[{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"18","year":"2023","has_accepted_license":"1","date_created":"2023-04-14T14:56:04Z","date_published":"2023-04-18T00:00:00Z","doi":"10.15479/at:ista:12826","page":"106","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria."},"title":"Neural control of optic flow-based navigation in Drosophila melanogaster","article_processing_charge":"No","author":[{"last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"04","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"checksum":"5f589a9af025f7eeebfd0c186209913e","file_id":"12857","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Thesis_Pokusaeva.docx","date_created":"2023-04-20T09:14:38Z","file_size":14507243,"date_updated":"2023-04-20T09:26:51Z","creator":"vpokusae"},{"date_created":"2023-04-20T09:14:44Z","file_name":"Thesis_Pokusaeva.pdf","creator":"vpokusae","date_updated":"2023-04-20T09:14:44Z","file_size":10090711,"checksum":"bbeed76db45a996b4c91a9abe12ce0ec","file_id":"12858","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"_id":"12826","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["570","571"],"date_updated":"2023-06-23T09:47:36Z","supervisor":[{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"department":[{"_id":"MaJö"},{"_id":"GradSch"}],"file_date_updated":"2023-04-20T09:26:51Z"},{"acknowledgement":"We acknowledge the financial support of the Natural Sciences and Engineering Research Council of Canada (NSERC RGPIN-2020-06377), the Spanish Ministry of Economy, Industry and Competitiveness (“Centro de Excelencia Severo Ochoa 2013-2017”, Plan Estatal PGC2018-099807-B-I00), of the CERCA Programme/Generalitat de Catalunya, and of the European Research Council (Synergy Grant 609989). VOP was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie programme (665385). We also acknowledge the support of the Spanish Ministry of Economy and Competitiveness (MEIC) to the EMBL partnership.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2022","day":"12","publication":"Genome Biology","date_published":"2022-04-12T00:00:00Z","doi":"10.1186/s13059-022-02665-3","date_created":"2023-01-16T09:48:44Z","article_number":"93","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"citation":{"mla":"Pokusaeva, Victoria, et al. “Strand Asymmetry Influences Mismatch Resolution during Single-Strand Annealing.” Genome Biology, vol. 23, 93, Springer Nature, 2022, doi:10.1186/s13059-022-02665-3.","short":"V. Pokusaeva, A.R. Diez, L. Espinar, A.T. Pérez, G.J. Filion, Genome Biology 23 (2022).","ieee":"V. Pokusaeva, A. R. Diez, L. Espinar, A. T. Pérez, and G. J. Filion, “Strand asymmetry influences mismatch resolution during single-strand annealing,” Genome Biology, vol. 23. Springer Nature, 2022.","ama":"Pokusaeva V, Diez AR, Espinar L, Pérez AT, Filion GJ. Strand asymmetry influences mismatch resolution during single-strand annealing. Genome Biology. 2022;23. doi:10.1186/s13059-022-02665-3","apa":"Pokusaeva, V., Diez, A. R., Espinar, L., Pérez, A. T., & Filion, G. J. (2022). Strand asymmetry influences mismatch resolution during single-strand annealing. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02665-3","chicago":"Pokusaeva, Victoria, Aránzazu Rosado Diez, Lorena Espinar, Albert Torelló Pérez, and Guillaume J. Filion. “Strand Asymmetry Influences Mismatch Resolution during Single-Strand Annealing.” Genome Biology. Springer Nature, 2022. https://doi.org/10.1186/s13059-022-02665-3.","ista":"Pokusaeva V, Diez AR, Espinar L, Pérez AT, Filion GJ. 2022. Strand asymmetry influences mismatch resolution during single-strand annealing. Genome Biology. 23, 93."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","last_name":"Pokusaeva","id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria"},{"first_name":"Aránzazu Rosado","full_name":"Diez, Aránzazu Rosado","last_name":"Diez"},{"first_name":"Lorena","last_name":"Espinar","full_name":"Espinar, Lorena"},{"full_name":"Pérez, Albert Torelló","last_name":"Pérez","first_name":"Albert Torelló"},{"first_name":"Guillaume J.","last_name":"Filion","full_name":"Filion, Guillaume J."}],"external_id":{"pmid":["35414014"],"isi":["000781953800001"]},"article_processing_charge":"No","title":"Strand asymmetry influences mismatch resolution during single-strand annealing","abstract":[{"lang":"eng","text":"Background: Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the contributions of DNA repair from those of DNA damage.\r\n\r\nResults: Here, we develop a genome-wide assay whereby the same DNA lesion is repaired in different genomic contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated if the break is repaired through single-strand annealing. The resolution of the mismatch showed a 60–80% bias in favor of the strand with the longest 3′ flap. The location of the lesion in the genome and the type of mismatch had little influence on the bias. Instead, we observe a complete reversal of the bias when the longest 3′ flap is moved to the opposite strand by changing the position of the double-strand break in the reporter.