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  • Cell Line  (524)
  • History, 21st Century  (459)
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  • 101
    Publication Date: 2008-05-27
    Description: Understanding the molecular underpinnings of cancer is of critical importance to the development of targeted intervention strategies. Identification of such targets, however, is notoriously difficult and unpredictable. Malignant cell transformation requires the cooperation of a few oncogenic mutations that cause substantial reorganization of many cell features and induce complex changes in gene expression patterns. Genes critical to this multifaceted cellular phenotype have therefore only been identified after signalling pathway analysis or on an ad hoc basis. Our observations that cell transformation by cooperating oncogenic lesions depends on synergistic modulation of downstream signalling circuitry suggest that malignant transformation is a highly cooperative process, involving synergy at multiple levels of regulation, including gene expression. Here we show that a large proportion of genes controlled synergistically by loss-of-function p53 and Ras activation are critical to the malignant state of murine and human colon cells. Notably, 14 out of 24 'cooperation response genes' were found to contribute to tumour formation in gene perturbation experiments. In contrast, only 1 in 14 perturbations of the genes responding in a non-synergistic manner had a similar effect. Synergistic control of gene expression by oncogenic mutations thus emerges as an underlying key to malignancy, and provides an attractive rationale for identifying intervention targets in gene networks downstream of oncogenic gain- and loss-of-function mutations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613942/" 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/PMC2613942/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McMurray, Helene R -- Sampson, Erik R -- Compitello, George -- Kinsey, Conan -- Newman, Laurel -- Smith, Bradley -- Chen, Shaw-Ree -- Klebanov, Lev -- Salzman, Peter -- Yakovlev, Andrei -- Land, Hartmut -- CA120317/CA/NCI NIH HHS/ -- CA90663/CA/NCI NIH HHS/ -- GM075299/GM/NIGMS NIH HHS/ -- K99 LM009477/LM/NLM NIH HHS/ -- K99 LM009477-01A1/LM/NLM NIH HHS/ -- R01 CA090663/CA/NCI NIH HHS/ -- R01 CA090663-03/CA/NCI NIH HHS/ -- R01 CA090663-04/CA/NCI NIH HHS/ -- R01 CA090663-05/CA/NCI NIH HHS/ -- R01 CA120317/CA/NCI NIH HHS/ -- R01 CA120317-01A1/CA/NCI NIH HHS/ -- R01 CA120317-02/CA/NCI NIH HHS/ -- R01 GM075299-01/GM/NIGMS NIH HHS/ -- R01 GM075299-02/GM/NIGMS NIH HHS/ -- R01 GM075299-03/GM/NIGMS NIH HHS/ -- R01 GM075299-03S1/GM/NIGMS NIH HHS/ -- T32 CA009363/CA/NCI NIH HHS/ -- T32 CA009363-25/CA/NCI NIH HHS/ -- T32 CA09363/CA/NCI NIH HHS/ -- England -- Nature. 2008 Jun 19;453(7198):1112-6. doi: 10.1038/nature06973. Epub 2008 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18500333" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Transformation, Neoplastic/*genetics ; Colon/cytology/pathology ; Colonic Neoplasms/*genetics ; Gene Expression Regulation, Neoplastic ; Genes, p53/genetics ; Genes, ras/genetics ; Genotype ; Humans ; Mice ; Mice, Nude ; Mutation/*genetics ; Neoplasm Transplantation ; Oncogenes/*genetics ; Phenotype
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  • 102
    Publication Date: 2008-11-11
    Description: Angiogenesis does not only depend on endothelial cell invasion and proliferation: it also requires pericyte coverage of vascular sprouts for vessel stabilization. These processes are coordinated by vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) through their cognate receptors on endothelial cells and vascular smooth muscle cells (VSMCs), respectively. PDGF induces neovascularization by priming VSMCs/pericytes to release pro-angiogenic mediators. Although VEGF directly stimulates endothelial cell proliferation and migration, its role in pericyte biology is less clear. Here we define a role for VEGF as an inhibitor of neovascularization on the basis of its capacity to disrupt VSMC function. Specifically, under conditions of PDGF-mediated angiogenesis, VEGF ablates pericyte coverage of nascent vascular sprouts, leading to vessel destabilization. At the molecular level, VEGF-mediated activation of VEGF-R2 suppresses PDGF-Rbeta signalling in VSMCs through the assembly of a previously undescribed receptor complex consisting of PDGF-Rbeta and VEGF-R2. Inhibition of VEGF-R2 not only prevents assembly of this receptor complex but also restores angiogenesis in tissues exposed to both VEGF and PDGF. Finally, genetic deletion of tumour cell VEGF disrupts PDGF-Rbeta/VEGF-R2 complex formation and increases tumour vessel maturation. These findings underscore the importance of VSMCs/pericytes in neovascularization and reveal a dichotomous role for VEGF and VEGF-R2 signalling as both a promoter of endothelial cell function and a negative regulator of VSMCs and vessel maturation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605188/" 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/PMC2605188/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greenberg, Joshua I -- Shields, David J -- Barillas, Samuel G -- Acevedo, Lisette M -- Murphy, Eric -- Huang, Jianhua -- Scheppke, Lea -- Stockmann, Christian -- Johnson, Randall S -- Angle, Niren -- Cheresh, David A -- GM 68524/GM/NIGMS NIH HHS/ -- P01 CA078045/CA/NCI NIH HHS/ -- P01 CA078045-050004/CA/NCI NIH HHS/ -- P01 CA078045-100004/CA/NCI NIH HHS/ -- P01 CA078045-109001/CA/NCI NIH HHS/ -- R01 CA095262/CA/NCI NIH HHS/ -- R01 CA095262-06/CA/NCI NIH HHS/ -- R01 CA118165/CA/NCI NIH HHS/ -- R01 HL078912/HL/NHLBI NIH HHS/ -- R01 HL078912-04/HL/NHLBI NIH HHS/ -- R21 CA129660/CA/NCI NIH HHS/ -- R21 CA129660-02/CA/NCI NIH HHS/ -- R37 CA050286/CA/NCI NIH HHS/ -- R37 CA050286-19/CA/NCI NIH HHS/ -- R37 CA050286-20/CA/NCI NIH HHS/ -- R37-CA082515/CA/NCI NIH HHS/ -- R37-CA50286/CA/NCI NIH HHS/ -- England -- Nature. 2008 Dec 11;456(7223):809-13. doi: 10.1038/nature07424. Epub 2008 Nov 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Surgery, School of Medicine, Moore's UCSD Cancer Center, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18997771" target="_blank"〉PubMed〈/a〉
    Keywords: Angiogenesis Inhibitors/pharmacology ; Animals ; Blood Vessels/*metabolism ; Cell Line ; Cells, Cultured ; Fibrosarcoma/blood supply ; Humans ; Mice ; Mice, Inbred C57BL ; Mice, Nude ; Neovascularization, Physiologic/drug effects/*physiology ; Pericytes/drug effects/*metabolism ; Platelet-Derived Growth Factor/*metabolism/pharmacology ; Receptor, Platelet-Derived Growth Factor beta/metabolism ; Receptors, Vascular Endothelial Growth Factor/metabolism ; Signal Transduction ; Vascular Endothelial Growth Factor A/*metabolism
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  • 103
    Publication Date: 2008-11-07
    Description: Xeroderma pigmentosum is a monogenic disease characterized by hypersensitivity to ultraviolet light. The cells of xeroderma pigmentosum patients are defective in nucleotide excision repair, limiting their capacity to eliminate ultraviolet-induced DNA damage, and resulting in a strong predisposition to develop skin cancers. The use of rare cutting DNA endonucleases-such as homing endonucleases, also known as meganucleases-constitutes one possible strategy for repairing DNA lesions. Homing endonucleases have emerged as highly specific molecular scalpels that recognize and cleave DNA sites, promoting efficient homologous gene targeting through double-strand-break-induced homologous recombination. Here we describe two engineered heterodimeric derivatives of the homing endonuclease I-CreI, produced by a semi-rational approach. These two molecules-Amel3-Amel4 and Ini3-Ini4-cleave DNA from the human XPC gene (xeroderma pigmentosum group C), in vitro and in vivo. Crystal structures of the I-CreI variants complexed with intact and cleaved XPC target DNA suggest that the mechanism of DNA recognition and cleavage by the engineered homing endonucleases is similar to that of the wild-type I-CreI. Furthermore, these derivatives induced high levels of specific gene targeting in mammalian cells while displaying no obvious genotoxicity. Thus, homing endonucleases can be designed to recognize and cleave the DNA sequences of specific genes, opening up new possibilities for genome engineering and gene therapy in xeroderma pigmentosum patients whose illness can be treated ex vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redondo, Pilar -- Prieto, Jesus -- Munoz, Ines G -- Alibes, Andreu -- Stricher, Francois -- Serrano, Luis -- Cabaniols, Jean-Pierre -- Daboussi, Fayza -- Arnould, Sylvain -- Perez, Christophe -- Duchateau, Philippe -- Paques, Frederic -- Blanco, Francisco J -- Montoya, Guillermo -- England -- Nature. 2008 Nov 6;456(7218):107-11. doi: 10.1038/nature07343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Macromolecular Crystallography Group, Spanish National Cancer Research Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987743" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CHO Cells ; Cell Line ; Cricetinae ; Cricetulus ; Crystallography, X-Ray ; DNA/chemistry/*genetics/*metabolism ; DNA Repair ; DNA Restriction Enzymes/*chemistry/genetics/*metabolism/toxicity ; DNA-Binding Proteins/*genetics ; Enzyme Stability ; *Genetic Engineering ; Humans ; Models, Molecular ; Phosphorylation ; Protein Multimerization ; Substrate Specificity ; Xeroderma Pigmentosum/*genetics
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  • 104
    Publication Date: 2008-02-01
    Description: The NAD-dependent protein deacetylase Sir2 (silent information regulator 2) regulates lifespan in several organisms. SIRT1, the mammalian orthologue of yeast Sir2, participates in various cellular functions and possibly tumorigenesis. Whereas the cellular functions of SIRT1 have been extensively investigated, less is known about the regulation of SIRT1 activity. Here we show that Deleted in Breast Cancer-1 (DBC1), initially cloned from a region (8p21) homozygously deleted in breast cancers, forms a stable complex with SIRT1. DBC1 directly interacts with SIRT1 and inhibits SIRT1 activity in vitro and in vivo. Downregulation of DBC1 expression potentiates SIRT1-dependent inhibition of apoptosis induced by genotoxic stress. Our results shed new light on the regulation of SIRT1 and have important implications in understanding the molecular mechanism of ageing and cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Ja-Eun -- Chen, Junjie -- Lou, Zhenkun -- England -- Nature. 2008 Jan 31;451(7178):583-6. doi: 10.1038/nature06500.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18235501" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/chemistry/genetics/*metabolism ; Aging ; Apoptosis/drug effects ; Catalytic Domain ; Cell Line ; Down-Regulation ; Etoposide/pharmacology ; Humans ; Immunoprecipitation ; Leucine Zippers ; Mutagens/pharmacology ; Protein Binding ; Protein Interaction Mapping ; Sirtuin 1 ; Sirtuins/*antagonists & inhibitors/chemistry/genetics/*metabolism
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  • 105
    Publication Date: 2008-02-29
    Description: Signalling by means of toll-like receptors (TLRs) is essential for the development of innate and adaptive immune responses. UNC93B1, essential for signalling of TLR3, TLR7 and TLR9 in both humans and mice, physically interacts with these TLRs in the endoplasmic reticulum (ER). Here we show that the function of the polytopic membrane protein UNC93B1 is to deliver the nucleotide-sensing receptors TLR7 and TLR9 from the ER to endolysosomes. In dendritic cells of 3d mice, which express an UNC93B1 missense mutant (H412R) incapable of TLR binding, neither TLR7 nor TLR9 exits the ER. Furthermore, the trafficking and signalling defects of the nucleotide-sensing TLRs in 3d dendritic cells are corrected by expression of wild-type UNC93B1. However, UNC93B1 is dispensable for ligand recognition and signal initiation by TLRs. To our knowledge, UNC93B1 is the first protein to be identified as a molecule specifically involved in trafficking of nucleotide-sensing TLRs. By inhibiting the interaction between UNC93B1 and TLRs it should be possible to achieve specific regulation of the nucleotide-sensing TLRs without compromising signalling via the cell-surface-disposed TLRs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, You-Me -- Brinkmann, Melanie M -- Paquet, Marie-Eve -- Ploegh, Hidde L -- England -- Nature. 2008 Mar 13;452(7184):234-8. doi: 10.1038/nature06726. Epub 2008 Feb 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA. ykim@wi.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18305481" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Dendritic Cells/metabolism ; *Endocytosis ; Endoplasmic Reticulum/metabolism ; Humans ; Ligands ; Lysosomes/*metabolism ; Membrane Glycoproteins/*metabolism ; Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Mutation ; Nucleotides/*metabolism ; Protein Transport ; Signal Transduction ; Toll-Like Receptor 7/*metabolism ; Toll-Like Receptor 9/*metabolism
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  • 106
    Publication Date: 2008-01-04
    Description: Mammalian homologues of Drosophila melanogaster transient receptor potential (TRP) are a large family of multimeric cation channels that act, or putatively act, as sensors of one or more chemical factor. Major research objectives are the identification of endogenous activators and the determination of cellular and tissue functions of these channels. Here we show the activation of TRPC5 (canonical TRP 5) homomultimeric and TRPC5-TRPC1 heteromultimeric channels by extracellular reduced thioredoxin, which acts by breaking a disulphide bridge in the predicted extracellular loop adjacent to the ion-selectivity filter of TRPC5. Thioredoxin is an endogenous redox protein with established intracellular functions, but it is also secreted and its extracellular targets are largely unknown. Particularly high extracellular concentrations of thioredoxin are apparent in rheumatoid arthritis, an inflammatory joint disease that disables millions of people worldwide. We show that TRPC5 and TRPC1 are expressed in secretory fibroblast-like synoviocytes from patients with rheumatoid arthritis, that endogenous TRPC5-TRPC1 channels of the cells are activated by reduced thioredoxin, and that blockade of the channels enhances secretory activity and prevents the suppression of secretion by thioredoxin. The data indicate the presence of a previously unrecognized ion-channel activation mechanism that couples extracellular thioredoxin to cell function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2645077/" 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/PMC2645077/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Shang-Zhong -- Sukumar, Piruthivi -- Zeng, Fanning -- Li, Jing -- Jairaman, Amit -- English, Anne -- Naylor, Jacqueline -- Ciurtin, Coziana -- Majeed, Yasser -- Milligan, Carol J -- Bahnasi, Yahya M -- Al-Shawaf, Eman -- Porter, Karen E -- Jiang, Lin-Hua -- Emery, Paul -- Sivaprasadarao, Asipu -- Beech, David J -- 077424/Wellcome Trust/United Kingdom -- 083857/Wellcome Trust/United Kingdom -- 18475/Arthritis Research UK/United Kingdom -- BB/D524875/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 Jan 3;451(7174):69-72. doi: 10.1038/nature06414.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Membrane and Systems Biology, Garstang Building, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18172497" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthritis, Rheumatoid/metabolism/pathology ; Cell Line ; Disulfides/chemistry/metabolism ; Electric Conductivity ; Humans ; Oxidation-Reduction/drug effects ; Patch-Clamp Techniques ; Rabbits ; TRPC Cation Channels/*agonists/chemistry/*metabolism ; Thioredoxins/chemistry/*pharmacology
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  • 107
    Publication Date: 2008-01-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grosshans, Helge -- Filipowicz, Witold -- England -- Nature. 2008 Jan 24;451(7177):414-6. doi: 10.1038/451414a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18216846" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; History, 20th Century ; History, 21st Century ; Humans ; Models, Genetic ; Molecular Biology/history ; Organ Specificity ; Protein Biosynthesis ; RNA Interference ; RNA, Double-Stranded/biosynthesis/genetics/metabolism ; RNA, Messenger/biosynthesis/genetics/metabolism ; RNA, Untranslated/biosynthesis/classification/*genetics/*metabolism ; Species Specificity ; Substrate Specificity ; Viruses/genetics/immunology
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  • 108
    Publication Date: 2008-03-21
    Description: REST/NRSF (repressor-element-1-silencing transcription factor/neuron-restrictive silencing factor) negatively regulates the transcription of genes containing RE1 sites. REST is expressed in non-neuronal cells and stem/progenitor neuronal cells, in which it inhibits the expression of neuron-specific genes. Overexpression of REST is frequently found in human medulloblastomas and neuroblastomas, in which it is thought to maintain the stem character of tumour cells. Neural stem cells forced to express REST and c-Myc fail to differentiate and give rise to tumours in the mouse cerebellum. Expression of a splice variant of REST that lacks the carboxy terminus has been associated with neuronal tumours and small-cell lung carcinomas, and a frameshift mutant (REST-FS), which is also truncated at the C terminus, has oncogenic properties. Here we show, by using an unbiased screen, that REST is an interactor of the F-box protein beta-TrCP. REST is degraded by means of the ubiquitin ligase SCF(beta-TrCP) during the G2 phase of the cell cycle to allow transcriptional derepression of Mad2, an essential component of the spindle assembly checkpoint. The expression in cultured cells of a stable REST mutant, which is unable to bind beta-TrCP, inhibited Mad2 expression and resulted in a phenotype analogous to that observed in Mad2(+/-) cells. In particular, we observed defects that were consistent with faulty activation of the spindle checkpoint, such as shortened mitosis, premature sister-chromatid separation, chromosome bridges and mis-segregation in anaphase, tetraploidy, and faster mitotic slippage in the presence of a spindle inhibitor. An indistinguishable phenotype was observed by expressing the oncogenic REST-FS mutant, which does not bind beta-TrCP. Thus, SCF(beta-TrCP)-dependent degradation of REST during G2 permits the optimal activation of the spindle checkpoint, and consequently it is required for the fidelity of mitosis. The high levels of REST or its truncated variants found in certain human tumours may contribute to cellular transformation by promoting genomic instability.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2707768/" 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/PMC2707768/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guardavaccaro, Daniele -- Frescas, David -- Dorrello, N Valerio -- Peschiaroli, Angelo -- Multani, Asha S -- Cardozo, Timothy -- Lasorella, Anna -- Iavarone, Antonio -- Chang, Sandy -- Hernando, Eva -- Pagano, Michele -- R01 GM057587/GM/NIGMS NIH HHS/ -- R01 GM057587-10/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Mar 20;452(7185):365-9. doi: 10.1038/nature06641.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, NYU Cancer Institute, New York University School of Medicine, 550 First Avenue, MSB 599, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18354482" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium-Binding Proteins/genetics/*metabolism ; Cell Cycle Proteins/genetics/*metabolism ; Cell Line ; *Chromosomal Instability ; G2 Phase ; Gene Expression Regulation ; Genomic Instability ; Humans ; Mad2 Proteins ; Mitosis ; Protein Binding ; Repressor Proteins/genetics/*metabolism ; SKP Cullin F-Box Protein Ligases/metabolism ; Spindle Apparatus/physiology ; Transcription Factors/genetics/*metabolism ; beta-Transducin Repeat-Containing Proteins/deficiency/genetics/*metabolism
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  • 109
    Publication Date: 2008-02-22
    Description: Phosphoinositides are a family of lipid signalling molecules that regulate many cellular functions in eukaryotes. Phosphatidylinositol-4,5-bisphosphate (PtdIns4,5P2), the central component in the phosphoinositide signalling circuitry, is generated primarily by type I phosphatidylinositol 4-phosphate 5-kinases (PIPKIalpha, PIPKIbeta and PIPKIgamma). In addition to functions in the cytosol, phosphoinositides are present in the nucleus, where they modulate several functions; however, the mechanism by which they directly regulate nuclear functions remains unknown. PIPKIs regulate cellular functions through interactions with protein partners, often PtdIns4,5P2 effectors, that target PIPKIs to discrete subcellular compartments, resulting in the spatial and temporal generation of PtdIns4,5P2 required for the regulation of specific signalling pathways. Therefore, to determine roles for nuclear PtdIns4,5P2 we set out to identify proteins that interacted with the nuclear PIPK, PIPKIalpha. Here we show that PIPKIalpha co-localizes at nuclear speckles and interacts with a newly identified non-canonical poly(A) polymerase, which we have termed Star-PAP (nuclear speckle targeted PIPKIalpha regulated-poly(A) polymerase) and that the activity of Star-PAP can be specifically regulated by PtdIns4,5P2. Star-PAP and PIPKIalpha function together in a complex to control the expression of select mRNAs, including the transcript encoding the key cytoprotective enzyme haem oxygenase-1 (refs 8, 9) and other oxidative stress response genes by regulating the 3'-end formation of their mRNAs. Taken together, the data demonstrate a model by which phosphoinositide signalling works in tandem with complement pathways to regulate the activity of Star-PAP and the subsequent biosynthesis of its target mRNA. The results reveal a mechanism for the integration of nuclear phosphoinositide signals and a method for regulating gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mellman, David L -- Gonzales, Michael L -- Song, Chunhua -- Barlow, Christy A -- Wang, Ping -- Kendziorski, Christina -- Anderson, Richard A -- R01 GM051968/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Feb 21;451(7181):1013-7. doi: 10.1038/nature06666.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Molecular and Cellular Pharmacology, University of Wisconsin Medical School, University of Wisconsin-Madison, 1300 University Avenue, Madison, Wisconsin 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18288197" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Nucleus/enzymology/genetics/*metabolism ; Heme Oxygenase-1/genetics ; Humans ; Mice ; Multiprotein Complexes/metabolism ; Oxidative Stress/genetics ; Phosphatidylinositol 4,5-Diphosphate ; Phosphatidylinositol Phosphates/*metabolism ; Phosphotransferases (Alcohol Group Acceptor)/deficiency/genetics/metabolism ; Polynucleotide Adenylyltransferase/chemistry/deficiency/genetics/*metabolism ; Protein Binding ; *RNA 3' End Processing ; RNA, Messenger/genetics/metabolism ; Substrate Specificity ; Transcription, Genetic
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  • 110
    Publication Date: 2008-02-08
    Description: Haematopoietic stem cells (HSCs) circulate in the bloodstream under steady-state conditions, but the mechanisms controlling their physiological trafficking are unknown. Here we show that circulating HSCs and their progenitors exhibit robust circadian fluctuations, peaking 5 h after the initiation of light and reaching a nadir 5 h after darkness. Circadian oscillations are markedly altered when mice are subjected to continuous light or to a 'jet lag' (defined as a shift of 12 h). Circulating HSCs and their progenitors fluctuate in antiphase with the expression of the chemokine CXCL12 in the bone marrow microenvironment. The cyclical release of HSCs and expression of Cxcl12 are regulated by core genes of the molecular clock through circadian noradrenaline secretion by the sympathetic nervous system. These adrenergic signals are locally delivered by nerves in the bone marrow, transmitted to stromal cells by the beta(3)-adrenergic receptor, leading to a decreased nuclear content of Sp1 transcription factor and the rapid downregulation of Cxcl12. These data indicate that a circadian, neurally driven release of HSC during the animal's resting period may promote the regeneration of the stem cell niche and possibly other tissues.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mendez-Ferrer, Simon -- Lucas, Daniel -- Battista, Michela -- Frenette, Paul S -- England -- Nature. 2008 Mar 27;452(7186):442-7. doi: 10.1038/nature06685. Epub 2008 Feb 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mount Sinai School of Medicine, Department of Medicine and Department of Gene and Cell Medicine, New York, New York 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256599" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Clocks/genetics/physiology/radiation effects ; Bone Marrow/*innervation/metabolism/radiation effects ; Bone Marrow Cells/metabolism/radiation effects ; Cell Line ; Chemokine CXCL12/genetics/metabolism ; Circadian Rhythm/*physiology/radiation effects ; Cues ; Gene Expression Regulation ; Hematopoietic Stem Cells/*cytology/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Osteoblasts ; Photic Stimulation ; Receptors, Adrenergic, beta-3/deficiency/genetics/metabolism ; Sp1 Transcription Factor/metabolism ; Stromal Cells/metabolism ; Sympathetic Nervous System/metabolism/radiation effects
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  • 111
    Publication Date: 2008-05-09
    Description: The architecture of human chromosomes in interphase nuclei is still largely unknown. Microscopy studies have indicated that specific regions of chromosomes are located in close proximity to the nuclear lamina (NL). This has led to the idea that certain genomic elements may be attached to the NL, which may contribute to the spatial organization of chromosomes inside the nucleus. However, sequences in the human genome that interact with the NL in vivo have not been identified. Here we construct a high-resolution map of the interaction sites of the entire genome with NL components in human fibroblasts. This map shows that genome-lamina interactions occur through more than 1,300 sharply defined large domains 0.1-10 megabases in size. These lamina-associated domains (LADs) are typified by low gene-expression levels, indicating that LADs represent a repressive chromatin environment. The borders of LADs are demarcated by the insulator protein CTCF, by promoters that are oriented away from LADs, or by CpG islands, suggesting possible mechanisms of LAD confinement. Taken together, these results demonstrate that the human genome is divided into large, discrete domains that are units of chromosome organization within the nucleus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guelen, Lars -- Pagie, Ludo -- Brasset, Emilie -- Meuleman, Wouter -- Faza, Marius B -- Talhout, Wendy -- Eussen, Bert H -- de Klein, Annelies -- Wessels, Lodewyk -- de Laat, Wouter -- van Steensel, Bas -- England -- Nature. 2008 Jun 12;453(7197):948-51. doi: 10.1038/nature06947. Epub 2008 May 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18463634" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Chromatin/genetics/metabolism ; *Chromosome Positioning ; Chromosomes, Human/genetics/*metabolism ; CpG Islands/genetics ; DNA-Binding Proteins/metabolism ; Fibroblasts ; Genome, Human ; Humans ; Lamin Type B/metabolism ; Nuclear Lamina/chemistry/*metabolism ; Promoter Regions, Genetic/genetics ; Protein Binding ; Repressor Proteins/metabolism
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  • 112
    Publication Date: 2008-01-25
    Description: Synaptic circuits in the retina transform visual input gathered by photoreceptors into messages that retinal ganglion cells (RGCs) send to the brain. Processes of retinal interneurons (amacrine and bipolar cells) form synapses on dendrites of RGCs in the inner plexiform layer (IPL). The IPL is divided into at least 10 parallel sublaminae; subsets of interneurons and RGCs arborize and form synapses in just one or a few of them. These lamina-specific circuits determine the visual features to which RGC subtypes respond. Here we show that four closely related immunoglobulin superfamily (IgSF) adhesion molecules--Dscam (Down's syndrome cell adhesion molecule), DscamL (refs 6-9), Sidekick-1 and Sidekick-2 (ref. 10)--are expressed in chick by non-overlapping subsets of interneurons and RGCs that form synapses in distinct IPL sublaminae. Moreover, each protein is concentrated within the appropriate sublaminae and each mediates homophilic adhesion. Loss- and gain-of-function studies in vivo indicate that these IgSF members participate in determining the IPL sublaminae in which synaptic partners arborize and connect. Thus, vertebrate Dscams, like Drosophila Dscams, play roles in neural connectivity. Together, our results on Dscams and Sidekicks suggest the existence of an IgSF code for laminar specificity in retina and, by implication, in other parts of the central nervous system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamagata, Masahito -- Sanes, Joshua R -- England -- Nature. 2008 Jan 24;451(7177):465-9. doi: 10.1038/nature06469.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18216854" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Adhesion ; Cell Line ; Chick Embryo ; Eye Proteins/genetics/*metabolism ; Gene Expression Profiling ; Humans ; Immunoglobulins/*chemistry ; Interneurons/metabolism ; Membrane Proteins/deficiency/genetics/*metabolism ; Neural Cell Adhesion Molecules/deficiency/genetics/*metabolism ; Organ Specificity ; Retina/*cytology/*metabolism ; Synapses/*metabolism
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  • 113
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2008-06-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Jun 5;453(7196):697. doi: 10.1038/453697a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18528339" target="_blank"〉PubMed〈/a〉
    Keywords: Genome, Human ; Genomics/*trends ; History, 20th Century ; History, 21st Century ; Human Genome Project/history ; Humans ; National Human Genome Research Institute (U.S.)/history/*organization & ; administration/trends ; United States
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  • 114
    Publication Date: 2008-02-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klagsbrun, Michael -- Moses, Marsha A -- England -- Nature. 2008 Feb 14;451(7180):781. doi: 10.1038/451781a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Surgery, Children's Hospital Boston and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA. michael.klagsbrun@childrens.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18273010" target="_blank"〉PubMed〈/a〉
    Keywords: Angiogenesis Inhibitors/therapeutic use ; Awards and Prizes ; Biomarkers ; History, 20th Century ; History, 21st Century ; Humans ; Neoplasms/*blood supply/drug therapy ; *Neovascularization, Pathologic/drug therapy ; United States
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  • 115
    Publication Date: 2008-03-07
    Description: Processes that regulate gene transcription are directly under the influence of the genome organization. The epigenome contains additional information that is not brought by DNA sequence, and generates spatial and functional constraints that complement genetic instructions. DNA methylation on CpGs constitutes an epigenetic mark generally correlated with transcriptionally silent condensed chromatin. Replication of methylation patterns by DNA methyltransferases maintains genome stability through cell division. Here we present evidence of an unanticipated dynamic role for DNA methylation in gene regulation in human cells. Periodic, strand-specific methylation/demethylation occurs during transcriptional cycling of the pS2/TFF1 gene promoter on activation by oestrogens. DNA methyltransferases exhibit dual actions during these cycles, being involved in CpG methylation and active demethylation of 5mCpGs through deamination. Inhibition of this process precludes demethylation of the pS2 gene promoter and its subsequent transcriptional activation. Cyclical changes in the methylation status of promoter CpGs may thus represent a critical event in transcriptional achievement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Metivier, Raphael -- Gallais, Rozenn -- Tiffoche, Christophe -- Le Peron, Christine -- Jurkowska, Renata Z -- Carmouche, Richard P -- Ibberson, David -- Barath, Peter -- Demay, Florence -- Reid, George -- Benes, Vladimir -- Jeltsch, Albert -- Gannon, Frank -- Salbert, Gilles -- England -- Nature. 2008 Mar 6;452(7183):45-50. doi: 10.1038/nature06544.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universite de Rennes I, CNRS, UMR 6026 Equipe SPARTE, IFR 140 GFAS, Campus de Beaulieu, 35042 Rennes cedex, France. Raphael.Metivier@univ-rennes1.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322525" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Chromatin Immunoprecipitation ; CpG Islands/genetics ; DNA (Cytosine-5-)-Methyltransferase/antagonists & inhibitors/metabolism ; *DNA Methylation/drug effects ; DNA Repair ; Deamination ; Estrogens/pharmacology ; *Gene Expression Regulation/drug effects ; Humans ; Kinetics ; Promoter Regions, Genetic/*genetics ; Thymine DNA Glycosylase/metabolism ; Transcription, Genetic/drug effects/*genetics ; Transcriptional Activation/drug effects/*genetics ; Tumor Suppressor Proteins/*genetics
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  • 116
    Publication Date: 2008-12-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Richerson, Peter J -- Boyd, Robert -- England -- Nature. 2008 Dec 18;456(7224):877. doi: 10.1038/456877a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Peter J. Richerson is in the Department of Environmental Science and Policy, University of California, Davis, California 95616, USA. pjricherson@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19092915" target="_blank"〉PubMed〈/a〉
    Keywords: Conflict (Psychology) ; *Cultural Evolution ; *Emigration and Immigration/history ; History, 20th Century ; History, 21st Century ; History, Ancient ; Internationality/history
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  • 117
    Publication Date: 2008-04-15
    Description: Eukaryotic cells store neutral lipids in cytoplasmic lipid droplets enclosed in a monolayer of phospholipids and associated proteins. These dynamic organelles serve as the principal reservoirs for storing cellular energy and for the building blocks for membrane lipids. Excessive lipid accumulation in cells is a central feature of obesity, diabetes and atherosclerosis, yet remarkably little is known about lipid-droplet cell biology. Here we show, by means of a genome-wide RNA interference (RNAi) screen in Drosophila S2 cells that about 1.5% of all genes function in lipid-droplet formation and regulation. The phenotypes of the gene knockdowns sorted into five distinct phenotypic classes. Genes encoding enzymes of phospholipid biosynthesis proved to be determinants of lipid-droplet size and number, suggesting that the phospholipid composition of the monolayer profoundly affects droplet morphology and lipid utilization. A subset of the Arf1-COPI vesicular transport proteins also regulated droplet morphology and lipid utilization, thereby identifying a previously unrecognized function for this machinery. These phenotypes are conserved in mammalian cells, suggesting that insights from these studies are likely to be central to our understanding of human diseases involving excessive lipid storage.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734507/" 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/PMC2734507/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guo, Yi -- Walther, Tobias C -- Rao, Meghana -- Stuurman, Nico -- Goshima, Gohta -- Terayama, Koji -- Wong, Jinny S -- Vale, Ronald D -- Walter, Peter -- Farese, Robert V -- R21 DK078254/DK/NIDDK NIH HHS/ -- R21 DK078254-01/DK/NIDDK NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 May 29;453(7195):657-61. doi: 10.1038/nature06928. Epub 2008 Apr 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18408709" target="_blank"〉PubMed〈/a〉
    Keywords: ADP-Ribosylation Factors/metabolism ; Animals ; Cell Line ; Coat Protein Complex I/metabolism ; Drosophila Proteins/*genetics ; Drosophila melanogaster/*cytology/*genetics ; Genes, Insect/*genetics ; Genome, Insect/*genetics ; *Genomics ; Lipid Metabolism/*genetics ; Lipolysis ; Phenotype ; Phosphatidylcholines/metabolism ; RNA Interference
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  • 118
    Publication Date: 2008-06-13
    Description: MicroRNAs (miRNAs) are small non-coding RNAs that participate in the spatiotemporal regulation of messenger RNA and protein synthesis. Aberrant miRNA expression leads to developmental abnormalities and diseases, such as cardiovascular disorders and cancer; however, the stimuli and processes regulating miRNA biogenesis are largely unknown. The transforming growth factor beta (TGF-beta) and bone morphogenetic protein (BMP) family of growth factors orchestrates fundamental biological processes in development and in the homeostasis of adult tissues, including the vasculature. Here we show that induction of a contractile phenotype in human vascular smooth muscle cells by TGF-beta and BMPs is mediated by miR-21. miR-21 downregulates PDCD4 (programmed cell death 4), which in turn acts as a negative regulator of smooth muscle contractile genes. Surprisingly, TGF-beta and BMP signalling promotes a rapid increase in expression of mature miR-21 through a post-transcriptional step, promoting the processing of primary transcripts of miR-21 (pri-miR-21) into precursor miR-21 (pre-miR-21) by the DROSHA (also known as RNASEN) complex. TGF-beta- and BMP-specific SMAD signal transducers are recruited to pri-miR-21 in a complex with the RNA helicase p68 (also known as DDX5), a component of the DROSHA microprocessor complex. The shared cofactor SMAD4 is not required for this process. Thus, regulation of miRNA biogenesis by ligand-specific SMAD proteins is critical for control of the vascular smooth muscle cell phenotype and potentially for SMAD4-independent responses mediated by the TGF-beta and BMP signalling pathways.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653422/" 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/PMC2653422/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davis, Brandi N -- Hilyard, Aaron C -- Lagna, Giorgio -- Hata, Akiko -- HD042149/HD/NICHD NIH HHS/ -- HL082854/HL/NHLBI NIH HHS/ -- HL086572/HL/NHLBI NIH HHS/ -- R01 HD042149/HD/NICHD NIH HHS/ -- R01 HD042149-05/HD/NICHD NIH HHS/ -- R01 HL082854/HL/NHLBI NIH HHS/ -- R01 HL082854-03/HL/NHLBI NIH HHS/ -- R21 HL086572/HL/NHLBI NIH HHS/ -- R21 HL086572-02/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 Jul 3;454(7200):56-61. doi: 10.1038/nature07086. Epub 2008 Jun 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18548003" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis Regulatory Proteins/metabolism ; Bone Morphogenetic Protein 4 ; Bone Morphogenetic Proteins/metabolism/pharmacology ; Breast Neoplasms/genetics ; Cell Line ; Cercopithecus aethiops ; DEAD-box RNA Helicases/metabolism ; Gene Expression Regulation/drug effects ; Humans ; Ligands ; Mice ; MicroRNAs/biosynthesis/*metabolism ; Muscle, Smooth/metabolism ; Phenotype ; Protein Binding ; *RNA Processing, Post-Transcriptional ; RNA-Binding Proteins/metabolism ; Ribonuclease III/*metabolism ; Signal Transduction/drug effects ; Smad Proteins/*metabolism ; Transforming Growth Factor beta/metabolism/pharmacology
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  • 119
    Publication Date: 2008-10-14
    Description: DNA double-strand breaks are generated by genotoxic agents and by cellular endonucleases as intermediates of several important physiological processes. The cellular response to genotoxic DNA breaks includes the activation of transcriptional programs known primarily to regulate cell-cycle checkpoints and cell survival. DNA double-strand breaks are generated in all developing lymphocytes during the assembly of antigen receptor genes, a process that is essential for normal lymphocyte development. Here we show that in murine lymphocytes these physiological DNA breaks activate a broad transcriptional program. This program transcends the canonical DNA double-strand break response and includes many genes that regulate diverse cellular processes important for lymphocyte development. Moreover, the expression of several of these genes is regulated similarly in response to genotoxic DNA damage. Thus, physiological DNA double-strand breaks provide cues that can regulate cell-type-specific processes not directly involved in maintaining the integrity of the genome, and genotoxic DNA breaks could disrupt normal cellular functions by corrupting these processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605662/" 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/PMC2605662/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bredemeyer, Andrea L -- Helmink, Beth A -- Innes, Cynthia L -- Calderon, Boris -- McGinnis, Lisa M -- Mahowald, Grace K -- Gapud, Eric J -- Walker, Laura M -- Collins, Jennifer B -- Weaver, Brian K -- Mandik-Nayak, Laura -- Schreiber, Robert D -- Allen, Paul M -- May, Michael J -- Paules, Richard S -- Bassing, Craig H -- Sleckman, Barry P -- R01 AI047829/AI/NIAID NIH HHS/ -- R01 AI047829-09/AI/NIAID NIH HHS/ -- R01 CA125195/CA/NCI NIH HHS/ -- R01 CA125195-02/CA/NCI NIH HHS/ -- England -- Nature. 2008 Dec 11;456(7223):819-23. doi: 10.1038/nature07392. Epub 2008 Oct 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18849970" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ataxia Telangiectasia Mutated Proteins ; B-Lymphocytes/drug effects/*metabolism ; Cell Cycle Proteins/drug effects ; Cell Line ; *DNA Breaks, Double-Stranded ; DNA-Binding Proteins/drug effects ; Enzyme Inhibitors/pharmacology ; Gene Expression Profiling ; Gene Expression Regulation, Developmental/drug effects/*genetics ; Homeodomain Proteins/metabolism ; Mice ; Mice, Knockout ; Mice, SCID ; NF-kappa B/metabolism ; Protein-Serine-Threonine Kinases/drug effects ; Tumor Suppressor Proteins/drug effects
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  • 120
    Publication Date: 2008-05-13
    Description: The recent discovery of CD4(+) T cells characterized by secretion of interleukin (IL)-17 (T(H)17 cells) and the naturally occurring regulatory FOXP3(+) CD4 T cell (nT(reg)) has had a major impact on our understanding of immune processes not readily explained by the T(H)1/T(H)2 paradigm. T(H)17 and nT(reg) cells have been implicated in the pathogenesis of human autoimmune diseases, including multiple sclerosis, rheumatoid arthritis, inflammatory bowel disease and psoriasis. Our recent data and the work of others demonstrated that transforming growth factor-beta (TGF-beta) and IL-6 are responsible for the differentiation of naive mouse T cells into T(H)17 cells, and it has been proposed that IL-23 may have a critical role in stabilization of the T(H)17 phenotype. A second pathway has been discovered in which a combination of TGF-beta and IL-21 is capable of inducing differentiation of mouse T(H)17 cells in the absence of IL-6 (refs 6-8). However, TGF-beta and IL-6 are not capable of differentiating human T(H)17 cells and it has been suggested that TGF-beta may in fact suppress the generation of human T(H)17 cells. Instead, it has been recently shown that the cytokines IL-1beta, IL-6 and IL-23 are capable of driving IL-17 secretion in short-term CD4(+) T cell lines isolated from human peripheral blood, although the factors required for differentiation of naive human CD4 to T(H)17 cells are still unknown. Here we confirm that whereas IL-1beta and IL-6 induce IL-17A secretion from human central memory CD4(+) T cells, TGF-beta and IL-21 uniquely promote the differentiation of human naive CD4(+) T cells into T(H)17 cells accompanied by expression of the transcription factor RORC2. These data will allow the investigation of this new population of T(H)17 cells in human inflammatory disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760130/" 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/PMC2760130/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Li -- Anderson, David E -- Baecher-Allan, Clare -- Hastings, William D -- Bettelli, Estelle -- Oukka, Mohamed -- Kuchroo, Vijay K -- Hafler, David A -- P01 AI039671/AI/NIAID NIH HHS/ -- P01 AI039671-14/AI/NIAID NIH HHS/ -- P01 NS038037/NS/NINDS NIH HHS/ -- P01 NS038037-080006/NS/NINDS NIH HHS/ -- R01 AI073542/AI/NIAID NIH HHS/ -- R01 AI073542-01/AI/NIAID NIH HHS/ -- R01 AI073542-02/AI/NIAID NIH HHS/ -- R01 AI073542-03/AI/NIAID NIH HHS/ -- R37 NS024247/NS/NINDS NIH HHS/ -- R37 NS024247-20/NS/NINDS NIH HHS/ -- U19 AI070352/AI/NIAID NIH HHS/ -- U19 AI070352-03/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Jul 17;454(7202):350-2. doi: 10.1038/nature07021. Epub 2008 May 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Immunology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18469800" target="_blank"〉PubMed〈/a〉
    Keywords: *Cell Differentiation ; Cell Line ; Cells, Cultured ; Gene Expression Regulation ; Humans ; Interleukin-17/metabolism ; Interleukins/*metabolism ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; T-Lymphocytes, Helper-Inducer/*cytology/*metabolism ; Transcription Factors/genetics/metabolism ; Transforming Growth Factor beta1/*metabolism
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  • 121
    Publication Date: 2008-05-27
    Description: Members of the epidermal growth factor receptor (EGFR) or ErbB/HER family and their activating ligands are essential regulators of diverse developmental processes. Inappropriate activation of these receptors is a key feature of many human cancers, and its reversal is an important clinical goal. A natural secreted antagonist of EGFR signalling, called Argos, was identified in Drosophila. We showed previously that Argos functions by directly binding (and sequestering) growth factor ligands that activate EGFR. Here we describe the 1.6-A resolution crystal structure of Argos bound to an EGFR ligand. Contrary to expectations, Argos contains no EGF-like domain. Instead, a trio of closely related domains (resembling a three-finger toxin fold) form a clamp-like structure around the bound EGF ligand. Although structurally unrelated to the receptor, Argos mimics EGFR by using a bipartite binding surface to entrap EGF. The individual Argos domains share unexpected structural similarities with the extracellular ligand-binding regions of transforming growth factor-beta family receptors. The three-domain clamp of Argos also resembles the urokinase-type plasminogen activator (uPA) receptor, which uses a similar mechanism to engulf the EGF-like module of uPA. Our results indicate that undiscovered mammalian counterparts of Argos may exist among other poorly characterized structural homologues. In addition, the structures presented here define requirements for the design of artificial EGF-sequestering proteins that would be valuable anti-cancer therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2526102/" 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/PMC2526102/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klein, Daryl E -- Stayrook, Steven E -- Shi, Fumin -- Narayan, Kartik -- Lemmon, Mark A -- R01 CA079992/CA/NCI NIH HHS/ -- R01 CA079992-10/CA/NCI NIH HHS/ -- R01 CA125432/CA/NCI NIH HHS/ -- R01 CA125432-01A1/CA/NCI NIH HHS/ -- England -- Nature. 2008 Jun 26;453(7199):1271-5. doi: 10.1038/nature06978. Epub 2008 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 809C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104-6059, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18500331" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Drosophila Proteins/*chemistry/*metabolism ; Drosophila melanogaster/*chemistry/cytology ; Epidermal Growth Factor/*chemistry/*metabolism ; Eye Proteins/*chemistry/*metabolism ; Humans ; Ligands ; Membrane Proteins/*chemistry/*metabolism ; Models, Molecular ; Nerve Tissue Proteins/*chemistry/*metabolism ; Protein Structure, Tertiary ; Receptor, Epidermal Growth Factor/antagonists & inhibitors/chemistry/*metabolism ; Receptors, Transforming Growth Factor beta/chemistry/metabolism ; Spodoptera
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  • 122
    Publication Date: 2008-04-25
