Biophysics: Microbes and Microscopy


See here, here, and here for suggested readings in Biophysics.

See here for a description of Prof. Parthasarathy's pop-science book about biophysics, So Simple a Beginning: How Four Physical Principles Shape Our Living World (2022).

Parthasarathy Lab, The University of Oregon

[preprint] Julia S. Ngo, Piyush Amitabh, Jonah G Sokoloff, Calvin Trinh, Travis J Wiles, Karen Guillemin, and Raghuveer Parthasarathy, "Bacterial Modulation of Intestinal Motility through Macrophage Redistribution." bioRxiv (2024). [DOI / Link]

T. Jarrod Smith, Deepika Sundarraman, Ellie Melancon, Laura Desban, Raghuveer Parthasarathy, and Karen Guillemin, "A mucin-regulated adhesin determines the spatial organization and inflammatory character of a bacterial symbiont in the vertebrate gut." Cell Host and Microbe 31: 1371-1375 (2023). [Link] [bioRxiv]

Deepika Sundarraman, T. Jarrod Smith, Jade V. Z. Kast, Karen Guillemin, and Raghuveer Parthasarathy, "Disaggregation as an interaction mechanism among intestinal bacteria." Biophysical Journal 121: 3458-3473 (2022). [Link] [Blog post]

Jennifer Hampton Hill, Michelle Sconce Massaquoi, Emily Goers Sweeney, Elena S. Wall, Philip Jahl, Rickesha Bell, Karen Kallio, Daniel Derrick, L. Charles Murtaugh, Raghuveer Parthasarathy, S. James Remington, June L. Round, Karen Guillemin, "BefA, a microbiota-secreted membrane disrupter disseminates to the pancreas and increases β cell mass" Cell Metabolism 34: 1779-1791.e9 (2022). [Link] [bioRxiv]

Raghuveer Parthasarathy, "Resource Letter: Biological Physics," The American Journal of Physics 89 (2021). [Link] [Preprint (earlier version)]

Philip E. Jahl and Raghuveer Parthasarathy, "Assessing the use of ellipsoidal microparticles for determining lipid membrane viscosity." Biophysical Journal 120: 5513-5520 (2021). [Link] [bioRxiv]

Brandon H Schlomann and Raghuveer Parthasarathy, "Gut bacterial aggregates as living gels." eLife 10: e71105 (2021). [Link] [Blog post]

Deepika Sundarraman*, Edouard A. Hay*, Dylan M. Martins*, Drew S. Shields, Noah L. Pettinari, and Raghuveer Parthasarathy, "Higher-Order Interactions Dampen Pairwise Competition in the Zebrafish Gut Microbiome." mBio 11:e01667-20 (2020). (Selected as an "Editor's Pick.") [Link] [Blog post]

T. J. Wiles*, B. H. Schlomann*, E. S. Wall, R. Betancourt, R. Parthasarathy, K. Guillemin, "Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation." PLoS Biology 18:(3): e3000661 (2020). [Link] [Blog post]

Philip E. Jahl, Raghuveer Parthasarathy, "Lipid Bilayer Hydrodynamic Drag." Phys. Rev. Research 2, 013132 (2020). [Link] [Blog post]

B. H. Schlomann*, T. J. Wiles*, E. S. Wall, K. Guillemin, R. Parthasarathy, "Sublethal antibiotics collapse gut bacterial populations by enhancing aggregation and expulsion." Proc. Natl. Acad. Sci. 116: 21392-21400 (2019). [Link] [bioRxiv Preprint] [Blog post] [Writeup in Nature Reviews Microbiology] [Writeup in Trends in Microbiology]

[Review] Brandon H Schlomann and Raghuveer Parthasarathy, "Timescales of gut microbiome dynamics." Current Opinion in Microbiology 50:56-63 (2019). [Link]

Brandon H Schlomann, Travis J Wiles, Elena S Wall, Karen Guillemin, Raghuveer Parthasarathy, "Bacterial cohesion predicts spatial distribution in the larval zebrafish intestine." Biophysical Journal 115: 1-7 (2018). [Link]. bioRxiv preprint (old version); Blog post.

Catherine D. Robinson, Helena S. Klein, Kyleah D. Murphy, Raghuveer Parthasarathy, Karen Guillemin, Brendan J. M. Bohannan, "Experimental bacterial adaptation to the zebrafish gut reveals a primary role for immigration." PLoS Biology 16: e2006893 (2018). [Link].

