Carrel name: keyword-gfp-cord Creating study carrel named keyword-gfp-cord Initializing database file: cache/cord-000933-nn9gj0z1.json key: cord-000933-nn9gj0z1 authors: Krzyzaniak, Magdalena Anna; Zumstein, Michael Thomas; Gerez, Juan Atilio; Picotti, Paola; Helenius, Ari title: Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein date: 2013-04-11 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1003309 sha: doc_id: 933 cord_uid: nn9gj0z1 file: cache/cord-001123-n2e4s7bu.json key: cord-001123-n2e4s7bu authors: Lin, Yue-Zhi; Yang, Fei; Zhang, Shu-Qin; Sun, Liu-Ke; Wang, Xue-Feng; Du, Cheng; Zhou, Jian-Hua title: The Soluble Form of the EIAV Receptor Encoded by an Alternative Splicing Variant Inhibits EIAV Infection of Target Cells date: 2013-11-22 journal: PLoS One DOI: 10.1371/journal.pone.0079299 sha: doc_id: 1123 cord_uid: n2e4s7bu file: cache/cord-018771-xqlb74px.json key: cord-018771-xqlb74px authors: Turinsky, Sebastian; Steuernagel, Claus title: Bluttransfusion date: 2013-04-04 journal: Praxis der Intensivmedizin DOI: 10.1007/978-3-642-34433-6_4 sha: doc_id: 18771 cord_uid: xqlb74px file: cache/cord-103509-hynnba03.json key: cord-103509-hynnba03 authors: Wong, Ten-Tsao; Liou, Gunn-Guang; Kan, Ming-Chung title: A self-assembled protein nanoparticle serving as a one-shot vaccine carrier date: 2020-09-18 journal: bioRxiv DOI: 10.1101/2020.09.16.299149 sha: doc_id: 103509 cord_uid: hynnba03 file: cache/cord-003705-ekhj8ae8.json key: cord-003705-ekhj8ae8 authors: Azkanaz, Maria; Rodríguez López, Aida; de Boer, Bauke; Huiting, Wouter; Angrand, Pierre-Olivier; Vellenga, Edo; Kampinga, Harm H; Bergink, Steven; Martens, Joost HA; Schuringa, Jan Jacob; van den Boom, Vincent title: Protein quality control in the nucleolus safeguards recovery of epigenetic regulators after heat shock date: 2019-06-14 journal: nan DOI: 10.7554/elife.45205 sha: doc_id: 3705 cord_uid: ekhj8ae8 file: cache/cord-258678-0atfsivf.json key: cord-258678-0atfsivf authors: Liu, Hong Yan; Gao, Xiaohu title: A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras date: 2013-11-07 journal: Sci Rep DOI: 10.1038/srep03129 sha: doc_id: 258678 cord_uid: 0atfsivf file: cache/cord-002320-m99amd4y.json key: cord-002320-m99amd4y authors: Mathur, Kalika; Anand, Abhishek; Dubey, Sunil Kumar; Sanan-Mishra, Neeti; Bhatnagar, Raj K.; Sunil, Sujatha title: Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity date: 2016-11-30 journal: Sci Rep DOI: 10.1038/srep38065 sha: doc_id: 2320 cord_uid: m99amd4y file: cache/cord-307067-cpc1yefj.json key: cord-307067-cpc1yefj authors: van Doremalen, Neeltje; Haddock, Elaine; Feldmann, Friederike; Meade-White, Kimberly; Bushmaker, Trenton; Fischer, Robert J.; Okumura, Atsushi; Hanley, Patrick W.; Saturday, Greg; Edwards, Nick J.; Clark, Madeleine H. A.; Lambe, Teresa; Gilbert, Sarah C.; Munster, Vincent J. title: A single dose of ChAdOx1 MERS provides protective immunity in rhesus macaques date: 2020-06-10 journal: Sci Adv DOI: 10.1126/sciadv.aba8399 sha: doc_id: 307067 cord_uid: cpc1yefj file: cache/cord-103868-iwpiti2h.json key: cord-103868-iwpiti2h authors: Harrison, Angela R.; Moseley, Gregory W. title: The Ebola virus interferon antagonist VP24 undergoes active nucleocytoplasmic trafficking date: 2020-08-11 journal: bioRxiv DOI: 10.1101/2020.08.10.245563 sha: doc_id: 103868 cord_uid: iwpiti2h file: cache/cord-002076-7t4d4vvo.json key: cord-002076-7t4d4vvo authors: Li, Yongfeng; Li, Lian-Feng; Yu, Shaoxiong; Wang, Xiao; Zhang, Lingkai; Yu, Jiahui; Xie, Libao; Li, Weike; Ali, Razim; Qiu, Hua-Ji title: Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology date: 2016-05-06 journal: Viruses DOI: 10.3390/v8050127 sha: doc_id: 2076 cord_uid: 7t4d4vvo file: cache/cord-102184-8u73adnk.json key: cord-102184-8u73adnk authors: Li, Jinzhi; Mahoney, Brennan Dale; Jacob, Miles Solomon; Caron, Sophie Jeanne Cécile title: Visual input into the Drosophila melanogaster mushroom body date: 2020-05-02 journal: bioRxiv DOI: 10.1101/2020.02.07.935924 sha: doc_id: 102184 cord_uid: 8u73adnk file: cache/cord-330176-1ugzkf22.json key: cord-330176-1ugzkf22 authors: Weeratunga, Prasanna; Uddin, Md Bashir; Kim, Myun Soo; Lee, Byeong-Hoon; Kim, Tae-Hwan; Yoon, Ji-Eun; Ma, Jin Yeul; Kim, Hongik; Lee, Jong-Soo title: RETRACTED ARTICLE: Interferon-mediated antiviral activities of Angelica tenuissima Nakai and its active components date: 2016-01-05 journal: J Microbiol DOI: 10.1007/s12275-016-5555-4 sha: doc_id: 330176 cord_uid: 1ugzkf22 file: cache/cord-001365-6u80p5sj.json key: cord-001365-6u80p5sj authors: Weger-Lucarelli, James; Chu, Haiyan; Aliota, Matthew T.; Partidos, Charalambos D.; Osorio, Jorge E. title: A Novel MVA Vectored Chikungunya Virus Vaccine Elicits Protective Immunity in Mice date: 2014-07-24 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0002970 sha: doc_id: 1365 cord_uid: 6u80p5sj file: cache/cord-316814-9fv9xrln.json key: cord-316814-9fv9xrln authors: Li, Hong-Ye; Chye, Mee-Len title: Use of GFP to Investigate Expression of Plant-Derived Vaccines date: 2009 journal: Viral Applications of Green Fluorescent Protein DOI: 10.1007/978-1-59745-559-6_19 sha: doc_id: 316814 cord_uid: 9fv9xrln file: cache/cord-253709-frauasts.json key: cord-253709-frauasts authors: Lan, Dongming; Huang, Guangrui; Shao, Hongwei; Zhang, Lichun; Ma, Lixin; Chen, Shangwu; Xu, Anlong title: An improved nonchromatographic method for the purification of recombinant proteins using elastin-like polypeptide-tagged proteases date: 2011-08-15 journal: Analytical Biochemistry DOI: 10.1016/j.ab.2011.04.034 sha: doc_id: 253709 cord_uid: frauasts file: cache/cord-319517-denczc6t.json key: cord-319517-denczc6t authors: Salipalli, Sandeep; Singh, Prafull Kumar; Borlak, Jürgen title: Recent advances in live cell imaging of hepatoma cells date: 2014-07-08 journal: BMC Cell Biol DOI: 10.1186/1471-2121-15-26 sha: doc_id: 319517 cord_uid: denczc6t file: cache/cord-001270-l8aa9cl3.json key: cord-001270-l8aa9cl3 authors: Wongsrikeao, Pimprapar; Saenz, Dyana; Rinkoski, Tommy; Otoi, Takeshige; Poeschla, Eric title: Antiviral restriction factor transgenesis in the domestic cat date: 2011-09-11 journal: Nat Methods DOI: 10.1038/nmeth.1703 sha: doc_id: 1270 cord_uid: l8aa9cl3 file: cache/cord-299509-7xjdryoq.json key: cord-299509-7xjdryoq authors: Scholte, Florine E. M.; Tas, Ali; Martina, Byron E. E.; Cordioli, Paolo; Narayanan, Krishna; Makino, Shinji; Snijder, Eric J.; van Hemert, Martijn J. title: Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates date: 2013-08-01 journal: PLoS One DOI: 10.1371/journal.pone.0071047 sha: doc_id: 299509 cord_uid: 7xjdryoq file: cache/cord-324720-acei0pn8.json key: cord-324720-acei0pn8 authors: Howe, Charles L; LaFrance-Corey, Reghann G; Sundsbak, Rhianna S; LaFrance, Stephanie J title: Inflammatory monocytes damage the hippocampus during acute picornavirus infection of the brain date: 2012-03-09 journal: J Neuroinflammation DOI: 10.1186/1742-2094-9-50 sha: doc_id: 324720 cord_uid: acei0pn8 file: cache/cord-280454-etf32afd.json key: cord-280454-etf32afd authors: Moustaqil, Mehdi; Ollivier, Emma; Chiu, Hsin-Ping; Van Tol, Sarah; Rudolffi-Soto, Paulina; Stevens, Christian; Bhumkar, Akshay; Hunter, Dominic J.B.; Freiberg, Alex; Jacques, David; Lee, Benhur; Sierecki, Emma; Gambin, Yann 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 journal: bioRxiv DOI: 10.1101/2020.06.05.135699 sha: doc_id: 280454 cord_uid: etf32afd file: cache/cord-315483-l6dm82pp.json key: cord-315483-l6dm82pp authors: Santhakumar, Diwakar; Rohaim, Mohammed Abdel Mohsen Shahaat; Hussein, Hussein A.; Hawes, Pippa; Ferreira, Helena Lage; Behboudi, Shahriar; Iqbal, Munir; Nair, Venugopal; Arns, Clarice W.; Munir, Muhammad title: Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses date: 2018-05-01 journal: Sci Rep DOI: 10.1038/s41598-018-24905-y sha: doc_id: 315483 cord_uid: l6dm82pp file: cache/cord-275307-d7htyfcl.json key: cord-275307-d7htyfcl authors: Gaglia, Marta Maria; Rycroft, Chris H.; Glaunsinger, Britt A. title: Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX date: 2015-12-08 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1005305 sha: doc_id: 275307 cord_uid: d7htyfcl file: cache/cord-273711-bxijla09.json key: cord-273711-bxijla09 authors: Zhao, Zhixun; Wu, Guohua; Zhu, Xueliang; Yan, Xinmin; Dou, Yongxi; Li, Jian; Zhu, Haixia; Zhang, Qiang; Cai, Xuepeng title: RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells date: 2012-02-17 journal: Virol J DOI: 10.1186/1743-422x-9-48 sha: doc_id: 273711 cord_uid: bxijla09 file: cache/cord-332881-mkm4ygh6.json key: cord-332881-mkm4ygh6 authors: Kirchhoff, Jana; Uhlenbruck, Sabine; Goris, Katherina; Keil, Günther M; Herrler, Georg title: Three viruses of the bovine respiratory disease complex apply different strategies to initiate infection date: 2014-02-18 journal: Vet Res DOI: 10.1186/1297-9716-45-20 sha: doc_id: 332881 cord_uid: mkm4ygh6 file: cache/cord-319842-4mnaicki.json key: cord-319842-4mnaicki authors: Jackson, William T; Giddings, Thomas H; Taylor, Matthew P; Mulinyawe, Sara; Rabinovitch, Marlene; Kopito, Ron R; Kirkegaard, Karla title: Subversion of Cellular Autophagosomal Machinery by RNA Viruses date: 2005-04-26 journal: PLoS Biol DOI: 10.1371/journal.pbio.0030156 sha: doc_id: 319842 cord_uid: 4mnaicki file: cache/cord-317142-qd61qvch.json key: cord-317142-qd61qvch authors: Muramatsu, Tomonari; Kim, Yong‐Tae; Nishii, Wataru; Terada, Takaho; Shirouzu, Mikako; Yokoyama, Shigeyuki title: Autoprocessing mechanism of severe acute respiratory syndrome coronavirus 3C‐like protease (SARS‐CoV 3CL (pro)) from its polyproteins date: 2013-03-27 journal: FEBS J DOI: 10.1111/febs.12222 sha: doc_id: 317142 cord_uid: qd61qvch file: cache/cord-346554-a98pjtxs.json key: cord-346554-a98pjtxs authors: Uddin, Md Bashir; Lee, Byeong-Hoon; Nikapitiya, Chamilani; Kim, Jae-Hoon; Kim, Tae-Hwan; Lee, Hyun-Cheol; Kim, Choul Goo; Lee, Jong-Soo; Kim, Chul-Joong title: Inhibitory effects of bee venom and its components against viruses in vitro and in vivo date: 2016-11-26 journal: J Microbiol DOI: 10.1007/s12275-016-6376-1 sha: doc_id: 346554 cord_uid: a98pjtxs file: cache/cord-345651-admlzeu4.json key: cord-345651-admlzeu4 authors: Wang, Gang; Liang, Rui; Liu, Ziwei; Shen, Zhou; Shi, Jiale; Shi, Yuejun; Deng, Feng; Xiao, Shaobo; Fu, Zhen F.; Peng, Guiqing title: The N-Terminal Domain of Spike Protein Is Not the Enteric Tropism Determinant for Transmissible Gastroenteritis Virus in Piglets date: 2019-03-30 journal: Viruses DOI: 10.3390/v11040313 sha: doc_id: 345651 cord_uid: admlzeu4 file: cache/cord-331414-i0oxm5mr.json key: cord-331414-i0oxm5mr authors: Kautz, Tiffany F.; Jaworski, Elizabeth; Routh, Andrew; Forrester, Naomi L. title: A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene date: 2020-06-19 journal: Viruses DOI: 10.3390/v12060660 sha: doc_id: 331414 cord_uid: i0oxm5mr file: cache/cord-354052-x4ckzw64.json key: cord-354052-x4ckzw64 authors: Li, Chunhua; Li, Zhen; Zou, Yong; Wicht, Oliver; van Kuppeveld, Frank J. M.; Rottier, Peter J. M.; Bosch, Berend Jan title: Manipulation of the Porcine Epidemic Diarrhea Virus Genome Using Targeted RNA Recombination date: 2013-08-02 journal: PLoS One DOI: 10.1371/journal.pone.0069997 sha: doc_id: 354052 cord_uid: x4ckzw64 file: cache/cord-272018-txdc0c3j.json key: cord-272018-txdc0c3j authors: Laing, Eric D.; Sterling, Spencer L.; Weir, Dawn L.; Beauregard, Chelsi R.; Smith, Ina L.; Larsen, Sasha E.; Wang, Lin-Fa; Snow, Andrew L.; Schaefer, Brian C.; Broder, Christopher C. title: Enhanced Autophagy Contributes to Reduced Viral Infection in Black Flying Fox Cells date: 2019-03-14 journal: Viruses DOI: 10.3390/v11030260 sha: doc_id: 272018 cord_uid: txdc0c3j file: cache/cord-353467-wbtzvm4i.json key: cord-353467-wbtzvm4i authors: Lambert, Carsten; Thomé, Nicole; Kluck, Christoph J.; Prange, Reinhild title: Functional incorporation of green fluorescent protein into hepatitis B virus envelope particles date: 2004-12-05 journal: Virology DOI: 10.1016/j.virol.2004.09.031 sha: doc_id: 353467 cord_uid: wbtzvm4i file: cache/cord-334855-s0ci3r8w.json key: cord-334855-s0ci3r8w authors: Andersen, Petter I.; Krpina, Klara; Ianevski, Aleksandr; Shtaida, Nastassia; Jo, Eunji; Yang, Jaewon; Koit, Sandra; Tenson, Tanel; Hukkanen, Veijo; Anthonsen, Marit W.; Bjoras, Magnar; Evander, Magnus; Windisch, Marc P.; Zusinaite, Eva; Kainov, Denis E. title: Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine date: 2019-10-18 journal: Viruses DOI: 10.3390/v11100964 sha: doc_id: 334855 cord_uid: s0ci3r8w file: cache/cord-274210-uaaj66xq.json key: cord-274210-uaaj66xq authors: Ding, Ning; Zhao, Kui; Lan, Yungang; Li, Zi; Lv, Xiaoling; Su, Jingjing; Lu, Huijun; Gao, Feng; He, Wenqi title: Induction of Atypical Autophagy by Porcine Hemagglutinating Encephalomyelitis Virus Contributes to Viral Replication date: 2017-02-28 journal: Front Cell Infect Microbiol DOI: 10.3389/fcimb.2017.00056 