Anne Muigai | Jomo Kenyatta University of Agriculture and Technology (original) (raw)
Papers by Anne Muigai
Sustainable Goat Production in Adverse Environments: Volume I
Veterinary Sciences
Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discrimi... more Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SL...
Tropical animal health and production, Jan 18, 2018
Livestock traders are a key conduit for incentives in livestock production systems. Their actions... more Livestock traders are a key conduit for incentives in livestock production systems. Their actions affect producer prices, investment decisions, and their livelihoods. However, smallholder farmers in rural communities of eastern Africa often have limited understanding of the marketing process and the interactions among market actors. This study was undertaken following the introduction of improved indigenous goat and sheep breeds in Climate Smart Villages of Nyando in western Kenya. We sought to understand the marketing of sheep and goats in five key rural markets used by the smallholder farmers of Nyando, to generate information on key market actors, their functions in the value chain, and their preferences for attributes in sheep and goats. Most traders (65%) in all the markets were men. Four different types of traders operated in the markets, producers, retailers, wholesalers, and brokers, each making a profit. Preference for selling sheep or goats and the animal attributes desire...
Virology journal, Feb 14, 2017
HIV-1 is highly variable genetically and at protein level, a property it uses to subvert antivira... more HIV-1 is highly variable genetically and at protein level, a property it uses to subvert antiviral immunity and treatment. The aim of this study was to assess if HIV subtype differences were associated with variations in glycosylation patterns and co-receptor tropism among HAART patients experiencing different virologic treatment outcomes. A total of 118 HIV env C2V3 sequence isolates generated previously from 59 Kenyan patients receiving highly active antiretroviral therapy (HAART) were examined for tropism and glycosylation patterns. For analysis of Potential N-linked glycosylation sites (PNGs), amino acid sequences generated by the NCBI's Translate tool were applied to the HIVAlign and the N-glycosite tool within the Los Alamos Database. Viral tropism was assessed using Geno2Pheno (G2P), WebPSSM and Phenoseq platforms as well as using Raymond's and Esbjörnsson's rules. Chi square test was used to determine independent variables association and ANOVA applied on scale v...
PloS one, 2017
Treatment failure is a key challenge in the management of HIV-1 infection. We conducted a mixed-m... more Treatment failure is a key challenge in the management of HIV-1 infection. We conducted a mixed-model survey of plasma nevirapine (NVP) concentrations (cNVP) and viral load in order to examine associations with treatment and adherence outcomes among Kenyan patients on prolonged antiretroviral therapy (ART). Blood plasma was collected at 1, 4 and 24 hours post-ART dosing from 58 subjects receiving NVP-containing ART and used to determine cNVP and viral load (VL). Median duration of treatment was 42 (range, 12-156) months, and 25 (43.1%) of the patients had virologic failure (VF). cNVP was significantly lower for VF than non- VF at 1hr (mean, 2,111ng/ml vs. 3,432ng/ml, p = 0.003) and at 4hr (mean 1,625ng/ml vs. 3,999ng/ml, p = 0.001) but not at 24hr post-ART dosing. Up to 53.4%, 24.1% and 22.4% of the subjects had good, fair and poor adherence respectively. cNVP levels peaked and were > = 3μg.ml at 4 hours in a majority of patients with good adherence and those without VF. Using a ...
Animal Genetics, 2016
The history of domestic sheep (Ovis aries) in Africa remains largely unknown. After being first i... more The history of domestic sheep (Ovis aries) in Africa remains largely unknown. After being first introduced from the Near East, sheep gradually spread through the African continent with pastoral societies. The eastern part of Africa was important either for the first diffusion of sheep southward or for putative secondary introductions from the Arabian Peninsula or southern Asia. We analysed mitochondrial DNA control region sequences of 91 domestic sheep from Kenya and found a high diversity of matrilines from the widespread haplogroup B, whereas only a single individual from haplogroup A was detected. Our phylogeography analyses of more than 500 available mitochondrial DNA sequences also identified ancestral haplotypes that were probably first introduced in Africa and are now widely distributed. Moreover, we found no evidence of an admixture between East and West African sheep. The presence of shared haplotypes in eastern and ancient southern African sheep suggests the possible southward movement of sheep along the eastern part of Africa. Finally, we found no evidence of an extensive introduction of sheep from southern Asia into Africa via the Indian Ocean trade. The overall findings on the phylogeography of East African domestic sheep set the grounds for understanding the origin and subsequent movements of sheep in Africa. The richness of maternal lineages in Kenyan breeds is of prime importance for future conservation and breeding programmes.
Establishment of Faidherbia albida trees on farm is often difficult despite the plant survival ad... more Establishment of Faidherbia albida trees on farm is often difficult despite the plant survival adaptive mechanisms such as drought and disease resistance. Adoption of the tree to agroforestry systems is also limited due to lack of knowledge on genetic variation of its provenances. Morphological characterization of F. albida provenances is therefore necessary to screen for natural genetic variation in seeds traits for selection of germplasm for long term agroforestry, timber production, fodder, soil fertility increment and environmental sustainability. In this study, seed traits of five provenances of F. albida: Taveta Wangingombe, Lupaso, Kuiseb and Manapools were examined. Divergent studies were analyzed based on seed morphology and geo-climatic conditions of the provenances. Seed length, width, thickness and weight were analyzed to determine the extent of phenotypic and genotypic variance and heritability. This study revealed significant differences among provenances (P≤0.05) for ...
Infectious Agents and Cancer, 2015
Background: The identification of suited early detection tests is one among the multiple requirem... more Background: The identification of suited early detection tests is one among the multiple requirements to reduce cervical cancer incidence in developing countries. Methods: We evaluated p16 INK4a /Ki-67 dual-stain cytology in a screening population in Thika district, Kenya and compared it to high-risk human papillomavirus (HR-HPV) DNA testing and visual inspection by acetic acid (VIA) and Lugol's iodine (VILI). Results: Valid results for all tests could be obtained in 477 women. 20.9 % (100/477) were tested positive for HR-HPV DNA, 3.1 % (15/477) had positive VIA/VILI and 8.2 % (39/477) positive p16 INK4a /Ki-67 cytology. Of 22 women that showed up for colposcopy and biopsy, 6 women were diagnosed with CIN3 and two with CIN2. All women with CIN2/3 were negative in VIA/VILI screening and positive by HR-HPV DNA testing. But HPV was also positive in 91.7 % (11/12) of women with normal histology. p16 INK4a /Ki-67 cytology was positive in all 6 women with CIN3, in one of the two CIN2 and in only 8.3 % (1/12) of women with normal histology. Conclusions: p16 INK4a /Ki-67 cytology is an interesting test for further studies in developing countries, since our findings point to a lower fraction of false positive test results using p16 INK4a /Ki-67 cytology compared to HPV DNA testing in a Kenyan screening population. VIA/VILI missed all histology-proven CIN2/3.
East African medical journal, 2011
To evaluate the extent of HIV-1 drug resistance among drug naive Kenyan individuals. Cross-sectio... more To evaluate the extent of HIV-1 drug resistance among drug naive Kenyan individuals. Cross-sectional study. Kenya Medical Research Institute HIV laboratory Nairobi, Kenya. A total of seventy eight HIV-1 positive drug naive subjects randomised from five Kenyan provincial hospitals between April and June 2004. A major non-nucleoside reverse transcriptase (NNRTI) an associated mutation was found in one patient (1.3%). NNRTI associated resistance mutations were present at amino acid codon sites G98A (2.56%); K103E (1.3%) and L100F (3.57%) prevalences. Baseline resistance may compromise the response to standard NNRTI-based first-line ART in 1.3 % of the study subjects. This indicates in general, that drug resistance among HIV-1 positive drug naive individual is at low thresholds (1.3%) but the problem could be more serious than reported here. Continuous resistance monitoring is therefore warranted to maintain individual and population-level ART effectiveness.
PLOS Neglected Tropical Diseases, 2015
Background Nontyphoidal Salmonellae (NTS) cause a large burden of invasive and gastrointestinal d... more Background Nontyphoidal Salmonellae (NTS) cause a large burden of invasive and gastrointestinal disease among young children in sub-Saharan Africa. No vaccine is currently available. Previous reports indicate the importance of the O-antigen of Salmonella lipopolysaccharide for virulence and resistance to antibody-mediated killing. We hypothesised that isolates with more O-antigen have increased resistance to antibody-mediated killing and are more likely to be invasive than gastrointestinal.
AIDS Research and Human Retroviruses, 2014
African Journal of Laboratory Medicine, 2014
Background: Since 1971, Kenya has had repeated cholera outbreaks. However, the cause of seasonal ... more Background: Since 1971, Kenya has had repeated cholera outbreaks. However, the cause of seasonal epidemics of cholera is not fully understood and neither are the factors that drive epidemics, both in Kenya and globally.Objectives: The objectives of the study were to determine the environmental reservoirs of V. cholerae during an interepidemic period in Kenya and to characterise their virulence factors.Methods: One hundred (50 clinical, 50 environmental) samples were tested for V. cholerae isolates using both simplex and multiplex polymerase chain reaction.Results: Both sediments and algae from fishing and landing bays yielded isolates of V. cholerae. Clinical strains were characterised along with the environmental strains for comparison. All clinical strains harboured ctxA, tcpA (El Tor), ompU, zot, ace, toxR, hylA (El Tor) and tcpI genes. Prevalence for virulence genes in environmental strains was hylA (El Tor) (10%), toxR (24%), zot (22%), ctxA (12%),tcpI (8%), hylA (26%) and tcpA...
