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1. Spatially resolved multiomics of human cardiac niches

Author

Kanemaru, Kazumasa, Cranley, James, Muraro, Daniele, Miranda, Antonio M. A., Ho, Siew Yen, Wilbrey-Clark, Anna, Patrick Pett, Jan, Polanski, Krzysztof, Richardson, Laura, Litvinukova, Monika, Kumasaka, Natsuhiko, Qin, Yue, Jablonska, Zuzanna, Semprich, Claudia I., Mach, Lukas, Dabrowska, Monika, Richoz, Nathan, Bolt, Liam, Mamanova, Lira, Kapuge, Rakeshlal, Barnett, Sam N., Perera, Shani, Talavera-López, Carlos, Mulas, Ilaria, Mahbubani, Krishnaa T., Tuck, Liz, Wang, Lu, Huang, Margaret M., Prete, Martin, Pritchard, Sophie, Dark, John, Saeb-Parsy, Kourosh, Patel, Minal, Clatworthy, Menna R., Hübner, Norbert, Chowdhury, Rasheda A., Noseda, Michela, and Teichmann, Sarah A.

Published
2023
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2. FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2

Author

Brevini, Teresa, Maes, Mailis, Webb, Gwilym J., John, Binu V., Fuchs, Claudia D., Buescher, Gustav, Wang, Lu, Griffiths, Chelsea, Brown, Marnie L., Scott, III, William E., Pereyra-Gerber, Pehuén, Gelson, William T. H., Brown, Stephanie, Dillon, Scott, Muraro, Daniele, Sharp, Jo, Neary, Megan, Box, Helen, Tatham, Lee, Stewart, James, Curley, Paul, Pertinez, Henry, Forrest, Sally, Mlcochova, Petra, Varankar, Sagar S., Darvish-Damavandi, Mahnaz, Mulcahy, Victoria L., Kuc, Rhoda E., Williams, Thomas L., Heslop, James A., Rossetti, Davide, Tysoe, Olivia C., Galanakis, Vasileios, Vila-Gonzalez, Marta, Crozier, Thomas W. M., Bargehr, Johannes, Sinha, Sanjay, Upponi, Sara S., Fear, Corrina, Swift, Lisa, Saeb-Parsy, Kourosh, Davies, Susan E., Wester, Axel, Hagström, Hannes, Melum, Espen, Clements, Darran, Humphreys, Peter, Herriott, Jo, Kijak, Edyta, Cox, Helen, Bramwell, Chloe, Valentijn, Anthony, Illingworth, Christopher J. R., Dahman, Bassam, Bastaich, Dustin R., Ferreira, Raphaella D., Marjot, Thomas, Barnes, Eleanor, Moon, Andrew M., Barritt, IV, Alfred S., Gupta, Ravindra K., Baker, Stephen, Davenport, Anthony P., Corbett, Gareth, Gorgoulis, Vassilis G., Buczacki, Simon J. A., Lee, Joo-Hyeon, Matheson, Nicholas J., Trauner, Michael, Fisher, Andrew J., Gibbs, Paul, Butler, Andrew J., Watson, Christopher J. E., Mells, George F., Dougan, Gordon, Owen, Andrew, Lohse, Ansgar W., Vallier, Ludovic, and Sampaziotis, Fotios

Published
2023
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3. Single-cell atlas of human liver development reveals pathways directing hepatic cell fates

Author

Wesley, Brandon T., Ross, Alexander D. B., Muraro, Daniele, Miao, Zhichao, Saxton, Sarah, Tomaz, Rute A., Morell, Carola M., Ridley, Katherine, Zacharis, Ekaterini D., Petrus-Reurer, Sandra, Kraiczy, Judith, Mahbubani, Krishnaa T., Brown, Stephanie, Garcia-Bernardo, Jose, Alsinet, Clara, Gaffney, Daniel, Horsfall, Dave, Tysoe, Olivia C., Botting, Rachel A., Stephenson, Emily, Popescu, Dorin-Mirel, MacParland, Sonya, Bader, Gary, McGilvray, Ian D., Ortmann, Daniel, Sampaziotis, Fotios, Saeb-Parsy, Kourosh, Haniffa, Muzlifah, Stevens, Kelly R., Zilbauer, Matthias, Teichmann, Sarah A., and Vallier, Ludovic