sha: doc_id: 274210 cord_uid: uaaj66xq file: cache/cord-338811-2bi2edcw.json key: cord-338811-2bi2edcw authors: Lennemann, Nicholas J.; Evans, Azia S.; Coyne, Carolyn B. title: Imaging-Based Reporter Systems to Define CVB-Induced Membrane Remodeling in Living Cells date: 2020-09-25 journal: Viruses DOI: 10.3390/v12101074 sha: doc_id: 338811 cord_uid: 2bi2edcw file: cache/cord-342189-ya05m58o.json key: cord-342189-ya05m58o authors: Banerjee, Abhik K.; Blanco, Mario R.; Bruce, Emily A.; Honson, Drew D.; Chen, Linlin M.; Chow, Amy; Bhat, Prashant; Ollikainen, Noah; Quinodoz, Sofia A.; Loney, Colin; Thai, Jasmine; Miller, Zachary D.; Lin, Aaron E.; Schmidt, Madaline M.; Stewart, Douglas G.; Goldfarb, Daniel; De Lorenzo, Giuditta; Rihn, Suzannah J.; Voorhees, Rebecca; Botten, Jason W.; Majumdar, Devdoot; Guttman, Mitchell title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date: 2020-10-08 journal: Cell DOI: 10.1016/j.cell.2020.10.004 sha: doc_id: 342189 cord_uid: ya05m58o file: cache/cord-348799-qu4zin3o.json key: cord-348799-qu4zin3o authors: Wu, Nannan; Nguyen, Xuan-Nhi; Wang, Li; Appourchaux, Romain; Zhang, Chengfei; Panthu, Baptiste; Gruffat, Henri; Journo, Chloé; Alais, Sandrine; Qin, Juliang; Zhang, Na; Tartour, Kevin; Catez, Frédéric; Mahieux, Renaud; Ohlmann, Theophile; Liu, Mingyao; Du, Bing; Cimarelli, Andrea 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 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008093 sha: doc_id: 348799 cord_uid: qu4zin3o file: cache/cord-004534-jqm1hxps.json key: cord-004534-jqm1hxps authors: nan title: Abstract date: 2009-06-09 journal: Eur Biophys J DOI: 10.1007/s00249-009-0478-1 sha: doc_id: 4534 cord_uid: jqm1hxps file: cache/cord-023026-2r84ndzv.json key: cord-023026-2r84ndzv authors: nan title: Posters date: 2013-06-14 journal: Glia DOI: 10.1002/glia.22530 sha: doc_id: 23026 cord_uid: 2r84ndzv file: cache/cord-257167-rz4r5sj7.json key: cord-257167-rz4r5sj7 authors: nan title: Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) date: 2006-12-31 journal: Neuroscience Research DOI: 10.1016/j.neures.2006.04.004 sha: doc_id: 257167 cord_uid: rz4r5sj7 file: cache/cord-023211-kt5gt26t.json key: cord-023211-kt5gt26t authors: nan title: Poster Session Abstracts date: 2007-08-29 journal: Pediatr Pulmonol DOI: 10.1002/ppul.20700 sha: doc_id: 23211 cord_uid: kt5gt26t Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-gfp-cord === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14119 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14040 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 13955 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14228 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-018771-xqlb74px author: Turinsky, Sebastian title: Bluttransfusion date: 2013-04-04 pages: extension: .txt txt: ./txt/cord-018771-xqlb74px.txt cache: ./cache/cord-018771-xqlb74px.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018771-xqlb74px.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-253709-frauasts.txt cache: ./cache/cord-253709-frauasts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253709-frauasts.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-103509-hynnba03.txt cache: ./cache/cord-103509-hynnba03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103509-hynnba03.txt' === file2bib.sh === id: cord-103868-iwpiti2h author: Harrison, Angela R. title: The Ebola virus interferon antagonist VP24 undergoes active nucleocytoplasmic trafficking date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-103868-iwpiti2h.txt cache: ./cache/cord-103868-iwpiti2h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103868-iwpiti2h.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-002320-m99amd4y.txt cache: ./cache/cord-002320-m99amd4y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002320-m99amd4y.txt' === file2bib.sh === id: cord-334855-s0ci3r8w author: Andersen, Petter I. title: Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine date: 2019-10-18 pages: extension: .txt txt: ./txt/cord-334855-s0ci3r8w.txt cache: ./cache/cord-334855-s0ci3r8w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334855-s0ci3r8w.txt' === file2bib.sh === id: cord-258678-0atfsivf author: Liu, Hong Yan title: A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras date: 2013-11-07 pages: extension: .txt txt: ./txt/cord-258678-0atfsivf.txt cache: ./cache/cord-258678-0atfsivf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258678-0atfsivf.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-273711-bxijla09.txt cache: ./cache/cord-273711-bxijla09.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273711-bxijla09.txt' === file2bib.sh === id: cord-316814-9fv9xrln author: Li, Hong-Ye title: Use of GFP to Investigate Expression of Plant-Derived Vaccines date: 2009 pages: extension: .txt txt: ./txt/cord-316814-9fv9xrln.txt cache: ./cache/cord-316814-9fv9xrln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316814-9fv9xrln.txt' === file2bib.sh === id: cord-002076-7t4d4vvo author: Li, Yongfeng title: Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology date: 2016-05-06 pages: extension: .txt txt: ./txt/cord-002076-7t4d4vvo.txt cache: ./cache/cord-002076-7t4d4vvo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002076-7t4d4vvo.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-001123-n2e4s7bu.txt cache: ./cache/cord-001123-n2e4s7bu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001123-n2e4s7bu.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-274210-uaaj66xq.txt cache: ./cache/cord-274210-uaaj66xq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274210-uaaj66xq.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-307067-cpc1yefj.txt cache: ./cache/cord-307067-cpc1yefj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307067-cpc1yefj.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-338811-2bi2edcw.txt cache: ./cache/cord-338811-2bi2edcw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338811-2bi2edcw.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-324720-acei0pn8.txt cache: ./cache/cord-324720-acei0pn8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324720-acei0pn8.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-317142-qd61qvch.txt cache: ./cache/cord-317142-qd61qvch.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317142-qd61qvch.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-330176-1ugzkf22.txt cache: ./cache/cord-330176-1ugzkf22.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-330176-1ugzkf22.txt' === file2bib.sh === id: cord-319842-4mnaicki author: Jackson, William T title: Subversion of Cellular Autophagosomal Machinery by RNA Viruses date: 2005-04-26 pages: extension: .txt txt: ./txt/cord-319842-4mnaicki.txt cache: ./cache/cord-319842-4mnaicki.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319842-4mnaicki.txt' === file2bib.sh === id: cord-001270-l8aa9cl3 author: Wongsrikeao, Pimprapar title: Antiviral restriction factor transgenesis in the domestic cat date: 2011-09-11 pages: extension: .txt txt: ./txt/cord-001270-l8aa9cl3.txt cache: ./cache/cord-001270-l8aa9cl3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001270-l8aa9cl3.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-345651-admlzeu4.txt cache: ./cache/cord-345651-admlzeu4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345651-admlzeu4.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-332881-mkm4ygh6.txt cache: ./cache/cord-332881-mkm4ygh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332881-mkm4ygh6.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-299509-7xjdryoq.txt cache: ./cache/cord-299509-7xjdryoq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299509-7xjdryoq.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-346554-a98pjtxs.txt cache: ./cache/cord-346554-a98pjtxs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346554-a98pjtxs.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-001365-6u80p5sj.txt cache: ./cache/cord-001365-6u80p5sj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-001365-6u80p5sj.txt' === file2bib.sh === id: cord-102184-8u73adnk author: Li, Jinzhi title: Visual input into the Drosophila melanogaster mushroom body date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-102184-8u73adnk.txt cache: ./cache/cord-102184-8u73adnk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-102184-8u73adnk.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-280454-etf32afd.txt cache: ./cache/cord-280454-etf32afd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-280454-etf32afd.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-003705-ekhj8ae8.txt cache: ./cache/cord-003705-ekhj8ae8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003705-ekhj8ae8.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-000933-nn9gj0z1.txt cache: ./cache/cord-000933-nn9gj0z1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000933-nn9gj0z1.txt' === file2bib.sh === id: cord-319517-denczc6t author: Salipalli, Sandeep title: Recent advances in live cell imaging of hepatoma cells date: 2014-07-08 pages: extension: .txt txt: ./txt/cord-319517-denczc6t.txt cache: ./cache/cord-319517-denczc6t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319517-denczc6t.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-348799-qu4zin3o.txt cache: ./cache/cord-348799-qu4zin3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-348799-qu4zin3o.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-275307-d7htyfcl.txt cache: ./cache/cord-275307-d7htyfcl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275307-d7htyfcl.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-315483-l6dm82pp.txt cache: ./cache/cord-315483-l6dm82pp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315483-l6dm82pp.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-342189-ya05m58o.txt cache: ./cache/cord-342189-ya05m58o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342189-ya05m58o.txt' === file2bib.sh === id: cord-004534-jqm1hxps author: nan title: Abstract date: 2009-06-09 pages: extension: .txt txt: ./txt/cord-004534-jqm1hxps.txt cache: ./cache/cord-004534-jqm1hxps.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 13 resourceName b'cord-004534-jqm1hxps.txt' === file2bib.sh === id: cord-023026-2r84ndzv author: nan title: Posters date: 2013-06-14 pages: extension: .txt txt: ./txt/cord-023026-2r84ndzv.txt cache: ./cache/cord-023026-2r84ndzv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-023026-2r84ndzv.txt' === file2bib.sh === id: cord-023211-kt5gt26t author: nan title: Poster Session Abstracts date: 2007-08-29 pages: extension: .txt txt: ./txt/cord-023211-kt5gt26t.txt cache: ./cache/cord-023211-kt5gt26t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 20 resourceName b'cord-023211-kt5gt26t.txt' === file2bib.sh === id: cord-257167-rz4r5sj7 author: nan title: Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) date: 2006-12-31 pages: extension: .txt txt: ./txt/cord-257167-rz4r5sj7.txt cache: ./cache/cord-257167-rz4r5sj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 29 resourceName b'cord-257167-rz4r5sj7.txt' Que is empty; done keyword-gfp-cord === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 5827 sentences = 282 flesch = 51 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. cache = ./cache/cord-001123-n2e4s7bu.txt txt = ./txt/cord-001123-n2e4s7bu.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 10347 sentences = 569 flesch = 54 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) . cache = ./cache/cord-000933-nn9gj0z1.txt txt = ./txt/cord-000933-nn9gj0z1.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 3187 sentences = 148 flesch = 48 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) cache = ./cache/cord-103509-hynnba03.txt txt = ./txt/cord-103509-hynnba03.txt === reduce.pl bib === id = cord-018771-xqlb74px author = Turinsky, Sebastian title = Bluttransfusion date = 2013-04-04 pages = extension = .txt mime = text/plain words = 1802 sentences = 279 flesch = 51 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. cache = ./cache/cord-018771-xqlb74px.txt txt = ./txt/cord-018771-xqlb74px.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 9362 sentences = 488 flesch = 49 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). cache = ./cache/cord-003705-ekhj8ae8.txt txt = ./txt/cord-003705-ekhj8ae8.txt === reduce.pl bib === id = cord-103868-iwpiti2h author = Harrison, Angela R. title = The Ebola virus interferon antagonist VP24 undergoes active nucleocytoplasmic trafficking date = 2020-08-11 pages = extension = .txt mime = text/plain words = 2255 sentences = 124 flesch = 45 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. cache = ./cache/cord-103868-iwpiti2h.txt txt = ./txt/cord-103868-iwpiti2h.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 5671 sentences = 338 flesch = 56 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. cache = ./cache/cord-002320-m99amd4y.txt txt = ./txt/cord-002320-m99amd4y.