Article
Environmental Sciences
Joana Antunes, Paula Sobral, Marta Martins, Vasco Branco
Summary: Nanoplastics have the potential to activate inflammatory pathways in human cells, leading to upregulation of proteins and increased production of inflammatory factors. The response varies depending on the cell type.
ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Yu Niu, Yongwei Zhao, Jintian He, Yang Yun, Mingming Shen, Zhending Gan, Lili Zhang, Tian Wang
Summary: The study demonstrated that supplementation with dihydroartemisinin improved intestinal morphology, regulated enterocyte proliferation and apoptosis, and alleviated intestinal inflammation through the TLR4/NOD/NF-kB signaling pathway in weaned piglets with intrauterine growth retardation.
Article
Cell Biology
Weihui Qi, Yanlin Chen, Shuaibo Sun, Xinxian Xu, Jingdi Zhan, Zijian Yan, Ping Shang, Xiaoyun Pan, Haixiao Liu
Summary: Osteoarthritis (OA) is a common degenerative disease, and controlling local chronic inflammation is crucial for delaying its development. Studies have shown that Linarin can effectively suppress the overproduction of inflammatory substances in chondrocytes and exert protective effects by intervening NF-KB activation.
Article
Microbiology
Mallika Somayajulu, Sharon A. A. McClellan, Shukkur Muhammed Farooq, Ahalya Pitchaikannu, Shunbin Xu, Linda Hazlett
Summary: This study demonstrates that glycyrrhizin protects against P. aeruginosa keratitis through blocking the TLR4 and TLR9 signaling pathways.
Article
Biotechnology & Applied Microbiology
Stefano Oliva, Francesca Diomede, Ylenia Della Rocca, Antonella Mazzone, Guya Diletta Marconi, Jacopo Pizzicannella, Oriana Trubiani, Giovanna Murmura
Summary: This study evaluated the effects of two different surfaces of dental implants on human periodontal ligament stem cells at an inflammation level and found that TiN-coated titanium can suppress the TLR4/MyD88/NF-kappa B p65/NLRP3 pathway and accelerate the deposition of extracellular matrix.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Immunology
Yaxing Zhao, Peng Liu, Haofan Luan, Hua Jiang, Yingmei Xu, Yuanqiang Zhang, Yubin Zhang, Ruiyan Li
Summary: A study has found that demethyleneberberine (DMB) has potential anti-inflammatory effects and could be used to treat conditions such as colitis induced by TNBS. It was shown that DMB can inhibit the activation of the TLR4 signaling pathway by non-covalently binding to the MD-2 protein. Therefore, DMB may be a promising drug to suppress inflammatory response.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Pedro Paulo Carneiro, Andreza S. Dorea, Walker N. Oliveira, Luiz Henrique Guimaraes, Claudia Brodskyn, Edgar M. Carvalho, Olivia Bacellar
Summary: Research has shown that the use of TLR2 and TLR4 antagonists can reduce the number of infected cells and internalized parasites in monocytes of CL patients, as well as decrease oxidative burst, IL-1 beta, TNF, and CXCL9 production. Additionally, TNF production in cells from CL lesions also decreased after neutralization of TLR2 and TLR4.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jiajun Zhang, Yingying Cui, Xinxin Zang, Tingting Feng, Fanruo Chen, Hui Wang, Guanghui Dang, Siguo Liu
Summary: Macrophages are the main immune cells responsible for defending against Mycobacterium tuberculosis infection. The NLRP3 protein plays a significant role in this defense, but the exact mechanism by which MTB evades this defense is unknown. This study identified the PE12 protein as an extracellular protein of MTB, which interacts with TLR4 in macrophages to inhibit the transcription and expression of NLRP3, leading to a reduction in inflammatory cytokines. The findings demonstrate the importance of PE12 in inhibiting the host immune response against MTB.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Pharmacology & Pharmacy
Deysi Viviana Tenazoa Wong, Renata Brito Falcao Holanda, Aurilene Gomes Cajado, Alessandro Maia Bandeira, Jorge Fernando Bessa Pereira, Joice Oliveira Amorim, Clarice Sampaio Torres, Luana Maria Moura Ferreira, Marina Helena Silva Lopes, Roberta Taiane Germano Oliveira, Anamaria Falcao Pereira, Rosane Oliveira Sant'Ana, Larissa Mont'alverne Arruda, Howard Lopes Ribeiro-Junior, Ronald Feitosa Pinheiro, Paulo Roberto Carvalho Almeida, Robson Francisco Carvalho, Fabio Figueiredo Chaves, Duilio Reis Rocha-Filho, Fernando Queiroz Cunha, Roberto Cesar Pereira Lima-Junior
Summary: The study revealed that colorectal cancer patients with TLR4 gene mutations are more prone to severe diarrhoea during irinotecan treatment, and mice lacking the Tlr4 gene showed exacerbated intestinal damage and inflammatory response.
