[{"date_created":"2021-08-17T08:58:47Z","year":"2018","month":"07","title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","date_updated":"2024-10-21T06:02:42Z","status":"public","main_file_link":[{"url":"https://doi.org/10.5061/dryad.bp25b65","open_access":"1"}],"citation":{"chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>.","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. Dryad. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>","ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow, Dryad, <a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>.","ieee":"A. M. Westram <i>et al.</i>, “Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.","ama":"Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>","mla":"Westram, Anja M., et al. <i>Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>.","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018)."},"article_processing_charge":"No","publisher":"Dryad","related_material":{"record":[{"id":"9917","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","_id":"9930","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2018-07-23T00:00:00Z","oa":1,"author":[{"full_name":"Westram, Anja M","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"first_name":"Anders","full_name":"Blomberg, Anders","last_name":"Blomberg"},{"last_name":"Mehlig","first_name":"Bernhard","full_name":"Mehlig, Bernhard"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"abstract":[{"lang":"eng","text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems."}],"day":"23","doi":"10.5061/dryad.bp25b65","type":"research_data_reference","department":[{"_id":"BeVi"}]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1503.02716"}],"date_updated":"2026-06-25T07:36:26Z","status":"public","month":"04","volume":288,"publication_status":"published","OA_type":"green","_id":"22042","oa_version":"Preprint","page":"1273-1298","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication":"Mathematische Zeitschrift","language":[{"iso":"eng"}],"mathsc":["35P25","35Q55"],"OA_place":"repository","type":"journal_article","scopus_import":"1","title":"Sobolev spaces adapted to the Schrödinger operator with inverse-square potential","publication_identifier":{"issn":["0025-5874"],"eissn":["1432-1823"]},"external_id":{"arxiv":["1503.02716"]},"intvolume":"       288","year":"2018","date_created":"2026-06-19T07:46:14Z","article_processing_charge":"No","publisher":"Springer Nature","citation":{"short":"R. Killip, C. Miao, M. Vişan, J. Zhang, J. Zheng, Mathematische Zeitschrift 288 (2018) 1273–1298.","ama":"Killip R, Miao C, Vişan M, Zhang J, Zheng J. Sobolev spaces adapted to the Schrödinger operator with inverse-square potential. <i>Mathematische Zeitschrift</i>. 2018;288(3-4):1273-1298. doi:<a href=\"https://doi.org/10.1007/s00209-017-1934-8\">10.1007/s00209-017-1934-8</a>","mla":"Killip, R., et al. “Sobolev Spaces Adapted to the Schrödinger Operator with Inverse-Square Potential.” <i>Mathematische Zeitschrift</i>, vol. 288, no. 3–4, Springer Nature, 2018, pp. 1273–98, doi:<a href=\"https://doi.org/10.1007/s00209-017-1934-8\">10.1007/s00209-017-1934-8</a>.","ieee":"R. Killip, C. Miao, M. Vişan, J. Zhang, and J. Zheng, “Sobolev spaces adapted to the Schrödinger operator with inverse-square potential,” <i>Mathematische Zeitschrift</i>, vol. 288, no. 3–4. Springer Nature, pp. 1273–1298, 2018.","ista":"Killip R, Miao C, Vişan M, Zhang J, Zheng J. 2018. Sobolev spaces adapted to the Schrödinger operator with inverse-square potential. Mathematische Zeitschrift. 288(3–4), 1273–1298.","chicago":"Killip, R., C. Miao, Monica Vişan, J. Zhang, and J. Zheng. “Sobolev Spaces Adapted to the Schrödinger Operator with Inverse-Square Potential.” <i>Mathematische Zeitschrift</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s00209-017-1934-8\">https://doi.org/10.1007/s00209-017-1934-8</a>.","apa":"Killip, R., Miao, C., Vişan, M., Zhang, J., &#38; Zheng, J. (2018). Sobolev spaces adapted to the Schrödinger operator with inverse-square potential. <i>Mathematische Zeitschrift</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00209-017-1934-8\">https://doi.org/10.1007/s00209-017-1934-8</a>"},"extern":"1","day":"01","abstract":[{"text":"We study the L p-theory for the Schrödinger operatorLa with inverse-square potential\r\na|x|^−2. Our main result describes when L p-based Sobolev spaces defined in terms of the\r\noperator (La)^s/2 agree with those defined via (−\u0002)^s/2.We consider all regularities 0 < s < 2.\r\nIn order to make the paper self-contained, we also review (with proofs) multiplier theorems,\r\nLittlewood–Paley theory, and Hardy-type inequalities associated to the operator La.","lang":"eng"}],"oa":1,"arxiv":1,"author":[{"full_name":"Killip, R.","first_name":"R.","last_name":"Killip"},{"last_name":"Miao","full_name":"Miao, C.","first_name":"C."},{"full_name":"Visan, Monica","first_name":"Monica","last_name":"Visan","id":"056daca0-b8d1-11f0-964f-f91054abf8ca"},{"first_name":"J.","full_name":"Zhang, J.","last_name":"Zhang"},{"first_name":"J.","full_name":"Zheng, J.","last_name":"Zheng"}],"date_published":"2018-04-01T00:00:00Z","issue":"3-4","article_type":"original","doi":"10.1007/s00209-017-1934-8"},{"type":"journal_article","OA_place":"repository","scopus_import":"1","publication":"SIAM Journal on Mathematical Analysis","keyword":["cubic-quintic NLS","nonvanishing boundary conditions","space-time resonances","scattering"],"language":[{"iso":"eng"}],"mathsc":["35Q55"],"_id":"22045","page":"2681-2739","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1702.04413"}],"date_updated":"2026-06-25T07:49:21Z","status":"public","publication_status":"published","volume":50,"month":"01","OA_type":"green","issue":"3","article_type":"original","doi":"10.1137/17m1116702","day":"01","abstract":[{"text":"We consider the initial-value problem for the cubic-quintic nonlinear Schrödinger equation (𝑖𝜕𝑡+Δ)⁢𝜓 =𝛼1⁢𝜓 −𝛼3⁢|𝜓|2⁢𝜓 +𝛼5⁢|𝜓|4⁢𝜓 in three spatial dimensions in the class of solutions with |𝜓⁡(𝑥)| →𝑐 >0 as |𝑥| →∞. Here 𝛼1, 𝛼3, 𝛼5, and 𝑐 are such that 𝜓⁡(𝑥) ≡𝑐 is an energetically stable equilibrium solution to this equation. Normalizing the boundary condition to 𝜓⁡(𝑥) →1 as |𝑥| →∞, we study the associated initial-value problem for 𝑢 =𝜓 −1 and prove a scattering result for small initial data in a weighted Sobolev space.","lang":"eng"}],"author":[{"full_name":"Killip, Rowan","first_name":"Rowan","last_name":"Killip"},{"first_name":"Jason","full_name":"Murphy, Jason","last_name":"Murphy"},{"last_name":"Visan","id":"056daca0-b8d1-11f0-964f-f91054abf8ca","first_name":"Monica","full_name":"Visan, Monica"}],"arxiv":1,"oa":1,"date_published":"2018-01-01T00:00:00Z","article_processing_charge":"No","publisher":"Society for Industrial & Applied Mathematics","extern":"1","citation":{"ieee":"R. Killip, J. Murphy, and M. Vişan, “The initial-value problem for the cubic-quintic NLS with nonvanishing boundary conditions,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 50, no. 3. Society for Industrial &#38; Applied Mathematics, pp. 2681–2739, 2018.","ista":"Killip R, Murphy J, Vişan M. 2018. The initial-value problem for the cubic-quintic NLS with nonvanishing boundary conditions. SIAM Journal on Mathematical Analysis. 50(3), 2681–2739.","apa":"Killip, R., Murphy, J., &#38; Vişan, M. (2018). The initial-value problem for the cubic-quintic NLS with nonvanishing boundary conditions. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/17m1116702\">https://doi.org/10.1137/17m1116702</a>","chicago":"Killip, Rowan, Jason Murphy, and Monica Vişan. “The Initial-Value Problem for the Cubic-Quintic NLS with Nonvanishing Boundary Conditions.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial &#38; Applied Mathematics, 2018. <a href=\"https://doi.org/10.1137/17m1116702\">https://doi.org/10.1137/17m1116702</a>.","short":"R. Killip, J. Murphy, M. Vişan, SIAM Journal on Mathematical Analysis 50 (2018) 2681–2739.","mla":"Killip, Rowan, et al. “The Initial-Value Problem for the Cubic-Quintic NLS with Nonvanishing Boundary Conditions.