African Journal of Biotechnology, 2010
Finding genes controlling quantitative traits will aid molecular breeding for crops and livestock... more Finding genes controlling quantitative traits will aid molecular breeding for crops and livestock with superior yields, growth rates, and evolutionary potential. Such genes can be located using the candidate gene approach, genome wide scans, or by within family mapping. Linkage disequilibrium (LD) or association mapping, is a candidate gene approach that relies on detecting a statistical association between the desired quantitative trait and a molecular marker allele. This approach is emerging as a leading tool for precise estimation of QTL positions, because it offers several advantages over family-based mapping: LD mapping detects associations with greater resolution, the associations detected are relevant population wide, and in plants, the use of natural populations would circumvent the need to raise large controlled crosses. However, LD approach is facing obstacles, with well over 60% of studies reporting associations in the medical genetics disapproved in subsequent tests. A large proportion of these false associations (or lack of it) result from population stratification, while the rest may be caused by other demographic and evolutionary processes that create a statistical association between a marker allele and the trait, such as bottlenecks, natural selection, hybridization and genetic drift. The problem is expected to escalate in plants, owing to the complex population structures. Regardless of the many recent methods that purport to take into account population stratification during association tests, we discuss the reasons why in plants, a priori knowledge of population structures is essential in any robust association analysis.
… JOURNAL OF ANIMAL …, 2006
... 7 : 943 - 952 July 2006 www.ajas.info The Genetic Diversity of Trans-caucasian Native Sheep B... more ... 7 : 943 - 952 July 2006 www.ajas.info The Genetic Diversity of Trans-caucasian Native Sheep Breeds Jibril Hirbo1, Anne Muigai1, 2, AN Naqvi*, ED Rege1 and Olivier Hanotte1 Department of Biological Sciences, Karakuram International University, Northern Areas, Gilgit ...
Letters in Applied Microbiology, 2003
![Research paper thumbnail of Genetic diversity in pigeonpea [Cajanus cajan (L.) Millsp.] landraces as revealed by simple sequence repeat markers](https://attachments.academia-assets.com/75653232/thumbnails/1.jpg)
](Genetic relationships among 88 pigeonpea accessions from a presumed centre of origin and diversit... more Genetic relationships among 88 pigeonpea accessions from a presumed centre of origin and diversity, India and a presumed secondary centre of diversity in East Africa were evaluated using six microsatellite markers. Forty-seven (47) alleles were detected in the populations studied, with a mean of eight alleles per locus. Populations were defined by region (India and East Africa) and sub-populations by country in the case of East Africa and State in the case of India. Substantial differentiation among regions was evident from Roger's modified distance and Wright's F statistic. Greatest genetic diversity in terms of number of alleles, number of rare alleles and Nei's unbiased estimate of gene diversity (H) was found in India as opposed to East Africa. This supports the hypothesis that India is the centre of diversity and East Africa is a secondary centre of diversity. Within East Africa, germplasm from Tanzania had the highest diversity according to Nei's unbiased estimate of gene diversity, followed by Kenya and Uganda. Germplasm from Kenya and Tanzania were more closely related than that of Uganda according to Roger's modified distance. Within India, results did not indicate a clear centre of diversity. Values of genetic distance indicated that genetic relationships followed geographical proximity.
