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  • 1
  • 2
    Publication Date: 2004-07-17
    Description: Resistance to the ABL kinase inhibitor imatinib (STI571 or Gleevec) in chronic myeloid leukemia (CML) occurs through selection for tumor cells harboring BCR-ABL kinase domain point mutations that interfere with drug binding. Crystallographic studies predict that most imatinib-resistant mutants should remain sensitive to inhibitors that bind ABL with less stringent conformational requirements. BMS-354825 is an orally bioavailable ABL kinase inhibitor with two-log increased potency relative to imatinib that retains activity against 14 of 15 imatinib-resistant BCR-ABL mutants. BMS-354825 prolongs survival of mice with BCR-ABL-driven disease and inhibits proliferation of BCR-ABL-positive bone marrow progenitor cells from patients with imatinib-sensitive and imatinib-resistant CML. These data illustrate how molecular insight into kinase inhibitor resistance can guide the design of second-generation targeted therapies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shah, Neil P -- Tran, Chris -- Lee, Francis Y -- Chen, Ping -- Norris, Derek -- Sawyers, Charles L -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):399-401.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Hematology and Oncology, Department of Medicine, The David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256671" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Antineoplastic Agents/metabolism/*pharmacology/therapeutic use ; Benzamides ; Binding Sites ; Cell Division/drug effects ; Cell Line ; Clinical Trials, Phase I as Topic ; Dasatinib ; Drug Resistance, Neoplasm ; Enzyme Inhibitors/metabolism/pharmacology/therapeutic use ; Fusion Proteins, bcr-abl/*antagonists & inhibitors/chemistry/genetics/metabolism ; Hematopoietic Stem Cells/drug effects ; Humans ; Imatinib Mesylate ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/*drug therapy ; Mice ; Mice, SCID ; Mutation ; Piperazines/*pharmacology/therapeutic use ; Protein Conformation ; Pyrimidines/metabolism/*pharmacology/therapeutic use ; Thiazoles/metabolism/*pharmacology/therapeutic use ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2018-11-21
    Description: Author(s): M. C. Tran, R. Ramanathan, M. McKague, D. Kaszlikowski, and T. Paterek Characterizing tradeoffs between simultaneous violations of multiple Bell inequalities in a large network has important physical consequences but is computationally demanding. We propose a graph-theoretic approach to efficiently produce Bell monogamy relations in arbitrary arrangements of qubits. Al... [Phys. Rev. A 98, 052325] Published Tue Nov 20, 2018
    Keywords: Quantum information
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1992-06-05
    Description: Regulation of interleukin-2 (IL-2) gene expression by the p50 and p65 subunits of the DNA binding protein NF-kappa B was studied in nontransformed CD4+ T lymphocyte clones. A homodimeric complex of the NF-kappa B p50 subunit was found in resting T cells. The amount of p50-p50 complex decreased after full antigenic stimulation, whereas the amount of the NF-kappa B p50-p65 heterodimer was increased. Increased expression of the IL-2 gene and activity of the IL-2 kappa B DNA binding site correlated with a decrease in the p50-p50 complex. Overexpression of p50 repressed IL-2 promoter expression. The switch from p50-p50 to p50-p65 complexes depended on a protein that caused sequestration of the p50-p50 complex in the nucleus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, S M -- Tran, A C -- Grilli, M -- Lenardo, M J -- New York, N.Y. -- Science. 1992 Jun 5;256(5062):1452-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunology, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1604322" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD4/*immunology ; Base Sequence ; Binding Sites ; Cell Line ; Cell Nucleus/physiology ; Chloramphenicol O-Acetyltransferase/genetics/metabolism ; Clone Cells ; Columbidae ; DNA/genetics ; *Gene Expression Regulation ; Interleukin-2/*genetics ; Macromolecular Substances ; Mice ; Molecular Sequence Data ; NF-kappa B/*metabolism ; Oligonucleotide Probes ; Promoter Regions, Genetic ; RNA, Messenger/metabolism ; Recombinant Fusion Proteins/metabolism ; T-Lymphocyte Subsets/*immunology ; Transfection ; Tumor Necrosis Factor-alpha/pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 1992-08-21
    Description: Anergy is a mechanism of T lymphocyte tolerance induced by antigen receptor stimulation in the absence of co-stimulation. Anergic T cells were shown to have a defect in antigen-induced transcription of the interleukin-2 gene. Analysis of the promoter indicated that the transcription factor AP-1 and its corresponding cis element were specifically down-regulated. Exposure of anergic T cells to interleukin-2 restored both antigen responsiveness and activity of the AP-1 element.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, S M -- Beverly, B -- Tran, A C -- Brorson, K -- Schwartz, R H -- Lenardo, M J -- New York, N.Y. -- Science. 1992 Aug 21;257(5073):1134-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1509265" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigen-Presenting Cells/immunology ; Antigens/*immunology ; Base Sequence ; Binding Sites ; Blotting, Northern ; Cell Line ; Concanavalin A/pharmacology ; *Gene Expression Regulation ; *Immune Tolerance ; Interleukin-2/*genetics/pharmacology ; Mice ; Molecular Sequence Data ; Mutation ; Promoter Regions, Genetic/genetics ; Proto-Oncogene Proteins c-jun/*physiology ; RNA, Messenger/metabolism ; Receptors, Antigen, T-Cell/immunology ; T-Lymphocytes/*immunology ; Transcription, Genetic ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2016-11-13
    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b02766
    Print ISSN: 0003-2700
    Electronic ISSN: 1520-6882
    Topics: Chemistry and Pharmacology
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  • 7
    Publication Date: 2011-11-01
    Description: A full description of the human proteome relies on the challenging task of detecting mature and changing forms of protein molecules in the body. Large-scale proteome analysis has routinely involved digesting intact proteins followed by inferred protein identification using mass spectrometry. This 'bottom-up' process affords a high number of identifications (not always unique to a single gene). However, complications arise from incomplete or ambiguous characterization of alternative splice forms, diverse modifications (for example, acetylation and methylation) and endogenous protein cleavages, especially when combinations of these create complex patterns of intact protein isoforms and species. 'Top-down' interrogation of whole proteins can overcome these problems for individual proteins, but has not been achieved on a proteome scale owing to the lack of intact protein fractionation methods that are well integrated with tandem mass spectrometry. Here we show, using a new four-dimensional separation system, identification of 1,043 gene products from human cells that are dispersed into more than 3,000 protein species created by post-translational modification (PTM), RNA splicing and proteolysis. The overall system produced greater than 20-fold increases in both separation power and proteome coverage, enabling the identification of proteins up to 105 kDa and those with up to 11 transmembrane helices. Many previously undetected isoforms of endogenous human proteins were mapped, including changes in multiply modified species in response to accelerated cellular ageing (senescence) induced by DNA damage. Integrated with the latest version of the Swiss-Prot database, the data provide precise correlations to individual genes and proof-of-concept for large-scale interrogation of whole protein molecules. The technology promises to improve the link between proteomics data and complex phenotypes in basic biology and disease research.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3237778/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3237778/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tran, John C -- Zamdborg, Leonid -- Ahlf, Dorothy R -- Lee, Ji Eun -- Catherman, Adam D -- Durbin, Kenneth R -- Tipton, Jeremiah D -- Vellaichamy, Adaikkalam -- Kellie, John F -- Li, Mingxi -- Wu, Cong -- Sweet, Steve M M -- Early, Bryan P -- Siuti, Nertila -- LeDuc, Richard D -- Compton, Philip D -- Thomas, Paul M -- Kelleher, Neil L -- F30 DA026672/DA/NIDA NIH HHS/ -- F30 DA026672-03/DA/NIDA NIH HHS/ -- GM 067193-08/GM/NIGMS NIH HHS/ -- P30 DA018310/DA/NIDA NIH HHS/ -- P30 DA018310-06/DA/NIDA NIH HHS/ -- P30DA 018310/DA/NIDA NIH HHS/ -- R01 GM067193/GM/NIGMS NIH HHS/ -- R01 GM067193-08/GM/NIGMS NIH HHS/ -- England -- Nature. 2011 Oct 30;480(7376):254-8. doi: 10.1038/nature10575.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22037311" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Cell Aging/genetics ; Cell Line ; DNA Damage ; Databases, Protein ; HMGA1a Protein/analysis ; HMGA1b Protein/analysis ; HeLa Cells ; Humans ; Phenotype ; Protein Isoforms/*analysis/*chemistry ; Protein Processing, Post-Translational ; Proteolysis ; Proteome/*analysis/*chemistry ; Proteomics/instrumentation/*methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2015-04-29
