[{"scopus_import":"1","pmid":1,"doi":"10.1038/s41586-019-1512-9","status":"public","oa_version":"None","intvolume":"       573","date_published":"2019-09-05T00:00:00Z","type":"journal_article","volume":573,"external_id":{"pmid":["31485056 "]},"language":[{"iso":"eng"}],"month":"09","OA_type":"closed access","quality_controlled":"1","extern":"1","publication_status":"published","article_processing_charge":"No","day":"05","date_updated":"2026-08-06T07:32:18Z","abstract":[{"lang":"eng","text":"Urban heat islands (UHIs) exacerbate the risk of heat-related mortality associated with global climate change. The intensity of UHIs varies with population size and mean annual precipitation, but a unifying explanation for this variation is lacking, and there are no geographically targeted guidelines for heat mitigation. Here we analyse summertime differences between urban and rural surface temperatures (ΔTs) worldwide and find a nonlinear increase in ΔTs with precipitation that is controlled by water or energy limitations on evapotranspiration and that modulates the scaling of ΔTs with city size. We introduce a coarse-grained model that links population, background climate, and UHI intensity, and show that urban–rural differences in evapotranspiration and convection efficiency are the main determinants of warming. The direct implication of these nonlinearities is that mitigation strategies aimed at increasing green cover and albedo are more efficient in dry regions, whereas the challenge of cooling tropical cities will require innovative solutions."}],"page":"55-60","publication":"Nature","author":[{"first_name":"Gabriele","full_name":"Manoli, Gabriele","last_name":"Manoli"},{"last_name":"Fatichi","full_name":"Fatichi, Simone","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"},{"last_name":"Schläpfer","full_name":"Schläpfer, Markus","first_name":"Markus"},{"first_name":"Kailiang","full_name":"Yu, Kailiang","last_name":"Yu"},{"full_name":"Crowther, Thomas W.","last_name":"Crowther","first_name":"Thomas W."},{"first_name":"Naika","full_name":"Meili, Naika","last_name":"Meili"},{"last_name":"Burlando","full_name":"Burlando, Paolo","first_name":"Paolo"},{"full_name":"Katul, Gabriel G.","last_name":"Katul","first_name":"Gabriel G."},{"full_name":"Bou-Zeid, Elie","last_name":"Bou-Zeid","first_name":"Elie"}],"title":"Magnitude of urban heat islands largely explained by climate and population","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"year":"2019","_id":"22571","citation":{"ieee":"G. Manoli <i>et al.</i>, “Magnitude of urban heat islands largely explained by climate and population,” <i>Nature</i>, vol. 573. Springer Nature, pp. 55–60, 2019.","ista":"Manoli G, Fatichi S, Schläpfer M, Yu K, Crowther TW, Meili N, Burlando P, Katul GG, Bou-Zeid E. 2019. Magnitude of urban heat islands largely explained by climate and population. Nature. 573, 55–60.","ama":"Manoli G, Fatichi S, Schläpfer M, et al. Magnitude of urban heat islands largely explained by climate and population. <i>Nature</i>. 2019;573:55-60. doi:<a href=\"https://doi.org/10.1038/s41586-019-1512-9\">10.1038/s41586-019-1512-9</a>","apa":"Manoli, G., Fatichi, S., Schläpfer, M., Yu, K., Crowther, T. W., Meili, N., … Bou-Zeid, E. (2019). Magnitude of urban heat islands largely explained by climate and population. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1512-9\">https://doi.org/10.1038/s41586-019-1512-9</a>","mla":"Manoli, Gabriele, et al. “Magnitude of Urban Heat Islands Largely Explained by Climate and Population.” <i>Nature</i>, vol. 573, Springer Nature, 2019, pp. 55–60, doi:<a href=\"https://doi.org/10.1038/s41586-019-1512-9\">10.1038/s41586-019-1512-9</a>.","chicago":"Manoli, Gabriele, Simone Fatichi, Markus Schläpfer, Kailiang Yu, Thomas W. Crowther, Naika Meili, Paolo Burlando, Gabriel G. Katul, and Elie Bou-Zeid. “Magnitude of Urban Heat Islands Largely Explained by Climate and Population.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1512-9\">https://doi.org/10.1038/s41586-019-1512-9</a>.","short":"G. Manoli, S. Fatichi, M. Schläpfer, K. Yu, T.W. Crowther, N. Meili, P. Burlando, G.G. Katul, E. Bou-Zeid, Nature 573 (2019) 55–60."},"das_tickbox":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","date_created":"2026-07-27T12:30:24Z","fulldoi":"https://doi.org/10.1038/s41586-019-1512-9"},{"file_date_updated":"2020-11-26T16:33:44Z","citation":{"ama":"Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. <i>Nature</i>. 2019;573(7773):291–295. doi:<a href=\"https://doi.org/10.1038/s41586-019-1519-2\">10.1038/s41586-019-1519-2</a>","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” <i>Nature</i>, vol. 573, no. 7773, Springer Nature, 2019, pp. 291–295, doi:<a href=\"https://doi.org/10.1038/s41586-019-1519-2\">10.1038/s41586-019-1519-2</a>.","apa":"Kampjut, D., &#38; Sazanov, L. A. (2019). Structure and mechanism of mitochondrial proton-translocating transhydrogenase. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1519-2\">https://doi.org/10.1038/s41586-019-1519-2</a>","ista":"Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 573(7773), 291–295.","ieee":"D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating transhydrogenase,” <i>Nature</i>, vol. 573, no. 7773. Springer Nature, pp. 291–295, 2019.","short":"D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1519-2\">https://doi.org/10.1038/s41586-019-1519-2</a>."},"oa":1,"article_type":"letter_note","issue":"7773","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-09-04T06:21:41Z","isi":1,"publisher":"Springer Nature","acknowledgement":" We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing was performed at the IST high-performance computing cluster.\r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385.","fulldoi":"https://doi.org/10.1038/s41586-019-1519-2","ec_funded":1,"article_processing_charge":"No","day":"12","publication_status":"published","date_updated":"2026-10-02T22:30:52Z","page":"291–295","abstract":[{"text":"Proton-translocating transhydrogenase (also known as nicotinamide nucleotide transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride between NADH and NADP+, coupled to the translocation of one proton across the membrane. Its main physiological function is the generation of NADPH, which is a substrate in anabolic reactions and a regulator of oxidative status; however, NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid deficiency in humans and metabolic abnormalities in mice, similar to those observed in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve a rotation of around 180° of the entire NADP(H)-binding domain that alternately participates in hydride transfer and proton-channel gating. However, owing to the lack of high-resolution structures of intact NNT, the details of this process remain unclear5,6. Here we present the cryo-electron microscopy structure of intact mammalian NNT in different conformational states. We show how the NADP(H)-binding domain opens the proton channel to the opposite sides of the membrane, and we provide structures of these two states. We also describe the catalytically important interfaces and linkers between the membrane and the soluble domains and their roles in nucleotide exchange. These structures enable us to propose a revised mechanism for a coupling process in NNT that is consistent with a large body of previous biochemical work. Our results are relevant to the development of currently unavailable NNT inhibitors, which may have therapeutic potential in ischaemia reperfusion injury, metabolic syndrome and some cancers7,8,9.","lang":"eng"}],"title":"Structure and mechanism of mitochondrial proton-translocating transhydrogenase","publication":"Nature","author":[{"orcid":"0000-0002-6018-3422","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen","last_name":"Kampjut","full_name":"Kampjut, Domen"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"_id":"6848","year":"2019","oa_version":"Submitted Version","type":"journal_article","date_published":"2019-09-12T00:00:00Z","intvolume":"       573","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"volume":573,"external_id":{"pmid":["31462775"],"isi":["000485415400061"]},"month":"09","file":[{"access_level":"open_access","file_id":"8821","success":1,"date_created":"2020-11-26T16:33:44Z","file_size":3066206,"relation":"main_file","content_type":"application/pdf","creator":"lsazanov","checksum":"52728cda5210a3e9b74cc204e8aed3d5","date_updated":"2020-11-26T16:33:44Z","file_name":"Manuscript_final_acc_withFigs_SI_opt_red.pdf"}],"ddc":["572"],"quality_controlled":"1","scopus_import":"1","pmid":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/","description":"News on IST Website"}],"record":[{"status":"public","relation":"dissertation_contains","id":"8340"}]},"doi":"10.1038/s41586-019-1519-2","has_accepted_license":"1","status":"public","department":[{"_id":"LeSa"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}]},{"fulldoi":"https://doi.org/10.1038/s41586-018-0396-4","isi":1,"publisher":"Nature Publishing Group","date_created":"2018-12-11T11:44:53Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"7719","article_type":"original","oa":1,"citation":{"ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>.","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>.","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512."