School of Biological Scienceshttp://ugspace.ug.edu.gh:8080/handle/123456789/47432024-03-28T18:51:43Z2024-03-28T18:51:43ZEvaluation Of Yield And Sub-Yield Components Of Cowpea (Vigna Unguiculata (L) Walp) AccessionsMensah, K.H.http://ugspace.ug.edu.gh:8080/handle/123456789/413582024-02-21T11:36:23Z2021-12-01T00:00:00ZEvaluation Of Yield And Sub-Yield Components Of Cowpea (Vigna Unguiculata (L) Walp) Accessions
Mensah, K.H.
One hundred and eight cowpea accessions were evaluated for yield and sub-yield components at the Department of Plant and Environmental Biology. They consisted of 60 F2 segregating, 44 accessions as test materials and 4 controls. The controls were Asontem Wang Kae, Padituya and Kirkhouse from CSIR-SARI. Data collected comprised of morphological and phytochemical traits. Descriptive, multivariate and genetic component analyses were carried out to evaluate the extent of variation. Rank summation index and contrast analysis were performed to select the best performing accessions. For the morphological traits studied, semierect growth habit with frequencies of 64.78%, 43.75% and 51.45% which occurred in the test materials, controls and the entire population. The majority of the accessions in the test materials exhibited red seed coat colour (19.59%) whereas in the controls most of the accession showed cream seed coat (50%). Overall, the majority of the accessions exhibited cream seed coat colour with a frequency of 35.35%. The chi-square test of association between qualitative traits showed was 125 significant associations in the test materials whereas the controls only showed 3 significant associations. The overall population exhibited 162 significant associations. In the multiple correspondence analysis (MCA) terminal leaf shape, growth habit, pod curvature and raceme position mostly led to variation in the first dimension which accounted for inertia of 51.40%. Thirteen farmer and consumer-preferred traits were used in the MCA plot. Asontem, UG8 and UG30 had a close relationship with similar phenotypic classes in the first quadrant of the MCA plot. UG1 and UG81 were outliers and had a distant relationship with majority of the phenotypic classes of the selected traits. The test materials had a significantly higher mean than the controls for the following traits; number of pods per plant, number of locules, seed weight and seed yield but lower than the controls for the following traits; days to first flower, days to 50% germination, days to first mature pod and days to 50% mature pod. Furthermore, the test materials were significantly higher in mean concentration for the following amino acids; gallic acid and vanillic acid, glycine, l-histidine, l-aspartic acid, l-valine and l-methionine. A total of 191, 537 and 413 significant pairwise correlations were observed in the test materials, controls and entire population respectively for all quantitative traits. The multiple regression analysis revealed that the underlying determinant of yield was most influenced by yield and yieldrelated components in the test materials and controls with contributions of 100% and 36.67% respectively. Phytochemical traits made the highest contribution of 25.95% to influencing variation in yield for the entire population. The first six principal components in the morphological traits accounted for a total variability of 47.17%, 55.40 %, 42.99% in the test materials, controls and entire population respectively. The first three principal components in the phytochemical traits accounted for a total variability of 51.81%, 100 %, 53.14% of the total variation in the test materials, controls and entire population respectively. The biplot showed that the relationships among accessions and morphological, phytochemical and all traits explained 46.63% and 99.49 and 94.48 % of the total variance respectively. The canonical discriminant analysis grouped against yield showed that the first CV accounted for 17.19% and 40.82% for the respective morphological and phytochemical traits. The cluster analysis based on morphological and phytochemical traits clustered the 108 accessions into 7 and 6 major groups respectively. The genetic component studies showed that seed yield had a high genotypic (63.1%) and phenotypic (243.8%) variances but low heritability of 18.41% while phytochemical traits had high GCV (>20), PCVs (>20) and heritability (>80%). Based on the lowest RSI scores, the 10 best performing accessions with high yield potential among the population evaluated were UG84, UG24, UG44, UG69, UG47, UG14, UG70, UG66, UG36, UG102 . The marginal analysis revealed that no accession was significantly higher in yield than the overall mean. However, it confirmed cluster grouping of accessions based on trait similarities and dissimilarities.
MPhil. Botany
2021-12-01T00:00:00ZPathogenomics And Antimicrobial Resistance Analysis In Neisseria GonorrhoeaeAgbodzi, B.http://ugspace.ug.edu.gh:8080/handle/123456789/413052024-02-16T13:11:22Z2021-01-01T00:00:00ZPathogenomics And Antimicrobial Resistance Analysis In Neisseria Gonorrhoeae
Agbodzi, B.
