--- _id: '514' abstract: - lang: eng text: 'Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum.' article_number: '16032' author: - first_name: Jean full_name: Simonnet, Jean last_name: Simonnet - first_name: Mérie full_name: Nassar, Mérie last_name: Nassar - first_name: Federico full_name: Stella, Federico id: 39AF1E74-F248-11E8-B48F-1D18A9856A87 last_name: Stella orcid: 0000-0001-9439-3148 - first_name: Ivan full_name: Cohen, Ivan last_name: Cohen - first_name: Bertrand full_name: Mathon, Bertrand last_name: Mathon - first_name: Charlotte full_name: Boccara, Charlotte id: 3FC06552-F248-11E8-B48F-1D18A9856A87 last_name: Boccara orcid: 0000-0001-7237-5109 - first_name: Richard full_name: Miles, Richard last_name: Miles - first_name: Desdemona full_name: Fricker, Desdemona last_name: Fricker citation: ama: Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 2017;8. doi:10.1038/ncomms16032 apa: Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms16032 chicago: Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032. ieee: J. Simonnet et al., “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032. mla: Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol. 8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032. short: J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017). date_created: 2018-12-11T11:46:54Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:01:16Z day: '01' ddc: - '571' department: - _id: JoCs doi: 10.1038/ncomms16032 file: - access_level: open_access checksum: 76d8a2b72a58e56adb410ec37dfa7eee content_type: application/pdf creator: system date_created: 2018-12-12T10:14:31Z date_updated: 2020-07-14T12:46:36Z file_id: '5083' file_name: IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf file_size: 2948357 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '07' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7305' pubrep_id: '937' quality_controlled: '1' scopus_import: 1 status: public title: Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '601' abstract: - lang: eng text: 'The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. ' article_number: '15741' article_processing_charge: No author: - first_name: Youwei full_name: Xu, Youwei last_name: Xu - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Chung full_name: Lee, Chung last_name: Lee - first_name: Kerstin full_name: Maier, Kerstin last_name: Maier - first_name: Björn full_name: Schwalb, Björn last_name: Schwalb - first_name: Dimitri full_name: Tegunov, Dimitri last_name: Tegunov - first_name: Jürgen full_name: Plitzko, Jürgen last_name: Plitzko - first_name: Henning full_name: Urlaub, Henning last_name: Urlaub - first_name: Patrick full_name: Cramer, Patrick last_name: Cramer citation: ama: Xu Y, Bernecky C, Lee C, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 2017;8. doi:10.1038/ncomms15741 apa: Xu, Y., Bernecky, C., Lee, C., Maier, K., Schwalb, B., Tegunov, D., … Cramer, P. (2017). Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15741 chicago: Xu, Youwei, Carrie Bernecky, Chung Lee, Kerstin Maier, Björn Schwalb, Dimitri Tegunov, Jürgen Plitzko, Henning Urlaub, and Patrick Cramer. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15741. ieee: Y. Xu et al., “Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 8, 15741. mla: Xu, Youwei, et al. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” Nature Communications, vol. 8, 15741, Nature Publishing Group, 2017, doi:10.1038/ncomms15741. short: Y. Xu, C. Bernecky, C. Lee, K. Maier, B. Schwalb, D. Tegunov, J. Plitzko, H. Urlaub, P. Cramer, Nature Communications 8 (2017). date_created: 2018-12-11T11:47:25Z date_published: 2017-06-06T00:00:00Z date_updated: 2021-01-12T08:05:40Z day: '06' ddc: - '570' doi: 10.1038/ncomms15741 extern: '1' file: - access_level: open_access checksum: 940742282a9a285dc4aeae0c2b5ebe96 content_type: application/pdf creator: dernst date_created: 2019-01-21T14:48:10Z date_updated: 2020-07-14T12:47:16Z file_id: '5865' file_name: 2017_NatureComm_Xu.pdf file_size: 3018075 relation: main_file file_date_updated: 2020-07-14T12:47:16Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7203' quality_controlled: '1' status: public title: Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '613' abstract: - lang: eng text: 'Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.' acknowledgement: We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG). article_number: '1535' article_processing_charge: Yes (in subscription journal) author: - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01683-1 apa: Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., & Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01683-1 chicago: Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01683-1. ieee: R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535. mla: Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1. short: R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017). date_created: 2018-12-11T11:47:30Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:06:15Z day: '01' ddc: - '576' - '579' department: - _id: CaGu - _id: GaTk doi: 10.1038/s41467-017-01683-1 ec_funded: 1 file: - access_level: open_access checksum: 44bb5d0229926c23a9955d9fe0f9723f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:05Z date_updated: 2020-07-14T12:47:20Z file_id: '5190' file_name: IST-2017-911-v1+1_s41467-017-01683-1.pdf file_size: 1951699 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7191' pubrep_id: '911' quality_controlled: '1' scopus_import: 1 status: public title: Shaping bacterial population behavior through computer interfaced control of individual cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '659' abstract: - lang: eng text: Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching. article_number: '14832' article_processing_charge: No author: - first_name: Frieda full_name: Kage, Frieda last_name: Kage - first_name: Moritz full_name: Winterhoff, Moritz last_name: Winterhoff - first_name: Vanessa full_name: Dimchev, Vanessa last_name: Dimchev - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Tobias full_name: Thalheim, Tobias last_name: Thalheim - first_name: Anika full_name: Freise, Anika last_name: Freise - first_name: Stefan full_name: Brühmann, Stefan last_name: Brühmann - first_name: Jana full_name: Kollasser, Jana last_name: Kollasser - first_name: Jennifer full_name: Block, Jennifer last_name: Block - first_name: Georgi A full_name: Dimchev, Georgi A last_name: Dimchev - first_name: Matthias full_name: Geyer, Matthias last_name: Geyer - first_name: Hams full_name: Schnittler, Hams last_name: Schnittler - first_name: Cord full_name: Brakebusch, Cord last_name: Brakebusch - first_name: Theresia full_name: Stradal, Theresia last_name: Stradal - first_name: Marie full_name: Carlier, Marie last_name: Carlier - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Josef full_name: Käs, Josef last_name: Käs - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832 apa: Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14832 chicago: Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14832. ieee: F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832. mla: Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832. short: F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017). date_created: 2018-12-11T11:47:46Z date_published: 2017-03-22T00:00:00Z date_updated: 2021-01-12T08:08:06Z day: '22' ddc: - '570' department: - _id: MiSi doi: 10.1038/ncomms14832 file: - access_level: open_access checksum: dae30190291c3630e8102d8714a8d23e content_type: application/pdf creator: system date_created: 2018-12-12T10:14:21Z date_updated: 2020-07-14T12:47:34Z file_id: '5072' file_name: IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf file_size: 9523746 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7075' pubrep_id: '902' quality_controlled: '1' scopus_import: 1 status: public title: FMNL formins boost lamellipodial force generation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '1104' abstract: - lang: eng text: In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code quasilinearly for its position, while distant cells remain largely invariant to the object's position and, instead, respond nonlinearly to changes in the object's speed. We develop a quantitative model that accounts for this effect and identify a disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems. article_number: '1964' article_processing_charge: No author: - first_name: Stephane full_name: Deny, Stephane last_name: Deny - first_name: Ulisse full_name: Ferrari, Ulisse last_name: Ferrari - first_name: Emilie full_name: Mace, Emilie last_name: Mace - first_name: Pierre full_name: Yger, Pierre last_name: Yger - first_name: Romain full_name: Caplette, Romain last_name: Caplette - first_name: Serge full_name: Picaud, Serge last_name: Picaud - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Olivier full_name: Marre, Olivier last_name: Marre citation: ama: Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y apa: Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02159-y chicago: Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-02159-y. ieee: S. Deny et al., “Multiplexed computations in retinal ganglion cells of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964. mla: Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y. short: S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017). date_created: 2018-12-11T11:50:10Z date_published: 2017-12-06T00:00:00Z date_updated: 2023-09-20T11:41:19Z day: '06' ddc: - '571' department: - _id: GaTk doi: 10.1038/s41467-017-02159-y ec_funded: 1 external_id: isi: - '000417241200004' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:16:06Z date_updated: 2018-12-12T10:16:06Z file_id: '5191' file_name: IST-2018-921-v1+1_s41467-017-02159-y.pdf file_size: 2872887 relation: main_file file_date_updated: 2018-12-12T10:16:06Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25CD3DD2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '604102' name: Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6266' pubrep_id: '921' quality_controlled: '1' scopus_import: '1' status: public title: Multiplexed computations in retinal ganglion cells of a single type tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '1080' abstract: - lang: eng text: Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods. article_number: '14114' article_processing_charge: No author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Alvin full_name: Makohon Moore, Alvin last_name: Makohon Moore - first_name: Jeffrey full_name: Gerold, Jeffrey last_name: Gerold - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Christine full_name: Iacobuzio Donahue, Christine last_name: Iacobuzio Donahue - first_name: Bert full_name: Vogelstein, Bert last_name: Vogelstein - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 2017;8. doi:10.1038/ncomms14114 apa: Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14114 chicago: Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14114. ieee: J. Reiter et al., “Reconstructing metastatic seeding patterns of human cancers,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114. mla: Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications, vol. 8, 14114, Nature Publishing Group, 2017, doi:10.1038/ncomms14114. short: J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017). date_created: 2018-12-11T11:50:02Z date_published: 2017-01-31T00:00:00Z date_updated: 2023-09-20T11:55:31Z day: '31' ddc: - '004' - '006' department: - _id: KrCh doi: 10.1038/ncomms14114 ec_funded: 1 external_id: isi: - '000393096600001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:15:15Z date_updated: 2018-12-12T10:15:15Z file_id: '5133' file_name: IST-2017-786-v1+1_ncomms14114.pdf file_size: 897050 relation: main_file file_date_updated: 2018-12-12T10:15:15Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6301' pubrep_id: '786' quality_controlled: '1' scopus_import: '1' status: public title: Reconstructing metastatic seeding patterns of human cancers tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '1085' abstract: - lang: eng text: Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution. article_number: '14251' article_processing_charge: No author: - first_name: Alison full_name: Wright, Alison last_name: Wright - first_name: Iulia full_name: Darolti, Iulia last_name: Darolti - first_name: Natasha full_name: Bloch, Natasha last_name: Bloch - first_name: Vicencio full_name: Oostra, Vicencio last_name: Oostra - first_name: Benjamin full_name: Sandkam, Benjamin last_name: Sandkam - first_name: Séverine full_name: Buechel, Séverine last_name: Buechel - first_name: Niclas full_name: Kolm, Niclas last_name: Kolm - first_name: Felix full_name: Breden, Felix last_name: Breden - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Judith full_name: Mank, Judith last_name: Mank citation: ama: Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 2017;8. doi:10.1038/ncomms14251 apa: Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14251 chicago: Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14251. ieee: A. Wright et al., “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251. mla: Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications, vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251. short: A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017). date_created: 2018-12-11T11:50:04Z date_published: 2017-01-31T00:00:00Z date_updated: 2023-09-20T11:48:16Z day: '31' ddc: - '570' - '576' department: - _id: BeVi doi: 10.1038/ncomms14251 external_id: isi: - '000392953700001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:15:22Z date_updated: 2018-12-12T10:15:22Z file_id: '5141' file_name: IST-2017-791-v1+1_ncomms14251.pdf file_size: 955256 relation: main_file file_date_updated: 2018-12-12T10:15:22Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6292' pubrep_id: '791' quality_controlled: '1' scopus_import: '1' status: public title: Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '993' abstract: - lang: eng text: In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development. article_number: '15140' article_processing_charge: Yes (in subscription journal) author: - first_name: Anna full_name: Levina (Martius), Anna id: 35AF8020-F248-11E8-B48F-1D18A9856A87 last_name: Levina (Martius) - first_name: Viola full_name: Priesemann, Viola last_name: Priesemann citation: ama: Levina (Martius) A, Priesemann V. Subsampling scaling. Nature Communications. 2017;8. doi:10.1038/ncomms15140 apa: Levina (Martius), A., & Priesemann, V. (2017). Subsampling scaling. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15140 chicago: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140. ieee: A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140. mla: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi:10.1038/ncomms15140. short: A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017). date_created: 2018-12-11T11:49:35Z date_published: 2017-05-04T00:00:00Z date_updated: 2023-09-22T09:54:07Z day: '04' ddc: - '005' - '571' department: - _id: GaTk - _id: JoCs doi: 10.1038/ncomms15140 ec_funded: 1 external_id: isi: - '000400560700001' file: - access_level: open_access checksum: 9880212f8c4c53404c7c6fbf9023c53a content_type: application/pdf creator: system date_created: 2018-12-12T10:15:05Z date_updated: 2020-07-14T12:48:19Z file_id: '5122' file_name: IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf file_size: 746224 relation: main_file file_date_updated: 2020-07-14T12:48:19Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6406' pubrep_id: '819' quality_controlled: '1' scopus_import: '1' status: public title: Subsampling scaling tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '955' abstract: - lang: eng text: 'Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.' article_number: '216' article_processing_charge: Yes (in subscription journal) author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8 apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8 chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8. ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216. mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8. short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017). date_created: 2018-12-11T11:49:23Z date_published: 2017-08-09T00:00:00Z date_updated: 2023-09-22T10:00:49Z day: '09' ddc: - '539' - '576' department: - _id: GaTk - _id: NiBa doi: 10.1038/s41467-017-00238-8 ec_funded: 1 external_id: isi: - '000407198800005' file: - access_level: open_access checksum: 29a1b5db458048d3bd5c67e0e2a56818 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:14Z date_updated: 2020-07-14T12:48:16Z file_id: '5064' file_name: IST-2017-864-v1+1_s41467-017-00238-8.pdf file_size: 998157 relation: main_file - access_level: open_access checksum: 7b78401e52a576cf3e6bbf8d0abadc17 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:15Z date_updated: 2020-07-14T12:48:16Z file_id: '5065' file_name: IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf file_size: 9715993 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6459' pubrep_id: '864' quality_controlled: '1' related_material: record: - id: '6071' relation: dissertation_contains status: public scopus_import: '1' status: public title: Evolution of new regulatory functions on biophysically realistic fitness landscapes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '798' abstract: - lang: eng text: Nonreciprocal circuit elements form an integral part of modern measurement and communication systems. Mathematically they require breaking of time-reversal symmetry, typically achieved using magnetic materials and more recently using the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities. Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered electromechanic interactions. Directional circulation is achieved with controlled phase-sensitive interference of six distinct electro-mechanical signal conversion paths. The presented circulator is compact, its silicon-on-insulator platform is compatible with both superconducting qubits and silicon photonics, and its noise performance is close to the quantum limit. With a high dynamic range, a tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter or wavelength converter, it could pave the way for superconducting qubit processors with multiplexed on-chip signal processing and readout. article_number: '1304' article_processing_charge: Yes (in subscription journal) author: - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Mahmoud full_name: Kalaee, Mahmoud last_name: Kalaee - first_name: Paul full_name: Dieterle, Paul last_name: Dieterle - first_name: Oskar full_name: Painter, Oskar last_name: Painter - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01304-x apa: Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O., & Fink, J. M. (2017). Mechanical on chip microwave circulator. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01304-x chicago: Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01304-x. ieee: S. Barzanjeh et al., “Mechanical on chip microwave circulator,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM. 2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304. mla: Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” Nature Communications, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01304-x. short: S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M. Fink, Nature Communications 8 (2017). date_created: 2018-12-11T11:48:33Z date_published: 2017-10-16T00:00:00Z date_updated: 2023-09-27T12:11:28Z day: '16' ddc: - '539' department: - _id: JoFi doi: 10.1038/s41467-017-01304-x ec_funded: 1 external_id: isi: - '000412999700021' file: - access_level: open_access checksum: b68dafa71d1834c23b742cd9987a3d5f content_type: application/pdf creator: system date_created: 2018-12-12T10:15:25Z date_updated: 2020-07-14T12:48:06Z file_id: '5145' file_name: IST-2017-867-v1+1_s41467-017-01304-x.pdf file_size: 1467696 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 258047B6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '707438' name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics' publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6855' pubrep_id: '867' quality_controlled: '1' scopus_import: '1' status: public title: Mechanical on chip microwave circulator tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '835' abstract: - lang: eng text: An outstanding question in animal development, tissue homeostasis and disease is how cell populations adapt to sensory inputs. During Drosophila larval development, hematopoietic sites are in direct contact with sensory neuron clusters of the peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for their survival and recruitment to these microenvironments, known as Hematopoietic Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes. These hemocyte responses depend on PNS activity, as shown by agonist treatment and transient silencing of sensory neurons. Activin-β has a key role in this regulation, which is apparent from reporter expression and mutant analyses. This mechanism of local sensory neurons controlling blood cell adaptation invites evolutionary parallels with vertebrate hematopoietic progenitors and the independent myeloid system of tissue macrophages, whose regulation by local microenvironments remain undefined. article_number: '15990' article_processing_charge: No author: - first_name: Kalpana full_name: Makhijani, Kalpana last_name: Makhijani - first_name: Brandy full_name: Alexander, Brandy last_name: Alexander - first_name: Deepti full_name: Rao, Deepti last_name: Rao - first_name: Sophia full_name: Petraki, Sophia last_name: Petraki - first_name: Leire full_name: Herboso, Leire last_name: Herboso - first_name: Katelyn full_name: Kukar, Katelyn last_name: Kukar - first_name: Itrat full_name: Batool, Itrat last_name: Batool - first_name: Stephanie full_name: Wachner, Stephanie id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87 last_name: Wachner - first_name: Katrina full_name: Gold, Katrina last_name: Gold - first_name: Corinna full_name: Wong, Corinna last_name: Wong - first_name: Michael full_name: O'Connor, Michael last_name: O'Connor - first_name: Katja full_name: Brückner, Katja last_name: Brückner citation: ama: Makhijani K, Alexander B, Rao D, et al. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 2017;8. doi:10.1038/ncomms15990 apa: Makhijani, K., Alexander, B., Rao, D., Petraki, S., Herboso, L., Kukar, K., … Brückner, K. (2017). Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15990 chicago: Makhijani, Kalpana, Brandy Alexander, Deepti Rao, Sophia Petraki, Leire Herboso, Katelyn Kukar, Itrat Batool, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15990. ieee: K. Makhijani et al., “Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Makhijani K, Alexander B, Rao D, Petraki S, Herboso L, Kukar K, Batool I, Wachner S, Gold K, Wong C, O’Connor M, Brückner K. 2017. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 8, 15990. mla: Makhijani, Kalpana, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” Nature Communications, vol. 8, 15990, Nature Publishing Group, 2017, doi:10.1038/ncomms15990. short: K. Makhijani, B. Alexander, D. Rao, S. Petraki, L. Herboso, K. Kukar, I. Batool, S. Wachner, K. Gold, C. Wong, M. O’Connor, K. Brückner, Nature Communications 8 (2017). date_created: 2018-12-11T11:48:45Z date_published: 2017-07-27T00:00:00Z date_updated: 2023-09-26T15:51:28Z day: '27' ddc: - '570' - '576' - '616' doi: 10.1038/ncomms15990 extern: '1' external_id: isi: - '000406360100001' file: - access_level: open_access checksum: 99a3d63308d4250eda0a35341171f80e content_type: application/pdf creator: system date_created: 2018-12-12T10:15:32Z date_updated: 2020-07-14T12:48:12Z file_id: '5153' file_name: IST-2017-859-v1+1_ncomms15990.pdf file_size: 3027104 relation: main_file file_date_updated: 2020-07-14T12:48:12Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6813' pubrep_id: '859' quality_controlled: '1' status: public title: Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '800' abstract: - lang: eng text: Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers. article_number: '758' article_processing_charge: No author: - first_name: Michael full_name: Strüber, Michael last_name: Strüber - first_name: Jonas full_name: Sauer, Jonas last_name: Sauer - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Marlene full_name: Bartos, Marlene last_name: Bartos citation: ama: Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00936-3 apa: Strüber, M., Sauer, J., Jonas, P. M., & Bartos, M. (2017). Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00936-3 chicago: Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00936-3. ieee: M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 8(1), 758. mla: Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications, vol. 8, no. 1, 758, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00936-3. short: M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017). date_created: 2018-12-11T11:48:34Z date_published: 2017-10-02T00:00:00Z date_updated: 2023-09-27T10:59:41Z day: '02' ddc: - '571' department: - _id: PeJo doi: 10.1038/s41467-017-00936-3 ec_funded: 1 external_id: isi: - '000412053100004' file: - access_level: open_access checksum: 7e2c7621afd5f802338e92e8619f024d content_type: application/pdf creator: system date_created: 2018-12-12T10:15:17Z date_updated: 2020-07-14T12:48:07Z file_id: '5135' file_name: IST-2017-914-v1+1_s41467-017-00936-3.pdf file_size: 4261832 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6853' pubrep_id: '914' quality_controlled: '1' scopus_import: '1' status: public title: Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '746' abstract: - lang: eng text: Metabotropic glutamate receptor subtype 5 (mGluR5) is crucially implicated in the pathophysiology of Fragile X Syndrome (FXS); however, its dysfunction at the sub-cellular level, and related synaptic and cognitive phenotypes are unexplored. Here, we probed the consequences of mGluR5/Homer scaffold disruption for mGluR5 cell-surface mobility, synaptic N-methyl-D-Aspartate receptor (NMDAR) function, and behavioral phenotypes in the second-generation Fmr1 knockout (KO) mouse. Using single-molecule tracking, we found that mGluR5 was significantly more mobile at synapses in hippocampal Fmr1 KO neurons, causing an increased synaptic surface co-clustering of mGluR5 and NMDAR. This correlated with a reduced amplitude of synaptic NMDAR currents, a lack of their mGluR5-Activated long-Term depression, and NMDAR/hippocampus dependent cognitive deficits. These synaptic and behavioral phenomena were reversed by knocking down Homer1a in Fmr1 KO mice. Our study provides a mechanistic link between changes of mGluR5 dynamics and pathological phenotypes of FXS, unveiling novel targets for mGluR5-based therapeutics. article_number: '1103' article_processing_charge: No author: - first_name: Elisabetta full_name: Aloisi, Elisabetta last_name: Aloisi - first_name: Katy full_name: Le Corf, Katy last_name: Le Corf - first_name: Julien full_name: Dupuis, Julien last_name: Dupuis - first_name: Pei full_name: Zhang, Pei last_name: Zhang - first_name: Melanie full_name: Ginger, Melanie last_name: Ginger - first_name: Virginie full_name: Labrousse, Virginie last_name: Labrousse - first_name: Michela full_name: Spatuzza, Michela last_name: Spatuzza - first_name: Matthias full_name: Georg Haberl, Matthias last_name: Georg Haberl - first_name: Lara full_name: Costa, Lara last_name: Costa - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Anke full_name: Tappe Theodor, Anke last_name: Tappe Theodor - first_name: Fillippo full_name: Drago, Fillippo last_name: Drago - first_name: Pier full_name: Vincenzo Piazza, Pier last_name: Vincenzo Piazza - first_name: Christophe full_name: Mulle, Christophe last_name: Mulle - first_name: Laurent full_name: Groc, Laurent last_name: Groc - first_name: Lucia full_name: Ciranna, Lucia last_name: Ciranna - first_name: Maria full_name: Catania, Maria last_name: Catania - first_name: Andreas full_name: Frick, Andreas last_name: Frick citation: ama: Aloisi E, Le Corf K, Dupuis J, et al. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01191-2 apa: Aloisi, E., Le Corf, K., Dupuis, J., Zhang, P., Ginger, M., Labrousse, V., … Frick, A. (2017). Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01191-2 chicago: Aloisi, Elisabetta, Katy Le Corf, Julien Dupuis, Pei Zhang, Melanie Ginger, Virginie Labrousse, Michela Spatuzza, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01191-2. ieee: E. Aloisi et al., “Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Aloisi E, Le Corf K, Dupuis J, Zhang P, Ginger M, Labrousse V, Spatuzza M, Georg Haberl M, Costa L, Shigemoto R, Tappe Theodor A, Drago F, Vincenzo Piazza P, Mulle C, Groc L, Ciranna L, Catania M, Frick A. 2017. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 8(1), 1103. mla: Aloisi, Elisabetta, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” Nature Communications, vol. 8, no. 1, 1103, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01191-2. short: E. Aloisi, K. Le Corf, J. Dupuis, P. Zhang, M. Ginger, V. Labrousse, M. Spatuzza, M. Georg Haberl, L. Costa, R. Shigemoto, A. Tappe Theodor, F. Drago, P. Vincenzo Piazza, C. Mulle, L. Groc, L. Ciranna, M. Catania, A. Frick, Nature Communications 8 (2017). date_created: 2018-12-11T11:48:17Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-27T12:27:30Z day: '01' ddc: - '571' department: - _id: RySh doi: 10.1038/s41467-017-01191-2 external_id: isi: - '000413571300004' file: - access_level: open_access checksum: 99ceee57549dc0461e3adfc037ec70a9 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:32Z date_updated: 2020-07-14T12:47:58Z file_id: '5287' file_name: IST-2017-915-v1+1_s41467-017-01191-2.pdf file_size: 1841650 relation: main_file file_date_updated: 2020-07-14T12:47:58Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6921' pubrep_id: '915' quality_controlled: '1' scopus_import: '1' status: public title: Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '614' abstract: - lang: eng text: 'Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.' article_number: '1486' article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Marion A full_name: Picard, Marion A id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01663-5 apa: Fraisse, C., Picard, M. A. L., & Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01663-5 chicago: Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01663-5. ieee: C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486. mla: Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01663-5. short: C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017). date_created: 2018-12-11T11:47:30Z date_published: 2017-12-01T00:00:00Z date_updated: 2024-02-21T13:47:47Z day: '01' ddc: - '570' - '576' department: - _id: BeVi - _id: NiBa doi: 10.1038/s41467-017-01663-5 external_id: pmid: - '29133797' file: - access_level: open_access checksum: 4da2651303c8afc2f7fc419be42a2433 content_type: application/pdf creator: dernst date_created: 2020-03-03T15:55:50Z date_updated: 2020-07-14T12:47:20Z file_id: '7562' file_name: 2017_NatureComm_Fraisse.pdf file_size: 1201520 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7190' pubrep_id: '910' quality_controlled: '1' related_material: record: - id: '7163' relation: popular_science status: public scopus_import: 1 status: public title: The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ...