Article
Multidisciplinary Sciences
Karol Nienaltowski, Rachel E. Rigby, Jaroslaw Walczak, Karolina E. Zakrzewska, Edyta Glow, Jan Rehwinkel, Michal Komorowski
Summary: The study introduces fractional response analysis (FRA) involving fractional cell counting to deconvolute heterogeneous multivariate responses of cellular populations. Experimental results demonstrate that cellular responses to cytokines scale linearly with the log of the cytokine dose, revealing the sensitivity of cellular populations to fold-changes in the dose.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Antoine Passemiers, Yves Moreau, Daniele Raimondi
Summary: This article presents a novel method called PORTIA for inferring gene regulatory networks (GRNs). The method is based on robust precision matrix estimation and is shown to outperform state-of-the-art methods in terms of speed while still maintaining good accuracy. The authors extensively validated PORTIA using benchmark datasets and propose a new scoring metric based on graph-theoretical concepts.
Article
Cell Biology
Shah Md Toufiqur Rahman, Mohammad Aqdas, Erik W. Martin, Francesco Tomassoni Ardori, Preeyaporn Songkiatisak, Kyu-Seon Oh, Stefan Uderhardt, Sangwon Yun, Quia C. Claybourne, Ross A. McDevitt, Valentina Greco, Ronald N. Germain, Lino Tessarollo, Myong-Hee Sung
Summary: This study introduces reporter mice with fluorescently labeled RelA and c-Rel proteins for real-time imaging of NF-KB signaling. The results show that quantitative features of signaling reflect different activating ligands, cell types, and age-related changes. Unexpectedly, the RelA:c-Rel heterodimer is depleted in the nuclei of stimulated cells.
Article
Biochemistry & Molecular Biology
Zitong Jerry Wang, Matt Thomson
Summary: The ability of cells to sense and respond to extracellular ligands in natural environments can be optimized by adapting to the spatial structure of the environment. Receptor localization in cells maximizes information acquisition, and dynamic redistribution of signaling receptors enhances cell navigation efficiency.
Article
Physics, Multidisciplinary
Jan Lewandowsky, Gerhard Bauch, Maximilian Stark
Summary: This article discusses the complexity issues of signal processing in digital communication receivers and proposes a design principle based on the information bottleneck method. By designing signal processing blocks with simple mathematical operations and strong quantization, the complexity of the receiver can be reduced. The article also compares different approaches to information bottleneck signal processing and provides a general view on this topic.
Review
Plant Sciences
Fumiyuki Soma, Fuminori Takahashi, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki
Summary: Drought is a severe abiotic stress that induces numerous genes in plants, including key regulators like SnRK2s and stress-responsive transcription factors. Abscisic acid (ABA) plays a crucial role in plant response to drought stress by activating signaling pathways and gene expression. Understanding the molecular mechanisms involved in drought stress responses, including phosphorylation signaling and gene regulation pathways, is essential for improving crop resilience to drought conditions.
Article
Biology
Xiaofeng Liang, Xiaobing Lin, Zien Lin, Weiyi Lin, Zhishen Peng, Shanshan Wei
Summary: This study investigated the role of cellular senescence in the tumor microenvironment of skin cutaneous melanoma (SKCM) using bioinformatics and machine learning. The results showed that genes associated with cellular senescence contribute to improved prognosis of SKCM by stimulating immune responses in the tumor microenvironment. Patients with high expression of cellular senescence-associated genes may benefit more from immune checkpoint inhibitor immunotherapy. Further research is needed to understand the pro-tumor function of cellular senescence in mesenchymal cells.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemical Research Methods
Haonan Feng, Ruiqing Zheng, Jianxin Wang, Fang-Xiang Wu, Min Li
Summary: Gene regulatory networks play a crucial role in biological processes, and existing expression data can be used to infer these networks using computational methods. However, identifying indirect regulatory links remains a challenge. In this study, a novel information-theory-based method is proposed to improve the identification of regulatory relationships between genes.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Review
Genetics & Heredity
Ildefonso M. de la Fuente, Luis Martinez, Jose Carrasco-Pujante, Maria Fedetz, Jose I. Lopez, Iker Malaina
Summary: The main sources of biomolecular order and complexity in cellular life include dissipative self-organization and molecular information processing, leading to the emergence of systemic functional structures in the cell. Through studies on enzymatic activity, functional coordination, metabolic networks, and molecular rhythms, it has been demonstrated that self-organization is central to understanding cellular processes. The quantification of biomolecular information flows in dissipative metabolic networks has enabled efficient self-regulatory control of metabolism, and the emergence of Hopfield-like dynamics characterized by associative memory has been observed in experiments with individual amoeba cells, indicating a fundamental evolutionary mechanism for cell adaptation.
