Upinder Singh

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Comparative genomic hybridizations of Entamoeba strains reveal unique genetic fingerprints that correlate with virulence
    Preetam H Shah
    Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
    Eukaryot Cell 4:504-15. 2005
  2. pmc Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference
    Jason A Hackney
    Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
    Nucleic Acids Res 35:2141-52. 2007
  3. pmc Robust gene silencing mediated by antisense small RNAs in the pathogenic protist Entamoeba histolytica
    Laura Morf
    Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305 5107, USA and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 5107, USA
    Nucleic Acids Res 41:9424-37. 2013
  4. pmc Small RNAs with 5'-polyphosphate termini associate with a Piwi-related protein and regulate gene expression in the single-celled eukaryote Entamoeba histolytica
    Hanbang Zhang
    Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA
    PLoS Pathog 4:e1000219. 2008
  5. ncbi request reprint Context-dependent roles of the Entamoeba histolytica core promoter element GAAC in transcriptional activation and protein complex assembly
    Upinder Singh
    Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
    Mol Biochem Parasitol 120:107-16. 2002
  6. pmc Recent insights into Entamoeba development: identification of transcriptional networks associated with stage conversion
    Upinder Singh
    Department of Microbiology and Immunology, Stanford University School of Medicine, S 143 Grant Building, 300 Pasteur Drive, Stanford, CA 94305 5107, USA
    Int J Parasitol 39:41-7. 2009
  7. ncbi request reprint Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite
    Gretchen M Ehrenkaufer
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell Microbiol 9:1426-44. 2007
  8. pmc New insights into Entamoeba histolytica pathogenesis
    Leigh A Baxt
    Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
    Curr Opin Infect Dis 21:489-94. 2008
  9. pmc Downregulation of an Entamoeba histolytica rhomboid protease reveals roles in regulating parasite adhesion and phagocytosis
    Leigh A Baxt
    Department of Microbiology and Immunology, Stanford University School of Medicine, S 143 Grant Building, 300 Pasteur Drive, Stanford, CA 94305, USA
    Eukaryot Cell 9:1283-93. 2010
  10. ncbi request reprint Transcriptional profiling of Entamoeba histolytica trophozoites
    Ryan C MacFarlane
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 5124, USA
    Int J Parasitol 35:533-42. 2005

Collaborators

Detail Information

Publications43

  1. pmc Comparative genomic hybridizations of Entamoeba strains reveal unique genetic fingerprints that correlate with virulence
    Preetam H Shah
    Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
    Eukaryot Cell 4:504-15. 2005
    ..This microarray-based genotyping assay can readily be applied to the study of E. histolytica clinical isolates to determine genetic diversity and potential genotypic-phenotypic associations...
  2. pmc Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference
    Jason A Hackney
    Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
    Nucleic Acids Res 35:2141-52. 2007
    ..Our analysis suggests that transcriptional regulatory networks can be identified using limited expression data. Thus, this approach is applicable to the multitude of systems for which microarray and genome sequence data are emerging...
  3. pmc Robust gene silencing mediated by antisense small RNAs in the pathogenic protist Entamoeba histolytica
    Laura Morf
    Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305 5107, USA and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 5107, USA
    Nucleic Acids Res 41:9424-37. 2013
    ..histolytica with many advantages over currently available technologies. Additionally, these data shed mechanistic insights into a eukaryotic RNA interference pathway with many novel aspects. ..
  4. pmc Small RNAs with 5'-polyphosphate termini associate with a Piwi-related protein and regulate gene expression in the single-celled eukaryote Entamoeba histolytica
    Hanbang Zhang
    Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA
    PLoS Pathog 4:e1000219. 2008
    ..elegans, and which appear to regulate gene expression. These data indicate that a silencing pathway mediated by 5'-polyphosphate siRNAs extends to single-celled eukaryotic organisms...
