Browsing by Author "Okello, John B. A."
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Item Ethno-Nomenclature of the Shea Tree (Vitellaria Paradoxa C.F. Gaertn.) and Its Products in the Shea Zones of Uganda(Global J Res. Med. Plants & Indigen. Med., 2012) Omujal, Francis; Agea, Jacob G.; Mulugo, Lucy W.; Vuzi, Peter C.; Namutebi, Agnes; Okello, John B. A.; Okonye, Godman; Nyanzi, Steven A.; Okullo, John B. L.A cross sectional survey was conducted in north-eastern Shea zones of Uganda to assess ethnonomenclature of the Shea tree (Vitellaria paradoxa C.F.Gaertn.) and products. The largely qualitative study that involved a total of six different ethnic groups was analyzed using emerging themes and patterns. Findings collected through individual and group interviews revealed variations and similarities in the ethno names. There was a wide variation in ethno-names of the Shea tree/products across and within the ethnic groups. The variations are explained by differences in languages spoken as well as dialects across the ethnic groups. It could also be a reflection of extensive range of occurrence of the Shea trees. Some ethnic groups e.g. Acholi and Langi; Madi and Lugbara had some similarities in the ethno-names. The similarity seemed to be explained by shared historical background and frequent interactions. Migration, intermarriages and frequent trade interactions had a contribution to the similarities between the ethnic groups. This study, however, did not investigate into the meanings of the ethno names, an area that should be taken up for further research.Item Population Genetic Structure of Savannah Elephants in Kenya: Conservation and Management Implications(Journal of heredity, 2008) Okello, John B. A.; Masembe, Charles; Rasmussen, Henrik B.; Wittemyer, George; Omondi, Patrick; Kahindi, Onesmas; Muwanika, Vincent B.; Arctander, Peter; Douglas-Hamilton, Iain; Nyakaana, Silvester; Siegismund, Hans R.We investigated population genetic structure and regional differentiation among African savannah elephants in Kenya using mitochondrial and microsatellite markers. We observed mitochondrial DNA (mtDNA) nucleotide diversity of 1.68% and microsatellite variation in terms of average number of alleles, expected and observed heterozygosities in the total study population of 10.20, 0.75, and 0.69, respectively. Hierarchical analysis of molecular variance of mtDNA variation revealed significant differentiation among the 3 geographical regions studied (FCT 5 0.264; P , 0.05) and a relatively lower differentiation among populations within regions (FSC 5 0.218; P , 0.0001). Microsatellite variation significantly differentiated among populations within regions (FSC 5 0.019; P , 0.0001) but not at the regional levels (FCT 5 0.000; P . 0.500). We attribute the high differentiation at the mitochondrial genome to the matrilineal social structure of elephant populations, female natal philopatry, and probably ancient vicariance. Lack of significant regional differentiation at the nuclear loci vis-a-vis strong differences at mtDNA loci between regions is likely the effect of subsequent homogenization through male-mediated gene flow. Our results depicting 3 broad regional mtDNA groups and the observed population genetic differentiation as well as connectivity patterns should be incorporated in the planning of future management activities such as translocations.Item Quantitative Assessment of the Sensitivity of Various Commercial Reverse Transcriptases Based on Armored HIV RNA(PLoS ONE, 2010) Okello, John B. A.; Rodriguez, Linda; Poinar, Debi; Bos, Kirsten; Okwi, Andrew L.; Bimenya, Gabriel S.; Sewankambo, Nelson K.; Henry, Kenneth R.; Kuch, Melanie; Poinar, Hendrik N.The in-vitro reverse transcription of RNA to its complementary DNA, catalyzed by the enzyme reverse transcriptase, is the most fundamental step in the quantitative RNA detection in genomic studies. As such, this step should be as analytically sensitive, efficient and reproducible as possible, especially when dealing with degraded or low copy RNA samples. While there are many reverse transcriptases in the market, all claiming to be highly sensitive, there is need for a systematic independent comparison of their applicability in quantification of rare RNA transcripts or low copy RNA, such as those obtained from archival tissues. Methodology/Principal Findings: We performed RT-qPCR to assess the sensitivity and reproducibility of 11 commercially available reverse transcriptases in cDNA synthesis from low copy number RNA levels. As target RNA, we used a serially known number of Armored HIV RNA molecules, and observed that 9 enzymes we tested were consistently sensitive to ,1,000 copies, seven of which were sensitive to ,100 copies, while only 5 were sensitive to ,10 RNA template copies across all replicates tested. Despite their demonstrated sensitivity, these five best performing enzymes (Accuscript, HIV-RT, M-MLV, Superscript III and Thermoscript) showed considerable variation in their reproducibility as well as their overall amplification efficiency. Accuscript and Superscript III were the most sensitive and consistent within runs, with Accuscript and Superscript II ranking as the most reproducible enzymes between assays. Conclusions/Significance: We therefore recommend the use of Accuscript or Superscript III when dealing with low copy number RNA levels, and suggest purification of the RT reactions prior to downstream applications (eg qPCR) to augment detection. Although the results presented in this study were based on a viral RNA surrogate, and applied to nucleic acid lysates derived from archival formalin-fixed paraffin embedded tissue, their relative performance on RNA obtained from other tissue types may vary, and needs future evaluation.Item Six new polymorphic microsatellite loci isolated and characterized from the African savannah elephant genome(Molecular Ecology Notes, 2005) Nyakaana, Silvester; Okello, John B. A.; Muwanika, Vincent B.; Siegismund, Hans R.The African savannah elephant (Loxodonta africana) is a ‘keystone’ species that plays a vital role in regulating the dynamics of both plant and animal communities and yet it is endangered and its numbers have been reduced to approximately 500 000 across their entire continental range. Molecular genetic markers are important tools for providing genetic information useful in formulating effective management and conservation strategies for the surviving elephant populations. We describe the isolation and characterization of six new polymorphic microsatellite markers in the African savannah elephant and demonstrate that these loci can be PCR (polymerase chain reaction)-multiplexed, a desirable attribute that saves costs in large-scale microsatellite screening.