Jing Yan, PhD
Assistant Professor, Molecular, Cellular and Developmental Biology
Research & Publications
Biography
Research Summary
Biofilms are ubiquitous surface-attached bacterial communities embedded in an extracellular matrix. We combine state-of-art imaging techniques, mutagenesis, mechanical measurements, and computer simulations to understand how bacteria build such multicellular communities cell by cell, what unique materials they use to do so, and what characteristics emerge at the level of the collective. Ultimately, we will use our understanding of bacterial biofilms to solve biofilm-related problems in medicine and in industry and to enhance the use of beneficial biofilms.
Coauthors
Research Image
Single-cell imaging of bacterial biofilms
Reconstructed 3D image of a Vibrio cholerae biofilm cluster. Color corresponds to height.
Selected Publications
- Bacteria surfing the elastic waveNijjer J, Cohen T, Yan J. Bacteria surfing the elastic wave. Nature Physics 2022, 19: 6-7. DOI: 10.1038/s41567-022-01862-y.
- Social evolution of shared biofilm matrix componentsTai J, Mukherjee S, Nero T, Olson R, Tithof J, Nadell C, Yan J. Social evolution of shared biofilm matrix components. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2123469119. PMID: 35771939, PMCID: PMC9271185, DOI: 10.1073/pnas.2123469119.
- Mechanical Resilience of Biofilms toward Environmental Perturbations Mediated by Extracellular MatrixZhang Q, Nguyen D, Tai J, Xu X, Nijjer J, Huang X, Li Y, Yan J. Mechanical Resilience of Biofilms toward Environmental Perturbations Mediated by Extracellular Matrix. Advanced Functional Materials 2022, 32 DOI: 10.1002/adfm.202110699.
- Mechanical forces drive a reorientation cascade leading to biofilm self-patterningNijjer J, Li C, Zhang Q, Lu H, Zhang S, Yan J. Mechanical forces drive a reorientation cascade leading to biofilm self-patterning. Nature Communications 2021, 12: 6632. PMID: 34789754, PMCID: PMC8599862, DOI: 10.1038/s41467-021-26869-6.
- Morphogenesis and cell ordering in confined bacterial biofilmsZhang Q, Li J, Nijjer J, Lu H, Kothari M, Alert R, Cohen T, Yan J. Morphogenesis and cell ordering in confined bacterial biofilms. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2107107118. PMID: 34330824, PMCID: PMC8346881, DOI: 10.1073/pnas.2107107118.
- Agent-based modeling of stress anisotropy driven nematic ordering in growing biofilmsLi C, Nijjer J, Feng L, Zhang Q, Yan J, Zhang S. Agent-based modeling of stress anisotropy driven nematic ordering in growing biofilms. Soft Matter 2024, 20: 3401-3410. PMID: 38563244, PMCID: PMC11041162, DOI: 10.1039/d3sm01535a.
- Lipoarabinomannan mediates localized cell wall integrity during division in mycobacteriaSparks I, Kado T, Prithviraj M, Nijjer J, Yan J, Morita Y. Lipoarabinomannan mediates localized cell wall integrity during division in mycobacteria. Nature Communications 2024, 15: 2191. PMID: 38467648, PMCID: PMC10928101, DOI: 10.1038/s41467-024-46565-5.
- Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonizationHuang X, Nero T, Weerasekera R, Matej K, Hinbest A, Jiang Z, Lee R, Wu L, Chak C, Nijjer J, Gibaldi I, Yang H, Gamble N, Ng W, Malaker S, Sumigray K, Olson R, Yan J. Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization. Nature Communications 2023, 14: 2104. PMID: 37055389, PMCID: PMC10102183, DOI: 10.1038/s41467-023-37660-0.
- New Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial EcologyTai J, Ferrell M, Yan J, Waters C. New Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial Ecology. 2023, 1404: 17-39. PMID: 36792869, PMCID: PMC10726288, DOI: 10.1007/978-3-031-22997-8_2.
- Mechanical Characterization and Single‐Cell Imaging of Bacterial BiofilmsMoreau A, Mukherjee S, Yan J. Mechanical Characterization and Single‐Cell Imaging of Bacterial Biofilms. Israel Journal Of Chemistry 2023, 63 DOI: 10.1002/ijch.202200075.