  5. ncbi request reprint Context-dependent roles of the Entamoeba histolytica core promoter element GAAC in transcriptional activation and protein complex assembly
    Upinder Singh
    Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
    Mol Biochem Parasitol 120:107-16. 2002
    ..The differing effect on transcription initiation in the hgl5 and fdx genes upon mutation of the GAAC element suggests a context-dependence of the GAAC-binding protein in gene expression...
  6. pmc Recent insights into Entamoeba development: identification of transcriptional networks associated with stage conversion
    Upinder Singh
    Department of Microbiology and Immunology, Stanford University School of Medicine, S 143 Grant Building, 300 Pasteur Drive, Stanford, CA 94305 5107, USA
    Int J Parasitol 39:41-7. 2009
    ..Recent progress in dissecting the transcriptional networks that regulate E. histolytica development is outlined in this paper...
  7. ncbi request reprint Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite
    Gretchen M Ehrenkaufer
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell Microbiol 9:1426-44. 2007
    ..These advances lay the groundwork for dissection of the molecular signals that initiate stage conversion and development of novel diagnostic and therapeutic measures targeting E. histolytica cysts...
  8. pmc New insights into Entamoeba histolytica pathogenesis
    Leigh A Baxt
    Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
    Curr Opin Infect Dis 21:489-94. 2008
    ..Entamoeba histolytica is an important global pathogen and a leading cause of parasitic death worldwide. This article summarizes significant research findings over the last year...
  9. pmc Downregulation of an Entamoeba histolytica rhomboid protease reveals roles in regulating parasite adhesion and phagocytosis
    Leigh A Baxt
    Department of Microbiology and Immunology, Stanford University School of Medicine, S 143 Grant Building, 300 Pasteur Drive, Stanford, CA 94305, USA
    Eukaryot Cell 9:1283-93. 2010
    ..These results suggest no significant role of EhROM1 in complement resistance but unexpected roles in parasite adhesion and phagocytosis...
  10. ncbi request reprint Transcriptional profiling of Entamoeba histolytica trophozoites
    Ryan C MacFarlane
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 5124, USA
    Int J Parasitol 35:533-42. 2005
    ..Using Caco-2 cells to model the host-parasite interaction, we verified that host cell killing was dependent on live ameba. However, surprisingly these events did not appear to induce major transcriptional changes in the parasites...
  11. pmc Short hairpin RNA-mediated knockdown of protein expression in Entamoeba histolytica
    Alicia S Linford
    Department of Microbiology, University of Virginia, Charlottesville, Virginia, USA
    BMC Microbiol 9:38. 2009
    ..We chose to test the use of RNA interference to knock down gene expression in Entamoeba histolytica...
  12. pmc Disruption of a locus encoding a nucleolar zinc finger protein decreases tachyzoite-to-bradyzoite differentiation in Toxoplasma gondii
    Padmini Vanchinathan
    Department of Internal Medicine, Division of Infectious Diseases, Stanford University School of Medicine, California 94305 5124, USA
    Infect Immun 73:6680-8. 2005
    ..This represents the first identification of a gene necessary for efficient conversion of tachyzoites to bradyzoites...
  13. pmc A developmentally regulated Myb domain protein regulates expression of a subset of stage-specific genes in Entamoeba histolytica
    Gretchen M Ehrenkaufer
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 5107, USA
    Cell Microbiol 11:898-910. 2009
    ..histolytica. Identification of transcriptional regulatory networks that control developmental pathways will provide novel insights into the biology of this important human pathogen...
  14. pmc Entamoeba histolytica modulates a complex repertoire of novel genes in response to oxidative and nitrosative stresses: implications for amebic pathogenesis
    João B Vicente
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 5107, USA
    Cell Microbiol 11:51-69. 2009
    ..histolytica...
  15. pmc Growth of the protozoan parasite Entamoeba histolytica in 5-azacytidine has limited effects on parasite gene expression
    Ibne Karim M Ali
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 5107, USA
    BMC Genomics 8:7. 2007
    ..However, the overall extent of DNA methylation and its subsequent effects on global gene expression in this parasite are currently unknown...
