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Von Der Heide R, Wenger M, Gilmore R, Walsh M, Sullivan B, Bittner J. Developmental changes in the capacity to process faces. J Vis 2010. [DOI: 10.1167/7.9.214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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52
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Gilmore R, Murray-Kolb L, Lee JM. Infants' visual habituation patterns show large within-session variability. J Vis 2010. [DOI: 10.1167/7.9.217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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53
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Von Der Heide R, Wenger M, Gilmore R, Howarth J, Sullivan B, Bittner J. Age-related differences in processing capacity for faces. J Vis 2010. [DOI: 10.1167/8.6.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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54
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Gilmore R, Harmon S, Keane G, Gannon C, O'Donnell JS. Variation in anticoagulant composition regulates differential effects of prothrombin complex concentrates on thrombin generation. J Thromb Haemost 2009; 7:2154-6. [PMID: 19740099 DOI: 10.1111/j.1538-7836.2009.03609.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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55
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Cross DJ, Gilmore R. Representation theory for strange attractors. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:056207. [PMID: 20365060 DOI: 10.1103/physreve.80.056207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 10/12/2009] [Indexed: 05/29/2023]
Abstract
Embeddings are diffeomorphisms between some unseen physical attractor and a reconstructed image. Different embeddings may or may not be equivalent under isotopy. We regard embeddings as representations of the attractor, review the labels required to distinguish inequivalent representations for an important class of dynamical systems, and discuss the systematic ways inequivalent embeddings become equivalent as the embedding dimension increases until there is finally only one "universal" embedding in a suitable dimension.
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Becker T, Bhushan S, Jarasch A, Armache JP, Funes S, Jossinet F, Gumbart J, Mielke T, Berninghausen O, Schulten K, Westhof E, Gilmore R, Mandon EC, Beckmann R. Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science 2009; 326:1369-73. [PMID: 19933108 DOI: 10.1126/science.1178535] [Citation(s) in RCA: 222] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. Although Sec complexes can form oligomers, it has been suggested that a single copy may serve as an active PCC. We determined subnanometer-resolution cryo-electron microscopy structures of eukaryotic ribosome-Sec61 complexes. In combination with biochemical data, we found that in both idle and active states, the Sec complex is not oligomeric and interacts mainly via two cytoplasmic loops with the universal ribosomal adaptor site. In the active state, the ribosomal tunnel and a central pore of the monomeric PCC were occupied by the nascent chain, contacting loop 6 of the Sec complex. This provides a structural basis for the activity of a solitary Sec complex in cotranslational protein translocation.
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Odufuye A, Bellolio M, Jain A, Dhillon R, Manivannan V, Gilmore R, Chandra R, Palamari B, Decker W, Stead L, Yerragondu N. 232: Emergency Department Hyperglycemia as a Predictor of Mortality and Functional Outcome After Intracerebral Hemorrhage by Diabetes Mellitus Status. Ann Emerg Med 2009. [DOI: 10.1016/j.annemergmed.2009.06.261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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58
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Manivannan V, Chandra R, Jain A, Bellolio M, Odufuye A, Dhillon R, Yerragondu N, Gilmore R, Decker W, Stead L. 358: Electrocardiographic Changes in Spontaneous Intracerebral Hemorrhage. Ann Emerg Med 2009. [DOI: 10.1016/j.annemergmed.2009.06.390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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59
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Mandon EC, Trueman SF, Gilmore R. Translocation of proteins through the Sec61 and SecYEG channels. Curr Opin Cell Biol 2009; 21:501-7. [PMID: 19450960 DOI: 10.1016/j.ceb.2009.04.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 04/15/2009] [Accepted: 04/16/2009] [Indexed: 10/20/2022]
Abstract
The Sec61 and SecYEG translocation channels mediate the selective transport of proteins across the endoplasmic reticulum and bacterial inner membrane, respectively. These channels are also responsible for the integration of membrane proteins. To accomplish these two critical events in protein expression, the transport channels undergo conformational changes to permit the export of lumenal domains and the integration of transmembrane spans. Novel insight into how these channels open during protein translocation has been provided by a combination of the analysis of new channel structures, biochemical characterization of translocation intermediates, molecular dynamics simulations, and in vivo and in vitro analysis of structure-based Sec61 and SecY mutants.
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60
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Ruiz-Canada C, Kelleher DJ, Gilmore R. Cotranslational and posttranslational N-glycosylation of polypeptides by distinct mammalian OST isoforms. Cell 2009; 136:272-83. [PMID: 19167329 DOI: 10.1016/j.cell.2008.11.047] [Citation(s) in RCA: 286] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 10/17/2008] [Accepted: 11/25/2008] [Indexed: 02/01/2023]
Abstract
Asparagine-linked glycosylation of polypeptides in the lumen of the endoplasmic reticulum is catalyzed by the hetero-oligomeric oligosaccharyltransferase (OST). OST isoforms with different catalytic subunits (STT3A versus STT3B) and distinct enzymatic properties are coexpressed in mammalian cells. Using siRNA to achieve isoform-specific knockdowns, we show that the OST isoforms cooperate and act sequentially to mediate protein N-glycosylation. The STT3A OST isoform is primarily responsible for cotranslational glycosylation of the nascent polypeptide as it enters the lumen of the endoplasmic reticulum. The STT3B isoform is required for efficient cotranslational glycosylation of an acceptor site adjacent to the N-terminal signal sequence of a secreted protein. Unlike STT3A, STT3B efficiently mediates posttranslational glycosylation of a carboxyl-terminal glycosylation site in an unfolded protein. These distinct and complementary roles for the OST isoforms allow sequential scanning of polypeptides for acceptor sites to insure the maximal efficiency of N-glycosylation.
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61
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Gilmore R, Doyle M, Holden F, White B, O'Donnell J. Activated protein C resistance, factor V Leiden and assessment of thrombotic risk. IRISH MEDICAL JOURNAL 2008; 101:256-257. [PMID: 18990960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Venous thromboembolism comprises deep vein thrombosis (DVT) and pulmonary embolism (PE). Acute venous thromboembolism (VTE) is a serious and potentially fatal disorder which often complicates the course of hospitalized patients, but also affects ambulatory and otherwise healthy people. The annual incidence of venous thromboembolism is 1 to 2 cases per 1000 person and the risk of the disorder rises exponentially with age, from an annual rate of less than 5 per 100,000 children to greater than 400 per 100,000 adults older than 80 years.
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Cunningham MS, Gilmore R, O’Donnell D, O’Donnell JS. Management of refractory venous thrombosis associated with malignancy using a supra-therapeutic enoxaparin regimen. Ir J Med Sci 2008; 178:339-41. [DOI: 10.1007/s11845-008-0200-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 07/14/2008] [Indexed: 11/29/2022]
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Letellier C, Moroz IM, Gilmore R. Comparison of tests for embeddings. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:026203. [PMID: 18850917 DOI: 10.1103/physreve.78.026203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Indexed: 05/26/2023]
Abstract
It is possible to compare results for the classical tests for embeddings of chaotic data with the results of a recently proposed test. The classical tests, which depend on real numbers (fractal dimensions, Lyapunov exponents) averaged over an attractor, are compared with a topological test that depends on integers. The comparison can only be done for mappings into three dimensions. We find that the classical tests fail to predict when a mapping is an embedding and when it is not. We point out the reasons for this failure, which are not restricted to three dimensions.
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Magnelli P, Cipollo JF, Ratner DM, Cui J, Kelleher D, Gilmore R, Costello CE, Robbins PW, Samuelson J. Unique Asn-linked oligosaccharides of the human pathogen Entamoeba histolytica. J Biol Chem 2008; 283:18355-64. [PMID: 18417475 DOI: 10.1074/jbc.m800725200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-Glycans of Entamoeba histolytica, the protist that causes amebic dysentery and liver abscess, are of great interest for multiple reasons. E. histolytica makes an unusual truncated N-glycan precursor (Man(5)GlcNAc(2)), has few nucleotide sugar transporters, and has a surface that is capped by the lectin concanavalin A. Here, biochemical and mass spectrometric methods were used to examine N-glycan biosynthesis and the final N-glycans of E. histolytica with the following conclusions. Unprocessed Man(5)GlcNAc(2), which is the most abundant E. histolytica N-glycan, is aggregated into caps on the surface of E. histolytica by the N-glycan-specific, anti-retroviral lectin cyanovirin-N. Glc(1)Man(5)GlcNAc(2), which is made by a UDP-Glc: glycoprotein glucosyltransferase that is part of a conserved N-glycan-dependent endoplasmic reticulum quality control system for protein folding, is also present in mature N-glycans. A swainsonine-sensitive alpha-mannosidase trims some N-glycans to biantennary Man(3)GlcNAc(2). Complex N-glycans of E. histolytica are made by the addition of alpha1,2-linked Gal to both arms of small oligomannose glycans, and Gal residues are capped by one or more Glc. In summary, E. histolytica N-glycans include unprocessed Man(5)GlcNAc(2), which is a target for cyanovirin-N, as well as unique, complex N-glycans containing Gal and Glc.
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Jiang Y, Cheng Z, Mandon EC, Gilmore R. An interaction between the SRP receptor and the translocon is critical during cotranslational protein translocation. ACTA ACUST UNITED AC 2008; 180:1149-61. [PMID: 18347066 PMCID: PMC2290843 DOI: 10.1083/jcb.200707196] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The signal recognition particle (SRP)-dependent targeting pathway facilitates rapid, efficient delivery of the ribosome-nascent chain complex (RNC) to the protein translocation channel. We test whether the SRP receptor (SR) locates a vacant protein translocation channel by interacting with the yeast Sec61 and Ssh1 translocons. Surprisingly, the slow growth and cotranslational translocation defects caused by deletion of the transmembrane (TM) span of yeast SRbeta (SRbeta-DeltaTM) are exaggerated when the SSH1 gene is disrupted. Disruption of the SBH2 gene, which encodes the beta subunit of the Ssh1p complex, likewise causes a growth defect when combined with SRbeta-DeltaTM. Cotranslational translocation defects in the ssh1DeltaSRbeta-DeltaTM mutant are explained by slow and inefficient in vivo gating of translocons by RNCs. A critical function for translocation channel beta subunits in the SR-channel interaction is supported by the observation that simultaneous deletion of Sbh1p and Sbh2p causes a defect in the cotranslational targeting pathway that is similar to the translocation defect caused by deletion of either subunit of the SR.
