References

Amara, J. F., T. Clackson, V. M. Rivera, T. Guo, T. Keenan, S. Natesan, R. Pollock, et al. 1997. “A Versatile Synthetic Dimerizer for the Regulation of Protein-Protein Interactions.” Proceedings of the National Academy of Sciences 94 (20): 10618–23. doi:10.1073/pnas.94.20.10618.

Baker, Monya. 2016. “1,500 Scientists Lift the Lid on Reproducibility.” Nature 533 (7604). Springer Nature: 452–54. doi:10.1038/533452a.

Brandenberg, Oliver F., Carsten Magnus, Roland R. Regoes, and Alexandra Trkola. 2015. “The HIV-1 Entry Process: A Stoichiometric View.” Trends in Microbiology 23 (12). Elsevier BV: 763–74. doi:10.1016/j.tim.2015.09.003.

Chan, K. Hung, Jack C. Hayya, and J. Keith Ord. 1977. “A Note on Trend Removal Methods: The Case of Polynomial Regression Versus Variate Differencing.” Econometrica 45 (3). JSTOR: 737. doi:10.2307/1911686.

Chen, Y., J. D. Muller, K. M. Berland, and E. Gratton. 1999. “Fluorescence fluctuation spectroscopy.” Methods 19 (2): 234–52. doi:10.1006/meth.1999.0854.

Dalal, R. B., M. A. Digman, A. F. Horwitz, V. Vetri, and E. Gratton. 2008. “Determination of particle number and brightness using a laser scanning confocal microscope operating in the analog mode.” Microsc. Res. Tech. 71 (1): 69–81. doi:10.1002/jemt.20526.

Declerck, Nathalie, and Catherine A. Royer. 2013. “Interactions in Gene Expression Networks Studied by Two-Photon Fluorescence Fluctuation Spectroscopy.” In Methods in Enzymology, 203–30. Elsevier. doi:10.1016/b978-0-12-405539-1.00007-5.

Digman, M. A., and E. Gratton. 2009. “Imaging barriers to diffusion by pair correlation functions.” Biophys. J. 97 (2): 665–73. doi:10.1016/j.bpj.2009.04.048.

Digman, M. A., R. Dalal, A. F. Horwitz, and E. Gratton. 2008. “Mapping the number of molecules and brightness in the laser scanning microscope.” Biophys. J. 94 (6): 2320–32. doi:10.1529/biophysj.107.114645.

Digman, M. A., P. W. Wiseman, C. Choi, Alan R. Horwitz, and E. Gratton. 2009. “Stoichiometry of Molecular Complexes at Adhesions in Living Cells.” Proceedings of the National Academy of Sciences 106 (7). National Academy of Sciences: 2170–5. doi:10.1073/pnas.0806036106.

Dunsing, Valentin, Madlen Luckner, Boris Zühlke, Roberto Petazzi, Andreas Herrmann, and Salvatore Chiantia. 2018. “Quantifying Protein Oligomerization in Living Cells: A Systematic Comparison of Fluorescent Proteins,” April. Cold Spring Harbor Laboratory. doi:10.1101/311175.

Einstein, A. 1905. “Über Die von Der Molekularkinetischen Theorie Der Wärme Geforderte Bewegung von in Ruhenden Flüssigkeiten Suspendierten Teilchen.” Annalen Der Physik 322 (8). Wiley: 549–60. doi:10.1002/andp.19053220806.

Einstein, Albert. 1905. “Concerning an Heuristic Point of View Toward the Emission and Transformation of Light.” Annalen Der Physik 17: 132–48.

FCSXpert. 2018. “What Is the Confocal Volume?” Sensor Technologies LLC. http://www.fcsxpert.com/classroom/theory/what-is-confocal-volume.html.

Fenz, Susanne F., Ana-Sunčana Smith, and Cornelia Monzel. 2017. “Measuring the Invisible: Determining the Size of Growing Nanodomains Using the Inverse FCS.” Biophysical Journal 112 (11). Elsevier BV: 2245–6. doi:10.1016/j.bpj.2017.04.014.

Förster, Th. 1948. “Zwischenmolekulare Energiewanderung Und Fluoreszenz.” Annalen Der Physik 437 (1-2). Wiley: 55–75. doi:10.1002/andp.19484370105.

