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Sjef; Rottier, Peter; Warren, Graham title: Sequence and topology of a model intracellular membrane protein, E1 glycoprotein, from a coronavirus date: 1984 journal: Nature DOI: 10.1038/308751a0 sha: doc_id: 341378 cord_uid: pw60qx7c file: cache/cord-317430-uvx8si42.json key: cord-317430-uvx8si42 authors: Chen, Yaping; Wang, Ji; Li, Xiangling; Hu, Ning; Voelcker, Nicolas H.; Xie, Xi; Elnathan, Roey title: Emerging Roles of 1D Vertical Nanostructures in Orchestrating Immune Cell Functions date: 2020-08-26 journal: Adv Mater DOI: 10.1002/adma.202001668 sha: doc_id: 317430 cord_uid: uvx8si42 file: cache/cord-356090-oj3d9ail.json key: cord-356090-oj3d9ail authors: Gorgun, D.; Lihan, M.; Kapoor, K.; Tajkhorshid, E. title: Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane date: 2020-10-27 journal: bioRxiv DOI: 10.1101/2020.10.27.357350 sha: doc_id: 356090 cord_uid: oj3d9ail file: cache/cord-349341-ap5n6ijl.json key: cord-349341-ap5n6ijl authors: Kopek, Benjamin G; Perkins, Guy; Miller, David J; Ellisman, Mark H; Ahlquist, Paul title: Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle date: 2007-08-14 journal: PLoS Biol DOI: 10.1371/journal.pbio.0050220 sha: doc_id: 349341 cord_uid: ap5n6ijl file: cache/cord-341129-eo0vjcmk.json key: cord-341129-eo0vjcmk authors: Kielian, Margaret; Rey, Félix A. title: Virus membrane-fusion proteins: more than one way to make a hairpin date: 2006 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro1326 sha: doc_id: 341129 cord_uid: eo0vjcmk 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-313599-5j19stye.json key: cord-313599-5j19stye authors: Wang, Xianfeng; Ding, Bin; Sun, Gang; Wang, Moran; Yu, Jianyong title: Electro-spinning/netting: A strategy for the fabrication of three-dimensional polymer nano-fiber/nets date: 2013-05-26 journal: Prog Mater Sci DOI: 10.1016/j.pmatsci.2013.05.001 sha: doc_id: 313599 cord_uid: 5j19stye file: cache/cord-001835-0s7ok4uw.json key: cord-001835-0s7ok4uw authors: nan title: Abstracts of the 29th Annual Symposium of The Protein Society date: 2015-10-01 journal: Protein Science DOI: 10.1002/pro.2823 sha: doc_id: 1835 cord_uid: 0s7ok4uw Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-membrane-cord parallel: Warning: No more processes: Decreasing number of running jobs to 67. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === 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: 88082 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: 85555 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: 87410 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: 91219 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: 90062 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: 89895 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: 87722 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: 89161 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: 87759 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: 88992 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: 85825 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: 90371 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: 86339 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: 88225 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: 89758 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: 90358 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: 89243 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: 89380 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: 91447 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: 91590 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: 89536 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: 91617 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: 90655 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: 90130 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-008480-p41oae8e author: O'Callaghan, Barbara title: Characterization of aminopeptidase N from Torpedo marmorata kidney date: 2004-11-12 pages: extension: .txt txt: ./txt/cord-008480-p41oae8e.txt cache: ./cache/cord-008480-p41oae8e.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-008480-p41oae8e.txt' === 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: 85569 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-017566-dvxrwzqw author: González, María Eugenia title: Viral Proteins that Enhance Membrane Permeability date: 2005 pages: extension: .txt txt: ./txt/cord-017566-dvxrwzqw.txt cache: ./cache/cord-017566-dvxrwzqw.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-017566-dvxrwzqw.txt' === file2bib.sh === id: cord-035248-m5517zgn author: Stokes, John W. title: Bleeding, Thromboembolism, and Clinical Outcomes in Venovenous Extracorporeal Membrane Oxygenation date: 2020-11-09 pages: extension: .txt txt: ./txt/cord-035248-m5517zgn.txt cache: ./cache/cord-035248-m5517zgn.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-035248-m5517zgn.txt' === file2bib.sh === id: cord-299270-fwbz3t25 author: Lemieux, M. Joanne title: Structure and function of proteins in membranes and nanodiscs date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-299270-fwbz3t25.txt cache: ./cache/cord-299270-fwbz3t25.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-299270-fwbz3t25.txt' === file2bib.sh === id: cord-103739-mmkrwj8t author: Snijder, Eric J. title: A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-103739-mmkrwj8t.txt cache: ./cache/cord-103739-mmkrwj8t.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-103739-mmkrwj8t.txt' === file2bib.sh === id: cord-287093-9mertwj7 author: Netherton, Christopher L title: Virus factories, double membrane vesicles and viroplasm generated in animal cells date: 2011-10-12 pages: extension: .txt txt: ./txt/cord-287093-9mertwj7.txt cache: ./cache/cord-287093-9mertwj7.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-287093-9mertwj7.txt' === file2bib.sh === id: cord-030961-5gzc7193 author: Wang, Jiajun title: Adhesive contact between cylindrical (Ebola) and spherical (SARS-CoV-2) viral particles and a cell membrane date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-030961-5gzc7193.txt cache: ./cache/cord-030961-5gzc7193.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-030961-5gzc7193.txt' === file2bib.sh === id: cord-023200-3caevjvh author: Falanga, Annarita title: Membranotropic peptides mediating viral entry date: 2018-02-13 pages: extension: .txt txt: ./txt/cord-023200-3caevjvh.txt cache: ./cache/cord-023200-3caevjvh.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-023200-3caevjvh.txt' === file2bib.sh === id: cord-303238-us3dybue author: Kanjanahaluethai, Amornrat title: Membrane Topology of Murine Coronavirus Replicase Nonstructural Protein 3 date: 2007-05-01 pages: extension: .txt txt: ./txt/cord-303238-us3dybue.txt cache: ./cache/cord-303238-us3dybue.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-303238-us3dybue.txt' === file2bib.sh === id: cord-253366-03cg831z author: Chakraborty, Hirak title: Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-253366-03cg831z.txt cache: ./cache/cord-253366-03cg831z.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-253366-03cg831z.txt' === file2bib.sh === id: cord-016938-pk76snuy author: Suh, Hwal (Matthew) title: Collagen Fabrication for the Cell-based Implants in Regenerative Medicine date: 2008 pages: extension: .txt txt: ./txt/cord-016938-pk76snuy.txt cache: ./cache/cord-016938-pk76snuy.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-016938-pk76snuy.txt' === file2bib.sh === id: cord-103812-ls6zgipi author: Norris, Rachael P. title: Gap junction internalization and processing in vivo: a 3D immuno-electron microscopy study date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-103812-ls6zgipi.txt cache: ./cache/cord-103812-ls6zgipi.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-103812-ls6zgipi.txt' === file2bib.sh === id: cord-013223-f43hks44 author: Chronopoulos, Antonios title: Emerging role of bacterial extracellular vesicles in cancer date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-013223-f43hks44.txt cache: ./cache/cord-013223-f43hks44.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 2 resourceName b'cord-013223-f43hks44.txt' === file2bib.sh === id: cord-327765-qdbgkm53 author: Kinnun, Jacob J. title: Lateral Heterogeneity and Domain Formation in Cellular Membranes date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-327765-qdbgkm53.txt cache: ./cache/cord-327765-qdbgkm53.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 2 resourceName b'cord-327765-qdbgkm53.txt' === file2bib.sh === id: cord-289541-y7lewk1t author: Zhang, Li-Zhi title: Fabrication of a lithium chloride solution based composite supported liquid membrane and its moisture permeation analysis date: 2006-05-01 pages: extension: .txt txt: ./txt/cord-289541-y7lewk1t.txt cache: ./cache/cord-289541-y7lewk1t.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-289541-y7lewk1t.txt' === file2bib.sh === id: cord-011888-3mvzkff6 author: Moore, John P. title: Oxone(®)-Mediated TEMPO-Oxidized Cellulose Nanomaterial Ultrafiltration and Dialysis Mixed-Matrix Hollow Fiber Membranes date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-011888-3mvzkff6.txt cache: ./cache/cord-011888-3mvzkff6.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-011888-3mvzkff6.txt' === file2bib.sh === id: cord-000884-zq8kqf6h author: Shen, Hsin-Hui title: Reconstitution of Membrane Proteins into Model Membranes: Seeking Better Ways to Retain Protein Activities date: 2013-01-14 pages: extension: .txt txt: ./txt/cord-000884-zq8kqf6h.txt cache: ./cache/cord-000884-zq8kqf6h.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-000884-zq8kqf6h.txt' === file2bib.sh === id: cord-298019-gf2asni1 author: Galdiero, Stefania title: gH625: A milestone in understanding the many roles of membranotropic peptides date: 2014-10-12 pages: extension: .txt txt: ./txt/cord-298019-gf2asni1.txt cache: ./cache/cord-298019-gf2asni1.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-298019-gf2asni1.txt' === file2bib.sh === id: cord-279463-bli8hwda author: Lipp, Joachim title: The membrane-spanning segment of invariant chain (Iγ) contains a potentially cleavable signal sequence date: 1986-09-26 pages: extension: .txt txt: ./txt/cord-279463-bli8hwda.txt cache: ./cache/cord-279463-bli8hwda.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 2 resourceName b'cord-279463-bli8hwda.txt' === file2bib.sh === id: cord-284690-ogu1gmcb author: da Cunha, Nicolau B. title: The next generation of antimicrobial peptides (AMPs) as molecular therapeutic tools for the treatment of diseases with social and economic impacts date: 2016-11-23 pages: extension: .txt txt: ./txt/cord-284690-ogu1gmcb.txt cache: ./cache/cord-284690-ogu1gmcb.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-284690-ogu1gmcb.txt' === file2bib.sh === id: cord-285620-oawrnmhy author: Fahimirad, Shohreh title: Efficient removal of water bacteria and viruses using electrospun nanofibers date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-285620-oawrnmhy.txt cache: ./cache/cord-285620-oawrnmhy.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-285620-oawrnmhy.txt' === file2bib.sh === id: cord-034898-zjfhpum2 author: Patangi, Sanjay Orathi title: Veno-arterial extracorporeal membrane oxygenation: Special reference for use in ‘post-cardiotomy cardiogenic shock’ — A review with an Indian perspective date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-034898-zjfhpum2.txt cache: ./cache/cord-034898-zjfhpum2.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-034898-zjfhpum2.txt' === file2bib.sh === id: cord-257754-pqxkyg8z author: Reggiori, Fulvio title: Membrane Origin for Autophagy date: 2006-07-21 pages: extension: .txt txt: ./txt/cord-257754-pqxkyg8z.txt cache: ./cache/cord-257754-pqxkyg8z.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-257754-pqxkyg8z.txt' === file2bib.sh === id: cord-104279-choywmwd author: nan title: Membrane protein sorting in the yeast secretory pathway: evidence that the vacuole may be the default compartment date: 1992-10-01 pages: extension: .txt txt: ./txt/cord-104279-choywmwd.txt cache: ./cache/cord-104279-choywmwd.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-104279-choywmwd.txt' === file2bib.sh === id: cord-346446-i7gpxcyo author: Zhang, Jianguo title: Biosynthetic Polymalic Acid as a Delivery Nanoplatform for Translational Cancer Medicine date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-346446-i7gpxcyo.txt cache: ./cache/cord-346446-i7gpxcyo.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-346446-i7gpxcyo.txt' === file2bib.sh === id: cord-272666-3uidpr79 author: Doyle, Nicole title: Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing date: 2018-09-06 pages: extension: .txt txt: ./txt/cord-272666-3uidpr79.txt cache: ./cache/cord-272666-3uidpr79.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-272666-3uidpr79.txt' === file2bib.sh === id: cord-265887-g5zhoyo9 author: Mukherjee, Shruti title: Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-265887-g5zhoyo9.txt cache: ./cache/cord-265887-g5zhoyo9.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-265887-g5zhoyo9.txt' === file2bib.sh === id: cord-009371-ub4p4ngr author: Mollenhauer, Hilton H. title: Alteration of intracellular traffic by monensin; mechanism, specificity and relationship to toxicity date: 1990-05-07 pages: extension: .txt txt: ./txt/cord-009371-ub4p4ngr.txt cache: ./cache/cord-009371-ub4p4ngr.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-009371-ub4p4ngr.txt' === file2bib.sh === id: cord-020712-l9cn0n99 author: Ohnishi, Shun-Ichi title: Chapter 9 Fusion of Viral Envelopes with Cellular Membranes date: 2008-05-30 pages: extension: .txt txt: ./txt/cord-020712-l9cn0n99.txt cache: ./cache/cord-020712-l9cn0n99.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-020712-l9cn0n99.txt' === file2bib.sh === id: cord-294842-aesiff1f author: Romero-Brey, Inés title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses date: 2014-07-22 pages: extension: .txt txt: ./txt/cord-294842-aesiff1f.txt cache: ./cache/cord-294842-aesiff1f.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-294842-aesiff1f.txt' === file2bib.sh === id: cord-020714-h1fevqcw author: Compans, Richard W. title: Membrane Glycoproteins of Enveloped Viruses date: 2008-05-30 pages: extension: .txt txt: ./txt/cord-020714-h1fevqcw.txt cache: ./cache/cord-020714-h1fevqcw.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-020714-h1fevqcw.txt' === file2bib.sh === id: cord-022504-tk7v4hoj author: nan title: Environmental and safety issues with nanoparticles date: 2012-03-16 pages: extension: .txt txt: ./txt/cord-022504-tk7v4hoj.txt cache: ./cache/cord-022504-tk7v4hoj.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-022504-tk7v4hoj.txt' === file2bib.sh === id: cord-317430-uvx8si42 author: Chen, Yaping title: Emerging Roles of 1D Vertical Nanostructures in Orchestrating Immune Cell Functions date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-317430-uvx8si42.txt cache: ./cache/cord-317430-uvx8si42.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-317430-uvx8si42.txt' === file2bib.sh === id: cord-336929-2rnkotqy author: Vieira, Flávia Sarmento title: Host‐cell lipid rafts: a safe door for micro‐organisms? date: 2012-01-03 pages: extension: .txt txt: ./txt/cord-336929-2rnkotqy.txt cache: ./cache/cord-336929-2rnkotqy.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-336929-2rnkotqy.txt' === file2bib.sh === id: cord-329448-kxxy60x9 author: Kumari, Sudha title: Endocytosis unplugged: multiple ways to enter the cell date: 2010-02-02 pages: extension: .txt txt: ./txt/cord-329448-kxxy60x9.txt cache: ./cache/cord-329448-kxxy60x9.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-329448-kxxy60x9.txt' === file2bib.sh === id: cord-353815-w35spqqt author: Huan, Yuchen title: Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-353815-w35spqqt.txt cache: ./cache/cord-353815-w35spqqt.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-353815-w35spqqt.txt' === file2bib.sh === id: cord-309384-vlk8cebh author: Kolter, Thomas title: Ganglioside Biochemistry date: 2012-12-19 pages: extension: .txt txt: ./txt/cord-309384-vlk8cebh.txt cache: ./cache/cord-309384-vlk8cebh.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-309384-vlk8cebh.txt' === file2bib.sh === id: cord-264996-og3sg0qw author: Howell, Gareth J. title: Cell Biology of Membrane Trafficking in Human Disease date: 2006-09-17 pages: extension: .txt txt: ./txt/cord-264996-og3sg0qw.txt cache: ./cache/cord-264996-og3sg0qw.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-264996-og3sg0qw.txt' === file2bib.sh === id: cord-313599-5j19stye author: Wang, Xianfeng title: Electro-spinning/netting: A strategy for the fabrication of three-dimensional polymer nano-fiber/nets date: 2013-05-26 pages: extension: .txt txt: ./txt/cord-313599-5j19stye.txt cache: ./cache/cord-313599-5j19stye.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 6 resourceName b'cord-313599-5j19stye.txt' === file2bib.sh === id: cord-014685-ihh30q6f author: nan title: Posters P788 - P999 date: 2005-09-21 pages: extension: .txt txt: ./txt/cord-014685-ihh30q6f.txt cache: ./cache/cord-014685-ihh30q6f.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 7 resourceName b'cord-014685-ihh30q6f.txt' === file2bib.sh === id: cord-004584-bcw90f5b author: nan title: Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date: 2011-08-06 pages: extension: .txt txt: ./txt/cord-004584-bcw90f5b.txt cache: ./cache/cord-004584-bcw90f5b.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 11 resourceName b'cord-004584-bcw90f5b.txt' === 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: 91544 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-001835-0s7ok4uw author: nan title: Abstracts of the 29th Annual Symposium of The Protein Society date: 2015-10-01 pages: extension: .txt txt: ./txt/cord-001835-0s7ok4uw.txt cache: ./cache/cord-001835-0s7ok4uw.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-001835-0s7ok4uw.txt' Que is empty; done keyword-membrane-cord === reduce.pl bib === id = cord-000884-zq8kqf6h author = Shen, Hsin-Hui title = Reconstitution of Membrane Proteins into Model Membranes: Seeking Better Ways to Retain Protein Activities date = 2013-01-14 pages = extension = .txt mime = text/plain words = 6861 sentences = 355 flesch = 39 summary = This review will discuss the reconstitution of membrane protein activities in four different types of model membrane—monolayers, supported lipid bilayers, liposomes and nanodiscs, comparing their advantages in membrane protein reconstitution. To simplify cell membrane systems, model membranes such as monolayers, bilayers, liposomes and nanodiscs have been developed, enabling detailed investigation of membrane protein structure in lipid membranes. There are a number of approaches used to create a model membrane in order to mimic properties of the native cell membrane, and we will review these various approaches for reconstituting membrane proteins into different types of model membrane-monolayers [5] , supported planar lipid bilayer [6] and liposomes [7] as shown in Figure 1A -C. By using this approach, it appears that both PLA2 and PLC are active at the monolayer model membrane, indicating that the kinetics of phospholipid hydrolysis at the air-water interface can be monitored by biophysical characterization techniques in situ such as PM-IRRAS and infrared reflection adsorption spectroscopy [22] . cache = ./cache/cord-000884-zq8kqf6h.txt txt = ./txt/cord-000884-zq8kqf6h.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-017566-dvxrwzqw author = González, María Eugenia title = Viral Proteins that Enhance Membrane Permeability date = 2005 pages = extension = .txt mime = text/plain words = 4482 sentences = 265 flesch = 45 summary = During the infection of cells by animal viruses, membrane permeability is modified at two different steps of the virus life cycle (Carrasco, 1995) (Figure 6 .1). The viral molecules involved are components of virions: glycoproteins when enveloped particles are analyzed or, still unidentified, domains of the structural proteins in the case of naked viruses. At late times of infection, when there is active translation of late viral mRNAs, the plasma membrane becomes permeable to small molecules and ions (Carrasco, 1978) ( Figure 6 .1). Different viral molecules may be responsible for this late enhancement of membrane permeability, including viroporins (Gonzalez and Carrasco, 2003) , glycoproteins, and even proteases (Chang et al., 1999; Blanco et al., 2003) . Entry of enveloped animal viruses leads to early membrane permeabilization, which is mediated by the formation of the two pores (fusion and TM) formed by viral fusion glycoproteins. cache = ./cache/cord-017566-dvxrwzqw.txt txt = ./txt/cord-017566-dvxrwzqw.txt === reduce.pl bib === id = cord-013223-f43hks44 author = Chronopoulos, Antonios title = Emerging role of bacterial extracellular vesicles in cancer date = 2020-10-15 pages = extension = .txt mime = text/plain words = 5793 sentences = 264 flesch = 29 summary = The increasing appreciation that microbiota-derived EV can enter the systemic circulation and be detected in human body fluids is likely to stimulate completely new areas of investigation in microbiome research, biomarkers and liquid biopsies, BEV-based therapeutics, onco-immunology, as well as fundamental microbial EV biology. In addition to potentially modulating the innate immune response via or more cytosolic DNA sensors, the possibility that pathogenic BEV-derived DNA can be transferred and detected in the nucleus of non-phagocytic cells (e.g. epithelial cells) [30] , raises the intriguing possibility that bacterial genetic material could be transferred to human somatic cells and integrated into the host genome. BEVs released by bacteria in the gut lumen can cross the epithelial barrier to gain access into the underlying submucosa enabling them to interact with various resident immune cell populations (dendritic cells, neutrophils and macrophages) as well as potentially disseminate more widely around the body via the systemic or lymphatic circulation to reach distant tissues and organs or even the brain (Fig. 2) . cache = ./cache/cord-013223-f43hks44.txt txt = ./txt/cord-013223-f43hks44.txt === reduce.pl bib === id = cord-023200-3caevjvh author = Falanga, Annarita title = Membranotropic peptides mediating viral entry date = 2018-02-13 pages = extension = .txt mime = text/plain words = 6062 sentences = 270 flesch = 41 summary = The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. [3, 4] The molecular details of the interactions at the interface of virus and cell surfaces are quite complex and highly variable, but there is a common idea that only a limited number of pathways allowing viruses to reach the sites of penetration exist, with enveloped and non-enveloped viruses presenting different and unrelated processes, but with general principles driving all fusion events. [16, 17] Viral fusion proteins undergo significant rearrangements from the pre-fusion to the post-fusion conformations which are triggered by either receptor binding, proteolytic cleavage or low endosomal pH, and eventually determine the exposure of previously sequestered hydrophobic peptides, loops, or patches, able to interact with and destabilize one or both the opposing membranes. cache = ./cache/cord-023200-3caevjvh.txt txt = ./txt/cord-023200-3caevjvh.txt === reduce.pl bib === id = cord-009371-ub4p4ngr author = Mollenhauer, Hilton H. title = Alteration of intracellular traffic by monensin; mechanism, specificity and relationship to toxicity date = 1990-05-07 pages = extension = .txt mime = text/plain words = 12395 sentences = 535 flesch = 46 summary = cache = ./cache/cord-009371-ub4p4ngr.txt txt = ./txt/cord-009371-ub4p4ngr.txt === reduce.pl bib === id = cord-022504-tk7v4hoj author = nan title = Environmental and safety issues with nanoparticles date = 2012-03-16 pages = extension = .txt mime = text/plain words = 14097 sentences = 709 flesch = 52 summary = During the process, large volumes of ultrapure water are consumed to clean the surface of the wafer, which generates large quantity of CMP wastewater typically having high solid content resulting from slurry abrasive particles of SiO 2 , Al 2 O 3 , or CeO 2 , depending on the nature of the CMP application. 7.2.6.2 Industrial processes with cleanrooms Cleanrooms and associated controlled environments (e.g., in the case of an ISO Class 3 cleanroom, the maximum permissible airborne particle concentration is less than 10 3 particles/m 3 for particles with the size of 0.1 m or larger, while the airborne particle concentration in ordinary indoor environments is on the order of 10 9 particles/m 3 or higher) are usually adopted to avoid particle contamination in industrial processes where precision products such as engineered nanoparticles, semiconductors, and other electronic or optical devices are fabricated because the deposition of particles onto product surfaces causes their yield reduction and quality deterioration. cache = ./cache/cord-022504-tk7v4hoj.txt txt = ./txt/cord-022504-tk7v4hoj.txt === reduce.pl bib === id = cord-030961-5gzc7193 author = Wang, Jiajun title = Adhesive contact between cylindrical (Ebola) and spherical (SARS-CoV-2) viral particles and a cell membrane date = 2020-08-28 pages = extension = .txt mime = text/plain words = 4335 sentences = 260 flesch = 55 summary = In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. In this work, we create a continuum model for the small-deflection adhesive contact mechanics of virus particle attachment onto the host cell membrane in terms of the principal biophysical properties of the virus, membrane, and their interaction. These results also help to retrieve conditions for lack of adhesion, pull-off force, and contact area between the virus particle and cell membrane. We now describe in outline the continuum models for adhesive contact between the virus and cell membrane, driven by adhesion and external displacement or force, and resisted by tension and elastic bending. In our models, the parameters that govern the adhesive contact mechanics are (more in Table 1 ) bending rigid κ, tension σ, adhesion free energy per receptor β, binding receptor density ρ, and the radius of the virus, R. cache = ./cache/cord-030961-5gzc7193.txt txt = ./txt/cord-030961-5gzc7193.txt === reduce.pl bib === id = cord-014685-ihh30q6f author = nan title = Posters P788 - P999 date = 2005-09-21 pages = extension = .txt mime = text/plain words = 38354 sentences = 1784 flesch = 45 summary = This study has attempted to analyse the structural properties of membrane peptides and proteins through the use of model systems that have been designed to mimic their natural counterparts: Podlubnaya 2 1 Institute of Theoretical and Experimental Biophysics RAS, 2 Pushchino State University Amyloid brils are formed by proteins or their peptides in the result of a conformational transition from alpha helix into beta-sheet structure. Analysis of the results of such studies indicate that folding of SNase fragments is dominated by developing the local and non-local nucleation sites from native-like secondary structures and by intensifying the longrange interactions of residues at nucleation sites with residues further removed in sequence. The results show that at different pH values the aggregation processes of both proteins follow different pathways determined by the variations in the native structure and by the details of the involved conformational changes. cache = ./cache/cord-014685-ihh30q6f.txt txt = ./txt/cord-014685-ihh30q6f.txt === reduce.pl bib === === reduce.pl bib === id = cord-011888-3mvzkff6 author = Moore, John P. title = Oxone(®)-Mediated TEMPO-Oxidized Cellulose Nanomaterial Ultrafiltration and Dialysis Mixed-Matrix Hollow Fiber Membranes date = 2020-06-15 pages = extension = .txt mime = text/plain words = 5936 sentences = 336 flesch = 58 summary = title: Oxone(®)-Mediated TEMPO-Oxidized Cellulose Nanomaterial Ultrafiltration and Dialysis Mixed-Matrix Hollow Fiber Membranes Ultrafiltration and dialysis were performed using bovine serum albumin (BSA), lysozyme, and urea to analyze various properties of each hollow fiber membrane type. Utilizing the procedure from Moore et al., OTO-CNMs Form I and Form II were synthesized and used in conjunction with cellulose triacetate (CTA) from Acros Organics (Fair Lawn, NJ, USA), N-methyl pyrrolidone (NMP) from VWR (Radnor, PA, USA), and deionized water to create novel membranes for filtration [21] . In this study on the implementation of two derivatives of cellulose nanomaterials into hollow fiber membranes for ultrafiltration and dialysis, OTO-CNM Form I and Form II mixed-matrix membranes have been quantitatively evaluated for the first time by determining model molecule selectivity (BSA, urea, and lysozyme), as well as transport rates (flux and diffusion rates). cache = ./cache/cord-011888-3mvzkff6.txt txt = ./txt/cord-011888-3mvzkff6.txt === reduce.pl bib === id = cord-103739-mmkrwj8t author = Snijder, Eric J. title = A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis date = 2020-03-24 pages = extension = .txt mime = text/plain words = 3808 sentences = 223 flesch = 48 summary = Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). 