6,087 results on '"Institute of Molecular and Cell Biology"'
Search Results
2. [BrainConnexion] - Neurodevice Phase I Trial
- Author
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Institute of Microelectronics, Institute of Molecular and Cell Biology, Institute for Infocomm Research, and Nanyang Technological University
- Published
- 2023
3. Health Status and Its Socio-economic Covariates of the Older Population in Poland - the Nationwide PolSenior2 Survey. (PolSenior2)
- Author
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Ministry of Health, Poland, Medical University of Silesia, Jagiellonian University, International Institute of Molecular and Cell Biology in Warsaw, SGH Warsaw School of Economics, Medical University of Lodz, National Institute of Public Health-National Institute of Hygiene, and Tomasz Zdrojewski, M.D., Ph.D., Assoc. Prof.
- Published
- 2019
4. Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
- Author
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National Science Centre (Poland), Foundation for Polish Science, International Institute of Molecular and Cell Biology (Poland), Ministerio de Economía, Industria y Competitividad (España), Wegrzyn, Katarzyna [0000-0002-3743-8597], Tomiczek, Bartlomiej [0000-0001-9295-663X], Wieczor, Milosz [0000-0003-4990-8629], Czub, Jacek [0000-0003-3639-6935], Moreno-del Álamo, María [0000-0002-6780-9686], Grochowina, Igor [0000-0003-2825-5315], Dutkiewicz, Rafal [0000-0003-4150-0450], Giraldo, R. [0000-0002-5358-7488], Konieczny, Igor [0000-0002-1588-5601], Wegrzyn, Katarzyna, Zabrocka, Elzbieta, Bury, Katarzyna, Tomiczek, Bartlomiej, Wieczor, Milosz, Czub, Jacek, Uciechowska, Urszula, Moreno-del Álamo, María, Walkow, Urszula, Grochowina, Igor, Dutkiewicz, Rafal, Bujnicki, Janusz M., Giraldo, R., Konieczny, Igor, National Science Centre (Poland), Foundation for Polish Science, International Institute of Molecular and Cell Biology (Poland), Ministerio de Economía, Industria y Competitividad (España), Wegrzyn, Katarzyna [0000-0002-3743-8597], Tomiczek, Bartlomiej [0000-0001-9295-663X], Wieczor, Milosz [0000-0003-4990-8629], Czub, Jacek [0000-0003-3639-6935], Moreno-del Álamo, María [0000-0002-6780-9686], Grochowina, Igor [0000-0003-2825-5315], Dutkiewicz, Rafal [0000-0003-4150-0450], Giraldo, R. [0000-0002-5358-7488], Konieczny, Igor [0000-0002-1588-5601], Wegrzyn, Katarzyna, Zabrocka, Elzbieta, Bury, Katarzyna, Tomiczek, Bartlomiej, Wieczor, Milosz, Czub, Jacek, Uciechowska, Urszula, Moreno-del Álamo, María, Walkow, Urszula, Grochowina, Igor, Dutkiewicz, Rafal, Bujnicki, Janusz M., Giraldo, R., and Konieczny, Igor
- Abstract
An essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA-protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the broad host range plasmid RK2, in addition to two winged helix domains, contains a third DNA-binding domain. The phylogenetic analysis revealed that the composition of this unique domain is typical within the described TrfA-like protein family. Both in vitro and in vivo experiments involving the constructed TrfA mutant proteins showed that the newly identified domain is essential for the formation of the protein complex with DNA, contributes to the avidity for interaction with DNA, and the replication activity of the initiator. The analysis of mutant proteins, each containing a single substitution, showed that each of the three domains composing TrfA is essential for the formation of the protein complex with DNA. Furthermore, the new domain, along with the winged helix domains, contributes to the sequence specificity of replication initiator interaction within the plasmid replication origin.
- Published
- 2021
5. Herpes Simplex Virus Gene Products Required for Viral Inhibition of Expression of G1-Phase Functions
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Song, Byeongwoon, Yeh, Kung-Chieh, Liu, Jian, and Knipe, David M.
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- 2001
- Full Text
- View/download PDF
6. Therapeutic strategies for pediatric obesity and their effect in cardiovascular disease risk markers
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Nascimento, H., Biological Science Department, Faculty of Pharmacy, University of Porto, Porto, Portugal, Institute for Molecular and Cell Biology (IBMC), University of Porto, Porto, Portugal, Quintanilha, A., Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal, Santos-Silva, A., and Belo, L.
- Subjects
Obesidade pediátrica, intervenção, doença cardiovascular ,Pediatric obesity ,intervention ,cardiovascular disease - Published
- 2014
7. Feedback inhibition underlies new computational functions of cerebellar interneurons
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Hunter E. Halverson, Jinsook Kim, Andrei Khilkevich, Michael D. Mauk, George J. Augustine, Lee Kong Chian School of Medicine (LKCMedicine), Institute of Molecular and Cell Biology, Singapore, and Institute of Molecular and Cell Biology, A*STAR
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Neurons ,Molecular Layer Interneurons ,General Immunology and Microbiology ,General Neuroscience ,General Medicine ,Cerebellar Learning ,General Biochemistry, Genetics and Molecular Biology ,Feedback ,Purkinje Cells ,Interneurons ,Cerebellum ,Medicine [Science] ,Feedback Inhibition - Abstract
The function of a feedback inhibitory circuit between cerebellar Purkinje cells and molecular layer interneurons (MLIs) was defined by combining optogenetics, neuronal activity recordings both in cerebellar slices and in vivo, and computational modeling. Purkinje cells inhibit a subset of MLIs in the inner third of the molecular layer. This inhibition is non-reciprocal, short-range (less than 200 μm) and is based on convergence of one to two Purkinje cells onto MLIs. During learning-related eyelid movements in vivo, the activity of a subset of MLIs progressively increases as Purkinje cell activity decreases, with Purkinje cells usually leading the MLIs. Computer simulations indicate that these relationships are best explained by the feedback circuit from Purkinje cells to MLIs and that this feedback circuit plays a central role in making cerebellar learning efficient. Ministry of Education (MOE) Published version Ministry of Education, Singapore: MOE2016-T2-1-097 & MOE2017-T3-1-002 (George J Augustine); National Institute of Mental Health: MH46904 & MH74006 (Michael D Mauk).
- Published
- 2022
8. Plk4 Regulates Centriole Asymmetry and Spindle Orientation in Neural Stem Cells
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Anthony Simon, Yuu Kimata, Maddalena Nano, Victor Racine, Daniel W. Buster, Alix Goupil, John M. Ryniawec, Carole Pennetier, Davide Gambarotto, Renata Basto, Delphine Gogendeau, Gregory C. Rogers, Damien Blanc, Centre de recherche de l'Institut Curie [Paris], Institut Curie [Paris], Department of Cell Biology, Sciences III, University of Geneva, Geneva, Switzerland, Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de génétique moléculaire (CGM), Centre National de la Recherche Scientifique (CNRS), Physico-Chimie-Curie (PCC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC), Institute of Molecular and Cell Biology - Molecular controls of Morphogenesis and Tumor Progression, and Institute of Molecular and Cell Biology
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Male ,PLK4 ,Centriole ,[SDV]Life Sciences [q-bio] ,Spindle Apparatus ,Protein Serine-Threonine Kinases ,centrosome positioning ,Biology ,symmetry breaking ,Cdh1 Proteins ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Neural Stem Cells ,spindle orientation ,Animals ,Drosophila Proteins ,Phosphorylation ,centrosomes ,Molecular Biology ,Cells, Cultured ,ComputingMilieux_MISCELLANEOUS ,Centrioles ,030304 developmental biology ,Centrosome ,0303 health sciences ,Astral microtubule nucleation ,Apical cortex ,Cell Cycle ,Cell Biology ,Spd2 ,Neural stem cell ,Cell biology ,Drosophila melanogaster ,Plk4 ,Female ,Stem cell ,Developmental biology ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Summary Defects in mitotic spindle orientation (MSO) disrupt the organization of stem cell niches impacting tissue morphogenesis and homeostasis. Mutations in centrosome genes reduce MSO fidelity, leading to tissue dysplasia and causing several diseases such as microcephaly, dwarfism, and cancer. Whether these mutations perturb spindle orientation solely by affecting astral microtubule nucleation or whether centrosome proteins have more direct functions in regulating MSO is unknown. To investigate this question, we analyzed the consequences of deregulating Plk4 (the master centriole duplication kinase) activity in Drosophila asymmetrically dividing neural stem cells. We found that Plk4 functions upstream of MSO control, orchestrating centriole symmetry breaking and consequently centrosome positioning. Mechanistically, we show that Plk4 acts through Spd2 phosphorylation, which induces centriole release from the apical cortex. Overall, this work not only reveals a role for Plk4 in regulating centrosome function but also links the centrosome biogenesis machinery with the MSO apparatus., Graphical Abstract, Highlights • Drosophila Plk4 mutant NSCs show defects in centriole asymmetry and spindle positioning • Apical centriole anchoring requires the PCM protein Spd-2 and the APC/C activator Fzr • Movement of the centriole toward the basal side of the cell requires Plk4 activity • At the mother centriole, Plk4 phosphorylates Spd2 to trigger PCM shedding and Fzr loss, Mitotic spindle orientation is tightly regulated during development and adulthood to maintain tissue organization and homeostasis. Spindle orientation requires the coordination between centrosomes and cortical cues. Gambarotto et al. report that the centrosome components Plk4 and Spd2 regulate centrosome asymmetry in interphase to influence spindle positioning in mitosis.
- Published
- 2019
9. Purification and characterization of DR_2577 (SlpA) a major S-layer protein from Deinococcus radiodurans
- Author
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Piano, Dario [Univ. of Cagliari, Cagliari (Italy); International Institute of Molecular and Cell Biology, Warsaw (Poland)]
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- 2015
- Full Text
- View/download PDF
10. Sustained activation of non-canonical NF-κB signalling drives glycolytic reprogramming in doxorubicin-resistant DLBCL
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Shen Kiat Lim, Chen Chen Peng, Shannon Low, Varsheni Vijay, Andrea Budiman, Beng Hooi Phang, Jing Quan Lim, Anand D. Jeyasekharan, Soon Thye Lim, Choon Kiat Ong, Suet-Mien Tan, Yinghui Li, School of Biological Sciences, and Institute of Molecular and Cell Biology, A*STAR
- Subjects
Cancer Research ,Oncology ,Non-Hodgkin Lymphoma ,Biological sciences [Science] ,Hematology ,Cell Signalling - Abstract
DLBCL is the most common lymphoma with high tumor heterogeneity. Treatment refractoriness and relapse from R-CHOP therapy in patients remain a clinical problem. Activation of the non-canonical NF-κB pathway is associated with R-CHOP resistance. However, downstream targets of non-canonical NF-κB mediating R-CHOP-induced resistance remains uncharacterized. Here, we identify the common mechanisms underlying both intrinsic and acquired resistance that are induced by doxorubicin, the main cytotoxic component of R-CHOP. We performed global transcriptomic analysis of (1) a panel of resistant versus sensitive and (2) isogenic acquired doxorubicin-resistant DLBCL cell lines following short and chronic exposure to doxorubicin respectively. Doxorubicin-induced stress in resistant cells activates a distinct transcriptional signature that is enriched in metabolic reprogramming and oncogenic signalling. Selective and sustained activation of non-canonical NF-κB signalling in these resistant cells exacerbated their survival by augmenting glycolysis. In response to doxorubicin, p52-RelB complexes transcriptionally activated multiple glycolytic regulators with prognostic significance through increased recruitment at their gene promoters. Targeting p52-RelB and their targets in resistant cells increased doxorubicin sensitivity in vitro and in vivo. Collectively, our study uncovered novel molecular drivers of doxorubicin-induced resistance that are regulated by non-canonical NF-κB pathway. We reveal new avenues of therapeutic targeting for R-CHOP-treated refractory/relapsed DLBCL patients. Nanyang Technological University National Medical Research Council (NMRC) National Research Foundation (NRF) Submitted/Accepted version This study is funded by the National Research Foundation (NRF) Singapore, under its Singapore NRF Fellowship (NRFNRFF2018-04). In addition, we thank the Nanyang Assistant Professorship (NAP) Startup-grant to Y.L. lab and National Medical Research Council (NMRC-OFLCG18May0028), Tanoto Foundation and Ling Foundation for their support.
- Published
- 2022
11. The African coelacanth genome provides insights into tetrapod evolution
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Mariko Forconi, Tereza Manousaki, Peter F. Stadler, Anna Maria Fausto, Simon D. M. White, Shigehiro Kuraku, Sumir Panji, Marcia Lara, Andreas Gnirke, Hervé Philippe, Shaohua Fan, Axel Meyer, Jean Nicolas Volff, Tsutomu Miyake, Sante Gnerre, Thorsten Burmester, Anne Nitsche, Igor Schneider, John J. Stegeman, Alison P. Lee, Kerstin Lindblad-Toh, Peter van Heusden, Chris T. Amemiya, Michael S. Campbell, Ettore Olmo, Vydianathan Ravi, Jason Turner-Maier, Denis Baurain, Gary W. Litman, Federica Di Palma, Nicolas Rohner, Manfred Schartl, Giuseppe Scapigliati, Oleg Simakov, Aaron M. Berlin, Barbara Picone, Ingo Braasch, Byrappa Venkatesh, David R. Nelson, Wilfried Haerty, Diana Tabbaa, M. Gail Mueller, Francesco Buonocore, Eric S. Lander, Gianluca De Moro, Uljana Hesse, Chris P. Ponting, Nathalie Feiner, Junaid Gamieldien, Clifford J. Tabin, Gregory L. Blatch, Tatsuya Ota, Steve Hoffmann, Maria Assunta Biscotti, John H. Postlethwait, Chris L. Organ, Jessica Alföldi, Lin Fan, Mark Robinson, Stephen M. J. Searle, Louise Williams, Mark E. Hahn, Sonja J. Prohaska, Jared V. Goldstone, Dariusz Przybylski, Iain MacCallum, Rosemary A. Dorrington, Joshua Z. Levin, Tatjana Sauka-Spengler, Kenta Sumiyama, Nil Ratan Saha, Henner Brinkmann, Jeremy Johnson, John P. Cannon, Filipe J. Ribeiro, Marco Gerdol, David B. Jaffe, Adriana Canapa, Hakim Tafer, Marco Barucca, Mark Yandell, Evan Mauceli, Alan Christoffels, Sibel I. Karchner, Adrienne L. Edkins, J. Joshua Smith, Bronwen Aken, Neil H. Shubin, Ted Sharpe, Domitille Chalopin, Alberto Pallavicini, Molecular Genetics Program, Benaroya Research Institute, Department of Biology, Northern Arizona University [Flagstaff], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Partenaires INRAE, Université de Montréal (UdeM), Institute of Neuroscience, University of Oregon [Eugene], University of Konstanz, Instituto de Ciências Biológicas, Federal University of Para - Universidade Federal do Para [Belem - Brésil], Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), Utah State University (USU), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Rhodes University, Grahamstown, Department of Life Sciences, Università degli studi di Trieste, Wellcome Trust Sanger Institute, Università Politecnica delle Marche [Ancona] (UNIVPM), Université de Liège, Victoria University [Melbourne], Department for Innovation in Biological, Agro-Food and Forest Systems, Tuscia University, University of Hamburg, Eccles Institute of Human Genetics, University of Utah, University of South Florida [Tampa] (USF), South African National Bioinformatics Institute (SANBI), University of the Western Cape, International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft-University of Konstanz, Biology Department (WHOI), Woods Hole Oceanographic Institution (WHOI), University of Oxford [Oxford], Leipzig University, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA, Keio University, All Children’s Hospital, University of Tennessee, Bioinformatics Group, Department of Computer Science, Universität Leipzig [Leipzig], Graduate University for Advanced Studies, Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore, European Molecular Biology Laboratory (EMBL), National Institute of Genetics (NIG), University of Chicago, Department Physiological Chemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), South African National Department of Science and Technology, National Human Genome Research Institute (NHGRI), European Science Foundation, Amemiya, Chris T., Alföldi, Jessica, Meyer, Axel, Lindblad-Toh, Kerstin, Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Trieste = University of Trieste, Università degli studi della Tuscia [Viterbo], University of the Western Cape (UWC), University of Oxford, Universität Leipzig, Julius-Maximilians-Universität Würzburg (JMU), Chris T., Amemiya, Jessica, Alföldi, Alison P., Lee, Shaohua, Fan, Hervé, Philippe, Iain, Maccallum, Ingo, Braasch, Tereza, Manousaki, Igor, Schneider, Nicolas, Rohner, Chris, Organ, Domitille, Chalopin, Jeramiah J., Smith, Mark, Robinson, Rosemary A., Dorrington, Gerdol, Marco, Bronwen, Aken, Maria Assunta, Biscotti, Marco, Barucca, Denis, Baurain, Aaron M., Berlin, Gregory L., Blatch, Francesco, Buonocore, Thorsten, Burmester, Michael S., Campbell, Adriana, Canapa, John P., Cannon, Alan, Christoffel, DE MORO, Gianluca, Adrienne L., Edkin, Lin, Fan, Anna Maria, Fausto, Nathalie, Feiner, Mariko, Forconi, Junaid, Gamieldien, Sante, Gnerre, Andreas, Gnirke, Jared V., Goldstone, Wilfried, Haerty, Mark E., Hahn, Uljana, Hesse, Steve, Hoffmann, Jeremy, Johnson, Sibel I., Karchner, Shigehiro, Kuraku, Marcia, Lara, Joshua Z., Levin, Gary W., Litman, Evan, Mauceli, Tsutomu, Miyake, M., Gail Mueller, David R., Nelson, Anne, Nitsche, Ettore, Olmo, Tatsuya, Ota, Pallavicini, Alberto, Sumir, Panji, Barbara, Picone, Chris P., Ponting, Sonja J., Prohaska, Dariusz, Przybylski, Nil Ratan, Saha, Vydianathan, Ravi, Filipe J., Ribeiro, Tatjana Sauka, Spengler, Giuseppe, Scapigliati, Stephen M. J., Searle, Ted, Sharpe, Oleg, Simakov, Peter F., Stadler, John J., Stegeman, Kenta, Sumiyama, Diana, Tabbaa, Hakim, Tafer, Jason Turner, Maier, Peter van, Heusden, Simon, White, Louise, William, Mark, Yandell, Henner, Brinkmann, Jean Nicolas, Volff, Clifford J., Tabin, Neil, Shubin, Manfred, Schartl, David B., Jaffe, John H., Postlethwait, Byrappa, Venkatesh, Federica Di, Palma, Eric S., Lander, Axel, Meyer, and Kerstin Lindblad, Toh
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0106 biological sciences ,terrestrial environment ,adaptation, ancestry, brain, excretion, finfish, gene expression, genome, immunity, olfaction, phylogenetics, protein, terrestrial environment, tetrapod ,[SDV]Life Sciences [q-bio] ,LATIMERIA-MENADOENSIS ,adaptation ,Chick Embryo ,MITOCHONDRIAL GENOME ,LIVING FOSSIL ,SEQUENCE ,GENES ,MODEL ,TRANSCRIPTION ,CHROMOSOMES ,RETENTION ,CHALUMNAE ,01 natural sciences ,Genome ,Animals, Genetically Modified ,Mice ,poisson ,Coelacanth ,Conserved Sequence ,Phylogeny ,Lungfish ,0303 health sciences ,Multidisciplinary ,biology ,Latimeria ,Fishes ,Genes, Homeobox ,Vertebrate ,Genomics ,Biological Evolution ,phylogenetics ,Enhancer Elements, Genetic ,évolution du génome ,Vertebrates ,excretion ,Comperative genomics ,Living fossil ,olfaction ,Genome evolution ,finfish ,brain ,Molecular Sequence Data ,tetrapod ,010603 evolutionary biology ,Article ,Evolution, Molecular ,03 medical and health sciences ,ddc:570 ,biology.animal ,Animals ,[INFO]Computer Science [cs] ,14. Life underwater ,030304 developmental biology ,Comparative genomics ,ancestry ,génome ,Extremities ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,biology.organism_classification ,immunity ,body regions ,Immunoglobulin M ,Evolutionary biology ,gene expression ,protein ,Sequence Alignment - Abstract
Acquisition and storage of Latimeria chalumnae samples was supported by grants from the African Coelacanth Ecosystem Programme of the South African National Department of Science and Technology. Generation of the Latimeria chalumnae and Protopterus annectens sequences by the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University was supported by grants from the National Human Genome Research Institute (NHGRI). K.L.T. is the recipient of a EURYI award from the European Science Foundation. We would also like to thank the Genomics Sequencing Platform of the Broad Institute for sequencing the L. chalumnae genome and L. chalumnae and P. annectens transcriptomes, S. Ahamada, R. Stobbs and the Association pour le Protection de Gombesa (APG) for their help in obtaining coelacanth samples, Y. Zhao for the use of data from Rana chensinensis, and L. Gaffney, C. Hamilton and J. Westlund for assistance with figure preparation. 10; International audience; The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
- Published
- 2013
12. A median fin derived from the lateral plate mesoderm and the origin of paired fins
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Keh-Weei Tzung, Robert L. Lalonde, Karin D. Prummel, Harsha Mahabaleshwar, Hannah R. Moran, Jan Stundl, Amanda N. Cass, Yao Le, Robert Lea, Karel Dorey, Monika J. Tomecka, Changqing Zhang, Eline C. Brombacher, William T. White, Henry H. Roehl, Frank J. Tulenko, Christoph Winkler, Peter D. Currie, Enrique Amaya, Marcus C. Davis, Marianne E. Bronner, Christian Mosimann, Tom J. Carney, Lee Kong Chian School of Medicine (LKCMedicine), and Institute of Molecular and Cell Biology, A*STAR
- Subjects
BMP Signaling ,Multidisciplinary ,Medicine [Science] ,Anal Fin - Abstract
The development of paired appendages was a key innovation during evolution and facilitated the aquatic to terrestrial transition of vertebrates. Largely derived from the lateral plate mesoderm (LPM), one hypothesis for the evolution of paired fins invokes derivation from unpaired median fins via a pair of lateral fin folds located between pectoral and pelvic fin territories1. Whilst unpaired and paired fins exhibit similar structural and molecular characteristics, no definitive evidence exists for paired lateral fin folds in larvae or adults of any extant or extinct species. As unpaired fin core components are regarded as exclusively derived from paraxial mesoderm, any transition presumes both co-option of a fin developmental programme to the LPM and bilateral duplication2. Here, we identify that the larval zebrafish unpaired pre-anal fin fold (PAFF) is derived from the LPM and thus may represent a developmental intermediate between median and paired fins. We trace the contribution of LPM to the PAFF in both cyclostomes and gnathostomes, supporting the notion that this is an ancient trait of vertebrates. Finally, we observe that the PAFF can be bifurcated by increasing bone morphogenetic protein signalling, generating LPM-derived paired fin folds. Our work provides evidence that lateral fin folds may have existed as embryonic anlage for elaboration to paired fins. Agency for Science, Technology and Research (A*STAR) Ministry of Education (MOE) Published version This work was funded by the Industry Aligned Fund (IAF) Agency for Science, Technology and Research (grant to T.J.C. and K.-W.T.); Ministry of Education (MoE) Tier 3 (grant 2016-T3-1-005 to T.J.C., C.W. and H.M.); Ministry of Education (MoE) Tier 1 (grant 2016-T1-001-055 to T.J.C. and C.Z.); Ministry of Education (MoE) Tier 2 (grant MOE-T2EP30221-0008 to C.W.); the Company of Biologists (travelling fellowship to M.J.T.); the National Science Foundation (grants IOS-1853949 to M.C.D. and 2203311 to C.M.); the Swiss National Science Foundation Sinergia (grant CRSII5_180345 to C.M.); the Swiss Bridge Foundation (C.M.); Additional Ventures Single Ventricle Research Fund (SVRF) (grant 1048003 to C.M.); the University of Colorado School of Medicine Anschutz Medical Campus and the Children’s Hospital Colorado Foundation (C.M.); the National Institutes of Health (NIH), National Institute of General Medical Sciences (grants 1T32GM141742-01 to H.R.M. and 3T32GM121742-02S1 to H.R.M.); Australian Research Council (discovery grant DP200103219 to F.J.T. and P.D.C); National Health and Medical Research Council (senior principal research fellow APP1136567 to P.D.C.); and the NIH (grant R35NS111564 to J.S. and M.E.B.).
- Published
- 2023
13. NF-κB/p52 augments ETS1 binding genome-wide to promote glioma progression
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Yinghui Li, Nicholas Sim, School of Biological Sciences, and Institute of Molecular and Cell Biology (IMCB), A*STAR
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ETS1 Protein ,Biological sciences [Science] ,Medicine (miscellaneous) ,Glioma ,General Agricultural and Biological Sciences ,General Biochemistry, Genetics and Molecular Biology - Abstract
Gliomas are highly invasive and chemoresistant cancers, making them challenging to treat. Chronic inflammation is a key driver of glioma progression as it promotes aberrant activation of inflammatory pathways such as NF-κB signalling, which drives cancer cell invasion and angiogenesis. NF-κB factors typically dimerise with its own family members, but emerging evidence of their promiscuous interactions with other oncogenic factors has been reported to promote transcription of new target genes and function. Here, we show that non-canonical NF-κB activation directly regulates p52 at the ETS1 promoter, activating its expression. This impacts the genomic and transcriptional landscape of ETS1 in a glioma-specific manner. We further show that enhanced non-canonical NF-κB signalling promotes the co-localisation of p52 and ETS1, resulting in transcriptional activation of non-κB and/or non-ETS glioma-promoting genes. We conclude that p52-induced ETS1 overexpression in glioma cells remodels the genome-wide regulatory network of p52 and ETS1 to transcriptionally drive cancer progression. Nanyang Technological University National Research Foundation (NRF) Published version This work is supported by the National Research Foundation (NRF), Singapore, under the Singapore NRF Fellowship (NRF-NRFF2018-04). Additionally, we thank Nanyang Technological University for the PhD scholarship support of N.S. and Nanyang Assistant Professorship start-up grant to Y.L. lab.
- Published
- 2023
14. GEMC1 and MCIDAS interactions with SWI/SNF complexes regulate the multiciliated cell-specific transcriptional program
- Author
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Michael Lewis, Berta Terré, Philip A. Knobel, Tao Cheng, Hao Lu, Camille Stephan-Otto Attolini, Jordann Smak, Etienne Coyaud, Isabel Garcia-Cao, Shalu Sharma, Chithran Vineethakumari, Jessica Querol, Gabriel Gil-Gómez, Gabriele Piergiovanni, Vincenzo Costanzo, Sandra Peiró, Brian Raught, Haotian Zhao, Xavier Salvatella, Sudipto Roy, Moe R. Mahjoub, Travis H. Stracker, Institut Català de la Salut, [Lewis M, Attolini CSO] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. [Terré B] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. MRC Clinical Trials Unit at UCL, London, UK. [Knobel PA] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. CDR-Life AG, Zurich, Switzerland. [Cheng T] Washington University in St Louis, Departments of Medicine (Nephrology), Cell Biology and Physiology, St. Louis, MO, USA. [Lu H] Institute of Molecular and Cell Biology, Proteos, Singapore, Singapore. [Querol J] Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus
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Cancer Research ,Cellular and Molecular Neuroscience ,fenómenos genéticos::regulación de la expresión génica [FENÓMENOS Y PROCESOS] ,Cell Physiological Phenomena::Cell Differentiation [PHENOMENA AND PROCESSES] ,Immunology ,Regulació genètica ,Cell Biology ,Diferenciació cel·lular ,Genetic Phenomena::Gene Expression Regulation [PHENOMENA AND PROCESSES] ,fenómenos fisiológicos celulares::diferenciación celular [FENÓMENOS Y PROCESOS] - Abstract
Cell signalling; Transcription Señalización celular; Transcripción Senyalització cel·lular; Transcripció Multiciliated cells (MCCs) project dozens to hundreds of motile cilia from their apical surface to promote the movement of fluids or gametes in the mammalian brain, airway or reproductive organs. Differentiation of MCCs requires the sequential action of the Geminin family transcriptional activators, GEMC1 and MCIDAS, that both interact with E2F4/5-DP1. How these factors activate transcription and the extent to which they play redundant functions remains poorly understood. Here, we demonstrate that the transcriptional targets and proximal proteomes of GEMC1 and MCIDAS are highly similar. However, we identified distinct interactions with SWI/SNF subcomplexes; GEMC1 interacts primarily with the ARID1A containing BAF complex while MCIDAS interacts primarily with BRD9 containing ncBAF complexes. Treatment with a BRD9 inhibitor impaired MCIDAS-mediated activation of several target genes and compromised the MCC differentiation program in multiple cell based models. Our data suggest that the differential engagement of distinct SWI/SNF subcomplexes by GEMC1 and MCIDAS is required for MCC-specific transcriptional regulation and mediated by their distinct C-terminal domains. We thank F. Guillemot, C. Lynch, M. Serrano, and S. Brody for antibodies, F. Supek for cells and reagents, A. Holland and C. Jewett for DEUP1 antibody and expansion microscopy suggestions, J. St-Germain for data analysis, J. Lüders for help with expansion microscopy, T. Dantas for sharing unpublished data and support from the IRB Functional Genomics and Biostatistics/Bioinformatics, Protein Expression and Mass Spectrometry Core Facilities. ML and BT were funded by Severo Ochoa FPI fellowships from the Ministry of Science, Innovation and Universities (MCIU), PK by an Advanced Postdoc Mobility fellowship from the Swiss National Science Foundation and the Kurt and Senta Herrmann Foundation and I.G.C by an AECC fellowship. THS was funded by the MCIU (PGC2018-095616-B-I00/GINDATA) and by the NIH Intramural Research Program, National Cancer Institute, Center for Cancer Research. X.S. was supported by MINECO (PID2019-110198RB-I00) and the European Research Council (CONCERT, contract number 648201). IRB Barcelona is the recipient of institutional funding from FEDER and the Centres of Excellence Severo Ochoa award to IRB Barcelona from MINECO (Government of Spain). MRM was funded by the National Heart, Lung and Blood Institute of the NIH (R01-HL128370). VC was funded by the Associazione Italiana per la Ricerca sul Cancro (AIRC), the European Research Council (ERC) grant 614541 and the GiovanniArmenise foundation career development award to VC. SR was funded by a Singapore National Medical Research Council (NMRC) Open Fund-Individual Research Grant (OFIRG19nov-0037). HZ was supported by National Cancer Institute (R01 CA220551).