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 6244 sentences = 329 flesch = 50 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. cache = ./cache/cord-307067-cpc1yefj.txt txt = ./txt/cord-307067-cpc1yefj.txt === reduce.pl bib === id = cord-258678-0atfsivf author = Liu, Hong Yan title = A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras date = 2013-11-07 pages = extension = .txt mime = text/plain words = 4788 sentences = 282 flesch = 51 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. cache = ./cache/cord-258678-0atfsivf.txt txt = ./txt/cord-258678-0atfsivf.txt === reduce.pl bib === id = cord-002076-7t4d4vvo author = Li, Yongfeng title = Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology date = 2016-05-06 pages = extension = .txt mime = text/plain words = 4996 sentences = 229 flesch = 36 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. cache = ./cache/cord-002076-7t4d4vvo.txt txt = ./txt/cord-002076-7t4d4vvo.txt === reduce.pl bib === id = cord-102184-8u73adnk author = Li, Jinzhi title = Visual input into the Drosophila melanogaster mushroom body date = 2020-05-02 pages = extension = .txt mime = text/plain words = 8655 sentences = 418 flesch = 57 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. cache = ./cache/cord-102184-8u73adnk.txt txt = ./txt/cord-102184-8u73adnk.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 2063 sentences = 112 flesch = 52 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. cache = ./cache/cord-253709-frauasts.txt txt = ./txt/cord-253709-frauasts.txt === reduce.pl bib === id = cord-316814-9fv9xrln author = Li, Hong-Ye title = Use of GFP to Investigate Expression of Plant-Derived Vaccines date = 2009 pages = extension = .txt mime = text/plain words = 2817 sentences = 204 flesch = 53 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. cache = ./cache/cord-316814-9fv9xrln.txt txt = ./txt/cord-316814-9fv9xrln.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 8471 sentences = 426 flesch = 51 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. cache = ./cache/cord-001365-6u80p5sj.txt txt = ./txt/cord-001365-6u80p5sj.txt === reduce.pl bib === id = cord-319517-denczc6t author = Salipalli, Sandeep title = Recent advances in live cell imaging of hepatoma cells date = 2014-07-08 pages = extension = .txt mime = text/plain words = 9184 sentences = 433 flesch = 46 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. cache = ./cache/cord-319517-denczc6t.txt txt = ./txt/cord-319517-denczc6t.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 9607 sentences = 442 flesch = 48 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) . cache = ./cache/cord-299509-7xjdryoq.txt txt = ./txt/cord-299509-7xjdryoq.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 7948 sentences = 396 flesch = 53 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. cache = ./cache/cord-330176-1ugzkf22.txt txt = ./txt/cord-330176-1ugzkf22.txt === reduce.pl bib === id = cord-001270-l8aa9cl3 author = Wongsrikeao, Pimprapar title = Antiviral restriction factor transgenesis in the domestic cat date = 2011-09-11 pages = extension = .txt mime = text/plain words = 6269 sentences = 333 flesch = 47 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 ). cache = ./cache/cord-001270-l8aa9cl3.txt txt = ./txt/cord-001270-l8aa9cl3.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 10152 sentences = 562 flesch = 56 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. cache = ./cache/cord-280454-etf32afd.txt txt = ./txt/cord-280454-etf32afd.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 5532 sentences = 348 flesch = 54 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). cache = ./cache/cord-324720-acei0pn8.txt txt = ./txt/cord-324720-acei0pn8.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 10776 sentences = 579 flesch = 47 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 ). cache = ./cache/cord-315483-l6dm82pp.txt txt = ./txt/cord-315483-l6dm82pp.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 10860 sentences = 537 flesch = 57 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) . cache = ./cache/cord-275307-d7htyfcl.txt txt = ./txt/cord-275307-d7htyfcl.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 6369 sentences = 339 flesch = 49 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. cache = ./cache/cord-332881-mkm4ygh6.txt txt = ./txt/cord-332881-mkm4ygh6.txt === reduce.pl bib === id = cord-319842-4mnaicki author = Jackson, William T title = Subversion of Cellular Autophagosomal Machinery by RNA Viruses date = 2005-04-26 pages = extension = .txt mime = text/plain words = 6936 sentences = 320 flesch = 39 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. cache = ./cache/cord-319842-4mnaicki.txt txt = ./txt/cord-319842-4mnaicki.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 4172 sentences = 242 flesch = 53 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 cache = ./cache/cord-273711-bxijla09.txt txt = ./txt/cord-273711-bxijla09.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 6356 sentences = 268 flesch = 56 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) . cache = ./cache/cord-317142-qd61qvch.txt txt = ./txt/cord-317142-qd61qvch.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 7836 sentences = 405 flesch = 55 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. cache = ./cache/cord-346554-a98pjtxs.txt txt = ./txt/cord-346554-a98pjtxs.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 6220 sentences = 265 flesch = 49 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 cache = ./cache/cord-345651-admlzeu4.txt txt = ./txt/cord-345651-admlzeu4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 11469 sentences = 647 flesch = 55 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. cache = ./cache/cord-342189-ya05m58o.txt txt = ./txt/cord-342189-ya05m58o.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 5129 sentences = 270 flesch = 45 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) . cache = ./cache/cord-274210-uaaj66xq.txt txt = ./txt/cord-274210-uaaj66xq.txt === reduce.pl bib === id = cord-023026-2r84ndzv author = nan title = Posters date = 2013-06-14 pages = extension = .txt mime = text/plain words = 138458 sentences = 6513 flesch = 40 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. cache = ./cache/cord-023026-2r84ndzv.txt txt = ./txt/cord-023026-2r84ndzv.txt === reduce.pl bib === id = cord-334855-s0ci3r8w author = Andersen, Petter I. title = Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine date = 2019-10-18 pages = extension = .txt mime = text/plain words = 4274 sentences = 272 flesch = 48 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 cache = ./cache/cord-334855-s0ci3r8w.txt txt = ./txt/cord-334855-s0ci3r8w.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 11391 sentences = 520 flesch = 48 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) . cache = ./cache/cord-348799-qu4zin3o.txt txt = ./txt/cord-348799-qu4zin3o.txt === reduce.pl bib === id = cord-023211-kt5gt26t author = nan title = Poster Session Abstracts date = 2007-08-29 pages = extension = .txt mime = text/plain words = 221224 sentences = 11772 flesch = 52 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. cache = ./cache/cord-023211-kt5gt26t.txt txt = ./txt/cord-023211-kt5gt26t.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 6671 sentences = 327 flesch = 43 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. cache = ./cache/cord-338811-2bi2edcw.txt txt = ./txt/cord-338811-2bi2edcw.txt === reduce.pl bib === id = cord-004534-jqm1hxps author = nan title = Abstract date = 2009-06-09 pages = extension = .txt mime = text/plain words = 139023 sentences = 6450 flesch = 42 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. cache = ./cache/cord-004534-jqm1hxps.txt txt = ./txt/cord-004534-jqm1hxps.txt === reduce.pl bib === id = cord-257167-rz4r5sj7 author = nan title = Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) date = 2006-12-31 pages = extension = .txt mime = text/plain words = 240925 sentences = 13617 flesch = 47 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). cache = ./cache/cord-257167-rz4r5sj7.txt txt = ./txt/cord-257167-rz4r5sj7.txt === reduce.pl bib === ===== Reducing email addresses cord-342189-ya05m58o cord-004534-jqm1hxps Creating transaction Updating adr table ===== Reducing keywords cord-000933-nn9gj0z1 cord-018771-xqlb74px cord-001123-n2e4s7bu cord-103509-hynnba03 cord-258678-0atfsivf cord-003705-ekhj8ae8 cord-002320-m99amd4y cord-103868-iwpiti2h cord-307067-cpc1yefj cord-102184-8u73adnk cord-001365-6u80p5sj cord-002076-7t4d4vvo cord-330176-1ugzkf22 cord-001270-l8aa9cl3 cord-316814-9fv9xrln cord-299509-7xjdryoq cord-253709-frauasts cord-324720-acei0pn8 cord-315483-l6dm82pp cord-280454-etf32afd cord-275307-d7htyfcl cord-273711-bxijla09 cord-319517-denczc6t cord-317142-qd61qvch cord-332881-mkm4ygh6 cord-319842-4mnaicki cord-331414-i0oxm5mr cord-272018-txdc0c3j cord-345651-admlzeu4 cord-346554-a98pjtxs cord-354052-x4ckzw64 cord-334855-s0ci3r8w cord-353467-wbtzvm4i cord-342189-ya05m58o cord-274210-uaaj66xq cord-338811-2bi2edcw cord-023026-2r84ndzv cord-023211-kt5gt26t cord-257167-rz4r5sj7 cord-004534-jqm1hxps cord-348799-qu4zin3o Creating transaction Updating wrd table ===== Reducing urls cord-003705-ekhj8ae8 cord-307067-cpc1yefj cord-102184-8u73adnk cord-324720-acei0pn8 cord-001270-l8aa9cl3 cord-273711-bxijla09 cord-315483-l6dm82pp cord-319842-4mnaicki cord-280454-etf32afd cord-317142-qd61qvch cord-334855-s0ci3r8w cord-342189-ya05m58o cord-004534-jqm1hxps cord-338811-2bi2edcw cord-257167-rz4r5sj7 cord-348799-qu4zin3o Creating transaction Updating url table ===== Reducing named entities cord-000933-nn9gj0z1 cord-018771-xqlb74px cord-103509-hynnba03 cord-001123-n2e4s7bu cord-258678-0atfsivf cord-003705-ekhj8ae8 cord-002320-m99amd4y cord-002076-7t4d4vvo cord-103868-iwpiti2h cord-330176-1ugzkf22 cord-307067-cpc1yefj cord-102184-8u73adnk cord-316814-9fv9xrln cord-253709-frauasts cord-001365-6u80p5sj cord-319517-denczc6t cord-001270-l8aa9cl3 cord-299509-7xjdryoq cord-280454-etf32afd cord-315483-l6dm82pp cord-275307-d7htyfcl cord-317142-qd61qvch cord-324720-acei0pn8 cord-319842-4mnaicki cord-332881-mkm4ygh6 cord-273711-bxijla09 cord-346554-a98pjtxs cord-345651-admlzeu4 cord-331414-i0oxm5mr cord-354052-x4ckzw64 cord-272018-txdc0c3j cord-353467-wbtzvm4i cord-338811-2bi2edcw cord-334855-s0ci3r8w cord-348799-qu4zin3o cord-342189-ya05m58o cord-004534-jqm1hxps cord-274210-uaaj66xq cord-023026-2r84ndzv cord-023211-kt5gt26t cord-257167-rz4r5sj7 Creating transaction Updating ent table ===== Reducing parts of speech cord-001123-n2e4s7bu cord-000933-nn9gj0z1 cord-018771-xqlb74px cord-103509-hynnba03 cord-258678-0atfsivf cord-003705-ekhj8ae8 cord-002076-7t4d4vvo cord-330176-1ugzkf22 cord-002320-m99amd4y cord-253709-frauasts cord-307067-cpc1yefj cord-103868-iwpiti2h cord-316814-9fv9xrln cord-001365-6u80p5sj cord-102184-8u73adnk cord-001270-l8aa9cl3 cord-319517-denczc6t cord-299509-7xjdryoq cord-324720-acei0pn8 cord-280454-etf32afd cord-273711-bxijla09 cord-275307-d7htyfcl cord-332881-mkm4ygh6 cord-319842-4mnaicki cord-315483-l6dm82pp cord-346554-a98pjtxs cord-317142-qd61qvch cord-345651-admlzeu4 cord-272018-txdc0c3j cord-331414-i0oxm5mr cord-354052-x4ckzw64 cord-274210-uaaj66xq cord-353467-wbtzvm4i cord-342189-ya05m58o cord-334855-s0ci3r8w cord-338811-2bi2edcw cord-348799-qu4zin3o cord-023026-2r84ndzv cord-004534-jqm1hxps cord-023211-kt5gt26t cord-257167-rz4r5sj7 Creating transaction Updating pos table Building ./etc/reader.txt cord-257167-rz4r5sj7 cord-023026-2r84ndzv cord-023211-kt5gt26t cord-023211-kt5gt26t cord-257167-rz4r5sj7 cord-023026-2r84ndzv number of items: 41 sum of words: 963,266 average size in words: 26,034 average readability score: 49 nouns: cells; cell; protein; expression; patients; mice; neurons; results; virus; activity; study; proteins; brain; gene; membrane; data; infection; role; analysis; time; system; effect; function; activation; response; treatment; studies; levels; control; disease; type; receptor; model; effects; astrocytes; changes; lung; mouse; number; surface; formation; mechanism; fluorescence; increase; genes; dna; development; presence; level; days verbs: using; shown; suggesting; increase; induced; expressed; found; compared; observe; indicate; identified; included; follows; investigate; binds; determine; demonstrated; perform; revealed; studied; reduced; involved; reported; associated; examined; mediated; based; contained; measured; develop; provide; regulated; known; treated; decreased; causes; detects; resulted; obtained; activate; inhibits; generates; analyzed; leading; require; played; related; infected; tested; allowed adjectives: different; specific; human; viral; neuronal; high; non; molecular; significant; single; important; functional; dependent; present; inflammatory; cellular; several; positive; neural; synaptic; low; higher; first; small; similar; new; primary; clinical; anti; respiratory; normal; epithelial; glial; various; many; large; novel; multiple; wild; cortical; hippocampal; immune; visual; potential; structural; like; early; antiviral; microglial; cystic adverbs: also; however; well; significantly; respectively; previously; therefore; furthermore; highly; recently; moreover; together; directly; even; specifically; first; interestingly; still; mainly; prior; currently; approximately; now; often; strongly; less; finally; alone; especially; rather; completely; fully; efficiently; similarly; partially; almost; yet; subsequently; selectively; next; additionally; least; indeed; importantly; widely; particularly; thereby; later; far; much pronouns: we; our; it; their; its; they; i; them; us; his; itself; one; themselves; he; isg20; her; my; you; your; a129; she; imagej; ifit5; mrnas; wtgfp; nlrp12; me; i-; egfp; ␤; ≥200; α1-pdx; type-; tag-1; sunset; shrna#3; s; rrna; pdgfar::gfp; pcdna3.1-v5-his; p70; p)ppgpp; ourselves; ours; or=0.12; na€; iu/; ireses; il13ra2; ifnar1 proper nouns: CF; Japan; GFP; CFTR; University; RNA; Univ; Fig; Tokyo; Department; C; Institute; USA; CNS; PCR; Dept; School; P.; ATP; Ca; CHIKV; mRNA; Science; S.; M.; WT; Sch; MS; GABA; J.; Medicine; Med; ER; Research; Na; II; T; K; A; SARS; C.; ∆F508; Sci; M; A.; RSV; Italy; Medical; Center; siRNA keywords: gfp; rna; cell; protein; university; study; result; sars; ifn; atp; virus; usa; supplementary; pcr; nmda; neuron; mouse; medical; lipid; lc3; institute; increase; gaba; fret; dna; department; cns; chikv; center; brain; biology; bdnf; ∆f508-cftr; ∆f508; wako; vsv; vp24; vero; united; tsukuba; transfusion; tokyo; tohoku; tgev; tenuissima; technology; tc-83; takashi; tab1; svz one topic; one dimension: cells file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623752/ titles(s): Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein three topics; one dimension: cells; cells; cells file(s): https://api.elsevier.com/content/article/pii/S016801020600085X, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079852/, https://www.ncbi.nlm.nih.gov/pubmed/26727903/ titles(s): Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) | Abstract | RETRACTED ARTICLE: Interferon-mediated antiviral activities of Angelica tenuissima Nakai and its active components five topics; three dimensions: patients cells cftr; cells protein cell; neurons japan brain; gfp cells virus; cleavage proteins protease file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167830/, https://api.elsevier.com/content/article/pii/S0092867420313106, https://api.elsevier.com/content/article/pii/S016801020600085X, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6570483/, https://doi.org/10.1016/j.ab.2011.04.034 titles(s): Poster Session Abstracts | SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses | Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) | Protein quality control in the nucleolus safeguards recovery of epigenetic regulators after heat shock | An improved nonchromatographic method for the purification of recombinant proteins using elastin-like polypeptide-tagged proteases Type: cord title: keyword-gfp-cord date: 2021-05-25 time: 13:31 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:gfp ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-334855-s0ci3r8w author: Andersen, Petter I. title: Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine date: 2019-10-18 words: 4274.0 sentences: 272.0 pages: flesch: 48.0 cache: ./cache/cord-334855-s0ci3r8w.txt txt: ./txt/cord-334855-s0ci3r8w.txt 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 abstract: Viruses are the major causes of acute and chronic infectious diseases in the world. According to the World Health Organization, there is an urgent need for better control of viral diseases. Repurposing existing antiviral agents from one viral disease to another could play a pivotal role in this process. 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. Moreover, we demonstrated novel activities of emetine against influenza A virus (FLUAV), niclosamide against HSV-2, brequinar against human immunodeficiency virus 1 (HIV-1), and homoharringtonine against EV1. Our findings may expand the spectrum of indications of these safe-in-man agents and reinforce the arsenal of available antiviral therapeutics pending the results of further in vitro and in vivo tests. url: https://doi.org/10.3390/v11100964 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 words: 9362.0 sentences: 488.0 pages: flesch: 49.0 cache: ./cache/cord-003705-ekhj8ae8.txt txt: ./txt/cord-003705-ekhj8ae8.txt 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). abstract: Maintenance of epigenetic modifiers is of utmost importance to preserve the epigenome and consequently appropriate cellular functioning. Here, we analyzed Polycomb group protein (PcG) complex integrity in response to heat shock (HS). Upon HS, various Polycomb Repressive Complex (PRC)1 and PRC2 subunits, including CBX proteins, but also other chromatin regulators, are found to accumulate in the nucleolus. In parallel, binding of PRC1/2 to target genes is strongly reduced, coinciding with a dramatic loss of H2AK119ub and H3K27me3 marks. Nucleolar-accumulated CBX proteins are immobile, but remarkably both CBX protein accumulation and loss of PRC1/2 epigenetic marks are reversible. This post-heat shock recovery of pan-nuclear CBX protein localization and reinstallation of epigenetic marks is HSP70 dependent. Our findings demonstrate that the nucleolus is an essential protein quality control center, which is indispensable for recovery of epigenetic regulators and maintenance of the epigenome after heat shock. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6570483/ 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 words: 11469.0 sentences: 647.0 pages: flesch: 55.0 cache: ./cache/cord-342189-ya05m58o.txt txt: ./txt/cord-342189-ya05m58o.txt 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. abstract: SARS-CoV-2 is a recently identified coronavirus that causes the respiratory disease known as COVID-19. Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis. Here, we comprehensively define the interactions between SARS-CoV-2 proteins and human RNAs. NSP16 binds to the mRNA recognition domains of the U1 and U2 splicing RNAs and acts to suppress global mRNA splicing upon SARS-CoV-2 infection. NSP1 binds to 18S ribosomal RNA in the mRNA entry channel of the ribosome and leads to global inhibition of mRNA translation upon infection. Finally, NSP8 and NSP9 bind to the 7SL RNA in the Signal Recognition Particle and interfere with protein trafficking to the cell membrane upon infection. Disruption of each of these essential cellular functions acts to suppress the interferon response to viral infection. Our results uncover a multipronged strategy utilized by SARS-CoV-2 to antagonize essential cellular processes to suppress host defenses. url: https://api.elsevier.com/content/article/pii/S0092867420313106 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 words: 5129.0 sentences: 270.0 pages: flesch: 45.0 cache: ./cache/cord-274210-uaaj66xq.txt txt: ./txt/cord-274210-uaaj66xq.txt 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) . abstract: Autophagy is a basic biological metabolic process involving in intracellular membrane transport pathways that recycle cellular components and eliminate intracellular microorganisms within the lysosome. Autophagy also plays an important part in virus infection and propagation. However, some pathogens, including viruses, have evolved unique trick to escape or exploit autophagy. This study explores the mechanism of autophagy induction by porcine hemagglutinating encephalomyelitis virus (PHEV) in Neuro-2a cells, and examines the role of autophagy in PHEV replication. PHEV triggered autophagy in Neuro-2a cells is dependent on the presence of bulk double- or single-membrane vacuoles, the accumulation of GFP-LC3 fluorescent dots, and the LC3 lipidation. In addition, PHEV induced an incomplete autophagic effect because the degradation level of p62 did not change in PHEV-infected cells. Further validation was captured using LysoTracker and lysosome-associated membrane protein by indirect immunofluorescence labeling in PHEV-infected cells. We also investigated the change in viral replication by pharmacological experiments with the autophagy inducer rapamycin or the autophagy inhibitor 3-MA, and the lysosomal inhibitor chloroquine (CQ). Suppression of autophagy by 3-MA increased viral replication, compared with the mock treatment, while promoting of autophagy by rapamycin reduced PHEV replication. CQ treatment enhanced the LC3 lipidation in PHEV-infected Neuro-2a cells but lowered PHEV replication. 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. url: https://doi.org/10.3389/fcimb.2017.00056 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 words: 10860.0 sentences: 537.0 pages: flesch: 57.0 cache: ./cache/cord-275307-d7htyfcl.txt txt: ./txt/cord-275307-d7htyfcl.txt 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) . abstract: Many viruses express factors that reduce host gene expression through widespread degradation of cellular mRNA. An example of this class of proteins is the mRNA-targeting endoribonuclease SOX from the gamma-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV). Previous studies indicated that cleavage of messenger RNAs (mRNA) by SOX occurs at specific locations defined by the sequence of the target RNA, which is at odds with the down-regulation of a large portion of cellular transcripts. In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. These data, coupled with targeted mutagenesis, reveal that while cleavage sites are specific and reproducible, they are defined by a degenerate sequence motif containing a small number of conserved residues rather than a strong consensus sequence. This degenerate element is well represented in both human and KSHV mRNA, and its presence correlates with RNA destabilization by SOX. This represents a new endonuclease targeting strategy, in which use of a degenerate targeting element enables RNA cleavage at specific locations without restricting the range of targets. Furthermore, it shows that strong target selectivity can be achieved without a high degree of sequence specificity. url: https://www.ncbi.nlm.nih.gov/pubmed/26646420/ 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 words: 2255.0 sentences: 124.0 pages: flesch: 45.0 cache: ./cache/cord-103868-iwpiti2h.txt txt: ./txt/cord-103868-iwpiti2h.txt 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. abstract: Viral interferon (IFN) antagonist proteins mediate evasion of IFN-mediated innate immunity and are often multifunctional, having distinct roles in viral replication processes. Functions of the Ebola virus (EBOV) IFN antagonist VP24 include nucleocapsid assembly during cytoplasmic replication and inhibition of IFN-activated signalling by STAT1. For the latter, VP24 prevents STAT1 nuclear import via competitive binding to nuclear import receptors (karyopherins). Many viral proteins, including proteins from viruses with cytoplasmic replication cycles, interact with the trafficking machinery to undergo nucleocytoplasmic transport, with key roles in pathogenesis. Despite established karyopherin interaction, the nuclear trafficking profile of VP24 has not been investigated. We find that VP24 becomes strongly nuclear following overexpression of karyopherin or inhibition of nuclear export pathways. Molecular mapping indicates that cytoplasmic localisation of VP24 depends on a CRM1-dependent nuclear export sequence at the VP24 C-terminus. Nuclear export is not required for STAT1 antagonism, consistent with competitive karyopherin binding being the principal antagonistic mechanism while export mediates return of nuclear VP24 to the cytoplasm for replication functions. Thus, nuclear export of VP24 might provide novel targets for antiviral approaches. Importance Ebola virus (EBOV) is the causative agent of ongoing outbreaks of severe haemorrhagic fever with case-fatality rates between 40 and 60%. 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. However, exploitation of host trafficking machinery for nucleocytoplasmic transport by EBOV has not been directly examined. We find that the EBOV protein VP24 is actively trafficked between the nucleus and cytoplasm, and identify the specific pathways and sequences involved. The data indicate that nucleocytoplasmic trafficking is important for the multifunctional nature of VP24, which has critical roles in immune evasion and viral replication, identifying a new mechanism in infection by this highly lethal pathogen, and potential target for antivirals. url: https://doi.org/10.1101/2020.08.10.245563 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 words: 5532.0 sentences: 348.0 pages: flesch: 54.0 cache: ./cache/cord-324720-acei0pn8.txt txt: ./txt/cord-324720-acei0pn8.txt 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). abstract: BACKGROUND: Neuropathology caused by acute viral infection of the brain is associated with the development of persistent neurological deficits. Identification of the immune effectors responsible for injuring the brain during acute infection is necessary for the development of therapeutic strategies that reduce neuropathology but maintain immune control of the virus. 