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Mukhopadhyay S, Bishayi R, Shaji A, Lee AH, Gupta R, Mohajeri M, Katiyar A, McKee B, Schmitz IR, Shin R, Lele TP, Lele PP. Dynamic Adaptation in Extant Porins Facilitates Antibiotic Tolerance in Energetic Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583920. [PMID: 38496420 PMCID: PMC10942424 DOI: 10.1101/2024.03.07.583920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Bacteria can tolerate antibiotics despite lacking the genetic components for resistance. The prevailing notion is that tolerance results from depleted cellular energy or cell dormancy. In contrast to this view, many cells in the tolerant population of Escherichia coli can exhibit motility - a phenomenon that requires cellular energy, specifically, the proton-motive force (PMF). As these motile-tolerant cells are challenging to isolate from the heterogeneous tolerant population, their survival mechanism is unknown. Here, we discovered that motile bacteria segregate themselves from the tolerant population under micro-confinement, owing to their unique ability to penetrate micron-sized channels. Single-cell measurements on the motile-tolerant population showed that the cells retained a high PMF, but they did not survive through active efflux alone. By utilizing growth assays, single-cell fluorescence studies, and chemotaxis assays, we showed that the cells survived by dynamically inhibiting the function of existing porins in the outer membrane. A drug transport model for porin-mediated intake and efflux pump-mediated expulsion suggested that energetic tolerant cells withstand antibiotics by constricting their porins. The novel porin adaptation we have uncovered is independent of gene expression changes and may involve electrostatic modifications within individual porins to prevent extracellular ligand entry.
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2
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Antani JD, Shaji A, Gupta R, Lele PP. Reassessing the Standard Chemotaxis Framework for Understanding Biased Migration in Helicobacter pylori. Annu Rev Chem Biomol Eng 2023; 15. [PMID: 38048436 DOI: 10.1146/annurev-chembioeng-100722-114625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Helicobacter pylori infections are a major cause of peptic ulcers and gastric cancers. The development of robust inflammation in response to these flagellated, motile bacteria is correlated with poor prognosis. Chemotaxis plays a crucial role in H. pylori colonization, enabling the bacteria to swim toward favorable chemical environments. Unlike the model species of bacterial chemotaxis, Escherichia coli, H. pylori cells possess polar flagella. They run forward by rotating their flagella counterclockwise, whereas backward runs are achieved by rotating their flagella clockwise. We delve into the implications of certain features of the canonical model of chemotaxis on our understanding of biased migration in polarly flagellated bacteria such as H. pylori. In particular, we predict how the translational displacement of H. pylori cells during a backward run could give rise to chemotaxis errors within the canonical framework. Also, H. pylori lack key chemotaxis enzymes found in E. coli, without which sensitive detection of ligands with a wide dynamic range seems unlikely. Despite these problems, H. pylori exhibit robust ability to migrate toward urea-rich sources. We emphasize various unresolved questions regarding the biophysical mechanisms of chemotaxis in H. pylori, shedding light on potential directions for future research. Understanding the intricacies of biased migration in H. pylori could offer valuable insights into how pathogens breach various protective barriers in the human host. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering , Volume 15 is June 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA; , , ,
- Current affiliation: Department of Ecology and Evolutionary Biology, Center for Phage Biology & Therapy, and Quantitative Biology Institute, Yale University, New Haven, Connecticut, USA
| | - Aakansha Shaji
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA; , , ,
| | - Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA; , , ,
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA; , , ,
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
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3
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Vidwans NA, Rhee KY, Lele PP, Vaddiraju S. Real-Time Deduction of Mechanisms and Kinetics Underlying Photocatalytic Water Disinfection: Cell Motility and Particle Tracking. ACS ES T Water 2023; 3:2938-2947. [PMID: 38204756 PMCID: PMC10778399 DOI: 10.1021/acsestwater.3c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The current methods used to study photocatalysis-assisted water disinfection at a laboratory scale may not lead to process scale-up for large-scale implementation. These methods do not capture the process complexity and address all the factors underlying disinfection kinetics, including the physical characteristics (e.g., shape and size) of the photocatalyst, the light intensity, the form of the catalyst (e.g., free-floating and immobilized), and the photocatalyst-microorganism interaction mode (e.g., collision mode and constant contact mode). This drawback can be overcome using in situ methods to track the interaction between the photocatalysts and the microorganisms (e.g., Escherichia coli) and thereby engineering the resulting disinfection kinetics. Contextually, this study employed microscopy and particle-tracking algorithms to quantify in situ cell motility of E. coli undergoing titanium dioxide (TiO2) nanowire-assisted photocatalysis, which was observed to correlate with cell viability closely. This experimentation also informed that the E. coli bacterium interacted with the photocatalysts through collisions (without sustained contact), which allowed for phenomenological modeling of the observed first-order kinetics of E. coli inactivation. Addition of fluorescent-tagging assays to microscopy revealed that cell membrane integrity loss is the primary mode of bacterial inactivation. This methodology is independent of the microorganism or the photocatalyst type and hence is expected to be beneficial for engineering disinfection kinetics.