    Description: Many long non-coding RNAs (lncRNAs) affect gene expression, but the mechanisms by which they act are still largely unknown. One of the best-studied lncRNAs is Xist, which is required for transcriptional silencing of one X chromosome during development in female mammals. Despite extensive efforts to define the mechanism of Xist-mediated transcriptional silencing, we still do not know any proteins required for this role. The main challenge is that there are currently no methods to comprehensively define the proteins that directly interact with a lncRNA in the cell. Here we develop a method to purify a lncRNA from cells and identify proteins interacting with it directly using quantitative mass spectrometry. We identify ten proteins that specifically associate with Xist, three of these proteins--SHARP, SAF-A and LBR--are required for Xist-mediated transcriptional silencing. We show that SHARP, which interacts with the SMRT co-repressor that activates HDAC3, is not only essential for silencing, but is also required for the exclusion of RNA polymerase II (Pol II) from the inactive X. Both SMRT and HDAC3 are also required for silencing and Pol II exclusion. In addition to silencing transcription, SHARP and HDAC3 are required for Xist-mediated recruitment of the polycomb repressive complex 2 (PRC2) across the X chromosome. Our results suggest that Xist silences transcription by directly interacting with SHARP, recruiting SMRT, activating HDAC3, and deacetylating histones to exclude Pol II across the X chromosome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516396/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516396/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McHugh, Colleen A -- Chen, Chun-Kan -- Chow, Amy -- Surka, Christine F -- Tran, Christina -- McDonel, Patrick -- Pandya-Jones, Amy -- Blanco, Mario -- Burghard, Christina -- Moradian, Annie -- Sweredoski, Michael J -- Shishkin, Alexander A -- Su, Julia -- Lander, Eric S -- Hess, Sonja -- Plath, Kathrin -- Guttman, Mitchell -- 1S10RR029591-01A1/RR/NCRR NIH HHS/ -- DP2 OD001686/OD/NIH HHS/ -- DP5 OD012190/OD/NIH HHS/ -- DP5OD012190/OD/NIH HHS/ -- T32GM07616/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 May 14;521(7551):232-6. doi: 10.1038/nature14443. Epub 2015 Apr 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA. ; 1] Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA [2] Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA. ; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25915022" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Cell Line ; Embryonic Stem Cells/enzymology/metabolism ; Female ; *Gene Silencing ; Heterogeneous-Nuclear Ribonucleoprotein U/metabolism ; Histone Deacetylases/*metabolism ; Histones/metabolism ; Male ; Mass Spectrometry/*methods ; Mice ; Nuclear Proteins/*metabolism ; Nuclear Receptor Co-Repressor 2/metabolism ; Polycomb Repressive Complex 2/metabolism ; Protein Binding ; RNA Polymerase II/metabolism ; RNA, Long Noncoding/genetics/*metabolism ; RNA-Binding Proteins/analysis/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Transcription, Genetic/*genetics ; X Chromosome/*genetics/metabolism ; X Chromosome Inactivation/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2018-07-20
    Description: Author(s): Abhinav Deshpande, Bill Fefferman, Minh C. Tran, Michael Foss-Feig, and Alexey V. Gorshkov We make the case for studying the complexity of approximately simulating (sampling) quantum systems for reasons beyond that of quantum computational supremacy, such as diagnosing phase transitions. We consider the sampling complexity as a function of time t due to evolution generated by spatially lo... [Phys. Rev. Lett. 121, 030501] Published Thu Jul 19, 2018
    Keywords: General Physics: Statistical and Quantum Mechanics, Quantum Information, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 10
    Publication Date: 2011-05-04
    Description: The precise identity of cancer cells of origin and the molecular events of tumor initiation in epidermal squamous cell carcinoma (SCC) are unknown. Here we show that malignancy potential is related to the developmental capacity of the initiating cancer cell in a genetically defined, intact, and inducible in vivo model. Specifically, these data demonstrate that SCCs can originate from inside the hair follicle stem cell (SC) niche or from immediate progenitors, whereas more developmentally restricted progeny, the transit amplifying (TA) cells, are unable to generate even benign tumors in the same genetic context. Using a temporal model of tumorigenesis in situ, we highlight the phenotypes of cancer progression from the hair follicle SC niche, including hyperplasia, epithelial to mesenchymal transition, and SCC formation. Furthermore, we provide insights into the inability of hair follicle TA cells to respond to tumorigenic stimuli.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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