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. Behavioral consequences of immune cell depletion were assessed by Morris water maze. RESULTS: Inflammatory monocytes, defined as CD45(hi)CD11b(++)F4/80(+)Gr1(+)1A8(-), and neutrophils, defined as CD45(hi)CD11b(+++)F4/80(-)Gr1(+)1A8(+), were found in the brain at 12 h after infection. Flow cytometry of brain-infiltrating leukocytes collected from LysM: GFP reporter mice confirmed the identification of neutrophils and inflammatory monocytes in the brain. Microscopy of sections from infected LysM:GFP mice showed that infiltrating cells were concentrated in the hippocampal formation. Immunostaining confirmed that neutrophils and inflammatory monocytes were localized to the hippocampal formation at 12 h after infection. Immunodepletion of inflammatory monocytes and neutrophils but not of neutrophils only resulted in preservation of hippocampal neurons. Immunodepletion of inflammatory monocytes also preserved cognitive function as assessed by the Morris water maze. CONCLUSIONS: Neutrophils and inflammatory monocytes rapidly and robustly responded to Theiler's virus infection by infiltrating the brain. Inflammatory monocytes preceded neutrophils, but both cell types were present in the hippocampal formation at a timepoint that is consistent with a role in triggering hippocampal pathology. Depletion of inflammatory monocytes and neutrophils with the Gr1 antibody resulted in hippocampal neuroprotection and preservation of cognitive function. Specific depletion of neutrophils with the 1A8 antibody failed to preserve neurons, suggesting that inflammatory monocytes are the key effectors of brain injury during acute picornavirus infection of the brain. These effector cells may be important therapeutic targets for immunomodulatory or immunosuppressive therapies aimed at reducing or preventing central nervous system pathology associated with acute viral infection. url: https://www.ncbi.nlm.nih.gov/pubmed/22405261/ 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 words: 6936.0 sentences: 320.0 pages: flesch: 39.0 cache: ./cache/cord-319842-4mnaicki.txt txt: ./txt/cord-319842-4mnaicki.txt 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. abstract: 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 show that several hallmarks of cellular autophagosomes can be identified in poliovirus-induced vesicles, including colocalization of LAMP1 and LC3, the human homolog of Saccharomyces cerevisiae Atg8p, and staining with the fluorophore monodansylcadaverine followed by fixation. Colocalization of LC3 and LAMP1 was observed early in the poliovirus replicative cycle, in cells infected with rhinoviruses 2 and 14, and in cells that express poliovirus proteins 2BC and 3A, known to be sufficient to induce double-membraned vesicles. Stimulation of autophagy increased poliovirus yield, and inhibition of the autophagosomal pathway by 3-methyladenine or by RNA interference against mRNAs that encode two different proteins known to be required for autophagy decreased poliovirus yield. We propose that, for poliovirus and rhinovirus, components of the cellular machinery of autophagosome formation are subverted to promote viral replication. Although autophagy can serve in the innate immune response to microorganisms, our findings are inconsistent with a role for the induced autophagosome-like structures in clearance of poliovirus. Instead, we argue that these double-membraned structures provide membranous supports for viral RNA replication complexes, possibly enabling the nonlytic release of cytoplasmic contents, including progeny virions, from infected cells. url: https://www.ncbi.nlm.nih.gov/pubmed/15884975/ 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 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Reporter genes for RNA viruses are well-known to be unstable due to putative RNA recombination events that excise inserted nucleic acids. RNA recombination has been demonstrated to be co-regulated with replication fidelity in alphaviruses, but it is unknown how recombination events at the minority variant level act, which is important for vaccine and trans-gene delivery design. Therefore, we sought to characterize the removal of a reporter gene by a low-fidelity alphavirus mutant over multiple replication cycles. To examine this, GFP was inserted into TC-83, a live-attenuated vaccine for the alphavirus Venezuelan equine encephalitis virus, as well as a low-fidelity variant of TC-83, and passaged until fluorescence was no longer observed. Short-read RNA sequencing using ClickSeq was performed to determine which regions of the viral genome underwent recombination and how this changed over multiple replication cycles. A rapid removal of the GFP gene was observed, where minority variants in the virus population accumulated small deletions that increased in size over the course of passaging. Eventually, these small deletions merged to fully remove the GFP gene. The removal was significantly enhanced during the passaging of low-fidelity TC-83, suggesting that increased levels of recombination are a defining characteristic of this mutant. url: https://www.ncbi.nlm.nih.gov/pubmed/32575413/ 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 words: 6369.0 sentences: 339.0 pages: flesch: 49.0 cache: ./cache/cord-332881-mkm4ygh6.txt txt: ./txt/cord-332881-mkm4ygh6.txt 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. abstract: Bovine respiratory disease complex (BRDC) is the major cause of serious respiratory tract infections in calves. The disease is multifactorial, with either stress or reduced immunity allowing several pathogens to emerge. 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. Comparative infection studies demonstrated that entry and release of BPIV3 occurred specifically via the apical membrane with ciliated cells being the major target cells. By contrast, airway epithelial cells were largely resistant to infection by BHV-1. When the epithelial barrier was abolished by opening tight junctions or by injuring the cell monolayer, BHV-1 infected mainly basal cells. Respiratory epithelial cells were also refractory to infection by BRSV. However, this virus infected neither differentiated epithelial cells nor basal cells when the integrity of the epithelial barrier was destroyed. In contrast to cells of the airway epithelium, subepithelial cells were susceptible to infection by BRSV. Altogether, these results indicate that the three viruses of the same disease complex follow different strategies to interact with the airway epithelium. Possible entry mechanisms are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/24548739/ 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 words: 10347.0 sentences: 569.0 pages: flesch: 54.0 cache: ./cache/cord-000933-nn9gj0z1.txt txt: ./txt/cord-000933-nn9gj0z1.txt 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) . abstract: Respiratory Syncytial Virus (RSV) is a highly pathogenic member of the Paramyxoviridae that causes severe respiratory tract infections. Reports in the literature have indicated that to infect cells the incoming viruses either fuse their envelope directly with the plasma membrane or exploit clathrin-mediated endocytosis. 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. A variety of perturbants were employed to characterize the cellular processes involved. We found that immediately after binding to cells RSV activated a signaling cascade involving the EGF receptor, Cdc42, PAK1, and downstream effectors. This led to a series of dramatic actin rearrangements; the cells rounded up, plasma membrane blebs were formed, and there was a significant increase in fluid uptake. If these effects were inhibited using compounds targeting Na(+)/H(+) exchangers, myosin II, PAK1, and other factors, no infection was observed. The RSV was rapidly and efficiently internalized by an actin-dependent process that had all hallmarks of macropinocytosis. Rather than fusing with the plasma membrane, the viruses thus entered Rab5-positive, fluid-filled macropinosomes, and fused with the membranes of these on the average 50 min after internalization. Rab5 was required for infection. To find an explanation for the endocytosis requirement, which is unusual among paramyxoviruses, we analyzed the fusion protein, F, and could show that, although already cleaved by a furin family protease once, it underwent a second, critical proteolytic cleavage after internalization. This cleavage by a furin-like protease removed a small peptide from the F1 subunits, and made the virus infectious. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623752/ 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 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bats are increasingly implicated as hosts of highly pathogenic viruses. The underlying virus–host interactions and cellular mechanisms that promote co-existence remain ill-defined, but physiological traits such as flight and longevity are proposed to drive these adaptations. Autophagy is a cellular homeostatic process that regulates ageing, metabolism, and intrinsic immune defense. We quantified basal and stimulated autophagic responses in black flying fox cells, and demonstrated that although black flying fox cells are susceptible to Australian bat lyssavirus (ABLV) infection, viral replication is dampened in these bat cells. Black flying fox cells tolerated prolonged ABLV infection with less cell death relative to comparable human cells, suggesting post-entry mechanisms interference with virus replication. An elevated basal autophagic level was observed and autophagy was induced in response to high virus doses. Pharmacological stimulation of the autophagy pathway reduced virus replication, indicating autophagy acts as an anti-viral mechanism. Enhancement of basal and virus-induced autophagy in bat cells connects related reports that long-lived species possess homeostatic processes that dampen oxidative stress and macromolecule damage. Exemplifying the potential that evolved cellular homeostatic adaptations like autophagy may secondarily act as anti-viral mechanisms, enabling bats to serve as natural hosts to an assortment of pathogenic viruses. Furthermore, our data suggest autophagy-inducing drugs may provide a novel therapeutic strategy for combating lyssavirus infection. url: https://doi.org/10.3390/v11030260 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 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The envelope of hepatitis B virus (HBV), containing the L, M, and S proteins, is essential for virus entry and maturation. For direct visualization of HBV, we determined whether envelope assembly could accommodate the green fluorescent protein (GFP). While the C-terminal addition of GFP to S trans-dominant negatively inhibited empty envelope particle secretion, the N-terminal GFP fusion to S (GFP.S) was co-integrated into the envelope, giving rise to fluorescent particles. Microscopy and topogenesis analyses demonstrated that the proper intracellular distribution and folding of GFP.S, required for particle export were rescued by interprotein interactions with wild-type S. Thereby, a dual location of GFP, inside and outside the envelope, was observed. GFP.S was also efficiently packaged into the viral envelope, and these GFP-tagged virions retained the capacity for attachment to HBV receptor-positive cells in vitro. Together, GFP-tagged virions should be suitable to monitor HBV uptake and egress in live hepatocytes. url: https://www.ncbi.nlm.nih.gov/pubmed/15527842/ 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 words: 2063.0 sentences: 112.0 pages: flesch: 52.0 cache: ./cache/cord-253709-frauasts.txt txt: ./txt/cord-253709-frauasts.txt 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. abstract: Abstract Proteins fused to the elastin-like polypeptide (ELP) tag can be selectively separated from crude cell extract without chromatography. To avoid the interference of the ELP tag on properties of the target protein, it is necessary to remove the ELP tag from target protein by protease digestion. Therefore, an additional chromatographic purification step is required to remove the proteases, and this is time- and labor-consuming. Here we demonstrate the utility of the ELP-tagged proteases for cleavage of ELP fusion proteins, allowing one-step removal of the cleaved ELP tag and ELP-tagged proteases without chromatography. url: https://doi.org/10.1016/j.ab.2011.04.034 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 words: 6671.0 sentences: 327.0 pages: flesch: 43.0 cache: ./cache/cord-338811-2bi2edcw.txt txt: ./txt/cord-338811-2bi2edcw.txt 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. abstract: Enteroviruses manipulate host membranes to form replication organelles, which concentrate viral and host factors to allow for efficient replication. However, this process has not been well-studied in living cells throughout the course of infection. 