African Archaeological Review, 2013
Indigenous African sheep genetic resources have been classified into two main groups, fat-tailed ... more Indigenous African sheep genetic resources have been classified into two main groups, fat-tailed and thin-tailed sheep. The fat-tailed sheep are the most widely distributed, being found in a large part of North Africa (from Egypt to Algeria) and in Eastern and Southern Africa (from Eritrea to South Africa). The thin-tailed sheep are present mainly in Morocco, Sudan and in West Africa. African sheep were domesticated outside Africa. They share a common ancestry with European and Asian sheep. Archaeological information supports separate introductions and dispersion histories for the African thin-tailed and fat-tailed sheep. The first sheep entered Africa via the Isthmus of Suez and/or the southern Sinai Peninsula, between 7500 and 7000 BP. They were likely of the thin-tailed type. Fat-tailed sheep entered Africa through its northeastern part and the Horn of Africa. Mitochondrial DNA analysis supports a common maternal ancestral origin for all African sheep, while autosomal and Y chromosome DNA analysis indicates a distinct genetic history for African thin-tailed and sub-Saharan fat-tailed sheep. The main ancestral population of southern African fat-tailed sheep likely originated in East Africa. Further work is needed to assess the possible dispersion of sheep from western Africa to the southern African regions.RésuméLes ressources génétiques africaines du mouton sont classifiées en deux groupes principaux, les moutons à queue grasse et les moutons à queue fine. Les moutons à queue grasse ont la distribution géographique la plus étendue, se rencontrant dans une grande partie de l’Afrique du Nord (depuis l’Égypte jusqu’à l’Algérie), et dans les régions les plus à l’est et au sud de l’Afrique (de l’Érythrée à l’Afrique du Sud). Les moutons à queue fine sont présents principalement au Maroc, au Soudan et en Afrique de l’Ouest. Les moutons africaines ont été domestiqués en dehors de l’Afrique. Ils partagent un ancêtre commun avec les moutons asiatiques et européens. Les informations archéologiques supportent une introduction distincte et une histoire de dispersion en partie séparée pour les moutons à queue grasse et à queue fine sur le continent. Les premiers moutons sont arrivés en Afrique par l’Isthme de Suez et/ou le sud de la Péninsule du Sinaï, entre 7500 et 7000 BP. Ils étaient probablement du type mouton à queue fine. Les moutons à queue grasse entrèrent en Afrique par le nord-est du continent et la corne de l’Afrique. Les résultats de l’ADN mitochondrial supportent une origine ancestrale maternelle commune pour tous les moutons africaines, tandis que les données des autosomes et du chromosome Y indiquent une histoire génétique distincte pour les moutons à queue grasse et à queue fine. La population ancestrale principale des moutons à queue grasse du sud du continent est probablement originaire de l’est de l’Afrique. Des études supplémentaires sont nécessaires pour attester la dispersion possible du mouton de l’Afrique de l’Ouest jusqu’au sud du continent.
European Journal of Clinical Microbiology & Infectious Diseases, Apr 1, 1998
Shigellosis in children is a major public health problem in developing countries. The disease is ... more Shigellosis in children is a major public health problem in developing countries. The disease is endemic throughout the developing world, where it causes major epidemics from time to time. The World Health Organisation (WHO) has estimated that 3.5 million children die from diarrhoeal diseases each year, 600000 of them from shigellosis alone [1]. Although early antibiotic treatment of dysentery has been recommended
African Journal of …, 2010
Microorganisms in the intestinal tracts of termites play a crucial role in the nutritional physio... more Microorganisms in the intestinal tracts of termites play a crucial role in the nutritional physiology of termites. The bacterial diversity in the fungus-cultivating Macrotermes michaelseni was examined using both molecular and culture dependent methods. Total DNA was extracted from the gut of the termite and 16S rRNA genes were amplified using bacterial specific primers. Representatives from forty-one (41) RFLP patterns from a total of one hundred and two (102) clones were sequenced. Most of the clones were affiliated with 3 main groups of the domain Bacteria: Cytophaga-Flexibacter-Bacteriodes (73), Proteobacteria (13), and the low G+C content Gram-positive bacteria (9). Two RFLPs related to planctomycetes, but deeper branching than known members of the phylum, were detected. In addition, 1 and 2 RFLPs represented the spirochetes and TM7-OP11 groups, respectively. In studies using culture dependent techniques, most of the isolates obtained belonged to the Gram-positive bacteria with a high G+C content. However, only one of the clones represented Gram-positive bacteria with High G+C content. These results show a high bacterial diversity in the intestinal microbiota of M. michaelseni, which continues to escape cultivation. As is the case in other termites many of the clones represent previously uncultured bacteria. The fact that most of the clones clustered with clones from Macrotermes gilvus provides further support for the hypothesis that microorganisms in intestinal tracts of termites have co-evolved with their hosts.
Microbiology Research Journal International
Aims: To investigate carriage and contamination rates of chicken broiler meat, the factors that a... more Aims: To investigate carriage and contamination rates of chicken broiler meat, the factors that are associated with Campylobacter spp. colonization and its phenotypic and genotypic antimicrobial resistance from Thika small-scale poultry farms. Study Design: The study design was cross-sectional and laboratory based, it employed simple random sampling across 18 small-scale farms. Site and Duration of Study: The study was conducted between August and December 2017 at Thika sub-county, a town located 42 Km North East of Nairobi. Methodology: One hundred and eighty five cloaca swab samples from live broilers and 158 neck swab samples from broiler carcasses were collected. Isolates were obtained by plating method using mCCDA, conventional methods and duplex PCR were used for the isolation and identification of Campylobacter species. Results: Carriage prevalence was at 15.67%, significantly (P = .000) lower than contamination prevalence detected at 30.37%. While the overall Campylobacter s...
Sustainable Goat Production in Adverse Environments: Volume I
Veterinary Sciences
Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discrimi... more Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SL...
