Article
Microbiology
Ran Mo, Yugeng Liu, Yuanyuan Chen, Yingjin Mao, Beile Gao
Summary: Microbes rely on signal transduction systems to sense and respond to environmental changes. The chemosensory system increases complexity through horizontal gene transfer, while the two-component system gains complexity through the fusion of histidine kinases and receiver domains. The presence and complexity of the c-di-GMP-mediated system are related to the size of the signaling network and can be easily rewired.
Article
Nanoscience & Nanotechnology
Julia Mueller, Anna C. Jaekel, Jonathan Richter, Markus Eder, Elisabeth Falgenhauer, Friedrich C. Simmel
Summary: This study develops a gentle extrusion-based bioprinting method for printing Escherichia coli into three-dimensional hydrogel structures. It demonstrates the control of interactions and chemical communication between bacteria placed at different positions within the bioprinted structure, and also showcases the fabrication of barrier structures using nonmotile bacteria to guide the movement of chemotactic bacteria. The combination of 3D bioprinting and synthetic biology approaches holds promise for the development of living biomaterials containing engineered bacteria as dynamic functional units.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Review
Biotechnology & Applied Microbiology
Kangsan Kim, Minjeong Kang, Byung-Kwan Cho
Summary: In recent years, there has been increasing interest in gut commensal engineering for therapeutic applications. Recent advancements in synthetic biology and systems biology have enabled effective utilization of gut commensals for therapy and diagnosis, including the rational design of synthetic microbial consortia and the construction of synthetic cells that can detect specific signals in the intestine and deliver therapeutic drugs in real-time.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
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)
Review
Microbiology
Madeline R. Barron, Vincent B. Young
Summary: The relationship between the gut environment and bacterial colonization is of great significance. The complex interactions between multiple factors in the gut environment make it difficult to uncover the characteristics of the system using reductionist methods. The systems biology approach provides a more comprehensive perspective. This article explores the relationship between the gut environment and bacterial colonization from the perspective of systems biology, and provides guidance for future research.
Article
Agronomy
Yu Sun, Lei Tian, Jingjing Chang, Shaohua Shi, Jianfeng Zhang, Hongwei Xie, Yaohui Cai, Dazhou Chen, Eiko E. Kuramae, Johannes A. van Veen, Weiqiang Li, Lam-Son Phan Tran, Chunjie Tian
Summary: The study found that the abundance of bacterial chemotaxis genes in the rhizospheres of wild rice was higher than in cultivated rice. The composition of chemotaxis genes was distinctly different between the two types of rice. Changes in rice root metabolite profiles impacted the selection of chemotaxis systems, and a core group of chemotactic bacteria were identified in the rhizosphere bacterial community.
Article
Microbiology
Bailey Marshall, Kaustubh Amritkar, Michael Wolfe, Betul Kacar, Robert Landick
Summary: Terpenoids have diverse applications, but their production still relies on nonrenewable sources. Efforts to engineer microbes for sustainable terpenoid production are ongoing. In this study, comparative genomics analysis revealed potential alternative pathways to bypass the first enzyme Dxs in terpenoid biosynthesis, but no alternative routes were found for enzymes IspG and IspH. These findings have implications for metabolic engineering and the understanding of terpenoid biosynthesis evolution.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Microbiology
Polina Beskrovnaya, Danielle L. Sexton, Mona Golmohammadzadeh, Ameena Hashimi, Elitza Tocheva
Summary: Sporulation is a specialized developmental program employed by bacteria to form dormant cells with increased resilience to stress, providing a major survival strategy for bacteria facing harsh environmental conditions. Different types of sporulation involve morphological changes regulated by non-homologous pathways, typically triggered by limited nutrients and requiring extensive membrane and peptidoglycan remodeling. Endospore and exospore formation by Firmicutes and Actinobacteria respectively play crucial roles in bacterial survival and species diversification.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Alexander Lalejini, Emily Dolson, Anya E. Vostinar, Luis Zaman
Summary: Directed microbial evolution utilizes evolutionary processes in the laboratory to create microorganisms with enhanced or novel functional traits. This study investigates the effectiveness of multiobjective selection algorithms from evolutionary computing in directing the evolution of microbial populations. The findings suggest that these algorithms outperform commonly used methods in laboratory settings, highlighting the potential for their application in directed evolution.