Gonorrhoea is a poorly controlled public health problem. With the global emergence of resistance to first line antibiotic treatment options, the infection has been predicted to be untreatable in the near future. This emerging trend highlights the need for constant genetic surveillance to unravel the mechanisms of resistance and inform therapy. This study therefore, sought to perform whole genome characterization of N. gonorrhoeae collected in Ghana to identify lineages of circulating strains, their antimicrobial resistance (AMR) and some virulence determinants. Gonococci isolates were cultured on gonococcal (GC) medium and identified using the API NH kit (Biomerieux, France). Genomic DNA was extracted from N. gonorrhoeae isolates using the QIAamp® DNeasy Ultraclean Microbial kit (Qiagen, Hilden, Germany). Whole genome sequencing (WGS) was performed on 56 isolates using both the Oxford Nanopore MinION and Illumina MiSeq sequencing platforms. The Comprehensive Antimicrobial Resistance Database (CARD) and PubMLST Neisseria database were used to catalogue chromosomal and plasmid genes implicated in AMR and assign sequence types (STs). The core genome MLST (cgMLST) approach was used for comparative genomics. The Virulence Factors of Pathogenic Bacteria Database (VFDB) was used to annotate virulence factors. In vitro resistance measured by disc diffusion revealed that (56)100%, (51)91% and (50)89.3% of the isolates were resistant to tetracycline, penicillin and ciprofloxacin respectively, while for the E-test method, (54)96.4%, (51)91% and (49)87.5% respectively were recorded. Four isolates exhibited reduced susceptibility to both cefixime and ceftriaxone as measured by disc diffusion. For these isolates, MIC ranges of 0.004 – 0.016 μg/ml and 0.016 - 0.75 μg/ml for ceftriaxone and cefixime respectively were recorded. No spectinomycin and azithromycin resistance was recorded using the E-test method. A total of 22 STs were identified by Multi-Locus Sequence Typing (MLST), with ST-14422 (n=10), ST-1927 (n=8) and ST-11210 (n=7) being the most prevalent. Six novel STs were also identified and submitted for the assignment of new sequence types (ST-15634-115641). Seven clusters of isolates with distinct AMR genotypes were identified after the cgMLST analysis, highlighting the presence of genome wide genetic variation. All isolates harboured chromosomal AMR determinants that confer resistance to beta-lactam antimicrobials and tetracycline. A total of (49)87.5% and (13)23% isolates contained fluoroquinolone and macrolide resistance markers respectively. Plasmids were highly prevalent: pTetM and pBlaTEM were found in 96%, and 92% of isolates, respectively. All isolates possessed the PI (B) variant of the porB gene which is associated with localized infection while high antigenic variations in the pillin genes was also detected. The study highlighted the need for constant genomic surveillance with the looming possible emergence of cephalosporin resistant isolates and isolates with highly variable antigens which could severely impact disease treatment.
MPhil. Molecular Biology
2021-01-01T00:00:00ZIn Vitro Studies Of The Effect Of Anopheles Gambiae Midgut Bacteria On The Development Of Plasmodium FalciparumAmetsi, Williams Godwinhttp://ugspace.ug.edu.gh:8080/handle/123456789/412992024-02-16T11:19:40Z2021-12-01T00:00:00ZIn Vitro Studies Of The Effect Of Anopheles Gambiae Midgut Bacteria On The Development Of Plasmodium Falciparum
Ametsi, Williams Godwin
During blood feeding, female Anopheles mosquitoes may ingest Plasmodium gametocytes which undergo transformation in the gut and develop into sporozoites that are infectious to humans. Bacteria inhabit the mosquito gut, and the number and diversity of these bacteria change following blood feeding. The presence of some bacteria species results in the reduced intensity of developing Plasmodium parasites. Little attention has been given to understanding this direct mechanism of bacteria on Plasmodium parasites, and the effects of bacteria on malaria parasite developmental genes are not completely understood. This limits the scope of how gut bacteria, for example Enterobacter and Serratia, which have been found with anti-Plasmodium effects can be further explored for alternative disease control strategies. Therefore, this study investigated the lethal effect of cell-free secreted bio-products of E. cloacae and S. marcescens on a key Plasmodium parasite developmental gene (Gamete release gene, GAMER) for its potential as a target for malaria transmission-blocking.