},"year":"2018","_id":"150","publication_identifier":{"eissn":["1476-4687"]},"publication":"Nature","title":"Inositol phosphates are assembly co-factors for HIV-1","author":[{"full_name":"Dick, Robert","last_name":"Dick","first_name":"Robert"},{"last_name":"Zadrozny","full_name":"Zadrozny, Kaneil K","first_name":"Kaneil K"},{"full_name":"Xu, Chaoyi","last_name":"Xu","first_name":"Chaoyi"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Schur, Florian","last_name":"Schur"},{"full_name":"Lyddon, Terri D","last_name":"Lyddon","first_name":"Terri D"},{"first_name":"Clifton L","last_name":"Ricana","full_name":"Ricana, Clifton L"},{"full_name":"Wagner, Jonathan M","last_name":"Wagner","first_name":"Jonathan M"},{"first_name":"Juan R","last_name":"Perilla","full_name":"Perilla, Juan R"},{"full_name":"Ganser, Pornillos Barbie K","last_name":"Ganser","first_name":"Pornillos Barbie K"},{"first_name":"Marc C","last_name":"Johnson","full_name":"Johnson, Marc C"},{"first_name":"Owen","full_name":"Pornillos, Owen","last_name":"Pornillos"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"}],"abstract":[{"text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.","lang":"eng"}],"page":"509–512","date_updated":"2023-09-12T07:44:37Z","publication_status":"published","day":"29","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/"}],"month":"08","volume":560,"external_id":{"isi":["000442483400046"],"pmid":["30158708"]},"language":[{"iso":"eng"}],"intvolume":"       560","date_published":"2018-08-29T00:00:00Z","type":"journal_article","oa_version":"Submitted Version","department":[{"_id":"FlSc"}],"status":"public","doi":"10.1038/s41586-018-0396-4","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"pmid":1,"scopus_import":"1"},{"doi":"10.1038/s41586-018-0197-9","pmid":1,"scopus_import":"1","status":"public","language":[{"iso":"eng"}],"volume":558,"external_id":{"pmid":["29875407"]},"type":"journal_article","date_published":"2018-06-06T00:00:00Z","intvolume":"       558","oa_version":"None","quality_controlled":"1","OA_type":"closed access","month":"06","date_updated":"2024-12-11T08:51:55Z","article_processing_charge":"No","day":"06","publication_status":"published","extern":"1","_id":"17931","year":"2018","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","title":"Comprehensive suppression of single-molecule conductance using destructive σ-interference","author":[{"last_name":"Garner","full_name":"Garner, Marc H.","first_name":"Marc H."},{"first_name":"Haixing","last_name":"Li","full_name":"Li, Haixing"},{"last_name":"Chen","full_name":"Chen, Yan","first_name":"Yan"},{"full_name":"Su, Timothy A.","last_name":"Su","first_name":"Timothy A."},{"first_name":"Zhichun","full_name":"Shangguan, Zhichun","last_name":"Shangguan"},{"first_name":"Daniel W.","last_name":"Paley","full_name":"Paley, Daniel W."},{"last_name":"Liu","full_name":"Liu, Taifeng","first_name":"Taifeng"},{"full_name":"Ng, Fay","last_name":"Ng","first_name":"Fay"},{"full_name":"Li, Hexing","last_name":"Li","first_name":"Hexing"},{"first_name":"Shengxiong","full_name":"Xiao, Shengxiong","last_name":"Xiao"},{"full_name":"Nuckolls, Colin","last_name":"Nuckolls","first_name":"Colin"},{"orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","last_name":"Venkataraman","full_name":"Venkataraman, Latha"},{"first_name":"Gemma C.","full_name":"Solomon, Gemma C.","last_name":"Solomon"}],"page":"415-419","abstract":[{"lang":"eng","text":"The tunnelling of electrons through molecules (and through any nanoscale insulating and dielectric material1) shows exponential attenuation with increasing length2, a length dependence that is reflected in the ability of the electrons to carry an electrical current. It was recently demonstrated3,4,5 that coherent tunnelling through a molecular junction can also be suppressed by destructive quantum interference6, a mechanism that is not length-dependent. For the carbon-based molecules studied previously, cancelling all transmission channels would involve the suppression of contributions to the current from both the π-orbital and σ-orbital systems. Previous reports of destructive interference have demonstrated a decrease in transmission only through the π-channel. Here we report a saturated silicon-based molecule with a functionalized bicyclo[2.2.2]octasilane moiety that exhibits destructive quantum interference in its σ-system. Although molecular silicon typically forms conducting wires7, we use a combination of conductance measurements and ab initio calculations to show that destructive σ-interference, achieved here by locking the silicon–silicon bonds into eclipsed conformations within a bicyclic molecular framework, can yield extremely insulating molecules less than a nanometre in length. Our molecules also exhibit an unusually high thermopower (0.97 millivolts per kelvin), which is a further experimental signature of the suppression of all tunnelling paths by destructive interference: calculations indicate that the central bicyclo[2.2.2]octasilane unit is rendered less conductive than the empty space it occupies. The molecular design presented here provides a proof-of-concept for a quantum-interference-based approach to single-molecule insulators."}],"article_type":"letter_note","issue":"7710","citation":{"short":"M.H. Garner, H. Li, Y. Chen, T.A. Su, Z. Shangguan, D.W. Paley, T. Liu, F. Ng, H. Li, S. Xiao, C. Nuckolls, L. Venkataraman, G.C. Solomon, Nature 558 (2018) 415–419.","chicago":"Garner, Marc H., Haixing Li, Yan Chen, Timothy A. Su, Zhichun Shangguan, Daniel W. Paley, Taifeng Liu, et al. “Comprehensive Suppression of Single-Molecule Conductance Using Destructive σ-Interference.” <i>Nature</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0197-9\">https://doi.org/10.1038/s41586-018-0197-9</a>.","ama":"Garner MH, Li H, Chen Y, et al. Comprehensive suppression of single-molecule conductance using destructive σ-interference. <i>Nature</i>. 2018;558(7710):415-419. doi:<a href=\"https://doi.org/10.1038/s41586-018-0197-9\">10.1038/s41586-018-0197-9</a>","apa":"Garner, M. H., Li, H., Chen, Y., Su, T. A., Shangguan, Z., Paley, D. W., … Solomon, G. C. (2018). Comprehensive suppression of single-molecule conductance using destructive σ-interference. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-018-0197-9\">https://doi.org/10.1038/s41586-018-0197-9</a>","mla":"Garner, Marc H., et al. “Comprehensive Suppression of Single-Molecule Conductance Using Destructive σ-Interference.” <i>Nature</i>, vol. 558, no. 7710, Springer Nature, 2018, pp. 415–19, doi:<a href=\"https://doi.org/10.1038/s41586-018-0197-9\">10.1038/s41586-018-0197-9</a>.","ista":"Garner MH, Li H, Chen Y, Su TA, Shangguan Z, Paley DW, Liu T, Ng F, Li H, Xiao S, Nuckolls C, Venkataraman L, Solomon GC. 2018. Comprehensive suppression of single-molecule conductance using destructive σ-interference. Nature. 558(7710), 415–419.","ieee":"M. H. Garner <i>et al.</i>, “Comprehensive suppression of single-molecule conductance using destructive σ-interference,” <i>Nature</i>, vol. 558, no. 7710. Springer Nature, pp. 415–419, 2018."},"fulldoi":"https://doi.org/10.1038/s41586-018-0197-9","date_created":"2024-09-09T08:17:04Z","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"fulldoi":"https://doi.org/10.1038/nature24650","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-06T12:14:20Z","publisher":"Springer Nature","article_type":"original","issue":"7683","citation":{"chicago":"Praetorius, Florian M, Benjamin Kick, Karl L. Behler, Maximilian N. Honemann, Dirk Weuster-Botz, and Hendrik Dietz. “Biotechnological Mass Production of DNA Origami.” <i>Nature</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nature24650\">https://doi.org/10.1038/nature24650</a>.","short":"F.M. Praetorius, B. Kick, K.L. Behler, M.N. Honemann, D. Weuster-Botz, H. Dietz, Nature 552 (2017) 84–87.","ama":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. Biotechnological mass production of DNA origami. <i>Nature</i>. 2017;552(7683):84-87. doi:<a href=\"https://doi.org/10.1038/nature24650\">10.1038/nature24650</a>","mla":"Praetorius, Florian M., et al. “Biotechnological Mass Production of DNA Origami.” <i>Nature</i>, vol. 552, no. 7683, Springer Nature, 2017, pp. 84–87, doi:<a href=\"https://doi.org/10.1038/nature24650\">10.1038/nature24650</a>.","apa":"Praetorius, F. M., Kick, B., Behler, K. L., Honemann, M. N., Weuster-Botz, D., &#38; Dietz, H. (2017). Biotechnological mass production of DNA origami. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature24650\">https://doi.org/10.1038/nature24650</a>","ista":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. 2017. Biotechnological mass production of DNA origami. Nature. 552(7683), 84–87.","ieee":"F. M. Praetorius, B. Kick, K. L. Behler, M. N. Honemann, D. Weuster-Botz, and H. Dietz, “Biotechnological mass production of DNA origami,” <i>Nature</i>, vol. 552, no. 7683. Springer Nature, pp. 84–87, 2017."},"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"year":"2017","_id":"14290","page":"84-87","abstract":[{"text":"DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features1,2,3,4,5,6,7,8,9,10,11,12. These structures are customizable in that they can be site-specifically functionalized13 or constructed to exhibit machine-like14,15 or logic-gating behaviour16. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials3,16,17,18,19,20,21,22, could be realized if more material could be used. In DNA origami, a nanostructure is assembled from a very long single-stranded scaffold molecule held in place by many short single-stranded staple oligonucleotides. Only the bacteriophage-derived scaffold molecules are amenable to scalable and efficient mass production23; the shorter staple strands are obtained through costly solid-phase synthesis24 or enzymatic processes25. Here we show that single strands of DNA of virtually arbitrary length and with virtually arbitrary sequences can be produced in a scalable and cost-efficient manner by using bacteriophages to generate single-stranded precursor DNA that contains target strand sequences interleaved with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA for several DNA origami using shaker-flask cultures, and demonstrate end-to-end production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank bioreactor. Our method is compatible with existing DNA origami design frameworks and retains the modularity and addressability of DNA origami objects that are necessary for implementing custom modifications using functional groups. With all of the production and purification steps amenable to scaling, we expect that our method will expand the scope of DNA nanotechnology in many areas of science and technology.","lang":"eng"}],"author":[{"full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"first_name":"Benjamin","last_name":"Kick","full_name":"Kick, Benjamin"},{"last_name":"Behler","full_name":"Behler, Karl L.","first_name":"Karl L."