Bio

Brief biography

Joel W. Ochieng, PhD, is a Senior Research Fellow and Leader of Agricultural Biotechnology the University of Nairobi. He completed his PhD in Plant Genetics under frontier scientist Prof Robert J. Henry (Queensland Professor of Innovation in Agriculture). Dr Ochieng is interested in studies of organismal evolution, understanding the processes that initiate and maintain variations in nature, with greater focus on variations of adaptive significance and the infusion of desired variations via genetic engineering.

Publications


2014

Ochieng, JW, Milugo TK.  2014.  Genetic diversity in Eucalypts. Genetics, Genomics and Breeding of Eucalypts. : CRC Press, Taylor & Francis

2013

Milugo, TK, Omosa LK, Ochanda JO, Owuor BO, Wamunyokoli FA, Oyugi JO, Ochieng JW.  2013.  Antagonistic effect of alkaloids and saponins on bioactivity in the quinine tree (Rauvolfia caffra sond.): further evidence to support biotechnology in traditional medicinal plants., 2013. BMC complementary and alternative medicine. 13:285. Abstract

The Quinine tree (Rauvolfia caffra) is used as a medicinal plant among traditional communities in many countries to manage tumors and other diseases associated with oxidative stress. To validate indigenous knowledge and possibly position this herb for technology uptake and utilization, we established the level of antioxidant activity in R. caffra, and probed for the presence of associated phytochemicals.

Shepherd, M, Kasem S, Ablett G, Ochieng J, Crawford A.  2013.  Developing a genetic classification for gene pool management of spotted gums. Abstract

Spotted gums (Genus Corymbia Section Politaria) occur as a species replacement series along the eastern seaboard of Australia, their distributions marked by regions of disjunction and sympatry. Their taxonomy remains controversial, with species assignment often challenging and reliant upon knowledge of geographic origin as well as subtle morphological or leaf oil variation. In this paper we explore a classification for spotted gums without assuming predefined geographic or taxonomic groups, instead using genetic structure at microsatellite marker loci (n=9) and a Bayesian model-based clustering approach implemented in STRUCTURE software. The C. torelliana outgroup (n=21; Section Cadagaria) formed a well resolved cluster (min. pairwise Fst = 0.19). Four populations were evident within the spotted gums (n=93) but structure was weak (pairwise Fst range 0.13 -0.05). Geography, both distance and topography were major determinants of structure, with migration among populations approximating a linear stepping-stone model. Corymbia maculata was resolved as a taxon and had the greatest genetic distance to any other population (min pairwise Fst 0.08). Three clusters were evident within the northern taxa but alignment with taxonomic groupings was poor. Corymbia citriodora material from north of a major disjunction in Central Queensland formed a Northern population. Corymbia citriodora, C. variegata and C. henryi material from below this disjunction but north of the Border Ranges, formed a Central population, whereas a Southern population was comprised of C. variegata and C. henryi from predominately south of the Border Ranges. Fewer ambiguous assignments occurred using genetic rather than taxonomic groups for self classification of the spotted gum reference population.

Ananga, AA, Georgiev V, Ochieng JW, Phills B, Tsolova V.  2013.  Production of Anthocyanins in Grape Cell Cultures: A potential Source of Raw Material for Pharmaceutical, Food, and Cosmetic Industries. The Mediterranean Genetic Code - Grapevine and Olive. : INTECH2013_anthocyanins_by_intech.pdf

2012

Davis, G, Ananga A, Krastanova S, Sutton S, Ochieng JW, Leong S, Tsolova V.  2012.  Elevated gene expression in chalcone synthase enzyme suggests an increased production of flavonoids in skin and synchronized red cell cultures of North American native grape berries., 2012 Jun. DNA and cell biology. 31(6):939-45. Abstract

