Article
Immunology
Neelakantan Thulasi Devika, Ashok Kumar Jangam, Vinaya Kumar Katneni, Prasanna Kumar Patil, Suganya Nathamuni, Mudagandur Shashi Shekhar
Summary: The study utilized constraint-based genome-scale metabolic modeling approach to screen and identify six candidate bacterial strains with growth enhancement and pathogen suppression capabilities, including three novel strains, for probiotic applications. This is the first study to apply genomic-scale metabolic models for aquaculture purposes and detect bacterial species limiting Vibrio harveyi growth.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Microbiology
Jessica A. Smith, Dawn E. Holmes, Trevor L. Woodard, Yang Li, Xinying Liu, Li-Ying Wang, David Meier, Ingrid A. Schwarz, Derek R. Lovley
Summary: Direct interspecies electron transfer (DIET) is an important process in anaerobic communities, but the interactions between DIET partners are not well understood. Geobacter metallireducens expressed type VI secretion system (T6SS) genes when co-cultured with Geobacter sulfurreducens. Disruption of the T6SS gene hcp eliminated the lag periods required for DIET initiation. The hcp-deficient mutant also showed faster reduction of Fe(III) oxide and established DIET quicker with Methanosarcina barkeri. The findings highlight the complex factors influencing DIET effectiveness.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Marisa R. Ferreira, Tomas M. Fernandes, David L. Turner, Carlos A. Salgueiro
Summary: Electroactive Geobacter bacteria have the ability to perform extracellular electron transfer and produce electric current while interacting with electrodes. This study investigates the structural and functional properties of the periplasmic triheme PpcA-family cytochromes in Geobacter metallireducens, providing important insights into their role in electron transfer efficiency and functionality.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Review
Biochemistry & Molecular Biology
Carolina H. Chung, Da-Wei Lin, Alec Eames, Sriram Chandrasekaran
Summary: Genome-scale metabolic models are powerful for understanding metabolism but lack cellular regulation. Integrative models encompassing six types of regulatory mechanisms have been developed to enhance predictive capabilities, with 22 methods discussed for simulating metabolic regulation. Challenges remain in constructing GEMs with regulation, and next-generation integrative GEMs will be crucial for discovering cell-type and disease-specific metabolic control mechanisms.
Review
Biotechnology & Applied Microbiology
Yu Chen, Feiran Li, Jens Nielsen
Summary: Yeast genome-scale metabolic models have a long history and diverse recent applications, including metabolic flux prediction, cell factory design, and multi-yeast comparative analysis. Integrating proteome constraints into the models can improve performance.
FEMS YEAST RESEARCH
(2022)
Article
Oncology
Helena A. Herrmann, Mate Rusz, Dina Baier, Michael A. Jakupec, Bernhard K. Keppler, Walter Berger, Gunda Koellensperger, Jurgen Zanghellini
Summary: The study reveals the metabolic reprogramming in drug-resistant cells sensitive to ruthenium- and platinum-based drugs. The findings suggest that the metabolic reprogramming in resistant cells is primarily limited to a select number of pathways.
Article
Geosciences, Multidisciplinary
Heewon Jung, Hyun-Seob Song, Christof Meile
Summary: We propose a modeling framework that integrates bio(geo)chemical and physical processes, and incorporates genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions.
GEOSCIENTIFIC MODEL DEVELOPMENT
(2023)
Review
Biochemical Research Methods
Mohammad Karim Khaleghi, Iman Shahidi Pour Savizi, Nathan E. Lewis, Seyed Abbas Shojaosadati
Summary: Recent advances in developing high-performing microbial and mammalian strains have allowed for sustainable production of bio-compounds, biofuels, and biopharmaceuticals. Constraint-based modeling and machine learning can be used independently or in combination to analyze and optimize fermentation parameters, serving as a complementary approach to generate more predictable models.
