[{"title":"A logic-based framework for verifying consensus algorithms","department":[{"_id":"ToHe"}],"publisher":"Springer","oa_version":"Submitted Version","ec_funded":1,"date_created":"2018-12-11T11:51:45Z","publist_id":"5817","abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in ensuring the reliability of many software applications. In this paper we consider distributed algorithms whose computations are organized in rounds. To verify the correctness of such algorithms, we reason about (i) properties (such as invariants) of the state, (ii) the transitions controlled by the algorithm, and (iii) the communication graph. We introduce a logic that addresses these points, and contains set comprehensions with cardinality constraints, function symbols to describe the local states of each process, and a limited form of quantifier alternation to express the verification conditions. We show its use in automating the verification of consensus algorithms. In particular, we give a semi-decision procedure for the unsatisfiability problem of the logic and identify a decidable fragment. We successfully applied our framework to verify the correctness of a variety of consensus algorithms tolerant to both benign faults (message loss, process crashes) and value faults (message corruption).","lang":"eng"}],"page":"161 - 181","volume":8318,"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1392","has_accepted_license":"1","year":"2014","oa":1,"status":"public","acknowledgement":"Supported by the Vienna Science and Technology Fund (WWTF) through grant PROSEED.","citation":{"apa":"Dragoi, C., Henzinger, T. A., Veith, H., Widder, J., & Zufferey, D. (2014). A logic-based framework for verifying consensus algorithms (Vol. 8318, pp. 161–181). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54013-4_10","chicago":"Dragoi, Cezara, Thomas A Henzinger, Helmut Veith, Josef Widder, and Damien Zufferey. “A Logic-Based Framework for Verifying Consensus Algorithms,” 8318:161–81. Springer, 2014. https://doi.org/10.1007/978-3-642-54013-4_10.","ieee":"C. Dragoi, T. A. Henzinger, H. Veith, J. Widder, and D. Zufferey, “A logic-based framework for verifying consensus algorithms,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA, 2014, vol. 8318, pp. 161–181.","ista":"Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. 2014. A logic-based framework for verifying consensus algorithms. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 8318, 161–181.","mla":"Dragoi, Cezara, et al. A Logic-Based Framework for Verifying Consensus Algorithms. Vol. 8318, Springer, 2014, pp. 161–81, doi:10.1007/978-3-642-54013-4_10.","short":"C. Dragoi, T.A. Henzinger, H. Veith, J. Widder, D. Zufferey, in:, Springer, 2014, pp. 161–181.","ama":"Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. A logic-based framework for verifying consensus algorithms. In: Vol 8318. Springer; 2014:161-181. doi:10.1007/978-3-642-54013-4_10"},"file_date_updated":"2020-07-14T12:44:48Z","conference":{"end_date":"2014-01-21","name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2014-01-19","location":"San Diego, USA"},"pubrep_id":"179","author":[{"last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","full_name":"Dragoi, Cezara"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"first_name":"Josef","last_name":"Widder","full_name":"Widder, Josef"},{"full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","orcid":"0000-0002-3197-8736","last_name":"Zufferey"}],"date_published":"2014-01-01T00:00:00Z","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-54013-4_10","date_updated":"2021-01-12T06:50:22Z","scopus_import":1,"quality_controlled":"1","intvolume":" 8318","publication_status":"published","file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:11:06Z","relation":"main_file","creator":"system","access_level":"open_access","file_size":444138,"checksum":"bffa33d39be77df0da39defe97eabf84","file_name":"IST-2014-179-v1+1_vmcai14.pdf","file_id":"4859","date_updated":"2020-07-14T12:44:48Z"}],"day":"01","ddc":["000","005"],"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"01"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","page":"167 - 181","year":"2014","_id":"1393","oa":1,"status":"public","citation":{"ieee":"A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,” in Proceedings of the on Future of Software Engineering, Hyderabad, India, 2014, pp. 167–181.","chicago":"Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic Programming.” In Proceedings of the on Future of Software Engineering, 167–81. ACM, 2014. https://doi.org/10.1145/2593882.2593900.","apa":"Gordon, A., Henzinger, T. A., Nori, A., & Rajamani, S. (2014). Probabilistic programming. In Proceedings of the on Future of Software Engineering (pp. 167–181). Hyderabad, India: ACM. https://doi.org/10.1145/2593882.2593900","ama":"Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In: Proceedings of the on Future of Software Engineering. ACM; 2014:167-181. doi:10.1145/2593882.2593900","short":"A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–181.","ista":"Gordon A, Henzinger TA, Nori A, Rajamani S. 2014. Probabilistic programming. Proceedings of the on Future of Software Engineering. FOSE: Future of Software Engineering, 167–181.","mla":"Gordon, Andrew, et al. “Probabilistic Programming.” Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–81, doi:10.1145/2593882.2593900."},"publisher":"ACM","publication":"Proceedings of the on Future of Software Engineering","department":[{"_id":"ToHe"}],"title":"Probabilistic programming","publist_id":"5816","date_created":"2018-12-11T11:51:45Z","ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Probabilistic programs are usual functional or imperative programs with two added constructs: (1) the ability to draw values at random from distributions, and (2) the ability to condition values of variables in a program via observations. Models from diverse application areas such as computer vision, coding theory, cryptographic protocols, biology and reliability analysis can be written as probabilistic programs. Probabilistic inference is the problem of computing an explicit representation of the probability distribution implicitly specified by a probabilistic program. Depending on the application, the desired output from inference may vary-we may want to estimate the expected value of some function f with respect to the distribution, or the mode of the distribution, or simply a set of samples drawn from the distribution. In this paper, we describe connections this research area called \\Probabilistic Programming" has with programming languages and software engineering, and this includes language design, and the static and dynamic analysis of programs. We survey current state of the art and speculate on promising directions for future