Article
Multidisciplinary Sciences
Qin Li, Torsten B. Meissner, Fang Wang, Ziming Du, Sai Ma, Sarika Kshirsagar, Tamara Tilburgs, Jason D. Buenrostro, Motonari Uesugi, Jack L. Strominger
Summary: HLA-C emerged during the evolution of pregnancy in great apes such as gorillas around 10 to 15 million years ago, playing a dual role in tolerance and immunity at the maternal-fetal interface. ELF3 is a key regulator of HLA-C, forming an autoregulatory feedback loop to establish their expression in trophoblasts. Wrenchnolol disrupts this positive-feedback loop by blocking the binding of MED23 to ELF3, resulting in down-regulation of HLA-C expression.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Hana El-Samad
Summary: Cells utilize feedback control mechanisms to regulate growth, division, repair, and responses to environmental changes, maintaining homeostasis of tissues and organs. Understanding the properties and challenges of biological feedback control networks is key to unraveling the essence of life.
Article
Engineering, Marine
Guoshuai Li, Xianku Zhang
Summary: In order to save energy and reduce carbon emissions in ships, a simple and robust green energy-saving control algorithm was proposed. The controller was designed using a third-order closed-loop gain shaping algorithm, and the final control law was obtained through the nonlinear switching feedback technique. The robustness of the system was proven using the Nyquist stability criterion. An evaluation model was established for energy-saving and carbon-reduction of the course-keeping controller. The proposed controller improved the ship's course-keeping accuracy, reduced the delay time and settling time of the controller, decreased the steering angle and frequency of the rudder, increased the robustness of the system, and achieved a 26.1% reduction in comprehensive energy-saving index under normal sea conditions. These improvements align with the requirements of navigation practice and are essential for safe, economical, green, and low-carbon navigation.
Article
Biochemistry & Molecular Biology
Liang Zhu, Lechen Liu, Aoli Wang, Jinwen Liu, Xin Huang, Tao Zan
Summary: Dermal fibrosis is a global disease that affects millions of people and causes physical and psychological distress. Fibroblast dysfunction plays a crucial role in the pathogenesis of dermal fibrosis, leading to excessive deposition of extracellular matrix. The positive feedback loop of fibroblast activation further worsens the condition. This review focuses on understanding the mechanisms and potential therapeutic targets to break this cycle.
Article
Engineering, Mechanical
Jianzhong Gao, Juping Ji, Yanping Liu, Feng Zhang, Ruiwu Wang, Hao Wang
Summary: This article presents a model for Alzheimer's disease, investigates the effect of calcium ions on the disease, and proposes two effective drug strategies for alleviating it. In addition, a stochastic model is formulated, and the existence and uniqueness of global positive solutions are analyzed. The configurational arrangement of stochastic coexistence equilibria is described using stochastic sensitivity function technique, and a tipping threshold is estimated. The results suggest that controlling noise through physical therapy can alleviate Alzheimer's disease.
NONLINEAR DYNAMICS
(2023)
Article
Engineering, Multidisciplinary
Xiaofei Fan, Xiunan Wang, Zhenkun Wang
Summary: This study develops a reaction-diffusion model with positive feedback loop to describe gene expression. The focus is on the long-term behavior of the system, including the determination of invariant regions and the global stability of equilibria. The results contribute to understanding the heterogeneity of cell characterization.
APPLIED MATHEMATICAL MODELLING
(2023)
Article
Engineering, Electrical & Electronic
Zhaolin Yang, Jing Jin, Xiaoming Liu, Taotao Yan, Xiaopeng Yu, Jianjun Zhou
Summary: This article presents a fully differential high-dynamic-range direct-conversion receiver for sub-1-GHz band applications, featuring integrated self-adaptive AGC loops. Designed with specific modules in RF and BB domains, the receiver achieves a low noise figure and wide gain tuning range.
IEEE TRANSACTIONS ON MICROWAVE THEORY AND TECHNIQUES
(2021)
Article
Automation & Control Systems
Roy S. Smith, Bassam Bamieh
Summary: Introducing stochastic components in a feedback loop can result in state behaviors different from those observed in a deterministic system. Multiplicative stochastic signals can lead to a richer set of state behaviors. These phenomena are also present in more complex stochastic dynamical systems.
IEEE CONTROL SYSTEMS MAGAZINE
(2021)
Article
Engineering, Electrical & Electronic
Baktash Behmanesh, Pietro Andreani
Summary: The expression of the loop gain in a circuit with one or more feedback loops is derived using transfer functions obtained through AC analysis. This method, while suitable for analog circuit simulator environments, does not require approximations or assumptions on the nature of the loop or the impedances.
