Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 41 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 26034 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 5 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 39 GFP 11 RNA 10 Fig 9 figure 9 cell 5 protein 4 study 4 result 4 University 3 SARS 3 IFN 3 ATP 2 virus 2 neuron 2 mouse 2 lipid 2 increase 2 fret 2 dna 2 USA 2 Supplementary 2 PCR 2 NMDA 2 Medical 2 Institute 2 GABA 2 Department 2 Center 2 CNS 2 CHIKV 2 Biology 2 BDNF 1 ∆F508-CFTR 1 ∆F508 1 tenuissima 1 structure 1 site 1 siRNA 1 role 1 response 1 reporter 1 ps3p 1 patient 1 ng2 1 neuronal 1 microglia 1 method 1 membrane 1 lung 1 lc3 Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 8476 cell 4071 protein 2779 % 2508 mouse 2362 study 2193 expression 2185 patient 2158 neuron 2065 virus 2040 result 1839 activity 1810 gene 1696 effect 1528 membrane 1432 brain 1427 level 1382 response 1339 receptor 1290 role 1240 infection 1239 function 1223 analysis 1217 system 1195 time 1146 control 1103 disease 1100 type 1083 mechanism 1040 model 1029 change 1004 datum 960 treatment 925 rat 910 activation 890 day 871 site 870 method 860 interaction 837 group 831 structure 786 process 783 lung 763 astrocyte 738 cf 737 region 728 number 727 culture 706 molecule 704 factor 692 surface Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1803 CF 1749 Japan 1466 GFP 1354 CFTR 1156 . 1071 University 853 RNA 667 al 593 Univ 565 Fig 551 Tokyo 546 Department 528 et 501 C 449 Institute 349 USA 342 CNS 338 PCR 337 Dept 324 School 292 P. 289 ATP 279 Ca 274 CHIKV 271 mRNA 270 Science 265 S. 262 M. 258 WT 250 Sch 248 MS 241 GABA 236 J. 235 Medicine 235 Med 235 ER 230 Research 229 Na 227 II 226 T 225 K 222 A 217 SARS 217 C. 210 ∆F508 210 Sci 210 M 210 A. 206 RSV 201 Italy Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 6505 we 1418 it 576 they 404 i 209 them 139 us 46 itself 18 one 15 themselves 15 he 13 isg20 7 you 5 she 5 imagej 5 ifit5 4 mrnas 3 wtgfp 3 nlrp12 3 me 3 i- 1 ␤ 1 α1-pdx 1 type- 1 tag-1 1 sunset 1 shrna#3 1 s 1 rrna 1 p70 1 ourselves 1 ours 1 or=0.12 1 na€ 1 ireses 1 il13ra2 1 ifnar1 1 icg-001 1 himself 1 her 1 hapg5p 1 grch37 1 fhvb2 1 carbon-11 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 29110 be 4617 have 3829 use 2458 show 1647 suggest 1506 increase 1467 induce 1280 express 1226 find 1069 compare 1025 observe 946 indicate 901 identify 882 include 876 follow 853 do 823 investigate 812 bind 807 determine 759 demonstrate 722 perform 692 reveal 688 study 673 reduce 671 involve 669 report 665 associate 664 examine 662 mediate 662 base 646 contain 644 measure 642 develop 635 provide 593 regulate 592 know 558 treat 558 decrease 543 cause 530 detect 526 result 520 obtain 519 activate 512 inhibit 511 generate 506 analyze 490 lead 471 require 461 play 457 relate Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 2413 not 2132 - 1619 also 1268 high 1112 different 1033 however 1025 specific 1022 well 952 human 940 other 862 more 848 such 844 only 817 viral 791 neuronal 789 low 703 significantly 700 non 680 single 675 molecular 663 significant 646 first 591 important 585 further 585 as 577 most 561 functional 557 dependent 555 present 533 here 524 then 524 small 521 inflammatory 517 large 514 thus 511 cellular 506 several 493 positive 478 neural 475 synaptic 455 early 454 new 449 similar 440 long 437 primary 435 respectively 429 clinical 419 anti 417 respiratory 406 previously Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 203 most 114 least 64 Most 58 high 49 good 24 large 12 low 12 great 11 strong 8 close 7 small 7 early 7 Panx1 6 late 6 big 4 bright 3 slow 3 simple 3 fast 3 common 3 Least 2 new 2 easy 2 deep 2 bad 2 -β 1 young 1 wtPEDV 1 weak 1 thick 1 ssRNA 1 slight 1 sick 1 safe 1 mild 1 long 1 cheap 1 broad 1 VirHostNet2.0 1 R19H07-GAL4AD 1 Cx30 1 -ir Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 374 most 90 least 10 well 3 highest 2 panx1 1 ® 1 -r Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 4 doi.org 2 www.ncbi.nlm.nih.gov 2 www.nature.com 2 www.mdpi.com 2 github.com 2 broadinstitute.github.io 1 www.who.int 1 www.nature 1 www.lamondlab.com 1 www.jneuroinflammation.com 1 www.genscript.com 1 www.genomatix.de 1 www.fruitfly.org 1 www.cdtdb.brain.riken.jp 1 www.ambion.com 1 www.ambion 1 v2.virtualflybrain.org 1 us.expasy.org 1 u759.curie.u-psud.fr 1 sustainabledevelopment.un.org 1 software.broadinstitute.org 1 rsb.info.nih.gov 1 publish.aps.org 1 n2t.net 1 en.wikipedia.org 1 creativecommons.org 1 ccpbsa.bioinformatik.uni-saarland.de 1 bowtie-bio.sourceforge.net 1 advances.sciencemag.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 2 http://www.nature.com/naturemethods/ 2 http://broadinstitute.github.io/picard/ 1 http://www.who.int/blueprint/priority-diseases/en/ 1 http://www.ncbi.nlm.nih.gov/projects/gorf 1 http://www.ncbi.nlm.nih.gov/ 1 http://www.nature 1 http://www.mdpi.com/1999-4915/12/10/1074/s1 1 http://www.mdpi.com/1999-4915/11/10/964/s1 1 http://www.lamondlab.com 1 http://www.jneuroinflammation.com/content/9/1/50 1 http://www.genscript.com/ssl-bin/app/rnai 1 http://www.genomatix.de 1 http://www.fruitfly.org/seq_tools/promoter.html 1 http://www.cdtdb.brain.riken.jp 1 http://www.ambion.com 1 http://www.ambion 1 http://v2.virtualflybrain.org/ 1 http://us.expasy.org/sprot/ 1 http://u759.curie.u-psud.fr/modelisation/LAH 1 http://sustainabledevelopment.un.org/ 1 http://software.broadinstitute.org/morpheus/ 1 http://rsb.info.nih.gov/ij/ 1 http://publish.aps.org/ 1 http://n2t.net/addgene:67137 1 http://github.com/timflutre/trimmomatic 1 http://github.com/alexdobin/STAR 1 http://en.wikipedia.org/wiki/Biomechanics 1 http://doi.org/10.7554/eLife.45205.015 1 http://doi.org/10.7554/eLife.45205.003 1 http://doi.org/10.1371/journal.ppat.1008093.g004 1 http://doi.org/10.1038/s41598-018-24905-y 1 http://creativecommons.org/licenses/by/4.0/ 1 http://ccpbsa.bioinformatik.uni-saarland.de 1 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml 1 http://advances.sciencemag.org/cgi/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 ohki@bio.phys.tohoku.ac.jp 1 mguttman@caltech.edu 1 thomas.andresen@nanotech.dtu.dk Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 25 cells were then 14 cells were also 10 cells were co 10 cells were not 10 cells were transiently 9 cells expressing gfp 8 mice did not 7 cells are not 7 expression was not 7 levels were significantly 6 cells did not 6 cells was significantly 6 effect was not 6 protein is not 5 cells do not 5 cells was also 5 cells were cultured 5 gfp expressing cells 5 gfp was not 4 % were female 4 analysis did not 4 cells are also 4 cells are more 4 cells expressing ∆f508 4 cells were significantly 4 expression was also 4 level was not 4 levels were not 4 mice are not 4 mice were then 4 neurons were also 4 patients are not 3 activity was also 3 activity was significantly 3 cells are susceptible 3 cells expressing isg20 3 cells has not 3 cells using lipofectamine 3 cells