Skip to main content Accessibility help
×
Hostname: page-component-cd9895bd7-7cvxr Total loading time: 0 Render date: 2024-12-22T16:16:23.855Z Has data issue: false hasContentIssue false

13 - Experimental Characterisation Techniques

from Part I - Physical Tools

Published online by Cambridge University Press:  12 December 2024

Thomas Andrew Waigh
Affiliation:
University of Manchester
Get access

Summary

Describes a range of physical techniques that can be applied to bacterial biophysics including sample culture, flow cytometry, microscopy, photonics, NMR, mass spectrometry and electrophoresis.

Type
Chapter
Information
The Physics of Bacteria
From Cells to Biofilms
, pp. 102 - 132
Publisher: Cambridge University Press
Print publication year: 2024

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Suggested Reading

Gunning, P. A.; Kirby, A. R.; Morris, V. J., Atomic Force Microscopy for Biologists. Imperial College Press: 1999. Lots of useful tips for sample preparation during AFM experiments.Google Scholar
Mersk, J., An Introduction to Optical Microscopy, 2nd ed. Cambridge University Press: 2019. Optical microscopes are primary tools to study the behaviour of bacteria and confocal microscopy is the standard method used with biofilms. The optical physics of such microscopes is covered in detail.Google Scholar
Waigh, T. A., Advances in the microrheology of complex fluids. Reports on Progress in Physics 2016, 79 (7), 074601. Reviews some applications of microrheology in complex fluids which include biofilms.CrossRefGoogle ScholarPubMed
Waigh, T. A., The Physics of Living Processes. Wiley: 2014. Contains a review of some standard experimental techniques important in biological physics.CrossRefGoogle Scholar
Zaccai, N. R.; Serdyuk, I. N.; Zaccai, J., Methods in Molecular Biophysics: Structure, Dynamics, Function for Biology and Medicine, 2nd ed. Cambridge University Press: 2017. Broad review of physical techniques used in molecular biology experiments.CrossRefGoogle Scholar

