This work was supported by the Academy of Finland (130750 and 218080 to J.T.H.), the Wellcome Trust (090532/Z/09/Z; 089026/Z/09/Z to T.A.B.), and by the MRC (MR/J007897/1 to J.T.H and T.A.B; MR/L009528/1 to T.A.B.).

<ol>
	<li>Nickell, S., Mihalache, O., Beck, F., Hegerl, R., Korinek, A., Baumeister, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+analysis+of+the+26S+proteasome+by+cryoelectron+tomography.">Structural analysis of the 26S proteasome by cryoelectron tomography.</a> Biochemical and biophysical research communications. 353 (1), 115-120 (2007).</li><li>Goldie, K. N., Wedig, T., Mitra, A. K., Aebi, U., Herrmann, H., Hoenger, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dissecting+the+3-D+structure+of+vimentin+intermediate+filaments+by+cryo-electron+tomography.">Dissecting the 3-D structure of vimentin intermediate filaments by cryo-electron tomography.</a> Journal of structural biology. 158 (3), 378-385 (2007).</li><li>Cheng, Y., Boll, W., Kirchhausen, T., Harrison, S. C., Walz, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cryo-electron+tomography+of+clathrin-coated+vesicles:+structural+implications+for+coat+assembly.">Cryo-electron tomography of clathrin-coated vesicles: structural implications for coat assembly.</a> Journal of molecular biology. 365 (3), (2007).</li><li>Gr&#252;newald, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+structure+of+herpes+simplex+virus+from+cryo-electron+tomography.">Three-dimensional structure of herpes simplex virus from cryo-electron tomography.</a> Science. 302 (5649), 1396-1398 (2003).</li><li>Murphy, G. E., Leadbetter, J. R., Jensen, G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+situ+structure+of+the+complete+Treponema+primitia+flagellar+motor.">In situ structure of the complete Treponema primitia flagellar motor.</a> Nature. 442 (7106), 1062-1064 (2006).</li><li>Medalia, O., Weber, I., Frangakis, A., Nicastro, D., Gerisch, G., Baumeister, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Macromolecular+architecture+in+eukaryotic+cells+visualized+by+cryoelectron+tomography.">Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography.</a> Science. 298 (5596), 1209-1213 (2002).</li><li>Heymann, J. B., Cardone, G., Winkler, D. C., Steven, A. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Computational+resources+for+cryo-electron+tomography+in+Bsoft.">Computational resources for cryo-electron tomography in Bsoft.</a> Journal of structural biology. 161 (3), 232-242 (2008).</li><li>Kremer, J., Mastronarde, D., McIntosh, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Computer+visualization+of+three-dimensional+image+data+using+IMOD.">Computer visualization of three-dimensional image data using IMOD.</a> Journal of structural biology. 116 (1), 71-76 (1996).</li><li>Casta&#241;o-D&#237;ez, D., Kudryashev, M., Arheit, M., Stahlberg, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamo:+a+flexible,+user-friendly+development+tool+for+subtomogram+averaging+of+cryo-EM+data+in+high-performance+computing+environments.">Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.</a> Journal of structural biology. 178 (2), 139-151 (2012).</li><li>Hrabe, T., Chen, Y., Pfeffer, S., Cuellar, L. K., Mangold, A. -. V., F&#246;rster, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PyTom:+a+python-based+toolbox+for+localization+of+macromolecules+in+cryo-electron+tomograms+and+subtomogram+analysis.">PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis.</a> Journal of structural biology. 178 (2), 177-188 (2012).</li><li>Fern&#225;ndez, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Computational+methods+for+electron+tomography.">Computational methods for electron tomography.</a> 43 (10), 1010-1030 (2012).</li><li>Briggs, J. A. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+biology+in+situ--the+potential+of+subtomogram+averaging).">Structural biology in situ--the potential of subtomogram averaging).</a> Current opinion in structural biology. 23 (2), 261-267 (2013).</li><li>Frangakis, A. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+macromolecular+complexes+in+cryoelectron+tomograms+of+phantom+cells.">Identification of macromolecular complexes in cryoelectron tomograms of phantom cells.</a> Proceedings of the National Academy of Sciences of the United States of America. 99 (22), 14153-14158 (2002).</li><li>Zanetti, G., Briggs, J. A. G., Gr&#252;newald, K., Sattentau, Q. J., Fuller, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cryo-electron+tomographic+structure+of+an+immunodeficiency+virus+envelope+complex+in+situ.">Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ.</a> PLoS pathogens. 2 (8), (2006).</li><li>Liu, J., Bartesaghi, A., Borgnia, M. J., Sapiro, G., Subramaniam, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+architecture+of+native+HIV-1+gp120+trimers.">Molecular architecture of native HIV-1 gp120 trimers.</a> Nature. 455 (7209), (2008).</li><li>Meyerson, J. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+molecular+structures+of+HIV+envelope+glycoproteins+using+cryo-electron+tomography+and+automated+sub-tomogram+averaging.">Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging.</a> Journal of visualized experiments : JoVE. (58), (2011).</li><li>Baker, T. S., Olson, N. H., Fuller, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adding+the+third+dimension+to+virus+life+cycles:+three-dimensional+reconstruction+of+icosahedral+viruses+from+cryo-electron+micrographs.">Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs.</a> Microbiology and molecular biology reviews : MMBR. 63 (4), 862-922 (1999).</li><li>Huiskonen, J. T., Butcher, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Membrane-containing+viruses+with+icosahedrally+symmetric+capsids.">Membrane-containing viruses with icosahedrally symmetric capsids.</a> Current opinion in structural biology. 17 (2), 229-236 (2007).</li><li>Liljeroos, L., Huiskonen, J. T., Ora, A., Susi, P., Butcher, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electron+cryotomography+of+measles+virus+reveals+how+matrix+protein+coats+the+ribonucleocapsid+within+intact+virions.">Electron cryotomography of measles virus reveals how matrix protein coats the ribonucleocapsid within intact virions.</a> Proceedings of the National Academy of Sciences of the United States of America. 108 (44), (2011).</li><li>Arranz, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+structure+of+native+influenza+virion+ribonucleoproteins.">The structure of native influenza virion ribonucleoproteins.</a> Science. 338 (6114), 1634-1637 (2012).</li><li>Karotki, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Eisosome+proteins+assemble+into+a+membrane+scaffold.">Eisosome proteins assemble into a membrane scaffold.</a> Journal of Cell Biology. 195 (5), 889-902 (2011).</li><li>Pietil&#228;, M. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Virion+architecture+unifies+globally+distributed+pleolipoviruses+infecting+halophilic+archaea.">Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea.</a> Journal of virology. 86 (9), 5067-5079 (2012).</li><li>Huiskonen, J. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electron+cryotomography+of+Tula+hantavirus+suggests+a+unique+assembly+paradigm+for+enveloped+viruses.">Electron cryotomography of Tula hantavirus suggests a unique assembly paradigm for enveloped viruses.</a> Journal of virology. 84 (10), 4889-4897 (2010).</li><li>Bowden, T. A., Bitto, D., McLees, A., Yeromonahos, C., Elliott, R. M., Huiskonen, J. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Orthobunyavirus+ultrastructure+and+the+curious+tripodal+glycoprotein+spike.">Orthobunyavirus ultrastructure and the curious tripodal glycoprotein spike.</a> PLoS pathogens. 9 (5), (2013).</li><li>Maurer, U. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Structure+of+Herpesvirus+Fusion+Glycoprotein+B-Bilayer+Complex+Reveals+the+Protein-Membrane+and+Lateral+Protein-Protein+Interaction.">The Structure of Herpesvirus Fusion Glycoprotein B-Bilayer Complex Reveals the Protein-Membrane and Lateral Protein-Protein Interaction.</a> Structure. 21 (8), 1396-1405 (1993).</li><li>Gan, L., Ladinsky, M. S., Jensen, G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromatin+in+a+marine+picoeukaryote+is+a+disordered+assemblage+of+nucleosomes.">Chromatin in a marine picoeukaryote is a disordered assemblage of nucleosomes.</a> Chromosoma. 122 (5), 377-386 (2013).</li><li>Scheres, S. H. W., Chen, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prevention+of+overfitting+in+cryo-EM+structure+determination.">Prevention of overfitting in cryo-EM structure determination.</a> Nature. 9 (9), 853-854 (2012).</li><li>Heymann, J. B., Belnap, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bsoft:+image+processing+and+molecular+modeling+for+electron+microscopy.">Bsoft: image processing and molecular modeling for electron microscopy.</a> Journal of structural biology. 157 (1), 3-18 (2007).</li><li>Goddard, T. D., Huang, C. C., Ferrin, T. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualizing+density+maps+with+UCSF+Chimera.">Visualizing density maps with UCSF Chimera.</a> Journal of structural biology. 157 (1), 281-287 (2007).</li><li>Faini, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+structures+of+COPI-coated+vesicles+reveal+alternate+coatomer+conformations+and+interactions.">The structures of COPI-coated vesicles reveal alternate coatomer conformations and interactions.</a> Science. 336 (6087), 1451-1454 (2012).</li><li>Wu, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fabs+enable+single+particle+cryoEM+studies+of+small+proteins.">Fabs enable single particle cryoEM studies of small proteins.</a> Structure. 20 (4), 582-592 (2012).</li></ol>