},{"first_name":"Maximilian N.","full_name":"Honemann, Maximilian N.","last_name":"Honemann"},{"full_name":"Weuster-Botz, Dirk","last_name":"Weuster-Botz","first_name":"Dirk"},{"last_name":"Dietz","full_name":"Dietz, Hendrik","first_name":"Hendrik"}],"title":"Biotechnological mass production of DNA origami","publication":"Nature","date_updated":"2023-11-07T12:24:49Z","extern":"1","day":"07","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","month":"12","language":[{"iso":"eng"}],"volume":552,"external_id":{"pmid":["29219963"]},"oa_version":"None","type":"journal_article","date_published":"2017-12-07T00:00:00Z","intvolume":"       552","status":"public","doi":"10.1038/nature24650","scopus_import":"1","pmid":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","date_created":"2025-06-10T09:13:08Z","fulldoi":"https://doi.org/10.1038/nature23898","citation":{"ieee":"V. Sunko <i>et al.</i>, “Maximal Rashba-like spin splitting via kinetic-energy-coupled inversion-symmetry breaking,” <i>Nature</i>, vol. 549, no. 7673. Springer Nature, pp. 492–496, 2017.","mla":"Sunko, Veronika, et al. “Maximal Rashba-like Spin Splitting via Kinetic-Energy-Coupled Inversion-Symmetry Breaking.” <i>Nature</i>, vol. 549, no. 7673, Springer Nature, 2017, pp. 492–96, doi:<a href=\"https://doi.org/10.1038/nature23898\">10.1038/nature23898</a>.","apa":"Sunko, V., Rosner, H., Kushwaha, P., Khim, S., Mazzola, F., Bawden, L., … King, P. D. C. (2017). Maximal Rashba-like spin splitting via kinetic-energy-coupled inversion-symmetry breaking. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature23898\">https://doi.org/10.1038/nature23898</a>","ama":"Sunko V, Rosner H, Kushwaha P, et al. Maximal Rashba-like spin splitting via kinetic-energy-coupled inversion-symmetry breaking. <i>Nature</i>. 2017;549(7673):492-496. doi:<a href=\"https://doi.org/10.1038/nature23898\">10.1038/nature23898</a>","ista":"Sunko V, Rosner H, Kushwaha P, Khim S, Mazzola F, Bawden L, Clark OJ, Riley JM, Kasinathan D, Haverkort MW, Kim TK, Hoesch M, Fujii J, Vobornik I, Mackenzie AP, King PDC. 2017. Maximal Rashba-like spin splitting via kinetic-energy-coupled inversion-symmetry breaking. Nature. 549(7673), 492–496.","chicago":"Sunko, Veronika, H. Rosner, P. Kushwaha, S. Khim, F. Mazzola, L. Bawden, O. J. Clark, et al. “Maximal Rashba-like Spin Splitting via Kinetic-Energy-Coupled Inversion-Symmetry Breaking.” <i>Nature</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nature23898\">https://doi.org/10.1038/nature23898</a>.","short":"V. Sunko, H. Rosner, P. Kushwaha, S. Khim, F. Mazzola, L. Bawden, O.J. Clark, J.M. Riley, D. Kasinathan, M.W. Haverkort, T.K. Kim, M. Hoesch, J. Fujii, I. Vobornik, A.P. Mackenzie, P.D.C. King, Nature 549 (2017) 492–496."},"oa":1,"issue":"7673","article_type":"letter_note","abstract":[{"lang":"eng","text":"Engineering and enhancing the breaking of inversion symmetry in solids—that is, allowing electrons to differentiate between ‘up’ and ‘down’—is a key goal in condensed-matter physics and materials science because it can be used to stabilize states that are of fundamental interest and also have potential practical applications. Examples include improved ferroelectrics for memory devices and materials that host Majorana zero modes for quantum computing1,2. Although inversion symmetry is naturally broken in several crystalline environments, such as at surfaces and interfaces, maximizing the influence of this effect on the electronic states of interest remains a challenge. Here we present a mechanism for realizing a much larger coupling of inversion-symmetry breaking to itinerant surface electrons than is typically achieved. The key element is a pronounced asymmetry of surface hopping energies—that is, a kinetic-energy-coupled inversion-symmetry breaking, the energy scale of which is a substantial fraction of the bandwidth. Using spin- and angle-resolved photoemission spectroscopy, we demonstrate that such a strong inversion-symmetry breaking, when combined with spin–orbit interactions, can mediate Rashba-like3,4 spin splittings that are much larger than would typically be expected. The energy scale of the inversion-symmetry breaking that we achieve is so large that the spin splitting in the CoO2- and RhO2-derived surface states of delafossite oxides becomes controlled by the full atomic spin–orbit coupling of the 3d and 4d transition metals, resulting in some of the largest known Rashba-like3,4 spin splittings. The core structural building blocks that facilitate the bandwidth-scaled inversion-symmetry breaking are common to numerous materials. Our findings therefore provide opportunities for creating spin-textured states and suggest routes to interfacial control of inversion-symmetry breaking in designer heterostructures of oxides and other material classes."}],"page":"492-496","author":[{"first_name":"Veronika","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","orcid":"0000-0003-2724-3523","full_name":"Sunko, Veronika","last_name":"Sunko"},{"first_name":"H.","full_name":"Rosner, H.","last_name":"Rosner"},{"first_name":"P.","last_name":"Kushwaha","full_name":"Kushwaha, P."},{"first_name":"S.","last_name":"Khim","full_name":"Khim, S."},{"full_name":"Mazzola, F.","last_name":"Mazzola","first_name":"F."},{"full_name":"Bawden, L.","last_name":"Bawden","first_name":"L."},{"first_name":"O. J.","full_name":"Clark, O. J.","last_name":"Clark"},{"first_name":"J. M.","full_name":"Riley, J. M.","last_name":"Riley"},{"last_name":"Kasinathan","full_name":"Kasinathan, D.","first_name":"D."},{"first_name":"M. W.","last_name":"Haverkort","full_name":"Haverkort, M. W."},{"first_name":"T. K.","full_name":"Kim, T. K.","last_name":"Kim"},{"first_name":"M.","last_name":"Hoesch","full_name":"Hoesch, M."},{"full_name":"Fujii, J.","last_name":"Fujii","first_name":"J."},{"last_name":"Vobornik","full_name":"Vobornik, I.","first_name":"I."},{"first_name":"A. P.","full_name":"Mackenzie, A. P.","last_name":"Mackenzie"},{"first_name":"P. D. C.","full_name":"King, P. D. C.","last_name":"King"}],"publication":"Nature","title":"Maximal Rashba-like spin splitting via kinetic-energy-coupled inversion-symmetry breaking","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"_id":"19810","year":"2017","extern":"1","publication_status":"published","article_processing_charge":"No","day":"28","arxiv":1,"date_updated":"2025-06-10T11:55:09Z","month":"09","OA_type":"green","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1708.03887","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","intvolume":"       549","type":"journal_article","date_published":"2017-09-28T00:00:00Z","external_id":{"pmid":["28959958"],"arxiv":["1708.03887"]},"volume":549,"language":[{"iso":"eng"}],"status":"public","OA_place":"repository","scopus_import":"1","pmid":1,"doi":"10.1038/nature23898"},{"extern":"1","article_processing_charge":"No","day":"28","publication_status":"published","date_updated":"2026-05-20T07:26:38Z","page":"551 - 554","abstract":[{"text":"RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species1-3. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins4-10. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation7. Upstream DNA emanates from the active centre cleft at an angle of approximately 105° with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human transcription.","lang":"eng"}],"author":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","last_name":"Bernecky"},{"full_name":"Herzog, Franz","last_name":"Herzog","first_name":"Franz"},{"first_name":"Wolfgang","full_name":"Baumeister, Wolfgang","last_name":"Baumeister"},{"full_name":"Plitzko, Jürgen","last_name":"Plitzko","first_name":"Jürgen"},{"first_name":"Patrick","full_name":"Cramer, Patrick","last_name":"Cramer"}],"title":"Structure of transcribing mammalian RNA polymerase II","publication":"Nature","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"year":"2016","_id":"602","citation":{"ieee":"C. Bernecky, F. Herzog, W. Baumeister, J. Plitzko, and P. Cramer, “Structure of transcribing mammalian RNA polymerase II,” <i>Nature</i>, vol. 529. Springer Nature, pp. 551–554, 2016.","ista":"Bernecky C, Herzog F, Baumeister W, Plitzko J, Cramer P. 2016. Structure of transcribing mammalian RNA polymerase II. Nature. 529, 551–554.","ama":"Bernecky C, Herzog F, Baumeister W, Plitzko J, Cramer P. Structure of transcribing mammalian RNA polymerase II. <i>Nature</i>. 2016;529:551-554. doi:<a href=\"https://doi.org/10.1038/nature16482\">10.1038/nature16482</a>","apa":"Bernecky, C., Herzog, F., Baumeister, W., Plitzko, J., &#38; Cramer, P. (2016). Structure of transcribing mammalian RNA polymerase II. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature16482\">https://doi.org/10.1038/nature16482</a>","mla":"Bernecky, Carrie, et al. “Structure of Transcribing Mammalian RNA Polymerase II.” <i>Nature</i>, vol. 529, Springer Nature, 2016, pp. 551–54, doi:<a href=\"https://doi.org/10.1038/nature16482\">10.1038/nature16482</a>.","chicago":"Bernecky, Carrie, Franz Herzog, Wolfgang Baumeister, Jürgen Plitzko, and Patrick Cramer. “Structure of Transcribing Mammalian RNA Polymerase II.” <i>Nature</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nature16482\">https://doi.org/10.1038/nature16482</a>.","short":"C. Bernecky, F. Herzog, W. Baumeister, J. Plitzko, P. Cramer, Nature 529 (2016) 551–554."},"article_type":"letter_note","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2018-12-11T11:47:26Z","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/nature16482","publist_id":"7205","scopus_import":"1","pmid":1,"doi":"10.1038/nature16482","status":"public","oa_version":"None","type":"journal_article","date_published":"2016-01-28T00:00:00Z","intvolume":"       529","language":[{"iso":"eng"}],"volume":529,"external_id":{"pmid":["26789250"]},"month":"01","OA_type":"closed access","quality_controlled":"1"},{"publist_id":"6799","fulldoi":"https://doi.org/10.1038/nature17995","acknowledgement":"We thank Y. Kulikova and G. Filion for discussion on statistical analysis and I. Osterman, R. Moretti and J. Meiler for technical assistance and M. Friesen for a critical reading of the manuscript. We thank H. Himmelbauer, CRG Genomic Unit and the Russian Science Foundation project (14-50-00150) for sequencing. Experiments were partially carried out using the equipment provided by the IBCH core facility (CKP IBCH). The work was supported by HHMI International Early Career Scientist Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329), Spanish Ministry of Economy and Competitiveness Centro de Excelencia Severo Ochoa 2013-2017 grant (SEV-2012-0208), Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat's AGAUR program (2014 SGR 0974), Russian Science Foundation (14-25-00129) and the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013, ERC grant agreement, 335980-EinME).","publisher":"Springer Nature","date_created":"2018-12-11T11:48:50Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_type":"original","citation":{"chicago":"Sarkisyan, Karen, Dmitry Bolotin, Margarita Meer, Dinara Usmanova, Alexander Mishin, George Sharonov, Dmitry Ivankov, et al. “Local Fitness Landscape of the Green Fluorescent Protein.” <i>Nature</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nature17995\">https://doi.org/10.1038/nature17995</a>.","short":"K. Sarkisyan, D. Bolotin, M. Meer, D. Usmanova, A. Mishin, G. Sharonov, D. Ivankov, N. Bozhanova, M. Baranov, O. Soylemez, N. Bogatyreva, P. Vlasov, E. Egorov, M. Logacheva, A. Kondrashov, D. Chudakov, E. Putintseva, I. Mamedov, D. Tawfik, K. Lukyanov, F. Kondrashov, Nature 533 (2016) 397–401.","ieee":"K. Sarkisyan <i>et al.