Tropical animal health and production, Jan 18, 2018
Livestock traders are a key conduit for incentives in livestock production systems. Their actions... more Livestock traders are a key conduit for incentives in livestock production systems. Their actions affect producer prices, investment decisions, and their livelihoods. However, smallholder farmers in rural communities of eastern Africa often have limited understanding of the marketing process and the interactions among market actors. This study was undertaken following the introduction of improved indigenous goat and sheep breeds in Climate Smart Villages of Nyando in western Kenya. We sought to understand the marketing of sheep and goats in five key rural markets used by the smallholder farmers of Nyando, to generate information on key market actors, their functions in the value chain, and their preferences for attributes in sheep and goats. Most traders (65%) in all the markets were men. Four different types of traders operated in the markets, producers, retailers, wholesalers, and brokers, each making a profit. Preference for selling sheep or goats and the animal attributes desire...
Virology journal, Feb 14, 2017
HIV-1 is highly variable genetically and at protein level, a property it uses to subvert antivira... more HIV-1 is highly variable genetically and at protein level, a property it uses to subvert antiviral immunity and treatment. The aim of this study was to assess if HIV subtype differences were associated with variations in glycosylation patterns and co-receptor tropism among HAART patients experiencing different virologic treatment outcomes. A total of 118 HIV env C2V3 sequence isolates generated previously from 59 Kenyan patients receiving highly active antiretroviral therapy (HAART) were examined for tropism and glycosylation patterns. For analysis of Potential N-linked glycosylation sites (PNGs), amino acid sequences generated by the NCBI's Translate tool were applied to the HIVAlign and the N-glycosite tool within the Los Alamos Database. Viral tropism was assessed using Geno2Pheno (G2P), WebPSSM and Phenoseq platforms as well as using Raymond's and Esbjörnsson's rules. Chi square test was used to determine independent variables association and ANOVA applied on scale v...
PloS one, 2017
Treatment failure is a key challenge in the management of HIV-1 infection. We conducted a mixed-m... more Treatment failure is a key challenge in the management of HIV-1 infection. We conducted a mixed-model survey of plasma nevirapine (NVP) concentrations (cNVP) and viral load in order to examine associations with treatment and adherence outcomes among Kenyan patients on prolonged antiretroviral therapy (ART). Blood plasma was collected at 1, 4 and 24 hours post-ART dosing from 58 subjects receiving NVP-containing ART and used to determine cNVP and viral load (VL). Median duration of treatment was 42 (range, 12-156) months, and 25 (43.1%) of the patients had virologic failure (VF). cNVP was significantly lower for VF than non- VF at 1hr (mean, 2,111ng/ml vs. 3,432ng/ml, p = 0.003) and at 4hr (mean 1,625ng/ml vs. 3,999ng/ml, p = 0.001) but not at 24hr post-ART dosing. Up to 53.4%, 24.1% and 22.4% of the subjects had good, fair and poor adherence respectively. cNVP levels peaked and were > = 3μg.ml at 4 hours in a majority of patients with good adherence and those without VF. Using a ...
Animal Genetics, 2016
The history of domestic sheep (Ovis aries) in Africa remains largely unknown. After being first i... more The history of domestic sheep (Ovis aries) in Africa remains largely unknown. After being first introduced from the Near East, sheep gradually spread through the African continent with pastoral societies. The eastern part of Africa was important either for the first diffusion of sheep southward or for putative secondary introductions from the Arabian Peninsula or southern Asia. We analysed mitochondrial DNA control region sequences of 91 domestic sheep from Kenya and found a high diversity of matrilines from the widespread haplogroup B, whereas only a single individual from haplogroup A was detected. Our phylogeography analyses of more than 500 available mitochondrial DNA sequences also identified ancestral haplotypes that were probably first introduced in Africa and are now widely distributed. Moreover, we found no evidence of an admixture between East and West African sheep. The presence of shared haplotypes in eastern and ancient southern African sheep suggests the possible southward movement of sheep along the eastern part of Africa. Finally, we found no evidence of an extensive introduction of sheep from southern Asia into Africa via the Indian Ocean trade. The overall findings on the phylogeography of East African domestic sheep set the grounds for understanding the origin and subsequent movements of sheep in Africa. The richness of maternal lineages in Kenyan breeds is of prime importance for future conservation and breeding programmes.
Establishment of Faidherbia albida trees on farm is often difficult despite the plant survival ad... more Establishment of Faidherbia albida trees on farm is often difficult despite the plant survival adaptive mechanisms such as drought and disease resistance. Adoption of the tree to agroforestry systems is also limited due to lack of knowledge on genetic variation of its provenances. Morphological characterization of F. albida provenances is therefore necessary to screen for natural genetic variation in seeds traits for selection of germplasm for long term agroforestry, timber production, fodder, soil fertility increment and environmental sustainability. In this study, seed traits of five provenances of F. albida: Taveta Wangingombe, Lupaso, Kuiseb and Manapools were examined. Divergent studies were analyzed based on seed morphology and geo-climatic conditions of the provenances. Seed length, width, thickness and weight were analyzed to determine the extent of phenotypic and genotypic variance and heritability. This study revealed significant differences among provenances (P≤0.05) for ...
Infectious Agents and Cancer, 2015
Background: The identification of suited early detection tests is one among the multiple requirem... more Background: The identification of suited early detection tests is one among the multiple requirements to reduce cervical cancer incidence in developing countries. Methods: We evaluated p16 INK4a /Ki-67 dual-stain cytology in a screening population in Thika district, Kenya and compared it to high-risk human papillomavirus (HR-HPV) DNA testing and visual inspection by acetic acid (VIA) and Lugol's iodine (VILI). Results: Valid results for all tests could be obtained in 477 women. 20.9 % (100/477) were tested positive for HR-HPV DNA, 3.1 % (15/477) had positive VIA/VILI and 8.2 % (39/477) positive p16 INK4a /Ki-67 cytology. Of 22 women that showed up for colposcopy and biopsy, 6 women were diagnosed with CIN3 and two with CIN2. All women with CIN2/3 were negative in VIA/VILI screening and positive by HR-HPV DNA testing. But HPV was also positive in 91.7 % (11/12) of women with normal histology. p16 INK4a /Ki-67 cytology was positive in all 6 women with CIN3, in one of the two CIN2 and in only 8.3 % (1/12) of women with normal histology. Conclusions: p16 INK4a /Ki-67 cytology is an interesting test for further studies in developing countries, since our findings point to a lower fraction of false positive test results using p16 INK4a /Ki-67 cytology compared to HPV DNA testing in a Kenyan screening population. VIA/VILI missed all histology-proven CIN2/3.
East African medical journal, 2011
To evaluate the extent of HIV-1 drug resistance among drug naive Kenyan individuals. Cross-sectio... more To evaluate the extent of HIV-1 drug resistance among drug naive Kenyan individuals. Cross-sectional study. Kenya Medical Research Institute HIV laboratory Nairobi, Kenya. A total of seventy eight HIV-1 positive drug naive subjects randomised from five Kenyan provincial hospitals between April and June 2004. A major non-nucleoside reverse transcriptase (NNRTI) an associated mutation was found in one patient (1.3%). NNRTI associated resistance mutations were present at amino acid codon sites G98A (2.56%); K103E (1.3%) and L100F (3.57%) prevalences. Baseline resistance may compromise the response to standard NNRTI-based first-line ART in 1.3 % of the study subjects. This indicates in general, that drug resistance among HIV-1 positive drug naive individual is at low thresholds (1.3%) but the problem could be more serious than reported here. Continuous resistance monitoring is therefore warranted to maintain individual and population-level ART effectiveness.
PLOS Neglected Tropical Diseases, 2015
Background Nontyphoidal Salmonellae (NTS) cause a large burden of invasive and gastrointestinal d... more Background Nontyphoidal Salmonellae (NTS) cause a large burden of invasive and gastrointestinal disease among young children in sub-Saharan Africa. No vaccine is currently available. Previous reports indicate the importance of the O-antigen of Salmonella lipopolysaccharide for virulence and resistance to antibody-mediated killing. We hypothesised that isolates with more O-antigen have increased resistance to antibody-mediated killing and are more likely to be invasive than gastrointestinal.
AIDS Research and Human Retroviruses, 2014
African Journal of Laboratory Medicine, 2014
Background: Since 1971, Kenya has had repeated cholera outbreaks. However, the cause of seasonal ... more Background: Since 1971, Kenya has had repeated cholera outbreaks. However, the cause of seasonal epidemics of cholera is not fully understood and neither are the factors that drive epidemics, both in Kenya and globally.Objectives: The objectives of the study were to determine the environmental reservoirs of V. cholerae during an interepidemic period in Kenya and to characterise their virulence factors.Methods: One hundred (50 clinical, 50 environmental) samples were tested for V. cholerae isolates using both simplex and multiplex polymerase chain reaction.Results: Both sediments and algae from fishing and landing bays yielded isolates of V. cholerae. Clinical strains were characterised along with the environmental strains for comparison. All clinical strains harboured ctxA, tcpA (El Tor), ompU, zot, ace, toxR, hylA (El Tor) and tcpI genes. Prevalence for virulence genes in environmental strains was hylA (El Tor) (10%), toxR (24%), zot (22%), ctxA (12%),tcpI (8%), hylA (26%) and tcpA...
