item: #1 of 43
id: cord-008613-tysyq6o4
author: Thomas, Sheila M.
title: Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5
date: 1988-09-09
words: 8438
flesch: 43
summary: The SV5 P gene has been shown to encode both the P protein (Mr = 44,000), and protein V (Mr = 24,000) by the arrest of translation in vitro of both P and V using a cDNA clone derived from SV5-specific mRNAs (Paterson et al., 1984) . and is part of the transcriptase complex (Buetti and Choppin, 1977) , while protein V is found in infected cells and is of unknown function (Peluso et al., 1977) .
keywords: amino; cdna; dna; et al; figure; frame; gene; mrna; nucleotides; protein; reading; region; residues; sequence; sv5; virus
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item: #2 of 43
id: cord-252433-0e9lonq4
author: Cullen, Bryan R.
title: Viral RNAs: Lessons from the Enemy
date: 2009-02-20
words: 3564
flesch: 48
summary: Although IRES elements were first discovered in RNA viruses, a subset of cellular mRNAs are now known to also contain IRESs. The RRE contains a single, high-affinity Rev-binding site and also functions as a scaffold for the multimerization of Rev on viral mRNAs.
keywords: cells; cellular; mrnas; rev; translation; viruses
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item: #3 of 43
id: cord-253259-hmn7mg8j
author: Shaw, A. L.
title: Three-dimensional visualization of the rotavirus hemagglutinin structure
date: 1993-08-27
words: 5997
flesch: 47
summary: Therefore, the most likely explanation for the loss of VP4 spikes from R-004 particles suggested by these results is that the heterologous VP4 becomes destabilized and falls off. One pending question is, at what stage does VP4 assembly take place, before or after the assembly of VP7?
keywords: et al; map; particles; protein; r-004; rotavirus; shell; spike; structure; vp4; vp7
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item: #4 of 43
id: cord-253302-keh7s758
author: Gong, Danyang
title: DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV
date: 2019-09-05
words: 11265
flesch: 40
summary: Although the portal vertex lacks true 5-fold symmetry, this classification with 5-fold symmetry imposed successfully distinguished between penton and portal vertices. Upon removing all redundant particles, 39,773 vertex sub-particles remained and were deemed sub-particles of the portal vertex, henceforth referred to as 'portal vertex sub-particles.'
keywords: binding; capsid; catc; density; dna; et al; figure; kshv; particles; penton; porf19; porf32; portal; reconstruction; sub; symmetry; vertex; vertex sub; vertices
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item: #5 of 43
id: cord-255856-0xqllbzz
author: Florman, Harvey M.
title: O-linked oligosaccharides of mouse egg ZP3 account for its sperm receptor activity
date: 1985-05-31
words: 8987
flesch: 45
summary: A specific size class of O-linked oligosaccharides, recovered following mild alkaline hydrolysis and reduction of ZP3, is shown to possess sperm receptor activity and to bind to sperm. When constituents of mouse egg zonae pellucidae were assayed individually for sperm receptor activity in vitro, ZP3 alone.was found to be functional Wassarman, 1980a, 1983; Wassarman and Bleil, 1982) .
keywords: activity; egg; et al; figure; oligosaccharides; pellucidae; receptor; receptor activity; sperm; sperm receptor; wassarman; zonae; zp2; zp3
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item: #6 of 43
id: cord-256156-mywhe6w9
author: Clausen, Thomas Mandel
title: SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2
date: 2020-09-14
words: 8996
flesch: 49
summary: To explore if HS, ACE2 and spike interact at the cell surface, we investigated the impact of ACE2 expression on S protein cell binding. Bound protein was washed with buffer and eluted with 0.2 M imidazole in washing buffer.
keywords: ace2; binding; cells; cov-2; et al; fig; heparin; human; infection; protein; r n; rbd; sars; site; spike; sulfate; surface; virus
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item: #7 of 43
id: cord-258372-w0j0n8mn
author: Gibson, Erin M.
title: How Support of Early Career Researchers Can Reset Science in the Post-COVID19 World
date: 2020-06-12
words: 3606
flesch: 37
summary: Even a short hiring freeze could have devastating effects on the ability of early career faculty labs to succeed. This pandemic has particularly impacted senior postdoctoral fellows seeking academic faculty positions and early career faculty seeking to establish themselves as independent investigators.
keywords: career; covid19; crisis; faculty; funding; researchers; science; scientists; universities
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item: #8 of 43
id: cord-259681-k9cnikqk
author: Johnson, David C.
title: O-linked oligosaccharides are acquired by herpes simplex virus glycoproteins in the Golgi apparatus
date: 1983-03-31
words: 5754
flesch: 37
summary: Other posttranslational modifications of HSVl glycoproteins (designated gB, gC, gD and gE) were related temporally to the discrete shifts in electrophoretic mobilities that signal acquisition of the O-linked oligosaccharides. HSVl glycoproteins were labeled with 35S-methionine in a pulse-chase experiment, and the mature and immature forms of the glycoproteins were precipitated with monoclonal antibodies prior to treatment with GalNAc oligosaccharidase.
keywords: cells; electrophoretic; forms; glycoproteins; hsvl; mobilities; oligosaccharides
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item: #9 of 43
id: cord-263468-996kl9jz
author: Cattaneo, Roberto
title: Biased hypermutation and other genetic changes in defective measles viruses in human brain infections
date: 1988-10-21
words: 7647
flesch: 41
summary: Expression of defective measles virus genes in brain tissues of patients with subacute sclerosing panencephalitis Restriction of measles virus gene expression in measles inclusion body encephalitis The transcription complex of vesicular stomatitis virus Matrix genes of measles virus and of canine distemper virus: cloning, nucleotide sequences, and deduced amino acid sequences Identification of a nonproductive, cell-associated form of measles virus by its resistance to inhibition by recombinant human interferon Defective translation of measles virus matrix protein in subacute sclerosing panencephalitis Accumulated measles virus mutations in a case of subacute sclerosing panencephalitis: interrupted matrix protein reading frame and transcription alteration Altered transcription from a defective measles virus genome derived from a diseased human brain Altered ratios of measles virus transcripts in diseased human brains Multiple viral mutations rather than host factors cause defective measles virus gene expression in a subacute scierosing panencephalitis ceil line Fluorographic detection of radioactivity in polyacrylamide gels with the water-soluble fluor, sodium salycilate Ribosomal initiation from an ACG codon in the Sendai virus P/C mRNA Nucleotide sequence of the gene encoding the matrix protein of a recent measles virus isolate Nucleotide sequence heterogeneity of an RNA phage population Measles virus nucleic acid sequences in human brain Studies on an attenuated measles virus vaccine: techniques for assay of effects of vaccination Extensive editing of cytochrome c oxidase From the sequence analysis presented in Figure 3 , it is immediately evident that mutations in this gene are more abundant than in other M genes and that U to C transitions account for a large majority of mutations.
keywords: brain; case; et al; figure; gene; measles; mutations; protein; rna; sequence; virus; viruses
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item: #10 of 43
id: cord-266480-u8o4eitu
author: Colubri, Andrés
title: Preventing outbreaks through interactive, experiential real-life simulations
date: 2020-09-02
words: 3169
flesch: 41
summary: This data reflects the spread of the virtual pathogen among the participants with a granularity that is nearly impossible to replicate in the real world--and it can be used like real outbreak data for epidemiological modeling and visualization. OO simulations at SMA.
keywords: data; health; outbreak; pandemic; simulation; students; transmission
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item: #11 of 43
id: cord-267046-ewnjgps5
author: Strauss, James H
title: Virus Evolution: How Does an Enveloped Virus Make a Regular Structure?
date: 2001-04-06
words: 311
flesch: 54
summary: (2001) shows that the bulk of E1 does not contribute rather than M might more resemble the alphavirus structo the outer portions of the spike but, instead, forms a ture, with short projecting spikes, but cleavage to M layer closely apposed to the lipid bilayer, analogous to removes the spikes. They also show that The Evolution of Enveloped Viruses E2 projects upward to the full-length of the spike.
keywords: virus
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item: #12 of 43
id: cord-269023-g21a9ik2
author: Mukherjee, Siddhartha
title: Before Virus, After Virus: A Reckoning
date: 2020-10-15
words: 5867
flesch: 54
summary: By the mid-1960s, Miller had realized that the thymus was the site of maturation for a different kind of immune cell-not a B cell, but a T cell, from the word 'T-hymus' (Max Cooper, working independently, had also established that two kinds of lymphocytes existed, and that the thymus was the maturation site for T cells). He had, in essence, observed the first steps in inflammation and immune response: the recruitment of immune cells to the site of injury.
keywords: antibodies; antibody; antigen; cells; covid-19; disease; immunity; infection; response; smallpox; t cells; virus
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item: #13 of 43
id: cord-270082-byxd4o4m
author: Doheny, Kimberly Floy
title: Identification of essential components of the S. cerevisiae kinetochore
date: 1993-05-21
words: 9945
flesch: 50
summary: In control experiments, we examined the stability of dicentric chromosome fragments containing either a nearly wild-type (ACDEI) or a highly defective (CDEIII-15C) secondary conditional CfN ( Figures 3A and 38 ). Yeast Strains and Media The c/f and wild-type parental strains containing chromosome fragments that can be monitored by a visual assay have been previously described (Spencer et al., 1990; Shero et al., 1991) .
keywords: cell; cen; centromere; cerevisiae; chromosome; complex; ctf13; dna; et al; figure; fragment; kinetochore; mutants; protein; sequence; strains; temperature; test; type
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item: #14 of 43
id: cord-271032-imc6woht
author: Schulte-Schrepping, Jonas
title: Severe COVID-19 is marked by a dysregulated myeloid cell compartment
date: 2020-08-05
words: 9745
flesch: 42
summary: Interestingly, immature cell clusters in severe COVID-19 showed signs of recent activation 390 like upregulation of CD64 (Mortaz et al., 2018) , RANK and RANKL (Riegel et al., 2012) , as 391 well as reduced CD62L expression (Mortaz et al., 2018) . Plotting cell cluster-specific surface marker expression onto 384 the UMAPs (Fig. 6C ) as well as statistical analyses of cell cluster distribution and surface 385 marker expression among different patient groups supported these observations (Fig. 386 6D+E) .
keywords: analysis; cell; cluster; cohort; covid-19; data; disease; expression; fig; genes; hla; marker; monocytes; neutrophils; patients; pbmc; samples; scrna; seq; table
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item: #15 of 43
id: cord-272520-7mci4mip
author: Goepfert, P. A.
title: Identification of an ER retrieval signal in a retroviral glycoprotein
date: 1995-08-25
words: 1213
flesch: 40
summary: Fourth, since tissue cultures infected with foamy viruses form syncytia and since virus budding from the plasma membrane occurs in some cell types (Gelderblom and Frank, 1987) , foamy virus glycoproteins must also escape through the Golgi stacks by the default secretory pathway. The conservation of this wellcharacterized ER localization signal within the glycoproteins of foamy viruses of human, chimpanzee, rhesus macaque, African green monkey, or bovine origin suggested that it fulfills a critical function in foamy virus biology.
keywords: foamy; virus
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item: #16 of 43
id: cord-279463-bli8hwda
author: Lipp, Joachim
title: The membrane-spanning segment of invariant chain (Iγ) contains a potentially cleavable signal sequence
date: 1986-09-26
words: 6280
flesch: 59
summary: Membrane insertion might occur in a loop-like fashion as this scheme can most easily explain how the different membrane topologies of membrane proteins are achieved (Engelman and Steitz, 1981) . Membrane proteins are also inserted into the ER membrane by an SRP-mediated mechanism (Anderson et al., 1983; Rottier et al., 1985; Spiess and Lodish, 1986; Lipp and Dobberstein, 1986) .
keywords: amino; insertion; membrane; protein; residues; segment; sequence; signal; terminal
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item: #17 of 43
id: cord-284609-1q75zw6b
author: King, Andrew M.Q.
title: Recombination in RNA
date: 1982-07-31
words: 4069
flesch: 45
summary: RNAase T1 fingerprints of virus RNA, prepared from representatives of each recombinant type, confirmed the approximate crossover sites that had been deduced from the inheritance of proteins. RNAase Tl fingerprints of virus RNA, prepared from representatives of each recombinant type, confirmed the approximate crossover sites that had been deduced from the inheritance of proteins.
keywords: parent; polypeptides; recombination; ret; rna; temperature; virus
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item: #18 of 43
id: cord-284944-hcgfe9wv
author: Silvin, Aymeric
title: Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19
date: 2020-08-05
words: 10810
flesch: 35
summary: Severe patients exhibited an expansion in the proportion of circulating neutrophils within the peripheral blood cell population (Figure 1E) , which was associated with an increase in their absolute number (Table S2) , as already reported . Focusing on neutrophil subsets, we noticed a slight increase in the fraction of CD10 Low CD101 + neutrophils in mild COVID-19 patients (Figure 1F) , whereas the fraction of CD10 Low CD101neutrophils was remarkably amplified in severe patients, suggesting an accumulation of immature subsets of neutrophils (Ng et al., 2019) in the peripheral blood of these patients ( Figure 1G and S1C-E).
keywords: analysis; blood; calprotectin; cd14; cd16; cells; controls; covid-19; covid-19 patients; disease; et al; expression; figure; fraction; hla; levels; low; monocytes; neutrophils; patients; plasma
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item: #19 of 43
id: cord-287349-1zcq7kzx
author: Chen, James
title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex
date: 2020-07-28
words: 2970
flesch: 27
summary: In Family Coronaviridae Crystal structure of Middle East respiratory syndrome coronavirus helicase From SARS to MERS: 10 years of research on highly 1162 pathogenic human coronaviruses Structure 1165 of replicating SARS-CoV-2 polymerase Dali server update Human Coronavirus 229E Nonstructural Protein 13: 1170 Characterization of Duplex-Unwinding, Nucleoside Triphosphatase, and RNA 5′-Triphosphatase Enzymatic Activities Associated with Severe Acute Respiratory Syndrome Coronavirus Helicase Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus 1179 Nsp13 upon ATP hydrolysis Structural basis of transcription arrest by coliphage HK022 nun in an 1183 DnaB Drives DNA Branch Migration and Dislodges 1186 Structure of the SARS-CoV nsp12 polymerase bound 1192 to nsp7 and nsp8 co-factors Transcriptional arrest: Escherichia coli RNA 1195 polymerase translocates backward, leaving the 3' end of the RNA intact and extruded RNA polymerase switches between inactivated and 1200 activated states By translocating back and forth along the DNA and the RNA Molecular Evolution of Multisubunit RNA Polymerases: 1204 Structural Analysis Cooperative 1207 translocation enhances the unwinding of duplex DNA by SARS coronavirus helicase nsP13 Discovery of an essential nucleotidylating activity associated with a newly delineated conserved 1213 domain in the RNA polymerase-containing protein of all nidoviruses What we know but 1217 do not understand about nidovirus helicases The EMBL-EBI search and sequence analysis tools APIs in 1221 2019 Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to 1229 polydisperse ensembles Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in 1233 coronavirus RNA synthesis Collaboration gets the most out of software Discovery of the first insect nidovirus, a missing evolutionary 1240 link in the emergence of the largest RNA virus genomes Cell the register of transcription by preventing backtracking of RNA polymerase Structure 1252 and function of the transcription elongation factor GreB bound to bacterial RNA polymerase Sequence 1256 requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA 1257 synthesis Analyzing resistance to 1264 design selective chemical inhibitors for AAA proteins cryoSPARC: algorithms for 1267 rapid unsupervised cryo-EM structure determination High-Throughput Deconvolution of Native Mass Spectra A 1274 planarian nidovirus expands the limits of RNA genome size Mechanistic basis of 1277 5'-3' translocation in SF1B helicases Advances in Experimental Medicine and Biology RELION: implementation of a Bayesian approach to cryo-EM structure 1283 determination Sequence logos: a new way to display consensus 1286 sequences Biochemical Characterization 1289 of the Equine Arteritis Virus Helicase Suggests a Close Functional The human coronavirus 229E superfamily 1 helicase has RNA and DNA duplex-unwinding activities with 5′-to-3′ polarity Remdesivir and SARS-CoV-2: structural requirements at 1302 both nsp12 RdRp and nsp14 Exonuclease active-sites Structure and Mechanism of 1305 Helicases and Nucleic Acid Translocases Coronaviruses lacking exoribonuclease 1308 activity are susceptible to lethal mutagenesis: evidence for proofreading and potential 1309 therapeutics Thinking Outside the Triangle: Replication Coronavirus RNA Synthesis and Processing Continuous and Discontinuous RNA 1318 Synthesis in Coronaviruses Protein AMPylation by an Evolutionarily Conserved 1322 One severe acute respiratory syndrome 1326 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities The Severe Acute Respiratory Syndrome (SARS) In this case backtracking is energetically disfavored since it only 291 shortens the product RNA duplex without recovering duplex nucleic acids somewhere else.
keywords: coronavirus; figure; helicase; nsp13; polymerase; rdrp; rna; sars; structural; transcription
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item: #20 of 43
id: cord-287815-alv30uk5
author: Mellman, Ira
title: The Golgi complex: In vitro veritas?
date: 1992-03-06
words: 9337
flesch: 37
summary: Nevertheless, the observed conservation of Golgi proteins between S. cerevisiae and mammals is most encouraging for our ability to confirm in living cells the function of components identified in vitro. I. Stereological studies Exit of newly synthesized membrane proteins from the trans cisterna of the Golgi complex to the plasma membrane The dynamic nature of the Golgi complex Isolation of a functional vesicular intermediate that mediates ER to Golgi transport in yeast Membrane traffic in endocytosis: insights from cell-free assays Reconstitution of steps in the constitutive secretorypathwayin permeabilized cells Three-dimensional architecture of the cortical region of the Golgi-apparatus in rat spermatids Reclustering of scattered Golgi elementsoccurs along microtubules Movement of internalized ligand-receptor complexes along a continuous endosomal reticulum Derived protein sequence, oligosaccharides, and membrane insertion of the 120 kD lysosomal membrane protein (Igpl20): identification of a highly conserved family of lysosomal membrane glycoproteins A recycling pathway between the endoplasmic reticulum and the Golgi apparatus for retention of unassembled MHC class I molecules Basolateral sorting in MDCKcells requiresadistinct cytoplasmicdomain determinant Selective inhibition of transcytosis by brefeldin A in MDCK cells Protein sulfation on tyrosine Biosynthetic protein transport in the secretory pathway Localization of mitochondria in living cells with rhodamine 123 Fluoride is not an activator of the smaller (20-25 kDa) GTP-binding proteins The rate of bulk flow from the Golgi to the plasma membrane Pathways of protein secretion in eukaryotes Elrefeldin A: cytosolic coat protein assembly, organelle structure, and membrane traffic Assembly of asparagine-linked a~ligosaccharides The biogenesis of lysosomes Dynamic behavior of endoplasmic reticulum in living cells The neuronal endomembranesystem Microtubule-dependent retrograde transport of proteins into the ER in the presence of brefeldin A suggests an ER recycling pathway Brefeldin A's effects on endosomes, lysosomes, and the TGN suggest a general mechanism for regulating organelle structure and membrane traffic Transport of secretory and membrane glycoproteins from the rough endoplasmic reticulum to the Golgi Hepatoma secretory proteins migrate from the rough endoplasmic reticulum to Golgi at characteristic rates Evidence for a molecular distinction between Golgi and cell surface forms of Immunocytochemical analysis of the transfer from the intermediate compartment to the Golgi complex of VSV G protein The El glycoprotein of an avian coronavirus is targeted to the cis Golgi complex Purification of a novel class of coated vesicles mediating biosynthetic protein transport through the Golgi stack Three dimensional structure of endosomes in BHK-21 cells Scale formation rn algae Novel blockade by brefeldin A of intracellular transport of secretory transport of secretory proteins in cultured rat hepatocytes Sequences within and adjacent to the transmembrane segment of a-2,6sialyltransferase specify Golgi retention Recycling glycoproteins do not return to the cis-Golgi The membrane spanning domain of 8-l ,4-galactosyltransferase specifies rrans Golgi localization A new type of coated vesicular carrier that appears not to contain clathrin: its possible role in protein transport within the Golgi stack Dissection of a single round of vesicular transport: sequential intermediates for intercisternal movement in the Golgi stack Brefeldin A, a drug that blocks secretion, prevents the assembly of non-clathrin-coated buds on Golgi cisternae Molecular trapping of a fluorescent ceramide analogue at the Golgi apparatus of fixed cells: interaction with endogenous lipids provides a trans-Golgi marker for both light and electron microscopy A novel fluorescent ceramide analog for studying membrane traffic in animal cells: accumulation at the Golgi apparatus results in altered spectral properties of the sphingolipid precursor Intracellular aspects of the process of protein secretion Clathnn, adaptors, and sorting Evidence that luminal ER proteins are sorted from secreted proteins in a post-ER compartment Control of protein exit from the endoplasmic reticulum Recycling of proterns between the endoplasmic reticulum and Golgi complex Brosyntheticprotetn transport and sorting by the endoplasmic reticulum and Golgi Three-dimensional electron microscopy: StructureoftheGolgr apparatus Perturbation of the morphology of the trans-Golgi network following brefeldin A treatment: redistribution of aTGN-specific integral membrane protein Distinct biochemical requirements for the budding, targeting, and fusion of ER-derived transport vesicles Post-translational protein modification in the endoplasmic reticulum.