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Affiliation(s)
- Niraj Ashutosh Vidwans
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Kathy Y Rhee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Sreeram Vaddiraju
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
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Lee AH, Gupta R, Nguyen HN, Schmitz IR, Siegele DA, Lele PP. Heterogeneous Distribution of Proton Motive Force in Nonheritable Antibiotic Resistance. mBio 2023; 14:e0238422. [PMID: 36598258 PMCID: PMC9973297 DOI: 10.1128/mbio.02384-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/21/2022] [Indexed: 01/05/2023] Open
Abstract
Bacterial infections that are difficult to eradicate are often treated by sequentially exposing the bacteria to different antibiotics. Although effective, this approach can give rise to epigenetic or other phenomena that may help some cells adapt to and tolerate the antibiotics. Characteristics of such adapted cells are dormancy and low energy levels, which promote survival without lending long-term genetic resistance against antibiotics. In this work, we quantified motility in cells of Escherichia coli that adapted and survived sequential exposure to lethal doses of antibiotics. In populations that adapted to transcriptional inhibition by rifampicin, we observed that ~1 of 3 cells continued swimming for several hours in the presence of lethal concentrations of ampicillin. As motility is powered by proton motive force (PMF), our results suggested that many adapted cells retained a high PMF. Single-cell growth assays revealed that the high-PMF cells resuscitated and divided upon the removal of ampicillin, just as the low-PMF cells did, a behavior reminiscent of persister cells. Our results are consistent with the notion that cells in a clonal population may employ multiple different mechanisms to adapt to antibiotic stresses. Variable PMF is likely a feature of a bet-hedging strategy: a fraction of the adapted cell population lies dormant while the other fraction retains high PMF to be able to swim out of the deleterious environment. IMPORTANCE Bacterial cells with low PMF may survive antibiotic stress due to dormancy, which favors nonheritable resistance without genetic mutations or acquisitions. On the other hand, cells with high PMF are less tolerant, as PMF helps in the uptake of certain antibiotics. Here, we quantified flagellar motility as an indirect measure of the PMF in cells of Escherichia coli that had adapted to ampicillin. Despite the disadvantage of maintaining a high PMF in the presence of antibiotics, we observed high PMF in ~30% of the cells, as evidenced by their ability to swim rapidly for several hours. These and other results were consistent with the idea that antibiotic tolerance can arise via different mechanisms in a clonal population.
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Affiliation(s)
- Annie H. Lee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Hong Nhi Nguyen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Isabella R. Schmitz
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Deborah A. Siegele
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
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5
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Manson MD, Nan B, Lele PP, Liu J, Duncan TM. Editorial: Biological rotary nanomotors. Front Microbiol 2022; 13:1012681. [PMID: 36212881 PMCID: PMC9532838 DOI: 10.3389/fmicb.2022.1012681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/29/2022] [Indexed: 01/28/2023] Open
Affiliation(s)
- Michael D. Manson
- Department of Biology, Texas A&M University, College Station, TX, United States,*Correspondence: Michael D. Manson
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Jun Liu
- Microbial Sciences Institute, Department of Microbial Pathogenesis, Yale University, New Haven, CT, United States
| | - Thomas M. Duncan
- Department of Biochemistry & Molecular Biology, Upstate Medical University, Syracuse, NY, United States
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Katiyar A, Zhang J, Antani JD, Yu Y, Scott KL, Lele PP, Reinhart‐King CA, Sniadecki NJ, Roux KJ, Dickinson RB, Lele TP. The Nucleus Bypasses Obstacles by Deforming Like a Drop with Surface Tension Mediated by Lamin A/C. Adv Sci (Weinh) 2022; 9:e2201248. [PMID: 35712768 PMCID: PMC9376816 DOI: 10.1002/advs.202201248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Migrating cells must deform their stiff cell nucleus to move through pores and fibers in tissue. Lamin A/C is known to hinder cell migration by limiting nuclear deformation and passage through confining channels, but its role in nuclear deformation and passage through fibrous environments is less clear. Cell and nuclear migration through discrete, closely spaced, slender obstacles which mimic the mechanical properties of collagen fibers are studied. Nuclei bypass slender obstacles while preserving their overall morphology by deforming around them with deep local invaginations of little resisting force. The obstacles do not impede the nuclear trajectory and do not cause rupture of the nuclear envelope. Nuclei likewise deform around single collagen fibers in cells migrating in 3D collagen gels. In contrast to its limiting role in nuclear passage through confining channels, lamin A/C facilitates nuclear deformation and passage through fibrous environments; nuclei in lamin-null (Lmna-/- ) cells lose their overall morphology and become entangled on the obstacles. Analogous to surface tension-mediated deformation of a liquid drop, lamin A/C imparts a surface tension on the nucleus that allows nuclear invaginations with little mechanical resistance, preventing nuclear entanglement and allowing nuclear passage through fibrous environments.
