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Slide 1: BUILDING FUNCTIONAL GENOMICS RESEARCH CAPACITY ON INSECTS VECTOR OF HUMAN DISEASE VECTOR IN AFRICA S. Doumbia1, MB. Coulibaly1, SF. Traore1, G. Dolo1, E. Adebiyi2 1 . DMEVE/ MRTC/Faculty of Medicine, University of Bamako, Mali; 2 . Department of Computer and Information Sciences (Bioinformatics Unit) College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
Slide 2: MALI Soudana-savana North savana Sahel Sahara desert W ater bodies MALI NIGER TCHAD SUDAN K ID A L G ao GAO N io n o KAYES K O U L IK O R O SEG OU M OPTI 2 0 250 500 S IK A S S O kilometers
Slide 3: MALI ICER UNIVERSITY OF BAMAKO MALI SERVICE CENTER FACULTY OF MEDICINE, PHARMACY & DENTISTRY (FMPOS) ACADEMIC / RESEARCH DEPARTMENTS ADMINISTRATION NIAID/RSO Mali/ICER Programs IT HIV/TB SEREFO MRTC / PARASITO/Pathogenesis MRTC / Vector Research
Slide 4: MRTC VECTOR RESEARCH GROUPS BIO-ECOLOGY & TRANSMISSION UNIT MOLECULAR BIOLOGY UNIT VECTOR PARASITE INTER ACTION GIS/ REMOTE SENSING UNIT FMPOS / MRTC / NIAID / LMVR VECTOR RESEARCH PROGRAM FILARIASIS UNIT LEISHMANIASIS UNIT GENOMICS / PROTEOMICS BIO INFORMATICS
Slide 5: MRTC VECTOR RESEARCH NETWORK UNIVERSITY OF MINNESOTA UNIVERSITY OF CALIFORNIA AT DAVIS UNIVERSITY OF JOHN HOPKINS UNIVERSITY OF COLORADO STATE FMPOS / MRTC / NIAID / LMVR ENTOMOLOGY PROGRAM NIH / NIAID / DIR / LPD / LMVR UNIVERSITY OF CALIFORNIA AT LOS ANGELES UNIVERSITY OF COLUMBIA UNIVERSITY OF NOTRE DAME WHO / TDR
Slide 6: MRTC-VECTOR RESEARCH GROUP * 6 SENIOR SCIENTISTS - Traoré Sékou F., MSc, PhD Entomology - Seydou Doumbia, MD. PhD , Epidemiology - Abdoulaye M. Toure, MD, Ph D, Parasitology - Guimogo Dolo, MSc, PhD Entomology - Djibril Sangaré MSc, PhD, Molecular entomology - Mamadou B Coulibaly Pharm D, PhD, Molecular entomology ** 10 JUNIOR SCIENTISTS - 5 MSc: (entomology, Molecular entomology, Biochemistry) - 5 MD & 1 Pharm D: All graduated from the University of BAMAKO. - 5 Licenses ( entomology) All graduated from the University of BAMAKO
Slide 7: BACKGROUND  The genome sequences for many diseases vector and parasites are now available and promise the development innovative approaches to control these diseases, Eg. Anopheles Gambiae, Plasmodium faliciparum and soon TSE TSE fly Considerable interest is now focused on identification of new insect vector target genes which may lead to genetically altered vectors the development of drugs, vaccines, insecticides and insect repellents This has renew interest in a vector-borne diseases control strategy based on replacing field insect vector populations by strains that are unable to transmit the pathogen to human  
Slide 8:  Africa, which is the most severely affected by these diseases, lacks adequate infrastructures and human resources required for rational use of genomic information Though African vector biologists have increasingly acquired advanced knowledge of molecular techniques, many of them lack basic knowledge in bioinformatics and genomic to take advantage of the genome sequences and translate it into meaningful control strategies African Center for Training in Functional Genomics of Insect vectors of Human Disease (AFROVECTGEN) has been initiated by WHO/TDR and the Department of Medical Entomology and Vector Ecology (DMEVE) of the MRTC  
Slide 9: OBJECTIVES OF AFROVECTGEN  Train African scientists involved in insect vectors of human diseases research to apply state-of-art bio informatics and functional genomics techniques Raise awareness and access to bioinformatics and insect vectors genomics resources among researchers of vector biology programs in the region To develop a training center at MRTC which could facilitate the establishment of a network involving African institutions and international institutions and trigger collaborative research in bioinformatics and genomics between African scientists and international partners  
Slide 10: POTENTIALS FOR A REGIONAL CENTER FOR TRAINING IN FUNCTIONAL GENOMIC OF DISEASE VECTORS  The strength of current research activities at the DMEVE/MRTC resides in four main program areas:  Molecular entomology  Vector population genetics  Vector-Parasite-Interactions (blood feeding of F1 mosquitoes to gametocyte careers)  Vector Ecology/Epidemiology and Geographical Information Systems The DMEVE/MRTC has developed a network of researchers to study Anopheles gambiae complex population genomics which can be used as resource for developing functional genomics Research activities in Africa
Slide 11: A MODEL OF NETWORKING  Study of “Population Genomic of the mosquito Anopheles gambiae in Africa”. This provide critical background information for malaria control strategies based on genetic manipulation: eg. patterns of gene flow, spatial changes in genetic structure of vector populations Studies of the genetics and genomics of mosquito immunity and parasite resistance in natural conditions. Natural resistance loci are identified and then mapped to isolate candidate resistance genes through sequence analysis, transcriptional profiling, and physiological studies Leishmaniasis research program sponsored by NIH/LMVR is focused on sand fly salivary gland proteins potential targets for vaccine. The research includes Transcriptome and proteome analysis of cDNA libraries of salivary gland proteins from different geographically isolated populations using bioinformatics. This network involves partner institutions from US and other African countries. It was developed through research grants funded by NIH and WHO/TDR   
Slide 12: Training Course On Functional Genomics Insect Vectors Of Human Diseases at Afrovectgen  General Information:  Course language (English)  Course duration 2 weeks  Participants: 20 (15 off-site, 5-6 in-country)  Target: Junior scientists, Ph.D. candidates or PostDoc, lecturers  Field: insect vector-borne diseases (e.g. vectors for malaria , leishmaniasis, filariasis, trypanosomiasis)  First course: (December 1- 16 2004), Second course Oct 26-Nov 10, 2005, Third course (Nov 29 – Dec 13, 2006)  Course website: http://sundjata.biology.ucla.edu/MRTC/Africangenomics/ 
Slide 13:  Applicants’ Profile :  First course (99 applications from 21 countries with 31% from Nigeria, 15% from Kenya, and 9% from Cameroon)  Selected: 15 off-site from 11 countries (Benin, Burkina Faso, Cameroon, Colombia, Côte D’ivoire, Kenya, Mauritania, Nigeria Senegal, Sudan, Uganda)  Second course (77 applications, 19 countries with 27% from Nigeria, 14% from Kenya, 8% from Ghana)  Selected: 16 off-site from 9 countries (Burkina Faso, Cameroon, Gambia, Ghana, Kenya, Nigeria, Sudan, Tanzania, Uganda) and 4 candidates from Mali  Third course (77 applications, 21 countries with 18% from Kenya, 16% from Nigeria, 9% from Sudan, and 6% from Ghana  14 off-site candidates from 12 countries (Cameroon, Cote d’Ivoire, Ethiopia, Ghana, Italy, Kenya, Niger, Nigeria, Sudan, Tanzania, Togo, Uganda)
Slide 14: COURSE CONTENT  Basic Molecular biology with focus on molecular entomology tools and techniques  Basic concepts of PCR (DNA extractions and diagnostic PCR)  Primers designing,  Genome sequencing, assembly  Sequencing technology, and strategies  DNA sequencing (procedure and technology),  and laboratory practices sessions population genetics/genomics  basic concept of Population genetics  simulation of natural selection for insecticide resistance  simulation of genetic modification of vector population.  gene flows and transposable elements  Technical and ethical issues related to transgenic insects as vector control strategy,  Genomic data analysis using open resource statistical packages such as ‘R’ statistical package were also covered 
Slide 15:  Applied Bioinformatics: Bioinformatics resources:  BLAST (NCBI)  Vectorbase,  “Anoexcel”: concept of piping bioinformatics data to an Excel spreadsheet   “Stripper” that strips primer and vector sequences from EST data Cluster5: A program that clusters EST or proteins based on Blast and CAP3 programs with results piped into spreadsheets  Functional genomics and proteomics        Principles and Technology of Microarrays; Microarray Data Normalization Methods; Microarray Data Acquisition and Analysis using: dChip Software for Oligo Arrays Methods for Filtering Microarray Data; Supervised and Unsupervised Classification Methods Applied to Gene Expression Data; Data interpretation tools (NetAffx, Gene Ontology, KEGG, GenMAPP); Hidden Markov Model (HMM) Tools
Slide 16: CHALLENGES AND PERSPECTIVES   Satisfaction of the demands (applications) Encourage application of knowledge acquired in bioinformatics and functional genomics during WHO/TDR sponsored workshops series of the past 3 years  We propose to extend the length of the training to cover a period of 3 months targeting 5 trainees    The first month to focus on intensive training in cutting edge Molecular techniques; applied bioinformatics and functional genomics with more practices The second month to be allocated to more genomic laboratory practices (e.g. sequencing, analyzing sequence data), seminars, literature search, and grant writing. During the third month, we will assist students to develop a project oriented toward functional genomics research  Very few research institution or Universities in the continent have adequate training resources (human and technology) for genomic Research. The MRTC provides research opportunity in genomic research for other African countries through international collaboration (networking)
Slide 17:  Mamadou B. Coulibaly, PharmD, Ph.D, DMEVE / MRTC/Faculty of Medicine, University of Bamako, Mali, Molecular biology Doulaye Dembele, Ph.D, IGBMC, CNRS and University Louis Pasteur, Strasbourg, France. Statistical methods applied to bioinformatics et microarray data analysis Huynh Chuong, Ph.D, Senior System analyst, National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA. Bioinformatics. Jennifer M. Anderson, Ph.D, Lab of Malaria and Vector Research / NIAID/ NIH, Rockville, MD, USA, applied bioinformatics to insect vectors and related software. Mark Wamalwa, Msc, Kenyatta University , Nairobi, KENYA, Microarray data analysis Kenneth Vernick, Ph.D, Associate Professor, Univ Minnesota, Minneapolis MN, USA. Functional genomics (microarray principles, methods and Applications, proteomics/ mass spectrometry) Mr. Charles E Taylor, Ph.D, Professor of Biology, UCLA, Los Angeles, California, USA. Population genetics (modeling/simulation aspects). Yongjian (Jason) Guo, Ph.D, Bioinformatics Specialist, Bioinformatics and Scientific IT Program (BSIP) NIAID Bethesda, MD 20892 Emmanuel Dialynas, Msc, Bioinformatics, I.M.B.B. FORTH, Insect Molecular Genetics Group Vassilika Vouton, P.O. Box 1527, GR-711 10 Heraklion, Crete, GREECE FACULTY        
Slide 18: Functional Genomic Training Course sponsored by WHO/TDR, Bamako 2006
Slide 19: IT at MRTC, Bamako
Slide 20: New NIH-Funded Functional Genomics Lab with Sequencing Machine, Real time PCR machines and 4 PCR machines, DMEV/MRTC, Faculty of Medicine, University of Bamako, Mali
Slide 21: ACKNOWLEDGEMENTS        Jose Ribeiro, L.M.V.R./NIAID/NIH, Rockville, USA; Jesus Valenzuela,. L.M.V.R./NIAID/NIH, Rockville, USA; Dr. Taylor’s lab at UCLA: http:// sundjata.biology.ucla.edu/MRTC/Africangenomics/ Administrative core of the course, Souleymane Karambe and Dr. R. Sakai NIAID/NIH, in particular Robert Gwadz and Chris Wallen for the support for IT infrastructure at MRTC PECET/FGIV This work was supported by WHO/TDR, grant ID-A40806