research.","lang":"eng"}],"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1145/2593882.2593900","open_access":"1"}],"day":"31","month":"05","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"conference":{"name":"FOSE: Future of Software Engineering","end_date":"2014-06-07","location":"Hyderabad, India","start_date":"2014-05-31"},"article_processing_charge":"No","doi":"10.1145/2593882.2593900","date_updated":"2021-01-12T06:50:22Z","author":[{"full_name":"Gordon, Andrew","last_name":"Gordon","first_name":"Andrew"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Aditya","last_name":"Nori","full_name":"Nori, Aditya"},{"first_name":"Sriram","last_name":"Rajamani","full_name":"Rajamani, Sriram"}],"date_published":"2014-05-31T00:00:00Z","quality_controlled":"1","scopus_import":1},{"date_published":"2014-02-01T00:00:00Z","author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Konrad"}],"article_processing_charge":"No","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-07T11:38:56Z","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"In this thesis I studied various individual and social immune defences employed by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi. The first two chapters of this thesis address the phenomenon of 'social immunisation'. Social immunisation, that is the immunological protection of group members due to social contact to a pathogen-exposed nestmate, has been described in various social insect species against different types of pathogens. However, in the case of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation exists at all. Its underlying mechanisms r any other properties were, however, unknown. In the first chapter of this thesis I identified the mechanistic basis of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium. I could show that nestmates of a pathogen-exposed individual contract low-level infections due to social interactions. These low-level infections are, however, non-lethal and cause an active stimulation of the immune system, which protects the nestmates upon subsequent pathogen encounters. In the second chapter of this thesis I investigated the specificity and colony level effects of social immunisation. I demonstrated that the protection conferred by social immunisation is highly specific, protecting ants only against the same pathogen strain. In addition, depending on the respective context, social immunisation may even cause fitness costs. I further showed that social immunisation crucially affects sanitary behaviour and disease dynamics within ant groups. In the third chapter of this thesis I studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic fungi, research concerning host fitness consequence is sparse. I showed that highly Laboulbenia-infected ants sustain fitness costs under resource limitation, however, gain fitness benefits when exposed to an entomopathogenus fungus. These effects are probably cause by a prophylactic upregulation of behavioural as well as physiological immune defences in highly infected ants."}],"department":[{"_id":"SyCr"}],"title":"Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus","publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:51:46Z","oa_version":"None","publist_id":"5814","status":"public","day":"01","citation":{"apa":"Konrad, M. (2014). Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","chicago":"Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and Technology Austria, 2014.","ieee":"M. Konrad, “Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology Austria, 2014.","mla":"Konrad, Matthias. Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus. Institute of Science and Technology Austria, 2014.","ista":"Konrad M. 2014. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","short":"M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology Austria, 2014.","ama":"Konrad M. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. 2014."},"month":"02","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"page":"131","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","_id":"1395","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia M"}],"year":"2014","publication_status":"published"},{"publisher":"Royal Society of Chemistry","publication":"Faraday Discussions","title":"The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics","date_created":"2023-08-10T06:38:19Z","oa_version":"None","extern":"1","abstract":[{"text":"The sensitivities of high-harmonic generation (HHG) and strong-field ionization (SFI) to coupled electronic and nuclear dynamics are studied, using the nitric oxide (NO) molecule as an example. A coherent superposition of electronic and rotational states of NO is prepared by impulsive stimulated Raman scattering and probed by simultaneous detection of HHG and SFI yields. We observe a fourfold higher sensitivity of high-harmonic generation to electronic dynamics and attribute it to the presence of inelastic quantum paths connecting coherently related electronic states [Kraus et al., Phys. Rev. Lett.111, 243005 (2013)]. Whereas different harmonic orders display very different sensitivities to rotational or electronic dynamics, strong-field ionization is found to be most sensitive to electronic motion. We introduce a general theoretical formalism for high-harmonic generation from coupled nuclear-electronic wave packets. We show that the unequal sensitivities of different harmonic orders to electronic or rotational dynamics result from the angle dependence of the photorecombination matrix elements which encode several autoionizing and shape resonances in the photoionization continuum of NO. We further study the dependence of rotational and electronic coherences on the intensity of the excitation pulse and support the observations with calculations.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":171,"page":"113-132","year":"2014","_id":"14018","article_type":"original","external_id":{"pmid":["25415558"]},"status":"public","publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"citation":{"ama":"Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics. Faraday Discussions. 2014;171:113-132. doi:10.1039/c4fd00018h","short":"D.R. Baykusheva, P.M. Kraus, S.B. Zhang, N. Rohringer, H.J. Wörner, Faraday Discussions 171 (2014) 113–132.","ista":"Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. 2014. The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics. Faraday Discussions. 171, 113–132.","mla":"Baykusheva, Denitsa Rangelova, et al. “The Sensitivities of High-Harmonic Generation and Strong-Field Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday Discussions, vol. 171, Royal Society of Chemistry, 2014, pp. 113–32, doi:10.1039/c4fd00018h.","ieee":"D. R. Baykusheva, P. M. Kraus, S. B. Zhang, N. Rohringer, and H. J. Wörner, “The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics,” Faraday Discussions, vol. 171. Royal Society of Chemistry, pp. 113–132, 2014.","chicago":"Baykusheva, Denitsa Rangelova, Peter M. Kraus, Song Bin Zhang, Nina Rohringer, and Hans Jakob Wörner. “The Sensitivities of High-Harmonic Generation and Strong-Field Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday Discussions. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4fd00018h.","apa":"Baykusheva, D. R., Kraus, P. M., Zhang, S. B., Rohringer, N., & Wörner, H. J. (2014). The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00018h"},"article_processing_charge":"No","doi":"10.1039/c4fd00018h","date_updated":"2023-08-22T08:58:12Z","date_published":"2014-04-14T00:00:00Z","author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"last_name":"Kraus","first_name":"Peter M.","full_name":"Kraus, Peter M."},{"full_name":"Zhang, Song Bin","last_name":"Zhang","first_name":"Song Bin"},{"last_name":"Rohringer","first_name":"Nina","full_name":"Rohringer, Nina"},{"full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob","last_name":"Wörner"}],"quality_controlled":"1","keyword":["Physical and Theoretical Chemistry"],"scopus_import":"1","publication_status":"published","intvolume":" 171","day":"14","pmid":1,"month":"04","language":[{"iso":"eng"}]},{"article_number":"064317","scopus_import":"1","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"quality_controlled":"1","author":[{"first_name":"K.","last_name":"Vasilatou","full_name":"Vasilatou, K."},{"first_name":"J. M.","last_name":"Michaud","full_name":"Michaud, J. M."},{"last_name":"Baykusheva","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova"},{"full_name":"Grassi, G.","last_name":"Grassi","first_name":"G."},{"full_name":"Merkt, F.","first_name":"F.","last_name":"Merkt"}],"date_published":"2014-08-14T00:00:00Z","date_updated":"2023-08-22T09:01:31Z","doi":"10.1063/1.4890744","article_processing_charge":"No","intvolume":" 141","publication_status":"published","language":[{"iso":"eng"}],"month":"08","pmid":1,"day":"14","oa_version":"None","date_created":"2023-08-10T06:38:30Z","title":"The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra","publication":"The Journal of Chemical Physics","publisher":"AIP Publishing","abstract":[{"text":"The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra of deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺) to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2 rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.","lang":"eng"}],"extern":"1","_id":"14019","year":"2014","volume":141,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Vasilatou, K., Michaud, J. M., Baykusheva, D. R., Grassi, G., & Merkt, F. (2014). The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4890744","ieee":"K. Vasilatou, J. M. Michaud, D. R. Baykusheva, G. Grassi, and F. Merkt, “The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra,” The Journal of Chemical Physics, vol. 141, no. 6. AIP Publishing, 2014.","chicago":"Vasilatou, K., J. M. Michaud, Denitsa Rangelova Baykusheva, G. Grassi, and F. Merkt. “The Cyclopropene Radical Cation: Rovibrational Level Structure at Low Energies from High-Resolution Photoelectron Spectra.” The Journal of Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4890744.","ista":"Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. 2014. The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. 141(6), 064317.","mla":"Vasilatou, K., et al. “The Cyclopropene Radical Cation: Rovibrational Level Structure at Low Energies from High-Resolution Photoelectron Spectra.” The Journal of Chemical Physics, vol. 141, no. 6, 064317, AIP Publishing, 2014, doi:10.1063/1.4890744.","short":"K. Vasilatou, J.M. Michaud, D.R. Baykusheva, G. Grassi, F. Merkt, The Journal of Chemical Physics 141 (2014).","ama":"Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. 2014;141(6). doi:10.1063/1.4890744"},"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"status":"public","external_id":{"pmid":["25134581"]},"article_type":"original","issue":"6"},{"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants."}],"author":[{"first_name":"Petra","last_name":"Marhavá","full_name":"Marhavá, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2014-12-01T00:00:00Z","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-07T11:39:38Z","date_created":"2018-12-11T11:51:49Z","oa_version":"None","publist_id":"5805","title":"Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","citation":{"ama":"Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. 2014.","mla":"Marhavá, Petra. Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2014.","ista":"Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","short":"P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.","chicago":"Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.","ieee":"P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.","apa":"Marhavá, P. (2014). Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria."},"month":"12","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"status":"public","day":"01","_id":"1402","supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"year":"2014","publication_status":"published","page":"90","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation"},{"article_number":"023001","author":[{"last_name":"Kraus","first_name":"P. M.","full_name":"Kraus, P. M."},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"last_name":"Wörner","first_name":"H. J.","full_name":"Wörner, H. J."}],"date_published":"2014-07-11T00:00:00Z","article_processing_charge":"No","date_updated":"2023-08-22T09:02:56Z","doi":"10.1103/physrevlett.113.023001","keyword":["General Physics and Astronomy"],"scopus_import":"1","quality_controlled":"1","intvolume":" 113","main_file_link":[{"url":"https://arxiv.org/abs/1311.3923","open_access":"1"}],"publication_status":"published","pmid":1,"day":"11","month":"07","language":[{"iso":"eng"}],"publication":"Physical Review Letters","title":"Two-pulse field-free orientation reveals anisotropy of molecular shape resonance","publisher":"American Physical Society","date_created":"2023-08-10T06:38:38Z","oa_version":"Preprint","arxiv":1,"abstract":[{"text":"We report the observation of macroscopic field-free orientation, i.e., more than 73% of CO molecules pointing in the same direction. This is achieved through an all-optical scheme operating at high particle densities (>10(17) cm(-3)) that combines one-color (ω) and two-color (ω+2ω) nonresonant femtosecond laser pulses. We show that the achieved orientation solely relies on the hyperpolarizability interaction as opposed to an ionization-depletion mechanism, thus, opening a wide range of applications. The achieved strong orientation enables us to reveal the molecular-frame anisotropies of the photorecombination amplitudes and phases caused by a shape resonance. The resonance appears as a local maximum in the even-harmonic emission around 28 eV. In contrast, the odd-harmonic emission is suppressed in this spectral region through the combined effects of an asymmetric photorecombination phase and a subcycle Stark effect, generic for polar molecules, that we experimentally identify.","lang":"eng"}],"extern":"1","volume":113,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"14020","year":"2014","oa":1,"status":"public","issue":"2","external_id":{"arxiv":["1311.3923"],"pmid":["25062172"]},"article_type":"original","citation":{"short":"P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Physical Review Letters 113 (2014).","ista":"Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. 