Published
2022
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4. Emergent thresholds in genetic regulatory networks: Protein patterning in Drosophila morphogenesis

Author

Dilão, Rui and Muraro, Daniele

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Molecular Networks
Abstract

We present a general methodology in order to build mathematical models of genetic regulatory networks. This approach is based on the mass action law and on the Jacob and Monod operon model. The mathematical models are built symbolically by the \emph{Mathematica} software package \emph{GeneticNetworks}. This package accepts as input the interaction graphs of the transcriptional activators and repressors and, as output, gives the mathematical model in the form of a system of ordinary differential equations. All the relevant biological parameters are chosen automatically by the software. Within this framework, we show that threshold effects in biology emerge from the catalytic properties of genes and its associated conservation laws. We apply this methodology to the segment patterning in \emph{Drosophila} early development and we calibrate and validate the genetic transcriptional network responsible for the patterning of the gap proteins Hunchback and Knirps, along the antero-posterior axis of the \emph{Drosophila} embryo. This shows that patterning at the gap genes stage is a consequence of the relations between the transcriptional regulators and their initial conditions along the embryo., Comment: 28 pages, 9 figures

Published
2009

5. mRNA diffusion explains protein gradients in \textit{Drosophila} early development

Author

Dilão, Rui and Muraro, Daniele

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Molecular Networks
Abstract

We propose a new model describing the production and the establishment of the stable gradient of the Bicoid protein along the antero-posterior axis of the embryo of \textit{Drosophila}. In this model, we consider that \textit{bicoid} mRNA diffuses along the antero-posterior axis of the embryo and the protein is produced in the ribosomes localized near the syncytial nuclei. Bicoid protein stays localized near the syncytial nuclei as observed in experiments. We calibrate the parameters of the mathematical model with experimental data taken during the cleavage stages 11 to 14 of the developing embryo of \textit{Drosophila}. We obtain good agreement between the experimental and the model gradients, with relative errors in the range 5-8%. The inferred diffusion coefficient of \textit{bicoid} mRNA is in the range 4.6\times 10^{-12}-1.5\times 10^{-11}m^2s^{-1}, in agreement with the theoretical predictions and experimental measurements for the diffusion of macromolecules in the cytoplasm. We show that the model based on the mRNA diffusion hypothesis is consistent with the known observational data, supporting the recent experimental findings of the gradient of \textit{bicoid} mRNA in \textit{Drosophila} [Spirov et al. (2009) Development 136:605-614]., Comment: 14 pages, 2 figures

Published
2009

6. Gene-level alignment of single cell trajectories

Author

Sumanaweera, Dinithi, primary, Suo, Chenqu, additional, Cujba, Ana-Maria, additional, Muraro, Daniele, additional, Dann, Emma, additional, Polanski, Krzysztof, additional, Steemers, Alexander S., additional, Lee, Woochan, additional, Oliver, Amanda J., additional, Park, Jong-Eun, additional, Meyer, Kerstin B., additional, Dumitrascu, Bianca, additional, and Teichmann, Sarah A., additional

Published
2023
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7. Gene-level alignment of single-cell trajectories

Author

Sumanaweera, Dinithi, Suo, Chenqu, Cujba, Ana-Maria, Muraro, Daniele, Dann, Emma, Polanski, Krzysztof, Steemers, Alexander S., Lee, Woochan, Oliver, Amanda J., Park, Jong-Eun, Meyer, Kerstin B., Dumitrascu, Bianca, and Teichmann, Sarah A.

Abstract

Single-cell data analysis can infer dynamic changes in cell populations, for example across time, space or in response to perturbation, thus deriving pseudotime trajectories. Current approaches comparing trajectories often use dynamic programming but are limited by assumptions such as the existence of a definitive match. Here we describe Genes2Genes, a Bayesian information-theoretic dynamic programming framework for aligning single-cell trajectories. It is able to capture sequential matches and mismatches of individual genes between a reference and query trajectory, highlighting distinct clusters of alignment patterns. Across both real world and simulated datasets, it accurately inferred alignments and demonstrated its utility in disease cell-state trajectory analysis. In a proof-of-concept application, Genes2Genes revealed that T cells differentiated in vitro match an immature in vivo state while lacking expression of genes associated with TNF signaling. This demonstrates that precise trajectory alignment can pinpoint divergence from the in vivo system, thus guiding the optimization of in vitro culture conditions.