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. This system thus allows for the monitoring of organelle-specific changes induced by infection in real-time. Using long-term time-lapse imaging of living cells infected with coxsackievirus B3 (CVB), we detected reporter translocation to the nucleus beginning ~4 h post-infection, which correlated with a loss of Golgi integrity and a collapse of the peripheral ER. Lastly, we applied our system to study the effects of a calcium channel inhibitor, 2APB, on virus-induced manipulation of host membranes. We found that 2APB treatment had no effect on the kinetics of infection or the percentage of infected cells. However, we observed aberrant ER structures in CVB-infected cells treated with 2APB and a significant decrease in viral-dependent cell lysis, which corresponded with a decrease in extracellular virus titers. Thus, our system provides a tractable platform to monitor the effects of inhibitors, gene silencing, and/or gene editing on viral manipulation of host membranes, which can help determine the mechanism of action for antivirals. url: https://doi.org/10.3390/v12101074 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 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine epidemic diarrhea virus (PEDV) causes severe economic losses in the swine industry in China and other Asian countries. Infection usually leads to an acute, often lethal diarrhea in piglets. Despite the impact of the disease, no system is yet available to manipulate the viral genome which has severely hampered research on this virus until today. We have established a reverse genetics system for PEDV based on targeted RNA recombination that allows the modification of the 3′-end of the viral genome, which encodes the structural proteins and the ORF3 protein. Using this system, we deleted the ORF3 gene entirely from the viral genome and showed that the ORF3 protein is not essential for replication of the virus in vitro. In addition, we inserted heterologous genes (i.e. the GFP and Renilla luciferase genes) at two positions in the viral genome, either as an extra expression cassette or as a replacement for the ORF3 gene. We demonstrated the expression of both GFP and Renilla luciferase as well as the application of these viruses by establishing a convenient and rapid virus neutralization assay. The new PEDV reverse genetics system will enable functional studies of the structural proteins and the accessory ORF3 protein and will allow the rational design and development of next generation PEDV vaccines. url: https://doi.org/10.1371/journal.pone.0069997 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 words: 2817.0 sentences: 204.0 pages: flesch: 53.0 cache: ./cache/cord-316814-9fv9xrln.txt txt: ./txt/cord-316814-9fv9xrln.txt 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. abstract: Plants are low-cost bioreactors for the production of various biopharmaceuticals including oral vaccines. Plant-derived oral vaccines are potentially useful in combating viral infections involving mucosal immunity. Transgenic plants have been generated to successfully produce mucosal vaccines against cholera, hepatitis B, foot-and-mouth disease, and Norwalk virus. As a first step toward the generation of oral vaccines against the severe acute respiratory syndrome coronavirus (SARS-CoV), we have expressed a recombinant S1 protein of the SARS-CoV in transformed tobacco. Since plant transformation and regeneration of stable transformants require considerable time, we initially used a green fluorescent protein (GFP) to tag the antigen in transient expression. GFP was fused to the carboxy-terminus of S1 for expression of S1-GFP to show expression of recombinant S1 by agroinfiltration of tobacco leaves. The GFP tag enables a relatively quick confirmation of antigen expression in plant cells by fluorescent microscopy. Such analysis using GFP that precedes stable plant transformation will enable the rapid screening of multiple constructs to attain optimal recombinant protein expression. Furthermore, this approach determines the subcellular localization of the recombinant protein in plant cells, providing information on optimal subcellular targeting for production in plant bioreactors. url: https://doi.org/10.1007/978-1-59745-559-6_19 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 words: 8655.0 sentences: 418.0 pages: flesch: 57.0 cache: ./cache/cord-102184-8u73adnk.txt txt: ./txt/cord-102184-8u73adnk.txt 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. abstract: The ability to integrate input from different sensory systems is a fundamental property of many brains. Yet, the patterns of neuronal connectivity that underlie such multisensory integration remain poorly characterized. The Drosophila melanogaster mushroom body — an associative center required for the formation of olfactory and visual memories — is an ideal system to investigate how different sensory channels converge in higher-order brain centers. The neurons connecting the mushroom body to the olfactory system have been described in great detail, but input from other sensory systems remains poorly defined. 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. Together with previous work that described a pathway conveying visual information from the medulla to the ventral accessory calyx of the mushroom body (Vogt et al., 2016), our study defines a second, parallel pathway that is anatomically poised to convey information from the visual system to the dorsal accessory calyx. This connectivity pattern — the segregation of the visual information into two separate pathways — could be a fundamental feature of the neuronal architecture underlying multisensory integration in associative brain centers. url: https://doi.org/10.1101/2020.02.07.935924 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 words: 4996.0 sentences: 229.0 pages: flesch: 36.0 cache: ./cache/cord-002076-7t4d4vvo.txt txt: ./txt/cord-002076-7t4d4vvo.txt 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. abstract: 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. Notably, the development of replicating-competent reporter-expressing viruses (RCREVs) has provided an excellent option to detect directly viral replication without the use of secondary labeling, which represents a significant advance in virology. 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. However, there remain various challenges associated with RCREVs, including pathogenicity alterations due to the insertion of a reporter gene, instability or loss of the reporter gene expression, or attenuation of reporter signals in vivo. Despite all these limitations, RCREVs have become powerful tools for both basic and applied virology with the development of new technologies for generating RCREVs, the inventions of novel reporters and the better understanding of regulation of viral replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4885082/ 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 words: 5827.0 sentences: 282.0 pages: flesch: 51.0 cache: ./cache/cord-001123-n2e4s7bu.txt txt: ./txt/cord-001123-n2e4s7bu.txt 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. abstract: Equine lentivirus receptor 1 (ELR1) has been identified as the sole receptor for equine infectious anemia virus (EIAV) and is a member of the tumor necrosis factor receptor (TNFR) superfamily. 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). One major spliced species (ELR1-IN) contained an insertion of 153 nt, which resulted in a premature stop codon situated 561 nt upstream of the predicted membrane spanning domain. The other major species (ELR1-DE) has a deletion of 109 nt that causes a shift of the open reading frame and generates a stop codon 312 nt downstream. Because ELR1-DE presumably encodes a peptide of a mere 23 residues, only ELR1-IN was further analyzed. The expression of a soluble form of ELR1 (sELR1) by ELR1-IN was confirmed by Western blot and immunofluorescence analyses. Similar to ELR1, the transcription level of ELR1-IN varied among individual horses and at different time points in the same individuals. The ratio of ELR1-IN mRNA species to ELR1 mRNA was approximately 1∶2.5. Pre-incubation of the recombinant sELR1 with EIAV significantly inhibited EIAV infection in equine macrophages, the primary in vivo target cell of the virus. Fetal equine dermal (FED) cells are susceptible to EIAV in vitro, and the replication of EIAV in FED cells transiently transfected with ELR1-IN was markedly reduced when compared with replication in cells transfected with the empty vector. Finally, the expression levels of both forms of the EIAV receptor were significantly regulated by infection with this virus. Taken together, our data indicate that sELR1 acts as a secreted cellular factor that inhibits EIAV infection in host cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838338/ 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 words: 4788.0 sentences: 282.0 pages: flesch: 51.0 cache: ./cache/cord-258678-0atfsivf.txt txt: ./txt/cord-258678-0atfsivf.txt 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. abstract: siRNA-aptamer chimeras have emerged as one of the most promising approaches for targeted delivery of siRNA due to the modularity of their diblock RNA structure, relatively lower cost over other targeted delivery approaches, and, most importantly, the outstanding potential for clinical translation. However, additional challenges must be addressed for efficient RNA interference (RNAi), in particular, endosomal escape. Currently, vast majority of siRNA delivery vehicles are based on cationic materials, which form complexes with negatively charged siRNA. Unfortunately, these approaches complicate the formulations again by forming large complexes with heterogeneous sizes, unfavorable surface charges, colloidal instability, and poor targeting ligand orientation. 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. The protein selectively tags along the siRNA block of individual chimera, rendering the overall size of the complex small, desirable for deep tissue penetration, and the aptamer block accessible for target recognition. More interestingly, we found that extending the c-terminal polyhistidine segment in the protein tag to 18 amino acids completely abolishes the RNA binding function of dsRBD. url: https://www.ncbi.nlm.nih.gov/pubmed/24196104/ 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 words: 5671.0 sentences: 338.0 pages: flesch: 56.0 cache: ./cache/cord-002320-m99amd4y.txt txt: ./txt/cord-002320-m99amd4y.txt 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. abstract: RNAi pathway is an antiviral defence mechanism employed by insects that result in degradation of viral RNA thereby curbing infection. Several viruses including flaviviruses encode viral suppressors of RNAi (VSRs) to counteract the antiviral RNAi pathway. Till date, no VSR has been reported in alphaviruses. The present study was undertaken to evaluate chikungunya virus (CHIKV) proteins for RNAi suppressor activity. We systematically analyzed all nine CHIKV proteins for RNAi suppressor activity using Sf21 RNAi sensor cell line based assay. Two non-structural proteins, namely, nsP2 and nsP3 were found to exhibit RNAi suppressor activity. We further validated the findings in natural hosts, namely in Aedes and in mammalian cell lines and further through EMSA and Agrobacterium infiltration in GFP silenced transgenic tobacco plants. Domains responsible for maximum RNAi suppressor activity were also identified within these proteins. RNA binding motifs in these domains were identified and their participation in RNAi suppression evaluated using site directed mutagenesis. Sequence alignment of these motifs across all species of known alphaviruses revealed conservation of these motifs emphasizing on a similar role of action in other species of alphaviruses as well. Further validation of RNAi suppressor activity of these proteins awaits establishment of specific virus infection models. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5128919/ 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 words: 10152.0 sentences: 562.0 pages: flesch: 56.0 cache: ./cache/cord-280454-etf32afd.txt txt: ./txt/cord-280454-etf32afd.txt 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. abstract: The genome of SARS-CoV-2 (SARS2) encodes for two viral proteases (NSP3/ papain-like protease and NSP5/ 3C-like protease or major protease) that are responsible for cleaving viral polyproteins for successful replication. NSP3 and NSP5 of SARS-CoV (SARS1) are known interferon antagonists. Here, we examined whether the protease function of SARS2 NSP3 and NSP5 target proteins involved in the host innate immune response. We designed a fluorescent based cleavage assay to rapidly screen the protease activity of NSP3 and NSP5 on a library of 71 human innate immune proteins (HIIPs), covering most pathways involved in human innate immunity. By expressing each of these HIIPs with a genetically encoded fluorophore in a cell-free system and titrating in the recombinant protease domain of NSP3 or NSP5, we could readily detect cleavage of cognate HIIPs on SDS-page gels. We identified 3 proteins that were specifically and selectively cleaved by NSP3 or NSP5: IRF-3, and NLRP12 and TAB1, respectively. Direct cleavage of IRF3 by NSP3 could explain the blunted Type- I 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. Surprisingly, both NLRP12 and TAB1 have each two distinct cleavage sites. We demonstrate that in mice, the second cleavage site of NLRP12 is absent. We pushed this comparative alignment of IRF-3 and NLRP12 homologs and show that the lack or presence of cognate cleavage motifs in IRF-3 and NLRP12 could contribute to the presentation of disease in cats and tigers, for example. Our findings provide an explanatory framework for in-depth studies into the pathophysiology of COVID-19 and should facilitate the search or development of more effective animal models for severe COVID-19. Finally, we discovered that one particular species of bats, David’s Myotis, possesses the five cleavage sites found in humans for NLRP12, TAB1 and IRF3. These bats are endemic from the Hubei province in China and we discuss its potential role as reservoir for the evolution of SARS1 and SASR2. url: https://doi.org/10.1101/2020.06.05.135699 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 words: 6356.0 sentences: 268.0 pages: flesch: 56.0 cache: ./cache/cord-317142-qd61qvch.txt txt: ./txt/cord-317142-qd61qvch.txt 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) . abstract: Like many other RNA viruses, severe acute respiratory syndrome coronavirus (SARS‐CoV) produces polyproteins containing several non‐structural proteins, which are then processed by the viral proteases. These proteases often exist within the polyproteins, and are excised by their own proteolytic activity (‘autoprocessing’). It is important to investigate the autoprocessing mechanism of these proteases from the point of view of anti‐SARS‐CoV drug design. In this paper, we describe a new method for investigating the autoprocessing mechanism of the main protease (M (pro)), which is also called the 3C‐like protease (3CL (pro)). Using our method, we measured the activities, under the same conditions, of the mature form and pro‐forms with the N‐terminal pro‐sequence, the C‐terminal pro‐sequence or both pro‐sequences, toward the pro‐form with both N‐ and C‐terminal pro‐sequences. The data indicate that the pro‐forms of the enzyme have proteolytic activity, and are stimulated by the same proteolytic activity. The stimulation occurs in two steps, with approximately eightfold stimulation by N‐terminal cleavage, approximately fourfold stimulation by C‐terminal cleavage, and 23‐fold stimulation by the cleavage of both termini, compared to the pro‐form with both the N‐ and C‐terminal pro‐sequences. Such cleavage mainly occurs in a trans manner; i.e. the pro‐form dimer cleaves the monomeric form. The stimulation by N‐terminal pro‐sequence removal is due to the cis (intra‐dimer and inter‐protomer) effect of formation of the new N‐terminus, whereas that by C‐terminal cleavage is due to removal of its trans (inter‐dimer) inhibitory effect. A numerical simulation of the maturation pathway is presented. url: https://doi.org/10.1111/febs.12222 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 words: 9184.0 sentences: 433.0 pages: flesch: 46.0 cache: ./cache/cord-319517-denczc6t.txt txt: ./txt/cord-319517-denczc6t.txt 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. abstract: Live cell imaging enables the study of dynamic processes of living cells in real time by use of suitable reporter proteins and the staining of specific cellular structures and/or organelles. With the availability of advanced optical devices and improved cell culture protocols it has become a rapidly growing research methodology. The success of this technique relies mainly on the selection of suitable reporter proteins, construction of recombinant plasmids possessing cell type specific promoters as well as reliable methods of gene transfer. 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. Moreover, different expression systems of marker proteins and the modes of gene transfer are discussed with emphasis on the study of lipid droplet formation in hepatocytes as an example. url: https://doi.org/10.1186/1471-2121-15-26 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 words: 10776.0 sentences: 579.0 pages: flesch: 47.0 cache: ./cache/cord-315483-l6dm82pp.txt txt: ./txt/cord-315483-l6dm82pp.txt 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 ). abstract: The intracellular actions of interferon (IFN)-regulated proteins, including IFN-induced proteins with tetratricopeptide repeats (IFITs), attribute a major component of the protective antiviral host defense. Here we applied genomics approaches to annotate the chicken IFIT locus and currently identified a single IFIT (chIFIT5) gene. The profound transcriptional level of this effector of innate immunity was mapped within its unique cis-acting elements. This highly virus- and IFN-responsive chIFIT5 protein interacted with negative sense viral RNA structures that carried a triphosphate group on its 5′ terminus (ppp-RNA). This interaction reduced the replication of RNA viruses in lentivirus-mediated IFIT5-stable chicken fibroblasts whereas CRISPR/Cas9-edited chIFIT5 gene knockout fibroblasts supported the replication of RNA viruses. Finally, we generated mosaic transgenic chicken embryos stably expressing chIFIT5 protein or knocked-down for endogenous chIFIT5 gene. Replication kinetics of RNA viruses in these transgenic chicken embryos demonstrated the antiviral potential of chIFIT5 in ovo. Taken together, these findings propose that IFIT5 specifically antagonize RNA viruses by sequestering viral nucleic acids in chickens, which are unique in innate immune sensing and responses to viruses of both poultry and human health significance. url: https://www.ncbi.nlm.nih.gov/pubmed/29717152/ 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 words: 9607.0 sentences: 442.0 pages: flesch: 48.0 cache: ./cache/cord-299509-7xjdryoq.txt txt: ./txt/cord-299509-7xjdryoq.txt 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) . abstract: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that re-emerged in 2004 and has caused massive outbreaks in recent years. The lack of a licensed vaccine or treatment options emphasize the need to obtain more insight into the viral life cycle and CHIKV-host interactions. Infectious cDNA clones are important tools for such studies, and for mechanism of action studies on antiviral compounds. Existing CHIKV cDNA clones are based on a single genome from an individual clinical isolate, which is expected to have evolved specific characteristics in response to the host environment, and possibly also during subsequent cell culture passaging. To obtain a virus expected to have the general characteristics of the recent E1-226V CHIKV isolates, we have constructed a new CHIKV full-length cDNA clone, CHIKV LS3, based on the consensus sequence of their aligned genomes. Here we report the characterization of this synthetic virus and a green fluorescent protein-expressing variant (CHIKV LS3-GFP). Their characteristics were compared to those of natural strain ITA07-RA1, which was isolated during the 2007 outbreak in Italy. In cell culture the synthetic viruses displayed phenotypes comparable to the natural isolate, and in a mouse model they caused lethal infections that were indistinguishable from infections with a natural strain. Compared to ITA07-RA1 and clinical isolate NL10/152, the synthetic viruses displayed similar sensitivities to several antiviral compounds. 3-deaza-adenosine was identified as a new inhibitor of CHIKV replication. Cyclosporin A had no effect on CHIKV replication, suggesting that cyclophilins -opposite to what was found for other +RNA viruses- do not play an essential role in CHIKV replication. The characterization of the consensus sequence-based synthetic viruses and their comparison to natural isolates demonstrated that CHIKV LS3 and LS3-GFP are suitable and representative tools to study CHIKV-host interactions, screen for antiviral compounds and unravel their mode of action. url: https://www.ncbi.nlm.nih.gov/pubmed/23936484/ doi: 10.1371/journal.pone.0071047 id: cord-018771-xqlb74px author: Turinsky, Sebastian title: Bluttransfusion date: 2013-04-04 words: 1802.0 sentences: 279.0 pages: flesch: 51.0 cache: ./cache/cord-018771-xqlb74px.txt txt: ./txt/cord-018771-xqlb74px.txt 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. abstract: Bei einem 58-jährigen Patienten mit einem Hb-Wert von 6,5 g/dl, der nach operativer Ausschaltung eines Bauchaortenaneurysmas auf der Intensivstation unerwartet nachblutet, soll eine Bluttransfusion durchgeführt werden. Wenige Minuten nach der Anforderung aus der Blutbank treffen die bestellten Erythrozytenkonzentrate ein – es sind Erythrozytenkonzentrate der Blutgruppe A. Sie sind eindeutig auf den Namen des Patienten ausgezeichnet, die Identität des Patienten wird erneut überprüft. Der durchgeführte Bedside-Test zeigt aber die Blutgruppe B! Was muss der Intensivarzt nun tun? url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123737/ 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 words: 7836.0 sentences: 405.0 pages: flesch: 55.0 cache: ./cache/cord-346554-a98pjtxs.txt txt: ./txt/cord-346554-a98pjtxs.txt 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. abstract: Bee venom (BV) from honey bee (Apis Melifera L.) contains at least 18 pharmacologically active components including melittin (MLT), phospholipase A(2) (PLA(2)), and apamin etc. BV is safe for human treatments dose dependently and proven to possess different healing properties including antibacterial and antiparasitidal properties. Nevertheless, antiviral properties of BV have not well investigated. Hence, we identified the potential antiviral properties of BV and its component against a broad panel of viruses. 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). Additionally, BV and MLT also inhibited the replication of non-enveloped viruses such as Enterovirus-71 (EV-71) and Coxsackie Virus (H3). Such antiviral properties were mainly explained by virucidal mechanism. Moreover, MLT protected mice which were challenged with lethal doses of pathogenic influenza A H1N1 viruses. Therefore, these results provides the evidence that BV and MLT could be a potential source as a promising antiviral agent, especially to develop as a broad spectrum antiviral agent. url: https://www.ncbi.nlm.nih.gov/pubmed/27888461/ 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 words: 6220.0 sentences: 265.0 pages: flesch: 49.0 cache: ./cache/cord-345651-admlzeu4.txt txt: ./txt/cord-345651-admlzeu4.txt 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 abstract: Transmissible gastroenteritis virus (TGEV) is the etiologic agent of transmissible gastroenteritis in pigs, and the N-terminal domain of TGEV spike protein is generally recognized as both the virulence determinant and enteric tropism determinant. Here, we assembled a full-length infectious cDNA clone of TGEV in a bacterial artificial chromosome. 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. S_NTD224 notably affected the TGEV growth kinetics in PK-15 cells but was not essential for recombinant virus survival. In animal experiments with 13 two-day-old piglets, the TGEV recombinant viruses with/without S_NTD224 deletion induced obvious clinical signs and mortality. Together, our results directly demonstrated that S_NTD224 of TGEV mildly influenced TGEV virulence but was not the enteric tropism determinant and provide new insights for the development of a new attenuated vaccine against TGEV. Importantly, the optimized reverse genetics platform used in this study will simplify the construction of mutant infectious clones and help accelerate progress in coronavirus research. url: https://www.ncbi.nlm.nih.gov/pubmed/30935078/ 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 words: 7948.0 sentences: 396.0 pages: flesch: 53.0 cache: ./cache/cord-330176-1ugzkf22.txt txt: ./txt/cord-330176-1ugzkf22.txt 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. abstract: Angelica tenuissima Nakai is a widely used commodity in traditional medicine. Nevertheless, no study has been conducted on the antiviral and immune-modulatory properties of an aqueous extract of Angelica tenuissima Nakai. In the present study, we evaluated the antiviral activities and the mechanism of action of an aqueous extract of Angelica tenuissima Nakai both in vitro and in vivo. 