Review
Immunology
Po-Tsang Lee, Fernando Y. Yamamoto, Chen-Fei Low, Jiun-Yan Loh, Chou-Min Chong
Summary: The gastrointestinal immune system plays a crucial role in regulating the symbiotic host-microbiome interactions and maintaining immune homeostasis. Fish gastrointestinal immune system has specialized gut-associated lymphoid tissues that establish tolerance towards commensal gut microbiome while mounting immune responses against enteric pathogens. Understanding the intestinal immune system is essential for developing oral vaccines and immunostimulants in aquaculture.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Xiaoming Zhang, Laura Kracht, Antonio M. Lerario, Marissa L. Dubbelaar, Nieske Brouwer, Evelyn M. Wesseling, Erik W. G. M. Boddeke, Bart J. L. Eggen, Susanne M. Kooistra
Summary: This study provides insight into epigenetic profiles and transcription factor networks associated with transcriptional signatures of tolerized and trained microglia in vivo, leading to a better understanding of innate immune memory of microglia.
JOURNAL OF NEUROINFLAMMATION
(2022)
Review
Fisheries
Qingshuang Zhang, Hongwei Yang, Tsegay Teame, Chao Ran, Yalin Yang, Yuanyuan Yao, Qianwen Ding, Shubin Liu, Shengkang Li, Zhen Zhang, Zhigang Zhou
Summary: Immunostimulants have multiple important functions in aquaculture, but improper use can lead to immune disorders. Modulating gut microbiota may be an effective approach to improve immune disorders caused by immunostimulants.
REVIEWS IN AQUACULTURE
(2023)
Review
Microbiology
Yu-Dian Zhou, Feng-Xia Liang, Hao-Ran Tian, Dan Luo, Ya-Yuan Wang, Shu-Rui Yang
Summary: Intestinal absorption of food is a source of glucose, and lifestyle and diet can lead to insulin resistance and impaired glucose tolerance, precursors of type 2 diabetes. Glycemic management is essential for long-term health, but its molecular mechanism is not fully understood. Disturbed microbiota affects gut homeostasis, intestinal barrier integrity, and systemic metabolism. Gut microbiota intervention can improve glucose tolerance, insulin sensitivity, and drug efficacy. Regulating gut microbiota through diet or pro/prebiotics can guide lifestyle interventions, while traditional Chinese medicine can effectively regulate intestinal homeostasis. Further research is needed to explore the microbiota-host relationship and therapeutic potential of targeting gut microbiota.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Agriculture, Multidisciplinary
Ying Li, Lezhen Dong, Zhishen Mu, Lingyi Liu, Junsi Yang, Zufang Wu, Daodong Pan, Lianliang Liu
Summary: This review article provides an overview of the unique structure, encapsulation, and targeted transport capabilities of lactoferrin (LF), as well as its applications in immunity and gut microbiota regulation. The microstructure and electrostatic interactions of LF are discussed, along with its nano self-assembly behavior as a cage-like protein. The article also highlights the potential impact of LF on immunological function through the regulation of gut microbiota.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Oncology
Amy Hui Ping Khor, Tomoyuki Koguchi, Hao Liu, Masanori Kakuta, Daisuke Matsubara, Ruimeng Wen, Yoji Sagiya, Seiya Imoto, Hidewaki Nakagawa, Koichi Matsuda, Chizu Tanikawa
Summary: p53, a tumor suppressor gene mutated in many cancers, has been found to be involved in regulating the gut microbiome and protecting the intestinal barrier through its downstream targets related to the innate immune system. Knockout mice lacking p53 are more susceptible to radiation-induced gastrointestinal toxicity and have shorter survival time, but treatment with antibiotics improves their outcomes.
Review
Medicine, General & Internal
Xiang Li, Shaoqiang Zhang, Gang Guo, Jing Han, Jun Yu
Summary: The gut microbiome plays a crucial role in cancer and cancer therapy. Individual variations in the gut microbiota may explain the heterogeneity in immune responses to immunotherapy. Understanding the functional role of the gut microbiome in regulating immunity and cancer is essential for precision medicine. Modifying the microbiota can enhance the efficacy of immunotherapy.