    Description: The functional heart is comprised of distinct mesoderm-derived lineages including cardiomyocytes, endothelial cells and vascular smooth muscle cells. Studies in the mouse embryo and the mouse embryonic stem cell differentiation model have provided evidence indicating that these three lineages develop from a common Flk-1(+) (kinase insert domain protein receptor, also known as Kdr) cardiovascular progenitor that represents one of the earliest stages in mesoderm specification to the cardiovascular lineages. To determine whether a comparable progenitor is present during human cardiogenesis, we analysed the development of the cardiovascular lineages in human embryonic stem cell differentiation cultures. Here we show that after induction with combinations of activin A, bone morphogenetic protein 4 (BMP4), basic fibroblast growth factor (bFGF, also known as FGF2), vascular endothelial growth factor (VEGF, also known as VEGFA) and dickkopf homolog 1 (DKK1) in serum-free media, human embryonic-stem-cell-derived embryoid bodies generate a KDR(low)/C-KIT(CD117)(neg) population that displays cardiac, endothelial and vascular smooth muscle potential in vitro and, after transplantation, in vivo. When plated in monolayer cultures, these KDR(low)/C-KIT(neg) cells differentiate to generate populations consisting of greater than 50% contracting cardiomyocytes. Populations derived from the KDR(low)/C-KIT(neg) fraction give rise to colonies that contain all three lineages when plated in methylcellulose cultures. Results from limiting dilution studies and cell-mixing experiments support the interpretation that these colonies are clones, indicating that they develop from a cardiovascular colony-forming cell. Together, these findings identify a human cardiovascular progenitor that defines one of the earliest stages of human cardiac development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Lei -- Soonpaa, Mark H -- Adler, Eric D -- Roepke, Torsten K -- Kattman, Steven J -- Kennedy, Marion -- Henckaerts, Els -- Bonham, Kristina -- Abbott, Geoffrey W -- Linden, R Michael -- Field, Loren J -- Keller, Gordon M -- R01 HL079275/HL/NHLBI NIH HHS/ -- R01 HL083126/HL/NHLBI NIH HHS/ -- R01 HL083126-03/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 May 22;453(7194):524-8. doi: 10.1038/nature06894. Epub 2008 Apr 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Gene and Cell Medicine, The Black Family Stem Cell Institute, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, New York 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432194" target="_blank"〉PubMed〈/a〉
    Keywords: Activins/pharmacology ; Bone Morphogenetic Protein 4 ; Bone Morphogenetic Proteins/pharmacology ; Cell Differentiation/drug effects ; Cell Line ; Cell Lineage/drug effects ; Embryonic Stem Cells/*cytology/drug effects/*metabolism/transplantation ; Fibroblast Growth Factor 2/pharmacology ; Humans ; Intercellular Signaling Peptides and Proteins/pharmacology ; Myocytes, Cardiac/*cytology/drug effects/metabolism ; Patch-Clamp Techniques ; Proto-Oncogene Proteins c-kit/genetics ; Vascular Endothelial Growth Factor A/pharmacology ; Vascular Endothelial Growth Factor Receptor-2/deficiency/genetics/*metabolism
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 123
    Publication Date: 2008-03-14
    Description: The Sir2 deacetylase regulates chromatin silencing and lifespan in Saccharomyces cerevisiae. In mice, deficiency for the Sir2 family member SIRT6 leads to a shortened lifespan and a premature ageing-like phenotype. However, the molecular mechanisms of SIRT6 function are unclear. SIRT6 is a chromatin-associated protein, but no enzymatic activity of SIRT6 at chromatin has yet been detected, and the identity of physiological SIRT6 substrates is unknown. Here we show that the human SIRT6 protein is an NAD+-dependent, histone H3 lysine 9 (H3K9) deacetylase that modulates telomeric chromatin. SIRT6 associates specifically with telomeres, and SIRT6 depletion leads to telomere dysfunction with end-to-end chromosomal fusions and premature cellular senescence. Moreover, SIRT6-depleted cells exhibit abnormal telomere structures that resemble defects observed in Werner syndrome, a premature ageing disorder. At telomeric chromatin, SIRT6 deacetylates H3K9 and is required for the stable association of WRN, the factor that is mutated in Werner syndrome. We propose that SIRT6 contributes to the propagation of a specialized chromatin state at mammalian telomeres, which in turn is required for proper telomere metabolism and function. Our findings constitute the first identification of a physiological enzymatic activity of SIRT6, and link chromatin regulation by SIRT6 to telomere maintenance and a human premature ageing syndrome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646112/" 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/PMC2646112/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Michishita, Eriko -- McCord, Ronald A -- Berber, Elisabeth -- Kioi, Mitomu -- Padilla-Nash, Hesed -- Damian, Mara -- Cheung, Peggie -- Kusumoto, Rika -- Kawahara, Tiara L A -- Barrett, J Carl -- Chang, Howard Y -- Bohr, Vilhelm A -- Ried, Thomas -- Gozani, Or -- Chua, Katrin F -- K08 AG028961/AG/NIA NIH HHS/ -- K08 AG028961-03/AG/NIA NIH HHS/ -- R01 AG028867/AG/NIA NIH HHS/ -- R01 AG028867-03/AG/NIA NIH HHS/ -- R01 GM079641/GM/NIGMS NIH HHS/ -- R01 GM079641-02/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Mar 27;452(7186):492-6. doi: 10.1038/nature06736. Epub 2008 Mar 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Division of Endocrinology, Gerontology and Metabolism, School of Medicine, Stanford University, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337721" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Cell Aging/genetics ; Cell Line ; Chromatin/genetics/*metabolism ; DNA Replication ; Exodeoxyribonucleases/metabolism ; Fibroblasts ; Histone Deacetylases/deficiency/genetics/*metabolism ; Histones/chemistry/metabolism ; Humans ; Lysine/metabolism ; Phenotype ; Protein Binding ; RecQ Helicases/metabolism ; Sirtuins/deficiency/genetics/*metabolism ; Telomerase/genetics/metabolism ; Telomere/genetics/*metabolism ; Werner Syndrome/genetics
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  • 124
    Publication Date: 2008-03-28
    Description: Clinical trials of small interfering RNA (siRNA) targeting vascular endothelial growth factor-A (VEGFA) or its receptor VEGFR1 (also called FLT1), in patients with blinding choroidal neovascularization (CNV) from age-related macular degeneration, are premised on gene silencing by means of intracellular RNA interference (RNAi). We show instead that CNV inhibition is a siRNA-class effect: 21-nucleotide or longer siRNAs targeting non-mammalian genes, non-expressed genes, non-genomic sequences, pro- and anti-angiogenic genes, and RNAi-incompetent siRNAs all suppressed CNV in mice comparably to siRNAs targeting Vegfa or Vegfr1 without off-target RNAi or interferon-alpha/beta activation. Non-targeted (against non-mammalian genes) and targeted (against Vegfa or Vegfr1) siRNA suppressed CNV via cell-surface toll-like receptor 3 (TLR3), its adaptor TRIF, and induction of interferon-gamma and interleukin-12. Non-targeted siRNA suppressed dermal neovascularization in mice as effectively as Vegfa siRNA. siRNA-induced inhibition of neovascularization required a minimum length of 21 nucleotides, a bridging necessity in a modelled 2:1 TLR3-RNA complex. Choroidal endothelial cells from people expressing the TLR3 coding variant 412FF were refractory to extracellular siRNA-induced cytotoxicity, facilitating individualized pharmacogenetic therapy. Multiple human endothelial cell types expressed surface TLR3, indicating that generic siRNAs might treat angiogenic disorders that affect 8% of the world's population, and that siRNAs might induce unanticipated vascular or immune effects.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642938/" 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/PMC2642938/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kleinman, Mark E -- Yamada, Kiyoshi -- Takeda, Atsunobu -- Chandrasekaran, Vasu -- Nozaki, Miho -- Baffi, Judit Z -- Albuquerque, Romulo J C -- Yamasaki, Satoshi -- Itaya, Masahiro -- Pan, Yuzhen -- Appukuttan, Binoy -- Gibbs, Daniel -- Yang, Zhenglin -- Kariko, Katalin -- Ambati, Balamurali K -- Wilgus, Traci A -- DiPietro, Luisa A -- Sakurai, Eiji -- Zhang, Kang -- Smith, Justine R -- Taylor, Ethan W -- Ambati, Jayakrishna -- R01 EY015422/EY/NEI NIH HHS/ -- R01 EY015422-04/EY/NEI NIH HHS/ -- R01 EY018350/EY/NEI NIH HHS/ -- R01 EY018350-02/EY/NEI NIH HHS/ -- R01 EY018836/EY/NEI NIH HHS/ -- R01 EY018836-01/EY/NEI NIH HHS/ -- England -- Nature. 2008 Apr 3;452(7187):591-7. doi: 10.1038/nature06765. Epub 2008 Mar 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ophthalmology, University of Kentucky, Lexington, Kentucky 40506, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18368052" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Endothelial Cells/metabolism ; Genetic Therapy/*methods ; Humans ; Immunity, Innate/*immunology ; Interferon-gamma/immunology ; Interleukin-12/immunology ; Macular Degeneration/complications/genetics/therapy ; Mice ; Mice, Inbred C57BL ; Neovascularization, Pathologic/genetics/*immunology/*prevention & control/therapy ; RNA, Small Interfering/chemistry/genetics/*immunology/*metabolism ; Toll-Like Receptor 3/chemistry/genetics/*metabolism ; Vascular Endothelial Growth Factor A/genetics
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  • 125
    Publication Date: 2008-05-30
    Description: Somatic cells can be reprogrammed to a pluripotent state through the ectopic expression of defined transcription factors. Understanding the mechanism and kinetics of this transformation may shed light on the nature of developmental potency and suggest strategies with improved efficiency or safety. Here we report an integrative genomic analysis of reprogramming of mouse fibroblasts and B lymphocytes. Lineage-committed cells show a complex response to the ectopic expression involving induction of genes downstream of individual reprogramming factors. Fully reprogrammed cells show gene expression and epigenetic states that are highly similar to embryonic stem cells. In contrast, stable partially reprogrammed cell lines show reactivation of a distinctive subset of stem-cell-related genes, incomplete repression of lineage-specifying transcription factors, and DNA hypermethylation at pluripotency-related loci. These observations suggest that some cells may become trapped in partially reprogrammed states owing to incomplete repression of transcription factors, and that DNA de-methylation is an inefficient step in the transition to pluripotency. We demonstrate that RNA inhibition of transcription factors can facilitate reprogramming, and that treatment with DNA methyltransferase inhibitors can improve the overall efficiency of the reprogramming process.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754827/" 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/PMC2754827/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mikkelsen, Tarjei S -- Hanna, Jacob -- Zhang, Xiaolan -- Ku, Manching -- Wernig, Marius -- Schorderet, Patrick -- Bernstein, Bradley E -- Jaenisch, Rudolf -- Lander, Eric S -- Meissner, Alexander -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-04/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 Jul 3;454(7200):49-55. doi: 10.1038/nature07056. Epub 2008 May 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18509334" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Azacitidine/pharmacology ; Cell Line ; Cell Lineage ; Cellular Reprogramming/*genetics ; Chromatin/metabolism ; DNA (Cytosine-5-)-Methyltransferase/antagonists & inhibitors/genetics/metabolism ; DNA Methylation ; Embryonic Stem Cells/metabolism ; Enzyme Inhibitors/pharmacology ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genome/genetics ; *Genomics ; Mice ; Pluripotent Stem Cells/cytology/*metabolism ; Transcription Factors/deficiency/genetics
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  • 126
    Publication Date: 2008-09-23
    Description: MicroRNAs (miRNAs) are short RNAs that direct messenger RNA degradation or disrupt mRNA translation in a sequence-dependent manner. For more than a decade, attempts to study the interaction of miRNAs with their targets were confined to the 3' untranslated regions of mRNAs, fuelling an underlying assumption that these regions are the principal recipients of miRNA activity. Here we focus on the mouse Nanog, Oct4 (also known as Pou5f1) and Sox2 genes and demonstrate the existence of many naturally occurring miRNA targets in their amino acid coding sequence (CDS). Some of the mouse targets analysed do not contain the miRNA seed, whereas others span exon-exon junctions or are not conserved in the human and rhesus genomes. miR-134, miR-296 and miR-470, upregulated on retinoic-acid-induced differentiation of mouse embryonic stem cells, target the CDS of each transcription factor in various combinations, leading to transcriptional and morphological changes characteristic of differentiating mouse embryonic stem cells, and resulting in a new phenotype. Silent mutations at the predicted targets abolish miRNA activity, prevent the downregulation of the corresponding genes and delay the induced phenotype. Our findings demonstrate the abundance of CDS-located miRNA targets, some of which can be species-specific, and support an augmented model whereby animal miRNAs exercise their control on mRNAs through targets that can reside beyond the 3' untranslated region.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tay, Yvonne -- Zhang, Jinqiu -- Thomson, Andrew M -- Lim, Bing -- Rigoutsos, Isidore -- AI54973/AI/NIAID NIH HHS/ -- DK47636/DK/NIDDK NIH HHS/ -- England -- Nature. 2008 Oct 23;455(7216):1124-8. doi: 10.1038/nature07299. Epub 2008 Sep 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stem Cell and Developmental Biology, Genome Institute of Singapore, Agency for Science Technology and Research, #08-01, Genome, 60 Biopolis Street, Singapore 138672, Singapore.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18806776" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blotting, Western ; Cell Differentiation/*genetics ; Cell Line ; DNA-Binding Proteins/*genetics/metabolism ; Embryonic Stem Cells/*cytology/metabolism ; *Gene Expression Regulation, Developmental ; HMGB Proteins/*genetics/metabolism ; Homeodomain Proteins/*genetics/metabolism ; Mice ; MicroRNAs/*genetics/metabolism ; Mutation ; Octamer Transcription Factor-3/*genetics/metabolism ; Open Reading Frames/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; SOXB1 Transcription Factors ; Transcription Factors/*genetics/metabolism
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  • 127
    Publication Date: 2008-08-30
    Description: Ligand-dependent activation of the hedgehog (Hh) signalling pathway has been associated with tumorigenesis in a number of human tissues. Here we show that, although previous reports have described a cell-autonomous role for Hh signalling in these tumours, Hh ligands fail to activate signalling in tumour epithelial cells. In contrast, our data support ligand-dependent activation of the Hh pathway in the stromal microenvironment. Specific inhibition of Hh signalling using small molecule inhibitors, a neutralizing anti-Hh antibody or genetic deletion of smoothened (Smo) in the mouse stroma results in growth inhibition in xenograft tumour models. Taken together, these studies demonstrate a paracrine requirement for Hh ligand signalling in the tumorigenesis of Hh-expressing cancers and have important implications for the development of Hh pathway antagonists in cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yauch, Robert L -- Gould, Stephen E -- Scales, Suzie J -- Tang, Tracy -- Tian, Hua -- Ahn, Christina P -- Marshall, Derek -- Fu, Ling -- Januario, Thomas -- Kallop, Dara -- Nannini-Pepe, Michelle -- Kotkow, Karen -- Marsters, James C -- Rubin, Lee L -- de Sauvage, Frederic J -- England -- Nature. 2008 Sep 18;455(7211):406-10. doi: 10.1038/nature07275. Epub 2008 Aug 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genentech Inc., 1 DNA Way, South San Francisco, California 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18754008" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Hedgehog Proteins/*metabolism ; Humans ; Ligands ; Mice ; Mice, Nude ; Neoplasm Transplantation ; Neoplasms/genetics/*metabolism ; Paracrine Communication/*physiology ; Receptors, G-Protein-Coupled/deficiency/genetics/metabolism ; Stromal Cells/*metabolism
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  • 128
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    Nature Publishing Group (NPG)
    Publication Date: 2008-10-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yeager, Ashley -- England -- Nature. 2008 Oct 30;455(7217):1154-5. doi: 10.1038/4551154a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18971982" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Embryo Research/economics/*legislation & jurisprudence ; *Embryonic Stem Cells/cytology ; *Federal Government ; Female ; Humans ; Michigan ; *State Government
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  • 129
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2008-11-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Browne, Janet -- England -- Nature. 2008 Nov 20;456(7220):324-5. doi: 10.1038/456324a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard University, USA. jbrowne@fas.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020602" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anniversaries and Special Events ; *Biological Evolution ; Chicago ; Finches/physiology ; Fossils ; Great Britain ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Literature, Modern/history ; *Models, Biological ; Mutagenesis ; Selection, Genetic
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  • 130
    Publication Date: 2008-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rogers Hollingsworth, J -- Muller, Karl H -- Hollingsworth, Ellen Jane -- England -- Nature. 2008 Jul 24;454(7203):412-3. doi: 10.1038/454412a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Wisconsin (Madison), 455 North Park Street, Madison, Wisconsin 53706, USA. hollingsjr@aol.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18650902" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Europe ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Science/economics/*history/standards/*trends ; United States
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  • 131
    Publication Date: 2008-04-11
    Description: Clathrin-coated vesicles are vehicles for intracellular trafficking in all nucleated cells, from yeasts to humans. Many studies have demonstrated their essential roles in endocytosis and cellular signalling processes at the plasma membrane. By contrast, very few of their non-endocytic trafficking roles are known, the best characterized being the transport of hydrolases from the Golgi complex to the lysosome. Here we show that clathrin is required for polarity of the basolateral plasma membrane proteins in the epithelial cell line MDCK. Clathrin knockdown depolarized most basolateral proteins, by interfering with their biosynthetic delivery and recycling, but did not affect the polarity of apical proteins. Quantitative live imaging showed that chronic and acute clathrin knockdown selectively slowed down the exit of basolateral proteins from the Golgi complex, and promoted their mis-sorting into apical carrier vesicles. Our results demonstrate a broad requirement for clathrin in basolateral protein trafficking in epithelial cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078870/" 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/PMC4078870/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deborde, Sylvie -- Perret, Emilie -- Gravotta, Diego -- Deora, Ami -- Salvarezza, Susana -- Schreiner, Ryan -- Rodriguez-Boulan, Enrique -- R01 EY008538/EY/NEI NIH HHS/ -- R01 GM034107/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Apr 10;452(7188):719-23. doi: 10.1038/nature06828.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ophthalmology, Dyson Vision Research Institute, LC-300, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18401403" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cathepsin D/metabolism ; Cell Line ; *Cell Polarity ; Clathrin/deficiency/genetics/*metabolism ; Clathrin Heavy Chains/genetics/metabolism ; Dogs ; Epithelial Cells/*cytology/metabolism ; Golgi Apparatus/metabolism ; Humans ; Inulin/metabolism ; Lysosomes/metabolism ; Protein Transport ; Receptors, LDL/metabolism ; Receptors, Transferrin/metabolism ; Tight Junctions/metabolism ; Time Factors ; trans-Golgi Network/metabolism
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  • 132
    Publication Date: 2008-03-14
    Description: Mechanisms underlying global changes in gene expression during tumour progression are poorly understood. SATB1 is a genome organizer that tethers multiple genomic loci and recruits chromatin-remodelling enzymes to regulate chromatin structure and gene expression. Here we show that SATB1 is expressed by aggressive breast cancer cells and its expression level has high prognostic significance (P 〈 0.0001), independent of lymph-node status. RNA-interference-mediated knockdown of SATB1 in highly aggressive (MDA-MB-231) cancer cells altered the expression of 〉1,000 genes, reversing tumorigenesis by restoring breast-like acinar polarity and inhibiting tumour growth and metastasis in vivo. Conversely, ectopic SATB1 expression in non-aggressive (SKBR3) cells led to gene expression patterns consistent with aggressive-tumour phenotypes, acquiring metastatic activity in vivo. SATB1 delineates specific epigenetic modifications at target gene loci, directly upregulating metastasis-associated genes while downregulating tumour-suppressor genes. SATB1 reprogrammes chromatin organization and the transcription profiles of breast tumours to promote growth and metastasis; this is a new mechanism of tumour progression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Hye-Jung -- Russo, Jose -- Kohwi, Yoshinori -- Kohwi-Shigematsu, Terumi -- England -- Nature. 2008 Mar 13;452(7184):187-93. doi: 10.1038/nature06781.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337816" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomarkers, Tumor/analysis ; Breast Neoplasms/diagnosis/*genetics/*pathology ; Cell Line ; Cell Line, Tumor ; Cell Polarity ; Disease Progression ; Epigenesis, Genetic/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/*genetics ; Humans ; Lung Neoplasms/pathology/secretion ; Lymphatic Metastasis/diagnosis/genetics/pathology ; Matrix Attachment Region Binding Proteins/deficiency/genetics/*metabolism ; Mice ; Mice, Nude ; Neoplasm Metastasis/diagnosis/*genetics/pathology ; Neoplasm Transplantation ; Phenotype ; Prognosis ; RNA Interference
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 133
    Publication Date: 2008-10-04
    Description: The long-standing view of Earth's Cenozoic glacial history calls for the first continental-scale glaciation of Antarctica in the earliest Oligocene epoch ( approximately 33.6 million years ago), followed by the onset of northern-hemispheric glacial cycles in the late Pliocene epoch, about 31 million years later. The pivotal early Oligocene event is characterized by a rapid shift of 1.5 parts per thousand in deep-sea benthic oxygen-isotope values (Oi-1) within a few hundred thousand years, reflecting a combination of terrestrial ice growth and deep-sea cooling. The apparent absence of contemporaneous cooling in deep-sea Mg/Ca records, however, has been argued to reflect the growth of more ice than can be accommodated on Antarctica; this, combined with new evidence of continental cooling and ice-rafted debris in the Northern Hemisphere during this period, raises the possibility that Oi-1 represents a precursory bipolar glaciation. Here we test this hypothesis using an isotope-capable global climate/ice-sheet model that accommodates both the long-term decline of Cenozoic atmospheric CO(2) levels and the effects of orbital forcing. We show that the CO(2) threshold below which glaciation occurs in the Northern Hemisphere ( approximately 280 p.p.m.v.) is much lower than that for Antarctica ( approximately 750 p.p.m.v.). Therefore, the growth of ice sheets in the Northern Hemisphere immediately following Antarctic glaciation would have required rapid CO(2) drawdown within the Oi-1 timeframe, to levels lower than those estimated by geochemical proxies and carbon-cycle models. Instead of bipolar glaciation, we find that Oi-1 is best explained by Antarctic glaciation alone, combined with deep-sea cooling of up to 4 degrees C and Antarctic ice that is less isotopically depleted (-30 to -35 per thousand) than previously suggested. Proxy CO(2) estimates remain above our model's northern-hemispheric glaciation threshold of approximately 280 p.p.m.v. until approximately 25 Myr ago, but have been near or below that level ever since. This implies that episodic northern-hemispheric ice sheets have been possible some 20 million years earlier than currently assumed (although still much later than Oi-1) and could explain some of the variability in Miocene sea-level records.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deconto, Robert M -- Pollard, David -- Wilson, Paul A -- Palike, Heiko -- Lear, Caroline H -- Pagani, Mark -- England -- Nature. 2008 Oct 2;455(7213):652-6. doi: 10.1038/nature07337.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geosciences, University of Massachusetts, Amherst, Massachusetts 01003, USA. deconto@geo.umass.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18833277" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; Atmosphere/*chemistry ; Calcium ; Carbon Dioxide/*analysis ; *Cold Climate ; Greenhouse Effect ; History, 21st Century ; History, Ancient ; *Ice Cover ; Magnesium ; Oxygen Isotopes ; Seasons