</i>, “Local fitness landscape of the green fluorescent protein,” <i>Nature</i>, vol. 533. Springer Nature, pp. 397–401, 2016.","ista":"Sarkisyan K, Bolotin D, Meer M, Usmanova D, Mishin A, Sharonov G, Ivankov D, Bozhanova N, Baranov M, Soylemez O, Bogatyreva N, Vlasov P, Egorov E, Logacheva M, Kondrashov A, Chudakov D, Putintseva E, Mamedov I, Tawfik D, Lukyanov K, Kondrashov F. 2016. Local fitness landscape of the green fluorescent protein. Nature. 533, 397–401.","apa":"Sarkisyan, K., Bolotin, D., Meer, M., Usmanova, D., Mishin, A., Sharonov, G., … Kondrashov, F. (2016). Local fitness landscape of the green fluorescent protein. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature17995\">https://doi.org/10.1038/nature17995</a>","ama":"Sarkisyan K, Bolotin D, Meer M, et al. Local fitness landscape of the green fluorescent protein. <i>Nature</i>. 2016;533:397-401. doi:<a href=\"https://doi.org/10.1038/nature17995\">10.1038/nature17995</a>","mla":"Sarkisyan, Karen, et al. “Local Fitness Landscape of the Green Fluorescent Protein.” <i>Nature</i>, vol. 533, Springer Nature, 2016, pp. 397–401, doi:<a href=\"https://doi.org/10.1038/nature17995\">10.1038/nature17995</a>."},"year":"2016","_id":"850","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","title":"Local fitness landscape of the green fluorescent protein","author":[{"full_name":"Sarkisyan, Karen","last_name":"Sarkisyan","orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"last_name":"Bolotin","full_name":"Bolotin, Dmitry","first_name":"Dmitry"},{"first_name":"Margarita","last_name":"Meer","full_name":"Meer, Margarita"},{"full_name":"Usmanova, Dinara","last_name":"Usmanova","first_name":"Dinara"},{"first_name":"Alexander","full_name":"Mishin, Alexander","last_name":"Mishin"},{"last_name":"Sharonov","full_name":"Sharonov, George","first_name":"George"},{"first_name":"Dmitry","last_name":"Ivankov","full_name":"Ivankov, Dmitry"},{"first_name":"Nina","last_name":"Bozhanova","full_name":"Bozhanova, Nina"},{"last_name":"Baranov","full_name":"Baranov, Mikhail","first_name":"Mikhail"},{"last_name":"Soylemez","full_name":"Soylemez, Onuralp","first_name":"Onuralp"},{"first_name":"Natalya","full_name":"Bogatyreva, Natalya","last_name":"Bogatyreva"},{"first_name":"Peter","full_name":"Vlasov, Peter","last_name":"Vlasov"},{"first_name":"Evgeny","last_name":"Egorov","full_name":"Egorov, Evgeny"},{"first_name":"Maria","full_name":"Logacheva, Maria","last_name":"Logacheva"},{"first_name":"Alexey","last_name":"Kondrashov","full_name":"Kondrashov, Alexey"},{"full_name":"Chudakov, Dmitriy","last_name":"Chudakov","first_name":"Dmitriy"},{"full_name":"Putintseva, Ekaterina","last_name":"Putintseva","first_name":"Ekaterina"},{"full_name":"Mamedov, Ilgar","last_name":"Mamedov","first_name":"Ilgar"},{"first_name":"Dan","last_name":"Tawfik","full_name":"Tawfik, Dan"},{"last_name":"Lukyanov","full_name":"Lukyanov, Konstantin","first_name":"Konstantin"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694"}],"abstract":[{"text":"Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea Victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design.","lang":"eng"}],"page":"397 - 401","date_updated":"2026-05-20T08:10:59Z","publication_status":"published","day":"19","article_processing_charge":"No","extern":"1","quality_controlled":"1","OA_type":"closed access","month":"05","volume":533,"external_id":{"pmid":["27193686"]},"language":[{"iso":"eng"}],"intvolume":"       533","type":"journal_article","date_published":"2016-05-19T00:00:00Z","oa_version":"None","status":"public","doi":"10.1038/nature17995","pmid":1,"scopus_import":"1"},{"date_updated":"2021-12-14T07:55:30Z","article_processing_charge":"No","day":"27","publication_status":"published","extern":"1","year":"2016","_id":"9456","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"title":"Mechanism for DNA transposons to generate introns on genomic scales","publication":"Nature","author":[{"full_name":"Huff, Jason T.","last_name":"Huff","first_name":"Jason T."},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"},{"full_name":"Roy, Scott W.","last_name":"Roy","first_name":"Scott W."}],"page":"533-536","abstract":[{"lang":"eng","text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution."}],"article_type":"letter_note","issue":"7626","oa":1,"citation":{"ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. 2016;538(7626):533-536. doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>","mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>.","apa":"Huff, J. T., Zilberman, D., &#38; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. Springer Nature . <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536.","ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” <i>Nature</i>, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.","chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>. Springer Nature , 2016. <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>.","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536."},"fulldoi":"https://doi.org/10.1038/nature20110","date_created":"2021-06-04T11:34:55Z","publisher":"Springer Nature ","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1038/nature20110","pmid":1,"scopus_import":"1","department":[{"_id":"DaZi"}],"status":"public","language":[{"iso":"eng"}],"volume":538,"external_id":{"pmid":["27760113"]},"date_published":"2016-10-27T00:00:00Z","type":"journal_article","intvolume":"       538","oa_version":"Submitted Version","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/"}],"month":"10"},{"citation":{"ieee":"S. Neyer <i>et al.</i>, “Structure of RNA polymerase I transcribing ribosomal DNA genes,” <i>Nature</i>, vol. 540, no. 7634. Springer Nature, pp. 607–610, 2016.","ista":"Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau V-V, Seybert A, Engel C, Scheffer MP, Cramer P, Frangakis AS. 2016. Structure of RNA polymerase I transcribing ribosomal DNA genes. Nature. 540(7634), 607–610.","mla":"Neyer, Simon, et al. “Structure of RNA Polymerase I Transcribing Ribosomal DNA Genes.” <i>Nature</i>, vol. 540, no. 7634, Springer Nature, 2016, pp. 607–10, doi:<a href=\"https://doi.org/10.1038/nature20561\">10.1038/nature20561</a>.","ama":"Neyer S, Kunz M, Geiss C, et al. Structure of RNA polymerase I transcribing ribosomal DNA genes. <i>Nature</i>. 2016;540(7634):607-610. doi:<a href=\"https://doi.org/10.1038/nature20561\">10.1038/nature20561</a>","apa":"Neyer, S., Kunz, M., Geiss, C., Hantsche, M., Hodirnau, V.-V., Seybert, A., … Frangakis, A. S. (2016). Structure of RNA polymerase I transcribing ribosomal DNA genes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature20561\">https://doi.org/10.1038/nature20561</a>","chicago":"Neyer, Simon, Michael Kunz, Christian Geiss, Merle Hantsche, Victor-Valentin Hodirnau, Anja Seybert, Christoph Engel, Margot P. Scheffer, Patrick Cramer, and Achilleas S. Frangakis. “Structure of RNA Polymerase I Transcribing Ribosomal DNA Genes.” <i>Nature</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nature20561\">https://doi.org/10.1038/nature20561</a>.","short":"S. Neyer, M. Kunz, C. Geiss, M. Hantsche, V.-V. Hodirnau, A. Seybert, C. Engel, M.P. Scheffer, P. Cramer, A.S. Frangakis, Nature 540 (2016) 607–610."},"issue":"7634","article_type":"letter_note","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Springer Nature","date_created":"2021-07-14T09:04:24Z","fulldoi":"https://doi.org/10.1038/nature20561","extern":"1","publication_status":"published","article_processing_charge":"No","day":"22","date_updated":"2021-07-22T09:22:20Z","abstract":[{"lang":"eng","text":"RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively."}],"page":"607-610","publication":"Nature","title":"Structure of RNA polymerase I transcribing ribosomal DNA genes","author":[{"full_name":"Neyer, Simon","last_name":"Neyer","first_name":"Simon"},{"first_name":"Michael","last_name":"Kunz","full_name":"Kunz, Michael"},{"first_name":"Christian","full_name":"Geiss, Christian","last_name":"Geiss"},{"first_name":"Merle","last_name":"Hantsche","full_name":"Hantsche, Merle"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau"},{"full_name":"Seybert, Anja","last_name":"Seybert","first_name":"Anja"},{"full_name":"Engel, Christoph","last_name":"Engel","first_name":"Christoph"},{"first_name":"Margot P.","last_name":"Scheffer","full_name":"Scheffer, Margot P."},{"full_name":"Cramer, Patrick","last_name":"Cramer","first_name":"Patrick"},{"first_name":"Achilleas S.","full_name":"Frangakis, Achilleas S.","last_name":"Frangakis"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"year":"2016","_id":"9654","oa_version":"None","intvolume":"       540","type":"journal_article","date_published":"2016-12-22T00:00:00Z","volume":540,"external_id":{"pmid":["27842382"]},"language":[{"iso":"eng"}],"month":"12","quality_controlled":"1","scopus_import":"1","pmid":1,"doi":"10.1038/nature20561","status":"public"},{"oa_version":"None","type":"journal_article","date_published":"2015-01-22T00:00:00Z","intvolume":"       517","language":[{"iso":"eng"}],"external_id":{"pmid":["25363765"]},"volume":517,"month":"01","OA_type":"closed access","quality_controlled":"1","scopus_import":"1","pmid":1,"doi":"10.1038/nature13838","status":"public","citation":{"ieee":"F. K. Schur <i>et al.</i>, “Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution,” <i>Nature</i>, vol. 517, no. 7535. Springer Nature, pp. 505–508, 2015.","ista":"Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 517(7535), 505–508.","mla":"Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” <i>Nature</i>, vol. 517, no. 7535, Springer Nature, 2015, pp. 505–08, doi:<a href=\"https://doi.org/10.1038/nature13838\">10.1038/nature13838</a>.","ama":"Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. <i>Nature</i>. 2015;517(7535):505-508. doi:<a href=\"https://doi.org/10.1038/nature13838\">10.1038/nature13838</a>","apa":"Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H., &#38; Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature13838\">https://doi.org/10.1038/nature13838</a>","chicago":"Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” <i>Nature</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nature13838\">https://doi.org/10.1038/nature13838</a>.","short":"F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs, Nature 517 (2015) 505–508."},"article_type":"letter_note","issue":"7535","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2018-12-11T11:48:39Z","publisher":"Springer Nature","acknowledgement":"This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples, and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich and T. Bharat for technical support and/or discussion. This study was technically supported by the European Molecular Biology Laboratory IT services unit.","fulldoi":"https://doi.org/10.1038/nature13838","publist_id":"6836","extern":"1","article_processing_charge":"No","day":"22","publication_status":"published","date_updated":"2026-05-19T08:19:41Z","page":"505 - 508","abstract":[{"text":"Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments.","lang":"eng"}],"title":"Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution","publication":"Nature","author":[{"first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian"},{"first_name":"Wim","last_name":"Hagen","full_name":"Hagen, Wim"},{"first_name":"Michaela","last_name":"Rumlová","full_name":"Rumlová, Michaela"},{"full_name":"Ruml, Tomáš","last_name":"Ruml","first_name":"Tomáš"},{"first_name":"B","full_name":"Müller, B","last_name":"Müller"},{"first_name":"Hans","last_name":"Kraüsslich","full_name":"Kraüsslich, Hans"},{"first_name":"John","last_name":"Briggs","full_name":"Briggs, John"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"year":"2015","_id":"814"},{"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"year":"2014","_id":"1862","page":"90 - 93","abstract":[{"lang":"eng","text":"The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses."}],"title":"Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules","author":[{"full_name":"Chen, Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"first_name":"Laurie","full_name":"Grandont, Laurie","last_name":"Grandont"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","last_name":"Li"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"first_name":"Sébastien","last_name":"Paque","full_name":"Paque, Sébastien"},{"first_name":"Anas","full_name":"Abuzeineh, Anas","last_name":"Abuzeineh"},{"first_name":"Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","full_name":"Rakusova, Hana","last_name":"Rakusova"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Perrot Rechenmann, Catherine","last_name":"Perrot Rechenmann","first_name":"Catherine"},{"full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"publication":"Nature","date_updated":"2025-09-29T13:10:05Z","ec_funded":1,"article_processing_charge":"No","day":"04","publication_status":"published","fulldoi":"https://doi.org/10.1038/nature13889","publist_id":"5237","acknowledgement":"We thank R. Dixit for performing complementary experiments, D. W. Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively, E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J. Leung for text optimization. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007, to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT) (to H.R.). This work benefited from the facilities and expertise of the Imagif Cell Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil Général de l’Essonne.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:25Z","isi":1,"publisher":"Nature Publishing Group","article_type":"original","issue":"729","citation":{"chicago":"Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque, Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature13889\">https://doi.org/10.1038/nature13889</a>.","short":"X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova, E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93.","ieee":"X. Chen <i>et al.</i>, “Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules,” <i>Nature</i>, vol. 516, no. 729. Nature Publishing Group, pp. 90–93, 2014.","mla":"Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” <i>Nature</i>, vol. 516, no. 729, Nature Publishing Group, 2014, pp. 90–93, doi:<a href=\"https://doi.org/10.1038/nature13889\">10.1038/nature13889</a>.","ama":"Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. <i>Nature</i>. 2014;516(729):90-93. doi:<a href=\"https://doi.org/10.1038/nature13889\">10.1038/nature13889</a>","apa":"Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., … Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature13889\">https://doi.org/10.1038/nature13889</a>","ista":"Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 516(729), 90–93."},"oa":1,"corr_author":"1","status":"public","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"EvBe"}],"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"doi":"10.1038/nature13889","scopus_import":"1","pmid":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/"}],"month":"12","language":[{"iso":"eng"}],"volume":516,"external_id":{"isi":["000346310800045"],"pmid":["25409144"]},"oa_version":"Submitted Version","type":"journal_article","date_published":"2014-12-04T00:00:00Z","intvolume":"       516"},{"extern":"1","publication_status":"published","article_processing_charge":"No","day":"01","date_updated":"2026-09-09T11:20:45Z","abstract":[{"text":"The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.","lang":"eng"}],"page":"109 - 114","publication":"Nature","author":[{"full_name":"Moroz, Leonid","last_name":"Moroz","first_name":"Leonid"},{"first_name":"Kevin","full_name":"Kocot, Kevin","last_name":"Kocot"},{"last_name":"Citarella","full_name":"Citarella, Mathew","first_name":"Mathew"},{"full_name":"Dosung, Sohn","last_name":"Dosung","first_name":"Sohn"},{"last_name":"Norekian","full_name":"Norekian, Tigran","first_name":"Tigran"},{"first_name":"Inna","full_name":"Povolotskaya, Inna","last_name":"Povolotskaya"},{"first_name":"Anastasia","full_name":"Grigorenko, Anastasia","last_name":"Grigorenko"},{"first_name":"Christopher","full_name":"Dailey, Christopher","last_name":"Dailey"},{"first_name":"Eugene","last_name":"Berezikov","full_name":"Berezikov, Eugene"},{"full_name":"Buckley, Katherine","last_name":"Buckley","first_name":"Katherine"},{"full_name":"Ptitsyn, Andrey","last_name":"Ptitsyn","first_name":"Andrey"},{"first_name":"Denis","last_name":"Reshetov","full_name":"Reshetov, Denis"},{"first_name":"Krishanu","full_name":"Mukherjee, Krishanu","last_name":"Mukherjee"},{"full_name":"Moroz, Tatiana","last_name":"Moroz","first_name":"Tatiana"},{"first_name":"Yelena","full_name":"Bobkova, Yelena","last_name":"Bobkova"},{"first_name":"Fahong","last_name":"Yu","full_name":"Yu, Fahong"},{"first_name":"Vladimir","last_name":"Kapitonov","full_name":"Kapitonov, Vladimir"},{"full_name":"Jurka, Jerzy","last_name":"Jurka","first_name":"Jerzy"},{"last_name":"Bobkov","full_name":"Bobkov, Yuriy","first_name":"Yuriy"},{"full_name":"Swore, Joshua","last_name":"Swore","first_name":"Joshua"},{"first_name":"David","full_name":"Girardo, David","last_name":"Girardo"},{"first_name":"Alexander","full_name":"Fodor, Alexander","last_name":"Fodor"},{"last_name":"Gusev","full_name":"Gusev, Fedor","first_name":"Fedor"},{"first_name":"Rachel","last_name":"Sanford","full_name":"Sanford, Rachel"},{"first_name":"Rebecca","last_name":"Bruders","full_name":"Bruders, Rebecca"},{"full_name":"Kittler, Ellen","last_name":"Kittler","first_name":"Ellen"},{"last_name":"Mills","full_name":"Mills, Claudia","first_name":"Claudia"},{"last_name":"Rast","full_name":"Rast, Jonathan","first_name":"Jonathan"},{"first_name":"Romain","full_name":"Derelle, Romain","last_name":"Derelle"},{"last_name":"Solovyev","full_name":"Solovyev, Victor","first_name":"Victor"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Billie","full_name":"Swalla, Billie","last_name":"Swalla"},{"full_name":"Sweedler, Jonathan","last_name":"Sweedler","first_name":"Jonathan"},{"last_name":"Rogaev","full_name":"Rogaev, Evgeny","first_name":"Evgeny"},{"first_name":"Kenneth","full_name":"Halanych, Kenneth","last_name":"Halanych"},{"full_name":"Kohn, Andrea","last_name":"Kohn","first_name":"Andrea"}],"title":"The ctenophore genome and the evolutionary origins of neural systems","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"_id":"863","year":"2014","citation":{"ieee":"L. Moroz <i>et al.</i>, “The ctenophore genome and the evolutionary origins of neural systems,” <i>Nature</i>, vol. 510, no. 7503. Nature Publishing Group, pp. 109–114, 2014.","mla":"Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” <i>Nature</i>, vol. 510, no. 7503, Nature Publishing Group, 2014, pp. 109–14, doi:<a href=\"https://doi.org/10.1038/nature13400\">10.1038/nature13400</a>.","ama":"Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary origins of neural systems. <i>Nature</i>. 2014;510(7503):109-114. doi:<a href=\"https://doi.org/10.1038/nature13400\">10.1038/nature13400</a>","apa":"Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya, I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural systems. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature13400\">https://doi.org/10.1038/nature13400</a>","ista":"Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114.","chicago":"Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature13400\">https://doi.org/10.1038/nature13400</a>.","short":"L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114."