Thoru Pederson

Summary

Affiliation: University of Massachusetts Medical School
Country: USA

Publications

  1. pmc As functional nuclear actin comes into view, is it globular, filamentous, or both?
    Thoru Pederson
    Program in Cell Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    J Cell Biol 180:1061-4. 2008
  2. pmc "Tall oaks fallen": Three Pioneers of Chromosome Science
    Thoru Pederson
    Program in Cell and Developmental Dynamics Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester, MA USA
    Nucleus 3:113-4. 2012
  3. doi request reprint The nuclear physique
    Thoru Pederson
    Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA Electronic address
    Int Rev Cell Mol Biol 307:1-13. 2014
  4. pmc The "study" role of past National Institutes of Health study sections
    Thoru Pederson
    Program in Cell and Developmental Dynamics and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Biol Cell 23:3281-4. 2012
  5. ncbi request reprint 50 years ago protein synthesis met molecular biology: the discoveries of amino acid activation and transfer RNA
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    FASEB J 19:1583-4. 2005
  6. pmc Nuclear actin extends, with no contraction in sight
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Biol Cell 16:5055-60. 2005
  7. ncbi request reprint New surprises in genetic coding and how an ingenious experiment was almost scooped, by evolution
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, Program in Cell Dynamics, University of Massachusetts Medical School, 377 Plantation St, Worcester, MA 01605, USA
    FASEB J 20:1759-60. 2006
  8. ncbi request reprint The spatial organization of the genome in mammalian cells
    Thoru Pederson
    Program in Cell Dynamics and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Curr Opin Genet Dev 14:203-9. 2004
  9. ncbi request reprint Reflections on the prize of prizes: Alfred Nobel
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, and The Worcester Foundation for Biomedical Research, Worcester, Massachusetts 01605, USA
    FASEB J 20:2186-9. 2006
  10. pmc Diffraction at the Brandenburg G(r)ate. Symposium on the optical analysis of biomolecular machines
    Thoru Pederson
    Program in Cell Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    EMBO Rep 7:1202-5. 2006

Research Grants

  1. RNA PROCESSING AND RIBONUCLEOPROTEIN
    Thoru Pederson; Fiscal Year: 2001
  2. RNA Transport Within the Nucleus
    Thoru Pederson; Fiscal Year: 2005

