School of Biological and Physical Sciences

Genomics and metagenomics analysis of non-typhoidal salmonella from children below five years and their immediate environment in disease-endemic Mukuru settlement in Nairobi, Kenya

2026-02-17T07:31:32Z

Genomics and metagenomics analysis of non-typhoidal salmonella from children below five years and their immediate environment in disease-endemic Mukuru settlement in Nairobi, Kenya KEBENEI, Collins Kipkorir Non-typhoidal Salmonella (NTS) remains a leading cause of morbidity and mortality in Sub-Saharan Africa, particularly among vulnerable children within informal settlements where safe water, sanitation, and hygiene (WASH) infrastructure are inadequate. The rising prevalence of antimicrobial-resistant NTS strains and the role of household environments as potential reservoirs sustaining endemic transmission remain poorly characterized in these high-risk informal settlements. This study aimed to investigate the occurrence, genetic diversity, antimicrobial resistance, pathogenic potential, and spatial distribution of NTS strains from environmental and clinical sources within Mukuru informal settlement, Nairobi, Kenya. By linking clinical and environmental NTS strains, the study provides insights into the persistence and transmission of antimicrobial-resistant strains. A case-control study conducted between June 2021 and June 2023 analyzed 2,675 clinical samples from children and 268 environmental samples, including drinking water, effluent, soil, and raw sewage, collected from case and control households. NTS isolation from clinical samples was performed using standard microbiological and biochemical techniques, followed by confirmation and serotyping through serological assays and whole-genome sequencing. Environmental samples underwent metagenomic sequencing and binning of NTS genomes. Whole-genome and metagenomic sequences were analysed to characterize genetic diversity, antimicrobial resistance genes (ARGs), and pathogenicity determinants. Core-genome SNP-based phylogenetic reconstruction assessed genomic relatedness, while spatial analyses mapped transmission patterns over time. NTS was detected in 1.57% of clinical samples, predominantly Salmonella Enteritidis (52.4%) and Salmonella Typhimurium (47.6%). Environmental samples from case households exhibited higher detection rates of NTS (33.3%) than those from homes of controls (7.1%), with effluent (45.2%) and drinking water (33.3%) showing the highest contamination levels. Core-SNP phylogenetic analysis revealed strong genomic relatedness between clinical and environmental NTS strains within households (F = 0.8171, R² = 0.0496, p = 0.459), affirming intra-household environmental-human transmission cycles. Effluent-derived strains often occupied basal phylogenetic positions, implicating household wastewater as a potential ancestral source. Antimicrobial resistance profiling revealed aminoglycoside resistance genes as the most prevalent across clinical and environmental NTS strains, with aac(6’)-Iaa_1 detected in 100% of clinical and 97.6% of environmental strains. Additional resistance genes included aph(6), aph(9)-Ia, oqxA, sul_1, cat2, and blaTEM-104_1. Notably, aph and oqxA genes were co-located within conserved resistance cassettes embedded in IncFIB(S)_1 and IncFII(S)_1 plasmids. These cassettes were flanked by mobile genetic elements, IS3, IS15, IS256, ISPm12, and transposons Tn3 and TnAs3, forming modular, horizontally transferable resistance islands. Pairwise comparisons revealed overlapping ARG profiles within household-case clusters, suggesting intra-household environmental-to-human ARG spillover (F = 1.816, R² = 0.131, p = 0.062). IncFIB(S)_1 (97.2% clinical, 29% environmental) and IncFII(S)_1 (97.2% clinical, 31.6% environmental) plasmids, harboring compact Type IV secretion systems, were the dominant replicons across clinical and environmental strains, suggesting high conjugation potential and ecological persistence. PERMANOVA revealed significant differences in plasmid profiles between clinical and environmental compartments (p_adj=0.01), except raw sewage (p_adj=0.154). Virulence gene profiling showed substantial overlap between clinical and effluent, drinking water, and soil NTS strains, with significant differences only between clinical and raw sewage strains (F=10.625, R²=0.202, p_adj=0.05). Spatial analysis revealed that high-intensity hotspots were consistently mapped to areas of infrastructural deficiency. These spatial patterns suggest that environmental matrices serve as reservoirs for antimicrobial-resistant NTS, underscoring the need for targeted WASH improvements and routine One Health surveillance to interrupt transmission in informal settlements. PhD Thesis

Culturable soil microbial community structure, nutrient dynamics and greenhouse gas emissions in Maize-Banana Based agroforestry system in Kisii County, Kenya