},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","issue":"7503","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:48:54Z","acknowledgement":"We thank Friday Harbor Laboratories for facilities during animal collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters, J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ, RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank F. Nivens for videos and P. L. Williams for database support. This work was supported by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH (1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310 to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H., L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033 (Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424), EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology Program 117 and Molette laboratory 22.","fulldoi":"https://doi.org/10.1038/nature13400","publist_id":"6785","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"pmid":1,"doi":"10.1038/nature13400","status":"public","OA_place":"publisher","oa_version":"None","intvolume":"       510","type":"journal_article","date_published":"2014-01-01T00:00:00Z","volume":510,"external_id":{"pmid":["24847885"]},"language":[{"iso":"eng"}],"month":"01","OA_type":"gold"},{"pmid":1,"scopus_import":"1","doi":"10.1038/nature08131","status":"public","intvolume":"       460","type":"journal_article","date_published":"2009-07-16T00:00:00Z","oa_version":"None","volume":460,"external_id":{"pmid":["19606145"]},"keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"month":"07","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","day":"16","extern":"1","date_updated":"2023-08-08T09:00:59Z","author":[{"last_name":"Nakanishi","full_name":"Nakanishi, Hideyuki","first_name":"Hideyuki"},{"first_name":"Kyle J. M.","full_name":"Bishop, Kyle J. M.","last_name":"Bishop"},{"full_name":"Kowalczyk, Bartlomiej","last_name":"Kowalczyk","first_name":"Bartlomiej"},{"last_name":"Nitzan","full_name":"Nitzan, Abraham","first_name":"Abraham"},{"full_name":"Weiss, Emily A.","last_name":"Weiss","first_name":"Emily A."},{"last_name":"Tretiakov","full_name":"Tretiakov, Konstantin V.","first_name":"Konstantin V."},{"first_name":"Mario M.","last_name":"Apodaca","full_name":"Apodaca, Mario M."},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"},{"full_name":"Stoddart, J. Fraser","last_name":"Stoddart","first_name":"J. Fraser"},{"full_name":"Grzybowski, Bartosz A.","last_name":"Grzybowski","first_name":"Bartosz A."}],"title":"Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles","publication":"Nature","abstract":[{"lang":"eng","text":"In traditional photoconductors1,2,3, the impinging light generates mobile charge carriers in the valence and/or conduction bands, causing the material’s conductivity to increase4. Such positive photoconductance is observed in both bulk and nanostructured5,6 photoconductors. Here we describe a class of nanoparticle-based materials whose conductivity can either increase or decrease on irradiation with visible light of wavelengths close to the particles’ surface plasmon resonance. The remarkable feature of these plasmonic materials is that the sign of the conductivity change and the nature of the electron transport between the nanoparticles depend on the molecules comprising the self-assembled monolayers (SAMs)7,8 stabilizing the nanoparticles. For SAMs made of electrically neutral (polar and non-polar) molecules, conductivity increases on irradiation. If, however, the SAMs contain electrically charged (either negatively or positively) groups, conductivity decreases. The optical and electrical characteristics of these previously undescribed inverse photoconductors can be engineered flexibly by adjusting the material properties of the nanoparticles and of the coating SAMs. In particular, in films comprising mixtures of different nanoparticles or nanoparticles coated with mixed SAMs, the overall photoconductance is a weighted average of the changes induced by the individual components. These and other observations can be rationalized in terms of light-induced creation of mobile charge carriers whose transport through the charged SAMs is inhibited by carrier trapping in transient polaron-like states9,10. The nanoparticle-based photoconductors we describe could have uses in chemical sensors and/or in conjunction with flexible substrates."}],"page":"371-375","year":"2009","_id":"13418","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"citation":{"short":"H. Nakanishi, K.J.M. Bishop, B. Kowalczyk, A. Nitzan, E.A. Weiss, K.V. Tretiakov, M.M. Apodaca, R. Klajn, J.F. Stoddart, B.A. Grzybowski, Nature 460 (2009) 371–375.","chicago":"Nakanishi, Hideyuki, Kyle J. M. Bishop, Bartlomiej Kowalczyk, Abraham Nitzan, Emily A. Weiss, Konstantin V. Tretiakov, Mario M. Apodaca, Rafal Klajn, J. Fraser Stoddart, and Bartosz A. Grzybowski. “Photoconductance and Inverse Photoconductance in Films of Functionalized Metal Nanoparticles.” <i>Nature</i>. Springer Nature, 2009. <a href=\"https://doi.org/10.1038/nature08131\">https://doi.org/10.1038/nature08131</a>.","ieee":"H. Nakanishi <i>et al.</i>, “Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles,” <i>Nature</i>, vol. 460, no. 7253. Springer Nature, pp. 371–375, 2009.","apa":"Nakanishi, H., Bishop, K. J. M., Kowalczyk, B., Nitzan, A., Weiss, E. A., Tretiakov, K. V., … Grzybowski, B. A. (2009). Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature08131\">https://doi.org/10.1038/nature08131</a>","ama":"Nakanishi H, Bishop KJM, Kowalczyk B, et al. Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles. <i>Nature</i>. 2009;460(7253):371-375. doi:<a href=\"https://doi.org/10.1038/nature08131\">10.1038/nature08131</a>","mla":"Nakanishi, Hideyuki, et al. “Photoconductance and Inverse Photoconductance in Films of Functionalized Metal Nanoparticles.” <i>Nature</i>, vol. 460, no. 7253, Springer Nature, 2009, pp. 371–75, doi:<a href=\"https://doi.org/10.1038/nature08131\">10.1038/nature08131</a>.","ista":"Nakanishi H, Bishop KJM, Kowalczyk B, Nitzan A, Weiss EA, Tretiakov KV, Apodaca MM, Klajn R, Stoddart JF, Grzybowski BA. 2009. Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles. Nature. 460(7253), 371–375."},"issue":"7253","article_type":"original","publisher":"Springer Nature","date_created":"2023-08-01T10:29:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1038/nature08131"},{"doi":"10.1038/nature07324","pmid":1,"scopus_import":"1","department":[{"_id":"DaZi"}],"status":"public","external_id":{"pmid":["18815594"]},"volume":456,"keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"intvolume":"       456","type":"journal_article","date_published":"2008-11-06T00:00:00Z","oa_version":"Submitted Version","quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/","open_access":"1"}],"month":"11","date_updated":"2021-12-14T08:54:36Z","publication_status":"published","day":"06","article_processing_charge":"No","extern":"1","year":"2008","_id":"9457","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","title":"Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks","author":[{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"first_name":"Devin","full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr"},{"full_name":"Ballinger, Tracy","last_name":"Ballinger","first_name":"Tracy"},{"last_name":"Henikoff","full_name":"Henikoff, Steven","first_name":"Steven"}],"abstract":[{"lang":"eng","text":"Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation."}],"page":"125-129","issue":"7218","article_type":"letter_note","oa":1,"citation":{"ista":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218), 125–129.","ama":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. 2008;456(7218):125-129. doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>","mla":"Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>, vol. 456, no. 7218, Springer Nature, 2008, pp. 125–29, doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>.","apa":"Zilberman, D., Coleman-Derr, D., Ballinger, T., &#38; Henikoff, S. (2008). Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>","ieee":"D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks,” <i>Nature</i>, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.","chicago":"Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>. Springer Nature, 2008. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>.","short":"D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129."},"fulldoi":"https://doi.org/10.1038/nature07324","publisher":"Springer Nature","date_created":"2021-06-04T11:49:32Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"language":[{"iso":"eng"}],"external_id":{"pmid":["18451854"]},"volume":453,"type":"journal_article","date_published":"2008-05-01T00:00:00Z","intvolume":"       453","oa_version":"None","OA_type":"closed access","month":"05","doi":"10.1038/nature06887","pmid":1,"status":"public","article_type":"original","issue":"7191","citation":{"ama":"Lämmermann T, Bader B, Monkley S, et al. Rapid leukocyte migration by integrin-independent flowing and squeezing. <i>Nature</i>. 2008;453(7191):51-55. doi:<a href=\"https://doi.org/10.1038/nature06887\">10.1038/nature06887</a>","apa":"Lämmermann, T., Bader, B., Monkley, S., Worbs, T., Wedlich Söldner, R., Hirsch, K., … Sixt, M. K. (2008). Rapid leukocyte migration by integrin-independent flowing and squeezing. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature06887\">https://doi.org/10.1038/nature06887</a>","mla":"Lämmermann, Tim, et al. “Rapid Leukocyte Migration by Integrin-Independent Flowing and Squeezing.” <i>Nature</i>, vol. 453, no. 7191, Nature Publishing Group, 2008, pp. 51–55, doi:<a href=\"https://doi.org/10.1038/nature06887\">10.1038/nature06887</a>.","ista":"Lämmermann T, Bader B, Monkley S, Worbs T, Wedlich Söldner R, Hirsch K, Keller M, Förster R, Critchley D, Fässler R, Sixt MK. 2008. Rapid leukocyte migration by integrin-independent flowing and squeezing. Nature. 453(7191), 51–55.","ieee":"T. Lämmermann <i>et al.