The authors have nothing to disclose.

<html> Connaissance de la structure virale de pointes de glycoprotéines de la membrane du virion est essentielle pour comprendre la réplication du virus et le développement de thérapies pour traiter et prévenir l&#39;infection. Cryo-microscopie électronique combinée avec une moyenne de particule est apparue comme la méthode la plus utilisée pour résoudre les structures de particules virales enveloppées, y compris les pointes de glycoprotéines. Cependant, cette méthode est limitée aux virus icosahedrally symétriques. Ici, grâce à l&#39;application de cryo-tomographie et subtomogram moyenne dans Jsubtomo, nous avons défini un protocole général pour la détermination de pointes de glycoprotéines sur pléomorphique virus enveloppés qui ne se prêtent pas à d&#39;autres méthodes structurelles en cours de biologie. Nos résultats représentatifs montrent que la résolution de cette méthode est suffisante pour révéler un aperçu de l&#39;architecture de domaine, oligomérisation, et plus l&#39;organisation de l&#39;ordre de pointes de glycoprotéines sur des virions intacts. jove_content &quot;&gt; L&#39;étape la plus critique dans le protocole construit deux modèles de départ fiables qui sont statistiquement indépendantes l&#39;une de l&#39;autre. exécution réussie de cette étape suppose que les pointes de glycoprotéine sont suffisamment importants et non emballés contre l&#39;autre trop serré, de sorte que les pics individuels peuvent visuellement reconnus et repris manuellement dans le tomographies, et deux modèles indépendants moyenne. Si cela n&#39;est pas possible, deux modifications du protocole peuvent être tentées. Tout d&#39;abord, deux modèles aléatoires indépendantes peuvent être construits en définissant d&#39;abord deux sous-ensembles aléatoires de subtomograms puis la moyenne des subtomograms 30 à l&#39;intérieur de ces sous-ensembles. D&#39;autre part, si la structure de la pointe isolée a été extraite par d&#39;autres moyens, par exemple par cristallographie aux rayons X, il peut être utilisé en tant que modèle de départ. Cependant, il faut veiller à faible ou filtre passe-bas ce modèle en utilisant un seuil de faible résolution (50-70 Å), que les deux modèles qui en résultent dans la prochaine ronde de raffinement serastatistiquement indépendantes qu&#39;au-delà de cette résolution. En raison de cette mise en garde, la première approche est recommandée. La résolution obtenue à partir de ce protocole dépend de quatre facteurs principaux: i. stratégie de collecte de données et de la qualité des données d&#39;entrée, ii. nombre des subtomograms, iii. la précision de l&#39;alignement des subtomograms, et iv. hétérogénéité des structures. Alors que la première et deuxième limitation peut être en grande partie résolu par l&#39;aide de détecteurs de haute signal-bruit directs électroniques combinés avec la FCE corrigé la tomographie et la collecte de données automatisée, la précision de l&#39;alignement est en outre affectée par la taille et la forme de la structure d&#39;intérêt lui-même. Lors de l&#39;application de ce protocole sur les petites pointes qui n&#39;ont pas traits saillants, il peut être avantageux de lier des fragments Fab à la pointe pour améliorer la précision d&#39;alignement et donc la résolution 31. Enfin, si les structures de calcul de la moyenne présentent des conformations multiples, sous-tomogrh méthodes de classification peuvent être utilisés pour différentes conformations moyenne séparément. À cette fin, Jsubtomo s&#39;intègre avec le paquet Dynamo, offrant classification de subtomogram puissant 9. Le protocole ci-dessus est complémentaire de la cristallographie aux rayons X des glycoprotéines virales isolées. Structures cristallographiques peuvent être montés dans des moyennes de sous-tomogramme d&#39;obtenir l&#39;orientation précise de la glycoprotéine par rapport à la membrane du virion. L&#39;application de cette méthode sera sans aucun doute continuer à faire la lumière sur la structure du virus enveloppés et physiopathologie.