was not 3 cells were further 3 cells were pre 3 cftr is not 3 cftr mediated cl 3 cftr mediated short 3 effect is more 3 effects were also 3 expression was higher 3 expression was significantly 3 expression was similarly 3 function is still Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 analysis showed no defect 2 cells showed no increase 2 cells were not significantly 1 activity was not evident 1 cells are not able 1 cells are not fully 1 cells are not only 1 cells are not yet 1 cells do not actively 1 cells has not so 1 cells have no significant 1 cells is not completely 1 cells revealed no alteration 1 cells showed no difference 1 cells showed not only 1 cells was not very 1 cells were not distinguishable 1 cells were not neurogenic 1 cf are not yet 1 cftr is not only 1 control was not dependent 1 effect are not fully 1 effect is not profound 1 effect was not due 1 effect was not only 1 expression did not significantly 1 functions is not exclusive 1 gene is not solely 1 genes are not well 1 gfp was not able 1 infection are not antiviral 1 infection is not clear 1 infection is not statistically 1 infection was not possible 1 level was not as 1 level was not different 1 levels showed no apparent 1 levels showed no difference 1 levels were not different 1 membranes are not easy 1 membranes are not visible 1 mice are not significantly 1 mice are not suitable 1 mice did not significantly 1 mice have no motor 1 mice show no different 1 mice showed no pathological 1 mice was not significantly 1 neurons are not dysfunctional 1 neurons is not well A rudimentary bibliography -------------------------- id = cord-334855-s0ci3r8w author = Andersen, Petter I. title = Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine date = 2019-10-18 keywords = EV1; FLUAV; GFP; HIV-1 summary = Here, we identified novel activities of obatoclax and emetine against herpes simplex virus type 2 (HSV-2), echovirus 1 (EV1), human metapneumovirus (HMPV) and Rift Valley fever virus (RVFV) in cell cultures. The expected response of the emetine-obatoclax drug combination on the viability of FLUAV-and mock-infected RPE cells was calculated using Bliss reference model [29] . After the initial screening, we identified four compounds (obatoclax, emetine, niclosamide and ganciclovir) that at none-cytotoxic concentrations rescued cells from virus-mediated death (Figure 2A) . Table S1 : Compounds, their suppliers and catalogue numbers; Table S2 : Developmental status of broad-spectrum antivirals used in the study; Table S3 : Human viruses and associated diseases; Figure S1 : The expected response of the emetine-obatoclax drug combination on the viability of FLUAV-and mock-infected RPE cells, as measured with the CTG assay using the Bliss reference model; Figure S2 doi = 10.3390/v11100964 id = cord-003705-ekhj8ae8 author = Azkanaz, Maria title = Protein quality control in the nucleolus safeguards recovery of epigenetic regulators after heat shock date = 2019-06-14 keywords = CBX2; CBX8; GFP; HSP70; PRC1; figure summary = To verify the HS-induced accumulation of PcG proteins in the nucleolus, we isolated nucleoli from heat shocked and untreated GFP-CBX8 expressing K562 cells ( Figure 2A ). Whereas initially considered as heat-induced damage, several lines of independent observations have suggested that this might rather reflect a regulated, HSP-dependent process in which the nucleolus serves as a temporal storage site for unfolded proteins during proteotoxic stress (Nollen et al., 2001; Ohtsuka et al., 1986; Welch and Feramisco, 1984) . Intra-nucleolar levels of H3K27me3 and H2AK119ub were not increased in heat shocked cells versus untreated cells, suggesting that PcG proteins are not involved in Polycomb-mediated silencing of nucleolar chromatin ( Figure 3E ). Independent LC-MS/MS analysis with K562 GFP-CBX8 cells confirmed these findings, implying that HS-induced nucleolar accumulation of various chromatin regulators, protein chaperones and proteasomal subunits is a conserved biological phenomenon (Figure 3-figure supplement 4A-E, Supplementary file 3). doi = 10.7554/elife.45205 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 keywords = GFP; IFN; NSP1; RNA; SARS; SRP; figure; protein summary = Here, we comprehensively define the interactions between each SARS-CoV-2 protein and human RNAs. We show that 10 viral proteins form highly specific interactions with mRNAs or ncRNAs, including those involved in progressive steps of host cell protein production. We show J o u r n a l P r e -p r o o f 5 that NSP16 binds to the mRNA recognition domains of the U1 and U2 RNA components of the spliceosome and acts to suppress global mRNA splicing in SARS-CoV-2-infected human cells. We identified several pathogenic functions of SARS-CoV-2 in human cells -including global inhibition of host mRNA splicing, protein translation, and membrane protein trafficking -and described the molecular mechanisms by which the virus acts to disrupt these essential cell processes. doi = 10.1016/j.cell.2020.10.004 id = cord-274210-uaaj66xq author = Ding, Ning title = Induction of Atypical Autophagy by Porcine Hemagglutinating Encephalomyelitis Virus Contributes to Viral Replication date = 2017-02-28 keywords = GFP; PHEV; figure; lc3 summary = These results show that PHEV infection induces atypical autophagy and causes the appearance of autophagosomes but blocks the fusion with lysosomes, which is necessary for the replication of PHEV in nerve cells. In this study, we confirmed that PHEV infection induces atypical autophagy and leads to the accumulation of autophagosomes while blocking their fusion with lysosomes, which creates conditions for the virus to replicate within nerve cells. In order to examine whether the autophagy is associated with viral replication in PHEV infection, we performed subcellular localization of viral proteins and LC3 or LAMP on PHEVinfected cells for the first time. In expect to recognize the effect of autophagy induced by PHEV infection on viral replication, we treated the Neuro-2a cells with 3-MA, the autophagic inhibitor targeting a class III phosphatidylinositol-3-kinase (PI3K) (Petiot et al., 2000) . doi = 10.3389/fcimb.2017.00056 id = cord-275307-d7htyfcl author = Gaglia, Marta Maria title = Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX date = 2015-12-08 keywords = Fig; GFP; RNA; SOX; cut; site summary = Development of a novel bioinformatics pipeline to detect highconfidence SOX cleavage sites across the transcriptome following PARE Prior analyses of individual mRNAs indicated that the KSHV RNase SOX cuts at specific locations within the RNA, in a manner dependent on the sequence surrounding the cleavage site [5] . This example shows the expected distribution for a cut site followed by exonucleolytic degradation due PARE libraries from two replicates of SOX-expressing or GFP control cells and extracted the 5'' end of each mapped read, which represents the cleavage site (S1 