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  • 134
    Publication Date: 2008-08-22
    Description: Investigation of the human antibody response to influenza virus infection has been largely limited to serology, with relatively little analysis at the molecular level. The 1918 H1N1 influenza virus pandemic was the most severe of the modern era. Recent work has recovered the gene sequences of this unusual strain, so that the 1918 pandemic virus could be reconstituted to display its unique virulence phenotypes. However, little is known about adaptive immunity to this virus. We took advantage of the 1918 virus sequencing and the resultant production of recombinant 1918 haemagglutinin (HA) protein antigen to characterize at the clonal level neutralizing antibodies induced by natural exposure of survivors to the 1918 pandemic virus. Here we show that of the 32 individuals tested that were born in or before 1915, each showed seroreactivity with the 1918 virus, nearly 90 years after the pandemic. Seven of the eight donor samples tested had circulating B cells that secreted antibodies that bound the 1918 HA. We isolated B cells from subjects and generated five monoclonal antibodies that showed potent neutralizing activity against 1918 virus from three separate donors. These antibodies also cross-reacted with the genetically similar HA of a 1930 swine H1N1 influenza strain, but did not cross-react with HAs of more contemporary human influenza viruses. The antibody genes had an unusually high degree of somatic mutation. The antibodies bound to the 1918 HA protein with high affinity, had exceptional virus-neutralizing potency and protected mice from lethal infection. Isolation of viruses that escaped inhibition suggested that the antibodies recognize classical antigenic sites on the HA surface. Thus, these studies demonstrate that survivors of the 1918 influenza pandemic possess highly functional, virus-neutralizing antibodies to this uniquely virulent virus, and that humans can sustain circulating B memory cells to viruses for many decades after exposure-well into the tenth decade of life.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848880/" 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/PMC2848880/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Xiaocong -- Tsibane, Tshidi -- McGraw, Patricia A -- House, Frances S -- Keefer, Christopher J -- Hicar, Mark D -- Tumpey, Terrence M -- Pappas, Claudia -- Perrone, Lucy A -- Martinez, Osvaldo -- Stevens, James -- Wilson, Ian A -- Aguilar, Patricia V -- Altschuler, Eric L -- Basler, Christopher F -- Crowe, James E Jr -- AI057158/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- CA55896/CA/NCI NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- R01 AI048677/AI/NIAID NIH HHS/ -- R01 AI048677-04/AI/NIAID NIH HHS/ -- U19 AI057229/AI/NIAID NIH HHS/ -- U19 AI62623/AI/NIAID NIH HHS/ -- U54 AI057157/AI/NIAID NIH HHS/ -- U54 AI057157-019002/AI/NIAID NIH HHS/ -- U54 AI57158/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Sep 25;455(7212):532-6. doi: 10.1038/nature07231. Epub 2008 Aug 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18716625" target="_blank"〉PubMed〈/a〉
    Keywords: Aged, 80 and over ; Animals ; Antibodies, Monoclonal/genetics/immunology/isolation & purification ; Antibodies, Viral/genetics/*immunology/*isolation & purification ; B-Lymphocytes/*immunology ; Cell Line ; Cross Reactions/immunology ; *Disease Outbreaks/history ; Dogs ; Female ; History, 20th Century ; Humans ; Influenza A Virus, H1N1 Subtype/genetics/*immunology/physiology ; Influenza, Human/*immunology/virology ; Kinetics ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Neutralization Tests ; *Survival
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  • 135
    Publication Date: 2008-12-02
    Description: MicroRNAs comprise a broad class of small non-coding RNAs that control expression of complementary target messenger RNAs. Dysregulation of microRNAs by several mechanisms has been described in various disease states including cardiac disease. Whereas previous studies of cardiac disease have focused on microRNAs that are primarily expressed in cardiomyocytes, the role of microRNAs expressed in other cell types of the heart is unclear. Here we show that microRNA-21 (miR-21, also known as Mirn21) regulates the ERK-MAP kinase signalling pathway in cardiac fibroblasts, which has impacts on global cardiac structure and function. miR-21 levels are increased selectively in fibroblasts of the failing heart, augmenting ERK-MAP kinase activity through inhibition of sprouty homologue 1 (Spry1). This mechanism regulates fibroblast survival and growth factor secretion, apparently controlling the extent of interstitial fibrosis and cardiac hypertrophy. In vivo silencing of miR-21 by a specific antagomir in a mouse pressure-overload-induced disease model reduces cardiac ERK-MAP kinase activity, inhibits interstitial fibrosis and attenuates cardiac dysfunction. These findings reveal that microRNAs can contribute to myocardial disease by an effect in cardiac fibroblasts. Our results validate miR-21 as a disease target in heart failure and establish the therapeutic efficacy of microRNA therapeutic intervention in a cardiovascular disease setting.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thum, Thomas -- Gross, Carina -- Fiedler, Jan -- Fischer, Thomas -- Kissler, Stephan -- Bussen, Markus -- Galuppo, Paolo -- Just, Steffen -- Rottbauer, Wolfgang -- Frantz, Stefan -- Castoldi, Mirco -- Soutschek, Jurgen -- Koteliansky, Victor -- Rosenwald, Andreas -- Basson, M Albert -- Licht, Jonathan D -- Pena, John T R -- Rouhanifard, Sara H -- Muckenthaler, Martina U -- Tuschl, Thomas -- Martin, Gail R -- Bauersachs, Johann -- Engelhardt, Stefan -- R01 CA059998/CA/NCI NIH HHS/ -- R01 CA78711/CA/NCI NIH HHS/ -- England -- Nature. 2008 Dec 18;456(7224):980-4. doi: 10.1038/nature07511. Epub 2008 Nov 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine I, Interdisziplinares Zentrum fur Klinische Forschung (IZKF), University of Wuerzburg, 97080 Wuerzburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19043405" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cardiomyopathies/*genetics/*metabolism/pathology/therapy ; Cell Line ; Cell Survival ; Cells, Cultured ; Disease Models, Animal ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Fibroblasts/*metabolism ; Gene Silencing ; Humans ; *MAP Kinase Signaling System ; Male ; Mice ; Mice, Transgenic ; MicroRNAs/*genetics ; Myocytes, Cardiac/cytology/metabolism ; Rats
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  • 136
    Publication Date: 2008-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zachos, James C -- Dickens, Gerald R -- Zeebe, Richard E -- England -- Nature. 2008 Jan 17;451(7176):279-83. doi: 10.1038/nature06588.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Sciences, University of California at Santa Cruz, Santa Cruz, California 95060, USA. jzachos@es.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202643" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon/analysis/*metabolism ; Carbon Dioxide/analysis/metabolism ; Ecosystem ; *Greenhouse Effect ; History, 21st Century ; History, Ancient ; Human Activities ; Models, Theoretical ; Oceans and Seas ; Temperature ; Time Factors
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  • 137
    Publication Date: 2008-05-16
    Description: Significant changes in physical and biological systems are occurring on all continents and in most oceans, with a concentration of available data in Europe and North America. Most of these changes are in the direction expected with warming temperature. Here we show that these changes in natural systems since at least 1970 are occurring in regions of observed temperature increases, and that these temperature increases at continental scales cannot be explained by natural climate variations alone. Given the conclusions from the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report that most of the observed increase in global average temperatures since the mid-twentieth century is very likely to be due to the observed increase in anthropogenic greenhouse gas concentrations, and furthermore that it is likely that there has been significant anthropogenic warming over the past 50 years averaged over each continent except Antarctica, we conclude that anthropogenic climate change is having a significant impact on physical and biological systems globally and in some continents.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenzweig, Cynthia -- Karoly, David -- Vicarelli, Marta -- Neofotis, Peter -- Wu, Qigang -- Casassa, Gino -- Menzel, Annette -- Root, Terry L -- Estrella, Nicole -- Seguin, Bernard -- Tryjanowski, Piotr -- Liu, Chunzhen -- Rawlins, Samuel -- Imeson, Anton -- England -- Nature. 2008 May 15;453(7193):353-7. doi: 10.1038/nature06937.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NASA/Goddard Institute for Space Studies and Columbia Center for Climate Systems Research, 2800 Broadway, New York, New York 10025, USA. crosenzweig@giss.nasa.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480817" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Databases, Factual ; *Ecosystem ; Forestry ; Geography ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; *Human Activities ; Ice ; Internationality ; Marine Biology ; Models, Statistical ; Temperature
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  • 138
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2008-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hand, Eric -- England -- Nature. 2008 Oct 9;455(7214):713. doi: 10.1038/455713a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18843322" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes/*economics ; California ; Fund Raising/*economics ; History, 21st Century ; Research Support as Topic/*economics
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  • 139
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2008-05-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moore, Andrew -- England -- Nature. 2008 May 1;453(7191):31-2. doi: 10.1038/453031a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Science & Society Programme at the European Molecular Biology Organization (EMBO), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451837" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biology/*education/history ; Computational Biology/education ; Curriculum/standards/*trends ; Evolution, Molecular ; History, 20th Century ; History, 21st Century ; Humans ; Internationality ; Models, Biological ; Teaching/history/*standards/*trends
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  • 140
    Publication Date: 2008-01-18
    Description: The RIG-like helicase (RLH) family of intracellular receptors detect viral nucleic acid and signal through the mitochondrial antiviral signalling adaptor MAVS (also known as Cardif, VISA and IPS-1) during a viral infection. MAVS activation leads to the rapid production of antiviral cytokines, including type 1 interferons. Although MAVS is vital to antiviral immunity, its regulation from within the mitochondria remains unknown. Here we describe human NLRX1, a highly conserved nucleotide-binding domain (NBD)- and leucine-rich-repeat (LRR)-containing family member (known as NLR) that localizes to the mitochondrial outer membrane and interacts with MAVS. Expression of NLRX1 results in the potent inhibition of RLH- and MAVS-mediated interferon-beta promoter activity and in the disruption of virus-induced RLH-MAVS interactions. Depletion of NLRX1 with small interference RNA promotes virus-induced type I interferon production and decreases viral replication. This work identifies NLRX1 as a check against mitochondrial antiviral responses and represents an intersection of three ancient cellular processes: NLR signalling, intracellular virus detection and the use of mitochondria as a platform for anti-pathogen signalling. This represents a conceptual advance, in that NLRX1 is a modulator of pathogen-associated molecular pattern receptors rather than a receptor, and identifies a key therapeutic target for enhancing antiviral responses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moore, Chris B -- Bergstralh, Daniel T -- Duncan, Joseph A -- Lei, Yu -- Morrison, Thomas E -- Zimmermann, Albert G -- Accavitti-Loper, Mary A -- Madden, Victoria J -- Sun, Lijun -- Ye, Zhengmao -- Lich, John D -- Heise, Mark T -- Chen, Zhijian -- Ting, Jenny P-Y -- England -- Nature. 2008 Jan 31;451(7178):573-7. doi: 10.1038/nature06501. Epub 2008 Jan 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology-Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18200010" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/antagonists & inhibitors/metabolism ; Animals ; Cell Line ; Cloning, Molecular ; Computational Biology ; Humans ; Interferon-beta/biosynthesis/genetics/metabolism ; Mice ; Mitochondria/*immunology/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; NF-kappa B/metabolism ; Protein Binding ; Protein Transport ; RNA, Small Interfering/genetics/metabolism ; Signal Transduction ; Virus Replication ; Viruses/*immunology
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  • 141
    Publication Date: 2008-09-17
    Description: The E2F1 transcription factor can promote proliferation or apoptosis when activated, and is a key downstream target of the retinoblastoma tumour suppressor protein (pRB). Here we show that E2F1 is a potent and specific inhibitor of beta-catenin/T-cell factor (TCF)-dependent transcription, and that this function contributes to E2F1-induced apoptosis. E2F1 deregulation suppresses beta-catenin activity in an adenomatous polyposis coli (APC)/glycogen synthase kinase-3 (GSK3)-independent manner, reducing the expression of key beta-catenin targets including c-MYC. This interaction explains why colorectal tumours, which depend on beta-catenin transcription for their abnormal proliferation, keep RB1 intact. Remarkably, E2F1 activity is also repressed by cyclin-dependent kinase-8 (CDK8), a colorectal oncoprotein. Elevated levels of CDK8 protect beta-catenin/TCF-dependent transcription from inhibition by E2F1. Thus, by retaining RB1 and amplifying CDK8, colorectal tumour cells select conditions that collectively suppress E2F1 and enhance the activity of beta-catenin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148807/" 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/PMC3148807/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morris, Erick J -- Ji, Jun-Yuan -- Yang, Fajun -- Di Stefano, Luisa -- Herr, Anabel -- Moon, Nam-Sung -- Kwon, Eun-Jeong -- Haigis, Kevin M -- Naar, Anders M -- Dyson, Nicholas J -- GM053203/GM/NIGMS NIH HHS/ -- GM071449/GM/NIGMS NIH HHS/ -- GM81607/GM/NIGMS NIH HHS/ -- P50 CA127003/CA/NCI NIH HHS/ -- P50 CA127003-02/CA/NCI NIH HHS/ -- P50-CA127003/CA/NCI NIH HHS/ -- R01 GM053203/GM/NIGMS NIH HHS/ -- R01 GM053203-13/GM/NIGMS NIH HHS/ -- R01 GM053203-14/GM/NIGMS NIH HHS/ -- R01 GM071449/GM/NIGMS NIH HHS/ -- R01 GM071449-04/GM/NIGMS NIH HHS/ -- R01 GM081607/GM/NIGMS NIH HHS/ -- R01 GM081607-01A1/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Sep 25;455(7212):552-6. doi: 10.1038/nature07310. Epub 2008 Sep 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Oncology, Massachusetts General Hospital Cancer Center and Harvard Medical School, 13th Street, Building 149, Charlestown, Massachusetts 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18794899" target="_blank"〉PubMed〈/a〉
    Keywords: Adenomatous Polyposis Coli Protein/metabolism ; Apoptosis ; Cell Line ; Cyclin-Dependent Kinase 8 ; Cyclin-Dependent Kinases/*metabolism ; E2F1 Transcription Factor/*antagonists & inhibitors/*metabolism ; Gene Expression Regulation ; Genes, myc/genetics ; Glycogen Synthase Kinase 3/metabolism ; Humans ; Retinoblastoma Protein/genetics/*metabolism ; Signal Transduction ; TCF Transcription Factors/metabolism ; *Transcription, Genetic ; Wnt Proteins/metabolism ; beta Catenin/*antagonists & inhibitors/*metabolism
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  • 142
    Publication Date: 2008-02-01
    Description: Ca2+/calmodulin-dependent regulation of voltage-gated CaV1-2 Ca2+ channels shows extraordinary modes of spatial Ca2+ decoding and channel modulation, vital for many biological functions. A single calmodulin (CaM) molecule associates constitutively with the channel's carboxy-terminal tail, and Ca2+ binding to the C-terminal and N-terminal lobes of CaM can each induce distinct channel regulations. As expected from close channel proximity, the C-lobe responds to the roughly 100-microM Ca2+ pulses driven by the associated channel, a behaviour defined as 'local Ca2+ selectivity'. Conversely, all previous observations have indicated that the N-lobe somehow senses the far weaker signals from distant Ca2+ sources. This 'global Ca2+ selectivity' satisfies a general signalling requirement, enabling a resident molecule to remotely sense cellular Ca2+ activity, which would otherwise be overshadowed by Ca2+ entry through the host channel. Here we show that the spatial Ca2+ selectivity of N-lobe CaM regulation is not invariably global but can be switched by a novel Ca2+/CaM-binding site within the amino terminus of channels (NSCaTE, for N-terminal spatial Ca2+ transforming element). Native CaV2.2 channels lack this element and show N-lobe regulation with a global selectivity. On the introduction of NSCaTE into these channels, spatial Ca2+ selectivity transforms from a global to local profile. Given this effect, we examined CaV1.2/CaV1.3 channels, which naturally contain NSCaTE, and found that their N-lobe selectivity is indeed local. Disruption of this element produces a global selectivity, confirming the native function of NSCaTE. Thus, differences in spatial selectivity between advanced CaV1 and CaV2 channel isoforms are explained by the presence or absence of NSCaTE. Beyond functional effects, the position of NSCaTE on the channel's amino terminus indicates that CaM can bridge the amino terminus and carboxy terminus of channels. Finally, the modularity of NSCaTE offers practical means for understanding the basis of global Ca2+ selectivity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262256/" 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/PMC4262256/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dick, Ivy E -- Tadross, Michael R -- Liang, Haoya -- Tay, Lai Hock -- Yang, Wanjun -- Yue, David T -- P30 DC005211/DC/NIDCD NIH HHS/ -- R01 MH065531/MH/NIMH NIH HHS/ -- R37 HL076795/HL/NHLBI NIH HHS/ -- T32 DC000023/DC/NIDCD NIH HHS/ -- England -- Nature. 2008 Feb 14;451(7180):830-4. doi: 10.1038/nature06529. Epub 2008 Jan 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Calcium Signals Laboratory, Departments of Biomedical Engineering and Neuroscience, The Johns Hopkins University School of Medicine, Ross Building, Room 713, 720 Rutland Avenue, Baltimore, Maryland 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18235447" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcium/*metabolism ; Calcium Channels/chemistry/genetics/*metabolism ; *Calcium Signaling ; Calmodulin/*metabolism ; Cell Line ; Evolution, Molecular ; Humans ; Molecular Sequence Data ; Substrate Specificity
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  • 143
    Publication Date: 2008-06-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kurtz, Steven -- England -- Nature. 2008 Jun 5;453(7196):707. doi: 10.1038/453707a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18528358" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Art ; Biological Warfare/prevention & control ; *Federal Government ; Food, Genetically Modified ; Guinea Pigs ; History, 21st Century ; Humans ; Research Personnel ; Science/*education ; Terrorism/prevention & control ; Time Factors ; United States
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  • 144
    Publication Date: 2008-03-28
    Description: T helper cells that produce IL-17 (T(H)17 cells) promote autoimmunity in mice and have been implicated in the pathogenesis of human inflammatory diseases. At mucosal surfaces, T(H)17 cells are thought to protect the host from infection, whereas regulatory T (T(reg)) cells control immune responses and inflammation triggered by the resident microflora. Differentiation of both cell types requires transforming growth factor-beta (TGF-beta), but depends on distinct transcription factors: RORgammat (encoded by Rorc(gammat)) for T(H)17 cells and Foxp3 for T(reg) cells. How TGF-beta regulates the differentiation of T cells with opposing activities has been perplexing. Here we demonstrate that, together with pro-inflammatory cytokines, TGF-beta orchestrates T(H)17 cell differentiation in a concentration-dependent manner. At low concentrations, TGF-beta synergizes with interleukin (IL)-6 and IL-21 (refs 9-11) to promote IL-23 receptor (Il23r) expression, favouring T(H)17 cell differentiation. High concentrations of TGF-beta repress IL23r expression and favour Foxp3+ T(reg) cells. RORgammat and Foxp3 are co-expressed in naive CD4+ T cells exposed to TGF-beta and in a subset of T cells in the small intestinal lamina propria of the mouse. In vitro, TGF-beta-induced Foxp3 inhibits RORgammat function, at least in part through their interaction. Accordingly, lamina propria T cells that co-express both transcription factors produce less IL-17 (also known as IL-17a) than those that express RORgammat alone. IL-6, IL-21 and IL-23 relieve Foxp3-mediated inhibition of RORgammat, thereby promoting T(H)17 cell differentiation. Therefore, the decision of antigen-stimulated cells to differentiate into either T(H)17 or T(reg) cells depends on the cytokine-regulated balance of RORgammat and Foxp3.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597437/" 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/PMC2597437/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Liang -- Lopes, Jared E -- Chong, Mark M W -- Ivanov, Ivaylo I -- Min, Roy -- Victora, Gabriel D -- Shen, Yuelei -- Du, Jianguang -- Rubtsov, Yuri P -- Rudensky, Alexander Y -- Ziegler, Steven F -- Littman, Dan R -- AI48779/AI/NIAID NIH HHS/ -- R01 AI048779/AI/NIAID NIH HHS/ -- R01 AI048779-05/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 May 8;453(7192):236-40. doi: 10.1038/nature06878. Epub 2008 Mar 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18368049" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation/drug effects ; Cell Line ; Cells, Cultured ; Forkhead Transcription Factors/genetics/*metabolism ; Gene Expression Regulation/drug effects ; Humans ; Interleukin-17/biosynthesis/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; Receptors, Interleukin/genetics/metabolism ; Receptors, Retinoic Acid/*antagonists & inhibitors/genetics/metabolism ; Receptors, Thyroid Hormone/*antagonists & inhibitors/genetics/metabolism ; T-Lymphocytes, Helper-Inducer/*cytology/*drug effects/metabolism ; Transforming Growth Factor beta/*pharmacology
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  • 145
    Publication Date: 2008-06-13
