David S Roos

E. Otis Kendall Professor of Biology
304B Carolyn Lynch Laboratories
droos@sas.upenn.edu
215-898-2118
Evolution
Microbiology
Cell and Developmental Biology
Genetics, Epigenetics, Genomics
Computational Biology
Research Interests: 

Studies in the Roos laboratory employ modern cell biological, molecular genetic, biochemical/pharmacological, immunological and genomic/bioinformatic techniques to study protozoan parasites, eukaryotic evolution, and the biology of host-pathogen interactions.  At present, our primary focus is on the phylum Apicomplexa, including Plasmodium (the causative agent of malaria) and Toxoplasma (notorious as a congenital pathogen, an opportunistic infection associated with AIDS and other immunosuppressed conditions, and a biosecurity threat to public water supplies).  We work on these organisms both because of their clinical and veterinary importance, and for the perspectives that they provide on eukaryotic biology and evolution.  Some recent reviews and commentary of possible interest:

  • Beiting DP & Roos DS (2011) A systems biological view of intracellular pathogens. Immunol Rev 240:117-28. PMID 21349090.
  • Chaudhary K & Roos DS (2005) Protozoan genomics for drug discovery. Nature Biotech 23:1089-91. PMID 16151400.
  • Roos DS (2005) Themes and variations in apicomplexan parasite biology. Science 309:72-3. PMID 15994520.
  • Joiner KA & Roos DS (2002) Secretory traffic in Toxoplasma gondii: Less is more. J Cell Biol 157:557-63. PMID 12011107.
  • Roos DS (2001) Bioinformatics -- Trying to swim in a sea of data. Science 291:1260-1. PMID 11233452.

Genetic Analysis of Parasite Biology and Host-Pathogen Interactions

The ability to saturate the T. gondii genome by insertional mutagenesis, target defined loci for genetic deletion or allelic replacement, and control the expression of recombinant proteins makes forward genetic approaches feasible in these parasites.  Similarly, the availability of extensive libraries of small molecules, host cell cDNAs and siRNA inhibitors, permits complementary reverse- and chemical-genetic approaches.  Successful expression of fluorescent, luminescent and enzymatic reporters facilitates analysis of transgenic parasites in living cells and animal tissues.  New genotyping methodology enables studies on a population scale.  These tools have been exploited to elucidate such diverse phenomena as the molecular mechanisms of drug action and resistance, temporal and developmental controls regulating differentiation through the complex parasite life cycle, host responses to infection, and the population biology of parasite evolution.  Selected references:

  • Khan A et al (2011) A monomorphic haplotype of chromosome Ia is associated with widespread success in clonal and nonclonal populations of Toxoplasma gondii. mBio 2:e00228. PMID 22068979.
  • Bahl A et al (2010) A novel multifunctional oligonucleotide microarray for Toxoplasma gondii. BMC Genomics 11:603. PMID 20974635.
  • Tait ED et al (2010) Virulence of Toxoplasma gondii is associated with distinct dendritic cell responses and reduced activation of CD8+ T cells. J Immunol 185:1502-122. PMID20592284.
  • Guiguemde WA et al (2010) Chemical genetics of Plasmodium falciparum. Nature 465:311-5. PMID 20485428.
  • Zhang M et al (2010) Plasmodium sporozoite development in the mammalian host is controlled by phosphorylation of eukaryotic initiation factor 2?. J Exper Med 207:1465-74. PMID 20584882.
  • Dzierszinski F et al (2007) Presentation of Toxoplasma gondii antigens via the endogenous MHC class I pathway in nonprofessional and professional antigen-presenting cells. Infect Immun 75:5200-9. PMID 17846116.
  • Boyle JP et al (2006) Just one cross appears capable of dramatically altering the population biology of the eukaryotic pathogen Toxoplasma gondii. PNAS 103:10514-9. PMID 16801557.
  • Shapira S et al (2005) Initiation and termination of NF-kappaB signaling by the intracellular protozoan parasite Toxoplasma gondii. J Cell Sci 118:3501-8. PMID 16079291.
  • Dzierszinski F, Nishi M, Ouko L & Roos DS (2004) Dynamics of Toxoplasma gondii differentiation. Eukaryotic Cell 3:992-1003. PMID 15302832.
  • Matrajt M, Donald RGK, Singh U & Roos DS (2002) Identification and characterization of differentiation mutants in the protozoan parasite Toxoplasma gondii. Molec Microbiol 44:735-7. PMID 11994154.

Evolutionary Cell Biology

These parasites exhibit a remarkable diversity of subcellular organelles, in a stripped-down package facilitating analysis of both common eukaryotic features and novel attributes of interest as therapeutic targets.  The former includes studies on Golgi biogenesis, vesicular trafficking, and cytoskeletal organization, while the latter includes the discovery, biochemical and cell biological characterization of the apicoplast — a nonphotosynthetic plastid acquired when an ancestral parasite 'ate' a eukaryotic alga, and retained the algal plastid (secondary endosymbiosis).  The 'apicoplast' is essential for parasite survival, and widely viewed as a promising target for drug development.  Current research focuses on the apical complex of specialized organelles that give this phylum its name, including 'micronemes' and 'rhoptries' essential for host cell invasion, modulation of host cell activities, and establishment of the unique intracellular niche in which parasites reside.  We are also exploring the unusual process by which parasites replicate, constructing daughters within the mother in a process conceptually analogous to viral self-assembly, suggesting unknown mechanisms of cell cycle regulation.  Selected references:

  • Jaffe EK et al (2011) Crystal structure of Toxoplasma gondii porphobilinogen synthase: Insights on octameric structure and porphobilinogen formation. J Biol Chem 286:15298-307. PMID 21383008.
  • Peixoto L et al (2010) Integrative genomic approaches highlight a family of parasite-specific kinases that regulate host responses. Cell Host & Microbe 8:208-18. PMID 20709297.
  • Chandramohandas R et al (2009) Apicomplexan parasites co-opt host calpains to facilitate their escape from infected host cells. Science 324:794-7. PMID 19342550.
  • Nishi M, Hu K, Murray JM & Roos DS (2008) How to build a parasite: Organellar dynamics during the cell cycle of Toxoplasma gondii. J Cell Sci 121:559-68. PMID 18411248.
  • Crawford MJ et al (2006) Toxoplasma gondii scavenges host-derived lipoic acid despite its de novo synthesis in the apicoplast. EMBO J 25:3214-22. PMID 16778769.
  • Hu K et al (2006) Cytoskeletal components of an invasion machine: The apical complex of Toxoplasma gondii. PLoS Pathogens 2:e13. PMID 16518471.
  • Harb OS et al (2004) Multiple functionally redundant signals mediate targeting to the apicoplast in Toxoplasma gondii. Eukaryotic Cell 3:663-674. PMID 15189987.
  • Ralph SA et al (2004) Metabolic pathway maps and functions of the Plasmodium falciparum apicoplast. Nature Rev Microbiol 2:203-16. PMID 15083156.
  • Pelletier L et al (2002) Golgi biogenesis in Toxoplasma gondii. Nature 418:548-52. PMID 12152082.
  • Hu K, Roos DS & Murray JM. A novel polymer of tubulin forms the conoid in Toxoplasma gondii. J Cell Biol 156:1039-50. PMID 11901169.
  • Hager KM, B Striepen, LG Tilney & DS Roos (1999) The nuclear envelope serves as an intermediary between the ER and Golgi complex in the intracellular parasite Toxoplasma gondii.  J Cell Sci 112:2631-2638.  PMID 10413671.
  • Fichera ME & Roos DS (1997) A plastid drug target in apicomplexan parasites. Nature 389:407-9. PMID 9389481.
  • Köhler S et al (1997) A plastid of probable green algal origin in apicomplexan parasites. Science 275:1485-8. PMID 9045615.

Computational Biology: Designing and Mining (Pathogen) Genome Databases

As genomic-scale datasets have come to the fore, we have played an active role in developing tools for generating, managing, mining, and analyzing this information, with a particular interest in comparative genomics.  Bioinformatics research projects have yielded algorithmic improvements in gene finding and the identification and validation of ortholog groups.  Working with a diverse group of colleagues around the world, we are also responsible for production informatics resources for ortholog identification (OrthoMCL.org), drug target prioritization (TDRtargets.org), and pathogen genomics (EuPathDB.org).  Coupling computational database mining with laboratory analysis provides new insights into eukaryotic biology and evolution, and facilitates the identification of targets for drug/vaccine/diagnostic development.  We are also actively engaged in cell biology and bioinformatics training programs around the world.  Selected references:

  • Reid AJ et al (2012) Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog 8:e1002567.  PMID 22457617.
  • Magariños MP et al (2012) TDR Targets: a chemogenomics resource for neglected diseases.  Nucl Acids Res 40:D1118-27.  PMID 22116064.
  • Stajich JE et al (2012) FungiDB and integrated functional genomics database for fungi. Nucl Acids Res 40:D675-81. PMID 22064857.
  • Peterson ME et al (2009) Evolutionary constraints on structural similarity in orthologs and paralogs. Prot Sci 18:1306-15. PMID 19472362.
  • Agüero F et al (2008) Genomic-scale prioritization of drug targets: TDRtargets.org. Nature Drug Discovery 7:900-7. PMID 18927591.
  • Liu Q, Crammer K, Pereira FCN & Roos DS (2008) Reranking candidate gene models with cross-species comparison for improved gene prediction. BMC Bioinformatics 9:433. PMID 18854050.
  • Liu Q, Mackey AJ, Roos DS & Pereira FCN (2008) Evigan: A hidden variable model for integrating gene evidence for eukaryotic gene prediction. Bioinformatics 24:597-605. PMID 19197439.
  • Chen F, Mackey AJ, Vermunt JK, Roos DS (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS1 2:e383. PMID 17440619.
  • Gardner MJ et al (2002) The genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419:498-511. PMID 12368864.
  • Kissinger JC et al (2002) The Plasmodium Genome Database. A eukaryotic genomics resource. Nature 419:490-2. PMID 12368860.
Courses Taught: 

Biology 202:  Introduction to Biochemistry & Cell Biology

Biology 406:  Molecular Mechanisms of Infectious Disease Biology

CAMB 549:  Parasites & Parasitism