Article
Engineering, Environmental
Martin Hvarregaard Thorsoe, Mikael Skou Andersen, Mark V. Brady, Morten Graversgaard, Emils Kilis, Anders Branth Pedersen, Samuli Pitzen, Helena Valve
Summary: This study assesses the domestic implementation of measures to limit diffuse agricultural pollution in the Baltic Sea region, finding that larger countries face more challenges while smaller countries perform better, influenced by domestic politics. While there is significant potential to reduce agricultural pollution through the European Agricultural Fund for Rural Development, limitations in application exist.
Review
Cell Biology
Xuehua Xu, Miao Pan, Tian Jin
Summary: The discovery of how phagocytes effectively find and kill pathogens through chemotaxis and phagocytosis sheds light on the evolutionarily conserved mechanisms underlying these processes in mammals.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Microbiology
Michael J. Sheedlo, Melanie D. Ohi, D. Borden Lacy, Timothy L. Coverid
Summary: Bacterial type IV secretion systems (T4SSs) are versatile nanomachines that can transfer DNA and deliver proteins into various target cells. Cryo-electron tomography has revealed the structures of T4SSs, allowing for comparison of their molecular architectures and core complex structures. Structural variation among T4SSs may confer specialized functional properties.
Article
Multidisciplinary Sciences
Nagasuryaprasad Kotikalapudi, Samuel Joshua Pragasam Sampath, Sinha Sukesh Narayan, Bhonde R. Ramesh, Harishankar Nemani, Sathish Kumar Mungamuri, Vijayalakshmi Venkatesan
Summary: This study demonstrates the potential therapeutic applications of human Placental MSCs in addressing obesity-related insulin resistance and complications, including restoring glucose homeostasis, regulating cytokines, activating the PI3K-Akt signaling pathway, and promoting peripheral blood glucose clearance.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Marissa A. Berry, Ekaterina P. Andrianova, Igor B. Zhulin
Summary: Chemosensory systems in bacteria and archaea are complex and multi-protein pathways that allow rapid cellular response to environmental changes. CheA histidine kinase, a central component of these systems, lacks a sensor domain and relies on dedicated chemoreceptors for sensing. This study provides a genomic survey of CheA domain composition from thousands of bacteria and archaea, revealing variations and deviations from the canonical architecture. It lays the foundation for better classification of CheA homologs and identifies targets for experimental investigations.
MICROBIOLOGY SPECTRUM
(2023)
Editorial Material
Multidisciplinary Sciences
Emiliano Donadio, Sebastian Di Martino, Sofia Heinonen
Summary: A foundation is reintroducing native species to restore ecosystems and develop ecotourism.
Article
Multidisciplinary Sciences
Sean Aller, Andrew Scott, Mitali Sarkar-Tyson, Orkun S. Soyer
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2018)
Article
Biotechnology & Applied Microbiology
Christian Zerfass, Joseph A. Christie-Oleza, Orkun S. Soyer
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Multidisciplinary Sciences
Jing Chen, Matthew J. Wade, Jan Dolfing, Orkun S. Soyer
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2019)
Review
Multidisciplinary Sciences
Zoe Schofield, Gabriel N. Meloni, Peter Tran, Christian Zerfass, Giovanni Sena, Yoshikatsu Hayashi, Murray Grant, Sonia A. Contera, Shelley D. Minteer, Minsu Kim, Arthur Prindle, Paulo Rocha, Mustafa B. A. Djamgoz, Teuta Pilizota, Patrick R. Unwin, Munehiro Asally, Orkun S. Soyer
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2020)
Article
Multidisciplinary Sciences
Hadrien Delattre, Jing Chen, Matthew J. Wade, Orkun S. Soyer
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2020)
Correction
Multidisciplinary Sciences
Zoe Schofield, Gabriel N. Meloni, Peter Tran, Christian Zerfass, Giovanni Sena, Yoshikatsu Hayashi, Murray Grant, Sonia A. Contera, Shelley D. Minteer, Minsu Kim, Arthur Prindle, Paulo R. F. Rocha, Mustafa B. A. Djamgoz, Teuta Pilizota, Patrick R. Unwin, Munehiro Asally, Orkun S. Soyer
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2020)
Article
Immunology
Helen Morcrette, Andrea Kovacs-Simon, Richard K. Tennant, John Love, Sariqa Wagley, Zheng R. Yang, David J. Studholme, Orkun S. Soyer, Olivia L. Champion, Clive S. Butler, Richard W. Titball
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2020)
Article
Chemistry, Analytical
Kelsey Cremin, Bryn A. Jones, James Teahan, Gabriel N. Meloni, David Perry, Christian Zerfass, Munehiro Asally, Orkun S. Soyer, Patrick R. Unwin
ANALYTICAL CHEMISTRY
(2020)
Article
Biology
Hadrien Delattre, Kalesh Sasidharan, Orkun S. Soyer
Summary: By utilizing genomic and structural information, a biomass function capturing the amino and nucleic acid requirements of SARSCoV-2 was developed and incorporated into a metabolic model of human lung cells. Through metabolic flux balance analysis, host-based metabolic perturbations inhibiting SARS-CoV-2 reproduction were identified.