Detail Information

Publications53

  1. pmc As functional nuclear actin comes into view, is it globular, filamentous, or both?
    Thoru Pederson
    Program in Cell Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    J Cell Biol 180:1061-4. 2008
    ..Both studies are critically discussed here, and although there are several issues to be resolved, it now seems reasonable to start thinking about functions for both monomeric and assembled actin in the nucleus...
  2. pmc "Tall oaks fallen": Three Pioneers of Chromosome Science
    Thoru Pederson
    Program in Cell and Developmental Dynamics Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester, MA USA
    Nucleus 3:113-4. 2012
    ..Here I offer remembrances of each of them, not as definitive memoirs but simply with the goal of informing the next generation about pioneers whose names they may hardly know today...
  3. doi request reprint The nuclear physique
    Thoru Pederson
    Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA Electronic address
    Int Rev Cell Mol Biol 307:1-13. 2014
    ..So, much credit is due to Ronald Hancock and Kwang Jeon, the coeditors of this volume, and all the authors for creating a work that is so au courant. ..
  4. pmc The "study" role of past National Institutes of Health study sections
    Thoru Pederson
    Program in Cell and Developmental Dynamics and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Biol Cell 23:3281-4. 2012
    ..We might ponder whether today's study sections, although more overworked than Sisyphus, should again take up this second function...
  5. ncbi request reprint 50 years ago protein synthesis met molecular biology: the discoveries of amino acid activation and transfer RNA
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    FASEB J 19:1583-4. 2005
  6. pmc Nuclear actin extends, with no contraction in sight
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Biol Cell 16:5055-60. 2005
    ....
  7. ncbi request reprint New surprises in genetic coding and how an ingenious experiment was almost scooped, by evolution
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, Program in Cell Dynamics, University of Massachusetts Medical School, 377 Plantation St, Worcester, MA 01605, USA
    FASEB J 20:1759-60. 2006
    ..Now it has been discovered that archaebacteria had been doing a related kind of "experiment" all along. Both involve a trick: changing an amino acid that is already attached to a "correct" transfer RNA...
  8. ncbi request reprint The spatial organization of the genome in mammalian cells
    Thoru Pederson
    Program in Cell Dynamics and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Curr Opin Genet Dev 14:203-9. 2004
    ..The arrangement of chromosomes in the nucleus also has been investigated by the analysis of chromosomal translocations, with some surprising recent findings...
  9. ncbi request reprint Reflections on the prize of prizes: Alfred Nobel
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, and The Worcester Foundation for Biomedical Research, Worcester, Massachusetts 01605, USA
    FASEB J 20:2186-9. 2006
  10. pmc Diffraction at the Brandenburg G(r)ate. Symposium on the optical analysis of biomolecular machines
    Thoru Pederson
    Program in Cell Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    EMBO Rep 7:1202-5. 2006
  11. ncbi request reprint The sea urchin's siren
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, Program in Cell Dynamics, University of Massachusetts Medical School, 377 Plantation Street, Worcester, MA 01605, USA
    Dev Biol 300:9-14. 2006
    ..Like all of us, I am excited to see the S. purpuratus genome appear and heartily congratulate, by writing this essay, the trailblazers whose intellectual courage and persistence has brought us to this happy position...
  12. ncbi request reprint Counterpoint: Statistical analysis in NIH peer review--identifying innovation
    Thoru Pederson
    University of Massachusetts Medical School, 377 Plantation St, Worcester, MA 01605, USA
    FASEB J 21:309-10; discussion 311. 2007
  13. ncbi request reprint Ribosomal protein mutations in Diamond-Blackfan anemia: might they operate upstream from protein synthesis?
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 377 Plantation St, Worcester, MA 01605, USA
    FASEB J 21:3442-5. 2007
    ....
  14. doi request reprint Turning a PAGE: the overnight sensation of SDS-polyacrylamide gel electrophoresis
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 377 Plantation St, Worcester, MA 01605, USA
    FASEB J 22:949-53. 2008
    ....
  15. doi request reprint The discovery of eukaryotic genome design and its forgotten corollary--the postulate of gene regulation by nuclear RNA
    Thoru Pederson
    Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    FASEB J 23:2019-21. 2009
    ..It seems fitting to recall the prescience of those who first raised such unorthodoxy. They powerfully catalyzed progress...
  16. pmc Regulatory RNAs derived from transfer RNA?
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    RNA 16:1865-9. 2010
    ..If their regulatory functions were to be confirmed, these newly revealed RNAs would add to the expanding repertoire of small noncoding RNAs and would also provide new perspectives on the coevolution of transfer RNA and messenger RNA...
  17. pmc Cytologically "compact" nuclear domains: reconsidering the nucleolus
    Thoru Pederson
    Department of Biochemistry, and Program in Cell and Developmental Dynamics, University of Massachusetts Medical School, Worcester, MA, USA
    Nucleus 1:444-5. 2010
    ..A new report demonstrates that the nucleolus accommodates the assembly of a virus, this amidst building ribosomes and performing other host cell functions...
  18. pmc An Olympian protozoan
    Thoru Pederson
    Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
    Nucleus 1:2-3. 2010