BRITISH JOURNAL OF PHARMACOLOGY
(2021)
Review
Endocrinology & Metabolism
Yongxiang Li, Qingyan Jiang, Lina Wang
Summary: Appetite is essential for normal metabolism, and inflammation can impact both homeostatic and non-homeostatic systems of appetite, with the physiological functions still largely unknown. This review focuses on the structures of these systems and discusses how TLR4-induced inflammatory signaling contributes to regulating appetite in both systems, providing potential for new therapeutic interventions.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Editorial Material
Immunology
Shikun Zhang, Xuetao Cao
Summary: Activation of Toll-like receptor 7 (TLR7) can induce lupus in mice, whereas activation of TLR9 can prevent it, even though both receptors interact with myeloid differentiation primary response gene 88 (MyD88) for downstream signaling. How TLR9 triggers anti-inflammatory responses in autoimmunity is still unclear.
TRENDS IN IMMUNOLOGY
(2023)
Article
Nutrition & Dietetics
Weifang Wang, Yunfeng Li, Guojing Han, Aimin Li, Xiaomei Kong
Summary: Supplementation of Lactobacillus can alleviate the inflammatory response in asthma, inhibit pulmonary fibrosis, and treat asthma, providing a new approach for improving asthma.
FRONTIERS IN NUTRITION
(2022)
Article
Neurosciences
Dongzhu Zhang, Xue Shen, Ke Pang, Zhao Yang, Anyong Yu
Summary: This study found that levels of VSIG4 in macrophages decreased after intracerebral hemorrhage, leading to macrophage M1 polarization. Up-regulation of VSIG4 inhibited macrophage M1 polarization, pro-inflammatory cytokine production, BBB disruption, and neurological deficits following ICH. Additionally, the anti-inflammatory effect of VSIG4 was mainly through blocking TLR4/NF-kappa beta signaling.
BRAIN RESEARCH BULLETIN
(2021)
Article
Multidisciplinary Sciences
George Maiti, Jihane Frikeche, Carly Yuen-Man Lam, Asim Biswas, Vishal Shinde, Marie Samanovic, Jonathan C. Kagan, Mark J. Mulligan, Shukti Chakravarti
Summary: The ECM protein lumican plays a significant role in regulating infections and inflammation, promoting TLR4 response while restricting TLR9 in immune cells. Lumican may be internalized by immune cells to modulate their transcriptional programs and effector responses, suggesting potential therapeutic applications in future treatments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell & Tissue Engineering
Lydia Bensemmane, Fabien Milliat, Xavier Treton, Christine Linard
Summary: SVF treatment modulates intestinal monocyte differentiation and accelerates the restoration of macrophage population, mitigating the radiation-induced gastrointestinal syndrome.
STEM CELL RESEARCH & THERAPY
(2023)
Review
Neurosciences
Jonathan E. Rubin, Catalina Vich, Matthew Clapp, Kendra Noneman, Timothy Verstynen
Summary: Neuroscientists have long been exploring how CBGT pathways use dopaminergic feedback signals to modify future decisions. By reviewing the literature on dopaminergic corticostriatal plasticity, they have converged on a normative, synaptic-level learning algorithm.
EUROPEAN JOURNAL OF NEUROSCIENCE
(2021)
Article
Mathematical & Computational Biology
Muhammad U. Abdulla, Ryan S. Phillips, Jonathan E. Rubin
Summary: Introducing the dynamics of extracellular potassium ion concentration and adjusting the parameters in an existing pre-BotC neuron bursting model have successfully induced the pre-inspiratory ramping behavior of respiratory neurons, which previous models failed to capture. The proposed model also provides a greater dynamic range of burst frequencies, durations, and duty cycles compared to existing models.
JOURNAL OF COMPUTATIONAL NEUROSCIENCE
(2022)
Review
Gastroenterology & Hepatology
David J. Hackam, Chhinder P. Sodhi
Summary: Necrotizing enterocolitis (NEC) is a serious gastrointestinal disease that affects premature infants, causing high morbidity and mortality. Recent research has provided new insights into the pathogenesis of NEC and potential therapies.
NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY
(2022)
Editorial Material
Pediatrics
David J. Hackam
Summary: This study suggests that anemia may increase the risk of necrotizing enterocolitis development through impaired tissue oxygenation, shifting the focus back onto the trigger for blood transfusion rather than the transfused blood itself.
PEDIATRIC RESEARCH
(2022)
Article
Biology
Ryan S. Phillips, Jonathan E. Rubin
Summary: Inspiratory breathing rhythms are generated through synchronized neuronal activity in the preBotzinger complex, with low-amplitude oscillations known as burstlets persisting even at physiological levels. The burstlet theory of respiratory rhythm generation suggests that these subthreshold events contribute to motor output generation. Intracellular calcium dynamics and calcium-activated nonselective cationic current play crucial roles in recruiting rhythmic and non-rhythmic components of the preBotzinger complex for rhythm generation and motor output recruitment.