Savannah L Logan, Christopher Dudley, Ryan P Baker, Michael J Taormina, Edouard A Hay, Raghuveer Parthasarathy, "Automated High-Throughput Light-Sheet Fluorescence Microscopy of Larval Zebrafish," PLOS ONE 13: e0198705 (2018). [Link]

Travis J. Wiles, Elena S. Wall, Brandon H. Schlomann, Edouard A. Hay, Raghuveer Parthasarathy, and Karen Guillemin, "Modernized tools for streamlined genetic manipulation and comparative study of wild and diverse proteobacterial lineages." mBio 9: e01877-18 (2018). [Link]. bioRxiv preprint (old version) [Link].

E. A. Hay and R. Parthasarathy, "Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets." PLOS Computational Biology 14(12): e1006628 (2018) [Link].

Brandon Schlomann, "Stationary moments, diffusion limits, and extinction times for logistic growth with random catastrophes." Journal of Theoretical Biology 454: 154-163 (2018). [Link]

S. L. Logan, J. Thomas, J. Yan, R. P. Baker, D. S. Shields, J. B. Xavier, B. K. Hammer, and R. Parthasarathy, "The Vibrio cholerae Type VI Secretion System Can Modulate Host Intestinal Mechanics to Displace Commensal Gut Bacteria." Proc. Natl. Acad. Sci. 115: E3779-E3787 (2018). [Link]; Blog post. Writeup in [link]

J. Ganz, R. P. Baker, M. K. Hamilton, E. Melancon, P. Diba, J. S. Eisen, and R. Parthasarathy, "Image velocimetry and spectral analysis enable quantitative characterization of larval zebrafish gut motility." Neurogastroenterology and Motility 30: e13351 (2018). [Link] [(2017 bioRxiv)]

[Review] Raghuveer Parthasarathy, "Monitoring microbial communities using light sheet fluorescence microscopy." Current Opinion in Microbiology 43:31-37 (2018). [Link] Preprint (peerJ): [Link].

Vincent L. Thoms*, Tristan T. Hormel*, Matthew A. Reyer, and Raghuveer Parthasarathy [* Equal contributors], "Tension Independence of Lipid Diffusion and Membrane Viscosity," Langmuir 33:12510-12515 (2017). [Link]

Michael J. Taormina*, Edouard A. Hay*, and Raghuveer Parthasarathy [* = equal contributors], "Passive and Active Microrheology of the Intestinal Fluid of the Larval Zebrafish." Biophysical Journal 113:957-965 (2017). [Link]

J. T. Nichols, B. Blanco-Sanchez, E. P. Brooks, R. Parthasarathy, J. Dowd, A. Subramanian, G. Nachtrab, K. D. Poss, T. F. Schilling, and C. B. Kimmel, "Ligament versus bone cell identity in the zebrafish hyoid skeleton is regulated by mef2ca." Development 143: 4430-4440 (2016). [PMID 27789622] [Link]

Travis J. Wiles, Matthew L. Jemielita, Ryan P. Baker, Brandon H. Schlomann, Savannah L. Logan, Julia Ganz, Ellie Melancon, Judith S. Eisen, Karen Guillemin, and Raghuveer Parthasarathy , "Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota." PLoS Biol. 14(7): e1002517 (2016). [Link.] (Earlier version (preprint) at bioRxiv.) Writeup in [Link]; [Blog post]

A. S. Rolig, R. Parthasarathy, A. R. Burns, B. J. M. Bohannan, and K. Guillemin, "Individual Members of the Microbiota Disproportionately Modulate Host Innate Immune Responses." Cell Host Microbe 18: 613-620 (2015). [PMID 26567512] [Link]

W. Z. Stephens, T. J. Wiles, E. S. Martinez, M. Jemielita, A. R. Burns, R. Parthasarathy, B. J. M. Bohannan, and K. Guillemin, "Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine." mBio 6: (2015). [PMID 26507229] [Link]

Tristan T. Hormel, Matthew A. Reyer, Raghuveer Parthasarathy, "Two-Point Microrheology of Phase-Separated Domains in Lipid Bilayers." Biophys. J. 109: 732-726 (2015). [PMID 26287625] [Link]

M. D. Hammers, M. J. Taormina, M. M. Cerda, L. A. Montoya, D. T. Seidenkranz, R. Parthasarathy, and M. D. Pluth, "A Bright Fluorescent Probe for H2S Enables Analyte-Responsive, 3D Imaging in Live Zebrafish Using Light Sheet Fluorescence Microscopy." J. Am. Chem. Soc. 137: 10216-10223 (2015), DOI:10.1021/jacs.5b04196. [PMID 26061541] [Link]
Cover art: We made the cover of JACS They didn't accept my overall design, but kept the zebrafish I painted. Here's a direct link to the cover image. -- RP

Raghuveer Parthasarathy, "The Physics of Life: an undergraduate general education biophysics course," Phys. Educ. 50:358-366 (2015). DOI:10.1088/0031-9120/50/3/358 [Link]

Ryan Baker, Michael J. Taormina, Matthew Jemielita, and Raghuveer Parthasarathy, "A combined light sheet fluorescence and differential interference contrast microscope for live imaging of multicellular specimens," J. Microscopy 258: 105-112 (2015). DOI: 10.1111/jmi.12220 [Link]

Matthew Jemielita, Michael J Taormina, Adam R Burns, Jennifer S Hampton, Annah S Rolig, Karen Guillemin, Raghuveer Parthasarathy, "Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut," mBio 5: e01751-14 (2014). [Link] [Blog post] Our work was selected as a featured image by mBio.

Tristan T. Hormel, Sarah Q. Kurihara, M. Kathleen Brennan, Matthew C. Wozniak, and Raghuveer Parthasarathy, "Measuring Lipid Membrane Viscosity Using Rotational and Translational Probe Diffusion," Phys. Rev. Lett. 112, 188101 (2014). [Link]. This paper was also featured with a "synopsis" in Physics: [Link] and as a "research highlight" in Nature Chemical Biology: [Link]. [Blog post]

Kyle J. Welch, Isaac Hastings-Hauss, Raghuveer Parthasarathy, and Eric I. Corwin, "Ballistic and diffusive dynamics in a two-dimensional ideal gas of macroscopic chaotic Faraday waves," Phys. Rev. E 89: 042143 (2014). [Link]

Alexander R. Small and Raghuveer Parthasarathy, "Superresolution Localization Methods," Annual Reviews of Physical Chemistry 65: 107-125 (2014). [Link]

Andrew F. Loftus, Sigrid Noreng, Vivian L. Hsieh, and Raghuveer Parthasarathy, "Robust Measurement of Membrane Bending Moduli Using Light Sheet Fluorescence Imaging of Vesicle Fluctuations," Langmuir 29: 14588-14594 (2013). [Link.] [Blog post]

Matthew Jemielita*, Michael J. Taormina*, April DeLaurier, Charles B. Kimmel, and Raghuveer Parthasarathy (*Equal authors), "Comparing phototoxicity during the development of a zebrafish craniofacial bone using confocal and light sheet fluorescence microscopy techniques," J. Biophotonics 6: 920-928 (2013). [Link]

Andrew F. Loftus, Vivian Hsieh, and Raghuveer Parthasarathy, "Modulation of membrane rigidity by the human vesicle trafficking proteins Sar1A and Sar1B," Biophys. Biochem. Res. Comm. 426: 585-589 (2012). Link.

Raghuveer Parthasarathy, "Rapid, accurate particle tracking by calculation of radial symmetry centers," Nature Methods 9: 724-726 (2012), DOI: 10.1038/nmeth.2071 . [Link]
Abstract: I introduce an algorithm for sub-pixel localization of imaged objects based on an analytic, non-iterative calculation of the best-fit radial symmetry center. This approach yields tracking accuracies that are near theoretical limits, similar to Gaussian fitting, but with orders of magnitude faster execution time, lower sensitivity to nearby particles, and applicability to any radially symmetric intensity distribution. I demonstrate the method with several types of data, including super-resolution microscopy images.
Also: There's an associated News and Views article (by Alex Small).

Michael J. Taormina, Matthew Jemielita, W. Zac Stephens, Adam R. Burns, Joshua V. Troll, Raghuveer Parthasarathy, and Karen Guillemin, "Investigating Bacterial-Animal Symbioses with Light Sheet Microscopy," Biol. Bulletin 223: 7-20 (2012). (Part of a special issue on "Discoveries in Animal Symbiosis in the 'omics' Age," August 2012.) [Link]

Emily Goers Sweeney, J. Nathan Henderson, John Goers, Christopher Wreden, Kevin G. Hicks, Jeneva K. Foster, Raghuveer Parthasarathy, S. James Remington, and Karen Guillemin, "Structure and Proposed Mechanism for the pH-Sensing Helicobacter pylori Chemoreceptor TlpB," Structure 20: 1177-1188 (2012). [Link]
Cover art: My artwork for this paper is on the cover of the July issue of Structure. -- RP