113(2), 023001.","mla":"Kraus, P. M., et al. “Two-Pulse Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical Review Letters, vol. 113, no. 2, 023001, American Physical Society, 2014, doi:10.1103/physrevlett.113.023001.","ama":"Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. 2014;113(2). doi:10.1103/physrevlett.113.023001","apa":"Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.113.023001","ieee":"P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse field-free orientation reveals anisotropy of molecular shape resonance,” Physical Review Letters, vol. 113, no. 2. American Physical Society, 2014.","chicago":"Kraus, P. M., Denitsa Rangelova Baykusheva, and H. J. Wörner. “Two-Pulse Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.113.023001."},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]}},{"day":"10","language":[{"iso":"eng"}],"month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1311.3923","open_access":"1"}],"intvolume":" 47","publication_status":"published","date_published":"2014-06-10T00:00:00Z","author":[{"first_name":"P M","last_name":"Kraus","full_name":"Kraus, P M"},{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva"},{"last_name":"Wörner","first_name":"H J","full_name":"Wörner, H J"}],"date_updated":"2023-08-22T09:04:30Z","doi":"10.1088/0953-4075/47/12/124030","article_processing_charge":"No","scopus_import":"1","keyword":["Condensed Matter Physics","Atomic and Molecular Physics","and Optics"],"quality_controlled":"1","article_number":"124030","oa":1,"status":"public","article_type":"original","external_id":{"arxiv":["1311.3923"]},"issue":"12","citation":{"ama":"Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. 2014;47(12). doi:10.1088/0953-4075/47/12/124030","short":"P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic, Molecular and Optical Physics 47 (2014).","mla":"Kraus, P. M., et al. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12, 124030, IOP Publishing, 2014, doi:10.1088/0953-4075/47/12/124030.","ista":"Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. 47(12), 124030.","chicago":"Kraus, P M, Denitsa Rangelova Baykusheva, and H J Wörner. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2014. https://doi.org/10.1088/0953-4075/47/12/124030.","ieee":"P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12. IOP Publishing, 2014.","apa":"Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/0953-4075/47/12/124030"},"publication_identifier":{"eissn":["1361-6455"],"issn":["0953-4075"]},"volume":47,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14021","year":"2014","arxiv":1,"abstract":[{"text":"We present the detailed analysis of a new two-pulse orientation scheme that achieves macroscopic field-free orientation at the high particle densities required for attosecond and high-harmonic spectroscopies (Kraus et al 2013 arXiv:1311.3923). Carbon monoxide molecules are oriented by combining one-colour and delayed two-colour non-resonant femtosecond laser pulses. High-harmonic generation is used to probe the oriented wave-packet dynamics and reveals that a very high degree of orientation (Nup/Ntotal = 0.73–0.82) is achieved. We further extend this approach to orienting carbonyl sulphide molecules. We show that the present two-pulse scheme selectively enhances orientation created by the hyperpolarizability interaction whereas the ionization-depletion mechanism plays no role. We further control and optimize orientation through the delay between the one- and two-colour pump pulses. Finally, we demonstrate a complementary encoding of electronic-structure features, such as shape resonances, in the even- and odd-harmonic spectrum. The achieved progress makes two-pulse field-free orientation an attractive tool for a broad class of time-resolved measurements.","lang":"eng"}],"extern":"1","title":"Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules","publication":"Journal of Physics B: Atomic, Molecular and Optical Physics","publisher":"IOP Publishing","oa_version":"Preprint","date_created":"2023-08-10T06:38:48Z"},{"language":[{"iso":"eng"}],"month":"08","citation":{"chicago":"Behrndt, Martin. “Forces Driving Epithelial Spreading in Zebrafish Epiboly.” IST Austria, 2014.","ieee":"M. Behrndt, “Forces driving epithelial spreading in zebrafish epiboly,” IST Austria, 2014.","apa":"Behrndt, M. (2014). Forces driving epithelial spreading in zebrafish epiboly. IST Austria.","ama":"Behrndt M. Forces driving epithelial spreading in zebrafish epiboly. 2014.","ista":"Behrndt M. 2014. Forces driving epithelial spreading in zebrafish epiboly. IST Austria.","mla":"Behrndt, Martin. Forces Driving Epithelial Spreading in Zebrafish Epiboly. IST Austria, 2014.","short":"M. Behrndt, Forces Driving Epithelial Spreading in Zebrafish Epiboly, IST Austria, 2014."},"day":"01","status":"public","publication_status":"published","year":"2014","_id":"1403","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"91","abstract":[{"text":"A variety of developmental and disease related processes depend on epithelial cell sheet spreading. In order to gain insight into the biophysical mechanism(s) underlying the tissue morphogenesis we studied the spreading of an epithelium during the early development of the zebrafish embryo. In zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk cell to completely engulf it at the end of gastrulation. Previous studies have proposed that an actomyosin ring forming within the yolk syncytial layer (YSL) acts as purse string that through constriction along its circumference pulls on the margin of the EVL. Direct biophysical evidence for this hypothesis has however been missing. The aim of the thesis was to understand how the actomyosin ring may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate the spreading of the epithelium. Using laser ablation to measure cortical tension within the actomyosin ring we found an anisotropic tension distribution, which was highest along the circumference of the ring. However the low degree of anisotropy was incompatible with the actomyosin