{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T19:22:51Z","timestamp":1771356171116,"version":"3.50.1"},"reference-count":35,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T00:00:00Z","timestamp":1771286400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"the US National Science Foundation","doi-asserted-by":"crossref","award":["2122027"],"award-info":[{"award-number":["2122027"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"name":"the Mizzou Forward Undergraduate Research Training Grant","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]},{"name":"the Research Excellence Program at the University of Missouri","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    The fundamental molecules of life are polymers. Prominent examples include nucleic acids and proteins, both of which exhibit a large array of mechanical properties and three-dimensional shapes. The bending rigidity of individual polymers is quantified by the persistence length. The shape of a polymer, dictated by the topology of the polymer backbone, a line trace through the center of the polymer along the contour path, is also an important characteristic. Common biomolecular architectures include linear, cyclic (ring-like), and branched structures; combinations of these can also exist, as in complex polymer networks. Determination of persistence length and shape are largely informative to polymer function and stability in biological environments. Here we demonstrate Persistence length Shape Polymer (PS Poly), a near-fully automated algorithm designed to obtain key physical attributes from single molecule images obtained in physiologically relevant fluid conditions via atomic force microscopy. The algorithm, which involves image reduction via skeletonization followed by end point and branch point detection, is capable of rapidly analyzing thousands of polymers with subpixel precision. Algorithm outputs were verified by analysis of deoxyribonucleic acid, a very well characterized macromolecule. The method was further demonstrated by application to candidalysin, a recently discovered and complex virulence factor from\n                    <jats:italic>Candida albicans<\/jats:italic>\n                    . Candidalysin forms polymers of highly variable shape and contour length and represents the first peptide toxin identified in a human fungal pathogen. PS Poly is a robust and general algorithm. It can be used to extract fundamental information about polymer backbone stiffness, architecture, and more generally, polymerization mechanisms.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0341464","type":"journal-article","created":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T18:49:01Z","timestamp":1771354141000},"page":"e0341464","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["PS Poly: A chain tracing algorithm to determine persistence length and categorize complex polymers by shape"],"prefix":"10.1371","volume":"21","author":[{"given":"Elizabeth A.","family":"Conley","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Creighton M.","family":"Lisowski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katherine G.","family":"Schaefer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harrison C.","family":"Davison","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie E.","family":"Baguio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ioan","family":"Kosztin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5811-7012","authenticated-orcid":true,"given":"Gavin M.","family":"King","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,2,17]]},"reference":[{"issue":"7597","key":"pone.0341464.ref001","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/nature17625","article-title":"Candidalysin is a fungal peptide toxin critical for mucosal infection","volume":"532","author":"DL Moyes","year":"2016","journal-title":"Nature"},{"key":"pone.0341464.ref002","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.75490","article-title":"The Candida albicans virulence factor candidalysin polymerizes in solution to form membrane pores and damage epithelial cells","volume":"11","author":"CM Russell","year":"2022","journal-title":"Elife"},{"issue":"2","key":"pone.0341464.ref003","doi-asserted-by":"crossref","first-page":"119","DOI":"10.4161\/viru.22913","article-title":"Candida albicans pathogenicity mechanisms","volume":"4","author":"FL