keywords: cells; cgn; cisternae; compartment; complex; enzymes; et al; function; glycosylation; golgi; membrane; protein; tgn; transport; vesicles; vitro
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item: #21 of 43
id: cord-289765-79cmcvfi
author: Morrison, Mike
title: How to Boost the Impact of Scientific Conferences
date: 2020-09-03
words: 2966
flesch: 50
summary: key: cord-289765-79cmcvfi authors: Morrison, Mike; Merlo, Kelsey; Woessner, Zach title: How to Boost the Impact of Scientific Conferences date: 2020-09-03 journal: Cell DOI: 10.1016/j.cell.2020.07.029 sha: doc_id: 289765 cord_uid: 79cmcvfi We can maximize the impact of scientific conferences by uploading all conference presentations, posters, and abstracts to highly trafficked public repositories for each content type. Figure 1 places the 'classic 3' scientific conference content types-presentations, posters, and conference abstracts-on a continuum ranging from 'easy to produce' to 'hard to produce' and from 'small impact' (on just a few people) to 'big impact' (reaching tens or hundreds of thousands of people).
keywords: conference; impact; media; science; scientists; talks
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item: #22 of 43
id: cord-291790-z5rwznmv
author: Li, Qianqian
title: The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity
date: 2020-07-17
words: 4910
flesch: 56
summary: 122 As expected, the two types of pseudotyped viruses are different in the infection efficiency in the 123 26 cell lines ( Figure 2) . The last column was employed as the 476 cells control without pseudotyped virus.
keywords: antibodies; cov-2; glycosylation; infectivity; mabs; mutants; sars; sensitivity; variants; virus
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item: #23 of 43
id: cord-294429-isivkz8b
author: Grifoni, Alba
title: Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals
date: 2020-05-20
words: 10283
flesch: 47
summary: CD4+ T cell responses to spike, the main target of most vaccine efforts, were robust and correlated with the magnitude of the anti-SARS-CoV-2 IgG and IgA titers. CD4 + T cell responses to the remainder of the SARS-CoV-2 orfeome were also detected in 100% of COVID-19 cases (p < 0.0079 vs. unexposed donors non-spike MP, Fig.
keywords: cases; cd4; cd8; cell; cell responses; cov-2; covid-19; disease; donors; et al; fig; human; responses; sars; specific; spike; t cell
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item: #24 of 43
id: cord-295062-8rl4kswe
author: Marsh, Mark
title: Virus Entry: Open Sesame
date: 2006-02-24
words: 8517
flesch: 34
summary: Microbiol Human immunodeficiency virus type 1 spinoculation enhances infection through virus binding Role of lipid rafts in virus replication Ultrastructural localization of gangliosides; GM1 is concentrated in caveolae Lipid rafts and caveolae as portals for endocytosis: new insights and common mechanisms Caveolar endocytosis of simian virus 40 reveals a new two-step vesicular-transport pathway to the ER Local actin polymerization and dynamin recruitment in SV40-induced internalization of caveolae Caveolinstabilized membrane domains as multifunctional transport and sorting devices in endocytic membrane traffic Genome-wide analysis of human kinases in clathrin-and caveolae/raft-mediated endocytosis Echovirus 1 endocytosis into caveosomes requires lipid rafts, dynamin II, and signaling events Viral entry, lipid rafts and caveosomes The neutral glycosphingolipid globotriaosylceramide promotes fusion mediated by a CD4-dependent CXCR4-utilizing HIV type 1 envelope glycoprotein Adaptable adaptors for coated vesicles Picornavirus-receptor interactions Assembly of endocytic machinery around individual influenza viruses during viral entry Viral RNA replication in association with cellular membranes Lv2, a novel postentry restriction, is mediated by both capsid and envelope Selective stimulation of caveolar endocytosis by glycosphingolipids and cholesterol Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein Interaction with decay-accelerating factor facilitates coxsackievirus B infection of polarized epithelial cells Influenza virus can enter and infect cells in the absence of clathrin-mediated endocytosis Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin How viruses enter animal cells Ganglioside-dependent cell attachment and endocytosis of murine polyomavirus-like particles Vaccinia virus motility Major histocompatibility complex class I molecules mediate association of SV40 with caveolae High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding The structure of simian virus 40 refined at 3.1 A resolution Virus maturation: dynamics and mechanism of a stabilizing structural transition that leads to infectivity Structural basis of nonenveloped virus cell entry The cytoplasmic body component TRIM5al-pha restricts HIV-1 infection in Old World monkeys Assembly and trafficking of caveolar domains in the cell: caveolae as stable, cargo-triggered, vesicular transporters Cellular RNA-editing enzymes can be packaged into virus particles and can introduce mutations in the viral genome during the reverse-transcription event that occurs shortly after virus entry.
keywords: cell; clathrin; endocytosis; entry; et al; infection; membrane; particles; pathways; penetration; proteins; receptors; surface; virus; viruses
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item: #25 of 43
id: cord-295894-us5x1jtg
author: Li, Bing
title: SnapShot: FABP Functions
date: 2020-08-20
words: 1253
flesch: 30
summary: In summary, accumulating evidence has demonstrated that FABP members not only exert overlapping functions in lipid binding and transport but exhibit unique characteristics in specific cells and tissues as well. Because of differences in their amino-acid sequences, FABP family members possess different lipid ligand-binding specificity and affinity.
keywords: fabp; lipid; macrophages
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item: #26 of 43
id: cord-301997-63160t7f
author: Schwer, Beate
title: Discontinuous transcription or RNA processing of vaccinia virus late messengers results in a 5′ poly(A) leader
date: 1987-07-17
words: 4746
flesch: 48
summary: The reason for this is that primer elongation experiments are complicated by a high degree of complementarity in late vaccinia RNA transcripts, both DNA strands are transcribed, genes can be overlapping, and there is readthrough of the RNA polymerase (Plucienniczak et al., 1985; Smith et al., 1984) . This paper concerns the study of the structure of the 5' terminus of vaccinia virus late RNA transcripts.
keywords: cdna; et al; late; promoter; rna; transcripts; vaccinia
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item: #27 of 43
id: cord-302020-ypsh3rjv
author: Kim, Dongwan
title: The Architecture of SARS-CoV-2 Transcriptome
date: 2020-04-23
words: 6130
flesch: 51
summary: Viral RNA modification was first described more than 40 years ago (Gokhale and Horner, 2017) . It was recently shown that HCoV-229E nsp8 has an adenylyltransferase activity, which may extend poly(A) tail of viral RNA (Tvarogová et al., 2019) .
keywords: cov-2; drs; figure; genome; length; modification; poly(a; reads; rna; rnas; sars; sequencing; viral
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item: #28 of 43
id: cord-305173-95o5z685
author: Martin, Thomas R.
title: A TRIFfic Perspective on Acute Lung Injury
date: 2008-04-18
words: 1843
flesch: 34
summary: Activation of innate immune pathways combined with the physical stresses created by mechanical ventilation cause a synergistic increase in lung injury, but the mechanisms underlying ALI are not clear (Dos Santos and Slutsky, 2006) . In order to identify susceptibility factors for lung injury, Imai and colleagues screened several strains of mice using a A TRIffic Perspective on Acute Lung Injury Thomas R. Martin 1, * and Mark M. Wurfel 1 simple model of lung injury, intratracheal instillation of 1.5 N hydrochloric acid (HCl), which approximates severe gastric acid aspiration.
keywords: injury; lung; tlr4
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item: #29 of 43
id: cord-305290-xnjwv0d7
author: Atkins, John F.
title: Ribosome gymnastics—Degree of difficulty 9.5, style 10.0
date: 1990-08-10
words: 8002
flesch: 57
summary: Coronaviruses use a combination of the above slippery sequences, namely U UUA AAC, for their frameshifting (Brierley et al., 1987 (Brierley et al., , 1989 Bredenbeek et al., 1990) . The involvement of a pseudoknot has been inferred for another coronavirus, mouse hepatitis virus (Bredenbeek et al., 1990) for some, but not all, retroviral examples (Brierley et al., 1989; ten Dam et al., 1990) and in a variety of other instances (ten Dam et al., 1990) .
keywords: codon; et al; frameshifting; gene; level; mrna; protein; readthrough; ribosomes; sequence; site; stop; trna; uga; virus
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item: #30 of 43
id: cord-307021-uppekume
author: Crooke, Elliott
title: ProOmpA is stabilized for membrane translocation by either purified E. coli trigger factor or canine signal recognition particle
date: 1988-09-23
words: 5580
flesch: 55
summary: Gel filtration analysis shows that the prominent polypeptide ( Figure 4C ) and trigger factor activity co-elute with an apparent size of 73,000 daltons ( Figure 5 ), indicating that trigger factor is a monomeric protein. Each translocation reaction contained 1.5 ug of membrane protein.
keywords: assembly; buffer; factor; membrane; proompa; protein; srp; translocation; trigger
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item: #31 of 43
id: cord-312115-foy3dsq4
author: Sekine, Takuya
title: Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19
date: 2020-08-14
words: 4930
flesch: 38
summary: Higher frequencies of T cell responses were also found in exposed seronegative family members compared to unexposed donors ( Figure S5E ). In contrast, memory T cell responses can persist for many years (Le Bert et al., 2020; Tang et al., 2011; Yang et al., 2006) and, in mice, protect against lethal challenge with SARS-CoV-1 (Channappanavar et al., 2014) .
