My laboratory is a member of the Giardia lamblia Genome Project Consortium, headed by the Josephine Bay Paul Center’s Dr. Mitchell Sogin. Giardia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist, often hypothesized to be the most basal eukaryote. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains approximately 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems. The study of complete genomes such as Giardia’s will increase our understanding of the early origin of eukaryotes. The genome project has entered the finishing stages (prediction of complete chromosomal sequences, gene prediction).

My laboratory’s primary research within the Giardia lamblia Genome Project is development of the web-based informatics (GiardiaDB), development of the core computational environment from sequencing pipeline to genome assembly, construction of software for computational assembly of the Giardia genome sequence, and leading computational aspects of finalizing the genome sequence. GiardiaDB is part of a larger effort in genome informatics of diverse prokaryotic and eukaryotic genomes, large-scale EST sequencing projects, and SAGE analysis. Visit our GMOD Server for more details.

Involvement of my laboratory in the Giardia lamblia genome project is part of a broader effort to understand infection, pathogenicity, transmission, and survival of infectious microorganisms. As part of the Program in Global Infectious Diseases, my laboratory is investigating patterns of genome-wide gene expression in Giardia (giardiasis: diarrhea, malabsorption), african Trypanosoma (trypanosomiasis: sleeping sickness), and Schistosoma (schistosomiasis). As the genome sequence of Giardia will soon be known and because Giardia’s life cycle can be reproduced in vitro, giardial gene expression is being examined using Serial Analysis of Gene Expression (SAGE) to monitor genome-wide levels of messenger RNA (mRNA) expression throughout its life cycle. Examination of genome-wide gene expression patterns will provide a coherent picture of activation and inactivation of biological pathways. SAGE quickly and very affordably detects 15 base nucleotide sequences from every mRNA transcript present in a sampled population of cells. The sequences are called ‘tags’ and the frequency of these tags determined by SAGE is directly reflective of relative transcript abundance. SAGE thus both identifies genes (15 bp can uniquely identify >85% of Giardia’s genes) and their relative levels of expression. Computationally, this requires joint analysis of genome sequences, predicted gene sequences, gene annotation, tag sequences, and tag frequencies. The Giardia SAGE project detects up- and down-regulation of genes related to giardial infection (excystation), pathogenicity (trophozoites), transmission (encystation), and survival in the environment (cysts). This research will provide a comprehensive understanding of changes in giardial gene expression in response to important host physiological signals and will serve as a valuable model for study of other parasites and complex eukaryotes, such as yeast and animals. It will provide a dynamic framework, in the context of the cell and life cycle, to the annotation of the Giardia genome, including the detection of unpredicted genes via detection of their tags.

SAGE is also being used to examine gene expression in African trypanosomes. Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense are protozoan parasites that cause African sleeping sickness in humans while Trypanosoma brucei brucei causes a wasting disease in cattle called Nagana. These parasites are morphologically indistinguishable and the only clear phenotypic distinction is the inability of T. b. brucei to infect humans. Analysis of human infectious and non-infectious lines of T. b. rhodesiense resulted in the identification of a trypanosome gene that is necessary for human infection (SRA). The SRA gene is absent in T. b. brucei, although similar gene sequences are present. To define the mechanism of human infectivity, another Josephine Bay Paul Center investigator (Dr. Stephen Hajduk) has selected for T. b. brucei lines resistant to human serum. These resistant lines of T. b. brucei are able to survive human serum despite lacking the SRA gene. Examination of genome-wide gene expression patterns in human serum susceptible and resistant T. b. brucei lines will provide a coherent picture of the biological pathways in trypanosomes that influence host range and human infection.

My laboratory also has a strong interest in molecular and statistical approaches to phylogenetic history. My laboratory has been examining overall phylogeny of the Gastropoda, with emphasis upon deep-sea groups endemic to hydrothermal vents, hydrocarbon seeps, and whale falls, using large and small subunit ribosomal sequences. Similar approaches have been used to examine eukaryote phylogeny, particularly regarding the origins of multicellularity and the nature of the first eukaryotes. Investigations of gene family diversity and phylogeny are being used to improve understanding of gene function, including studies of protein disulphide isomerases, Mybs, histones, fermentation enzymes, hydrogenases, and cytochrome P450s. New projects include bioinformatics approaches for detection of transcription factors in eukaryotic genomes, with subsequent study of the evolution of transcriptional control.

Recent Publications:

Palm, D., M. Weiland, A.G. McArthur, J. Winiecka-Krusnell, M.J. Cipriano, S.R. Birkeland, S.E. Pacocha, B.J. Davids, F.D Gillin, E. Linder, & S.V. Svard. 2005. Developmental changes in the adhesive disk during Giardia differentiation. Molecular and Biochemical Parasitology, 141, 199-207.

Weiland, M.E-L., A.G. McArthur, H.G. Morrison, M.L. Sogin, & S.G. Svard. 2005. Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia. International Journal for Parasitology, 35, 617-626.

Wilson, J.Y., A.G. McArthur, & J.J. Stegeman. 2005. Characterization of a cetacean aromatase (CYP19) and the phylogeny and functional conservation of vertebrate aromatase. General and Comparative Endocrinology, 140, 74-83.

Best, A.A., H.G. Morrison, A.G. McArthur, M.L. Sogin, & G.J. Olsen. 2004. Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia. Genome Research, 14, 1537-1547.