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Affiliation(s)
- Aditya Katiyar
- Department of Biomedical EngineeringTexas A&M University101 Bizzell St.College StationTX77843USA
| | - Jian Zhang
- Department of Biomedical EngineeringVanderbilt University2301 Vanderbilt PlaceNashvilleTN37235USA
| | - Jyot D. Antani
- Artie McFerrin Department of Chemical EngineeringTexas A&M University3122 TAMUCollege StationTX77843USA
| | - Yifan Yu
- Department of Chemical EngineeringUniversity of Florida1030 Center DriveGainesvilleFL32611USA
| | - Kelsey L. Scott
- Enabling Technologies GroupSanford Research2301 East 60th St NSioux FallsSD57104USA
| | - Pushkar P. Lele
- Artie McFerrin Department of Chemical EngineeringTexas A&M University3122 TAMUCollege StationTX77843USA
| | - Cynthia A. Reinhart‐King
- Department of Biomedical EngineeringVanderbilt University2301 Vanderbilt PlaceNashvilleTN37235USA
| | - Nathan J. Sniadecki
- Department of Mechanical EngineeringDepartment of Lab Medicine and PathologyInstitute for Stem Cell and Regenerative MedicineCenter for Cardiac BiologyUniversity of WashingtonStevens Way, Box 352600SeattleWA98195USA
| | - Kyle J. Roux
- Enabling Technologies GroupSanford Research2301 East 60th St NSioux FallsSD57104USA
- Department of PediatricsSanford School of MedicineUniversity of South Dakota414 E Clark StVermillionSD57069USA
| | - Richard B. Dickinson
- Department of Chemical EngineeringUniversity of Florida1030 Center DriveGainesvilleFL32611USA
| | - Tanmay P. Lele
- Department of Biomedical EngineeringTexas A&M University101 Bizzell St.College StationTX77843USA
- Artie McFerrin Department of Chemical EngineeringTexas A&M University3122 TAMUCollege StationTX77843USA
- Department of Translational Medical SciencesTexas A&M University2121 W Holcombe St.HoustonTX77030USA
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Gupta R, Yuan J, Lele PP. Bacterial Proprioception: Can a Bacterium Sense Its Movement? Front Microbiol 2022; 13:928408. [PMID: 35875555 PMCID: PMC9302961 DOI: 10.3389/fmicb.2022.928408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The evolution of the bacterial flagellum gave rise to motility and repurposing of a signaling network, now termed the chemotaxis network, enabled biasing of cell movements. This made it possible for the bacterium to seek out favorable chemical environments. To enable chemotaxis, the chemotaxis network sensitively detects extracellular chemical stimuli and appropriately modulates flagellar functions. Additionally, the flagellar motor itself is capable of detecting mechanical stimuli and adapts its structure and function in response, likely triggering a transition from planktonic to surface-associated lifestyles. Recent work has shown a link between the flagellar motor's response to mechanical stimuli and the chemotactic output. Here, we elaborate on this link and discuss how it likely helps the cell sense and adapt to changes in its swimming speeds in different environments. We discuss the mechanism whereby the motor precisely tunes its chemotaxis output under different mechanical loads, analogous to proprioception in higher order organisms. We speculate on the roles bacterial proprioception might play in a variety of phenomena including the transition to surface-associated lifestyles such as swarming and biofilms.
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Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei, China
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
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8
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Gupta R, Rhee KY, Beagle SD, Chawla R, Perdomo N, Lockless SW, Lele PP. Indole modulates cooperative protein-protein interactions in the flagellar motor. PNAS Nexus 2022; 1. [PMID: 35719892 PMCID: PMC9205328 DOI: 10.1093/pnasnexus/pgac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Indole is a major component of the bacterial exometabolome, and the mechanisms for its wide-ranging effects on bacterial physiology are biomedically significant, although they remain poorly understood. Here, we determined how indole modulates the functions of a widely conserved motility apparatus, the bacterial flagellum. Our experiments in Escherichia coli revealed that indole influences the rotation rates and reversals in the flagellum’s direction of rotation via multiple mechanisms. At concentrations higher than 1 mM, indole decreased the membrane potential to dissipate the power available for the rotation of the motor that operates the flagellum. Below 1 mM, indole did not dissipate the membrane potential. Instead, experiments and modeling indicated that indole weakens cooperative protein interactions within the flagellar complexes to inhibit motility. The metabolite also induced reversals in the rotational direction of the motor to promote a weak chemotactic response, even when the chemotaxis response regulator, CheY, was lacking. Experiments further revealed that indole does not require the transporter Mtr to cross the membrane and influence motor functions. Based on these findings, we propose that indole modulates intra- and inter-protein interactions in the cell to influence several physiological functions.
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Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Kathy Y Rhee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Sarah D Beagle
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Ravi Chawla
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Nicolas Perdomo
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
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Wong GCL, Antani JD, Lele PP, Chen J, Nan B, Kühn MJ, Persat A, Bru JL, Høyland-Kroghsbo NM, Siryaporn A, Conrad JC, Carrara F, Yawata Y, Stocker R, V Brun Y, Whitfield GB, Lee CK, de Anda J, Schmidt WC, Golestanian R, O'Toole GA, Floyd KA, Yildiz FH, Yang S, Jin F, Toyofuku M, Eberl L, Nomura N, Zacharoff LA, El-Naggar MY, Yalcin SE, Malvankar NS, Rojas-Andrade MD, Hochbaum AI, Yan J, Stone HA, Wingreen NS, Bassler BL, Wu Y, Xu H, Drescher K, Dunkel J. Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation. Phys Biol 2021; 18. [PMID: 33462162 PMCID: PMC8506656 DOI: 10.1088/1478-3975/abdc0e] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/14/2021] [Indexed: 11/29/2022]
Abstract
Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor.