    Description: Innate immune defences are essential for the control of virus infection and are triggered through host recognition of viral macromolecular motifs known as pathogen-associated molecular patterns (PAMPs). Hepatitis C virus (HCV) is an RNA virus that replicates in the liver, and infects 200 million people worldwide. Infection is regulated by hepatic immune defences triggered by the cellular RIG-I helicase. RIG-I binds PAMP RNA and signals interferon regulatory factor 3 activation to induce the expression of interferon-alpha/beta and antiviral/interferon-stimulated genes (ISGs) that limit infection. Here we identify the polyuridine motif of the HCV genome 3' non-translated region and its replication intermediate as the PAMP substrate of RIG-I, and show that this and similar homopolyuridine or homopolyriboadenine motifs present in the genomes of RNA viruses are the chief feature of RIG-I recognition and immune triggering in human and murine cells. 5' terminal triphosphate on the PAMP RNA was necessary but not sufficient for RIG-I binding, which was primarily dependent on homopolymeric ribonucleotide composition, linear structure and length. The HCV PAMP RNA stimulated RIG-I-dependent signalling to induce a hepatic innate immune response in vivo, and triggered interferon and ISG expression to suppress HCV infection in vitro. These results provide a conceptual advance by defining specific homopolymeric RNA motifs within the genome of HCV and other RNA viruses as the PAMP substrate of RIG-I, and demonstrate immunogenic features of the PAMP-RIG-I interaction that could be used as an immune adjuvant for vaccine and immunotherapy approaches.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856441/" 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/PMC2856441/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saito, Takeshi -- Owen, David M -- Jiang, Fuguo -- Marcotrigiano, Joseph -- Gale, Michael Jr -- P01 DA021353/DA/NIDA NIH HHS/ -- R01 AI060389/AI/NIAID NIH HHS/ -- R01 AI060389-01/AI/NIAID NIH HHS/ -- R01 AI060389-02/AI/NIAID NIH HHS/ -- R01 AI060389-03/AI/NIAID NIH HHS/ -- R01 AI060389-04/AI/NIAID NIH HHS/ -- R01 AI060389-05/AI/NIAID NIH HHS/ -- R01 AI060389-06/AI/NIAID NIH HHS/ -- R01 AI060389-07/AI/NIAID NIH HHS/ -- R01 AI060389-08/AI/NIAID NIH HHS/ -- R01 AI060389-09/AI/NIAID NIH HHS/ -- R01 DA024563/DA/NIDA NIH HHS/ -- R01 DA024563-01/DA/NIDA NIH HHS/ -- R01 DA024563-02/DA/NIDA NIH HHS/ -- R01 DA024563-03/DA/NIDA NIH HHS/ -- R01AI060389/AI/NIAID NIH HHS/ -- R01DA021353/DA/NIDA NIH HHS/ -- U19 AI040035/AI/NIAID NIH HHS/ -- U19 AI040035-100004/AI/NIAID NIH HHS/ -- U19 AI040035-110004/AI/NIAID NIH HHS/ -- U19 AI040035-120004/AI/NIAID NIH HHS/ -- U19 AI040035-130004/AI/NIAID NIH HHS/ -- U19 AI040035-140004/AI/NIAID NIH HHS/ -- U19AI40035/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Jul 24;454(7203):523-7. doi: 10.1038/nature07106. Epub 2008 Jun 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98195-7650, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18548002" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/immunology/metabolism ; Animals ; Cell Line ; DEAD-box RNA Helicases/deficiency/genetics/*metabolism ; Genome, Viral/genetics ; Hepacivirus/*genetics/*immunology/pathogenicity ; Humans ; Immunity, Innate/*immunology ; Interferon-beta/biosynthesis/genetics/immunology ; Ligands ; Liver/immunology/virology ; Mice ; RNA, Viral/*genetics/*immunology ; Uridine/genetics/immunology/metabolism ; Virus Replication/genetics
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  • 146
    Publication Date: 2008-04-25
    Description: The cellular machinery promoting phagocytosis of corpses of apoptotic cells is well conserved from worms to mammals. An important component is the Caenorhabditis elegans engulfment receptor CED-1 (ref. 1) and its Drosophila orthologue, Draper. The CED-1/Draper signalling pathway is also essential for the phagocytosis of other types of 'modified self' including necrotic cells, developmentally pruned axons and dendrites, and axons undergoing Wallerian degeneration. Here we show that Drosophila Shark, a non-receptor tyrosine kinase similar to mammalian Syk and Zap-70, binds Draper through an immunoreceptor tyrosine-based activation motif (ITAM) in the Draper intracellular domain. We show that Shark activity is essential for Draper-mediated signalling events in vivo, including the recruitment of glial membranes to severed axons and the phagocytosis of axonal debris and neuronal cell corpses by glia. We also show that the Src family kinase (SFK) Src42A can markedly increase Draper phosphorylation and is essential for glial phagocytic activity. We propose that ligand-dependent Draper receptor activation initiates the Src42A-dependent tyrosine phosphorylation of Draper, the association of Shark and the activation of the Draper pathway. These Draper-Src42A-Shark interactions are strikingly similar to mammalian immunoreceptor-SFK-Syk signalling events in mammalian myeloid and lymphoid cells. Thus, Draper seems to be an ancient immunoreceptor with an extracellular domain tuned to modified self, and an intracellular domain promoting phagocytosis through an ITAM-domain-SFK-Syk-mediated signalling cascade.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493287/" 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/PMC2493287/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ziegenfuss, Jennifer S -- Biswas, Romi -- Avery, Michelle A -- Hong, Kyoungja -- Sheehan, Amy E -- Yeung, Yee-Guide -- Stanley, E Richard -- Freeman, Marc R -- 1R01CA26504/CA/NCI NIH HHS/ -- 1R01GM55293/GM/NIGMS NIH HHS/ -- 1R01NS053538/NS/NINDS NIH HHS/ -- R37 CA026504/CA/NCI NIH HHS/ -- R37 CA026504-30/CA/NCI NIH HHS/ -- England -- Nature. 2008 Jun 12;453(7197):935-9. doi: 10.1038/nature06901. Epub 2008 Apr 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605-2324, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432193" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Axons/metabolism/pathology ; Cell Line ; Cell Membrane/metabolism ; Central Nervous System ; Drosophila Proteins/chemistry/*metabolism ; Intracellular Signaling Peptides and Proteins/*metabolism ; Membrane Proteins/chemistry/*metabolism ; Neuroglia/*cytology ; *Phagocytosis ; Phosphorylation ; Protein Binding ; Protein Structure, Tertiary ; Protein Transport ; Protein-Tyrosine Kinases/*metabolism ; Proto-Oncogene Proteins pp60(c-src)/*metabolism ; *Signal Transduction ; Two-Hybrid System Techniques
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  • 147
    Publication Date: 2008-08-30
    Description: Stem cells are defined as self-renewing cell populations that can differentiate into multiple distinct cell types. However, hundreds of different human cell lines from embryonic, fetal and adult sources have been called stem cells, even though they range from pluripotent cells-typified by embryonic stem cells, which are capable of virtually unlimited proliferation and differentiation-to adult stem cell lines, which can generate a far more limited repertoire of differentiated cell types. The rapid increase in reports of new sources of stem cells and their anticipated value to regenerative medicine has highlighted the need for a general, reproducible method for classification of these cells. We report here the creation and analysis of a database of global gene expression profiles (which we call the 'stem cell matrix') that enables the classification of cultured human stem cells in the context of a wide variety of pluripotent, multipotent and differentiated cell types. Using an unsupervised clustering method to categorize a collection of approximately 150 cell samples, we discovered that pluripotent stem cell lines group together, whereas other cell types, including brain-derived neural stem cell lines, are very diverse. Using further bioinformatic analysis we uncovered a protein-protein network (PluriNet) that is shared by the pluripotent cells (embryonic stem cells, embryonal carcinomas and induced pluripotent cells). Analysis of published data showed that the PluriNet seems to be a common characteristic of pluripotent cells, including mouse embryonic stem and induced pluripotent cells and human oocytes. Our results offer a new strategy for classifying stem cells and support the idea that pluripotency and self-renewal are under tight control by specific molecular networks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637443/" 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/PMC2637443/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muller, Franz-Josef -- Laurent, Louise C -- Kostka, Dennis -- Ulitsky, Igor -- Williams, Roy -- Lu, Christina -- Park, In-Hyun -- Rao, Mahendra S -- Shamir, Ron -- Schwartz, Philip H -- Schmidt, Nils O -- Loring, Jeanne F -- K12 5K12HD000849-20/HD/NICHD NIH HHS/ -- P20 GM075059/GM/NIGMS NIH HHS/ -- P20 GM075059-01/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Sep 18;455(7211):401-5. doi: 10.1038/nature07213. Epub 2008 Aug 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. fj.mueller@zip-kiel.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18724358" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Artificial Intelligence ; Cell Differentiation ; Cell Line ; Computational Biology ; Databases, Factual ; Embryonic Stem Cells/classification/metabolism ; *Gene Expression Profiling ; Humans ; Mice ; Multipotent Stem Cells/classification/metabolism ; Oligonucleotide Array Sequence Analysis ; Oocytes/classification/metabolism ; Phenotype ; Pluripotent Stem Cells/classification/metabolism ; Protein Binding ; Stem Cells/*classification/*metabolism
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  • 148
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2008-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Jan 31;451(7178):500. doi: 10.1038/451500a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18235454" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Culture ; Germany ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Italy ; Natural History/*history/*trends ; Periodicals as Topic/trends ; Research Personnel/history ; Specimen Handling/*history/*trends ; *Universities/history
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  • 149
    Publication Date: 2008-06-20
    Description: Changes in the climate system's energy budget are predominantly revealed in ocean temperatures and the associated thermal expansion contribution to sea-level rise. Climate models, however, do not reproduce the large decadal variability in globally averaged ocean heat content inferred from the sparse observational database, even when volcanic and other variable climate forcings are included. The sum of the observed contributions has also not adequately explained the overall multi-decadal rise. Here we report improved estimates of near-global ocean heat content and thermal expansion for the upper 300 m and 700 m of the ocean for 1950-2003, using statistical techniques that allow for sparse data coverage and applying recent corrections to reduce systematic biases in the most common ocean temperature observations. Our ocean warming and thermal expansion trends for 1961-2003 are about 50 per cent larger than earlier estimates but about 40 per cent smaller for 1993-2003, which is consistent with the recognition that previously estimated rates for the 1990s had a positive bias as a result of instrumental errors. On average, the decadal variability of the climate models with volcanic forcing now agrees approximately with the observations, but the modelled multi-decadal trends are smaller than observed. We add our observational estimate of upper-ocean thermal expansion to other contributions to sea-level rise and find that the sum of contributions from 1961 to 2003 is about 1.5 +/- 0.4 mm yr(-1), in good agreement with our updated estimate of near-global mean sea-level rise (using techniques established in earlier studies) of 1.6 +/- 0.2 mm yr(-1).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Domingues, Catia M -- Church, John A -- White, Neil J -- Gleckler, Peter J -- Wijffels, Susan E -- Barker, Paul M -- Dunn, Jeff R -- England -- Nature. 2008 Jun 19;453(7198):1090-3. doi: 10.1038/nature07080.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Australian Weather and Climate Research, CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania 7001, Australia. catia.domingues@csiro.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563162" target="_blank"〉PubMed〈/a〉
    Keywords: Forecasting ; Greenhouse Effect ; History, 20th Century ; History, 21st Century ; *Hot Temperature ; Models, Theoretical ; Oceans and Seas ; Research Design ; Seawater/*analysis ; Time Factors ; Volcanic Eruptions
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  • 150
    Publication Date: 2008-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zwiers, Francis -- Hegerl, Gabriele -- England -- Nature. 2008 May 15;453(7193):296-7. doi: 10.1038/453296a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480804" target="_blank"〉PubMed〈/a〉
    Keywords: *Ecosystem ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; *Human Activities ; Meta-Analysis as Topic ; Models, Statistical
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  • 151
    Publication Date: 2008-02-22
    Description: The innate immune system recognizes nucleic acids during infection and tissue damage. Whereas viral RNA is detected by endosomal toll-like receptors (TLR3, TLR7, TLR8) and cytoplasmic RIG-I and MDA5, endosomal TLR9 and cytoplasmic DAI bind DNA, resulting in the activation of nuclear factor-kappaB and interferon regulatory factor transcription factors. However, viruses also trigger pro-inflammatory responses, which remain poorly defined. Here we show that internalized adenoviral DNA induces maturation of pro-interleukin-1beta in macrophages, which is dependent on NALP3 and ASC, components of the innate cytosolic molecular complex termed the inflammasome. Correspondingly, NALP3- and ASC-deficient mice display reduced innate inflammatory responses to adenovirus particles. Inflammasome activation also occurs as a result of transfected cytosolic bacterial, viral and mammalian (host) DNA, but in this case sensing is dependent on ASC but not NALP3. The DNA-sensing pro-inflammatory pathway functions independently of TLRs and interferon regulatory factors. Thus, in addition to viral and bacterial components or danger signals in general, inflammasomes sense potentially dangerous cytoplasmic DNA, strengthening their central role in innate immunity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muruve, Daniel A -- Petrilli, Virginie -- Zaiss, Anne K -- White, Lindsay R -- Clark, Sharon A -- Ross, P Joel -- Parks, Robin J -- Tschopp, Jurg -- England -- Nature. 2008 Mar 6;452(7183):103-7. doi: 10.1038/nature06664. Epub 2008 Feb 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of Calgary, Alberta T2N 4N1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18288107" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/genetics/immunology/physiology ; Animals ; Apoptosis Regulatory Proteins ; Carrier Proteins/genetics/*immunology ; Cell Line ; Cytoskeletal Proteins/deficiency/genetics/*immunology ; Cytosol/*metabolism/microbiology/*virology ; DNA/*immunology ; DNA, Viral/immunology ; Humans ; Immunity, Innate/*immunology ; Inflammation/*immunology/virology ; Interleukin-1beta/immunology/metabolism/secretion ; Macrophages, Peritoneal/immunology/metabolism ; Mice ; Mice, Inbred C57BL ; Protein Processing, Post-Translational
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  • 152
    Publication Date: 2008-09-17
    Description: TRPML1 (mucolipin 1, also known as MCOLN1) is predicted to be an intracellular late endosomal and lysosomal ion channel protein that belongs to the mucolipin subfamily of transient receptor potential (TRP) proteins. Mutations in the human TRPML1 gene cause mucolipidosis type IV disease (ML4). ML4 patients have motor impairment, mental retardation, retinal degeneration and iron-deficiency anaemia. Because aberrant iron metabolism may cause neural and retinal degeneration, it may be a primary cause of ML4 phenotypes. In most mammalian cells, release of iron from endosomes and lysosomes after iron uptake by endocytosis of Fe(3+)-bound transferrin receptors, or after lysosomal degradation of ferritin-iron complexes and autophagic ingestion of iron-containing macromolecules, is the chief source of cellular iron. The divalent metal transporter protein DMT1 (also known as SLC11A2) is the only endosomal Fe(2+) transporter known at present and it is highly expressed in erythroid precursors. Genetic studies, however, suggest the existence of a DMT1-independent endosomal and lysosomal Fe(2+) transport protein. By measuring radiolabelled iron uptake, by monitoring the levels of cytosolic and intralysosomal iron and by directly patch-clamping the late endosomal and lysosomal membrane, here we show that TRPML1 functions as a Fe(2+) permeable channel in late endosomes and lysosomes. ML4 mutations are shown to impair the ability of TRPML1 to permeate Fe(2+) at varying degrees, which correlate well with the disease severity. A comparison of TRPML1(-/- )ML4 and control human skin fibroblasts showed a reduction in cytosolic Fe(2+) levels, an increase in intralysosomal Fe(2+) levels and an accumulation of lipofuscin-like molecules in TRPML1(-/-) cells. We propose that TRPML1 mediates a mechanism by which Fe(2+) is released from late endosomes and lysosomes. Our results indicate that impaired iron transport may contribute to both haematological and degenerative symptoms of ML4 patients.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301259/" 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/PMC4301259/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, Xian-Ping -- Cheng, Xiping -- Mills, Eric -- Delling, Markus -- Wang, Fudi -- Kurz, Tino -- Xu, Haoxing -- T32 HL007572/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 Oct 16;455(7215):992-6. doi: 10.1038/nature07311. Epub 2008 Sep 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Department of Molecular, Cellular, and Developmental Biology, The University of Michigan, 3089 Natural Science Building (Kraus), 830 North University, Ann Arbor, Michigan 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18794901" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Membrane Permeability ; Endosomes/*metabolism ; Fibroblasts ; Fluorescence ; Humans ; Ion Transport ; Iron/analysis/*metabolism ; Lysosomes/*metabolism ; Mice ; Mucolipidoses/*metabolism ; Protons ; TRPM Cation Channels/deficiency/genetics/*metabolism ; Transfection ; Transient Receptor Potential Channels
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  • 153
    Publication Date: 2008-07-18
    Description: Partial agonists are ligands that bind to receptors but produce only a small maximum response even at concentrations where all receptors are occupied. In the case of ligand-activated ion channels, it has been supposed since 1957 that partial agonists evoke a small response because they are inefficient at eliciting the change of conformation between shut and open states of the channel. We have investigated partial agonists for two members of the nicotinic superfamily-the muscle nicotinic acetylcholine receptor and the glycine receptor-and find that the open-shut reaction is similar for both full and partial agonists, but the response to partial agonists is limited by an earlier conformation change ('flipping') that takes place while the channel is still shut. This has implications for the interpretation of structural studies, and in the future, for the design of partial agonists for therapeutic use.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629928/" 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/PMC2629928/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lape, Remigijus -- Colquhoun, David -- Sivilotti, Lucia G -- 074491/Wellcome Trust/United Kingdom -- G0400869/Medical Research Council/United Kingdom -- G0400869(72542)/Medical Research Council/United Kingdom -- England -- Nature. 2008 Aug 7;454(7205):722-7. doi: 10.1038/nature07139. Epub 2008 Jul 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University College London, Medical Sciences Building, Gower Street, London WC1E 6BT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18633353" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; *Drug Partial Agonism ; Glycine/pharmacology ; Humans ; Membrane Potentials/drug effects ; Muscles/metabolism ; Nicotinic Agonists/*pharmacology ; Protein Conformation ; Protein Subunits/agonists/chemistry/genetics/metabolism ; Quaternary Ammonium Compounds/pharmacology ; Rats ; Receptors, Glycine/agonists/chemistry/genetics/metabolism ; Receptors, Nicotinic/chemistry/genetics/*metabolism ; Structure-Activity Relationship ; Taurine/pharmacology
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  • 154
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    Nature Publishing Group (NPG)
    Publication Date: 2008-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Jan 17;451(7176):224. doi: 10.1038/451224a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202602" target="_blank"〉PubMed〈/a〉
    Keywords: Congresses as Topic/*economics/history ; Drug Industry/economics/history ; Foundations/*economics/*organization & administration/trends ; *Fund Raising/trends ; History, 20th Century ; History, 21st Century ; London ; Nobel Prize ; Research Personnel/history
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  • 155
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    Nature Publishing Group (NPG)
    Publication Date: 2008-06-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nath, Indira -- England -- Nature. 2008 Jun 19;453(7198):1002. doi: 10.1038/4531002a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Indira Nath is in the LEPRA - Blue Peter Research Centre, Cherlapally, Hyderabad 501301, India. indiranath@bprcleprasociety.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563148" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Child ; Culicidae/genetics/*physiology ; Developing Countries ; Female ; Great Britain ; History, 20th Century ; History, 21st Century ; Humans ; Insect Control/*history ; Malaria/*prevention & control/transmission ; Pregnancy ; Public Health/history
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  • 156
    Publication Date: 2008-01-18
    Description: Germ cells are the only cells that transmit genetic information to the next generation, and they therefore must be prevented from differentiating inappropriately into somatic cells. A common mechanism by which germline progenitors are protected from differentiation-inducing signals is a transient and global repression of RNA polymerase II (RNAPII)-dependent transcription. In both Drosophila and Caenorhabditis elegans embryos, the repression of messenger RNA transcription during germ cell specification correlates with an absence of phosphorylation of Ser 2 residues in the carboxy-terminal domain of RNAPII (hereafter called CTD), a critical modification for transcriptional elongation. Here we show that, in Drosophila embryos, a small protein encoded by polar granule component (pgc) is essential for repressing CTD Ser 2 phosphorylation in newly formed pole cells, the germline progenitors. Ectopic Pgc expression in somatic cells is sufficient to repress CTD Ser 2 phosphorylation. Furthermore, Pgc interacts, physically and genetically, with positive transcription elongation factor b (P-TEFb), the CTD Ser 2 kinase complex, and prevents its recruitment to transcription sites. These results indicate that Pgc is a cell-type-specific P-TEFb inhibitor that has a fundamental role in Drosophila germ cell specification. In C. elegans embryos, PIE-1 protein segregates to germline blastomeres, and is thought to repress mRNA transcription through interaction with P-TEFb. Thus, inhibition of P-TEFb is probably a common mechanism during germ cell specification in the disparate organisms C. elegans and Drosophila.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2719856/" 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/PMC2719856/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hanyu-Nakamura, Kazuko -- Sonobe-Nojima, Hiroko -- Tanigawa, Akie -- Lasko, Paul -- Nakamura, Akira -- R01 HD036631/HD/NICHD NIH HHS/ -- R01 HD036631-10/HD/NICHD NIH HHS/ -- England -- Nature. 2008 Feb 7;451(7179):730-3. doi: 10.1038/nature06498. Epub 2008 Jan 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Germline Development, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18200011" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans ; Cell Line ; Chromatin/genetics/*metabolism ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/*cytology/embryology/genetics/*metabolism ; Gene Expression Regulation, Developmental ; Germ Cells/cytology/*metabolism ; Phosphorylation ; Phosphoserine/metabolism ; Positive Transcriptional Elongation Factor B/antagonists & ; inhibitors/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; RNA Polymerase II/chemistry/metabolism ; Stem Cells/cytology/metabolism
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  • 157
    Publication Date: 2008-07-11
    Description: All viruses rely on host cell proteins and their associated mechanisms to complete the viral life cycle. Identifying the host molecules that participate in each step of virus replication could provide valuable new targets for antiviral therapy, but this goal may take several decades to achieve with conventional forward genetic screening methods and mammalian cell cultures. Here we describe a novel genome-wide RNA interference (RNAi) screen in Drosophila that can be used to identify host genes important for influenza virus replication. After modifying influenza virus to allow infection of Drosophila cells and detection of influenza virus gene expression, we tested an RNAi library against 13,071 genes (90% of the Drosophila genome), identifying over 100 for which suppression in Drosophila cells significantly inhibited or stimulated reporter gene (Renilla luciferase) expression from an influenza-virus-derived vector. The relevance of these findings to influenza virus infection of mammalian cells is illustrated for a subset of the Drosophila genes identified; that is, for three implicated Drosophila genes, the corresponding human homologues ATP6V0D1, COX6A1 and NXF1 are shown to have key functions in the replication of H5N1 and H1N1 influenza A viruses, but not vesicular stomatitis virus or vaccinia virus, in human HEK 293 cells. Thus, we have demonstrated the feasibility of using genome-wide RNAi screens in Drosophila to identify previously unrecognized host proteins that are required for influenza virus replication. This could accelerate the development of new classes of antiviral drugs for chemoprophylaxis and treatment, which are urgently needed given the obstacles to rapid development of an effective vaccine against pandemic influenza and the probable emergence of strains resistant to available drugs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2574945/" 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/PMC2574945/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hao, Linhui -- Sakurai, Akira -- Watanabe, Tokiko -- Sorensen, Ericka -- Nidom, Chairul A -- Newton, Michael A -- Ahlquist, Paul -- Kawaoka, Yoshihiro -- GM35072/GM/NIGMS NIH HHS/ -- R01 AI044386/AI/NIAID NIH HHS/ -- R01 AI044386-10/AI/NIAID NIH HHS/ -- R01 AI047446/AI/NIAID NIH HHS/ -- R01 AI047446-09/AI/NIAID NIH HHS/ -- R01 AI069274/AI/NIAID NIH HHS/ -- R01 AI069274-03/AI/NIAID NIH HHS/ -- R01 GM035072/GM/NIGMS NIH HHS/ -- R01 GM035072-23/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Aug 14;454(7206):890-3. doi: 10.1038/nature07151. Epub 2008 Jul 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Molecular Virology, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18615016" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Drosophila melanogaster/*genetics/*virology ; Gene Expression Regulation ; Genome, Insect/genetics ; Host-Pathogen Interactions/*physiology ; Humans ; Influenza A virus/*physiology ; Luciferases, Renilla/metabolism ; *RNA Interference ; Vaccinia virus/physiology ; Vesiculovirus/physiology ; Virus Replication/*physiology
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  • 158
    Publication Date: 2008-01-18
    Description: Human cells possess an antiviral activity that inhibits the release of retrovirus particles, and other enveloped virus particles, and is antagonized by the HIV-1 accessory protein, Vpu. This antiviral activity can be constitutively expressed or induced by interferon-alpha, and it consists of protein-based tethers, which we term 'tetherins', that cause retention of fully formed virions on infected cell surfaces. Using deductive constraints and gene expression analyses, we identify CD317 (also called BST2 or HM1.24), a membrane protein of previously unknown function, as a tetherin. Specifically, CD317 expression correlated with, and induced, a requirement for Vpu during HIV-1 and murine leukaemia virus particle release. Furthermore, in cells where HIV-1 virion release requires Vpu expression, depletion of CD317 abolished this requirement. CD317 caused retention of virions on cell surfaces and, after endocytosis, in CD317-positive compartments. Vpu co-localized with CD317 and inhibited these effects. Inhibition of Vpu function and consequent mobilization of tetherin's antiviral activity is a potential therapeutic strategy in HIV/AIDS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neil, Stuart J D -- Zang, Trinity -- Bieniasz, Paul D -- England -- Nature. 2008 Jan 24;451(7177):425-30. doi: 10.1038/nature06553. Epub 2008 Jan 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Aaron Diamond AIDS Research Center and Laboratory of Retrovirology, The Rockefeller University, 455 First Avenue, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18200009" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD/genetics/*metabolism ; Cell Line ; Cell Membrane/virology ; Endocytosis ; GPI-Linked Proteins ; Gene Expression Profiling ; HIV Infections/metabolism/therapy/virology ; HIV-1/*metabolism ; HeLa Cells ; Human Immunodeficiency Virus Proteins/antagonists & inhibitors/*metabolism ; Humans ; Interferon-alpha/pharmacology ; Leukemia Virus, Murine/metabolism ; Membrane Glycoproteins/*antagonists & inhibitors/genetics/*metabolism ; Mutant Proteins/genetics/metabolism ; Oligonucleotide Array Sequence Analysis ; Protein Transport ; Viral Regulatory and Accessory Proteins/antagonists & inhibitors/*metabolism ; Virion/metabolism ; Virus Replication ; gag Gene Products, Human Immunodeficiency Virus/metabolism
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  • 159
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    Nature Publishing Group (NPG)
    Publication Date: 2008-06-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harris, Alan -- England -- Nature. 2008 Jun 26;453(7199):1178-9. doi: 10.1038/4531178a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Space Science Institute, 4603 Orange Knoll Avenue, La Canada, California 91011-3364, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18580926" target="_blank"〉PubMed〈/a〉
    Keywords: *Earth (Planet) ; *Environmental Monitoring/history/statistics & numerical data ; History, 20th Century ; History, 21st Century ; *Meteoroids ; United States ; United States National Aeronautics and Space Administration
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  • 160
    Publication Date: 2008-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nelson, Bryn -- England -- Nature. 2008 Nov 6;456(7218):26-8. doi: 10.1038/456026a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987711" target="_blank"〉PubMed〈/a〉
    Keywords: Boston ; Computational Biology/trends ; Drug Industry/organization & administration/*trends ; Gene Expression Profiling ; Gene Regulatory Networks/genetics ; Genetic Predisposition to Disease/genetics ; Genome, Human/*genetics ; Genomics/*trends ; History, 21st Century ; Humans ; Individuality ; Washington
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  • 161
    Publication Date: 2008-05-02
    Description: Mitochondria use transport proteins of the eukaryotic mitochondrial carrier family (MCF) to mediate the exchange of diverse substrates, including ATP, with the host cell cytosol. According to classical endosymbiosis theory, insertion of a host-nuclear-encoded MCF transporter into the protomitochondrion was the key step that allowed the host cell to harvest ATP from the enslaved endosymbiont. Notably the genome of the microsporidian Encephalitozoon cuniculi has lost all of its genes for MCF proteins. This raises the question of how the recently discovered microsporidian remnant mitochondrion, called a mitosome, acquires ATP to support protein import and other predicted ATP-dependent activities. The E. cuniculi genome does contain four genes for an unrelated type of nucleotide transporter used by plastids and bacterial intracellular parasites, such as Rickettsia and Chlamydia, to import ATP from the cytosol of their eukaryotic host cells. The inference is that E. cuniculi also uses these proteins to steal ATP from its eukaryotic host to sustain its lifestyle as an obligate intracellular parasite. Here we show that, consistent with this hypothesis, all four E. cuniculi transporters can transport ATP, and three of them are expressed on the surface of the parasite when it is living inside host cells. The fourth transporter co-locates with mitochondrial Hsp70 to the E. cuniculi mitosome. Thus, uniquely among eukaryotes, the traditional relationship between mitochondrion and host has been subverted in E. cuniculi, by reductive evolution and analogous gene replacement. Instead of the mitosome providing the parasite cytosol with ATP, the parasite cytosol now seems to provide ATP for the organelle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsaousis, Anastasios D -- Kunji, Edmund R S -- Goldberg, Alina V -- Lucocq, John M -- Hirt, Robert P -- Embley, T Martin -- MC_U105663139/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2008 May 22;453(7194):553-6. doi: 10.1038/nature06903. Epub 2008 Apr 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Cell and Molecular Biosciences, Catherine Cookson Building, Framlington Place, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18449191" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/*metabolism ; Animals ; Biological Transport ; Carrier Proteins/genetics/immunology/metabolism ; Cell Line ; Encephalitozoon cuniculi/*cytology/genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Fungal Proteins/genetics/immunology/metabolism ; Genome, Fungal/genetics ; Genome, Mitochondrial/genetics ; Mitochondria/genetics/*metabolism ; Models, Biological ; Molecular Sequence Data ; Rabbits ; Rats ; Symbiosis
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  • 162
    Publication Date: 2008-08-23
    Description: Adipose tissue is central to the regulation of energy balance. Two functionally different types of fat are present in mammals: white adipose tissue, the primary site of triglyceride storage, and brown adipose tissue, which is specialized in energy expenditure and can counteract obesity. Factors that specify the developmental fate and function of white and brown adipose tissue remain poorly understood. Here we demonstrate that whereas some members of the family of bone morphogenetic proteins (BMPs) support white adipocyte differentiation, BMP7 singularly promotes differentiation of brown preadipocytes even in the absence of the normally required hormonal induction cocktail. BMP7 activates a full program of brown adipogenesis including induction of early regulators of brown fat fate PRDM16 (PR-domain-containing 16; ref. 4) and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha; ref. 5), increased expression of the brown-fat-defining marker uncoupling protein 1 (UCP1) and adipogenic transcription factors PPARgamma and CCAAT/enhancer-binding proteins (C/EBPs), and induction of mitochondrial biogenesis via p38 mitogen-activated protein (MAP) kinase-(also known as Mapk14) and PGC-1-dependent pathways. Moreover, BMP7 triggers commitment of mesenchymal progenitor cells to a brown adipocyte lineage, and implantation of these cells into nude mice results in development of adipose tissue containing mostly brown adipocytes. Bmp7 knockout embryos show a marked paucity of brown fat and an almost complete absence of UCP1. Adenoviral-mediated expression of BMP7 in mice results in a significant increase in brown, but not white, fat mass and leads to an increase in energy expenditure and a reduction in weight gain. These data reveal an important role of BMP7 in promoting brown adipocyte differentiation and thermogenesis in vivo and in vitro, and provide a potential new therapeutic approach for the treatment of obesity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745972/" 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/PMC2745972/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tseng, Yu-Hua -- Kokkotou, Efi -- Schulz, Tim J -- Huang, Tian Lian -- Winnay, Jonathon N -- Taniguchi, Cullen M -- Tran, T Thien -- Suzuki, Ryo -- Espinoza, Daniel O -- Yamamoto, Yuji -- Ahrens, Molly J -- Dudley, Andrew T -- Norris, Andrew W -- Kulkarni, Rohit N -- Kahn, C Ronald -- K08 DK064906/DK/NIDDK NIH HHS/ -- K08 DK64906/DK/NIDDK NIH HHS/ -- P30 DK040561/DK/NIDDK NIH HHS/ -- P30 DK040561-13/DK/NIDDK NIH HHS/ -- P30 DK46200/DK/NIDDK NIH HHS/ -- R01 DK 060837/DK/NIDDK NIH HHS/ -- R01 DK077097/DK/NIDDK NIH HHS/ -- R01 DK077097-01A1/DK/NIDDK NIH HHS/ -- R01 DK077097-02/DK/NIDDK NIH HHS/ -- R01 DK67536/DK/NIDDK NIH HHS/ -- R21 DK070722/DK/NIDDK NIH HHS/ -- R21 DK070722-01/DK/NIDDK NIH HHS/ -- R21 DK070722-02/DK/NIDDK NIH HHS/ -- England -- Nature. 2008 Aug 21;454(7207):1000-4. doi: 10.1038/nature07221.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section on Obesity and Hormone Action, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02215, USA. yu-hua.tseng@joslin.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18719589" target="_blank"〉PubMed〈/a〉
    Keywords: 3T3-L1 Cells ; *Adipogenesis ; Adipose Tissue, Brown/*growth & development/*metabolism ; Adipose Tissue, White/growth & development ; Animals ; Bone Morphogenetic Protein 7 ; Bone Morphogenetic Proteins/*metabolism ; Cell Line ; *Energy Metabolism/genetics ; Male ; Mesenchymal Stromal Cells/cytology/physiology ; Mice ; Mice, Inbred C57BL ; Mice, Nude ; Mitochondria/physiology ; Thermogenesis ; Transforming Growth Factor beta/*metabolism ; p38 Mitogen-Activated Protein Kinases/metabolism
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  • 163
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    Nature Publishing Group (NPG)
    Publication Date: 2008-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ledford, Heidi -- England -- Nature. 2008 Oct 23;455(7216):1023-8. doi: 10.1038/4551023a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948925" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Consciousness/physiology ; Continental Population Groups ; Epigenesis, Genetic ; History, 20th Century ; History, 21st Century ; Humans ; Models, Theoretical ; *Science/history ; Stem Cells ; *Terminology as Topic
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  • 164
    Publication Date: 2008-04-15
    Description: In insects, each olfactory sensory neuron expresses between one and three ligand-binding members of the olfactory receptor (OR) gene family, along with the highly conserved and broadly expressed Or83b co-receptor. The functional insect OR consists of a heteromeric complex of unknown stoichiometry but comprising at least one variable odorant-binding subunit and one constant Or83b family subunit. Insect ORs lack homology to G-protein-coupled chemosensory receptors in vertebrates and possess a distinct seven-transmembrane topology with the amino terminus located intracellularly. Here we provide evidence that heteromeric insect ORs comprise a new class of ligand-activated non-selective cation channels. Heterologous cells expressing silkmoth, fruitfly or mosquito heteromeric OR complexes showed extracellular Ca2+ influx and cation-non-selective ion conductance on stimulation with odorant. Odour-evoked OR currents are independent of known G-protein-coupled second messenger pathways. The fast response kinetics and OR-subunit-dependent K+ ion selectivity of the insect OR complex support the hypothesis that the complex between OR and Or83b itself confers channel activity. Direct evidence for odorant-gated channels was obtained by outside-out patch-clamp recording of Xenopus oocyte and HEK293T cell membranes expressing insect OR complexes. The ligand-gated ion channel formed by an insect OR complex seems to be the basis for a unique strategy that insects have acquired to respond to the olfactory environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Koji -- Pellegrino, Maurizio -- Nakagawa, Takao -- Nakagawa, Tatsuro -- Vosshall, Leslie B -- Touhara, Kazushige -- England -- Nature. 2008 Apr 24;452(7190):1002-6. doi: 10.1038/nature06850. Epub 2008 Apr 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrated Biosciences, The University of Tokyo, Chiba 277-8562, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18408712" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bombyx ; Calcium/metabolism ; Cell Line ; Culicidae ; Drosophila melanogaster ; Electric Conductivity ; HeLa Cells ; Heterotrimeric GTP-Binding Proteins ; Humans ; Insects/*chemistry ; *Ion Channel Gating ; Kinetics ; Ligands ; Odors/analysis ; Oocytes/metabolism ; Patch-Clamp Techniques ; Protein Subunits/chemistry/metabolism ; Receptors, Odorant/*chemistry/*metabolism ; Smell ; Xenopus laevis
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  • 165
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    Nature Publishing Group (NPG)
    Publication Date: 2008-10-25
    Description: Science policies based on techno-nationalist thinking and fantasies about the past technological revolutions will get us nowhere fast, says David Edgerton.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edgerton, David -- England -- Nature. 2008 Oct 23;455(7216):1030-1. doi: 10.1038/4551030a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for the History of Science, Technology and Medicine, Imperial College London, London SW7 2AZ, UK. d.edgerton@imperial.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948929" target="_blank"〉PubMed〈/a〉
    Keywords: History, 19th Century ; History, 20th Century ; History, 21st Century ; Research/economics/history/trends ; Technology/*economics/history/*trends
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  • 166
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    Nature Publishing Group (NPG)
    Publication Date: 2008-01-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2008 Jan 10;451(7175):114-5. doi: 10.1038/451114a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18185550" target="_blank"〉PubMed〈/a〉
    Keywords: History, 20th Century ; History, 21st Century ; *International Cooperation/history ; Nuclear Warfare/*history/*prevention & control/trends ; Security Measures/history/trends ; Terrorism/prevention & control/trends
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  • 167
    Publication Date: 2008-06-06
    Description: Drosophila neuroblasts and ovarian stem cells are well characterized models for stem cell biology. In both cell types, one daughter cell self-renews continuously while the other undergoes a limited number of divisions, stops to proliferate mitotically and differentiates. Whereas neuroblasts segregate the Trim-NHL (tripartite motif and Ncl-1, HT2A and Lin-41 domain)-containing protein Brain tumour (Brat) into one of the two daughter cells, ovarian stem cells are regulated by an extracellular signal from the surrounding stem cell niche. After division, one daughter cell looses niche contact. It undergoes 4 transit-amplifying divisions to form a cyst of 16 interconnected cells that reduce their rate of growth and stop to proliferate mitotically. Here we show that the Trim-NHL protein Mei-P26 (refs 7, 8) restricts growth and proliferation in the ovarian stem cell lineage. Mei-P26 expression is low in stem cells but is strongly induced in 16-cell cysts. In mei-P26 mutants, transit-amplifying cells are larger and proliferate indefinitely leading to the formation of an ovarian tumour. Like brat, mei-P26 regulates nucleolar size and can induce differentiation in Drosophila neuroblasts, suggesting that these genes act through the same pathway. We identify Argonaute-1, a component of the RISC complex, as a common binding partner of Brat and Mei-P26, and show that Mei-P26 acts by inhibiting the microRNA pathway. Mei-P26 and Brat have a similar domain composition that is also found in other tumour suppressors and might be a defining property of a new family of microRNA regulators that act specifically in stem cell lineages.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988194/" 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/PMC2988194/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neumuller, Ralph A -- Betschinger, Joerg -- Fischer, Anja -- Bushati, Natascha -- Poernbacher, Ingrid -- Mechtler, Karl -- Cohen, Stephen M -- Knoblich, Juergen A -- P 16629/Austrian Science Fund FWF/Austria -- England -- Nature. 2008 Jul 10;454(7201):241-5. doi: 10.1038/nature07014. Epub 2008 Jun 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr Bohr Gasse 3, 1030 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18528333" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Argonaute Proteins ; Cell Cycle ; Cell Differentiation ; Cell Enlargement ; Cell Line ; *Cell Lineage ; Cell Nucleolus/metabolism ; Cell Size ; DNA-Binding Proteins/metabolism ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/classification/*cytology/genetics ; Eukaryotic Initiation Factors ; Female ; MicroRNAs/genetics/*metabolism ; Mutation ; Neurons/cytology/metabolism ; Ovary/*cytology/metabolism ; Stem Cells/*cytology/*metabolism
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  • 168
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    Nature Publishing Group (NPG)
    Publication Date: 2008-10-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hassan, Mohamed -- England -- Nature. 2008 Oct 2;455(7213):598-9. doi: 10.1038/455598a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉TWAS, the Academy of Sciences for the Developing World in Trieste, Italy. mhassan@twas.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18833263" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes/history ; Animals ; Cattle ; China ; Congresses as Topic/*history ; Cooperative Behavior ; Developing Countries/history ; History, 20th Century ; History, 21st Century ; Humans ; Science/*history/trends
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  • 169
    Publication Date: 2008-10-31
    Description: AB(5) toxins comprise an A subunit that corrupts essential eukaryotic cell functions, and pentameric B subunits that direct target-cell uptake after binding surface glycans. Subtilase cytotoxin (SubAB) is an AB(5) toxin secreted by Shiga toxigenic Escherichia coli (STEC), which causes serious gastrointestinal disease in humans. SubAB causes haemolytic uraemic syndrome-like pathology in mice through SubA-mediated cleavage of BiP/GRP78, an essential endoplasmic reticulum chaperone. Here we show that SubB has a strong preference for glycans terminating in the sialic acid N-glycolylneuraminic acid (Neu5Gc), a monosaccharide not synthesized in humans. Structures of SubB-Neu5Gc complexes revealed the basis for this specificity, and mutagenesis of key SubB residues abrogated in vitro glycan recognition, cell binding and cytotoxicity. SubAB specificity for Neu5Gc was confirmed using mouse tissues with a human-like deficiency of Neu5Gc and human cell lines fed with Neu5Gc. Despite lack of Neu5Gc biosynthesis in humans, assimilation of dietary Neu5Gc creates high-affinity receptors on human gut epithelia and kidney vasculature. This, and the lack of Neu5Gc-containing body fluid competitors in humans, confers susceptibility to the gastrointestinal and systemic toxicities of SubAB. Ironically, foods rich in Neu5Gc are the most common source of STEC contamination. Thus a bacterial toxin's receptor is generated by metabolic incorporation of an exogenous factor derived from food.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723748/" 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/PMC2723748/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Byres, Emma -- Paton, Adrienne W -- Paton, James C -- Lofling, Jonas C -- Smith, David F -- Wilce, Matthew C J -- Talbot, Ursula M -- Chong, Damien C -- Yu, Hai -- Huang, Shengshu -- Chen, Xi -- Varki, Nissi M -- Varki, Ajit -- Rossjohn, Jamie -- Beddoe, Travis -- R01 AI068715-01A1/AI/NIAID NIH HHS/ -- R01 AI068715-02/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Dec 4;456(7222):648-52. doi: 10.1038/nature07428. Epub 2008 Oct 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Protein Crystallography Unit and ARC Centre of Excellence for Structural and Functional Microbial Genomics, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18971931" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Toxins/chemistry/genetics/*metabolism/*toxicity ; Cell Death/drug effects ; Cell Line ; Crystallography, X-Ray ; Escherichia coli Proteins/*chemistry/genetics/metabolism/*toxicity ; Humans ; Mice ; Microscopy, Fluorescence ; Models, Molecular ; Neuraminic Acids/administration & dosage/*metabolism/pharmacology ; Polysaccharides/*chemistry/*metabolism ; Protein Binding ; Protein Subunits ; Shiga-Toxigenic Escherichia coli/chemistry/pathogenicity ; Sialic Acids/chemistry/metabolism ; Species Specificity ; Substrate Specificity ; Subtilisins/*chemistry/genetics/metabolism/*toxicity ; Survival Analysis
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  • 170
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    Nature Publishing Group (NPG)
    Publication Date: 2008-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2008 Jan 17;451(7176):233. doi: 10.1038/451233a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202610" target="_blank"〉PubMed〈/a〉
    Keywords: Congresses as Topic/economics/history/*organization & administration/trends ; Drug Industry/history/organization & administration/trends ; Foundations/history/*organization & administration/*trends ; History, 20th Century ; History, 21st Century ; London
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  • 171
    Publication Date: 2008-10-14