    ..Ciliated protozoa of the genus Tetrahymena have provided a uniquely enabling platform for monumental discoveries in the molecular biology of the nucleus...
  19. ncbi request reprint The molecular cytology of gene expression: fluorescent RNA as both a stain and tracer in vivo
    T Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 USA
    Eur J Histochem 48:57-64. 2004
    ..Several examples of Fluorescent RNA Cytochemistry are presented, collectively illustrating the range of applicability this approach offers in the toolbox of gene expression, studied as in vivo cell biology...
  20. pmc Can telomerase be put in its place?
    Thoru Pederson
    Program in Cell Dynamics and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    J Cell Biol 164:637-9. 2004
    ..In this issue, Jady et al. place the Cajal body on the intranuclear traffic route of telomerase RNA (Jady et al., 2004)...
  21. ncbi request reprint A century of DNA reaches the bedside
    Thoru Pederson
    Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, 377 Plantation Street, Suite 337, Worcester, Massachusetts 01605, USA
    Pharos Alpha Omega Alpha Honor Med Soc 65:27-32. 2002
  22. ncbi request reprint Historical review: an energy reservoir for mitosis, and its productive wake
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester 01605, USA
    Trends Biochem Sci 28:125-9. 2003
    ..But the notion that mitotic progression involves the cyclic build-up and consumption of key factors endured and, as we all now know so well, eventually triumphed...
  23. pmc Fluorescent RNA cytochemistry: tracking gene transcripts in living cells
    T Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 377 Plantation Street, Worcester, MA 01605, USA
    Nucleic Acids Res 29:1013-6. 2001
    ....
  24. pmc Half a century of "the nuclear matrix"
    T Pederson
    Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Mol Biol Cell 11:799-805. 2000
    ....
  25. ncbi request reprint Movement and localization of RNA in the cell nucleus
    T Pederson
    Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester 01605, USA
    FASEB J 13:S238-42. 1999
    ..The methods we have developed and these initial results represent the first major step toward a comprehensive understanding of RNA traffic in the cell nucleus...
  26. ncbi request reprint Actin in the nucleus: what form and what for?
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 377 Plantation Street, Worcester, MA 01605 2300, USA
    J Struct Biol 140:3-9. 2002
    ..We present ideas for advancing the nuclear actin field and call for a renewed attack on this major problem in cell biology...
  27. pmc RNA interference and mRNA silencing, 2004: how far will they reach?
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Mol Biol Cell 15:407-10. 2004
    ..This essay summarizes recent developments and offers some personalized perspectives, with emphasis on what we do not yet know...
  28. ncbi request reprint Dynamics and genome-centricity of interchromatin domains in the nucleus
    Thoru Pederson
    Department of Biochemistry and Molecular Pharmacology, and Program in Cell Dynamics University of Massachusetts Medical School, Worcester, MA 01605, USA
    Nat Cell Biol 4:E287-91. 2002
    ....
  29. pmc Nucleophosmin is a binding partner of nucleostemin in human osteosarcoma cells
    Hanhui Ma
    Program in Cell Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Biol Cell 19:2870-5. 2008
    ..These results support the notion that cell cycle regulatory proteins congress and interact in the nucleolus, adding to the emerging concept that this nuclear domain has functions beyond ribosome production...
  30. pmc A nonribosomal landscape in the nucleolus revealed by the stem cell protein nucleostemin
    Joan C Ritland Politz
    Department of Biochemistry and Molecular Pharmacology and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Biol Cell 16:3401-10. 2005
    ....
  31. ncbi request reprint Nuclear export of signal recognition particle RNA in mammalian cells
    Christina N Alavian
    Department of Biochemistry and Molecular Pharmacology and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Biochem Biophys Res Commun 313:351-5. 2004
    ..These results indicate that the steady-state concentration of SRP RNA in the nucleolus is sensitive to perturbations in nuclear import/export pathways...
  32. pmc MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells
    Joan C Ritland Politz
    Department of Biochemistry and Molecular Pharmacology and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Proc Natl Acad Sci U S A 103:18957-62. 2006
    ..These results suggest that miR-206 may associate both with nascent ribosomes in the nucleolus and with exported, functional ribosomes in the cytoplasm...
  33. pmc Diffusion-based transport of nascent ribosomes in the nucleus
    Joan C Ritland Politz
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Mol Biol Cell 14:4805-12. 2003
    ..Once nucleoplasmic, the subunits moved in the same random manner and also sometimes visited another nucleolus before leaving the nucleus...
  34. doi request reprint Nucleostemin: a multiplex regulator of cell-cycle progression
    Hanhui Ma
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01609, USA
    Trends Cell Biol 18:575-9. 2008
    ..This new finding expands our understanding of the multiple modes of NS action and reinforces the concept that the nucleolus has key roles in cell-cycle progression...
  35. pmc In search of nonribosomal nucleolar protein function and regulation
    Thoru Pederson
    Program in Cell Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    J Cell Biol 184:771-6. 2009
    ..This review discusses our thoughts on the discovery of nonribosomal proteins in the nucleolus...
  36. pmc Depletion of the nucleolar protein nucleostemin causes G1 cell cycle arrest via the p53 pathway