Published
2024
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9. Spatially resolved multiomics of human cardiac niches

Author

Kanemaru, Kazumasa, primary, Cranley, James, additional, Muraro, Daniele, additional, Miranda, Antonio M.A., additional, Pett, Jan Patrick, additional, Litvinukova, Monika, additional, Kumasaka, Natsuhiko, additional, Ho, Siew Yen, additional, Polanski, Krzysztof, additional, Richardson, Laura, additional, Mach, Lukas, additional, Dabrowska, Monika, additional, Richoz, Nathan, additional, Barnett, Sam N., additional, Perera, Shani, additional, Wilbrey-Clark, Anna L, additional, Talavera-López, Carlos, additional, Mulas, Ilaria, additional, Mahbubani, Krishnaa T., additional, Bolt, Liam, additional, Mamanova, Lira, additional, Tuck, Liz, additional, Wang, Lu, additional, Huang, Margaret M., additional, Prete, Martin, additional, Pritchard, Sophie, additional, Dark, John, additional, Saeb-Parsy, Kourosh, additional, Patel, Minal, additional, Clatworthy, Menna R., additional, Chowdhury, Rasheda A., additional, Noseda, Michela, additional, and Teichmann, Sarah A., additional

Published
2023
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11. Validation of a Morphogenesis Model of Drosophila Early Development by a Multi-objective Evolutionary Optimization Algorithm

Author

Dilão, Rui, Muraro, Daniele, Nicolau, Miguel, Schoenauer, Marc, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Pizzuti, Clara, editor, Ritchie, Marylyn D., editor, and Giacobini, Mario, editor

Published
2009
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14. Single-cell atlas of human liver development reveals pathways directing hepatic cell fates

Author

Wesley, Brandon T., primary, Ross, Alexander D. B., additional, Muraro, Daniele, additional, Miao, Zhichao, additional, Saxton, Sarah, additional, Tomaz, Rute A., additional, Morell, Carola M., additional, Ridley, Katherine, additional, Zacharis, Ekaterini D., additional, Petrus-Reurer, Sandra, additional, Kraiczy, Judith, additional, Mahbubani, Krishnaa T., additional, Brown, Stephanie, additional, Garcia-Bernardo, Jose, additional, Alsinet, Clara, additional, Gaffney, Daniel, additional, Tysoe, Olivia C., additional, Botting, Rachel A., additional, Stephenson, Emily, additional, Popescu, Dorin-Mirel, additional, MacParland, Sonya, additional, Bader, Gary, additional, McGilvray, Ian D., additional, Ortmann, Daniel, additional, Sampaziotis, Fotios, additional, Saeb-Parsy, Kourosh, additional, Haniffa, Muzlifah, additional, Stevens, Kelly R., additional, Zilbauer, Matthias, additional, Teichmann, Sarah A., additional, and Vallier, Ludovic, additional

Published
2022
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15. Modeling HNF1B-associated monogenic diabetes using human iPSCs reveals an early stage impairment of the pancreatic developmental program

Author

El-Khairi, Ranna, Olszanowski, Evelyn, Muraro, Daniele, Madrigal, Pedro, Tilgner, Katarzyna, Chhatriwala, Mariya, Vyas, Sapna, Chia, Crystal Y, Vallier, Ludovic, Rodríguez-Seguí, Santiago A, Madrigal, Pedro [0000-0003-1959-8199], Vallier, Ludovic [0000-0002-3848-2602], and Apollo - University of Cambridge Repository

Subjects
HNF1B, Organogenesis, Induced Pluripotent Stem Cells, β cell, Fluorescent Antibody Technique, Haploinsufficiency, Models, Biological, Immunophenotyping, monogenic, Insulin-Secreting Cells, Diabetes Mellitus, Humans, Cell Lineage, pancreas, in vitro, Hepatocyte Nuclear Factor 1-beta, Gene Editing, iPSC, diabetes, MODY5, Gene Expression Profiling, Gene Expression Regulation, Developmental, Cell Differentiation, differentiation, human induced pluripotent stem cells, Disease Susceptibility, CRISPR-Cas Systems, Biomarkers, Signal Transduction
Abstract

Heterozygous mutations in HNF1B in humans result in a multisystem disorder, including pancreatic hypoplasia and diabetes mellitus. Here we used a well-controlled human induced pluripotent stem cell pancreatic differentiation model to elucidate the molecular mechanisms underlying HNF1B-associated diabetes. Our results show that lack of HNF1B blocks specification of pancreatic fate from the foregut progenitor (FP) stage, but HNF1B haploinsufficiency allows differentiation of multipotent pancreatic progenitor cells (MPCs) and insulin-secreting β-like cells. We show that HNF1B haploinsufficiency impairs cell proliferation in FPs and MPCs. This could be attributed to impaired induction of key pancreatic developmental genes, including SOX11, ROBO2, and additional TEAD1 target genes whose function is associated with MPC self-renewal. In this work we uncover an exhaustive list of potential HNF1B gene targets during human pancreas organogenesis whose downregulation might underlie HNF1B-associated diabetes onset in humans, thus providing an important resource to understand the pathogenesis of this disease.

Published
2021

16. O07 FXR antagonists as new agents for COVID19

Author

Brevini, Teresa, primary, Maes, Mailis, additional, Webb, Gwilym J, additional, Gelson, William TH, additional, Forrest, Sally, additional, Mlcochova, Petra, additional, Dillon, Scott, additional, Varankar, Sagar, additional, Darvish-Damavandi, Mahnaz, additional, Mulcahy, Victoria L, additional, Kuc, Rhoda E, additional, Williams, Thomas L, additional, Galanakis, Vasileios, additional, Vila-Gonzalez, Marta, additional, Tysoe, Olivia C, additional, Muraro, Daniele, additional, Crozier, Thomas WM, additional, Bargehr, Johannes, additional, Sinha, Sanjay, additional, Upponi, Sara S, additional, Swift, Lisa, additional, Saeb-Parsy, Kourosh, additional, Davies, Susan E, additional, Marjot, Thomas, additional, Barnes, Eleanor, additional, Lohse, Ansgar W, additional, Moon, Andrew M, additional, Sidney Barritt, A, additional, Gupta, Ravindra K, additional, Baker, Stephen, additional, Davenport, Anthony P, additional, Corbett, Gareth, additional, Buczacki, Simon JA, additional, Lee, Joo-Hyeon, additional, Gibbs, Paul, additional, Butler, Andrew J, additional, Watson, Christopher JE, additional, Mells, George F, additional, Dougan, Gordon, additional, Vallier, Ludovic, additional, and Sampaziotis, Fotios, additional

Published
2021
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17. Modeling HNF1B-associated monogenic diabetes using human iPSCs reveals an early stage impairment of the pancreatic developmental program

Author

El-Khairi, Ranna, primary, Olszanowski, Evelyn, additional, Muraro, Daniele, additional, Madrigal, Pedro, additional, Tilgner, Katarzyna, additional, Chhatriwala, Mariya, additional, Vyas, Sapna, additional, Chia, Crystal Y., additional, Vallier, Ludovic, additional, and Rodríguez-Seguí, Santiago A., additional

Published
2021
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18. TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells

Author

Osnato, Anna, primary, Brown, Stephanie, additional, Krueger, Christel, additional, Andrews, Simon, additional, Collier, Amanda J, additional, Nakanoh, Shota, additional, Quiroga Londoño, Mariana, additional, Wesley, Brandon T, additional, Muraro, Daniele, additional, Brumm, A Sophie, additional, Niakan, Kathy K, additional, Vallier, Ludovic, additional, Ortmann, Daniel, additional, and Rugg-Gunn, Peter J, additional

Published
2021
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19. Author response: TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells

Author

Osnato, Anna, primary, Brown, Stephanie, additional, Krueger, Christel, additional, Andrews, Simon, additional, Collier, Amanda J, additional, Nakanoh, Shota, additional, Quiroga Londoño, Mariana, additional, Wesley, Brandon T, additional, Muraro, Daniele, additional, Brumm, A Sophie, additional, Niakan, Kathy K, additional, Vallier, Ludovic, additional, Ortmann, Daniel, additional, and Rugg-Gunn, Peter J, additional

Published
2021
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20. FXR inhibition reduces ACE2 expression, SARS-CoV-2 infection and may improve COVID-19 outcome