- Interfacial cavitationHenzel T, Nijjer J, Chockalingam S, Wahdat H, Crosby A, Yan J, Cohen T. Interfacial cavitation. PNAS Nexus 2022, 1: pgac217. PMID: 36714841, PMCID: PMC9802248, DOI: 10.1093/pnasnexus/pgac217.
- Molecular Mechanism of Vibrio cholerae biofilm adhesionWeerasekera R, Hinbest A, Nero T, Huang X, Yan J, Olson R. Molecular Mechanism of Vibrio cholerae biofilm adhesion. The FASEB Journal 2022, 36 DOI: 10.1096/fasebj.2022.36.s1.l7499.
- Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancementBarrasso K, Chac D, Debela M, Geigel C, Steenhaut A, Seda A, Dunmire C, Harris J, Larocque R, Midani F, Qadri F, Yan J, Weil A, Ng W. Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement. ELife 2022, 11: e73010. PMID: 35343438, PMCID: PMC8993218, DOI: 10.7554/elife.73010.
- Bacterial Surface Detachment during Nebulization with Contaminated Reusable Home NebulizersHarris JC, Collins MS, Huang PH, Schramm CM, Nero T, Yan J, Murray TS. Bacterial Surface Detachment during Nebulization with Contaminated Reusable Home Nebulizers. Microbiology Spectrum 2022, 10: e02535-21. PMID: 35107362, PMCID: PMC8809330, DOI: 10.1128/spectrum.02535-21.
- Nonlinear inclusion theory with application to the growth and morphogenesis of a confined bodyLi J, Kothari M, Chockalingam S, Henzel T, Zhang Q, Li X, Yan J, Cohen T. Nonlinear inclusion theory with application to the growth and morphogenesis of a confined body. Journal Of The Mechanics And Physics Of Solids 2022, 159: 104709. DOI: 10.1016/j.jmps.2021.104709.
- Searching for the Secret of Stickiness: How Biofilms Adhere to SurfacesJiang Z, Nero T, Mukherjee S, Olson R, Yan J. Searching for the Secret of Stickiness: How Biofilms Adhere to Surfaces. Frontiers In Microbiology 2021, 12: 686793. PMID: 34305846, PMCID: PMC8295476, DOI: 10.3389/fmicb.2021.686793.
- Active phase separation by turning towards regions of higher densityZhang J, Alert R, Yan J, Wingreen N, Granick S. Active phase separation by turning towards regions of higher density. Nature Physics 2021, 17: 961-967. DOI: 10.1038/s41567-021-01238-8.
- CO 2 -Driven diffusiophoresis for maintaining a bacteria-free surfaceShim S, Khodaparast S, Lai CY, Yan J, Ault JT, Rallabandi B, Shardt O, Stone HA. CO 2 -Driven diffusiophoresis for maintaining a bacteria-free surface. Soft Matter 2021, 17: 2568-2576. PMID: 33514979, DOI: 10.1039/d0sm02023k.
- Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substratesFei C, Mao S, Yan J, Alert R, Stone H, Bassler B, Wingreen N, Košmrlj A. Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 7622-7632. PMID: 32193350, PMCID: PMC7148565, DOI: 10.1073/pnas.1919607117.
- Surviving as a Community: Antibiotic Tolerance and Persistence in Bacterial BiofilmsYan J, Bassler B. Surviving as a Community: Antibiotic Tolerance and Persistence in Bacterial Biofilms. Cell Host & Microbe 2019, 26: 15-21. PMID: 31295420, PMCID: PMC6629468, DOI: 10.1016/j.chom.2019.06.002.
- Surfactant-Mediated Assembly of Amphiphilic Janus Spheres.Tsyrenova A, Miller K, Yan J, Olson E, Anthony SM, Jiang S. Surfactant-Mediated Assembly of Amphiphilic Janus Spheres. Langmuir : The ACS Journal Of Surfaces And Colloids 2019, 35: 6106-6111. PMID: 30950625, DOI: 10.1021/acs.langmuir.9b00500.
- Mechanical instability and interfacial energy drive biofilm morphogenesisYan J, Fei C, Mao S, Moreau A, Wingreen NS, Košmrlj A, Stone HA, Bassler BL. Mechanical instability and interfacial energy drive biofilm morphogenesis. ELife 2019, 8: e43920. PMID: 30848725, PMCID: PMC6453567, DOI: 10.7554/elife.43920.
- Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary PeelingYan J, Moreau A, Khodaparast S, Perazzo A, Feng J, Fei C, Mao S, Mukherjee S, Košmrlj A, Wingreen N, Bassler B, Stone H. Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary Peeling. Advanced Materials 2019, 31: e1807586. PMID: 30667139, DOI: 10.1002/adma.201807586.
- Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary PeelingYan J, Moreau A, Khodaparast S, Perazzo A, Feng J, Fei C, Mao S, Mukherjee S, Košmrlj A, Wingreen NS, Bassler BL, Stone HA. Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary Peeling. Advanced Materials 2018, 30: e1804153. PMID: 30368924, PMCID: PMC8865467, DOI: 10.1002/adma.201804153.
- Verticalization of bacterial biofilmsBeroz F, Yan J, Meir Y, Sabass B, Stone H, Bassler B, Wingreen N. Verticalization of bacterial biofilms. Nature Physics 2018, 14: 954-960. PMID: 30906420, PMCID: PMC6426328, DOI: 10.1038/s41567-018-0170-4.
- Extracellular-matrix-mediated osmotic pressure drives Vibrio cholerae biofilm expansion and cheater exclusionYan J, Nadell CD, Stone HA, Wingreen NS, Bassler BL. Extracellular-matrix-mediated osmotic pressure drives Vibrio cholerae biofilm expansion and cheater exclusion. Nature Communications 2017, 8: 327. PMID: 28835649, PMCID: PMC5569112, DOI: 10.1038/s41467-017-00401-1.
- Effective temperature concept evaluated in an active colloid mixture.Han M, Yan J, Granick S, Luijten E. Effective temperature concept evaluated in an active colloid mixture. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: 7513-7518. PMID: 28674007, PMCID: PMC5530701, DOI: 10.1073/pnas.1706702114.
- Environmental fluctuation governs selection for plasticity in biofilm productionYan J, Nadell CD, Bassler BL. Environmental fluctuation governs selection for plasticity in biofilm production. The ISME Journal: Multidisciplinary Journal Of Microbial Ecology 2017, 11: 1569-1577. PMID: 28338673, PMCID: PMC5520152, DOI: 10.1038/ismej.2017.33.
- Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilmsNadell CD, Ricaurte D, Yan J, Drescher K, Bassler BL. Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms. ELife 2017, 6: e21855. PMID: 28084994, PMCID: PMC5283829, DOI: 10.7554/elife.21855.
- Reconfiguring active particles by electrostatic imbalance.Yan J, Han M, Zhang J, Xu C, Luijten E, Granick S. Reconfiguring active particles by electrostatic imbalance. Nature Materials 2016, 15: 1095-9. PMID: 27400388, DOI: 10.1038/nmat4696.
- Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imagingYan J, Sharo AG, Stone HA, Wingreen NS, Bassler BL. Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: e5337-e5343. PMID: 27555592, PMCID: PMC5018804, DOI: 10.1073/pnas.1611494113.
- A Scalable Platform for Functional Nanomaterials via Bubble‐BurstingFeng J, Nunes J, Shin S, Yan J, Kong Y, Prud'homme R, Arnaudov L, Stoyanov S, Stone H. A Scalable Platform for Functional Nanomaterials via Bubble‐Bursting. Advanced Materials 2016, 28: 4047-4052. PMID: 27007617, DOI: 10.1002/adma.201505994.
- Colloidal superstructures programmed into magnetic Janus particles.Yan J, Bae SC, Granick S. Colloidal superstructures programmed into magnetic Janus particles. Advanced Materials (Deerfield Beach, Fla.) 2015, 27: 874-9. PMID: 25503513, DOI: 10.1002/adma.201403857.
- Rotating crystals of magnetic Janus colloids.Yan J, Bae SC, Granick S. Rotating crystals of magnetic Janus colloids. Soft Matter 2015, 11: 147-53. PMID: 25372218, DOI: 10.1039/c4sm01962h.
- Colloidal ribbons and rings from Janus magnetic rods.Yan J, Chaudhary K, Chul Bae S, Lewis JA, Granick S. Colloidal ribbons and rings from Janus magnetic rods. Nature Communications 2013, 4: 1516. PMID: 23443544, DOI: 10.1038/ncomms2520.
- Linking synchronization to self-assembly using magnetic Janus colloids.Yan J, Bloom M, Bae SC, Luijten E, Granick S. Linking synchronization to self-assembly using magnetic Janus colloids. Nature 2012, 491: 578-81. PMID: 23172215, DOI: 10.1038/nature11619.