2026-02-17T06:41:08Z

Culturable soil microbial community structure, nutrient dynamics and greenhouse gas emissions in Maize-Banana Based agroforestry system in Kisii County, Kenya BUYELA, Daniel Khasabulli Microbial community structure are the characteristics of a group of microorganisms as measured by any metric of taxa or gene composition, diversity and abundance via a range of molecular or cultural techniques. Soil microbial community structure is an important biological component of soil function. Microbial community affect the belowground dynamics and fate of nutrients which can influence soil fertility. Soil microorganisms play a significant role in the efflux of greenhouse gases (GHG). To better comprehend agroforestry systems that can enhance soil nutrients and combat climate change, it is vital to ascertain the effects of agroforestry systems (AFS) on the soil microbial community structure. Declining soil fertility as a result of continuous cropping is a major problem facing farmers in Kisii County. The link between the microbial community and GHG emissions remains poorly understood due to the diversity and complexity of microorganisms in soils. Further, there is little understanding of the morphological and molecular characteristics of these microbes. There is paucity of information on the role of microbes on soil nutrient dynamics and greenhouse gas efflux in maize-banana based AFS in Kisii county. For smallholder farmers to adapt agroforestry systems for their potential to increase soil fertility and reduce GHC emissions, there is a dearth of simple methodologies. Therefore, the objective of this study was to assess soil microbial community structure, nutrient dynamics and greenhouse gas emissions in a maize-banana based agroforestry system in Kisii County. This study was conducted at Kenya Agricultural and Livestock Research Organization farm in Kisii County. This study was conducted on an established agroforestry experimental plots which were set using a completely randomized block design with maize and banana intercropped with agroforestry trees. Soil samples were taken randomly at 10 different spots per plot at a depth of 0-15cm. Soil microbial biomass was determined using the chloroform fumigation extraction and their population determined by direct counting. Microbes were isolated in pure cultures, characterized morphologically and molecularly, and their phylogenetic relationships determined. Total organic carbon(C), nitrogen(N), phosphorus(P), potassium(K), calcium(Ca) and magnesium(Mg) were determined. Soil GHG (carbon dioxide, methane, and nitrous oxide) measurements were done using closed chambers. Soil pH was determined using a combined pH meter. Morphological and molecular data was subjected to cluster analysis. Data was subjected to analysis of variance and means separated using Least Significant Differences (P ≤ 0.05) after testing for normality. Correlation analysis was carried out on soil microbial biomass, microbial populations, soil carbon, nutrients and GHG. Microbial biomass and population were significantly higher in intercrop treatment with maize-banana, Sesbania sesban (MBSS). Most of bacterial isolates were Gram-negative bacilli and cocii with a few Gram-positive bacilli belonging to thirteen genera, while fungal isolates belonged to seven genera. Bacteria isolates clustered into five orders and fungal isolates clustered into three orders. Morphological genograms clustered isolates in two groups at 75% similarity level. Molecularly, sequences of bacterial isolates had >97% similarity match with gene bank isolates except MBCC2 while all fungal isolates had >97% similarity match with Genebank isolates. Soils from agroforestry tree species combinations treatment MBSS had higher values of C, N, P, K, Ca and Mg levels. Plots with Calliandra calothyrsus agroforetry tree species had low values GHG emissions. Sesbania sesban has the ability to increase soil microbial biomass and population which in turn act to improve soil health through microbial organic matter decomposition and thus recommended for use in maize-banana based agroforestry system. The study recommends the use Calliandra PhD Thesis