Gach, Johannes S., Margaux Bouzin, Marcus P. Wong, Veronika Chromikova, Andrea Gorlani, Kuan-Ting Yu, Brijesh Sharma, Enrico Gratton, and Donald N. Forthal. 2017. “Human Immunodeficiency Virus Type-1 (HIV-1) Evades Antibody-Dependent Phagocytosis.” Edited by Alexandra Trkola. PLOS Pathogens 13 (12). Public Library of Science (PLoS): e1006793. doi:10.1371/journal.ppat.1006793.

Hammamatsu. 2007. “Photomultiplier Tubes: Basics and Applications.” Hammamatsu. https://www.hamamatsu.com/resources/pdf/etd/PMT_handbook_v3aE.pdf.

Hebert, B., S. Costantino, and P. W. Wiseman. 2005. “Spatiotemporal image correlation spectroscopy (STICS) theory, verification, and application to protein velocity mapping in living CHO cells.” Biophys. J. 88 (5): 3601–14. doi:10.1529/biophysj.104.054874.

Herold, N., M. Anders-Osswein, B. Glass, M. Eckhardt, B. Muller, and H.-G. Krausslich. 2014. “HIV-1 Entry in SupT1-R5, CEM-Ss, and Primary CD4 T Cells Occurs at the Plasma Membrane and Does Not Require Endocytosis.” Journal of Virology 88 (24). American Society for Microbiology: 13956–70. doi:10.1128/jvi.01543-14.

Hoischen, Christian, Shamci Monajembashi, Klaus Weisshart, and Peter Hemmerich. 2018. “Multimodal Light Microscopy Approaches to Reveal Structural and Functional Properties of Promyelocytic Leukemia Nuclear Bodies.” Frontiers in Oncology 8 (May). Frontiers Media SA. doi:10.3389/fonc.2018.00125.

Iliopoulou, Maro, Rory Nolan, Luis Alvarez, Yasunori Watanabe, Charles A. Coomer, G. Maria Jakobsdottir, Thomas A. Bowden, and Sergi Padilla-Parra. 2018. “A dynamic three step mechanism drives the HIV-1 prefusion reaction.” Nat. Struct. Mol. Biol. 25 (9). doi:10.1038/s41594-018-0113-x.

Jakobsdottir, G. Maria, Maro Iliopoulou, Rory Nolan, Luis Alvarez, Alex A. Compton, and Sergi Padilla-Parra. 2017. “On the Whereabouts of HIV-1 Cellular Entry and Its Fusion Ports.” Trends in Molecular Medicine 23 (10). Elsevier BV: 932–44. doi:10.1016/j.molmed.2017.08.005.

Jameson, D. M., J. A. Ross, and J. P. Albanesi. 2009. “Fluorescence fluctuation spectroscopy: ushering in a new age of enlightenment for cellular dynamics.” Biophys Rev 1 (3): 105–18. doi:10.1007/s12551-009-0013-8.

Jones, Daniel M, Luis A Alvarez, Rory Nolan, Margarita Ferriz, Raquel Sainz Urruela, Xènia Massana-Muñoz, Hila Novak-Kotzer, Michael L Dustin, and Sergi Padilla-Parra. 2017. “Dynamin-2 Stabilizes the Hiv-1 Fusion Pore with a Low Oligomeric State.” Cell Reports 18 (2). Elsevier: 443–53. doi:10.1016/j.celrep.2016.12.032.

Kapanidis, Achillefs N., Ted A. Laurence, Nam Ki Lee, Emmanuel Margeat, Xiangxu Kong, and Shimon Weiss. 2005. “Alternating-Laser Excitation of Single Molecules.” Accounts of Chemical Research 38 (7). American Chemical Society (ACS): 523–33. doi:10.1021/ar0401348.

Kisley, Lydia, and Christy F. Landes. 2014. “Molecular Approaches to Chromatography Using Single Molecule Spectroscopy.” Analytical Chemistry 87 (1). American Chemical Society (ACS): 83–98. doi:10.1021/ac5039225.

Kwon, Young Do, Marie Pancera, Priyamvada Acharya, Ivelin S Georgiev, Emma T Crooks, Jason Gorman, M Gordon Joyce, et al. 2015. “Crystal Structure, Conformational Fixation and Entry-Related Interactions of Mature Ligand-Free HIV-1 Env.” Nature Structural & Molecular Biology 22 (7). Springer Nature: 522–31. doi:10.1038/nsmb.3051.

Laboratory for Fluorescence Dynamics. 2018. Globals for Images: SimFCS 4. University of California, Irvine. http://www.lfd.uci.edu/globals/.

