Article
Multidisciplinary Sciences
Mohammad Mazharul Islam, Andrea Goertzen, Pankaj K. Singh, Rajib Saha
Summary: In this study, a highly curated PDAC genome-scale metabolic model was reconstructed and used to explore the unique metabolic traits of PDAC. New therapeutic targets were identified, providing a better understanding of the metabolic vulnerabilities in PDAC and potential guidance for the development of novel therapeutic strategies.
Article
Microbiology
Ulf W. Liebal, Lena Ullmann, Christian Lieven, Philipp Kohl, Daniel Wibberg, Thiemo Zambanini, Lars M. Blank
Summary: The first genome-scale metabolic model of Ustilago maydis, iUma22, was reported for the simulation of metabolic activities and biotechnological research. The model, reconstructed from sequencing and annotation, allows for studies of metabolic adaptations to different environmental niches and highlights missing metabolic pathways in different strains of U. maydis.
Article
Oncology
Seungyoon Nam, Yongmin Lee
Summary: Gastric cancer is a deadly cancer with different histological subtypes. This study used transcriptome analysis to identify differential metabolic pathways between the diffuse and intestinal subtypes of gastric cancer, including cholesterol homeostasis, xenobiotic metabolism, fatty acid metabolism, the MTORC1 pathway, and glycolysis.
Article
Biology
Jonathan M. Monk
Summary: This article analyzes the metabolic diversity and speciation of Escherichia through the construction of genome-scale models. The results indicate that strain-specific metabolic capabilities correspond to different species and nutrient niches. This work marks a first step towards a curated reconstruction of pan-Escherichia metabolism.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Sara Benito-Vaquerizo, Ivette Parera Olm, Thijs de Vroet, Peter J. Schaap, Diana Z. Sousa, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Summary: This study used computational and experimental methods to study the metabolism of Anaerotignum neopropionicum, a propionate-producing bacterium. The construction of the genome-scale metabolic model iANEO_SB607 provided insight into the acrylate pathway for fermentation of ethanol into propionate, shedding light on the energetic aspects of the cell.
MICROBIAL CELL FACTORIES
(2022)
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
Biochemistry & Molecular Biology
Jyotshana Gautam, Zhaohui Xu
Summary: By integrating mathematical modeling and experimental results, a metabolic model of Thermotoga sp. strain RQ7 was constructed to quantitatively simulate its metabolism at the genome scale. The model serves as a useful tool for designing growth media, identifying metabolic engineering strategies, and exploring the physiological potentials of this biotechnologically significant organism.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Fidias D. Gonzalez Camargo, Mary Santamaria-Torres, Monica P. Cala, Marcela Guevara-Suarez, Silvia Restrepo Restrepo, Andrea Sanchez-Camargo, Miguel Fernandez-Nino, Maria Corujo, Ada Carolina Gallo Molina, Javier Cifuentes, Julian A. Serna, Juan C. Cruz, Carolina Munoz-Camargo, Andres F. Gonzalez Barrios
Summary: Colombia has faced complex social problems due to illicit crops, but efforts have been made to regulate these crops, particularly Cannabis sativa, leading to advancements in medical cannabis, crop improvement, and exploration of alternative uses. A genome-scale metabolic reconstruction of C. sativa was described and contextualized using metabolic data obtained from plants grown in Colombia. The reconstruction revealed pathways related to fatty acid biosynthesis, steroids, amino acids, and various metabolisms. Key metabolites with anticancer properties were identified and their potential applications discussed. Cytotoxicity assays demonstrated high anticancer activity against certain types of cancer cells while having negligible impact on healthy human skin cells.
Article
Biotechnology & Applied Microbiology
Rafaela Zandonade Ventorim, Mauricio Alexander de Moura Ferreira, Eduardo Luis Menezes de Almeida, Eduard J. Kerkhoven, Wendel Batista da Silveira
Summary: This study presents the first genome-scale metabolic reconstruction of P. laurentii, an oleaginous yeast. The reconstruction provides insights into the metabolic capabilities of P. laurentii and its potential as a single cell oil platform to meet energy demand.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biology
Abhijit Paul, Salman Azhar, Phonindra Nath Das, Nandadulal Bairagi, Samrat Chatterjee
Summary: This study identifies factors contributing to the impaired metabolism-secretion coupling in pancreatic beta-cells in diabetes, including reduced mitochondrial fatty acid oxidation and oxidative phosphorylation, increased reactive oxygen species generation, attenuated antioxidant defense systems, and altered plasma metabolites associated with cardiovascular disease.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Yufeng Guo, Liqiu Su, Qi Liu, Yan Zhu, Zongjie Dai, Qinhong Wang
Summary: Yarrowia lipolytica is a versatile chassis cell used in biotechnological applications, and this study developed a high-quality genome-scale metabolic model for this cell, providing insights into its metabolic mechanism and guiding metabolic engineering.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(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.