Article
Biochemical Research Methods
Catalina T. Vich, Matthew Clapp, Jonathan E. T. Rubin, Timothy Verstynen
Summary: In this study, the authors use simulated decision-making to investigate the mapping between neural activity in the cortico-basal ganglia-thalamic (CBGT) circuit and behavioral outcomes. They find that three core sets of CBGT subnetworks play important roles in the action selection process and are involved in adapting decision policies across exploitative and exploratory situations.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biology
Ryan S. Phillips, Hidehiko Koizumi, Yaroslav Molkov, Jonathan E. Rubin, Jeffrey C. Smith
Summary: This study experimentally confirmed the roles of neuronal persistent sodium current (I-NaP) and calcium-activated non-selective cation current (I-CAN) in the respiratory oscillator. The results showed that I-NaP is essential for rhythm generation, while I-CAN plays a crucial role in determining the amplitude of rhythmic output.
Article
Ecology
Jonathan E. Rubin, David J. D. Earn, Priscilla E. Greenwood, Todd L. Parsons, Karen C. Abbott
Summary: This study focuses on the variability of cycle periods in cyclic populations and proposes a new mechanistic hypothesis for the generation of cycle period variation by environmental stochasticity.
Article
Mathematics, Applied
X. Duan, J. E. Rubin, D. Swigon
Summary: Our recent work on linear and affine dynamical systems has provided a general framework for inferring parameters of a differential equation model from discrete data points. It introduced a new class of inverse problems where qualitative information about parameters and dynamics is determined for regions of the data space. Rigorous mathematical results have justified this approach and identified common features for certain classes of models. In this work, we present a numerical investigation that shows how these features extend to the Lotka-Volterra system, even when perturbations are present. Our work also reveals new properties and non-uniqueness in the associated diagrams.
Article
Gastroenterology & Hepatology
Johannes W. W. Duess, Maame E. E. Sampah, Carla M. M. Lopez, Koichi Tsuboi, Daniel J. J. Scheese, Chhinder P. P. Sodhi, David J. J. Hackam
Summary: Necrotizing enterocolitis (NEC) is a devastating disease in premature infants, caused by dietary and bacterial factors in a vulnerable host. Intestinal perforation can lead to severe infection and sepsis. Toll-like receptor 4 has been identified as a critical regulator of NEC development. This review article presents recent findings on microbial signaling, the immature immune system, intestinal ischemia, systemic inflammation, and potential therapeutic approaches.
Article
Neurosciences
S. R. John, W. H. Barnett, A. P. L. Abdala, D. B. Zoccal, J. E. Rubin, Y. I. Molkov
Summary: The Kolliker-Fuse nucleus (KF) plays a crucial role in both normal breathing and respiratory abnormalities, such as those seen in Rett syndrome. However, little is known about the dynamics of KF neurons and their synaptic connections. In this study, computational models were used to investigate the activity of KF and its interactions with other components of the respiratory neural circuitry. Two models were developed to simulate normal breathing and breathing abnormalities, and their properties were found to be consistent with experimental observations. These findings provide insights into the dynamics and local network interactions of KF, and offer predictions for future experimental testing.
JOURNAL OF PHYSIOLOGY-LONDON
(2023)
Article
Biochemical Research Methods
John E. Parker, Asier Aristieta, Aryn H. Gittis, Jonathan E. Rubin
Summary: This work presents a toolbox that implements a methodology for automated classification of neural responses based on spike train recordings. The toolbox provides a user-friendly and efficient approach to detect various types of neuronal responses that may not be identified by traditional methods.
JOURNAL OF NEUROSCIENCE METHODS
(2024)
Article
Mathematics, Applied
Choongseok Park, Jonathan E. Rubin
Summary: This study presents an analysis of activity patterns in a neuronal network consisting of three mutually inhibitory neurons. The network model exhibits various activity patterns, including a propagating solution that contradicts the network architecture and shows sudden turn-around of trajectories during fast transitions. A linearized model is used to perform a thorough analysis of the oscillations and reveals novel adaptive escape and adaptive release phase transition mechanisms.
SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS
(2022)
Meeting Abstract
Mathematical & Computational Biology
Muhammad Abdulla, Ryan Phillips, Jonathan Rubin
JOURNAL OF COMPUTATIONAL NEUROSCIENCE
(2021)
Article
Mathematics, Applied
Jonathan E. Rubin, Justyna Signerska-Rynkowska, Jonathan D. Touboul
Summary: This study investigates the responses of neurons to transient inputs, focusing on the postinhibitory facilitation and slope detection phenomena in nonlinear adaptive hybrid models. The research provides a framework for mathematical analysis of responses associated with Type III neurons, contributing to a better understanding of computational properties in such systems.
SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS
(2021)
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)