Article
Biochemical Research Methods
Joshua Rees-Garbutt, Jake Rightmyer, Oliver Chalkley, Lucia Marucci, Claire Grierson
Summary: Theoretical minimal gene sets for Mycoplasma genitalium have been simulated and found to be unable to produce dividing cells, indicating the need to reintroduce specific genes. This underscores the importance of identifying species-specific low essential genes and their interactions.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Martina Maritan, Ludovic Autin, Jonathan Karr, Markus W. Covert, Arthur J. Olson, David S. Goodsell
Summary: Building structural models of entire cells presents a challenge that requires integration of multiple sources of biological data and enhanced computational modeling methods. The study presents 3D structural models of an entire Mycoplasma genitalium cell, combining experimental and homology-modeled structures to provide a structural representation for all proteins, DNA, and RNA molecules. The models establish a framework for further research and exploration of mesoscale properties, highlighting the importance of data gathering methodologies.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Hongzhong Lu, Eduard J. Kerkhoven, Jens Nielsen
Summary: This review discusses the latest developments in multiscale models of yeast and demonstrates how incorporating enzymatic parameters and other cellular networks can enhance the comprehensive description of cellular physiology. These new models significantly improve predictive performance and expand the applications of Saccharomyces cerevisiae in cell factory design and basic studies of yeast physiology.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Immunology
Roisin McMorrow, Giorgia Zambito, Alex Nigg, Karishma Lila, Thierry P. P. van den Bosch, Clemens W. G. M. Lowik, Laura Mezzanotte
Summary: In this study, a dual color bioluminescent mouse model was used to investigate the location and function of T-cells during tumor growth and checkpoint blockade treatment. The results showed differences in total T-cell bioluminescence between highly infiltrated 'hot' tumors and poorly infiltrated 'cold' tumors. An increase in bioluminescence signal was observed in the tumor-draining lymph nodes after checkpoint blockade treatment.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Nutrition & Dietetics
Adam Drewnowski, Nicola McKeown, Katrina Kissock, Eleanor Beck, Heddie Mejborn, Florent Vieux, Jessica Smith, Gabriel Masset, Chris J. Seal
Summary: Healthy eating patterns advocate for whole grains, vegetables, fruits, and other nutritious foods, however, whole grains are often not included in nutrient profiling models. Most nutrient profiling models identify healthy foods as those with limited energy, saturated fat, sugar, and sodium content. As global dietary guidance shifts towards food and food groups, future nutrient density metrics may need to align with this approach.
ADVANCES IN NUTRITION
(2021)
Article
Chemistry, Medicinal
Sebastian Schieferdecker, Freddy A. Bernal, K. Philip Wojtas, Francois Keiff, Yan Li, Hans-Martin Dahse, Florian Kloss
Summary: In this study, a set of BTZs were synthesized and evaluated for their antimycobacterial activity. High potency was achieved through piperidine and piperazine substitutions, and promising candidates were identified. It was found that target inhibition is not the only requirement for suitable antimycobacterial agents. Extensively validated machine learning models successfully predicted whole cell activity class.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Zaida Luthey-Schulten, Zane R. Thornburg, Benjamin R. Gilbert
Summary: A complete description of the state of a cell requires knowledge of various factors, along with theoretical models and simulations to interpret the data. In simple and well-studied bacterial systems, obtaining sufficient information to establish a dynamical whole-cell model poses challenges.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Lin Tang
Summary: This paper presents a comprehensive modeling approach for cellular networks of cells with a minimal genome.
Article
Biophysics
Agnieszka Obarska-Kosinska, Benedikt Rennekamp, Aysecan Uenal, Frauke Graeter
Summary: Researchers developed full-atom models of collagen fibrils for 20 different species with diverse cross-link types and localization for structure-based analyses and simulations of type I collagen in health and disease. Parameters of the modeled cross-links for an Amber force field were provided to facilitate simulations.