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Banerjee S, Vishwanath P, Cui J, Kelleher DJ, Gilmore R, Robbins PW, Samuelson J. The evolution of N-glycan-dependent endoplasmic reticulum quality control factors for glycoprotein folding and degradation. Proc Natl Acad Sci U S A 2007; 104:11676-81. [PMID: 17606910 PMCID: PMC1905923 DOI: 10.1073/pnas.0704862104] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Asn-linked glycans (N-glycans) play important roles in the quality control (QC) of glycoprotein folding in the endoplasmic reticulum (ER) lumen and in ER-associated degradation (ERAD) of proteins by cytosolic proteasomes. A UDP-Glc:glycoprotein glucosyltransferase glucosylates N-glycans of misfolded proteins, which are then bound and refolded by calreticulin and/or calnexin in association with a protein disulfide isomerase. Alternatively, an alpha-1,2-mannosidase (Mns1) and mannosidase-like proteins (ER degradation-enhancing alpha-mannosidase-like proteins 1, 2, and 3) are part of a process that results in the dislocation of misfolded glycoproteins into the cytosol, where proteins are degraded in the proteasome. Recently we found that numerous protists and fungi contain 0-11 sugars in their N-glycan precursors versus 14 sugars in those of animals, plants, fungi, and Dictyostelium. Our goal here was to determine what effect N-glycan precursor diversity has on N-glycan-dependent QC systems of glycoprotein folding and ERAD. N-glycan-dependent QC of folding (UDP-Glc:glycoprotein glucosyltransferase, calreticulin, and/or calnexin) was present and active in some but not all protists containing at least five mannose residues in their N-glycans and was absent in protists lacking Man. In contrast, N-glycan-dependent ERAD appeared to be absent from the majority of protists. However, Trypanosoma and Trichomonas genomes predicted ER degradation-enhancing alpha-mannosidase-like protein and Mns1 orthologs, respectively, each of which had alpha-mannosidase activity in vitro. Phylogenetic analyses suggested that the diversity of N-glycan-dependent QC of glycoprotein folding (and possibly that of ERAD) was best explained by secondary loss. We conclude that N-glycan precursor length has profound effects on N-glycan-dependent QC of glycoprotein folding and ERAD.
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Abstract
Many membrane proteins are inserted into cellular membranes via a carboxy-terminal tail-anchor segment, but the mechanism of insertion is poorly understood. In this issue of Cell, Stefanovic and Hegde (2007) report the identification and initial characterization of a soluble ATP-dependent receptor for the insertion of newly synthesized tail-anchored membrane proteins.
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Bellolio MF, Vaidyanathan L, Gilmore R, Kashyap R, Enduri S, Decker WW, Stead L. Ischemic Stroke in Young Adults: Etiology and Outcome. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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69
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Gilmore R, Bellolio F, Mishra S, Bhagra A, Decker WW, Stead L. Defining a Threshold for Hyperglycemia-related Mortality Risk Following Acute Ischemic Stroke. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.1139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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70
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Dajani N, Bhagra A, DeJesus R, Enduri S, Bellolio MF, Gilmore R, Decker WW, Stead L. Volume of Infarct on Magnetic Resonance Diffusion Weighted Imaging is Correlated to Stroke Etiology. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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71
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Bellolio MF, Vaidyanathan L, Enduri S, Kayshap R, Gilmore R, Bhagra A, Decker WW, Stead LG. Subsequent Vascular Event Following an Acute Ischemic Stroke. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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72
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Mishra S, Gilmore R, Bellolio MF, Bhagra A, Enduri S, Decker WW, Stead L. Does Initial Emergency Department Hyperglycemia Simply Represent Underlying Undiagnosed Diabetes in Patients Presenting with Acute Ischemic Stroke. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Hoff A, Yassa A, Bellolio MF, Vaidyanathan L, Gilmore R, Decker WW, Stead L. Adherence to Inpatient JCAHO Prophylaxis Measures after Acute Ischemic Stroke Results in Better Functional Outcome. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Nash D, Vaidyanathan L, Bellolio F, Enduri S, Mishra S, Gilmore R, Decker WW, Stead L. Hemoglobin: A Predictor of Functional Outcome Following an Acute Ischemic Stroke. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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75
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Bellolio M, Bhagra A, Gilmore R, Enduri S, Decker WW, Jaffe A, Brown R, Stead L. A Risk Stratification Tool in Patients Presenting with Transient Ischemic Attack for Subsequent Acute Coronary Syndrome: The Thrombolysis in Myocardial Infarction Score. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.1049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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