    Description: Susceptibility to Crohn's disease, a complex inflammatory disease involving the small intestine, is controlled by over 30 loci. One Crohn's disease risk allele is in ATG16L1, a gene homologous to the essential yeast autophagy gene ATG16 (ref. 2). It is not known how ATG16L1 or autophagy contributes to intestinal biology or Crohn's disease pathogenesis. To address these questions, we generated and characterized mice that are hypomorphic for ATG16L1 protein expression, and validated conclusions on the basis of studies in these mice by analysing intestinal tissues that we collected from Crohn's disease patients carrying the Crohn's disease risk allele of ATG16L1. Here we show that ATG16L1 is a bona fide autophagy protein. Within the ileal epithelium, both ATG16L1 and a second essential autophagy protein ATG5 are selectively important for the biology of the Paneth cell, a specialized epithelial cell that functions in part by secretion of granule contents containing antimicrobial peptides and other proteins that alter the intestinal environment. ATG16L1- and ATG5-deficient Paneth cells exhibited notable abnormalities in the granule exocytosis pathway. In addition, transcriptional analysis revealed an unexpected gain of function specific to ATG16L1-deficient Paneth cells including increased expression of genes involved in peroxisome proliferator-activated receptor (PPAR) signalling and lipid metabolism, of acute phase reactants and of two adipocytokines, leptin and adiponectin, known to directly influence intestinal injury responses. Importantly, Crohn's disease patients homozygous for the ATG16L1 Crohn's disease risk allele displayed Paneth cell granule abnormalities similar to those observed in autophagy-protein-deficient mice and expressed increased levels of leptin protein. Thus, ATG16L1, and probably the process of autophagy, have a role within the intestinal epithelium of mice and Crohn's disease patients by selective effects on the cell biology and specialized regulatory properties of Paneth cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695978/" 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/PMC2695978/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cadwell, Ken -- Liu, John Y -- Brown, Sarah L -- Miyoshi, Hiroyuki -- Loh, Joy -- Lennerz, Jochen K -- Kishi, Chieko -- Kc, Wumesh -- Carrero, Javier A -- Hunt, Steven -- Stone, Christian D -- Brunt, Elizabeth M -- Xavier, Ramnik J -- Sleckman, Barry P -- Li, Ellen -- Mizushima, Noboru -- Stappenbeck, Thaddeus S -- Virgin, Herbert W 4th -- AI062773/AI/NIAID NIH HHS/ -- DK43351/DK/NIDDK NIH HHS/ -- P30 DK040561/DK/NIDDK NIH HHS/ -- P30 DK040561-13/DK/NIDDK NIH HHS/ -- P30 DK043351/DK/NIDDK NIH HHS/ -- P30 DK043351-18/DK/NIDDK NIH HHS/ -- P30 DK052574-09/DK/NIDDK NIH HHS/ -- P30 DK52574/DK/NIDDK NIH HHS/ -- R01 AI062773/AI/NIAID NIH HHS/ -- R01 AI062773-01A1/AI/NIAID NIH HHS/ -- R01 AI062832/AI/NIAID NIH HHS/ -- R01 AI062832-04/AI/NIAID NIH HHS/ -- T32 AR007279/AR/NIAMS NIH HHS/ -- T32 AR007279-30/AR/NIAMS NIH HHS/ -- T32 AR07279/AR/NIAMS NIH HHS/ -- U54 AI057160/AI/NIAID NIH HHS/ -- U54 AI057160-010005/AI/NIAID NIH HHS/ -- U54 AI057160-05S10018/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Nov 13;456(7219):259-63. doi: 10.1038/nature07416. Epub 2008 Oct 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18849966" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Autophagy/*genetics ; Carrier Proteins/genetics/*metabolism ; Cell Line ; Crohn Disease/genetics/pathology ; Exocytosis/genetics ; Homozygote ; Humans ; Mice ; Mice, Inbred C57BL ; Mutation ; Paneth Cells/*metabolism/pathology
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  • 172
    Publication Date: 2008-07-04
    Description: Herpesviruses are characterized by their ability to maintain life-long latent infections in their animal hosts. However, the mechanisms that allow establishment and maintenance of the latent state remain poorly understood. Herpes simplex virus 1 (HSV-1) establishes latency in neurons of sensory ganglia, where the only abundant viral gene product is a non-coding RNA, the latency associated transcript (LAT). Here we show that LAT functions as a primary microRNA (miRNA) precursor that encodes four distinct miRNAs in HSV-1 infected cells. One of these miRNAs, miR-H2-3p, is transcribed in an antisense orientation to ICP0-a viral immediate-early transcriptional activator that is important for productive HSV-1 replication and thought to have a role in reactivation from latency. We show that miR-H2-3p is able to reduce ICP0 protein expression, but does not significantly affect ICP0 messenger RNA levels. We also identified a fifth HSV-1 miRNA in latently infected trigeminal ganglia, miR-H6, which derives from a previously unknown transcript distinct from LAT. miR-H6 shows extended seed complementarity to the mRNA encoding a second HSV-1 transcription factor, ICP4, and inhibits expression of ICP4, which is required for expression of most HSV-1 genes during productive infection. These results may explain the reported ability of LAT to promote latency. Thus, HSV-1 expresses at least two primary miRNA precursors in latently infected neurons that may facilitate the establishment and maintenance of viral latency by post-transcriptionally regulating viral gene expression.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666538/" 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/PMC2666538/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Umbach, Jennifer Lin -- Kramer, Martha F -- Jurak, Igor -- Karnowski, Heather W -- Coen, Donald M -- Cullen, Bryan R -- R01 AI067968/AI/NIAID NIH HHS/ -- R01 AI067968-02/AI/NIAID NIH HHS/ -- R01 AI067968-03/AI/NIAID NIH HHS/ -- T32 CA009111/CA/NCI NIH HHS/ -- England -- Nature. 2008 Aug 7;454(7205):780-3. doi: 10.1038/nature07103. Epub 2008 Jul 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18596690" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cell Line ; Down-Regulation ; *Gene Expression Regulation, Viral ; Genome, Viral/genetics ; Herpesvirus 1, Human/*genetics/physiology ; Humans ; Immediate-Early Proteins/biosynthesis/genetics ; Male ; Mice ; MicroRNAs/*genetics/*metabolism ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics/metabolism ; RNA, Viral/*genetics/*metabolism ; Ubiquitin-Protein Ligases/biosynthesis/genetics ; Virus Latency/*genetics/physiology
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  • 173
    Publication Date: 2008-01-04
    Description: Post-translational modification (PTM) of proteins plays an important part in mediating protein interactions and/or the recruitment of specific protein targets. PTM can be mediated by the addition of functional groups (for example, acetylation or phosphorylation), peptides (for example, ubiquitylation or sumoylation), or nucleotides (for example, poly(ADP-ribosyl)ation). Poly(ADP-ribosyl)ation often involves the addition of long chains of ADP-ribose units, linked by glycosidic ribose-ribose bonds, and is critical for a wide range of processes, including DNA repair, regulation of chromosome structure, transcriptional regulation, mitosis and apoptosis. Here we identify a novel poly(ADP-ribose)-binding zinc finger (PBZ) motif in a number of eukaryotic proteins involved in the DNA damage response and checkpoint regulation. The PBZ motif is also required for post-translational poly(ADP-ribosyl)ation. We demonstrate interaction of poly(ADP-ribose) with this motif in two representative human proteins, APLF (aprataxin PNK-like factor) and CHFR (checkpoint protein with FHA and RING domains), and show that the actions of CHFR in the antephase checkpoint are abrogated by mutations in PBZ or by inhibition of poly(ADP-ribose) synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahel, Ivan -- Ahel, Dragana -- Matsusaka, Takahiro -- Clark, Allison J -- Pines, Jonathon -- Boulton, Simon J -- West, Stephen C -- England -- Nature. 2008 Jan 3;451(7174):81-5. doi: 10.1038/nature06420.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genetic Recombination and, Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18172500" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Cell Cycle ; Cell Cycle Proteins/*chemistry/*metabolism ; Cell Line ; DNA Damage ; *DNA Repair ; DNA-(Apurinic or Apyrimidinic Site) Lyase ; Humans ; Molecular Sequence Data ; Neoplasm Proteins/chemistry/metabolism ; Phosphoproteins/chemistry/metabolism ; Poly Adenosine Diphosphate Ribose/biosynthesis/*metabolism ; Protein Binding ; Protein Processing, Post-Translational ; Ubiquitination ; Zinc Fingers/*physiology
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  • 174
    Publication Date: 2008-07-11
    Description: Ebola virus (EBOV) entry requires the surface glycoprotein (GP) to initiate attachment and fusion of viral and host membranes. Here we report the crystal structure of EBOV GP in its trimeric, pre-fusion conformation (GP1+GP2) bound to a neutralizing antibody, KZ52, derived from a human survivor of the 1995 Kikwit outbreak. Three GP1 viral attachment subunits assemble to form a chalice, cradled by the GP2 fusion subunits, while a novel glycan cap and projected mucin-like domain restrict access to the conserved receptor-binding site sequestered in the chalice bowl. The glycocalyx surrounding GP is likely central to immune evasion and may explain why survivors have insignificant neutralizing antibody titres. KZ52 recognizes a protein epitope at the chalice base where it clamps several regions of the pre-fusion GP2 to the amino terminus of GP1. This structure provides a template for unravelling the mechanism of EBOV GP-mediated fusion and for future immunotherapeutic development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700032/" 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/PMC2700032/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Jeffrey E -- Fusco, Marnie L -- Hessell, Ann J -- Oswald, Wendelien B -- Burton, Dennis R -- Saphire, Erica Ollmann -- R01 AI067927/AI/NIAID NIH HHS/ -- R01 AI067927-03/AI/NIAID NIH HHS/ -- R21 AI053423/AI/NIAID NIH HHS/ -- R21 AI053423-02/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Jul 10;454(7201):177-82. doi: 10.1038/nature07082.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, Mail Drop IMM-2, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18615077" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Viral/genetics/*immunology ; Binding Sites, Antibody ; Cathepsins/metabolism ; Cell Line ; Cricetinae ; Cricetulus ; Crystallography, X-Ray ; Democratic Republic of the Congo ; Ebolavirus/*chemistry/immunology ; Glycoproteins/*chemistry/*immunology/metabolism ; Glycosylation ; Humans ; Membrane Fusion ; Models, Molecular ; Protein Conformation ; Receptors, Virus/chemistry/metabolism ; *Survivors
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  • 175
    Publication Date: 2008-07-29
    Description: Influenza A virus is a major human and animal pathogen with the potential to cause catastrophic loss of life. The virus reproduces rapidly, mutates frequently and occasionally crosses species barriers. The recent emergence in Asia of avian influenza related to highly pathogenic forms of the human virus has highlighted the urgent need for new effective treatments. Here we demonstrate the importance to viral replication of a subunit interface in the viral RNA polymerase, thereby providing a new set of potential drug binding sites entirely independent of surface antigen type. No current medication targets this heterotrimeric polymerase complex. All three subunits, PB1, PB2 and PA, are required for both transcription and replication. PB1 carries the polymerase active site, PB2 includes the capped-RNA recognition domain, and PA is involved in assembly of the functional complex, but so far very little structural information has been reported for any of them. We describe the crystal structure of a large fragment of one subunit (PA) of influenza A RNA polymerase bound to a fragment of another subunit (PB1). The carboxy-terminal domain of PA forms a novel fold, and forms a deep, highly hydrophobic groove into which the amino-terminal residues of PB1 can fit by forming a 3(10) helix.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Obayashi, Eiji -- Yoshida, Hisashi -- Kawai, Fumihiro -- Shibayama, Naoya -- Kawaguchi, Atsushi -- Nagata, Kyosuke -- Tame, Jeremy R H -- Park, Sam-Yong -- England -- Nature. 2008 Aug 28;454(7208):1127-31. doi: 10.1038/nature07225. Epub 2008 Jul 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Protein Design Laboratory, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama 230-0045, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18660801" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Line ; Crystallization ; Crystallography, X-Ray ; Humans ; Influenza A Virus, H1N1 Subtype/*enzymology/genetics ; Protein Binding ; Protein Subunits/*chemistry/genetics/*metabolism ; RNA Replicase/*chemistry/genetics/*metabolism ; Viral Proteins/*chemistry/genetics/*metabolism ; Virus Replication
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  • 176
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2008-02-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hayden, Erika Check -- England -- Nature. 2008 Feb 14;451(7180):763-5. doi: 10.1038/451763a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18272992" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information/ethics ; Genome, Human/genetics ; Genomics/*history ; History, 20th Century ; History, 21st Century ; Human Genome Project/history ; Humans ; Molecular Biology/*history ; Sequence Analysis, DNA/*history ; United States
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  • 177
    Publication Date: 2008-04-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Akunyili, Dora -- England -- Nature. 2008 Apr 24;452(7190):924. doi: 10.1038/452924a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18441547" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Drug Industry/economics/*ethics/standards ; Fraud/*prevention & control/*statistics & numerical data ; History, 21st Century ; Humans ; India ; International Cooperation ; Nigeria
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  • 178
    Publication Date: 2008-11-07
    Description: The hedgehog (Hh) signalling pathway has an evolutionarily conserved role in patterning fields of cells during metazoan development, and is inappropriately activated in cancer. Hh pathway activity is absolutely dependent on signalling by the seven-transmembrane protein smoothened (Smo), which is regulated by the Hh receptor patched (Ptc). Smo signals to an intracellular multi-protein complex containing the Kinesin related protein Costal2 (Cos2), the protein kinase Fused (Fu) and the transcription factor Cubitus interruptus (Ci). In the absence of Hh, this complex regulates the cleavage of full-length Ci to a truncated repressor protein, Ci75, in a process that is dependent on the proteasome and priming phosphorylations by Protein kinase A (PKA). Binding of Hh to Ptc blocks Ptc-mediated Smo inhibition, allowing Smo to signal to the intracellular components to attenuate Ci cleavage. Because of its homology with the Frizzled family of G-protein-coupled receptors (GPCR), a likely candidate for an immediate Smo effector would be a heterotrimeric G protein. However, the role that G proteins may have in Hh signal transduction is unclear and quite controversial, which has led to widespread speculation that Smo signals through a variety of novel G-protein-independent mechanisms. Here we present in vitro and in vivo evidence in Drosophila that Smo activates a G protein to modulate intracellular cyclic AMP levels in response to Hh. Our results demonstrate that Smo functions as a canonical GPCR, which signals through Galphai to regulate Hh pathway activation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744466/" 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/PMC2744466/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ogden, Stacey K -- Fei, Dennis Liang -- Schilling, Neal S -- Ahmed, Yashi F -- Hwa, John -- Robbins, David J -- CA82628/CA/NCI NIH HHS/ -- HL074190/HL/NHLBI NIH HHS/ -- R01 CA082628/CA/NCI NIH HHS/ -- R01 CA082628-11/CA/NCI NIH HHS/ -- R01 HL074190/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 Dec 18;456(7224):967-70. doi: 10.1038/nature07459.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, New Hampshire 03755, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987629" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Choristoma/metabolism ; Cyclic AMP/metabolism ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/genetics/*metabolism ; GTP-Binding Protein alpha Subunits, Gi-Go/genetics/*metabolism ; Hedgehog Proteins/genetics/*metabolism ; Kinesin/metabolism ; Mutation/genetics ; Receptors, Cell Surface/genetics/metabolism ; Receptors, G-Protein-Coupled/genetics/*metabolism ; *Signal Transduction
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  • 179
    Publication Date: 2008-09-30
    Description: Mammalian Toll-like receptors (TLRs) 3, 7, 8 and 9 initiate immune responses to infection by recognizing microbial nucleic acids; however, these responses come at the cost of potential autoimmunity owing to inappropriate recognition of self nucleic acids. The localization of TLR9 and TLR7 to intracellular compartments seems to have a role in facilitating responses to viral nucleic acids while maintaining tolerance to self nucleic acids, yet the cell biology regulating the transport and localization of these receptors remains poorly understood. Here we define the route by which TLR9 and TLR7 exit the endoplasmic reticulum and travel to endolysosomes in mouse macrophages and dendritic cells. The ectodomains of TLR9 and TLR7 are cleaved in the endolysosome, such that no full-length protein is detectable in the compartment where ligand is recognized. Notably, although both the full-length and cleaved forms of TLR9 are capable of binding ligand, only the processed form recruits MyD88 on activation, indicating that this truncated receptor, rather than the full-length form, is functional. Furthermore, conditions that prevent receptor proteolysis, including forced TLR9 surface localization, render the receptor non-functional. We propose that ectodomain cleavage represents a strategy to restrict receptor activation to endolysosomal compartments and prevent TLRs from responding to self nucleic acids.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596276/" 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/PMC2596276/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ewald, Sarah E -- Lee, Bettina L -- Lau, Laura -- Wickliffe, Katherine E -- Shi, Guo-Ping -- Chapman, Harold A -- Barton, Gregory M -- AI072429/AI/NIAID NIH HHS/ -- CA009179/CA/NCI NIH HHS/ -- HL67204/HL/NHLBI NIH HHS/ -- R01 AI072429/AI/NIAID NIH HHS/ -- R01 AI072429-01A2/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Dec 4;456(7222):658-62. doi: 10.1038/nature07405. Epub 2008 Sep 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Immunology & Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, 405 Life Sciences Addition, Berkeley, California 94720-3200, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18820679" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cells, Cultured ; Dendritic Cells/cytology/metabolism ; Endoplasmic Reticulum/metabolism ; Female ; Golgi Apparatus/metabolism ; Ligands ; Lysosomes/metabolism ; Macrophages/cytology/metabolism ; Male ; Membrane Glycoproteins/chemistry/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Mice ; Myeloid Differentiation Factor 88/metabolism ; Phagosomes/metabolism ; *Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Protein Transport ; Toll-Like Receptor 7/chemistry/metabolism ; Toll-Like Receptor 9/*chemistry/*metabolism
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  • 180
    Publication Date: 2008-09-27
    Description: Across the Greenland-Scotland ridge there is a continuous flow of cold dense water, termed 'overflow', from the Nordic seas to the Atlantic Ocean. This is a main contributor to the production of North Atlantic Deep Water that feeds the lower limb of the Atlantic meridional overturning circulation, which has been predicted to weaken as a consequence of climate change. The two main overflow branches pass the Denmark Strait and the Faroe Bank channel. Here we combine results from direct current measurements in the Faroe Bank channel for 1995-2005 with an ensemble hindcast experiment for 1948-2005 using an ocean general circulation model. For the overlapping period we find a convincing agreement between model simulations and observations on monthly to interannual timescales. Both observations and model data show no significant trend in volume transport. In addition, for the whole 1948-2005 period, the model indicates no persistent trend in the Faroe Bank channel overflow or in the total overflow transport, in agreement with the few available historical observations. Deepening isopycnals in the Norwegian Sea have tended to decrease the pressure difference across the Greenland-Scotland ridge, but this has been compensated for by the effect of changes in sea level. In contrast with earlier studies, we therefore conclude that the Faroe Bank channel overflow, and also the total overflow, did not decrease consistently from 1950 to 2005, although the model does show a weakening total Atlantic meridional overturning circulation as a result of changes south of the Greenland-Scotland ridge.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olsen, Steffen M -- Hansen, Bogi -- Quadfasel, Detlef -- Osterhus, Svein -- England -- Nature. 2008 Sep 25;455(7212):519-22. doi: 10.1038/nature07302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Danish Meteorological Institute, Lyngbyvej 100, 2100 Copenhagen, Denmark. smo@dmi.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818655" target="_blank"〉PubMed〈/a〉
    Keywords: Atlantic Ocean ; Computer Simulation ; Denmark ; Greenhouse Effect ; Greenland ; History, 20th Century ; History, 21st Century ; Ice/analysis ; Models, Theoretical ; Pressure ; Scotland ; Seawater/*analysis ; *Water Movements
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  • 181
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    Nature Publishing Group (NPG)
    Publication Date: 2008-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vance, Erik -- England -- Nature. 2008 Apr 3;452(7187):525-6. doi: 10.1038/452525a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18385709" target="_blank"〉PubMed〈/a〉
    Keywords: Anatomy/economics/education ; Animals ; Cetacea/*anatomy & histology ; History, 20th Century ; History, 21st Century ; New York City
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  • 182
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    Nature Publishing Group (NPG)
    Publication Date: 2008-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fauci, Anthony S -- England -- Nature. 2008 May 15;453(7193):289-90. doi: 10.1038/453289a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute of Allergy and Infectious Diseases (NIAID) at the US National Institutes of Health in Bethesda, Maryland, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480799" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/history ; Anti-HIV Agents/history/supply & distribution/therapeutic use ; Drug Resistance, Viral ; HIV/drug effects/genetics/isolation & purification/physiology ; HIV Infections/drug therapy/*history/prevention & control/virology ; History, 20th Century ; History, 21st Century ; Humans ; Time Factors ; Zidovudine/history/pharmacology/therapeutic use
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  • 183
    Publication Date: 2008-06-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chandler, David -- England -- Nature. 2008 Jun 26;453(7199):1164-8. doi: 10.1038/4531164a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18580921" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Dinosaurs ; Earth (Planet) ; Environmental Monitoring/history ; History, 20th Century ; History, 21st Century ; *Minor Planets ; Moon ; United States ; United States National Aeronautics and Space Administration
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  • 184
    Publication Date: 2008-01-11