Plasmodium falciparum 3D7 and Dd2 cultures at 1% parasitaemia were independently exposed to spent Luria-Bertani (LB) medium from varying concentrations of Enterobacter cloacae and Serratia marcescens. The parasite killing effect of the bacteria were assessed with SYBR green fluorescent assay after 48 hours of co-culture. Spent media with final bacteria concentration between 10e+10-10e+20 reduced parasitaemia (P<0.001) compared to parasite culture without bacteria treatment. Using real-time (quantitative) PCR, it was found that the expression of GAMER was down regulated by 2 folds after 1 hour of screening P. falciparum 3D7 with cell-free spent medium of E. cloacae cultured for 8 hours in LB broth (Ec-8). However, the expression of GAMER was unaffected after 6 and 12 hours of screening P. falciparum 3D7 with Ec-8. These data provide information for further studies on gene and protein targets for transmission blocking interventions.
MPhil. Molecular Cell Biology Of Infectious Diseases
2021-12-01T00:00:00ZSelection Dynamics Of Circumsporozoite Protein (Csp) Vaccine Target In Ghana: The Contribution Of Human Leukocyte Antigen (Hla) VariationKpaka, J.N.http://ugspace.ug.edu.gh:8080/handle/123456789/412832024-02-15T14:50:20Z2021-07-01T00:00:00ZSelection Dynamics Of Circumsporozoite Protein (Csp) Vaccine Target In Ghana: The Contribution Of Human Leukocyte Antigen (Hla) Variation
Kpaka, J.N.
Implementation of RTS,S/AS01 vaccine for malaria is underway in three (3) African countries, Ghana, Kenya, and Malawi. This vaccine, which targets the Plasmodium falciparum circumsporozoite protein (CSP) provides partial protection for infants and children against clinical and severe malaria infections. Reasons for this reduced efficacy or immunogenicity are poorly understood, but CSP variation has been implicated. Human leukocyte antigen (HLA) has also been observed to influence RTS,S-mediated protection. This study aims to define the variants of CSP and determine its distribution between Begoro and Cape Coast in Ghana over three years. Further, the influence of HLA genotype in terms of parasite frequency and RTS,S/AS01 response was assessed.
About 50μl of peripheral blood was collected from participants in Begoro and Cape Coast in 2014, 2015, and 2016, dried blood spot (DBS) prepared and DNA was extracted. The C-terminal of Plasmodium falciparum CSP and the human leukocyte antigen (HLA) class II gene in humans were deep sequenced. The translated amino acid haplotypes of the CSP were aligned and compared to the reference 3D7 vaccine strain. The HLA class II haplotypes were grouped into superfamily and their association with the CSP variants was ascertained.
The CSP haplotypes are evenly distributed between Begoro and Cape Coast. There were 31 Th2R haplotypes in Begoro and 30 Th2R haplotypes in Cape Coast; 15 Th3R haplotypes in Begoro and 13 in Cape Coast. About 83.9% of Th2R and 96.5% of Th3R haplotypes in Begoro are shared with Cape Coast. The amino acid changes with reference to the 3D7 vaccine strain at the Th2R epitope range from 1 to 6 and 1 to 4 at theTh3R epitope. There is a 53% and 60% reduction in the 3D7 Th2R and Th3R haplotypes, respectively, from 2014 to 2016, but 3D7 is still common in Ghana, Kenya, and Malawi. The 3D7 haplotype does not correlate with HLA-DRB1, but there is with HLA-DQA1 and HLA-DPB1.
Begoro and Cape Coast are two different ecological zones in Ghana but the parasite population is homogenous. The Th2R epitope of CSP is polymorphic than the Th3R epitope and this higher polymorphism is driving a higher non-synonymous amino acid substitution at the Th2R epitope than the Th3R epitope which may have vaccine implication. A decline in frequency of 3D7 parasite population may also affect the performance in the vaccine in Begoro and Cape Coast. Initial correlations indicate that HLA-DPB1 (01:01/17:01) correlates with the 3D7 vaccine strain, but HLA-DPB1 (01:01/17:01) and other variants of HLA-DQA1 also correlates with other Th2R haplotypes and may compete with the vaccine haplotype for antigen presentation to CD+4 T cells. This may have implications for the efficacy of the RTS,S/AS01 vaccine in Ghana.
MPhil. Molecular Cell Biology Of Infectious Diseases
2021-07-01T00:00:00Z