Electron cryo-tomographie est une technique d&#39;imagerie cryo-microscopie électronique permettant le calcul d&#39;un à trois dimensions (3D) de reconstruction des échantillons biologiques complexes. Spécimens appropriés vont de complexes macromoléculaires purifiés 1, 2 filaments, vésicules enrobées 3, et les virus polymorphes de la membrane 4 à 5 cellules procaryotes entiers et même des zones minces de cellules eucaryotes entiers 6. Après la collecte de données d&#39;une inclinaison de la série, les volumes tomographiques 3D, ou des tomographies, peut être calculée en utilisant plusieurs logiciels, y compris celles bSoft 7 et 8 MID. Deux aspects inhérents à l&#39;étude d&#39;échantillons biologiques par la limite d&#39;électrons cryo-tomographie l&#39;interprétation biologique des volumes tomographiques correspondant. Tout d&#39;abord, en raison de la limitation de la dose d&#39;électrons qui peut être appliquée à des matières biologiques avant d&#39;introduire dégâts d&#39;irradiation importante, signaratios l-bruit dans les données tomographiques sont généralement très faibles. Deuxièmement, à la suite d&#39;un échantillonnage limité géométrie d&#39;inclinaison lors de la collecte de données, des vues de l&#39;objet restent absents, conduisant à une soi-disant «manque de coin &#39;artefact dans le volume tomographique. Cependant, ces deux limitations peuvent être surmontées si le volume tomographique contient répéter des structures identiques, tels que des complexes macromoléculaires, qui peuvent être avec succès moyennes 9-12. Avant moyenne des structures de reconstructions de tomographie, les objets d&#39;intérêt doivent être trouvés et alignés à la même orientation. La localisation de ces structures peut être réalisée par corrélation croisée d&#39;une structure de matrice dans le volume tomographique utilisant une approche souvent dénommé modèle correspondant 13. Le modèle utilisé dans ce processus d&#39;adaptation peut être dérivé de cryo-microscopie électronique ou électronique de cryo-tomographie par reconstruction 3D combiné, ou il peut être une carte de densité de simulationune structure atomique. Plusieurs forfaits de calcul ont été développés pour mener à bien ces tâches 11. Calcul de la moyenne des pics de la glycoprotéine du virus de la membrane, comme le VIH-1, a été une approche particulièrement efficace pour l&#39;étude de la structure 14 à 16. Une bonne compréhension de la structure fait partie intégrante de révéler à la fois les bases moléculaires des interactions virus-hôte et l&#39;orientation du développement de la conception antiviral et un vaccin. Bien que la cristallographie macromoléculaire est la technique de choix pour la haute résolution (généralement mieux que 4 Å) Analyse structurale des glycoprotéines virales et de leurs complexes, les structures de rayons X résultant de cette méthode sont des protéines isolées de l&#39;environnement membranaire naturel sur le virion . Ainsi, les détails importants tels que l&#39;architecture d&#39;ordre supérieur de glycoprotéines virales, dans le contexte du virion, demeurent insuffisantes. D&#39;autre part, cryo-microscopie électronique et reconstruction de particule uniquedes virus enveloppés ensemble est limité à virions à symétrie icosaédrique 17,18. Cryotomography électronique associée à l&#39;alignement de sous-volume est donc apparue comme une technique complémentaire qui permet l&#39;étude des pics de la glycoprotéine de forme irrégulière, les virus polymorphes in situ. Nous avons développé un logiciel nommé Jsubtomo (www.opic.ox.ac.uk/jsubtomo) pour la détection, l&#39;alignement et la moyenne des sous-volumes tomographiques. Jsubtomo a été utilisée dans la détermination de la structure d&#39;un certain nombre de structures cellulaires et virales 19-26. Ici, nous présentons un protocole détaillé, qui permet de déterminer les structures de pic viral de la surface. Pour contourner excès de raffinement structures moyennes en corrélant le bruit, le schéma de raffinement «étalon-or» est adoptée 10,27. Enfin, les stratégies pour la visualisation et l&#39;interprétation des résultats typiques sont discutés.