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 50, no. 3, Society for Industrial &#38; Applied Mathematics, 2018, pp. 2681–739, doi:<a href=\"https://doi.org/10.1137/17m1116702\">10.1137/17m1116702</a>.","ama":"Killip R, Murphy J, Vişan M. The initial-value problem for the cubic-quintic NLS with nonvanishing boundary conditions. <i>SIAM Journal on Mathematical Analysis</i>. 2018;50(3):2681-2739. doi:<a href=\"https://doi.org/10.1137/17m1116702\">10.1137/17m1116702</a>"},"das_tickbox":"1","title":"The initial-value problem for the cubic-quintic NLS with nonvanishing boundary conditions","external_id":{"arxiv":["1702.04413"]},"publication_identifier":{"issn":["0036-1410","1095-7154"]},"date_created":"2026-06-19T07:49:03Z","year":"2018","intvolume":"        50"},{"language":[{"iso":"eng"}],"publication":"Geometric and Functional Analysis","scopus_import":"1","type":"journal_article","OA_place":"repository","OA_type":"green","volume":28,"publication_status":"published","month":"07","date_updated":"2026-06-29T09:55:53Z","status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1708.05362","open_access":"1"}],"quality_controlled":"1","_id":"22055","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1062-1090","date_published":"2018-07-01T00:00:00Z","oa":1,"author":[{"last_name":"Killip","full_name":"Killip, Rowan","first_name":"Rowan"},{"first_name":"Monica","full_name":"Visan, Monica","id":"056daca0-b8d1-11f0-964f-f91054abf8ca","last_name":"Visan"},{"last_name":"Zhang","full_name":"Zhang, Xiaoyi","first_name":"Xiaoyi"}],"arxiv":1,"abstract":[{"lang":"eng","text":"We present a general method for obtaining conservation laws for integrable PDE at negative regularity and exhibit its application to KdV, NLS, and mKdV. Our method works uniformly for these problems posed both on the line and on the circle."}],"day":"01","doi":"10.1007/s00039-018-0444-0","article_type":"original","issue":"4","intvolume":"        28","date_created":"2026-06-19T07:56:48Z","year":"2018","publication_identifier":{"eissn":["1420-8970"],"issn":["1016-443X"]},"external_id":{"arxiv":["1708.05362"]},"title":"Low regularity conservation laws for integrable PDE","das_tickbox":"1","extern":"1","citation":{"ama":"Killip R, Vişan M, Zhang X. Low regularity conservation laws for integrable PDE. <i>Geometric and Functional Analysis</i>. 2018;28(4):1062-1090. doi:<a href=\"https://doi.org/10.1007/s00039-018-0444-0\">10.1007/s00039-018-0444-0</a>","mla":"Killip, Rowan, et al. “Low Regularity Conservation Laws for Integrable PDE.” <i>Geometric and Functional Analysis</i>, vol. 28, no. 4, Springer Nature, 2018, pp. 1062–90, doi:<a href=\"https://doi.org/10.1007/s00039-018-0444-0\">10.1007/s00039-018-0444-0</a>.","short":"R. Killip, M. Vişan, X. Zhang, Geometric and Functional Analysis 28 (2018) 1062–1090.","apa":"Killip, R., Vişan, M., &#38; Zhang, X. (2018). Low regularity conservation laws for integrable PDE. <i>Geometric and Functional Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00039-018-0444-0\">https://doi.org/10.1007/s00039-018-0444-0</a>","chicago":"Killip, Rowan, Monica Vişan, and Xiaoyi Zhang. “Low Regularity Conservation Laws for Integrable PDE.” <i>Geometric and Functional Analysis</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s00039-018-0444-0\">https://doi.org/10.1007/s00039-018-0444-0</a>.","ista":"Killip R, Vişan M, Zhang X. 2018. Low regularity conservation laws for integrable PDE. Geometric and Functional Analysis. 28(4), 1062–1090.","ieee":"R. Killip, M. Vişan, and X. Zhang, “Low regularity conservation laws for integrable PDE,” <i>Geometric and Functional Analysis</i>, vol. 28, no. 4. Springer Nature, pp. 1062–1090, 2018."},"article_processing_charge":"No","publisher":"Springer Nature"},{"type":"journal_article","publication":"Oberwolfach Reports","language":[{"iso":"eng"}],"page":"1681-1745","_id":"22093","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","status":"public","date_updated":"2026-07-02T05:51:37Z","main_file_link":[{"url":"https://doi.org/10.4171/OWR/2017/27","open_access":"1"}],"OA_type":"free access","publication_status":"published","month":"04","volume":14,"issue":"2","doi":"10.4171/owr/2017/27","abstract":[{"lang":"eng","text":"Nonlinear dispersive equations are models for nonlinear waves in a wide range of physical contexts. Mathematically they display an interplay between linear dispersion and nonlinear interactions, which can result in a wide range of outcomes from finite time blow-up to solitons and scattering. They are linked to many areas of mathematics and physics, ranging from integrable systems and harmonic analysis to fluid dynamics, geometry, general relativity and probability."}],"day":"28","date_published":"2018-04-28T00:00:00Z","oa":1,"author":[{"full_name":"Koch, Herbert","first_name":"Herbert","last_name":"Koch"},{"last_name":"Raphaël","full_name":"Raphaël, Pierre","first_name":"Pierre"},{"full_name":"Tataru, Daniel","first_name":"Daniel","last_name":"Tataru"},{"full_name":"Visan, Monica","first_name":"Monica","id":"056daca0-b8d1-11f0-964f-f91054abf8ca","last_name":"Visan"}],"citation":{"mla":"Koch, Herbert, et al. “Nonlinear Waves and Dispersive Equations.” <i>Oberwolfach Reports</i>, vol. 14, no. 2, EMS Press, 2018, pp. 1681–745, doi:<a href=\"https://doi.org/10.4171/owr/2017/27\">10.4171/owr/2017/27</a>.","ama":"Koch H, Raphaël P, Tataru D, Vişan M. Nonlinear waves and dispersive equations. <i>Oberwolfach Reports</i>. 2018;14(2):1681-1745. doi:<a href=\"https://doi.org/10.4171/owr/2017/27\">10.4171/owr/2017/27</a>","short":"H. Koch, P. Raphaël, D. Tataru, M. Vişan, Oberwolfach Reports 14 (2018) 1681–1745.","apa":"Koch, H., Raphaël, P., Tataru, D., &#38; Vişan, M. (2018). Nonlinear waves and dispersive equations. <i>Oberwolfach Reports</i>. EMS Press. <a href=\"https://doi.org/10.4171/owr/2017/27\">https://doi.org/10.4171/owr/2017/27</a>","chicago":"Koch, Herbert, Pierre Raphaël, Daniel Tataru, and Monica Vişan. “Nonlinear Waves and Dispersive Equations.” <i>Oberwolfach Reports</i>. EMS Press, 2018. <a href=\"https://doi.org/10.4171/owr/2017/27\">https://doi.org/10.4171/owr/2017/27</a>.","ieee":"H. Koch, P. Raphaël, D. Tataru, and M. Vişan, “Nonlinear waves and dispersive equations,” <i>Oberwolfach Reports</i>, vol. 14, no. 2. EMS Press, pp. 1681–1745, 2018.","ista":"Koch H, Raphaël P, Tataru D, Vişan M. 2018. Nonlinear waves and dispersive equations. Oberwolfach Reports. 14(2), 1681–1745."},"extern":"1","publisher":"EMS Press","article_processing_charge":"No","title":"Nonlinear waves and dispersive equations","das_tickbox":"1","intvolume":"        14","date_created":"2026-06-19T08:55:08Z","year":"2018","publication_identifier":{"eissn":["1660-8941"],"issn":["1660-8933"]}},{"article_processing_charge":"No","publisher":"Nature Publishing Group","file":[{"date_created":"2019-04-09T07:41:57Z","file_size":8167169,"date_updated":"2020-07-14T12:45:58Z","creator":"dernst","file_name":"2017_NatureNeuroscience_Deliu.pdf","content_type":"application/pdf","relation":"main_file","checksum":"60abd0f05b7cdc08a6b0ec460884084f","access_level":"open_access","file_id":"6255"}],"citation":{"short":"E. Deliu, N. Arecco, J. Morandell, C. Dotter, X. Contreras, C. Girardot, E. Käsper, A. Kozlova, K. Kishi, I. Chiaradia, K. Noh, G. Novarino, Nature Neuroscience 21 (2018) 1717–1727.","ama":"Deliu E, Arecco N, Morandell J, et al. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. <i>Nature Neuroscience</i>. 2018;21(12):1717-1727. doi:<a href=\"https://doi.org/10.1038/s41593-018-0266-2\">10.1038/s41593-018-0266-2</a>","mla":"Deliu, Elena, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” <i>Nature Neuroscience</i>, vol. 21, no. 12, Nature Publishing Group, 2018, pp. 1717–27, doi:<a href=\"https://doi.org/10.1038/s41593-018-0266-2\">10.1038/s41593-018-0266-2</a>.","ieee":"E. Deliu <i>et al.</i>, “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition,” <i>Nature Neuroscience</i>, vol. 21, no. 12. Nature Publishing Group, pp. 1717–1727, 2018.","ista":"Deliu E, Arecco N, Morandell J, Dotter C, Contreras X, Girardot C, Käsper E, Kozlova A, Kishi K, Chiaradia I, Noh K, Novarino G. 2018. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 21(12), 1717–1727.","chicago":"Deliu, Elena, Niccoló Arecco, Jasmin Morandell, Christoph Dotter, Ximena Contreras, Charles Girardot, Eva Käsper, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41593-018-0266-2\">https://doi.org/10.1038/s41593-018-0266-2</a>.","apa":"Deliu, E., Arecco, N., Morandell, J., Dotter, C., Contreras, X., Girardot, C., … Novarino, G. (2018). Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41593-018-0266-2\">https://doi.org/10.1038/s41593-018-0266-2</a>"},"ddc":["570"],"file_date_updated":"2020-07-14T12:45:58Z","external_id":{"isi":["000451324700010"]},"year":"2018","date_created":"2018-12-11T11:44:05Z","intvolume":"        21","has_accepted_license":"1","title":"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition","doi":"10.1038/s41593-018-0266-2","acknowledgement":"This work was supported by the Simons Foundation Autism Research Initiative (grant 401299) to G.N. and the DFG (SPP1738 grant NO 1249) to K.-M.N.","issue":"12","article_type":"original","author":[{"first_name":"Elena","full_name":"Deliu, Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","last_name":"Deliu"},{"last_name":"Arecco","full_name":"Arecco, Niccoló","first_name":"Niccoló"},{"first_name":"Jasmin","full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell"},{"full_name":"Dotter, Christoph","first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter"},{"last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena"},{"first_name":"Charles","full_name":"Girardot, Charles","last_name":"Girardot"},{"full_name":"Käsper, Eva","first_name":"Eva","last_name":"Käsper"},{"full_name":"Kozlova, Alena","first_name":"Alena","last_name":"Kozlova","id":"C50A9596-02D0-11E9-976E-E38CFE5CBC1D"},{"full_name":"Kishi, Kasumi","first_name":"Kasumi","orcid":"0000-0001-6060-4795","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi"},{"id":"B6467F20-02D0-11E9-BDA5-E960C241894A","last_name":"Chiaradia","first_name":"Ilaria","full_name":"Chiaradia, Ilaria","orcid":"0000-0002-9529-4464"},{"last_name":"Noh","first_name":"Kyung","full_name":"Noh, Kyung"},{"first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"}],"oa":1,"date_published":"2018-11-19T00:00:00Z","day":"19","abstract":[{"lang":"eng","text":"SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder."}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"6074"},{"id":"12364","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/","relation":"press_release","description":"News on IST Homepage"}]},"quality_controlled":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"3","page":"1717 - 1727","oa_version":"Submitted Version","isi":1,"month":"11","publication_status":"published","volume":21,"publist_id":"8054","date_updated":"2026-07-03T22:30:25Z","status":"public","scopus_import":"1","corr_author":"1","department":[{"_id":"GaNo"},{"_id":"EdHa"}],"type":"journal_article","language":[{"iso":"eng"}],"pubrep_id":"1071","project":[{"_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299"}],"publication":"Nature Neuroscience"},{"file_date_updated":"2021-02-11T11:17:14Z","ddc":["576","579"],"citation":{"apa":"Steinrück, M. (2018). <i>The influence of sequence context on the evolution of bacterial gene expression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>.","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","mla":"Steinrück, Magdalena. <i>The Influence of Sequence Context on the Evolution of Bacterial Gene Expression</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>.","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018."},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file":[{"file_size":9190845,"date_updated":"2020-07-14T12:45:43Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Steinrueck_final.docx","creator":"dernst","date_created":"2019-02-08T10:51:22Z","embargo_to":"open_access","file_id":"5941","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","access_level":"closed","relation":"source_file"},{"date_created":"2019-02-08T10:51:22Z","content_type":"application/pdf","file_name":"Thesis_Steinrueck_final.pdf","creator":"dernst","date_updated":"2021-02-11T11:17:14Z","file_size":7521973,"embargo":"2019-11-02","access_level":"open_access","checksum":"3def8b7854c8b42d643597ce0215efac","relation":"main_file","file_id":"5942"}],"title":"The influence of sequence context on the evolution of bacterial gene expression","has_accepted_license":"1","year":"2018","date_created":"2018-12-11T11:44:14Z","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th1059","abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"day":"30","date_published":"2018-10-30T00:00:00Z","author":[{"last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719","full_name":"Steinrück, Magdalena","first_name":"Magdalena"}],"oa":1,"_id":"26","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"109","oa_version":"Published Version","related_material":{"record":[{"id":"704","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2026-04-08T14:15:35Z","status":"public","publist_id":"8029","degree_awarded":"PhD","month":"10","publication_status":"published","OA_place":"publisher","type":"dissertation","department":[{"_id":"CaGu"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"pubrep_id":"1059","language":[{"iso":"eng"}]},{"isi":1,"publication_status":"published","volume":208,"month":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-07-03T22:31:28Z","publist_id":"7274","status":"public","related_material":{"record":[{"relation":"popular_science","id":"5571","status":"public"},{"id":"5572","status":"public","relation":"popular_science"},{"id":"17119","status":"public","relation":"dissertation_contains"}]},"quality_controlled":"1","_id":"542","oa_version":"Published Version","page":"365 - 375","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"pubrep_id":"1058","project":[{"grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"publication":"Genetics","scopus_import":"1","corr_author":"1","ec_funded":1,"department":[{"_id":"BeVi"}],"type":"journal_article","external_id":{"isi":["000419356300024"]},"date_created":"2018-12-11T11:47:04Z","year":"2018","intvolume":"       208","has_accepted_license":"1","title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","publisher":"Genetics Society of America","file":[{"file_id":"5132","checksum":"2123845e7031a0cf043905be160f9e69","access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"system","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","date_updated":"2020-07-14T12:46:50Z","file_size":1311661,"date_created":"2018-12-12T10:15:14Z"}],"article_processing_charge":"No","citation":{"ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” <i>Genetics</i>, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","apa":"Kelemen, R. K., &#38; Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>","chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>.","short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>.","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. 2018;208(1):365-375. doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>"},"ddc":["576"],"file_date_updated":"2020-07-14T12:46:50Z","author":[{"last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","first_name":"Réka K","full_name":"Kelemen, Réka K"},{"first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"oa":1,"date_published":"2018-01-01T00:00:00Z","day":"01","abstract":[{"lang":"eng","text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter."}],"doi":"10.1534/genetics.117.300513","issue":"1","article_type":"original"},{"degree_awarded":"PhD","publication_status":"published","month":"06","publist_id":"8003","status":"public","date_updated":"2026-04-08T14:13:44Z","related_material":{"record":[{"id":"682","status":"public","relation":"part_of_dissertation"}]},"_id":"51","page":"186","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","pubrep_id":"1032","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","supervisor":[{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"}],"OA_place":"publisher","type":"dissertation","department":[{"_id":"RySh"}],"year":"2018","date_created":"2018-12-11T11:44:22Z","publication_identifier":{"issn":["2663-337X"]},"title":"From the left to the right: A tale of asymmetries, environments, and hippocampal development","has_accepted_license":"1","citation":{"ama":"Case MJ. From the left to the right: A tale of asymmetries, environments, and hippocampal development. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1032\">10.15479/AT:ISTA:th_1032</a>","mla":"Case, Matthew J. <i>From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1032\">10.15479/AT:ISTA:th_1032</a>.","short":"M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development, Institute of Science and Technology Austria, 2018.","apa":"Case, M. J. (2018). <i>From the left to the right: A tale of asymmetries, environments, and hippocampal development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1032\">https://doi.org/10.15479/AT:ISTA:th_1032</a>","chicago":"Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1032\">https://doi.org/10.15479/AT:ISTA:th_1032</a>.","ista":"Case MJ. 2018. From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria.","ieee":"M. J. Case, “From the left to the right: A tale of asymmetries, environments, and hippocampal development,” Institute of Science and Technology Austria, 2018."},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file":[{"embargo_to":"open_access","date_created":"2019-04-09T07:16:26Z","content_type":"application/msword","creator":"dernst","file_name":"2018_Thesis_Case_Source.doc","file_size":141270528,"date_updated":"2021-02-11T23:30:13Z","access_level":"closed","checksum":"dcc7b55619d8509dd62b8e99d6cdee44","relation":"source_file","file_id":"6251"},{"relation":"main_file","access_level":"open_access","checksum":"f69fdd5c8709c4e618aa8c1a1221153d","file_id":"6252","date_created":"2019-04-09T07:16:23Z","file_name":"2018_Thesis_Case.pdf","creator":"dernst","content_type":"application/pdf","embargo":"2019-07-05","date_updated":"2021-02-11T11:17:14Z","file_size":15193621}],"file_date_updated":"2021-02-11T23:30:13Z","ddc":["571","576"],"date_published":"2018-06-27T00:00:00Z","author":[{"full_name":"Case, Matthew J","first_name":"Matthew J","last_name":"Case","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"abstract":[{"text":"Asymmetries have long been known about in the central nervous system. From gross anatomical differences, such as the presence of the parapineal organ in only one hemisphere of the developing zebrafish, to more subtle differences in activity between both hemispheres, as seen in freely roaming animals or human participants under PET and fMRI imaging analysis. The presence of asymmetries has been demonstrated to have huge behavioural implications, with their disruption often leading to the generation of neurological disorders, memory problems, changes in personality, and in an organism's health and well-being. For my Ph.D. work I aimed to tackle two important avenues of research. The first being the process of input-side dependency in the hippocampus, with the goal of finding a key gene responsible for its development (Gene X). The second project was to do with experience-induced laterality formation in the hippocampus. Specifically, how laterality in the synapse density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental enrichment. Through unilateral tracer injections into the CA3, I was able to selectively measure the properties of synapses within the CA1 and investigate how they differed based upon which hemisphere the presynaptic neurone originated. Having found the existence of a previously unreported reversed (left-isomerism) i.v. mutant, through morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate a key gene responsible for the process of left or right determination of inputs to the CA1 s.r.. This work relates to the previous finding of input-side dependent asymmetry in the wild-type rodent, where the origin of the projecting neurone to the CA1 will determine the morphology of a synapse, to a greater degree than the hemisphere in which the projection terminates. Using left- and right-isomerism i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like (Evl) as a potential target for Gene X. In relation to this topic, I also highlight my work in the recently published paper of how knockout of PirB can lead to a lack of input-side dependency in the murine hippocampus. For the second question, I show that the environmental enrichment paradigm will lead to an asymmetry in the synapse densities in the hippocampus of mice. I also highlight that the nature of the enrichment is of less consequence than the process of enrichment itself. I demonstrate that the CA3 region will dramatically alter its projection targets, in relation to environmental stimulation, with the asymmetry in synaptic density, caused by enrichment, relying heavily on commissural fibres. I also highlight the vital importance of input-side dependent asymmetry, as a necessary component of experience-dependent laterality formation in the CA1 s.r.. However, my results suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism also at play. Upon further investigation, I highlight the significant, and highly important, finding that the changes seen in the CA1 s.r. were predominantly caused through projections from the left-CA3, with the right-CA3 having less involvement in this mechanism.","lang":"eng"}],"day":"27","doi":"10.15479/AT:ISTA:th_1032"},{"doi":"10.15479/AT:ISTA:th_1042","day":"27","abstract":[{"text":"The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. ","lang":"eng"}],"author":[{"first_name":"Igor","full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn"}],"oa":1,"date_published":"2018-08-27T00:00:00Z","file_date_updated":"2021-02-11T23:30:22Z","ddc":["573"],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file":[{"date_created":"2019-04-08T13:36:01Z","embargo_to":"open_access","file_size":7666687,"date_updated":"2021-02-11T23:30:22Z","creator":"dernst","file_name":"2018_Thesis_Gridchyn_source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"7db4415e435590fa33542c7b0a0321d7","access_level":"closed","file_id":"6236"},{"file_id":"6237","access_level":"open_access","checksum":"f96f3fe8979f7b1e6db6acaca962b10c","relation":"main_file","content_type":"application/pdf","file_name":"2018_Thesis_Gridchyn.pdf","creator":"dernst","file_size":6034153,"date_updated":"2021-02-11T11:17:18Z","embargo":"2019-08-29","date_created":"2019-04-08T13:36:01Z"}],"citation":{"short":"I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018.","mla":"Gridchyn, Igor. <i>Reactivation Content Is Important for Consolidation of Spatial Memory</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">10.15479/AT:ISTA:th_1042</a>.","ama":"Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">10.15479/AT:ISTA:th_1042</a>","ista":"Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria.","ieee":"I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018.","apa":"Gridchyn, I. (2018). <i>Reactivation content is important for consolidation of spatial memory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">https://doi.org/10.15479/AT:ISTA:th_1042</a>","chicago":"Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">https://doi.org/10.15479/AT:ISTA:th_1042</a>."