ring functioning as a purse string only. Additionally, we observed retrograde cortical flow from vegetal parts of the ring into the EVL margin. Interpreting the experimental data using a theoretical distribution that models the tissues as active viscous gels led us to proposen that the actomyosin ring has a twofold contribution to EVL epiboly. It not only acts as a purse string through constriction along its circumference, but in addition constriction along the width of the ring generates pulling forces through friction-resisted cortical flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly proceeded normally indicating that the flow-friction mechanism is sufficient to drive the process. Aiming to understand what cellular mechanism(s) may facilitate the spreading of the epithelium we found that tension-oriented EVL cell divisions limit tissue anisotropy by releasing tension along the division axis and promote epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions in which oriented-cell division is impaired or the epithelium is mechanically challenged. Taken together our study of EVL epiboly suggests a novel mechanism of force generation for actomyosin rings through friction-resisted cortical flow and highlights the importance of tension-oriented cell divisions in epithelial morphogenesis.","lang":"eng"}],"alternative_title":["IST Austria Thesis"],"date_updated":"2023-10-17T12:16:58Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2282"},{"status":"public","relation":"part_of_dissertation","id":"2950"},{"id":"3373","status":"public","relation":"part_of_dissertation"}]},"date_published":"2014-08-01T00:00:00Z","author":[{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin","last_name":"Behrndt","first_name":"Martin"}],"publist_id":"5804","acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"None","date_created":"2018-12-11T11:51:49Z","publisher":"IST Austria","department":[{"_id":"CaHe"}],"title":"Forces driving epithelial spreading in zebrafish epiboly"},{"abstract":[{"lang":"eng","text":"The co-evolution of hosts and pathogens is characterized by continuous adaptations of both parties. Pathogens of social insects need to adapt towards disease defences at two levels: 1) individual immunity of each colony member consisting of behavioural defence strategies as well as humoral and cellular immune responses and 2) social immunity that is collectively performed by all group members comprising behavioural, physiological and organisational defence strategies.\r\n\r\nTo disentangle the selection pressure on pathogens by the collective versus individual level of disease defence in social insects, we performed an evolution experiment using the Argentine Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution over 10 serial host passages to two different evolution host treatments: (1) only individual host immunity in a single host treatment, and (2) simultaneously acting individual and social immunity in a social host treatment, in which an exposed ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen evolution experiment, the 6 Metarhizium spp. strains were characterised concerning conidiospore size killing rates in singly and socially reared ants, their competitiveness under coinfecting conditions and their influence on ant behaviour. We analysed how the ancestral atrain mixture changed in conidiospere size, killing rate and strain composition dependent on host treatment (single or social hosts) during 10 passages and found that killing rate and conidiospere size of the pathogen increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting the evolved strain mixtures that evolved under either the single or social host treatment under both single and social current rearing conditions in a full factorial design experiment revealed that the additional collective defences in insect societies add new selection pressure for their coevolving pathogens that compromise their ability to adapt to its host at the group level. To our knowledge, this is the first study directly measuring the influence of social immunity on pathogen evolution."}],"author":[{"full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock"}],"date_published":"2014-04-01T00:00:00Z","alternative_title":["IST Austria Thesis"],"date_updated":"2021-01-12T06:50:30Z","oa_version":"None","date_created":"2018-12-11T11:51:49Z","publist_id":"5803","title":"Evolution of a fungal pathogen towards individual versus social immunity in ants","department":[{"_id":"SyCr"}],"publisher":"IST Austria","citation":{"apa":"Stock, M. (2014). Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria.","ieee":"M. Stock, “Evolution of a fungal pathogen towards individual versus social immunity in ants,” IST Austria, 2014.","chicago":"Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants.” IST Austria, 2014.","mla":"Stock, Miriam. Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants. IST Austria, 2014.","ista":"Stock M. 2014. Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria.","short":"M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants, IST Austria, 2014.","ama":"Stock M. Evolution of a fungal pathogen towards individual versus social immunity in ants. 2014."},"language":[{"iso":"eng"}],"month":"04","acknowledgement":"This work was funded by the DFG and the ERC.","status":"public","day":"01","_id":"1404","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia M","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia M"}],"publication_status":"published","year":"2014","page":"101","type":"dissertation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"status":"public","issue":"47","article_type":"original","external_id":{"pmid":["25346175"]},"citation":{"chicago":"Stahl, Evi, Thomas Martin, Florian M Praetorius, and Hendrik Dietz. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/ange.201405991.","ieee":"E. Stahl, T. Martin, F. M. Praetorius, and H. Dietz, “Facile and scalable preparation of pure and dense DNA origami solutions,” Angewandte Chemie International Edition, vol. 126, no. 47. Wiley, pp. 12949–12954, 2014.","apa":"Stahl, E., Martin, T., Praetorius, F. M., & Dietz, H. (2014). Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/ange.201405991","ama":"Stahl E, Martin T, Praetorius FM, Dietz H. Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. 2014;126(47):12949-12954. doi:10.1002/ange.201405991","ista":"Stahl E, Martin T, Praetorius FM, Dietz H. 2014. Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. 126(47), 12949–12954.","mla":"Stahl, Evi, et al. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte Chemie International Edition, vol. 126, no. 47, Wiley, 2014, pp. 12949–54, doi:10.1002/ange.201405991.","short":"E. Stahl, T. Martin, F.M. Praetorius, H. Dietz, Angewandte Chemie International Edition 126 (2014) 12949–12954."