LIFE SCIENCE ALLIANCE
(2021)
Article
Biochemical Research Methods
Clarmyra Hayes, Elisenda Feliu, Orkun S. Soyer
Summary: The study focuses on the capacity of multisite enzymes to generate bistable dynamics in reaction networks, showing that multiple substrate-enzyme complexes have the potential for bistable dynamics. A generic model of an enzyme with n-substrate binding sites is constructed, providing an analytical solution for steady-state concentrations of enzyme-substrate complexes. By analyzing these expressions, mechanisms of bistability are understood and parameter combinations for bistability are derived, demonstrating how specific enzyme kinetic parameters and enzyme levels can influence bistability in multisite enzyme networks.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biology
Robert West, Hadrien Delattre, Elad Noor, Elisenda Feliu, Orkun S. Soyer
Summary: A mathematical framework is developed to analyze the impact of co-substrate cycling on metabolic flux. Co-substrate cycling imposes an additional flux limit on a reaction, in addition to the limit imposed by the kinetics of the primary enzyme. By regulating the total pool size and turnover rate of the cycled co-substrate, flux dynamics in branched and coupled pathways can be controlled.
Article
Chemistry, Analytical
Kelsey Cremin, Gabriel N. Meloni, Dimitrios Valavanis, Orkun S. Soyer, Patrick R. Unwin
Summary: Ultramicroelectrode (UME) or microelectrode probes are commonly used for single-cell measurements of cellular properties and processes. The sensitivity of these measurements is limited by the magnitude of cellular and UME fluxes, as well as the stability of UME response. This study combines scanning electrochemical microscopy (SECM) and finite element method (FEM) modeling to measure and simulate the oxygen consumption rate (OCR) in single HeLa cells. The results suggest that the present detection sensitivity of the technique is close to or below the range of actual single-cell OCR, and improvements in the stability and precision of SECM measurements are needed.
ACS MEASUREMENT SCIENCE AU
(2023)
Review
Biology
Kelsey Cremin, Sarah J. N. Duxbury, Jerko Rosko, Orkun S. S. Soyer
Summary: Spatial organization is a common feature in the microbial world. Recent interest has focused on understanding the role of spatial organization in microbial physiology, coexistence, and evolution. Studies have shown that spatial organization influences these aspects by feedback between local conditions, cell physiology and movement, and evolution. This mini review highlights the importance of spatio-temporal measurements and mathematical models to study emergent dynamics in spatially organized microbial systems (SOMS). Future studies should focus on the initial formation of SOMS and their emergent dynamics, utilizing model systems that mimic natural ones.
Article
Biology
Connah G. M. Johnson, Alexander G. Fletcher, Orkun S. Soyer
Summary: In this study, the authors introduce ChemChaste, an extension that enables spatial simulation of multicellular and bulk biochemistry. ChemChaste allows for the simulation of an arbitrary number of spatially diffusing chemicals, spatially heterogeneous chemical diffusion coefficients, and the inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface for defining parameters without direct interaction with Chaste's core C++ code.
Article
Biotechnology & Applied Microbiology
Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, Orkun S. Soyer, J. Kimberly Summers, Antoine Limasset, A. Murat Eren, Rayan Chikhi, Aaron E. Darling
Summary: STRONG is a novel method that identifies strains de novo from multiple metagenome samples by using assembly graphs to extract coverages of SCGs in each MAG and determine the number of strains, their haplotypes or sequences, and abundances. The method is validated using synthetic communities and real samples.