},"has_accepted_license":"1","title":"Reactivation content is important for consolidation of spatial memory","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:44:21Z","year":"2018","department":[{"_id":"JoCs"}],"OA_place":"publisher","type":"dissertation","corr_author":"1","supervisor":[{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"pubrep_id":"1042","page":"104","_id":"48","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","publist_id":"8006","date_updated":"2026-04-08T14:13:15Z","month":"08","publication_status":"published","degree_awarded":"PhD"},{"publication_status":"published","month":"04","volume":30,"isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-07-03T22:32:14Z","publist_id":"7417","status":"public","related_material":{"record":[{"relation":"dissertation_contains","id":"6269","status":"public"}]},"quality_controlled":"1","_id":"412","oa_version":"Published Version","page":"700 - 716","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"project":[{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"publication":"The Plant Cell","scopus_import":"1","corr_author":"1","ec_funded":1,"department":[{"_id":"JiFr"}],"type":"journal_article","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"external_id":{"pmid":["29511054"],"isi":["000429441400018"]},"intvolume":"        30","date_created":"2018-12-11T11:46:20Z","year":"2018","has_accepted_license":"1","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","pmid":1,"article_processing_charge":"No","publisher":"American Society of Plant Biologists","file":[{"relation":"main_file","access_level":"open_access","checksum":"4e165e653b67d3f0684697f21aace5a1","file_id":"11406","date_created":"2022-05-23T09:12:38Z","date_updated":"2022-05-23T09:12:38Z","file_size":4407538,"file_name":"2018_PlantCell_Adamowski.pdf","success":1,"creator":"dernst","content_type":"application/pdf"}],"citation":{"mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” <i>The Plant Cell</i>, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:<a href=\"https://doi.org/10.1105/tpc.17.00785\">10.1105/tpc.17.00785</a>.","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. <i>The Plant Cell</i>. 2018;30(3):700-716. doi:<a href=\"https://doi.org/10.1105/tpc.17.00785\">10.1105/tpc.17.00785</a>","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2018. <a href=\"https://doi.org/10.1105/tpc.17.00785\">https://doi.org/10.1105/tpc.17.00785</a>.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., &#38; Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.17.00785\">https://doi.org/10.1105/tpc.17.00785</a>","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” <i>The Plant Cell</i>, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018."},"file_date_updated":"2022-05-23T09:12:38Z","ddc":["580"],"oa":1,"author":[{"last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","full_name":"Adamowski, Maciek"},{"last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","last_name":"Kania","first_name":"Urszula","full_name":"Kania, Urszula"},{"first_name":"Matous","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc"},{"first_name":"Geert","full_name":"De Jaeger, Geert","last_name":"De Jaeger"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2018-04-09T00:00:00Z","day":"09","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana."}],"doi":"10.1105/tpc.17.00785","issue":"3","acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","article_type":"original"},{"doi":"10.15479/AT:ISTA:th_930","date_published":"2018-01-01T00:00:00Z","author":[{"last_name":"Hurny","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3638-1426","first_name":"Andrej","full_name":"Hurny, Andrej"}],"oa":1,"abstract":[{"lang":"eng","text":"The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth."}],"day":"01","citation":{"ieee":"A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018.","ista":"Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria.","apa":"Hurny, A. (2018). <i>Identification and characterization of novel auxin-cytokinin cross-talk components</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">https://doi.org/10.15479/AT:ISTA:th_930</a>","chicago":"Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">https://doi.org/10.15479/AT:ISTA:th_930</a>.","short":"A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018.","mla":"Hurny, Andrej. <i>Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">10.15479/AT:ISTA:th_930</a>.","ama":"Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">10.15479/AT:ISTA:th_930</a>"},"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","file":[{"creator":"dernst","file_name":"2018_Hurny_thesis_source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":28112114,"date_updated":"2020-12-02T23:30:08Z","embargo_to":"open_access","date_created":"2019-04-05T09:37:56Z","file_id":"6226","relation":"source_file","access_level":"closed","checksum":"0c9d6d1c80d9857e6e545213467bbcb2"},{"date_created":"2019-04-05T09:37:55Z","embargo":"2019-07-10","file_size":12524427,"date_updated":"2020-12-02T09:52:16Z","file_name":"2018_Hurny_thesis.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","checksum":"ecbe481a1413d270bd501b872c7ed54f","access_level":"open_access","file_id":"6227"}],"ddc":["570"],"file_date_updated":"2020-12-02T23:30:08Z","date_created":"2018-12-11T11:47:03Z","year":"2018","publication_identifier":{"issn":["2663-337X"]},"title":"Identification and characterization of novel auxin-cytokinin cross-talk components","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"corr_author":"1","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"OA_place":"publisher","type":"dissertation","department":[{"_id":"EvBe"}],"pubrep_id":"930","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1024"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"539","page":"147","oa_version":"Published Version","degree_awarded":"PhD","month":"01","publication_status":"published","publist_id":"7277","status":"public","date_updated":"2026-04-08T14:13:30Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"pubrep_id":"1031","language":[{"iso":"eng"}],"type":"dissertation","OA_place":"publisher","department":[{"_id":"CaHe"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","status":"public","date_updated":"2026-04-16T10:07:33Z","publist_id":"8004","degree_awarded":"PhD","month":"06","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"50","oa_version":"Published Version","page":"95","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"661"},{"relation":"part_of_dissertation","id":"1100","status":"public"},{"status":"public","id":"676","relation":"part_of_dissertation"}]},"abstract":[{"text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation.","lang":"eng"}],"day":"22","date_published":"2018-06-22T00:00:00Z","oa":1,"author":[{"orcid":"0000-0001-5199-9940","first_name":"Daniel","full_name":"Capek, Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:TH_1031","title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration","has_accepted_license":"1","date_created":"2018-12-11T11:44:21Z","year":"2018","publication_identifier":{"issn":["2663-337X"]},"ddc":["570","591","596"],"file_date_updated":"2021-02-11T23:30:21Z","citation":{"ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria.","ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","apa":"Capek, D. (2018). <i>Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">https://doi.org/10.15479/AT:ISTA:TH_1031</a>","chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">https://doi.org/10.15479/AT:ISTA:TH_1031</a>.","short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","mla":"Capek, Daniel. <i>Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">10.15479/AT:ISTA:TH_1031</a>.","ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">10.15479/AT:ISTA:TH_1031</a>"},"file":[{"embargo":"2019-06-25","file_size":31576521,"date_updated":"2021-02-11T11:17:17Z","creator":"dernst","file_name":"2018_Thesis_Capek.pdf","content_type":"application/pdf","date_created":"2019-04-08T13:42:26Z","file_id":"6238","relation":"main_file","access_level":"open_access","checksum":"d3eca3dcacb67bffdde6e6609c31cdd0"},{"embargo_to":"open_access","date_created":"2019-04-08T13:42:27Z","creator":"dernst","file_name":"2018_Thesis_Capek_source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2021-02-11T23:30:21Z","file_size":38992956,"relation":"source_file","access_level":"closed","checksum":"876deb14067e638aba65d209668bd821","file_id":"6239"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria"},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"LifeSc"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"6263","oa_version":"Published Version","page":"91","related_material":{"record":[{"relation":"part_of_dissertation","id":"1027","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"696"},{"id":"1619","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2026-04-08T14:15:06Z","status":"public","publication_status":"published","month":"12","degree_awarded":"PhD","department":[{"_id":"ToBo"}],"OA_place":"publisher","type":"dissertation","supervisor":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Tobias","first_name":"Tobias","orcid":"0000-0003-4398-476X"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file_date_updated":"2021-02-11T11:17:17Z","ddc":["570","576","579"],"file":[{"date_created":"2019-04-09T13:49:24Z","embargo":"2020-01-25","date_updated":"2021-02-11T11:17:17Z","file_size":5656866,"file_name":"2018_Thesis_Lukacisinova.