Author

Brevini, Teresa, primary, Maes, Mailis, additional, Webb, Gwilym J., additional, Gelson, William T. H., additional, Forrest, Sally, additional, Mlcochova, Petra, additional, Dillon, Scott, additional, Varankar, Sagar, additional, Darvish-Damavandi, Mahnaz, additional, Mulcahy, Victoria L., additional, Kuc, Rhoda E., additional, Williams, Thomas L., additional, Galanakis, Vasileios, additional, Vila-Gonzalez, Marta, additional, Tysoe, Olivia C., additional, Muraro, Daniele, additional, Crozier, Thomas W. M., additional, Bargehr, Johannes, additional, Sinha, Sanjay, additional, Upponi, Sara S., additional, Swift, Lisa, additional, Saeb-Parsy, Kourosh, additional, Davies, Susan E., additional, Marjot, Thomas, additional, Barnes, Eleanor, additional, Lohse, Ansgar W., additional, Moon, Andrew M., additional, Sidney Barritt, A., additional, Gupta, Ravindra K., additional, Baker, Stephen, additional, Davenport, Anthony P., additional, Corbett, Gareth, additional, Buczacki, Simon J. A., additional, Lee, Joo-Hyeon, additional, Gibbs, Paul, additional, Butler, Andrew J., additional, Watson, Christopher J. E., additional, Mells, George F., additional, Dougan, Gordon, additional, Vallier, Ludovic, additional, and Sampaziotis, Fotios, additional

Published
2021
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21. Regional Differences in Human Biliary Tissues and Corresponding In Vitro-Derived Organoids

Author

Rimland, Casey A, Tilson, Samantha G, Morell, Carola M, Tomaz, Rute A, Lu, Wei-Yu, Adams, Simone E, Georgakopoulos, Nikitas, Otaizo-Carrasquero, Francisco, Myers, Timothy G, Ferdinand, John R, Gieseck, Richard L, Sampaziotis, Fotios, Tysoe, Olivia C, Ross, Alexander, Kraiczy, Judith M, Wesley, Brandon, Muraro, Daniele, Zilbauer, Matthias, Oniscu, Gabriel C, Hannan, Nicholas RF, Forbes, Stuart J, Saeb-Parsy, Kourosh, Wynn, Thomas A, Vallier, Ludovic, Rimland, Casey A [0000-0002-5187-6921], Myers, Timothy G [0000-0002-7059-5906], Gieseck, Richard L [0000-0003-0200-581X], Tysoe, Olivia C [0000-0002-1061-1484], Forbes, Stuart J [0000-0003-3715-2561], and Apollo - University of Cambridge Repository

Subjects
Common Bile Duct, Keratin-19, Tissue and Organ Procurement, Gallbladder, Cell Differentiation, Epithelial Cells, Organoids, Mice, Bile Ducts, Intrahepatic, Gene Expression Regulation, Liver, Bile Ducts, Extrahepatic, Animals, Bile, Humans, RNA-Seq
Abstract

BACKGROUND AND AIMS: Organoids provide a powerful system to study epithelia in vitro. Recently, this approach was applied successfully to the biliary tree, a series of ductular tissues responsible for the drainage of bile and pancreatic secretions. More precisely, organoids have been derived from ductal tissue located outside (extrahepatic bile ducts; EHBDs) or inside the liver (intrahepatic bile ducts; IHBDs). These organoids share many characteristics, including expression of cholangiocyte markers such as keratin (KRT) 19. However, the relationship between these organoids and their tissues of origin, and to each other, is largely unknown. APPROACH AND RESULTS: Organoids were derived from human gallbladder, common bile duct, pancreatic duct, and IHBDs using culture conditions promoting WNT signaling. The resulting IHBD and EHBD organoids expressed stem/progenitor markers leucine-rich repeat-containing G-protein-coupled receptor 5/prominin 1 and ductal markers KRT19/KRT7. However, RNA sequencing revealed that organoids conserve only a limited number of regional-specific markers corresponding to their location of origin. Of particular interest, down-regulation of biliary markers and up-regulation of cell-cycle genes were observed in organoids. IHBD and EHBD organoids diverged in their response to WNT signaling, and only IHBDs were able to express a low level of hepatocyte markers under differentiation conditions. CONCLUSIONS: Taken together, our results demonstrate that differences exist not only between extrahepatic biliary organoids and their tissue of origin, but also between IHBD and EHBD organoids. This information may help to understand the tissue specificity of cholangiopathies and also to identify targets for therapeutic development.