Table) . Indeed, the sequences flanking the set of reproducible SOX cut sites (identified with a confidence level of 99.99%) were a closer match to the motif compared to those surrounding GFP-specific fragment ends, as shown by the distribution of the log likelihood scores (Fig 6A) . doi = 10.1371/journal.ppat.1005305 id = cord-103868-iwpiti2h author = Harrison, Angela R. title = The Ebola virus interferon antagonist VP24 undergoes active nucleocytoplasmic trafficking date = 2020-08-11 keywords = GFP; VP24 summary = Functions of the Ebola virus (EBOV) IFN antagonist VP24 include nucleocapsid assembly during cytoplasmic replication and inhibition of IFN-activated signalling by STAT1. Proteins of many viruses with cytoplasmic replication cycles similar to EBOV interact with the nuclear trafficking machinery, resulting in active nucleocytoplasmic shuttling important to immune evasion and other intranuclear functions. Thus, it appears that active In this study we have shown that EBOV VP24 undergoes active trafficking between the nucleus 275 and cytoplasm involving CRM1-dependent nuclear export via a NES at the VP24 C-terminus. Notably, the EBOV 287 matrix protein VP40 has also been reported to localise to the nucleus in infected and transfected 288 cells (16, 50); however, a direct role for active trafficking pathways to regulate localisation, 289 distinct from mechanisms such as diffusion or interaction with other host factors, has not been 290 defined. doi = 10.1101/2020.08.10.245563 id = cord-324720-acei0pn8 author = Howe, Charles L title = Inflammatory monocytes damage the hippocampus during acute picornavirus infection of the brain date = 2012-03-09 keywords = CD45; GFP; figure; gr1 summary = METHODS: The identity of brain-infiltrating leukocytes was determined using microscopy and flow cytometry at several acute time points following intracranial infection of mice with the Theiler''s murine encephalomyelitis virus. Likewise, the population of CD45 hi cells could be distinguished by surface F4/80 expression, with some F4/80 + Figure 1 Histological evidence of rapid immune cell infiltration into the hippocampus of mice acutely infected with Theiler''s murine encephalomyelitis virus (TMEV). We were unable to identify a population of inflammatory monocytes in the blood in the infected mice, suggesting either that these cells are not circulating at this time or that so many have been recruited to the brain that the Figure 2 Flow cytometric assessment of the infiltrate present in the brain of mice acutely infected with Theiler''s murine encephalomyelitis virus (TMEV). doi = 10.1186/1742-2094-9-50 id = cord-319842-4mnaicki author = Jackson, William T title = Subversion of Cellular Autophagosomal Machinery by RNA Viruses date = 2005-04-26 keywords = GFP; LAMP1; LC3; RNA; cell summary = Infection of human cells with poliovirus induces the proliferation of double-membraned cytoplasmic vesicles whose surfaces are used as the sites of viral RNA replication and whose origin is unknown. Here, we explore the role of several constituents of autophagosome machinery in poliovirus-and rhinovirusinfected cells by monitoring: the presence of autophagosomal protein LC3 in virally induced vesicles, the acquisition of colocalization of LC3 and LAMP1 in virally infected cells, the viral induction of punctate structures that stain with monodansylcadaverine (MDC), and the effects of perturbing the autophagosomal pathway pharmacologically and via RNA interference on intracellular and extracellular virus yield. To determine whether the autophagosome-like membranes induced during poliovirus infection perform an antiviral function or facilitate viral replication, we tested the effect on poliovirus yield of pretreating H1-HeLa cells with either tamoxifen or rapamycin, known inducers of autophagy. doi = 10.1371/journal.pbio.0030156 id = cord-331414-i0oxm5mr author = Kautz, Tiffany F. title = A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene date = 2020-06-19 keywords = GFP; RNA; TC-83; figure summary = doi = 10.3390/v12060660 id = cord-332881-mkm4ygh6 author = Kirchhoff, Jana title = Three viruses of the bovine respiratory disease complex apply different strategies to initiate infection date = 2014-02-18 keywords = BHV-1-GFP; BPIV3; BRSV; GFP summary = We investigated the susceptibility of bovine airway epithelial cells (BAEC) to infection by the three major viruses associated with the BRDC: bovine respiratory syncytial virus (BRSV), bovine herpesvirus type 1 (BHV-1) and bovine parainfluenza virus type 3 (BPIV3). For this purpose, two culture systems for well-differentiated BAEC were used: the air-liquid interface (ALI) system, where filter-grown BAEC differentiate into a pseudostratified respiratory epithelium and precision-cut lung slices (PCLS) where BAEC are maintained in the original tissue organisation. We have reported recently that well-differentiated respiratory epithelial cells are susceptible to infection by BPIV3 whereas they are rather resistant to infection by BRSV [7] . BPIV3 efficiently infected the airway epithelial cells using sialic acids on the apical surface as a receptor determinant for virus entry from the apical side. When BHV-1-GFP was applied to the apical side of the well-differentiated airway epithelial cells, infected cells were detected only occasionally. doi = 10.1186/1297-9716-45-20 id = cord-000933-nn9gj0z1 author = Krzyzaniak, Magdalena Anna title = Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein date = 2013-04-11 keywords = FACS; Fig; GFP; RSV; Rab5; cell; virus summary = To study the entry process in human tissue culture cells (HeLa, A549), we used fluorescence microscopy and developed quantitative, FACS-based assays to follow virus binding to cells, endocytosis, intracellular trafficking, membrane fusion, and infection. To determine the pathway of RSV entry into HeLa and A549 cells, we developed quantitative fluorescence-activated cell sorting (FACS) assays and complemented them with confocal microscopy to monitor cell binding of RSV, endocytosis, fusion, and infection. Since we did not detect free capsids that would stain only for N or P (data not shown), we used the presence of the capsid antigens to distinguish between intact RSVs and VLPs. When purified virus preparations were incubated with HeLa cells at 4uC, immunoblotting after SDS-PAGE showed that more than half of the input N and P associated with the cells indicating that RSV binding in the cold was efficient (Fig. 1C) . doi = 10.1371/journal.ppat.1003309 id = cord-272018-txdc0c3j author = Laing, Eric D. title = Enhanced Autophagy Contributes to Reduced Viral Infection in Black Flying Fox Cells date = 2019-03-14 keywords = ABLV; GFP; NBF; cell; figure summary = doi = 10.3390/v11030260 id = cord-353467-wbtzvm4i author = Lambert, Carsten title = Functional incorporation of green fluorescent protein into hepatitis B virus envelope particles date = 2004-12-05 keywords = GFP; GFP.S; HBV; SHA summary = doi = 10.1016/j.virol.2004.09.031 id = cord-253709-frauasts author = Lan, Dongming title = An improved nonchromatographic method for the purification of recombinant proteins using elastin-like polypeptide-tagged proteases date = 2011-08-15 keywords = ELP; GFP summary = title: An improved nonchromatographic method for the purification of recombinant proteins using elastin-like polypeptide-tagged proteases Abstract Proteins fused to the elastin-like polypeptide (ELP) tag can be selectively separated from crude cell extract without chromatography. Proteins fused to the elastin-like polypeptide (ELP) tag can be selectively separated from crude cell extract without chromatography. Among them, Meyer and Chilkoti reported a nonchromatographic method for purification of recombinant proteins using an elastin-like polypeptide (ELP) 2 tag [1] . This characteristic transition allows the recombinant ELP fusion protein to be isolated from the cell lysate by repeated steps of aggregation, centrifugation, and resolubilization without chromatography. Recombinant ELP fusion proteins at different expression levels can be efficiently recovered by the ITC method [4, 5] . ELP-3C protease was produced at a high level with an apparent molecular weight of approximately 58 kDa. To aggregate ELP-3C protease, solid NaCl was added into the cleared lysate to a final concentration of 2 M at room temperature to trigger the phase transition of ELP. doi = 10.1016/j.ab.2011.04.034 id = cord-338811-2bi2edcw author = Lennemann, Nicholas J. title = Imaging-Based Reporter Systems to Define CVB-Induced Membrane Remodeling in Living Cells date = 2020-09-25 keywords = CVB; GFP; figure summary = To define the dynamic process of enterovirus membrane remodeling of major secretory pathway organelles, we have developed plasmid-based reporter systems that utilize viral protease-dependent release of a nuclear-localized fluorescent protein from the endoplasmic reticulum (ER) membrane during infection, while retaining organelle-specific fluorescent protein markers such as the ER and Golgi. To monitor enterovirus infection in real-time, we adapted cell-based reporter methodologies previously used for flaviviruses and hepatitis C virus that rely on viral protease cleavage-dependent translocation of a membrane-anchored cytoplasmic fluorescent proteins to the nucleus [27] [28] [29] . CVB infection of RepER expressing U2OS cells resulted in a clear translocation of GFP-NLS reporter to the nucleus and eventual dispersal due to cell lysis, while the mCherry-KDEL was maintained in the membranous structure of the ER (Video S1 and Figure 2a) . Live-cell imaging of CVB infected cells expressing these reporters allowed for the real-time visualization of virus-induced changes to the host cell, including the collapse of the peripheral ER network and loss of Golgi integrity. doi = 10.3390/v12101074 id = cord-354052-x4ckzw64 author = Li, Chunhua title = Manipulation of the Porcine Epidemic Diarrhea Virus Genome Using Targeted RNA Recombination date = 2013-08-02 keywords = GFP; ORF3; PEDV summary = doi = 10.1371/journal.pone.0069997 id = cord-316814-9fv9xrln author = Li, Hong-Ye title = Use of GFP to Investigate Expression of Plant-Derived Vaccines date = 2009 keywords = GFP; SARS summary = Agroinfiltration is a more recent technique that can be applied to investigate transient expression in plant cells by which an Agrobacterium liquid culture is infiltrated into intact plant leaves (7) . By simple infiltration of Agrobacterium cells carrying appropriate gene constructs into tobacco plants leaves, transient expression assays can be performed within 3 days without using expensive instruments or complicated procedures. Two days after agroinfiltration, expression and subcellular localization of the GFP fusion proteins in tobacco leaves can be determined by simple observation under fluorescence or confocal laser scanning microscopy. 7. Generate plasmid pCV12 (Fig. 1 ) or similar nuclear transformation vector for expression of a fusion protein consisting of the SARS-CoV S1 and GFP. Production of tobacco leaves transiently expressing a protein fusion consisting of the SARS-CoV S1 protein fused with the GFP was carried out using Agrobacterium-mediated transformation with plasmid pCV12. doi = 10.1007/978-1-59745-559-6_19 id = cord-102184-8u73adnk author = Li, Jinzhi title = Visual input into the Drosophila melanogaster mushroom body date = 2020-05-02 keywords = GFP; Kenyon; figure; neuron summary = Here, we use a range of anatomical and genetic techniques to identify two novel types of mushroom body input neuron that connect visual processing centers — namely the lobula and the posterior lateral protocerebrum — to the dorsal accessory calyx of the mushroom body. Altogether, based on the results obtained using both the GRASP technique and the dye/photo-labeling technique, we conclude that LOPN is a true input 265 neuron of the a/bp Kenyon cells and that it conveys information from the lobula, a visual processing center, to the dorsal accessory calyx. To identify the neurons that project to the post-synaptic terminals formed by the PLPPNs in the posterior lateral protocerebrum, a poorly characterized visual processing center, we used the targeted photo-labeling technique described above ( Figure 8A ). Our results suggest that the LOPN and PLPPNs that we identified in our screen connect to the a/bp Kenyon cells and that, together, these two types of projection neuron represent a large fraction of the input neurons of the dorsal accessory calyx. doi = 10.1101/2020.02.07.935924 id = cord-002076-7t4d4vvo author = Li, Yongfeng title = Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology date = 2016-05-06 keywords = EGFP; GFP; reporter; virus summary = Commonly used tests based on wild-type viruses, such as immunostaining, cannot meet the demands for rapid detection of viral replication, high-throughput screening for antivirals, as well as for tracking viral proteins or virus transport in real time. This article reviews the applications of RCREVs in diagnostic and molecular virology, including rapid neutralization tests, high-throughput screening systems, identification of viral receptors and virus-host interactions, dynamics of viral infections in vitro and in vivo, vaccination approaches and others. Replicating-competent reporter-expressing viruses (RCREVs) are one type of artificially modified viruses that not only retain the viral genetic characteristics but also possess the new properties of the reporter genes, which represent a useful tool for quantitative analysis of viral replication and tracking viral protein transport in both living cells and animals. doi = 10.3390/v8050127 id = cord-001123-n2e4s7bu author = Lin, Yue-Zhi title = The Soluble Form of the EIAV Receptor Encoded by an Alternative Splicing Variant Inhibits EIAV Infection of Target Cells date = 2013-11-22 keywords = EIAV; ELR1; ELR1-IN; GFP summary = title: The Soluble Form of the EIAV Receptor Encoded by an Alternative Splicing Variant Inhibits EIAV Infection of Target Cells In addition to the previously described membrane-associated form of ELR1, two other major alternative splicing variant mRNAs were identified in equine monocyte-derived macrophages (eMDMs). This result strongly indicated that overexpressed recombinant sELR1 was able to inhibit EIAV infection in vitro, probably by competing with the membrane-associated receptor for the binding of virions on target cells. Thus, the soluble form of ELR1, tagged with HA, was overexpressed in FED cells, a major target of EIAV in vitro, by transfection with the sELR1 expression vector pcDNA3.1-ELR1-IN. The regulated expression levels of both the soluble and membrane-associated forms of ELR1 by EIAV reveal the possible role of sELR1 in the interaction between virus and host. doi = 10.1371/journal.pone.0079299 id = cord-258678-0atfsivf author = Liu, Hong Yan title = A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras date = 2013-11-07 keywords = GFP; RNA; chimera; siRNA summary = Here, we report the development of a small and simple protein tag that complements the therapeutic and targeting functionalities of chimera with two functional domains: a dsRNA binding domain (dsRBD) for siRNA docking and a pH-dependent polyhistidine to disrupt endosomal membrane. Therefore, it is of critical importance to design a delivery system that is simple for potential regulatory approval and mass production, universal for all siRNAaptamer chimera, neutral and siRNA-binding specific to ensure aptamer targeting, and small to avoid major alteration of chimera''s biodistribution profile. To assess their dsRNA binding activity, siRNA-aptamer chimera labeled with fluorophore FAM were incubated with the protein tags and probed with gel electrophoresis (1% agarose). To evaluate the targeting specificity of the aptamer block, PSMA-positive LNCaP cells and PSMA-negative PC3 cells were treated with complex of chimera and dsRBD-His 18 (chimera/protein tag molar ratio at 152, 100 nM chimera) in serum free medium for 2 hours, followed by incubation in complete medium for another 12 h. doi = 10.1038/srep03129 id = cord-002320-m99amd4y author = Mathur, Kalika title = Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity date = 2016-11-30 keywords = CHIKV; Fig; GFP; RNA summary = Systematic analysis of all CHIKV proteins using a Sf21 RNAi sensor cell line based assay revealed that non-structural proteins nsP2 and nsP3 exhibited RNAi suppressor activity. Using cell lysate of the transfected cell expressing nsP2 and nsP3, we evaluated their ability to bind double stranded RNA by using [γ 32P] labeled shRNA of GFP and running the bound complex in a 6% polyacrylamide gel (Fig. 3e) . Having confirmed that both nsP2 and nsP3 exhibit RNAi suppressor activities, efforts were taken to characterise the proteins better and to identify those specific domains that were and NS4B (dengue virus) were taken as positive controls and empty vector was used as negative control. Taken together, the current study has identified CHIKV proteins nsP2 and nsP3 to exhibit RNAi suppressor activity in the in-vitro system that was further demonstrated in its natural hosts, namely, an Aedes and mammalian cell line. doi = 10.1038/srep38065 id = cord-280454-etf32afd author = Moustaqil, Mehdi title = SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts date = 2020-06-05 keywords = Fig; GFP; IRF3; NLRP12; SARS; TAB1; cleavage summary = title: SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts Direct cleavage of IRF3 by NSP3 could explain the blunted TypeI IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of IL-6 and inflammatory response observed in COVID-19 patients. In this report, we show that the viral proteases PLpro and 3CLpro of SARS-CoV2 lead to the in-vitro proteolytic cleavage of three important proteins of the host immune response: IRF3, TAB1 and NLRP12 (Fig. 1B) . The presence of the five human-like cleavage sites for IRF3, TAB1 and NLRP12 in a single species shows that it is possible that the SARS viruses could have gained the new functionality of cleaving these Human Innate Immune Proteins in a single reservoir host, potentially in Myotis Davidii. doi = 10.1101/2020.06.05.135699 id = cord-317142-qd61qvch author = Muramatsu, Tomonari title = Autoprocessing mechanism of severe acute respiratory syndrome coronavirus 3C‐like protease (SARS‐CoV 3CL (pro)) from its polyproteins date = 2013-03-27 keywords = 3CL; GFP summary = In vitro 3CL pro autoprocessing system First we developed a SARS 3CL protease autoprocessing system by use of the Escherichia coli cell-free protein synthesis system, with the N-and C-terminal 10 amino acid pro-sequences accompanied by an S tag and a His tag, respectively (Fig. 1A) . Over the course of the cell-free protein synthesis reaction (30°C, 4 h), the N-and C-terminal processing sites of the catalytically active construct (wild-type, WT in Fig. 1A) were completely cleaved by the enzyme''s endogenous proteolytic activity, as shown in Fig. 1B ,C (WT). To investigate the activities of the pro-forms of SARS-3CL pro in detail, we developed a ''trans-cleaving assay'', using a substrate in which the core region of the 3CL protease was exchanged with GFP (green fluorescent protein) ( Fig. 2A) . We estimated the activity of the enzyme (or pro-enzyme) toward the N-and C-terminal processing sites in the GFP substrate on the basis of the dilution ratio at which 50% cleavage was achieved (Fig. 2C) . doi = 10.1111/febs.12222 id = cord-319517-denczc6t author = Salipalli, Sandeep title = Recent advances in live cell imaging of hepatoma cells date = 2014-07-08 keywords = GFP; cell; fluorescent; fret; gene; lipid; protein summary = This review aims to provide an overview of the recent developments in the field of marker proteins (bioluminescence and fluorescent) and methodologies (fluorescent resonance energy transfer, fluorescent recovery after photobleaching and proximity ligation assay) employed as to achieve an improved imaging of biological processes in hepatoma cells. The success of live cell imaging relies on various factors including the specific imaging system, climate controlling devices for cultured cells under investigation, construction of recombinant plasmid DNA, transfer and expression of candidate genes and/or fluorescent proteins in mammalian cells. T4SS (Bartonella sp.) 60-70% 50% >70% >60% 50-60% [76] [77] [78] lipofection (1 μg) methods were used for transfection of plasmid encoding fluorescent protein (pEGFP and pEYFP) tagged to human and mouse ADRP genes in Huh-7 cells as to study the pathways of lipid droplet metabolism. doi = 10.1186/1471-2121-15-26 id = cord-315483-l6dm82pp author = Santhakumar, Diwakar title = Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses date = 2018-05-01 keywords = DF-1; Fig; GFP; IFN; NDV; RNA; Supplementary; ifit5 summary = To