Single-particle tracking

In life sciences, single-particle tracking is broadly used to quantify the dynamics of molecules/proteins in live cells (of bacteria, yeast, mammalian cells and live Drosophila embryos).{{Cite journal |last1=Höfling |first1=Felix|last2=Franosch|first2=Thomas|date=2013-03-12|title=Anomalous transport in the crowded world of biological cells|journal=Reports on Progress in Physics|volume=76|issue=4|pages=046602 |doi=10.1088/0034-4885/76/4/046602 |pmid=23481518|issn=0034-4885|bibcode=2013RPPh...76d6602H |arxiv=1301.6990|s2cid=40921598}}{{cite journal |last1=Podh |first1=Nitesh Kumar |last2=Paliwal |first2=Sheetal |last3=Dey |first3=Partha |last4=Das |first4=Ayan |last5=Morjaria |first5=Shruti |last6=Mehta |first6=Gunjan |title=In-vivo Single-Molecule Imaging in Yeast: Applications and Challenges |journal=Journal of Molecular Biology |date=5 November 2021 |volume=433 |issue=22 |pages=167250 |doi=10.1016/j.jmb.2021.167250|pmid=34537238 |s2cid=237573437 }}{{Cite journal|last1=Barkai|first1=Eli |last2=Garini|first2=Yuval|last3=Metzler |first3=Ralf|date=2012|title=Strange kinetics of single molecules in living cells |journal=Physics Today|volume=65|issue=8|pages=29–35|doi=10.1063/pt.3.1677|issn=0031-9228 |bibcode=2012PhT....65h..29B}}{{Citation|last1=Mir|first1=Mustafa|title=Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy|volume=1814|date=2018|work=Nanoscale Imaging: Methods and Protocols|pages=541–559|editor-last=Lyubchenko|editor-first=Yuri L.|series=Methods in Molecular Biology|publisher=Springer|place=New York |doi=10.1007/978-1-4939-8591-3_32|isbn=978-1-4939-8591-3 |pmc=6225527|pmid=29956254|last2=Reimer|first2=Armando|last3=Stadler|first3=Michael|last4=Tangara |first4=Astou|last5=Hansen|first5=Anders S.|last6=Hockemeyer|first6=Dirk |last7=Eisen|first7=Michael B. |last8=Garcia|first8=Hernan|last9=Darzacq|first9=Xavier}}{{Cite journal |last1=Ball|first1=David A.|last2=Mehta|first2=Gunjan D.|last3=Salomon-Kent|first3=Ronit|last4=Mazza |first4=Davide|last5=Morisaki|first5=Tatsuya|last6=Mueller|first6=Florian|last7=McNally|first7=James G. |last8=Karpova |first8=Tatiana S.|date=December 2016|title=Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin|journal=Nucleic Acids Research|volume=44|issue=21|pages=e160 |doi=10.1093/nar/gkw744|pmid=27566148|pmc=5137432|issn=0305-1048}} It has been extensively used to study the transcription factor dynamics in live cells.{{Cite journal|last1=Mehta|first1=Gunjan D. |last2=Ball|first2=David A.|last3=Eriksson|first3=Peter R.|last4=Chereji |first4=Razvan V.|last5=Clark |first5=David J.|last6=McNally|first6=James G. |last7=Karpova|first7=Tatiana S.|date=2018-12-06 |title=Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast|journal=Molecular Cell|volume=72 |issue=5|pages=875–887.e9 |doi=10.1016/j.molcel.2018.09.009|pmid=30318444|pmc=6289719|issn=1097-2765}}{{Cite journal|last1=Morisaki|first1=Tatsuya|last2=Müller |first2=Waltraud G. |last3=Golob|first3=Nicole |last4=Mazza|first4=Davide|last5=McNally|first5=James G.|date=2014-07-18|title=Single-molecule analysis of transcription factor binding at transcription sites in live cells |journal=Nature Communications |volume=5|issue=1|pages=4456 |doi=10.1038/ncomms5456|pmid=25034201|pmc=4144071|issn=2041-1723|bibcode=2014NatCo...5.4456M}}{{Cite journal|last1=Presman|first1=Diego M.|last2=Ball |first2=David A.|last3=Paakinaho|first3=Ville|last4=Grimm|first4=Jonathan B.|last5=Lavis|first5=Luke D.|last6=Karpova|first6=Tatiana S.|last7=Hager|first7=Gordon L.|date=2017-07-01|title=Quantifying transcription factor binding dynamics at the single-molecule level in live cells|journal=Methods |series=The 4D Nucleome|volume=123|pages=76–88|doi=10.1016/j.ymeth.2017.03.014|pmid=28315485|pmc=5522764 |issn=1046-2023|hdl=11336/64420}} This method has been extensively used in the last decade to understand the target-search mechanism of proteins in live cells. It addresses fundamental biological questions such as how a protein of interest finds its target in the complex cellular environment? how long does it take to find its target site for binding? what is the residence time of proteins binding to DNA? Recently, SPT has been used to study the kinetics of protein translating and processing in vivo. For molecules which bind large structures such as ribosomes, SPT can be used to extract information about the binding kinetics. As ribosome binding increases the effective size of the smaller molecule, the diffusion rate decreases upon binding. By monitoring these changes in diffusion behavior, direct measurements of binding events are obtained.{{Cite journal|last1=Volkov|first1=Ivan L. |last2=Lindén|first2=Martin|last3=Aguirre Rivera|first3=Javier|last4=Ieong|first4=Ka-Weng|last5=Metelev |first5=Mikhail|last6=Elf|first6=Johan|last7=Johansson|first7=Magnus|date=June 2018|title=tRNA tracking for direct measurements of protein synthesis kinetics in live cells|journal=Nature Chemical Biology|volume=14 |issue=6|pages=618–626|doi=10.1038/s41589-018-0063-y|issn=1552-4469|pmc=6124642|pmid=29769736}}{{Cite journal|last1=Metelev|first1=Mikhail|last2=Volkov|first2=Ivan L.