Review
Critical Care Medicine
Sahil Gupta, James N. Tsoporis, Song-Hui Jia, Claudia C. dos Santos, Thomas G. Parker, John C. Marshall
Summary: This article discusses how host cells recognize danger signals using pattern recognition receptors, focusing on Toll-like receptors (TLRs) as the most studied class of PRRs. It reviews the expression, regulation, and function of different TLRs, emphasizing TLR-4, and how TLR adaptor protein binding directs intracellular signaling to activate or terminate an innate immune response. The recent progress in research on the involvement of S100 proteins as ligands for TLR-4 in inflammatory disease is also highlighted.
Article
Biochemical Research Methods
Upinder Bhalla
Summary: Chemical signals play a crucial role in cell computations, and modeling these complex networks can be challenging. HillTau provides a simplified way to model these networks, condensing multiple reaction steps into single steps defined by a small number of parameters. It is fast, simple, and fits well with full chemical formulations, making it a valuable tool for modeling signaling network functions and fitting complicated networks. HillTau is especially useful for system abstraction, model reduction, data-driven optimization, and fast approximations to complex cellular signaling.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biology
Connah G. M. Johnson, Alexander G. Fletcher, Orkun S. Soyer
Summary: In this study, the authors introduce ChemChaste, an extension that enables spatial simulation of multicellular and bulk biochemistry. ChemChaste allows for the simulation of an arbitrary number of spatially diffusing chemicals, spatially heterogeneous chemical diffusion coefficients, and the inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface for defining parameters without direct interaction with Chaste's core C++ code.
Article
Biochemistry & Molecular Biology
Eberhard O. Voit, Daniel V. Olivenca
Summary: Choosing the most suitable representations is crucial for biomedical systems analysis. Ordinary differential equations (ODEs) are the most prevalent choice due to their flexibility and ease of use. However, selecting a mathematical format for the equations is not trivial and often lacks objective guidance. Power-law approximations are simple and overcome limitations in describing nonlinear features of biomedical phenomena. Nonetheless, ODE models also have limitations, leading to the proposal of an alternative approach called discrete Biochemical Systems Theory (dBST).
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Automation & Control Systems
Alain Sanchez-Ruiz, Juan Jose Valera-Garcia, Iraitz Legarra, Inigo Torre, Sebastian Telleria, Inigo Atutxa
Summary: This article presents a systematic modeling approach for MVDC multidrive systems to analyze the power quality of the MVDC bus, focusing on the interaction between the harmonics injected by converters and the natural resonances of the system. The proposed methodology demonstrates applicability for real case studies of high-power medium-voltage MVDC multidrive systems.
IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS
(2021)
Article
Multidisciplinary Sciences
Bo Wang, Eric R. Gamazon
Summary: This study used deep mutational scanning experiments and neural networks to model and predict the biochemical phenotypes of the spike receptor-binding domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) zinc-binding peptidase domain in SARS-CoV-2. The results demonstrated that the neural networks were able to accurately predict binding affinity, protein expression, and antibody escape, surpassing the predictive power of conventional methods in structural biology. Integration of the physicochemical properties of amino acids further improved the accuracy of the predictions.
Article
Biochemical Research Methods
Oya Karasan, Alper Sen, Banu Tiryaki, A. Ercument Cicek
Summary: Codon optimization is an essential tool in biotechnology for synthesizing genes to be expressed in other organisms. The authors propose a unifying modeling approach that can optimize any combination of measures using graph/network representations. Their method is tested on commonly used objectives and shown to be effective for the largest proteins available.
Review
Cell Biology
Guoxun Chen
Summary: Obesity and type 2 diabetes are major public health concerns, with nutrition playing a key role in these issues. Vitamin A has been found to regulate glucose and fat metabolism, while interactions between insulin and RA signaling systems impact the expression of genes involved in hepatic glucose and lipid metabolism.
