Article
Neurosciences
Clara Posner, Sohum Mehta, Jin Zhang
Summary: Cells respond to environmental cues by encoding information in compartmentalized biochemical signaling reactions. Genetically encoded fluorescent biosensors enable the monitoring of signaling events in live cells. Temporal and spatiotemporal computational models can be used to interpret biosensor experiments and explore hypotheses difficult to test experimentally.
JOURNAL OF PHYSIOLOGY-LONDON
(2023)
Article
Materials Science, Multidisciplinary
Kamalnath Kadirvel, Hamish L. Fraser, Yunzhi Wang
Summary: Although most high-entropy alloys are multi-phase rather than single-phase solid solutions at equilibrium, recent studies have expanded the compositional space for the exploration of novel microstructures with enhanced functional or mechanical properties. Understanding the phase transformation pathways and microstructural evolution in multi-phase high-entropy alloys can aid in designing alloys and processes for specific engineering applications. This study investigates the effects of equilibrium volume fractions, free energy landscapes, and elastic modulus mismatch on the microstructural evolution of two-phase high-entropy alloys and provides insights for designing desired microstructures.
Review
Biochemistry & Molecular Biology
Nauf Bou Antoun, Athina-Myrto Chioni
Summary: Cancer is a leading cause of death worldwide. Drug resistance, whether intrinsic or acquired, plays a crucial role in cancer relapse. Various factors and signaling pathways are involved in the development of drug resistance, and a deeper understanding of these mechanisms is necessary to improve cancer treatment outcomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Genetics & Heredity
Aoife A. Nolan, Nourhan K. Aboud, Walter Kolch, David Matallanas
Summary: Oncogenic RAS mutations are key drivers of human cancers, making RAS inhibition a crucial goal in oncology. Efforts to block effector pathways like RAF-MEK-ERK have been largely disappointing, leading researchers to investigate RAF-dependent pathways independent of catalytic activity as potential targets for blocking oncogenic RAS signaling. The roles of RAF kinase-independent functions in apoptosis, cell cycle progression, and cell migration have been well documented.
Article
Mechanics
Nicolas Moreno, Marco Ellero
Summary: We propose a fully Lagrangian heterogeneous multiscale method (LHMM) for modeling complex fluids with microscopic features. The method discretizes the fluctuating Navier-Stokes equations using smoothed dissipative particle dynamics (SDPD) and exploits the multiscale features of SDPD to account for thermal fluctuations. The LHMM is validated using different flow configurations and fluid types, showing its flexibility in modeling complex fluids at the microscale.
JOURNAL OF FLUID MECHANICS
(2023)
Review
Biochemistry & Molecular Biology
Margherita Sisto, Sabrina Lisi
Summary: Autoimmunity is a chronic process that leads to inflammation, tissue damage, and subsequent tissue remodelling and organ fibrosis. Most chronic autoimmune fibrotic disorders have in common a persistent and sustained production of growth factors, proteolytic enzymes, angiogenic factors, and fibrogenic cytokines, resulting in the deposition of connective tissue elements or epithelial to mesenchymal transformation (EMT) that progressively remodels and destroys normal tissue architecture leading to organ failure. However, there are currently no approved treatments that directly target the molecular mechanisms of fibrosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Chih-Yao Chung, Gabriel E. Valdebenito, Anitta R. Chacko, Michael R. Duchen
Summary: Mutations in mitochondrial DNA have a significant impact on cellular energy homeostasis and signaling pathways, influencing disease presentation and progression.
