Biotechnology and Bioinformatics
Biotechnology and Bioinformatics Research Directorate (BTBIRD)
- About BTBIRD
- Researchers at BTBIRD
Biotechnology and Bioinformatics Research Directorate (BTBIRD) was established at AHRI in 2017. This directorate is focused on improving medical care in Ethiopia by adopting and developing new or improved tools and methods for diagnosis, prevention, and treatment of diseases through various technologies including bioinformatics, genomics, and recombinant technology. Further, BTBID works to serve as a hub for technology transfer and capacity building of health biotechnology in universities and research institutes.
The directorate conducts research in a wide range of topics with the collaboration of all the other directorates at AHRI.
Simply put, our research focuses on manipulating organisms, biological processes, cells, and cellular components to develop new or improved tools and products that are useful in research and health care, and bioinformatics, analyzing samples sequenced at AHRI or beyond.
Some of the current area of work
- Preparation and evaluation of in house monoclonal antibodies against commercial antibodies for clinical and research use
- Intravenous immunoglobulin (IVIg) preparation
- Human Leukocyte Antigen (HLA) Typing
- In house production of diagnostic kit (direct agglutination test(DAT)) for the visceral leishmaniasis diagnosis
- In house production of trans-isolate media(TIM) for the transport of cerebrospinal fluids for primary cultures from patients with bacterial meningitis
- In house production of viral load and drug resistance testing for different viral diseases such as HIV, viral Hepatitis etc
- Developing flow cytometry based diagnostics for leukemia
- Genomics and Bioinformatics Research
Preparation and evaluation of in house monoclonal antibodies against commercial antibodies for clinical and research use
Monoclonal antibodies are antibodies designed in the laboratory to recognize and bind to specific proteins. These antibodies have immense use in research, diagnostics and therapeutics. Currently, a third of new drugs that are introduced make use of monoclonal antibodies.
In this project, we are involved in locally producing laboratory scale mouse anti-human CD4 and CD38 monoclonal antibodies (mAb) using hybridoma technology. Anti-CD4 monoclonal antibodies can replace commercialized antibodies to monitor treatment response to anti-retroviral therapy of HIV patients. CD38 is a prognostic marker for lymphocytic leukemia. Therefore, anti-CD38 monoclonal antibodies can be used to monitor the prognosis of lymphocytic leukemia. The project is meant to transfer the technology of mAb preparationand fluorescence labeling by using local expertise and international partners. Three complementary approaches are used for this project i.e., in house preparation of hybridomas, production of monoclonal antibodies from purchased hybridomas, and labeling purchased monoclonal antibodies.
Intravenous immunoglobulin (IVIg) preparation
Intravenous immunoglobulin (IVIg) is sterile IgG prepared by purifying human plasma pooled from large number of donors. IVIG is composed of more than 95% unmodified IgG, which has intact Fc-dependent effector functions, and trace amounts of immunoglobulin A (IgA) or immunoglobulin M (IgM). IVIg is mainly used to treat people with immunodeficiency disorders and sometimes it is co-administered with other medications for people who are fighting chronic infections. The demand for IVIg is increasing globally. Personal communication with medical doctors in Ethiopia has revealed that IVIG is also needed in this country; however, scientific studies assessing the need for IVIg in Ethiopia have not been conducted yet.
The IVIg purification project was initiated with seed money from AHRI. Following that, ministry of health of Ethiopia donated a significant amount of money from their sustainable development goals (SDG) fund to facilitate IVIg technology transfer and laboratory scale production.
Human Leukocyte Antigen (HLA) Typing
Kidney transplant is the best long-term therapeutic strategy for individuals with end stage kidney disease. In some transplant cases, there could be humoral or cellular mediated immune responses against the transplanted kidney, even in the presence of immunosuppressants. This leads to organ rejection, which leaves the patient in a worse medical condition. Most rejection reactions are directed at human leukocyte antigens (HLAs) expressed on the transplanted kidney. In order to avoid rejection during kidney transplant, multiple HLA compatibility tests must be done for the patient-donor pair.
This project will provide compatibility tests for the kidney transplant program at St. Paul’s Hospital. The three types of compatibility tests we do are serology typing, molecular typing, and flow cytometry crossmatch. Until now, these tests were done at a company in Germany or India and it took two weeks to get the results, which was unpromising for patients that were at the end stages of kidney disease; so is the need for local capacity of doing the tests in Ethiopia. AHRI took the initiative and trained its staff at the University of Michigan and established HLA laboratory at AHRI. In collaboration with St Paul Kidney transplant program, validation has been done with few samples tested simultaneously at both our facility and at the company in Germany. All our results were concordant with the results from the German company.