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Affiliation(s)
- Gerard C L Wong
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States of America
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States of America
| | - Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA24061, United States of America
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, Texas, TX 77845, United States of America
| | - Marco J Kühn
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Persat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jean-Louis Bru
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America
| | | | - Albert Siryaporn
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America.,Department of Physics & Astronomy, University of California-Irvine, California, CA 92697, United States of America
| | - Jacinta C Conrad
- William A Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, TX 77204, United States of America
| | - Francesco Carrara
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Yutaka Yawata
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Yves V Brun
- University of Montreal, Faculty of Medicine, Montreal, Quebec, H3C 3J7, Canada
| | - Gregory B Whitfield
- University of Montreal, Faculty of Medicine, Montreal, Quebec, H3C 3J7, Canada
| | - Calvin K Lee
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Jaime de Anda
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - William C Schmidt
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), D-37077 Göttingen, Germany.,Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States of America
| | - Kyle A Floyd
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, CA 95060, United States of America
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, CA 95060, United States of America
| | - Shuai Yang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Fan Jin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Chemistry, University of Southern California, Los Angeles, California, CA 90089, United States of America
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Chemistry, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Biological Sciences, University of Southern California, Los Angeles, California, CA 90089, United States of America
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, CT 06516, United States of America.,Microbial Sciences Institute, Yale University, New Haven, Connecticut, CT 06516, United States of America
| | - Nikhil S Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, CT 06516, United States of America.,Microbial Sciences Institute, Yale University, New Haven, Connecticut, CT 06516, United States of America
| | - Mauricio D Rojas-Andrade
- Department of Materials Science and Engineering, University of California-Irvine, Irvine, California CA 92697, United States of America
| | - Allon I Hochbaum
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America.,Department of Materials Science and Engineering, University of California-Irvine, Irvine, California CA 92697, United States of America.,Department of Chemistry, University of California-Irvine, Irvine, California, CA 92697, United States of America.,Department of Chemical and Biomolecular Engineering, University of California-Irvine, Irvine, California, CA 92697, United States of America
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, CT 06511, United States of America
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, NJ 08544, United States of America
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, NJ 08544, United States of America.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, NJ 08544, United States of America
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, NJ 08544, United States of America.,The Howard Hughes Medical Institute, Chevy Chase, Maryland MD 20815, United States of America
| | - Yilin Wu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Haoran Xu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139-4307, United States of America
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10
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Antani JD, Sumali AX, Lele TP, Lele PP. Asymmetric random walks reveal that the chemotaxis network modulates flagellar rotational bias in Helicobacter pylori. eLife 2021; 10:63936. [PMID: 33493107 PMCID: PMC7834020 DOI: 10.7554/elife.63936] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
The canonical chemotaxis network modulates the bias for a particular direction of rotation in the bacterial flagellar motor to help the cell migrate toward favorable chemical environments. How the chemotaxis network in Helicobacter pylori modulates flagellar functions is unknown, which limits our understanding of chemotaxis in this species. Here, we determined that H. pylori swim faster (slower) whenever their flagella rotate counterclockwise (clockwise) by analyzing their hydrodynamic interactions with bounding surfaces. This asymmetry in swimming helped quantify the rotational bias. Upon exposure to a chemo-attractant, the bias decreased and the cells tended to swim exclusively in the faster mode. In the absence of a key chemotaxis protein, CheY, the bias was zero. The relationship between the reversal frequency and the rotational bias was unimodal. Thus, H. pylori’s chemotaxis network appears to modulate the probability of clockwise rotation in otherwise counterclockwise-rotating flagella, similar to the canonical network.
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Affiliation(s)
- Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Anita X Sumali
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Tanmay P Lele
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77840, College Station, TX 77840, United States.,Department of Translational Medical Sciences, Texas A&M University, Houston, TX 77030, United States
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
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11
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Katiyar A, Antani JD, McKee BP, Gupta R, Lele PP, Lele TP. A method for direct imaging of x-z cross-sections of fluorescent samples. J Microsc 2020; 281:224-230. [PMID: 33020917 DOI: 10.1111/jmi.12965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 01/08/2023]
Abstract
The x-z cross-sectional profiles of fluorescent objects can be distorted in confocal microscopy, in large part due to mismatch between the refractive index of the immersion medium of typical high numerical aperture objectives and the refractive index of the medium in which the sample is present. Here, we introduce a method to mount fluorescent samples parallel to the optical axis. This mounting allows direct imaging of what would normally be an x-z cross-section of the object, in the x-y plane of the microscope. With this approach, the x-y cross-sections of fluorescent beads were seen to have significantly lower shape-distortions as compared to x-z cross-sections reconstructed from confocal z-stacks. We further tested the method for imaging of nuclear and cellular heights in cultured cells, and found that they are significantly flatter than previously reported. This approach allows improved imaging of the x-z cross-section of fluorescent samples. LAY DESCRIPTION: Optical distortions are common in confocal microscopy. In particular, the mismatch between the refractive index of the immersion medium of the microscope objective and the refractive index of the sample medium distorts the shapes of fluorescent objects in the x-z plane of the microscope. Here, we introduced a method to eliminate the shape-distortion in the x-z cross-sections. This was achieved by mounting fluorescent samples on vertical glass slides such that the cross-sections orthogonal to the glass surface could be imaged in the x-y plane of the microscope. Our method successfully improved the imaging of nuclear and cellular heights in cultured cells and revealed that the heights were significantly flatter than previously reported with conventional approaches.
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Affiliation(s)
- A Katiyar
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77840, U.S.A
| | - J D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas, 77843, U.S.A
| | - B P McKee
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, 32611, U.S.A
| | - R Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas, 77843, U.S.A
| | - P P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas, 77843, U.S.A
| | - T P Lele
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77840, U.S.A
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12
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Rhee KY, Chawla R, Lele PP. Protein expression-independent response of intensity-based pH-sensitive fluorophores in Escherichia coli. PLoS One 2020; 15:e0234849. [PMID: 32555627 PMCID: PMC7302705 DOI: 10.1371/journal.pone.0234849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 12/02/2022] Open
Abstract
Fluorescent proteins that modulate their emission intensities when protonated serve as excellent probes of the cytosolic pH. Since the total fluorescence output fluctuates significantly due to variations in the fluorophore levels in cells, eliminating the dependence of the signal on protein concentration is crucial. This is typically accomplished with the aid of ratiometric fluorescent proteins such as pHluorin. However, pHluorin is excited by blue light, which can complicate pH measurements by adversely impacting bacterial physiology. Here, we characterized the response of intensity-based, pH-sensitive fluorescent proteins that excite at longer wavelengths where the blue light effect is diminished. The pH-response was interpreted in terms of an analytical model that assumed two emission states for each fluorophore: a low intensity protonated state and a high intensity deprotonated state. The model suggested a scaling to eliminate the dependence of the signal on the expression levels as well as on the illumination and photon-detection settings. Experiments successfully confirmed the scaling predictions. Thus, the internal pH can be readily determined with intensity-based fluorophores with appropriate calibrations irrespective of the fluorophore concentration and the signal acquisition setup. The framework developed in this work improves the robustness of intensity-based fluorophores for internal pH measurements in E. coli, potentially extending their applications.