confirm the sequence of the cDNA and to identify the genomic structure of the identified IFIT gene, the transcript was amplified from RNA extracted from NDV-infected CEFs. Complete sequence analysis of the gene revealed an open reading frame (ORF) of 1440 bps (479 amino acids excluding stop codon) with high sequence identity (48% and 67%) with the human and duck IFIT5 proteins, respectively ( Supplementary Fig. 1B) . The levels of chIFN-β gene induction was proportional to the NDV replication (Fig. 2D) , therefore, it can be inferred that the virus-induced expression of chicken IFIT5 is IFN-dependent and that chIFIT5 is an early-ISG with capacity to modulate initial steps of virus life cycle. To compare anti-viral effects of chIFIT5 (only IFIT gene identified in chickens so far) with its orthologous and homologous human proteins, huIFIT1, huIFIT2, huIFIT3 and huIFIT5 were expressed in chicken cells and antiviral affect was monitored (Fig. 5A ). doi = 10.1038/s41598-018-24905-y id = cord-299509-7xjdryoq author = Scholte, Florine E. M. title = Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates date = 2013-08-01 keywords = CHIKV; Fig; ITA07-RA1; LS3; LS3-GFP; RNA; Vero summary = Infectious cDNA clones of viruses have become invaluable tools that allow reverse genetics studies to elucidate the contribution of specific amino acids or RNA structures to viraemia, virulence, antigenicity, replication kinetics, interactions with host factors, adaptation to new vectors, and many other aspects of the viral life cycle. To obtain a virus that -in terms of virulence, sensitivity to antiviral compounds, and CHIKV-host interactions -is expected to have the general characteristics of the E1-226V CHIKV strains that were circulating during the 2005-2009 outbreaks, we have constructed a completely synthetic CHIKV cDNA clone based on the consensus sequence of the aligned genomes of these recent isolates. Indirect immunofluorescence analysis of Vero E6 cells infected with CHIKV LS3, LS3-GFP, or ITA07-RA1 at various time points showed that the localization and expression kinetics of E2 and dsRNA were similar for the natural isolate and the synthetic viruses (Fig. 6) . doi = 10.1371/journal.pone.0071047 id = cord-018771-xqlb74px author = Turinsky, Sebastian title = Bluttransfusion date = 2013-04-04 keywords = GFP; Patienten; Transfusion; der summary = Ein leukozytendepletiertes EK wird unmittelbar vor der Transfusion gewaschen und muss dann innerhalb von 6 h ohne weitere Lagerung transfundiert werden. Sowohl der zunehmende Mangel an Blutprodukten als auch diverse andere Umstände wie die Ablehnung durch den Patienten oder eine verzögerte Verfügbarkeit von Blutprodukten im Notfall machen es erforderlich, Alternativen zur Transfusion von Fremdblut zu kennen. B. bei schwerer Blutungsanämie, durch Beatmung mit einer FiO 2 = 1,0 eine Zunahme des physikalisch im Blut gelösten Sauerstoffs erreicht werden, die etwa dem Effekt der Transfusion von 1-2 EK entspricht. Bei schweren anaphylaktischen Transfusionsreaktionen, wie sie häufiger bei Patienten mit IgA-Mangel und der Ausbildung von Anti-IgA-Antikörpern auftreten können, besteht die Indikation zur Transfusion gewaschener Blutprodukte. Ist im Rahmen einer lebensbedrohlichen Situation eine Transfusion mit Rhesus-positivem Blut unvermeidlich, so kann die Bildung von Antikörpern durch eine Immunisierung gegen das Rhesusantigen verhindert werden (Gabe von Anti-D-Immunglobulin, z. doi = 10.1007/978-3-642-34433-6_4 id = cord-346554-a98pjtxs author = Uddin, Md Bashir title = Inhibitory effects of bee venom and its components against viruses in vitro and in vivo date = 2016-11-26 keywords = EV-71; GFP; MLT; VSV summary = Co-incubation of non-cytotoxic amounts of BV and MLT, the main component of BV, significantly inhibited the replication of enveloped viruses such as Influenza A virus (PR8), Vesicular Stomatitis Virus (VSV), Respiratory Syncytial Virus (RSV), and Herpes Simplex Virus (HSV). To compare the antiviral effects of BV to VSV-GFP infection, the levels of viral replication (which reflected by GFP expression) were photographed (under 200X magnification) at 12 or 24 hpi of VSV-GFP, and calculated the virus titer by standard plaque assay with some modifications. To find out the effective time point which MLT exhibits virucidal activity, 2.0 μg/ml of MLT and VSV-GFP (MOI=0.2) were co-incubated for 5, 10, 20, and 30 min at 4°C, and then mixture was inoculated to HEK293T cell monolayers in 6 well plates. doi = 10.1007/s12275-016-6376-1 id = cord-345651-admlzeu4 author = Wang, Gang title = The N-Terminal Domain of Spike Protein Is Not the Enteric Tropism Determinant for Transmissible Gastroenteritis Virus in Piglets date = 2019-03-30 keywords = BAC; GFP; TGEV; figure summary = Using a novel approach, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems efficiently and rapidly rescued another recombinant virus with a 224-amino-acid deletion in the N-terminal domain of the TGEV Spike gene (S_NTD224), which is analogous to the N-terminal domain of porcine respiratory coronavirus. Homologous recombination was then performed using the ClonExpress II One Step Cloning Kit (Vazyme, Nanjing, Jiangsu, China) according to the manufacturer''s instructions using 200 ng of recycled linearized pTGEV-GFP BAC, 45 ng of PCR products of S_NTD and two pairs of primers (rec-672SF/δS-NTDR and rec-672SR/δS-NTDF) ( Table 2) . To construct an infectious clone of TGEV, six overlapping cDNA fragments designated A to F were generated by reverse transcriptase PCR (RT-PCR) using total RNA extracted from PK-15 cells infected with TGEV WH-1 ( Figure 1A ,B). Complete genomic sequences, a key residue in the spike protein and deletions in nonstructural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus doi = 10.3390/v11040313 id = cord-330176-1ugzkf22 author = Weeratunga, Prasanna title = RETRACTED ARTICLE: Interferon-mediated antiviral activities of Angelica tenuissima Nakai and its active components date = 2016-01-05 keywords = Angelica; Fig; GFP; IFN; Nakai; tenuissima summary = In vitro, an effective dose of Angelica tenuissima Nakai markedly inhibited the replication of Influenza A virus (PR8), Vesicular stomatitis virus (VSV), Herpes simplex virus (HSV), Coxsackie virus, and Enterovirus (EV-71) on epithelial (HEK293T/HeLa) and immune (RAW264.7) cells. To investigate the antiviral effects in immune cells, we first assessed the replication of divergent GFP-expressing viruses that were treated or untreated with cytotoxic-free (data not shown) Angelica tenuissima Nakai in RAW264.7 cells. These results suggest that the aqueous extract of Angelica tenuissima Nakai can induce the secretion of IFNs and pro-inflammatory cytokines, which can stimulate the cellular antiviral state for inhibition of viral replication. The aqueous extract of Angelica tenuissima Nakai inhibit the diverse viral infection through the induction of Type I IFN signaling and pro-inflammatory