African Journal of Biotechnology, 2010
Finding genes controlling quantitative traits will aid molecular breeding for crops and livestock... more Finding genes controlling quantitative traits will aid molecular breeding for crops and livestock with superior yields, growth rates, and evolutionary potential. Such genes can be located using the candidate gene approach, genome wide scans, or by within family mapping. Linkage disequilibrium (LD) or association mapping, is a candidate gene approach that relies on detecting a statistical association between the desired quantitative trait and a molecular marker allele. This approach is emerging as a leading tool for precise estimation of QTL positions, because it offers several advantages over family-based mapping: LD mapping detects associations with greater resolution, the associations detected are relevant population wide, and in plants, the use of natural populations would circumvent the need to raise large controlled crosses. However, LD approach is facing obstacles, with well over 60% of studies reporting associations in the medical genetics disapproved in subsequent tests. A large proportion of these false associations (or lack of it) result from population stratification, while the rest may be caused by other demographic and evolutionary processes that create a statistical association between a marker allele and the trait, such as bottlenecks, natural selection, hybridization and genetic drift. The problem is expected to escalate in plants, owing to the complex population structures. Regardless of the many recent methods that purport to take into account population stratification during association tests, we discuss the reasons why in plants, a priori knowledge of population structures is essential in any robust association analysis.
… JOURNAL OF ANIMAL …, 2006
... 7 : 943 - 952 July 2006 www.ajas.info The Genetic Diversity of Trans-caucasian Native Sheep B... more ... 7 : 943 - 952 July 2006 www.ajas.info The Genetic Diversity of Trans-caucasian Native Sheep Breeds Jibril Hirbo1, Anne Muigai1, 2, AN Naqvi*, ED Rege1 and Olivier Hanotte1 Department of Biological Sciences, Karakuram International University, Northern Areas, Gilgit ...
Letters in Applied Microbiology, 2003
Genetic relationships among 88 pigeonpea accessions from a presumed centre of origin and diversit... more Genetic relationships among 88 pigeonpea accessions from a presumed centre of origin and diversity, India and a presumed secondary centre of diversity in East Africa were evaluated using six microsatellite markers. Forty-seven (47) alleles were detected in the populations studied, with a mean of eight alleles per locus. Populations were defined by region (India and East Africa) and sub-populations by country in the case of East Africa and State in the case of India. Substantial differentiation among regions was evident from Roger's modified distance and Wright's F statistic. Greatest genetic diversity in terms of number of alleles, number of rare alleles and Nei's unbiased estimate of gene diversity (H) was found in India as opposed to East Africa. This supports the hypothesis that India is the centre of diversity and East Africa is a secondary centre of diversity. Within East Africa, germplasm from Tanzania had the highest diversity according to Nei's unbiased estimate of gene diversity, followed by Kenya and Uganda. Germplasm from Kenya and Tanzania were more closely related than that of Uganda according to Roger's modified distance. Within India, results did not indicate a clear centre of diversity. Values of genetic distance indicated that genetic relationships followed geographical proximity.
African Archaeological Review, 2013
Indigenous African sheep genetic resources have been classified into two main groups, fat-tailed ... more Indigenous African sheep genetic resources have been classified into two main groups, fat-tailed and thin-tailed sheep. The fat-tailed sheep are the most widely distributed, being found in a large part of North Africa (from Egypt to Algeria) and in Eastern and Southern Africa (from Eritrea to South Africa). The thin-tailed sheep are present mainly in Morocco, Sudan and in West Africa. African sheep were domesticated outside Africa. They share a common ancestry with European and Asian sheep. Archaeological information supports separate introductions and dispersion histories for the African thin-tailed and fat-tailed sheep. The first sheep entered Africa via the Isthmus of Suez and/or the southern Sinai Peninsula, between 7500 and 7000 BP. They were likely of the thin-tailed type. Fat-tailed sheep entered Africa through its northeastern part and the Horn of Africa. Mitochondrial DNA analysis supports a common maternal ancestral origin for all African sheep, while autosomal and Y chromosome DNA analysis indicates a distinct genetic history for African thin-tailed and sub-Saharan fat-tailed sheep. The main ancestral population of southern African fat-tailed sheep likely originated in East Africa. Further work is needed to assess the possible dispersion of sheep from western Africa to the southern African regions.RésuméLes ressources génétiques africaines du mouton sont classifiées en deux groupes principaux, les moutons à queue grasse et les moutons à queue fine. Les moutons à queue grasse ont la distribution géographique la plus étendue, se rencontrant dans une grande partie de l’Afrique du Nord (depuis l’Égypte jusqu’à l’Algérie), et dans les régions les plus à l’est et au sud de l’Afrique (de l’Érythrée à l’Afrique du Sud). Les moutons à queue fine sont présents principalement au Maroc, au Soudan et en Afrique de l’Ouest. Les moutons africaines ont été domestiqués en dehors de l’Afrique. Ils partagent un ancêtre commun avec les moutons asiatiques et européens. Les informations archéologiques supportent une introduction distincte et une histoire de dispersion en partie séparée pour les moutons à queue grasse et à queue fine sur le continent. Les premiers moutons sont arrivés en Afrique par l’Isthme de Suez et/ou le sud de la Péninsule du Sinaï, entre 7500 et 7000 BP. Ils étaient probablement du type mouton à queue fine. Les moutons à queue grasse entrèrent en Afrique par le nord-est du continent et la corne de l’Afrique. Les résultats de l’ADN mitochondrial supportent une origine ancestrale maternelle commune pour tous les moutons africaines, tandis que les données des autosomes et du chromosome Y indiquent une histoire génétique distincte pour les moutons à queue grasse et à queue fine. La population ancestrale principale des moutons à queue grasse du sud du continent est probablement originaire de l’est de l’Afrique. Des études supplémentaires sont nécessaires pour attester la dispersion possible du mouton de l’Afrique de l’Ouest jusqu’au sud du continent.
European Journal of Clinical Microbiology & Infectious Diseases, Apr 1, 1998
Shigellosis in children is a major public health problem in developing countries. The disease is ... more Shigellosis in children is a major public health problem in developing countries. The disease is endemic throughout the developing world, where it causes major epidemics from time to time. The World Health Organisation (WHO) has estimated that 3.5 million children die from diarrhoeal diseases each year, 600000 of them from shigellosis alone [1]. Although early antibiotic treatment of dysentery has been recommended
African Journal of …, 2010
Microorganisms in the intestinal tracts of termites play a crucial role in the nutritional physio... more Microorganisms in the intestinal tracts of termites play a crucial role in the nutritional physiology of termites. The bacterial diversity in the fungus-cultivating Macrotermes michaelseni was examined using both molecular and culture dependent methods. Total DNA was extracted from the gut of the termite and 16S rRNA genes were amplified using bacterial specific primers. Representatives from forty-one (41) RFLP patterns from a total of one hundred and two (102) clones were sequenced. Most of the clones were affiliated with 3 main groups of the domain Bacteria: Cytophaga-Flexibacter-Bacteriodes (73), Proteobacteria (13), and the low G+C content Gram-positive bacteria (9). Two RFLPs related to planctomycetes, but deeper branching than known members of the phylum, were detected. In addition, 1 and 2 RFLPs represented the spirochetes and TM7-OP11 groups, respectively. In studies using culture dependent techniques, most of the isolates obtained belonged to the Gram-positive bacteria with a high G+C content. However, only one of the clones represented Gram-positive bacteria with High G+C content. These results show a high bacterial diversity in the intestinal microbiota of M. michaelseni, which continues to escape cultivation. As is the case in other termites many of the clones represent previously uncultured bacteria. The fact that most of the clones clustered with clones from Macrotermes gilvus provides further support for the hypothesis that microorganisms in intestinal tracts of termites have co-evolved with their hosts.
Microbiology Research Journal International
Aims: To investigate carriage and contamination rates of chicken broiler meat, the factors that a... more Aims: To investigate carriage and contamination rates of chicken broiler meat, the factors that are associated with Campylobacter spp. colonization and its phenotypic and genotypic antimicrobial resistance from Thika small-scale poultry farms. Study Design: The study design was cross-sectional and laboratory based, it employed simple random sampling across 18 small-scale farms. Site and Duration of Study: The study was conducted between August and December 2017 at Thika sub-county, a town located 42 Km North East of Nairobi. Methodology: One hundred and eighty five cloaca swab samples from live broilers and 158 neck swab samples from broiler carcasses were collected. Isolates were obtained by plating method using mCCDA, conventional methods and duplex PCR were used for the isolation and identification of Campylobacter species. Results: Carriage prevalence was at 15.67%, significantly (P = .000) lower than contamination prevalence detected at 30.37%. While the overall Campylobacter s...
by Marta Mirazon Lahr, Frances Rivera, Ronika K. Power, Federica Crivellaro, José-Manuel Maíllo-Fernández, Christopher Kiarie, Julie Lawrence, E. Mbua, Anne Muigai, Denis Misiko Mukhongo, Ann Van Baelen, Alex Wilshaw, and Robert Foley
The nature of inter-group relations among prehistoric hunter-gatherers remains disputed, with arg... more The nature of inter-group relations among prehistoric hunter-gatherers remains disputed, with arguments in favour and against the existence of warfare before the development of sedentary societies. Here we report on a case of inter-group violence towards a group of hunter-gatherers from Nataruk, west of Lake Turkana, which during the late Pleistocene/early Holocene period extended about 30 km beyond its present-day shore. Ten of the twelve articulated skeletons found at Nataruk show evidence of having died violently at the edge of a lagoon, into which some of the bodies fell. The remains from Nataruk are unique, preserved by the particular conditions of the lagoon with no evidence of deliberate burial. They offer a rare glimpse into the life and death of past foraging people, and evidence that warfare was part of the repertoire of inter-group
relations among prehistoric hunter-gatherers.