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Affiliation(s)
- Kathy Y. Rhee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
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13
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Antani JD, Lele PP. Anisotropic Swimming Modes in Helicobacter pylori. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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14
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Abstract
Surface sensing in bacteria is a precursor to the colonization of biotic and abiotic surfaces, and an important cause of drug resistance and virulence. As a motile bacterium approaches and adheres to a surface from the bulk fluid, the mechanical forces that act on it change. Bacteria are able to sense these changes in the mechanical load through a process termed mechanosensing. Bacterial mechanosensing has featured prominently in recent literature as playing a key role in surface sensing. However, the changes in mechanical loads on different parts of the cell at a surface vary in magnitudes as well as in signs. This confounds the determination of a causal relationship between the activation of specific mechanosensors and surface sensing. Here, we explain how contrasting mechanical stimuli arise on a surface-adherent cell and how known mechanosensors respond to these stimuli. The evidence for mechanosensing in select bacterial species is reinterpreted, with a focus on mechanosensitive molecular motors. We conclude with proposed criteria that bacterial mechanosensors must satisfy to successfully mediate surface sensing.
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Affiliation(s)
- Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Tanmay P Lele
- Department of Chemical Engineering, University of Florida, Gainesville, Fl, USA
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
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15
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Orr AA, Yang J, Sule N, Chawla R, Hull KG, Zhu M, Romo D, Lele PP, Jayaraman A, Manson MD, Tamamis P. Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr. Biophys J 2019; 118:492-504. [PMID: 31839263 DOI: 10.1016/j.bpj.2019.11.3382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/05/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
The attractant chemotaxis response of Escherichia coli to norepinephrine requires that it be converted to 3,4-dihydroxymandelic acid (DHMA) by the monoamine oxidase TynA and the aromatic aldehyde dehydrogenase FeaB. DHMA is sensed by the serine chemoreceptor Tsr, and the attractant response requires that at least one subunit of the periplasmic domain of the Tsr homodimer (pTsr) has an intact serine-binding site. DHMA that is generated in vivo by E. coli is expected to be a racemic mixture of the (R) and (S) enantiomers, so it has been unclear whether one or both chiral forms are active. Here, we used a combination of state-of-the-art tools in molecular docking and simulations, including an in-house simulation-based docking protocol, to investigate the binding properties of (R)-DHMA and (S)-DHMA to E. coli pTsr. Our studies computationally predicted that (R)-DHMA should promote a stronger attractant response than (S)-DHMA because of a consistently greater-magnitude piston-like pushdown of the pTsr α-helix 4 toward the membrane upon binding of (R)-DHMA than upon binding of (S)-DHMA. This displacement is caused primarily by interaction of DHMA with Tsr residue Thr156, which has been shown by genetic studies to be critical for the attractant response to L-serine and DHMA. These findings led us to separate the two chiral species and test their effectiveness as chemoattractants. Both the tethered cell and motility migration coefficient assays validated the prediction that (R)-DHMA is a stronger attractant than (S)-DHMA. Our study demonstrates that refined computational docking and simulation studies combined with experiments can be used to investigate situations in which subtle differences between ligands may lead to diverse chemotactic responses.
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Affiliation(s)
- Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Jingyun Yang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Nitesh Sule
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Kenneth G Hull
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Mingzhao Zhu
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Daniel Romo
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Michael D Manson
- Department of Biology, Texas A&M University, College Station, Texas.
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.
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16
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Abstract
Escherichia coli swarm on semi-solid surfaces with the aid of flagella. It has been hypothesized that swarmer cells overcome the increased viscous drag near surfaces by developing higher flagellar thrust and by promoting surface wetness with the aid of a flagellar switch. The switch enables reversals between clockwise (CW) and counterclockwise (CCW) directions of rotation of the flagellar motor. Here, we measured the behavior of flagellar motors in swarmer cells. Results indicated that although the torque was similar to that in planktonic cells, the tendency to rotate CCW was higher in swarmer cells. This suggested that swarmers likely have a smaller pool of phosphorylated CheY. Results further indicated that the upregulation of the flagellin gene was not critical for flagellar thrust or swarming. Consistent with earlier reports, moisture added to the swarm surface restored swarming in a CCW-only mutant, but not in a FliG mutant that rotated motors CW-only (FliGCW). Fluorescence assays revealed that FliGCW cells grown on agar surfaces carried fewer flagella than planktonic FliGCW cells. The surface-dependent reduction in flagella correlated with a reduction in the number of putative flagellar preassemblies. These results hint toward a possibility that the conformational dynamics of switch proteins play a role in the proper assembly of flagellar complexes and flagellar export, thereby aiding bacterial swarming.
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Affiliation(s)
- Katie M Ford
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Aravindh Nagarajan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Madeline M Johnson
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
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17
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Diethmaier C, Chawla R, Canzoneri A, Kearns DB, Lele PP, Dubnau D. Viscous drag on the flagellum activates Bacillus subtilis entry into the K-state. Mol Microbiol 2017; 106:367-380. [PMID: 28800172 DOI: 10.1111/mmi.13770] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2017] [Indexed: 12/23/2022]
Abstract
Bacillus subtilis flagella are not only required for locomotion but also act as sensors that monitor environmental changes. Although how the signal transmission takes place is poorly understood, it has been shown that flagella play an important role in surface sensing by transmitting a mechanical signal to control the DegS-DegU two-component system. Here we report a role for flagella in the regulation of the K-state, which enables transformability and antibiotic tolerance (persistence). Mutations impairing flagellar synthesis are inferred to increase DegU-P, which inhibits the expression of ComK, the master regulator for the K-state, and reduces transformability. Tellingly, both deletion of the flagellin gene and straight filament (hagA233V ) mutations increased DegU phosphorylation despite the fact that both mutants had wild type numbers of basal bodies and the flagellar motors were functional. We propose that higher viscous loads on flagellar motors result in lower DegU-P levels through an unknown signaling mechanism. This flagellar-load based mechanism ensures that cells in the motile subpopulation have a tenfold enhanced likelihood of entering the K-state and taking up DNA from the environment. Further, our results suggest that the developmental states of motility and competence are related and most commonly occur in the same epigenetic cell type.