Review
Nanoscience & Nanotechnology
Xiaodong Zhang, Xiaokai Chen, Yanli Zhao
Summary: Artificial nanosystems have the ability to modulate immune responses and can be used in vaccine development and treatment of bacterial infections and diseases. This review discusses the recent advances of nanosystems in vaccine development and immune activation, as well as the application of immune-suppressive nanosystems.
ACS APPLIED NANO MATERIALS
(2022)
Review
Pharmacology & Pharmacy
Jun Lu, Xiang He, Lijuan Zhang, Ran Zhang, Wenzheng Li
Summary: Acetylation modifications play a crucial role in the pathological process of cancer and can affect immune system function and tumor immunity. Understanding the role of acetylation in cancer is essential for developing new therapies.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Rossella Cianci, Laura Franza, Raffaele Borriello, Danilo Pagliari, Antonio Gasbarrini, Giovanni Gambassi
Summary: Heart failure is a complex health issue where the immune system and microbiota modulation play important roles in its pathogenesis and progression.
Review
Immunology
Guosen Ou, Huachong Xu, Jialin Wu, Shiqi Wang, Yaokang Chen, Li Deng, Xiaoyin Chen
Summary: Influenza A, a common subtype of flu, causes millions of severe infections and hundreds of thousands of deaths each year. Vaccination is the traditional method to prevent influenza A, but its effectiveness is limited due to antigenic changes in the virus and lag in vaccine production. Therefore, alternative therapies are being explored. Recent studies have shown that regulating the gut microbiota can enhance the immune response against influenza A.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Nelly Amenyogbe, Pedro Dimitriu, Kinga K. Smolen, Eric M. Brown, Casey P. Shannon, Scott J. Tebbutt, Phillip J. Cooper, Arnaud Marchant, Tessa Goetghebuer, Monika Esser, Brett B. Finlay, Tobias R. Kollmann, William W. Mohn
Summary: This study identified differences in immune responses correlating to gut microbiomes across biogeographically diverse settings and evaluated biological plausibility using a mouse model.
Review
Biochemistry & Molecular Biology
Ludovico Abenavoli, Giuseppe Guido Maria Scarlata, Maria Rosaria Paravati, Luigi Boccuto, Francesco Luzza, Emidio Scarpellini
Summary: Liver transplantation is the preferred treatment for patients with certain liver conditions, but rejection after transplantation is a significant issue. The gut microbiota is involved in the gut-liver axis and can affect the immune response, potentially leading to graft rejection. Evaluating changes in the gut microbiota composition is essential for monitoring the success of liver transplantation and implementing appropriate preventive measures.
Article
Biochemistry & Molecular Biology
Yiwei Zhang, Jian Zhou, Zhiyuan Wei, Hui Dong, Di Yang, Yuanyu Deng, Jiahui Li, Saiyu Shi, Yi Sun, Huimin Lu, Jizhao Yuan, Bing Ni, Yuzhang Wu, Yi Tian, Chao Han
Summary: Dendritic cells play a crucial role in the immune system by regulating defense against pathogens and tolerance to self. This review highlights the significance of mRNA stability regulation in dendritic cells for their function and immune therapy.
Review
Immunology
Sonakshi Rastogi, Sneha Mohanty, Sapna Sharma, Prabhanshu Tripathi
Summary: This review summarizes the recent progress in understanding the effects of dietary metabolites, particularly short-chain fatty acids (SCFAs), on the gut-lung axis and its impact on lung health. The role of the gut-lung axis in SARS-CoV-2 mediated inflammation is also highlighted. By analyzing global research progress and knowledge gaps, the study predicts future research directions.
