Program brochure of

First African Virtual Conference on Bioinformatics

(Afbix rsquo09)

Organized by

Bioinformaticsorg

In collaboration with

RSGshyAfrica and RSGshy Morocco

February 19shy20 2009

httpwikibioinformaticsorgAfbix09

afbix09bioinformaticsorg 1

Contents

Prologue

Concept of virtual hubs

Keynote speakers

Program

Program Chairs ndash Committee

Abstracts

List of participating hubs and confirmed participants

afbix09bioinformaticsorg 2

Prologue

We are delighted to bring you this brochure containing a list of abstracts for the first African

Virtual Conference on Bioinformatics (Afbix rsquo09) In addition to research on tropical diseases

pathogenesis and their vectors the field of bioinformatics has become an important part of life

science studies in Africa But with the great geographical expanse of the continent it is often

impractical or uneconomical for African researchers to come together for conferences That is in

person The Bioinformatics Organization (BioinformaticsOrg) has therefore collaborated with

the African Society of Bioinformatics amp Computational Biology (ASBCB) and Regional Student

Groups (RSGs) in Africa to develop a bioinformatics conference that utilizes local institutions in

Africa as virtual hubs

At the outset we would like to thank all of the keynote and other invited speakers for having

accepted our kind invitation to present a talk And thanks you to the workaholics of all

committee members and reviewers who planned this event well and made this a fruitful

beginning for virtual conferences in Africa

We look forward to see you during the virtual conference

Have a great conference ahead

Sincerely

Chairs and the Team Afbix lsquo09

afbix09bioinformaticsorg 3

Concept of virtual hubs

Considering the fact that there is still time to open affordable bandwidth in Africa we at

BioinformaticsOrg thought of distributing this virtual conference through hubs across all parts

of Africa In that process 20shy30 participants per hub can pay a fee for the hub which would act

as a cumulative reduced registration fee for the individual This may be the first of its kind in

the virtual world where this concept is introduced

BioinformaticsOrg has a subscription to an online meeting system which allows users to

connect and form a virtual classroom

Hub

BioinformaticsOrgrsquos virtual world

through the online meeting system

Hub

Individual participant(s)

Prototype of virtual conference

afbix09bioinformaticsorg 4

Keynote speakers

Dr Trevor Sewell Dr Richard F Wintle

Dr Ivan Gerling Dr Dan Masiga

afbix09bioinformaticsorg 5

Program(All times Greenwich Meridian time GMT)

February 19

Morning session

bull 0900shy0920 shy Welcome By Mtakai Ngara and Segun Fatumo

Subshytheme 1 Structural Biology Applied to Infectious Diseases

bull 0930shy1030 shy Keynote 1 Dr Trevor Sewell Title TBA bull 1040shy1100 shy Coffee break with virtual posters bull 1100shy1140 shy Invited Speaker 1 Dr Ezekiel Adebiyi Computational Biologists in

Malaria Research SignificanceChallenges and Suggestions on way forward bull 1150shy1210 shy Oral presenter 1 Khalid Moum bull 1220shy1240 shy Presentation about achievements from BioinformaticsOrg ndash Jeff Bizzaro bull 1250shy1350 shy LunchDinner (virtual) networking )

Afternoon session

SubshyTheme 2 Applied Genomics to Infectious Diseases

bull 1400shy1500 shy Keynote 2 Dr Richard Wintle Title TBA bull 1510shy1550 shy Invited speaker 2 Dr Raphael D Isokpehi Aquaporins at the Hostshy

Parasite Interface in Malaria1550shy1610 shy Coffee break with Virtual posters bull 1600shy1630 ndash Oral presenter 2 Segun Fatumobull 1640shy1710 ndash Oral presenter 3 John Tan

afbix09bioinformaticsorg 6

February 20

Morning session

SubshyTheme 3 Career Development in Bioinformatics and Opportunities for Researchers in Africa

bull 0900shy1000 shy Keynote 3 Dr Dan MasigashyChair ASBCB bull 1000shy1100 shy ISCB Student Council shy SC Chair Abhishek Pratap amp RSGs in Africa shy

RSG regional leaders bull 1100shy1130 shy Coffee break with virtual posters bull 1130shy1210 ndash LunchDinner NetworkingAdvertisements

Afternoon session

bull 1220shy1350 shy A tutorial on Mitochondrial systems biology a sequel to Mitochondriomics by Prashanth Suravajhala Bioinformatics Organization

SubshyTheme 4 Proteomic applications to Tropical Diseases

bull 1400shy1500 shy Keynote 4 Dr Ivan Gerling bull 1510shy1550 shy Invited speaker 3 Dr Lawrence Okoror Proteomics a major tool for

vaccine preparation Lassa virus as a case study bull 1600shy1730 ndash A tutorial on the UCSC Genome Browser by Warren Lathe

