Article
Mathematics
Ning Jiang, Jiangyan Liang, Yi-Long Luo, Min Tang, Yaming Zhang
Summary: This study investigates the well-posedness of biological models with AHL-dependent cell mobility in engineered Escherichia coli populations. The local existence for large initial data is proven for a recently proposed kinetic model. The positivity and local conservation laws for density and nutrient concentration are justified with specific initial assumptions. Based on these properties, a global extension in time near the equilibrium is achieved. By considering the asymptotic behaviors of the CheZ turnover rate, an anisotropic diffusion model for engineered Escherichia coli populations (AD-EECP) is derived, and a key extra a priori estimate is found to overcome the difficulties from the nonlinearity of the diffusion structure. The local well-posedness, positivity, and local conservation laws for density and nutrient of the AD-EECP are justified, and the global existence around the stable steady-state is obtained.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2022)
Article
Mathematics, Applied
Wenbin Lyu, Zhi-An Wang
Summary: This paper investigates a parabolic-elliptic chemotaxis model with density-suppressed motility and general logistic source in an n-dimensional smooth bounded domain with Neumann boundary conditions. The main focus is on exploring the strength of logistic damping necessary to ensure the global boundedness of solutions, and establishing the asymptotic behavior of solutions under certain conditions.
ADVANCES IN NONLINEAR ANALYSIS
(2023)
Article
Mathematics, Applied
Xueyan Tao, Zhong Bo Fang
Summary: This work investigates the density-suppressed motility model and proves the existence of globally bounded classical solutions under certain conditions. It also demonstrates that the solutions can stabilize towards a specific equilibrium state.
ZEITSCHRIFT FUR ANGEWANDTE MATHEMATIK UND PHYSIK
(2022)
Review
Microbiology
Vadim M. Gumerov, Ekaterina P. Andrianova, Igor B. Zhulin
Summary: Chemosensory system is a complex and specialized signal transduction mode in bacteria and archaea, which can respond rapidly to environmental changes. Both experimental and computational studies have revealed substantial diversity in system design, functional regulation, cellular localization, and phyletic distribution of chemosensory pathways.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Biophysics
Guangzhe Liu, Zhaorong Liu, Lailai Zhu, Rongjing Zhang, Junhua Yuan
Summary: This study demonstrates that fluid flow and cell body rotation influence the run-and-tumble behavior of flagellated bacteria. Fluid flow increases running time and decreases tumbling time, while cell body rotation only decreases tumbling time.
BIOPHYSICAL JOURNAL
(2021)
Article
Physics, Fluids & Plasmas
Shlomit Peled, Shawn D. Ryan, Sebastian Heidenreich, Markus Baer, Gil Ariel, Avraham Be'er
Summary: Heterogeneous systems of active matter exhibit complex emergent dynamical patterns. Mixed swarms of cells with different aspect ratios were studied experimentally and in simulations, revealing that long cells act as nucleation sites for rapidly moving short cells, enhancing swarming speeds. However, high fractions of long cells can create bottlenecks for efficient swarming.
Article
Chemistry, Multidisciplinary
Apoorva Vishwakarma, Francis Dang, Allison Ferrell, Hazel A. Barton, Abraham Joy
Summary: Over 80% of chronic bacterial infections in humans are linked to biofilms, which provide significant resistance to antibiotics and host immune responses. Water-soluble synthetic peptidomimetic polyurethanes have shown potential in disrupting established biofilms and inhibiting biofilm formation without toxicity to mammalian cells.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Mathematics, Applied
Zhi-An Wang, Xin Xu
Summary: This paper investigates the stationary problem of density-suppressed motility models in one dimension with Neumman boundary conditions, using global bifurcation theory and the Helly compactness theorem to explore the conditions under which non-constant stationary solutions exist. The results show that in the absence of cell growth, solutions exhibit monotonicity and a global bifurcation diagram can be obtained by treating the chemical diffusion rate as a bifurcation parameter. However, with cell growth, the structure of the global bifurcation diagram becomes much more complex and solutions lose their monotonicity property, requiring a minimum range of growth rate for non-constant stationary solutions to exist.
IMA JOURNAL OF APPLIED MATHEMATICS
(2021)
Article
Mathematical & Computational Biology
Jiawei Chu, Hai -Yang Jin
Summary: In this paper, we study the global stability of a predator-prey system with defense switching mechanism and density-suppressed dispersal strategy. We establish the existence of global classical solutions with uniform-in-time boundedness using the method of energy estimates and Moser iteration. The global stability of co-existence equilibrium is proved by using Lyapunov functionals and LaSalle's invariant principle. The linear stability analysis and numerical simulations suggest that density-suppressed dispersal may trigger pattern formation.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2022)
Article
Microbiology
Victoria Palma, Maria Soledad Gutierrez, Orlando Vargas, Raghuveer Parthasarathy, Paola Navarrete
Summary: Bacterial motility is a common characteristic that can be studied through various methods, with three-dimensional imaging being advantageous in microscopic approaches. Understanding bacterial motility is also important for studying bacterial-host interactions.
Article
Chemistry, Physical
Elena Sese-Sansa, Demian Levis, Ignacio Pagonabarraga
Summary: This article discusses a dynamical field theory for self-propelled particles subjected to generic torques and forces. By coarse-graining their microscopic dynamics, the study investigates the instabilities of macroscopic and finite structures, and the influence of intrinsic torques on phase separation and non-equilibrium patterns.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Mathematics
Jing Li, Zhi-An Wang
Summary: The paper introduces a density-suppressed motility model to explain the self-trapping mechanism inducing spatial and temporal pattern formations observed in bacterial motion experiments. By constructing super- and sub-solutions, the conditions and characteristics of traveling wave solutions in the system are revealed, along with a discussion on the effects of different motility functions on wave patterns and speeds.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2021)
Article
Biochemical Research Methods
George Courcoubetis, Manasi S. Gangan, Sean Lim, Xiaokan Guo, Stephan Haas, James Q. Boedicker
Summary: This study examines the formation and dynamics of bacterial aggregates in soft agar and their collective movement. The movement of the aggregates is driven by the change in motility of individual cells and the regulation of cell density. The results show that bacteria swim towards regions with high concentrations of attractant molecules and stop swimming in crowded areas, leading to the migration and merging of the aggregates. This work identifies a new mechanism for collective bacterial motility and control.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Mathematics, Applied
Wenbin Lyu, Jiahao Wang
Summary: This paper is concerned with a chemotaxis system with density-dependent motility and indirect signal absorption. By some basic inequalities, we obtain that the convergence rate of solutions is exponential as time tends to infinity for such kind of models with l < 2, which improves on a recent result in [14], where the convergence rate of solutions is algebraic. (c) 2023 Elsevier Inc. All rights reserved.
JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Yoshiharu Krockenberger, Ai Ikeda, Hideki Yamamoto
Summary: Research suggests that tuning the copper-oxygen bond configuration to the state of minimal energy is crucial for the emergence of high-temperature superconductivity, with differences in atomic stripe formation on CuO2 planes in infinite-layer phases observed in different compounds.
Article
Virology
Ye-Fan Hu, Jing-Chu Hu, Hin Chu, Thomas Yau, Bao-Zhong Zhang, Jian-Dong Huang
Summary: The impact of the Omicron variant on antibodies and vaccines is still unknown. However, analysis suggests that it may weaken the neutralizing potential of current therapeutic antibodies to varying degrees and could have a similar impact on COVID-19 vaccines.
Article
Multidisciplinary Sciences
Yuting Chen, Eriona Hysolli, Anlu Chen, Stephen Casper, Songlei Liu, Kevin Yang, Chenli Liu, George Church
Summary: This study demonstrates the first application of whole-genome recoding technology in human cells, achieving successful conversion of TAG to TAA for 33 essential genes via a single transfection. It also reveals off-target events in gene exons and introduces a computational tool called GRIT for recoding, showcasing the feasibility of recoding and highly multiplex editing in mammalian cells.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Ting Wei, Wangsheng Lai, Qian Chen, Yi Zhang, Chenjian Sun, Xionglei He, Guoping Zhao, Xiongfei Fu, Chenli Liu
Summary: In this study, a system called SPACE was introduced for rapid and extensively parallelizable evolution of biomolecules by incorporating spatial dimensions into the phage-assisted continuous evolution system. The system leverages competition over space and allows for the emergence of improved or new protein functions.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Review
Microbiology
Matthew Scott, Terence Hwa
Summary: This review describes how physiological constraints are sensed through metabolic fluxes and how flux-controlled regulation gives rise to simple empirical relations between protein levels and the rate of cell growth.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Rohan Balakrishnan, Matteo Mori, Igor Segota, Zhongge Zhang, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Article
Microbiology
Chenhao Wu, Matteo Mori, Miriam Abele, Amir Banaei-Esfahani, Zhongge Zhang, Hiroyuki Okano, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Summary: Bacterial fitness depends on their ability to adapt to changing environments. Escherichia coli, for example, primarily expresses protein synthesis machinery in rich growth medium and biosynthetic enzymes in minimal medium. By analysing timing of enzyme expression, quantitative proteomics has revealed a positive relation between onset time of enzyme synthesis and enzyme reserve in E. coli. A coarse-grained kinetic model based on proteomes has been developed to capture enzyme recovery kinetics and infer regulatory strategies underlying the gene expression program of E. coli.
NATURE MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jingwen Zhu, Pan Chu, Xiongfei Fu
Summary: Global regulation of cell growth rate on gene expression perturbs gene networks and impacts cell-fate determination. Using a synthetic circuit, researchers discovered that growth rates can induce a bifurcation in the landscape, leading to changes in cell-fate decisions. This bifurcation is caused by unbalanced gene expression response to growth variations. These findings highlight the importance of growth regulation in cell-fate determination processes.
NATURE CHEMICAL BIOLOGY
(2023)
Review
Virology
Siva Sundara Kumar Durairajan, Abhay Kumar Singh, Udhaya Bharathy Saravanan, Mayurikaa Namachivayam, Moorthi Radhakrishnan, Jian-Dong Huang, Rahul Dhodapkar, Hongjie Zhang
Summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can invade the gastrointestinal system, causing symptoms such as vomiting, diarrhea, and abdominal pain. Understanding the mechanisms of infection and transmission in the gastrointestinal tract is crucial for early detection and targeted therapeutics against COVID-19-induced gastrointestinal infection and inflammatory bowel disease (IBD).
Article
Microbiology
Arion Iffland-Stettner, Hiroyuki Okano, Matti Gralka, Ghita Guessous, Kapil Amarnath, Otto X. X. Cordero, Terence Hwa, Sebastian Bonhoeffer
Summary: A genome-scale metabolic model of V. splendidus 1A01 was reconstructed, offering solutions to the technical problems associated with model reconstruction for a marine bacterial strain like V. splendidus 1A01.
Article
Multidisciplinary Sciences
Matteo Mori, Chuankai Cheng, Brian R. Taylor, Hiroyuki Okano, Terence Hwa
Summary: This article presents a theoretical framework called FDM to quantify the contribution of each metabolic reaction to cellular functions. It highlights the importance of energy allocation in cell growth.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Ghita Guessous, Vadim Patsalo, Rohan Balakrishnan, Tolga caglar, James R. Williamson, Terence Hwa
Summary: Chitin-degrading bacteria have developed a mechanism of utilizing chitinases to sustain growth and dispersal, enabling them to explore new habitats without compromising their fitness on previously colonized ones.
NATURE MICROBIOLOGY
(2023)
Article
Materials Science, Multidisciplinary
Bao-Zhong Zhang, Yee-Man Au-Yeung, Terrence Tsz-Tai Yuen, Xiaoyun Xu, Hua-Rui Gong, Zheng Zeng, Renhao Li, Jinlian Hu, Hin Chu, Jian-Dong Huang
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Physics, Multidisciplinary
Liang Luo, Yang Bai, Xiongfei Fu
Summary: Classic models of cell size control consider that cells divide when reaching a threshold, e.g., size, age, or size extension. The molecular basis of the threshold involves multiple layers of regulation as well as gene noise. This work highlights the importance of examining gene noise in size control.
PHYSICAL REVIEW RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Jiawen Chen, Ting Li, Chun Ye, Jiasheng Zhong, Jian-Dong Huang, Yiquan Ke, Haitao Sun
Summary: Traditionally, the lung in a healthy state is considered sterile, but the development of non-culture-dependent techniques has revealed the presence of low-biomass microbiomes in the lungs. The lung microbiome is similar to the oral microbiome, suggesting a passive transfer of microorganisms from the oral cavity to the lungs. The composition of the lung microbiome is influenced by elimination, immigration, and relative growth within its communities. The lung microbiome plays a role in lung diseases and the lung-brain axis, but the causal connection between specific diseases and the lung microbiome is not well understood.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