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Affiliation(s)
- Christine Diethmaier
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station Texas, TX, USA
| | | | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station Texas, TX, USA
| | - David Dubnau
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
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18
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Abstract
The role of flagellar motors in bacterial motility and chemotaxis is well-understood. Recent discoveries suggest that flagellar motors are able to remodel in response to a variety of environmental stimuli and are among the triggers for surface colonization and infections. The precise mechanisms by which motors remodel and promote cellular adaptation likely depend on key motor attributes. The photomultiplier-based bead-tracking technique presented here enables accurate biophysical characterization of motor functions, including adaptations in motor speeds and switch-dynamics. This approach offers the advantage of real-time tracking and the ability to probe motor behavior over extended durations. The protocols discussed can be readily extended to study flagellar motors in a variety of bacterial species.
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Affiliation(s)
- Katie M Ford
- Artie McFerrin Department of Chemical Engineering, Texas A&M University
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University;
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19
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Lele PP, Roland T, Shrivastava A, Chen Y, Berg HC. The flagellar motor of Caulobacter crescentus generates more torque when a cell swims backward. Nat Phys 2016; 12:175-178. [PMID: 27499800 PMCID: PMC4973516 DOI: 10.1038/nphys3528] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/22/2015] [Indexed: 06/06/2023]
Abstract
Caulobacter crescentus, a monotrichous bacterium, swims by rotating a single right-handed helical filament. CW motor rotation thrusts the cell forward 1, a mode of motility known as the pusher mode; CCW motor rotation pulls the cell backward, a mode of motility referred to as the puller mode 2. The situation is opposite in E. coli, a peritrichous bacterium, where CCW rotation of multiple left-handed filaments drives the cell forward. The flagellar motor in E. coli generates more torque in the CCW direction than the CW direction in swimming cells 3,4. However, monotrichous bacteria including C. crescentus swim forward and backward at similar speeds, prompting the assumption that motor torques in the two modes are the same 5,6. Here, we present evidence that motors in C. crescentus develop higher torques in the puller mode than in the pusher mode, and suggest that the anisotropy in torque-generation is similar in two species, despite the differences in filament handedness and motor bias (probability of CW rotation).
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Affiliation(s)
- Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station TX 77843-3122
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138
| | - Thibault Roland
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138
| | - Abhishek Shrivastava
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138
| | | | - Howard C. Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138
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20
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Abstract
Stimulation of Escherichia coli by exponential ramps of chemoattractants generates step changes in the concentration of the response regulator, CheY-P. Because flagellar motors are ultrasensitive, this should change the fraction of time that motors spin clockwise, the CWbias. However, early work failed to show changes in CWbias when ramps were shallow. This was explained by a model for motor remodeling that predicted plateaus in plots of CWbias versus [CheY-P]. We looked for these plateaus by examining distributions of CWbias in populations of cells with different mean [CheY-P]. We did not find such plateaus. Hence, we repeated the work on shallow ramps and found that motors did indeed respond. These responses were quantitatively described by combining motor remodeling with ultrasensitivity in a model that exhibited high sensitivities over a wide dynamic range.
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Affiliation(s)
- Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843–3122, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Abhishek Shrivastava
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thibault Roland
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Howard C. Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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21
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Shrivastava A, Lele PP, Berg HC. A rotary motor drives Flavobacterium gliding. Curr Biol 2015; 25:338-341. [PMID: 25619763 DOI: 10.1016/j.cub.2014.11.045] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/10/2014] [Accepted: 11/17/2014] [Indexed: 12/23/2022]
Abstract
Cells of Flavobacterium johnsoniae, a rod-shaped bacterium devoid of pili or flagella, glide over glass at speeds of 2-4 μm/s [1]. Gliding is powered by a protonmotive force [2], but the machinery required for this motion is not known. Usually, cells move along straight paths, but sometimes they exhibit a reciprocal motion, attach near one pole and flip end over end, or rotate. This behavior is similar to that of a Cytophaga species described earlier [3]. Development of genetic tools for F. johnsoniae led to discovery of proteins involved in gliding [4]. These include the surface adhesin SprB that forms filaments about 160 nm long by 6 nm in diameter, which, when labeled with a fluorescent antibody [2] or a latex bead [5], are seen to move longitudinally down the length of a cell, occasionally shifting positions to the right or the left. Evidently, interaction of these filaments with a surface produces gliding. To learn more about the gliding motor, we sheared cells to reduce the number and size of SprB filaments and tethered cells to glass by adding anti-SprB antibody. Cells spun about fixed points, mostly counterclockwise, rotating at speeds of 1 Hz or more. The torques required to sustain such speeds were large, comparable to those generated by the flagellar rotary motor. However, we found that a gliding motor runs at constant speed rather than at constant torque. Now, there are three rotary motors powered by protonmotive force: the bacterial flagellar motor, the Fo ATP synthase, and the gliding motor.
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Affiliation(s)
- Abhishek Shrivastava
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Pushkar P Lele
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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22
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Abstract
The analysis of Fluorescence Recovery After Photobleaching (FRAP) experiments involves mathematical modeling of the fluorescence recovery process. An important feature of FRAP experiments that tends to be ignored in the modeling is that there can be a significant loss of fluorescence due to bleaching during image capture. In this paper, we explicitly include the effects of bleaching during image capture in the model for the recovery process, instead of correcting for the effects of bleaching using reference measurements. Using experimental examples, we demonstrate the usefulness of such an approach in FRAP analysis.