OpenHelixcom bull 1740shy1820 ndash Invited speaker 4 Dr Scott Emrich bull 1830shy1920 shy Invited speaker 5 Dr Michael Ferdigbull 1930shy2000 shy Noura Chelbat Vote of thanks conference wrapshyup and adieu

afbix09bioinformaticsorg 7

Program Chairs and Committee

Chairs Mtakai Ngara (ILRI Kenya) Noura Chelbat (Austria) JW Bizzaro (President BioinformaticsOrg ) Prashanth Suravajhala (Associate Director BioinformaticsOrg)

Program Committee

Chair Segun Fatumo (Covenant University Nigeria)

Noura Chelbat (Institute of Bioinformatics JKU Linz shyAustria) Sarath Chandra Janga (University of Cambridge UK) Abhishek Pratap (USA) Prashanth Suravajhala Sheila Ommeh (Kenya) Kavisha Ramdayal (SANBI South Africa) Souiai Ouissem (Tunisia)

Technical Committee

Chair Nelson Ndegwa

Working group Sheila Ommeh Kavisha Ramdayal Kenneth Babu Souiai Ouissem Stanley Mbandi Amina El Gonnouni Geoffrey Siwo Marion Adebiyi Dennis Zofou Amal Maurady

afbix09bioinformaticsorg 8

Abstracts

All the abstracts are in accordance with the ones that the authors communicated with us and

therefore DO NOT contain the revisions The readersrsquo discretion is advised However

scientific and technical revisions for abstracts if any have been amended by authors upon

receiving comments from reviewers Should you require the full length articles you could

communicate with authors directly after the conference The full length articles of select

abstracts will be communicated to the Journal of Bioinformatics and Computational Biology

and Bioinformation

afbix09bioinformaticsorg 9

1

MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population

LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9

BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7

CHEacuteRIFH8 KHYATTI M1

Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc

PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations

EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)

RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age

CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations

Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP

afbix09bioinformaticsorg 10

2

Inferring the metabolic network of Plasmodium falciparum in the host

Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2

1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology

University of Heidelberg Germany

In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual

reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)

with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK

and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that

the automatic reconstruction of pathways generates manifold paths that need an expert manual

verification as eg In the PlasmoCyc database there may be pathways incomplete or not

completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be

filled by an elaborated comparison to the human metabolic network as the parasite may take

advantage of human enzymes The parasite may use them outside the parasitersquos organism in the

red blood cell and in the apicoplast organelle We reconstructed the metabolic network of

Plasmodium falciparum and found that the network got more complete when including the

human enzymes Furthermore we could show that the metabolism got more robust as the

number of essential reactions was substantially reduced when taking human enzymes into

account

Keywords chokepoints essential reactions Plasmodium Drug targets

afbix09bioinformaticsorg 11

3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients

K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5

L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1

1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco

Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been

found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans

the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed

that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and

environmental factors

It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory

molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are

important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC

pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these

grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of

ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of

NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain

reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from

peripheral lymphocytes

The results of the present study obtained from a large sample indicate that young patients from North Africa with

the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217

OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger

and older onset patients are genetically different and may involve different mechanisms

Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding

author khalidmoumgmailcom

afbix09bioinformaticsorg 12

4

Designing of Vector and Vector map based on genome of Emiliania huxleyi phage

Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4

1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India

Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi

afbix09bioinformaticsorg 13

5

Computational Evaluation of Some Malaria Drug Targets

Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2

1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology

University of Heidelberg Germany

The most severe form of malaria a disease that affects over 300 million people annually is

caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and

has led to the death of millions both children and adult alike Although there are already existing

antishymalarial drugs but the development of resistance by the parasite against existing drugs has

necessitated the importance of identifying new drug targets In a recent publication [Fatumo et

al2008] 22 potential drug targets based on an automated metabolic pathway database called

PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by

[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database

(Malaria Parasite Metabolic Pathways) against pathways generated automatically like

PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done

The study shows that the automatically generated pathwaysdatabases need an expert manual

verification Consequently in this work we evaluated the drug targets predicted by Fatumo et

al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the

protein structures and identified the binding sites for the refined list of the drug targets

afbix09bioinformaticsorg 14

6 Abstract truncated

FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE

HUMAN YshyCHROMOSOME

Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore

lydiajothigmailcom

Various genes across the human genome are found to be functionally related or

dependent Functional annotation of a few genes of the human Yshychromosome coding for

hypothetical proteins and those with unknown role can help us better understand the structure

and role of human genes thereby understanding sexshylinked male chromosome This could also

provide us new strategies to combat human diseases Of the307 genes of the human Y

chromosomes those coding for hypothetical proteins were short listed using bioinformatics

tools while function of proteins coded by these genes were predicted by manual annotation to

assign the most probable function This prediction was done using the tools JAFA CPH

PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence

score of the candidates were made based on similar results that were obtained from different

number of tools

The study can also be extended to the current build of the human genome and provide clue to the

various diseases linked to the human Y chromosome Out of the twenty five genes for which

functions were predicted three genes have their functions predicted with 90 percent accuracy

These can lead to a wet laboratory analysis where the predicted function for these three genes

can be verified

afbix09bioinformaticsorg 15

7

Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions

1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia

1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University

2Malaria Research and Training Centre (MRTC)University of Bamako Mali

Corresponding author ltOluwagbemi Olugbengagt

Background

Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease

Methodology

In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data

Results

The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito

afbix09bioinformaticsorg 16

8

Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation

Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis

This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities

afbix09bioinformaticsorg 17

9 Abstract truncated

AfriPFdb The African Plasmodium falciparum database

1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M

IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines

As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)

Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation

Key words Malaria Plasmodium falciparum Database Drugs and Vaccines

corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18

10

FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa

countries

Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben

Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1

1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte

contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de

Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc

Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter

transcriptional activity of this gene Recent evidence suggests an association of this

polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this

relationship

Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North

Africa countries Tunisia Algeria and Morocco were determined using polymerase chain

reaction based restriction fragment length polymorphism (PCRshyRFLP)

Results No Associations with cancer risk were estimated We observed a no significant

difference in distribution of the genotype CC and TC between cases and controls the OR was

respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005

in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant

OR=061 In male we found a p=003 with an OR=066 the difference is significant between

cases and controls with TC genotype but this is not statistically significant

Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of

nasopharyngeal carcinoma in Maghrebian population

Key Words NPC FAS L PCRshyRFLP

afbix09bioinformaticsorg 19

11

Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage

Marion Adebiyi1 Yah Clarence2

1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom

2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom

Correspondence Corresponding Author olumarionhotmailcomAbstract

Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs

Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage

afbix09bioinformaticsorg 20

12

DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER

Shishir Kumar Gupta Archana Singh

Department of Bioinformatics CSJM University Kanpur India

eshymail shishirbioinfogmailcom

Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare

KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer

afbix09bioinformaticsorg 21

13

Experimental study for PCRshybased detection of Malaria infection at the Liver stage

Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4

1Department of Computer and Information Sciences Covenant University Ota Nigeria

2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria

3Department of Biological Sciences Covenant University Ota Nigeria

4Malaria Research Training Center (MRTC) University of Bamako Mali

Corresponding Author vcosamoryahoocom

Malaria transmission involves three different developmental stages namely Human liver stage

human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood

stage Generally there is no doubt that there are some available drugs that can cure the disease

but the problem in most cases is poor or late diagnosis resulting to complications and even death

However most studies do not consider the genes that code for proteins expressed at the nonshy

infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of

human malaria parasites is practically prohibited and therefore mouse model malaria parasites P

berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic

technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver

stage so that timely intervention can be made to alleviate the problem of the disease

Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal

especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough

may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to

diagnostic chip used for detecting other diseases like HIV

Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip

afbix09bioinformaticsorg 22

14

Polphasic approach for phylogenetic analysis and classification of a bacterial strain

Rishika Bisariya

Bioinformatics VIT University Vellore Tamil Nadu India

Rishikabisariyagmailcom

A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the

parade ground South Delhi The strain was identified as a member of genus Herminiimonas by

polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the

universal bacterial primers For phylogenetic analysis closely related reference strains alongwith

one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For

the construction of the phylogenetic trees the software packages TREECON and CLUSTALX

version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining

and maximum parsimony method and evaluated by bootstrap resampling (100 replications)

The nucleotide sequence was then translated into amino acid sequence by using the proteomics

tool TRANSLATE

Keywords Polyphasic approach phylogenetic analysis bootstrap resampling

afbix09bioinformaticsorg 23

15

Computational Identification of functional related gene in Malaria parasites

Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2

1Department of Computer and Information SciencesCovenant University

PMB 1023 Ota Nigeria

2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)

69120 HeidelbergGermany

Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)