An ecotourism model for conservation of the Maasai Mau forest, Kenya

2025-11-11T08:06:52Z

An ecotourism model for conservation of the Maasai Mau forest, Kenya ALOO, Charles Ochuka Ecotourism has emerged as a sustainable economic sector with favourable environment friendly practices in the recent past attracting high attention in the developing countries. It has therefore emerged as a strong tool for income generation, socio-cultural preservation and biodiversity friendly. However, it is not clear among scholars how ecotourism it contributes to environmental conservation given that some of the activities involved are not well understood on their link to forest conservation. Thus, a model which gives more insight on the relationship of the various ecotourism elements to forest conservation is necessary. This study sought to develop an ecotourism model that would provide guideline for the conservation of Maasai Mau forest, Kenya . Specific objectives were to assess the influence of livelihood practices of Mau forest adjacent community on Forest conservation, to establish the influence of economic activities of Maasai Mau forest adjacent community on Forest conservation; to ascertain the influence of socio-cultural practices of Maasai Mau forest adjacent community on Forest conservation and to develop an ecotourism model that would provide conservation guidelines for Maasai Mau Forest, Kenya . The study employed a triangulation mixed method design involving quantitative and qualitative techniques. Target population comprised of 962 respondents. The sample size was 384 respondents from which stratified random sampling was used to achieve 6 heads of government agencies(KWS and KFS), 29 hotel and restaurant service providers, 339 community forest associations and 12 Travel & Tour Operators. Questionnaires with five point Likert scales were administered on the sampled community forest associations (CFAs) and hotels and restaurant service providers; interviews were used to collect data from the six government agencies top managers, from tour and travel while Focus group discussions (FGDs) were used to collect data from 12 travel and tour operators. Qualitative data was analysed through thematic analysis. Means, standard deviations, frequency counts and percentages were used for descriptive statistics while regression analysis was used to compare the relationships between livelihood practices, economic activities, socio-cultural practices, and conservation. It was found that livelihood practices (M=2.74; SD=1.250), economic activities (M=2.61; SD=1.250), and socio cultural practices (2.86; SD=1.232) moderately influences the conservation of Maasai Mau forest. It is also illustrated economic activities have a negative and significant influence (β = -0.189, t(353)=-3.255, p<.05), influence of livelihood practices are positive and significant (β =0.256, t(353)=5.441, p<.05) and socio-cultural practices of the adjacent community have positive and significant effect (β =0.307, t(353)=5.587, p<.05) on the conservation of Maasai Mau forest. This implies that for unit increase in economic activities lead to -0.189 unit changes in the conservation of the forest. For every unit increase in livelihood practices and socio cultural practices, there is 0.256 and .307 unit changes in the conservation of Maasai Mau forest respectively. The overall model explained a significant variance of 34.6% in forest conservation(R2=.346, F(3,354)=62.193, p<.05). This implies that the model is a good fit and therefore can make a good guide for forest conservation. It is concluded that increase in economic activities leads more to forest depletion. This implies that ecotourism model can guide local communities to generate new sources of livelihood from the natural forest, reinforce traditional culture and contribute to the environmental conservation. The study findings on an ecotourism model may provide guideline for suitable forest conservation approaches capable of ameliorating the problems currently being witnessed round Maasai Mau Forest. PhD Thesis

Reformulating the gravitational geodetic and frame-dragging effects in a complex Spacetime frame

2025-11-06T12:56:19Z

Reformulating the gravitational geodetic and frame-dragging effects in a complex Spacetime frame KIBANDE, Wellingtone Einstein's general theory of relativity governs dynamics in a gravitational field. Linearization of the non-linear field equations converts them to solvable forms. The clear similarity between linearized equations and Maxwell's equations in electrodynamics prompts inference that the gravitational field is inherently composed of electric and magnetic forces as constituent elements. Notably, the electric force component aligns seamlessly with the well-known Newtonian gravity force, while the magnetic force component manifests dynamic phenomena, including the predicted geodetic and frame-dragging effects. A significant constraint emerges in the use of the four-dimensional Minkowski spacetime frame for the derivation and exploration of field equations. This frame, unfortunately, lacks a fully defined unit vector in the temporal direction, thereby impeding essential mathematical operations such as the curl and cross product of vectors that intricately describe dynamic properties. In an endeavour to surmount this impediment, a ground breaking approach is introduced: A novel four-dimensional complex spacetime frame. This frame extends the conventional three-dimensional Euclidean space by incorporating an imaginary temporal axis defined by a unit vector. It has rigorously shown that this innovative approach solves the previously encountered limitations in Minkowski spacetime, facilitating the execution of mathematical operations including curl and cross-product of vectors in a more standard manner. This work presents a comprehensive reformulation of the relativistic gravitational field theory within the novel complex spacetime frame. The resulting field equations are deployed through re-examination of some relativistic effects namely geodetic and frame-dragging effects, with a distinct emphasis on achieving an elevated degree of precision and accuracy in predicting relativistic properties. The end result of this scholarly endeavour is to discern comparative analysis of the obtained results vis-à-vis the empirical findings derived from the Gravity Probe-B experiment. A gravitoelectromagnetic (GEM) field potential four-vector and field strength tensor defined within Minkowski spacetime was calculated and their applications to gyroscope dynamics were discussed leading to a gyromagnetic ratio η=4. A gravitational field strength in a complex spacetime frame was obtained. Electric and magnetic forces in a complex spacetime frame were obtained. expressions for frame-dragging and geodetic effects were obtained. A comparison between obtained results, the results of the GP-B experiment and earlier theoretical result was done. Gyroscope dynamics were found to be characterised by frame-dragging (Lense-Thirring) and geodetic effects. The frame-dragging effect was found to be -2B ⃗_g×q ̂×S ⃗ and that of geodetic effect was found to -3/2 v ⃗/c×E ⃗_g×q ̂×S ⃗ . The directions of the relativistic effects are specified. Comparing with established theoretical findings, it was noted that the magnitude of geodetic effect was exactly equal to that obtained earlier theoretically and experimentally but the numerical value of frame-dragging effect was much smaller. As opposed to earlier results, our findings include the directional components of the relativistic effects providing additional information. A re-evaluation of other physical theories is suggested in future research. PhD Thesis

Piperonyl butoxide net utilization and durability on malaria transmission in Muhoroni sub-county, western Kenya

2025-11-06T12:44:04Z

Piperonyl butoxide net utilization and durability on malaria transmission in Muhoroni sub-county, western Kenya OYWERI, Job Nyamwaro Pyrethroid-treated nets have reduced malaria in endemic areas, but insecticide resistance has hindered progress, prompting WHO to recommend piperonyl butoxide (PBO) based LLINs. Kenya adopted PBO nets, but their usage and effect on malaria infection is not well documented. Additionally, their recommended three-year lifespan is challenged by fabric decay and insecticidal decay, both of which can influence malaria transmission. The current study objectives were: to determine the effect of PBO net usage on malaria infection in Muhoroni sub-county, Western Kenya, to assess the influence of PBO net integrity on malaria incidence at the household level in Muhoroni sub-county, Western Kenya and to examine the influence of PBO net bioefficacy on malaria incidence in Muhoroni sub-county, Western Kenya. A cross-sectional net usage survey was conducted on 12 randomly selected villages comprising of six villages per intervention arm (pyrethroid and PBO-LLINs) one-year post-net distribution. Using a standardized semi-structured questionnaire, 181 and 199 households in the pyrethroid and PBO-LLINs were randomly surveyed respectively. Finger-prick blood smears and dry blood spots (DBS) on filter papers were collected for microscopy and real-time PCR (RT-PCR) malaria diagnosis respectively. A repeated cross-sectional study design was employed to evaluate net integrity every six months and bioefficacy every three months, for a period of up to 18 months. Distinctive households ranging from 101-107 households/group/visit were surveyed with 116-135 nets (pyrethroid) and 137-169 nets (PBO) assessed. Inconsistently used nets were excluded from the study. Six nets per group were retrieved from households with different wall characteristics (mud plastered, mud unplastered/exposed mud, and cemented/block/brick) for residual bioefficacy testing using WHO cone bioassays. Monthly malaria active case detections were carried out by community health promoters (CHPs) in the surveyed households. The influence of net utilization on malaria infection was determined using logistic regression. A simple logistic regression model and Fisher-Freeman Halton exact test were used to determine the influence of PBO physical integrity and bioefficacy on malaria incidence respectively. Malaria parasite prevalence by qPCR was lower in the PBO-LLIN group 29% vs. 34.7%. The use of PBO net decreased the risk of a malaria infection by 39.8% [OR=0.602 (95% CI=0.373-0.971), P=0.038]. At 18 months, there was lower torn rate in the PBO-LLIN compared to pyrethroid-LLIN group (21.8% (31/142) vs. 45.2% (61/135) with pHI scores of 1618.6±1056.7 and 2494.1±1696.4 respectively. By the 18th month, bioefficacy against susceptible mosquitoes decreased for both net types (PBO: 98.1% to 18.5%, pyrethroid-LLIN: 97.6% to 18.4%), and for resistant mosquitoes as well (PBO: 55.6% to 11.8%, pyrethroid-LLIN: 36.9% to 6.8%). Malaria incidence was consistently lower (23.6 cases/1000 people/month vs. 16.2 cases/1000 people/month) among households using PBO-LLINs compared to pyrethroid-LLINs over 18 months. Compromised physical integrity (torn) and bioefficacy (not effective) of the PBO-LLINs were significantly associated with higher malaria incidences in households. To sustain PBO-LLIN effectiveness, the Ministry of Health should strengthen community education on consistent and proper net use, consider periodic assessments of fabric integrity and bioefficacy within 18 months post-distribution and integrate community-based monitoring to identify and replace ineffective nets promptly. PhD Thesis

Entanglement of atom-field states in the anti-Jaynes-Cummings interaction: rabi oscillations and quantum teleportation of entangled atomic qubits