In house production of trans-isolate media (TIM) for the transport of cerebrospinal fluids for primary cultures from patients with bacterial meningitis
The Bacterial and Viral Diseases Research Directorate is currently conducting research to determine prevalence and serogroup distribution of meningococcal meningitis among vaccinated and non-vaccinated Ethiopians. As a part of this study, it has been initiated to produce trans-isolate media (TIM), which supports survival of meningitis strains during transport to the laboratory. Most bacterial causes of meningitis remain unconfirmed because of failure to grow isolates in culture due to the distance from laboratories. Bacterial causes of meningitis die easily outside of the host and require enriched media and body temperature to grow. TIM provides nutrients for live transportation. The technology for in house TIM production has been acquired so that quality assured readymade vials of TIM is provided for clinicians and researchers.
Genomics and Bioinformatics Research
A team of scientists from AHRI have secured a grant for a project called TBGEN, which will study host-parasite interactions in tuberculosis. We are using this project to establish and build genomics and bioinformatics research at AHRI. In order to prepare for the project, we have already started giving training to staff and students at AHRI. One of the trainings we gave on bioinformatics is described briefly below.
Bioinformatics training at AHRI
Institutional initiatives strengthening capacity at AHRI focuses on building a bioinformatics training center, next generation sequencing (NGS) facility and computing platform to support researchers and postgraduates in Ethiopia. The facilities benefit both ongoing and new project initiatives such as on pathogen evolution, virulence determinants and epidemiology of important pathogens, including M. tuberculosis.
Training workshop on Mycobacterium whole genome sequence data analysis
As part of capacity building in bioinformatics in Ethiopia, an introductory course on bioinformatics was conducted between 24- 28 December 2018 at AHRI. The training was aimed at delivering hands on practical introduction to NGS data analysis of Mycobacterium tuberculosis complex (MTBC) genome. Every workshop day included, 40 minutes presentation, three hours hands on practical and 20 minutes discussion. The presentation topics were on next generation sequencing technologies, examples of sequence data file formats and a stepwise description of each bioinformatics workflow during NGS data analysis.
There were 12 participants (7 from AHRI, 1 each from EPHI, NHADIC, AAU-IBT, EBTI, and AASSTU) and 4 trainers (2 from AHRI, one from AAU-IBT and one from EBTI) from health and biotechnology research institutes in Ethiopia.
At the end of the training, participants had an opportunity to reflect on the training experience. Though they have expressed their satisfaction on acquiring basic skills in handling NGS data, they have highlighted the need to improve computational power of the workstations at the bioinformatics laboratory and address fluctuations of internet connectivity.
Dr. Markos Abebe, PhD
Acting Director of BTBIRD
Markos Abebe(PhD) is a Lead Scientist at the Armauer Hansen Research Institute (AHRI) and Adjunct Associate Professor of Immunology at Addis Ababa University, Institute of Biotechnology. He received his BSC (in Biology in 1986) and MSc (in Parasitology/Immunology in 2001) from Addis Ababa University. He received his PhD from the University Of Copenhagen, Denmark in 2008 in TB immunology. He attended several relevant trainings in a number of European countries. He received the first AHRI Tore Godal Prize Award in 2001 for his contribution in infectious disease research, particularly on Female Genital Tuberculosis. His main research interest is in understanding the mechanism of host-parasite interaction and identification of biomarkers and development of diagnostics. He received grants from EDCTP and DFG for his postdoctoral research. Dr Markos published a number of scientific papers in peer reviewed journals and advised a number of MSc and PhD students. He is well experienced in research leadership and management and played momentous role in networking local and international research institutes in the advancement of medical research and training in the country. He became member of the Ethiopian Academy of Sciences in February 2016. Currently he is leading the Biotechnology and Bioinformatics Research Directorate at AHRI.
Dr Yonas Kassahun
Holds Phd in molecular genetics from university of Dublin, Ireland. During this period, I have worked on bioinformatics and Bayesian based statistical approach implemented for admixture mapping analysis of African cattle hybrid zones. The analysis gave a quantitative measure of the degree of chromosomal mosaicism in hybrid zones, the dynamics of genome introgression and identified regions with some evidence of the imprint of natural selection. My research focused on the application of bioinformatics models of admixture mapping to decipher complex genetic traits analysis. The study highlights for the first time using african cattle breeds to elucidate ancestral differences correlated for genetic susceptibility in Mycobacterium bovis using high density markers covering whole genome. Furthermore, african cattle phylogeography, genetic population structure and relevant quantitative trait loci (QTL) analysis were described using bioinformatics inference and in relation to continental reference cattle genome data. Follow up position as postdoctoral fellow at AHRI focused on comparative genomics of M bovis using NGS data, pathogen genomics and bioinformatics training and supervision.
Dawit Hailu obtained his B.Sc. in Biological Sciences from Nagoya University, Japan in 2015. During this time, he worked on identifying novel substrate genes for the E3 ubiquitin ligases Asb 11 and Asb 13 using genetic and biochemistry techniques on mammalian culture cells. Then, he completed his masters at the same university in 2017, where he worked mainly on identifying novel substrate target gene for the Saccharomyces Cerevisiae E3 ubiquitin ligase DIA2, which plays role in invasive growth. Dawit has been trained on sample library preparation for next generation sequencing and is currently working on strengthening the DNA sequencing facility at AHRI together with Biotechnology and Bioinformatics team members.
Project Data Manager, TBGEN
Bethlehem has earned her BSC Degree from HiLCoE School of Computer Science and Technology in Computer Science and currently studying her MSC Degree in Information Science and Systems at Addis Ababa University. She has worked in Software Development, Oracle Technical Consultancy, IT Management areas and in projects involving machine learning. She has interest in data science areas of big data analytics in Artificial Intelligence and Bioinformatics. Currently she is working in TBGEN Project data management and analytics of the human and bacteria sequenced genomic data and on the establishment of the Bioinformatics center.
Amanuel is a computer Engineer interested in biological (Life) science. He obtained his BSC in Electrical and computer Engineering (Computer Engineering focus area) from Institute of technology, University of Gondar in 2017. His BSC Thesis Project was designing and implementing PDF to speech converting device for visually impaired people. He has a couple of certificates on computer related trainings. He is more interested and wants to pursue his career on machine learning regarding genomics. Currently, he is working in Bioinformatics team as an assistant data manager on a genetics study project called TBGEN.
Melaku Tilahun is associate researcher at the Armauer Hansen Research Institute (AHRI) .He received BSc degree from Jimma University in Medical Laboratory Science and completed his MSc Degree in Clinical Laboratory Science with Diagnostic and Public Health Microbiology Specialty in Addis Ababa University, Ethiopia. He has worked as a Laboratory Manager of the Institute. During his stay at the institute he was participating in different research projects and he has published his works in different open access peer reviewed journals. Currently he has joined Arba Minch University, Ethiopia to study his PhD Degree in the field of Biotechnology with specialty of Medical Biotechnology. Melaku’s main research interest is studying the epidemiology and genomics of M.tuberculosisto understand the transmission dynamics and the genetic basis of antibiotic resistance and to provide information for current discrepancies between genotype and phenotype drug resistance.
Tewodros Tariku is a PhD candidate at Addis Ababa University, Ethiopia, conducting his dissertation study on the genetic basis of podoconiosis, a non-filarial elephantiasis of the lower leg, that affects more than 1 million people in Ethiopia. He employed genome-wide association (GWA) analysis approach in diverse ethnic groups in Ethiopia to identify genetic variants that increase risk to podoconiosis, and findings suggest the involvement of variants located in the HLA-class II region. He obtained his bachelor’s degree in Biology from Bahir Dar University and a master’s degree in Microbiology from Addis Ababa University. He is interested in the application of data analytics and data science tools to health and biological data to generate new evidences and improve decision making in public health and basic research.
Elena Hailu has been a researcher at AHRI since October 2003 and currently joined Institute of Biotechnology at Addis Ababa University to study her Ph.D. Emory University, USA provided her a support for PhD work through NIH/Fogarty International Center Global Infectious Diseases grant.Previously, she obtained her MSc degree in Biochemistry with distinction from Moscow Academy of Veterinary medicine and Biotechnology, Russia in 1993. Her main research interest is to investigate how TB pathology might be influenced by Mycobacterium tuberculosis strain diversity. She was part of the group that discovered and characterized the new Lineage 7 of M. tuberculosis in Ethiopia. She was a winner of “Association of Physicians Links with Developing Countries Scheme” and got training in Brighton and Sussex Medical School, UK. She attended several courses, workshops and conferences aboard. She has a list of publication in peer reviewed journals. Elena is committed to the capacity building in Ethiopia particularly establishing the sequencing facility at AHRI.
Fikir T. Bekele
Fiker obtained her B.A. in Molecular Biology at Pomona College. During this time sheworked on investigating the interaction between a bacteria cell membrane model and Temporin-SHf, an antimicrobial peptide. Then, she completed her masters in the Department of Pathology at the University of Cambridge, where she studied cellular and humoral immune responses against S. mansoniinfection before and after treatment with praziquantel. Currently, Fiker is working on preparing and evaluating in house monoclonal antibodies against commercial antibodies for clinical and research use. In the future, she would like to pursue Ph.D in vaccine development.
Dr Rosa Tsegaye
Rosa Tsegaye is project data manager at Armauer Hansen Research Institute (AHRI). Mainly, she is working on scientific research. Her research interest is on bioinformatics. She has completed her Ph.D in data science from Hildesheim University, German. The focus of her research was on machine learning for natural language processing. Before her Ph.D, she was working in Yahoo! Research lab as an intern data scientist. Prior to that she received her second masters in data mining and knowledge management from different Europe universities (Université Lumière (France), Polytech’Nantes Università degli Studi del Piemonte Orientale (UPO), Alesandria (Italy), Universitat Polit ècnica de Catalunya (UPC), Barcelona (Spain), Universitatea Politehnica din Bucuresti, Bucharest (Romania)), and her first masters in networks and distributed systems from Chalmers University, Sweden. She received her bachelor degree from Arba Minch University in computer science and information technology.
Dr. Markos Abebe, PhD
Acting Director of BTBIRD