In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data

Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics

afbix09bioinformaticsorg 24

16

In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2

1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria

Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development

Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs

Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs

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Participating Hubs

East Africa Hub ILRI Nairobi

South Africa SANBI Cape Town

West Africa Covenant University Nigeria

Morocco SMBI

USA University of Notre Dame

List of Confirmed Participants

Name Affiliation

Abhishek Tripathi University of Notre Dame

Abiodun Adebayo Covenant University

Adele Kruger SANBI

Adesola Ajayi Covenant University

Alecia Naidu SANBI

Allan Kamau SANBI

Amit Kumar India

Andrew Rider University of Notre Dame

Angela Eni Covenant University

Angela Makolo IITA

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Asako Tan University of Notre Dame

Becky Miller University of Notre Dame

Bisibori Bett Agricultural Research Institute

Bonaventure O Aman -

Changde Cheng University of Notre Dame

Chinwe Ekenna Covenant University

Dedan Githae University of Manchester

Dr Ashley Pretorius SANBI

Dr Gordon Harkins SANBI

Dr James Patterson SANBI

Dr Mandeep Kaur SANBI

Dr Mike Ferdig University of Notre Dame

Dr Scott Emrich University of Notre Dame

Dr Stuart Meier SANBI

Dr Sundararajan

Seshadri SANBI

Dr Sunil Sagar SANBI

Edwin Murungi SANBI

Edwin Siu University of Notre Dame

Ekow Oppon SANBI

Esther Kanduma -

Eunice Machuka Kenyatta UniversityKARITRCICIPE

Eva Kalemera

Aluvaala KEMRIITROMIDUniversity of Nairobi

Ezekiel Adebiyi Covenant University

Feziwe Mpondo SANBI

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Frederick Kamanu

Kinyua SANBI

Gbenga Oluwagbemi Covenant University

Geoffrey Siwo University of Notre Dame

George Tinega KARITRCUniversity of Nairobi

Huxley Makonde JKUAT

Irene Kasumba University of Notre Dame

Irene Njoki Kiiru Kenyatta University

Isaac Njaci University of Manchester

Itunu Ewejobi Covenant University

James Atika Kenyatta University

Jelili Oyelade Covenant University

Jenica Abdrudan University of Notre Dame

Jessica Hewitt University of Notre Dame

John Maduka UNN

John Smith University of London

John Tan University of Notre Dame

Joseph Njoroge Egerton University

Kamau Peter Kuria University of Jomo

Kiboi Muthui -

Kuda Kupara ICIPE

Kunle Ibikunle Covenant University

Lydia Charles India

Magbubah Essack SANBI

Maria Unger University of Notre Dame

Mario Jonas SANBI

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Marion Adebiyi Covenant University

Mark Wacker University of Notre Dame

Mark Wamalwa SANBI

Mary Ngendo Kenyatta University

Monique Maqungo SANBI

Mulongo Moses ILRI

Musa Nur Gabere SANBI

Mushal Allam SANBI

Olawande Daramola Covenant University

Olubanke Ogunlana Covenant University

Onyeka Emebo Covenant University

Pamela Tamez University of Notre Dame

Paul Ogongo Institute of Primate Research

Pauline Mcloone Covenant University

Pierre Mulamba

Mutombo SANBI

Ryne Gorsuch University of Notre Dame

Saleem Adam SANBI

Samson Machohi Tea Research Foundation of Kenya

Samuel Kojo Kwofie SANBI

Sarah Mwangi SANBI

Sean McLaughlin SANBI

Sebastian Fernandez University of Notre Dame

Sebastian Schmeier SANBI

Segun Fatumo Covenant University

Serah Waithira Kahiu JKUATILRI

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Siah Habi Biomed Institute

Sonal Patel ILRI

Sumir Panji SANBI

Susanta Behura University of Notre Dame

Timothy Kuria

Kamanu SANBI

Tracey Kibler SANBI

Ulf Schaefer SANBI

Unizik Uzochukwu -

Upeka Samarakoon University of Notre Dame

Victor Osamor Covenant University

Watchman Kwesi National University of Ghana

FAOUZI Abdellah Pasteur Institut

HAMDI Salsabil Pasteur Institut

NAJI fadwa Pasteur Institut

MOUMAD Khalid Pasteur Institut

LAANTRI Nadia Pasteur Institut

BOUHALI ZRIOUIL Sanaacirc

Pasteur Institut

BOUNACEUR Safaa Pasteur Institut

BENRAHMA Houda Pasteur Institut

CHARIF Majida Pasteur Institut

ELOUALID Abdelmajid Pasteur Institut

OUATOU Sanaa Pasteur Institut

ANGA Latifa Pasteur Institut

BOUDABBOUCH Najma

Pasteur Institut

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BAKHOUCH Khadija Pasteur Institut

FARIAT Nadia Pasteur Institut

Fouzia Radouani Pasteur Institut

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