References

Jensen, H. J., Complexity Science: The Study of Emergence. Cambridge University Press: 2023.Google Scholar
Waigh, T. A., The Physics of Living Processes. Wiley: 2014.CrossRefGoogle Scholar
Leake, M. C., Single-Molecular Cellular Biophysics. Cambridge University Press: 2013.CrossRefGoogle Scholar
Zaccai, N. R.; Serdyuk, I. N.; Zaccai, J., Methods in Molecular Biophysics. Cambridge University Press: 2017.CrossRefGoogle Scholar
Locke, A.; Fitzgerald, S.; Mahadevan-Jansen, A., Advances in optical detection of human associated pathogenic bacteria. Molecules 2020, 25 (22), 5256.CrossRefGoogle ScholarPubMed
Xu, Y.; Dhaouadi, Y.; Stoodley, P.; Ren, D., Sensing the unreachable: Challenges and opportunities in biofilm detection. Current Opinion in Biotechnology 2020, 64, 7984.CrossRefGoogle ScholarPubMed
Hart, J. W.; Waigh, T. A.; Lu, J. R.; Roberts, I. S., Microrheology and spatial heterogeneity of Staphylococcus aureus biofilms modulated by hydrodynamic shear and biofilm-degrading enzymes. Langmuir 2019, 35 (9), 35533561.CrossRefGoogle ScholarPubMed
Rogers, S. S.; van der Walle, C.; Waigh, T. A., Microrheology of bacterial biofilms in vitro: Staphylococcus aureus and Pseudomonas aeruginosa. Langmuir 2008, 24 (23), 1354913555.CrossRefGoogle ScholarPubMed
Novick, A.; Szilard, L., Experiments with the chemostat on spontaneous mutations of bacteria. Proceedings of the National Academy of Sciences of the United States of America 1950, 36 (12), 708719.CrossRefGoogle ScholarPubMed
McBain, A. J., In vitro biofilm models. In Advances in Applied Microbiology, Laskin, A. I., Ed. Elsevier: 2009; Vol. 69, pp. 100126.Google Scholar
Capuccino, J. G.; Welsh, C., Microbiology: A Laboratory Manual. Pearson: 2018.Google Scholar
Torok, E.; Moran, E.; Cooke, F., Oxford Handbook of Infectious Diseases and Microbiology. Oxford University Press: 2016.CrossRefGoogle Scholar
Woyke, T.; Doud, D. F. R.; Schulz, F., The trajectory of microbial single-cell sequencing. Nature Methods 2017, 14 (11), 10451054.CrossRefGoogle ScholarPubMed
Balagadde, F. K.; You, L.; Hansen, C. L.; Arnold, F. H.; Quake, S. R., Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 2005, 309 (5731), 137140.CrossRefGoogle Scholar
Connell, J. L.; Ritschdorff, E. T.; Whiteley, M.; Shear, J. B., 3D printing of microscopic bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 2013, 110 (46), 1838018385.CrossRefGoogle ScholarPubMed
Waigh, T. A.; Rau, C., X-ray and neutron imaging with colloids. Current Opinion in Colloid and Interface Science 2012, 17 (1), 1322.CrossRefGoogle Scholar
deBoer, J. F.; Milner, T. E.; vanGemert, M. J. C.; Nelson, J. S., Two-dimensional birefringence imaging in biological tissue by polarization-sensitive optical coherence tomography. Optics Letters 1997, 22 (12), 934936.CrossRefGoogle Scholar
Pasquina-Lemonche, L.; et al., The architecture of the Gram positive bacterial cell wall. Nature 2020, 582 (7811), 294297.CrossRefGoogle ScholarPubMed
Phanphak, S.; Georgiades, P.; Li, R.; King, J.; Roberts, I. S.; Waigh, T. A., Super-resolution fluorescence microscopy study of the production of K1 capsules by Escherichia coli: Evidence for the differential distribution of the capsule at the poles and the equator of the cell. Langmuir 2019, 35 (16), 56355646.CrossRefGoogle ScholarPubMed
Morris, V. J.; Kirby, A. R.; Gunning, A. P., Atomic Force Microscopy for Biologists, 2nd ed. Imperial College Press: 2009.CrossRefGoogle Scholar
Lau, P. C. Y.; Dutcher, J. R.; Beveridge, T. J.; Lam, J. S., Absolute quantitation of bacterial biofilm adhesion and viscoelasticity by microbead force spectroscopy. Biophysical Journal 2009, 96 (7), 29352948.CrossRefGoogle ScholarPubMed
Esteban-Ferrer, D.; Edwards, M. A.; Fumagalli, L.; Juarez, A.; Gomila, G., Electric polarization properties of single bacteria measured with electrostatic force microscopy. ACS Nano 2014, 8 (10), 98439849.CrossRefGoogle ScholarPubMed
Mertz, J., Introduction to Optical Microscopy. Cambridge University Press: 2019.CrossRefGoogle Scholar
