BUILDING FUNCTIONAL GENOMICS RESEARCH CAPACITY ON INSECTS VECTOR OF HUMAN DISEASE VECTOR IN AFRICA

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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

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MALI
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MALI ICER
UNIVERSITY OF BAMAKO
MALI SERVICE CENTER
FACULTY OF MEDICINE, PHARMACY DENTISTRY (FMPOS)
ACADEMIC / RESEARCH DEPARTMENTS
ADMINISTRATION NIAID/RSO
IT
Mali/ICER Programs
MRTC / Vector Research
MRTC / PARASITO/Pathogenesis
HIV/TB SEREFO
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MRTC VECTOR RESEARCH GROUPS
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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
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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

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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

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• 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

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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

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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

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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

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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
  Post-Doc, 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/M
  RTC/Africangenomics/

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• 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 Divoire,
  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 dIvoire, Ethiopia, Ghana, Italy,
  Kenya, Niger, Nigeria, Sudan, Tanzania, Togo,
  Uganda)

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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

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• 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

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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)

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FACULTY

• 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

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Functional Genomic Training Course sponsored by
WHO/TDR, Bamako 2006
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IT at MRTC, Bamako
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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
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ACKNOWLEDGEMENTS

• Jose Ribeiro, L.M.V.R./NIAID/NIH, Rockville, USA
  
• Jesus Valenzuela,.  L.M.V.R./NIAID/NIH,
  Rockville, USA
• Dr. Taylors 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