  16. pmc Oxidative stress resistance genes contribute to the pathogenic potential of the anaerobic protozoan parasite, Entamoeba histolytica
    Elena Rastew
    Department of Internal Medicine, Stanford University School of Medicine, Stanford, CA, USA
    Int J Parasitol 42:1007-15. 2012
    ..Our data imply that stress response genes may play multi-factorial roles in amoebic pathogenesis...
  17. pmc Toxoplasma gondii asexual development: identification of developmentally regulated genes and distinct patterns of gene expression
    Michael D Cleary
    Department of Microbiology and Immunology, Stanford University, Stanford, California 94305 5124, USA
    Eukaryot Cell 1:329-40. 2002
    ..This analysis permits the first in-depth look at changes in gene expression during development of this complex protozoan parasite...
  18. pmc Regulation of H2O2 stress-responsive genes through a novel transcription factor in the protozoan pathogen Entamoeba histolytica
    Richard J Pearson
    Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
    J Biol Chem 288:4462-74. 2013
    ..Overexpression of EHI_108720 increased parasite virulence. Insight into how E. histolytica responds to oxidative stress increases our understanding of how this important human pathogen establishes invasive disease...
  19. pmc Trichostatin A effects on gene expression in the protozoan parasite Entamoeba histolytica
    Gretchen M Ehrenkaufer
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 5107, USA
    BMC Genomics 8:216. 2007
    ..Additionally, a number of active histone modifying enzymes have been identified in the parasite genome. However, the overall extent of gene regulation tied to histone acetylation is not known...
  20. ncbi request reprint Transcriptional regulatory networks in Entamoeba histolytica
    Gretchen M Ehrenkaufer
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 5107, USA
    Curr Drug Targets 9:931-7. 2008
    ....
  21. pmc Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes
    Hanbang Zhang
    Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305 5107, USA
    BMC Genomics 14:53. 2013
    ..Small RNA mediated gene silencing is a well-conserved regulatory pathway. In the parasite Entamoeba histolytica an endogenous RNAi pathway exists, however, the depth and diversity of the small RNA population remains unknown...
  22. ncbi request reprint Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome
    Carol A Gilchrist
    Department of Internal Medicine, University of Virginia, Charlottesville, VA 22908 1340, USA
    Mol Biochem Parasitol 147:163-76. 2006
    ....
  23. ncbi request reprint Genomic DNA microarrays for Entamoeba histolytica: applications for use in expression profiling and strain genotyping
    Ryan MacFarlane
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 5124, USA
    Exp Parasitol 110:196-202. 2005
    ..We present a synopsis of our results to date and potential future applications of microarray technology for the study of Entamoeba biology...
  24. pmc Identification of differentially expressed genes in virulent and nonvirulent Entamoeba species: potential implications for amebic pathogenesis
    Ryan C MacFarlane
    Department of Medicine, Division of Infectious Diseases, S 143 Grant Building, 300 Pasteur Drive, Stanford, CA 94305, USA
    Infect Immun 74:340-51. 2006
    ..histolytica HM-1:IMSS. Our results, identifying expression profiles and patterns indicative of a virulence phenotype, may be useful in characterizing the transcriptional framework of virulence...
  25. pmc Entamoeba histolytica: a snapshot of current research and methods for genetic analysis
    Laura Morf
    Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, CA, United States
    Curr Opin Microbiol 15:469-75. 2012
    ..We end by highlighting some of the many questions that remain to be answered in order to fully understand this important human pathogen...
  26. pmc A detoxifying oxygen reductase in the anaerobic protozoan Entamoeba histolytica
    João B Vicente
    Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA
    Eukaryot Cell 11:1112-8. 2012
    ..This observation represents a new mechanism of oxygen resistance in the anaerobic protozoan pathogen E. histolytica...
  27. pmc Coding and noncoding genomic regions of Entamoeba histolytica have significantly different rates of sequence polymorphisms: implications for epidemiological studies
    Dhruva Bhattacharya
    Department of Microbiology and Immunology, Division of Infectious Diseases, Stanford, CA 94305, USA
    J Clin Microbiol 43:4815-9. 2005
    ..07% and 0.37%, respectively), indicating that these regions are subject to different selection pressures. Additionally, single nucleotide polymorphisms (SNPs) potentially associated with specific clinical outcomes were identified...