Article
Multidisciplinary Sciences
Rodolfo Ciuffa, Federico Uliana, Jonathan Mannion, Martin Mehnert, Tencho Tenev, Cathy Marulli, Ari Satanowski, Lena Maria Leone Keller, Pilar Natalia Rodilla Ramirez, Alessandro Ori, Matthias Gstaiger, Pascal Meier, Ruedi Aebersold
Summary: Protein-protein interactions (PPIs) are the main mode of proteome organization in cells. Traditional PPI networks lack contextual information. Generating context-dependent PPI networks is necessary for structural and systems-level modeling, but remains challenging. In this study, an experimental/computational strategy is described to achieve contextual modeling of PPIs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Chemistry, Multidisciplinary
Ayan Chatterjee, Antara Reja, Sumit Pal, Dibyendu Das
Summary: This article discusses the use of minimal peptide assemblies to emulate the structure and function of existing enzymes, aiming to understand the origins of catalytically active binding pockets in early life. Additionally, the study focuses on catalytic systems under non-equilibrium conditions to shed light on the role of bioenergetics in the chemical emergence of complex behavior.
CHEMICAL SOCIETY REVIEWS
(2022)
Article
Computer Science, Information Systems
Tao Zheng, Aigong Xu, Xinchao Xu, Mingyue Liu
Summary: In this study, the effects of three types of deterministic errors in a conventional inertial measurement unit (IMU) on a navigation system are theoretically deduced and verified by simulation. Navigation experiments are carried out to investigate the effects of these errors and a two-position continuous calibration scheme is designed to calibrate the IMU. The calibration results show significant improvement in the position and heading accuracy of the navigation system.
Article
Multidisciplinary Sciences
Alexander Lavin, Ciaran M. Gilligan-Lee, Alessya Visnjic, Siddha Ganju, Dava Newman, Sujoy Ganguly, Danny Lange, Atilim Gunes Baydin, Amit Sharma, Adam Gibson, Stephan Zheng, Eric P. Xing, Chris Mattmann, James Parr, Yarin Gal
Summary: This article introduces the development process of machine learning systems, emphasizing the importance of a systematic engineering approach. It highlights the challenges and risks in the rushed development process and proposes the Machine Learning Technology Readiness Levels framework as a solution.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Shao-Ting Chiu, Wen-Wei Tseng, An-Chi Wei
Summary: Mitochondria, semi-autonomous organelles in eukaryotic cells, play a crucial role in energy production and metabolism. This study proposed a mathematical model to simulate the signaling process between mitochondria and the nucleus in response to mitochondrial damage. The dynamics and robustness of the signaling pathway were analyzed, providing insights for drug design against yeast and fungi.
Review
Endocrinology & Metabolism
Jean-Pierre Vilardaga, Lisa J. Clark, Alex D. White, Ieva Sutkeviciute, Ji Young Lee, Ivet Bahar
Summary: The classical paradigm of G protein-coupled receptor signaling is being revised as several receptors have been found to engage in sustained signaling responses from subcellular compartments. PTH1R, an important GPCR for calcium and phosphate regulation, can mediate different modes of cAMP signaling. Recent studies have uncovered the structural and signaling mechanisms of PTH1R and its potential pharmacological outputs. Understanding the spatial and temporal aspects of PTH1R signaling is important for drug development targeting metabolic bone and mineral diseases.
Article
Multidisciplinary Sciences
Peter J. Gawthrop, Michael Pan
Summary: The sensitivity of systems biology models can indicate important parameters for physiological function and guide parameter estimation. However, kinetic models of biochemical systems often lose thermodynamic consistency after parameter perturbations. In this study, we analyze the sensitivity of biological reaction networks using a bond graph representation, where parameter sensitivities are treated as bond graph components. We derive a sensitivity system that expresses parameter variation as additional system inputs, which can be linearized to provide local sensitivity to parameters in terms of linear system properties. This approach helps identify essential reactions and metabolites in maintaining the function of biological pathways, as demonstrated using a model of the Pentose Phosphate Pathway.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)