cytokines, leading to an antiviral state in epithelial and immune cells. doi = 10.1007/s12275-016-5555-4 id = cord-001365-6u80p5sj author = Weger-Lucarelli, James title = A Novel MVA Vectored Chikungunya Virus Vaccine Elicits Protective Immunity in Mice date = 2014-07-24 keywords = CD4; CHIK; GFP; MVA summary = Despite the presence of high levels of neutralizing antibodies elicited by most of the VACV vectored VEEV vaccine candidates, they were ineffective in providing protection against airborne infection, suggesting they were unable to elicit a sufficient T cell mediated immune response, which has been shown to be critical for protection against lethal VEEV encephalitis [34, 35] . Most importantly, depletion of CD4 + T cells in vaccinated mice resulted in loss of protection, with 100% succumbing to infection upon challenge with wild-type CHIKV, indicating an indispensable role of MVA-CHIK immune CD4+ T cells in protection. Expression of E2 was observed in the supernatant of CHIKV infected cells, but there Prior to boost (where applicable) and challenge, mice were bled and serum was monitored for both total Ig(G+M) and neutralizing activity by TCID 50 was no detection of E2 expression in MVA-CHIK, suggesting that the protein was not being secreted. doi = 10.1371/journal.pntd.0002970 id = cord-103509-hynnba03 author = Wong, Ten-Tsao title = A self-assembled protein nanoparticle serving as a one-shot vaccine carrier date = 2020-09-18 keywords = AH3-GFP; Fig; protein summary = From these two clues, it was hypothesized that AH3-GFP fusion protein form stable protein complex through hydrophobic interaction mediated by N-terminal AH3 peptide. Using the same protocol, AH3-GFP was found to co-sedimented with the bacterial membrane (Fig. S3A) as well as the AH3-sfGFP-hM2e fusion protein but not a free GFP protein (Fig S3B) These results are consistent with our protein structure modeling that Arg11 serves as a main contact point for dimer stacking also it mediates the electrostatic interaction with mutated Glu13 (Fig. 3E ). These results suggest that the two point mutations of AH3 in I8L and K13E enable the formation of a stable, high antigenic protein complex that stimulates long lasting immune responses in a single immunization. The result suggests that although carrier protein AH3-sfGFP also has high antigenicity, it did not interfere with the immune response against the heterologous protein, hM2e (Fig. 5B, 5C) doi = 10.1101/2020.09.16.299149 id = cord-001270-l8aa9cl3 author = Wongsrikeao, Pimprapar title = Antiviral restriction factor transgenesis in the domestic cat date = 2011-09-11 keywords = Fig; GFP; IVF; Supplementary; cat summary = In contrast to primates, feline species lack antiviral TRIM5α genes 11 but have potently restrictive APOBEC3 proteins 9, 10 , which sets up intriguing possibilities for testing such genes at the whole-animal level, for conferring gene-based immunity with them or engineered variants 12, 13 , and potentially for HIV-1 disease model development 10 . In experiments summarized in Supplementary Table 1 , we subjected 195 in vitro-matured grade I and II domestic cat oocytes to perivitelline space microinjection (PVSMI) with lentiviral vector TSinG 5 ; we performed injection 10-12 h before or 10-12 h after in vitro fertilization (IVF) (Supplementary Fig. 1 ). We consistently observed embryo-pervasive, abundant expression of both proteins encoded by dual gene vectors in cat blastocysts when we injected lentiviral vector before IVF ( Fig. 1b and Supplementary Table 2 ). doi = 10.1038/nmeth.1703 id = cord-348799-qu4zin3o author = Wu, Nannan title = The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation date = 2019-10-10 keywords = Fig; GFP; HEK293; ISG20; RNA; cell summary = This lack of specificity was not present in cells however, given that the ectopic expression of ISG20 did not lead to the indiscriminate degradation of cellular RNAs (ribosomal as well as small nucleolar RNAs previously shown to be associated to ISG20 [2] ), nor of an Hepatitis C virus (HCV)-derived Luciferase reporter mRNA produced in vitro and then transfected into cells (S4C and S4D Fig) , suggesting that in cells the RNase activity of ISG20 is tightly controlled. Self mimicry allows the escape of target genes'' mRNAs from the effects of ISG20 VSV infection and ectopic DNA or RNA transfection do not bear much in common apart from the fact that both represent artificial injections into the cell of non-self genetic material from without. To further determine whether ISG20 acted on translation initiation and more specifically through specific initiation factors (eIFs), capped and polyadenylated mRNAs coding luciferase under the control of several 5'' untranslated regions (5'' UTRs) were generated in vitro and directly transfected in ISG20-expressing cells (Fig 3D) . doi = 10.1371/journal.ppat.1008093 id = cord-273711-bxijla09 author = Zhao, Zhixun title = RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells date = 2012-02-17 keywords = GFP; GTPV; RNA summary = title: RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells When Vero cells were transfected with shRNA expression vectors (p61/GFP, p70/GFP, p165/GFP and p296/GFP) and then infected with GTPV, GTPV-ORF095-70 was found to be the most effective inhibition site in decreasing cytopathic effect (CPE) induced by GTPV. These results suggest that the siRNA generated by in vitro transcription effectively and specifically inhibit the expression of GTPV ORF095 conserved regions in BHK-21 cells. To investigate whether or not knockout of ORF095 relieves cytopathic effect (CPE) induced by GTPV, Vero cells were transfected by plasmids expressing ORF095 protein-targeted shRNAs (p61/GFP, p70/GFP, p165/GFP and p296/GFP), respectively. Therefore, ORF095 gene is a good target to suppress GTPV replication by RNAi. In conclusion, this study demonstrates that vector-based shRNA methodology can effectively inhibit GTPV replication on Vero cells. RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells doi = 10.1186/1743-422x-9-48 id = cord-004534-jqm1hxps author = nan title = Abstract date = 2009-06-09 keywords = AFM; ATP; Biology; Biophysics; Chemistry; Department; FCS; France; GFP; Genova; Germany; Hyp; Institute; Italy; Molecular; Physics; RNA; Sciences; University; cell; dna; fluorescence; fret; interaction; lipid; membrane; protein; result; structure; study summary = HIV-1 to efficiently complete a replication cycle has to integrate its genome into the host cellular DNA.After HIV-1 enters target cells,neosynthesized viral DNA forms along with other proteins the pre-integration complex (PIC).PICs are then transported into the nucleus where integration,catalyzed by the viral integrase,takes place.HIV-1 viral particles engineered to incorporate integrase fused to EGFP have proven effective to study PICs within nuclei of infected cells.In this study we report the live imaging analysis of nuclear PIC dynamics obtained