BIOTECHNOLOGY JOURNAL
(2021)
Review
Oncology
Itziar Frades, Carles Foguet, Marta Cascante, Marcos J. Arauzo-Bravo
Summary: Immune and cancer cells compete for nutrients within the tumor microenvironment, leading to a metabolic battle between these cell populations. Tumor cells reprogram their metabolism for advantages, requiring quantification of metabolic fluxes through genome-scale constraint-based or kinetic modeling. The dynamic interplay of various cell types in the tumor microenvironment shapes the tumor's physiology.
Article
Biochemistry & Molecular Biology
Blas Blazquez, David San Leon, Antonia Rojas, Marta Tortajada, Juan Nogales
Summary: In this study, a high-quality genome-scale model (iBB1018) was constructed for accurate prediction of metabolic capabilities in B. subtilis. The model showed great accuracy in predicting carbon source utilization and identified potential novel carbon sources. Furthermore, the model was used for constructing the panphenome of B. subtilis, revealing the large metabolic versatility of the species and the importance of accessory metabolism at a species level.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jean-Christophe Lachance, Dominick Matteau, Joelle Brodeur, Colton J. Lloyd, Nathan Mih, Zachary A. King, Thomas F. Knight, Adam M. Feist, Jonathan M. Monk, Bernhard O. Palsson, Pierre-Etienne Jacques, Sebastien Rodrigue
Summary: Mesoplasma florum, a fast-growing near-minimal organism, was used as a model to explore rational genome designs and construct the iJL208 metabolic model. Through this work, a rational approach to genome design was established, laying the groundwork for model-driven whole-genome engineering.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Review
Biochemical Research Methods
Elie Desmond-Le Quemener, Roman Moscoviz, Nicolas Bernet, Andrew Marcus
Summary: The study of mathematical modeling of DIET and MIET in anaerobic ecosystems offers new strategies for improving biotechnologies. While the modeling of DIET kinetics is still in its early stages, recent concepts introduced for modeling electroactive biofilms should be further developed. DIET shows potential to increase IET rates compared to H 2 -MIET, but additional characterizations of biological components supporting IET are needed to enhance predictions.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Mohammadreza Yasemi, Mario Jolicoeur
Summary: By using the gDCBM framework, the time-resolved dynamics of CHO cell metabolism can be modeled, which enables the sequential prediction of intracellular fluxes during growth and non-growth phases and transparently reveals the shortcomings in such practice.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Jason L. Vailionis, Weishu Zhao, Ke Zhang, Dmitry A. Rodionov, Gina L. Lipscomb, Tania N. N. Tanwee, Hailey C. O'Quinn, Ryan G. Bing, Robert M. Kelly, Michael W. W. Adams, Ying Zhang
Summary: A genome-scale metabolic model was developed for the growth of Pyrococcus furiosus, an archaeon that ferments carbohydrates and peptides at 100 degrees C. The model investigates the energy balance of P. furiosus and reveals the importance of acetate production and the coupling of ATP synthase and hydrogenase in generating a sodium gradient. The model is used to guide genetic engineering designs for ethanol production and provides valuable insights for bio-based chemical and fuel production.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Zi-Han Liang, Hong Sun, Yang Li, Anyi Hu, Qiang Tang, Han-Qing Yu
Summary: A novel approach is proposed to enhance microbial extracellular electron transfer (EET) by controlling the hydrolyzation of ATP. This approach accelerates carbon substrate consumption, increases biomass accumulation, and expands the intracellular NADH pool, resulting in enhanced EET capability. The method consistently exhibits improved efficiency in the bioconversion of model xenobiotics. This study provides a new perspective and feasible strategy to enhance microbial EET for efficient xenobiotic conversion.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Radhakrishnan Mahadevan, Axel von Kamp, Steffen Klamt