Published
2021

22. Cholangiocyte organoids can repair bile ducts after transplantation in the human liver

Author

Sampaziotis, Fotios, primary, Muraro, Daniele, additional, Tysoe, Olivia C., additional, Sawiak, Stephen, additional, Beach, Timothy E., additional, Godfrey, Edmund M., additional, Upponi, Sara S., additional, Brevini, Teresa, additional, Wesley, Brandon T., additional, Garcia-Bernardo, Jose, additional, Mahbubani, Krishnaa, additional, Canu, Giovanni, additional, Gieseck, Richard, additional, Berntsen, Natalie L., additional, Mulcahy, Victoria L., additional, Crick, Keziah, additional, Fear, Corrina, additional, Robinson, Sharayne, additional, Swift, Lisa, additional, Gambardella, Laure, additional, Bargehr, Johannes, additional, Ortmann, Daniel, additional, Brown, Stephanie E., additional, Osnato, Anna, additional, Murphy, Michael P., additional, Corbett, Gareth, additional, Gelson, William T. H., additional, Mells, George F., additional, Humphreys, Peter, additional, Davies, Susan E., additional, Amin, Irum, additional, Gibbs, Paul, additional, Sinha, Sanjay, additional, Teichmann, Sarah A., additional, Butler, Andrew J., additional, See, Teik Choon, additional, Melum, Espen, additional, Watson, Christopher J. E., additional, Saeb-Parsy, Kourosh, additional, and Vallier, Ludovic, additional

Published
2021
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23. Regional Differences in Human Biliary Tissues and Corresponding In Vitro–Derived Organoids

Author

Rimland, Casey A., primary, Tilson, Samantha G., additional, Morell, Carola M., additional, Tomaz, Rute A., additional, Lu, Wei‐Yu, additional, Adams, Simone E., additional, Georgakopoulos, Nikitas, additional, Otaizo‐Carrasquero, Francisco, additional, Myers, Timothy G., additional, Ferdinand, John R., additional, Gieseck, Richard L., additional, Sampaziotis, Fotios, additional, Tysoe, Olivia C., additional, Ross, Alexander, additional, Kraiczy, Judith M., additional, Wesley, Brandon, additional, Muraro, Daniele, additional, Zilbauer, Matthias, additional, Oniscu, Gabriel C., additional, Hannan, Nicholas R.F., additional, Forbes, Stuart J., additional, Saeb‐Parsy, Kourosh, additional, Wynn, Thomas A., additional, and Vallier, Ludovic, additional

Published
2021
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25. Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation

Author

Ortmann, Daniel, primary, Brown, Stephanie, additional, Czechanski, Anne, additional, Aydin, Selcan, additional, Muraro, Daniele, additional, Huang, Yuanhua, additional, Tomaz, Rute A., additional, Osnato, Anna, additional, Canu, Giovanni, additional, Wesley, Brandon T., additional, Skelly, Daniel A., additional, Stegle, Oliver, additional, Choi, Ted, additional, Churchill, Gary A., additional, Baker, Christopher L., additional, Rugg-Gunn, Peter J., additional, Munger, Steven C., additional, Reinholdt, Laura G., additional, and Vallier, Ludovic, additional

Published
2020
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26. Cholangiocyte organoids are plastic and their identity is controlled by their local microenvironment

Author

Sampaziotis, Fotis, primary, Muraro, Daniele, additional, Tysoe, Olivia C., additional, Beach, Timothy, additional, Sawiak, Stephen, additional, Godfrey, Edmund, additional, Upponi, Sara, additional, Wesley, Brandon, additional, Garcia-Bernardo, Jose, additional, Brevini, Teresa, additional, Mahbubani, Krishnaa, additional, Cannu, Giovanni, additional, Gieseck, Richard, additional, Berntsen, Natalie Lie, additional, Mulcahy, Victoria, additional, Crick, Keziah, additional, Fear, Corina, additional, Robinson, Sharayne, additional, Swift, Lisa, additional, Ortmann, Daniel, additional, Osnato, Anna, additional, Brown, Stephanie, additional, Murphy, Michael, additional, Gelson, William, additional, Mells, George, additional, Davies, Susan, additional, Amin, Irum, additional, Gibbs, Paul, additional, Teichmann, Sarah, additional, Butler, Andrew, additional, See, Teik Choon, additional, Melum, Espen, additional, Watson, Chris, additional, Saeb-Parsy, Kourosh, additional, and Vallier, Ludovic, additional