TRENDS IN CELL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Chen-Chen Jiang, Li-Shan Lin, Sen Long, Xiao-Yan Ke, Kohji Fukunaga, Ying-Mei Lu, Feng Han
Summary: Autism spectrum disorder (ASD) is a common and complex neurodevelopmental disorder with a strong genetic basis. Despite the limited understanding of its etiology, risk factors, and disease progression, significant progress has been made in genetics, identifying hundreds of genes associated with a high risk for autism. The involvement of signal transduction molecular events in pathological processes has important implications for precise molecular targeting in autism. This review provides insights into the mechanisms and clinical implications of signal transduction in autism, as well as future challenges and perspectives.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Review
Biochemistry & Molecular Biology
Jasna Lojk, Janja Marc
Summary: The Wnt signalling pathway is crucial for bone development, homeostasis, and mineral density regulation. It includes both canonical/beta-catenin and non-canonical pathways, which play important roles in bone cell differentiation, maturation, and function, as well as in bone tissue structure regulation. Further research is needed to explore the significance of non-canonical Wnt signalling pathways in bone biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Yue Zhang, Ruirui Wang, Xiaodong Wang, Caihong Zhao, Hailong Shen, Ling Yang
Summary: Seed germination plays a significant role in plant development and crop yield. Recent studies have found that nitric oxide (NO) acts as both a nitrogen source during seed development and a participant in stress responses to salt, drought, and high temperature. NO influences seed germination by integrating various signaling pathways. However, the precise network mechanism of NO's regulation of seed germination is still unclear due to the instability of NO gas activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Guangze Zhao, Sana Aghakeshmiri, Yankuan T. Chen, Huifang M. Zhang, Fione Yip, Decheng Yang
Summary: NFAT5 is sensitive to both osmotic and non-osmotic stress signals, playing a protective role against detrimental effects. Dysregulation of NFAT5 expression may cause pathological conditions, dictated by target gene regulation and signaling pathway activation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Developmental Biology
Stephanie A. Campbell, Tabea L. Stephan, Jeremy Lotto, Rebecca Cullum, Sibyl Drissler, Pamela A. Hoodless
Summary: This article discusses the signaling pathways and transcriptional regulators that drive liver cell development and primary liver cancers, as well as emerging models derived from pluripotent stem cells, 3D organoids, and bioengineering for improved studies of signaling pathways in liver cancer and regenerative medicine.
Review
Agronomy
Beatriz Val-Torregrosa, Mireia Bundo, Blanca San Segundo
Summary: Rice production is affected by various stresses, including nutrient stress. Improper use of pesticides can have harmful effects on the environment and human health. Understanding the interaction between nutrient stress and disease resistance is essential for optimizing fertilizer and pesticide use in rice production.
Article
Developmental Biology
Paula Murphy, Chris Armit, Bill Hill, Shanmugasundaram Venkataraman, Patrick Frankel, Richard A. Baldock, Duncan R. Davidson
Summary: This study provides an integrated analysis of key genes in the 3D space of the mouse embryo, revealing new organization of expression patterns and territories where Wnt and Fzd genes are co-expressed.
Article
Agricultural Engineering
Begona Renau-Morata, Sergio G. Nebauer, Victor Garcia-Carpintero, Joaquin Canizares, Eugenio Gomez Minguet, Marcelino de los Mozos, Rosa Molina
Summary: The study aims to gain insights into the regulatory networks controlling flowering time in saffron, showing the important roles of ABA, gibberellins, and IAA in flower induction. These findings pave the way for further understanding the transition from vegetative to reproductive phase in saffron.