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Affiliation(s)
- Jun Wu
- Department of Chemical Engineering, University of Florida, Gainesville Florida, United States of America
| | - Nandini Shekhar
- Department of Chemical Engineering, University of Florida, Gainesville Florida, United States of America
| | - Pushkar P. Lele
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tanmay P. Lele
- Department of Chemical Engineering, University of Florida, Gainesville Florida, United States of America
- * E-mail:
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23
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Lele PP, Furst EM. Assemble-and-stretch method for creating two- and three-dimensional structures of anisotropic particles. Langmuir 2009; 25:8875-8878. [PMID: 19572535 DOI: 10.1021/la901743q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We fabricate two-dimensional ordered arrays of anisotropic particles by embedding hexagonally close-packed monolayers of spherical latex particles in polymer films and subjecting them to an extensional strain. Furthermore, by stacking several films, we create three-dimensional structures. An important advantage of this approach is the ability to independently control the particle orientation in each layer of the structure. Additionally, the symmetry of a layer is controlled by the orientation of the original array of spherical particles versus the stretch direction. This technique may be readily used to generate structures for photonic applications, as well as to aid fundamental studies of packing of anisotropic particles.
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Affiliation(s)
- Pushkar P Lele
- Department of Chemical Engineering and Center for Molecular and Engineering Thermodynamics, University of Delaware, 150 Academy Street, Newark, Delaware 19716, USA
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24
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Singh JP, Lele PP, Nettesheim F, Wagner NJ, Furst EM. One- and two-dimensional assembly of colloidal ellipsoids in ac electric fields. Phys Rev E Stat Nonlin Soft Matter Phys 2009; 79:050401. [PMID: 19518404 DOI: 10.1103/physreve.79.050401] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Indexed: 05/13/2023]
Abstract
We investigate the assembly of colloidal ellipsoids in ac electric fields. Polystyrene latex ellipsoids with aspect ratios 3.0, 4.3, and 7.6 orient with the applied field and, at sufficient field strengths, interact to form particle chains at an angle with respect to the field. The characteristic chain angle decreases with increasing aspect ratio. The angled chains combine laterally to form an open centered rectangular two-dimensional structures belonging to the c2mm plane group. This chaining and assembly behavior is explained based on calculations of the particle pair interactions explicitly accounting for the electric field and shape of the ellipsoids.
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Affiliation(s)
- John P Singh
- Department of Chemical Engineering and Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, Delaware 19716, USA
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25
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Lele PP, Mittal M, Furst EM. Anomalous particle rotation and resulting microstructure of colloids in AC electric fields. Langmuir 2008; 24:12842-12848. [PMID: 18950210 DOI: 10.1021/la802225u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We study the transition of ordered structures to disordered bands and vortices in colloidal suspensions subjected to AC electric fields. We map the critical frequencies and field biases at which particles form disordered bands and vortices. These results are interpreted based on the trajectory dynamics of particle pairs using blinking optical tweezers. Under conditions that vortices are observed, individual particle pairs rotate out of alignment with the field. The direction and magnitude of these interactions determine the orientation and average angular velocity of the band revolution. Increasing the frequency of the electric field reduces the anomalous rotation of the particles pairs, consistent with the frequency dependence of the suspension order-to-disorder transition. This anomalous rotation is consistent with a torque on doublets generated by the mutual polarization of particles and phase lag of the induced dipoles.
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Affiliation(s)
- Pushkar P Lele
- Department of Chemical Engineering and Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, DE, USA
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26
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Mittal M, Lele PP, Kaler EW, Furst EM. Polarization and interactions of colloidal particles in ac electric fields. J Chem Phys 2008; 129:064513. [DOI: 10.1063/1.2969103] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Basauri L, Lele PP. A simple method for production of trackless focal lesions with focused ultrasound: statistical evaluation of the effects of irradiation on the central nervous system of the cat. J Physiol 2007; 160:513-534.2. [PMID: 16992120 PMCID: PMC1359561 DOI: 10.1113/jphysiol.1962.sp006863] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Newman WH, Lele PP, Bowman HF. Limitations and significance of thermal washout data obtained during microwave and ultrasound hyperthermia. Int J Hyperthermia 1990; 6:771-84. [PMID: 2394925 DOI: 10.3109/02656739009140824] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
It is common in clinical hyperthermia to calculate an 'effective blood flow' by neglecting tissue thermal conduction and fitting thermal washout data to a simple, perfusion-dominated exponential model. We have applied this approach to characterize thermal dissipative mechanisms in patients treated at the Harvard-MIT Hyperthermia Center, by analysing thermal washout curves which were obtained during treatment sessions by momentarily interrupting the applied heating. Unfortunately, these measurements of 'effective blood flow' in patient sessions have given inconsistent results. These inconsistencies arise from uncertainties inherent in the clinical situation: the actual thermal boundary conditions and the spatiotemporal characteristics of the heating field. To quantify these observations a Green's function solution to the tissue bioheat equation has been derived, to enable temperature fields produced by various heating geometries to be easily calculated. This has been applied to the analysis of temperature decay curves following local energy deposition representative of ultrasound and microwave hyperthermia therapy devices. These results show that thermal washout data are as dependent on patient- and session-specific parameters as on tissue properties and perfusion. For measurements of effective blood flow following ultrasonic heating, errors are dependent on the measurement position within the heated volume, heating geometry, and duration of heating prior to the decay; for microwave heating, results are dependent on the position of the measurement point within the heated field, the heating frequency, and the surface boundary conditions, whether heated, cooled, or insulated. Thus, any effective tissue property calculated without correctly modelling the heating geometry, boundary conditions and initial conditions will be of a qualitative rather than quantitative nature, and may lead to erroneous and misleading conclusions concerning tissue and tumour response.
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Affiliation(s)
- W H Newman
- Harvard-MIT Hyperthermia Center, Cambridge, MA 02139
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Affiliation(s)
- P P Lele
- Harvard-MIT Hyperthermia Center, Massachusetts Institute of Technology, Cambridge 02139
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Lele PP. Advanced ultrasonic techniques for local tumor hyperthermia. Radiol Clin North Am 1989; 27:559-75. [PMID: 2648459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Scanned, intensity-modulated, focused ultrasound (SIMFU) presently is the modality of choice for localized, controlled heating of deep as well as superficial tumors noninvasively. With the present SIMFU system, it was possible to heat 88 per cent of deep tumors up to 12 cm in depth and 15 cm in diameter, to 43 degrees C in 3 to 4 minutes. The infiltrative tumor margins could be heated to the desired therapeutic temperature. The temperature outside the treatment field fell off sharply. Excellent objective responses were obtained without local or systemic toxicity. Multiinstitutional clinical trials of local hyperthermia by this promising technique are clearly warranted.
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Affiliation(s)
- P P Lele
- Hyperthermia Center, Massachusetts Institute of Technology, Cambridge
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Sleefe GE, Lele PP. Tissue characterization based on scatterer number density estimation. IEEE Trans Ultrason Ferroelectr Freq Control 1988; 35:749-57. [PMID: 18290212 DOI: 10.1109/58.9332] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The authors propose a robust model for characterizing the statistical nature of signals obtained from ultrasonic backscatter processes. The model can accommodate frequency-dependent attenuation, spatially varying media statistics, arbitrary beam geometries, and arbitrary pulse shapes. On the basis of this model, statistical schemes are proposed for estimating the scatterer number density (SND) of tissues. The algorithm for estimating the scatterer number incorporates measurements of both the statistical moments of the backscattered signals and the point spread function of the acoustic system. The number density algorithm has been applied to waveforms obtained from ultrasonic phantoms with known number densities and in vitro mammalian tissues. There is an excellent agreement among theoretical, histological, and experimental results. The application of this technique for noninvasive clinical tissue characterization is discussed.
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Affiliation(s)
- G E Sleefe
- Lab. for Med. Ultrasonics, MIT, Cambridge, MA
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Abstract
Knowledge of tissue thermal transport properties is imperative for any therapeutic medical tool which employs the localized application of heat to perfused biological tissue. In this study, several techniques are proposed to measure local tissue thermal diffusion by heating with a focused ultrasound field. Transient as well as near steady-state heat inputs are discussed and examined for their suitability as a measurement technique for either tissue thermal diffusivity or perfusion rate. It is shown that steady-state methods are better suited for the measurement of perfusion; however the uncertainty in the perfusion measurement is directly related to knowledge of the tissue's intrinsic thermal diffusivity. Results are presented for a transient thermal pulse technique for the measurement of the thermal diffusivity of perfused and nonperfused tissues, in vitro and in vivo. Measurements conducted in plexiglas, animal muscle, kidney and brain concur with tabulated values and show a scatter from 5-15 percent from the mean; measurements made in perfused muscle and brain compare well with the nonperfused values. An estimate of the error introduced by the effect of perfusion shows that except for highly perfused kidney tissue the effect of perfusion is less than the experimental scatter. This validation of the tissue heat transfer model will allow its eventual extension to the simultaneous measurement of local tissue thermal diffusivity and perfusion.
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Lele PP, Parker KJ. Temperature distributions in tissues during local hyperthermia by stationary or steered beams of unfocused or focused ultrasound. Br J Cancer Suppl 1982; 5:108-21. [PMID: 6950746 PMCID: PMC2149280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Temperature distributions resulting from insonation with stationary or steered beams of unfocused or focused ultrasound were measured in tissue-equivalent phantom, beef muscle in vitro, dog muscle mass, and transplanted murine tumours in vivo. Arrays of 4 to 6 thermocouples stepped through the volume of interest under computer control were used to measure the steady-state temperatures at 600 to 800 locations in both in vitro and in vivo experiments. The results were confirmed in spontaneous tumours in dog patients using fewer multi-thermocouple probes. Plane wave ultrasound was found to result in spatially non-uniform hyperthermia even in superficial tumours. The region of maximum temperature rise was small in extent and was situated at a depth which varied in the different models from 0.5 to 1.0 cm. Neither its location nor its extent could be varied by spatial manipulations of the transducer or by changing the insonation parameters except the ultrasonic frequency. A second region of hyperthermia was produced at depth by reflective heating if an ultrasonically reflective target, such as bone or air-containing tissue, was located below the target tissue. On the other hand, using available steered, focused ultrasound techniques, tumours (whether situated superficially or at depth) could be heated to a uniform, controllable temperature without undesirable temperature elevation in surrounding normal tissues. The use of steered, focused ultrasound permits deposition of energy to be tailored to the specific needs of each individual tumour. The small size of the focal region enables heating of tumours even when located near ultrasound reflecting targets.
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Lele PP. Induction of deep, local hyperthermia by ultrasound and electromagnetic fields: problems and choices. Radiat Environ Biophys 1980; 17:205-217. [PMID: 7443976 DOI: 10.1007/bf01323647] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The feasibility, and the biophysical and engineering concepts underlying the use of electromagnetic energy and ultrasound for production of deep, local hyperthermia are discussed. Focused ultrasound currently is the only modality that can be used for producing controllable levels of hyperthermia localized to deep seated tumors, non-invasively and safely. The ultrasonic focus needs to moved within the tissues around the periphery of the tumor to achieve uniform temperature distributions.
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Robinson TC, Lele PP. An analysis of lesion development in the brain and in plastics by high-intensity focused ultrasound at low-megahertz frequencies. J Acoust Soc Am 1972; 51:1333-1351. [PMID: 5032950 DOI: 10.1121/1.1912979] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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