},"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"volume":126,"page":"12949-12954","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"14301","year":"2014","abstract":[{"lang":"eng","text":"DNA has become a prime material for assembling complex three-dimensional objects that promise utility in various areas of application. However, achieving user-defined goals with DNA objects has been hampered by the difficulty to prepare them at arbitrary concentrations and in user-defined solution conditions. Here, we describe a method that solves this problem. The method is based on poly(ethylene glycol)-induced depletion of species with high molecular weight. We demonstrate that our method is applicable to a wide spectrum of DNA shapes and that it achieves excellent recovery yields of target objects up to 97 %, while providing efficient separation from non-integrated DNA strands. DNA objects may be prepared at concentrations up to the limit of solubility, including the possibility for bringing DNA objects into a solid phase. Due to the fidelity and simplicity of our method we anticipate that it will help to catalyze the development of new types of applications that use self-assembled DNA objects."}],"extern":"1","publication":"Angewandte Chemie International Edition","title":"Facile and scalable preparation of pure and dense DNA origami solutions","publisher":"Wiley","date_created":"2023-09-06T12:51:14Z","oa_version":"Published Version","pmid":1,"day":"17","month":"11","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1002/ange.201405991","open_access":"1"}],"intvolume":" 126","publication_status":"published","author":[{"full_name":"Stahl, Evi","first_name":"Evi","last_name":"Stahl"},{"full_name":"Martin, Thomas","first_name":"Thomas","last_name":"Martin"},{"last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M"},{"first_name":"Hendrik","last_name":"Dietz","full_name":"Dietz, Hendrik"}],"date_published":"2014-11-17T00:00:00Z","article_processing_charge":"No","date_updated":"2023-11-07T12:14:30Z","doi":"10.1002/ange.201405991","scopus_import":"1","quality_controlled":"1"},{"pmid":1,"day":"21","month":"03","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1309.5662","open_access":"1"}],"intvolume":" 10","publication_status":"published","date_published":"2014-03-21T00:00:00Z","author":[{"full_name":"Takagi, Daisuke","last_name":"Takagi","first_name":"Daisuke"},{"first_name":"Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"full_name":"Braunschweig, Adam B.","last_name":"Braunschweig","first_name":"Adam B."},{"full_name":"Shelley, Michael J.","first_name":"Michael J.","last_name":"Shelley"},{"full_name":"Zhang, Jun","first_name":"Jun","last_name":"Zhang"}],"article_processing_charge":"No","date_updated":"2023-02-23T13:47:35Z","doi":"10.1039/c3sm52815d","keyword":["General Chemistry","Condensed Matter Physics"],"scopus_import":"1","quality_controlled":"1","article_number":"1784","oa":1,"status":"public","issue":"11","external_id":{"arxiv":["1309.5662"],"pmid":["24800268"]},"article_type":"original","citation":{"mla":"Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:10.1039/c3sm52815d.","ista":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.","short":"D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014).","ama":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 2014;10(11). doi:10.1039/c3sm52815d","apa":"Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., & Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c3sm52815d","chicago":"Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter. Royal Society of Chemistry , 2014. https://doi.org/10.1039/c3sm52815d.","ieee":"D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” Soft Matter, vol. 10, no. 11. Royal Society of Chemistry , 2014."},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"volume":10,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","type":"journal_article","_id":"9050","year":"2014","arxiv":1,"abstract":[{"lang":"eng","text":"Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter."}],"extern":"1","publication":"Soft Matter","title":"Hydrodynamic capture of microswimmers into sphere-bound orbits","publisher":"Royal Society of Chemistry ","date_created":"2021-02-01T13:43:31Z","oa_version":"Preprint"},{"date_created":"2021-02-18T14:31:11Z","oa_version":"Published Version","publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","title":"Light-activated self-propelled colloids","publisher":"The Royal Society","abstract":[{"lang":"eng","text":"Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles."}],"extern":"1","arxiv":1,"_id":"9166","year":"2014","volume":372,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","type":"journal_article","citation":{"mla":"Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:10.1098/rsta.2013.0372.","short":"J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 372 (2014).","ista":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372(2029), 20130372.","ama":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2014;372(2029). doi:10.1098/rsta.2013.0372","apa":"Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., & Chaikin, P. M. (2014). Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rsta.2013.0372","chicago":"Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2014. https://doi.org/10.1098/rsta.2013.0372.","ieee":"J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin, “Light-activated self-propelled colloids,” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372, no. 2029. The Royal Society, 2014."},"publication_identifier":{"issn":["1364-503X"],"eissn":["1471-2962"]},"oa":1,"status":"public","issue":"2029","external_id":{"arxiv":["1410.7278"],"pmid":["25332383"]},"article_type":"original","article_number":"20130372","keyword":["General Engineering","General Physics and Astronomy","General Mathematics"],"scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci"},{"full_name":"Sacanna, S.","first_name":"S.","last_name":"Sacanna"},{"last_name":"Kim","first_name":"S.-H.","full_name":"Kim, S.-H."},{"first_name":"G.-R.","last_name":"Yi","full_name":"Yi, G.-R."