106 double-membrane spherules (DMSs) 107 We first set out to analyse the ultrastructure of MERS-CoV-infected Huh7 cells under sample 108 preparation conditions favourable for autoradiography (see Materials and Methods) (Fig 1, S1 109 Video). Association of polioviral proteins of the P2 89 genomic region with the viral replication complex and virus-induced membrane synthesis as 90 visualized by electron microscopic immunocytochemistry and autoradiography cache = ./cache/cord-103739-mmkrwj8t.txt txt = ./txt/cord-103739-mmkrwj8t.txt === reduce.pl bib === id = cord-016938-pk76snuy author = Suh, Hwal (Matthew) title = Collagen Fabrication for the Cell-based Implants in Regenerative Medicine date = 2008 pages = extension = .txt mime = text/plain words = 6409 sentences = 292 flesch = 37 summary = As atelocollagen has no telopeptides that integrate with other atelocollagen molecules, basic technology to produce intramolecular and intermolecular bonds for construction of the extracellular matrix with adequate mechanical properties required by tissue where the artificial cell-based implant is delivered is the recrosslinking method using chemical reagents or physical dynamics. Collagen can be fabricated into various forms of gel, fiber, membrane with or without pores, and it can even be grafted onto the non-viable metal, ceramic and synthetic biomaterials to introduce biological layer on surface. To produce an artificial skin, autologous dermal fibroblasts of rat were seeded into the EDC crosslinked porous collagen-laminin membrane and cultured in minimum essential medium (MEM) for 3 days to provide the cell-niche adaptation period. Although collagen based gel is favorable to fabricate cell conductive substitute, weak mechanical property is a barrier for application in the physiological stress bearing tissues, and, to resolve this problem, hybridization of collagen with polymeric biomaterials has been suggested. cache = ./cache/cord-016938-pk76snuy.txt txt = ./txt/cord-016938-pk76snuy.txt === reduce.pl bib === id = cord-008480-p41oae8e author = O'Callaghan, Barbara title = Characterization of aminopeptidase N from Torpedo marmorata kidney date = 2004-11-12 pages = extension = .txt mime = text/plain words = 4411 sentences = 263 flesch = 53 summary = Depending on solubilization conditions, both the antigen and peptidase activity were recovered either as a broad peak with a sedimentation coefficient of 18S (2% CHAPS) or as a single peak of 7.8S (1% CHAPS plus 0.2 % C(12)E(9)), showing that Torpedo aminopeptidase N behaves as an oligomer stabilized by hydrophobic interactions, easily converted into a 160 kDa monomer. The antigen is highly concentrated in the apical membrane of proximal tubule epithelial cells (600 gold particles/μm(2) of brush border membrane) whereas no labeling could be detected in other cell types or in other membranes of the same cells (basolatéral membranes, vacuoles or vesicles). Hybrids were selected in hypoxanthine, aminopterin and thymidine medium and superuatants from the culture wefts containing hybrid cells were tested for the presence of antibodies binding to the apical membrane of tubular epithelial cells on Torpedo kidney frozen sections. cache = ./cache/cord-008480-p41oae8e.txt txt = ./txt/cord-008480-p41oae8e.txt === reduce.pl bib === id = cord-284690-ogu1gmcb author = da Cunha, Nicolau B. title = The next generation of antimicrobial peptides (AMPs) as molecular therapeutic tools for the treatment of diseases with social and economic impacts date = 2016-11-23 pages = extension = .txt mime = text/plain words = 9481 sentences = 450 flesch = 35 summary = The use of viral vectors based on the tobacco mosaic virus (TMV) and potato virus X (PVX) for cloning and massively expressing AMP genes in Nicotiana benthamiana appears to be an interesting new approach to considerably enhance recombinant peptide production before structural and functional characterization. However, frequent gene silencing at the transcriptional level and instability of genes cloned in vectors for stable or transient expression remain major challenges limiting the efficient production of AMPs. Another persistent issue is the poor quality of the peptides endogenously synthesized in bacteria, yeast, and plants, particularly resulting from undesirable post-translational modifications [2, 33] . Some drawbacks presented by plant expression systems are solved by the CRISPR system, a revolutionary genome-editing technology that presents myriad possibilities for genetic manipulation at the genomic level and provides unprecedented tools (CRISPRi and CRISPRa) to precisely control gene expression and the structural modification of AMPs. Despite its current minor limitations (e.g. off-target effects), CRISPR could have a key role in the future development of clinical drugs as biotechnological antiinfective agents, including the rational biosynthesis of next-generation antimicrobials. cache = ./cache/cord-284690-ogu1gmcb.txt txt = ./txt/cord-284690-ogu1gmcb.txt === reduce.pl bib === id = cord-298019-gf2asni1 author = Galdiero, Stefania title = gH625: A milestone in understanding the many roles of membranotropic peptides date = 2014-10-12 pages = extension = .txt mime = text/plain words = 8586 sentences = 354 flesch = 37 summary = While they have been initially discovered in viral fusion proteins and have been involved in the mechanism of viral entry, it is now clear that their features and their mode of interaction with membrane bilayers can be exploited to design viral inhibitors as well as to favor delivery of cargos across the cell membrane and across the blood–brain barrier. Peptides with a propensity for membrane binding can also interfere with enveloped virus entry by direct physical interaction with the hydrophobic surfaces present on cell membranes and/or fusion proteins. Since not all membranotropic peptides are able to cross the membrane bilayer, it is essential to identify structural characteristics of hydrophobic peptides know to enter the cell membrane to highlight any feature that is involved in the penetration which may help in the design of novel delivery tools. Dendrimer functionalization with a membrane-interacting domain of herpes simplex virus type 1: towards intracellular delivery cache = ./cache/cord-298019-gf2asni1.txt txt = ./txt/cord-298019-gf2asni1.txt === reduce.pl bib === id = cord-020712-l9cn0n99 author = Ohnishi, Shun-Ichi title = Chapter 9 Fusion of Viral Envelopes with Cellular Membranes date = 2008-05-30 pages = extension = .txt mime = text/plain words = 11708 sentences = 735 flesch = 56 summary = Residues 80-100 in El and residues 100-131 in G, which have sequence homology among the strains, may be such stretches though not strongly hydrophobic (Table 262 SHUN-ICHI OHNlSHl and the putative fusogenic segment should be able to interact with the target membrane, inducing some disturbance eventually leading to fusion (Fig. Ib) . Presence of receptors for the amino-terminal segments in target membranes has been suggested from studies on inhibition of virus replication by small peptides with amino acid sequences similar to that of the viral amino terminus (Richardson et al., 1980; Richardson and Choppin, 1983) . Why is a specific amino acid sequence of F glycoprotein required for the membrane fusion reaction between envelope of HVJ (Sendai virus) and target cell membranes? pH-Dependent membrane fusion activity of a synthetic twenty amino acid peptide with the same sequence as that of the hydrophobic segment in influenza virus hemagglutinin cache = ./cache/cord-020712-l9cn0n99.txt txt = ./txt/cord-020712-l9cn0n99.txt === reduce.pl bib === === reduce.pl bib === id = cord-253366-03cg831z author = Chakraborty, Hirak title = Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics date = 2020-07-22 pages = extension = .txt mime = text/plain words = 5024 sentences = 282 flesch = 47 summary = In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. An efficient membrane fusion mechanism between SARS-CoV-2 and host cell could also be responsible for the high level of infection. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Identification of the membraneactive regions of the severe acute respiratory syndrome coronavirus spike membrane glycoprotein using a 16/18-mer peptide scan: implications for the viral fusion mechanism Interaction of a peptide from the pre-transmembrane domain of the severe acute respiratory syndrome coronavirus spike protein with phospholipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes cache = ./cache/cord-253366-03cg831z.txt txt = ./txt/cord-253366-03cg831z.txt === reduce.pl bib === id = cord-020714-h1fevqcw author = Compans, Richard W. title = Membrane Glycoproteins of Enveloped Viruses date = 2008-05-30 pages = extension = .txt mime = text/plain words = 14149 sentences = 684 flesch = 43 summary = Other advantages of enveloped viruses in studies of membrane structure and biogenesis include the ease of biosynthetic labeling of viruses grown in cell culture with specific radioactive precursors and the availability of mutants in defined gene products, some of which are proving to be useful in the analysis of viral membrane assembly. Apart from minor differences in carbohydrates of glycoproteins, virion proteins are indistinguishable when the virus is propagated in a variety of cells; therefore there appears to be little or no determining influence of viral proteins on the composition of the lipid bilayer. Based upon the estimated carbohydrate content (12,000 daltons) of the HA glycoprotein obtained by Laver (1971) and Schwarz and Klenk (1974) and the size estimates of the type I and I1 glycopeptides of influenza virus grown in MDBK cells, it was estimated that HA, contains a single type I glycopeptide whereas HA, possesses two type I and one or two type I1 oligosaccharide side-chains for the WSN strain (Nakamura and Com pans, 1978b) . cache = ./cache/cord-020714-h1fevqcw.txt txt = ./txt/cord-020714-h1fevqcw.txt === reduce.pl bib === id = cord-289541-y7lewk1t author = Zhang, Li-Zhi title = Fabrication of a lithium chloride solution based composite supported liquid membrane and its moisture permeation analysis date = 2006-05-01 pages = extension = .txt mime = text/plain words = 4040 sentences = 292 flesch = 60 summary = The membrane is composed of three layers: two hydrophobic protective layers and a sandwiched hydrophilic support layer in which LiCl solution is immobilized to facilitate water vapor transfer. Further, the supported liquid layer only accounts for 12% of the total moisture transfer resistance in the cell, indicating that there is much potential for further performance improvement. The core material of an MTHR ventilator are vapor-permeable membranes, therefore both heat and moisture are transferred between these two air streams when they flow through the unit. However, moisture diffusion coefficients in such polymer membranes are usually very low, in the order of 10 −12 to 10 −13 m 2 s −1 [11, 18] , while MTHR ventilators only have limited transmembrane vapor partial pressure difference, consequently performances are quite limited currently. To improve the performances of MTHR ventilators, in this study, a novel membrane, a composite SLM, which employs LiCl liquid solution immobilized in a porous support membrane to facilitate the transport of moisture, is prepared. cache = ./cache/cord-289541-y7lewk1t.txt txt = ./txt/cord-289541-y7lewk1t.txt === reduce.pl bib === id = cord-034898-zjfhpum2 author = Patangi, Sanjay Orathi title = Veno-arterial extracorporeal membrane oxygenation: Special reference for use in ‘post-cardiotomy cardiogenic shock’ — A review with an Indian perspective date = 2020-11-07 pages = extension = .txt mime = text/plain words = 7527 sentences = 448 flesch = 39 summary = title: Veno-arterial extracorporeal membrane oxygenation: Special reference for use in 'post-cardiotomy cardiogenic shock' — A review with an Indian perspective Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is an important modality of managing post-cardiotomy cardiogenic shock with variable outcomes which would otherwise be universally fatal. Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) has gained popularity over the years as a 'bailout' option after conventional circulatory support methods have proved refractory in the operating room (OR)/intensive care unit (ICU). Long-term survival and major outcomes in post-cardiotomy extracorporeal membrane oxygenation for adult patients in cardiogenic shock Usefulness of cardiac biomarkers to predict cardiac recovery in patients on extracorporeal membrane oxygenation support for refractory cardiogenic shock Nosocomial infections in adult cardiogenic shock patients supported by venoarterial extracorporeal membrane oxygenation Clinical outcomes in patients after extracorporeal membrane oxygenation support for postcardiotomy cardiogenic shock: a single-centre experience of 92 cases cache = ./cache/cord-034898-zjfhpum2.txt txt = ./txt/cord-034898-zjfhpum2.txt === reduce.pl bib === id = cord-104279-choywmwd author = nan title = Membrane protein sorting in the yeast secretory pathway: evidence that the vacuole may be the default compartment date = 1992-10-01 pages = extension = .txt mime = text/plain words = 9856 sentences = 411 flesch = 52 summary = First, to determine if the lumenal domain was sorted to the vacuole when expressed in the secretory pathway as a soluble protein, a gene fusion was used to create the protein ctFss-B, consisting of the NH2-terminal ER-targeting signal sequence of prepro-t~ factor fused to the lumenal domain of DPAP B at residue 49 ( Fig. 1 B) . To ad-dress the possibility that the mutant constructs analyzed in this study were mislocalized to the plasma membrane followed by rapid endocytic uptake to the vacuole, indirect immunofluorescence experiments were performed on BB-Inv, B-A-B, A20-BB, and/x22-AA-B expressed in a secl strain at 34~ As a positive control for accumulation in secretory vesicles, the localization of the fusion protein Fusl-LacZp was analyzed (Trueheart et al., 1987) . cache = ./cache/cord-104279-choywmwd.txt txt = ./txt/cord-104279-choywmwd.txt === reduce.pl bib === id = cord-035248-m5517zgn author = Stokes, John W. title = Bleeding, Thromboembolism, and Clinical Outcomes in Venovenous Extracorporeal Membrane Oxygenation date = 2020-11-09 pages = extension = .txt mime = text/plain words = 2386 sentences = 141 flesch = 28 summary = Our objective was to examine the relative frequencies of bleeding and thromboembolic events and their associations with survival among a cohort of consecutive patients receiving venovenous extracorporeal membrane oxygenation. Our objective was to examine the relative frequencies of bleeding and thromboembolic events and their associations with survival among a cohort of consecutive patients receiving venovenous extracorporeal membrane oxygenation. Conclusions: In this cohort of patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation, bleeding occurred more frequently than thromboembolism and was associated with worse survival. Conclusions: In this cohort of patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation, bleeding occurred more frequently than thromboembolism and was associated with worse survival. We collected the following data from the electronic health record: patient characteristics in the 24 hours prior to ECMO initiation; bleeding and thromboembolic events during venovenous ECMO as previously defined (5); and clinical outcomes, including in-hospital survival, ECMO duration, and hospital length of stay. cache = ./cache/cord-035248-m5517zgn.txt txt = ./txt/cord-035248-m5517zgn.txt === reduce.pl bib === id = cord-279463-bli8hwda author = Lipp, Joachim title = The membrane-spanning segment of invariant chain (Iγ) contains a potentially cleavable signal sequence date = 1986-09-26 pages = extension = .txt mime = text/plain words = 6276 sentences = 367 flesch = 62 summary = As type II membrane proteins contain only a single stretch of hydrophobic amino acid residues, this might function as a signal for membrane insertion as well as a membrane anchor (Markoff et al., 1984; Spiess and Lodish, 1986) . plycat is an in-frame fusion between the 5' region of ly encoding the cytoplas, mic, membrane-spanning segment plus 12 amino acids of the exoplasmic portion of ly and the gene encoding the cytoplasmic protein chloramphenicol acetyltransferase (CAT). After protease digestion in the presence of microsomal membranes, lyCAT* is reduced in molecular weight by about 2 kd, suggesting that it exposes 20-30 amino acid residues on the cytoplasmic side ( Figure 3 , lanes 2 and 3). This signal sequence is located in the amino-terminal half of the membrane-spanning segment, and it is cleaved when the preceding cytoplasmic domain is removed. cache = ./cache/cord-279463-bli8hwda.txt txt = ./txt/cord-279463-bli8hwda.txt === reduce.pl bib === id = cord-257754-pqxkyg8z author = Reggiori, Fulvio title = Membrane Origin for Autophagy date = 2006-07-21 pages = extension = .txt mime = text/plain words = 9205 sentences = 481 flesch = 46 summary = In addition, a study analyzing conditional knock-out mice defective for autophagy has revealed that the mutant animal accumulates numerous ubiquitinated aggregates in the cytosol, suggesting that this covalent protein modification could serve to specifically target to autophagosomes large structures that have to be eliminated (Komatsu et al., 2005) . In contrast to mammalian cells where several isolation membranes can be simultaneously activated, a single perivacuolar site of organization for double-membrane vesicle formation (named the pre-autophagosomal structure, PAS) is observed in the yeast S. Because the three mammalian Atg8 homologs are diVerently expressed in various tissues (Tanida et al., 2004) , another intriguing option is that these proteins are involved in supplying the autophagosome with membranes derived from diVerent compartments depending on the cell type; for example, GATE-16 from the Golgi complex and GABARAP from the same organelle as well as the synaptic cisternae (Kittler et al., 2001; Kneussel et al., 2000; Sagiv et al., 2000) . cache = ./cache/cord-257754-pqxkyg8z.txt txt = ./txt/cord-257754-pqxkyg8z.txt === reduce.pl bib === === reduce.pl bib === id = cord-287093-9mertwj7 author = Netherton, Christopher L title = Virus factories, double membrane vesicles and viroplasm generated in animal cells date = 2011-10-12 pages = extension = .txt mime = text/plain words = 4308 sentences = 227 flesch = 39 summary = In this review, we discuss how three supergroups of (+)RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses. In this review, we discuss how three supergroups of (+)strand RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses (NCLDV). The RNA-dependent RNA polymerases (RdRp) of the (+)strand RNA viruses are targeted to the cytoplasmic face of membrane-bound organelles and subsequent assembly of the replicase complex induces membrane curvature and the formation of densely packed membrane vesicles (reviewed in [1, 2] ) ( Figure 1 ). This suggests that replication may take place on CM and that genomes are transferred to vesicular packets for envelopment and budding, while excess viral RNA may be stored in DMVs. Picornaviruses generate densely packed DMVs between 200 and 400 nm in diameter, a series of single membraned vesicles resulting from fragmentation of the Golgi, and autophagosomes possibly generated as a bystander response to infection [11 ,12-16] . cache = ./cache/cord-287093-9mertwj7.txt txt = ./txt/cord-287093-9mertwj7.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-327765-qdbgkm53 author = Kinnun, Jacob J. title = Lateral Heterogeneity and Domain Formation in Cellular Membranes date = 2020-09-15 pages = extension = .txt mime = text/plain words = 5431 sentences = 346 flesch = 47 summary = where a 0 is the area per molecule, R is the domain radius, ε is the dielectric constant of the interfacial water, ε 0 is the permittivity of free space, e is Euler's number, and δ is the molecular cut-off distance ∼ 0.5nm 26 Lipids and membrane proteins have varying intrinsic hydrophobic thicknesses. In terms of specific theoretical energetics, this contribution to line tension is less 6 J o u r n a l P r e -p r o o f Figure 2 : (a) The registration of domains across membrane leaflets maximizes dynamics, is entropically favorable, and is one mechanism for domain coalescence (adapted from Haataja et al. In other words, the simple phenomenological free energy approach presented here provides a conceptual framework for understanding the scattering data and interpreting the wide range of phase behaviors observed for lateral lipid organization in cell membranes. Lipid lateral diffusion in bilayers with phosphatidylcholine, sphingomyelin and cholesterol: An NMR study of dynamics and lateral phase separation cache = ./cache/cord-327765-qdbgkm53.txt txt = ./txt/cord-327765-qdbgkm53.txt === reduce.pl bib === id = cord-299270-fwbz3t25 author = Lemieux, M. Joanne title = Structure and function of proteins in membranes and nanodiscs date = 2020-08-22 pages = extension = .txt mime = text/plain words = 3034 sentences = 145 flesch = 39 summary = Abstract The field of membrane structural biology represents a fast-moving field with exciting developments including native nanodiscs that allow preparation of complexes of post-translationally modified proteins bound to biological lipids. Comparisons with the performance of conventional detergents suggests that the development of neutral or basic copolymers related to SMA could offer advantages, providing avenues for solubilization and analysis of a broader array of biological membrane:protein assemblies (memteins). The individual components of erythrocyte membranes including Rh proteins are well known, but their multimeric lipid complexes are dissociated in detergent-based preparations and hence no longer recognizable or extractable using conformation-specific antibodies. A set of ABCG2 protein constructs were designed with N-terminal GFP or SNAP and His 6 tags and solubilized from HEK cells using SMA(2:1) copolymer, as were CD28 and CD86 Antibiotics include lipid-specific peptides that self-associate into pores, which permeabilize bacterial membranes. cache = ./cache/cord-299270-fwbz3t25.txt txt = ./txt/cord-299270-fwbz3t25.txt === reduce.pl bib === === reduce.pl bib === id = cord-303238-us3dybue author = Kanjanahaluethai, Amornrat title = Membrane Topology of Murine Coronavirus Replicase Nonstructural Protein 3 date = 2007-05-01 pages = extension = .txt mime = text/plain words = 4789 sentences = 247 flesch = 50 summary = The papain-like protease (PLpro) encoded by the coronavirus that causes severe acute respiratory syndrome (SARS-CoV) processes three sites in the replicase polyprotein (Harcourt et al., 2004) , and has recently been shown to have de-ubiquitinating activity (Barretto et al., 2005; Lindner et al., 2005) . To extend these studies of membrane association of coronavirus replicase products, we analyzed the amino acid sequence of MHV-JHM nsp3 (from glycine-833 to glycine-2840) for probability of transmembrane helices using the five different programs designed to search for putative membrane-spanning sequences: Phobius, TMHMM, HMMTOP, SOSUI and TMpred (Fig. 2) . In contrast, when CMMs were added to the mixture, protein products that included all or part of nsp3-TM (PLP2-2485, -2390 and -2258) were detected predominantly in the pelleted fraction, consistent with membrane association (Fig. 3B ). cache = ./cache/cord-303238-us3dybue.txt txt = ./txt/cord-303238-us3dybue.txt === reduce.pl bib === id = cord-265887-g5zhoyo9 author = Mukherjee, Shruti title = Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date = 2020-08-11 pages = extension = .txt mime = text/plain words = 9085 sentences = 538 flesch = 41 summary = (56) Apart from these highly conserved sequences throughout the genus, there are distinct potent glycosylation sites along the stretch that can serve as chaperone interacting motifs to help in the protein folding and/or aid in J o u r n a l P r e -p r o o f Journal Pre-proof trafficking along with the cellular machinery.(57) Glycosylation of particular asparagine residues (Asn 45, Asn 48, Asn 64, and Asn 68) in the SARS-CoV has been shown to be crucial in maintaining the proteinoligomerization events associated with the host membranes. (41) The formation of a disulfide bond may also play a crucial role in the oligomerization of the E protein, forming stable dimers, trimers, and pentamers depending on its functional requirement.