BIOPHYSICAL JOURNAL
(2021)
Article
Biology
Caroline Frischmon, Carlise Sorenson, Michael Winikoff, Katarzyna P. Adamala
Summary: Build-a-Cell is a global network of researchers aiming to develop synthetic living cells within the next decade, revolutionizing the biotechnology industry by providing a more complete understanding of biology through large-scale collaboration and integration of cellular functions.
Article
Engineering, Electrical & Electronic
Pritesh Mistry, Peter Hughes, Abirami Gunasekaran, Gareth Tucker, Adam Bevan
Summary: This study utilizes real-world Diesel Multiple Unit sensor data to predict engine failures through remote condition monitoring. A methodology based on windowing of data achieves an accuracy of 88% in predictive modeling. The use of explainable AI methods provides feature importance explanations for the model's performance. The proposed methodology is not only useful for the railway industry but also applicable for predictive maintenance of various systems.
Review
Engineering, Biomedical
Kenny Zhuoran Wu, Christabella Adine, Aleksandr Mitriashkin, Benjamin Jun Jie Aw, N. Gopalakrishna Iyer, Eliza Li Shan Fong
Summary: Patient-derived in vitro tumor models are too simple and do not capture important characteristics of the tumor microenvironment (TME), limiting their use for personalized drug testing. In vivo models are costly and time-consuming. Ex vivo patient-derived tumor explant (PDE) cultures retain the intact TME but have low throughput and viability. However, with growing recognition of the importance of patient-specific TME, there is an urgent need to improve and utilize PDE cultures for personalized medicine in cancer patients.
ADVANCED HEALTHCARE MATERIALS
(2023)
Article
Chemistry, Analytical
Pelagia-Irene Gouma
Summary: There is ongoing discussion about how viruses are transmitted in the air and the need for monitoring environmental presence of an active pathogen. Current detection methods using nucleic acid and antigen tests fail to differentiate between viable and non-viable viruses. This perspective presents an innovative approach using a live-cell sensor microdevice that captures and becomes infected by viruses, providing early warning signals for the presence of pathogens.
Editorial Material
Multidisciplinary Sciences
Janet Rossant, Jianping Fu
Summary: Scientists should carefully consider the necessity of using embryo models based on human stem cells in their work due to the practical and ethical challenges involved.
Article
Multidisciplinary Sciences
Jorn Bethune, April Kleppe, Soren Besenbacher
Summary: The mutation rate of a specific position in the human genome is influenced by the sequence context surrounding it. Traditional modeling methods become less effective for larger values of k due to sparse data. To address this issue, a new method called k-mer pattern partition is proposed, which groups similar k-mers. This new method improves the prediction of mutation rates and allows for the creation of models using wider sequence contexts. Additionally, a software package called Genovo is developed to predict different types of mutations for each gene based on the k-mer pattern partition model.
NATURE COMMUNICATIONS
(2022)
Meeting Abstract
Biophysics
Markus Covert
BIOPHYSICAL JOURNAL
(2019)
Article
Biochemistry & Molecular Biology
Keara Lane, Marta Andres-Terre, Takamasa Kudo, Denise M. Monack, Markus W. Covert
Review
Immunology
Stevan Jeknic, Takamasa Kudo, Markus W. Covert
FRONTIERS IN IMMUNOLOGY
(2019)
Article
Biology
Hee Won Yang, Steven D. Cappell, Ariel Jaimovich, Chad Liu, Mingyu Chung, Leighton H. Daigh, Lindsey R. Pack, Yilin Fan, Sergi Regot, Markus Covert, Tobias Meyer
Article
Biochemistry & Molecular Biology
Katie Bodner, Arin L. Melkonian, Angela I. M. Barth, Takamasa Kudo, Yu Tanouchi, Markus W. Covert
Review
Biochemistry & Molecular Biology
Katie Bodner, Arin L. Melkonian, Markus W. Covert
Summary: Bacteriophages play a crucial role in human health by altering the severity of bacterial infections, and recent studies have uncovered their ability to modulate the physiology of mammalian cells. Understanding the interactions between phages and mammalian cells has important implications for phage therapy.
TRENDS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Markus W. Covert, Taryn E. Gillies, Takamasa Kudo, Eran Agmon
Summary: Quantitative systems biology is at a turning point, with the potential to have a global impact in biological research and applications. Drawing lessons from meteorology, there is an opportunity to forecast the next steps and achieve similar global influence in the field through mathematical modeling.
Article
Biochemical Research Methods
Eran Agmon, Ryan K. Spangler, Christopher J. Skalnik, William Poole, Shayn M. Peirce, Jerry H. Morrison, Markus W. Covert
Summary: Vivarium is a software tool for building integrative multiscale models, providing an interface that allows computational biologists to easily define mechanistic models and combine them as an integrated multiscale model. It streamlines the integrative modeling effort by making individual models into modules that can be wired together and run with Vivarium's discrete-event simulation engine. This tool has been demonstrated to successfully build composite models that combine various modeling frameworks, and it has the potential to support future efforts in integrating more types of models at different biological scales.
Article
Biochemistry & Molecular Biology
Martina Maritan, Ludovic Autin, Jonathan Karr, Markus W. Covert, Arthur J. Olson, David S. Goodsell
Summary: Building structural models of entire cells presents a challenge that requires integration of multiple sources of biological data and enhanced computational modeling methods. The study presents 3D structural models of an entire Mycoplasma genitalium cell, combining experimental and homology-modeled structures to provide a structural representation for all proteins, DNA, and RNA molecules. The models establish a framework for further research and exploration of mesoscale properties, highlighting the importance of data gathering methodologies.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Takamasa Kudo, Keara Lane, Markus W. Covert
Summary: By integrating live-cell imaging with pooled library-based screening, we developed a method that enables intracellular multiplexing and allows for long-term observation and analysis of phenotypes of interest, directly connecting behavior to the cellular genotype.
Article
Mathematical & Computational Biology
Travis A. Ahn-Horst, Luis Santiago Mille, Gwanggyu Sun, Jerry H. Morrison, Markus W. Covert
Summary: Growth and environmental responses are crucial for organisms' survival and adaptation. A study on a whole-cell model of E. coli found that small molecule feedback inhibition pathways and dysregulated amino acid synthesis pathways play important roles in growth regulation and concentration fluctuations at the single-cell level, respectively.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Heejo Choi, Markus W. Covert
Summary: In this study, a whole-cell model was used to investigate the inconsistencies between in vitro tRNA aminoacylation measurements and in vivo protein synthesis demands in E. coli. The results showed that kinetic measurements of aminoacyl-tRNA synthetase were insufficient for cellular proteome maintenance, leading to significant impacts on cellular phenotypes. This study deepens our understanding of translation in an in vivo context.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Christopher K. Skalnik, Sean Cheah, Mica H. Yang, Mattheus M. Wolff, Ryan Spangler, Lee W. Talman, Jerry Morrison, Shayn Peirce, Eran Agmon, Markus Covert
Summary: This study used a detailed mathematical model of individual Escherichia coli cells to investigate their response to different antibiotics, taking into account cell-to-cell variations in gene and protein expression. The research is important for understanding the development of antibiotic resistance and developing new mechanistic models.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Katie Bodner, Arin L. Melkonian, Markus W. Covert
Article
Multidisciplinary Sciences
Derek N. Macklin, Travis A. Ahn-Horst, Heejo Choi, Nicholas A. Ruggero, Javier Carrera, John C. Mason, Gwanggyu Sun, Eran Agmon, Mialy M. DeFelice, Inbal Maayan, Keara Lane, Ryan K. Spangler, Taryn E. Gillies, Morgan L. Paull, Sajia Akhter, Samuel R. Bray, Daniel S. Weaver, Ingrid M. Keseler, Peter D. Karp, Jerry H. Morrison, Markus W. Covert