keywords: cells; cov-2; covid-19; et al; figure; individuals; memory; responses; sars
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item: #32 of 43
id: cord-318276-so5jooj0
author: Bertholet, Christine
title: Vaccinia virus produces late mRNAs by discontinuous synthesis
date: 1987-07-17
words: 6229
flesch: 53
summary: Another interesting question is whether the leader RNA sequences are also translated. Synthesis of polyriboadenylic acid How do eucaryotic ribosomes select initiation regions in messenger RNA? Bifunctional messenger RNAs in eukaryotes The role of RNA priming rn viral and trypanosomal mRNA synthesis Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus, a cytoplasmic RNA virus Arrangement of late mRNAs transcribed from a 7.1-kilobase EcoRl vaccinia virus DNA fragment Molecular Cloning: A Laboratory Manual Control of induced thymidine kinase activity rn the poxvirus infected cell The induction and repression of thymidine kinase in the poxvirus-infected HeLa cell Analysis of single-and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange Reproduction of poxviruses Replication of poxviruses Identification of a novel Y branch structure as an intermediate in trypanosome mRNA processing: evidence for Pans splicing Hybridization and sedimentation studies on early and late vaccinia messenger RNA A cDNA clomng vector that permrts expression of cDNA inserts in mammalian cells Soluble endoribonuclease activity from vaccinia virus: specific cleavage of virion-assocrated highmolecular weight RNA La crosse virions contain a primer-stimulated RNA polymerase and a methylated cap-dependent endonuclease A unique cap (m7GpppXm)-dependent influenza vrnon endonuclease cleaves capped RNAs to generate the primers that rmtiate vrral RNA transcnption Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase
keywords: cdna; dna; figure; gene; late; rna; rnas; sequences; vaccinia; virus
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item: #33 of 43
id: cord-321308-rwxhdg8r
author: Grubaugh, Nathan D.
title: Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear
date: 2020-07-03
words: 1506
flesch: 50
summary: The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus Superspreading and the effect of individual variation on disease emergence A Unique Clade of SARS-CoV-2 Viruses is Associated with Lower Viral Loads in Patient Upper Airways Recently Identified Mutations in the Ebola Virus-Makona Genome Do Not Alter Pathogenicity in Animal Models Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry Comparing viral load and clinical outcomes in Washington State across D614G mutation in spike protein of SARS-CoV-2 key: cord-321308-rwxhdg8r authors: Grubaugh, Nathan D.; Hanage, William P.; Rasmussen, Angela L. title: Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear date: 2020-07-03 journal: Cell DOI: 10.1016/j.cell.2020.06.040 sha: doc_id: 321308 cord_uid: rwxhdg8r Abstract Korber et al.
keywords: d614
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item: #34 of 43
id: cord-321868-xk4yuibj
author: Belcourt, Michael F.
title: Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site
date: 1990-07-27
words: 9596
flesch: 60
summary: In addition, Ty elements lack the characteristic homopolymeric run of nucleotides (slippery sequences) at the site of frameshifting that characterizes frameshift sites of retroviruses and coronaviruses (Brierley et al., 1989; Jacks et al., 1988a) . These two characteristics suggest a model for frameshifting that retains features of frameshift sites in other systems.
keywords: agg; codon; cuu; et al; frameshift site; frameshifting; gene; nucleotide; pause; plasmid; reading; sequence; site; trna; yeast
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item: #35 of 43
id: cord-326916-bakwk4tm
author: Fauver, Joseph R.
title: Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States
date: 2020-05-07
words: 5565
flesch: 43
summary: To delineate the roles of domestic and international virus spread in the emergence of new United States COVID-19 outbreaks, we sequenced SARS-CoV-2 viruses collected from cases identified in Connecticut. By March 18, the five countries comprised 78% of reported non-United States cases, whereas the five states comprised 48% of reported domestic cases outside of Connecticut and New York.
keywords: cases; connecticut; cov-2; covid-19; data; international; new; number; sars; states; travel; united
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item: #36 of 43
id: cord-327349-rxb6zfoc
author: Au, Lewis
title: Cancer, COVID-19, and antiviral immunity: the CAPTURE study
date: 2020-09-03
words: 4534
flesch: 25
summary: key: cord-327349-rxb6zfoc authors: Au, Lewis; Boos, Laura Amanda; Swerdlow, Anthony; Byrne, Fiona; Shepherd, Scott T.C.; Fendler, Annika; Turajlic, Samra title: Cancer, COVID-19, and antiviral immunity: the CAPTURE study date: 2020-09-03 journal: Cell DOI: 10.1016/j.cell.2020.09.005 sha: doc_id: 327349 cord_uid: rxb6zfoc The SARS-CoV-2 pandemic has posed a significant challenge for risk evaluation and mitigation amongst cancer patients. Susceptibility to and severity of COVID-19 in cancer patients has not been studied in a prospective and broadly applicable manner.
keywords: cancer; capture; cov-2; covid-19; immune; infection; outcomes; patients; response; risk; sars; study
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item: #37 of 43
id: cord-328289-3h3kmjlz
author: Iadecola, Costantino
title: Effects of COVID-19 on the nervous system
date: 2020-08-19
words: 6543
flesch: 28
summary: Furthermore, several autopsy series have revealed a notable lack of immune cell infiltration (Kantonen et al., 2020; Reichard et al., 2020; Solomon et al., 2020) . Consistent with hypoxic brain injury, autopsy studies in COVID-19 have shown neuronal damage in brain regions most vulnerable to hypoxia, including neocortex, hippocampus and cerebellum (Kantonen et al., 2020; Reichard et al., 2020; Solomon et al., 2020) .