Landini, G., D.A. Randell, S. Fouad, and A. Galton. 2016. “Automatic Thresholding from the Gradients of Region Boundaries.” Journal of Microscopy 265 (2). Wiley: 185–95. doi:10.1111/jmi.12474.

Leica. 2012. “Sensors for True Confocal Scanning.” Leica Microsystems. https://www.leica-microsystems.com/science-lab/sensors-for-true-confocal-scanning/.

Liu, Qingbo, Priyamvada Acharya, Michael A Dolan, Peng Zhang, Christina Guzzo, Jacky Lu, Alice Kwon, et al. 2017. “Quaternary Contact in the Initial Interaction of CD4 with the HIV-1 Envelope Trimer.” Nature Structural & Molecular Biology 24 (4). Springer Nature: 370–78. doi:10.1038/nsmb.3382.

Ly, Sonny, Feliza Bourguet, Nicholas O. Fischer, Edmond Y. Lau, Matthew A. Coleman, and Ted A. Laurence. 2014. “Quantifying Interactions of a Membrane Protein Embedded in a Lipid Nanodisc Using Fluorescence Correlation Spectroscopy.” Biophysical Journal 106 (2). Elsevier BV: L05–L08. doi:10.1016/j.bpj.2013.12.014.

Ma, Xiaochu, Maolin Lu, Jason Gorman, Daniel S Terry, Xinyu Hong, Zhou Zhou, Hong Zhao, et al. 2018. “HIV-1 Env Trimer Opens Through an Asymmetric Intermediate in Which Individual Protomers Adopt Distinct Conformations.” eLife 7 (March). eLife Sciences Organisation, Ltd. doi:10.7554/elife.34271.

Marechal, V., M.-C. Prevost, C. Petit, E. Perret, J.-M. Heard, and O. Schwartz. 2001. “Human Immunodeficiency Virus Type 1 Entry into Macrophages Mediated by Macropinocytosis.” Journal of Virology 75 (22). American Society for Microbiology: 11166–77. doi:10.1128/jvi.75.22.11166-11177.2001.

Ménager, Mickaël M., and Dan R. Littman. 2016. “Actin Dynamics Regulates Dendritic Cell-Mediated Transfer of HIV-1 to T Cells.” Cell 164 (4). Elsevier BV: 695–709. doi:10.1016/j.cell.2015.12.036.

Mieruszynski, Stephen, Candida Briggs, Michelle A. Digman, Enrico Gratton, and Mark R Jones. 2015. “Live Cell Characterization of DNA Aggregation Delivered Through Lipofection.” Scientific Reports 5 (1). Springer Nature. doi:10.1038/srep10528.

Miyauchi, Kosuke, Yuri Kim, Olga Latinovic, Vladimir Morozov, and Gregory B. Melikyan. 2009. “HIV Enters Cells via Endocytosis and Dynamin-Dependent Fusion with Endosomes.” Cell 137 (3). Elsevier BV: 433–44. doi:10.1016/j.cell.2009.02.046.

Moutin, E., V. Compan, F. Raynaud, C. Clerte, N. Bouquier, G. Labesse, M. L. Ferguson, L. Fagni, C. A. Royer, and J. Perroy. 2014. “The Stoichiometry of Scaffold Complexes in Living Neurons - DLC2 Functions as a Dimerization Engine for GKAP.” Journal of Cell Science 127 (16). The Company of Biologists: 3451–62. doi:10.1242/jcs.145748.

Munro, J. B., J. Gorman, X. Ma, Z. Zhou, J. Arthos, D. R. Burton, W. C. Koff, et al. 2014. “Conformational Dynamics of Single HIV-1 Envelope Trimers on the Surface of Native Virions.” Science 346 (6210). American Association for the Advancement of Science (AAAS): 759–63. doi:10.1126/science.1254426.

Nolan, Rory, L Alvarez, Jonathan Elegheert, Maro Iliopoulou, G Maria Jakobsdottir, Marina Rodriguez-Muñoz, A Radu Aricescu, and Sergi Padilla Parra. 2017. “Nandb—number and Brightness in R with a Novel Automatic Detrending Algorithm.” Bioinformatics 33 (21). Oxford University Press: 3508–10. doi:10.1093/bioinformatics/btx434.

Nolan, Rory, Luis Alvarez, Samuel C. Griffiths, Jonathan Elegheert, Christian Siebold, and Sergi Padilla-Parra. 2018. “Calibration-Free in-Vitro Quantification of Protein Homo-Oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software.” Journal of Visualized Experiments 137 (e58157). MyJove Corporation. doi:10.3791/58157.