Article
Biotechnology & Applied Microbiology
Vivienne Mol, Martyn Bennett, Benjamin J. Sanchez, Beata K. Lisowska, Markus J. Herrgard, Alex Toftgaard Nielsen, David J. Leak, Nikolaus Sonnenschein
Summary: This study presents p-thermo, the most comprehensive genome-scale model to date of Parageobacillus thermoglucosidasius NCIMB 11955, which accurately predicts the metabolism of this bacteria and resolves an uncharacterized bottleneck in anaerobic metabolism.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Subasree Sridhar, Prerna Bhalla, Justin Kullu, Sriya Veerapaneni, Swagatika Sahoo, Nirav Bhatt, G. K. Suraishkumar
Summary: Reactive species play important roles in many diseases, but are often not adequately modeled in current genome-scale metabolic models. By developing a scalable RS reactions module, researchers were able to integrate RS reactions into human metabolic models and highlight dysregulations in important cancer pathways, suggesting varying susceptibility to ferroptosis-targeting treatments in different cancers.
METABOLIC ENGINEERING
(2023)
Review
Microbiology
Almut Heinken, Arianna Basile, Johannes Hertel, Cyrille Thinnes, Ines Thiele
Summary: Microbial community modeling through COBRA provides a complementary approach to meta-omics analyses, linking microbial composition and function changes to disease etiology. It helps stratify patients and controls, identify host pathways affected by the microbiome, and propose novel interventions for diseases.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021
(2021)
Article
Engineering, Environmental
Nerea Uri-Carreno, Per H. Nielsen, Krist V. Gernaey, Qian Wang, Ulla Gro Nielsen, Marta Nierychlo, Susan H. Hansen, Lisette Thomsen, Xavier Flores-Alsina
Summary: Membrane-Aerated Biofilm Reactors (MABRs) are an effective alternative for wastewater treatment plants (WWTP) with enhanced nitrogen removal capacity and reduced energy consumption. This study demonstrates the impact of oxidation-reduction potential (ORP) on the performance of MABRs, showing that low ORP conditions can hinder nitrification. By increasing ORP and replacing/cleaning membranes, nitrification rates and the abundance of nitrifying organisms were significantly improved. The study also suggests that low ORP conditions promote the reduction of iron and sulfur compounds, leading to deposition in the biofilm and inhibiting nitrifiers growth.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Rebecca M. Lennen, Hyun Gyu Lim, Kristian Jensen, Elsayed T. Mohammed, Patrick V. Phaneuf, Myung Hyun Noh, Sailesh Malla, Rosa A. Borner, Ksenia Chekina, Emre Ozdemir, Ida Bonde, Anna Koza, Jerome Maury, Lasse E. Pedersen, Lars Y. Schoning, Nikolaus Sonnenschein, Bernhard O. Palsson, Alex T. Nielsen, Morten O. A. Sommer, Markus J. Herrgard, Adam M. Feist
Summary: This study used an automated platform to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals and uncovered the tolerance mechanisms. The results showed that cells are tolerized through frequent mutation of membrane transporters, cell wall-associated proteins, transcription and translation machineries, and stress signaling proteins. Osmotic stress plays a significant role in tolerance, and pre-tolerized starting isolates can greatly enhance the subsequent production of chemicals.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Dalimil Bujdos, Barbora Popelarova, Daniel C. Volke, Pablo I. Nikel, Nikolaus Sonnenschein, Pavel Dvorak
Summary: This study investigates the basis for the co-utilization of sugars in Pseudomonas putida KT2440 bacteria and proposes a novel genetic engineering strategy to enhance the growth and production of valuable compounds from glucose and cellobiose.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Gisela Nadal-Rey, John M. Kavanagh, Benny Cassells, Sjef Cornelissen, David F. Fletcher, Krist V. Gernaey, Dale D. McClure
Summary: This study used the particle lifeline approach to quantify the effect of reactor design on industrial organisms. The results showed that cells in the stirred tank reactor experienced longer fluctuations of starvation and overflow metabolism compared to those in the bubble column, due to differences in mixing between the two designs. These findings are important for optimizing large-scale reactor designs and developing scale down systems.
BIOCHEMICAL ENGINEERING JOURNAL
(2023)
Article
Engineering, Chemical
Martin Lyregaard, Sten Bay Jorgensen, Jens Abildskov
Summary: Linear tray models based on liquid phase plug flow are developed for absorption and desorption in separation columns. The models focus on point efficiency and incorporate the Lewis enhancement effects. They can evaluate stationary profiles and tray efficiencies of systems with arbitrary numbers of trays and parallel streams.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Engineering, Environmental
Nikolaus I. Vollmer, Carina L. Gargalo, Krist V. Gernaey, Stig I. Olsen, Guerkan Sin
Summary: This study conducted a detailed life cycle assessment of an integrated xylitol biorefinery that utilizes wheat straw as feedstock. Through optimization and techno-economic analysis, the environmental impacts of the biorefinery were evaluated and compared to the current chemical production processes of xylitol. The results showed lower impacts compared to standard chemical production but slightly higher impacts compared to a proprietary production process.