by time-lapse microscopy.Intranuclear trajectories of IN-EGFP-labeled PIC were collected in three dimensions and examined by both mean squared displacement (MSD) and cage diameter (CD) analysis.In CD the maximum distances measured between two positions occupied by a PIC in a time window of 2 minutes were calculated while in our MSD analysis 5-minute long trajectory segments were considered.Remarkably,MSD revealed the presence of an underlying active transport mechanism.To test the possible role of actin filaments,PIC nuclear trafficking was analyzed in cells treated with latrunculin B (actin polymerization inhibitor).Preliminary results suggest that the disruption of actin function impairs the active nuclear movement of PICs. Second harmonic generation microscopy reveals sarcomere contractile dynamics of cardiomyocytes N. doi = 10.1007/s00249-009-0478-1 id = cord-023026-2r84ndzv author = nan title = Posters date = 2013-06-14 keywords = ATP; Alzheimer; BBB; BDNF; CNS; EAE; GABA; GFAP; GFP; GLT-1; IL-6; LPS; MBP; NMDA; OPC; PCR; SCI; SOD1; SVZ; Schwann; University; astrocyte; brain; cell; expression; increase; microglia; mouse; ng2; protein; result; role; study summary = Thus, this work provides the basis to identify molecular pathways regulated by distinct niche/environmental signals and involved in the heterogeneity of adult OPCs. Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative demyelinating disease of the central nervous system (CNS) characterized by inflammation, which leads to formation of demyelinating areas due to loss of oligodendrocytes, astrogliosis and, finally, axonal degeneration. Taken together, these results demonstrate the important role of miR-200b in modulating the MAPK pathway via c-Jun which in turn affects different aspects of the inflammatory process accompanying microglia activation including cytokine response, NO production, phagocytosis and neuronal cell death. For this purpose, coronal cryostat free-floating sections from the brain of both adult transgenic mice and their corresponding wild-type (Wt) littermates, were processed for the study of astrocytes using GFAP immunohistochemistry and microglia using antibodies against Iba1 and several markers commonly related to the activated phenotype of these microglial cells, such as CD16/32 (Fc receptor), F4/80, CD11b, CD206, CD150 and MHC-II. doi = 10.1002/glia.22530 id = cord-023211-kt5gt26t author = nan title = Poster Session Abstracts date = 2007-08-29 keywords = ASL; ATP; BMI; CFF; CFQ; CFRD; CFTR; Center; Cystic; DHA; FEV1; FVC; Fibrosis; Foundation; GFP; HBE; Hospital; IL-8; Isc; MRSA; Medical; NBD1; NIH; PCR; PKA; Pseudomonas; USA; United; University; airway; cell; conclusion; dna; increase; lung; method; patient; result; study; ∆F508; ∆F508-CFTR summary = Previous studies performed using fluorescence halide efflux measurements and short-circuit current voltage clamp have shown that treatment with PPARγ (peroxisome proliferator activated receptor gamma) agonists, such as pioglitazone and FLL (FMOC-L-leucine), resulted in an increased biosynthesis and trafficking of ∆F508-CFTR to the cell surface. Physiology, School of Medical Sciences, University of Bristol, Bristol, United Kingdom Recent progress in the development of small molecule correctors and potentiators capable of restoring CFTR function have increased the need for pre-clinical test models including cultured airway epithelial cells from human CF patients as well as CF mouse models. Clinical studies have linked increased sputum and peripheral blood neutrophil MPO activity with increased airflow obstruction in cystic fibrosis (CF) patients of the same age, gender, airway bacterial flora, and CFTR genotype. Because patients expressing low levels of normal CFTR mRNA (5-20%) have mild disease symptoms, these studies demonstrate that the incorporation of the ciliated cell-specific FOXJ1 promoter into gene therapy vectors may be useful for treatment of CF. doi = 10.1002/ppul.20700 id = cord-257167-rz4r5sj7 author = nan title = Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) date = 2006-12-31 keywords = Anatomy; BDNF; BSI; Biology; Brain; CA1; CNS; CREST; Center; Chiba; Department; Dept; Div; Division; Engineering; Fos; GABA; GFP; Graduate; Hiroshi; Institute; JST; Japan; KAKENHI; Kobe; Kyoto; LTD; LTP; Laboratory; Life; Medical; Medicine; NMDA; Nagoya; National; Neuroscience; Niigata; Okazaki; Osaka; PS1A; PS2P; PS3A; Physiology; Purkinje; RIKEN; Research; Saitama; Sato; School; Science; Sendai; Takashi; Technology; Tohoku; Tokyo; Tsukuba; USA; University; Wako; activity; cell; effect; mouse; neuron; neuronal; ps3p; response; result; study summary = SY1-3-11-3 SAD: A novel kinase implicated in phosphoproteome at the presynaptic active zone Toshihisa Ohtsuka Department of Clinical and Molecular Pathology, Faculty of Medicine/Graduate School of Medicine, University of Toyama, Toyama, Japan SAD is a serine/threonine kianse, which has been shown to regulate various neuronal functions during development, including clustering synaptic vesicles, maturation of synapses, and axon/dendrite polarization: these have recently been revealed by genetic studies in C. The results suggest that EAAT4 plays a major role in regulating the concentration of CF transmitters, possibly glutamate, in the route of its extrasynaptic diffusion, and determining the degree of CF-induced inhibition of GABA release from BCs depending on the regional difference of EAAT4 expression in postsynaptic PCs. Chitoshi Takayama 1 , Yoshiro Inoue 1 1 Department of Molecular Neuroanatomy, Hokkaido University School of Medicine, Sapporo, Japan GABA mediates inhibitory transmission in the adult central nervous system (CNS). doi = 10.1016/j.neures.2006.04.004 id = cord-307067-cpc1yefj author = van Doremalen, Neeltje title = A single dose of ChAdOx1 MERS provides protective immunity in rhesus macaques date = 2020-06-10 keywords = ChAdOx1; DPI; GFP; MERS; animal summary = For Middle East respiratory syndrome coronavirus (MERS-CoV), we show that rhesus macaques seroconverted rapidly after a single intramuscular vaccination with ChAdOx1 MERS. A prime-boost regimen of ChAdOx1 MERS boosted antibody titers, and viral replication was completely absent from the respiratory tract tissue of these rhesus macaques. Viral load was higher for lower respiratory tract tissue obtained from animals vaccinated with ChAdOx1 GFP (n = 6) than from animals receiving a prime-only (n = 6) or a prime-boost regimen of ChAdOx1 MERS (n = 2) (Fig. 4B ). Notably, antigenic differences have been reported between S proteins from the Middle East and Africa (8), potentially affecting the efficacy of a vaccine based In conclusion, we show that a single vaccination with ChAdOx1 MERS results in protection against disease progression and virus replication associated with MERS-CoV challenge in the rhesus macaque, and a prime-boost regimen reduced viral replication further. doi = 10.1126/sciadv.aba8399