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- 2023
15. Transcriptional regulation during aberrant activation of NF-κB signalling in cancer
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Yinghui Li, Kamalakshi Deka, School of Biological Sciences, and Institute of Molecular and Cell Biology, A*STAR
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NF-κB Signalling ,Biological sciences [Science] ,General Medicine ,Cancer - Abstract
The NF-κB signalling pathway is a major signalling cascade involved in the regulation of inflammation and innate immunity. It is also increasingly recognised as a crucial player in many steps of cancer initiation and progression. The five members of the NF-κB family of transcription factors are activated through two major signalling pathways, the canonical and non-canonical pathways. The canonical NF-κB pathway is prevalently activated in various human malignancies as well as inflammation-related disease conditions. Meanwhile, the significance of non-canonical NF-κB pathway in disease pathogenesis is also increasingly recognized in recent studies. In this review, we discuss the double-edged role of the NF-κB pathway in inflammation and cancer, which depends on the severity and extent of the inflammatory response. We also discuss the intrinsic factors, including selected driver mutations, and extrinsic factors, such as tumour microenvironment and epigenetic modifiers, driving aberrant activation of NF-κB in multiple cancer types. We further provide insights into the importance of the interaction of NF-κB pathway components with various macromolecules to its role in transcriptional regulation in cancer. Finally, we provide a perspective on the potential role of aberrant NF-κB activation in altering the chromatin landscape to support oncogenic development. National Research Foundation (NRF) Published version This work is funded by the National Research Foundation (NRF) Singapore, under its Singapore NRF Fellowship (NRF-NRFF2018-04).
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- 2023
16. Photobiocatalytic Oxyfunctionalization with High Reaction Rate using a Baeyer–Villiger Monooxygenase from Burkholderia xenovorans in Metabolically Engineered Cyanobacteria
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Elif Erdem, Lenny Malihan-Yap, Leen Assil-Companioni, Hanna Grimm, Giovanni Davide Barone, Carole Serveau-Avesque, Agnes Amouric, Katia Duquesne, Véronique de Berardinis, Yagut Allahverdiyeva, Véronique Alphand, Robert Kourist, Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Graz University of Technology [Graz] (TU Graz), Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto = University of Porto, Instituto de Biologia Molecular e Celular - institute for molecular and cell biology [Porto, Portugal] (IBMC), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Turku, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
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photosynthesis ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,biocatalysis ,[CHIM.ORGA]Chemical Sciences/Organic chemistry ,010405 organic chemistry ,[CHIM.CATA]Chemical Sciences/Catalysis ,General Chemistry ,010402 general chemistry ,enzyme catalysis ,cyanobacteria ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Baeyer−Villiger oxidation ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience; Baeyer−Villiger monooxygenases (BVMOs) catalyze the oxidation of ketones to lactones under very mild reaction conditions. This enzymatic route is hindered by the requirement of a stoichiometric supply of auxiliary substrates for cofactor recycling and difficulties with supplying the necessary oxygen. The recombinant production of BVMO in cyanobacteria allows the substitution of auxiliary organic cosubstrates with water as an electron donor and the utilization of oxygen generated by photosynthetic water splitting. Herein, we report the identification of a BVMO from Burkholderia xenovorans (BVMO Xeno) that exhibits higher reaction rates in comparison to currently identified BVMOs. We report a 10fold increase in specific activity in comparison to cyclohexanone monooxygenase (CHMO Acineto) in Synechocystis sp. PCC 6803 (25 vs 2.3 U g DCW −1 at an optical density of OD 750 = 10) and an initial rate of 3.7 ± 0.2 mM h −1. While the cells containing CHMO Acineto showed a considerable reduction of cyclohexanone to cyclohexanol, this unwanted side reaction was almost completely suppressed for BVMO Xeno , which was attributed to the much faster lactone formation and a 10-fold lower K M value of BVMO Xeno toward cyclohexanone. Furthermore, the whole-cell catalyst showed outstanding stereoselectivity. These results show that, despite the self-shading of the cells, high specific activities can be obtained at elevated cell densities and even further increased through manipulation of the photosynthetic electron transport chain (PETC). The obtained rates of up to 3.7 mM h −1 underline the usefulness of oxygenic cyanobacteria as a chassis for enzymatic oxidation reactions. The photosynthetic oxygen evolution can contribute to alleviating the highly problematic oxygen mass-transfer limitation of oxygendependent enzymatic processes.
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- 2021
17. TENT5 cytoplasmic noncanonical poly(A) polymerases regulate the innate immune response in animals
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Liudkovska, Vladyslava, Krawczyk, Paweł S., Brouze, Aleksandra, Gumińska, Natalia, Wegierski, Tomasz, Cysewski, Dominik, Mackiewicz, Zuzanna, Ewbank, Jonathan J., Drabikowski, Krzysztof, Mroczek, Seweryn, Dziembowski, Andrzej, International Institute of Molecular and Cell Biology [Warsaw] (IIMCB), University of Warsaw (UW), Institute of Biochemistry and Biophysics [Warsaw] (IBB), Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Turing Centre for Living Systems [Marseille] (TCLS)
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Multidisciplinary ,[SDV]Life Sciences [q-bio] - Abstract
Innate immunity is the first line of host defense against pathogens. Here, through global transcriptome and proteome analyses, we uncover that newly described cytoplasmic poly(A) polymerase TENT-5 (terminal nucleotidyltransferase 5) enhances the expression of secreted innate immunity effector proteins in Caenorhabditis elegans . Direct RNA sequencing revealed that multiple mRNAs with signal peptide–encoding sequences have shorter poly(A) tails in tent-5 –deficient worms. Those mRNAs are translated at the endoplasmic reticulum where a fraction of TENT-5 is present, implying that they represent its direct substrates. Loss of tent-5 makes worms more susceptible to bacterial infection. Notably, the role of TENT-5 in innate immunity is evolutionarily conserved. Its orthologs, TENT5A and TENT5C, are expressed in macrophages and induced during their activation. Analysis of macrophages devoid of TENT5A/C revealed their role in the regulation of secreted proteins involved in defense response. In summary, our study reveals cytoplasmic polyadenylation to be a previously unknown component of the posttranscriptional regulation of innate immunity in animals.
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- 2022
18. Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences
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Ying Zhang, Vinay Tergaonkar, Xinya Li, Melissa J. Fullwood, Yu Zhang, Fan Cao, Sambhavi Animesh, Yan Ping Loh, Yichao Cai, Wee Joo Chng, Chee Keong Kwoh, Semih Can Akıncılar, Fullwood, Melissa J [0000-0003-0692-4434], Apollo - University of Cambridge Repository, School of Biological Sciences, School of Computer Science and Engineering, and Institute of Molecular and Cell Biology, A*STAR
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FOS: Computer and information sciences ,Bioinformatics ,QH301-705.5 ,DNA sequence ,Method ,Computational biology ,Biology ,QH426-470 ,DNA sequencing ,Machine Learning ,chemistry.chemical_compound ,Hi-C ,RNA polymerase ,Gene expression ,Machine learning ,3D genome organization ,Genetics ,Humans ,Biology (General) ,ChIA-PET ,Genome ,Leukemia ,Artificial neural network ,Base Sequence ,Biological sciences [Science] ,Computational Biology ,3D Genome Organization ,Human genetics ,Chromatin ,chemistry ,CTCF ,Computer science and engineering [Engineering] ,Neural Networks, Computer ,Chromatin interactions - Abstract
Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interaction neural network (ChINN), to predict chromatin interactions between open chromatin regions using only DNA sequences. ChINN predicts CTCF- and RNA polymerase II-associated and Hi-C chromatin interactions. ChINN shows good across-sample performances and captures various sequence features for chromatin interaction prediction. We apply ChINN to 6 chronic lymphocytic leukemia (CLL) patient samples and a published cohort of 84 CLL open chromatin samples. Our results demonstrate extensive heterogeneity in chromatin interactions among CLL patient samples. Ministry of Education (MOE) National Research Foundation (NRF) Published version This research is supported by the National Research Foundation (NRF) Singapore through an NRF Fellowship awarded to M.J.F (NRF-NRFF2012-054) and NTU start-up funds awarded to M.J.F. This research is supported by the RNA Biology Center at the Cancer Science Institute of Singapore, NUS, as part of funding under the Singapore Ministry of Education Academic Research Fund Tier 3 awarded to Daniel Tenen as lead PI with M.J.F as co-investigator (MOE2014-T3-1-006). This research is supported by a National Research Foundation Competitive Research Programme grant awarded to V.T. as lead PI and M.J.F. as co-PI (NRF-CRP17-2017-02). This research is supported by the National Research Foundation Singapore and the Singapore Ministry of Education under its Research Centres of Excellence initiative. This research is supported by a Ministry of Education Tier II grant awarded to M.J.F (T2EP30120-0020).
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- 2021
19. Single-Cell Transcriptome of Wet AMD Patient-Derived Endothelial Cells in Angiogenic Sprouting
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Natalie Jia Ying Yeo, Vanessa Wazny, Nhi Le Uyen Nguyen, Chun-Yi Ng, Kan Xing Wu, Qiao Fan, Chui Ming Gemmy Cheung, Christine Cheung, Lee Kong Chian School of Medicine (LKCMedicine), and Institute of Molecular and Cell Biology, A*STAR
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Vascular Endothelial Growth Factor A ,Fibrin ,Vascular Endothelial Growth Factors ,Interleukins ,Organic Chemistry ,Endothelial Cells ,Angiogenesis Inhibitors ,General Medicine ,age-related macular degeneration ,blood outgrowth endothelial cells ,sprouting angiogenesis ,single-cell transcriptome ,endothelial cell states ,Catalysis ,Choroidal Neovascularization ,Computer Science Applications ,Inorganic Chemistry ,Blood Outgrowth Endothelial Cells ,Age-Related Macular Degeneration ,Wet Macular Degeneration ,Humans ,Medicine [Science] ,Physical and Theoretical Chemistry ,Amino Acids ,Transcriptome ,Molecular Biology ,Spectroscopy - Abstract
Age-related macular degeneration (AMD) is a global leading cause of visual impairment in older populations. 'Wet' AMD, the most common subtype of this disease, occurs when pathological angiogenesis infiltrates the subretinal space (choroidal neovascularization), causing hemorrhage and retinal damage. Gold standard anti-vascular endothelial growth factor (VEGF) treatment is an effective therapy, but the long-term prevention of visual decline has not been as successful. This warrants the need to elucidate potential VEGF-independent pathways. We generated blood out-growth endothelial cells (BOECs) from wet AMD and normal control subjects, then induced angiogenic sprouting of BOECs using a fibrin gel bead assay. To deconvolute endothelial heterogeneity, we performed single-cell transcriptomic analysis on the sprouting BOECs, revealing a spectrum of cell states. Our wet AMD BOECs share common pathways with choroidal neovascularization such as extracellular matrix remodeling that promoted proangiogenic phenotype, and our 'activated' BOEC subpopulation demonstrated proinflammatory hallmarks, resembling the tip-like cells in vivo. We uncovered new molecular insights that pathological angiogenesis in wet AMD BOECs could also be driven by interleukin signaling and amino acid metabolism. A web-based visualization of the sprouting BOEC single-cell transcriptome has been created to facilitate further discovery research. Agency for Science, Technology and Research (A*STAR) Ministry of Education (MOE) Nanyang Technological University Published version The team from Nanyang Technological University Singapore was funded by the Nanyang Assistant Professorship and Academic Research Fund grants (MOE2018-T2-1-042 and RG88/21) from the Ministry of Education, Singapore. N.J.Y.Y and V.W. were supported by the Nanyang President’s Graduate Scholarship. C.C. and C.M.G.C. were funded by the SERI-IMCB Program in Retinal Angiogenic Diseases (SIPRAD) grant (SPF2014/002) from Agency for Science, Technology and Research, Singapore.
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- 2022
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20. Variable allelic expression of imprinted genes at the Peg13, Trappc9, Ago2 cluster in single neural cells
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Michael Claxton, Michela Pulix, Michelle K. Y. Seah, Ralph Bernardo, Peng Zhou, Sultan Aljuraysi, Triantafillos Liloglou, Philippe Arnaud, Gavin Kelsey, Daniel M. Messerschmidt, Antonius Plagge, University of Liverpool, University of Copenhagen = Københavns Universitet (UCPH), Institute of Molecular and Cell Biology [Singapore, Singapore] (IMCB / A*STAR), Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), University of Cambridge [UK] (CAM), Arnaud, Philippe, Apollo - University of Cambridge Repository, and Plagge, Antonius [0000-0001-6592-1343]
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Trappc9 ,Ago2 ,allelic expression ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,[SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN] ,Cell Biology ,[SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,genomic imprinting ,Peg13 ,Cell and Developmental Biology ,neural stem cell ,neurosphere ,[SDV.BBM.MN] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN] ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,single-cell analysis ,[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Developmental Biology - Abstract
Peer reviewed: True, Acknowledgements: We would like to thank all staff of the animal facility for their dedicated work. We would also like to thank Abigail Clark and Megan Green for contributions to early stages of the project., Genomic imprinting is an epigenetic process through which genes are expressed in a parent-of-origin specific manner resulting in mono-allelic or strongly biased expression of one allele. For some genes, imprinted expression may be tissue-specific and reliant on CTCF-influenced enhancer-promoter interactions. The Peg13 imprinting cluster is associated with neurodevelopmental disorders and comprises canonical imprinted genes, which are conserved between mouse and human, as well as brain-specific imprinted genes in mouse. The latter consist of Trappc9, Chrac1 and Ago2, which have a maternal allelic expression bias of ∼75% in brain. Findings of such allelic expression biases on the tissue level raise the question of how they are reflected in individual cells and whether there is variability and mosaicism in allelic expression between individual cells of the tissue. Here we show that Trappc9 and Ago2 are not imprinted in hippocampus-derived neural stem cells (neurospheres), while Peg13 retains its strong bias of paternal allele expression. Upon analysis of single neural stem cells and in vitro differentiated neurons, we find not uniform, but variable states of allelic expression, especially for Trappc9 and Ago2. These ranged from mono-allelic paternal to equal bi-allelic to mono-allelic maternal, including biased bi-allelic transcriptional states. Even Peg13 expression deviated from its expected paternal allele bias in a small number of cells. Although the cell populations consisted of a mosaic of cells with different allelic expression states, as a whole they reflected bulk tissue data. Furthermore, in an attempt to identify potential brain-specific regulatory elements across the Trappc9 locus, we demonstrate tissue-specific and general silencer activities, which might contribute to the regulation of its imprinted expression bias.