Review
Biochemical Research Methods
Shyam Srinivasan, William R. Cluett, Radhakrishnan Mahadevan
BIOTECHNOLOGY JOURNAL
(2015)
Review
Biochemical Research Methods
Naveen Venayak, Nikolaos Anesiadis, William R. Cluett, Radhakrishnan Mahadevan
CURRENT OPINION IN BIOTECHNOLOGY
(2015)
Article
Cell Biology
M. Ahsanul Islam, Karsten Zengler, Elizabeth A. Edwards, Radhakrishnan Mahadevan, Gregory Stephanopoulos
INTEGRATIVE BIOLOGY
(2015)
Article
Cell Biology
Pratish Gawand, Fatumina Said Abukar, Naveen Venayak, Siavash Partow, Adilson E. Motter, Radhakrishnan Mahadevan
INTEGRATIVE BIOLOGY
(2015)
Article
Biotechnology & Applied Microbiology
Laurence Yang, Shyamsundhar Srinivasan, Radhakrishnan Mahadevan, William R. Cluett
METABOLIC ENGINEERING
(2015)
Article
Biotechnology & Applied Microbiology
Steffen Klamt, Radhakrishnan Mahadevan
METABOLIC ENGINEERING
(2015)
Review
Biochemical Research Methods
Shyam Srinivasan, William R. Cluett, Radhakrishnan Mahadevan
BIOTECHNOLOGY JOURNAL
(2015)
Article
Biochemical Research Methods
Nadeera Jayasinghe, Ashley Franks, Kelly P. Nevin, Radhakrishnan Mahadevan
BIOTECHNOLOGY JOURNAL
(2014)
Article
Medicine, General & Internal
Jessica Butler, Corri Black, Peter Craig, Chris Dibben, Ruth Dundas, Michelle Hilton Boon, Marjorie Johnston, Frank Popham
Editorial Material
Biology
Suzanne L. K. Stewart, Charlotte R. Pennington, Goncalo R. da Silva, Nick Ballou, Jessica Butler, Zoltan Dienes, Caroline Jay, Stephanie Rossit, Anna Samara
Summary: This article emphasizes the importance of improving research integrity and reproducibility, and proposes coordinated changes, promoting a positive research culture, a unified stance on improving research quality, establishing common foundations for open and transparent research practice, and routinizing this practice.
BMC RESEARCH NOTES
(2022)
Article
Multidisciplinary Sciences
Lynn Robertson, Rute Vieira, Jessica Butler, Marjorie Johnston, Simon Sawhney, Corri Black
Summary: This study aimed to identify and describe multimorbidity clusters in a large, unselected hospitalized patient population. Ten clusters of conditions were identified, each containing patients with similar diseases. There were differences in patient characteristics among different clusters, which could help provide more personalized care for specific patient groups.
SCIENTIFIC REPORTS
(2022)
Editorial Material
Biology
Stephen H. Bradley, Nicholas J. DeVito, Kelly E. Lloyd, Patricia Logullo, Jessica E. Butler
Summary: Poor quality medical research has negative consequences such as misleading healthcare professionals and policymakers, undermining trust in science and medicine, and wasting public funds. To address these issues, recommendations include promoting transparency, establishing better incentives, and reducing biases.
BMC RESEARCH NOTES
(2022)
Article
Psychiatry
William P. Ball, Corri Black, Sharon Gordon, Barbala Ostrovska, Shantini Paranjothy, Adelene Rasalam, David Ritchie, Helen Rowlands, Magdalena Rzewuska, Elaine Thompson, Katie Wilde, Jessica E. Butler
Summary: One in eight children in the United Kingdom are estimated to have a mental health condition, but many do not receive support or treatment. The COVID-19 pandemic has negatively impacted mental health and disrupted care. Boys receive double the prescriptions compared to girls, and the most deprived areas have double the prescribing rate. The increase in mental health prescriptions and changes in referrals align with emerging evidence of increasing poor mental health.
Article
Biotechnology & Applied Microbiology
Nicholas D. Gold, Christopher M. Gowen, Francois-Xavier Lussier, Sarat C. Cautha, Radhakrishnan Mahadevan, Vincent J. J. Martin
MICROBIAL CELL FACTORIES
(2015)