I am a biotechnologist with an experience spanning 9 years in different institutions in various lab activities. I am currently working as a research assistant at the KALRO Biotechnology Centre. As mentioned, I have sufficient exposition in various lab activities, just to mention a few: sample collection and processing; ELISA; DNA/RNA extraction; FACS analysis, cell sorting and counting; disease scoring; conventional PCR and qPCR; sample processing for NGS sequencing based on the IonTorrent platform; developing & optimizing standard operating procedures for various equipment and techniques in a molecular biology lab, setting and executing experiments; data collection and report writing. I also have bioinformatics skills just to mention a few, de novo and reference guided assembly, creating and managing sequence databases, genome annotation and much more; I have training in using R. I am a published author with several papers in my name
Abstract
Diseases caused by viruses are known to cause the heaviest economic losses in tree tomato. A survey was conducted in 26 farms from three agro-ecological zones (upper highlands, lower highland, and midlands) in Machakos, Nairobi, Embu, Tharaka Nithi, Meru, Elgeyo Marakwet, Nandi, Baringo and Nakuru counties, and 358 leaf samples collected. Next generation sequencing (NGS) revealed potato virus Y (PVY), tomato mild mottle virus (TMMoV, 9243 bp, MW537585), Ethiopian tobacco bushy top virus (4199 bp, MW883068), and associated RNA satellite (522 bp, MW713579), and lastly potato spindle tuber viroid (359 bp, MZ054164). RT-PCR and sanger sequencing revealed sequences with a high percentage identity with the NGS results: 90% for ETBTV, 99% for satETBTV-E, 96% for TMMoV and 98% for PSTVd. The RT-PCR results also revealed PVY as being the most prevalent, with 46% of all farms having samples which tested positive for it. Both PSTVd and TMMoV were present in two farms, from Embu and Meru, and Meru and Nandi respectively. ETBTV and satETBTV-E, were present in one farm from Tharaka Nithi. Pepper enomavirus, tobacco mottle virus, tomato chlorosis virus, Kenyan potato cytohabdovirus and tamarillo fruit ring virus were also detected using NGS, but their presence is yet to be validated using RT-PCR. No sample from the upper highlands tested positive for any of the viruses tested. There was no significant difference between in PVY incidence between the lower highland and midlands zones. This study provides a good baseline for the development of disease management strategies for virus diseases.
Research Supervisors
Prof Douglas W. Miano Prof Rama Devi Narla Dr. Paul K. Kuria