Anthocyanins are antioxidants and are among the natural products synthesized via the flavonoid biosynthesis pathway. Anthocyanins have been recommended for dietary intake in the prevention of cardiovascular diseases, cancer, and age-related conditions such as Alzheimer's disease or dementia. With an increasingly aging population in many parts of the world, strategies for the commercial production of in vitro synchronized red cell cultures as natural antioxidants will be a significant contribution to human medicine. Red pigmented fruits such as grapes (Vitis sp.) are a major source of bioavailable anthocyanins and other polyphenols. Since the level of antioxidants varies among cultivars, this study is the first one that phytochemically and genetically characterizes native grape cultivars of North America to determine the optimal cultivar and berry cells for the production of anthocyanins as antioxidants. Using real-time PCR and bioinformatics approaches, we tested for the transcript expression of the chalcone synthase (CHS) gene, an enzyme involved in the flavonoid and anthocyanin biosynthesis pathway, in different parts of physiologically mature grape berries and in vitro synchronized red cells. A low level of expression was recorded in berry flesh, compared with an elevated expression in berry skins and in vitro synchronized red cells, suggesting increased production of flavonoids in skin and cell cultures. This preliminary study demonstrates the potential of functional genomics in natural products research as well as in systematic studies of North American native grapes, specifically in muscadine (Vitis rotundifolia).

Ananga, AA, E CE, Ochieng JW, Kumar S, Kambiranda D, Vasanthaiah H, Tsolova V, Senwo Z, F KF, Anike FN.  2012.  Prospects for Transgenic and Molecular Breeding for Cold Tolerance in Canola (Brassica napus). Oilseeds. : INTECH2012_oilseeds_by_intech_june_2012.pdf
Davis, G, Ananga A, Krastanova S, Sutton S, Ochieng JW, Leong S, Tsolova V.  2012.  Elevated gene expression in chalcone synthase enzyme suggests an increased production of flavonoids in skin and synchronized red cell cultures of North American native grape berries., 2012 Jun. DNA and cell biology. 31(6):939-45. Abstract2012_davis_et_al_dna_and_cell_biology.pdf

Anthocyanins are antioxidants and are among the natural products synthesized via the flavonoid biosynthesis pathway. Anthocyanins have been recommended for dietary intake in the prevention of cardiovascular diseases, cancer, and age-related conditions such as Alzheimer's disease or dementia. With an increasingly aging population in many parts of the world, strategies for the commercial production of in vitro synchronized red cell cultures as natural antioxidants will be a significant contribution to human medicine. Red pigmented fruits such as grapes (Vitis sp.) are a major source of bioavailable anthocyanins and other polyphenols. Since the level of antioxidants varies among cultivars, this study is the first one that phytochemically and genetically characterizes native grape cultivars of North America to determine the optimal cultivar and berry cells for the production of anthocyanins as antioxidants. Using real-time PCR and bioinformatics approaches, we tested for the transcript expression of the chalcone synthase (CHS) gene, an enzyme involved in the flavonoid and anthocyanin biosynthesis pathway, in different parts of physiologically mature grape berries and in vitro synchronized red cells. A low level of expression was recorded in berry flesh, compared with an elevated expression in berry skins and in vitro synchronized red cells, suggesting increased production of flavonoids in skin and cell cultures. This preliminary study demonstrates the potential of functional genomics in natural products research as well as in systematic studies of North American native grapes, specifically in muscadine (Vitis rotundifolia).

2011

Ouma, C, Roca AL, were T, Raballah EO, Oguge NO, Jura WGZO, Ochieng JW, Hanotte O, Georgiadis N.  2011.  Genetic structure of hartebeest populations Straddling a transition zone between Morphotypes. J. Basic & Appl. Sci. Res. 1(3):131-149.2011_ouma_et_al_jbasr.pdf

2010

Ochieng, JW, Shepherd M, Baverstock PR, Nikles G, Lee D, Henry RJ.  2010.  Two sympatric spotted gum species are molecularly homogeneous. Conservation Genetics. 11(1):45-56.2010_ochieng_et_al_coge.pdf

2008

Ananga, AO, Cebert E, Soliman K, Kantety R, Konan K, Ochieng JW.  2008.  Phylogenetic relationships within and among Brassica species from RAPD Loci associated with blackleg resistance. Afr. Journal of Biotechnology . 7(9):1287-1293.2008_ananga_et_al_ajb.pdf
Tilahun, Y, Soliman K, Lawrence KS, Cseke LJ, Ochieng JW.  2008.  Nuclear ribosomal DNA diversity of a cotton pest (Rotylenchulus reniformis) in the United States. Afr. Journal of Biotechnology. 7(18):3217-3224.2008_tilahun_et_al_ajb.pdf
Shepherd, M, Kasem S, Ablett G, Ochieng JW, Crawford A.  2008.  Genetic structuring in the spotted gum complex (genus Corymbia, section Politaria). Australian Systematic Botany . 21:1-11.2008_shepherd_et_al_asb.pdf
Ochieng, JW, Shepherd M, Baverstock PR, Nikles G, Lee D, Henry RJ.  2008.  Genetic variation within two sympatric spotted gum eucalypts exceeds between species variation. Silvae Genetica. 57:249-256.2008_ochieng_et_al_silgen.pdf

2007

Ochieng, JW, Baverstock PR, Steane DA, Shepherd M, Henry RJ.  2007.  Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs. Abstract

Divergent paralogs can create both obstacles and opportunities for phylogenetic reconstruction. Phylogenetic relationships among eucalypt genera have been incongruent among datasets in previous studies, where morphological characters supported monophyly of the genus Corymbia, while intergenic spacers of the nuclear ribosomes (ITS) and chloroplast loci (trnL, trnH, psbA) showed Corymbia as either equivocal or paraphyletic. Ribosomal DNA occurs in multiple copies in a genome. We cloned and sequenced the nrITS to investigate if gene duplication was the cause of incongruence among trees in the eucalypts. Three ITS riboforms, two of them widespread, were recovered within some genomes. One of the ITS riboforms recovered a robust phylogeny showing Corymbia as a monophyletic genus, corroborating the evidence from morphology, fossil data, a recent ITS/ETS dataset and microsatellites (SSRs). Compelling evidence suggested that this divergent riboform is a pseudogene, i.e., non-functional paralog: comparatively lower GC content suggesting lower structural stability, deamination-like mutations at potential methylation sites, lack of conserved helices and hairpins and conspicuously lower thermodynamic stability in secondary structures. Phylogenies from the apparently functional riboform retained Corymbia as paraphyletic. We show here that pseudogenes can recover a well-corroborated phylogeny whereas their functional paralogs show misleading hypotheses. We explain that phylogenetic signals may be obscured when functional constraints in ITS necessitate compensatory mutations in the secondary structure helices involved in RNA transcription, whereas pseudogenes mutate under neutrality.

Ochieng, JW, Muigai AWT, Ude GN.  2007.  Localizing genes using Linkage Disequilibrium in Plants: Integrating Lessons from the Medical Genetics. Afr. Journal of Biotechnology . 6(6):650-657.2007_ochieng_et_al__ajb_ld.pdf
Ochieng, JW, Muigai AWT, Ude GN.  2007.  Phylogenetics in Plant Biotechnology: Principles, obstacles and opportunities for the resource poor. Afr. Journal of Biotechnology . 6(6):639-649.2007_ochieng_et_al_ajb_phy.pdf
Ochieng, JW, Steane DA, Ladiges PY, Baverstock PR, Henry RJ, Shepherd M.  2007.  Microsatellites retain phylogenetic signals across genera in eucalypts (Myrtaceae). Genetics and Molecular Biology. 30(4):1125-1134.2007_ochieng_et_al_gmb.pdf
Ochieng, JW, Henry RJ, Baverstock PR, Steane DA, Shepherd M.  2007.  Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs., 2007 Aug. Molecular phylogenetics and evolution. 44(2):752-64. Abstract

Divergent paralogs can create both obstacles and opportunities for phylogenetic reconstruction. Phylogenetic relationships among eucalypt genera have been incongruent among datasets in previous studies, where morphological characters supported monophyly of the genus Corymbia, while intergenic spacers of the nuclear ribosomes (ITS) and chloroplast loci (trnL, trnH, psbA) showed Corymbia as either equivocal or paraphyletic. Ribosomal DNA occurs in multiple copies in a genome. We cloned and sequenced the nrITS to investigate if gene duplication was the cause of incongruence among trees in the eucalypts. Three ITS riboforms, two of them widespread, were recovered within some genomes. One of the ITS riboforms recovered a robust phylogeny showing Corymbia as a monophyletic genus, corroborating the evidence from morphology, fossil data, a recent ITS/ETS dataset and microsatellites (SSRs). Compelling evidence suggested that this divergent riboform is a pseudogene, i.e., non-functional paralog: comparatively lower GC content suggesting lower structural stability, deamination-like mutations at potential methylation sites, lack of conserved helices and hairpins and conspicuously lower thermodynamic stability in secondary structures. Phylogenies from the apparently functional riboform retained Corymbia as paraphyletic. We show here that pseudogenes can recover a well-corroborated phylogeny whereas their functional paralogs show misleading hypotheses. We explain that phylogenetic signals may be obscured when functional constraints in ITS necessitate compensatory mutations in the secondary structure helices involved in RNA transcription, whereas pseudogenes mutate under neutrality.