INDUSTRIAL CROPS AND PRODUCTS
(2021)
Article
Mathematical & Computational Biology
Steven Woodhouse, Nir Piterman, Christoph M. Wintersteiger, Berthold Goettgens, Jasmin Fisher
BMC SYSTEMS BIOLOGY
(2018)
Editorial Material
Biochemistry & Molecular Biology
Michael K. Yu, Jianzhu Ma, Jasmin Fisher, Jason F. Kreisberg, Benjamin J. Raphael, Trey Ideker
Article
Cell Biology
Yasmin Z. Paterson, David Shorthouse, Markus W. Pleijzier, Nir Piterman, Claus Bendtsen, Benjamin A. Hall, Jasmin Fisher
INTEGRATIVE BIOLOGY
(2018)
Article
Cell Biology
Ali Sinan Koksal, Kirsten Beck, Dylan R. Cronin, Aaron McKenna, Nathan D. Camp, Saurabh Srivastava, Matthew E. MacGilvray, Rastislav Bodik, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher, Anthony Gitter
Article
Multidisciplinary Sciences
Peter Kreuzaler, Matthew A. Clarke, Elizabeth J. Brown, Catherine H. Wilson, Roderik M. Kortlever, Nir Piterman, Trevor Littlewood, Gerard I. Evan, Jasmin Fisher
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Review
Biotechnology & Applied Microbiology
Petra Schneider, W. Patrick Walters, Alleyn T. Plowright, Norman Sieroka, Jennifer Listgarten, Robert A. Goodnow, Jasmin Fisher, Johanna M. Jansen, Jose S. Duca, Thomas S. Rush, Matthias Zentgraf, John Edward Hill, Elizabeth Krutoholow, Matthias Kohler, Jeff Blaney, Kimito Funatsu, Chris Luebkemann, Gisbert Schneider
NATURE REVIEWS DRUG DISCOVERY
(2020)
Article
Automation & Control Systems
Yehia Abd Alrahman, Nir Piterman
Summary: The proposed formalism models and reasons about reconfigurable multi-agent systems, where agents interact and communicate in different modes to pursue joint tasks. Agents can dynamically synchronize, exchange data, adapt behavior, and reconfigure communication interfaces, executing independently in the system and influencing each other through message exchange.
AUTONOMOUS AGENTS AND MULTI-AGENT SYSTEMS
(2021)
Editorial Material
Multidisciplinary Sciences
Sarah A. Teichmann, Muzlifah Haniffa, Jasmin Fisher
Summary: Diversity is a creative force that broadens views and enhances ideas, increasing productivity and the impact of science. Every research organization, whether in academia or industry, needs better inclusion policies to harness the benefits of diversity. We share our suggestions on promoting inclusion in academia and creating a better research culture for all, drawing from our experiences as women in science.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Laure Talarmain, Matthew A. Clarke, David Shorthouse, Lilia Cabrera-Cosme, David G. Kent, Jasmin Fisher, Benjamin A. Hall
Summary: The study reveals that HOXA9 plays a binary switch function in acute myeloid leukaemia (AML) and can serve as a clinical stratification and prognostic marker. Computational network modeling of chronic myeloproliferative neoplasms (MPN) suggests that the relationship between HOXA9, JAK2, and TET2 explains the branching progression of different clinical characteristics, and predicts a connection between the RUNX1 and MYB genes and a suppressive role for the NOTCH pathway.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Rowan Howell, James Davies, Matthew A. Clarke, Anna Appios, Yashoda Jayal, Ben Ringham-Terry, Isabel Boned Del Rio, Jasmin Fisher, Clare L. Bennett
Summary: Researchers have developed an in silico model to investigate the interaction between melanomas and Langerhans cells (LCs). The model suggests that melanomas do not activate LC migration to lymph nodes until they reach a critical size, due to a positive TNF-alpha feedback loop. Experimental testing confirms that treating primary tumors with MAPK pathway inhibitors can prevent LC migration. The study also predicts treatment combinations that can bypass LC dysfunction.
Proceedings Paper
Automation & Control Systems
Shaun Azzopardi, Nir Piterman, Gerardo Schneider
Summary: Temporal synthesis aims to construct reactive programs that meet a given declarative formula. By combining automata monitors as triggers for LTL formulas, a more expressive language is proposed. This approach allows for minimal reasoning about the monitor state space and provides a tool for constructing controllers.
AUTOMATED TECHNOLOGY FOR VERIFICATION AND ANALYSIS, ATVA 2021
(2021)
Review
Oncology
Matthew A. Clarke, Jasmin Fisher
NATURE REVIEWS CANCER
(2020)
Proceedings Paper
Computer Science, Artificial Intelligence
Matthew A. Clarke, Steven Woodhouse, Nir Piterman, Benjamin A. Hall, Jasmin Fisher
AUTOMATED REASONING FOR SYSTEMS BIOLOGY AND MEDICINE
(2019)