},{"full_name":"Pine, D. J.","first_name":"D. J.","last_name":"Pine"},{"full_name":"Chaikin, P. M.","first_name":"P. M.","last_name":"Chaikin"}],"date_published":"2014-11-28T00:00:00Z","article_processing_charge":"No","doi":"10.1098/rsta.2013.0372","date_updated":"2021-02-22T10:44:16Z","intvolume":" 372","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsta.2013.0372"}],"publication_status":"published","month":"11","language":[{"iso":"eng"}],"pmid":1,"day":"28"},{"issue":"4","day":"22","status":"public","acknowledgement":"We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter, D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse, the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan, and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo, and G. Sheng for critically reading the manuscript. This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H. and the RIKEN Foreign Postdoctoral Researcher Program to B.D.","month":"05","language":[{"iso":"eng"}],"citation":{"ista":"Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 7(4), 941–950.","short":"B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950.","mla":"Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports, vol. 7, no. 4, Cell Press, 2014, pp. 941–50, doi:10.1016/j.celrep.2014.03.066.","ama":"Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 2014;7(4):941-950. doi:10.1016/j.celrep.2014.03.066","apa":"Dong, B., Hannezo, E. B., & Hayashi, S. (2014). Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2014.03.066","ieee":"B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape,” Cell Reports, vol. 7, no. 4. Cell Press, pp. 941–950, 2014.","chicago":"Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports. Cell Press, 2014. https://doi.org/10.1016/j.celrep.2014.03.066."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":7,"page":"941 - 950","year":"2014","publication_status":"published","_id":"925","intvolume":" 7","article_processing_charge":"No","doi":"10.1016/j.celrep.2014.03.066","date_updated":"2021-01-12T08:21:57Z","date_published":"2014-05-22T00:00:00Z","author":[{"full_name":"Dong, Bo","last_name":"Dong","first_name":"Bo"},{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hayashi, Shigeo","last_name":"Hayashi","first_name":"Shigeo"}],"extern":"1","abstract":[{"text":"The morphological stability of biological tubes is crucial for the efficient circulation of fluids and gases. Failure of this stability causes irregularly shaped tubes found in multiple pathological conditions. Here, we report that Drosophila mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis accompanied by the ectopic accumulation and overactivation of Crumbs in swollen endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM) of the tracheal tube is a viscoelastic material coupled with the apical membrane. We present a simple mechanical model in which aECM elasticity, apical membrane growth, and their interaction are three vital parameters determining the stability of biological tubes. Our findings demonstrate a mechanical role for the extracellular matrix and suggest that the interaction of the apical membrane and an elastic aECM determines the final morphology of biological tubes independent of cell shape.","lang":"eng"}],"publisher":"Cell Press","publication":"Cell Reports","title":"Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape","publist_id":"6515","date_created":"2018-12-11T11:49:14Z","oa_version":"None"},{"oa_version":"None","date_created":"2018-12-11T11:49:14Z","publist_id":"6516","title":"Growth homeostatic regulation and stem cell dynamics in tissues","publication":"Journal of the Royal Society Interface","publisher":"Royal Society of London","abstract":[{"text":"The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea.","lang":"eng"}],"extern":"1","date_published":"2014-04-06T00:00:00Z","author":[{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prost","first_name":"Jacques","full_name":"Prost, Jacques"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"}],"date_updated":"2021-01-12T08:21:57Z","doi":"10.1098/rsif.2013.0895","article_processing_charge":"No","intvolume":" 11","_id":"926","publication_status":"published","year":"2014","volume":11,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2014). Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2013.0895","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and stem cell dynamics in tissues,” Journal of the Royal Society Interface, vol. 11, no. 93. Royal Society of London, 2014.","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface. Royal Society of London, 2014. https://doi.org/10.1098/rsif.2013.0895.","mla":"Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface, vol. 11, no. 93, Royal Society of London, 2014, doi:10.1098/rsif.2013.0895.","short":"E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface 11 (2014).","ista":"Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).","ama":"Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 2014;11(93). doi:10.1098/rsif.2013.0895"},"language":[{"iso":"eng"}],"month":"04","acknowledgement":"We thank Jens Elgeti and Silvia Fre for fruitful discussions.","status":"public","day":"06","issue":"93"},{"publisher":"National Academy of Sciences","publication":"PNAS","title":"Theory of epithelial sheet morphology in three dimensions","publist_id":"6517","date_created":"2018-12-11T11:49:14Z","oa_version":"None","article_processing_charge":"No","doi":"10.1073/pnas.1312076111","date_updated":"2021-01-12T08:21:58Z","author":[{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"first_name":"Jacques","last_name":"Prost","full_name":"Prost, Jacques"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"}],"date_published":"2014-01-01T00:00:00Z","extern":"1","abstract":[{"text":"Morphogenesis during embryo development requires the coordination of mechanical forces to generate the macroscopic shapes of organs. We propose a minimal theoretical model, based on cell adhesion and actomyosin contractility, which describes the various shapes of epithelial cells and the bending and buckling of epithelial sheets, as well as the relative stability of cellular tubes and spheres. We show that, to understand these processes, a full 3D description of the cells is needed, but that simple scaling laws can still be derived. The morphologies observed in vivo can be understood as stable points of mechanical equations and the transitions between them are either continuous or discontinuous. We then focus on epithelial sheet bending, a ubiquitous morphogenetic process. We calculate the curvature of an epithelium as a function of actin belt tension as well as of cell-cell and and cell-substrate tension. The model allows for a comparison of the relative stabilities of spherical or cylindrical cellular structures (acini or tubes). Finally, we propose a unique type of buckling instability of epithelia, driven by a flattening of individual cell shapes, and discuss experimental tests to verify our predictions.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":111,"page":"27 - 32","year":"2014","publication_status":"published","_id":"927","intvolume":" 111","issue":"1","day":"01","status":"public","month":"01","language":[{"iso":"eng"}],"citation":{"ista":"Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology in three dimensions. PNAS. 111(1), 27–32.","short":"E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32.","mla":"Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. 27–32, doi:10.1073/pnas.1312076111.","ama":"Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three dimensions. PNAS. 2014;111(1):27-32. doi:10.1073/pnas.1312076111","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2014). Theory of epithelial sheet morphology in three dimensions. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1312076111","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology in three dimensions,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. 27–32, 2014.","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1312076111."}},{"quality_controlled":"1","scopus_import":"1","date_updated":"2021-12-14T08:22:36Z","doi":"10.1016/j.cell.2014.01.029","article_processing_charge":"No","author":[{"full_name":"Huff, Jason T.","first_name":"Jason T.","last_name":"Huff"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"date_published":"2014-03-13T00:00:00Z","publication_status":"published","intvolume":" 156","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"language":[{"iso":"eng"}],"month":"03","day":"13","pmid":1,"oa_version":"Published Version","date_created":"2021-06-04T12:00:16Z","publisher":"Elsevier","department":[{"_id":"DaZi"}],"title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","publication":"Cell","extern":"1","abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"year":"2014","_id":"9458","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"1286-1297","volume":156,"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"citation":{"chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.01.029.","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","apa":"Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029."},"article_type":"original","external_id":{"pmid":["24630728"]},"issue":"6","status":"public","oa":1},{"article_processing_charge":"No","doi":"10.1073/pnas.1418564111","date_updated":"2021-12-14T08:23:26Z","author":[{"first_name":"Zsuzsanna","last_name":"Mérai","full_name":"Mérai, Zsuzsanna"},{"full_name":"Chumak, Nina","last_name":"Chumak","first_name":"Nina"},{"first_name":"Marcelina","last_name":"García-Aguilar","full_name":"García-Aguilar, Marcelina"},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"full_name":"Bindics, János","first_name":"János","last_name":"Bindics"},{"last_name":"Ślusarz","first_name":"Lucyna","full_name":"Ślusarz, Lucyna"},{"full_name":"Arnoux, Stéphanie","last_name":"Arnoux","first_name":"Stéphanie"},{"full_name":"Opravil, Susanne","first_name":"Susanne","last_name":"Opravil"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"full_name":"Tamaru, Hisashi","first_name":"Hisashi","last_name":"Tamaru"}],"date_published":"2014-11-11T00:00:00Z","quality_controlled":"1","scopus_import":"1","publication_status":"published","intvolume":" 111","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1418564111"}],"day":"11","pmid":1,"month":"11","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","department":[{"_id":"DaZi"}],"date_created":"2021-06-07T07:23:43Z","oa_version":"Published Version","extern":"1","abstract":[{"text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":111,"page":"16166-16171","year":"2014","_id":"9479","issue":"45","external_id":{"pmid":["25344531"]},"article_type":"original","oa":1,"status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 2014;111(45):16166-16171. doi:10.1073/pnas.1418564111","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.","ieee":"Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” Proceedings of the National Academy of Sciences, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1418564111"}},{"date_updated":"2021-12-14T08:24:48Z","doi":"10.1016/j.tplants.2014.01.014","article_processing_charge":"No","author":[{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"date_published":"2014-05-04T00:00:00Z","quality_controlled":"1","scopus_import":"1","publication_status":"published","intvolume":" 19","day":"04","pmid":1,"language":[{"iso":"eng"}],"month":"05","publisher":"Elsevier","department":[{"_id":"DaZi"}],"title":"DNA methylation as a system of plant genomic immunity","publication":"Trends in Plant Science","oa_version":"None","date_created":"2021-06-07T14:38:09Z","extern":"1","abstract":[{"lang":"eng","text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression."}],"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"320-326","volume":19,"year":"2014","_id":"9519","external_id":{"pmid":["24618094 "]},"article_type":"review","issue":"5","status":"public","publication_identifier":{"eissn":["1878-4372"],"issn":["1360-1385"]},"citation":{"ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:10.1016/j.tplants.2014.01.014.","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","apa":"Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014"}},{"abstract":[{"lang":"eng","text":"Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture."}],"extern":"1","arxiv":1,"date_created":"2021-06-23T06:29:35Z","oa_version":"Published Version","publication":"The Electronic Journal of Combinatorics","title":"On the number of spanning trees in random regular graphs","publisher":"The Electronic Journal of Combinatorics","citation":{"apa":"Greenhill, C., Kwan, M. A., & Wind, D. (2014). On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics. https://doi.org/10.37236/3752","chicago":"Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics, 2014. https://doi.org/10.37236/3752.","ieee":"C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in random regular graphs,” The Electronic Journal of Combinatorics, vol. 21, no. 1. The Electronic Journal of Combinatorics, 2014.","ista":"Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.","mla":"Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics, vol. 21, no. 1, P1.45, The Electronic Journal of Combinatorics, 2014, doi:10.37236/3752.","short":"C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics 21 (2014).","ama":"Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 2014;21(1). doi:10.37236/3752"},"publication_identifier":{"eissn":["1077-8926"]},"status":"public","oa":1,"issue":"1","article_type":"original","external_id":{"arxiv":["1309.6710"]},"_id":"9594","year":"2014","volume":21,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"journal_article","scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Greenhill, Catherine","last_name":"Greenhill","first_name":"Catherine"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan"},{"full_name":"Wind, David","first_name":"David","last_name":"Wind"}],"date_published":"2014-02-28T00:00:00Z","article_processing_charge":"No","doi":"10.37236/3752","date_updated":"2023-02-23T14:02:12Z","article_number":"P1.45","month":"02","language":[{"iso":"eng"}],"day":"28","intvolume":" 21","main_file_link":[{"url":"https://doi.org/10.37236/3752","open_access":"1"}],"publication_status":"published"}]