</i>, “Rapid leukocyte migration by integrin-independent flowing and squeezing,” <i>Nature</i>, vol. 453, no. 7191. Nature Publishing Group, pp. 51–55, 2008.","short":"T. Lämmermann, B. Bader, S. Monkley, T. Worbs, R. Wedlich Söldner, K. Hirsch, M. Keller, R. Förster, D. Critchley, R. Fässler, M.K. Sixt, Nature 453 (2008) 51–55.","chicago":"Lämmermann, Tim, Bernhard Bader, Susan Monkley, Tim Worbs, Roland Wedlich Söldner, Karin Hirsch, Markus Keller, et al. “Rapid Leukocyte Migration by Integrin-Independent Flowing and Squeezing.” <i>Nature</i>. Nature Publishing Group, 2008. <a href=\"https://doi.org/10.1038/nature06887\">https://doi.org/10.1038/nature06887</a>."},"publist_id":"2186","fulldoi":"https://doi.org/10.1038/nature06887","date_created":"2018-12-11T12:06:00Z","publisher":"Nature Publishing Group","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-05-29T09:25:29Z","day":"01","article_processing_charge":"No","publication_status":"published","extern":"1","year":"2008","_id":"3941","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","title":"Rapid leukocyte migration by integrin-independent flowing and squeezing","author":[{"last_name":"Lämmermann","full_name":"Lämmermann, Tim","first_name":"Tim"},{"full_name":"Bader, Bernhard","last_name":"Bader","first_name":"Bernhard"},{"full_name":"Monkley, Susan","last_name":"Monkley","first_name":"Susan"},{"last_name":"Worbs","full_name":"Worbs, Tim","first_name":"Tim"},{"first_name":"Roland","full_name":"Wedlich Söldner, Roland","last_name":"Wedlich Söldner"},{"first_name":"Karin","full_name":"Hirsch, Karin","last_name":"Hirsch"},{"full_name":"Keller, Markus","last_name":"Keller","first_name":"Markus"},{"last_name":"Förster","full_name":"Förster, Reinhold","first_name":"Reinhold"},{"last_name":"Critchley","full_name":"Critchley, David","first_name":"David"},{"first_name":"Reinhard","last_name":"Fässler","full_name":"Fässler, Reinhard"},{"full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"page":"51 - 55","abstract":[{"text":"All metazoan cells carry transmembrane receptors of the integrin family, which couple the contractile force of the actomyosin cytoskeleton to the extracellular environment. In agreement with this principle, rapidly migrating leukocytes use integrin-mediated adhesion when moving over two-dimensional surfaces. As migration on two-dimensional substrates naturally overemphasizes the role of adhesion, the contribution of integrins during three-dimensional movement of leukocytes within tissues has remained controversial. We studied the interplay between adhesive, contractile and protrusive forces during interstitial leukocyte chemotaxis in vivo and in vitro. We ablated all integrin heterodimers from murine leukocytes, and show here that functional integrins do not contribute to migration in three-dimensional environments. Instead, these cells migrate by the sole force of actin-network expansion, which promotes protrusive flowing of the leading edge. Myosin II-dependent contraction is only required on passage through narrow gaps, where a squeezing contraction of the trailing edge propels the rigid nucleus.","lang":"eng"}]},{"article_type":"letter_note","issue":"7079","citation":{"ama":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual quantum computation through quantum interrogation. <i>Nature</i>. 2006;439(7079):949-952. doi:<a href=\"https://doi.org/10.1038/nature04523\">10.1038/nature04523</a>","mla":"Hosten, Onur, et al. “Counterfactual Quantum Computation through Quantum Interrogation.” <i>Nature</i>, vol. 439, no. 7079, Nature Publishing Group, 2006, pp. 949–52, doi:<a href=\"https://doi.org/10.1038/nature04523\">10.1038/nature04523</a>.","apa":"Hosten, O., Rakher, M., Barreiro, J., Peters, N., &#38; Kwiat, P. (2006). Counterfactual quantum computation through quantum interrogation. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature04523\">https://doi.org/10.1038/nature04523</a>","ista":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2006. Counterfactual quantum computation through quantum interrogation. Nature. 439(7079), 949–952.","ieee":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual quantum computation through quantum interrogation,” <i>Nature</i>, vol. 439, no. 7079. Nature Publishing Group, pp. 949–952, 2006.","short":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, Nature 439 (2006) 949–952.","chicago":"Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Quantum Computation through Quantum Interrogation.” <i>Nature</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/nature04523\">https://doi.org/10.1038/nature04523</a>."},"publist_id":"7235","fulldoi":"https://doi.org/10.1038/nature04523","date_created":"2018-12-11T11:47:18Z","publisher":"Nature Publishing Group","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-05-08T11:42:23Z","day":"23","article_processing_charge":"No","publication_status":"published","extern":"1","year":"2006","_id":"579","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","title":"Counterfactual quantum computation through quantum interrogation","author":[{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten"},{"full_name":"Rakher, Matthew","last_name":"Rakher","first_name":"Matthew"},{"first_name":"Julio","full_name":"Barreiro, Julio","last_name":"Barreiro"},{"first_name":"Nicholas","last_name":"Peters","full_name":"Peters, Nicholas"},{"full_name":"Kwiat, Paul","last_name":"Kwiat","first_name":"Paul"}],"page":"949 - 952","abstract":[{"lang":"eng","text":"The logic underlying the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to surprising effects. Counterfactual computation constitutes a striking example: the potential outcome of a quantum computation can be inferred, even if the computer is not run 1. Relying on similar arguments to interaction-free measurements 2 (or quantum interrogation3), counterfactual computation is accomplished by putting the computer in a superposition of 'running' and 'not running' states, and then interfering the two histories. Conditional on the as-yet-unknown outcome of the computation, it is sometimes possible to counterfactually infer information about the solution. Here we demonstrate counterfactual computation, implementing Grover's search algorithm with an all-optical approach4. It was believed that the overall probability of such counterfactual inference is intrinsically limited1,5, so that it could not perform better on average than random guesses. However, using a novel 'chained' version of the quantum Zeno effect6, we show how to boost the counterfactual inference probability to unity, thereby beating the random guessing limit. Our methods are general and apply to any physical system, as illustrated by a discussion of trapped-ion systems. Finally, we briefly show that, in certain circumstances, counterfactual computation can eliminate errors induced by decoherence. "}],"language":[{"iso":"eng"}],"external_id":{"pmid":["16495993"]},"volume":439,"date_published":"2006-02-23T00:00:00Z","type":"journal_article","intvolume":"       439","oa_version":"None","quality_controlled":"1","OA_type":"closed access","month":"02","doi":"10.1038/nature04523","pmid":1,"scopus_import":"1","status":"public"},{"extern":"1","article_processing_charge":"No","day":"24","publication_status":"published","date_updated":"2025-01-03T11:13:23Z","page":"904-907","abstract":[{"lang":"eng","text":"Since it was first suggested1 that a single molecule might function as an active electronic component, a number of techniques have been developed to measure the charge transport properties of single molecules2,3,4,5,6,7,8,9,10,11,12. Although scanning tunnelling microscopy observations under high vacuum conditions can allow stable measurements of electron transport, most measurements of a single molecule bonded in a metal–molecule–metal junction exhibit relatively large variations in conductance. As a result, even simple predictions about how molecules behave in such junctions have still not been rigorously tested. For instance, it is well known13,14 that the tunnelling current passing through a molecule depends on its conformation; but although some experiments have verified this effect15,16,17,18, a comprehensive mapping of how junction conductance changes with molecular conformation is not yet available. In the simple case of a biphenyl—a molecule with two phenyl rings linked by a single C–C bond—conductance is expected to change with the relative twist angle between the two rings, with the planar conformation having the highest conductance. Here we use amine link groups to form single-molecule junctions with more reproducible current–voltage characteristics19. This allows us to extract average conductance values from thousands of individual measurements on a series of seven biphenyl molecules with different ring substitutions that alter the twist angle of the molecules. We find that the conductance for the series decreases with increasing twist angle, consistent with a cosine-squared relation predicted for transport through π-conjugated biphenyl systems13."}],"author":[{"orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","full_name":"Venkataraman, Latha","last_name":"Venkataraman"},{"last_name":"Klare","full_name":"Klare, Jennifer E.","first_name":"Jennifer E."},{"first_name":"Colin","last_name":"Nuckolls","full_name":"Nuckolls, Colin"},{"full_name":"Hybertsen, Mark S.","last_name":"Hybertsen","first_name":"Mark S."},{"last_name":"Steigerwald","full_name":"Steigerwald, Michael L.","first_name":"Michael L."}],"publication":"Nature","title":"Dependence of single-molecule junction conductance on molecular conformation","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"year":"2006","_id":"18041","citation":{"ieee":"L. Venkataraman, J. E. Klare, C. Nuckolls, M. S. Hybertsen, and M. L. Steigerwald, “Dependence of single-molecule junction conductance on molecular conformation,” <i>Nature</i>, vol. 442, no. 7105. Springer Nature, pp. 904–907, 2006.","mla":"Venkataraman, Latha, et al. “Dependence of Single-Molecule Junction Conductance on Molecular Conformation.” <i>Nature</i>, vol. 442, no. 7105, Springer Nature, 2006, pp. 904–07, doi:<a href=\"https://doi.org/10.1038/nature05037\">10.1038/nature05037</a>.","apa":"Venkataraman, L., Klare, J. E., Nuckolls, C., Hybertsen, M. S., &#38; Steigerwald, M. L. (2006). Dependence of single-molecule junction conductance on molecular conformation. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature05037\">https://doi.org/10.1038/nature05037</a>","ama":"Venkataraman L, Klare JE, Nuckolls C, Hybertsen MS, Steigerwald ML. Dependence of single-molecule junction conductance on molecular conformation. <i>Nature</i>. 2006;442(7105):904-907. doi:<a href=\"https://doi.org/10.1038/nature05037\">10.1038/nature05037</a>","ista":"Venkataraman L, Klare JE, Nuckolls C, Hybertsen MS, Steigerwald ML. 2006. Dependence of single-molecule junction conductance on molecular conformation. Nature. 442(7105), 904–907.","short":"L. Venkataraman, J.E. Klare, C. Nuckolls, M.S. Hybertsen, M.L. Steigerwald, Nature 442 (2006) 904–907.","chicago":"Venkataraman, Latha, Jennifer E. Klare, Colin Nuckolls, Mark S. Hybertsen, and Michael L. Steigerwald. “Dependence of Single-Molecule Junction Conductance on Molecular Conformation.” <i>Nature</i>. Springer Nature, 2006. <a href=\"https://doi.org/10.1038/nature05037\">https://doi.org/10.1038/nature05037</a>."},"article_type":"letter_note","issue":"7105","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-09-09T15:07:33Z","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/nature05037","scopus_import":"1","pmid":1,"doi":"10.1038/nature05037","status":"public","oa_version":"None","type":"journal_article","date_published":"2006-08-24T00:00:00Z","intvolume":"       442","language":[{"iso":"eng"}],"volume":442,"external_id":{"pmid":["16929295"]},"month":"08","OA_type":"closed access","quality_controlled":"1"},{"doi":"10.1038/nature03633","pmid":1,"status":"public","language":[{"iso":"eng"}],"external_id":{"pmid":["15988527 "]},"volume":435,"date_published":"2005-06-30T00:00:00Z","type":"journal_article","intvolume":"       435","oa_version":"None","month":"06","date_updated":"2026-07-15T13:02:15Z","article_processing_charge":"No","day":"30","publication_status":"published","extern":"1","year":"2005","_id":"3001","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","author":[{"first_name":"Tomasz","full_name":"Paciorek, Tomasz","last_name":"Paciorek"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"last_name":"Ruthardt","full_name":"Ruthardt, Nadia","first_name":"Nadia"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"last_name":"Stierhof","full_name":"Stierhof, York","first_name":"York"},{"last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen"},{"full_name":"Morris, David","last_name":"Morris","first_name":"David"},{"first_name":"Neil","last_name":"Emans","full_name":"Emans, Neil"},{"full_name":"Jürgens, Gerd","last_name":"Jürgens","first_name":"Gerd"},{"first_name":"Niko","last_name":"Geldner","full_name":"Geldner, Niko"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí"}],"title":"Auxin inhibits endocytosis and promotes its own efflux from cells","page":"1251 - 1256","abstract":[{"lang":"eng","text":"One of the mechanisms by which signalling molecules regulate cellular behaviour is modulating subcellular protein translocation. This mode of regulation is often based on specialized vesicle trafficking, termed constitutive cycling, which consists of repeated internalization and recycling of proteins to and from the plasma membrane. No such mechanism of hormone action has been shown in plants although several proteins, including the PIN auxin efflux facilitators, exhibit constitutive cycling. Here we show that a major regulator of plant development, auxin, inhibits endocytosis. This effect is specific to biologically active auxins and requires activity of the Calossin-like protein BIG. By inhibiting the internalization step of PIN constitutive cycling, auxin increases levels of PINs at the plasma membrane. Concomitantly, auxin promotes its own efflux from cells by a vesicle-trafficking-dependent mechanism. Furthermore, asymmetric auxin translocation during gravitropism is correlated with decreased PIN internalization. Our data imply a previously undescribed mode of plant hormone action: by modulating PIN protein trafficking, auxin regulates PIN abundance and activity at the cell surface, providing a mechanism for the feedback regulation of auxin transport."}],"article_type":"original","issue":"7046","das_tickbox":"1","citation":{"ieee":"T. Paciorek <i>et al.</i>, “Auxin inhibits endocytosis and promotes its own efflux from cells,” <i>Nature</i>, vol. 435, no. 7046. Nature Publishing Group, pp. 1251–1256, 2005.","mla":"Paciorek, Tomasz, et al. “Auxin Inhibits Endocytosis and Promotes Its Own Efflux from Cells.” <i>Nature</i>, vol. 435, no. 7046, Nature Publishing Group, 2005, pp. 1251–56, doi:<a href=\"https://doi.org/10.1038/nature03633\">10.1038/nature03633</a>.","ama":"Paciorek T, Zažímalová E, Ruthardt N, et al. Auxin inhibits endocytosis and promotes its own efflux from cells. <i>Nature</i>. 2005;435(7046):1251-1256. doi:<a href=\"https://doi.org/10.1038/nature03633\">10.1038/nature03633</a>","apa":"Paciorek, T., Zažímalová, E., Ruthardt, N., Petrášek, J., Stierhof, Y., Kleine Vehn, J., … Friml, J. (2005). Auxin inhibits endocytosis and promotes its own efflux from cells. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature03633\">https://doi.org/10.1038/nature03633</a>","ista":"Paciorek T, Zažímalová E, Ruthardt N, Petrášek J, Stierhof Y, Kleine Vehn J, Morris D, Emans N, Jürgens G, Geldner N, Friml J. 2005. Auxin inhibits endocytosis and promotes its own efflux from cells. Nature. 435(7046), 1251–1256.","chicago":"Paciorek, Tomasz, Eva Zažímalová, Nadia Ruthardt, Jan Petrášek, York Stierhof, Jürgen Kleine Vehn, David Morris, et al. “Auxin Inhibits Endocytosis and Promotes Its Own Efflux from Cells.” <i>Nature</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/nature03633\">https://doi.org/10.1038/nature03633</a>.","short":"T. Paciorek, E. Zažímalová, N. Ruthardt, J. Petrášek, Y. Stierhof, J. Kleine Vehn, D. Morris, N. Emans, G. Jürgens, N. Geldner, J. Friml, Nature 435 (2005) 1251–1256."},"publist_id":"3702","fulldoi":"https://doi.org/10.1038/nature03633","date_created":"2018-12-11T12:00:47Z","publisher":"Nature Publishing Group","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"language":[{"iso":"eng"}],"volume":433,"external_id":{"pmid":["15635403"]},"oa_version":"None","date_published":"2005-01-01T00:00:00Z","type":"journal_article","intvolume":"       433","OA_type":"closed access","month":"01","doi":"10.1038/nature03184","pmid":1,"status":"public","article_type":"original","issue":"7021","citation":{"ista":"Billou I, Xu J, Wildwater M, Willemsen V, Paponov I, Friml J, Heldstra R, Aida M, Palme K, Scheres B. 2005. The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature. 433(7021), 39–44.","mla":"Billou, Ikram, et al. “The PIN Auxin Efflux Facilitator Network Controls Growth and Patterning in Arabidopsis Roots.” <i>Nature</i>, vol. 433, no. 7021, Nature Publishing Group, 2005, pp. 39–44, doi:<a href=\"https://doi.org/10.1038/nature03184\">10.1038/nature03184</a>.","apa":"Billou, I., Xu, J., Wildwater, M., Willemsen, V., Paponov, I., Friml, J., … Scheres, B. (2005). The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature03184\">https://doi.org/10.1038/nature03184</a>","ama":"Billou I, Xu J, Wildwater M, et al. The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. <i>Nature</i>. 2005;433(7021):39-44. doi:<a href=\"https://doi.org/10.1038/nature03184\">10.1038/nature03184</a>","ieee":"I. Billou <i>et al.</i>, “The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots,” <i>Nature</i>, vol. 433, no. 7021. Nature Publishing Group, pp. 39–44, 2005.","short":"I. Billou, J. Xu, M. Wildwater, V. Willemsen, I. Paponov, J. Friml, R. Heldstra, M. Aida, K. Palme, B. Scheres, Nature 433 (2005) 39–44.","chicago":"Billou, Ikram, Jian Xu, Marjolein Wildwater, Viola Willemsen, Ivan Paponov, Jiří Friml, Renze Heldstra, Mitsuhiro Aida, Klaus Palme, and Ben Scheres. “The PIN Auxin Efflux Facilitator Network Controls Growth and Patterning in Arabidopsis Roots.” <i>Nature</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/nature03184\">https://doi.org/10.1038/nature03184</a>."},"publist_id":"4448","fulldoi":"https://doi.org/10.1038/nature03184","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:57:46Z","publisher":"Nature Publishing Group","date_updated":"2026-08-07T08:01:24Z","extern":"1","day":"01","article_processing_charge":"No","publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"year":"2005","_id":"2455","page":"39 - 44","abstract":[{"lang":"eng","text":"Local accumulation of the plant growth regulator auxin mediates pattern formation in Arabidopsis roots and influences outgrowth and development of lateral root- and shoot-derived primordia. However, it has remained unclear how auxin can simultaneously regulate patterning and organ outgrowth and how its distribution is stabilized in a primordium-specif ic manner. Here we show that five PIN genes collectively control auxin distribution to regulate cell division and cell expansion in the primary root. Furthermore, the joint action of these genes has an important role in pattern formation by focusing the auxin maximum and restricting the expression domain of PLETHORA (PLT) genes, major determinants for root stem cell specification. In turn, PLT genes are required for PIN gene transcription to stabilize the auxin maximum at the distal root tip. Our data reveal an interaction network of auxin transport facilitators and root fate determinants that control patterning and growth of the root primordium."}],"publication":"Nature","author":[{"last_name":"Billou","full_name":"Billou, Ikram","first_name":"Ikram"},{"last_name":"Xu","full_name":"Xu, Jian","first_name":"Jian"},{"full_name":"Wildwater, Marjolein","last_name":"Wildwater","first_name":"Marjolein"},{"first_name":"Viola","last_name":"Willemsen","full_name":"Willemsen, Viola"},{"first_name":"Ivan","full_name":"Paponov, Ivan","last_name":"Paponov"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Renze","last_name":"Heldstra","full_name":"Heldstra, Renze"},{"last_name":"Aida","full_name":"Aida, Mitsuhiro","first_name":"Mitsuhiro"},{"first_name":"Klaus","last_name":"Palme","full_name":"Palme, Klaus"},{"last_name":"Scheres","full_name":"Scheres, Ben","first_name":"Ben"}],"title":"The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots"}]