for petrogenesis and tectonic setting

Metavolcanics and mafic intrusive rocks of the Paleoproterozoic Birimian terrane in the southeastern part of the West African Craton, Ghana, were analyzed for major and trace elements and Nd and Sr isotopic data to constrain the geodynamic evolution of the Birimian Supergroup. The metavolcanic rocks consist of metabasalts, meta-andesites, and amphibolites, whereas the mafic intrusions are mainly gabbros, hornblendites, and dolerites. The rocks are tholeiitic in composition and show the classic features of arc magmatism. The metavolcanics display significant enrichments in large ion lithophile elements (LILE) and light rare earth elements, relative to high field strength elements (HFSE) and heavy rare earth elements. The multielement patterns of the rocks also show positive Pb, Ba, Th, and Sr and negative Nb, Ta, and Ce anomalies that are typical characteristics of subduction-related magmas. They also have La/Nb ratios <3 and La/Ta ratios <43 that are similar to other Archean and Birimian greenstone belts in West Africa. The rocks have εNd (2.1 Ga) values of -0.96 to +2.60, and Nd model ages of 2.24-2.51 Ga (TDM1) and 2.16-2.45 Ga (TDM2), indicating their juvenile character with possible contributions from pre-Birimian crustal materials in their sources. The εNd values suggest a depleted source and further indicate that they were probably produced in an almost entirely oceanic environment with minor influence from the continental crust. The Nd isotopic results are consistent with the island arc model, which views Paleoproterozoic terranes of the West African Craton in the context of subduction-accretion processes. Accordingly, these processes may have played a role in the formation of the Columbia supercontinent during the Paleoproterozoic (2.1-1.8 Ga) orogenic events.

Source: UG