    Hanhui Ma
    Program in Cell Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Biol Cell 18:2630-5. 2007
    ..These results demonstrate that, in the cells investigated, the level of NS is regulated by p14(ARF) and the control of the G1/S transition by NS operates in a p53-dependent manner...
  37. pmc The nucleolus stress response is coupled to an ATR-Chk1-mediated G2 arrest
    Hanhui Ma
    Department of Biochemistry and Molecular Pharmacology and Program in Cell and Developmental Dynamics, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Biol Cell 24:1334-42. 2013
    ....
  38. pmc MicroRNAs with a nucleolar location
    Joan C Ritland Politz
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    RNA 15:1705-15. 2009
    ....
  39. pmc Rapid, diffusional shuttling of poly(A) RNA between nuclear speckles and the nucleoplasm
    Joan C Ritland Politz
    Department of Biochemistry, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Biol Cell 17:1239-49. 2006
    ....
  40. pmc Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors
    Hanhui Ma
    Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
    Proc Natl Acad Sci U S A 110:21048-53. 2013
    ..These methods may have significant potential both for basic chromosome and genome research as well as in clinical applications. ..
  41. pmc Networking development by Boolean logic
    Shikui Tu
    Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
    Nucleus 4:89-91. 2013
    ....
  42. pmc Signal recognition particle RNA localization within the nucleolus differs from the classical sites of ribosome synthesis
    Joan C Politz
    Department of Biochemistry and Molecular Pharmacology, Program in Cell Dynamics, University of Massachusetts Medical School, 377 Plantation Street, Worcester, MA 01605, USA
    J Cell Biol 159:411-8. 2002
    ..These results demonstrate that SRP RNA concentrates in an intranucleolar location other than the classical stations of ribosome biosynthesis, suggesting that there may be nucleolar regions that are specialized for other functions...
  43. ncbi request reprint Human cell lines expressing hormone regulated T7 RNA polymerase localized at distinct intranuclear sites
    S V Yarovoi
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 377 Plantation Street, Worcester, MA 01605, USA
    Gene 275:73-81. 2001
    ..Both of these observed intranuclear localizations have relevance to the potential applications of this system...
  44. ncbi request reprint Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells
    J C Politz
    Department of Biochemistry and Molecular Biology, Biomedical Imaging Center, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Curr Biol 9:285-91. 1999
    ....
  45. pmc Signal recognition particle components in the nucleolus
    J C Politz
    Department of Biochemistry, University of Massachusetts Medical School, 377 Plantation Street, Suite 337, Worcester, MA 01605, USA
    Proc Natl Acad Sci U S A 97:55-60. 2000
    ..Our findings support the notion that the nucleolus is the site of assembly and/or interaction between the family of ribonucleoproteins involved in protein synthesis, in addition to ribosomes themselves...
  46. pmc The plurifunctional nucleolus
    T Pederson
    Worcester Foundation for Biomedical Research and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester Foundation Campus, 222 Maple Avenue, Shrewsbury, MA 01545, USA
    Nucleic Acids Res 26:3871-6. 1998
    ..The plurifunctional nucleolus concept has a strong footing in contemporary data and adds a new perspective to our current picture of the spatial-functional design of the cell nucleus...
  47. ncbi request reprint Genome function and nuclear architecture: from gene expression to nanoscience
    TIMOTHY P O'BRIEN
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genome Res 13:1029-41. 2003
    ..Advancing these concepts will require coordinated networks of physicists, chemists, and materials scientists collaborating with cell, developmental, and genome biologists...
  48. ncbi request reprint Signal recognition particle assembly in relation to the function of amplified nucleoli of Xenopus oocytes
    John Sommerville
    Division of Cell and Molecular Biology, School of Biology, University of St Andrews, KY16 9TS, UK
    J Cell Sci 118:1299-307. 2005
    ....
  49. ncbi request reprint Proteomics of the nucleolus: more proteins, more functions?
    Thoru Pederson
    Trends Biochem Sci 27:111-2. 2002
  50. pmc RNA polymerase III transcripts and the PTB protein are essential for the integrity of the perinucleolar compartment
    Chen Wang
    Department of Cell and Molecular Biology, Northwestern University Medical School, Chicago, Illinois 60611, USA
    Mol Biol Cell 14:2425-35. 2003
    ..Together, these findings suggest, as a working model, that PNCs may be involved in the metabolism of specific pol III transcripts in the transformed state and that PTB is one of the key elements mediating this process...
  51. ncbi request reprint Gene territories and cancer
    Thoru Pederson
    Nat Genet 34:242-3. 2003
  52. ncbi request reprint Meeting Holly Smith, through two generations of his disciples
    Thoru Pederson
    Pharos Alpha Omega Alpha Honor Med Soc 71:48-9. 2008

Research Grants8

  1. RNA PROCESSING AND RIBONUCLEOPROTEIN
    Thoru Pederson; Fiscal Year: 2001
    ..The same studies should provide information on sequences required for nuclear export. These two inter-related projects test the hypothesis that the nucleolus is a more pluri-functional organelle than previously thought. ..
  2. RNA Transport Within the Nucleus
    Thoru Pederson; Fiscal Year: 2005
    ..Another aspect of the project will address the intranuclear traffic of these RNAs in relation to proteins known to be involved in nuclear import or RNA export, i.e. the Ran-GTPase and TAP. ..