<table border="0" cellpadding="0" cellspacing="0" width="686">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Name of Material/ Equipment</td>
			<td style="width:184px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:167px;">Comments/Description</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Jsubtomo (ver 1.3.1)</td>
			<td style="width:184px;">University of Oxford</td>
			<td style="width:119px;">n/a</td>
			<td>www.opic.ac.uk/jsubtomo</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Bsoft (ver 1.8.7)</td>
			<td style="width:184px;">NIAMS, NIH</td>
			<td style="width:119px;">n/a</td>
			<td>bsoft.ws</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">UCSF Chimera</td>
			<td style="width:184px;">UCSF</td>
			<td style="width:119px;">n/a</td>
			<td>www.cgl.ucsf.edu/chimera</td>
		</tr>
	</tbody>
</table>

averaging of viral envelope glycoprotein spikes from electron cryotomography reconstructions using jsubtomo

Les virus enveloppés utilisent des glycoprotéines membranaires sur leur surface d&#39;entrée de médiation dans des cellules hôtes. Analyse la structure tridimensionnelle de ces glycoprotéine &#39;pointes&#39; est souvent techniquement difficile, mais important pour la compréhension de la pathogenèse virale et dans la conception de médicaments. Ici, un protocole est présenté pour virale détermination de la structure de pointe par le biais de la moyenne de calcul de données cryo-tomographie électronique. Cryo-tomographie est une technique en microscopie électronique utilisée pour obtenir des reconstructions tridimensionnelles tomographiques de volume, ou des tomographies, des échantillons biologiques tels que les virus polymorphes de la membrane dans un état quasi-native, congelé-hydraté. Ces tomographies révèlent des structures d&#39;intérêt en trois dimensions, mais à faible résolution. Moyenne de calcul de sous-volumes, ou sous-tomographies, est nécessaire pour obtenir plus de détails de la résolution de la répétition des motifs structuraux, tels que pointes de glycoprotéines virales. Une approche de calcul détaillé pour aligning et moyenne sous-tomographies à l&#39;aide du logiciel Jsubtomo est décrite. Cette approche permet la visualisation de la structure de pointes de glycoprotéines virales à une résolution de l&#39;ordre de 20-40 Å et l&#39;étude de l&#39;étude de la hausse des commandes pic-à-pic interactions sur la membrane du virion. Les résultats typiques sont présentés pour le virus Bunyamwera, un virus enveloppé de la famille des Bunyaviridae. Cette famille est un groupe structurellement divers agents pathogènes constituent une menace pour la santé humaine et animale.

Nous démontrons l&#39;application de la moyenne flux de travail sous-tomographie décrit ci-dessus pour le complexe de la glycoprotéine d&#39;enveloppe du virus Bunyamwera (Orthobunyavirus, Bunyaviridae) en utilisant un ensemble de données publiées antérieurement mis 24. paramètres de collecte de données et le raffinement sont listés dans le Tableau 1. Une tomographie représentatif est montré à la figure 2. <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td> Paramètre (unité) </td><td> Valeur </td></tr><tr><td> La collecte des données </td><td></td></tr><tr><td> Tension (kV) </td><td> 300 </td></tr><tr><td> Grossissement calibré (X) </td><td> 111000 </td></tr><tr><td> La taille du pixel (A) </td><td> 5.4 </td></tr><tr><td> Dose estimée (e - / Å 2) </td><td> 100 </td></tr><tr><td> Underfocus (pm) </td><td> 4,0-4,5 </td&gt; </tr><tr><td> Zéro FCE (A) une </td><td> 26-30 </td></tr><tr><td> Plage d&#39;inclinaison (°) </td><td> -60 À 60 </td></tr><tr><td> Tilt échantillonnage (°) </td><td> 3 </td></tr><tr><td> Données et raffinement </td><td></td></tr><tr><td> Tomographies </td><td> 11 </td></tr><tr><td> Virions </td><td> 29 </td></tr><tr><td> Graines par virion </td><td> 106 </td></tr><tr><td> Nombre total de graines </td><td> 3074 </td></tr><tr><td> Spikes détectés </td><td> 1346 </td></tr><tr><td> Spikes après de supprimer les chevauchements </td><td> 1401 </td></tr><tr><td> Spikes après sélection sur la base de corrélation croisée </td><td> 1022 </td></tr><tr><td> Spikes inclus dans la moyenne finale </td><td> 1022 </td></tr><tr><td> Symétrie </td><td> C3 </td></tr><tr><td> Échantillonnage angulaire (°) </td><td> 8 </td></tr><tr><td> Résolutiongamme utilisée dans le raffinement (Å) </td><td> 42-334 </td></tr><tr><td> Résolution estimation finale (A) b </td><td> 35 </td></tr></tbody></table> Tableau 1: la collecte des données et statistiques Bunyamwera de raffinement. un FCT, la fonction de transfert de contraste. b Calculé à l&#39;aide de Fourier coque corrélation entre deux structures indépendamment raffinés au seuil de 0,143. <img alt="Figure 2" fo:content-width="6in" src="/files/ftp_upload/51714/51714fig2highres.jpg" width="600" /> Figure 2:. Slice par une tomographie de virions Bunyamwera Plusieurs vues de côté pic évident dans la périphérie de chaque virion sont indiqués par des flèches. La tomographie a été filtré passe-bas à 60 Å. Barre d&#39;échelle de 100 nm. Tout d&#39;abord, nous avons affiné un modèle initial en utilisant 205 pointes, récolté manuellement ( <strong&gt; Figure 3). Trois symétrie du centre-pic le plus évident était sans appliquer de symétrie (figure 3B) et a été imposée dans les rondes subséquentes de raffinement (figure 3C). Pour détecter automatiquement tous les pics sur la surface du virion, nous avons généré 106 graines de chaque virion au rayon de 43 nm et un espacement de 20 degrés (figure 4A) et de façon itérative affiné leurs positions par rapport à la membrane (figure 4B). <img alt="Figure 3" fo:content-width="6in" src="/files/ftp_upload/51714/51714fig3highres.jpg" width="600" /> Figure 3: Le raffinement de la structure de la matrice initiale. (A) cylindrique en moyenne (C100) modèle construit à partir des positions définies manuellement de pointes. (B) En moyenne densité après cinq tours de raffinement sans symétrie (C1) a imposé affiche une hausse de trois foiscaractéristiques symétriques. La résolution du modèle est de 48 Å. (C) moyenne de la pointe a été résolu à 41 Å après cinq tours de raffinement avec triple symétrie. <img alt="Figure 4" fo:content-width="6in" src="/files/ftp_upload/51714/51714fig4highres.jpg" width="600" /> Figure 4:. Raffinement des graines AB) Un sous-ensemble de graines avant (A) et après (B) raffinement sont présentés sur une densite de virion de la figure 2 Graines à (B) ont été codés par couleur en fonction de la transversale respective. coefficients de corrélation (bleu, faible corrélation, le rouge, haute corrélation). Les meilleurs corrélation glycoprotéine correctifs de pointes (top 75% après la suppression des chevauchements; ~ 1000 pointes) ont été utilisés pour calculer la moyenne finale. La moyenne a été résolu à 35 Å de résolution (Figure 5). Il a révélé une structure de pointe trimérique dans le milieu, enOutre une contribution de six crampons voisins. Modèles composites des virions, calculés en plaçant la structure en des positions connues, ont révélé placement des pointes sur la surface du virion (Figure 6A). De temps en temps, des taches commandés localement des pointes étaient évidents (figure 6B). <img alt="Figure 5" fo:content-width="6in" src="/files/ftp_upload/51714/51714fig5highres.jpg" width="600" /> Figure 5: Structure raffinée d&#39;un patch de la couche de pointes de glycoprotéines après template matching. (AB) Deux cartes «même» et «bizarre», reconstruites à partir de deux moitiés des données sont présentées. Les deux cartes montrent un degré remarquable de similitude, la vérification de l&#39;valable jusqu&#39;au de l&#39;approche. L&#39;orientation autour de l&#39;axe de temps est différente de la pointe que les deux cartes ont été reconstruits entièrement indépendamment l&#39;un de l&#39;autre. (C) moyenne des deux cartes est indiqué enla résolution finale de 35 Å. <img alt="Figure 6" fo:content-width="6in" src="/files/ftp_upload/51714/51714fig6highres.jpg" width="600" /> Figure 6: Placement des pointes sur le virion Bunyamwera. (A) du modèle composite d&#39;un virion. Voir vecteurs (bâtons) indiquent les orientations des pointes. Les couleurs indiquent la corrélation entre chaque pic et la structure du modèle (bleu, une faible corrélation, le rouge, forte corrélation). (B) Un gros plan d&#39;une pièce ordonnée de pointes.

Watch this Scientific Journal Video about Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo at JoVE.com

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

An approach is presented for determining structures of viral membrane glycoprotein complexes using a combination of electron cryo-tomography and sub-tomogram averaging with the computational package Jsubtomo.

Moyenne de la glycoprotéine d&#39;enveloppe virale Pointes de Electron Cryotomography reconstructions utilisant Jsubtomo

Enveloped viruses utilize membrane glycoproteins on their surface to mediate entry into host cells. Three-dimensional structural analysis of these ...

averaging-viral-envelope-glycoprotein-spikes-from-electron

Research

JoVE Journal

Immunology and Infection

12.0K vues.  University of Oxford. An approach is presented for determining structures of viral membrane glycoprotein complexes using a combination of electron cryo-tomography and sub-tomogram averaging with the computational package Jsubtomo.

Vidéo: Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Using a Pan-Viral Microarray Assay (Virochip) to Screen Clinical Samples for Viral Pathogens

The diagnosis of viral causes of many infectious diseases is difficult due to the inherent sequence diversity of viruses as well as the ongoing emergence of novel viral pathogens, such as SARS coronavirus and 2009 pandemic H1N1 influenza virus, that are not detectable by traditional methods. To address these challenges, we have previously developed and validated a pan-viral microarray platform called the Virochip with the capacity to detect all known viruses as well as novel variants on the basis of conserved sequence homology1. Using the Virochip, we have identified the full spectrum of viruses associated with respiratory infections, including cases of unexplained critical illness in hospitalized patients, with a sensitivity equivalent to or superior to conventional clinical testing2-5. The Virochip has also been used to identify novel viruses, including the SARS coronavirus6,7, a novel rhinovirus clade5, XMRV (a retrovirus linked to prostate cancer)8, avian bornavirus (the cause of a wasting disease in parrots)9, and a novel cardiovirus in children with respiratory and diarrheal illness10. The current version of the Virochip has been ported to an Agilent microarray platform and consists of ~36,000 probes derived from over ~1,500 viruses in GenBank as of December of 2009. Here we demonstrate the steps involved in processing a Virochip assay from start to finish (~24 hour turnaround time), including sample nucleic acid extraction, PCR amplification using random primers, fluorescent dye incorporation, and microarray hybridization, scanning, and analysis.

Using a Pan-Viral Microarray Assay Virochip to Screen Clinical Samples for Viral Pathogens

The Virochip is a pan-viral microarray designed to simultaneously detect all known viruses as well as novel viruses on the basis of conserved sequence homology. Here we demonstrate how to run a Virochip assay to analyze clinical samples for the presence of both known and unknown viruses.

En utilisant un dosage Microarray pan-virale (Virochip) pour cribler des échantillons cliniques pour les pathogènes viraux

The diagnosis of viral causes of many infectious diseases is difficult due to the inherent sequence diversity of viruses as well as the ongoing emergence ...

Recherche

Immunologie et infection

Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging

Since its discovery nearly 30 years ago, more than 60 million people have been infected with the human immunodeficiency virus (HIV) <a href="http://www.usaid.gov">(www.usaid.gov)</a>. The virus infects and destroys CD4+ T-cells thereby crippling the immune system, and causing an acquired immunodeficiency syndrome (AIDS) 2. Infection begins when the HIV Envelope glycoprotein "spike" makes contact with the CD4 receptor on the surface of the CD4+ T-cell. This interaction induces a conformational change in the spike, which promotes interaction with a second cell surface co-receptor 5,9. The significance of these protein interactions in the HIV infection pathway makes them of profound importance in fundamental HIV research, and in the pursuit of an HIV vaccine.
The need to better understand the molecular-scale interactions of HIV cell contact and neutralization motivated the development of a technique to determine the structures of the HIV spike interacting with cell surface receptor proteins and molecules that block infection. Using cryo-electron tomography and 3D image processing, we recently demonstrated the ability to determine such structures on the surface of native virus, at &tilde;20 &Aring; resolution 9,14. This approach is not limited to resolving HIV Envelope structures, and can be extended to other viral membrane proteins and proteins reconstituted on a liposome. In this protocol, we describe how to obtain structures of HIV envelope glycoproteins starting from purified HIV virions and proceeding stepwise through preparing vitrified samples, collecting, cryo-electron microscopy data, reconstituting and processing 3D data volumes, averaging and classifying 3D protein subvolumes, and interpreting results to produce a protein model. The computational aspects of our approach were adapted into modules that can be accessed and executed remotely using the Biowulf GNU/Linux parallel processing cluster at the NIH <a href="http://biowulf.nih.gov">(http://biowulf.nih.gov)</a>. This remote access, combined with low-cost computer hardware and high-speed network access, has made possible the involvement of researchers and students working from school or home.

The protocol describes a high-throughput approach to determining structures of membrane proteins using cryo-electron tomography and 3D image processing. It covers the details of specimen preparation, data collection, data processing and interpretation, and concludes with the production of a representative target for the approach, the HIV-1 Envelope glycoprotein. These computational procedures are designed in a way that enables researchers and students to work remotely and contribute to data processing and structural analysis.

Détermination des structures moléculaires des glycoprotéines d&#39;enveloppe du VIH en utilisant microscopie cryo-électronique et automatisée Sous-tomogramme moyenne

Since its discovery nearly 30 years ago, more than 60 million people have been infected with the human immunodeficiency virus (HIV) (www.usaid.gov). The ...

Cost-effective Method for Microbial Source Tracking Using Specific Human and Animal Viruses

Microbial contamination of the environment represents a significant health risk. Classical bacterial fecal indicators have shown to have significant limitations, viruses are more resistant to many inactivation processes and standard fecal indicators do not inform on the source of contamination. The development of cost-effective methods for the concentration of viruses from water and molecular assays facilitates the applicability of viruses as indicators of fecal contamination and as microbial source tracking (MST) tools. Adenoviruses and polyomaviruses are DNA viruses infecting specific vertebrate species including humans and are persistently excreted in feces and/or urine in all geographical areas studied. In previous studies, we suggested the quantification of human adenoviruses (HAdV) and JC polyomaviruses (JCPyV) by quantitative PCR (qPCR) as an index of human fecal contamination. Recently, we have developed qPCR assays for the specific quantification of porcine adenoviruses (PAdV) and bovine polyomaviruses (BPyV) as animal fecal markers of contamination with sensitivities of 1-10 genome copies per test tube. In this study, we present the procedure to be followed to identify the source of contamination in water samples using these tools. As example of representative results, analysis of viruses in ground water presenting high levels of nitrates is shown.
Detection of viruses in low or moderately polluted waters requires the concentration of the viruses from at least several liters of water into a much smaller volume, a procedure that usually includes two concentration steps in series. This somewhat cumbersome procedure and the variability observed in viral recoveries significantly hamper the simultaneous processing of a large number of water samples.
In order to eliminate the bottleneck caused by the two-step procedures we have applied a one-step protocol developed in previous studies and applicable to a diversity of water matrices. The procedure includes: acidification of ten-liter water samples, flocculation by skimmed milk, gravity sedimentation of the flocculated materials, collection of the precipitate and centrifugation, resuspension of the precipitate in 10 ml phosphate buffer. The viral concentrate is used for the extraction of viral nucleic acids and the specific adenoviruses and polyomaviruses of interest are quantified by qPCR. High number of samples may be simultaneously analyzed using this low-cost concentration method.
The procedure has been applied to the analysis of bathing waters, seawater and river water and in this study, we present results analyzing groundwater samples. This high-throughput quantitative method is reliable, straightforward, and cost-effective.

The study describes a cost-effective method for the identification of the source of fecal/urine contamination or contamination by nitrates in water using qPCR for the specific quantification of human/porcine/bovine DNA viruses, adenoviruses and polyomaviruses, proposed as MST tools.

Rentable méthode de suivi des sources microbiennes spécifiques utilisant des virus humains et animaux

Microbial contamination of the environment represents a significant health risk. Classical bacterial fecal indicators have shown to have significant ...

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

RNA viruses use RNA dependent RNA polymerases to replicate their genomes. The intrinsically high error rate of these enzymes is a large contributor to the generation of extreme population diversity that facilitates virus adaptation and evolution. Increasing evidence shows that the intrinsic error rates, and the resulting mutation frequencies, of RNA viruses can be modulated by subtle amino acid changes to the viral polymerase. Although biochemical assays exist for some viral RNA polymerases that permit quantitative measure of incorporation fidelity, here we describe a simple method of measuring mutation frequencies of RNA viruses that has proven to be as accurate as biochemical approaches in identifying fidelity altering mutations. The approach uses conventional virological and sequencing techniques that can be performed in most biology laboratories. Based on our experience with a number of different viruses, we have identified the key steps that must be optimized to increase the likelihood of isolating fidelity variants and generating data of statistical significance. The isolation and characterization of fidelity altering mutations can provide new insights into polymerase structure and function1-3. Furthermore, these fidelity variants can be useful tools in characterizing mechanisms of virus adaptation and evolution4-7.

The present article describes the steps required to isolate and characterize RNA polymerase fidelity variants of RNA viruses and how to use mutation frequency data to confirm fidelity changes in tissue culture.

Isolement des variantes des virus à ARN de Fidelity et caractérisation de la fréquence de mutation de virus

RNA viruses use RNA dependent RNA polymerases to replicate their genomes. The intrinsically high error rate of these enzymes is a large contributor to the ...

Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography

Viruses, particularly bacteriophages (phages), are the most numerous biological entities on Earth1,2. Viruses modulate host cell abundance and diversity, contribute to the cycling of nutrients, alter host cell phenotype, and influence the evolution of both host cell and viral communities through the lateral transfer of genes 3. Numerous studies have highlighted the staggering genetic diversity of viruses and their functional potential in a variety of natural environments. 
Metagenomic techniques have been used to study the taxonomic diversity and functional potential of complex viral assemblages whose members contain single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and RNA genotypes 4-9. Current library construction protocols used to study environmental DNA-containing or RNA-containing viruses require an initial nuclease treatment in order to remove nontargeted templates 10. However, a comprehensive understanding of the collective gene complement of the virus community and virus diversity requires knowledge of all members regardless of genome composition. Fractionation of purified nucleic acid subtypes provides an effective mechanism by which to study viral assemblages without sacrificing a subset of the community&#x2019;s genetic signature. 
Hydroxyapatite, a crystalline form of calcium phosphate, has been employed in the separation of nucleic acids, as well as proteins and microbes, since the 1960s11. By exploiting the charge interaction between the positively-charged Ca2+ ions of the hydroxyapatite and the negatively charged phosphate backbone of the nucleic acid subtypes, it is possible to preferentially elute each nucleic acid subtype independent of the others. We recently employed this strategy to independently fractionate the genomes of ssDNA, dsDNA and RNA-containing viruses in preparation of DNA sequencing 12. Here, we present a method for the fractionation and recovery of ssDNA, dsDNA and RNA viral nucleic acids from mixed viral assemblages using hydroxyapatite chromotography.

We describe an efficient method to separate single-stranded DNA, double-stranded DNA and RNA molecules from environmental viral communities. Nucleic acids are fractionated using hydroxyapatite chromatography with increasing concentrations of phosphate-containing buffers. This method permits the isolation of all viral nucleic acid types from environmental samples.

Séparation de l&#39;ADN simple brin, double brin de l&#39;ADN et l&#39;ARN à partir d&#39;un environnement communautaire viral en utilisant chromatographie d&#39;hydroxyapatite

Viruses, particularly bacteriophages (phages), are the most numerous biological entities on Earth1,2.  Viruses modulate host cell abundance and diversity, ...

Preparation of Viral DNA from Nucleocapsids

Viruses are obligate cellular parasites, and thus the study of their DNA requires isolating viral material away from host cell contaminants and DNA. Several downstream applications require large quantities of pure viral DNA, which is provided by this protocol. These applications include viral genome sequencing, where the removal of host DNA is crucial to optimize data output for viral sequences, and the production of new viral recombinant strains, where co-transfection of purified plasmid and linear viral DNA facilitates recombination.1,2,3 
This procedure utilizes a combination of extractions and density-based centrifugation to isolate purified linear herpesvirus nucleocapsid DNA from infected cells.4,5 The initial purification steps aim to isolate purified viral capsids, which contain and protect the viral DNA during the extractions and centrifugation steps that remove cellular proteins and DNA. Lysis of nucleocapsids then releases viral DNA, and two final phenol-chloroform steps remove remaining proteins. The final DNA captured from solution is highly concentrated and pure, with an average OD260/280 of 1.90. Depending on the quantity of infected cells used, yields of viral DNA range from 150-800 &mu;g or more. The purity of this DNA makes it stable during long-term storage at 4C. This DNA is thus ideally suited for high-throughput sequencing, high fidelity PCR reactions, and transfections. 
Prior to beginning the protocol, it is important to know the average number of cells per dish (e.g. an average of 8 x 106 PK-15 cells in a confluent 15 cm dish), and the titer of the viral stock to be used (e.g. 1 x 108 plaque-forming units per ml). These are necessary to calculate the appropriate multiplicity of infection (MOI) for the protocol.6 For instance, to infect one 15 cm dish of PK-15 cells with the above viral stock, at an MOI of 5, you would use 400 &mu;l of viral stock and dilute it with 3.6 ml of medium (total inoculation volume of 4 ml for one 15 cm plate).
Multiple viral DNA preparations can be prepared at the same time. The number of simultaneous preparations is limited only by the number of tubes held by the ultracentrifuge rotor (one per virus; see step 3.9 below). Here we describe the procedure as though being done for one virus.

We describe the process of isolating high purity herpesvirus nucleocapsid DNA from infected cells. The final DNA captured from solution is of high concentration and purity, making it ideally suited for high-throughput sequencing, high fidelity PCR reactions, and transfections to produce new viral recombinants.

Préparation de l&#39;ADN viral à partir des nucléocapsides

Viruses are obligate cellular parasites, and thus the study of their DNA requires isolating viral material away from host cell contaminants and DNA. ...

Imaging of HIV-1 Envelope-induced Virological Synapse and Signaling on Synthetic Lipid Bilayers

Human immunodeficiency virus type 1 (HIV-1) infection occurs most efficiently via cell to cell transmission2,10,11. This cell to cell transfer between CD4+ T cells involves the formation of a virological synapse (VS), which is an F-actin-dependent cell-cell junction formed upon the engagement of HIV-1 envelope gp120 on the infected cell with CD4 and the chemokine receptor (CKR) CCR5 or CXCR4 on the target cell 8. In addition to gp120 and its receptors, other membrane proteins, particularly the adhesion molecule LFA-1 and its ligands, the ICAM family, play a major role in VS formation and virus transmission as they are present on the surface of virus-infected donor cells and target cells, as well as on the envelope of HIV-1 virions1,4,5,6,7,13. VS formation is also accompanied by intracellular signaling events that are transduced as a result of gp120-engagement of its receptors. Indeed, we have recently showed that CD4+ T cell interaction with gp120 induces recruitment and phosphorylation of signaling molecules associated with the TCR signalosome including Lck, CD3&zeta;, ZAP70, LAT, SLP-76, Itk, and PLC&gamma;15.
In this article, we present a method to visualize supramolecular arrangement and membrane-proximal signaling events taking place during VS formation. We take advantage of the glass-supported planar bi-layer system as a reductionist model to represent the surface of HIV-infected cells bearing the viral envelope gp120 and the cellular adhesion molecule ICAM-1. The protocol describes general procedures for monitoring HIV-1 gp120-induced VS assembly and signal activation events that include i) bi-layer preparation and assembly in a flow cell, ii) injection of cells and immunofluorescence staining to detect intracellular signaling molecules on cells interacting with HIV-1 gp120 and ICAM-1 on bi-layers, iii) image acquisition by TIRF microscopy, and iv) data analysis. This system generates high-resolution images of VS interface beyond that achieved with the conventional cell-cell system as it allows detection of distinct clusters of individual molecular components of VS along with specific signaling molecules recruited to these sub-domains.

This article describes a method to visualize formation of an HIV-1 envelope-induced virological synapse on glass supported planar bilayers by total internal reflection fluorescence (TIRF) microscopy. The method can also be combined with immunofluorescence staining to detect activation and redistribution of signaling molecules that occur during HIV-1 envelope-induced virological synapse formation.

Imagerie de VIH-1 Enveloppe induite Synapse virologique et de signalisation sur bicouches lipidiques synthétiques

Human immunodeficiency virus type 1 (HIV-1) infection occurs most efficiently via cell to cell transmission2,10,11. This cell to cell transfer between ...

Conformational Evaluation of HIV-1 Trimeric Envelope Glycoproteins Using a Cell-based ELISA Assay

HIV-1 envelope glycoproteins (Env) mediate viral entry into target cells and are essential to the infectious cycle. Understanding how those glycoproteins are able to fuel the fusion process through their conformational changes could lead to the design of better, more effective immunogens for vaccine strategies. Here we describe a cell-based ELISA assay that allows studying the recognition of trimeric HIV-1 Env by monoclonal antibodies. Following expression of HIV-1 trimeric Env at the surface of transfected cells, conformation specific anti-Env antibodies are incubated with the cells. A horseradish peroxidase-conjugated secondary antibody and a simple chemiluminescence reaction are then used to detect bound antibodies. This system is highly flexible and can detect Env conformational changes induced by soluble CD4 or cellular proteins. It requires minimal amount of material and no highly-specialized equipment or know-how. Thus, this technique can be established for medium to high throughput screening of antigens and antibodies, such as newly-isolated antibodies.

Understanding viral surface antigens conformations is required to evaluate antibody neutralization and guide the design of effective vaccine immunogens. Here we describe a cell-based ELISA assay that allows the study of the recognition of trimeric HIV-1 Env expressed at the surface of transfected cells by specific anti-Env antibodies.

Évaluation de conformation du VIH-1 trimère glycoprotéines d&#39;enveloppe l&#39;aide d&#39;un base de cellules test ELISA

HIV-1 envelope glycoproteins (Env) mediate viral entry into target cells and are essential to the infectious cycle. Understanding how those glycoproteins ...

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

Coxiella burnetii, the agent causing Q fever, is an obligate intracellular bacterium. PCR based diagnostic assays have been developed for detecting C. burnetii DNA in cell cultures and clinical samples. PCR requires specialized equipment and extensive end user training, and therefore, it is not suitable for routine work especially in a resource-constrained area. We have developed a loop-mediated isothermal amplification (LAMP) assay to detect the presence of C. burnetii in patient samples. This method is performed at a single temperature around 60 &#176;C in a water bath or heating block. The sensitivity of this LAMP assay is very similar to PCR with a detection limit of about 25 copies per reaction. This report describes the preparation of the reaction using lyophilized reagents and visualization of results using hydroxynaphthol blue (HNB) or a UV lamp with fluorescent intercalating dye in the reaction. The LAMP reagents were lyophilized and stored at room temperature (RT) for one month without loss of detection sensitivity. This LAMP assay is particularly robust because the reaction mixture preparation does not involve complex steps. This method is ideal for use in resource-limited settings where Q fever is endemic.

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

We described here a simple loop-mediated isothermal amplification (LAMP) method using lyophilized reagents for the detection of C. burnetii in patient samples.

Le développement de lyophilisé boucle médiées isothermes Amplification Réactifs pour la détection des<em&gt; Coxiella burnetii</em

Coxiella burnetii, the agent causing Q fever, is an obligate intracellular bacterium. PCR based diagnostic assays have been developed for detecting C. ...

Measuring Influenza Neuraminidase Inhibition Antibody Titers by Enzyme-linked Lectin Assay

Antibodies to neuraminidase (NA), the second most abundant surface protein on influenza virus, contribute toward protection against influenza. Traditional methods to measure NA inhibiting (NI) antibody titers are not practical for routine serology. This protocol describes the enzyme-linked lectin assay (ELLA), a practical alternative method to measure NI titers that is performed in 96 well plates coated with a large glycoprotein substrate, fetuin. NA cleaves terminal sialic acids from fetuin, exposing the penultimate sugar, galactose. Peanut agglutinin (PNA) is a lectin with specificity for galactose and therefore the extent of desialylation can be quantified using a PNA-horseradish peroxidase conjugate, followed by addition of a chromogenic peroxidase substrate. The optical density that is measured is proportional to NA activity. To measure NI antibody titers, serial dilutions of sera are incubated at 37 &#176;C O/N on fetuin-coated plates with a fixed amount of NA. The reciprocal of the highest serum dilution that results in &#8805;50% inhibition of NA activity is designated as the NI antibody titer. The ELLA provides a practical format for routine evaluation of human antibody responses following influenza infection or vaccination.

We describe the enzyme-linked lectin assay (ELLA) for measuring influenza neuraminidase (NA)-inhibition antibody titers in sera. The assay uses peanut agglutinin to quantify galactose residues that become accessible when NA removes sialic acid from fetuin-coated, 96-well plates.

Mesure de la grippe neuraminidase Inhibition Titres d&#39;anticorps par-enzymatique lectine Assay

Antibodies to neuraminidase (NA), the second most abundant surface protein on influenza virus, contribute toward protection against influenza. Traditional ...