2023-09-18T10:13:28Z

Entanglement of atom-field states in the anti-Jaynes-Cummings interaction: rabi oscillations and quantum teleportation of entangled atomic qubits MAYERO, Christopher The quantum Rabi model (QRM), the simplest single-mode spin-boson model, was initially simplified using rotating wave approximation (RWA), yielding the Jaynes Cummings (JC) model in rotating frame (RF). The QRM was later symmetrised into its rotating JC and counter-rotating (CR) anti-Jaynes-Cummings (AJC) components, yielding an exactly solvable AJC model in the counter-rotating frame (CRF). This work presents the dynamics generated when a two-level atom (fermionic system) interacts with a quantised electromagnetic field mode (bosonic system) in the AJC model. The evolution of the atomic state during the AJC interaction with field mode initially and separately in three basic non-classical states of light is considered. In each respective atom-field interaction, we provided the corresponding extensively studied JC interaction as a com parison. We have shown that when the field mode is in an initial Fock state (idealised light), Rabi oscillations during the AJC interaction occur in the reverse sense relative to that during the JC interaction. In addition, quantum teleportation of a two-atom entan gled anti-symmetric state at unit fidelity indicates that maximally entangled atom-field states generated in the AJC interaction are effective quantum channels, and the observed long-lived entanglement during the AJC interaction specify that the atomic qubits ex hibit long coherence time vital for computational processes. What is more, two-qubit controlled-NOT (C-NOT) gate operation and single qubit Walsh-Hadamard gate oper ation is demonstrated each giving standard outcomes as expected. In the former, the target qubit is flipped when the control qubit is in an initial ground state |g⟩ and remain unchanged when the control qubit is in an initial excited state |e⟩ while in the latter the atomic basis states {|e⟩, |g⟩} were rotated into diagonal basis states {|+⟩, |−⟩}. When the field mode in an initial coherent state is considered during the AJC interaction, fully quantised atom-field interaction is realised since the field is dominantly sub-Poissonian. Finally, when an initial squeezed coherent state is considered during the AJC interaction, at all time intervals the atom-field quantum systems are entangled (mixed), i.e, at no point did the quantum systems evolve to pure state, the degree of mixedness increased with every increase in the squeeze parameter and ringing revivals at an expected col lapse phase are observed when higher values of squeeze parameter is applied. This thesis work presents the first ever demonstration of quantum Rabi oscillations, entanglement dynamics, successful quantum teleportation, photon statistics and effective quantum gate operations in an AJC interaction between a two-level atom and a quantised electromag netic field mode. In contrast to the standard JC interaction which has generally been iv used in quantum information theory (QIT) and quantum computation, the AJC inter action provides the advantage of starting with both an atom and field mode each in an initial ground state, i.e, an atom in spin-down state and field mode in vacuum state, a property which is essentially unachievable in the JC interaction when an initial Fock state is considered. We now recommend application of the AJC model in the emerging field of quantum technology, which has a potential to revolutionise a wide range of industries and applications, from finance and logistics to healthcare and energy. More specifically, the results of this work in its present form, will be of immense contribution to QIT and physical realisation of quantum computation

Synthesis and characterization of fish scales (Oreochromis niloticus) derived biochar and magnetic composites and their application in removal of anionic indigo carmine and cationic crystal violet dyes from synthetic and industrial wastewater

2022-12-19T16:21:19Z

Synthesis and characterization of fish scales (Oreochromis niloticus) derived biochar and magnetic composites and their application in removal of anionic indigo carmine and cationic crystal violet dyes from synthetic and industrial wastewater OINDO, George Achieng’ The global and regional increase in demand for textile products have led to increased quantities of dye wastewater in the environment, which is a potential source of carcinogenic compounds. This situation not only hampers photosynthetic activities of benthic plants but also affects aesthetic quality of water sources. Apart from many available wood biomass, fish scales of Tilapia (Oreochromis niloticus) are also abundant wastes in the environment that can be processed and applied as materials in abstraction of indigo carmine (IC) and crystal violet (CV)dyes from wastewater.Nevertheless, physical and chemical characteristics of raw fish scales and their biochars are not known. The main objective of this study was to synthesize and characterize fish scale biochars(FSB) and magnetic composites (FSB@Fe3O4) at varying temperatures and apply them in remediation of industrial dye effluents. Pulverized raw fish scales (RFS) were pyrolysed over temperature of 200 oC - 800 oC and magnetic composites,FSB@400 oC-Fe3O4, FSB@600 oC-Fe3O4 and FSB@800 oC-Fe3O4, were synthesized by chemical co-precipitation method. The adsorbents were characterizedfor peak optical absorbance, functional groups, magnetic strength, surface morphology, particle size, elemental compositions, surface charge, surface area, thermal stability and crystallinity. The potential of pulverized RFS, FSB and FSB@Fe3O4 compared to activated charcoal (AC) for abstraction of IC and CV dyes from aqueous solutions was determined as a function of initial dye concentration, contact time, dye solution pH, adsorbent dosage and temperature. Peak optical absorbance was 252-320 nm with FSB@600 oC posting the lowest peak of all the magnetic composites studied. The adsorbents contained CO32-, PO43-, Fe-O and -OH as confirmed by EDX and XRD analysis. TEM results displayed spotted ring-like patterns on the surface of FSB and catenation of identical spherically shaped flowers was observed on FSB@Fe3O4. Magnetization values for VSM analysis ranged between 8 to 10 emu/g, sufficient for adsorbent recovery with a magnet. The pHpzc ranged between 3.80-8.42, while TGA showed that a rise in temperature led to a rise and a decline in weight loss for RFS, FSB and FSB@Fe3O4, correspondingly. BET surface areas were 94.05 and 102.67 m2/g for FSB@600 oCand FSB@600 oC-Fe3O4, respectively. Adsorption results demonstrated that the quantity (q) of the dyes adsorbed by FSB and FSB@Fe3O4 increased with initial dye concentration, material load and solution temperature. Lower quantities of IC and higher quantities of CV were recorded at higher pH levels. Statistics fittedpseudo-second-order kinetic models while the Langmuir isotherm presented the best fit of all the models tested. The optimum pH 2 and pH 8-10 were favourable for adsorption of IC and CV, respectively. Wastewater remediation data revealed that for location A, FSB@600 oC significantly reduced IC and CV by 72.00% and 96.96%, correspondingly. Reusability results showed that the adsorbents conserved their initial adsorption capacities for the abstraction of IC for five consecutive cycles without significant depletion. However, substantial decrease in adsorption capacities at the fifth regeneration cycle was observed for CV. Fish scale biomass can be applied in the synthesis of adsorbents that can be adopted as easily accessible materials for remediation of industrial dye wastewater. PhD Thesis

Evaluation of morphophysiological, biochemical and yield responses of Bambara groundnut landraces to sodium chloride salinity

2022-12-19T16:13:36Z

Evaluation of morphophysiological, biochemical and yield responses of Bambara groundnut landraces to sodium chloride salinity AMBEDE, Jane Gayalwa Soil salinity limits crop growth, development and productivity in agricultural soils worldwide and contributes to food insecurity. It is induced by accumulation of high levels of particularly sodium and chloride ions within the rooting zone. Bambara groundnut {Vigna subterranea (L.) Verdc} is underutilized and fairly neglected indigenous African food legume with potential to alleviate food and nutritional insecurity in tropical regions of Africa. The crop has potential to be grown in semi-arid areas or under irrigation, both of which offer potentially saline conditions. The effect of sodium chloride (NaCl) salinity on growth and physiology of this plant continues to attract research, more so on the locally grown landraces. There are still unanswered questions on the effect of NaCl salinity on photosynthetic pigments, compatible solutes, nodulation and yield. Therefore, the overall objective of the study was to evaluate morphophysiological, biochemical and yield responses of Bambara groundnut landraces in response to NaCl salinity. The specific objectives were to determine the effects of NaCl salinity on growth, gas exchange (transpiration rate (Tr), stomatal conductance (gs) and C02 assimilation rate(Cr)), mineral nutrients (sodium, potassium and calcium), proline, leaf pigments (chlorophyll a, b, total chlorophyll and carotenoids), nodulation and yield parameters in Bambara. Experiments were laid out in a greenhouse at Maseno University in a completely randomized design, involving 15 factors of 5 NaCl salinity treatments: (0/control, 2, 4, 6 and 8) in dSm-1, and 3 Bambara groundnut landraces. There were 3 replications. Ten large similar sized seeds of three local landraces: red seed coat (RSC), white (WSC) and black (BSC) were each sown in a 20-liter pot containing moist loam soil with pH of 4.7. All the seeds were coated with Bradyrhizobium strain USDA 110, to enhance biological nitrogen fixation of the seedlings. Thinning was done 7 days after emergence, leaving 5 plants per pot. NaCl salinity treatments commenced 7 days after thinning. Data collection commenced on the 3rd day after initiating salinity treatments and was repeated after every 2 or 4 weeks. Plant height (PH), root length (RL), width and length of leaf were measured using a meter rule, and leaves and branches were counted. Seedling fresh and dry weights were measured using electronic weighing balance. Leaf area (LA), root to shoot ratio (R:S) and percent water content (%WC) were calculated. Gas exchange parameters were determined using portable infra-red gas analyzer. Plant mineral nutrient, proline and leaf pigment content were determined using atomic absorption spectrometry, colorimetric assay and spectrophotometer respectively. Nodules, pods and seeds were counted. Data were subjected to analysis of variance using the SAS Statistical Computer Package and separation of means using the Least Significance Difference at 5% level. Plant growth parameters, PH, LA, leaf number, shoot and root fresh weights of the three landraces significantly (p≤0.05) reduced as NaCl salinity increased. Increase in salinity had adverse effect on leaf pigments, and number of pods and seeds in all the landraces. Salinity did not influence root dry weight (RDW) of the RSC and BSC landraces. There were significant (p ≤ 0.05) interactions between NaCl salinity treatments and Bambara such that the number of branches and Na+ content increased in all the landraces. Salinity increased shoot dry weight (SDW) in salinity treatments of 2, 4 and 6 dSm-1 in RSC landrace, RDWin salinity treatments of 4, 6 and 8 dSm-1 in WSC landrace, RL in salinity treatment of 2 dSm-1in all the landraces, R: S ratio in salinity treatment of 4 dSm-1 in WSC and BSC land races, and 2, 4 and 6 dSm-1 in RSC landrace, and %WC in salinity treatment of 2 dSm-1 in WSC and 4 dSm-1in BSC landrace. Salinity also increased K+ and Ca 2+in salinity treatment of 2 dSm-1in all the landraces, and carotenoid content in salinity treatment of 2 dSm-1 in WSC landrace. Cr, gs, Tr and number of nodules significantly increased in salinity treatment of 2 dSm-1 in all the landraces however Cr, Tr and number of nodules also increased in RSC landrace atsalinity treatment of 4 dSm-1. Increased proline content in all the landraces under salinity could be an indicator of salt tolerance due to osmotic adjustment. Salinity negatively influenced morphophysiological, biochemical and yield responses of Bambara groundnut landraces. The RSC landrace responded better to NaCl salinity on average followed by BSC and least was WSC. The three landraces can do well where soil NaCl salinity reaches 4dSm-1 electrical conductivity.