    Description: Stem cell self-renewal implies proliferation under continued maintenance of multipotency. Small changes in numbers of stem cells may lead to large differences in differentiated cell numbers, resulting in significant physiological consequences. Proliferation is typically regulated in the G1 phase, which is associated with differentiation and cell cycle arrest. However, embryonic stem (ES) cells may lack a G1 checkpoint. Regulation of proliferation in the 'DNA damage' S/G2 cell cycle checkpoint pathway is known for its role in the maintenance of chromatin structural integrity. Here we show that autocrine/paracrine gamma-aminobutyric acid (GABA) signalling by means of GABA(A) receptors negatively controls ES cell and peripheral neural crest stem (NCS) cell proliferation, preimplantation embryonic growth and proliferation in the boundary-cap stem cell niche, resulting in an attenuation of neuronal progenies from this stem cell niche. Activation of GABA(A) receptors leads to hyperpolarization, increased cell volume and accumulation of stem cells in S phase, thereby causing a rapid decrease in cell proliferation. GABA(A) receptors signal through S-phase checkpoint kinases of the phosphatidylinositol-3-OH kinase-related kinase family and the histone variant H2AX. This signalling pathway critically regulates proliferation independently of differentiation, apoptosis and overt damage to DNA. These results indicate the presence of a fundamentally different mechanism of proliferation control in these stem cells, in comparison with most somatic cells, involving proteins in the DNA damage checkpoint pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andang, Michael -- Hjerling-Leffler, Jens -- Moliner, Annalena -- Lundgren, T Kalle -- Castelo-Branco, Goncalo -- Nanou, Evanthia -- Pozas, Ester -- Bryja, Vitezslav -- Halliez, Sophie -- Nishimaru, Hiroshi -- Wilbertz, Johannes -- Arenas, Ernest -- Koltzenburg, Martin -- Charnay, Patrick -- El Manira, Abdeljabbar -- Ibanez, Carlos F -- Ernfors, Patrik -- G0601943/Medical Research Council/United Kingdom -- England -- Nature. 2008 Jan 24;451(7177):460-4. doi: 10.1038/nature06488. Epub 2008 Jan 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18185516" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autocrine Communication ; Blastocyst/cytology/enzymology/metabolism ; Cell Count ; Cell Cycle ; Cell Line ; Cell Proliferation ; Cell Size ; DNA Damage ; GABA-A Receptor Agonists ; GABA-A Receptor Antagonists ; Histones/deficiency/genetics/*metabolism ; Mice ; Neural Crest/cytology/metabolism ; Paracrine Communication ; Patch-Clamp Techniques ; Phosphatidylinositol 3-Kinases/metabolism ; Phosphorylation ; Receptors, GABA-A/genetics/*metabolism ; Stem Cells/*cytology/enzymology/*metabolism ; gamma-Aminobutyric Acid/metabolism
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  • 185
    Publication Date: 2008-01-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anderson, David -- Brenner, Sydney -- England -- Nature. 2008 Jan 10;451(7175):139. doi: 10.1038/451139a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉David Anderson is in the Division of Biology, 216-276 Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA.wuwei@caltech.edu; sbrenner@salk.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18185579" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/genetics ; Animals ; Drosophila melanogaster/genetics/physiology ; History, 20th Century ; History, 21st Century ; Molecular Biology/*history ; Neurobiology/history
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  • 186
    Publication Date: 2008-05-24
    Description: Phenotypic cell-to-cell variability within clonal populations may be a manifestation of 'gene expression noise', or it may reflect stable phenotypic variants. Such 'non-genetic cell individuality' can arise from the slow fluctuations of protein levels in mammalian cells. These fluctuations produce persistent cell individuality, thereby rendering a clonal population heterogeneous. However, it remains unknown whether this heterogeneity may account for the stochasticity of cell fate decisions in stem cells. Here we show that in clonal populations of mouse haematopoietic progenitor cells, spontaneous 'outlier' cells with either extremely high or low expression levels of the stem cell marker Sca-1 (also known as Ly6a; ref. 9) reconstitute the parental distribution of Sca-1 but do so only after more than one week. This slow relaxation is described by a gaussian mixture model that incorporates noise-driven transitions between discrete subpopulations, suggesting hidden multi-stability within one cell type. Despite clonality, the Sca-1 outliers had distinct transcriptomes. Although their unique gene expression profiles eventually reverted to that of the median cells, revealing an attractor state, they lasted long enough to confer a greatly different proclivity for choosing either the erythroid or the myeloid lineage. Preference in lineage choice was associated with increased expression of lineage-specific transcription factors, such as a 〉200-fold increase in Gata1 (ref. 10) among the erythroid-prone cells, or a 〉15-fold increased PU.1 (Sfpi1) (ref. 11) expression among myeloid-prone cells. Thus, clonal heterogeneity of gene expression level is not due to independent noise in the expression of individual genes, but reflects metastable states of a slowly fluctuating transcriptome that is distinct in individual cells and may govern the reversible, stochastic priming of multipotent progenitor cells in cell fate decision.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Hannah H -- Hemberg, Martin -- Barahona, Mauricio -- Ingber, Donald E -- Huang, Sui -- P01 CA045548/CA/NCI NIH HHS/ -- R21 CA123284/CA/NCI NIH HHS/ -- England -- Nature. 2008 May 22;453(7194):544-7. doi: 10.1038/nature06965.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vascular Biology Programme, Department of Pathology and Surgery, Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497826" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, Ly/genetics/metabolism ; Cell Differentiation ; Cell Line ; Cell Lineage/*genetics ; Clone Cells/cytology/metabolism ; Erythroid Cells/cytology/metabolism ; GATA1 Transcription Factor/metabolism ; *Gene Expression Profiling ; Hematopoietic Stem Cells/*cytology/*metabolism ; Membrane Proteins/genetics/metabolism ; Mice ; Myeloid Cells/cytology/metabolism ; Proto-Oncogene Proteins/metabolism ; Stochastic Processes ; Trans-Activators/metabolism ; Transcription, Genetic/*genetics
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  • 187
    Publication Date: 2008-11-04
    Description: Protein-RNA interactions have critical roles in all aspects of gene expression. However, applying biochemical methods to understand such interactions in living tissues has been challenging. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova revealed extremely reproducible RNA-binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3' untranslated regions, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597294/" 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/PMC2597294/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Licatalosi, Donny D -- Mele, Aldo -- Fak, John J -- Ule, Jernej -- Kayikci, Melis -- Chi, Sung Wook -- Clark, Tyson A -- Schweitzer, Anthony C -- Blume, John E -- Wang, Xuning -- Darnell, Jennifer C -- Darnell, Robert B -- MC_U105185858/Medical Research Council/United Kingdom -- R01 NS034389/NS/NINDS NIH HHS/ -- R01 NS034389-09/NS/NINDS NIH HHS/ -- R01 NS034389-10/NS/NINDS NIH HHS/ -- R01 NS034389-11/NS/NINDS NIH HHS/ -- R01 NS034389-12/NS/NINDS NIH HHS/ -- R01 NS034389-13A1/NS/NINDS NIH HHS/ -- R01 NS040955/NS/NINDS NIH HHS/ -- R01 NS040955-05/NS/NINDS NIH HHS/ -- R01 NS34389/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Nov 27;456(7221):464-9. doi: 10.1038/nature07488. Epub 2008 Nov 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18978773" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing/*genetics ; Animals ; Antigens, Neoplasm/genetics/*metabolism ; Cell Line ; Cross-Linking Reagents/chemistry/metabolism ; Exons/genetics ; Genome/*genetics ; Genomics ; Humans ; Immunoprecipitation ; Mice ; Neocortex/*cytology ; Neurons/*metabolism ; Organ Specificity ; Polyadenylation/genetics ; RNA, Messenger/genetics/*metabolism ; RNA-Binding Proteins/genetics/*metabolism
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  • 188
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    Nature Publishing Group (NPG)
    Publication Date: 2008-02-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Padian, Kevin -- England -- Nature. 2008 Feb 7;451(7179):632-4. doi: 10.1038/451632a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Paleontology, University of California, Berkeley, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256649" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biology/*history ; Classification ; Ecology/history ; Extinction, Biological ; Female ; Genetic Speciation ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Humans ; Male ; Mating Preference, Animal ; Phylogeny ; Population Dynamics ; *Selection, Genetic ; Sex Characteristics
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  • 189
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    Nature Publishing Group (NPG)
    Publication Date: 2008-02-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armand, M -- Tarascon, J-M -- England -- Nature. 2008 Feb 7;451(7179):652-7. doi: 10.1038/451652a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉LRCS, CNRS UMR-6007, Universite de Picardie Jules Verne, Amiens, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256660" target="_blank"〉PubMed〈/a〉
    Keywords: Air ; Automobiles/history ; Bioelectric Energy Sources/economics/history/trends ; Biomass ; Biomimetics ; Cell Phones/history ; Conservation of Energy Resources/economics/history/*methods/*trends ; Electrochemistry/economics/history ; Electronics/economics/history/trends ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Lithium/chemistry ; Nanotechnology/trends ; Oxygen/chemistry
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  • 190
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    Nature Publishing Group (NPG)
    Publication Date: 2008-08-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Check Hayden, Erika -- England -- Nature. 2008 Jul 31;454(7204):565-9. doi: 10.1038/454565a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18668076" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/adverse effects/economics/*history/immunology ; Animals ; Biomedical Research/*history ; Clinical Trials as Topic/economics/history ; HIV Infections/economics/history/*prevention & control ; History, 20th Century ; History, 21st Century ; Humans
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  • 191
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    Publication Date: 2008-08-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scully, Tony -- England -- Nature. 2008 Aug 21;454(7207):934-6. doi: 10.1038/454934a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18719561" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chile ; Decapodiformes/*cytology/*physiology ; Electrophysiology/*history/trends ; History, 20th Century ; History, 21st Century ; Laboratories ; Neurons/physiology
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  • 192
    Publication Date: 2008-05-23
    Description: Dengue haemorrhagic fever and dengue shock syndrome, the most severe responses to dengue virus (DV) infection, are characterized by plasma leakage (due to increased vascular permeability) and low platelet counts. CLEC5A (C-type lectin domain family 5, member A; also known as myeloid DAP12-associating lectin (MDL-1)) contains a C-type lectin-like fold similar to the natural-killer T-cell C-type lectin domains and associates with a 12-kDa DNAX-activating protein (DAP12) on myeloid cells. Here we show that CLEC5A interacts with the dengue virion directly and thereby brings about DAP12 phosphorylation. The CLEC5A-DV interaction does not result in viral entry but stimulates the release of proinflammatory cytokines. Blockade of CLEC5A-DV interaction suppresses the secretion of proinflammatory cytokines without affecting the release of interferon-alpha, supporting the notion that CLEC5A acts as a signalling receptor for proinflammatory cytokine release. Moreover, anti-CLEC5A monoclonal antibodies inhibit DV-induced plasma leakage, as well as subcutaneous and vital-organ haemorrhaging, and reduce the mortality of DV infection by about 50% in STAT1-deficient mice. Our observation that blockade of CLEC5A-mediated signalling attenuates the production of proinflammatory cytokines by macrophages infected with DV (either alone or complexed with an enhancing antibody) offers a promising strategy for alleviating tissue damage and increasing the survival of patients suffering from dengue haemorrhagic fever and dengue shock syndrome, and possibly even other virus-induced inflammatory diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Szu-Ting -- Lin, Yi-Ling -- Huang, Ming-Ting -- Wu, Ming-Fang -- Cheng, Shih-Chin -- Lei, Huan-Yao -- Lee, Chien-Kuo -- Chiou, Tzyy-Wen -- Wong, Chi-Huey -- Hsieh, Shie-Liang -- GM62116/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 May 29;453(7195):672-6. doi: 10.1038/nature07013. Epub 2008 May 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department and Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18496526" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Cell Adhesion Molecules/genetics/metabolism ; Cell Line ; Dengue Virus/*metabolism/*pathogenicity ; Host-Pathogen Interactions ; Humans ; Interferon-alpha ; Lectins, C-Type/antagonists & inhibitors/genetics/immunology/*metabolism ; Macrophages/virology ; Membrane Proteins/metabolism ; Mice ; Phosphorylation ; Protein Binding ; Receptors, Cell Surface/antagonists & inhibitors/genetics/immunology/*metabolism ; STAT1 Transcription Factor/deficiency/genetics ; Tumor Necrosis Factor-alpha/secretion ; Virus Replication
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 193
    Publication Date: 2008-08-23
    Description: Brown fat can increase energy expenditure and protect against obesity through a specialized program of uncoupled respiration. Here we show by in vivo fate mapping that brown, but not white, fat cells arise from precursors that express Myf5, a gene previously thought to be expressed only in the myogenic lineage. We also demonstrate that the transcriptional regulator PRDM16 (PRD1-BF1-RIZ1 homologous domain containing 16) controls a bidirectional cell fate switch between skeletal myoblasts and brown fat cells. Loss of PRDM16 from brown fat precursors causes a loss of brown fat characteristics and promotes muscle differentiation. Conversely, ectopic expression of PRDM16 in myoblasts induces their differentiation into brown fat cells. PRDM16 stimulates brown adipogenesis by binding to PPAR-gamma (peroxisome-proliferator-activated receptor-gamma) and activating its transcriptional function. Finally, Prdm16-deficient brown fat displays an abnormal morphology, reduced thermogenic gene expression and elevated expression of muscle-specific genes. Taken together, these data indicate that PRDM16 specifies the brown fat lineage from a progenitor that expresses myoblast markers and is not involved in white adipogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583329/" 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/PMC2583329/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seale, Patrick -- Bjork, Bryan -- Yang, Wenli -- Kajimura, Shingo -- Chin, Sherry -- Kuang, Shihuan -- Scime, Anthony -- Devarakonda, Srikripa -- Conroe, Heather M -- Erdjument-Bromage, Hediye -- Tempst, Paul -- Rudnicki, Michael A -- Beier, David R -- Spiegelman, Bruce M -- R01 AR044031/AR/NIAMS NIH HHS/ -- R01 AR044031-11/AR/NIAMS NIH HHS/ -- R37 DK031405/DK/NIDDK NIH HHS/ -- R37 DK031405-27/DK/NIDDK NIH HHS/ -- England -- Nature. 2008 Aug 21;454(7207):961-7. doi: 10.1038/nature07182.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana-Farber Cancer Institute and the Department of Cell Biology, Harvard Medical School, 1 Jimmy Fund Way, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18719582" target="_blank"〉PubMed〈/a〉
    Keywords: Adipocytes, Brown/cytology/*metabolism ; Adipocytes, White/metabolism ; Adipose Tissue, Brown/cytology ; Animals ; COS Cells ; *Cell Differentiation/genetics ; Cell Line ; Cercopithecus aethiops ; DNA-Binding Proteins/genetics/*metabolism ; *Gene Expression Regulation, Developmental ; Male ; Mice ; Muscle Development/genetics ; Muscle, Skeletal/cytology/growth & development/*metabolism ; Myogenic Regulatory Factor 5/genetics ; PPAR gamma/genetics ; Transcription Factors/genetics/*metabolism
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  • 194
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2008-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2008 Jul 31;454(7204):556. doi: 10.1038/454556a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18670399" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Consent Forms/ethics/*standards ; *Embryonic Stem Cells/cytology ; Ethics Committees ; Female ; Humans ; Informed Consent/*ethics/standards ; National Institutes of Health (U.S.) ; Tissue and Organ Procurement/ethics/standards ; United States
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 195
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2008-06-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pearson, Helen -- England -- Nature. 2008 Jun 12;453(7197):846-9. doi: 10.1038/453846a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18548045" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes/economics/*history/*organization & administration ; Biomedical Research/economics/*history/*organization & administration ; Clinical Trials as Topic ; Financial Management ; History, 20th Century ; History, 21st Century ; Humans ; Internationality ; Neoplasms/therapy ; *Technology Transfer
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 196
    Publication Date: 2008-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Houghton, John -- England -- Nature. 2008 Oct 9;455(7214):737-8. doi: 10.1038/455737a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉john.houghton@jri.org.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18843350" target="_blank"〉PubMed〈/a〉
    Keywords: Congresses as Topic/*history ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; *Human Activities ; International Cooperation ; Spain
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  • 197
    Publication Date: 2008-07-25
    Description: Copper is a cofactor for many cellular enzymes and transporters. It can be loaded onto secreted and endomembrane cuproproteins by translocation from the cytosol into membrane-bound organelles by ATP7A or ATP7B transporters, the genes for which are mutated in the copper imbalance syndromes Menkes disease and Wilson disease, respectively. Endomembrane cuproproteins are thought to incorporate copper stably on transit through the trans-Golgi network, in which ATP7A accumulates by dynamic cycling through early endocytic compartments. Here we show that the pigment-cell-specific cuproenzyme tyrosinase acquires copper only transiently and inefficiently within the trans-Golgi network of mouse melanocytes. To catalyse melanin synthesis, tyrosinase is subsequently reloaded with copper within specialized organelles called melanosomes. Copper is supplied to melanosomes by ATP7A, a cohort of which localizes to melanosomes in a biogenesis of lysosome-related organelles complex-1 (BLOC-1)-dependent manner. These results indicate that cell-type-specific localization of a metal transporter is required to sustain metallation of an endomembrane cuproenzyme, providing a mechanism for exquisite spatial control of metalloenzyme activity. Moreover, because BLOC-1 subunits are mutated in subtypes of the genetic disease Hermansky-Pudlak syndrome, these results also show that defects in copper transporter localization contribute to hypopigmentation, and hence perhaps other systemic defects, in Hermansky-Pudlak syndrome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812007/" 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/PMC2812007/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Setty, Subba Rao Gangi -- Tenza, Daniele -- Sviderskaya, Elena V -- Bennett, Dorothy C -- Raposo, Graca -- Marks, Michael S -- 064583/Wellcome Trust/United Kingdom -- R01 EY015625/EY/NEI NIH HHS/ -- R01 EY015625-05/EY/NEI NIH HHS/ -- R21 GM078474/GM/NIGMS NIH HHS/ -- R21 GM078474-02/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Aug 28;454(7208):1142-6. doi: 10.1038/nature07163. Epub 2008 Jul 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18650808" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*metabolism ; Animals ; Carrier Proteins/genetics/metabolism ; Cation Transport Proteins/*metabolism ; Cell Line ; Copper/*metabolism/pharmacology ; Endosomes/metabolism ; Humans ; Melanocytes/cytology/drug effects/enzymology/metabolism ; Melanosomes/drug effects/*enzymology/metabolism ; Mice ; Monophenol Monooxygenase/*metabolism ; Organ Specificity ; Qa-SNARE Proteins/metabolism ; Tyrosine/*metabolism ; trans-Golgi Network/metabolism
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  • 198
    Publication Date: 2008-09-19
    Description: Most organic and organometallic catalysts have been discovered through serendipity or trial and error, rather than by rational design. Computational methods, however, are rapidly becoming a versatile tool for understanding and predicting the roles of such catalysts in asymmetric reactions. Such methods should now be regarded as a first line of attack in the design of catalysts.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717898/" 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/PMC2717898/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Houk, K N -- Cheong, Paul Ha-Yeon -- GM 36700/GM/NIGMS NIH HHS/ -- R01 GM036700/GM/NIGMS NIH HHS/ -- R01 GM036700-23/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Sep 18;455(7211):309-13. doi: 10.1038/nature07368.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, Department of Chemistry and Biochemistry, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA. houk@chem.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18800129" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Chemistry/history/*methods ; *Computational Biology/history ; *Computer Simulation ; Drug Design ; History, 20th Century ; History, 21st Century ; Kinetics ; Molecular Structure
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  • 199
    Publication Date: 2008-10-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pekar, Stephen F -- England -- Nature. 2008 Oct 2;455(7213):602-3. doi: 10.1038/455602a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18833265" target="_blank"〉PubMed〈/a〉
    Keywords: Antarctic Regions ; Atmosphere/chemistry ; Carbon Dioxide/*analysis ; *Cold Climate ; Greenhouse Effect ; History, 21st Century ; History, Ancient ; *Ice Cover
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  • 200
    Publication Date: 2009-06-02
    Description: The generation of induced pluripotent stem (iPS) cells has enabled the derivation of patient-specific pluripotent cells and provided valuable experimental platforms to model human disease. Patient-specific iPS cells are also thought to hold great therapeutic potential, although direct evidence for this is still lacking. Here we show that, on correction of the genetic defect, somatic cells from Fanconi anaemia patients can be reprogrammed to pluripotency to generate patient-specific iPS cells. These cell lines appear indistinguishable from human embryonic stem cells and iPS cells from healthy individuals. Most importantly, we show that corrected Fanconi-anaemia-specific iPS cells can give rise to haematopoietic progenitors of the myeloid and erythroid lineages that are phenotypically normal, that is, disease-free. These data offer proof-of-concept that iPS cell technology can be used for the generation of disease-corrected, patient-specific cells with potential value for cell therapy applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720823/" 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/PMC2720823/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raya, Angel -- Rodriguez-Piza, Ignasi -- Guenechea, Guillermo -- Vassena, Rita -- Navarro, Susana -- Barrero, Maria Jose -- Consiglio, Antonella -- Castella, Maria -- Rio, Paula -- Sleep, Eduard -- Gonzalez, Federico -- Tiscornia, Gustavo -- Garreta, Elena -- Aasen, Trond -- Veiga, Anna -- Verma, Inder M -- Surralles, Jordi -- Bueren, Juan -- Izpisua Belmonte, Juan Carlos -- R01 HL053670/HL/NHLBI NIH HHS/ -- R01 HL053670-14/HL/NHLBI NIH HHS/ -- England -- Nature. 2009 Jul 2;460(7251):53-9. doi: 10.1038/nature08129. Epub 2009 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Regenerative Medicine in Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19483674" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Cellular Reprogramming ; Fanconi Anemia/*pathology/*therapy ; Health ; Hematopoietic Stem Cells/*cytology/metabolism ; Humans ; Pluripotent Stem Cells/*cytology/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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