Drescher, K.; Dunkel, J.; Nadell, C. D.; Bassler, B. L., Architectural transitions in Vibrio cholerae biofilms at single-cell resolution. Proceedings of the National Academy of Sciences of the United States of America 2016, 113 (14), E2066–E2072.Google ScholarPubMed
Hauth, J.; Chodorski, J.; Wirsen, A.; Ulber, R., Improved FRAP measurements on biofilms. Biophysical Journal 2020, 118 (10), 23542365.CrossRefGoogle ScholarPubMed
Golding, I.; Paulsson, J.; Zawilski, S. M.; Cox, E. C., Real-time kinetics of gene activity in individual bacterial cells. Cell 2005, 123 (6), 10251036.CrossRefGoogle Scholar
Zhao, X.; Hilliard, L. R.; Mechery, S. J.; Wang, Y.; Bagwe, R. P.; Jin, S.; Tan, W., A rapid bioassay for single bacterial cell quantitation using bioconjugated nanoparticles. Proceedings of the National Academy of Sciences of the United States of America 2004, 101 (42), 1502715032.CrossRefGoogle ScholarPubMed
Aglott, J. W.; Hardie, K. R., Fluorescent nanosensors reveal dynamics in pH gradients during biofilm formation. npj Biofilms and Microbiomes 2021, 7, 50.Google Scholar
Li, R.; Georgiades, P.; Cox, H.; Phanphak, S.; Roberts, I. S.; Waigh, T. A.; Lu, J. R., Quenched stochastic optical reconstruction microscopy (qSTORM) with graphene oxide. Scientific Reports 2018, 8 (1), 16928.CrossRefGoogle ScholarPubMed
Shi, H.; Shi, Q.; Grodner, B.; Lenz, J. S.; Zipfel, W. R.; Brito, I. L.; de Vlaminck, I., Highly multiplexed spatial mapping of microbial communities. Nature 2020, 588 (7839), 676681.CrossRefGoogle ScholarPubMed
Celli, J. P.; et al., Helicobacter pylori moves through mucus by reducing mucin viscoelasticity. Proceedings of the National Academy of Sciences of the United States of America 2009, 106 (34), 1432114326.CrossRefGoogle ScholarPubMed
Cox, H.; Georgiades, P.; Xu, H.; Waigh, T. A.; Lu, J. R., Self-assembly of mesoscopic peptide surfactant fibrils investigated by STORM super-resolution fluorescence microscopy. Biomacromolecules 2017, 18 (11), 34813491.CrossRefGoogle ScholarPubMed
Berk, V.; Fong, J. C. N.; Dempsey, G. T.; Develioglu, O. N.; Zhuang, X.; Liphardt, J.; Yildiz, F. H.; Chu, S., Molecular architecture and assembly principles of Vibrio cholerae biofilms. Science 2012, 337 (6091), 236239.CrossRefGoogle ScholarPubMed
Wagner, M.; Horn, H., OCT in biofilm research: A comprehensive review. Biotechnology and Bioengineering 2017, 114 (7), 1386.CrossRefGoogle ScholarPubMed
Gierl, L.; Stoy, K.; Faina, A.; Hora, H.; Wagner, M., An open-source robotic platform that enables automated monitoring of replicate biofilm cultivation using OCT. npj Biofilms and Microbiomes 2020, 6 (1), 18.CrossRefGoogle Scholar
White, B. R.; et al., In vivo dynamic human retinal blood flow imaging using ultra-high-speed spectral domain optical Doppler tomography. Optics Express 2003, 11 (25), 34903497.CrossRefGoogle Scholar
Murphy, D. B.; Davidson, M. W., Fundamentals of Light Microscopy and Electronic Imaging, 2nd ed. Wiley: 2012.CrossRefGoogle Scholar
Martinez, V. A.; et al., Differential dynamic microscopy: A high-throughput method for characterizing the motility of microorganisms. Biophysical Journal 2012, 103 (8), 16371647.CrossRefGoogle ScholarPubMed
Popescu, G., Quantitative Phase Imaging of Cells and Tissues. McGraw-Hill: 2011.Google Scholar
Miller, S. D.; Haddock, S. H. D.; Elvidge, C. D.; Lee, T. F., Detection of a bioluminescent milky sea from space. Proceedings of the National Academy of Sciences of the United States of America 2005, 102 (40), 1418114184.CrossRefGoogle ScholarPubMed
Hill, S. C.; et al., Real-time measurement of fluorescence spectra from single airborne biological particles. Field Analytical Chemistry and Technology 1999, 3 (4–5), 221239.3.0.CO;2-7>CrossRefGoogle Scholar
Giovannetti, V.; Lloyd, S.; Maccone, L., Advances in quantum metrology. Nature Photonics 2011, 5 (4), 222229.CrossRefGoogle Scholar
Chao, J. L.; Perevedentseva, E.; CHung, P. H.; Liu, K. K.; Cheng, C. Y.; Chang, C. C.; Cheng, C. L., Nanometer-sized diamond particle as a probe for biolabelling. Biophysical Journal 2007, 93 (6), 21992208.CrossRefGoogle Scholar