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- 2022
21. MCI-frcnn: A deep learning method for topological micro-domain boundary detection
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Simon Zhongyuan Tian, Pengfei Yin, Kai Jing, Yang Yang, Yewen Xu, Guangyu Huang, Duo Ning, Melissa J. Fullwood, Meizhen Zheng, School of Biological Sciences, Cancer Science Institute of Singapore, NUS, and Institute of Molecular and Cell Biology, A*STAR
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Deep Learning ,Biological sciences [Science] ,Topological Micro-Domain ,Cell Biology ,Developmental Biology - Abstract
Chromatin structural domains, or topologically associated domains (TADs), are a general organizing principle in chromatin biology. RNA polymerase II (RNAPII) mediates multiple chromatin interactive loops, tethering together as RNAPII-associated chromatin interaction domains (RAIDs) to offer a framework for gene regulation. RAID and TAD alterations have been found to be associated with diseases. They can be further dissected as micro-domains (micro-TADs and micro-RAIDs) by clustering single-molecule chromatin-interactive complexes from next-generation three-dimensional (3D) genome techniques, such as ChIA-Drop. Currently, there are few tools available for micro-domain boundary identification. In this work, we developed the MCI-frcnn deep learning method to train a Faster Region-based Convolutional Neural Network (Faster R-CNN) for micro-domain boundary detection. At the training phase in MCI-frcnn, 50 images of RAIDs from Drosophila RNAPII ChIA-Drop data, containing 261 micro-RAIDs with ground truth boundaries, were trained for 7 days. Using this well-trained MCI-frcnn, we detected micro-RAID boundaries for the input new images, with a fast speed (5.26 fps), high recognition accuracy (AUROC = 0.85, mAP = 0.69), and high boundary region quantification (genomic IoU = 76%). We further applied MCI-frcnn to detect human micro-TADs boundaries using human GM12878 SPRITE data and obtained a high region quantification score (mean gIoU = 85%). In all, the MCI-frcnn deep learning method which we developed in this work is a general tool for micro-domain boundary detection. Ministry of Education (MOE) National Research Foundation (NRF) Published version This work was supported by grants from the National Natural Science Foundation of China (32170644), the National Key R&D Program of China (20222YFC3400400), the Shenzhen Fundamental Research Programme (JCYJ20220530115211026), and the Shenzhen Innovation Committee of Science and Technology (ZDSYS20200811144002008). MF is supported by the National Research Foundation Singapore and the Singapore Ministry of Education under its Research Centres of Excellence initiative and by a Ministry of Education Tier II grant awarded to MF (T2EP30120- 0020).
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- 2022
22. Acknowledging and citing core facilities
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Kivinen, Katja, GAM van Luenen, Henri, Alcalay, Myriam, Bock, Christoph, Dodzian, Joanna, Hoskova, Katerina, Hoyle, Danielle, Hradil, Ondrej, Christensen, Sofie Kjellerup, Korn, Bernhard, Kosteas, Theodoros, Morales, Mònica, Skowronek, Krzysztof, Theodorou, Vasiliki, van Minnebruggen, Geert, Salamero, Jean, Premvardhan, Lavanya, Institute for Molecular Medicine Finland [Helsinki] (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Netherlands Cancer Institute (NKI), Antoni van Leeuwenhoek Hospital, European Institute of Oncology [Milan] (ESMO), Research Center for Molecular Medicine of the Austrian Academy of Sciences [Vienna, Austria] (CeMM ), Austrian Academy of Sciences (OeAW), International Institute of Molecular and Cell Biology [Warsaw] (IIMCB), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), The Babraham Institute [Cambridge, UK], EU-LIFE Alliance [Barcelona], Friedrich Miescher Institute for Biomedical Research (FMI), Novartis Research Foundation, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Foundation for Research and Technology - Hellas (FORTH), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), and Institut Curie [Paris]
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[SDV]Life Sciences [q-bio] ,[SHS]Humanities and Social Sciences - Abstract
International audience
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- 2022
23. Light-driven hydroxylation of testosterone by Synechocystis sp. PCC 6803 expressing the heterologous CYP450 monooxygenase CYP110D1
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Francesco Mascia, Sara B. Pereira, Catarina C. Pacheco, Paulo Oliveira, Jennifer Solarczek, Anett Schallmey, Robert Kourist, Véronique Alphand, Paula Tamagnini, Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Microélectronique, Electromagnétisme et Photonique - Laboratoire d'Hyperfréquences et Caractérisation (IMEP-LAHC), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Aix Marseille Université (AMU), Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto = University of Porto, Instituto de Biologia Molecular e Celular - institute for molecular and cell biology [Porto, Portugal] (IBMC), Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], and Graz University of Technology [Graz] (TU Graz)
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[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,[CHIM.ORGA]Chemical Sciences/Organic chemistry ,Environmental Chemistry ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Pollution - Abstract
International audience; The selective hydroxylation of steroids through chemical synthesis is a complex reaction with a high environmental impact. The use of photoautotrophic microorganisms expressing heterologous monooxygenases could overcome this problem by fueling the reaction with electrons and O2 derived from the light-dependent oxidation of water, occurring during photosynthesis. Here, the light-driven selective hydroxylation of testosterone into 15β-hydroxytestosterone was achieved using whole-cells of the unicellular cyanobacterium Synechocystis sp. PCC 6803 expressing the heterologous CYP450 monooxygenase, CYP110D1. Additionally, the reaction conditions including cell density, aeration, and substrate concentration were optimized, leading to a maximum specific activity of 1 U gCDW−1. This value is about 2-fold higher than the one achieved using the model heterotrophic bacterium, E. coli, in which was necessary to express not only CYP110D1 but also its electron partners, and to use glucose as a sacrificial electron donor. Altogether, the results obtained here demonstrate the higher efficiency and sustainability (94% atom economy) of testosterone hydroxylation using our engineered Synechocystis chassis, compared to biocatalysis with heterotrophic microorganisms or chemical synthesis
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- 2022
24. Accurate Identification of DNA Replication Origin by Fusing Epigenomics and Chromatin Interaction Information
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Fu-Ying Dao, Hao Lv, Melissa J. Fullwood, Hao Lin, School of Biological Sciences, and Institute of Molecular and Cell Biology, A∗STAR
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Multidisciplinary ,Cell Lines ,Biological sciences [Science] ,DNA - Abstract
DNA replication initiation is a complex process involving various genetic and epigenomic signatures. The correct identification of replication origins (ORIs) could provide important clues for the study of a variety of diseases caused by replication. Here, we design a computational approach named iORI-Epi to recognize ORIs by incorporating epigenome-based features, sequence-based features, and 3D genome-based features. The iORI-Epi displays excellent robustness and generalization ability on both training datasets and independent datasets of K562 cell line. Further experiments confirm that iORI-Epi is highly scalable in other cell lines (MCF7 and HCT116). We also analyze and clarify the regulatory role of epigenomic marks, DNA motifs, and chromatin interaction in DNA replication initiation of eukaryotic genomes. Finally, we discuss gene enrichment pathways from the perspective of ORIs in different replication timing states and heuristically dissect the effect of promoters on replication initiation. Our computational methodology is worth extending to ORI identification in other eukaryotic species. Published version
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- 2022
25. Trans-interaction of risk loci 6p24.1 and 10q11.21 is associated with endothelial damage in coronary artery disease
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Kai Yi Tay, Kan Xing Wu, Florence Wen Jing Chioh, Matias Ilmari Autio, Nicole Min Qian Pek, Balakrishnan Chakrapani Narmada, Sock-Hwee Tan, Adrian Fatt-Hoe Low, Michelle Mulan Lian, Elaine Guo Yan Chew, Hwee Hui Lau, Shih Ling Kao, Adrian Kee Keong Teo, Jia Nee Foo, Roger Sik Yin Foo, Chew Kiat Heng, Mark Yan Yee Chan, Christine Cheung, Lee Kong Chian School of Medicine (LKCMedicine), School of Biological Sciences, Institute of Molecular and Cell Biology (IMCB), A*STAR, and Genome Institute of Singapore
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Genotype ,Single Nucleotide Polymorphisms ,Humans ,Endothelial Cells ,Medicine [Science] ,Coronary Artery Disease ,Cardiology and Cardiovascular Medicine ,Polymorphism, Single Nucleotide ,Alleles - Abstract
Background and aims: Single nucleotide polymorphism rs6903956 has been identified as one of the genetic risk factors for coronary artery disease (CAD). However, rs6903956 lies in a non-coding locus on chromosome 6p24.1. We aim to interrogate the molecular basis of 6p24.1 containing rs6903956 risk alleles in endothelial disease biology. Methods and Results: We generated induced pluripotent stem cells (iPSCs) from CAD patients (AA risk genotype at rs6903956) and non-CAD subjects (GG non-risk genotype at rs6903956). CRISPR-Cas9-based deletions (Δ63- 89bp) on 6p24.1, including both rs6903956 and a short tandem repeat variant rs140361069 in linkage disequilibrium, were performed to generate isogenic iPSC-derived endothelial cells. Edited CAD endothelial cells, with removal of ‘A’ risk alleles, exhibited a global transcriptional downregulation of pathways relating to abnormal vascular physiology and activated endothelial processes. A CXC chemokine ligand on chromosome 10q11.21, CXCL12, was uncovered as a potential effector gene in CAD endothelial cells. Underlying this effect was the preferential inter-chromosomal interaction of 6p24.1 risk locus to a weak promoter of CXCL12, confirmed by chromatin conformation capture assays on our iPSC-derived endothelial cells. Functionally, risk genotypes AA/AG at rs6903956 were associated significantly with elevated levels of circulating damaged endothelial cells in CAD patients. Circulating endothelial cells isolated from patients with risk genotypes AA/AG were also found to have 10 folds higher CXCL12 transcript copies/cell than those with non-risk genotype GG. Conclusions: Our study reveals the trans-acting impact of 6p24.1 with another CAD locus on 10q11.21 and is associated with intensified endothelial injury. Ministry of Education (MOE) Nanyang Technological University National Research Foundation (NRF) Published version The National Research Foundation, Singapore (Project Number 370062002) funded the Singapore Coronary Artery Disease Genetics Study (SCADGENS) and genotyping of the participants. The team from Nanyang Technological University Singapore was funded by an Academic Research Fund Tier 1 grant (2018-T1-001-030) from the Ministry of Education, Singapore, Human Frontier Science Program Research Grant (RGY0069/2019), and the Nanyang Assistant Professorship. K.Y. T. is supported by NTU Research Scholarship. H.H.L. is supported by the Institute of Molecular and Cell Biology (IMCB) Scientific Staff Development Award (SSDA) for her part-time Ph.D. A.K.K.T. is supported by IMCB, A*STAR, Precision Medicine and Personalised Therapeutics Joint Research Grant 2019, the 2nd A*STAR-AMED Joint Grant Call 192B9002 and NUHSRO/2021/035/NUSMed/04/NUS-IMCB Joint Lab/LOA.
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- 2022
26. Slit-Robo signalling establishes a Sphingosine-1-phosphate gradient to polarise fin mesenchyme
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Harsha Mahabaleshwar, PV Asharani, Tricia Yi Loo, Shze Yung Koh, Melissa R Pitman, Samuel Kwok, Jiajia Ma, Bo Hu, Fang Lin, Xue Li Lok, Stuart M Pitson, Timothy E Saunders, Tom J Carney, Lee Kong Chian School of Medicine (LKCMedicine), Institute of Molecular and Cell Biology (IMCB), A*STAR, Mahabaleshwar, Harsha, Asharani, PV, Loo, Tricia Yi, Koh, Shze Yung, Pitman, Melissa R, Kwok, Samuel, Ma, Jiajia, Hu, Bo, Lin, Fang, Li Lok, Xue, Pitson, Stuart M, Saunders, Timothy E, and Carney, Tom J
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QL ,QH ,fin ,Intracellular Signaling Peptides and Proteins ,Gene Expression Regulation, Developmental ,Articles ,Robo ,Zebrafish Proteins ,Biochemistry ,Mesoderm ,Slit ,Sphingosine ,Genetics ,sphingosine-1-phosphate ,Animals ,Medicine [Science] ,Mesenchyme ,Lysophospholipids ,Molecular Biology ,Zebrafish - Abstract
Immigration of mesenchymal cells into the growing fin and limb buds drives distal outgrowth, with subsequent tensile forces between these cells essential for fin and limb morphogenesis. Morphogens derived from the apical domain of the fin, orientate limb mesenchyme cell polarity, migration, division and adhesion. The zebrafish mutant stomp displays defects in fin morphogenesis including blister formation and associated loss of orientation and adhesion of immigrating fin mesenchyme cells. Positional cloning of stomp identifies a mutation in the gene encoding the axon guidance ligand, Slit3. We provide evidence that Slit ligands derived from immigrating mesenchyme act via Robo receptors at the apical ectodermal ridge (AER) to promote release of sphingosine-1-phosphate (S1P). S1P subsequently diffuses back to the mesenchyme to promote their polarisation, orientation, positioning and adhesion to the interstitial matrix of the fin fold. We thus demonstrate the coordination of the Slit-Robo and S1P signalling pathways in fin fold morphogenesis. Our work introduces a mechanism regulating the orientation, positioning and adhesion of its constituent cells. Ministry of Education (MOE) Work in the TJC and TES labs was funded by a Ministry of Education of Singapore AcRF Tier 3 grant (MOE2016-T3-1-005). Work in the FL lab was supported by funding from the National Science Foundation, IOS-1354457. SMP is supported by Senior Research Fellowships (1042589and1156693) from the National Health and Medical Research Council of Australia.
