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  • 1
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    A novel cyclic helix B peptide inhibits dendritic cell maturation during amelioration of acute kidney graft rejection through Jak-2/STAT3/SOCS1 (2015)
    Springer Nature
    Details
    Publication Date: 2015-11-27
    Description: A novel cyclic helix B peptide inhibits dendritic cell maturation during amelioration of acute kidney graft rejection through Jak-2/STAT3/SOCS1 Cell Death and Disease 6, e1993 (November 2015). doi:10.1038/cddis.2015.338 Authors: C Yang, Y Zhang, J Wang, L Li, L Wang, M Hu, M Xu, Y Long, R Rong & T Zhu
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 2
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    Crystal structures of Elp1 subunits of Elongator [Biochemistry] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-08-26
    Description: The evolutionarily conserved Elongator complex, which is composed of six subunits elongator protein 1 (Elp1 to -6), plays vital roles in gene regulation. The molecular hallmark of familial dysautonomia (FD) is the splicing mutation of Elp1 [also known as IκB kinase complex-associated protein (IKAP)] in the nervous system that is...
    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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  • 3
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    Priming of rice antiherbivore defense by silicon [Ecology] (2013)
    National Academy of Sciences
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    Publication Date: 2013-09-18
    Description: Although the function of silicon (Si) in plant physiology has long been debated, its beneficial effects on plant resistance against abiotic and biotic stresses, including insect herbivory, have been well documented. In addition, the jasmonate (JA) signaling pathway plays a crucial role in mediating antiherbivore defense responses in plants. However,...
    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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    Non-cultivated plants present a season-long route of pesticide exposure for honey bees (2016)
    Springer Nature
    Details
    Publication Date: 2016-06-02
    Description: Article The extent to which non-crop plants may be contaminated by insecticides is not known. Here, the authors show that pollen collected by honey bees living in areas of intensive maize production is contaminated by a wide range of pesticides throughout the growing season, with the principle pollen source being non-crop plants. Nature Communications doi: 10.1038/ncomms11629 Authors: Elizabeth Y. Long, Christian H. Krupke
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 5
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    The structural basis for the oligomerization of the N-terminal domain of SATB1 (2012)
    Oxford University Press
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    Publication Date: 2012-05-13
    Description: Special AT-rich sequence-binding protein 1 (SATB1) is a global chromatin organizer and gene expression regulator essential for T-cell development and breast cancer tumor growth and metastasis. The oligomerization of the N-terminal domain of SATB1 is critical for its biological function. We determined the crystal structure of the N-terminal domain of SATB1. Surprisingly, this domain resembles a ubiquitin domain instead of the previously proposed PDZ domain. Our results also reveal that SATB1 can form a tetramer through its N-terminal domain. The tetramerization of SATB1 plays an essential role in its binding to highly specialized DNA sequences. Furthermore, isothermal titration calorimetry results indicate that the SATB1 tetramer can bind simultaneously to two DNA targets. Based on these results, we propose a molecular model whereby SATB1 regulates the expression of multiple genes both locally and at a distance.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    PDGF-BB and TGF-β1 on cross-talk between endothelial and smooth muscle cells in vascular remodeling induced by low shear stress [Cell Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-02-02
    Description: Shear stress, especially low shear stress (LowSS), plays an important role in vascular remodeling during atherosclerosis. Endothelial cells (ECs), which are directly exposed to shear stress, convert mechanical stimuli into intracellular signals and interact with the underlying vascular smooth muscle cells (VSMCs). The interactions between ECs and VSMCs modulate the LowSS-induced vascular remodeling. With the use of proteomic analysis, the protein profiles of rat aorta cultured under LowSS (5 dyn/cm2) and normal shear stress (15 dyn/cm2) were compared. By using Ingenuity Pathway Analysis to identify protein–protein association, a network was disclosed that involves two secretary molecules, PDGF-BB and TGF-β1, and three other linked proteins, lamin A, lysyl oxidase, and ERK 1/2. The roles of this network in cellular communication, migration, and proliferation were further studied in vitro by a cocultured parallel-plate flow chamber system. LowSS up-regulated migration and proliferation of ECs and VSMCs, increased productions of PDGF-BB and TGF-β1, enhanced expressions of lysyl oxidase and phospho-ERK1/2, and decreased Lamin A in ECs and VSMCs. These changes induced by LowSS were confirmed by using PDGF-BB recombinant protein, siRNA, and neutralizing antibody. TGF-β1 had similar influences on ECs as PDGF-BB, but not on VSMCs. Our results suggest that ECs convert the LowSS stimuli into up-regulations of PDGF-BB and TGF-β1, but these two factors play different roles in LowSS-induced vascular remodeling. PDGF-BB is involved in the paracrine control of VSMCs by ECs, whereas TGF-β1 participates in the feedback control from VSMCs to ECs.
    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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    Structural insights into Paf1 complex assembly and histone binding (2013)
    Oxford University Press
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    Publication Date: 2013-12-07
    Description: The highly conserved Paf1 complex (PAF1C) plays critical roles in RNA polymerase II transcription elongation and in the regulation of histone modifications. It has also been implicated in other diverse cellular activities, including posttranscriptional events, embryonic development and cell survival and maintenance of embryonic stem cell identity. Here, we report the structure of the human Paf1/Leo1 subcomplex within PAF1C. The overall structure reveals that the Paf1 and Leo1 subunits form a tightly associated heterodimer through antiparallel beta-sheet interactions. Detailed biochemical experiments indicate that Leo1 binds to PAF1C through Paf1 and that the Ctr9 subunit is the key scaffold protein in assembling PAF1C. Furthermore, we show that the Paf1/Leo1 heterodimer is necessary for its binding to histone H3, the histone octamer, and nucleosome in vitro . Our results shed light on the PAF1C assembly process and substrate recognition during various PAF1C-coordinated histone modifications.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Temperature, Pressure, and Composition of the Mantle Source Region of Late Cenozoic Basalts in Hainan Island, SE Asia: a Consequence of a Young Thermal Mantle Plume close to Subduction Zones? (2011)
    Oxford University Press
    Details
    Publication Date: 2011-12-23
    Description: Basaltic lavas from Hainan Island near the northern edge of the South China Sea have an age range of between late Miocene (about 13 Ma) and Holocene, with a peak age of late Pliocene to middle Pleistocene. The basaltic province is dominated by tholeiites with subordinate alkali basalts. Most analysed samples display light rare earth element (LREE) enriched REE patterns and ocean island basalt (OIB)-like incompatible element distributions. The basalts contain abundant undeformed high-Mg olivine phenocrysts (up to Fo 90·7 ) that are high in CaO and MnO, indicating high-magnesian parental magmas. Independent barometers indicate that clinopyroxenes in the basalts crystallized over a wide range of pressures of 2–25 kbar (dominantly at 10–15 kbar) and that the melt cooled from about 1350°C to 1100°C during their crystallization. The compositional characteristics of the basalts indicate that their generation most probably involved both low-silica and high-silica melts, as represented by the alkali basalts and tholeiites, respectively. Our results show that the source region for the Hainan basalts is highly heterogeneous. The source for the tholeiites is mainly composed of peridotite and recycled oceanic crust, whereas the source for the bulk of the low-Th alkali basalts consists predominantly of peridotite and low-silica eclogite (garnet pyroxenite). Some high-Th (≥ 4 ppm) alkali basalts may have been produced by partial melting of low-silica garnet pyroxenite (eclogite). We estimated the primary melt compositions for the Hainan basalts using the most forsteritic olivine (Fo 90·7 ) composition and the most primitive bulk-rock samples (MgO 〉 9·0 wt % and CaO 〉8·0 wt %), assuming a constant Fe–Mg exchange partition coefficient of K D = 0·31 and Fe 3+ /Fe T = 0·1. The effective melting pressure ( P f ) and melting temperature ( T ) of the primary melts are P f = 18–32 kbar (weighted average = 23·8 ± 1·8 kbar) and T = 1420–1520°C for the tholeiites, and P f = 25–32 (weighted average = 28·3 ± 1·4 kbar) and T = 1480–1530°C for the alkali basalts. The P f – T data form an array that plots systematically above the dry lherzolite solidus but below the base of the lithosphere (~55 km) and intersects the dry peridotite solidus at a pressure of about 50 kbar. The mantle potential temperature beneath Hainan Island, based on the estimate primary melt compositions, varies from about 1500 to 1580°C with a weighted average of 1541 ± 10°C. The high-magnesian olivine phenocrysts, high mantle potential temperature, and the presence of recycled oceanic crust in the source region provide independent support for the Hainan plume model that has previously been proposed largely based on geophysical observations. The Hainan plume thus provides a rare example of a young mantle plume associated with deep slab subduction.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
    Published by Oxford University Press
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  • 9
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    APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3'-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb ( http://mosas.sysu.edu.cn/utr ), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3'-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Localization of the G protein betagamma complex in living cells during chemotaxis (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-11
    Description: Gradients of chemoattractants elicit signaling events at the leading edge of a cell even though chemoattractant receptors are uniformly distributed on the cell surface. In highly polarized Dictyostelium discoideum amoebas, membrane-associated betagamma subunits of heterotrimeric guanine nucleotide-binding proteins (G proteins) were localized in a shallow anterior-posterior gradient. A uniformly applied chemoattractant generated binding sites for pleckstrin homology (PH) domains on the inner surface of the membrane in a pattern similar to that of the Gbetagamma subunits. Loss of cell polarity resulted in uniform distribution of both the Gbetagamma subunits and the sensitivity of PH domain recruitment. These observations indicate that Gbetagamma subunits are not sufficiently localized to restrict signaling events to the leading edge but that their distribution may determine the relative chemotactic sensitivity of polarized cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jin, T -- Zhang, N -- Long, Y -- Parent, C A -- Devreotes, P N -- GM-28007/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Feb 11;287(5455):1034-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10669414" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Membrane/metabolism ; Cell Polarity ; Chemotactic Factors/pharmacology ; Chemotaxis/*physiology ; Cyclic AMP/pharmacology ; Dictyostelium/metabolism/*physiology ; *GTP-Binding Protein beta Subunits ; *GTP-Binding Protein gamma Subunits ; GTP-Binding Proteins/*metabolism ; *Heterotrimeric GTP-Binding Proteins ; Recombinant Fusion Proteins/metabolism ; Signal Transduction
    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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