(105) Thus even though the TMD spans the lipid bilayer, the CxxC motif could serve as an essential key to defining the membrane-associated oligomerization events-providing newer targets for preemptive therapeutic intervention. cache = ./cache/cord-265887-g5zhoyo9.txt txt = ./txt/cord-265887-g5zhoyo9.txt === reduce.pl bib === === reduce.pl bib === id = cord-272666-3uidpr79 author = Doyle, Nicole title = Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing date = 2018-09-06 pages = extension = .txt mime = text/plain words = 7472 sentences = 358 flesch = 52 summary = In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. In a subsequent study by others, it was shown that expression of only nsp3 and 4 from either MERS-CoV or SARS-CoV was able to induce DMV formation, and furthermore, addition of nsp6 made no difference to their shape or size, and did not induce the spherule-like structures seen following infection with whole virus [26] . cache = ./cache/cord-272666-3uidpr79.txt txt = ./txt/cord-272666-3uidpr79.txt === reduce.pl bib === id = cord-103812-ls6zgipi author = Norris, Rachael P. title = Gap junction internalization and processing in vivo: a 3D immuno-electron microscopy study date = 2020-06-30 pages = extension = .txt mime = text/plain words = 4803 sentences = 296 flesch = 55 summary = Less is understood about their internalization, which forms double membrane vesicles containing cytosol and membranes from another cell, called connexosomes or annular gap junctions. Gap junction internalization can also be considered to be a form of trogocytosis (Joly and Hudriser, 2003) in which a portion of the plasma membrane and cytosol of the neighboring cell is transferred to the engulfing cell (See Fig. 1A ). Serial sections were then imaged to obtain threedimensional information; this distinguished between internalized connexosomes and gap junctions in the process of invagination. In 7 of the 56 modified connexosomes, a patch of unlabeled outer membrane bulged outward from a labeled inner membrane ( suggesting that different types of vesicles were involved. Five serial sections through a modified connexosome containing several internal vesicles labeled with Cx43. cache = ./cache/cord-103812-ls6zgipi.txt txt = ./txt/cord-103812-ls6zgipi.txt === reduce.pl bib === id = cord-285620-oawrnmhy author = Fahimirad, Shohreh title = Efficient removal of water bacteria and viruses using electrospun nanofibers date = 2020-08-16 pages = extension = .txt mime = text/plain words = 6761 sentences = 361 flesch = 38 summary = This review intends to provide a detailed summary of the recent advances in the fabrication of antibacterial and antiviral electrospun nanofibers and discuss their application efficiency as a water filtration membrane. The present work reviews previous studies on the production and application of electrospun nanofibers as antimicrobial water filtration membranes. The objectives of this review were to: (i) introduce the different procedures, which have been applied for incorporation of the various antimicrobial agents into electrospun nanofibers (ii) discuss the different antimicrobial tests used for proving antimicrobial activity of the fabricated electrospun water filters (iii) study the efficiency of the produced antimicrobial electrospun application in the water treatment industry. Based on the majority of researches studied in this review, blending and post-modification strategies are two commonly used techniques to incorporate biocide agents into nanofibers aiming for water disinfection application (Shalaby et al., 2018; He et al., 2018; Makaremi et al., 2016) . cache = ./cache/cord-285620-oawrnmhy.txt txt = ./txt/cord-285620-oawrnmhy.txt === reduce.pl bib === === reduce.pl bib === id = cord-264996-og3sg0qw author = Howell, Gareth J. title = Cell Biology of Membrane Trafficking in Human Disease date = 2006-09-17 pages = extension = .txt mime = text/plain words = 20320 sentences = 1072 flesch = 42 summary = Many of these transport intermediates or vesicles, whether derived from the ER, other internal organelles, or the plasma membrane, are ''coated'' with unique protein complexes, tethering factors, and regulatory factors that ensure correct targeting to an acceptor compartment. Breast cancer Caveolin-1 Deletion or dominant negative mutation of caveolin-1 promotes tumor progression Breast cancer (Bouras et al., 2004; Williams and Lisanti, 2005) (Hayasaka et al., 1993; Matsuyama et al., 2002) Chediak-Higashi syndrome (CHS) CHS1/Lyst Lyst involved in regulation of protein secretion from lysosomes -enlarged lysosomes Partial albinism, recurrent bacterial infections, impaired chemotaxis and abnormal natural killer cell function (Shiflett et al., 2002; Ward et al., 2003) 214500 Choroideremia (CHM) Rab Escort Protein 1 (REP1) RAB27a remains cytosolic due to defective geranylgeranyl modification in CHM lymphoblasts X-linked form of retinal degeneration 303100 Various mechanisms control the traYcking of proteins from the TGN by the formation and delivery of membrane-derived transport vesicles to the plasma membrane, endosomes, or lysosomal structures (Ponnambalam and Baldwin, 2003) . cache = ./cache/cord-264996-og3sg0qw.txt txt = ./txt/cord-264996-og3sg0qw.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-309384-vlk8cebh author = Kolter, Thomas title = Ganglioside Biochemistry date = 2012-12-19 pages = extension = .txt mime = text/plain words = 16840 sentences = 960 flesch = 38 summary = A principal difference between ganglioside biosynthesis in the Golgi apparatus and degradation in the endolysosomal compartment is that during GSL formation, membranebound glycosyltransferases interact with their membranebound glycolipid substrates by diffusion within the twodimensional plane of the lipid bilayer. As glycosidase substrates, GSLs with four carbohydrate residues or less require the additional presence of small lipid binding glycoproteins, either the GM2 activator protein or one of the four saposins A-D. In vitro, in addition to enzymes and activator proteins, also an appropriate membrane-lipid composition of the ganglioside-containing membrane is required for degradation [222] . Due to the deficiency of two enzyme activities, β-hexosaminidases A and B, storage of negatively charged glycolipids characteristic for Tay-Sachs disease and, in addition, of uncharged substrates such as GA2 in the brain and globoside in visceral organs (Figure 16 ) is observed. cache = ./cache/cord-309384-vlk8cebh.txt txt = ./txt/cord-309384-vlk8cebh.txt === reduce.pl bib === === reduce.pl bib === id = cord-004584-bcw90f5b author = nan title = Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date = 2011-08-06 pages = extension = .txt mime = text/plain words = 106850 sentences = 5038 flesch = 41 summary = Our goals are two-fold: (1) to monitor conformational changes in each domain upon its binding to specific ligands and then to correlate the observed changes with structural differences between the CRDs and (2) to investigate the interaction between the CRDs and lipid model membranes. Cholesterol-assisted lipid and protein interactions such as the integration into lipid nanodomains are considered to play a functional part in a whole range of membrane-associated processes, but their direct and non-invasive observation in living cells is impeded by the resolution limit of [200nm of a conventional far-field optical microscope. Therefore, to investigate the dynamic and complex membrane lateral organization in living cells, we have developed an original approach based on molecule diffusion measurements performed by fluorescence correlation spectroscopy at different spatial scales (spot variable FCS, svFCS) (1). cache = ./cache/cord-004584-bcw90f5b.txt txt = ./txt/cord-004584-bcw90f5b.txt === reduce.pl bib === === reduce.pl bib === id = cord-294842-aesiff1f author = Romero-Brey, Inés title = Membranous Replication Factories Induced by Plus-Strand RNA Viruses date = 2014-07-22 pages = extension = .txt mime = text/plain words = 11038 sentences = 520 flesch = 40 summary = Three-dimensional reconstructions of the WNV KUN replication sites revealed an intimate association of the rough ER (rER) with the bounding membrane of the VPs [20] (Figure 2B ), resembling the vesicles observed in DENV-infected cells. In cells infected with TBEV, one of the most important tick-transmitted viruses in Europe and Asia, virus particles and membrane-connected vesicles were also observed inside the ER [25] , similar to what was described for DENV and WNV KUN . Importantly, pulse-radiolabeling experiments localized sites of active RNA replication to the outer surface of single-membrane tubules [71] and isolation of the membranous replication factories and their subsequent visualization by EM revealed that they form rosette-like structures composed of virus-induced cytoplasmic vesicles [124] . Formation of plant RNA virus replication complexes on membranes: Role of an endoplasmic reticulum-targeted viral protein cache = ./cache/cord-294842-aesiff1f.txt txt = ./txt/cord-294842-aesiff1f.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-353815-w35spqqt author = Huan, Yuchen title = Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields date = 2020-10-16 pages = extension = .txt mime = text/plain words = 12266 sentences = 623 flesch = 38 summary = This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. Tryptophan (Trp), as a non-polar amino acid, has a remarkable effect on the interface region of the lipid bilayer, whereas Arg, as a basic amino acid, confers peptide charge and hydrogen bond interactions, which are essential properties to combine with the bacterial membrane's abundant anionic component. And it seems that Trp residues play the role of natural aromatic activators of Arg-rich AMPs by ion-pair-π interactions (Walrant et al., 2020) , thereby promoting enhanced peptide-membrane interactions (Chan et al., 2006) . Furthermore, L4H4, which is designed based on the linear cationic amphiphilic peptide magainin, also shows good antibacterial activity and cell penetration properties by inserting four histidine sequences in leucine and alanine (Lointier et al., 2020) . cache = ./cache/cord-353815-w35spqqt.txt txt = ./txt/cord-353815-w35spqqt.txt === reduce.pl bib === id = cord-346446-i7gpxcyo author = Zhang, Jianguo title = Biosynthetic Polymalic Acid as a Delivery Nanoplatform for Translational Cancer Medicine date = 2020-10-22 pages = extension = .txt mime = text/plain words = 6094 sentences = 281 flesch = 35 summary = pullulan, the addition of exogenous carbonates augments CO 2 fixation and pyruvate carboxylation into oxaloacetate by pyruvate carboxylase in the cytoplasm, abolishing the intramitochondrial pathways for L-malate production and ensuing PMLA synthesis ( Figure 2 ) [23, 30] . At pH 7.4, the terminal α-carboxylic acid in the side chain is deprotonated and ionized; this would be repelled from the cell membrane, but, because of strong hydrophobic interactions, indole in the side chain can attract and intercalate into phospholipids, generating PMLA tritryptophan-lipid complexes and releasing binding energy to stabilize the structure. To increase the interaction between the biopolymer and the plasma membrane, methylation of carboxylic acid groups with different levels of diazomethane was used to generate a PMLA-Me x H 100−x copolymer (where x is the percentage of methyl units) [77, 78] . Analysis of the L-malate biosynthesis pathway involved in poly(beta-L-malic acid) production in Aureobasidium melanogenum GXZ-6 by addition of metabolic intermediates and inhibitors cache = ./cache/cord-346446-i7gpxcyo.txt txt = ./txt/cord-346446-i7gpxcyo.txt === reduce.pl bib === id = cord-336929-2rnkotqy author = Vieira, Flávia Sarmento title = Host‐cell lipid rafts: a safe door for micro‐organisms? date = 2012-01-03 pages = extension = .txt mime = text/plain words = 9925 sentences = 494 flesch = 41 summary = In addition to the lipid components, a variety of cell receptors and signalling proteins are known to be associated with membrane rafts. Many animal viruses exploit the endocytic machinery of their host cell for infection, and lipid rafts are often a site for entry, assembly and budding of microbial pathogens, as confirmed by biochemical approaches and microscopy evidence (Kovbasnjuk et al., 2001; Suomalainen, 2002; Lu et al., 2008) . Interestingly, it had already been demonstrated that Brucella abortus infection is related with PrP C (cellular PrP), one of the lipid raft-associated molecules on the plasma membrane of different cell types. In the macrophage-like cell line RAW 264.7, for example, LPS stimulation induces translocation of CD14, ERK-2 (extracellular-signalregulated kinase 2) and p38 to lipid rafts, but other proteins also involved in the LPS signalling response do not migrate within these microdomains (Triantafilou et al., 2007; Olsson and Sundler, 2006) . cache = ./cache/cord-336929-2rnkotqy.txt txt = ./txt/cord-336929-2rnkotqy.txt === reduce.pl bib === id = cord-329448-kxxy60x9 author = Kumari, Sudha title = Endocytosis unplugged: multiple ways to enter the cell date = 2010-02-02 pages = extension = .txt mime = text/plain words = 11521 sentences = 541 flesch = 31 summary = These factors include one or more underlying principle in cargo enrichment, necessitating specific coat and coat-associated protein assembly, a scission mechanism, and a means to integrate these steps; several molecules and membrane parameters can influence and diversify an endocytic process. CtBP1/BARS (C-terminal-binding protein-1/brefeldin A ribosylation substrate) proteins were originally demonstrated to regulate dynamin-independent fluid uptake in a variety of cell lines, and were later reported to localize to the site of and affect macropinosome membrane closure in a phosphorylation-dependent manner [36] . Overexpression of dominant negative, GTP-binding mutants of dynamin also blocked receptor-mediated endocytosis in various cells, suggesting a role for the GTPase activity of dynamin in the clathrin-dependent endocytic process outside the nervous system. The identification of an endocytic pathway as distinct has been primarily based on associated cargo proteins or lipids, and molecular regulators; the contribution of kinetics and detailed physical mechanism to such categorization is not generally available except in some wellcharacterized situations, namely clathrin-pit endocytosis or endocytosis by actin-dependent forces in yeast. cache = ./cache/cord-329448-kxxy60x9.txt txt = ./txt/cord-329448-kxxy60x9.txt === reduce.pl bib === === reduce.pl bib === id = cord-317430-uvx8si42 author = Chen, Yaping title = Emerging Roles of 1D Vertical Nanostructures in Orchestrating Immune Cell Functions date = 2020-08-26 pages = extension = .txt mime = text/plain words = 11481 sentences = 673 flesch = 39 summary = [6] In particular, SiNW arrays demonstrated high efficiency (>90%) in transfecting exogenous genetic materials into primary immune cells-which are notoriously hard to transfect-while maintaining high viability and immunological competence; [27, 28, 36] siRNAs were transfected via SiNWs into primary B cells and CD4 + T cells to knock down predicted target genes, facilitating discovery of essential signaling pathways and genetic regulatory circuits for immune cell activation and differentiation; [27, 28] SiNWs were used to administer a small-molecule inhibitor of the enzyme Polo-like kinase (Plk) into bone-marrow derived dendritic cells (BMDCs), confirming the essential role of Plk2 and Plk4 in regulating antiviral gene expression in these cell; [37] by using vertical carbon nanosyringe arrays (CNSAs) under applied centrifugal g-force, pEGFP plasmids were transfected www.advmat.de www.advancedsciencenews.com into primary lymphocytes with significantly higher efficiency than conventional Lipofectamine 2000-mediated method. cache = ./cache/cord-317430-uvx8si42.txt txt = ./txt/cord-317430-uvx8si42.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-313599-5j19stye author = Wang, Xianfeng title = Electro-spinning/netting: A strategy for the fabrication of three-dimensional polymer nano-fiber/nets date = 2013-05-26 pages = extension = .txt mime = text/plain words = 25077 sentences = 1216 flesch = 45 summary = NFN possess the general properties and functions of conventional electrospun nanofibers and other 1D nanostructures fabricated using different techniques, as well as the impressive feature characters (e.g. extremely small diameter, high porosity, Steiner tree network geometry, controllable coverage rate) that distinguish themselves from their counterparts, the properties donated by the polymer phase, and the 2D net-like geometry. Therefore, strongly interconnected thin MPEG spider-web-like nano-nets with thick PA-6 nanofibers are responsible to increase mechanical strength and hydrophilic nature of PA-6 fibrous membranes, which make composite MPEG/PA-6 NFN membranes great potential in air filtration and different biomedical application. More recently, our group has presented continuous efforts toward the aim of generating PANI-based nanostructured materials and for the first time fabricated composite PANI/PA-6 NFN membranes (Fig. 20a) , which were used as a platform for efficient sensing reaction by providing high specific surface area and porosity. cache = ./cache/cord-313599-5j19stye.txt txt = ./txt/cord-313599-5j19stye.txt === reduce.pl bib === id = cord-001835-0s7ok4uw author = nan title = Abstracts of the 29th Annual Symposium of The Protein Society date = 2015-10-01 pages = extension = .txt mime = text/plain words = 138514 sentences = 6150 flesch = 40 summary = Altogether, these results indicate that, although PHDs might be more selective for HIF as a substrate as it was initially thought, the enzymatic activity of the prolyl hydroxylases is possibly influenced by a number of other proteins that can directly bind to PHDs. Non-natural aminoacids via the MIO-enzyme toolkit Alina Filip 1 , Judith H Bartha-V ari 1 , Gergely B an oczy 2 , L aszl o Poppe 2 , Csaba Paizs 1 , Florin-Dan Irimie 1 1 Biocatalysis and Biotransformation Research Group, Department of Chemistry, UBB, 2 Department of Organic Chemistry and Technology An attractive enzymatic route to enantiomerically pure to the highly valuable a-or b-aromatic amino acids involves the use of aromatic ammonia lyases (ALs) and aminomutases (AMs). Continuing our studies of the effect of like-charged residues on protein-folding mechanisms, in this work, we investigated, by means of NMR spectroscopy and molecular-dynamics simulations, two short fragments of the human Pin1 WW domain [hPin1(14-24); hPin1(15-23)] and one single point mutation system derived from hPin1(14-24) in which the original charged residues were replaced with non-polar alanine residues. cache = ./cache/cord-001835-0s7ok4uw.txt txt = ./txt/cord-001835-0s7ok4uw.txt ===== Reducing email addresses cord-289541-y7lewk1t cord-274101-vm9nh8lc cord-004584-bcw90f5b cord-004534-jqm1hxps cord-001835-0s7ok4uw Creating transaction Updating adr table ===== Reducing keywords cord-006556-hmzoxqu3 cord-006947-nrzjedhi cord-013223-f43hks44 cord-017566-dvxrwzqw cord-000884-zq8kqf6h cord-023200-3caevjvh cord-009371-ub4p4ngr cord-030961-5gzc7193 cord-022504-tk7v4hoj cord-014685-ihh30q6f cord-011888-3mvzkff6 cord-015866-65zrbo1w cord-103739-mmkrwj8t cord-016938-pk76snuy cord-008480-p41oae8e cord-298019-gf2asni1 cord-284690-ogu1gmcb cord-020712-l9cn0n99 cord-022354-aqtceqqo cord-253366-03cg831z cord-289541-y7lewk1t cord-020714-h1fevqcw cord-104279-choywmwd cord-035248-m5517zgn cord-279463-bli8hwda cord-034898-zjfhpum2 cord-257754-pqxkyg8z cord-287093-9mertwj7 cord-276456-oa6hh7ky cord-020788-a33vcapl cord-274101-vm9nh8lc cord-327765-qdbgkm53 cord-299270-fwbz3t25 cord-028738-ing07qma cord-303238-us3dybue cord-022538-1g9kmpdi cord-265887-g5zhoyo9 cord-272666-3uidpr79 cord-103812-ls6zgipi cord-338827-1moy43hr cord-285620-oawrnmhy cord-264996-og3sg0qw cord-333757-h12aozg2 cord-309384-vlk8cebh cord-269756-tid8a464 cord-319754-5isw53wl cord-004584-bcw90f5b cord-294842-aesiff1f cord-325915-dw989txm cord-323319-u5hfkjv8 cord-330110-pamxy4av cord-314402-kjzkk51t cord-314604-w61sqy17 cord-300429-b0zev8zb cord-339172-210dwhgj cord-325712-9kbnyqt3 cord-353815-w35spqqt cord-336929-2rnkotqy cord-329448-kxxy60x9 cord-346446-i7gpxcyo cord-341378-pw60qx7c cord-317430-uvx8si42 cord-356090-oj3d9ail cord-004534-jqm1hxps cord-349341-ap5n6ijl cord-341129-eo0vjcmk cord-313599-5j19stye cord-001835-0s7ok4uw Creating transaction Updating wrd table ===== Reducing urls cord-006556-hmzoxqu3 cord-023200-3caevjvh cord-030961-5gzc7193 cord-014685-ihh30q6f cord-015866-65zrbo1w cord-284690-ogu1gmcb cord-265887-g5zhoyo9 cord-285620-oawrnmhy cord-272666-3uidpr79 cord-314402-kjzkk51t cord-004584-bcw90f5b cord-300429-b0zev8zb cord-339172-210dwhgj cord-353815-w35spqqt cord-317430-uvx8si42 cord-004534-jqm1hxps cord-349341-ap5n6ijl cord-001835-0s7ok4uw Creating transaction Updating url table ===== Reducing named entities cord-006556-hmzoxqu3 cord-013223-f43hks44 cord-006947-nrzjedhi cord-017566-dvxrwzqw cord-000884-zq8kqf6h cord-023200-3caevjvh cord-009371-ub4p4ngr cord-030961-5gzc7193 cord-022504-tk7v4hoj cord-011888-3mvzkff6 cord-103739-mmkrwj8t cord-016938-pk76snuy cord-008480-p41oae8e cord-014685-ihh30q6f cord-015866-65zrbo1w cord-284690-ogu1gmcb cord-298019-gf2asni1 cord-020712-l9cn0n99 cord-020714-h1fevqcw cord-022354-aqtceqqo cord-253366-03cg831z cord-289541-y7lewk1t cord-034898-zjfhpum2 cord-035248-m5517zgn cord-104279-choywmwd cord-279463-bli8hwda cord-257754-pqxkyg8z cord-287093-9mertwj7 cord-274101-vm9nh8lc cord-276456-oa6hh7ky cord-020788-a33vcapl cord-327765-qdbgkm53 cord-299270-fwbz3t25 cord-028738-ing07qma cord-303238-us3dybue cord-022538-1g9kmpdi cord-265887-g5zhoyo9 cord-103812-ls6zgipi cord-285620-oawrnmhy cord-338827-1moy43hr cord-333757-h12aozg2 cord-272666-3uidpr79 cord-269756-tid8a464 cord-319754-5isw53wl cord-264996-og3sg0qw cord-325915-dw989txm cord-309384-vlk8cebh cord-294842-aesiff1f cord-330110-pamxy4av cord-323319-u5hfkjv8 cord-314402-kjzkk51t cord-300429-b0zev8zb cord-314604-w61sqy17 cord-339172-210dwhgj cord-353815-w35spqqt cord-325712-9kbnyqt3 cord-336929-2rnkotqy cord-346446-i7gpxcyo cord-341378-pw60qx7c cord-329448-kxxy60x9 cord-356090-oj3d9ail cord-317430-uvx8si42 cord-341129-eo0vjcmk cord-349341-ap5n6ijl cord-004584-bcw90f5b cord-313599-5j19stye cord-004534-jqm1hxps cord-001835-0s7ok4uw Creating transaction Updating ent table ===== Reducing parts of speech cord-017566-dvxrwzqw cord-013223-f43hks44 cord-000884-zq8kqf6h cord-023200-3caevjvh cord-030961-5gzc7193 cord-103739-mmkrwj8t cord-006556-hmzoxqu3 cord-011888-3mvzkff6 cord-016938-pk76snuy cord-008480-p41oae8e cord-009371-ub4p4ngr cord-253366-03cg831z cord-298019-gf2asni1 cord-289541-y7lewk1t cord-035248-m5517zgn cord-022504-tk7v4hoj cord-284690-ogu1gmcb cord-279463-bli8hwda cord-034898-zjfhpum2 cord-006947-nrzjedhi cord-020712-l9cn0n99 cord-257754-pqxkyg8z cord-276456-oa6hh7ky cord-287093-9mertwj7 cord-104279-choywmwd cord-327765-qdbgkm53 cord-020714-h1fevqcw cord-015866-65zrbo1w cord-022354-aqtceqqo cord-299270-fwbz3t25 cord-028738-ing07qma cord-303238-us3dybue cord-274101-vm9nh8lc cord-265887-g5zhoyo9 cord-103812-ls6zgipi cord-272666-3uidpr79 cord-020788-a33vcapl cord-285620-oawrnmhy cord-333757-h12aozg2 cord-022538-1g9kmpdi cord-338827-1moy43hr cord-323319-u5hfkjv8 cord-314402-kjzkk51t cord-314604-w61sqy17 cord-341378-pw60qx7c cord-269756-tid8a464 cord-319754-5isw53wl cord-330110-pamxy4av cord-325915-dw989txm cord-014685-ihh30q6f cord-346446-i7gpxcyo cord-309384-vlk8cebh cord-325712-9kbnyqt3 cord-294842-aesiff1f cord-339172-210dwhgj cord-300429-b0zev8zb cord-356090-oj3d9ail cord-353815-w35spqqt cord-336929-2rnkotqy cord-341129-eo0vjcmk cord-264996-og3sg0qw cord-329448-kxxy60x9 cord-317430-uvx8si42 cord-349341-ap5n6ijl cord-313599-5j19stye cord-004584-bcw90f5b cord-004534-jqm1hxps cord-001835-0s7ok4uw Creating transaction Updating pos table Building ./etc/reader.txt cord-004534-jqm1hxps cord-001835-0s7ok4uw cord-004584-bcw90f5b cord-264996-og3sg0qw cord-276456-oa6hh7ky cord-325712-9kbnyqt3 number of items: 68 sum of words: 616,790 average size in words: 14,685 average readability score: 43 nouns: membrane; protein; proteins; cell; cells; virus; fusion; membranes; lipid; structure; surface; peptide; formation; activity; peptides; domain; particles; interaction; interactions; results; studies; acid; role; process; model; properties; structures; water; mechanism; type; transport; residues; molecules; study; vesicles; function; receptor; binding; analysis; time; system; fluorescence; viruses; changes; host; data; energy; dna; effect; domains verbs: used; shown; binding; induced; form; contain; based; found; studied; suggest; increases; observed; providing; including; require; involved; associated; allowing; determined; leads; investigated; revealed; indicates; causes; mediated; known; resulting; obtained; demonstrated; occurs; followed; identified; developed; produced; described; generated; comparing; interacts; makes; presenting; performed; reported; reduced; supported; expressed; applied; play; regulate; remains; affected adjectives: different; viral; high; molecular; structural; specific; single; human; cellular; several; important; small; low; new; large; hydrophobic; biological; non; many; active; various; functional; conformational; dependent; like; similar; antimicrobial; higher; intracellular; free; complex; bacterial; present; first; cytoplasmic; major; possible; key; recent; novel; experimental; potential; outer; able; essential; immune; native; multiple; particular; common adverbs: also; however; well; therefore; highly; recently; even; still; respectively; often; furthermore; directly; previously; significantly; moreover; first; mainly; together; now; much; strongly; rather; widely; fully; currently; less; negatively; interestingly; generally; usually; finally; particularly; especially; specifically; yet; far; approximately; probably; commonly; easily; relatively; typically; successfully; additionally; subsequently; completely; clearly; indeed; thereby; partially pronouns: we; it; their; its; our; they; i; them; us; itself; his; themselves; one; he; my; me; she; you; gh625; rab8; your; u; stnfα; s; ppifs; imagej; fbp17; cb562; −; yourself; yegfp; theirs; protoxin; p110a; ourselves; oneself; nsp4; nsp1; mrnas; monomera; iv-3l3r.; ifitm3; her; hapg5p; gate16; em; cord-325915-dw989txm; c840; asap2 proper nouns: Fig; RNA; C; University; SARS; Golgi; pH; ER; II; K; A; Institute; HA; M.; S.; B; NFN; A.; E.; ATP; Na; J.; Arb; ECLS; CoV; S; DNA; T; N; P.; NMR; C.; M; Department; Italy; FP; HIV-1; D; F; Germany; ECMO; Protein; L.; G.; R.; DPAP; Chemistry; Ca; HIV; HCV keywords: membrane; protein; cell; virus; rna; fusion; lipid; peptide; golgi; dna; sars; university; surface; study; structure; particle; interaction; institute; department; atp; activity; acid; result; replication; process; molecular; high; hcv; gram; effect; ecmo; bsa; transport; snare; size; signal; nanoparticle; germany; fret; france; form; fluorescence; fcs; extracorporeal; domain; concentration; complex; chemistry; channel; change one topic; one dimension: membrane file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102020/ titles(s): Extracorporeal Life Support: Four Decades and Counting three topics; one dimension: protein; membrane; membrane file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079852/, https://www.ncbi.nlm.nih.gov/pubmed/32287484/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158284/ titles(s): Abstract | Electro-spinning/netting: A strategy for the fabrication of three-dimensional polymer nano-fiber/nets | ENVIRONMENTAL AND SAFETY ISSUES WITH NANOPARTICLES five topics; three dimensions: protein membrane fusion; membrane virus cells; membrane membranes protein; membrane protein particles; membrane endocytosis proteins file(s): https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.2823, https://doi.org/10.1586/erv.11.111, https://www.ncbi.nlm.nih.gov/pubmed/32287484/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158284/, https://api.elsevier.com/content/article/pii/S0070215306740017 titles(s): Abstracts of the 29th Annual Symposium of The Protein Society | Downstream processing of cell culture-derived virus particles | Electro-spinning/netting: A strategy for the fabrication of three-dimensional polymer nano-fiber/nets | ENVIRONMENTAL AND SAFETY ISSUES WITH NANOPARTICLES | Membrane Origin for Autophagy Type: cord title: keyword-membrane-cord date: 2021-05-25 time: 15:31 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:membrane ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-006556-hmzoxqu3 author: Alibrahim, Omar S. title: Extracorporeal Life Support: Four Decades and Counting date: 2017-04-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Extracorporeal membrane oxygenation (ECMO) or extracorporeal life support (ECLS) is a form of heart lung bypass that is used to support neonates, pediatrics, and adult patients with cardiorespiratory failure for days or weeks till organ recovery or transplantation. Venoarterial (VA) and venovenous (VV) ECLS are the most common modes of support. ECLS circuit components and monitoring have been evolving over the last 40 years. The technology is safer, simpler, and more durable with fewer complications. The use of neonatal respiratory ECLS use has been declining over the last two decades, while adult respiratory ECLS is growing especially since the H1N1 influenza pandemic in 2009. This review provides an overview of ECLS evolution over the last four decades, its use in neonatal, pediatric and adults, description of basic principles, circuit components, complications, and outcomes as well as a quick look into the future. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102020/ doi: 10.1007/s40140-017-0210-0 id: cord-341378-pw60qx7c author: Armstrong, John title: Sequence and topology of a model intracellular membrane protein, E1 glycoprotein, from a coronavirus date: 1984 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In the eukaryotic cell, both secreted and plasma membrane proteins are synthesized at the endoplasmic reticulum, then transported, via the Golgi complex, to the cell surface(1–4). Each of the compartments of this transport pathway carries out particular metabolic functions(5–8), and therefore presumably contains a distinct complement of membrane proteins. Thus, mechanisms must exist for localizing such proteins to their respective destinations. However, a major obstacle to the study of such mechanisms is that the isolation and detailed analysis of such internal membrane proteins pose formidable technical problems. We have therefore used the E1 glycoprotein from coronavirus MHV-A59 as a viral model for this class of protein. Here we present the primary structure of the protein, determined by analysis of cDNA clones prepared from viral mRNA. In combination with a previous study of its assembly into the endoplasmic reticulum membrane(9), the sequence reveals several unusual features of the protein which may be related to its intracellular localization. url: https://www.ncbi.nlm.nih.gov/pubmed/6325918/ doi: 10.1038/308751a0 id: cord-319754-5isw53wl author: Balgoma, David title: Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date: 2020-08-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host cell lipid metabolism, and the role played by diverse lipids in regard to the infection effectiveness. All these aspects have currently been tackled separately as independent issues and focused on the function of proteins. Here, we review the role of cholesterol and other lipids in ssRNA+ infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32878290/ doi: 10.3390/metabo10090356 id: cord-269756-tid8a464 author: Basso, Luis G. M. title: SARS-CoV fusion peptides induce membrane surface ordering and curvature date: 2016-11-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral membrane fusion is an orchestrated process triggered by membrane-anchored viral fusion glycoproteins. The S2 subunit of the spike glycoprotein from severe acute respiratory syndrome (SARS) coronavirus (CoV) contains internal domains called fusion peptides (FP) that play essential roles in virus entry. Although membrane fusion has been broadly studied, there are still major gaps in the molecular details of lipid rearrangements in the bilayer during fusion peptide-membrane interactions. Here we employed differential scanning calorimetry (DSC) and electron spin resonance (ESR) to gather information on the membrane fusion mechanism promoted by two putative SARS FPs. DSC data showed the peptides strongly perturb the structural integrity of anionic vesicles and support the hypothesis that the peptides generate opposing curvature stresses on phosphatidylethanolamine membranes. ESR showed that both FPs increase lipid packing and head group ordering as well as reduce the intramembrane water content for anionic membranes. Therefore, bending moment in the bilayer could be generated, promoting negative curvature. The significance of the ordering effect, membrane dehydration, changes in the curvature properties and the possible role of negatively charged phospholipids in helping to overcome the high kinetic barrier involved in the different stages of the SARS-CoV-mediated membrane fusion are discussed. url: https://doi.org/10.1038/srep37131 doi: 10.1038/srep37131 id: cord-253366-03cg831z author: Chakraborty, Hirak title: Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics date: 2020-07-22 words: 5024.0 sentences: 282.0 pages: flesch: 47.0 cache: ./cache/cord-253366-03cg831z.txt txt: ./txt/cord-253366-03cg831z.txt summary: In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. An efficient membrane fusion mechanism between SARS-CoV-2 and host cell could also be responsible for the high level of infection. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Identification of the membraneactive regions of the severe acute respiratory syndrome coronavirus spike membrane glycoprotein using a 16/18-mer peptide scan: implications for the viral fusion mechanism Interaction of a peptide from the pre-transmembrane domain of the severe acute respiratory syndrome coronavirus spike protein with phospholipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes abstract: The emerging and re-emerging viral diseases are continuous threats to the wellbeing of human life. Previous outbreaks of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS had evidenced potential threats of coronaviruses in human health. The recent pandemic due to SARS-CoV-2 is overwhelming and has been going beyond control. Vaccines and antiviral drugs are ungently required to mitigate the pandemic. Therefore, it is important to comprehend the mechanistic details of viral infection process. The fusion between host cell and virus being the first step of infection, understanding the fusion mechanism could provide crucial information to intervene the infection process. Interestingly, all enveloped viruses contain fusion protein on their envelope that acts as fusion machine. For coronaviruses, the spike or S glycoprotein mediates successful infection through receptor binding and cell fusion. The cell fusion process requires merging of virus and host cell membranes, and that is essentially performed by the S2 domain of the S glycoprotein. In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. We have further discussed about the cell fusion of SARS-CoV-2 in the context of present pandemic situation. url: https://api.elsevier.com/content/article/pii/S0301462220301460 doi: 10.1016/j.bpc.2020.106438 id: cord-317430-uvx8si42 author: Chen, Yaping title: Emerging Roles of 1D Vertical Nanostructures in Orchestrating Immune Cell Functions date: 2020-08-26 words: 11481.0 sentences: 673.0 pages: flesch: 39.0 cache: ./cache/cord-317430-uvx8si42.txt txt: ./txt/cord-317430-uvx8si42.txt summary: [6] In particular, SiNW arrays demonstrated high efficiency (>90%) in transfecting exogenous genetic materials into primary immune cells-which are notoriously hard to transfect-while maintaining high viability and immunological competence; [27, 28, 36] siRNAs were transfected via SiNWs into primary B cells and CD4 + T cells to knock down predicted target genes, facilitating discovery of essential signaling pathways and genetic regulatory circuits for immune cell activation and differentiation; [27, 28] SiNWs were used to administer a small-molecule inhibitor of the enzyme Polo-like kinase (Plk) into bone-marrow derived dendritic cells (BMDCs), confirming the essential role of Plk2 and Plk4 in regulating antiviral gene expression in these cell; [37] by using vertical carbon nanosyringe arrays (CNSAs) under applied centrifugal g-force, pEGFP plasmids were transfected www.advmat.de www.advancedsciencenews.com into primary lymphocytes with significantly higher efficiency than conventional Lipofectamine 2000-mediated method. abstract: Engineered nano–bio cellular interfaces driven by 1D vertical nanostructures (1D‐VNS) are set to prompt radical progress in modulating cellular processes at the nanoscale. Here, tuneable cell–VNS interfacial interactions are probed and assessed, highlighting the use of 1D‐VNS in immunomodulation, and intracellular delivery into immune cells—both crucial in fundamental and translational biomedical research. With programmable topography and adaptable surface functionalization, 1D‐VNS provide unique biophysical and biochemical cues to orchestrate innate and adaptive immunity, both ex vivo and in vivo. The intimate nanoscale cell–VNS interface leads to membrane penetration and cellular deformation, facilitating efficient intracellular delivery of diverse bioactive cargoes into hard‐to‐transfect immune cells. The unsettled interfacial mechanisms reported to be involved in VNS‐mediated intracellular delivery are discussed. By identifying up‐to‐date progress and fundamental challenges of current 1D‐VNS technology in immune‐cell manipulation, it is hoped that this report gives timely insights for further advances in developing 1D‐VNS as a safe, universal, and highly scalable platform for cell engineering and enrichment in advanced cancer immunotherapy such as chimeric antigen receptor‐T therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/32844502/ doi: 10.1002/adma.202001668 id: cord-013223-f43hks44 author: Chronopoulos, Antonios title: Emerging role of bacterial extracellular vesicles in cancer date: 2020-10-15 words: 5793.0 sentences: 264.0 pages: flesch: 29.0 cache: ./cache/cord-013223-f43hks44.txt txt: ./txt/cord-013223-f43hks44.txt summary: The increasing appreciation that microbiota-derived EV can enter the systemic circulation and be detected in human body fluids is likely to stimulate completely new areas of investigation in microbiome research, biomarkers and liquid biopsies, BEV-based therapeutics, onco-immunology, as well as fundamental microbial EV biology. In addition to potentially modulating the innate immune response via or more cytosolic DNA sensors, the possibility that pathogenic BEV-derived DNA can be transferred and detected in the nucleus of non-phagocytic cells (e.g. epithelial cells) [30] , raises the intriguing possibility that bacterial genetic material could be transferred to human somatic cells and integrated into the host genome. BEVs released by bacteria in the gut lumen can cross the epithelial barrier to gain access into the underlying submucosa enabling them to interact with various resident immune cell populations (dendritic cells, neutrophils and macrophages) as well as potentially disseminate more widely around the body via the systemic or lymphatic circulation to reach distant tissues and organs or even the brain (Fig. 2) . abstract: Shedding of microbial extracellular vesicles constitutes a universal mechanism for inter-kingdom and intra-kingdom communication that is conserved among prokaryotic and eukaryotic microbes. In this review we delineate fundamental aspects of bacterial extracellular vesicles (BEVs) including their biogenesis, cargo composition, and interactions with host cells. We critically examine the evidence that BEVs from the host gut microbiome can enter the circulatory system to disseminate to distant organs and tissues. The potential involvement of BEVs in carcinogenesis is evaluated and future research ideas explored. We further discuss the potential of BEVs in microbiome-based liquid biopsies for cancer diagnostics and bioengineering strategies for cancer therapy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7557313/ doi: 10.1038/s41388-020-01509-3 id: cord-276456-oa6hh7ky author: Collins, R.N. title: 5.14 The Biophysics of Membrane Fusion date: 2012-05-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A crucial interplay between protein conformations and lipid membrane energetics emerges as the guiding principle for the regulation and mechanism of membrane fusion in biological systems. As some of the basics of fusion become clear, a myriad of compelling questions come to the fore. Is the interior of the fusion pore protein or lipid? Why is synaptic release so fast? Why is PIP(2) needed for exocytosis? How does fusion peptide insertion lead to fusion of viruses to cell membranes? What role does the TMD play? How can studies on membrane fission contribute to our understanding of membrane fusion? What exactly are SNARE proteins doing? url: https://api.elsevier.com/content/article/pii/B9780123749208005233 doi: 10.1016/b978-0-12-374920-8.00523-3 id: cord-020714-h1fevqcw author: Compans, Richard W. title: Membrane Glycoproteins of Enveloped Viruses date: 2008-05-30 words: 14149.0 sentences: 684.0 pages: flesch: 43.0 cache: ./cache/cord-020714-h1fevqcw.txt txt: ./txt/cord-020714-h1fevqcw.txt summary: Other advantages of enveloped viruses in studies of membrane structure and biogenesis include the ease of biosynthetic labeling of viruses grown in cell culture with specific radioactive precursors and the availability of mutants in defined gene products, some of which are proving to be useful in the analysis of viral membrane assembly. Apart from minor differences in carbohydrates of glycoproteins, virion proteins are indistinguishable when the virus is propagated in a variety of cells; therefore there appears to be little or no determining influence of viral proteins on the composition of the lipid bilayer. Based upon the estimated carbohydrate content (12,000 daltons) of the HA glycoprotein obtained by Laver (1971) and Schwarz and Klenk (1974) and the size estimates of the type I and I1 glycopeptides of influenza virus grown in MDBK cells, it was estimated that HA, contains a single type I glycopeptide whereas HA, possesses two type I and one or two type I1 oligosaccharide side-chains for the WSN strain (Nakamura and Com pans, 1978b) . abstract: This chapter focuses on the recent information of the glycoprotein components of enveloped viruses and points out specific findings on viral envelopes. Although enveloped viruses of different major groups vary in size and shape, as well as in the molecular weight of their structural polypeptides, there are general similarities in the types of polypeptide components present in virions. The types of structural components found in viral membranes are summarized briefly in the chapter. All the enveloped viruses studied to date possess one or more glycoprotein species and lipid as a major structural component. The presence of carbohydrate covalently linked to proteins is demonstrated by the incorporation of a radioactive precursor, such as glucosamine or fucose, into viral polypeptides, which is resolved by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis. Enveloped viruses share many common features in the organization of their structural components, as indicated by several approaches, including electron microscopy, surface-labeling, and proteolytic digestion experiments, and the isolation of subviral components. The chapter summarizes the detailed structure of the glycoproteins of four virus groups: (1) influenza virus glycoproteins, (2) rhabdovirus G protein, (3) togavirus glycoprotein, and (4) paramyxovirus glycoproteins The information obtained includes the size and shape of viral glycoproteins, the number of polypeptide chains in the complete glycoprotein structure, and compositional data on the polypeptide and oligosaccharide portions of the molecules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146817/ doi: 10.1016/s0070-2161(08)60750-9 id: cord-314604-w61sqy17 author: Crone, Niek S. A. title: Modulation of Coiled-Coil Binding Strength and Fusogenicity through Peptide Stapling date: 2020-02-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: [Image: see text] Peptide stapling is a technique which has been widely employed to constrain the conformation of peptides. One of the effects of such a constraint can be to modulate the interaction of the peptide with a binding partner. Here, a cysteine bis-alkylation stapling technique was applied to generate structurally isomeric peptide variants of a heterodimeric coiled-coil forming peptide. These stapled variants differed in the position and size of the formed macrocycle. C-terminal stapling showed the most significant changes in peptide structure and stability, with calorimetric binding analysis showing a significant reduction of binding entropy for stapled variants. This entropy reduction was dependent on cross-linker size and was accompanied by a change in binding enthalpy, illustrating the effects of preorganization. The stapled peptide, along with its binding partner, were subsequently employed as fusogens in a liposome model system. An increase in both lipid- and content-mixing was observed for one of the stapled peptide variants: this increased fusogenicity was attributed to increased coiled-coil binding but not to membrane affinity, an interaction theorized to be a primary driving force in this fusion system. url: https://www.ncbi.nlm.nih.gov/pubmed/32058706/ doi: 10.1021/acs.bioconjchem.0c00009 id: cord-006947-nrzjedhi author: Dasgupta, S title: Nano- and microparticles at fluid and biological interfaces date: 2017-09-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Systems with interfaces are abundant in both technological applications and biology. While a fluid interface separates two fluids, membranes separate the inside of vesicles from the outside, the interior of biological cells from the environment, and compartmentalize cells into organelles. The physical properties of interfaces are characterized by interface tension, those of membranes are characterized by bending and stretching elasticity. Amphiphilic molecules like surfactants that are added to a system with two immiscible fluids decrease the interface tension and induce a bending rigidity. Lipid bilayer membranes of vesicles can be stretched or compressed by osmotic pressure; in biological cells, also the presence of a cytoskeleton can induce membrane tension. If the thickness of the interface or the membrane is small compared with its lateral extension, both can be described using two-dimensional mathematical surfaces embedded in three-dimensional space. We review recent work on the interaction of particles with interfaces and membranes. This can be micrometer-sized particles at interfaces that stabilise emulsions or form colloidosomes, as well as typically nanometer-sized particles at membranes, such as viruses, parasites, and engineered drug delivery systems. In both cases, we first discuss the interaction of single particles with interfaces and membranes, e.g. particles in external fields, non-spherical particles, and particles at curved interfaces, followed by interface-mediated interaction between two particles, many-particle interactions, interface and membrane curvature-induced phenomena, and applications. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104866/ doi: 10.1088/1361-648x/aa7933 id: cord-272666-3uidpr79 author: Doyle, Nicole title: Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing date: 2018-09-06 words: 7472.0 sentences: 358.0 pages: flesch: 52.0 cache: ./cache/cord-272666-3uidpr79.txt txt: ./txt/cord-272666-3uidpr79.txt summary: In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. In a subsequent study by others, it was shown that expression of only nsp3 and 4 from either MERS-CoV or SARS-CoV was able to induce DMV formation, and furthermore, addition of nsp6 made no difference to their shape or size, and did not induce the spherule-like structures seen following infection with whole virus [26] . abstract: Positive-strand RNA viruses, such as coronaviruses, induce cellular membrane rearrangements during replication to form replication organelles allowing for efficient viral RNA synthesis. Infectious bronchitis virus (IBV), a pathogenic avian Gammacoronavirus of significant importance to the global poultry industry, has been shown to induce the formation of double membrane vesicles (DMVs), zippered endoplasmic reticulum (zER) and tethered vesicles, known as spherules. These membrane rearrangements are virally induced; however, it remains unclear which viral proteins are responsible. In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. Three non-structural transmembrane proteins, nsp3, nsp4, and nsp6, were expressed in cells singularly or in combination and the effects on cellular membranes investigated using electron microscopy and electron tomography. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. This study highlights further differences in the mechanism of membrane rearrangements between members of the coronavirus family. url: https://doi.org/10.3390/v10090477 doi: 10.3390/v10090477 id: cord-285620-oawrnmhy author: Fahimirad, Shohreh title: Efficient removal of water bacteria and viruses using electrospun nanofibers date: 2020-08-16 words: 6761.0 sentences: 361.0 pages: flesch: 38.0 cache: ./cache/cord-285620-oawrnmhy.txt txt: ./txt/cord-285620-oawrnmhy.txt summary: This review intends to provide a detailed summary of the recent advances in the fabrication of antibacterial and antiviral electrospun nanofibers and discuss their application efficiency as a water filtration membrane. The present work reviews previous studies on the production and application of electrospun nanofibers as antimicrobial water filtration membranes. The objectives of this review were to: (i) introduce the different procedures, which have been applied for incorporation of the various antimicrobial agents into electrospun nanofibers (ii) discuss the different antimicrobial tests used for proving antimicrobial activity of the fabricated electrospun water filters (iii) study the efficiency of the produced antimicrobial electrospun application in the water treatment industry. Based on the majority of researches studied in this review, blending and post-modification strategies are two commonly used techniques to incorporate biocide agents into nanofibers aiming for water disinfection application (Shalaby et al., 2018; He et al., 2018; Makaremi et al., 2016) . abstract: Abstract Pathogenic contamination has been considered as a significant worldwide water quality concern. Due to providing promising opportunities for the production of nanocomposite membranes with tailored porosity, adjustable pore size, and scaled-up ability of biomolecules incorporation, electrospinning has become the center of attention. This review intends to provide a detailed summary of the recent advances in the fabrication of antibacterial and antiviral electrospun nanofibers and discuss their application efficiency as a water filtration membrane. The current review attempts to give a functionalist perspective of the fundamental progress in construction strategies of antibacterial and antiviral electrospun nanofibers. The review provides a list of antibacterial and antiviral agents commonly used as water membrane filters and discusses the challenges in the incorporation process. We have thoroughly studied the recent application of functionalized electrospun nanofibers in the water disinfection process, with an emphasis on their efficiency. Moreover, different antibacterial and antiviral assay techniques for membranes are discussed, the gaps and limitations are highlighted and promising strategies to overcome barriers are studies. url: https://www.ncbi.nlm.nih.gov/pubmed/32866832/ doi: 10.1016/j.scitotenv.2020.141673 id: cord-023200-3caevjvh author: Falanga, Annarita title: Membranotropic peptides mediating viral entry date: 2018-02-13 words: 6062.0 sentences: 270.0 pages: flesch: 41.0 cache: ./cache/cord-023200-3caevjvh.txt txt: ./txt/cord-023200-3caevjvh.txt summary: The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. [3, 4] The molecular details of the interactions at the interface of virus and cell surfaces are quite complex and highly variable, but there is a common idea that only a limited number of pathways allowing viruses to reach the sites of penetration exist, with enveloped and non-enveloped viruses presenting different and unrelated processes, but with general principles driving all fusion events. [16, 17] Viral fusion proteins undergo significant rearrangements from the pre-fusion to the post-fusion conformations which are triggered by either receptor binding, proteolytic cleavage or low endosomal pH, and eventually determine the exposure of previously sequestered hydrophobic peptides, loops, or patches, able to interact with and destabilize one or both the opposing membranes. abstract: The means used by enveloped viruses to bypass cellular membranes are well characterized; however, the mechanisms used by non‐enveloped viruses to deliver their genome inside the cell remain unresolved and poorly defined. The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. Thus, in spite of noticeable differences in entry, this short stretches of membranotropic peptides are probably associated with similar entry‐related events. This review will uncover the intrinsic features of viral membranotropic peptides involved in viral entry of both naked viruses and the ones encircled with a biological membrane with the objective to better elucidate their different functional properties and possible applications in the biomedical field. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167733/ doi: 10.1002/pep2.24040 id: cord-298019-gf2asni1 author: Galdiero, Stefania title: gH625: A milestone in understanding the many roles of membranotropic peptides date: 2014-10-12 words: 8586.0 sentences: 354.0 pages: flesch: 37.0 cache: ./cache/cord-298019-gf2asni1.txt txt: ./txt/cord-298019-gf2asni1.txt summary: While they have been initially discovered in viral fusion proteins and have been involved in the mechanism of viral entry, it is now clear that their features and their mode of interaction with membrane bilayers can be exploited to design viral inhibitors as well as to favor delivery of cargos across the cell membrane and across the blood–brain barrier. Peptides with a propensity for membrane binding can also interfere with enveloped virus entry by direct physical interaction with the hydrophobic surfaces present on cell membranes and/or fusion proteins. Since not all membranotropic peptides are able to cross the membrane bilayer, it is essential to identify structural characteristics of hydrophobic peptides know to enter the cell membrane to highlight any feature that is involved in the penetration which may help in the design of novel delivery tools. Dendrimer functionalization with a membrane-interacting domain of herpes simplex virus type 1: towards intracellular delivery abstract: Here, we review the current knowledge about viral derived membranotropic peptides, and we discuss how they may be used for many therapeutic applications. While they have been initially discovered in viral fusion proteins and have been involved in the mechanism of viral entry, it is now clear that their features and their mode of interaction with membrane bilayers can be exploited to design viral inhibitors as well as to favor delivery of cargos across the cell membrane and across the blood–brain barrier. The peptide gH625 has been extensively used for all these purposes and provides a significant contribution to the field. We describe the roles of this sequence in order to close the gap between the many functions that are now emerging for membranotropic peptides. url: https://api.elsevier.com/content/article/pii/S0005273614003411 doi: 10.1016/j.bbamem.2014.10.006 id: cord-017566-dvxrwzqw author: González, María Eugenia title: Viral Proteins that Enhance Membrane Permeability date: 2005 words: 4482.0 sentences: 265.0 pages: flesch: 45.0 cache: ./cache/cord-017566-dvxrwzqw.txt txt: ./txt/cord-017566-dvxrwzqw.txt summary: During the infection of cells by animal viruses, membrane permeability is modified at two different steps of the virus life cycle (Carrasco, 1995) (Figure 6 .1). The viral molecules involved are components of virions: glycoproteins when enveloped particles are analyzed or, still unidentified, domains of the structural proteins in the case of naked viruses. At late times of infection, when there is active translation of late viral mRNAs, the plasma membrane becomes permeable to small molecules and ions (Carrasco, 1978) ( Figure 6 .1). Different viral molecules may be responsible for this late enhancement of membrane permeability, including viroporins (Gonzalez and Carrasco, 2003) , glycoproteins, and even proteases (Chang et al., 1999; Blanco et al., 2003) . Entry of enveloped animal viruses leads to early membrane permeabilization, which is mediated by the formation of the two pores (fusion and TM) formed by viral fusion glycoproteins. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122156/ doi: 10.1007/0-387-28146-0_6 id: cord-356090-oj3d9ail author: Gorgun, D. title: Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane date: 2020-10-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infection of human cells by the SARS-CoV2 relies on its binding to a specific receptor and subsequent fusion of the viral and host cell membranes. The fusion peptide (FP), a short peptide segment in the spike protein, plays a central role in the initial penetration of the virus into the host cell membrane, followed by the fusion of the two membranes. Here, we use an array of molecular dynamics (MD) simulations taking advantage of the Highly Mobile Membrane Mimetic (HMMM) model, to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level, and to characterize the membrane-bound form of the peptide. Six independent systems were generated by changing the initial positioning and orientation of the FP with respect to the membrane, and each system was simulated in five independent replicas. In 60% of the simulations, the FP reaches a stable, membrane-bound configuration where the peptide deeply penetrated into the membrane. Clustering of the results reveals two major membrane binding modes, the helix-binding mode and the loop-binding mode. Taken into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, we propose that the helix-binding mode represents more closely the biologically relevant form. In the helix-binding mode, the helix is stabilized in an oblique angle with respect to the membrane with its N-terminus tilted towards the membrane core. Analysis of the FP-lipid interactions shows the involvement of specific residues of the helix in membrane binding previously described as the fusion active core residues. Taken together, the results shed light on a key step involved in SARS-CoV2 infection with potential implications in designing novel inhibitors. SIGNIFICANCE A key step in cellular infection by the SARS-CoV2 virus is its attachment to and penetration into the plasma membrane of human cells. These processes hinge upon the membrane interaction of the viral fusion peptide, a segment exposed by the spike protein upon its conformational changes after encountering the host cell. In this study, using molecular dynamics simulations, we describe how the fusion peptide from the SARS-CoV2 virus binds human cellular membranes and characterize, at an atomic level, lipid-protein interactions important for the stability of the bound state. url: https://doi.org/10.1101/2020.10.27.357350 doi: 10.1101/2020.10.27.357350 id: cord-020788-a33vcapl author: Gottardi, Cara J. title: Signals and Mechanisms of Sorting in Epithelial Polarity date: 2008-05-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This chapter discusses epithelial-membrane polarity, sorting pathways in polarized cells, and the sorting-signal paradigm. Polarized epithelial cells have long captured the attention of cell biologists and cell physiologists. At the electron-microscopic level, one of the most apparent and fundamental features of this cell type is its polarized organization of intracellular organelles and its structurally and compositionally distinct lumenal (apical) and serosal (basolateral) plasma-membrane domains. The polarized epithelial phenotype is an absolute necessity for organ-system function. In the most general sense, these cells organize to form a continuous, single layer of cells, or epithelium, which serves as a semi-permeable barrier between apposing and biologically distinct compartments. Within the tubules of the nephron, these cells orchestrate complex ion-transporting processes that ultimately control the overall fluid balance of the organism. At the surface of the gastrointestinal tract, specialized versions of this cell type control the digestion, absorption, and immuno-protection of the organism. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147917/ doi: 10.1016/s1569-2558(08)60020-x id: cord-022354-aqtceqqo author: HUNTER, ERIC title: Membrane Insertion and Transport of Viral Glycoproteins: A Mutational Analysis date: 2012-12-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155604/ doi: 10.1016/b978-0-12-203460-2.50007-x id: cord-264996-og3sg0qw author: Howell, Gareth J. title: Cell Biology of Membrane Trafficking in Human Disease date: 2006-09-17 words: 20320.0 sentences: 1072.0 pages: flesch: 42.0 cache: ./cache/cord-264996-og3sg0qw.txt txt: ./txt/cord-264996-og3sg0qw.txt summary: Many of these transport intermediates or vesicles, whether derived from the ER, other internal organelles, or the plasma membrane, are ''''coated'''' with unique protein complexes, tethering factors, and regulatory factors that ensure correct targeting to an acceptor compartment. Breast cancer Caveolin-1 Deletion or dominant negative mutation of caveolin-1 promotes tumor progression Breast cancer (Bouras et al., 2004; Williams and Lisanti, 2005) (Hayasaka et al., 1993; Matsuyama et al., 2002) Chediak-Higashi syndrome (CHS) CHS1/Lyst Lyst involved in regulation of protein secretion from lysosomes -enlarged lysosomes Partial albinism, recurrent bacterial infections, impaired chemotaxis and abnormal natural killer cell function (Shiflett et al., 2002; Ward et al., 2003) 214500 Choroideremia (CHM) Rab Escort Protein 1 (REP1) RAB27a remains cytosolic due to defective geranylgeranyl modification in CHM lymphoblasts X-linked form of retinal degeneration 303100 Various mechanisms control the traYcking of proteins from the TGN by the formation and delivery of membrane-derived transport vesicles to the plasma membrane, endosomes, or lysosomal structures (Ponnambalam and Baldwin, 2003) . abstract: Understanding the molecular and cellular mechanisms underlying membrane traffic pathways is crucial to the treatment and cure of human disease. Various human diseases caused by changes in cellular homeostasis arise through a single gene mutation(s) resulting in compromised membrane trafficking. Many pathogenic agents such as viruses, bacteria, or parasites have evolved mechanisms to subvert the host cell response to infection, or have hijacked cellular mechanisms to proliferate and ensure pathogen survival. Understanding the consequence of genetic mutations or pathogenic infection on membrane traffic has also enabled greater understanding of the interactions between organisms and the surrounding environment. This review focuses on human genetic defects and molecular mechanisms that underlie eukaryote exocytosis and endocytosis and current and future prospects for alleviation of a variety of human diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/16984815/ doi: 10.1016/s0074-7696(06)52005-4 id: cord-353815-w35spqqt author: Huan, Yuchen title: Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields date: 2020-10-16 words: 12266.0 sentences: 623.0 pages: flesch: 38.0 cache: ./cache/cord-353815-w35spqqt.txt txt: ./txt/cord-353815-w35spqqt.txt summary: This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. Tryptophan (Trp), as a non-polar amino acid, has a remarkable effect on the interface region of the lipid bilayer, whereas Arg, as a basic amino acid, confers peptide charge and hydrogen bond interactions, which are essential properties to combine with the bacterial membrane''s abundant anionic component. And it seems that Trp residues play the role of natural aromatic activators of Arg-rich AMPs by ion-pair-π interactions (Walrant et al., 2020) , thereby promoting enhanced peptide-membrane interactions (Chan et al., 2006) . Furthermore, L4H4, which is designed based on the linear cationic amphiphilic peptide magainin, also shows good antibacterial activity and cell penetration properties by inserting four histidine sequences in leucine and alanine (Lointier et al., 2020) . abstract: Antimicrobial peptides (AMPs) are a class of small peptides that widely exist in nature and they are an important part of the innate immune system of different organisms. AMPs have a wide range of inhibitory effects against bacteria, fungi, parasites and viruses. The emergence of antibiotic-resistant microorganisms and the increasing of concerns about the use of antibiotics resulted in the development of AMPs, which have a good application prospect in medicine, food, animal husbandry, agriculture and aquaculture. This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. The research progress on antivirus peptides, especially anti-coronavirus (COVID-19) peptides, has been introduced given the COVID-19 pandemic worldwide in 2020. url: https://www.ncbi.nlm.nih.gov/pubmed/33178164/ doi: 10.3389/fmicb.2020.582779 id: cord-303238-us3dybue author: Kanjanahaluethai, Amornrat title: Membrane Topology of Murine Coronavirus Replicase Nonstructural Protein 3 date: 2007-05-01 words: 4789.0 sentences: 247.0 pages: flesch: 50.0 cache: ./cache/cord-303238-us3dybue.txt txt: ./txt/cord-303238-us3dybue.txt summary: The papain-like protease (PLpro) encoded by the coronavirus that causes severe acute respiratory syndrome (SARS-CoV) processes three sites in the replicase polyprotein (Harcourt et al., 2004) , and has recently been shown to have de-ubiquitinating activity (Barretto et al., 2005; Lindner et al., 2005) . To extend these studies of membrane association of coronavirus replicase products, we analyzed the amino acid sequence of MHV-JHM nsp3 (from glycine-833 to glycine-2840) for probability of transmembrane helices using the five different programs designed to search for putative membrane-spanning sequences: Phobius, TMHMM, HMMTOP, SOSUI and TMpred (Fig. 2) . In contrast, when CMMs were added to the mixture, protein products that included all or part of nsp3-TM (PLP2-2485, -2390 and -2258) were detected predominantly in the pelleted fraction, consistent with membrane association (Fig. 3B ). abstract: Mouse hepatitis virus (MHV) is a member of the family Coronaviridae. These positive strand RNA viruses encode a replicase polyprotein that is processed into 16 nonstructural proteins (nsps). The nsps assemble with membranes to generate double membrane vesicles, which are the sites of viral RNA synthesis. MHV nsp3 contains multiple domains including two papain-like protease domains, PLP1 and PLP2, and a predicted transmembrane (TM) domain. In this study, we determined the membrane topology of nsp3-TM and showed that TM-mediated tethering of PLP2 is important for processing at cleavage site 3. Biochemical analysis revealed that nsp3 is an integral membrane protein that is inserted into endoplasmic reticulum (ER) membranes co-translationally and glycosylated at asparagine-2357. Proteinase K digestion experiments indicate that the TM domain of nsp3 has 4 membrane-spanning helices. We show that nsp3-TM is sufficient to mediate ER membrane association of a cytosolic protein. This study is the first detailed analysis of the topology and function of the coronavirus nsp3 TM domain. url: https://www.ncbi.nlm.nih.gov/pubmed/17222884/ doi: 10.1016/j.virol.2006.12.009 id: cord-341129-eo0vjcmk author: Kielian, Margaret title: Virus membrane-fusion proteins: more than one way to make a hairpin date: 2006 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Structure–function studies have defined two classes of viral membrane-fusion proteins that have radically different architectures but adopt a similar overall 'hairpin' conformation to induce fusion of the viral and cellular membranes and therefore initiate infection. In both classes, the hairpin conformation is achieved after a conformational change is triggered by interaction with the target cell. This review will focus in particular on the properties of the more recently described class II proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/16357862/ doi: 10.1038/nrmicro1326 id: cord-327765-qdbgkm53 author: Kinnun, Jacob J. title: Lateral Heterogeneity and Domain Formation in Cellular Membranes date: 2020-09-15 words: 5431.0 sentences: 346.0 pages: flesch: 47.0 cache: ./cache/cord-327765-qdbgkm53.txt txt: ./txt/cord-327765-qdbgkm53.txt summary: where a 0 is the area per molecule, R is the domain radius, ε is the dielectric constant of the interfacial water, ε 0 is the permittivity of free space, e is Euler''s number, and δ is the molecular cut-off distance ∼ 0.5nm 26 Lipids and membrane proteins have varying intrinsic hydrophobic thicknesses. In terms of specific theoretical energetics, this contribution to line tension is less 6 J o u r n a l P r e -p r o o f Figure 2 : (a) The registration of domains across membrane leaflets maximizes dynamics, is entropically favorable, and is one mechanism for domain coalescence (adapted from Haataja et al. In other words, the simple phenomenological free energy approach presented here provides a conceptual framework for understanding the scattering data and interpreting the wide range of phase behaviors observed for lateral lipid organization in cell membranes. Lipid lateral diffusion in bilayers with phosphatidylcholine, sphingomyelin and cholesterol: An NMR study of dynamics and lateral phase separation abstract: As early as the development of the fluid mosaic model for cellular membranes, researchers began observing the telltale signs of lateral heterogeneity. Over the decades this has led to the development of the lipid raft hypothesis and the ensuing controversy that has unfolded. Here, we review the physical concepts behind domain formation in lipid membranes, both of their structural and dynamic origins. This, then leads into a discussion of coarse-grained, phenomenological approaches that describe the wide range of phases associated with lipid lateral heterogeneity. We use these physical concepts to describe the interaction between raft-lipid species, such as long-chain saturated lipids, sphingomyelin, and cholesterol with non-raft forming lipids, such as those with short acyl chains or unsaturated fatty acids. While debate has persisted on the biological relevance of lipid domains, recent research, described here, continues to identify biological roles for rafts and new experimental approaches have revealed the existence of lipid domains in living systems. Given the recent progress on both the biological and structural aspects of raft formation, the research area of membrane lateral heterogeneity will not only expand, but will continue to produce exciting results. url: https://api.elsevier.com/content/article/pii/S0009308420301079 doi: 10.1016/j.chemphyslip.2020.104976 id: cord-339172-210dwhgj author: Knoops, Kèvin title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Positive-strand RNA viruses, a large group including human pathogens such as SARS-coronavirus (SARS-CoV), replicate in the cytoplasm of infected host cells. Their replication complexes are commonly associated with modified host cell membranes. Membrane structures supporting viral RNA synthesis range from distinct spherular membrane invaginations to more elaborate webs of packed membranes and vesicles. Generally, their ultrastructure, morphogenesis, and exact role in viral replication remain to be defined. Poorly characterized double-membrane vesicles (DMVs) were previously implicated in SARS-CoV RNA synthesis. We have now applied electron tomography of cryofixed infected cells for the three-dimensional imaging of coronavirus-induced membrane alterations at high resolution. Our analysis defines a unique reticulovesicular network of modified endoplasmic reticulum that integrates convoluted membranes, numerous interconnected DMVs (diameter 200–300 nm), and “vesicle packets” apparently arising from DMV merger. The convoluted membranes were most abundantly immunolabeled for viral replicase subunits. However, double-stranded RNA, presumably revealing the site of viral RNA synthesis, mainly localized to the DMV interior. Since we could not discern a connection between DMV interior and cytosol, our analysis raises several questions about the mechanism of DMV formation and the actual site of SARS-CoV RNA synthesis. Our data document the extensive virus-induced reorganization of host cell membranes into a network that is used to organize viral replication and possibly hide replicating RNA from antiviral defense mechanisms. Together with biochemical studies of the viral enzyme complex, our ultrastructural description of this “replication network” will aid to further dissect the early stages of the coronavirus life cycle and its virus-host interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/18798692/ doi: 10.1371/journal.pbio.0060226 id: cord-309384-vlk8cebh author: Kolter, Thomas title: Ganglioside Biochemistry date: 2012-12-19 words: 16840.0 sentences: 960.0 pages: flesch: 38.0 cache: ./cache/cord-309384-vlk8cebh.txt txt: ./txt/cord-309384-vlk8cebh.txt summary: A principal difference between ganglioside biosynthesis in the Golgi apparatus and degradation in the endolysosomal compartment is that during GSL formation, membranebound glycosyltransferases interact with their membranebound glycolipid substrates by diffusion within the twodimensional plane of the lipid bilayer. As glycosidase substrates, GSLs with four carbohydrate residues or less require the additional presence of small lipid binding glycoproteins, either the GM2 activator protein or one of the four saposins A-D. In vitro, in addition to enzymes and activator proteins, also an appropriate membrane-lipid composition of the ganglioside-containing membrane is required for degradation [222] . Due to the deficiency of two enzyme activities, β-hexosaminidases A and B, storage of negatively charged glycolipids characteristic for Tay-Sachs disease and, in addition, of uncharged substrates such as GA2 in the brain and globoside in visceral organs (Figure 16 ) is observed. abstract: Gangliosides are sialic acid-containing glycosphingolipids. They occur especially on the cellular surfaces of neuronal cells, where they form a complex pattern, but are also found in many other cell types. The paper provides a general overview on their structures, occurrence, and metabolism. Key functional, biochemical, and pathobiochemical aspects are summarized. url: https://www.ncbi.nlm.nih.gov/pubmed/25969757/ doi: 10.5402/2012/506160 id: cord-349341-ap5n6ijl author: Kopek, Benjamin G title: Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle date: 2007-08-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens. All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles. However, the exact sites of RNA synthesis and crucial topological relationships between relevant membranes, vesicle interiors, surrounding lumens, and cytoplasm generally are poorly defined. We applied electron microscope tomography and complementary approaches to flock house virus (FHV)–infected Drosophila cells to provide the first 3-D analysis of such replication complexes. The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5'-triphosphate incorporation localized between inner and outer mitochondrial membranes inside ∼50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. All such FHV spherules were outer mitochondrial membrane invaginations with interiors connected to the cytoplasm by a necked channel of ∼10-nm diameter, which is sufficient for ribonucleotide import and product RNA export. Tomographic, biochemical, and other results imply that FHV spherules contain, on average, three RNA replication intermediates and an interior shell of ∼100 membrane-spanning, self-interacting protein As. The results identify spherules as the site of protein A and nascent RNA accumulation and define spherule topology, dimensions, and stoichiometry to reveal the nature and many details of the organization and function of the FHV RNA replication complex. The resulting insights appear relevant to many other positive-strand RNA viruses and support recently proposed structural and likely evolutionary parallels with retrovirus and double-stranded RNA virus virions. url: https://www.ncbi.nlm.nih.gov/pubmed/17696647/ doi: 10.1371/journal.pbio.0050220 id: cord-329448-kxxy60x9 author: Kumari, Sudha title: Endocytosis unplugged: multiple ways to enter the cell date: 2010-02-02 words: 11521.0 sentences: 541.0 pages: flesch: 31.0 cache: ./cache/cord-329448-kxxy60x9.txt txt: ./txt/cord-329448-kxxy60x9.txt summary: These factors include one or more underlying principle in cargo enrichment, necessitating specific coat and coat-associated protein assembly, a scission mechanism, and a means to integrate these steps; several molecules and membrane parameters can influence and diversify an endocytic process. CtBP1/BARS (C-terminal-binding protein-1/brefeldin A ribosylation substrate) proteins were originally demonstrated to regulate dynamin-independent fluid uptake in a variety of cell lines, and were later reported to localize to the site of and affect macropinosome membrane closure in a phosphorylation-dependent manner [36] . Overexpression of dominant negative, GTP-binding mutants of dynamin also blocked receptor-mediated endocytosis in various cells, suggesting a role for the GTPase activity of dynamin in the clathrin-dependent endocytic process outside the nervous system. The identification of an endocytic pathway as distinct has been primarily based on associated cargo proteins or lipids, and molecular regulators; the contribution of kinetics and detailed physical mechanism to such categorization is not generally available except in some wellcharacterized situations, namely clathrin-pit endocytosis or endocytosis by actin-dependent forces in yeast. abstract: Endocytosis occurs at the cell surface and involves internalization of the plasma membrane (PM) along with its constituent membrane proteins and lipids. Endocytosis is involved in sampling of the extracellular milieu and also serves to regulate various processes initiated at the cell surface. These include nutrient uptake, signaling from cell-surface receptors, and many other processes essential for cell and tissue functioning in metazoans. It is also central to the maintenance of PM lipid and protein homeostasis. There are multiple means of internalization that operate concurrently, at the cell surface. With advancement in high-resolution visualization techniques, it is now possible to track multiple endocytic cargo at the same time, revealing a remarkable diversity of endocytic processes in a single cell. A combination of live cell imaging and efficient genetic manipulations has also aided in understanding the functional hierarchy of molecular players in these mechanisms of internalization. Here we provide an account of various endocytic routes, their mechanisms of operation and occurrence across phyla. url: https://www.ncbi.nlm.nih.gov/pubmed/20125123/ doi: 10.1038/cr.2010.19 id: cord-299270-fwbz3t25 author: Lemieux, M. Joanne title: Structure and function of proteins in membranes and nanodiscs date: 2020-08-22 words: 3034.0 sentences: 145.0 pages: flesch: 39.0 cache: ./cache/cord-299270-fwbz3t25.txt txt: ./txt/cord-299270-fwbz3t25.txt summary: Abstract The field of membrane structural biology represents a fast-moving field with exciting developments including native nanodiscs that allow preparation of complexes of post-translationally modified proteins bound to biological lipids. Comparisons with the performance of conventional detergents suggests that the development of neutral or basic copolymers related to SMA could offer advantages, providing avenues for solubilization and analysis of a broader array of biological membrane:protein assemblies (memteins). The individual components of erythrocyte membranes including Rh proteins are well known, but their multimeric lipid complexes are dissociated in detergent-based preparations and hence no longer recognizable or extractable using conformation-specific antibodies. A set of ABCG2 protein constructs were designed with N-terminal GFP or SNAP and His 6 tags and solubilized from HEK cells using SMA(2:1) copolymer, as were CD28 and CD86 Antibiotics include lipid-specific peptides that self-associate into pores, which permeabilize bacterial membranes. abstract: Abstract The field of membrane structural biology represents a fast-moving field with exciting developments including native nanodiscs that allow preparation of complexes of post-translationally modified proteins bound to biological lipids. This has led to conceptual advances including biological membrane:protein assemblies or “memteins” as the fundamental functional units of biological membranes. Tools including cryo-electron microscopy and X-ray crystallography are maturing such that it is becoming increasingly feasible to solve structures of large, multicomponent complexes, while complementary methods including nuclear magnetic resonance spectroscopy yield unique insights into interactions and dynamics. Challenges remain, including elucidating exactly how lipids and ligands are recognized at atomic resolution and transduce signals across asymmetric bilayers. In this special volume some of the latest thinking and methods are gathered through the analysis of a range of transmembrane targets. Ongoing work on areas including polymer design, protein labelling and microfluidic technologies will ensure continued progress on improving resolution and throughput, providing deeper understanding of this most important group of targets. url: https://api.elsevier.com/content/article/pii/S0005273620302881 doi: 10.1016/j.bbamem.2020.183445 id: cord-279463-bli8hwda author: Lipp, Joachim title: The membrane-spanning segment of invariant chain (Iγ) contains a potentially cleavable signal sequence date: 1986-09-26 words: 6276.0 sentences: 367.0 pages: flesch: 62.0 cache: ./cache/cord-279463-bli8hwda.txt txt: ./txt/cord-279463-bli8hwda.txt summary: As type II membrane proteins contain only a single stretch of hydrophobic amino acid residues, this might function as a signal for membrane insertion as well as a membrane anchor (Markoff et al., 1984; Spiess and Lodish, 1986) . plycat is an in-frame fusion between the 5'' region of ly encoding the cytoplas, mic, membrane-spanning segment plus 12 amino acids of the exoplasmic portion of ly and the gene encoding the cytoplasmic protein chloramphenicol acetyltransferase (CAT). After protease digestion in the presence of microsomal membranes, lyCAT* is reduced in molecular weight by about 2 kd, suggesting that it exposes 20-30 amino acid residues on the cytoplasmic side ( Figure 3 , lanes 2 and 3). This signal sequence is located in the amino-terminal half of the membrane-spanning segment, and it is cleaved when the preceding cytoplasmic domain is removed. abstract: Abstract The human invariant chain (Iγ) of class II histocompatibility antigens spans the membrane of the endoplasmic reticulum once. It exposes a small amino-terminal domain on the cytoplasmic side and a carboxyterminal, glycosylated domain on the exoplasmic side of the membrane. When the exoplasmic domain of Iγ is replaced by the cytoplasmic protein chloramphenicol acetyltransferase (CAT), CAT becomes the exoplasmic, glycosylated domain of the resulting membrane protein IγCAT∗. Deletion of the hydrophilic cytoplasmic domain from IγCAT gives rise to a secreted protein from which an amino-terminal segment is cleaved, most likely by signal peptidase. We conclude that the membrane-spanning region of Iγ contains a signal sequence in its amino-terminal half and that hydrophilic residues at the amino-terminal end of a signal sequence can determine cleavage by signal peptidase. url: https://www.ncbi.nlm.nih.gov/pubmed/3530500/ doi: 10.1016/0092-8674(86)90710-5 id: cord-022538-1g9kmpdi author: Makino, Hisao title: ENVIRONMENTAL AND SAFETY ISSUES WITH NANOPARTICLES date: 2008-05-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This chapter evaluates the relationship between nanoparticles and the environment, and describes the trouble caused by nanoparticles as well as the safety issues. The relationship between nanoparticles and the environment is clarified from the viewpoint of the kind of influence nanoparticles generated either artificially or naturally have on the environment, such as in atmosphere, groundwater, wastewaters, and exhaust gases. Indoor nanoparticles originate from the several sources such as products of chemical reactions, nonvolatile residues (NVRs) of liquid droplets, printers/photocopiers, combustion, bioaerosols, and infiltration of outdoor air. The influence of nanoparticles on the indoor environment is discussed in the chapter. It describes the sources of nanoparticle generation in general industrial processes such as grinding processes, and in cleanroom or controlled environment industrial processes, such as exhaled air, ionizers, and haze by chemical reaction on solid surfaces. The chapter discusses safety issues related to nanoparticles such as possibility of dust explosion, health risks and biological effects of nanoparticle materials such as carbon nanotubes, fullerenes, nanosized metal oxides, and carbon black. The chapter also discusses methods for removing nanoparticles from gas and liquid as technology to control the influence of nanoparticles on the environment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158284/ doi: 10.1016/b978-044453122-3.50010-6 id: cord-333757-h12aozg2 author: Modis, Yorgo title: Class II Fusion Proteins date: 2013-07-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Enveloped viruses rely on fusion proteins in their envelope to fuse the viral membrane to the host-cell membrane. This key step in viral entry delivers the viral genome into the cytoplasm for replication. Although class II fusion proteins are genetically and structurally unrelated to class I fusion proteins, they use the same physical principles and topology as other fusion proteins to drive membrane fusion. Exposure of a fusion loop first allows it to insert into the host-cell membrane. Conserved hydrophobic residues in the fusion loop act as an anchor, which penetrates only partway into the outer bilayer leaflet of the host-cell membrane. Subsequent folding back of the fusion protein on itself directs the C-terminal viral transmembrane anchor towards the fusion loop. This fold-back forces the host-cell membrane (held by the fusion loop) and the viral membrane (held by the C-terminal transmembrane anchor) against each other, resulting in membrane fusion. In class II fusion proteins, the fold-back is triggered by the reduced pH of an endosome, and is accompanied by the assembly of fusion protein monomers into trimers. The fold-back occurs by domain rearrangement rather than by an extensive refolding of secondary structure, but this domain rearrangement and the assembly of monomers into trimers together bury a large surface area. The energy that is thus released exerts a bending force on the apposed viral and cellular membranes, causing them to bend towards each other and, eventually, to fuse. url: https://www.ncbi.nlm.nih.gov/pubmed/23884590/ doi: 10.1007/978-1-4614-7651-1_8 id: cord-009371-ub4p4ngr author: Mollenhauer, Hilton H. title: Alteration of intracellular traffic by monensin; mechanism, specificity and relationship to toxicity date: 1990-05-07 words: 12395.0 sentences: 535.0 pages: flesch: 46.0 cache: ./cache/cord-009371-ub4p4ngr.txt txt: ./txt/cord-009371-ub4p4ngr.txt summary: abstract: Monensin, a monovalent ion-selective ionophore, facilitates the transmembrane exchange of principally sodium ions for protons. The outer surface of the ionophore-ion comples is composed largely of nonpolar hydrocarbon, which imparts a high solubility to the complexes in nonpolar solvents. In biological systems, these complexes are freely soluble in the lipid components of membranes and, presumably, diffuse or shuttle through the membranes from one aqueous membrane interface to the other. The net effect for monensin is a trans-membrane exchange of sodium ions for protons. However, the interaction of an ionophore with biological membranes, and its ionophoric expression, is highly dependent on the biochemical configuration of the membrane itself. One apparent consequence of this exchange is the neutralization of acidic intracellular compartments such as the trans Golgi apparatus cisternae and associated elements, lysosomes, and certain endosomes. This is accompanied by a disruption of trans Golgi apparatus cisternae and of lysosome and acidic endosome function. At the same time, Golgi apparatus cisternae appear to swell, presumably due to osmotic uptake of water resulting from the inward movement of ions. Monensin effects on Golgi apparatus are observed in cells from a wide range of plant and animal species. The action of monensin is most often exerted on the trans half of the stacked cisternae, often near the point of exit of secretory vesicles at the trans face of the stacked cisternae, or, especially at low monensin concentrations or short exposure times, near the middle of the stacked cisternae. The effects of monensin are quite rapid in both animal and plant cells; i.e., changes in Golgi apparatus may be observed after only 2–5 min of exposure. It is implicit in these observations that the uptake of osmotically active cations is accompanied by a concomitant efflux of H(+) and that a net influx of protons would be required to sustain the ionic exchange long enough to account for the swelling of cisternae observed in electron micrographs. In the Golgi apparatus, late processing events such as terminal glycosylation and proteolytic cleavages are most susceptible to inhibition by monensin. Yet, many incompletely processed molecules may still be secreted via yet poorly understood mechanisms that appear to bypass the Golgi apparatus. In endocytosis, monensin does not prevent internalization. However, intracellular degradation of internalized ligands may be prevented. It is becoming clear that endocytosis involves both acidic and non-acidic compartments and that monensin inhibits those processes that normally occur in acidic compartments. Thus, monensin, which is capable of collapsing Na(+) and H(+) gradients, has gained wide-spread acceptance as a tool for studying Golgi apparatus function and for localizing and identifying the molecular pathways of subcellular vesicular traffic involving acid compartments. Among its advantages are the low concentrations at which inhibitions are produced (0.01–1.0 μM), a minimum of troublesome side effects (e.g., little or no change of protein synthesis or ATP levels) and a reversible action. Because the affinity of monensin for Na(+) is ten times that for K(+), its nearest competitor, monensin mediates primarily a Na(+)-H(+) exchange. Monensin has little tendency to bind calcium. Not only is monensin of importance as an experimental tool, it is of great commercial value as a coccidiostat for poultry and to promote more efficient utilization of feed in cattle. The mechanisms by which monensin interact with coccidia and rumen microflora to achieved these benefits are reasonably well documented. However, the interactions between monensin and the tissues of the host animal are not well understood although the severe toxicological manifestations of monensin poisoning are well known. Equine species are particularly susceptible to monensin poisoning, and a common effect of monensin poisoning is vacuolization and/or swelling of mitochondria in striated muscle. Other pathological injuries to striated muscle, spleen, lung, liver and kidney also have been noted. A consistent observation is cardiac myocyte degeneration as well as vacuolization. Differences in cellular response resulting from exposure to monensin (i.e., Golgi apparatus swelling in cultured cells, isolated tissues, and plants vs.mitochondrial swelling in animals fed monensin) suggest that myocardial damage is due either to a monensin metabolite or is a secondary response to some other derivation. However, as pointed out by Bergen and Bates [26], the underlying mode of action of ionophores is on transmembrane ion fluxes which dissipate cation and proton gradients. Consequently, some or all of the observed monensin effects in vivo in animals could be secondary phenomena caused by disruption of normal membrane physiology resulting from altered ion fluxes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148783/ doi: 10.1016/0304-4157(90)90008-z id: cord-011888-3mvzkff6 author: Moore, John P. title: Oxone(®)-Mediated TEMPO-Oxidized Cellulose Nanomaterial Ultrafiltration and Dialysis Mixed-Matrix Hollow Fiber Membranes date: 2020-06-15 words: 5936.0 sentences: 336.0 pages: flesch: 58.0 cache: ./cache/cord-011888-3mvzkff6.txt txt: ./txt/cord-011888-3mvzkff6.txt summary: title: Oxone(®)-Mediated TEMPO-Oxidized Cellulose Nanomaterial Ultrafiltration and Dialysis Mixed-Matrix Hollow Fiber Membranes Ultrafiltration and dialysis were performed using bovine serum albumin (BSA), lysozyme, and urea to analyze various properties of each hollow fiber membrane type. Utilizing the procedure from Moore et al., OTO-CNMs Form I and Form II were synthesized and used in conjunction with cellulose triacetate (CTA) from Acros Organics (Fair Lawn, NJ, USA), N-methyl pyrrolidone (NMP) from VWR (Radnor, PA, USA), and deionized water to create novel membranes for filtration [21] . In this study on the implementation of two derivatives of cellulose nanomaterials into hollow fiber membranes for ultrafiltration and dialysis, OTO-CNM Form I and Form II mixed-matrix membranes have been quantitatively evaluated for the first time by determining model molecule selectivity (BSA, urea, and lysozyme), as well as transport rates (flux and diffusion rates). abstract: Recent exploration of cellulose nanomaterials has resulted in the creation of Oxone(®)-Mediated TEMPO-Oxidized Cellulose Nanomaterials (OTO-CNMs). These materials, when incorporated into a polymer matrix, have properties showing increased flux, decreased membrane resistance, and improved clearance, making them an ideal material for dialysis. This study is the first to focus on the implementation of OTO-CNMs into hollow fiber membranes and a comparison of these membranes for ultrafiltration and dialysis. Ultrafiltration and dialysis were performed using bovine serum albumin (BSA), lysozyme, and urea to analyze various properties of each hollow fiber membrane type. The results presented in this study provide the first quantitative evaluation of the clearance and sieving characteristics of Oxone(®)-Mediated TEMPO-Oxidized Cellulose-Nanomaterial-doped cellulose triacetate mixed-matrix hemodialyzers. While the cellulose nanomaterials increased flux (10–30%) in ultrafiltration mode, this was offset by increased removal of albumin. However, in dialysis mode, these materials drastically increased the mass transfer of components (50–100%), which could lead to significantly lower dialysis times for patients. This change in the performance between the two different modes is most likely due to the increased porosity of the cellulose nanomaterials. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7361684/ doi: 10.3390/polym12061348 id: cord-265887-g5zhoyo9 author: Mukherjee, Shruti title: Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date: 2020-08-11 words: 9085.0 sentences: 538.0 pages: flesch: 41.0 cache: ./cache/cord-265887-g5zhoyo9.txt txt: ./txt/cord-265887-g5zhoyo9.txt summary: (56) Apart from these highly conserved sequences throughout the genus, there are distinct potent glycosylation sites along the stretch that can serve as chaperone interacting motifs to help in the protein folding and/or aid in J o u r n a l P r e -p r o o f Journal Pre-proof trafficking along with the cellular machinery.(57) Glycosylation of particular asparagine residues (Asn 45, Asn 48, Asn 64, and Asn 68) in the SARS-CoV has been shown to be crucial in maintaining the proteinoligomerization events associated with the host membranes. (41) The formation of a disulfide bond may also play a crucial role in the oligomerization of the E protein, forming stable dimers, trimers, and pentamers depending on its functional requirement.(105) Thus even though the TMD spans the lipid bilayer, the CxxC motif could serve as an essential key to defining the membrane-associated oligomerization events-providing newer targets for preemptive therapeutic intervention. abstract: The Envelope (E) protein in SARS Coronavirus (CoV) is a small structural protein, incorporated as part of the envelope. A major fraction of the protein has been known to be associated with the host membranes, particularly organelles related to intracellular trafficking, prompting CoV packaging and propagation. Studies have elucidated the central hydrophobic transmembrane domain of the E protein being responsible for much of the viroporin activity in favor of the virus. However, newer insights into the organizational principles at the membranous compartments within the host cells suggest further complexity of the system. The lesser hydrophobic Carboxylic-terminal of the protein harbors interesting amino acid sequences- suggesting at the prevalence of membrane-directed amyloidogenic properties that remains mostly elusive. These highly conserved segments indicate at several potential membrane-associated functional roles that can redefine our comprehensive understanding of the protein. This should prompt further studies in designing and characterizing of effective targeted therapeutic measures. url: https://api.elsevier.com/content/article/pii/S0301462220301605 doi: 10.1016/j.bpc.2020.106452 id: cord-325712-9kbnyqt3 author: Nathan, Lakshmi title: Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms date: 2019-07-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The most widely-used assays for studying viral entry, including infectivity, cofloatation, and cell-cell fusion assays, yield functional information but provide low resolution of individual entry steps. Structural characterization provides high-resolution conformational information, but on its own is unable to address the functional significance of these conformations. Single virion tracking microscopy techniques provide more detail on the intermediate entry steps than infection assays and more functional information than structural methods, bridging the gap between these methods. In addition, single virion approaches also provide dynamic information about the kinetics of entry processes. This chapter reviews single virion tracking techniques and describes how they can be applied to study specific virus entry steps. These techniques provide information complementary to traditional ensemble approaches. Single virion techniques may either probe virion behavior in live cells or in biomimetic platforms. Synthesizing information from ensemble, structural, and single virion techniques ultimately yields a more complete understanding of the viral entry process than can be achieved by any single method alone. url: https://www.ncbi.nlm.nih.gov/pubmed/31317494/ doi: 10.1007/978-3-030-14741-9_2 id: cord-287093-9mertwj7 author: Netherton, Christopher L title: Virus factories, double membrane vesicles and viroplasm generated in animal cells date: 2011-10-12 words: 4308.0 sentences: 227.0 pages: flesch: 39.0 cache: ./cache/cord-287093-9mertwj7.txt txt: ./txt/cord-287093-9mertwj7.txt summary: In this review, we discuss how three supergroups of (+)RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses. In this review, we discuss how three supergroups of (+)strand RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses (NCLDV). The RNA-dependent RNA polymerases (RdRp) of the (+)strand RNA viruses are targeted to the cytoplasmic face of membrane-bound organelles and subsequent assembly of the replicase complex induces membrane curvature and the formation of densely packed membrane vesicles (reviewed in [1, 2] ) ( Figure 1 ). This suggests that replication may take place on CM and that genomes are transferred to vesicular packets for envelopment and budding, while excess viral RNA may be stored in DMVs. Picornaviruses generate densely packed DMVs between 200 and 400 nm in diameter, a series of single membraned vesicles resulting from fragmentation of the Golgi, and autophagosomes possibly generated as a bystander response to infection [11 ,12-16] . abstract: Many viruses reorganise cellular membrane compartments and the cytoskeleton to generate subcellular microenvironments called virus factories or ‘viroplasm’. These create a platform to concentrate replicase proteins, virus genomes and host proteins required for replication and also protect against antiviral defences. There is growing interest in understanding how viruses induce such large changes in cellular organisation, and recent studies are beginning to reveal the relationship between virus factories and viroplasm and the cellular structures that house them. In this review, we discuss how three supergroups of (+)RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/22440839/ doi: 10.1016/j.coviro.2011.09.008 id: cord-103812-ls6zgipi author: Norris, Rachael P. title: Gap junction internalization and processing in vivo: a 3D immuno-electron microscopy study date: 2020-06-30 words: 4803.0 sentences: 296.0 pages: flesch: 55.0 cache: ./cache/cord-103812-ls6zgipi.txt txt: ./txt/cord-103812-ls6zgipi.txt summary: Less is understood about their internalization, which forms double membrane vesicles containing cytosol and membranes from another cell, called connexosomes or annular gap junctions. Gap junction internalization can also be considered to be a form of trogocytosis (Joly and Hudriser, 2003) in which a portion of the plasma membrane and cytosol of the neighboring cell is transferred to the engulfing cell (See Fig. 1A ). Serial sections were then imaged to obtain threedimensional information; this distinguished between internalized connexosomes and gap junctions in the process of invagination. In 7 of the 56 modified connexosomes, a patch of unlabeled outer membrane bulged outward from a labeled inner membrane ( suggesting that different types of vesicles were involved. Five serial sections through a modified connexosome containing several internal vesicles labeled with Cx43. abstract: Gap junctions have well-established roles in cell-cell communication by way of forming permeable intercellular channels. Less is understood about their internalization, which forms double membrane vesicles containing cytosol and membranes from another cell, called connexosomes or annular gap junctions. Here, we systematically studied the fate of connexosomes in intact ovarian follicles. High pressure frozen, serial sectioned tissue was immunogold labeled for Connexin 43. Within a volume of electron micrographs, every labeled structure was categorized and counted. Surface area measurements indicate that large connexosomes undergo fission. Subsequent modifications are separation of inner and outer membranes, loss of Cx43 from the outer membrane, and outward budding of the modified membranes. We also documented several clear examples of organelle transfer from one cell to another by gap junction internalization. We discuss how connexosome formation and processing may be a novel means for gap junctions to mediate cell-cell communication. url: https://doi.org/10.1101/2020.06.29.178475 doi: 10.1101/2020.06.29.178475 id: cord-008480-p41oae8e author: O''Callaghan, Barbara title: Characterization of aminopeptidase N from Torpedo marmorata kidney date: 2004-11-12 words: 4411.0 sentences: 263.0 pages: flesch: 53.0 cache: ./cache/cord-008480-p41oae8e.txt txt: ./txt/cord-008480-p41oae8e.txt summary: Depending on solubilization conditions, both the antigen and peptidase activity were recovered either as a broad peak with a sedimentation coefficient of 18S (2% CHAPS) or as a single peak of 7.8S (1% CHAPS plus 0.2 % C(12)E(9)), showing that Torpedo aminopeptidase N behaves as an oligomer stabilized by hydrophobic interactions, easily converted into a 160 kDa monomer. The antigen is highly concentrated in the apical membrane of proximal tubule epithelial cells (600 gold particles/μm(2) of brush border membrane) whereas no labeling could be detected in other cell types or in other membranes of the same cells (basolatéral membranes, vacuoles or vesicles). Hybrids were selected in hypoxanthine, aminopterin and thymidine medium and superuatants from the culture wefts containing hybrid cells were tested for the presence of antibodies binding to the apical membrane of tubular epithelial cells on Torpedo kidney frozen sections. abstract: A major antigen of the brush border membrane of Torpedo marmorata kidney was identified and purified by immunoprecipitation. The sequence of its 18 N terminal amino acids was determined and found to be very similar to that of mammalian aminopeptidase N (EC 3.4.11.2). Indeed aminopeptidase N activity was efficiently immunoprecipitated by monoclonal antibody 180K1. The purified antigen gives a broad band at 180 kDa after SDS-gel electrophoresis, which, after treatment by endoglycosidase F, is converted to a thinner band at 140 kDa. This antigen is therefore heavily glycosylated. Depending on solubilization conditions, both the antigen and peptidase activity were recovered either as a broad peak with a sedimentation coefficient of 18S (2% CHAPS) or as a single peak of 7.8S (1% CHAPS plus 0.2 % C(12)E(9)), showing that Torpedo aminopeptidase N behaves as an oligomer stabilized by hydrophobic interactions, easily converted into a 160 kDa monomer. The antigen is highly concentrated in the apical membrane of proximal tubule epithelial cells (600 gold particles/μm(2) of brush border membrane) whereas no labeling could be detected in other cell types or in other membranes of the same cells (basolatéral membranes, vacuoles or vesicles). Monoclonal antibodies prepared here will be useful tools for further functional and structural studies of Torpedo kidney aminopeptidase N. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131328/ doi: 10.1016/s0248-4900(94)80003-0 id: cord-020712-l9cn0n99 author: Ohnishi, Shun-Ichi title: Chapter 9 Fusion of Viral Envelopes with Cellular Membranes date: 2008-05-30 words: 11708.0 sentences: 735.0 pages: flesch: 56.0 cache: ./cache/cord-020712-l9cn0n99.txt txt: ./txt/cord-020712-l9cn0n99.txt summary: Residues 80-100 in El and residues 100-131 in G, which have sequence homology among the strains, may be such stretches though not strongly hydrophobic (Table 262 SHUN-ICHI OHNlSHl and the putative fusogenic segment should be able to interact with the target membrane, inducing some disturbance eventually leading to fusion (Fig. Ib) . Presence of receptors for the amino-terminal segments in target membranes has been suggested from studies on inhibition of virus replication by small peptides with amino acid sequences similar to that of the viral amino terminus (Richardson et al., 1980; Richardson and Choppin, 1983) . Why is a specific amino acid sequence of F glycoprotein required for the membrane fusion reaction between envelope of HVJ (Sendai virus) and target cell membranes? pH-Dependent membrane fusion activity of a synthetic twenty amino acid peptide with the same sequence as that of the hydrophobic segment in influenza virus hemagglutinin abstract: This chapter reviews some characteristic features of membrane fusion activity for each virus and discusses the mechanisms of membrane fusion, especially low pH-induced membrane fusion. It concentrates on the interaction of the hydrophobic segment with the target cell membrane lipid bilayer and suggests the entrance of the segment into the lipid bilayer hydrophobic core as a key step in fusion. The envelope is a lipid bilayer membrane with the virus specific glycoproteins spanning it. The bilayer originates from the host cell membrane and has a lipid composition and transbilayer distribution quite similar to the host's. The viral glycoproteins have the functions of binding to the target cell surface and fusion with the cell membranes. The two functions are carried by a single glycoprotein in influenza virus (HA), vesicular stomatitis virus (VSV) G glycoprotein, and Semliki Forest virus SFV E glycoprotein. In Sendai virus (HVJ), the functions are carried by separate glycoproteins, hemagglutinin-neuraminidase (HN) for binding and fusion glycoprotein (F) for fusion. When viruses encounter target cells, they first bind to the cell surface through an interaction of the viral glycoprotein with receptors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146812/ doi: 10.1016/s0070-2161(08)60137-9 id: cord-034898-zjfhpum2 author: Patangi, Sanjay Orathi title: Veno-arterial extracorporeal membrane oxygenation: Special reference for use in ‘post-cardiotomy cardiogenic shock’ — A review with an Indian perspective date: 2020-11-07 words: 7527.0 sentences: 448.0 pages: flesch: 39.0 cache: ./cache/cord-034898-zjfhpum2.txt txt: ./txt/cord-034898-zjfhpum2.txt summary: title: Veno-arterial extracorporeal membrane oxygenation: Special reference for use in ''post-cardiotomy cardiogenic shock'' — A review with an Indian perspective Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is an important modality of managing post-cardiotomy cardiogenic shock with variable outcomes which would otherwise be universally fatal. Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) has gained popularity over the years as a ''bailout'' option after conventional circulatory support methods have proved refractory in the operating room (OR)/intensive care unit (ICU). Long-term survival and major outcomes in post-cardiotomy extracorporeal membrane oxygenation for adult patients in cardiogenic shock Usefulness of cardiac biomarkers to predict cardiac recovery in patients on extracorporeal membrane oxygenation support for refractory cardiogenic shock Nosocomial infections in adult cardiogenic shock patients supported by venoarterial extracorporeal membrane oxygenation Clinical outcomes in patients after extracorporeal membrane oxygenation support for postcardiotomy cardiogenic shock: a single-centre experience of 92 cases abstract: The ultimate goals of cardiovascular physiology are to ensure adequate end-organ perfusion to satisfy the local metabolic demand, to maintain homeostasis and achieve ‘milieu intérieur’. Cardiogenic shock is a state of pump failure which results in tissue hypoperfusion and its associated complications. There are a wide variety of causes which lead to this deranged physiology, and one such important and common scenario is the post-cardiotomy state which is encountered in cardiac surgical units. Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is an important modality of managing post-cardiotomy cardiogenic shock with variable outcomes which would otherwise be universally fatal. VA-ECMO is considered as a double-edged sword with the advantages of luxurious perfusion while providing an avenue for the failing heart to recover, but with the problems of anticoagulation, inflammatory and adverse systemic effects. Optimal outcomes after VA-ECMO are heavily reliant on a multitude of factors and require a multi-disciplinary team to handle them. This article aims to provide an insight into the pathophysiology of VA-ECMO, cannulation techniques, commonly encountered problems, monitoring, weaning strategies and ethical considerations along with a literature review of current evidence-based practices. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7647874/ doi: 10.1007/s12055-020-01051-7 id: cord-274101-vm9nh8lc author: Perez Espitia, Paula Judith title: Bioactive Peptides: Synthesis, Properties, and Applications in the Packaging and Preservation of Food date: 2012-02-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract: Bioactive peptides are protein fragments which have a positive impact on the functions and conditions of living beings. Peptides have shown several useful properties for human health, including antimicrobial, antifungal, antiviral, and antitumor activities. These compounds are produced by almost all species of life. However, they are produced in limited quantities in nature. As a result, researchers have tried to synthesize bioactive peptides to study their properties and applications in various areas. Among their applications in food preservation, peptides have been incorporated into packaging materials. This review begins with a brief description of the methods used for the synthesis, purification, and characterization of peptides. Also, the main bioproperties and mechanisms of action of peptides are discussed. Finally, some applications of peptides are presented, especially their use in active packaging, their effects on the polymeric matrix, and peptide migration. url: https://www.ncbi.nlm.nih.gov/pubmed/32368201/ doi: 10.1111/j.1541-4337.2011.00179.x id: cord-257754-pqxkyg8z author: Reggiori, Fulvio title: Membrane Origin for Autophagy date: 2006-07-21 words: 9205.0 sentences: 481.0 pages: flesch: 46.0 cache: ./cache/cord-257754-pqxkyg8z.txt txt: ./txt/cord-257754-pqxkyg8z.txt summary: In addition, a study analyzing conditional knock-out mice defective for autophagy has revealed that the mutant animal accumulates numerous ubiquitinated aggregates in the cytosol, suggesting that this covalent protein modification could serve to specifically target to autophagosomes large structures that have to be eliminated (Komatsu et al., 2005) . In contrast to mammalian cells where several isolation membranes can be simultaneously activated, a single perivacuolar site of organization for double-membrane vesicle formation (named the pre-autophagosomal structure, PAS) is observed in the yeast S. Because the three mammalian Atg8 homologs are diVerently expressed in various tissues (Tanida et al., 2004) , another intriguing option is that these proteins are involved in supplying the autophagosome with membranes derived from diVerent compartments depending on the cell type; for example, GATE-16 from the Golgi complex and GABARAP from the same organelle as well as the synaptic cisternae (Kittler et al., 2001; Kneussel et al., 2000; Sagiv et al., 2000) . abstract: Autophagy is a degradative transport route conserved among all eukaryotic organisms. During starvation, cytoplasmic components are randomly sequestered into large double‐membrane vesicles called autophagosomes and delivered into the lysosome/vacuole where they are destroyed. Cells are able to modulate autophagy in response to their needs, and under certain circumstances, cargoes, such as aberrant protein aggregates, organelles, and bacteria can be selectively and exclusively incorporated into autophagosomes. As a result, this pathway plays an active role in many physiological processes, and it is induced in numerous pathological situations because of its ability to rapidly eliminate unwanted structures. Despite the advances in understanding the functions of autophagy and the identification of several factors, named Atg proteins that mediate it, the mechanism that leads to autophagosome formation is still a mystery. A major challenge in unveiling this process arises from the fact that the origin and the transport mode of the lipids employed to compose these structures is unknown. This compendium will review and analyze the current data about the possible membrane source(s) with a particular emphasis on the yeast Saccharomyces cerevisiae, the leading model organism for the study of autophagosome biogenesis, and on mammalian cells. The information acquired investigating the pathogens that subvert autophagy in order to replicate in the host cells will also be discussed because it could provide important hints for solving this mystery. url: https://api.elsevier.com/content/article/pii/S0070215306740017 doi: 10.1016/s0070-2153(06)74001-7 id: cord-294842-aesiff1f author: Romero-Brey, Inés title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses date: 2014-07-22 words: 11038.0 sentences: 520.0 pages: flesch: 40.0 cache: ./cache/cord-294842-aesiff1f.txt txt: ./txt/cord-294842-aesiff1f.txt summary: Three-dimensional reconstructions of the WNV KUN replication sites revealed an intimate association of the rough ER (rER) with the bounding membrane of the VPs [20] (Figure 2B ), resembling the vesicles observed in DENV-infected cells. In cells infected with TBEV, one of the most important tick-transmitted viruses in Europe and Asia, virus particles and membrane-connected vesicles were also observed inside the ER [25] , similar to what was described for DENV and WNV KUN . Importantly, pulse-radiolabeling experiments localized sites of active RNA replication to the outer surface of single-membrane tubules [71] and isolation of the membranous replication factories and their subsequent visualization by EM revealed that they form rosette-like structures composed of virus-induced cytoplasmic vesicles [124] . Formation of plant RNA virus replication complexes on membranes: Role of an endoplasmic reticulum-targeted viral protein abstract: In this review, we summarize the current knowledge about the membranous replication factories of members of plus-strand (+) RNA viruses. We discuss primarily the architecture of these complex membrane rearrangements, because this topic emerged in the last few years as electron tomography has become more widely available. A general denominator is that two “morphotypes” of membrane alterations can be found that are exemplified by flaviviruses and hepaciviruses: membrane invaginations towards the lumen of the endoplasmatic reticulum (ER) and double membrane vesicles, representing extrusions also originating from the ER, respectively. We hypothesize that either morphotype might reflect common pathways and principles that are used by these viruses to form their membranous replication compartments. url: https://doi.org/10.3390/v6072826 doi: 10.3390/v6072826 id: cord-028738-ing07qma author: Roy, Nimisha title: Prototype of a Smart Microfluidic Platform for the Evaluation of SARS-Cov-2 Pathogenesis, Along with Estimation of the Effectiveness of Potential Drug Candidates and Antigen–Antibody Interactions in Convalescent Plasma Therapy date: 2020-07-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Originating in China during December 2019, the novel corona-virus, SARS-CoV-2, has created mayhem worldwide in a very short time. The outbreak has been so rapid and widespread that the only option to treat the patients was administering drugs already available in the market like chloroquine/hydroxychloroquine (an antimalarial drug) and remedesivir. A large number of patients have been cured but the attribution to survival by these drugs has been controversial. Till date, we do not have any specific drug or vaccine available for COVID-19 and the pandemic seems to be far from over. To handle the current challenges posed by the outbreak effectively, we need to employ innovative interdisciplinary approaches. Organ-on-chip (OOC), particularly lung-on-chip, is one such approach which combines the potential of microfluidics, cell culture and molecular biology into a single miniaturised platform. The device is realized to be capable of simulating in-vivo physiological responses of an organ. In the current study, an OOC, which is a multichannel 3D cell culture microfluidic device, is made via soft lithography technique, using polydimethylsiloxane-polymer and diverse polymeric porous/semipermeable membranes. Several polymer membranes i.e. PDMS, polyvinylidene fluoride (PVDF), nitrocellulose, polyester etc., integrated into the microdevices, were efficiently explored to realize their better cell-adhesion and viability property. We also propose for the application of a simple, smart and cost-effective lung-on-chip platform to study the SARS-CoV-2 pathogenesis in humans, drug toxicity testing and provide insights into antigen–antibody interactions. This platform will enable us to study multiple phenomena at a micro-level generating more reliable data and a better understanding of the underlying mechanisms of SARS-CoV-2 infection and pathogenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7340772/ doi: 10.1007/s41403-020-00148-0 id: cord-000884-zq8kqf6h author: Shen, Hsin-Hui title: Reconstitution of Membrane Proteins into Model Membranes: Seeking Better Ways to Retain Protein Activities date: 2013-01-14 words: 6861.0 sentences: 355.0 pages: flesch: 39.0 cache: ./cache/cord-000884-zq8kqf6h.txt txt: ./txt/cord-000884-zq8kqf6h.txt summary: This review will discuss the reconstitution of membrane protein activities in four different types of model membrane—monolayers, supported lipid bilayers, liposomes and nanodiscs, comparing their advantages in membrane protein reconstitution. To simplify cell membrane systems, model membranes such as monolayers, bilayers, liposomes and nanodiscs have been developed, enabling detailed investigation of membrane protein structure in lipid membranes. There are a number of approaches used to create a model membrane in order to mimic properties of the native cell membrane, and we will review these various approaches for reconstituting membrane proteins into different types of model membrane-monolayers [5] , supported planar lipid bilayer [6] and liposomes [7] as shown in Figure 1A -C. By using this approach, it appears that both PLA2 and PLC are active at the monolayer model membrane, indicating that the kinetics of phospholipid hydrolysis at the air-water interface can be monitored by biophysical characterization techniques in situ such as PM-IRRAS and infrared reflection adsorption spectroscopy [22] . abstract: The function of any given biological membrane is determined largely by the specific set of integral membrane proteins embedded in it, and the peripheral membrane proteins attached to the membrane surface. The activity of these proteins, in turn, can be modulated by the phospholipid composition of the membrane. The reconstitution of membrane proteins into a model membrane allows investigation of individual features and activities of a given cell membrane component. However, the activity of membrane proteins is often difficult to sustain following reconstitution, since the composition of the model phospholipid bilayer differs from that of the native cell membrane. This review will discuss the reconstitution of membrane protein activities in four different types of model membrane—monolayers, supported lipid bilayers, liposomes and nanodiscs, comparing their advantages in membrane protein reconstitution. Variation in the surrounding model environments for these four different types of membrane layer can affect the three-dimensional structure of reconstituted proteins and may possibly lead to loss of the proteins activity. We also discuss examples where the same membrane proteins have been successfully reconstituted into two or more model membrane systems with comparison of the observed activity in each system. Understanding of the behavioral changes for proteins in model membrane systems after membrane reconstitution is often a prerequisite to protein research. It is essential to find better solutions for retaining membrane protein activities for measurement and characterization in vitro. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565336/ doi: 10.3390/ijms14011589 id: cord-103739-mmkrwj8t author: Snijder, Eric J. title: A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis date: 2020-03-24 words: 3808.0 sentences: 223.0 pages: flesch: 48.0 cache: ./cache/cord-103739-mmkrwj8t.txt txt: ./txt/cord-103739-mmkrwj8t.txt summary: Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). 106 double-membrane spherules (DMSs) 107 We first set out to analyse the ultrastructure of MERS-CoV-infected Huh7 cells under sample 108 preparation conditions favourable for autoradiography (see Materials and Methods) (Fig 1, S1 109 Video). Association of polioviral proteins of the P2 89 genomic region with the viral replication complex and virus-induced membrane synthesis as 90 visualized by electron microscopic immunocytochemistry and autoradiography abstract: Zoonotic coronavirus (CoV) infections, like those responsible for the current SARS-CoV-2 epidemic, cause grave international public health concern. In infected cells, the CoV RNA-synthesizing machinery associates with modified endoplasmic reticulum membranes that are transformed into the viral replication organelle (RO). While double-membrane vesicles (DMVs) appear to be a pan-coronavirus RO element, studies to date describe an assortment of additional coronavirus-induced membrane structures. Despite much speculation, it remains unclear which RO element(s) accommodate viral RNA synthesis. Here we provide detailed 2D and 3D analyses of CoV ROs and show that diverse CoVs essentially induce the same membrane modifications, including the small open double-membrane spherules (DMSs) previously thought to be restricted to gamma- and delta-CoV infections and proposed as sites of replication. Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. RNA synthesis could not be linked to DMSs or any other cellular or virus-induced structure. Our results provide a unifying model of the CoV RO and clearly establish DMVs as the central hub for viral RNA synthesis and a potential drug target in coronavirus infection. url: https://doi.org/10.1101/2020.03.24.005298 doi: 10.1101/2020.03.24.005298 id: cord-300429-b0zev8zb author: Sobocińska, Justyna title: Protein Palmitoylation and Its Role in Bacterial and Viral Infections date: 2018-01-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: S-palmitoylation is a reversible, enzymatic posttranslational modification of proteins in which palmitoyl chain is attached to a cysteine residue via a thioester linkage. S-palmitoylation determines the functioning of proteins by affecting their association with membranes, compartmentalization in membrane domains, trafficking, and stability. In this review, we focus on S-palmitoylation of proteins, which are crucial for the interactions of pathogenic bacteria and viruses with the host. We discuss the role of palmitoylated proteins in the invasion of host cells by bacteria and viruses, and those involved in the host responses to the infection. We highlight recent data on protein S-palmitoylation in pathogens and their hosts obtained owing to the development of methods based on click chemistry and acyl-biotin exchange allowing proteomic analysis of protein lipidation. The role of the palmitoyl moiety present in bacterial lipopolysaccharide and lipoproteins, contributing to infectivity and affecting recognition of bacteria by innate immune receptors, is also discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/29403483/ doi: 10.3389/fimmu.2017.02003 id: cord-338827-1moy43hr author: Stillwell, William title: Membrane Transport date: 2016-07-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Life depends on a membrane's ability to precisely control the level of solutes in the aqueous compartments, inside and outside, bathing the membrane. The membrane determines what solutes enter and leave a cell. Transmembrane transport is controlled by complex interactions between membrane lipids, proteins, and carbohydrates. How the membrane accomplishes these tasks is the topic of this chapter. url: https://www.sciencedirect.com/science/article/pii/B9780444637727000191 doi: 10.1016/b978-0-444-63772-7.00019-1 id: cord-035248-m5517zgn author: Stokes, John W. title: Bleeding, Thromboembolism, and Clinical Outcomes in Venovenous Extracorporeal Membrane Oxygenation date: 2020-11-09 words: 2386.0 sentences: 141.0 pages: flesch: 28.0 cache: ./cache/cord-035248-m5517zgn.txt txt: ./txt/cord-035248-m5517zgn.txt summary: Our objective was to examine the relative frequencies of bleeding and thromboembolic events and their associations with survival among a cohort of consecutive patients receiving venovenous extracorporeal membrane oxygenation. Our objective was to examine the relative frequencies of bleeding and thromboembolic events and their associations with survival among a cohort of consecutive patients receiving venovenous extracorporeal membrane oxygenation. Conclusions: In this cohort of patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation, bleeding occurred more frequently than thromboembolism and was associated with worse survival. Conclusions: In this cohort of patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation, bleeding occurred more frequently than thromboembolism and was associated with worse survival. We collected the following data from the electronic health record: patient characteristics in the 24 hours prior to ECMO initiation; bleeding and thromboembolic events during venovenous ECMO as previously defined (5); and clinical outcomes, including in-hospital survival, ECMO duration, and hospital length of stay. abstract: OBJECTIVES: Bleeding and thromboembolism are common during venovenous extracorporeal membrane oxygenation. The relative frequency of these complications and their impact on clinical outcomes have not been described, and no randomized trials exist to guide anticoagulation strategies in extracorporeal membrane oxygenation. Our objective was to examine the relative frequencies of bleeding and thromboembolic events and their associations with survival among a cohort of consecutive patients receiving venovenous extracorporeal membrane oxygenation. DESIGN: Retrospective cohort study. SETTING: A single academic medical center. PATIENTS: Adult patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation. Eligibility criteria for this analysis were selected to emulate the population that would be recruited for a randomized trial of anticoagulation strategies during venovenous extracorporeal membrane oxygenation. Patients were excluded if they had active bleeding or thromboembolism prior to extracorporeal membrane oxygenation initiation, a history of trauma or surgery in the 7 days prior to extracorporeal membrane oxygenation initiation, an arterial extracorporeal membrane oxygenation cannula, or if they received greater than 48 hours of extracorporeal membrane oxygenation support at another institution INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Outcomes included bleeding and thromboembolic events, duration of extracorporeal membrane oxygenation support, hospital length of stay, and in-hospital survival among 55 patients receiving venovenous extracorporeal membrane oxygenation. Bleeding events occurred in 25 patients (45.5%), and thromboembolism occurred in eight patients (14.5%). Bleeding events were associated with longer duration of extracorporeal membrane oxygenation support (p = 0.007) and worse in-hospital survival (p = 0.02). Thromboembolic events did not appear to be associated with clinical outcomes. CONCLUSIONS: In this cohort of patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation, bleeding occurred more frequently than thromboembolism and was associated with worse survival. These results highlight the need for randomized trials to evaluate the safety and efficacy of continuous IV anticoagulation among patients receiving venovenous extracorporeal membrane oxygenation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655084/ doi: 10.1097/cce.0000000000000267 id: cord-016938-pk76snuy author: Suh, Hwal (Matthew) title: Collagen Fabrication for the Cell-based Implants in Regenerative Medicine date: 2008 words: 6409.0 sentences: 292.0 pages: flesch: 37.0 cache: ./cache/cord-016938-pk76snuy.txt txt: ./txt/cord-016938-pk76snuy.txt summary: As atelocollagen has no telopeptides that integrate with other atelocollagen molecules, basic technology to produce intramolecular and intermolecular bonds for construction of the extracellular matrix with adequate mechanical properties required by tissue where the artificial cell-based implant is delivered is the recrosslinking method using chemical reagents or physical dynamics. Collagen can be fabricated into various forms of gel, fiber, membrane with or without pores, and it can even be grafted onto the non-viable metal, ceramic and synthetic biomaterials to introduce biological layer on surface. To produce an artificial skin, autologous dermal fibroblasts of rat were seeded into the EDC crosslinked porous collagen-laminin membrane and cultured in minimum essential medium (MEM) for 3 days to provide the cell-niche adaptation period. Although collagen based gel is favorable to fabricate cell conductive substitute, weak mechanical property is a barrier for application in the physiological stress bearing tissues, and, to resolve this problem, hybridization of collagen with polymeric biomaterials has been suggested. abstract: Though transplantation of cells, tissue or organ has been regarded as an ideal approach, scarcity of donor is a practical barrier in clinics. Current progresses in cell engineering has opened a new era, providing tools for host-regeneration by implanting manipulated cells in forms of cell therapy, which includes delivery of single cells or multicellular structural support of hybridized cells, as a representative individualized treatment method. This chapter mainly concerns on the cellbased implant made of cells and collagen, the main structural protein in extracellular matrix in mammalian tissue, as it has been regarded as a promising method for manufacturing a biologically mimicked artificial tissues. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121374/ doi: 10.1007/978-3-540-75409-1_8 id: cord-330110-pamxy4av author: Teissier, Elodie title: Mechanism of Inhibition of Enveloped Virus Membrane Fusion by the Antiviral Drug Arbidol date: 2011-01-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The broad-spectrum antiviral arbidol (Arb) inhibits cell entry of enveloped viruses by blocking viral fusion with host cell membrane. To better understand Arb mechanism of action, we investigated its interactions with phospholipids and membrane peptides. We demonstrate that Arb associates with phospholipids in the micromolar range. NMR reveals that Arb interacts with the polar head-group of phospholipid at the membrane interface. Fluorescence studies of interactions between Arb and either tryptophan derivatives or membrane peptides reconstituted into liposomes show that Arb interacts with tryptophan in the micromolar range. Interestingly, apparent binding affinities between lipids and tryptophan residues are comparable with those of Arb IC50 of the hepatitis C virus (HCV) membrane fusion. Since tryptophan residues of membrane proteins are known to bind preferentially at the membrane interface, these data suggest that Arb could increase the strength of virus glycoprotein's interactions with the membrane, due to a dual binding mode involving aromatic residues and phospholipids. The resulting complexation would inhibit the expected viral glycoprotein conformational changes required during the fusion process. Our findings pave the way towards the design of new drugs exhibiting Arb-like interfacial membrane binding properties to inhibit early steps of virus entry, i.e., attractive targets to combat viral infection. url: https://doi.org/10.1371/journal.pone.0015874 doi: 10.1371/journal.pone.0015874 id: cord-336929-2rnkotqy author: Vieira, Flávia Sarmento title: Host‐cell lipid rafts: a safe door for micro‐organisms? date: 2012-01-03 words: 9925.0 sentences: 494.0 pages: flesch: 41.0 cache: ./cache/cord-336929-2rnkotqy.txt txt: ./txt/cord-336929-2rnkotqy.txt summary: In addition to the lipid components, a variety of cell receptors and signalling proteins are known to be associated with membrane rafts. Many animal viruses exploit the endocytic machinery of their host cell for infection, and lipid rafts are often a site for entry, assembly and budding of microbial pathogens, as confirmed by biochemical approaches and microscopy evidence (Kovbasnjuk et al., 2001; Suomalainen, 2002; Lu et al., 2008) . Interestingly, it had already been demonstrated that Brucella abortus infection is related with PrP C (cellular PrP), one of the lipid raft-associated molecules on the plasma membrane of different cell types. In the macrophage-like cell line RAW 264.7, for example, LPS stimulation induces translocation of CD14, ERK-2 (extracellular-signalregulated kinase 2) and p38 to lipid rafts, but other proteins also involved in the LPS signalling response do not migrate within these microdomains (Triantafilou et al., 2007; Olsson and Sundler, 2006) . abstract: The lipid raft hypothesis proposed that these microdomains are small (10–200 nM), highly dynamic and enriched in cholesterol, glycosphingolipids and signalling phospholipids, which compartmentalize cellular processes. These membrane regions play crucial roles in signal transduction, phagocytosis and secretion, as well as pathogen adhesion/interaction. Throughout evolution, many pathogens have developed mechanisms to escape from the host immune system, some of which are based on the host membrane microdomain machinery. Thus lipid rafts might be exploited by pathogens as signalling and entry platforms. In this review, we summarize the role of lipid rafts as players in the overall invasion process used by different pathogens to escape from the host immune system. url: https://doi.org/10.1042/bc20090138 doi: 10.1042/bc20090138 id: cord-030961-5gzc7193 author: Wang, Jiajun title: Adhesive contact between cylindrical (Ebola) and spherical (SARS-CoV-2) viral particles and a cell membrane date: 2020-08-28 words: 4335.0 sentences: 260.0 pages: flesch: 55.0 cache: ./cache/cord-030961-5gzc7193.txt txt: ./txt/cord-030961-5gzc7193.txt summary: In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. In this work, we create a continuum model for the small-deflection adhesive contact mechanics of virus particle attachment onto the host cell membrane in terms of the principal biophysical properties of the virus, membrane, and their interaction. These results also help to retrieve conditions for lack of adhesion, pull-off force, and contact area between the virus particle and cell membrane. We now describe in outline the continuum models for adhesive contact between the virus and cell membrane, driven by adhesion and external displacement or force, and resisted by tension and elastic bending. In our models, the parameters that govern the adhesive contact mechanics are (more in Table 1 ) bending rigid κ, tension σ, adhesion free energy per receptor β, binding receptor density ρ, and the radius of the virus, R. abstract: A critical event during the process of cell infection by a viral particle is attachment, which is driven by adhesive interactions and resisted by bending and tension. The biophysics of this process has been studied extensively, but the additional role of externally applied force or displacement has generally been neglected. In this work, we study the adhesive force-displacement response of viral particles against a cell membrane. We have built two models: one in which the viral particle is cylindrical (say, representative of a filamentous virus such as Ebola) and another in which it is spherical (such as SARS-CoV-2 and Zika). Our interest is in initial adhesion, in which case deformations are small, and the mathematical model for the system can be simplified considerably. The parameters that characterize the process combine into two dimensionless groups that represent normalized membrane bending stiffness and tension. In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. (The zero external force contact width and pull-off force are both zero.) For large values of normalized membrane tension, the adhesion between virus and cell membrane is weak but stable. (The contact width at zero external force has a small value.) Our results for pull-off force and zero force contact width help to quantify conditions that could aid the development of therapies based on denying the virus entry into the cell by blocking its initial adhesion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42558-020-00026-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7453191/ doi: 10.1007/s42558-020-00026-3 id: cord-313599-5j19stye author: Wang, Xianfeng title: Electro-spinning/netting: A strategy for the fabrication of three-dimensional polymer nano-fiber/nets date: 2013-05-26 words: 25077.0 sentences: 1216.0 pages: flesch: 45.0 cache: ./cache/cord-313599-5j19stye.txt txt: ./txt/cord-313599-5j19stye.txt summary: NFN possess the general properties and functions of conventional electrospun nanofibers and other 1D nanostructures fabricated using different techniques, as well as the impressive feature characters (e.g. extremely small diameter, high porosity, Steiner tree network geometry, controllable coverage rate) that distinguish themselves from their counterparts, the properties donated by the polymer phase, and the 2D net-like geometry. Therefore, strongly interconnected thin MPEG spider-web-like nano-nets with thick PA-6 nanofibers are responsible to increase mechanical strength and hydrophilic nature of PA-6 fibrous membranes, which make composite MPEG/PA-6 NFN membranes great potential in air filtration and different biomedical application. More recently, our group has presented continuous efforts toward the aim of generating PANI-based nanostructured materials and for the first time fabricated composite PANI/PA-6 NFN membranes (Fig. 20a) , which were used as a platform for efficient sensing reaction by providing high specific surface area and porosity. abstract: Since 2006, a rapid development has been achieved in a subject area, so called electro-spinning/netting (ESN), which comprises the conventional electrospinning process and a unique electro-netting process. Electro-netting overcomes the bottleneck problem of electrospinning technique and provides a versatile method for generating spider-web-like nano-nets with ultrafine fiber diameter less than 20 nm. Nano-nets, supported by the conventional electrospun nanofibers in the nano-fiber/nets (NFN) membranes, exhibit numerious attractive characteristics such as extremely small diameter, high porosity, and Steiner tree network geometry, which make NFN membranes optimal candidates for many significant applications. The progress made during the last few years in the field of ESN is highlighted in this review, with particular emphasis on results obtained in the author’s research units. After a brief description of the development of the electrospinning and ESN techniques, several fundamental properties of NFN nanomaterials are addressed. Subsequently, the used polymers and the state-of-the-art strategies for the controllable fabrication of NFN membranes are highlighted in terms of the ESN process. Additionally, we highlight some potential applications associated with the remarkable features of NFN nanostructure. Our discussion is concluded with some personal perspectives on the future development in which this wonderful technique could be pursued. url: https://www.ncbi.nlm.nih.gov/pubmed/32287484/ doi: 10.1016/j.pmatsci.2013.05.001 id: cord-015866-65zrbo1w author: Wardhan, Rashmi title: Membrane Transport date: 2018-01-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Every living cell has to exchange molecules across the membrane for cellular functions. The hydrophobic or lipophilic molecules do not require energy for crossing the membrane. They can diffuse freely from higher to lower concentration till equilibrium is established. This process is called passive transport or diffusion. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119958/ doi: 10.1007/978-981-10-7101-0_6 id: cord-325915-dw989txm author: Wolf, Michael W title: Downstream processing of cell culture-derived virus particles date: 2014-01-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Manufacturing of cell culture-derived virus particles for vaccination and gene therapy is a rapidly growing field in the biopharmaceutical industry. The process involves a number of complex tasks and unit operations ranging from selection of host cells and virus strains for the cultivation in bioreactors to the purification and formulation of the final product. For the majority of cell culture-derived products, efforts focused on maximization of bioreactor yields, whereas design and optimization of downstream processes were often neglected. Owing to this biased focus, downstream procedures today often constitute a bottleneck in various manufacturing processes and account for the majority of the overall production costs. For efficient production methods, particularly in sight of constantly increasing economic pressure within human healthcare systems, highly productive downstream schemes have to be developed. Here, we discuss unit operations and downstream trains to purify virus particles for use as vaccines and vectors for gene therapy. url: https://doi.org/10.1586/erv.11.111 doi: 10.1586/erv.11.111 id: cord-323319-u5hfkjv8 author: Xu, Mengchang title: Analysis of the biodegradation performance and biofouling in a halophilic MBBR-MBR to improve the treatment of disinfected saline wastewater date: 2020-10-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Disinfectant-containing wastewaters have been generated from many places, including marine industries. The synthetic NaClO-containing wastewaters have been effectively treated in a saline MBBR-MBR (moving bed biofilm reactor & membrane bioreactor) system containing marine microorganisms. A low concentration of NaCl (below 100 mg/L) is not enough to kill the microorganisms, but can affect their bioactivity and induce membrane biofouling. A linear relationship has been obtained for the half-life of membrane biofouling as a function of the NaClO concentration (10-100 mg/L): [half-life] = 25－0.12×[NaClO concentration]. The COD and NH(3)-N removals are the highest at a salinity of 30 g/L for the marine bioreactors. The behaviour of the typical biofoulants, measured real-timely by fluorescence spectroscopy, can indicate the levels of membrane biofouling and microbial activity, responding to the NaClO and NaCl influences. Based on the behavior of biofoulants, this work has also proposed a novel strategy of biofoulants monitoring for membrane antifouling, where antifouling responses can be carried out when the concentration of biofoulants significantly increases. url: https://doi.org/10.1016/j.chemosphere.2020.128716 doi: 10.1016/j.chemosphere.2020.128716 id: cord-346446-i7gpxcyo author: Zhang, Jianguo title: Biosynthetic Polymalic Acid as a Delivery Nanoplatform for Translational Cancer Medicine date: 2020-10-22 words: 6094.0 sentences: 281.0 pages: flesch: 35.0 cache: ./cache/cord-346446-i7gpxcyo.txt txt: ./txt/cord-346446-i7gpxcyo.txt summary: pullulan, the addition of exogenous carbonates augments CO 2 fixation and pyruvate carboxylation into oxaloacetate by pyruvate carboxylase in the cytoplasm, abolishing the intramitochondrial pathways for L-malate production and ensuing PMLA synthesis ( Figure 2 ) [23, 30] . At pH 7.4, the terminal α-carboxylic acid in the side chain is deprotonated and ionized; this would be repelled from the cell membrane, but, because of strong hydrophobic interactions, indole in the side chain can attract and intercalate into phospholipids, generating PMLA tritryptophan-lipid complexes and releasing binding energy to stabilize the structure. To increase the interaction between the biopolymer and the plasma membrane, methylation of carboxylic acid groups with different levels of diazomethane was used to generate a PMLA-Me x H 100−x copolymer (where x is the percentage of methyl units) [77, 78] . Analysis of the L-malate biosynthesis pathway involved in poly(beta-L-malic acid) production in Aureobasidium melanogenum GXZ-6 by addition of metabolic intermediates and inhibitors abstract: Poly(β-L-malic acid) (PMLA) is a natural polyester produced by numerous microorganisms. Regarding its biosynthetic machinery, a nonribosomal peptide synthetase (NRPS) is proposed to direct polymerization of L-malic acid in vivo. Chemically versatile and biologically compatible, PMLA can be used as an ideal carrier for several molecules, including nucleotides, proteins, chemotherapeutic drugs, and imaging agents, and can deliver multimodal theranostics through biological barriers such as the blood–brain barrier. We focus on PMLA biosynthesis in microorganisms, summarize the physicochemical and physiochemical characteristics of PMLA as a naturally derived polymeric delivery platform at nanoscale, and highlight the attachment of functional groups to enhance cancer detection and treatment. url: https://www.sciencedirect.com/science/article/pii/S0968000420302449 doi: 10.1016/j.tibs.2020.09.008 id: cord-289541-y7lewk1t author: Zhang, Li-Zhi title: Fabrication of a lithium chloride solution based composite supported liquid membrane and its moisture permeation analysis date: 2006-05-01 words: 4040.0 sentences: 292.0 pages: flesch: 60.0 cache: ./cache/cord-289541-y7lewk1t.txt txt: ./txt/cord-289541-y7lewk1t.txt summary: The membrane is composed of three layers: two hydrophobic protective layers and a sandwiched hydrophilic support layer in which LiCl solution is immobilized to facilitate water vapor transfer. Further, the supported liquid layer only accounts for 12% of the total moisture transfer resistance in the cell, indicating that there is much potential for further performance improvement. The core material of an MTHR ventilator are vapor-permeable membranes, therefore both heat and moisture are transferred between these two air streams when they flow through the unit. However, moisture diffusion coefficients in such polymer membranes are usually very low, in the order of 10 −12 to 10 −13 m 2 s −1 [11, 18] , while MTHR ventilators only have limited transmembrane vapor partial pressure difference, consequently performances are quite limited currently. To improve the performances of MTHR ventilators, in this study, a novel membrane, a composite SLM, which employs LiCl liquid solution immobilized in a porous support membrane to facilitate the transport of moisture, is prepared. abstract: A novel composite supported liquid membrane has been prepared for ventilation air moisture recovery. The membrane is composed of three layers: two hydrophobic protective layers and a sandwiched hydrophilic support layer in which LiCl solution is immobilized to facilitate water vapor transfer. A test is conducted to measure the moisture permeation rate through the composite membrane. Various resistances in the cell and in the composite membrane are clarified. Linear equilibrium relations between humidity, temperature, and LiCl concentration in the liquid solution layer are obtained to aid in the model set-up. It has been found that the mean moisture permeation rate through the composite membrane is around 1.14 × 10(−4) kg m(−2) s(−1), almost two times higher than that through a solid hydrophilic cellulose acetate membrane with comparative thickness. Further, the supported liquid layer only accounts for 12% of the total moisture transfer resistance in the cell, indicating that there is much potential for further performance improvement. url: https://doi.org/10.1016/j.memsci.2005.09.035 doi: 10.1016/j.memsci.2005.09.035 id: cord-314402-kjzkk51t author: Zou, Guijin title: EML webinar overview: Simulation-assisted discovery of membrane targeting nanomedicine date: 2020-06-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The COVID-19 pandemic has brought infectious diseases again to the forefront of global public health concerns. In this EML webinar (Gao, 2020), we discuss some recent work on simulation-assisted discovery of membrane targeting nanomedicine to counter increasing antimicrobial resistance and potential application of similar ideas to the current pandemic. A recent report led by the world health organization (WHO) warned that 10 million people worldwide could die of bacterial infections each year by 2050. To avert the crisis, membrane targeting antibiotics are drawing increasing attention due to their intrinsic advantage of low resistance development. In collaboration with a number of experimental groups, we show examples of simulation-assisted discovery of molecular agents capable of selectively penetrating and aggregating in bacterial lipid membranes, causing membrane permeability/rupture. Through systematic all-atom molecular dynamics simulations and free energy analysis, we demonstrate that the membrane activity of the molecular agents correlates with their ability to enter, perturb and permeabilize the lipid bilayers. Further study on different cell membranes demonstrates that the selectivity results from the presence of cholesterol in mammalian but not in bacterial membranes, as the cholesterol can condense the hydrophobic region of membrane, preventing the penetration of the molecular agents. Following the molecular penetration, we establish a continuum theory and derive the energetic driving force for the domain aggregation and pore growth on lipid membrane. We show that the energy barrier to membrane pore formation can be significantly lowered through molecular aggregation on a large domain with intrinsic curvature and a sharp interface. The theory is consistent with experimental observations and validated with coarse-grained molecular dynamics simulations of molecular domain aggregation leading to pore formation in a lipid membrane. The mechanistic modelling and simulation provide some fundamental principles on how molecular antimicrobials interact with bacterial membranes and damage them through domain aggregation and pore formation. For treating viral infections and cancer therapy, we discuss potential size- and lipid-type-based selectivity principles for developing membrane active nanomedicine. These studies suggest a general simulation-assisted platform to accelerate discovery and innovation in nanomedicine against infectious diseases. EML Webinar speakers are updated at https://imechanica.org/node/24132 url: https://www.ncbi.nlm.nih.gov/pubmed/32537481/ doi: 10.1016/j.eml.2020.100817 id: cord-284690-ogu1gmcb author: da Cunha, Nicolau B. title: The next generation of antimicrobial peptides (AMPs) as molecular therapeutic tools for the treatment of diseases with social and economic impacts date: 2016-11-23 words: 9481.0 sentences: 450.0 pages: flesch: 35.0 cache: ./cache/cord-284690-ogu1gmcb.txt txt: ./txt/cord-284690-ogu1gmcb.txt summary: The use of viral vectors based on the tobacco mosaic virus (TMV) and potato virus X (PVX) for cloning and massively expressing AMP genes in Nicotiana benthamiana appears to be an interesting new approach to considerably enhance recombinant peptide production before structural and functional characterization. However, frequent gene silencing at the transcriptional level and instability of genes cloned in vectors for stable or transient expression remain major challenges limiting the efficient production of AMPs. Another persistent issue is the poor quality of the peptides endogenously synthesized in bacteria, yeast, and plants, particularly resulting from undesirable post-translational modifications [2, 33] . Some drawbacks presented by plant expression systems are solved by the CRISPR system, a revolutionary genome-editing technology that presents myriad possibilities for genetic manipulation at the genomic level and provides unprecedented tools (CRISPRi and CRISPRa) to precisely control gene expression and the structural modification of AMPs. Despite its current minor limitations (e.g. off-target effects), CRISPR could have a key role in the future development of clinical drugs as biotechnological antiinfective agents, including the rational biosynthesis of next-generation antimicrobials. abstract: Anti-infective drugs have had a key role in the contemporary world, contributing to dramatically decrease mortality rates caused by infectious diseases worldwide. Antimicrobial peptides (AMPs) are multifunctional effectors of the innate immune system of mucosal surfaces and present antimicrobial activity against a range of pathogenic viruses, bacteria, and fungi. However, the discovery and development of new antibacterial drugs is a crucial step to overcome the great challenge posed by the emergence of antibiotic resistance. In this review, we outline recent advances in the development of novel AMPs with improved antimicrobial activities that were achieved through characteristic structural design. In addition, we describe recent progress made to overcome some of the major limitations that have hindered peptide biosynthesis. url: https://www.sciencedirect.com/science/article/pii/S1359644616304135 doi: 10.1016/j.drudis.2016.10.017 id: cord-001835-0s7ok4uw author: nan title: Abstracts of the 29th Annual Symposium of The Protein Society date: 2015-10-01 words: 138514.0 sentences: 6150.0 pages: flesch: 40.0 cache: ./cache/cord-001835-0s7ok4uw.txt txt: ./txt/cord-001835-0s7ok4uw.txt summary: Altogether, these results indicate that, although PHDs might be more selective for HIF as a substrate as it was initially thought, the enzymatic activity of the prolyl hydroxylases is possibly influenced by a number of other proteins that can directly bind to PHDs. Non-natural aminoacids via the MIO-enzyme toolkit Alina Filip 1 , Judith H Bartha-V ari 1 , Gergely B an oczy 2 , L aszl o Poppe 2 , Csaba Paizs 1 , Florin-Dan Irimie 1 1 Biocatalysis and Biotransformation Research Group, Department of Chemistry, UBB, 2 Department of Organic Chemistry and Technology An attractive enzymatic route to enantiomerically pure to the highly valuable a-or b-aromatic amino acids involves the use of aromatic ammonia lyases (ALs) and aminomutases (AMs). Continuing our studies of the effect of like-charged residues on protein-folding mechanisms, in this work, we investigated, by means of NMR spectroscopy and molecular-dynamics simulations, two short fragments of the human Pin1 WW domain [hPin1(14-24); hPin1(15-23)] and one single point mutation system derived from hPin1(14-24) in which the original charged residues were replaced with non-polar alanine residues. abstract: nan url: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.2823 doi: 10.1002/pro.2823 id: cord-004534-jqm1hxps author: nan title: Abstract date: 2009-06-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079852/ doi: 10.1007/s00249-009-0478-1 id: cord-004584-bcw90f5b author: nan title: Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date: 2011-08-06 words: 106850.0 sentences: 5038.0 pages: flesch: 41.0 cache: ./cache/cord-004584-bcw90f5b.txt txt: ./txt/cord-004584-bcw90f5b.txt summary: Our goals are two-fold: (1) to monitor conformational changes in each domain upon its binding to specific ligands and then to correlate the observed changes with structural differences between the CRDs and (2) to investigate the interaction between the CRDs and lipid model membranes. Cholesterol-assisted lipid and protein interactions such as the integration into lipid nanodomains are considered to play a functional part in a whole range of membrane-associated processes, but their direct and non-invasive observation in living cells is impeded by the resolution limit of [200nm of a conventional far-field optical microscope. Therefore, to investigate the dynamic and complex membrane lateral organization in living cells, we have developed an original approach based on molecule diffusion measurements performed by fluorescence correlation spectroscopy at different spatial scales (spot variable FCS, svFCS) (1). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080017/ doi: 10.1007/s00249-011-0734-z id: cord-014685-ihh30q6f author: nan title: Posters P788 - P999 date: 2005-09-21 words: 38354.0 sentences: 1784.0 pages: flesch: 45.0 cache: ./cache/cord-014685-ihh30q6f.txt txt: ./txt/cord-014685-ihh30q6f.txt summary: This study has attempted to analyse the structural properties of membrane peptides and proteins through the use of model systems that have been designed to mimic their natural counterparts: Podlubnaya 2 1 Institute of Theoretical and Experimental Biophysics RAS, 2 Pushchino State University Amyloid brils are formed by proteins or their peptides in the result of a conformational transition from alpha helix into beta-sheet structure. Analysis of the results of such studies indicate that folding of SNase fragments is dominated by developing the local and non-local nucleation sites from native-like secondary structures and by intensifying the longrange interactions of residues at nucleation sites with residues further removed in sequence. The results show that at different pH values the aggregation processes of both proteins follow different pathways determined by the variations in the native structure and by the details of the involved conformational changes. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080055/ doi: 10.1007/s00249-005-0504-x id: cord-022504-tk7v4hoj author: nan title: Environmental and safety issues with nanoparticles date: 2012-03-16 words: 14097.0 sentences: 709.0 pages: flesch: 52.0 cache: ./cache/cord-022504-tk7v4hoj.txt txt: ./txt/cord-022504-tk7v4hoj.txt summary: During the process, large volumes of ultrapure water are consumed to clean the surface of the wafer, which generates large quantity of CMP wastewater typically having high solid content resulting from slurry abrasive particles of SiO 2 , Al 2 O 3 , or CeO 2 , depending on the nature of the CMP application. 7.2.6.2 Industrial processes with cleanrooms Cleanrooms and associated controlled environments (e.g., in the case of an ISO Class 3 cleanroom, the maximum permissible airborne particle concentration is less than 10 3 particles/m 3 for particles with the size of 0.1 m or larger, while the airborne particle concentration in ordinary indoor environments is on the order of 10 9 particles/m 3 or higher) are usually adopted to avoid particle contamination in industrial processes where precision products such as engineered nanoparticles, semiconductors, and other electronic or optical devices are fabricated because the deposition of particles onto product surfaces causes their yield reduction and quality deterioration. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158170/ doi: 10.1016/b978-0-444-56336-1.50007-2 id: cord-104279-choywmwd author: nan title: Membrane protein sorting in the yeast secretory pathway: evidence that the vacuole may be the default compartment date: 1992-10-01 words: 9856.0 sentences: 411.0 pages: flesch: 52.0 cache: ./cache/cord-104279-choywmwd.txt txt: ./txt/cord-104279-choywmwd.txt summary: First, to determine if the lumenal domain was sorted to the vacuole when expressed in the secretory pathway as a soluble protein, a gene fusion was used to create the protein ctFss-B, consisting of the NH2-terminal ER-targeting signal sequence of prepro-t~ factor fused to the lumenal domain of DPAP B at residue 49 ( Fig. 1 B) . To ad-dress the possibility that the mutant constructs analyzed in this study were mislocalized to the plasma membrane followed by rapid endocytic uptake to the vacuole, indirect immunofluorescence experiments were performed on BB-Inv, B-A-B, A20-BB, and/x22-AA-B expressed in a secl strain at 34~ As a positive control for accumulation in secretory vesicles, the localization of the fusion protein Fusl-LacZp was analyzed (Trueheart et al., 1987) . abstract: The targeting signals of two yeast integral membrane dipeptidyl aminopeptidases (DPAPs), DPAP B and DPAP A, which reside in the vacuole and the Golgi apparatus, respectively, were analyzed. No single domain of DPAP B is required for delivery to the vacuolar membrane, because removal or replacement of either the cytoplasmic, transmembrane, or lumenal domain did not affect the protein's transport to the vacuole. DPAP A was localized by indirect immunofluorescence to non-vacuolar, punctate structures characteristic of the yeast Golgi apparatus. The 118-amino acid cytoplasmic domain of DPAP A is sufficient for retention of the protein in these structures, since replacement of the cytoplasmic domain of DPAP B with that of DPAP A resulted in an immunolocalization pattern indistinguishable from that of wild type DPAP A. Overproduction of DPAP A resulted in its mislocalization to the vacuole, because cells expressing high levels of DPAP A exhibited vacuolar as well as Golgi staining. Deletion of 22 residues of the DPAP A cytoplasmic domain resulted in mislocalization of the mutant protein to the vacuole. Thus, the cytoplasmic domain of DPAP A is both necessary and sufficient for Golgi retention, and removal of the retention signal, or saturation of the retention apparatus by overproducing DPAP A, resulted in transport to the vacuole. Like wild type DPAP B, the delivery of mutant membrane proteins to the vacuole was unaffected in the secretory vesicle-blocked sec1 mutant; thus, transport to the vacuole was not via the plasma membrane followed by endocytosis. These data are consistent with a model in which membrane proteins are delivered to the vacuole along a default pathway. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2289628/ doi: nan ==== 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