Browsing by Author "Okao-Okuja, Geofrey"

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    Occurrence of Bondar’s Nesting Whitefly, Paraleyrodes bondari (Hemiptera: Aleyrodidae), on cassava in Uganda
    (Revista Brasileira de entomologia, 2018) Abu Omongo, Christopher; Namuddu, Annet; Okao-Okuja, Geofrey; Alicai, Titus; Brunschot, Sharon van; Ouvrard, David; Colvin, John
    Cassava is a valued calorific source to millions of Africans who eat it daily and a vital staple for their food security. One of the key constraints to this crop is white flies which are both a vector of viral diseases and a direct pest. Although the African cassava white fly is known to cause physical damage on cassava with considerable tuberous yield loss, a recent white fly outbreak caused unusually severe damage, which prompted the current reported investigation. Molecular identification of white fly adults sampled from the affected cassava field revealed the presence of a new white fly species, Paraleyrodes bondari. This communication is the first report of the occurrence of P. bondari on cassava in Uganda.
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    Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa
    (Genes, 2019) Boykin, Laura M.; Sseruwagi, Peter; Alicai, Titus; Ateka, Elijah; Umar Mohammed, Ibrahim; Stanton, Jo-Ann L.; Kayuki, Charles; Mark, Deogratius; Fute, Tarcisius; Erasto, Joel; Bachwenkizi, Hilda; Muga, Brenda; Mumo, Naomi; Mwangi, Jenniffer; Abidrabo, Phillip; Okao-Okuja, Geofrey; Omuut, Geresemu; Akol, Jacinta; Apio, Hellen B.; Osingada, Francis; Kehoe, Monica A.; Eccles, David; Savill, Anders; Lamb, Stephen; Kinene, Tonny; Rawle, Christopher B.; Muralidhar, Abishek; Mayall, Kirsty; Tairo, Fred; Ndunguru, Joseph
    In this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an e ective point-of-need field diagnostic system. The PDQeX extractsDNAusing a cocktail of thermophilic proteinases and cell wall-degrading enzymes, thermo-responsive extractor cartridges and a temperature control unit. This closed system delivers purified DNA with no cross-contamination. The MinIT is a newly released data processing unit that converts MinION raw signal output into nucleotide base called data locally in real-time, removing the need for high-specification computers and large file transfers from the field. All three devices are battery powered with an exceptionally small footprint that facilitates transport and setup. To evaluate and validate capability of the system for unbiased pathogen identification by real-time sequencing in a farmer’s field setting, we analysed samples collected from cassava plants grown by subsistence farmers in three sub-Sahara African countries (Tanzania, Uganda and Kenya). A range of viral pathogens, all with similar symptoms, greatly reduce yield or destroy cassava crops. Eight hundred (800) million people worldwide depend on cassava for food and yearly income, and viral diseases are a significant constraint to its production. Early pathogen detection at a molecular level has great potential to rescue crops within a single growing season by providing results that inform decisions on disease management, use of appropriate virus-resistant or replacement planting. This case study presented conditions of working in-field with limited or no access to mains power, laboratory infrastructure, Internet connectivity and highly variable ambient temperature. An additional challenge is that, generally, plant material contains inhibitors of downstream molecular processes making e ective DNA purification critical. We successfully undertook real-time on-farm genome sequencing of samples collected from cassava plants on three farms, one in each country. Cassava mosaic begomoviruses were detected by sequencing leaf, stem, tuber and insect samples. The entire process, from arrival on farm to diagnosis, including sample collection, processing and provisional sequencing results was complete in under 3 h. The need for accurate, rapid and on-site diagnosis grows as globalized human activity accelerates. This technical breakthrough has applications that are relevant to human and animal health, environmental management and conservation.