--- _id: '9097' abstract: - lang: eng text: Psoriasis is a chronic inflammatory skin disease clinically characterized by the appearance of red colored, well-demarcated plaques with thickened skin and with silvery scales. Recent studies have established the involvement of a complex signalling network of interactions between cytokines, immune cells and skin cells called keratinocytes. Keratinocytes form the cells of the outermost layer of the skin (epidermis). Visible plaques in psoriasis are developed due to the fast proliferation and unusual differentiation of keratinocyte cells. Despite that, the exact mechanism of the appearance of these plaques in the cytokine-immune cell network is not clear. A mathematical model embodying interactions between key immune cells believed to be involved in psoriasis, keratinocytes and relevant cytokines has been developed. The complex network formed of these interactions poses several challenges. Here, we choose to study subnetworks of this complex network and initially focus on interactions involving TNFα, IL-23/IL-17, and IL-15. These are chosen based on known evidence of their therapeutic efficacy. In addition, we explore the role of IL-15 in the pathogenesis of psoriasis and its potential as a future drug target for a novel treatment option. We perform steady state analyses for these subnetworks and demonstrate that the interactions between cells, driven by cytokines could cause the emergence of a psoriasis state (hyper-proliferation of keratinocytes) when levels of TNFα, IL-23/IL-17 or IL-15 are increased. The model results explain and support the clinical potentiality of anti-cytokine treatments. Interestingly, our results suggest different dynamic scenarios underpin the pathogenesis of psoriasis, depending upon the dominant cytokines of subnetworks. We observed that the increase in the level of IL-23/IL-17 and IL-15 could lead to psoriasis via a bistable route, whereas an increase in the level of TNFα would lead to a monotonic and gradual disease progression. Further, we demonstrate how this insight, bistability, could be exploited to improve the current therapies and develop novel treatment strategies for psoriasis. acknowledgement: RP acknowledges the Department of Science and Technology, India for the support through the DST-INSPIRE Faculty Award (DST/INSPIRE/04/2015/001939). This work was supported by the Engineering and Physical Sciences Research Council (EPSRC), United Kingdom (Grant numbers EP/J018295/1, EP/J018392/1, EP/N014391/1). The contribution of RP was also supported by the later Grant. This work was generously supported by the Welcome Trust Institutional Strategic Support Award (204909/Z/16/Z) too. The contribution of MG was supported by the EPSRC via EP/N014391/1 and a Wellcome Trust Institutional Strategic Support Award (WT105618MA). The contribution of YA was generously supported by the Wellcome Trust Institutional Strategic Support Award (WT105618MA). article_number: '2204' article_processing_charge: No article_type: original author: - first_name: Rakesh full_name: Pandey, Rakesh last_name: Pandey - first_name: Yusur full_name: Al-Nuaimi, Yusur last_name: Al-Nuaimi - first_name: Rajiv Kumar full_name: Mishra, Rajiv Kumar id: 46CB58F2-F248-11E8-B48F-1D18A9856A87 last_name: Mishra - first_name: Sarah K. full_name: Spurgeon, Sarah K. last_name: Spurgeon - first_name: Marc full_name: Goodfellow, Marc last_name: Goodfellow citation: ama: Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. Scientific Reports. 2021;11. doi:10.1038/s41598-020-80507-7 apa: Pandey, R., Al-Nuaimi, Y., Mishra, R. K., Spurgeon, S. K., & Goodfellow, M. (2021). Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-80507-7 chicago: Pandey, Rakesh, Yusur Al-Nuaimi, Rajiv Kumar Mishra, Sarah K. Spurgeon, and Marc Goodfellow. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17 and IL-15 in a Network Involved in the Pathogenesis of Psoriasis.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-020-80507-7. ieee: R. Pandey, Y. Al-Nuaimi, R. K. Mishra, S. K. Spurgeon, and M. Goodfellow, “Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis,” Scientific Reports, vol. 11. Springer Nature, 2021. ista: Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. 2021. Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. Scientific Reports. 11, 2204. mla: Pandey, Rakesh, et al. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17 and IL-15 in a Network Involved in the Pathogenesis of Psoriasis.” Scientific Reports, vol. 11, 2204, Springer Nature, 2021, doi:10.1038/s41598-020-80507-7. short: R. Pandey, Y. Al-Nuaimi, R.K. Mishra, S.K. Spurgeon, M. Goodfellow, Scientific Reports 11 (2021). date_created: 2021-02-07T23:01:12Z date_published: 2021-01-26T00:00:00Z date_updated: 2022-08-19T07:22:23Z day: '26' ddc: - '570' department: - _id: PeJo doi: 10.1038/s41598-020-80507-7 file: - access_level: open_access checksum: e8a68df48750712671f5c47b0228e531 content_type: application/pdf creator: dernst date_created: 2021-02-09T07:33:23Z date_updated: 2021-02-09T07:33:23Z file_id: '9106' file_name: 2021_ScientificReports_Pandey.pdf file_size: 2885056 relation: main_file success: 1 file_date_updated: 2021-02-09T07:33:23Z has_accepted_license: '1' intvolume: ' 11' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2021' ... --- _id: '9905' abstract: - lang: eng text: Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period. acknowledgement: We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL). article_number: '15729' article_processing_charge: Yes article_type: original author: - first_name: Simon full_name: Rella, Simon id: B4765ACA-AA38-11E9-AC9A-0930E6697425 last_name: Rella - first_name: Yuliya A. full_name: Kulikova, Yuliya A. last_name: Kulikova - first_name: Emmanouil T. full_name: Dermitzakis, Emmanouil T. last_name: Dermitzakis - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-95025-3 apa: Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3 chicago: Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-95025-3. ieee: S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021. ista: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729. mla: Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3. short: S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021). date_created: 2021-08-15T22:01:26Z date_published: 2021-07-30T00:00:00Z date_updated: 2023-08-11T10:42:58Z day: '30' ddc: - '570' - '610' department: - _id: FyKo doi: 10.1038/s41598-021-95025-3 ec_funded: 1 external_id: isi: - '000683329100001' pmid: - '34330988' file: - access_level: open_access checksum: ac86892ed17e6724c7251844da5cef5c content_type: application/pdf creator: asandaue date_created: 2021-08-16T11:36:49Z date_updated: 2021-08-16T11:36:49Z file_id: '9927' file_name: 2021_ScientificReports_Rella.pdf file_size: 3432001 relation: main_file success: 1 file_date_updated: 2021-08-16T11:36:49Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/ scopus_import: '1' status: public title: Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2021' ... --- _id: '7487' abstract: - lang: eng text: 'Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis playing a key role in cancer metabolic reprogramming. Humans express two types of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2 is repressed in many tumor cells and a better understanding of its function in tumorigenesis may further the development of new therapeutic approaches. We analyzed GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7 cells. We studied GLS2 expression after induction of differentiation with phorbol ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we investigated cell cycle progression and levels of p53, p21 and c-Myc proteins. Using the baculovirus system, human GLS2 protein was overexpressed, purified and analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform. We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry and subcellular fractionation gave consistent results demonstrating nuclear and mitochondrial locations, with the latter being predominant. Nuclear targeting was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins. We assessed the subnuclear location finding a widespread distribution of GLS2 in the nucleoplasm without clear overlapping with specific nuclear substructures. GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore, human GLS2 was identified as being hypusinated by MS analysis, a posttranslational modification which may be relevant for its nuclear targeting and/or function. Our studies provide evidence for a tumor suppressor role of GLS2 in certain types of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in cancer cells induced an antiproliferative response with cell cycle arrest at the G2/M phase.' article_number: '2259' article_processing_charge: No article_type: original author: - first_name: Amada R. full_name: López De La Oliva, Amada R. last_name: López De La Oliva - first_name: José A. full_name: Campos-Sandoval, José A. last_name: Campos-Sandoval - first_name: María C. full_name: Gómez-García, María C. last_name: Gómez-García - first_name: Carolina full_name: Cardona, Carolina last_name: Cardona - first_name: Mercedes full_name: Martín-Rufián, Mercedes last_name: Martín-Rufián - first_name: Fernando J. full_name: Sialana, Fernando J. last_name: Sialana - first_name: Laura full_name: Castilla, Laura last_name: Castilla - first_name: Narkhyun full_name: Bae, Narkhyun id: 3A5F7CD8-F248-11E8-B48F-1D18A9856A87 last_name: Bae - first_name: Carolina full_name: Lobo, Carolina last_name: Lobo - first_name: Ana full_name: Peñalver, Ana last_name: Peñalver - first_name: Marina full_name: García-Frutos, Marina last_name: García-Frutos - first_name: David full_name: Carro, David last_name: Carro - first_name: Victoria full_name: Enrique, Victoria last_name: Enrique - first_name: José C. full_name: Paz, José C. last_name: Paz - first_name: Raghavendra G. full_name: Mirmira, Raghavendra G. last_name: Mirmira - first_name: Antonia full_name: Gutiérrez, Antonia last_name: Gutiérrez - first_name: Francisco J. full_name: Alonso, Francisco J. last_name: Alonso - first_name: Juan A. full_name: Segura, Juan A. last_name: Segura - first_name: José M. full_name: Matés, José M. last_name: Matés - first_name: Gert full_name: Lubec, Gert last_name: Lubec - first_name: Javier full_name: Márquez, Javier last_name: Márquez citation: ama: López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-58264-4 apa: López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona, C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-58264-4 chicago: López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García, Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla, et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-58264-4. ieee: A. R. López De La Oliva et al., “Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020. ista: López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D, Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 10(1), 2259. mla: López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:10.1038/s41598-020-58264-4. short: A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona, M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M. García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J. Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020). date_created: 2020-02-16T23:00:49Z date_published: 2020-02-10T00:00:00Z date_updated: 2023-08-18T06:35:13Z day: '10' ddc: - '570' department: - _id: CaBe doi: 10.1038/s41598-020-58264-4 external_id: isi: - '000560694800012' pmid: - '32042057' file: - access_level: open_access checksum: c780bd87476a9c9e12668ff66de3dc96 content_type: application/pdf creator: dernst date_created: 2020-02-18T07:43:21Z date_updated: 2020-07-14T12:47:59Z file_id: '7495' file_name: 2020_ScientificReport_Lopez.pdf file_size: 4703751 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41598-020-80651-0 scopus_import: '1' status: public title: Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '7632' abstract: - lang: eng text: The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical network supporting goal-directed behaviour, with functions including sensorimotor transformations and decision making. In primates, this network links performed and observed actions via mirror neurons, which fire both when individuals perform an action and when they observe the same action performed by a conspecific. Mirror neurons are believed to be important for social learning, but it is not known whether mirror-like neurons occur in similar networks in other social species, such as rodents, or if they can be measured in such models using paradigms where observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching and wheel-running tasks, and found that cell populations in both areas robustly encoded several naturalistic behaviours. However, neural responses to the same set of observed actions were absent, although we verified that observer mice were attentive to performers and that PPC neurons responded reliably to visual cues. Statistical modelling also indicated that executed actions outperformed observed actions in predicting neural responses. These results raise the possibility that sensorimotor action recognition in rodents could take place outside of the parieto-frontal circuit, and underscore that detecting socially-driven neural coding depends critically on the species and behavioural paradigm used. article_number: '5559' article_processing_charge: No article_type: original author: - first_name: Tuce full_name: Tombaz, Tuce last_name: Tombaz - first_name: Benjamin A. full_name: Dunn, Benjamin A. last_name: Dunn - first_name: Karoline full_name: Hovde, Karoline last_name: Hovde - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Bartul full_name: Mimica, Bartul last_name: Mimica - first_name: Pranav full_name: Mamidanna, Pranav last_name: Mamidanna - first_name: Yasser full_name: Roudi, Yasser last_name: Roudi - first_name: Jonathan R. full_name: Whitlock, Jonathan R. last_name: Whitlock citation: ama: Tombaz T, Dunn BA, Hovde K, et al. Action representation in the mouse parieto-frontal network. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-62089-6 apa: Tombaz, T., Dunn, B. A., Hovde, K., Cubero, R. J., Mimica, B., Mamidanna, P., … Whitlock, J. R. (2020). Action representation in the mouse parieto-frontal network. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-62089-6 chicago: Tombaz, Tuce, Benjamin A. Dunn, Karoline Hovde, Ryan J Cubero, Bartul Mimica, Pranav Mamidanna, Yasser Roudi, and Jonathan R. Whitlock. “Action Representation in the Mouse Parieto-Frontal Network.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-62089-6. ieee: T. Tombaz et al., “Action representation in the mouse parieto-frontal network,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020. ista: Tombaz T, Dunn BA, Hovde K, Cubero RJ, Mimica B, Mamidanna P, Roudi Y, Whitlock JR. 2020. Action representation in the mouse parieto-frontal network. Scientific reports. 10(1), 5559. mla: Tombaz, Tuce, et al. “Action Representation in the Mouse Parieto-Frontal Network.” Scientific Reports, vol. 10, no. 1, 5559, Springer Nature, 2020, doi:10.1038/s41598-020-62089-6. short: T. Tombaz, B.A. Dunn, K. Hovde, R.J. Cubero, B. Mimica, P. Mamidanna, Y. Roudi, J.R. Whitlock, Scientific Reports 10 (2020). date_created: 2020-04-05T22:00:47Z date_published: 2020-03-27T00:00:00Z date_updated: 2023-08-18T10:25:13Z day: '27' ddc: - '570' department: - _id: SaSi doi: 10.1038/s41598-020-62089-6 external_id: isi: - '000560406800007' file: - access_level: open_access checksum: e6cfaaaf7986532132934400038b824a content_type: application/pdf creator: dernst date_created: 2020-04-06T10:44:23Z date_updated: 2020-07-14T12:48:01Z file_id: '7644' file_name: 2020_ScientificReports_Tombaz.pdf file_size: 2621249 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Scientific reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Action representation in the mouse parieto-frontal network tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '7931' abstract: - lang: eng text: In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data. article_number: '8635' article_processing_charge: No article_type: original author: - first_name: Leonid A. full_name: Uroshlev, Leonid A. last_name: Uroshlev - first_name: Eldar T. full_name: Abdullaev, Eldar T. last_name: Abdullaev - first_name: Iren R. full_name: Umarova, Iren R. last_name: Umarova - first_name: Irina A. full_name: Il’Icheva, Irina A. last_name: Il’Icheva - first_name: Larisa A. full_name: Panchenko, Larisa A. last_name: Panchenko - first_name: Robert V. full_name: Polozov, Robert V. last_name: Polozov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Yury D. full_name: Nechipurenko, Yury D. last_name: Nechipurenko - first_name: Sergei L. full_name: Grokhovsky, Sergei L. last_name: Grokhovsky citation: ama: Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1 apa: Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1 chicago: Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-65406-1. ieee: L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020. ista: Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635. mla: Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1. short: L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020). date_created: 2020-06-07T22:00:51Z date_published: 2020-05-25T00:00:00Z date_updated: 2023-08-21T07:00:17Z day: '25' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41598-020-65406-1 external_id: isi: - '000560774200007' file: - access_level: open_access checksum: 099e51611a5b7ca04244d03b2faddf33 content_type: application/pdf creator: dernst date_created: 2020-06-08T06:27:32Z date_updated: 2020-07-14T12:48:05Z file_id: '7947' file_name: 2020_ScientificReports_Uroshlev.pdf file_size: 1001724 relation: main_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A method for identification of the methylation level of CpG islands from NGS data tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '8643' abstract: - lang: eng text: The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors. acknowledgement: 'We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).' article_number: '16220' article_processing_charge: No article_type: original author: - first_name: Alfonso full_name: Deichler, Alfonso last_name: Deichler - first_name: Denisse full_name: Carrasco, Denisse last_name: Carrasco - first_name: Luciana full_name: Lopez-Jury, Luciana last_name: Lopez-Jury - first_name: Tomas A full_name: Vega Zuniga, Tomas A id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87 last_name: Vega Zuniga - first_name: Natalia full_name: Marquez, Natalia last_name: Marquez - first_name: Jorge full_name: Mpodozis, Jorge last_name: Mpodozis - first_name: Gonzalo full_name: Marin, Gonzalo last_name: Marin citation: ama: Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0 apa: Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0 chicago: Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0. ieee: A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020. ista: Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220. mla: Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0. short: A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020). date_created: 2020-10-11T22:01:14Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-08-22T09:58:21Z day: '01' ddc: - '570' department: - _id: MaJö doi: 10.1038/s41598-020-72848-0 external_id: isi: - '000577142600032' file: - access_level: open_access checksum: f6dd99954f1c0ffb4da5a1d2d739bf31 content_type: application/pdf creator: dernst date_created: 2020-10-12T12:39:10Z date_updated: 2020-10-12T12:39:10Z file_id: '8651' file_name: 2020_ScientificReport_Deichler.pdf file_size: 3906744 relation: main_file success: 1 file_date_updated: 2020-10-12T12:39:10Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '6867' abstract: - lang: eng text: A novel magnetic scratch method achieves repeatability, reproducibility and geometric control greater than pipette scratch assays and closely approximating the precision of cell exclusion assays while inducing the cell injury inherently necessary for wound healing assays. The magnetic scratch is affordable, easily implemented and standardisable and thus may contribute toward better comparability of data generated in different studies and laboratories. article_number: '12625' article_processing_charge: No author: - first_name: M. full_name: Fenu, M. last_name: Fenu - first_name: T. full_name: Bettermann, T. last_name: Bettermann - first_name: C. full_name: Vogl, C. last_name: Vogl - first_name: Nasser full_name: Darwish-Miranda, Nasser id: 39CD9926-F248-11E8-B48F-1D18A9856A87 last_name: Darwish-Miranda orcid: 0000-0002-8821-8236 - first_name: J. full_name: Schramel, J. last_name: Schramel - first_name: F. full_name: Jenner, F. last_name: Jenner - first_name: I. full_name: Ribitsch, I. last_name: Ribitsch citation: ama: Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-48930-7 apa: Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner, F., & Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-48930-7 chicago: Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel, F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-48930-7. ieee: M. Fenu et al., “A novel magnet-based scratch method for standardisation of wound-healing assays,” Scientific Reports, vol. 9, no. 1. Springer Nature, 2019. ista: Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch I. 2019. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 9(1), 12625. mla: Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports, vol. 9, no. 1, 12625, Springer Nature, 2019, doi:10.1038/s41598-019-48930-7. short: M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner, I. Ribitsch, Scientific Reports 9 (2019). date_created: 2019-09-15T22:00:42Z date_published: 2019-09-02T00:00:00Z date_updated: 2023-08-29T07:55:15Z day: '02' ddc: - '570' department: - _id: Bio doi: 10.1038/s41598-019-48930-7 external_id: isi: - '000483697800007' pmid: - '31477739' file: - access_level: open_access checksum: 9cfd986d4108e288cc72276ef047ab0c content_type: application/pdf creator: dernst date_created: 2019-09-16T12:42:40Z date_updated: 2020-07-14T12:47:42Z file_id: '6879' file_name: 2019_ScientificReports_Fenu.pdf file_size: 3523795 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A novel magnet-based scratch method for standardisation of wound-healing assays tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ...