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  • 1
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    Distinctive roles of PHAP proteins and prothymosin-alpha in a death regulatory pathway (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-11
    Description: A small molecule, alpha-(trichloromethyl)-4-pyridineethanol (PETCM), was identified by high-throughput screening as an activator of caspase-3 in extracts of a panel of cancer cells. PETCM was used in combination with biochemical fractionation to identify a pathway that regulates mitochondria-initiated caspase activation. This pathway consists of tumor suppressor putative HLA-DR-associated proteins (PHAP) and oncoprotein prothymosin-alpha (ProT). PHAP proteins promoted caspase-9 activation after apoptosome formation, whereas ProT negatively regulated caspase-9 activation by inhibiting apoptosome formation. PETCM relieved ProT inhibition and allowed apoptosome formation at a physiological concentration of deoxyadenosine triphosphate. Elimination of ProT expression by RNA interference sensitized cells to ultraviolet irradiation-induced apoptosis and negated the requirement of PETCM for caspase activation. Thus, this chemical-biological combinatory approach has revealed the regulatory roles of oncoprotein ProT and tumor suppressor PHAP in apoptosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Xuejun -- Kim, Hyun-Eui -- Shu, Hongjun -- Zhao, Yingming -- Zhang, Haichao -- Kofron, James -- Donnelly, Jennifer -- Burns, Dave -- Ng, Shi-Chung -- Rosenberg, Saul -- Wang, Xiaodong -- GMRO1-57158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jan 10;299(5604):223-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12522243" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Apoptosis ; Apoptotic Protease-Activating Factor 1 ; Caspase 3 ; Caspase 9 ; Caspases/metabolism ; Cell Extracts ; Cytochrome c Group/metabolism ; Deoxyadenine Nucleotides/metabolism/pharmacology ; Enzyme Activation ; HeLa Cells ; Humans ; Intracellular Signaling Peptides and Proteins ; Mitochondria/metabolism ; Molecular Sequence Data ; *Neuropeptides ; Nuclear Proteins/chemistry/isolation & purification/*metabolism/pharmacology ; Protein Precursors/chemistry/isolation & purification/*metabolism/pharmacology ; Proteins/chemistry/isolation & purification/*metabolism/pharmacology ; Pyridines/chemistry/*pharmacology ; RNA Interference ; Recombinant Proteins/metabolism/pharmacology ; Signal Transduction ; Thymosin/*analogs & derivatives/chemistry/isolation & ; purification/*metabolism/pharmacology ; Tumor Suppressor Proteins/chemistry/isolation & purification/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-27
    Description: The RNA interference (RNAi) pathway is initiated by processing long double-stranded RNA into small interfering RNA (siRNA). The siRNA-generating enzyme was purified from Drosophila S2cells and consists of two stoichiometric subunits: Dicer-2(DCR-2) and a previously unknown protein that we named R2D2. R2D2 is homologous to the Caenorhabditis elegans RNAi protein RDE-4. Association with R2D2 does not affect the enzymatic activity of DCR-2. Rather, the DCR-2/R2D2 complex, but not DCR-2 alone, binds to siRNA and enhances sequence-specific messenger RNA degradation mediated by the RNA-initiated silencing complex (RISC). These results indicate that R2D2 bridges the initiation and effector steps of the Drosophila RNAi pathway by facilitating siRNA passage from Dicer to RISC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Qinghua -- Rand, Tim A -- Kalidas, Savitha -- Du, Fenghe -- Kim, Hyun-Eui -- Smith, Dean P -- Wang, Xiaodong -- DC02539/DC/NIDCD NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1921-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512631" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Argonaute Proteins ; Biotinylation ; Caenorhabditis elegans/genetics/metabolism ; Caenorhabditis elegans Proteins/chemistry ; Cell Line ; Chemical Precipitation ; Drosophila Proteins/chemistry/genetics/*isolation & purification/*metabolism ; Drosophila melanogaster/*genetics/metabolism ; Electrophoretic Mobility Shift Assay ; Endoribonucleases/genetics/isolation & purification/*metabolism ; Kinetics ; Molecular Sequence Data ; Mutation ; Protein Structure, Tertiary ; RNA Helicases/genetics/*isolation & purification/*metabolism ; *RNA Interference ; RNA, Double-Stranded/metabolism ; RNA, Messenger/metabolism ; RNA, Small Interfering/*metabolism ; RNA-Binding Proteins/chemistry/genetics/isolation & purification/*metabolism ; RNA-Induced Silencing Complex/isolation & purification/metabolism ; Recombinant Proteins/metabolism ; Ribonuclease III
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Formation of apoptosome is initiated by cytochrome c-induced dATP hydrolysis and subsequent nucleotide exchange on Apaf-1 (2005)
    National Academy of Sciences
    Details
    Publication Date: 2005-10-26
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Hierarchical star formation across the ring galaxy NGC 6503 (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: We present a detailed clustering analysis of the young stellar population across the star-forming ring galaxy NGC 6503, based on the deep Hubble Space Telescope photometry obtained with the Legacy ExtraGalactic UV Survey. We apply a contour-based map analysis technique and identify in the stellar surface density map 244 distinct star-forming structures at various levels of significance. These stellar complexes are found to be organized in a hierarchical fashion with 95 per cent being members of three dominant super-structures located along the star-forming ring. The size distribution of the identified structures and the correlation between their radii and numbers of stellar members show power-law behaviours, as expected from scale-free processes. The self-similar distribution of young stars is further quantified from their autocorrelation function, with a fractal dimension of ~1.7 for length-scales between ~20 pc and 2.5 kpc. The young stellar radial distribution sets the extent of the star-forming ring at radial distances between 1 and 2.5 kpc. About 60 per cent of the young stars belong to the detected stellar structures, while the remaining stars are distributed among the complexes, still inside the ring of the galaxy. The analysis of the time-dependent clustering of young populations shows a significant change from a more clustered to a more distributed behaviour in a time-scale of ~60 Myr. The observed hierarchy in stellar clustering is consistent with star formation being regulated by turbulence across the ring. The rotational velocity difference between the edges of the ring suggests shear as the driving mechanism for this process. Our findings reveal the interesting case of an inner ring forming stars in a hierarchical fashion.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Prosocial value representation in MPFC [Psychological and Cognitive Sciences] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-06-24
    Description: Despite the importance of valuing another person’s welfare for prosocial behavior, currently we have only a limited understanding of how these values are represented in the brain and, more importantly, how they give rise to individual variability in prosociality. In the present study, participants underwent functional magnetic resonance imaging while...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Quorum sensing-mediated metabolic slowing [Microbiology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-10-15
    Description: Acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) controls the production of numerous intra- and extracellular products across many species of Proteobacteria. Although these cooperative activities are often costly at an individual level, they provide significant benefits to the group. Other potential roles for QS include the restriction of nutrient acquisition and...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    Molecular basis of GKRP as allosteric switch of GK [Biochemistry] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-06-19
    Description: Glucokinase (GK) is a monomeric allosteric enzyme and plays a pivotal role in blood glucose homeostasis. GK is regulated by GK regulatory protein (GKRP), and indirectly by allosteric effectors of GKRP. Despite the critical roles of GK and GKRP, the molecular basis for the allosteric regulation mechanism of GK by...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Suppression of stored-beam oscillation and observation of flux improvement during top-up injection (2017)
    American Physical Society (APS)
    Details
    Publication Date: 2017-09-02
    Description: Author(s): Y-G. Son, J.-Y. Kim, C. Mitsuda, K. Kobayashi, J. Ko, T-Y. Lee, J-Y. Choi, D-E. Kim, H-S. Seo, H-S. Han, K-S. Park, C-D. Park, and S. Shin This paper describes a start-to-end study of the suppression of stored-beam oscillation during top-up injection at the Pohang Light Source (PLS-II) beam line. The fast counterkicker implemented in PLS-II suppresses stored-beam oscillations in the vertical plane. During top-up injection in the magnet... [Phys. Rev. Accel. Beams 20, 082803] Published Wed Aug 30, 2017
    Keywords: Beam Control, Diagnostics, and Feedback
    Electronic ISSN: 1098-4402
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    JiffyNet: a web-based instant protein network modeler for newly sequenced species (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-23
    Description: Revolutionary DNA sequencing technology has enabled affordable genome sequencing for numerous species. Thousands of species already have completely decoded genomes, and tens of thousands more are in progress. Naturally, parallel expansion of the functional parts list library is anticipated, yet genome-level understanding of function also requires maps of functional relationships, such as functional protein networks. Such networks have been constructed for many sequenced species including common model organisms. Nevertheless, the majority of species with sequenced genomes still have no protein network models available. Moreover, biologists might want to obtain protein networks for their species of interest on completion of the genome projects. Therefore, there is high demand for accessible means to automatically construct genome-scale protein networks based on sequence information from genome projects only. Here, we present a public web server, JiffyNet, specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a query species with only protein sequences provided. Assessment of the networks by JiffyNet demonstrated generally high predictive ability for pathway annotations. Furthermore, JiffyNet provides network visualization and analysis pages for wide variety of molecular concepts to facilitate network-guided hypothesis generation. JiffyNet is freely accessible at http://www.jiffynet.org .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-29
    Description: Saccharomyces cerevisiae , i.e. baker’s yeast, is a widely studied model organism in eukaryote genetics because of its simple protocols for genetic manipulation and phenotype profiling. The high abundance of publicly available data that has been generated through diverse ‘omics’ approaches has led to the use of yeast for many systems biology studies, including large-scale gene network modeling to better understand the molecular basis of the cellular phenotype. We have previously developed a genome-scale gene network for yeast, YeastNet v2, which has been used for various genetics and systems biology studies. Here, we present an updated version, YeastNet v3 (available at http://www.inetbio.org/yeastnet/ ), that significantly improves the prediction of gene–phenotype associations. The extended genome in YeastNet v3 covers up to 5818 genes (~99% of the coding genome) wired by 362 512 functional links. YeastNet v3 provides a new web interface to run the tools for network-guided hypothesis generations. YeastNet v3 also provides edge information for all data-specific networks (~2 million functional links) as well as the integrated networks. Therefore, users can construct alternative versions of the integrated network by applying their own data integration algorithm to the same data-specific links.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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