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- 2022
27. Ankyrin G restricts ion channel diffusion at the axonal initial segment before the establishment of the diffusion barrier
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Victor Racine, Daniel Choquet, Anna Brachet, Jean-Baptiste Sibarita, Bénédicte Dargent, Marie Irondelle, Marie-Pierre Fache, Christophe Leterrier, Neurobiologie des Canaux Ioniques, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de la Méditerranée - Aix-Marseille 2, Institute of Molecular and Cell Biology - Molecular controls of Morphogenesis and Tumor Progression, Institute of Molecular and Cell Biology, Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut interdisciplinaire de Neurosciences, Centre National de la Recherche Scientifique (CNRS), Leterrier, Christophe, Université de la Méditerranée - Aix-Marseille 2-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Interdisciplinaire de Neurosciences (IINS)
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Ankyrins ,animal structures ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,Amino Acid Motifs ,Molecular Sequence Data ,Biology ,Article ,Sodium Channels ,Cell Line ,Cell membrane ,03 medical and health sciences ,Mice ,0302 clinical medicine ,medicine ,Ankyrin ,Animals ,Amino Acid Sequence ,Phosphorylation ,Casein Kinase II ,Ion channel ,Research Articles ,030304 developmental biology ,Action potential initiation ,chemistry.chemical_classification ,0303 health sciences ,Binding Sites ,Sodium channel ,Cell Membrane ,[SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,Cell Biology ,Molecular biology ,Axons ,Transport protein ,Protein Transport ,Membrane ,medicine.anatomical_structure ,Membrane protein ,chemistry ,Biophysics ,Sequence Alignment ,030217 neurology & neurosurgery - Abstract
Ion channel immobilization by ankyrin G is regulated by casein kinase 2 in immature hippocampal neurons., In mammalian neurons, the precise accumulation of sodium channels at the axonal initial segment (AIS) ensures action potential initiation. This accumulation precedes the immobilization of membrane proteins and lipids by a diffusion barrier at the AIS. Using single-particle tracking, we measured the mobility of a chimeric ion channel bearing the ankyrin-binding motif of the Nav1.2 sodium channel. We found that ankyrin G (ankG) limits membrane diffusion of ion channels when coexpressed in neuroblastoma cells. Site-directed mutants with decreased affinity for ankG exhibit increased diffusion speeds. In immature hippocampal neurons, we demonstrated that ion channel immobilization by ankG is regulated by protein kinase CK2 and occurs as soon as ankG accumulates at the AIS of elongating axons. Once the diffusion barrier is formed, ankG is still required to stabilize ion channels. In conclusion, our findings indicate that specific binding to ankG constitutes the initial step for Nav channel immobilization at the AIS membrane and precedes the establishment of the diffusion barrier.
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- 2010
28. Antipsychotics increase vesicular glutamate transporter 2 (VGLUT2) expression in thalamolimbic pathways
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Sylvie Dumas, Severine Farley, Larissa Moutsimilli, Marie-Anne El Khoury, Victor Racine, Flavie Mathieu, Jean-Baptiste Sibarita, Bruno Giros, Christophe Chamot, Salah El Mestikawy, Eleni T. Tzavara, Neurobiologie et Psychiatrie, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Institute of Molecular and Cell Biology - Molecular controls of Morphogenesis and Tumor Progression, Institute of Molecular and Cell Biology, Helios Biosciences - c/o Paris Biotech, Helios Biosciences, Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC)
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Male ,medicine.drug_class ,medicine.medical_treatment ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,Biology ,Lithium ,Vesicular Glutamate Transport Protein 2 ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Glutamatergic ,Mice ,0302 clinical medicine ,Thalamus ,Vesicular transporter ,Neural Pathways ,medicine ,Limbic ,Limbic System ,Antipsychotics ,Animals ,RNA, Messenger ,Prefrontal cortex ,Antipsychotic ,Clozapine ,030304 developmental biology ,Pharmacology ,0303 health sciences ,Analysis of Variance ,Diazepam ,Ventral striatum ,Glutamate receptor ,Antidepressants ,Typical antipsychotic ,3. Good health ,Mice, Inbred C57BL ,Amphetamine ,medicine.anatomical_structure ,Gene Expression Regulation ,Glutamate ,Neuroscience ,030217 neurology & neurosurgery ,medicine.drug ,Antipsychotic Agents - Abstract
International audience; Recently the two vesicular-glutamate-transporters VGLUT1 and VGLUT2 have been cloned and characterized. VGLUT1 and VGLUT2 together label all glutamatergic neurons, but because of their distinct expression patterns in the brain they facilitate our ability to define between a VGLUT1-positive cortical and a VGLUT2-positive subcortical glutamatergic systems. We have previously demonstrated an increased cortical VGLUT1 expression as marker of antidepressant activity. Here, we assessed the effects of different psychotropic drugs on brain VGLUT2 mRNA and protein expression. The typical antipsychotic haloperidol, and the atypicals clozapine and risperidone increased VGLUT2 mRNA selectively in the central medial/medial parafascicular, paraventricular and intermediodorsal thalamic nuclei; VGLUT2 protein was accordingly amplified in paraventricular and ventral striatum and in prefrontal cortex. The antidepressants fluoxetine and desipramine and the sedative anxiolytic diazepam had no effect. These results highlight the implication of thalamo-limbic glutamatergic pathways in the action of antipsychotics. Increased VGLUT2 expression in these neurons might constitute a marker for antipsychotic activity and subcortical glutamate neurotransmission might be a possible novel target for future generation antipsychotics.
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- 2007
29. The human Nup107–160 nuclear pore subcomplex contributes to proper kinetochore functions
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Jean-Baptiste Sibarita, Tim J. Yen, Victor Racine, Stéphanie Bolhy, Valérie Doye, Ramin Shiekhattar, Vincent Galy, Annabelle Alves, Etienne Formstecher, Tatsuo Fukagawa, Michela Zuccolo, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Ecole Doctorale Gènes Génomes Cellules, Université Paris-Sud - Paris 11 (UP11), Laboratoire de Biologie du Développement (LBD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Hybrigenics [Paris], Hybrigenics, Institute of Molecular and Cell Biology - Molecular controls of Morphogenesis and Tumor Progression, Institute of Molecular and Cell Biology, Interdisciplinary Institute for Neuroscience (IINS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), National Institute of Genetics (NIG), Laboratory of Molecular Cell Biology, National Institutes of Health [Bethesda] (NIH), Institute for Cancer Research, The Fox Chase Cancer Center, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
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Prometaphase ,Chromosomal Proteins, Non-Histone ,[SDV]Life Sciences [q-bio] ,Spindle Apparatus ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,[SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC] ,Biology ,Microtubules ,Models, Biological ,Article ,General Biochemistry, Genetics and Molecular Biology ,Ndc80 complex ,Minor Histocompatibility Antigens ,03 medical and health sciences ,0302 clinical medicine ,Microtubule ,Chromosomes, Human ,Humans ,Nuclear pore ,Kinetochores ,Molecular Biology ,Metaphase ,Mitosis ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,0303 health sciences ,General Immunology and Microbiology ,Kinetochore ,General Neuroscience ,GTPase-Activating Proteins ,Microfilament Proteins ,Nuclear Proteins ,Cell biology ,Nuclear Pore Complex Proteins ,Cytoskeletal Proteins ,Protein Transport ,RNA Interference ,Nucleoporin ,030217 neurology & neurosurgery ,HeLa Cells ,Molecular Chaperones ,Protein Binding - Abstract
We previously demonstrated that a fraction of the human Nup107–160 nuclear pore subcomplex is recruited to kinetochores at the onset of mitosis. However, the molecular determinants for its kinetochore targeting and the functional significance of this localization were not investigated. Here, we show that the Nup107–160 complex interacts with CENP-F, but that CENP-F only moderately contributes to its targeting to kinetochores. In addition, we show that the recruitment of the Nup107–160 complex to kinetochores mainly depends on the Ndc80 complex. We further demonstrate that efficient depletion of the Nup107–160 complex from kinetochores, achieved either by combining siRNAs targeting several of its subunits excluding Seh1, or by depleting Seh1 alone, induces a mitotic delay. Further analysis of Seh1-depleted cells revealed impaired chromosome congression, reduced kinetochore tension and kinetochore–microtubule attachment defects. Finally, we show that the presence of the Nup107–160 complex at kinetochores is required for the recruitment of Crm1 and RanGAP1–RanBP2 to these structures. Together, our data thus provide the first molecular clues underlying the function of the human Nup107–160 complex at kinetochores.
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- 2007
30. SMCHD1 variants may induce variegated expression in Facio Scapulo Humeral Dystophy and Bosma Arhinia and microphtalmia syndrome
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Camille Dion, Bruno Reversade, Shifeng Xue, Raphaël Chevalier, Frédérique Magdinier, Mégane Delourme, Anaïs Baudot, Camille Laberthonnière, Adélaïde J, Hirst D, Jérôme D. Robin, Chaffanet M, Jérôme Déjardin, Karine Nguyen, Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), National University of Singapore (NUS), Institute of Molecular and Cell Biology [Singapore, Singapore] (IMCB / A*STAR), Koç University, Institut de génétique humaine (IGH), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and CHAFFANET, Max
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Regulation of gene expression ,Genetics ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,SMC protein ,DNA methylation ,Gene expression ,[SDV.GEN] Life Sciences [q-bio]/Genetics ,Biology ,Enhancer ,Gene ,Function (biology) ,Chromatin - Abstract
An expanding number of genetic syndromes are linked to mutations in genes encoding factors that guide chromatin organization. Recently, distinct genetic syndromes have been linked to mutations in theSMCHD1gene. However, the function of this non-canonical SMC protein remains partly defined in Human tissues. To address this question, we determined its epi-signature in type 2 Facio Scapulo Humeral Dystrophy (FSHD2) and Bosma Arhinia and Microphtalmia Syndrome (BAMS) linked to heterozygous mutations in this gene. By combining RNA-Seq, DNA methylation profiling and ChIP-Seq, we showed that SMCHD1 regulates repressed chromatin but alsocis-regulatory elements and enhancers. Our results emphasize dual functions for SMCHD1, in chromatin compaction, chromatin insulation and gene regulation with variable outcomes and targets depending on tissues. We propose that altered DNA methylation and long-range chromatin organization at a number of loci required for development and tissue differentiation, trigger variegated gene expression in rare genetic diseases linked to heterozygousSMCHD1mutations.
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- 2022
31. Centrosome–nuclear axis repositioning drives the assembly of a bipolar spindle scaffold to ensure mitotic fidelity
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Jorge G Ferreira, Martial Balland, Vanessa Nunes, Matthieu Piel, Irène Wang, Domingos Castro, Margarida Dantas, Helder Maiato, Nicolas Carpi, Paulo Aguiar, Elisa Vitiello, Instituto de Biologia Molecular e Celular - institute for molecular and cell biology [Porto, Portugal] (IBMC), Universidade do Porto, Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Biologie Cellulaire et Cancer, Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Instituto de Ciências Biomédicas de Abel Salazar (ICBAS)
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Rotation ,Cell division ,Nuclear Envelope ,Movement ,Mitosis ,Spindle Apparatus ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,Biology ,Prophase ,Actin-Related Protein 2-3 Complex ,03 medical and health sciences ,0302 clinical medicine ,Cell Adhesion ,medicine ,Molecular motor ,Humans ,Cytoskeleton ,Cell Shape ,Molecular Biology ,030304 developmental biology ,Centrosome ,0303 health sciences ,Cell Cycle ,Dyneins ,Articles ,Cell Biology ,Cell biology ,Spindle apparatus ,HEK293 Cells ,medicine.anatomical_structure ,Nucleus ,030217 neurology & neurosurgery ,HeLa Cells - Abstract
International audience; MBoC | ARTICLE Centrosome-nuclear axis repositioning drives the assembly of a bipolar spindle scaffold to ensure mitotic fidelity ABSTRACT During the initial stages of cell division, the cytoskeleton is extensively reorganized so that a bipolar mitotic spindle can be correctly assembled. This process occurs through the action of molecular motors, cytoskeletal networks, and the nucleus. How the combined activity of these different components is spatiotemporally regulated to ensure efficient spindle assembly remains unclear. To investigate how cell shape, cytoskeletal organization, and molecular motors cross-talk to regulate initial spindle assembly, we use a combination of micropatterning with high-resolution imaging and 3D cellular reconstruction. We show that during prophase, centrosomes and nucleus reorient so that centrosomes are positioned on the shortest nuclear axis at nuclear envelope (NE) breakdown. We also find that this orientation depends on a combination of centrosome movement controlled by Arp2/3-mediated regulation of microtubule dynamics and Dynein-generated forces on the NE that regulate nuclear reorientation. Finally, we observe this centrosome configuration favors the establishment of an initial bipolar spindle scaffold, facilitating chromosome capture and accurate segregation, without compromising division plane orientation.
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- 2020
32. Enabling open-ended questions in team-based learning using automated marking: impact on student achievement, learning and engagement
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Sophia Huey Shan Tan, Guillaume Thibault, Anna Chia Yin Chew, Preman Rajalingam, Lee Kong Chian School of Medicine (LKCMedicine), School of Biological Sciences, Mechanobiology Institute, National University of Singapore, Institute of Molecular and Cell Biology, A*STAR, Singapore, and Center for Teaching, Learning and Pedagogy
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Deep Learning ,Automated Marking ,Education [Social sciences] ,Computer Science Applications ,Education - Abstract
Background: Different types of assessments influence learning and learning behaviour. Multiple-choice questions (MCQs) reward partial knowledge and encourage surface learning, while open-ended questions (OEQs) promote deeper learning. Currently, MCQs is part of team-based learning (TBL) curriculum, and it is challenging to implement OEQs as immediate feedback is necessary. Objectives: We asked if MCQ and OEQs affect student achievement, student learning and student engagement differently in a TBL classroom. Methods: MCQs and OEQs test scores of N = 66 students were automatically captured in Learning Activity Management System (LAMS) and were compared using a switching replications quasi-experimental design with pre- and post-tests to answer the research questions. Student learning approaches and engagement in the team activities were assessed using the study process questionnaire and the structure of observed learning outcomes taxonomy respectively. Results and Conclusions: Students get significantly higher MCQ scores than OEQs for the same set of questions, but the reverse is true for application exercises (AEs), which focus on higher-level application. Most students significantly deepened their learning approaches before OEQs, while poorly prepared students were less engaged during OEQ discussions. Interestingly students subjected to OEQs took less time and scored higher in AE discussions, suggesting better focus on higher-level thinking. Implications: This project is significant as it bridges our understanding of the value of OEQs and TBL. Our approach is transferable to other courses, and thus it can improve the quality of teaching and learning in tertiary education. Nanyang Technological University Nanyang Technological University, Grant/Award Number: EdeX.
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- 2022
33. The unfolded protein response reverses the effects of glucose on lifespan in chemically-sterilized C. elegans
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Caroline Beaudoin-Chabot, Lei Wang, Cenk Celik, Aishah Tul-Firdaus Abdul Khalid, Subhash Thalappilly, Shiyi Xu, Jhee Hong Koh, Venus Wen Xuan Lim, Ann Don Low, Guillaume Thibault, School of Biological Sciences, and Institute of Molecular and Cell Biology, A*STAR
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Multidisciplinary ,Longevity ,General Physics and Astronomy ,General Chemistry ,Endoplasmic Reticulum Stress ,Stress ,General Biochemistry, Genetics and Molecular Biology ,Ageing ,Glucose ,Unfolded Protein Response ,Animals ,Medicine [Science] ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins - Abstract
Metabolic diseases often share common traits, including accumulation of unfolded proteins in the endoplasmic reticulum (ER). Upon ER stress, the unfolded protein response (UPR) is activated to limit cellular damage which weakens with age. Here, we show that Caenorhabditis elegans fed a bacterial diet supplemented high glucose at day 5 of adulthood (HGD-5) extends their lifespan, whereas exposed at day 1 (HGD-1) experience shortened longevity. We observed a metabolic shift only in HGD-1, while glucose and infertility synergistically prolonged the lifespan of HGD-5, independently of DAF-16. Notably, we identified that UPR stress sensors ATF-6 and PEK-1 contributed to the longevity of HGD-5 worms, while ire-1 ablation drastically increased HGD-1 lifespan. Together, we postulate that HGD activates the otherwise quiescent UPR in aged worms to overcome ageing-related stress and restore ER homeostasis. In contrast, young animals subjected to HGD provokes unresolved ER stress, conversely leading to a detrimental stress response. Ministry of Education (MOE) Ministry of Health (MOH) National Medical Research Council (NMRC) Published version This work was supported by the Singapore Ministry of Education Academic Research Fund Tier 2 (2018-T2-1-002) and Tier 1 (2019-T1-002-011) as well as the Ministry of Health, Singapore, National Medical Research Council Open Fund Individual Research Grant (MOH-000566).
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- 2022
34. Discovery of a genetic module essential for assigning left–right asymmetry in humans and ancestral vertebrates
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Emmanuelle Szenker-Ravi, Tim Ott, Muznah Khatoo, Anne Moreau de Bellaing, Wei Xuan Goh, Yan Ling Chong, Anja Beckers, Darshini Kannesan, Guillaume Louvel, Priyanka Anujan, Vydianathan Ravi, Carine Bonnard, Sébastien Moutton, Patric Schoen, Mélanie Fradin, Estelle Colin, André Megarbane, Linda Daou, Ghassan Chehab, Sylvie Di Filippo, Caroline Rooryck, Jean-François Deleuze, Anne Boland, Nicolas Arribard, Rukiye Eker, Sumanty Tohari, Alvin Yu-Jin Ng, Marlène Rio, Chun Teck Lim, Birgit Eisenhaber, Frank Eisenhaber, Byrappa Venkatesh, Jeanne Amiel, Hugues Roest Crollius, Christopher T. Gordon, Achim Gossler, Sudipto Roy, Tania Attie-Bitach, Martin Blum, Patrice Bouvagnet, Bruno Reversade, ACS - Heart failure & arrhythmias, ARD - Amsterdam Reproduction and Development, Genome Institute of Singapore (GIS), University of Hohenheim, Groupement Hospitalier Lyon-Est (GHE), Hospices Civils de Lyon (HCL), Institute of Molecular and Cell Biology [Singapore, Singapore] (IMCB / A*STAR), National University Hospital [Singapore] (NUH), Centre Hospitalier Universitaire de Liège (CHU-Liège), Hannover Medical School [Hannover] (MHH), REBIRTH Cluster of Excellence [Hannover], Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Hammersmith Hospital NHS Imperial College Healthcare, Skin Research Institute of Singapore [Singapore, Singapore] (SRIS / A*STAR), Maison de Santé Protestante de Bordeaux-Bagatelle (MSPB), Praxis Dr Patric SCHÖN [Oberschleissheim, Germany] (2PS), CHU Pontchaillou [Rennes], Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Gilbert and Rose-Marie Chagoury School of Medicine [Lebanese American University], Lebanese American University (LAU), Institut Jérôme Lejeune, Université Saint-Joseph de Beyrouth (USJ), Lebanese University [Beirut] (LU), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Maladies Rares: Génétique et Métabolisme (Bordeaux) (U1211 INSERM/MRGM), Université de Bordeaux (UB)-Groupe hospitalier Pellegrin-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Hôpital Universitaire des Enfants Reine Fabiola [Bruxelles, Belgique] (HUDERF), Istanbul University, Assistance publique-Hôpitaux de Paris - Espace éthique (AP-HP Espace éthique), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Necker - Enfants Malades [AP-HP], Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Singapore Institute of Food and Biotechnology Innovation [Singapore, Singapore] (SIFBI / A*STAR ), Bioinformatics Institute [Singapore, Singapore] (BII / A*STAR), Nanyang Technological University [Singapour], National University of Singapore (NUS), Service de Génétique Médicale [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Maison de la Femme de la Mère et de l'Enfant [CHU de la Martinique] (MFME [Fort de France]), CHU de la Martinique [Fort de France], Koc University School of Medicine [Istanbul, Turkey] (KUSOM), and CarMeN, laboratoire
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[SDV] Life Sciences [q-bio] ,Loss of Function Mutation ,[SDV]Life Sciences [q-bio] ,Vertebrates ,Metalloproteases ,Genetics ,Animals ,Humans ,Proteins ,Gene Regulatory Networks ,Cilia ,Biological Evolution ,Body Patterning - Abstract
Erratum in Publisher Correction: Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates. Szenker-Ravi E, Ott T, Khatoo M, Moreau de Bellaing A, Goh WX, Chong YL, Beckers A, Kannesan D, Louvel G, Anujan P, Ravi V, Bonnard C, Moutton S, Schoen P, Fradin M, Colin E, Megarbane A, Daou L, Chehab G, Di Filippo S, Rooryck C, Deleuze JF, Boland A, Arribard N, Eker R, Tohari S, Ng AY, Rio M, Lim CT, Eisenhaber B, Eisenhaber F, Venkatesh B, Amiel J, Crollius HR, Gordon CT, Gossler A, Roy S, Attie-Bitach T, Blum M, Bouvagnet P, Reversade B.Nat Genet. 2022 Jun;54(6):906. doi: 10.1038/s41588-022-01053-8.PMID: 35304595 No abstract available.; International audience; The vertebrate left-right axis is specified during embryogenesis by a transient organ: the left-right organizer (LRO). Species including fish, amphibians, rodents and humans deploy motile cilia in the LRO to break bilateral symmetry, while reptiles, birds, even-toed mammals and cetaceans are believed to have LROs without motile cilia. We searched for genes whose loss during vertebrate evolution follows this pattern and identified five genes encoding extracellular proteins, including a putative protease with hitherto unknown functions that we named ciliated left-right organizer metallopeptide (CIROP). Here, we show that CIROP is specifically expressed in ciliated LROs. In zebrafish and Xenopus, CIROP is required solely on the left side, downstream of the leftward flow, but upstream of DAND5, the first asymmetrically expressed gene. We further ascertained 21 human patients with loss-of-function CIROP mutations presenting with recessive situs anomalies. Our findings posit the existence of an ancestral genetic module that has twice disappeared during vertebrate evolution but remains essential for distinguishing left from right in humans.
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- 2022
35. Label-free assessment of differentiation efficiency in iPSC-derived spinal cord progenitor cells via Magnetic Resonance Relaxometry (MRR)
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Tan, Jerome Zu Yao, Chen, Jiahui, Roxby, Daniel, Chooi, Wai Hon, Nguyen, Tan Dai, Ng, Shi-Yan, Chew, Sing Yian, Han, Jongyoon, Interdisciplinary Graduate School (IGS), School of Chemistry, Chemical Engineering and Biotechnology, 14th Stem Cell Society Singapore Symposium 2022, Campus for Research Excellence And Technological Enterprise (CREATE), Institute of Molecular and Cell Biology, A*STAR, and NTU Institute for Health Technologies
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Bioengineering [Engineering] ,Medicine::Tissue engineering [Science] ,Cell Therapy ,Critical Quality Attribute - Abstract
The advent of induced pluripotent stem cells (iPSC) has provided a promising solution to the replacement of damaged neurons, especially in spinal cord injuries. Despite its merits, differentiation of iPSCs is a highly variable process, prompting the need to reliably assess the degree of differentiation across batches, and validate their quality. iPSC phenotypes are detected through labelling cells with fluorescent markers or immunofluorescence staining based methods, which perturb or destroy cells, preventing their further use. In this study, human iPSCs derived from Cord Lining Endothelial cells were differentiated into Spinal-cord Progenitor Cells (SCPCs) through a 10-day process. Label-free measurement of these cells were performed at different timepoints using Magnetic Resonance Relaxometry (MRR), a rapid and label-free technique to obtain critical cellular iron (Fe3+) content. MRR only requires
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- 2022
36. Blood vessel occlusion by Cryptococcus neoformans is a mechanism for haemorrhagic dissemination of infection
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Robert Evans, Aleksandra Bojarczuk, Renshaw Sa, Johnston Sa, Lagendijk Ak, Gibson Jf, Kamuyango A, Ingham Pw, Hogan Bm, Richard Hotham, Lee Kong Chian School of Medicine (LKCMedicine), and Institute of Molecular and Cell Biology (A*Star) Singapore
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medicine.medical_specialty ,Cryptococcus Neoformans ,Immunology ,Biology ,Meningitis, Cryptococcal ,Microbiology ,03 medical and health sciences ,0302 clinical medicine ,Text mining ,Virology ,Internal medicine ,Genetics ,medicine ,Animals ,Humans ,Medicine [Science] ,Molecular Biology ,Zebrafish ,030304 developmental biology ,0303 health sciences ,business.industry ,Mechanism (biology) ,Blood vessel occlusion ,Cryptococcosis ,Blood Vessel Occlusion ,3. Good health ,Cardiology ,Cryptococcus neoformans ,Parasitology ,business ,030217 neurology & neurosurgery - Abstract
Meningitis caused by infectious pathogens is associated with vessel damage and infarct formation, however the physiological cause is often unknown. Cryptococcus neoformans is a human fungal pathogen and causative agent of cryptococcal meningitis, where vascular events are observed in up to 30% of patients, predominantly in severe infection. Therefore, we aimed to investigate how infection may lead to vessel damage and associated pathogen dissemination using a zebrafish model that permitted noninvasive in vivo imaging. We find that cryptococcal cells become trapped within the vasculature (dependent on their size) and proliferate there resulting in vasodilation. Localised cryptococcal growth, originating from a small number of cryptococcal cells in the vasculature was associated with sites of dissemination and simultaneously with loss of blood vessel integrity. Using a cell-cell junction tension reporter we identified dissemination from intact blood vessels and where vessel rupture occurred. Finally, we manipulated blood vessel tension via cell junctions and found increased tension resulted in increased dissemination. Our data suggest that global vascular vasodilation occurs following infection, resulting in increased vessel tension which subsequently increases dissemination events, representing a positive feedback loop. Thus, we identify a mechanism for blood vessel damage during cryptococcal infection that may represent a cause of vascular damage and cortical infarction during cryptococcal meningitis. Agency for Science, Technology and Research (A*STAR) Nanyang Technological University Published version JFG was supported by an award from the Singapore A*STAR Research Attachment Programme (ARAP) in partnership with the University of Sheffield. Work in the PWI lab was funded by the A*STAR Institute of Molecular and Cell Biology (IMCB) and the Lee Kong Chian School of Medicine. RJE was supported by a British Infection Association postdoctoral fellowship (https://www.britishinfection.org/). AKL was supported by a University of Queensland Postdoctoral Fellowship. BMH by an NHMRC/ National Heart Foundation Career Development Fellowship (1083811). SAJ, AB, RJE, AK and RH, were supported by Medical Research Council and Department for International Development Career Development Award Fellowship MR/J009156/1 (http://www.mrc.ac.uk/). SAJ was additionally supported by a Krebs Institute Fellowship (http:// krebsinstitute.group.shef.ac.uk/), and Medical Research Council Centre grant (G0700091). AK was supported by a Wellcome Trust Strategic Award in Medical Mycology and Fungal Immunology (097377/Z/11/Z). SAR was supported by a Medical Research Council Programme Grant (MR/M004864/1). Light sheet microscopy was carried out in the Wolfson Light Microscopy Facility, supported by a BBSRC ALERT14 award for light-sheet microscopy (BB/M012522/1).
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- 2022
37. Human PERK rescues unfolded protein response-deficient yeast cells
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Wei Sheng, Yap, Guillaume, Thibault, School of Biological Sciences, and Institute of Molecular and Cell Biology, A*STAR
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PERK ,endocrine system ,Unfolded Protein Response ,Yeast Human ,Medicine [Science] ,Synthetic Biology ,IRE1 ,Endoplasmic Reticulum Stress - Abstract
Stress pathways monitor intracellular systems and deploy a range of regulatory mechanisms upon stress. One of the best characterised pathways with wide implications in disease, the unfolded protein response (UPR), is the endoplasmic reticulum (ER) guarding to maintain homeostasis. In eukaryotes, the UPR comprises of three highly conserved transducers leading to the regulation of hundreds of targets by activating UPR-specific transcription factors (Fun and Thibault, 2019). Developed UPR inhibitors to treat diseases have serious potential long term side effects on the functions of the pancreas, the immune system, and the liver as the UPR programme is too broad to be inhibited from the upstream players (Hetz et al., 2013). Additionally, the inhibition or deletion of one of the three ER stress transducers, IRE1, PERK, and ATF6, leads to a compensatory mechanism from the remaining two ER stress transducers. This phenomenon may complicate a search for new ER stress transducer inhibitors. Here, we report a fully functional human PERK (hPERK) chimeric protein expressed in Saccharomyces cerevisiae that could be used for high throughput screen to identify new PERK inhibitory or activating compounds.
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- 2022
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38. MYC overexpression leads to increased chromatin interactions at superenhancers and MYC binding sites
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Melissa Fullwood, KAIJING CHEN, Yi Xiang See, School of Biological Sciences, Cancer Science Institute of Singapore, National University of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, and Institute of Molecular and Cell Biology, A*STAR
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Biological sciences::Molecular biology [Science] ,Chromatin Interactions ,Genetics ,Biological sciences::Genetics [Science] ,Genetics (clinical) ,Cancer - Abstract
The MYC oncogene encodes for the MYC protein and is frequently dysregulated across multiple cancer cell types, making it an attractive target for cancer therapy. MYC overexpression leads to MYC binding at active enhancers, resulting in a global transcriptional amplification of active genes. Since superenhancers are frequently dysregulated in cancer, we hypothesized that MYC preferentially invades into superenhancers and alters the cancer genome organization. To that end, we performed ChIP-seq, RNA-seq, 4C-seq and SIQHiC (Spike-in Quantitative Hi-C) on the U2OS osteosarcoma cell line with tetracycline-inducible MYC. MYC overexpression in U2OS cells modulated histone acetylation and increased MYC binding at superenhancers. SIQHiC analysis revealed increased global chromatin contact frequency, particularly at chromatin interactions connecting MYC binding sites at promoters and enhancers. Immunofluorescence staining showed that MYC molecules formed punctate foci at these transcriptionally active domains after MYC overexpression. These results demonstrate the accumulation of overexpressed MYC at promoter-enhancer hubs and suggest that MYC invades into enhancers through spatial proximity. At the same time, the increased protein-protein interactions may strengthen these chromatin interactions to increase chromatin contact frequency. CTCF siRNA knockdown in MYC overexpressed U2OS cells demonstrated that removal of architectural proteins can disperse MYC and abrogate the increase in chromatin contacts. By elucidating the chromatin landscape of MYC driven cancers, we can potentially target MYC associated chromatin interactions for cancer therapy. Ministry of Education (MOE) Accepted version This research is supported by the RNA Biology Center at the Cancer Science Institute of Singapore, NUS, as part of funding under the Singapore Ministry of Education Academic Research Fund Tier 3 grant awarded to Daniel Tenen (MOE2014-T3-1-006). This research is supported by the NRF Singapore and the Singapore Ministry of Education under its Research Centres of Excellence initiative and a Singapore Ministry of Education Academic Research Fund Tier 2 grant awarded to M.J.F. (MOET2EP30120-0009).
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- 2022
39. Robust non-toxic macroscale beads with antibacterial and contaminant scavenging properties for aquaculture
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Zhang, Penghui, Carney, Tom J., Schroën, Karin, Boom, Remko M., Chan-Park, Mary B., School of Chemical and Biomedical Engineering, Lee Kong Chian School of Medicine (LKCMedicine), Institute of Molecular and Cell Biology, A*STAR, NTU Food Technology Centre, and Centre for Antimicrobial Bioengineering
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Bioengineering [Engineering] ,Antibacterial Performance ,technology, industry, and agriculture ,Life Science ,Aquaculture ,macromolecular substances ,Aquatic Science ,Food Process Engineering ,VLAG - Abstract
Non-toxic macroscale (few millimeters in diameter) cationic antibacterial beads were made for suppression of bacteria in fish culture. The beads were formed by the diffusion-driven layer by layer (dd-LBL) process using graphene oxide substrate and branched polyethyleneimine and were stabilized by post-assembly crosslinking process in which carboxyl groups on the graphene oxide were crosslinked with amine groups on the branched polyethyleneimine using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS) chemistry. The crosslinked beads have negligible in vitro toxicity to 3T3 cells and zebrafish embryos. Further, the crosslinked beads exhibit excellent antibacterial activity, which can reach over 99.9% inactivation against Escherichia coli (E. coli) in 30 min even with ultrahigh (~ 108 CFU/mL) E. coli concentration. The antibacterial activity of the crosslinked beads can be regenerated with a simple procedure and remains high in the 10th cycle of regeneration. The crosslinked beads have much improved mechanical stability compared to the raw (uncrosslinked) beads. The highly porous structure and abundant functional groups of the crosslinked beads give them high adsorption capacity towards various forms of organic matter such as fish waste. Addition of zeolite nanoparticles during the bead formation process and subsequent chemical crosslinking with hyaluronic acid makes these beads suitable for removal of total ammonia nitrogen (TAN) while preserving the antibacterial activity and biocompatibility. Agency for Science, Technology and Research (A*STAR) Ministry of Education (MOE) Ministry of Health (MOH) Nanyang Technological University This work was funded and supported by the Singapore MOE Tier 3 grants (MOE2013-T3-1-002 and MOE2018-T3-1-003), a Singapore MOH Industry Alignment Fund (NMRC/MOHIAFCAT2/ 003/2014), an A*Star Specialty Chemical grant (SERC A1786a0032), CARIE (Centre for Aquaculture Research Innovation and Education), and an NTU iFood Grant. Zhang P.H. acknowledges the support of NTU through a PhD scholarship.
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- 2022
40. Colorimetric and fluorescent TRAP assays for visualising and quantifying fish osteoclast activity
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Lalith Prabha Ethiraj, En Lei Samuel Fong, Ranran Liu, Madelynn Chan, Christoph Winkler, Tom James Carney, Lee Kong Chian School of Medicine (LKCMedicine), Tan Tock Seng Hospital, and Institute of Molecular and Cell Biology (IMCB), A*STAR
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Isoenzymes ,Histology ,Tartrate-Resistant Acid Phosphatase ,Acid Phosphatase ,Biophysics ,Osteoclast ,Animals ,Osteoclasts ,Medicine [Science] ,Colorimetry ,Cell Biology ,Zebrafish - Abstract
Histochemical detection of tartrate-resistant acid phosphatase (TRAP) activity is a fundamental technique for visualizing osteoclastic bone resorption and assessing osteoclast activity status in tissues. This approach has mostly employed colorimetric detection, which has limited quantification of activity in situ and co-labelling with other skeletal markers. Here we report simple colorimetric and fluorescent TRAP assays in zebrafish and medaka, two important model organisms for investigating the pathogenesis of bone disorders. We show fluorescent TRAP staining, utilising the ELF97 substrate, is a rapid, robust and stable system to visualise and quantify osteoclast activity in zebrafish, and is compatible with other fluorescence stains, transgenic lines and antibody approaches. Using this approach, we show that TRAP activity is predominantly found around the base of the zebrafish pharyngeal teeth, where osteoclast activity state appears to be heterogeneous. Published version
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- 2021
41. A high-throughput genetic screening protocol to measure lipid bilayer stress-induced unfolded protein response in Saccharomyces cerevisiae
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Nurulain Ho, Wei Sheng Yap, Guillaume Thibault, School of Biological Sciences, and Institute of Molecular and Cell Biology, A*STAR
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Saccharomyces cerevisiae Proteins ,Science (General) ,Lipid Bilayers ,Saccharomyces cerevisiae ,Gene Expression ,General Biochemistry, Genetics and Molecular Biology ,Cell membrane ,Q1-390 ,Model Organisms ,Gene expression ,Protocol ,medicine ,Genetics ,Flow Cytometry/Mass Cytometry ,Lipid bilayer ,General Immunology and Microbiology ,biology ,Chemistry ,General Neuroscience ,Endoplasmic reticulum ,Cell Membrane ,Biological sciences [Science] ,Endoplasmic Reticulum Stress ,biology.organism_classification ,Synthetic genetic array ,High Throughput Screening ,High-Throughput Screening Assays ,Cell biology ,medicine.anatomical_structure ,Genetic Techniques ,Unfolded Protein Response ,Unfolded protein response ,Cell-based Assays ,Signal transduction ,Signal Transduction - Abstract
Summary The endoplasmic reticulum (ER) stress is defined by the accumulation of unfolded proteins at the ER and perturbation at the ER membrane, known as lipid bilayer stress (LBS). In turn, ER stress triggers the unfolded protein response (UPR) to restore ER homeostasis. Here, we provide a modified protocol based on the synthetic genetic array analysis in Saccharomyces cerevisiae to identify genetic perturbations that induce the UPR by LBS. This method is adaptable to other canonical stress pathways. For complete details on the use and execution of this protocol, please refer to Ho et al. (2020), Jonikas et al. (2009) and Baryshnikova et al. (2010)., Graphical abstract, Highlights • Generation and validation of IRE1 and IRE1ΔLD query strains with a UPR reporter • Detailed protocol of query strains mated to the yeast deletion library using SGA • High-throughput measurement of reporter fluorescence levels by flow cytometry • Data analysis to identify gene deletions activating the UPR by lipid bilayer stress, The endoplasmic reticulum (ER) stress is defined by the accumulation of unfolded proteins at the ER and perturbation at the ER membrane, known as lipid bilayer stress (LBS). In turn, ER stress triggers the unfolded protein response (UPR) to restore ER homeostasis. Here, we provide a modified protocol based on the synthetic genetic array analysis in Saccharomyces cerevisiae to identify genetic perturbations that induce the UPR by LBS. This method is adaptable to other canonical stress pathways.
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- 2021
42. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest
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Rüdiger Bode, Martin Mascher, Serge Casaregola, Anasua Sarkar, Guilhem Savel, Patrick Wincker, Valérie Barbe, Martin Giersberg, Marina Marcet-Houben, Keith Baronian, Nils Stein, Véronique Leh-Louis, Christine Sacerdot, Guy-Franck Richard, Jan Riechen, Ingrid Lafontaine, Jean Luc Souciet, Urs Hähnel, Eric Westhof, Joseph Schacherer, Uwe Scholz, Sebastian Worch, Sebastian Beier, Pascal Durrens, Erik Böer, Anke Trautwein-Schult, Christian Marck, Toni Gabaldón, Cécile Fairhead, Anja Hartmann, Claire Jubin, Bernard Dujon, Cécile Neuvéglise, Małgorzata Czernicka, Claudine Bleykasten, David James Sherman, Laurence Despons, Marie Laure Straub, Paul P. Jung, Marc Lemaire, Dagmara Jankowska, Tiphaine Martin, Benoit Vacherie, Emmanuel Talla, Agnès Thierry, José Almeida Cruz, André Goffeau, Gotthard Kunze, Claude Gaillardin, Philippe Baret, Guillaume Morel, Przemysław Piotr Gierski, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Yeast Genetics, Leibniz Institute of Plant Research (IPK), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona], Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et de Technologies de Saclay (IBITECS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université catholique de Louvain, Institut des Sciences de la Vie, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL), School of Biological Sciences, University of Canterbury, Institute of Biochemistry, Universität Greifswald - University of Greifswald, Université de Strasbourg (UNISTRA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Génétique moléculaire, génomique, microbiologie (GMGM), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire des levures (YMG), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program ' Génotypage et Génomique Comparée ' , the ACI IMPBIO ' Génolevures En Ligne ' and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia, SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161)., Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université Catholique de Louvain = Catholic University of Louvain (UCL), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Canterbury [Christchurch], International Institute of Molecular and Cell Biology [Warsaw] (IIMCB), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Kunze, Gotthard, Neuvéglise, Cécile, UCL - SST/ELI/ELIA - Agronomy, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
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Yarrowia lipolytica ,n-butanol ,yeast ,genome ,tannic acid ,metabolism ,biotechnology ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,Technological development ,Butyric acid ,Applied Microbiology and Biotechnology ,Genome ,Blastobotrys ,Saccharomycotina ,[INFO.INFO-BT]Computer Science [cs]/Biotechnology ,N-butanol ,2. Zero hunger ,0303 health sciences ,biology ,Segmental duplications ,Genomics ,Phylogenetics ,General Energy ,Biochemistry ,Biotechnology ,Nitrogen ,Saccharomyces cerevisiae ,Biotecnologia agrícola ,Computational biology ,Management, Monitoring, Policy and Law ,Biotechnological potentials ,Arxula ,Arxula adeninivorans ,03 medical and health sciences ,Carbon and nitrogen ,030304 developmental biology ,Saccharomycetes ,Comparative genomics ,Tannic acid ,030306 microbiology ,Renewable Energy, Sustainability and the Environment ,Protein ,Research ,Fundamental studies ,Yarrowia ,Llevats -- Genètica ,biology.organism_classification ,Yeast ,Carbon ,Metabolism ,Genes ,Organic acid - Abstract
Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant./nResults: The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. Conclusions: The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications. This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program “Génotypage et Génomique Comparée”, the ACI IMPBIO “Génolevures En Ligne” and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia; SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161). B.D. is a member of Institut Universitaire de France
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- 2014
43. Interleukin-10 induces interferon-γ-dependent emergency myelopoiesis
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Ana, Cardoso, Ana Catarina, Martins, Ana Raquel, Maceiras, Wei, Liu, Isabel, Castro, António G, Castro, António, Bandeira, James P, Di Santo, Ana, Cumano, Yan, Li, Paulo, Vieira, Margarida, Saraiva, Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto = University of Porto, Instituto de Biologia Molecular e Celular - institute for molecular and cell biology [Porto, Portugal] (IBMC), Lymphocytes et Immunité - Lymphocytes and Immunity, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Medical School (University of Nanjing), Nanjing University (NJU), University of Minho [Braga], Cellule Pasteur, Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité, Immunité Innée - Innate Immunity, A. Cardoso (SFRH/BD/84704/2012) and A.C.M. (SFRH/BD/136800/2018) were supported by the Portuguese Foundation for Science and Technology (FCT) through PhD grants.This study was partially supported by grants from the National Key Research and Development Program of China (2019YFA0802900), National Natural Science Foundation of China (32070942), and Fundamental Research Funds for the Central Universities.The M.S. lab was financed by a FCT-ANR grant (MyeloTEN-FCTANR/ BIM-MEC/0007/2013). We acknowledge the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by FCT.This work was funded by National Funds through FCT, I.P., under the project UIDB/04293/2020, and backed by the COST Action BM1404 European Network of Investigators Triggering Exploratory Research on Myeloid Regulatory Cells (http://www.mye-euniter.eu), which is supported by the Horizon 2020—EU Framework Program Research and Innovation Programme. M.S. is funded by FCT through Estímulo Individual ao Emprego Científico.A. Cumano and P.V. were financed by ANR Twothyme and by REVIVE (Investissement d’Avenir, ANR-10-LABX-73). A.B., A. Cumano, and P.V. were also financed by the Institut Pasteur, INSERM, and ANR (project MYELOTEN, ANR-13-ISV1-0003-01)., We thank Vincent Rouilly for statistical advice and Werner Müller (University of Manchester), Rui Appelberg (i3S), and Bruno Silva-Santos (iMM) for providing the IL-10Rα-, IFN-γ-, and TCRγδ-deficient animals, respectively. We thank Anne O’Garra for helpful discussions and for critical reading of the manuscript. We also thank Delfim Duarte and Maria José Teles for helpful discussions and for helping with the hemogram quantification. We thank Caetano Reis e Sousa for help with the preparation of the graphical abstract. We thank the support of the personnel in the animal facilities, the i3S scientific platforms Translational Cytometry (TraCy), and Histology and Electron Microscopy (HEMS). HEMS is a member of the national infrastructure PPBI (Portuguese Platform of Bioimaging, PPBI-POCI-01-0145-FEDER-022122)., ANR-10-LABX-0073,REVIVE,Stem Cells in Regenerative Biology and Medicine(2010), ANR-13-ISV1-0003,MYELOTEN,DEREGULATION DE L'HEMATOPOIESE PAR LA SUREXPRESSION DE L'INTERLEUKINE-10 : IMPLICATIONS DANS LE DEVELOPPEMENT DE PATHOLOGIES HEMATOLOGIQUES(2013), European Project, Vougny, Marie-Christine, Laboratoires d'excellence - Stem Cells in Regenerative Biology and Medicine - - REVIVE2010 - ANR-10-LABX-0073 - LABX - VALID, Blanc – Accords bilatéraux 2013 - DEREGULATION DE L'HEMATOPOIESE PAR LA SUREXPRESSION DE L'INTERLEUKINE-10 : IMPLICATIONS DANS LE DEVELOPPEMENT DE PATHOLOGIES HEMATOLOGIQUES - - MYELOTEN2013 - ANR-13-ISV1-0003 - Blanc – Accords bilatéraux 2013 - VALID, COST Action BM1404 MyeEUNITER - INCOMING, Universidade do Porto, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), and Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)
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CD4-Positive T-Lymphocytes ,Mice, Knockout ,Myelopoiesis ,[SDV.IMM] Life Sciences [q-bio]/Immunology ,T cells ,emergency myelopoiesis ,CD8-Positive T-Lymphocytes ,Interleukin-10 ,Interferon-gamma ,Mice ,IL-10 ,Animals ,[SDV.IMM]Life Sciences [q-bio]/Immunology ,IFN-γ ,Myeloid Progenitor Cells - Abstract
International audience; In emergency myelopoiesis (EM), expansion of the myeloid progenitor compartment and increased myeloid cell production are observed and often mediated by the pro-inflammatory cytokine interferon gamma (IFN-γ). Interleukin-10 (IL-10) inhibits IFN-γ secretion, but paradoxically, its therapeutic administration to humans causes hematologic changes similar to those observed in EM. In this work, we use different in vivo systems, including a humanized immune system mouse model, to show that IL-10 triggers EM, with a significant expansion of the myeloid progenitor compartment and production of myeloid cells. Hematopoietic progenitors display a prominent IFN-γ transcriptional signature, and we show that IFN-γ mediates IL-10-driven EM. We also find that IL-10, unexpectedly, reprograms CD4 and CD8 T cells toward an activation state that includes IFN-γ production by these T cell subsets in vivo. Therefore, in addition to its established anti-inflammatory properties, IL-10 can induce IFN-γ production and EM, opening additional perspectives for the design of IL-10-based immunotherapies.
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- 2021
44. Left Atrial Phasic Function in Older Adults Is Associated with Fibrotic and Low-Grade Inflammatory Pathways
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Angela S. Koh, Anthony Siau, Fei Gao, Florence W.J. Chioh, Shuang Leng, Xiaodan Zhao, Liang Zhong, Ru San Tan, Poh Ling Koh, Jean-Paul Kovalik, Wee Shiong Lim, Gina S. Lee, Woon-Puay Koh, Christine Cheung, Lee Kong Chian School of Medicine (LKCMedicine), and Institute of Molecular and Cell Biology, A*STAR
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Aging ,Medicine [Science] ,Geriatrics and Gerontology ,Cardiovascular ,Left Atrium - Abstract
Introduction: Concomitant risk factors challenge the mechanistic understanding of cardiac aging. We determined the degree to which the left atrial function could be distinguished by advanced cardiac magnetic resonance (CMR) imaging in older adults and assessed associations between the left atrial function and the plasma biomarkers related to biological aging and cardiovascular disease [serum monocyte chemoattractant protein-1 (MCP1), matrix metallopeptidase 9 (MMP-9), B-type natriuretic peptides (BNPs), galectin-3 (Gal-3), high-sensitivity cardiac troponin I (hsTn1), high-sensitivity C-reactive protein (hs-CRP), and soluble urokinase plasminogen activator receptor (sUPAR)]. Methods: Among a cross-sectional population-based cohort of older adults, longitudinal LA strain including reservoir strain (ϵs), conduit strain (ϵe), and booster strain (ϵa) as well as peak strain rates (SRs, SRe, SRa) were determined using CMR and studied in association with blood biomarkers. Results: We studied 243 community adults (42.8% female, mean age 70.3 ± 9.5 years). In bivariate analysis, ϵe and SRe were reduced in gradation with increasing risk factors (all p values
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- 2021
45. Circulating <scp>microRNA</scp> breast cancer biomarker detection in patient sera with surface plasmon resonance imaging biosensor
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Patrick M. Y. Chan, Ann Siew Gek Lee, Ern Yu Tan, Malini Olivo, Hann Qian Lim, Ghayathri Balasundaram, Sau Yeen Loke, Bee Kiang Chong, Chi Lok Wong, Lee Kong Chian School of Medicine (LKCMedicine), Institute of Molecular and Cell Biology, A*STAR, and Tan Tock Seng Hospital
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Breast Cancer Biomarker ,General Physics and Astronomy ,Breast Neoplasms ,Biosensing Techniques ,General Biochemistry, Genetics and Molecular Biology ,Nuclear magnetic resonance ,Breast cancer ,Surface plasmon resonance imaging ,Circulating miRNA ,Biomarkers, Tumor ,medicine ,Humans ,Medicine [Science] ,General Materials Science ,In patient ,Circulating MicroRNA ,Plasmon ,Chemistry ,General Engineering ,Resonance ,General Chemistry ,Surface Plasmon Resonance ,medicine.disease ,Biomarker (cell) ,Female ,Gold ,Biosensor - Abstract
In this article, we report for the first time, the detection of circulating miRNA as a breast cancer biomarker in patient sera using surface plasmon resonance imaging biosensor. The advantage of this approach lies in the rapid, label-free and sensitive detection. The sensor excites plasmonic resonance on the gold sensor surface and specific DNA-miRNA molecular bindings elucidate responses in the plasmonic resonance image. Experiments of detecting synthetic miRNA molecules (miR-1249) were performed and the sensor resolution was found to be 63.5 nM. The sensor was further applied to screen 17 patient serum samples from National Cancer Centre Singapore and Tan Tock Seng Hospital. Sensor intensity response was found to differ by 20% between malignant and benign cases and thus forms, a potential and an important metric in distinguishing benignity and malignancy. Agency for Science, Technology and Research (A*STAR) This work was supported by Agency of Science, Technology and Research (A*STAR), under its Industry alignment fund prepositioning programme, Award H19H6a0025 , Agency for Science, Technology and Research’s (A*STAR) BMRC Central Research Fund (CRF, UIBR) Award and A*ccelerate under GAP funding (ETPL/14-R15GAP-0027). This project was partially funded by the NCC Research Fund.
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- 2021
46. Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis
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Caner Akıl, Linh T. Tran, Magali Orhant-Prioux, Yohendran Baskaran, Yosuke Senju, Shuichi Takeda, Phatcharin Chotchuang, Duangkamon Muengsaen, Albert Schulte, Edward Manser, Laurent Blanchoin, Robert C. Robinson, Institute of Molecular and Cell Biology, A*STAR, National University of Singapore (NUS), Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan, CytoMorphoLab, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7), JST CREST, grant number JPMJCR19S5, Japan, Japan Society for the Promotion of Science (JSPS), grant number JP20H00476 and 20K06589, Moore-Simons Project on the Origin of the Eukaryotic Cell, grant number GBMF9743, A*STAR, Singapore National Medical Research Council (NMRC grant OFIRG/0067/2018), Vidyasirimedhi Institute of Science and Technology (VISTEC), and Wesco Scientific Promotion Foundation
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Medicine (miscellaneous) ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,MESH: Actins ,Archaea ,Actins ,General Biochemistry, Genetics and Molecular Biology ,Actin Cytoskeleton ,MESH: Gelsolin ,MESH: Archaea ,MESH: Calcium ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Calcium ,MESH: Actin Cytoskeleton ,General Agricultural and Biological Sciences ,Gelsolin - Abstract
Charting the emergence of eukaryotic traits is important for understanding the characteristics of organisms that contributed to eukaryogenesis. Asgard archaea and eukaryotes are the only organisms known to possess regulated actin cytoskeletons. Here, we determined that gelsolins (2DGels) from Lokiarchaeota (Loki) and Heimdallarchaeota (Heim) are capable of regulating eukaryotic actin dynamics in vitro and when expressed in eukaryotic cells. The actin filament severing and capping, and actin monomer sequestering, functionalities of 2DGels are strictly calcium controlled. We determined the X-ray structures of Heim and Loki 2DGels bound actin monomers. Each structure possesses common and distinct calcium-binding sites. Loki2DGel has an unusual WH2-like motif (LVDV) between its two gelsolin domains, in which the aspartic acid coordinates a calcium ion at the interface with actin. We conclude that the calcium-regulated actin cytoskeleton predates eukaryogenesis and emerged in the predecessors of the last common ancestor of Loki, Heim and Thorarchaeota. Calcium-regulated actin filament assembly predates eukaryogenesis and was present in the last common ancestor of Asgard archaea Loki, Heim, and Thorarchaeota.
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- 2022
47. Subtle spectral effects accompanying the assembly of bacteriochlorophylls into cyclic light harvesting complexes revealed by high-resolution fluorescence spectroscopy
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Freiberg, Arvi [Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia and Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu (Estonia)]
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- 2014
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48. Computation studies into architecture and energy transfer properties of photosynthetic units from filamentous anoxygenic phototrophs
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Freiberg, Arvi [Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia and Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu (Estonia)]
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- 2014
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49. Dynamics and potential significance of spontaneous activity in the habenula
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null Suryadi, Ruey-Kuang Cheng, Elliot Birkett, Suresh Jesuthasan, Lock Yue Chew, School of Physical and Mathematical Sciences, Lee Kong Chian School of Medicine (LKCMedicine), Institute of Molecular and Cell Biology, and Complexity Institute
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Criticality ,General Neuroscience ,Biological sciences [Science] ,Avalanche ,General Medicine - Abstract
The habenula is an evolutionarily conserved structure of the vertebrate brain that is essential for behavioural flexibility and mood control. It is spontaneously active and is able to access diverse states when the animal is exposed to sensory stimuli. Here we investigate the dynamics of habenula spontaneous activity, to gain insight into how sensitivity is optimized. Two-photon calcium imaging was performed in resting zebrafish larvae at single cell resolution. An analysis of avalanches of inferred spikes suggests that the habenula is subcritical. Activity had low covariance and a small mean, arguing against dynamic criticality. A multiple regression estimator of autocorrelation time suggests that the habenula is neither fully asynchronous nor perfectly critical, but is reverberating. This pattern of dynamics may enable integration of information and high flexibility in the tuning of network properties, thus providing a potential mechanism for the optimal responses to a changing environment. Significance Statement: Spontaneous activity in neurons shapes the response to stimuli. One structure with a high level of spontaneous neuronal activity is the habenula, a regulator of broadly acting neuromodulators involved in mood and learning. How does this activity influence habenula function? We show here that the habenula of a resting animal is near criticality, in a state termed reverberation. This pattern of dynamics is consistent with high sensitivity and flexibility, and may enable the habenula to respond optimally to a wide range of stimuli. Ministry of Education (MOE) Published version This work was funded by the Singapore Ministry of Education through an Academic Research Fund Tier 1 Award (MOE2016-T1-001-152) and a Tier 2 Award (MOE2017-T2-1-058).
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- 2021
50. Matriptase activation of Gq drives epithelial disruption and inflammation via RSK and DUOX
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Thomas J. Carney, Changqing Zhang, Lynda J. Partridge, Claire A. Scott, Jiajia Ma, Vinay Tergaonkar, Ser Sue Ng, Sudipto Roy, Ying Na Ho, Katherine S. Marsay, Harsha Mahabaleshwar, Weibin Zhang, Christopher K.J. Teow, Enrique Amaya, Lee Kong Chian School of Medicine (LKCMedicine), and Institute of Molecular and Cell Biology, A*STAR
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0301 basic medicine ,MAPK/ERK pathway ,Embryo, Nonmammalian ,Neutrophils ,Cell ,Polymerase Chain Reaction ,Animals, Genetically Modified ,0302 clinical medicine ,Gq ,Biology (General) ,Zebrafish ,biology ,Chemistry ,RSK ,General Neuroscience ,Serine Endopeptidases ,General Medicine ,Par2 ,Cell biology ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Medicine ,Epithelia ,Matriptase ,Hai1 ,Research Article ,QH301-705.5 ,Science ,Peptides, Cyclic ,ST14 ,Gene Expression Regulation, Enzymologic ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,St14 ,medicine ,Animals ,Medicine [Science] ,Calcium Signaling ,Cell adhesion ,Diacylglycerol kinase ,Inflammation ,General Immunology and Microbiology ,Cadherin ,Genetics and Genomics ,Cell Biology ,DNA ,Hydrogen Peroxide ,Hydrogen peroxide ,Enzyme Activation ,030104 developmental biology ,inflammation ,Mutation ,Cancer cell ,biology.protein ,GTP-Binding Protein alpha Subunits, Gq-G11 ,RNA ,Calcium ,Epidermis - Abstract
Epithelial tissues are primed to respond to insults by activating epithelial cell motility and rapid inflammation. Such responses are also elicited upon overexpression of the membrane-bound protease, Matriptase, or mutation of its inhibitor, Hai1. Unrestricted Matriptase activity also predisposes to carcinoma. How Matriptase leads to these cellular outcomes is unknown. We demonstrate that zebrafish hai1a mutants show increased H2O2, NfκB signalling, and IP3R -mediated calcium flashes, and that these promote inflammation, but do not generate epithelial cell motility. In contrast, inhibition of the Gq subunit in hai1a mutants rescues both the inflammation and epithelial phenotypes, with the latter recapitulated by the DAG analogue, PMA. We demonstrate that hai1a has elevated MAPK pathway activity, inhibition of which rescues the epidermal defects. Finally, we identify RSK kinases as MAPK targets disrupting adherens junctions in hai1a mutants. Our work maps novel signalling cascades mediating the potent effects of Matriptase on epithelia, with implications for tissue damage response and carcinoma progression., eLife digest Cancer occurs when normal processes in the cell become corrupted or unregulated. Many proteins can contribute, including one enzyme called Matriptase that cuts other proteins at specific sites. Matriptase activity is tightly controlled by a protein called Hai1. In mice and zebrafish, when Hai1 cannot adequately control Matriptase activity, invasive cancers with severe inflammation develop. However, it is unclear how unregulated Matriptase leads to both inflammation and cancer invasion. One outcome of Matriptase activity is removal of proteins called Cadherins from the cell surface. These proteins have a role in cell adhesion: they act like glue to stick cells together. Without them, cells can dissociate from a tissue and move away, a critical step in cancer cells invading other organs. However, it is unknown exactly how Matriptase triggers the removal of Cadherins from the cell surface to promote invasion. Previous work has shown that Matriptase switches on a receptor called Proteinase-activated receptor 2, or Par2 for short, which is known to activate many enzymes, including one called phospholipase C. When activated, this enzyme releases two signals into the cell: a sugar called inositol triphosphate, IP3; and a lipid or fat called diacylglycerol, DAG. It is possible that these two signals have a role to play in how Matriptase removes Cadherins from the cell surface. To find out, Ma et al. mapped the effects of Matriptase in zebrafish lacking the Hai1 protein. This revealed that Matriptase increases IP3 and DAG levels, which initiate both inflammation and invasion. IP3 promotes inflammation by switching on pro-inflammatory signals inside the cell such as the chemical hydrogen peroxide. At the same time, DAG promotes cell invasion by activating a well-known cancer signalling pathway called MAPK. This pathway activates a protein called RSK. Ma et al. show that this protein is required to remove Cadherins from the surface of cells, thus connecting Matriptase’s activation of phospholipase C with its role in disrupting cell adhesion. An increase in the ratio of Matriptase to HAI-1 (the human equivalent of Hai1) is present in many cancers. For this reason, the signal cascades described by Ma et al. may be of interest in developing treatments for these cancers. Understanding how these signals work together could lead to more direct targeted anti-cancer approaches in the future.
- Published
- 2021
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