Mayer","year":"2013","journal-title":"Virulence"},{"issue":"5","key":"pone.0341464.ref004","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1038\/s41557-020-0440-5","article-title":"The synthesis, properties and potential applications of cyclic polymers","volume":"12","author":"FM Haque","year":"2020","journal-title":"Nat Chem"},{"issue":"11","key":"pone.0341464.ref005","doi-asserted-by":"crossref","first-page":"5924","DOI":"10.1021\/cr900068q","article-title":"Hyperbranched and highly branched polymer architectures--synthetic strategies and major characterization aspects","volume":"109","author":"BI Voit","year":"2009","journal-title":"Chem Rev"},{"issue":"19","key":"pone.0341464.ref006","doi-asserted-by":"crossref","first-page":"11701","DOI":"10.1021\/acs.chemrev.0c00617","article-title":"Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems","volume":"121","author":"DJ M\u00fcller","year":"2021","journal-title":"Chem Rev"},{"issue":"1","key":"pone.0341464.ref007","doi-asserted-by":"crossref","first-page":"55","DOI":"10.3390\/ijms24010055","article-title":"Atomic Force Microscopy Reveals Complexity Underlying General Secretory System Activity","volume":"24","author":"DR Weaver","year":"2022","journal-title":"Int J Mol Sci"},{"issue":"4","key":"pone.0341464.ref008","doi-asserted-by":"crossref","first-page":"4220","DOI":"10.1021\/acsnano.8b09234","article-title":"Imaging DNA Equilibrated onto Mica in Liquid Using Biochemically Relevant Deposition Conditions","volume":"13","author":"PR Heenan","year":"2019","journal-title":"ACS Nano"},{"issue":"5","key":"pone.0341464.ref009","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1006\/jmbi.1996.0687","article-title":"Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis","volume":"264","author":"C Rivetti","year":"1996","journal-title":"J Mol Biol"},{"key":"pone.0341464.ref010","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198520597.001.0001","volume-title":"Polymer Physics","author":"M Rubinstein","year":"2003"},{"key":"pone.0341464.ref011","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/1751-0473-9-16","article-title":"Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains","volume":"9","author":"G Lamour","year":"2014","journal-title":"Source Code Biol Med"},{"key":"pone.0341464.ref012","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.ymeth.2021.01.008","article-title":"TopoStats - A program for automated tracing of biomolecules from AFM images","volume":"193","author":"JG Beton","year":"2021","journal-title":"Methods"},{"issue":"5","key":"pone.0341464.ref013","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1021\/ma502264c","article-title":"FiberApp: An Open-Source Software for Tracking and Analyzing Polymers, Filaments, Biomacromolecules, and Fibrous Objects","volume":"48","author":"I Usov","year":"2015","journal-title":"Macromolecules"},{"issue":"10","key":"pone.0341464.ref014","doi-asserted-by":"crossref","first-page":"5435","DOI":"10.1039\/D0NR08564B","article-title":"High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes","volume":"13","author":"SF Konrad","year":"2021","journal-title":"Nanoscale"},{"issue":"2","key":"pone.0341464.ref015","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/nnano.2006.63","article-title":"High flexibility of DNA on short length scales probed by atomic force microscopy","volume":"1","author":"PA Wiggins","year":"2006","journal-title":"Nat Nanotechnol"},{"issue":"4","key":"pone.0341464.ref016","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1016\/j.bpj.2009.06.015","article-title":"DNA deformations near charged surfaces: electron and atomic force microscopy views","volume":"97","author":"FGA Faas","year":"2009","journal-title":"Biophys J"},{"issue":"1","key":"pone.0341464.ref017","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1529\/biophysj.106.096966","article-title":"Bending dynamics of fluctuating biopolymers probed by automated high-resolution filament tracking","volume":"93","author":"CP Brangwynne","year":"2007","journal-title":"Biophys J"},{"issue":"3","key":"pone.0341464.ref018","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1017\/S1431927619000308","article-title":"DSeg: A Dynamic Image Segmentation Program to Extract Backbone Patterns for Filamentous Bacteria and Hyphae Structures","volume":"25","author":"H Zhang","year":"2019","journal-title":"Microsc