Physiological, biochemical and yield responses of maize and banana plants under Calliandra calothyrsus, Sesbania sesban and Leucaena diversifolia intercropping in Vihiga county, Kenya

2022-12-19T16:11:33Z

Physiological, biochemical and yield responses of maize and banana plants under Calliandra calothyrsus, Sesbania sesban and Leucaena diversifolia intercropping in Vihiga county, Kenya SIMIYU, Wamalwa. Dennis Increasing population leads to demand for more food. Consequently, there is need to expand agricultural land, necessitating cutting down of trees. This however, leads to soil degradation. Nutrient depleted soils and poor cropping systems such as continuous cropping, have contributed to the declining yield, which is a major problem facing farmers in Western Kenya. Intercropping with agroforestry tree species can alleviate soil infertility problems and increase crop productivity through enhanced biological nitrogen fixation, growth and photosynthesis hence ensuring food security. However, intercropping with agroforestry trees may lead to competition for both above ground and below ground resources between crops and trees hence affecting growth, physiology, biochemistry and yield of the component crops. Intercropping maize and bananas with agroforestry trees such as Calliandracalothyrsus, Sesbaniasesban and Leucaenadiversifolia have the potential to improve the growth and productivity of both maize and bananas and as a result alleviate food insecurity. However, the influence of the agroforestry trees species on the growth, gas exchange, nutrient uptake and yield of the crops is yet to be established. This study sought to investigate the influence of intercropping agroforestry tree species on maize and banana height, number of green leaves, leaf area, stem diameter, transpiration rate, intercellular CO2 concentration, net photosynthesis, total chlorophyll content, uptake of N, P, K, Mg, Ca nutrients and yield. The field trials were set up at Maseno University farm in Vihiga County. Seeds of agroforestry trees were acquired from KEFRI – Muguga, planted in a seedbed and the seedlings raised in nurseries. Five months old Williams’ variety tissue banana seedlings were obtained from KALRO-Thika. Hybrid maize seeds, H513 were bought from Kenya seed company Kitale. Banana holes were dug 90cm x 90cm x 60cm deep and 20 Kg of cow dung manure + 20 Kg of top soil + 200g of NPK fertilizer added before planting the banana at a depth of 0.3m for proper anchorage. Maize were planted at 0.75 m inter row by 0.3 m spacing. Randomized Complete Block Design with 3 replications and seven treatment levels (maize without fertilizer, maize banana Calliandracalothyrsus, maize banana Leucaenadiversifolia, maize banana Sesbaniasesban, maize-banana, banana monocrop and maize with fertilizer) were used. Fifteen maize and four banana plants in each treatment were sampled in a zigzag method and tagged for data collection. Data on plant height, stem diameter, number of leaves, leaf area, and yield (grain weight, banana bunch weight, banana number of fingers and finger length) were determined. Gas exchange and chlorophyll content index parameters were measured using infrared gas analyser and SPAD meter, respectively on the 3rd fully sun exposed leaf of the tagged plants. Kjeldahl method was used to determine plant tissue N content. Ca, Mg and P contents were determined using atomic absorption spectrophotometer, while atomic emission spectrophotometer was used to determine K contents. Data collected from the study was subjected to analysis of variance using GenStat statistical package. Treatment means were also separated and compared using the least significant difference. Correlation analysis was carried out on plant height, leaf area, net photosynthetic rate, intercellular CO2 concentration and transpiration rate to determine the relationship between the parameters. There were significant increases (P ≤ 0.05) in plant height of maize, stem diameter, number of leaves, net photosynthesis, intercellular CO2 concentration, transpiration rate, chlorophyll content, nutrient uptake and yield under maize + banana + sesbaniasesban (MBS) intercropping. There were no significant differences (P ≥ 0.05) in plant height of banana plants under the agroforestry tree species intercropping. Bunch weight and finger length were significantly higher under MBS. There was significant strong positive correlations (P ≤ 0.05) between net photosynthesis and leaf area, net photosynthesis and transpiration rate, net photosynthesis and intercellular CO2 concentration, leaf area and intercellular CO2 concentration in both maize and banana plants. These agroforestry trees enhanced growth, physiological, biochemical and yield of maize and bananas. Therefore, intercropping of maize, banana and Sesbaniasesban is recommended as it increased the yields of both maize and banana through improved growth, photosynthetic rate and mineral nutrient uptake. This study allows us understand the interaction mechanisms of the crops of maize and banana crops with the three agroforestry tree species to resources. PhD Thesis

