- Email: [email protected]
Foreword—MBP thematic issue on genomics
Molecular & Biochemical Parasitology 118 (2001) 127– 128 www.parasitology-online.com.
Editorial
Foreword —MBP thematic issue on genomics
The revolution in biology that has resulted from the adoption of new methodologies of automated instrumentation, robotics, mass screening and combinatorial approaches is undoubted. There is a massive amount of new data now being amassed including sequence information and analysis of the mRNA and protein repertoires in various cell types. The genome has been joined by the transcriptome, the proteome, the metabolome, and the vaccinome. The editors of Molecular and Biochemical Parasitology thought that it would be of interest to provide a snapshot of how these approaches are being applied to parasitic diseases. As organisers and participants in a symposium entitled ‘‘The Past, Present and Future of Genomic Sequence Information’’ held during the 49th Annual Meeting of the American Society of Tropical Medicine and Hygiene in Houston TX last November, we have been invited to guest edit for Molecular and Biochemical Parasitology a Thematic Issue on Genomics, focusing mainly on malaria and including a selection of the contributions to the Symposium. The goal of the Symposium was to provide a perspective on the potential for genomic sequence as it relates to vaccine and drug development, by integrating information from the Malaria genome project with the rest of the genomics and proteomics fields. Speakers reviewed and updated new developments in the sequencing, annotation and analysis of the Plasmodium falciparum, yoelii and berghei genomes, introduced the PlasmoDB database and tools to use the data, and illustrated how genomics and proteomics data could potentially be exploited for the development of new vaccines or drugs. These themes are explored in greater detail in the accompanying original research articles. Thus the complex organisation of the subtelomeric regions of the currently available fully sequenced P. falciparum chromosomes is dissected (Pizzi and Frontali). Such analyses must ultimately encompass the entire genome and algorithms designed to help illuminate patterns will help us make
sense of newly sequenced genomes (Stern et al.). Is the current annotation correct? Perhaps not. New algorithms will challenge the initial picture of the gene content of Plasmodium chromosomes (Crawley et al.) and careful manual examination of existing predictions is shown to be a powerful approach (Huestis and Fischer). Many of us have our favourite genes and one bounty of the genome sequencing is the unexpected revelation that the single gene a laboratory was focussing upon is a member of a multi-gene family (Holt et al.) and the role and conservation of those proteins (Kaneko et al.). Furthermore it might be conserved in the many species of Plasmodium whose genomes are coming under the sequencers’ knife. The surprising extent of general genome conservation at an organisational level is emphasised in a comparison of diverged species of Plasmodium such as P. 6i6ax and P. falciparum (Tchavtchitch et al.). This conservation is reflected in gene content of genomes and extends beyond Plasmodium as is illustrated by genome profiling (Carlton et al.). Lastly, it is hoped that this trove of gene information will lead to new therapies for malaria, drugs, vaccines, and perhaps as yet undreamt-of strategies. If this hope is realized then during the testing phase of such treatment we will need to have rapid and sensitive methods to detect parasitaemia and two articles describe the application of quantitative PCR-based detection of Plasmodium which may prove to be the workhorse detection methodology in vaccine testing centres (Whitney et al.; Hermsen et al.). This revolutionary change is not confined to malaria but encompasses the whole of Parasitology as was illustrated by a recent meeting held at the Royal Society which is summarised in this issue (Burchall et al.). We hope that you enjoy the articles presented in this focus on the state-of-the art of (malaria) genomics, and that it may leave you with the desire to explore opportunities offered by such recent advances. As you read these
0166-6851/01/$ - see front matter © 2001 Elsevier Science B.V. All rights reserved. PII: S 0 1 6 6 - 6 8 5 1 ( 0 1 ) 0 0 3 8 9 - 9
128
Editorial
articles you may also choose to ponder how we can meet the challenge of involving scientists from endemic countries in the use of methodologies of undoubted power but high expense.