Le Sage, D.; et al., Optical magnetic imaging of living cells. Nature 2013, 496 (7446), 486.CrossRefGoogle ScholarPubMed
Taylor, M. A.; Janousek, J.; Daria, V.; Knittel, J.; Hage, B.; Bachor, H. A.; Bowen, W. P., Biological measurement beyond the quantum limit. Nature Photonics 2013, 7 (3), 229233.CrossRefGoogle Scholar
Taylor, M. A.; Bowen, W. P., Quantum metrology and its application in biology. Physics Reports 2016, 615 (5700), 159.CrossRefGoogle Scholar
Lubin, G.; Oron, D.; Rossman, U.; Tenne, R.; Yallapragada, V. J., Photon correlations in spectroscopy and microscopy. ACS Photonics 2022, 9, 28912904.CrossRefGoogle Scholar
Parson, W. W., Modern Optical Spectroscopy, 2nd ed. Springer: 2015.CrossRefGoogle Scholar
Lee, K. S.; et al., An automated Raman-based platform for the sorting of live cells by functional properties. Nature Microbiology 2019, 4 (6), 10351048.CrossRefGoogle ScholarPubMed
Hill, E. H.; Marzan, L. M., Toward plasmonic monitoring of surface effects on bacterial quorum sensing. Current Opinion in Colloid and Interface Science 2017, 32, 110.CrossRefGoogle Scholar
Bodelon, G.; et al., Detection and imaging of quorum sensing in P. aeruginosa biofilm communities by surface-enhanced resonance Raman scattering. Nature Materials 2016, 15 (11), 12031211.CrossRefGoogle Scholar
McNeil-Watson, F.; Tscharnuter, W.; Miller, J., A new instrument for the measurement of very small electrophoretic mobilities using phase analysis light scattering (PALS). Colloids and Surfaces A 1998, 140 (1–3), 5357.CrossRefGoogle Scholar
Waz, N. T.; et al., Influence of the polysaccharide capsule on the bactericidal activity of indolicidin on Streptococcus pneumoniae. Frontiers in Microbiology 2022, 13, 898815.CrossRefGoogle ScholarPubMed
Ashkin, A.; Dziedzic, J. M., Optical trapping and manipulation of viruses and bacteria. Science 1987, 235 (4795), 15171520.CrossRefGoogle ScholarPubMed
Uthe, B.; Sader, J. E.; Pelton, M., Optical measurement of the picosecond fluid mechanics in simple liquids generated by vibrating nanoparticles: A review. Reports on Progress in Physics 2022, 85 (10), 103001.CrossRefGoogle ScholarPubMed
Galy, O.; Latour-Lambert, P.; Zrelli, K.; Ghigo, J. M.; Beloin, C.; Henry, N., Mapping of bacterial biofilm local mechanics by magnetic microparticle actuation. Biophysical Journal 2012, 103 (6), 14001408.CrossRefGoogle ScholarPubMed
Haward, S. J., Microfluidic extensional rheometry using stagnation point flow. Biomicrofluidics 2016, 10 (4), 043401.CrossRefGoogle ScholarPubMed
Waigh, T. A., Advances in the microrheology of complex fluids. Reports on Progress in Physics 2016, 79 (7), 074601.CrossRefGoogle ScholarPubMed
Geisel, S.; Secchi, E.; Vermant, J., Experimental challenges in determining the rheological properties of bacterial biofilms. Interface Focus 2022, 12 (6), 20220032.CrossRefGoogle ScholarPubMed
Pavlovsky, L.; Younger, J. G.; Solomon, M. J., In situ rheology of Staphylococcus epidermidis bacterial biofilms. Soft Matter 2013, 9 (1), 122131.CrossRefGoogle ScholarPubMed
Sabass, B.; Koch, M. D.; Liu, G.; Shaevitz, J. W., Force generation by groups of migrating bacteria. Proceedings of the National Academy of Sciences of the United States of America 2017, 114 (28), 72667271.CrossRefGoogle ScholarPubMed
Separovic, F.; Hofferek, V.; Duff, A. P.; McConville, M. J.; Sani, M. A., In-cell DNP NMR reveals multiple targeting effect of antimicrobial peptide. Journal of Structural Biology: X 2022, 6 (12), 100074.Google ScholarPubMed
Seymour, J. D.; Gage, J. P.; Codd, S. L.; Gerlach, R., Anomalous fluid transport in porous media induced by biofilm growth. Physical Review Letters 2004, 93 (19), 198103.CrossRefGoogle ScholarPubMed
Van de Vyver, H.; et al., A novel mouse model of Staphylococcus aureus vascular graft infection: Noninvasive imaging of biofilm development in vivo. The American Journal of Pathology 2017, 187 (2), 268.CrossRefGoogle ScholarPubMed