|last3=Lundin|first3=Erik |last4=Gynnå|first4=Arvid H. |last5=Elf|first5=Johan|last6=Johansson|first6=Magnus|date=2020-10-12 |title=Direct measurements of mRNA translation kinetics in living cells|journal=Nature Communications |volume=13 |issue=1 |page=1852 |doi=10.1038/s41467-022-29515-x|pmid=35388013 |pmc=8986856 |biorxiv=10.1101/2020.10.12.335505|s2cid=222803093}} Furthermore, exogenous particles are employed as probes to assess the mechanical properties of the medium, a technique known as passive microrheology.{{Cite journal|last=Wirtz|first=Denis|date=2009|title=Particle-Tracking Microrheology of Living Cells: Principles and Applications|journal=Annual Review of Biophysics |volume=38|issue=1|pages=301–326 |doi=10.1146/annurev.biophys.050708.133724|pmid=19416071|issn=1936-122X |citeseerx=10.1.1.295.9645}} This technique has been applied to investigate the motion of lipids and proteins within membranes,{{cite journal |doi=10.1146/annurev.biophys.26.1.373 |pmid=9241424|title=Single-Particle Tracking: Applications to Membrane Dynamics|journal=Annual Review of Biophysics and Biomolecular Structure|volume=26|pages=373–399 |year=1997|last1=Saxton |first1=Michael J.|last2=Jacobson|first2=Ken}}{{Citation|last=Krapf|first=Diego|date=2015|chapter-url=http://linkinghub.elsevier.com/retrieve/pii/S1063582315000034|pages=167–207|publisher=Elsevier |doi=10.1016/bs.ctm.2015.03.002|pmid=26015283|isbn=9780128032954|access-date=2018-08-20|chapter=Mechanisms Underlying Anomalous Diffusion in the Plasma Membrane|title=Lipid Domains|volume=75|series=Current Topics in Membranes|s2cid=34712482 }} molecules in the nucleus and cytoplasm,{{Cite journal |last=Golding|first=Ido|date=2006|title=Physical Nature of Bacterial Cytoplasm|journal=Physical Review Letters|volume=96|issue=9|pages=098102 |doi=10.1103/PhysRevLett.96.098102|pmid=16606319 |bibcode=2006PhRvL..96i8102G}} organelles and molecules therein,{{Cite journal|last1=Nixon-Abell|first1=Jonathon|last2=Obara|first2=Christopher J.|last3=Weigel |first3=Aubrey V.|last4=Li|first4=Dong |last5=Legant|first5=Wesley R.|last6=Xu|first6=C. Shan|last7=Pasolli|first7=H. Amalia|last8=Harvey |first8=Kirsten|last9=Hess|first9=Harald F.|date=2016-10-28|title=Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER|journal=Science|volume=354|issue=6311 |pages=aaf3928|doi=10.1126/science.aaf3928|issn=0036-8075|pmid=27789813|pmc=6528812}} lipid granules,{{Cite journal|last=Tolić-Nørrelykke|first=Iva Marija|date=2004|title=Anomalous Diffusion in Living Yeast Cells|journal=Physical Review Letters|volume=93|issue=7|pages=078102|pmid=15324280 |doi=10.1103/PhysRevLett.93.078102 |bibcode=2004PhRvL..93g8102T|s2cid=2544882}}{{Cite journal |last=Jeon|first=Jae-Hyung|date=2011|title=In Vivo Anomalous Diffusion and Weak Ergodicity Breaking of Lipid Granules|journal=Physical Review Letters|volume=106 |issue=4|pages=048103|pmid=21405366 |doi=10.1103/PhysRevLett.106.048103|bibcode=2011PhRvL.106d8103J|arxiv=1010.0347|s2cid=1049771}}{{Cite journal|last1=Chen|first1=Yu|last2=Rees|first2=Thomas W|last3=Ji|first3=Liangnian |last4=Chao |first4=Hui|date=2018|title=Mitochondrial dynamics tracking with iridium(III) complexes|journal=Current Opinion in Chemical Biology |volume=43|pages=51–57|doi=10.1016/j.cbpa.2017.11.006|pmid=29175532|issn=1367-5931|doi-access=free}} vesicles, and particles introduced in the cytoplasm or the nucleus. Additionally, single-particle tracking has been extensively used in the study of reconstituted lipid bilayers,{{Cite journal|last1=Knight |first1=Jefferson D.|last2=Falke|first2=Joseph J.|date=2009|title=Single-Molecule Fluorescence Studies of a PH Domain: New Insights into the Membrane Docking Reaction|journal=Biophysical Journal|volume=96|issue=2|pages=566–582 |doi=10.1016/j.bpj.2008.10.020|issn=0006-3495|pmc=2716689 |pmid=19167305|bibcode=2009BpJ....96..566K}} intermittent diffusion between 3D and either 2D (e.g., a membrane) {{Cite journal|last1=Campagnola|first1=Grace |last2=Nepal|first2=Kanti|last3=Schroder |first3=Bryce W.|last4=Peersen|first4=Olve B.|last5=Krapf|first5=Diego|date=2015-12-07|title=Superdiffusive motion of membrane-targeting C2 domains|journal=Scientific Reports|volume=5 |issue=1|pages=17721 |doi=10.1038/srep17721|pmc=4671060|pmid=26639944|arxiv=1506.03795|bibcode=2015NatSR...517721C|issn=2045-2322}} or 1D (e.g., a DNA polymer) phases, and synthetic entangled actin networks.{{Cite journal|last=Wong|first=I. Y.|date=2004|title=Anomalous Diffusion Probes Microstructure Dynamics of Entangled F-Actin Networks|journal=Physical Review Letters|volume=92|issue=17|pages=178101 |doi=10.1103/PhysRevLett.92.178101 |pmid=15169197|bibcode=2004PhRvL..92q8101W|s2cid=16461939}}{{Cite journal|last1=Wang|first1=Bo|last2=Anthony|first2=Stephen M.|last3=Bae|first3=Sung Chul |last4=Granick|first4=Steve|date=2009-09-08|title=Anomalous yet Brownian|journal=Proceedings of the National Academy of Sciences|volume=106|issue=36|pages=15160–15164|doi=10.1073/pnas.0903554106|pmc=2776241 |pmid=19666495|bibcode=2009PNAS..10615160W|doi-access=free}}

The most common type of particles used in single particle tracking are based either on scatterers, such as polystyrene beads or gold nanoparticles that can be tracked using bright field illumination, or fluorescent particles. For fluorescent tags, there are many different options with their own advantages and disadvantages, including quantum dots, fluorescent proteins, organic fluorophores, and cyanine dyes.

On a fundamental level, once the images are obtained, single-particle tracking is a two step process. First the particles are detected and then the localized different particles are connected in order to obtain individual trajectories.

Besides performing particle tracking in 2D, there are several imaging modalities for 3D particle tracking, including multifocal plane microscopy,{{cite journal|last1=Ram|first1=Sripad|last2=Prabhat|first2=Prashant|last3=Chao|first3=Jerry|last4=Sally Ward|first4=E.|last5=Ober|first5=Raimund J.|year=2008|title=High accuracy 3D quantum dotifocal plane microscopy for the study of fast intracellular dynamics in live cells|journal=Biophysical Journal|volume=95|issue=12|pages=6025–6043|doi=10.1529/biophysj.108.140392|pmid=18835896|pmc=2599831|bibcode=2008BpJ....95.6025R}} double helix point spread function microscopy,{{cite journal|last1=Badieirostami|first1=M.|last2=Lew|first2=M. D.|last3=Thompson|first3=M. A.|last4=Moerner|first4=W. E.|year=2010|title=Three-dimensional localization precision of the double-helix point spread function versus astigmatism and biplane|journal=Applied Physics Letters|volume=97|issue=16|pages=161103|doi=10.1063/1.3499652|pmid=21079725|pmc=2980550|bibcode=2010ApPhL..97p1103B}} and introducing astigmatism via a cylindrical lens or adaptive optics.

{{main|Brownian motion}}

• Brownian motion
• Diffusion
• Microrheology
• Nanoparticle tracking analysis
• Single-molecule experiment
• Single particle trajectory
• Tethered particle motion

{{reflist}}

• [https://imagej.net/TrackMate TrackMate]
• [https://www.utsouthwestern.edu/labs/danuser/software/#utrack_anc U-Track]
• [https://www.oxinst.com/learning/view/article/double-helix-and-super-resolution Double helix PSF method (Andor)]
• [http://inadilic.fr/data/ Examples of simulated or experimental single-particle trajectories]

Category:Laboratory techniques