| My research program is focused on the study
of the biology of parasitism and host-pathogen interactions using
genomic
approaches with the ultimate goal of better understanding infection
and survival mechanisms. These approaches include the development
and application of molecular, computational and phylogenetic
tools. In the long term, our research will contribute to better
diagnosis, prevention and therapeutics of parasite- and bacteria-caused
diseases in humans, animals and plants.
Genome Sequencing and Analysis 
Genome sequences represent an invaluable resource for scientists
working to understand the biology of various pathogens. The
analysis of genome contents undoubtedly constitute a first
important step toward the development of better drugs, vaccines
and methods for pathogen control. Such projects have been
an important activity of my laboratory since 1998. Using
the latest sequencing and bioinformatics tools, we have decoded
and annotated large portions of the African and American
trypanosome genomes, causative agents of African sleeping
sickness and Chagas disease, respectively. Both of
these flagellated protozoan parasites are deadly pathogens,
invariably fatal to infected humans (and domestic animals).
They possess several highly unusual molecular mechanisms
including trans-splicing of polycistronic transcripts, editing
of mitochondrial RNA transcripts, and apparent lack of RNA
polymerase II promoters for most protein-encoding genes.
They also possess complex mechanisms for antigenic variation,
and unique organelles such as the kinetoplast and the glycosome.
We have also recently completed the sequencing of the Schistosoma
mansoni and Perkinsus marinus genomes. S. mansoni is a trematode
parasite that causes schistosomiasis (Bilharzia), a highly
prevalent tropical disease and leading cause of severe morbidity
in many developing countries. P. marinus is a facultative
intracellular parasite of the eastern oyster.
Comparative Genomics of Human Pathogens 
A special area of interest within my group is the comparative
genomics of pathogens with an emphasis on the study of the
evolution of genome architecture and content in pathogens,
as well as the identification of genes that are phylogenetically
restricted or that have been transferred horizontally. Our
recent investigations have focused on three trypanosomatid
parasites. The three pathogens (Trypanosoma brucei, Trypanosoma
cruzi and Leishmania major) are distantly related but have
distinctive life cycles, different insect vectors, and, perhaps
most importantly, different disease characteristics.
Despite high levels of divergence at the sequence level, the
three species exhibit a striking conservation of gene order,
suggesting that selection has maintained gene order among the
trypanosomatids over hundreds of millions of years of evolution.
Computation of clusters of orthology allows us to i) examine
global synteny as well as the selective and mutational forces
that act on chromosomal and genome structure, ii) dissect insertion/deletion
events, gene duplication between species, and comparative chromosomal
architecture for better insights into the evolutionary relationship
of the trypanosomatids, and iii) define the ‘core’ proteome
of a trypanosomatid and during that process, identify genes
that appear to be restricted to each of the species. Such gene
products could provide targets for drug design as well as vaccine
candidates.
Our current comparative efforts encompass a variety of pathogenic and non-pathogenic trypanosomatid strains for which
sequencing projects are underway. Comparative analyses of these genomes will not
only reveal great insights into the evolution of trypanosomatids,
but will allow us to identify subsets of genes specifically
linked to virulence and survival mechanisms.
Functional Proteomics - Elucidation of kinetoplastid interactomes and host-pathogen protein-protein interactions
We have initiated a large-scale project aimed at investigating protein-protein interactions (PPIs) in trypanosomatids using the yeast two-hybrid (Y2H) methodology. In order to validate a variety of platforms for high-throughput testing of PPIs in kinetoplastids, we carried out a comprehensive evaluation of the physical interactions between subunits of Trypanosoma brucei proteasome 26S. As this project expands to characterize the full interactomes, we expect it to result in a significant improvement of the annotation of predicted proteins (particularly hypothetical proteins) and the identification of kinetoplastid-specific hubs of interacting proteins that can be exploited as drug targets. We are also making progress towards investigating the trypanosomatid ‘infectome’, by examining the interactions selected subset of T. brucei, T. cruzi and L. major proteins against the human ORFeome.
Functional Genomics - Characterization of a novel surface protein family (MASP) in Trypanosoma cruzi
Comparison of the gene content of the three parasites (El-Sayed
et al., 2005) revealed a conserved core of ~6200 genes. Many
of the species-specific genes encode for large families of
surface proteins. In T. cruzi, those include trans-sialidases,
mucins and a novel large gene family that we named mucin-associated
surface protein or MASP. The MASP family contains 1377 members
corresponding to ~6% of the T.cruzi diploid genome and is characterized
by conserved N- and C-terminal domains and a central highly
variable region. Despite the large size of the MASP family
in T.cruzi and its likely location on the parasite surface,
it has remained undetected. We are using combination
of approaches to functionally characterize the MASP family.
Our specific goals are as follows: 1) Investigate the expression
profile of MASP throughout the T.cruzi life cycle and in distinct
host cells; 2) Analyze the cellular
location of MASP; 3)
Investigate a potential role for MASP in host cell attachment
and invasion; 4) Test by ELISA whether MASP is recognized by
sera from chagasic patients; and 5) Investigate the mechanisms
of control of MASP expression throughout the parasite’s
life cycle. This work is being done in close collaboration
with Dr. Daniella Bartholomeu at the Universidade Federal de
Minas Gerais, Belo Horizonte, Brazil.
The Human Microbiome and Disease
Several connections between abnormal gut microflora and gastrointestinal (GI) disease have been established with abnormal flora observed in Crohn’s disease, Irritable Bowel Syndrome and many food allergies. Positive results from the intentional modulation of the gut flora in these cases have been reported recently. Furthermore, connections between gut dysbiosis and other human disorders not typically linked with gut health, such as autism spectrum disorder (ASD), have been made. Autism is a disorder characterized by a spectrum of developmental disorders affecting various aspects of social development. No underlying etiology has been determined. Early studies have correlated gut dysfunction with ASD and suggested a possible role for the GI microflora in the symptoms of autistic children. GI symptoms are common in childhood developmental disorders on the autistic spectrum. Anecdotal evidence also exists for the benefit of using GI-targeted antifungal, antibiotic and probiotic therapy, all of which affect gut flora. We are investigating the gut microflora in autistic children compared to neurotypical controls using culture-independent, high-throughput metagenomic approaches to: 1) Investigate the difference in microflora communities using 16S and 18S ribosomal DNA sequencing; 2) Develop biomarker profiles for the ASD gut by assessing differences in microbial community memberships between ASD and healthy children through sequence assembly, annotation and comparative analysis of gene content; and 3) Characterize the metabolic potential of the ASD gut microflora by community genomics. A thorough understanding of the composition, genomic content and functional potential of gut microflora communities in ASD children vs. neurotypical children is a critical and first step towards understanding the complex etiology of ASD.
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