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Structural and Computational Biology and Molecular Biophysics

Houston, Texas

A BCM research lab.
Structural and Computational Biology & Molecular Biophysics
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Gad Shaulsky, Ph.D.

Gad Shaulsky, Ph.D.Professor, Molecular and Human Genetics

Baylor College of Medicine


B.Sc. Biology, Tel Aviv University, Israel (1985)
M.Sc. Biochemistry, Tel Aviv University, Israel (1986)
Ph.D. Cell Biology, The Weizmann Institute of Science, Rehovot, Israel (1991)
Postdoctoral: Department of Biology, UC San Diego

Research Interests:

Self-recognition in Dictyostelium
Self-recognition in Dictyostelium. Two strains, labeled in green and red, segregate from each other during the aggregation phase of development thanks to a novel self-recognition mechanism. Photography: Shigenori Hirose.

Functional genomics: In the past we have used microarrays to discover gene function in development, de-differentiation, spore germination, drug resistance, and chemotaxis (e.g. Booth et al., 2005; Van Driessche et al., 2007). We also showed that the transcriptome is a good phenotyping tool for discovering epistatic relationships between genes in the cAMP-dependent Protein Kinase regulatory pathway (Van Driessche et al., 2005). Recently, we started to use RNA-sequencing as our main platform for transcriptional profiling. We compared the developmental transcriptomes of D. discoideum and D. purpureum, two Dictyostelium species whose genomes are as different from each other as the genomes of humans and jawed fish, but whose developmental morphologies are very similar. We found vast similarities between the two transcriptomes (Parikh et al., 2010). The data are available for interactive exploration on dictyExpress. In collaboration with Dr. Adam Kuspa at BCM we are generating thousands of mutant Dictyostelium strains and we are analyzing them using transcriptional profiling. We are currently focused on several transcription factors and on the response of Dictyostelium cells to different types of bacteria.

The evolution of social behavior in Dictyostelium: Social organisms must deal with cheaters - individuals that reap the benefits of sociality without paying the costs. In Dictyostelium, some cells sacrifice themselves and benefit other cells that may be genetically different, providing a fertile ground for cheating. In collaboration with Drs. Strassmann and Queller at Rice University and with Dr. Adam Kuspa at BCM, we found over 100 genes that participate in social interactions (Santorelli et al., 2008). We are using genetic tools to characterize mechanisms that determine social interactions and test how cooperators resist cheating (Khare and Shaulsky, 2006; Khare et al., 2009; Khare and Shaulsky, 2010).

Allorecognition in Dictyostelium: Multicellular organisms can distinguish self from non-self through various mechanisms. We have found that D. discoideum cells preferentially cooperate with their relatives (Ostrowski et al., 2008), possibly reducing their exposure to strains that can cheat on them. We are now investigating the molecular mechanisms that underlie kin discrimination. We found two cell-cell adhesion genes, tgrB1 and tgrC1, that are highly polymorphic in natural populations and are required for allorecognition (Benabentos et al., 2009). Gene replacement experiments have shown that the sequence polymorphism in these genes is sufficient to explain allorecognition in this system (Hirose et al., 2011). We are investigating the cellular and genetic mechanisms that regulate allorecognition.

Data Mining: We are collaborating with Dr. Blaz Zupan and his group at the University of Ljubljana in Slovenia to develop new concepts in genetic analysis. Previously we have developed a tool that performs automated epistasis analysis, GenePath. We also developed dictyExpress, a web tool that can access and analyze our transcriptional profiling data. We are in the process of developing a tool for automated analysis of RNA-sequencing data.

Selected Publications

  • Nasser W, Santhanam B, Miranda ER, Parikh A, Juneja K, Rot G, Dinh C, Chen R, Zupan B, Shaulsky G and Kuspa A. Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions. Curr Biol, 23(10):862-72 (2013). PubMed
  • Miranda ER, Rot G, Toplak M, Santhanam B, Curk T, Shaulsky G and Zupan B. Transcriptional profiling of Dictyostelium with RNA sequencing. Methods Mol Biol, 983:139-71 (2013). PubMed
  • Shigenori H, Benabentos R, Ho HI, Kuspa A and Shaulsky G. Self-recognition in social amoebae is mediated by allelic pairs of tiger genes. Science, 333: 467-70 (2011).
  • Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis WF, Kuspa A, Shaulsky G. Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol., 11(3): R35 (2010). Pub Med
  • Khare A and Shaulsky G. Cheating by exploitation of developmental prestalk patterning in Dictyostelium discoideum. PLoS Genet., 6(2): e1000854 (2010). Pub Med
  • Khare A, Santorelli LA, Strassmann JE, Queller DC, Kuspa A and Shaulsky G. Cheater-resistance is not futile. Nature, 461(7266): 980-2 (2009). Pub Med
  • Benabentos R, Hirose S, Sucgang R, Curk T, Katoh M, Ostrowski EA, Strassmann JE, Queller DC, Zupan B, Shaulsky G and Kuspa A. Polymorphic Members of the lag Gene Family Mediate Kin Discrimination in Dictyostelium. Curr. Biol., 19(7): 567-572 (2009). Pub Med

Contact Information:

Department: Molecular and Human Genetics
Address: Baylor College of Medicine
One Baylor Plaza
Room S930
Houston, Texas 77030, U.S.A.
Phone: 713-798-8082
Fax: 713-798-1021

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