Dunham, S. J. B.; Ellis, J. F.; Sweedler, J. V., Mass spectrometry imaging of complex microbial communities. Accounts of Chemical Research 2017, 50 (1), 96104.CrossRefGoogle ScholarPubMed
Etayash, H.; Khan, M. F.; Kaur, K.; Thundat, T., Microfluidic cantilever detects bacteria and measures their susceptibility to antibiotics in small confined volumes. Nature Communications 2016, 7, 12947.CrossRefGoogle ScholarPubMed
Azulay, D. N.; et al., Multiscale X-ray study of Bacillus subtilis biofilms reveals interlinked structural hierarchy and elemental heterogeneity. Proceedings of the National Academy of Sciences of the United States of America 2022, 119 (4), e2118107119.Google ScholarPubMed
Gong, H.; et al., Aggregated amphiphilic antimicrobial peptides embedded in bacterial membranes. ACS Applied Materials and Interfaces 2020, 12 (40), 4442044432.CrossRefGoogle ScholarPubMed
Dogsa, I.; Kriechbaum, M.; Stopar, D.; Laggner, P., Structure of bacterial extracellular polymeric substances at different pH values as determined by SAXS. Biophysical Journal 2005, 89 (4), 27112720.CrossRefGoogle ScholarPubMed
Chemla, Y., A new study of bacterial motion: Superconducting quantum interference device microscopy of magnetotactic bacteria. Biophysical Journal 1999, 76 (6), 33233330.CrossRefGoogle ScholarPubMed
Hsiao, W. W. W.; Hui, Y. Y.; Tsai, P. C.; Chang, H. C., Fluorescent nanodiamond: A versatile tool for long-term cell tracking, super-resolution imaging, and nanoscale temperature sensing. Accounts of Chemical Research 2016, 49 (3), 400407.CrossRefGoogle ScholarPubMed
Rosenblatt, C.; Torres de Araujo, F. F.; Frankel, R. B., Birefringence determination of magnetic moments of magnetotactic bacteria. Biophysical Journal 1982, 40 (1), 8385.CrossRefGoogle ScholarPubMed
Faivre, D.; Fischer, A.; Garcia-Rubio, I.; Mastrogiacomo, G.; Gehring, A. U., Development of cellular magnetic dipoles in magnetotactic bacteria. Biophysical Journal 2010, 99 (4), 12681273.CrossRefGoogle ScholarPubMed
Zvelebil, M. J.; Baum, J. O., Understanding Bioinformatics. Garland Science: 2007.CrossRefGoogle Scholar
Ceri, H.; Olson, M. E.; Stremick, C.; Read, R. R.; Morck, D.; Buret, A., The calgary biofilm device: New technology for rapid determination of antibiotic susceptibilities of bacterial biofilms. Journal of Clinical Microbiology 1999, 37 (6), 17711776.CrossRefGoogle ScholarPubMed
Evanko, D., Measuring a bacteria’s sweet tooth. Nature Methods 2005, 2 (2), 8889.CrossRefGoogle Scholar
Whiteley, M.; Bungera, G.; Bumgarner, R. E.; Passek, M. R.; Teltzel, G. M.; Lory, S.; Greenberg, E. P., Gene expression in P. aeruginosa biofilms. Nature 2001, 413 (6858), 860.CrossRefGoogle Scholar
Edgar, R.; et al., High-sensitivity bacterial detection using biotin-tagged phage and quantum-dot nanocomplexes. Proceedings of the National Academy of Sciences of the United States of America 2006, 103 (13), 48414845.CrossRefGoogle ScholarPubMed
Viovy, J. L., Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms. Reviews of Modern Physics 2000, 72 (3), 813872.CrossRefGoogle Scholar
Castellarnau, M.; Errachid, A.; Madrid, C.; Juarez, A.; Samitier, J., Dielectrophoresis as a tool to characterize and differentiate isogenic mutants of Escherichia coli. Biophysical Journal 2006, 91 (10), 39373945.CrossRefGoogle ScholarPubMed
Dague, E.; Duval, J.; Jorand, F.; Thomas, F.; Gaboriaud, F., Probing surface structures of Shewanella spp. by microelectrophoresis. Biophysical Journal 2006, 90 (7), 26122621.CrossRefGoogle ScholarPubMed
Berg, H. C.; Turner, L., Torque generated by the flagellar motor of Escherichia coli. Biophysical Journal 1993, 65 (5), 22012216.CrossRefGoogle ScholarPubMed
Lewandowki, Z.; Beyenal, H., Fundamentals of Biofilm Research. CRC Press: 2013.CrossRefGoogle Scholar
Chen, C.; Smye, S. W.; Robinson, M. P.; Evans, J. A., Membrane electroporation theories: A review. Medical and Biological Engineering and Computing 2006, 44 (1–2), 514.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×