Influence of landscape heterogeneity on plasmodium infection in Nyakach sub-county, western Kenya

2022-12-19T15:52:35Z

Influence of landscape heterogeneity on plasmodium infection in Nyakach sub-county, western Kenya OTAMBO, Wilfred. Ouma Despite scaled up intervention strategies in Kenya, existing control and treatment tools have not suppressed Plasmodium infection. Persistence of malaria has been attributed to submicroscopic infection with densities too low to be detected by standard diagnostic methods. Although landscape heterogeneity may contribute to the persistence of malaria, its role in persistence of submicroscopic infections is unknown. Landscape heterogeneity is defined here as variation in topography and rainfall seasonality. The topography of Nyakach Sub-County ranges from Lake Victoria's shores to the highland plateau, with habitat stability thought to influence diverse vector ecology and Plasmodium infection. Dynamic changes in vector ecology will always pose a challenge to intervention strategies. It is unknown, however, what effect landscape heterogeneity has on malaria entomological indices in maintaining year round vector population. Variation in the ecological landscape may result in differential risk exposures to malaria contributing to variation in febrile incidences in the community. It remains to be seen whether year-round clinical malaria persistence is influenced by landscape heterogeneity. The current study investigated the influence of landscape heterogeneity on Plasmodium infection in Nyakach Sub-County, western Kenya. The specific objectives were to determine the influence of topography and seasonality on prevalence of submicroscopic malaria, entomological indices of malaria, and incidence of clinical malaria in Nyakach Sub-County, western Kenya. A cross-sectional study design was used to collect data on prevalence of submicroscopic infection and entomological survey while longitudinal study design was used to collect data on the incidences of clinical malaria in lakeshore, hillside and highland plateau throughout wet and dry seasons. 1,777 finger prick blood smears and dry blood spots on filter paper were collected for microscopic inspection and real time-PCR diagnosis of Plasmodium infection over the wet and the dry season of 2019 and 2020. Larval sampling was conducted in all larval habitats using a standard dipper and adult Anopheles mosquitoes sampled using Pyrethrum Spray Catches. Finger-prick blood samples were collected from 2,205 febrile cases and tested for malaria parasites using ultra-sensitive Alere® malaria rapid diagnostic tests. Mixed effect model, negative binomial, and binary logistic regression determined the influence of topography and seasonality on: prevalence of submicroscopic infection; Anopheles larval and adult vector densities and abundance; and incidence of clinical malaria. The prevalence of submicroscopic infection was 14.2% (253/1,777). The likelihood of submicroscopic infection was higher in the lakeshore in both the wet and dry seasons (AOR: 2.71, 95% CI=1.85-3.95; p<0.0001) and hillside (AOR: 1.74, 95% CI=1.17–2.61, p=0.007) than in the highland plateau zones. Anopheles larval densities were 3.23 (95% CI=2.50-4.18, p<0.0001) and 1.81 (95% CI=1.32-2.48, p<0.0001) times higher in the lakeshore and hillside zones, respectively, than on the highland plateau and 4.59 (95% CI=3.61-5.83, p<0.0001) higher in wet season than dry season. Adult Anopheles abundance were 1.72 (95% CI=1.02-2.90, p=0.041) times higher in the lakeshore zone than on the highland plateau, and 2.17 (95% CI=1.48-3.20, p<0.0001) times higher in wet season than in dry season. Clinical malaria incidences were 2.02 (95% CI=1.62-2.50, p<0.0001) times higher lakeshore and 1.4 (OR: 1.42, 95% CI=1.13-1.79, p=0.002) times higher in hillside zone than on the highland plateau, and 1.49 (95% CI=1.24-1.80, p<0.0001) times higher in wet season, than in dry season. Landscape heterogeneity influenced prevalence of submicroscopic infection, entomological indices of malaria, and incidence of clinical malaria. Empirical evidence on the role of landscape heterogeneity on malaria, emphasizes importance of: developing strategies for identifying malaria transmission determinants in diverse landscapes; tailoring malaria control interventions to specific landscape attributes and improve the accuracy of malaria diagnosis and treatment. PhD Thesis