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. Such inhibition can be described by the induction of the antiviral state in cells by antiviral, IFNrelated gene induction and secretion of IFNs and pro-inflammatory cytokines. In vivo, Angelica tenuissima Nakai treated BALB/c mice displayed higher survivability and lower lung viral titers when challenged with lethal doses of highly pathogenic influenza A subtypes (H1N1, H5N2, H7N3, and H9N2). We also found that Angelica tenuissima Nakai can induce the secretion of IL-6, IFN-λ, and local IgA in bronchoalveolar lavage fluid (BALF) of Angelica tenuissima Nakai treated mice, which correlating with the observed prophylactic effects. In HPLC analysis, we found the presence of several compounds in the aqueous fraction and among them; we evaluated antiviral properties of ferulic acid. Therefore, an extract of Angelica tenuissima Nakai and its components, including ferulic acid, play roles as immunomodulators and may be potential candidates for novel anti-viral/anti-influenza agents. url: https://www.ncbi.nlm.nih.gov/pubmed/26727903/ 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 words: 8471.0 sentences: 426.0 pages: flesch: 51.0 cache: ./cache/cord-001365-6u80p5sj.txt txt: ./txt/cord-001365-6u80p5sj.txt 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. abstract: BACKGROUND: Chikungunya virus (CHIKV) is a re-emerging arbovirus associated with febrile illness often accompanied by rash and arthralgia that may persist for several years. Outbreaks are associated with high morbidity and create a public health challenge for countries affected. Recent outbreaks have occurred in both Europe and the Americas, suggesting CHIKV may continue to spread. Despite the sustained threat of the virus, there is no approved vaccine or antiviral therapy against CHIKV. Therefore, it is critical to develop a vaccine that is both well tolerated and highly protective. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we describe the construction and characterization of a modified Vaccinia virus Ankara (MVA) virus expressing CHIKV E3 and E2 proteins (MVA-CHIK) that protected several mouse models from challenge with CHIKV. In particular, BALB/c mice were completely protected against viremia upon challenge with CHIKV after two doses of MVA-CHIK. Additionally, A129 mice (deficient in IFNα/β) were protected from viremia, footpad swelling, and mortality. While high anti-virus antibodies were elicited, low or undetectable levels of neutralizing antibodies were produced in both mouse models. However, passive transfer of MVA-CHIK immune serum to naïve mice did not protect against mortality, suggesting that antibodies may not be the main effectors of protection afforded by MVA-CHIK. Furthermore, depletion of CD4(+), but not CD8(+) T-cells from vaccinated mice resulted in 100% mortality, implicating the indispensable role of CD4(+) T-cells in the protection afforded by MVA-CHIK. CONCLUSIONS/SIGNIFICANCE: The results presented herein demonstrate the potential of MVA to effectively express CHIKV E3-E2 proteins and generate protective immune responses. Our findings challenge the assumption that only neutralizing antibodies are effective in providing protection against CHIKV, and provides a framework for the development of novel, more effective vaccine strategies to combat CHIKV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109897/ 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 words: 3187.0 sentences: 148.0 pages: flesch: 48.0 cache: ./cache/cord-103509-hynnba03.txt txt: ./txt/cord-103509-hynnba03.txt 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) abstract: In this paper, we are exploring the role of an amphipathic helical peptide in mediating the self-assembly of a fusion protein into a protein nanoparticle and the application of the nanoparticle as a one-shot vaccine carrier. Out of several candidates, an amphipathic helical peptide derived from M2 protein of type A influenza virus is found to stimulate high antigenicity when fused to a fluorescent protein genetically. This fusion protein was found to form protein nanoparticle spontaneously when expressed and purified protein stimulates long-lasting antibody responses in single immunization. Through modeling peptide structure and nanoparticle assembly, we have improved this vaccine carrier in complex stability. The revised vaccine carrier is able to stimulate constant antibody titer to a heterologous antigen for at least six months in single immunization. The immune response against a heterologous antigen can be boosted further by additional immunization in spite of high immune responses to carrier protein. url: https://doi.org/10.1101/2020.09.16.299149 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 words: 6269.0 sentences: 333.0 pages: flesch: 47.0 cache: ./cache/cord-001270-l8aa9cl3.txt txt: ./txt/cord-001270-l8aa9cl3.txt 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 ). abstract: Studies of the domestic cat have contributed to many scientific advances, including the present understanding of the mammalian cerebral cortex. A practical capability for cat transgenesis is needed to realize the distinctive potential of research on this neurobehaviorally complex, accessible species for advancing human and feline health. For example, humans and cats are afflicted with pandemic AIDS lentiviruses that are susceptible to species-specific restriction factors. Here we introduced genes encoding such a factor, rhesus macaque TRIMCyp, and eGFP, into the cat germline. The method establishes gamete-targeted transgenesis for the first time in a carnivore. We observed uniformly transgenic outcomes, widespread expression, no mosaicism and no F1 silencing. TRIMCyp transgenic cat lymphocytes resisted feline immunodeficiency virus replication. This capability to experimentally manipulate the genome of an AIDS-susceptible species can be used to test the potential of restriction factors for HIV gene therapy and to build models of other infectious and noninfectious diseases. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nmeth.1703) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006694/ 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 words: 11391.0 sentences: 520.0 pages: flesch: 48.0 cache: ./cache/cord-348799-qu4zin3o.txt txt: ./txt/cord-348799-qu4zin3o.txt 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) . abstract: ISG20 is a broad spectrum antiviral protein thought to directly degrade viral RNA. However, this mechanism of inhibition remains controversial. Using the Vesicular Stomatitis Virus (VSV) as a model RNA virus, we show here that ISG20 interferes with viral replication by decreasing protein synthesis in the absence of RNA degradation. Importantly, we demonstrate that ISG20 exerts a translational control over a large panel of non-self RNA substrates including those originating from transfected DNA, while sparing endogenous transcripts. This activity correlates with the protein’s ability to localize in cytoplasmic processing bodies. Finally, these functions are conserved in the ISG20 murine ortholog, whose genetic ablation results in mice with increased susceptibility to viral infection. Overall, our results posit ISG20 as an important defense factor able to discriminate the self/non-self origins of the RNA through translation modulation. url: https://doi.org/10.1371/journal.ppat.1008093 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 words: 4172.0 sentences: 242.0 pages: flesch: 53.0 cache: ./cache/cord-273711-bxijla09.txt txt: ./txt/cord-273711-bxijla09.txt 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 abstract: BACKGROUND: Goatpox is an economically important disease in goat and sheep-producing areas of the world. Many vaccine strategies developed to control the disease are not yet completely successful. Hairpin expression vectors have been used to induce gene silencing in a large number of studies on viruses. However, none of these studies has been attempted to study GTPV. In the interest of exploiting improved methods to control goat pox, it is participated that RNAi may provide effective protection against GTPV. In this study we show the suppression of Goatpox virus (GTPV) replication via knockdown of virion core protein using RNA interference. RESULTS: Four short interfering RNA (siRNA) sequences (siRNA-61, siRNA-70, siRNA-165 and siRNA-296) against a region of GTPV ORF095 were selected. Sense and antisense siRNA-encoding sequences separated by a hairpin loop sequence were designed as short hairpin RNA (shRNA) expression cassettes under the control of a human U6 promoter. ORF095 amplicon was generated using PCR, and then cloned into pEGFP-N1 vector, named as p095/EGFP. p095/EGFP and each of the siRNA expression cassettes (p61, p70, p165 and p296) were co-transfected into BHK-21 cells. Fluorescence detection, flow cytometric analysis, retro transcription PCR (RT-PCR) and real time PCR were used to check the efficiency of RNAi. The results showed that the ORF095-specific siRNA-70 effectively down-regulated the expression of ORF095. 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. The results presented here indicated that DNA-based siRNA could effectively inhibit the replication of GTPV (approximately 463. 5-fold reduction of viral titers) on Vero cells. CONCLUSIONS: This study demonstrates that vector-based shRNA methodology can effectively inhibit GTPV replication on Vero cells. Simultaneously, this work represents a strategy for controlling goatpox, potentially facilitating new experimental approaches in the analysis of both viral and cellular gene functions during of GTPV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/22340205/ doi: 10.1186/1743-422x-9-48 id: cord-004534-jqm1hxps author: nan title: Abstract date: 2009-06-09 words: 139023.0 sentences: 6450.0 pages: flesch: 42.0 cache: ./cache/cord-004534-jqm1hxps.txt txt: ./txt/cord-004534-jqm1hxps.txt 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. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079852/ doi: 10.1007/s00249-009-0478-1 id: cord-023026-2r84ndzv author: nan title: Posters date: 2013-06-14 words: 138458.0 sentences: 6513.0 pages: flesch: 40.0 cache: ./cache/cord-023026-2r84ndzv.txt txt: ./txt/cord-023026-2r84ndzv.txt 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. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165910/ doi: 10.1002/glia.22530 id: cord-023211-kt5gt26t author: nan title: Poster Session Abstracts date: 2007-08-29 words: 221224.0 sentences: 11772.0 pages: flesch: 52.0 cache: ./cache/cord-023211-kt5gt26t.txt txt: ./txt/cord-023211-kt5gt26t.txt 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. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167830/ 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 words: 240925.0 sentences: 13617.0 pages: flesch: 47.0 cache: ./cache/cord-257167-rz4r5sj7.txt txt: ./txt/cord-257167-rz4r5sj7.txt 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). abstract: nan url: https://api.elsevier.com/content/article/pii/S016801020600085X 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 words: 6244.0 sentences: 329.0 pages: flesch: 50.0 cache: ./cache/cord-307067-cpc1yefj.txt txt: ./txt/cord-307067-cpc1yefj.txt 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. abstract: Developing a vaccine to protect against the lethal effects of the many strains of coronavirus is critical given the current global pandemic. For Middle East respiratory syndrome coronavirus (MERS-CoV), we show that rhesus macaques seroconverted rapidly after a single intramuscular vaccination with ChAdOx1 MERS. The vaccine protected against respiratory injury and pneumonia and reduced viral load in lung tissue by several orders of magnitude. MERS-CoV replication in type I and II pneumocytes of ChAdOx1 MERS–vaccinated animals was absent. 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. We also found that antibodies elicited by ChAdOx1 MERS in rhesus macaques neutralized six different MERS-CoV strains. Transgenic human dipeptidyl peptidase 4 mice vaccinated with ChAdOx1 MERS were completely protected against disease and lethality for all different MERS-CoV strains. The data support further clinical development of ChAdOx1 MERS. url: https://doi.org/10.1126/sciadv.aba8399 doi: 10.1126/sciadv.aba8399 ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel