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Genomes and Genes | Thoru PedersonSummaryAffiliation: University of Massachusetts Medical School Country: USA Publications
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The "study" role of past National Institutes of Health study sectionsThoru 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...
Historical review: an energy reservoir for mitosis, and its productive wakeThoru 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...- The sea urchin's sirenThoru 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... - 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)... - The molecular cytology of gene expression: fluorescent RNA as both a stain and tracer in vivoT 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... - The spatial organization of the genome in mammalian cellsThoru 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... 
Turning a PAGE: the overnight sensation of SDS-polyacrylamide gel electrophoresisThoru 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....- 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... - 50 years ago protein synthesis met molecular biology: the discoveries of amino acid activation and transfer RNAThoru Pederson
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
FASEB J 19:1583-4. 2005 - New surprises in genetic coding and how an ingenious experiment was almost scooped, by evolutionThoru 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... - Reflections on the prize of prizes: Alfred NobelThoru 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 - Diffraction at the Brandenburg G(r)ate. Symposium on the optical analysis of biomolecular machinesThoru 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 - Counterpoint: Statistical analysis in NIH peer review--identifying innovationThoru Pederson
University of Massachusetts Medical School, 377 Plantation St, Worcester, MA 01605, USA
FASEB J 21:309-10; discussion 311. 2007 - 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.... - 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... - The discovery of eukaryotic genome design and its forgotten corollary--the postulate of gene regulation by nuclear RNAThoru 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... - An Olympian protozoanThoru 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... - Movement and localization of RNA in the cell nucleusT 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... - 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.... - Fluorescent RNA cytochemistry: tracking gene transcripts in living cellsT 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.... - Nuclear actin extends, with no contraction in sightThoru 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.... - Cytologically "compact" nuclear domains: reconsidering the nucleolusThoru 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... - A century of DNA reaches the bedsideThoru 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 - 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... - Dynamics and genome-centricity of interchromatin domains in the nucleusThoru 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.... - 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... - Nucleophosmin is a binding partner of nucleostemin in human osteosarcoma cellsHanhui 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... - A nonribosomal landscape in the nucleolus revealed by the stem cell protein nucleosteminJoan 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.... - Nuclear export of signal recognition particle RNA in mammalian cellsChristina 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... - MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cellsJoan 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... - Nucleostemin: a multiplex regulator of cell-cycle progressionHanhui 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... - Depletion of the nucleolar protein nucleostemin causes G1 cell cycle arrest via the p53 pathwayHanhui 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... - Diffusion-based transport of nascent ribosomes in the nucleusJoan 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... - In search of nonribosomal nucleolar protein function and regulationThoru 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... - MicroRNAs with a nucleolar locationJoan C Ritland Politz
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
RNA 15:1705-15. 2009.... - Rapid, diffusional shuttling of poly(A) RNA between nuclear speckles and the nucleoplasmJoan C Ritland Politz
Department of Biochemistry, University of Massachusetts Medical School, Worcester, MA 01605, USA
Mol Biol Cell 17:1239-49. 2006.... - The nucleolus stress response is coupled to an ATR-Chk1-mediated G2 arrestHanhui Ma
Department of Biochemistry and Molecular Pharmacology and Program in Cell and Developmental Dynamics, University of Massachusetts Medical School, Worcester, MA 01605
Mol Biol Cell 24:1334-42. 2013.... - Signal recognition particle RNA localization within the nucleolus differs from the classical sites of ribosome synthesisJoan 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... - Movement of nuclear poly(A) RNA throughout the interchromatin space in living cellsJ 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.... - Human cell lines expressing hormone regulated T7 RNA polymerase localized at distinct intranuclear sitesS 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... - Signal recognition particle components in the nucleolusJ 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... - The plurifunctional nucleolusT 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... - Genome function and nuclear architecture: from gene expression to nanoscienceTIMOTHY 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... - RNA polymerase III transcripts and the PTB protein are essential for the integrity of the perinucleolar compartmentChen 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... - Proteomics of the nucleolus: more proteins, more functions?Thoru Pederson
Trends Biochem Sci 27:111-2. 2002 - Signal recognition particle assembly in relation to the function of amplified nucleoli of Xenopus oocytesJohn Sommerville
Division of Cell and Molecular Biology, School of Biology, University of St Andrews, KY16 9TS, UK
J Cell Sci 118:1299-307. 2005.... - Gene territories and cancerThoru Pederson
Nat Genet 34:242-3. 2003 - Meeting Holly Smith, through two generations of his disciplesThoru Pederson
Pharos Alpha Omega Alpha Honor Med Soc 71:48-9. 2008
Research Grants
- RNA PROCESSING AND RIBONUCLEOPROTEINThoru 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. ..
- RNA Transport Within the NucleusThoru 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. ..