2006

Ochieng, JW;, Baverstock PR;, Henry RJ;, Shepherd M.  2006.  Implications for Association Mapping..
Ochieng, W.  2006.  Viral load, CD4+ T-lymphocyte counts and antibody titres in HIV-1 infected untreated children in Kenya; implication for immunodeficiency and AIDS progression. Abstract

ere are limited reports on HIV-1 RNA load, CD4+ T-lymphocytes and antibody responses in relation to disease progression in HIV-1 infected untreated children in Africa. METHODS: To describe the relationships between these parameters, we conducted a longitudinal cohort study involving 51 perinatally HIV-1 infected children aged between 1 and 13 years. HIV status was determined by ELISA and confirmed by western blot and PCR. Antibodies were quantified by limiting dilution ELISA, plasma HIV-1 RNA load by RT-PCR and CD4+ T-lymphocytes by FACSCount. RESULTS: Asymptomatic and symptomatic disease had, respectively, a rise in median HIV-1 RNA load from 1,195 to 132,543 and from 42,962 to 1,109,281 copies/ml in children below 6 years. The increase in viral load was 10-fold higher for asymptomatic compared to other categories and 2-fold faster for children less than 6 years than those above. Similarly, symptomatic children below 6 years had initial median CD4+ T-lymphocyte counts of 647 (22%) cells/muL, declining to 378 (20%) while those above 6 years had initial values of below 335 (15%) but which increased to 428 (17%). Median viral load correlated significantly with median CD4+ T-lymphocyte percentage in children above 6 years (p=0.026) but not below. CONCLUSIONS: Viral load is lower in older than younger children and correlates significantly with percentage CD4+ T-lymphocytes. Survival by HIV-1 infected children requires a competent immune response early in infection to counter the rapidly replicating virus. Interventions aimed at boosting the naïve immune system may prolong survival in these children.

2005

Shepherd, M, Lee DJ, Baker N, Kasem S, Ochieng JW, Bihua C;, Henry RJ.  2005.  Corymbia genetics at Southern Cross University (Presentation Corymbia Research Meeting).

2004

Jianlin, H, Ochieng JW, Lkhagva B, Hanotte O.  2004.  Genetic diversity and relationship of domestic bactrian camels (Camelus bactrianus) in China and Mongolia. Journal of Camel Practice & Research. 11(2):97-99.2004_jianlin_et_al_jcpr.pdf

2003

Mburu, DN, Ochieng JW, Kuria SG, Jianlin H, Kaufmann B, Rege JEO, Hanotte O.  2003.  Genetic diversity and relationships of indigenous Kenyan camel (Camelus dromedarius) populations: implications for their classification., 2003 Feb. Animal genetics. 34(1):26-32. Abstract

The genetic diversity and relationships amongst the dromedary (Camelus dromedarius) populations are poorly documented. Four recognized Kenyan dromedary breeds (Somali, Turkana, Rendille, Gabbra) and dromedary from Pakistan and the Arabian Peninsula (Saudi Arabia, United Arab Emirates) were studied using 14 microsatellite loci. Phylogenetic analysis showed that Kenyan dromedaries are distinct from Arabian and Pakistani populations. Expected heterozygosity and allelic diversity values indicate that Kenyan dromedaries are less diverse than non-Kenyan populations. With the exception of the Somali population, the Kenyan dromedaries are poorly differentiated (average FST=0.009), with only one to two loci separating the Gabbra, Rendille and Turkana populations studied (P < 0.05). Individual assignments were performed using the maximum likelihood method. A correct breed assignment of only 39-48% was observed for the Kenyan dromedaries, using an allocation stringency of a log of the odds ratio >2. Our results do not support the present classification of the indigenous Kenyan dromedary into four distinct breeds based on socio-geographical criteria. Instead, our results point to just two separate genetic entities, the Somali and a group including the Gabbra, Rendille and Turkana populations.