Microanal"},{"issue":"13","key":"pone.0341464.ref019","doi-asserted-by":"crossref","first-page":"2599","DOI":"10.1016\/j.bpj.2021.05.011","article-title":"AutoSmarTrace: Automated chain tracing and flexibility analysis of biological filaments","volume":"120","author":"M Schneider","year":"2021","journal-title":"Biophys J"},{"issue":"4","key":"pone.0341464.ref020","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0094766","article-title":"Multi-platform compatible software for analysis of polymer bending mechanics","volume":"9","author":"JS Graham","year":"2014","journal-title":"PLoS One"},{"key":"pone.0341464.ref021","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.4312","article-title":"A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton","volume":"6","author":"J Nunez-Iglesias","year":"2018","journal-title":"PeerJ"},{"issue":"6","key":"pone.0341464.ref022","doi-asserted-by":"crossref","first-page":"107370","DOI":"10.1016\/j.jbc.2024.107370","article-title":"Polymerization mechanism of the Candida albicans virulence factor candidalysin","volume":"300","author":"KG Schaefer","year":"2024","journal-title":"J Biol Chem"},{"issue":"10","key":"pone.0341464.ref023","doi-asserted-by":"crossref","first-page":"2553","DOI":"10.1038\/s41564-024-01794-8","article-title":"Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin","volume":"9","author":"J Lin","year":"2024","journal-title":"Nat Microbiol"},{"key":"pone.0341464.ref024","unstructured":"KingGavinM. https:\/\/github.com\/KingGavinM\/"},{"issue":"1","key":"pone.0341464.ref025","doi-asserted-by":"crossref","first-page":"9094","DOI":"10.1038\/s41598-023-36066-8","article-title":"An efficient multilevel image thresholding method based on improved heap-based optimizer","volume":"13","author":"EH Houssein","year":"2023","journal-title":"Sci Rep"},{"issue":"3","key":"pone.0341464.ref026","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1145\/357994.358023","article-title":"A fast parallel algorithm for thinning digital patterns","volume":"27","author":"TY Zhang","year":"1984","journal-title":"Commun ACM"},{"key":"pone.0341464.ref027","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9781139015165","volume-title":"Graph Algorithms","author":"S Even","year":"2011"},{"key":"pone.0341464.ref028","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.453","article-title":"scikit-image: image processing in Python","volume":"2","author":"S van der Walt","year":"2014","journal-title":"PeerJ"},{"key":"pone.0341464.ref029","volume-title":"Python 3 Reference Manual","author":"G Van Rossum","year":"2009"},{"key":"pone.0341464.ref030","first-page":"11","article-title":"Proceedings of the 7th Python in Science Conference","author":"AA Hagberg","year":"2008","journal-title":"Pasadena, CA USA"},{"issue":"3","key":"pone.0341464.ref031","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"P Virtanen","year":"2020","journal-title":"Nat Methods"},{"issue":"6","key":"pone.0341464.ref032","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1209\/epl\/i2006-10390-3","article-title":"Persistence length of semiflexible polymers and bending rigidity renormalization","volume":"76","author":"P Gutjahr","year":"2006","journal-title":"Europhys Lett"},{"issue":"23","key":"pone.0341464.ref033","doi-asserted-by":"crossref","first-page":"238302","DOI":"10.1103\/PhysRevLett.113.238302","article-title":"Persistence-length renormalization of polymers in a crowded environment of hard disks","volume":"113","author":"S Sch\u00f6bl","year":"2014","journal-title":"Phys Rev Lett"},{"key":"pone.0341464.ref034","author":"M Newville","year":"2014","journal-title":"LMFIT: Non-Linear Least-Square Minimization and Curve-Fitting for Python"},{"issue":"8","key":"pone.0341464.ref035","doi-asserted-by":"crossref","first-page":"286","DOI":"10.3390\/polym8080286","article-title":"Semiflexible Chains at Surfaces: Worm-Like Chains and beyond","volume":"8","author":"J Baschnagel","year":"2016","journal-title":"Polymers (Basel)"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0341464","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T18:49:07Z","timestamp":1771354147000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0341464"}},"subtitle":[],"editor":[{"given":"Santiago","family":"Casado Rojo","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,2,17]]},"references-count":35,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0341464","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,17]]}}}