[{"has_accepted_license":"1","year":"2017","day":"01","publication":"Nature Genetics","page":"358 - 366","date_published":"2017-03-01T00:00:00Z","doi":"10.1038/ng.3764","date_created":"2018-12-11T11:47:43Z","acknowledgement":"We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"citation":{"mla":"Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:10.1038/ng.3764.","short":"A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee, F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban, M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature Genetics 49 (2017) 358–366.","ieee":"A. Makohon Moore et al., “Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer,” Nature Genetics, vol. 49, no. 3. Nature Publishing Group, pp. 358–366, 2017.","ama":"Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 2017;49(3):358-366. doi:10.1038/ng.3764","apa":"Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D., … Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng.3764","chicago":"Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics. Nature Publishing Group, 2017. https://doi.org/10.1038/ng.3764.","ista":"Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 49(3), 358–366."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7092","author":[{"first_name":"Alvin","last_name":"Makohon Moore","full_name":"Makohon Moore, Alvin"},{"first_name":"Ming","last_name":"Zhang","full_name":"Zhang, Ming"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter"},{"full_name":"Božić, Ivana","last_name":"Božić","first_name":"Ivana"},{"first_name":"Benjamin","last_name":"Allen","full_name":"Allen, Benjamin"},{"first_name":"Deepanjan","id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45","last_name":"Kundu","full_name":"Kundu, Deepanjan"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Fay","last_name":"Wong","full_name":"Wong, Fay"},{"first_name":"Yuchen","full_name":"Jiao, Yuchen","last_name":"Jiao"},{"first_name":"Zachary","full_name":"Kohutek, Zachary","last_name":"Kohutek"},{"first_name":"Jungeui","full_name":"Hong, Jungeui","last_name":"Hong"},{"first_name":"Marc","last_name":"Attiyeh","full_name":"Attiyeh, Marc"},{"last_name":"Javier","full_name":"Javier, Breanna","first_name":"Breanna"},{"full_name":"Wood, Laura","last_name":"Wood","first_name":"Laura"},{"first_name":"Ralph","last_name":"Hruban","full_name":"Hruban, Ralph"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"},{"full_name":"Papadopoulos, Nickolas","last_name":"Papadopoulos","first_name":"Nickolas"},{"first_name":"Kenneth","last_name":"Kinzler","full_name":"Kinzler, Kenneth"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"},{"first_name":"Christine","last_name":"Iacobuzio Donahue","full_name":"Iacobuzio Donahue, Christine"}],"article_processing_charge":"No","external_id":{"pmid":["28092682"]},"title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication_identifier":{"issn":["10614036"]},"publication_status":"published","file":[{"file_id":"7050","checksum":"e442dc3b7420a36ec805e9bb45cc1a2e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_NatureGenetics_Makohon.pdf","date_created":"2019-11-19T08:13:50Z","creator":"dernst","file_size":908099,"date_updated":"2020-07-14T12:47:33Z"}],"language":[{"iso":"eng"}],"issue":"3","volume":49,"ec_funded":1,"abstract":[{"lang":"eng","text":"The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease."}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","month":"03","intvolume":" 49","date_updated":"2022-06-10T09:55:08Z","ddc":["000"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:33Z","_id":"653","article_type":"original","type":"journal_article","status":"public"},{"year":"2017","publication_status":"published","publication_identifier":{"isbn":["9781450349468"]},"language":[{"iso":"eng"}],"publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","day":"30","page":"1001-1017","date_created":"2019-06-06T13:21:29Z","ec_funded":1,"doi":"10.1145/3133956.3134031","date_published":"2017-10-30T00:00:00Z","abstract":[{"text":"A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs.\r\n\r\nEssentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called \"depth-robustness\") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice.\r\n\r\nIn this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we:\r\n*Prove that their depth-robustness is asymptotically maximal.\r\n*Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF.\r\n*Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks. \r\nWe find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice.\r\n\r\nAlong the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT).\r\n","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/443"}],"oa":1,"scopus_import":1,"quality_controlled":"1","publisher":"ACM Press","month":"10","citation":{"ieee":"J. F. Alwen, J. Blocki, and B. Harsha, “Practical graphs for optimal side-channel resistant memory-hard functions,” in Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, Dallas, TX, USA, 2017, pp. 1001–1017.","short":"J.F. Alwen, J. Blocki, B. Harsha, in:, Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–1017.","ama":"Alwen JF, Blocki J, Harsha B. Practical graphs for optimal side-channel resistant memory-hard functions. In: Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. ACM Press; 2017:1001-1017. doi:10.1145/3133956.3134031","apa":"Alwen, J. F., Blocki, J., & Harsha, B. (2017). Practical graphs for optimal side-channel resistant memory-hard functions. In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security (pp. 1001–1017). Dallas, TX, USA: ACM Press. https://doi.org/10.1145/3133956.3134031","mla":"Alwen, Joel F., et al. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–17, doi:10.1145/3133956.3134031.","ista":"Alwen JF, Blocki J, Harsha B. 2017. Practical graphs for optimal side-channel resistant memory-hard functions. Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 1001–1017.","chicago":"Alwen, Joel F, Jeremiah Blocki, and Ben Harsha. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, 1001–17. ACM Press, 2017. https://doi.org/10.1145/3133956.3134031."},"date_updated":"2021-01-12T08:07:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F","last_name":"Alwen"},{"full_name":"Blocki, Jeremiah","last_name":"Blocki","first_name":"Jeremiah"},{"last_name":"Harsha","full_name":"Harsha, Ben","first_name":"Ben"}],"title":"Practical graphs for optimal side-channel resistant memory-hard functions","department":[{"_id":"KrPi"}],"_id":"6527","conference":{"name":"CCS: Conference on Computer and Communications Security","start_date":"2017-10-30","end_date":"2017-11-03","location":"Dallas, TX, USA"},"type":"conference","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"status":"public"},{"citation":{"ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736.","chicago":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144915.","ieee":"A. Kicheva and N. Rivron, “Creating to understand – developmental biology meets engineering in Paris,” Development, vol. 144, no. 5. Company of Biologists, pp. 733–736, 2017.","short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","apa":"Kicheva, A., & Rivron, N. (2017). Creating to understand – developmental biology meets engineering in Paris. Development. Company of Biologists. https://doi.org/10.1242/dev.144915","ama":"Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering in Paris. Development. 2017;144(5):733-736. doi:10.1242/dev.144915","mla":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:10.1242/dev.144915."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"full_name":"Rivron, Nicolas","last_name":"Rivron","first_name":"Nicolas"}],"publist_id":"7089","title":"Creating to understand – developmental biology meets engineering in Paris","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}],"has_accepted_license":"1","year":"2017","day":"01","publication":"Development","page":"733 - 736","doi":"10.1242/dev.144915","date_published":"2017-03-01T00:00:00Z","date_created":"2018-12-11T11:47:44Z","quality_controlled":"1","publisher":"Company of Biologists","oa":1,"date_updated":"2021-01-12T08:07:54Z","ddc":["571"],"file_date_updated":"2020-07-14T12:47:33Z","department":[{"_id":"AnKi"}],"_id":"654","type":"journal_article","status":"public","pubrep_id":"987","publication_identifier":{"issn":["09501991"]},"publication_status":"published","file":[{"date_created":"2018-12-12T10:15:20Z","file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","creator":"system","date_updated":"2020-07-14T12:47:33Z","file_size":228206,"checksum":"eef22a0f42a55b232cb2d1188a2322cb","file_id":"5139","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"5","volume":144,"ec_funded":1,"abstract":[{"lang":"eng","text":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations."}],"oa_version":"Submitted Version","scopus_import":1,"month":"03","intvolume":" 144"},{"month":"08","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.01666"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA'15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity."}],"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781509040964"]},"publication_status":"published","status":"public","type":"conference","conference":{"end_date":"2017-06-30","location":"Aachen, Germany","start_date":"2017-06-25","name":"ISIT: International Symposium on Information Theory"},"_id":"6526","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T08:07:53Z","publisher":"IEEE","quality_controlled":"1","oa":1,"doi":"10.1109/isit.2017.8006529","date_published":"2017-08-09T00:00:00Z","date_created":"2019-06-06T12:53:09Z","day":"09","publication":"2017 IEEE International Symposium on Information Theory (ISIT)","year":"2017","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"article_number":"8006529","title":"On the complexity of estimating Rènyi divergences","author":[{"last_name":"Skórski","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"}],"external_id":{"arxiv":["1702.01666"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017 IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, 2017.","short":"M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017.","ama":"Skórski M. On the complexity of estimating Rènyi divergences. In: 2017 IEEE International Symposium on Information Theory (ISIT). IEEE; 2017. doi:10.1109/isit.2017.8006529","apa":"Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In 2017 IEEE International Symposium on Information Theory (ISIT). Aachen, Germany: IEEE. https://doi.org/10.1109/isit.2017.8006529","mla":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” 2017 IEEE International Symposium on Information Theory (ISIT), 8006529, IEEE, 2017, doi:10.1109/isit.2017.8006529.","ista":"Skórski M. 2017. On the complexity of estimating Rènyi divergences. 2017 IEEE International Symposium on Information Theory (ISIT). ISIT: International Symposium on Information Theory, 8006529.","chicago":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In 2017 IEEE International Symposium on Information Theory (ISIT). IEEE, 2017. https://doi.org/10.1109/isit.2017.8006529."}},{"publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2017","day":"06","publication":"eLife","doi":"10.7554/eLife.23136","date_published":"2017-03-06T00:00:00Z","date_created":"2018-12-11T11:47:44Z","article_number":"e23136","citation":{"ista":"Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella grow through an injection diffusion mechanism. eLife. 6, e23136.","chicago":"Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.23136.","ama":"Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through an injection diffusion mechanism. eLife. 2017;6. doi:10.7554/eLife.23136","apa":"Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier, E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.23136","short":"T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier, C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017).","ieee":"T. Renault et al., “Bacterial flagella grow through an injection diffusion mechanism,” eLife, vol. 6. eLife Sciences Publications, 2017.","mla":"Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife, vol. 6, e23136, eLife Sciences Publications, 2017, doi:10.7554/eLife.23136."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Thibaud","full_name":"Renault, Thibaud","last_name":"Renault"},{"full_name":"Abraham, Anthony","last_name":"Abraham","first_name":"Anthony"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Paradis, Guillaume","last_name":"Paradis","first_name":"Guillaume"},{"full_name":"Rainville, Simon","last_name":"Rainville","first_name":"Simon"},{"last_name":"Charpentier","full_name":"Charpentier, Emmanuelle","first_name":"Emmanuelle"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tu, Yuhai","last_name":"Tu","first_name":"Yuhai"},{"full_name":"Namba, Keiichi","last_name":"Namba","first_name":"Keiichi"},{"first_name":"James","last_name":"Keener","full_name":"Keener, James"},{"last_name":"Minamino","full_name":"Minamino, Tohru","first_name":"Tohru"},{"last_name":"Erhardt","full_name":"Erhardt, Marc","first_name":"Marc"}],"publist_id":"7082","title":"Bacterial flagella grow through an injection diffusion mechanism","abstract":[{"text":"The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"03","intvolume":" 6","publication_identifier":{"issn":["2050084X"]},"publication_status":"published","file":[{"creator":"system","file_size":5520359,"date_updated":"2020-07-14T12:47:33Z","file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","date_created":"2018-12-12T10:08:53Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"39e1c3e82ddac83a30422fa72fa1a383","file_id":"4716"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4717","checksum":"a6d542253028f52e00aa29739ddffe8f","file_size":11242920,"date_updated":"2020-07-14T12:47:33Z","creator":"system","file_name":"IST-2017-904-v1+2_elife-23136-figures-v2.pdf","date_created":"2018-12-12T10:08:54Z"}],"language":[{"iso":"eng"}],"volume":6,"license":"https://creativecommons.org/licenses/by/4.0/","_id":"655","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"904","date_updated":"2021-01-12T08:07:55Z","ddc":["579"],"file_date_updated":"2020-07-14T12:47:33Z","department":[{"_id":"CaGu"}]}]