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","checksum":"fc60585c9eaad868ac007004ef130908","access_level":"open_access","file_id":"6264"},{"relation":"source_file","access_level":"closed","checksum":"264057ec0a92ab348cc83b41f021ba92","file_id":"6265","date_created":"2019-04-09T13:49:23Z","embargo_to":"open_access","file_size":5168054,"date_updated":"2020-07-14T12:47:25Z","file_name":"2018_Thesis_Lukacisinova_source.docx","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"ieee":"M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018.","ista":"Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria.","apa":"Lukacisinova, M. (2018). <i>Genetic determinants of antibiotic resistance evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1072\">https://doi.org/10.15479/AT:ISTA:th1072</a>","chicago":"Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1072\">https://doi.org/10.15479/AT:ISTA:th1072</a>.","short":"M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018.","mla":"Lukacisinova, Marta. <i>Genetic Determinants of Antibiotic Resistance Evolution</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1072\">10.15479/AT:ISTA:th1072</a>.","ama":"Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1072\">10.15479/AT:ISTA:th1072</a>"},"has_accepted_license":"1","title":"Genetic determinants of antibiotic resistance evolution","publication_identifier":{"issn":["2663-337X"]},"date_created":"2019-04-09T13:57:15Z","year":"2018","doi":"10.15479/AT:ISTA:th1072","day":"28","abstract":[{"lang":"eng","text":"Antibiotic  resistance  can  emerge  spontaneously  through  genomic  mutation  and  render treatment   ineffective.   To   counteract   this process, in   addition   to   the   discovery   and description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand its  determinantsis  needed. To address  this challenge,  this  thesisuncoversnew  genetic determinants   of   resistance   evolvability   using   a   customized   robotic   setup, exploressystematic   ways   in   which   resistance   evolution   is   perturbed   due   to dose-responsecharacteristics  of  drugs and  mutation  rate  differences,and  mathematically  investigates the evolutionary fate of one specific type of evolvability modifier -a stress-induced mutagenesis allele.We  find  severalgenes  which  strongly  inhibit  or  potentiate  resistance  evolution.  In  order to identify   them,   we   first developedan   automated   high-throughput   feedback-controlled protocol whichkeeps the population size and selection pressure approximately constant for hundreds  of  cultures  by  dynamically  re-diluting  the  cultures  and  adjusting  the  antibiotic concentration.  We  implementedthis  protocol  on  a  customized  liquid  handling  robot  and propagated  100  different  gene  deletion  strains  of Escherichia  coliin  triplicate  for  over  100 generations  in  tetracycline  and  in  chloramphenicol,  and  comparedtheir  adaptation  rates.We  find  a  diminishing  returns  pattern,  where  initially  sensitive  strains  adapted  more compared to less sensitive ones.  Our data uncover that deletions of certain genes which do not  affect  mutation  rate,including  efflux  pump  components,  a  chaperone  and severalstructural  and regulatory  genes  can strongly  and  reproducibly  alterresistance  evolution. Sequencing   analysis of   evolved   populations   indicates   that   epistasis   with   resistance mutations  is  the  most  likelyexplanation. This  work  could  inspire  treatment  strategies  in which  targeted  inhibitors  of  evolvability  mechanisms  will  be  given  alongside  antibiotics  to slow down resistance evolution and extend theefficacy of antibiotics.We implemented  astochasticpopulation  genetics  model, toverifyways  in  which  general properties,  namely,  dose-response  characteristics  of  drugs  and  mutation  rates,  influence evolutionary  dynamics.  In  particular,  under  the  exposure  to  antibiotics  with  shallow  dose-response  curves,bacteria  have  narrower  distributions  of  fitness  effects  of  new  mutations. We  show  that in  silicothis  also  leads  to  slower  resistance  evolution.  We see and  confirm with experiments that increased mutation rates, apart from speeding up evolution, also leadto high reproducibility of phenotypic adaptation in a context of continually strong selection pressure.Knowledge  of  these  patterns  can  aid  in  predicting  the  dynamics  of  antibiotic resistance evolutionand adapting treatment schemes accordingly.Focusing on   a   previously   described   type   of   evolvability   modifier –a   stress-induced mutagenesis  allele –we  find  conditions  under  which  it  can  persist  in  a  population  under periodic  selectionakin  to  clinical  treatment. We  set  up  a  deterministic infinite  populationcontinuous  time  model  tracking  the  frequencies  of  a  mutator  and  resistance  allele  and evaluate  various  treatment  schemes  in  how  well  they  maintain  a stress-induced mutator allele. In particular,a high diversity  of stresses  is  crucial  for  the  persistence of the  mutator allele. This leads to a general trade-off where exactly those diversifying treatment schemes which  are  likely  to  decrease  levels  of  resistance  could  lead  to  stronger  selection  of  highly evolvable genotypes.In  the  long  run,  this  work  will  lead  to  a  deeper  understanding  of  the  genetic  and  cellular mechanisms involved in antibiotic resistance evolution and could inspire new strategies for slowing down its rate. "}],"oa":1,"author":[{"full_name":"Lukacisinova, Marta","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova"}],"date_published":"2018-12-28T00:00:00Z"},{"file_date_updated":"2021-02-11T11:17:16Z","ddc":["571","573"],"publisher":"Institute of Science and Technology Austria","file":[{"file_id":"6267","access_level":"open_access","checksum":"9d2c2dca04b00e485470c28b262af59a","relation":"main_file","file_size":4906420,"date_updated":"2021-02-11T11:17:16Z","embargo":"2019-11-24","content_type":"application/pdf","file_name":"2018_Thesis_McKenzie.pdf","creator":"dernst","date_created":"2019-04-09T14:12:40Z"},{"access_level":"closed","checksum":"50b58c272899601bc6fd9642c4dc97f1","relation":"source_file","file_id":"6268","embargo_to":"open_access","date_created":"2019-04-09T14:12:40Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst","file_name":"2018_Thesis_McKenzie_source.docx","file_size":5053545,"date_updated":"2020-07-14T12:47:25Z"}],"article_processing_charge":"No","citation":{"apa":"Mckenzie, C. (2018). <i>Design and characterization of methods and biological components to realize synthetic neurotransmission </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th_1055\">https://doi.org/10.15479/at:ista:th_1055</a>","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:th_1055\">https://doi.org/10.15479/at:ista:th_1055</a>.","ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria.","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:th_1055\">10.15479/at:ista:th_1055</a>","mla":"Mckenzie, Catherine. <i>Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:th_1055\">10.15479/at:ista:th_1055</a>.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018."},"has_accepted_license":"1","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","publication_identifier":{"issn":["2663-337X"]},"year":"2018","date_created":"2019-04-09T14:13:39Z","doi":"10.15479/at:ista:th_1055","day":"31","abstract":[{"lang":"eng","text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. "}],"author":[{"full_name":"Mckenzie, Catherine","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie"}],"oa":1,"date_published":"2018-10-31T00:00:00Z","_id":"6266","page":"95","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"new_edition","status":"public","id":"7132"}]},"status":"public","date_updated":"2026-04-08T14:14:05Z","month":"10","publication_status":"published","degree_awarded":"PhD","department":[{"_id":"HaJa"}],"OA_place":"publisher","type":"dissertation","corr_author":"1","supervisor":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","full_name":"Janovjak, Harald L","first_name":"Harald L","orcid":"0000-0002-8023-9315"}],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"pubrep_id":"1055"},{"publication":"Nature Communications","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"}],"language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"PeJo"}],"ec_funded":1,"scopus_import":"1","date_updated":"2026-07-03T22:32:39Z","status":"public","publist_id":"8034","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":9,"month":"11","publication_status":"published","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"21","oa_version":"Published Version","quality_controlled":"1","article_number":"4605","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/"}],"record":[{"relation":"dissertation_contains","id":"6363","status":"public"}]},"abstract":[{"lang":"eng","text":"Parvalbumin-positive (PV+) GABAergic interneurons in hippocampal microcircuits are thought to play a key role in several higher network functions, such as feedforward and feedback inhibition, network oscillations, and pattern separation. Fast lateral inhibition mediated by GABAergic interneurons may implement a winner-takes-all mechanism in the hippocampal input layer. However, it is not clear whether the functional connectivity rules of granule cells (GCs) and interneurons in the dentate gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings from up to seven GCs and up to four PV+ interneurons in the dentate gyrus, we find that connectivity is structured in space, synapse-specific, and enriched in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV+ interneuron) is ~ 10-times more abundant than recurrent inhibition (in which a GC inhibits itself). Thus, unique connectivity rules may enable the dentate gyrus to perform specific higher-order computations"}],"day":"02","date_published":"2018-11-02T00:00:00Z","oa":1,"author":[{"id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia ","first_name":"Claudia ","orcid":"0000-0003-4710-2082"},{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán","full_name":"Guzmán, José","first_name":"José","orcid":"0000-0003-2209-5242"},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Xiaomin","full_name":"Zhang, Xiaomin","orcid":"0000-0003-0256-6529"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"article_type":"original","issue":"1","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J..","doi":"10.1038/s41467-018-06899-3","title":"Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus","has_accepted_license":"1","intvolume":"         9","year":"2018","date_created":"2018-12-11T11:44:12Z","external_id":{"isi":["000449069700009"]},"file_date_updated":"2020-07-14T12:45:28Z","ddc":["570"],"citation":{"ieee":"C. Espinoza Martinez, J. Guzmán, X. Zhang, and P. M. Jonas, “Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus,” <i>Nature Communications</i>, vol. 9, no. 1. Nature Publishing Group, 2018.","ista":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. 2018. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 9(1), 4605.","apa":"Espinoza Martinez, C., Guzmán, J., Zhang, X., &#38; Jonas, P. M. (2018). Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-018-06899-3\">https://doi.org/10.1038/s41467-018-06899-3</a>","chicago":"Espinoza Martinez, Claudia , José Guzmán, Xiaomin Zhang, and Peter M Jonas. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-018-06899-3\">https://doi.org/10.1038/s41467-018-06899-3</a>.","short":"C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications 9 (2018).","ama":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-06899-3\">10.1038/s41467-018-06899-3</a>","mla":"Espinoza Martinez, Claudia, et al. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” <i>Nature Communications</i>, vol. 9, no. 1, 4605, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-06899-3\">10.1038/s41467-018-06899-3</a>."},"publisher":"Nature Publishing Group","file":[{"file_size":4651930,"date_updated":"2020-07-14T12:45:28Z","creator":"dernst","file_name":"2018_NatureComm_Espinoza.pdf","content_type":"application/pdf","date_created":"2018-12-17T15:41:57Z","file_id":"5715","relation":"main_file","checksum":"9fe2a63bd95a5067d896c087d07998f3","access_level":"open_access"}],"article_processing_charge":"No"},{"type":"journal_article","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"JoBo"}],"ec_funded":1,"scopus_import":"1","publication":"Nature Ecology and Evolution","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"},{"name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"648440"},{"grant_number":"24573","name":"Design principles underlying genetic switch architecture","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"_id":"67","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","page":"1633 - 1643","quality_controlled":"1","related_material":{"record":[{"relation":"popular_science","id":"5585","status":"public"},{"relation":"dissertation_contains","id":"6371","status":"public"}]},"publist_id":"7987","date_updated":"2026-07-03T22:32:37Z","status":"public","publication_status":"published","volume":2,"month":"09","isi":1,"article_type":"original","issue":"10","doi":"10.1038/s41559-018-0651-y","abstract":[{"lang":"eng","text":"Gene regulatory networks evolve through rewiring of individual components—that is, through changes in regulatory connections. However, the mechanistic basis of regulatory rewiring is poorly understood. Using a canonical gene regulatory system, we quantify the properties of transcription factors that determine the evolutionary potential for rewiring of regulatory connections: robustness, tunability and evolvability. In vivo repression measurements of two repressors at mutated operator sites reveal their contrasting evolutionary potential: while robustness and evolvability were positively correlated, both were in trade-off with tunability. Epistatic interactions between adjacent operators alleviated this trade-off. A thermodynamic model explains how the differences in robustness, tunability and evolvability arise from biophysical characteristics of repressor–DNA binding. The model also uncovers that the energy matrix, which describes how mutations affect repressor–DNA binding, encodes crucial information about the evolutionary potential of a repressor. The biophysical determinants of evolutionary potential for regulatory rewiring constitute a mechanistic framework for understanding network evolution."}],"day":"10","date_published":"2018-09-10T00:00:00Z","oa":1,"author":[{"orcid":"0000-0001-7777-546X","full_name":"Igler, Claudia","first_name":"Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mato","full_name":"Lagator, Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"},{"first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"ddc":["570"],"file_date_updated":"2020-07-14T12:47:37Z","citation":{"ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. <i>Nature Ecology and Evolution</i>. 2018;2(10):1633-1643. doi:<a href=\"https://doi.org/10.1038/s41559-018-0651-y\">10.1038/s41559-018-0651-y</a>","mla":"Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:<a href=\"https://doi.org/10.1038/s41559-018-0651-y\">10.1038/s41559-018-0651-y</a>.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. <i>Nature Ecology and Evolution</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41559-018-0651-y\">https://doi.org/10.1038/s41559-018-0651-y</a>","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” <i>Nature Ecology and Evolution</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41559-018-0651-y\">https://doi.org/10.1038/s41559-018-0651-y</a>.","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643."},"article_processing_charge":"No","publisher":"Nature Publishing Group","file":[{"date_created":"2020-05-14T11:28:52Z","file_size":1135973,"date_updated":"2020-07-14T12:47:37Z","content_type":"application/pdf","creator":"dernst","file_name":"2018_NatureEcology_Igler.pdf","access_level":"open_access","checksum":"383a2e2c944a856e2e821ec8e7bf71b6","relation":"main_file","file_id":"7830"}],"title":"Evolutionary potential of transcription factors for gene regulatory rewiring","has_accepted_license":"1","intvolume":"         2","date_created":"2018-12-11T11:44:27Z","year":"2018","external_id":{"isi":["000447947600021"]}},{"year":"2018","date_created":"2018-12-12T12:31:40Z","month":"07","status":"public","date_updated":"2026-07-03T22:32:37Z","title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"has_accepted_license":"1","citation":{"ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>.","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","mla":"Igler, Claudia, et al. <i>Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>"},"related_material":{"record":[{"relation":"research_paper","id":"67","status":"public"},{"status":"public","id":"6371","relation":"research_paper"}]},"file":[{"file_id":"5611","relation":"main_file","checksum":"1435781526c77413802adee0d4583cce","access_level":"open_access","file_name":"IST-2018-108-v1+1_data_figures.xlsx","creator":"system","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","date_updated":"2020-07-14T12:47:07Z","file_size":16507,"date_created":"2018-12-12T13:02:45Z"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5585","oa_version":"Published Version","ddc":["576"],"license":"https://creativecommons.org/publicdomain/zero/1.0/","file_date_updated":"2020-07-14T12:47:07Z","date_published":"2018-07-20T00:00:00Z","author":[{"full_name":"Igler, Claudia","first_name":"Claudia","orcid":"0000-0001-7777-546X","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler"},{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato","full_name":"Lagator, Mato"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P"},{"first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"oa":1,"datarep_id":"108","abstract":[{"lang":"eng","text":"Mean repression values and standard error of the mean are given for all operator mutant libraries."}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"},{"grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture"}],"day":"20","ec_funded":1,"doi":"10.15479/AT:ISTA:108","type":"research_data","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"type":"dissertation","OA_place":"publisher","department":[{"_id":"SiHi"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"pubrep_id":"1057","language":[{"iso":"eng"}],"_id":"10","page":"1 - 139","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","publist_id":"8046","date_updated":"2026-04-08T14:12:45Z","status":"public","degree_awarded":"PhD","publication_status":"published","month":"11","doi":"10.15479/AT:ISTA:th1057","abstract":[{"text":"Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain.","lang":"eng"}],"day":"21","date_published":"2018-11-21T00:00:00Z","author":[{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","full_name":"Laukoter, Susanne","first_name":"Susanne","orcid":"0000-0002-7903-3010"}],"oa":1,"ddc":["570"],"file_date_updated":"2021-02-11T11:17:16Z","citation":{"ista":"Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria.","ieee":"S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018.","apa":"Laukoter, S. (2018). <i>Role of genomic imprinting in cerebral cortex development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">https://doi.org/10.15479/AT:ISTA:th1057</a>","chicago":"Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">https://doi.org/10.15479/AT:ISTA:th1057</a>.","short":"S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018.","ama":"Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">10.15479/AT:ISTA:th1057</a>","mla":"Laukoter, Susanne. <i>Role of Genomic Imprinting in Cerebral Cortex Development</i>. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">10.15479/AT:ISTA:th1057</a>."},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file":[{"file_id":"6396","relation":"source_file","checksum":"41fdbf5fdce312802935d88a8ad9932c","access_level":"closed","file_size":17949175,"date_updated":"2019-11-23T23:30:03Z","creator":"dernst","file_name":"Thesis_LaukoterSusanne_FINAL.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-05-10T07:47:04Z","embargo_to":"open_access"},{"file_id":"6397","relation":"main_file","checksum":"53001a9a0c9e570e598d861bb0af28aa","access_level":"open_access","embargo":"2019-11-21","date_updated":"2021-02-11T11:17:16Z","file_size":21187245,"file_name":"Thesis_LaukoterSusanne_FINAL.pdf","creator":"dernst","content_type":"application/pdf","date_created":"2019-05-10T07:47:04Z"}],"title":"Role of genomic imprinting in cerebral cortex development","has_accepted_license":"1","year":"2018","date_created":"2018-12-11T11:44:08Z","publication_identifier":{"issn":["2663-337X"]}},{"external_id":{"isi":["000451735700054"],"arxiv":["1804.09522"]},"publication_identifier":{"issn":["0034-6748"]},"year":"2018","date_created":"2019-01-10T14:22:23Z","intvolume":"        89","title":"30 GHz-voltage controlled oscillator operating at 4 K","publisher":"AIP Publishing","article_processing_charge":"No","citation":{"short":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018).","ama":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. <i>Review of Scientific Instruments</i>. 2018;89(11). doi:<a href=\"https://doi.org/10.1063/1.5038258\">10.1063/1.5038258</a>","mla":"Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” <i>Review of Scientific Instruments</i>, vol. 89, no. 11, 114701, AIP Publishing, 2018, doi:<a href=\"https://doi.org/10.1063/1.5038258\">10.1063/1.5038258</a>.","ista":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 89(11), 114701.","ieee":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R. Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” <i>Review of Scientific Instruments</i>, vol. 89, no. 11. AIP Publishing, 2018.","chicago":"Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” <i>Review of Scientific Instruments</i>. AIP Publishing, 2018. <a href=\"https://doi.org/10.1063/1.5038258\">https://doi.org/10.1063/1.5038258</a>.","apa":"Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., &#38; Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. <i>Review of Scientific Instruments</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5038258\">https://doi.org/10.1063/1.5038258</a>"},"arxiv":1,"author":[{"full_name":"Hollmann, Arne","first_name":"Arne","last_name":"Hollmann"},{"last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","first_name":"Daniel"},{"last_name":"Kucharski","first_name":"Maciej","full_name":"Kucharski, Maciej"},{"last_name":"Kissinger","first_name":"Dietmar","full_name":"Kissinger, Dietmar"},{"full_name":"Fischer, Gunter","first_name":"Gunter","last_name":"Fischer"},{"first_name":"Lars R.","full_name":"Schreiber, Lars R.","last_name":"Schreiber"}],"oa":1,"date_published":"2018-11-01T00:00:00Z","day":"01","abstract":[{"text":"Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field.","lang":"eng"}],"doi":"10.1063/1.5038258","issue":"11","isi":1,"month":"11","volume":89,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.09522"}],"status":"public","date_updated":"2026-07-03T22:33:11Z","related_material":{"record":[{"id":"10058","status":"public","relation":"dissertation_contains"}]},"article_number":"114701","quality_controlled":"1","_id":"5816","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Review of Scientific Instruments","scopus_import":"1","department":[{"_id":"GeKa"}],"type":"journal_article"}]