\r\n\r\nConclusions: These results suggest that the processing of the double-strand break has a major influence on the repair of mismatches during single-strand annealing."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 23","publication_identifier":{"issn":["1474-760X"]},"publication_status":"published","file":[{"file_name":"2022_GenomeBiology_Pokusaeva.pdf","date_created":"2023-01-27T09:01:40Z","creator":"dernst","file_size":4939342,"date_updated":"2023-01-27T09:01:40Z","success":1,"checksum":"17bb091fec04d82ba20a3458c4cfd2bd","file_id":"12419","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://github.com/cellcomplexitylab/strand_asymmetry ","relation":"software"},{"url":"https://hub.docker.com/r/gui11aume/strand_asymmetry","relation":"software"}]},"volume":23,"ec_funded":1,"_id":"12226","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-04T09:27:00Z","ddc":["570"],"department":[{"_id":"MaJö"}],"file_date_updated":"2023-01-27T09:01:40Z"},{"_id":"6419","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-25T10:30:37Z","ddc":["570"],"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:47:30Z","abstract":[{"lang":"eng","text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 15","publication_identifier":{"eissn":["15537404"]},"publication_status":"published","file":[{"checksum":"cf3889c8a8a16053dacf9c3776cbe217","file_id":"6445","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-05-14T08:26:08Z","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:30Z","file_size":3726017}],"language":[{"iso":"eng"}],"volume":15,"issue":"4","related_material":{"record":[{"id":"9789","status":"public","relation":"research_data"},{"status":"public","id":"9790","relation":"research_data"},{"id":"9797","status":"public","relation":"research_data"}]},"ec_funded":1,"article_number":"e1008079","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","ieee":"V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva"},{"first_name":"Dinara R.","full_name":"Usmanova, Dinara R.","last_name":"Usmanova"},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V.","first_name":"Ekaterina V."},{"full_name":"Espinar, Lorena","last_name":"Espinar","first_name":"Lorena"},{"first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","last_name":"Sarkisyan"},{"first_name":"Alexander S.","full_name":"Mishin, Alexander S.","last_name":"Mishin"},{"full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva","first_name":"Natalya S."},{"last_name":"Ivankov","full_name":"Ivankov, Dmitry","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","full_name":"Avvakumov, Sergey","last_name":"Avvakumov"},{"first_name":"Inna S.","full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya"},{"first_name":"Guillaume J.","last_name":"Filion","full_name":"Filion, Guillaume J."},{"last_name":"Carey","full_name":"Carey, Lucas B.","first_name":"Lucas B."},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"external_id":{"isi":["000466866000029"]},"article_processing_charge":"No","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"10","publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1008079","date_published":"2019-04-10T00:00:00Z","date_created":"2019-05-13T07:58:38Z"},{"oa_version":"Published Version","publisher":"Public Library of Science","month":"04","year":"2019","day":"10","date_created":"2021-08-06T08:50:15Z","date_published":"2019-04-10T00:00:00Z","doi":"10.1371/journal.pgen.1008079.s011","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6419"}]},"_id":"9790","type":"research_data_reference","status":"public","citation":{"ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.","ieee":"V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011","mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011."},"date_updated":"2023-08-25T10:30:36Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dinara R.","full_name":"Usmanova, Dinara R.","last_name":"Usmanova"},{"first_name":"Ekaterina V.","full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva"},{"last_name":"Espinar","full_name":"Espinar, Lorena","first_name":"Lorena"},{"last_name":"Sarkisyan","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"first_name":"Alexander S.","full_name":"Mishin, Alexander S.","last_name":"Mishin"},{"first_name":"Natalya S.","full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva"},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey","last_name":"Avvakumov"},{"full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya","first_name":"Inna S."},{"last_name":"Filion","full_name":"Filion, Guillaume J.","first_name":"Guillaume J."},{"last_name":"Carey","full_name":"Carey, Lucas B.","first_name":"Lucas B."},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"department":[{"_id":"FyKo"}],"title":"A statistical summary of segment libraries and sequencing results"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Pokusaeva, Victoria, et al. 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