Nolan, Rory, and Sergi Padilla-Parra. 2017a. “exampletestr - an Easy Start to Unit Testing R Packages.” Wellcome Open Research 2 (June). F1000 Research, Ltd.: 31. doi:10.12688/wellcomeopenres.11635.2.

———. 2017b. “filesstrings: An R Package for File and String Manipulation.” The Journal of Open Source Software 2 (14). The Open Journal: 260. doi:10.21105/joss.00260.

———. 2018. “ijtiff: An R Package Providing TIFF I/O for ImageJ Users.” Journal of Open Source Software 3 (23). The Open Journal: 633. doi:10.21105/joss.00633.

Nolan, Rory, Maro Iliopoulou, Luis Alvarez, and Sergi Padilla-Parra. 2017. “Detecting Protein Aggregation and Interaction in Live Cells: A Guide to Number and Brightness.” Methods. doi:10.1016/j.ymeth.2017.12.001.

Ozorowski, Gabriel, Jesper Pallesen, Natalia de Val, Dmitry Lyumkis, Christopher A. Cottrell, Jonathan L. Torres, Jeffrey Copps, et al. 2017. “Open and Closed Structures Reveal Allostery and Pliability in the HIV-1 Envelope Spike.” Nature 547 (7663). Springer Nature: 360–63. doi:10.1038/nature23010.

Padilla-Parra, Sergi. 2009. “Developpments Methodologiques Pour La Quantification Des Interactions Proteiques En Cellules Vivantes Par Microscopie de Fluorescence.” PhD thesis, Universite Paris Diderot.

Qian, H., and E. L. Elson. 1990. “Distribution of molecular aggregation by analysis of fluctuation moments.” Proc. Natl. Acad. Sci. U.S.A. 87 (14): 5479–83. doi:10.1073/pnas.87.14.5479.

Qin, L., I. Kufareva, L. G. Holden, C. Wang, Y. Zheng, C. Zhao, G. Fenalti, et al. 2015. “Crystal Structure of the Chemokine Receptor CXCR4 in Complex with a Viral Chemokine.” Science 347 (6226). American Association for the Advancement of Science (AAAS): 1117–22. doi:10.1126/science.1261064.

R Core Team. 2016. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.

Rienzo, Carmine Di, Francesco Cardarelli, Mariagrazia Di Luca, Fabio Beltram, and Enrico Gratton. 2016. “Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells.” Biophysical Journal 111 (4). Elsevier BV: 841–51. doi:10.1016/j.bpj.2016.07.005.

Rueden, C. T., J. Schindelin, M. C. Hiner, B. E. DeZonia, A. E. Walter, E. T. Arena, and K. W. Eliceiri. 2017. “ImageJ2: ImageJ for the next generation of scientific image data.” BMC Bioinformatics 18 (1): 529. doi:10.1186/s12859-017-1934-z.

Sahoo, Harekrushna, and Petra Schwille. 2011. “FRET and FCS-Friends or Foes?” ChemPhysChem 12 (3). Wiley: 532–41. doi:10.1002/cphc.201000776.

Schindelin, J., I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, et al. 2012. “Fiji: an open-source platform for biological-image analysis.” Nat. Methods 9 (7): 676–82. doi:10.1038/nmeth.2019.

Stroustrup, Bjarne. 2013. The C++ Programming Language. 4th ed. Addison-Wesley Professional.

Tan, Q., Y. Zhu, J. Li, Z. Chen, G. W. Han, I. Kufareva, T. Li, et al. 2013. “Structure of the CCR5 Chemokine Receptor-HIV Entry Inhibitor Maraviroc Complex.” Science 341 (6152). American Association for the Advancement of Science (AAAS): 1387–90. doi:10.1126/science.1241475.

Wu, Lijun, Norma P. Gerard, Richard Wyatt, Hyeryun Choe, Cristina Parolin, Nancy Ruffing, Alessândra Borsetti, et al. 1996. “CD4-Induced Interaction of Primary HIV-1 Gp120 Glycoproteins with the Chemokine Receptor CCR-5.” Nature 384 (6605). Springer Nature: 179–83. doi:10.1038/384179a0.

Zhao, M., L. Jin, B. Chen, Y. Ding, H. Ma, and D. Chen. 2003. “Afterpulsing and its correction in fluorescence correlation spectroscopy experiments.” Appl Opt 42 (19): 4031–6.