  28. pmc RNA interference in Entamoeba histolytica: implications for parasite biology and gene silencing
    Hanbang Zhang
    Stanford University School of Medicine, S 143 Grant Building, 300 Pasteur Drive, Stanford, CA 94305, USA
    Future Microbiol 6:103-17. 2011
    ....
  29. pmc Loss of dsRNA-based gene silencing in Entamoeba histolytica: implications for approaches to genetic analysis
    Ryan C MacFarlane
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 5124, USA
    Exp Parasitol 119:296-300. 2008
    ..Thus, users of the dsRNA silencing approach should proceed with caution and regularly confirm gene down regulation. The development and use of constructs for inducible expression of dsRNA may help alleviate this potential problem...
  30. ncbi request reprint Approaches to characterizing Entamoeba histolytica transcriptional regulation
    Richard J Pearson
    Department of Internal Medicine, Division of Infectious Diseases, S 143 Grant Building, 300 Pasteur Drive, Stanford, CA 94305, USA
    Cell Microbiol 12:1681-90. 2010
    ..In this review, we have looked at how molecular technological advances have shaped our understanding of transcriptional regulation in amoeba and what we may expect from the application of powerful new techniques...
  31. pmc Nucleus-localized antisense small RNAs with 5'-polyphosphate termini regulate long term transcriptional gene silencing in Entamoeba histolytica G3 strain
    Hanbang Zhang
    Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305 5107, USA
    J Biol Chem 286:44467-79. 2011
    ..To our knowledge, this is the first study to show that 5'- polyphosphate antisense sRNAs can mediate TGS, and it is the first example of RNAi-mediated TGS in protozoan parasites...
  32. pmc Identification of an Entamoeba histolytica serine-, threonine-, and isoleucine-rich protein with roles in adhesion and cytotoxicity
    Ryan C MacFarlane
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 5124, USA
    Eukaryot Cell 6:2139-46. 2007
    ..This work validates the fact that genes expressed exclusively in virulent strains may represent virulence determinants and highlights the need for further functional analyses of other genes with similar expression profiles...
  33. pmc A pseudouridine synthase homologue is critical to cellular differentiation in Toxoplasma gondii
    Matthew Z Anderson
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    Eukaryot Cell 8:398-409. 2009
    ..Our results suggest a surprising and important role for RNA modification in this biological process...
  34. ncbi request reprint Genetic analysis of tachyzoite to bradyzoite differentiation mutants in Toxoplasma gondii reveals a hierarchy of gene induction
    Upinder Singh
    D305 Fairchild Building, Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305 5124, USA
    Mol Microbiol 44:721-33. 2002
    ..gondii. Our approach shows the utility of this system as a model to study developmental biology in single-celled eukaryotes including protozoa and fungi...
  35. ncbi request reprint DNA microarrays in parasitology: strengths and limitations
    John C Boothroyd
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Trends Parasitol 19:470-6. 2003
    ..However, many parasitologists work on organisms whose genomes have been only partially sequenced and where little, if any, annotation is available. The focus of this review is on how to use and apply microarrays to these situations...
  36. pmc Transient and stable transfection in the protozoan parasite Entamoeba invadens
    Gretchen M Ehrenkaufer
    Division of Infectious Diseases, Department of Internal Medicine, Stanford University, Stanford, CA 94305 5107, USA
    Mol Biochem Parasitol 184:59-62. 2012
    ..invadens have been limited by the lack of genetic tools in this species. Here, we report a new method for both transient and stable transfection of E. invadens. These new tools will greatly enhance research into Entamoeba development...
  37. pmc Functional characterization of spliceosomal introns and identification of U2, U4, and U5 snRNAs in the deep-branching eukaryote Entamoeba histolytica
    Carrie A Davis
    Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
    Eukaryot Cell 6:940-8. 2007
    ..Finally, we provided molecular evidence for the E. histolytica U2, U4, and U5 snRNAs. These data lay the foundation for further dissection of the role of RNA processing in E. histolytica gene expression...
  38. pmc An Entamoeba histolytica rhomboid protease with atypical specificity cleaves a surface lectin involved in phagocytosis and immune evasion
    Leigh A Baxt
    Department of Internal Medicine and Microbiology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Genes Dev 22:1636-46. 2008
    ..Collectively these results implicate rhomboid proteases for the first time in immune evasion and suggest that a common function of rhomboid enzymes in widely divergent protozoan pathogens is to break down adhesion proteins...
  39. pmc Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States
    Audrie Lin
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 8:e53838. 2013
    ..In contrast, little is known about the gut microbiota and its variation over time in older children and adolescents, especially in developing countries...
  40. pmc Antiparasitic therapy
    Shanthi Kappagoda
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 5107, USA
    Mayo Clin Proc 86:561-83. 2011
    ....
  41. ncbi request reprint DNA content analysis on microarrays
    Upinder Singh
    Department of Internal Medicine, Stanford University, CA, USA
    Methods Mol Biol 270:237-48. 2004
    ..This chapter outlines the utilization of DNA microarrays to study genomic content...
  42. ncbi request reprint Identification and characterization of differentiation mutants in the protozoan parasite Toxoplasma gondii
    Mariana Matrajt
    Department of Biology, University of Pennsylvania, Philadelphia 19104 6018, USA
    Mol Microbiol 44:735-47. 2002
    ..Microarray hybridizations show that these mutants behave more like tachyzoites at a global level, even under bradyzoite differentiation conditions...
  43. ncbi request reprint The genome of the protist parasite Entamoeba histolytica
    Brendan Loftus
    TIGR, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 433:865-8. 2005
    ..Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen...

Research Grants13

  1. Investigating Entamoeba histolytica Colonic Pathogenesis
    Upinder Singh; Fiscal Year: 2003
    ....
  2. Investigating Entamoeba histolytica Colonic Pathogenesis
    Upinder Singh; Fiscal Year: 2010
    ..Events such as the Tsunami or upheaval in the political and social infrastructure of a region can allow disease to emerge. We are interested in understanding the molecular mechanisms that the parasite uses to cause disease. ..
  3. Investigating Entamoeba histolytica Colonic Pathogenesis
    Upinder Singh; Fiscal Year: 2009
    ..Events such as the Tsunami or upheaval in the political and social infrastructure of a region can allow disease to emerge. We are interested in understanding the molecular mechanisms that the parasite uses to cause disease. ..
  4. Identification of Transcriptional Regulatory Networks in Entamoeba Histolytica
    Upinder Singh; Fiscal Year: 2007
    ..Events such as the Tsunami or upheaval in the political and social infrastructure of a region can allow disease to emerge. We are interested in understanding the molecular mechanisms that the parasite uses to cause disease. ..
  5. Developing Tools to Study Encystation in Entamoeba Histolytica
    Upinder Singh; Fiscal Year: 2007
    ..We are interested in understanding the life stages of the parasite with the goal of identifying new ways to diagnose, treat, and prevent human infections. ..
  6. Investigating Entamoeba histolytica Colonic Pathogenesis
    Upinder Singh; Fiscal Year: 2007
    ..abstract_text> ..
  7. Assessing Genetic Diveristy in Entamoeba Histolytica
    Upinder Singh; Fiscal Year: 2006
    ..This approach will also provide a number of novel genetic targets for the development of improved epidemiological markers, diagnostic assays, and treatment strategies. ..
  8. Investigating Entamoeba histolytica Colonic Pathogenesis
    Upinder Singh; Fiscal Year: 2006
    ..abstract_text> ..
  9. Investigating Entamoeba histolytica Colonic Pathogenesis
    Upinder Singh; Fiscal Year: 2010
    ..Events such as the Tsunami or upheaval in the political and social infrastructure of a region can allow disease to emerge. We are interested in understanding the molecular mechanisms that the parasite uses to cause disease. ..