keywords: acute; brain; cells; covid-19; disease; encephalitis; entry; et al; evidence; human; infection; manifestations; patients; sars; system; virus
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item: #38 of 43
id: cord-334123-wb45ww7f
author: Schimmel, Paul
title: RNA pseudoknots that interact with components of the translation apparatus
date: 1989-07-14
words: 3336
flesch: 56
summary: Regardless of the detailed interpretation of the experiments, the analysis of RNA structure by these methods is instructive and has provided one of the first examples of a functional probe for pseudoknot formation. key: cord-334123-wb45ww7f authors: Schimmel, Paul title: RNA pseudoknots that interact with components of the translation apparatus date: 1989-07-14 journal: Cell DOI: 10.1016/0092-8674(89)90395-4 sha: doc_id: 334123 cord_uid: wb45ww7f nan It is not a long extrapolation to recognize that the unanticipated structural motifs that were found in tRNA are underpinnings of the RNA pseudoknot.
keywords: et al; pseudoknot; structure; trna
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item: #39 of 43
id: cord-336696-c3rbmysh
author: Oberfeld, Blake
title: SnapShot: COVID-19
date: 2020-04-30
words: 1231
flesch: 34
summary: The causative agent was characterized as a novel coronavirus, initially referred to as 2019-nCoV and renamed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) (Zhou et al., 2020b) . Human coronaviruses include 229E, NL63, OC43, and HKU1, which are associated with mild seasonal illness, as well as viruses responsible for past outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS).
keywords: covid-19; disease; sars
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item: #40 of 43
id: cord-339093-mwxkvwaz
author: Li, Wei
title: High potency of a bivalent human VH domain in SARS-CoV-2 animal models
date: 2020-09-04
words: 11471
flesch: 51
summary: V H ab8 antibody was identified by panning of the phage library. Single antibody domains (sAbd), e.g., camelid V H H (15 kDa) exhibit strong antigen binding and high stability (Harmsen and De Haard, 2007) .
keywords: ab8; ace2; antibodies; antibody; binding; cells; cov-2; et al; figure; human; igg1; infection; neutralization; protein; rbd; sars; v h; viral; virus
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item: #41 of 43
id: cord-342189-ya05m58o
author: Banerjee, Abhik K.
title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses
date: 2020-10-08
words: 11499
flesch: 45
summary: Because viral membrane proteins also require trafficking to the ER, viral disruption of SRP might negatively impact viral propagation, unless viral proteins are trafficked in an SRP-independent manner ( Figure S7E ) or if NSP8/9 selectively impacts host (but not viral) proteins. Understanding the interactions between viral proteins and components of human cells is essential for elucidating their pathogenic mechanisms and for development of effective therapeutics.
keywords: binding; cells; cov-2; et al; expression; figure; gene; gfp; host; human; ifn; infection; membrane; mrna; nsp1; protein; ribosome; rna; sars; splicing; srp; translation
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item: #42 of 43
id: cord-345103-b2wkm03g
author: Yao, Hangping
title: Molecular architecture of the SARS-CoV-2 virus
date: 2020-09-06
words: 5759
flesch: 41
summary: The spike copy number per virion is comparable to HIV (Liu et al., 2008) , but ~5 times less than the Lassa virus (LASV) (Li et al., 2016) or ~10 times less than the Influenza J o u r n a l P r e -p r o o f virus (Harris et al., 2006) . The electron beam induced motion was corrected using a combination of MotionCor (Li et al., 2013) and MotionCor2 (Zheng et al., 2017) by averaging eight frames for each tilt.
keywords: coronavirus; cov-2; cryo; et al; figure; protein; rbd; resolution; rnps; sars; spike; virions; virus
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item: #43 of 43
id: cord-350855-gofzhff7
author: Hou, Yixuan J.
title: SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract
date: 2020-05-27
words: 3432
flesch: 17
summary: The oral-lung axis: the impact of oral health on lung health Pharmacological rescue of 1319 conditionally reprogrammed cystic fibrosis bronchial epithelial cells Chronic e-cigarette exposure 1323 alters the human bronchial epithelial proteome Quantitative aspiration during sleep 1326 in normal subjects Stabilization of a full-length infectious cDNA clone of transmissible gastroenteritis 1329 coronavirus by insertion of an intron The 1332 species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV 1333 and naming it SARS-CoV-2 Comorbidity and its impact on 1590 patients 1336 with Covid-19 in China: a nationwide analysis SARS-CoV-2 cell 1340 entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease 1341 inhibitor Clinical features of patients infected with 2019 novel coronavirus in Wuhan Pharyngeal aspiration in 1346 normal adults and patients with depressed consciousness Angiotensin-converting enzyme 2 protects from severe 1349 acute lung failure The proteolytic regulation of virus cell entry by furin and other 1351 proprotein convertases Pulmonary angiotensin-converting enzyme 2 (ACE2) and inflammatory 1353 lung disease Influenza A virus infection causes chronic lung disease linked to sites of active 1356 viral RNA remnants Nrf2 expression modifies 1358 influenza A entry and replication in nasal epithelial cells. RNA/cytospin 369 detected ~20% of upper respiratory cells expressing ACE2 vs ~4% for scRNAseq 370 ( Figure 4F ).
keywords: ace2; cells; coronavirus; cov-2; expression; figure; human; infection; lung; nasal; sars; virus
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