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS
(2023)
Article
Biochemical Research Methods
Christopher Barrett, Andrei C. Bura, Qijun He, Fenix W. Huang, Thomas J. X. Li, Michael S. Waterman, Christian M. Reidys
Summary: This study explores the impact of macrolevel pandemic dynamics on the genomic evolution of SARS-CoV-2, suggesting that social behavioral measures could influence the mutational patterns of the virus. The findings demonstrate complex interactions within mutational clades and highlight the adaptability of the virus, despite its genetic stability.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Anupam Dey, Debashis Barik
Summary: Bistability in living systems is closely related to decision making processes, with the operating principles of a bistable switch from a positive feedback loop well understood. Investigating feed-forward signaling of a positive feedback loop reveals the generation of various emergent bistable switches in hybrid motifs. The emergent behaviors of these switches depend on logic gate configuration and regulatory thresholds, rather than the nature of the positive feedback loop.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Engineering, Marine
Boxu Min, Xianku Zhang
Summary: This paper proposed a ship tracking control strategy, including a robust course-keeping controller and a MILOS guidance system, using nonlinear feedback technique and three techniques to enhance the track-keeping effect, simulation results show advantages over conventional LOS guidance.
Article
Immunology
Jixin Li, Yanan He, Yanjun Qu, Chengcheng Ren, Xiaotong Wang, Yan Cheng, Liyuan Sun, Xin Zhang, Guangmei Zhang
Summary: This study investigated the role of BST2 in the development of endometriosis. The results showed that BST2 was significantly upregulated in ectopic endometrial tissues and cells, and promoted proliferation, migration, and lymphangiogenesis while inhibiting apoptosis. The underlying mechanism involved the transcription factor IRF6 and the NF-kappa B signaling pathway. These findings provide novel insights into the potential therapeutic target and biomarker for endometriosis.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Genetics & Heredity
Anna Terebus, Farid Manuchehrfar, Youfang Cao, Jie Liang
Summary: The study provides comprehensive characterizations of the stochastic multimodality of feed-forward loops (FFLs), including how switching between different network phenotypes is controlled and the topological sensitivity of the multimodality of the landscapes to regulation intensities. Results show that slow binding and unbinding dynamics of transcription factor to promoter result in strong stochastic behavior of FFLs different from deterministic models, and strong input intensity may lead to up to 6 stable phenotypes.
FRONTIERS IN GENETICS
(2021)
Article
Medicine, General & Internal
Adithya Chedere, Kishore Hari, Saurav Kumar, Annapoorni Rangarajan, Mohit Kumar Jolly
Summary: The double-negative feedback loop between AMPK and Akt in breast cancer cells plays a crucial role in regulating cell adaptation to stress conditions. This feedback loop results in two distinct cell states that can co-exist and switch between each other under specific parameters. Experimental validation and clinical data analysis support the prediction that this feedback loop can generate multi-stability and drive phenotypic switching and heterogeneity in cancer cell populations.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Biochemical Research Methods
Satyajit D. Rao, Oleg A. Igoshin
Summary: By studying the interplay of positive and negative feedback loops in bacterial gene regulatory networks, we demonstrated the advantages of this combination and its impact on the steady-state and dynamic responses of the network. Mathematical modeling was used to explain experimentally observed dynamical properties and make testable predictions for further experiments.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Joel D. Mallory, Xian F. Mallory, Anatoly B. Kolomeisky, Oleg A. Igoshin
Summary: The study reveals that proofreading optimizes the rate of virus production, but further optimization would lead to a significant increase in the cost. Minimizing cost is crucial for functional virus production.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Microbiology
Satyajit D. Rao, Pratik Datta, Maria Laura Gennaro, Oleg A. Igoshin
Summary: This study reveals the presence of hysteresis in the response of pathogenic Mycobacterium tuberculosis to surface stress, while it is absent in nonpathogenic Mycobacterium smegmatis. By combining quantitative experiments and mathematical modeling, interactions between the two master regulators of stress response, MprAB and sigma(E), were shown to shape the dynamic properties of the surface stress network. The proposed role of chaperone DnaK in stress sensing provides a novel system-level understanding of bacterial stress response dynamics.
Article
Microbiology
Zhuo Chen, Priyanka Srivastava, Brenda Zarazua-Osorio, Anuradha Marathe, Masaya Fujita, Oleg A. Igoshin
Summary: In Bacillus subtilis, the master regulator Spo0A controls both biofilm and sporulation pathways. However, the kinases KinA and KinC, although acting via Spo0A, have differential effects on downstream pathways. This study reveals that KinC not only activates but also downregulates Spo0A, and its effect is stage-dependent. This mechanism reduces single-cell heterogeneity of Spo0A activity and ultimately determines the fraction of cells activating biofilm gene expression.
Article
Biochemical Research Methods
Ludovico Calabrese, Jacopo Grilli, Matteo M. Osella, Christopher Kempes, Marco Cosentino M. Lagomarsino, Luca Ciandrini, Jason M. Haugh, Oleg A. Igoshin
Summary: Cells adopt strategies to allocate resources under limited availability. Our study shows that at slow growth, protein degradation is balanced by maintenance ribosomes. We find that protein degradation increases at slow growth, possibly due to active waste management and recycling.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Amanda M. Nash, Maria Jarvis, Samira Aghlara-Fotovat, Sudip Mukherjee, Andrea Hernandez, Andrew D. Hecht, Peter D. Rios, Sofia Ghani, Ira Joshi, Douglas Isa, Yufei Cui, Shirin Nouraein, Jared Z. Lee, Chunyu Xu, David Y. Zhang, Rahul A. Sheth, Weiyi Peng, Jose Oberholzer, Oleg A. Igoshin, Amir A. Jazaeri, Omid Veiseh
Summary: In this study, a cytokine delivery platform composed of polymer-encapsulated human RPE cells was developed to overcome the limitations of high-dose infusions in cytokine therapy. The tumor-adjacent administration of these capsules demonstrated effective and controlled dose modulation, leading to successful peritoneal cancer immunotherapy without systemic toxicities. The IL2-producing cytokine factory treatment eradicated peritoneal tumors in preclinical animal models, providing rationale for future clinical testing in humans.
Article
Chemistry, Physical
Tripti Midha, Joel D. Mallory, Anatoly B. Kolomeisky, Oleg A. Igoshin
Summary: Cleavage of dinucleotides after misincorporational pauses increases transcriptional elongation accuracy, and accessory proteins such as GreA and TFIIS further improve accuracy. This study developed a chemical-kinetic model that reveals the balance between speed and accuracy in transcriptional proofreading. The results show that long pauses are essential for high accuracy, while cleavage-factor-stimulated proofreading optimizes speed and improves both speed and accuracy compared to other cleavage methods.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Microbiology
Zhuo Chen, Brenda Zarazua-Osorio, Priyanka Srivastava, Masaya Fujita, Oleg A. Igoshin
Summary: In this study, the researchers used mathematical modeling and experiments to show that a regulator called Spo0A controls cell differentiation in Bacillus subtilis. They also explained why biofilm formation and sporulation appear to be mutually exclusive on a single-cell level.
Review
Microbiology
Patrick Murphy, Jessica Comstock, Trosporsha Khan, Jiangguo Zhang, Roy Welch, Oleg A. Igoshin
Summary: The soil bacterium Myxococcus xanthus exhibits diverse behaviors, including starvation-induced multicellular development and dispersal of aggregates. This study examines the cell behaviors driving both aggregation and dispersal, finding that reversal bias and aggregate size are correlated. Using different strains, the researchers demonstrate that aggregate dispersal is under genetic control.
Meeting Abstract
Immunology
Guillaume Carmona, Amanda Nash, Maria Jarvis, Ryan Newman, Jake Schladenhauffen, Samira Aghlara-Fotovat, Andrea Hernandez, Shirin Nouraein, Sudip Mukherjee, Andrew Hecht, Yufei Cui, Jared Lee, Peter Rios, David Zhang, Chunyu Xu, Rahul Sheth Sheth, Weiyi Peng, Jose Oberholzer, Oleg Igoshin, Amir Jazaeri, Omid Veiseh
JOURNAL OF IMMUNOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Misha Perepelitsa, Ilya Timofeyev, Patrick Murphy, Oleg A. Igoshin
Summary: This study develops a model to describe the alignment behavior of self-propelled rods, and derives the evolution equation for the kinetic density function using a set of microscopic-level rules. The results show that the alignment based on purely physical collisions is less robust.
Meeting Abstract
Biotechnology & Applied Microbiology
Guillaume Carmona, Amanda Nash, Ryan Newman, Jake Schladenhauffen, Maria Jarvis, Samira Aghlarafotovat, Sudip Mukherjee, Andrea Hernandez, Andrew Hecht, Peter Rios, Yufei Cui, Jared Lee, Chunyu Xu, David Zhang, Rahul Sheth, Weiyi Peng, Jose Oberholzer, Oleg Igoshin, Amir Jazaeri, Omid Veiseh
Article
Multidisciplinary Sciences
Qiwei Yu, Anatoly B. Kolomeisky, Oleg A. Igoshin
Summary: Many biological processes use kinetic proofreading to differentiate between correct and incorrect substrates, sacrificing higher energy dissipation for lower error rates. Understanding the physico-chemical constraints for minimizing dissipation and error is crucial for enzyme evolution. This study identifies a fundamental error-cost bound that limits the performance of proofreading networks under any parameter variations while maintaining substrate discrimination. The bound is kinetically controlled and determined by the difference in transition state energies.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Multidisciplinary Sciences
Tianyou Yao, Seth Coleman, Thu Vu Phuc Nguyen, Ido Golding, Oleg A. Igoshin
Summary: Research shows that replication in lambda bacteriophages helps them make the decision between infection and lysogeny. In the early stages of infection, viral gene expression simply scales with MOI; however, in the later stages, modulation of viral replication by decision genes amplifies gene expression differences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Zhuo Chen, Priyanka Srivastava, Brenda Zarazua-Osorio, Anuradha Marathe, Masaya Fujita, Oleg A. Igoshin
Summary: In Bacillus subtilis, the kinase KinC not only regulates biofilm genes but also downregulates sporulation genes, resulting in a negative effect on SpoOA activity. During fast growth, KinC acts as a phosphate source to activate SpoOA, while during slow growth, KinC becomes a phosphate sink leading to decreased SpoOA activity. This mechanism increases overall biofilm matrix production activity by reducing single-cell SpoOA activity heterogeneity and controlling the fraction of cells activating biofilm gene expression.