FRONTIERS IN IMMUNOLOGY
(2022)
Editorial Material
Computer Science, Artificial Intelligence
Naren Ramakrishnan, Chang-Tien Lu, Madhav Marathe, Achla Marathe, Anil Vullikanti, Stephen Eubank, Scotland Leman, Michael Roan, John S. Brownstein, Kristen Summers, Lise Getoor, Aravind Srinivasan, Tanzeem Choudhury, Dipak Gupta, David Mares
IEEE INTELLIGENT SYSTEMS
(2015)
Article
Physics, Fluids & Plasmas
Yasamin Khorramzadeh, Mina Youssef, Stephen Eubank, Shahir Mowlaei
Article
Multidisciplinary Sciences
Maksudul Alam, Xinwei Deng, Casandra Philipson, Josep Bassaganya-Riera, Keith Bisset, Adria Carbo, Stephen Eubank, Raquel Hontecillas, Stefan Hoops, Yongguo Mei, Vida Abedi, Madhav Marathe
Review
Infectious Diseases
Kathleen A. Alexander, Claire E. Sanderson, Madav Marathe, Bryan L. Lewis, Caitlin M. Rivers, Jeffrey Shaman, John M. Drake, Eric Lofgren, Virginia M. Dato, Marisa C. Eisenberg, Stephen Eubank
PLOS NEGLECTED TROPICAL DISEASES
(2015)
Article
Mathematics, Interdisciplinary Applications
Benjamin M. Althouse, Samuel V. Scarpino, Lauren Ancel Meyers, John W. Ayers, Marisa Bargsten, Joan Baumbach, John S. Brownstein, Lauren Castro, Hannah Clapham, Derek A. T. Cummings, Sara Del Valle, Stephen Eubank, Geoffrey Fairchild, Lyn Finelli, Nicholas Generous, Dylan George, David R. Harper, Laurent Hebert-Dufresne, Michael A. Johansson, Kevin Konty, Marc Lipsitch, Gabriel Milinovich, Joseph D. Miller, Elaine O. Nsoesie, Donald R. Olson, Michael Paul, Philip M. Polgreen, Reid Priedhorsky, Jonathan M. Read, Isabel Rodriguez-Barraquer, Derek J. Smith, Christian Stefansen, David L. Swerdlow, Deborah Thompson, Alessandro Vespignani, Amy Wesolowski
Article
Infectious Diseases
Matthew Biggerstaff, David Alper, Mark Dredze, Spencer Fox, Isaac Chun-Hai Fung, Kyle S. Hickmann, Bryan Lewis, Roni Rosenfeld, Jeffrey Shaman, Ming-Hsiang Tsou, Paola Velardi, Alessandro Vespignani, Lyn Finelli
BMC INFECTIOUS DISEASES
(2016)
Article
Biochemical Research Methods
Nargesalsadat Dorratoltaj, Achla Marathe, Bryan L. Lewis, Samarth Swarup, Stephen G. Eubank, Kaja M. Abbas
PLOS COMPUTATIONAL BIOLOGY
(2017)
Review
Multidisciplinary Sciences
Nargesalsadat Dorratoltaj, Ryan Nikin-Beers, Stanca M. Ciupe, Stephen G. Eubank, Kaja M. Abbas
Article
Biology
Madhurima Nath, Yihui Ren, Yasamin Khorramzadeh, Stephen Eubank
JOURNAL OF THEORETICAL BIOLOGY
(2018)
Article
Medicine, General & Internal
Abhijin Adiga, Shuyu Chu, Stephen Eubank, Christopher J. Kuhlman, Bryan Lewis, Achla Marathe, Madhav Marathe, Eric K. Nordberg, Samarth Swarup, Anil Vullikanti, Mandy L. Wilson
Correction
Multidisciplinary Sciences
Eric T. Lofgren, M. Elizabeth Halloran, Caitlin M. Rivers, John M. Drake, Travis C. Porco, Bryan Lewis, Wan Yang, Alessandro Vespignani, Jeffrey Shaman, Joseph N. S. Eisenberg, Marisa C. Eisenberg, Madhav Marathe, Samuel V. Scarpino, Kathleen A. Alexander, Rafael Meza, Matthew J. Ferrari, James M. Hyman, Lauren A. Meyers, Stephen Eubank
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Biochemical Research Methods
Prithwish Chakraborty, Bryan Lewis, Stephen Eubank, John S. Brownstein, Madhav Marathe, Naren Ramakrishnan
PLOS COMPUTATIONAL BIOLOGY
(2018)
Article
Geochemistry & Geophysics
Anne-Marie Wefing, Jennifer Arps, Patrick Blaser, Claudia Wienberg, Dierk Hebbeln, Norbert Frank
Article
Physics, Fluids & Plasmas
Yihui Ren, Stephen Eubank, Madhurima Nath
Proceedings Paper
Computer Science, Artificial Intelligence
Madhurima Nath, Stephen Eubank, Mina Youssef, Yasamin Khorramzadeh, Shahir Mowlaei
COMPLEX NETWORKS VI
(2015)
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)