FRONTIERS IN GENETICS
(2021)
Article
Entomology
Miltan Chandra Roy, Yonggyun Kim
Summary: This study explored cellular immune responses of the mealworm Tenebrio molitor, showing that calcium signaling is associated with eicosanoid mediation, triggering the immune responses in the insect hemocytes.
ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA
(2021)
Article
Computer Science, Information Systems
Jan Lewandowsky, Sumedh Jitendra Dongare, Rocio Martin Lima, Marc Adrat, Matthias Schrammen, Peter Jax
Summary: The information bottleneck method aims to preserve as much relevant mutual information as possible under compression, with applications in various fields like communication and machine learning. By considering parameterized systems, the efficiency of preserving relevant information in communication receivers can be further improved.
Article
Mechanics
Kai Segadlo, Bastian Epping, Alexander van Meegen, David Dahmen, Michael Kraemer, Moritz Helias
Summary: Understanding the capabilities and limitations of different network architectures is crucial for machine learning. Through Bayesian inference and mean-field theory, we can uncover the connections and differences between recurrent and deep networks. The study finds that recurrent networks typically converge slower than deep networks, and the convergence speed depends on the parameters of the weight prior as well as the depth or number of time steps.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Materials Science, Biomaterials
Chima V. Maduka, Mohammed Alhaj, Evran Ural, Maxwell M. Kuhnert, Oluwatosin M. Habeeb, Anthony L. Schilmiller, Kurt D. Hankenson, Stuart B. Goodman, Ramani Narayan, Christopher H. Contag
Summary: The stereochemistry of polylactide (PLA) affects its thermal and physicochemical properties, including degradation profiles. However, the role of PLA stereochemistry and its immune responses in vivo and in vitro remains unclear. In this study, a bioenergetic model was used to investigate the immune cellular responses to different PLA stereochemistries. The findings provide mechanistic explanations for the diverse immune responses to PLA and emphasize the importance of immunometabolism in the biocompatibility of biomaterials used in medicine.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2023)
Article
Biology
Pedro Rodrigues, Rafael S. Costa, Rui Henriques
Summary: This study compares the role of different machine learning methods in studying the regulatory processes of cells affected by the SARS-CoV-2 virus. The results show that pattern-based biclustering algorithms have better performance in functional enrichment analysis and can aid in knowledge extraction. Furthermore, the comparative analysis of the results identifies potential pathophysiological characteristics of COVID-19 and compares them with other relevant studies.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Kaige Chen, Zheng Zhang, Jiachen Zhang, Ziyuan Fang, Wang Dong, Yucai Wang, Min Li
Summary: This study explores a new antigen-caged adjuvant strategy, in which a controlled bio-mineralization method is used to prepare antigen-caged metal adjuvants. The results demonstrate that this strategy can enhance the adjuvanticity of aluminum adjuvants and promote the internalization of antigen and adjuvant by antigen-presenting cells, leading to robust humoral and cellular immune responses.
Article
Physics, Multidisciplinary
Ying Tang
Summary: The study shows that in driven quantum systems, the free energy change can be amplified by adding a magnetic field, and this quantum effect is reflected in an extended free energy equality, supporting the extraction of additional free energy from the magnetic field.
COMMUNICATIONS PHYSICS
(2021)
Article
Multidisciplinary Sciences
Yu-Ling Chang, Maura Rossetti, David W. Gjertson, Liudmilla Rubbi, Michael Thompson, Dennis J. Montoya, Marco Morselli, Felicia Ruffin, Alexander Hoffmann, Matteo Pellegrini, Vance G. Fowler Jr, Michael R. Yeaman, Elaine F. Reed
Summary: The study found that persistent methicillin-resistant Staphylococcus aureus (MRSA) bacteremia may be related to the DNA methylation profiles of patients, with different methylation signatures existing in patients experiencing antibiotic-persistent MRSA infection (APMB) compared to those with antibiotic-resolving MRSA infection (ARMB). These distinct methylation patterns, enriched in neutrophils, allowed for the prediction of APMB with an average area under the curve of 0.85, indicating a potential risk stratification strategy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Ying Tang, Adewunmi Adelaja, Felix X-F Ye, Eric Deeds, Roy Wollman, Alexander Hoffmann
Summary: The authors propose a mathematical framework for inferring the mutual information encoded in temporal signaling dynamics and use it to study how information is transmitted over time in response to different stimuli in NF kappa B, MAPK and p53 signaling pathways.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Quen J. Chen, Sho Ohta, Katherine M. Sheu, Roberto Spreafico, Adewunmi Adelaja, Brooks Taylor, Alexander Hoffmann
Summary: The NF-κB transcription factor can reprogram the epigenome of macrophages by activating latent enhancers, but it only responds to certain stimuli, depending on the temporal dynamics of NF-κB activity. Non-oscillatory NF-κB can open chromatin and activate immune response genes by disrupting histone-DNA interactions, thereby modulating expression.
Article
Biochemical Research Methods
Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann
Summary: This study explores the identifiability of gene regulatory strategies using a mechanistic modeling approach and computational workflow. Results show that most GRS can be easily distinguished, but a third require more quantitative data. By developing an advanced error model and incorporating it into a Bayesian framework, GRS models for individual genes can be identified with multiple datasets, allowing for better allocation of experimental resources. Applying this workflow to immune response genes in macrophages revealed more combinatorial control than previously thought, supported by chromatin immuno-precipitation analysis.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Medicine, Research & Experimental
Harry Pickering, Subha Sen, Janice Arakawa-Hoyt, Kenichi Ishiyama, Yumeng Sun, Rajesh Parmar, Richard S. Ahn, Gemalene Sunga, Megan Llamas, Alexander Hoffmann, Mario Deng, Suphamai Bunnapradist, Joanna M. Schaenman, David W. Gjertson, Maura Rossetti, Lewis L. Lanier, Elaine F. Reed
Summary: This study characterized longitudinal immune responses to CMV in kidney transplant recipients with viremia. High levels of IL-15 and expansion of NK cells were observed before viremia, while mature NK cells and inhibitory receptors were expanded after viremia. Memory NK cells and NK-like CD28(-)CD8(+) T cells were associated with control of viremia, highlighting their importance in effective CMV control.
Review
Biochemistry & Molecular Biology
Marie Oliver Metzig, Alexander Hoffmann
Summary: Cell biology research has made significant contributions in improving anti-cancer therapies by studying different forms of regulated cell death, identifying master regulators such as NF kappa B, and translating these findings. In the era of immunotherapy, the targeted induction of immunogenic cell death is becoming increasingly important for optimizing anti-tumor immunity.
Article
Physics, Multidisciplinary
Ying Tang, Dinghua Shi, Linyuan Lu
Summary: The study investigates the optimization of synchronization in phase oscillators with higher-order interactions, finding that optimized networks exhibit more homogeneity in nodes' degree for undirected interactions, while they are generally structurally asymmetric for directed interactions. By controlling the network topology of higher-order interactions, synchronization phenomena beyond pairwise interactions can be achieved.
COMMUNICATIONS PHYSICS
(2022)
Article
Multidisciplinary Sciences
Diane Lefaudeux, Supriya Sen, Kevin Jiang, Alexander Hoffmann
Summary: This study investigates mRNA export rates for innate immune genes and finds that the export rate is gene-specific. Additionally, the export rate does not determine temporal gene responsiveness but complements mRNA decay rates to ensure similar abundances of short- and long-lived mRNAs.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Katherine M. Sheu, Aditya A. Guru, Alexander Hoffmann
Summary: Immune sentinel macrophages respond to pathogens through immune response genes. The capacity for stimulus-specific gene expression, known as stimulus-response specificity (SRS), is crucial for macrophage function. Using information theory and machine learning, we developed an experimental workflow to quantify SRS and found that it is influenced by specific immune genes with low heterogeneity and separate signaling pathways.
Editorial Material
Cell Biology
Alexander Hoffmann
Summary: The study focuses on understanding the function and species-specificity of short sequence elements in the core promoter that determine gene transcription activity. Through massively parallel measurements of synthetic core promoters, a statistical learning model was developed to identify the sequence differences between human and Drosophila core promoters. This model was then used to design gene core promoters that are specifically recognized by the human transcriptional machinery.
GENES & DEVELOPMENT
(2023)
Article
Computer Science, Artificial Intelligence
Ying Tang, Jiayu Weng, Pan Zhang
Summary: Stochastic reaction networks are widely used to model stochastic processes in physics, chemistry, and biology. A new approach based on evolving a variational autoregressive neural network provides an efficient way to track the time evolution of the joint probability distribution for general reaction networks.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Allergy
Hector I. Navarro, Yi Liu, Anna Fraser, Diane Lefaudeux, Jennifer J. Chia, Linda Vong, Chaim M. Roifman, Alexander Hoffmann
Summary: This study characterized RelB-deficient autoimmunity by transcriptomic profiling and found that loss of RelB leads to excessive induction of interferon-stimulated genes and suppression of inflammatory response genes. The genetic evidence also suggests that the autoimmune pathology in RelB-deficient mice is independent of interferon.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