Nijman, IJ, Otsen M, Verkaar ELC, de Ruijter C, Hanekamp E, Ochieng JW, Shamshad S, Rege JEO, Hanotte O, Barwegen MW, Sulawati T, Lenstra JA.  2003.  Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites., 2003 Jan. Heredity. 90(1):10-6. Abstract

Hybridization between wild and domestic bovine species occurs worldwide either spontaneously or by organized crossing. We have analysed hybridization of banteng (Bos javanicus) and zebu (Bos indicus) in south-east Asian cattle using mitochondrial DNA (PCR-RFLP and sequencing), AFLP, satellite fragment length polymorphisms (SFLP or PCR-RFLP of satellite DNA) and microsatellite genotyping. The Indonesian Madura zebu breed is reputed to be of hybrid zebu-banteng origin, but this has never been documented and Bali cattle are considered to be a domesticated form of banteng. The banteng mitochondrial type was found in all animals sampled on the isle of Bali, Indonesia, but only in 35% of the animals from a Malaysian Bali-cattle population. The Madura animals also carried mitochondrial DNA of either zebu and banteng origin. In both populations, zebu introgression was confirmed by AFLP and SFLP. Microsatellite analysis of the Malaysian Bali population revealed for 12 out of 15 loci screened, Bali-cattle-specific alleles, several of which were also found in wild banteng animals. The tools we have described are suitable for the detection of species in introgression studies, which are essential for the genetic description of local breeds and the preservation of their economic and cultural value.

2002

Yoon, DH, Ochieng JW, Lee HK, Oh SJ, Cho BW, Cheong IC, Hanotte O.  2002.  Genetic diversity and relationships of three Eastern Asian cattle breeds. AbstractBook

Ten cattle populations, 3 Asian (Hanwoo, Yanbian, Wagyu), 2 African, and 2 European Bos taurus as well as 2 Asian B. indicus and one Bali cattle, B. banteng, were characterized with 13 microsatellite markers. A total of 364 animals from the different cattle populations were used in the study. Allele frequencies were used to estimate expected heterozygosities (He), genetic distances (Ds), and to perform principal component analysis. 165 alleles were observed across all loci. The data supported a common origin for the Hanwoo and Yanbian cattle (Ds=0.013). No evidence for a major West European taurine introgression into the Wagyu was observed. The Eastern Asian cattle were found to be genetically distinct from the European and African taurine and from the Asian zebu. It is recommended that the genetic uniqueness of these cattle breeds be maintained in conservation and improvement programmes

Hanotte, O, Bradley DG, Ochieng JW, Verjee Y, Hill EW, Rege EJO.  2002.  African pastoralism: genetic imprints of origins and migrations., 2002 Apr 12. Science (New York, N.Y.). 296(5566):336-9. Abstract

The genetic history of African cattle pastoralism is controversial and poorly understood. We reveal the genetic signatures of its origins, secondary movements, and differentiation through the study of 15 microsatellite loci in 50 indigenous cattle breeds spanning the present cattle distribution in Africa. The earliest cattle originated within the African continent, but Near East and European genetic influences are also identified. The initial expansion of African Bos taurus was likely from a single region of origin. It reached the southern part of the continent by following an eastern route rather than a western one. The B. indicus genetic influence shows a major entry point through the Horn and the East Coast of Africa and two modes of introgression into the continent.

2000

Jianlin, H, Mburu D, Ocheng JW, Rege JEO, Hanotte O.  2000.  Usefulness of New World Camelidae microsatellite primers for amplification of polymorphic loci in Old World camelids. Animal Genetics. 31(6):404-406.2000_jianlin_et_al_angen.pdf
Hanotte, O, Tawah CL, Bradley D, Okomo M, Verjee Y, Ochieng JW, Rege JE.  2000.  Geographic distribution and frequency of taurine (Bos taurus) and zebu (Bos indicus) Y chromosome Haplotypes amongst sub-Saharan African Cattle breeds. Molecular Ecology. 9(4):387-396.2000_hanotte_et_al_mecol.pdf

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