Published
2020
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27. NOD2 and TLR2 Signal via TBK1 and PI31 to Direct Cross-Presentation and CD8 T Cell Responses

Author

Corridoni, Daniele, primary, Shiraishi, Seiji, additional, Chapman, Thomas, additional, Steevels, Tessa, additional, Muraro, Daniele, additional, Thézénas, Marie-Laëtitia, additional, Prota, Gennaro, additional, Chen, Ji-Li, additional, Gileadi, Uzi, additional, Ternette, Nicola, additional, Cerundolo, Vincenzo, additional, and Simmons, Alison, additional

Published
2019
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28. Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics

Author

Yiangou, Loukia, primary, Grandy, Rodrigo A., additional, Morell, Carola M., additional, Tomaz, Rute A., additional, Osnato, Anna, additional, Kadiwala, Juned, additional, Muraro, Daniele, additional, Garcia-Bernardo, Jose, additional, Nakanoh, Shota, additional, Bernard, William G., additional, Ortmann, Daniel, additional, McCarthy, Davis J., additional, Simonic, Ingrid, additional, Sinha, Sanjay, additional, and Vallier, Ludovic, additional

Published
2019
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32. Snapin promotes HIV ‐1 transmission from dendritic cells by dampening TLR 8 signaling

Author

Khatamzas, Elham, primary, Hipp, Madeleine Maria, additional, Gaughan, Daniel, additional, Pichulik, Tica, additional, Leslie, Alasdair, additional, Fernandes, Ricardo A, additional, Muraro, Daniele, additional, Booth, Sarah, additional, Zausmer, Kieran, additional, Sun, Mei‐Yi, additional, Kessler, Benedikt, additional, Rowland‐Jones, Sarah, additional, Cerundolo, Vincenzo, additional, and Simmons, Alison, additional

Published
2017
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33. THREE-DIMENSIONAL COUPLED FEM MODELLING AND PROGRAMMING OF PARTIALLY SATURATED POROUS MEDIA

Author

Muraro, Daniele

Subjects
FEM, porous media, hybrid mixture theory, partially saturated soils, three-dimensional domains, Settore ICAR/08 - Scienza delle Costruzioni, FEM, coupled problems, partially saturated soils, porous media, hybrid mixture theory, three-dimensional domains, coupled problems, ICAR/08 Scienza delle costruzioni
Abstract

The purpose of the work presented in this thesis is to investigate the fully and partially saturated behaviour of soils, behaviour that can be extended also to geomaterials like concrete. The physical - mathematical approach proposed within this manuscript is a coupled thermo-hydro-mechanical model, suitable for consolidation / subsidence analyses of unsaturated soils. This coupled formulation, can therefore be qualified as u – pw – pg – (T), by the introduction of basic state variables involved in the processes, that here are: the displacements field u, the liquid (water) pressure field pw, the gas (dry air and water vapour) pressure field pg, and eventually the temperature T that is involved on the modelling of non – isothermal process. Due to the coexistence of two different fluid phases, liquid and gaseous one, this model can be regarded as a multiphase approach to a deforming porous medium as proposed by Lewis and Schrefler in the framework of the hybrid mixture theory for porous media firstly presented by Hassanizadeh and Gray and Zienkiewicz et al. The evolution at macroscopic scale of the state variables above mentioned, in particular of pressures of both liquid and gas, is basically influenced by the microstructure of the material that characterizes the behaviour of a soil with relation on capillary effects and deformability. The physical approach proposed here is based on averaging techniques applied to the physical quantities that can be estimated in a representative elementary volume (REV) . With the addition of water retention functions that provide a description of the relation that exists among capillary pressure and the degree of water saturation, a complete set of fluid balance equations and mechanical and thermodynamic equilibrium equations can be obtained for the medium in a macroscopic scale. A coupled (thermo)-hydro-mechanical formulation u – p – (T) that deals with a fully saturated porous medium has been implemented with success in the past in the F.E. two-dimensional program PLASCON and its further extensions to three- dimensionality with PLASCON3D. The present work focused on the extension and upgrading of the relative simple single phase theory along with its numerical implementations, towards a more realistic multiphase description of the porous material, where voids may be filled up with both liquid and gas that interacts each other by mean of the concept of capillary pressure. An improved code PLASCON3D_PS based on the fully coupled u – pw – pg – (T) formulation and developed from previous versions has been realized. Due to the lack in literature of three-dimensional coupled numerical and experimental tests, some numerical results of benchmark tests and real case problems, that derive from two-dimensional domains, will be presented.

Published
2014

37. Prioritisation and Network Analysis of Crohn's Disease Susceptibility Genes

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Lauffenburger, Douglas A., Muraro, Daniele, Simmons, Alison, Massachusetts Institute of Technology. Department of Biological Engineering, Lauffenburger, Douglas A., Muraro, Daniele, and Simmons, Alison

Abstract

Recent Genome-Wide Association Studies (GWAS) have revealed numerous Crohn's disease susceptibility genes and a key challenge now is in understanding how risk polymorphisms in associated genes might contribute to development of this disease. For a gene to contribute to disease phenotype, its risk variant will likely adversely communicate with a variety of other gene products to result in dysregulation of common signaling pathways. A vital challenge is to elucidate pathways of potentially greatest influence on pathological behaviour, in a manner recognizing how multiple relevant genes may yield integrative effect. In this work we apply mathematical analysis of networks involving the list of recently described Crohn's susceptibility genes, to prioritise pathways in relation to their potential development of this disease. Prioritisation was performed by applying a text mining and a diffusion based method (GRAIL, GPEC). Prospective biological significance of the resulting prioritised list of proteins is highlighted by changes in their gene expression levels in Crohn's patients intestinal tissue in comparison with healthy donors., United States. Army Research Office (Institute for Collaborative Biotechnologies Contract W911NF-09-D-0001)

Published
2014

38. mRNA diffusion explains protein gradients in \textit{Drosophila} early development

Author

Dil��o, Rui and Muraro, Daniele

Subjects
animal structures, Molecular Networks (q-bio.MN), FOS: Biological sciences, fungi, embryonic structures, Quantitative Biology - Molecular Networks, Quantitative Biology - Quantitative Methods, Quantitative Methods (q-bio.QM)
Abstract

We propose a new model describing the production and the establishment of the stable gradient of the Bicoid protein along the antero-posterior axis of the embryo of \textit{Drosophila}. In this model, we consider that \textit{bicoid} mRNA diffuses along the antero-posterior axis of the embryo and the protein is produced in the ribosomes localized near the syncytial nuclei. Bicoid protein stays localized near the syncytial nuclei as observed in experiments. We calibrate the parameters of the mathematical model with experimental data taken during the cleavage stages 11 to 14 of the developing embryo of \textit{Drosophila}. We obtain good agreement between the experimental and the model gradients, with relative errors in the range 5-8%. The inferred diffusion coefficient of \textit{bicoid} mRNA is in the range 4.6\times 10^{-12}-1.5\times 10^{-11}m^2s^{-1}, in agreement with the theoretical predictions and experimental measurements for the diffusion of macromolecules in the cytoplasm. We show that the model based on the mRNA diffusion hypothesis is consistent with the known observational data, supporting the recent experimental findings of the gradient of \textit{bicoid} mRNA in \textit{Drosophila} [Spirov et al. (2009) Development 136:605-614]., 14 pages, 2 figures

Published
2009

42. Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots

Author

Muraro, Daniele, primary, Mellor, Nathan, additional, Pound, Michael P., additional, Help, Hanna, additional, Lucas, Mikaël, additional, Chopard, Jérôme, additional, Byrne, Helen M., additional, Godin, Christophe, additional, Hodgman, T. Charlie, additional, King, John R., additional, Pridmore, Tony P., additional, Helariutta, Ykä, additional, Bennett, Malcolm J., additional, and Bishopp, Anthony, additional

Published
2013
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50. AS163 - Cholangiocyte organoids are plastic and their identity is controlled by their local microenvironment.

Author

Sampaziotis, Fotis, Muraro, Daniele, Tysoe, Olivia C., Beach, Timothy, Sawiak, Stephen, Godfrey, Edmund, Upponi, Sara, Wesley, Brandon, Garcia-Bernardo, Jose, Brevini, Teresa, Mahbubani, Krishnaa, Cannu, Giovanni, Gieseck, Richard, Berntsen, Natalie Lie, Mulcahy, Victoria, Crick, Keziah, Fear, Corina, Robinson, Sharayne, Swift, Lisa, and Ortmann, Daniel

Subjects
*ORGANOIDS, *LIVER regeneration
Published
2020
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