Raghuveer Parthasarathy, "Cars and Kinetic Energy - Some Simple Physics with Real-World Relevance," The Physics Teacher 50: 395-397 (2012). [Publisher Link] [Local link]

[Book Chapter] Raghuveer Parthasarathy, "Optics: Basic Physics," in Handbook of Biomedical Optics, ed. D.A. Boas, C. Pitris, N. Ramanujam (CRC Press, 2011). [Link]

[Retracted] Christopher W. Harland, Miranda J. Bradley, and Raghuveer Parthasarathy, "Phospholipid bilayers are viscoelastic," Proc. Natl. Acad. Sci. USA 107: 19146-19150 (2010). Link The conclusions of this paper are wrong -- a consequence of insufficiently precise analysis. Our retraction notice was published in August 2011; you can read the page proof here or a version with graphs (not allowed in the official retraction notice) here. We deeply regret any confusion or wasted effort caused by our flawed paper, and we are happy to provide additional information or resources on technical issues related to the paper's methods.
A postscript: Spurred by these events, I've been thinking about whether there can exist a particle tracking method that is as accurate as direct fitting of Gaussian intensity profiles to particle images (the present state-of-the-art) but that is computationally much faster. I have come up with a new sort of tracking, based on maximizing radial symmetry, that works well. For a very brief description, see here. For a longer discussion and tests of the method, see my 2012 Nature Methods paper noted above, and my Particle Tracking page. -- RP.

Edward I. Settles*, Andrew F. Loftus*, Alesia N. McKeown, and Raghuveer Parthasarathy, "The vesicle trafficking protein Sar1 lowers lipid membrane rigidity," Biophys. J. 99: 1539-1545 (2010). [* = equal contributors] [ Link]

[Preview / Commentary paper; not a peer-reviewed article] Anica M. Wandler, Raghuveer Parthasarathy, and Karen Guillemin, "A greasy foothold for Helicobacter pylori," Cell Host & Microbe 7: 338-339 (2010). [Link] [PubMed]

Yupeng Kong and Raghuveer Parthasarathy, "Different modulation mechanisms of attractive colloidal interactions by lipid and protein functionalization," Langmuir 26: 10541-10545 (2010). [Link]

Kamil Godula, Marissa L. Umbel, David Rabuka, Zsofia Botyanszki, Carolyn R. Bertozzi, and Raghuveer Parthasarathy, "Control of the molecular orientation of membrane-anchored biomimetic glycopolymers," J. Am. Chem. Soc. 131: 10263-10268 (2009). [Link] See also the cover of Nature Chemical Biology, July 2010: Journal link, a bigger image with some text, and a better description.

Yupeng Kong and Raghuveer Parthasarathy, "Modulation of attractive colloidal interactions by lipid membrane functionalization," Soft Matter, 5: 2027-2029 (2009) [Link]

Christopher W. Harland*, Zsofia Botyanszki*, David Rabuka, Carolyn R. Bertozzi, and Raghuveer Parthasarathy, "Synthetic trehalose glycolipids confer desiccation resistance to supported lipid monolayers," Langmuir 25: 5193-5198, (2009) [*These authors contributed equally to this work][Link], [PMC Link]

Gregory T. Tietjen, Yupeng Kong, and Raghuveer Parthasarathy "An efficient method for the creation of tunable optical line traps via control of gradient and scattering forces," Opt. Express 16: 10341-10348 (2008) [Link]

Christopher W. Harland, David Rabuka, Carolyn R. Bertozzi, and Raghuveer Parthasarathy. "The M. tuberculosis virulence factor trehalose dimycolate imparts desiccation resistance to model mycobacterial membranes," Biophys. J. 94: 4718-4724 (2008). [Link]

Jay T. Groves, Raghuveer Parthasarathy, and Martin B. Forstner, "Fluorescence Imaging of Membrane Dynamics," Annu. Rev. Biomed. Eng. 10: 311-338 (2008). [Link]

Raghuveer Parthasarathy, David Rabuka, Carolyn Bertozzi, and Jay T. Groves, "Molecular Orientation of Membrane-Anchored Mucin Glycoprotein Mimics, J. Phys. Chem. B, 111: 12133-12135 (2007). [ACS]

David Rabuka, Raghuveer Parthasarathy, Goo Soo Lee, Xing Chen, Jay T. Groves, and Carolyn Bertozzi, "Hierarchical Assembly of Model Cell Surfaces: Synthesis of Mucin Mimetic Polymers and Their Display on Supported Bilayers," J. Amer. Chem. Soc., 129: 5462-5471 (2007). [ACS]

Raghuveer Parthasarathy and Jay T. Groves, "Curvature and spatial organization in biological membranes," Soft Matter, 3: 24-33 (2007). [Link to Soft Matter] [ Journal Cover ]

Membrane biophysics (2004 to 2006)

Raghuveer Parthasarathy, Cheng-han Yu, and Jay T. Groves, "Curvature modulated phase separation in lipid bilayer membranes," Langmuir, 22: 5095-5099 (2006). [ACS]

Raghuveer Parthasarathy and Jay T. Groves, "Coupled membrane fluctuations and protein mobility in supported intermembrane junctions," J. Phys. Chem. B, 110: 8513-8516 (2006). [ACS]

Raghuveer Parthasarathy, Paul A. Cripe, and Jay T. Groves, "Electrostatically Driven Spatial Patterns in Lipid Membrane Composition," Phys. Rev. Lett. 95: 048101 (2005).  [PubMed]

Raghuveer Parthasarathy and Jay T. Groves, "Protein Patterns at Lipid Bilayer Junctions," Proc. Natl. Acad. Sci. 101: 12798-12803 (2004).  [PubMed]

Raghuveer Parthasarathy and Jay T. Groves, "Optical techniques for imaging membrane topography," Cell Biochem. Biophys. 41: 391-414 (2004).  [PubMed]

Raghuveer Parthasarathy, Bryan L. Jackson, Thomas J. Lowery, Amy P. Wong, and Jay T. Groves, "Nonequilibrium Adhesion Patterns at Lipid Bilayer Junctions," J. Phys. Chem. B 108: 649-657 (2004).  [ACS]

Nanocrystals and nanowires (2001 to 2004)

Raghuveer Parthasarathy, Xiao-Min Lin, Klara Elteto, T. F. Rosenbaum, and Heinrich M. Jaeger, "Percolating through Networks of Random Thresholds: Finite Temperature Electron Tunneling in Metal Nanocrystal Arrays," Phys. Rev. Lett. 92: 076801 (2004).

Xiao-Min Lin, Raghuveer Parthasarathy, and Heinrich M. Jaeger, "Nanocrystal Arrays: Self-assembly and physical properties," in the Dekker Encoclyopedia of Nanoscience and Nanotechnology, ed. J.A. Schwarz, C.I. Contescu, K. Putyera (Dekker, 2004).

Thomas Scheibel, Raghuveer Parthasarathy, George Sawicki, Xiao-Min Lin, Heinrich Jaeger, and Susan L. Lindquist, "Conducting nanowires built by controlled self-assembly of amyloid fibers and selective metal deposition," Proc. Natl. Acad. Sci. 100: 4527-4532 (2003). [PNAS]

Raghuveer Parthasarathy, Xiao-Min Lin, and Heinrich M. Jaeger, "Electronic transport in metal nanocrystal arrays: the effect of structural disorder on scaling behavior," Phys. Rev. Lett. 87: 186807 (2001).

Xiao-Min Lin, Raghuveer Parthasarathy, and Heinrich M. Jaeger, "Direct patterning of self-assembled nanocrystal monolayers by electron beams," Appl. Phys. Lett. 78: 1915-1917 (2001). [Link]

Other topics (old)

H. M. Rønnow, R. Parthasarathy, J. Jensen, G. Aeppli, T. F. Rosenbaum, and D. F. McMorrow, "Quantum phase transition of a magnet in a spin bath," Science 308: 389-392 (2005). [Link]

S. Ghosh, R. Parthasarathy, T. F. Rosenbaum, and G. Aeppli, "Coherent spin oscillations in a disordered magnet," Science 296: 2195-2198 (2002). [Link]

S. Anders, R. Parthasarathy, H. M. Jaeger, P. Guptasarma, D. G. Hinks, and R. van Veen, "Dynamics of the second peak in the magnetization of Bi2Sr2CaCu2O8 crystals," Phys. Rev. B 58: 6639-6644 (1998).

D. H. Cobden, G. Pilling, R. Parthasarathy, P. L. McEuen, I. M. Castleton, E. H. Linfield, D. A. Ritchie, and G. A. C. Jones, "Current flow past an etched barrier: field emission from a two-dimensional electron gas," Europhys. Lett. 41: 327-332 (1998).

R. Parthasarathy, C. Franck, R. Treffers, D. Cudaback, C. Heiles, C. Hancox, and R. Millan, "A rooftop radio observatory: an undergraduate telescope system at the University of California at Berkeley," Am. J. Phys. 66: 768-771 (1998).[Link]