Ross L. Coppel Monash Uni6ersity, Victoria, Australia
Denise L. Doolan Na6al Medical Research Center, Maryland, USA E-mail: [email protected]
Andrew P. Waters Leiden Uni6ersity Medical Centre, Leiden, The Netherlands
Editorial
Foreword —MBP thematic issue on genomics
The revolution in biology that has resulted from the adoption of new methodologies of automated instrumentation, robotics, mass screening and combinatorial approaches is undoubted. There is a massive amount of new data now being amassed including sequence information and analysis of the mRNA and protein repertoires in various cell types. The genome has been joined by the transcriptome, the proteome, the metabolome, and the vaccinome. The editors of Molecular and Biochemical Parasitology thought that it would be of interest to provide a snapshot of how these approaches are being applied to parasitic diseases. As organisers and participants in a symposium entitled ‘‘The Past, Present and Future of Genomic Sequence Information’’ held during the 49th Annual Meeting of the American Society of Tropical Medicine and Hygiene in Houston TX last November, we have been invited to guest edit for Molecular and Biochemical Parasitology a Thematic Issue on Genomics, focusing mainly on malaria and including a selection of the contributions to the Symposium. The goal of the Symposium was to provide a perspective on the potential for genomic sequence as it relates to vaccine and drug development, by integrating information from the Malaria genome project with the rest of the genomics and proteomics fields. Speakers reviewed and updated new developments in the sequencing, annotation and analysis of the Plasmodium falciparum, yoelii and berghei genomes, introduced the PlasmoDB database and tools to use the data, and illustrated how genomics and proteomics data could potentially be exploited for the development of new vaccines or drugs. These themes are explored in greater detail in the accompanying original research articles. Thus the complex organisation of the subtelomeric regions of the currently available fully sequenced P. falciparum chromosomes is dissected (Pizzi and Frontali). Such analyses must ultimately encompass the entire genome and algorithms designed to help illuminate patterns will help us make
sense of newly sequenced genomes (Stern et al.). Is the current annotation correct? Perhaps not. New algorithms will challenge the initial picture of the gene content of Plasmodium chromosomes (Crawley et al.) and careful manual examination of existing predictions is shown to be a powerful approach (Huestis and Fischer). Many of us have our favourite genes and one bounty of the genome sequencing is the unexpected revelation that the single gene a laboratory was focussing upon is a member of a multi-gene family (Holt et al.) and the role and conservation of those proteins (Kaneko et al.). Furthermore it might be conserved in the many species of Plasmodium whose genomes are coming under the sequencers’ knife. The surprising extent of general genome conservation at an organisational level is emphasised in a comparison of diverged species of Plasmodium such as P. 6i6ax and P. falciparum (Tchavtchitch et al.). This conservation is reflected in gene content of genomes and extends beyond Plasmodium as is illustrated by genome profiling (Carlton et al.). Lastly, it is hoped that this trove of gene information will lead to new therapies for malaria, drugs, vaccines, and perhaps as yet undreamt-of strategies. If this hope is realized then during the testing phase of such treatment we will need to have rapid and sensitive methods to detect parasitaemia and two articles describe the application of quantitative PCR-based detection of Plasmodium which may prove to be the workhorse detection methodology in vaccine testing centres (Whitney et al.; Hermsen et al.). This revolutionary change is not confined to malaria but encompasses the whole of Parasitology as was illustrated by a recent meeting held at the Royal Society which is summarised in this issue (Burchall et al.). We hope that you enjoy the articles presented in this focus on the state-of-the art of (malaria) genomics, and that it may leave you with the desire to explore opportunities offered by such recent advances. As you read these
0166-6851/01/$ - see front matter © 2001 Elsevier Science B.V. All rights reserved. PII: S 0 1 6 6 - 6 8 5 1 ( 0 1 ) 0 0 3 8 9 - 9
128
Editorial
articles you may also choose to ponder how we can meet the challenge of involving scientists from endemic countries in the use of methodologies of undoubted power but high expense.
Ross L. Coppel Monash Uni6ersity, Victoria, Australia
Denise L. Doolan Na6al Medical Research Center, Maryland, USA E-mail: [email protected]
Andrew P. Waters Leiden Uni6ersity Medical Centre, Leiden, The Netherlands