INTERNATIONAL JOURNAL OF LIFE CYCLE ASSESSMENT
(2023)
Article
Biochemistry & Molecular Biology
Paul Cachera, Helen Olsson, Hilde Coumou, Mads L. Jensen, Benjamin J. Sanchez, Tomas Strucko, Marcel van den Broek, Jean-Marc Daran, Michael K. Jensen, Nikolaus Sonnenschein, Michael Lisby, Uffe H. Mortensen
Summary: CRI-SPA allows simple and rapid transfer of chromosomal genetic features between different strains of Saccharomyces cerevisiae. It is highly efficient and reproducible, and even allows marker-free transfer of genetic features. The simplicity, speed, and reliability of CRI-SPA make it a versatile tool for studying biological processes at a systems level.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Engineering, Environmental
Sebastian O. N. Topalian, Pedram Ramin, Kasper Kjellberg, Christian Kazadi Mbamba, Damien J. Batstone, Krist V. Gernaey, Xavier Flores-Alsina
Summary: In this study, a dynamic polymer dosing strategy is developed for an industrial centrifuge system that receives highly variable rates and quality of feed solids from a wastewater treatment plant. The strategy includes data extraction, data wrangling, model development, and model analysis, using partial least squares and random forest models to predict polymer dosages. The approach has the potential to save operators a significant amount of time and improve efficiency.
JOURNAL OF WATER PROCESS ENGINEERING
(2023)
Article
Education, Scientific Disciplines
Fiammetta Caccavale, Carina L. Gargalo, Krist V. Gernaey, Ulrich Kruhne
Summary: In times of educational disruption, significant advances have been made in adopting digitalization strategies. It is important for chemical engineers to be adequately educated to face the challenges of Industry 4.0 and acquire new skills. This study establishes a pedagogical framework to teach Python to chemical engineers, with courses covering topics such as chemical reaction engineering and machine learning. The students found the course to be useful and achieved practical problem-solving using Python.
EDUCATION FOR CHEMICAL ENGINEERS
(2023)
Article
Education, Scientific Disciplines
Isuru A. Udugama, Martin Atkins, Christoph Bayer, James Carson, Duygu Dikicioglu, Krist Gernaey, Jarka Glassey, Matthew Taylor, Brent R. Young
Summary: Educators in chemical engineering have a history of using digital tools for solving engineering problems, but it can be challenging to determine which tool is best for teaching specific concepts. A survey of department heads and committee members in IChemE institutions found that Microsoft Excel (VBA), commercial simulators, and scripting tools were ideal for teaching core subjects, while 3D models and Virtual/Augmented Reality were suited for teaching process design, safety, and sustainability. Non-technical factors such as simplicity, maintenance, and cost also play a role in tool adoption.
EDUCATION FOR CHEMICAL ENGINEERS
(2023)
Proceedings Paper
Automation & Control Systems
Marcus Krogh Nielsen, Jens Dynesen, Jess Dragheim, Ib Christensen, Sten Bay Jorgensen, Jakob Kjobsted Huusom, Krist V. Gernaey, John Bagterp Jorgensen
Summary: In this paper, a novel kinetic growth model for Methylococcus capsulatus (Bath) is presented, which incorporates growth and pH coupling. The model is applied to a laboratory-scale continuous stirred tank reactor for single-cell protein production. The simulation method ensures non-negativity in state and algebraic variables, and introduces linear scaling for numerical stability. A numerical experiment of economic optimal control for single-cell protein production is conducted, demonstrating non-trivial input profiles for biomass growth and pH tracking.
2023 EUROPEAN CONTROL CONFERENCE, ECC
(2023)
Article
Chemistry, Analytical
Isabella Jul-Jorgensen, Krist V. Gernaey, Christian A. Hundahl
Summary: Cleaning Validation is a critical process in pharmaceutical manufacturing, ensuring that cross-contamination levels remain within acceptable limits. The recent development of handheld Fourier-Transform IR (FTIR) spectroscopy provides a feasible solution for real-time release in pharmaceutical manufacturing plants. This paper addresses the challenges of model development for multi-product plants without complete traceability, utilizing a partial least squares discriminant analysis model based on total organic carbon (TOC) measurements to determine cleanliness. The model is tested on artificial samples printed with a chemical printer for multiple products, incorporating different surface roughness spectra, and evaluated based on sensitivity, specificity, and class error.
Review
Environmental Sciences
Elham Ramin, Lourenco Faria, Carina L. Gargalo, Pedram Ramin, Xavier Flores-Alsina, Maj M. Andersen, Krist V. Gernaey
Summary: This study presents the first global review of water innovation practices in industrial symbiosis cases, proposing six categories of practices and highlighting regional variations and knowledge gaps, emphasizing the need for further research.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2024)
Article
Computer Science, Interdisciplinary Applications
Carina L. Gargalo, Haoshui Yu, Nikolaus Vollmer, Ahmad Arabkoohsar, Krist Gernaey, Guerkan Sin
Summary: With the increasing concern for climate change, renewable and sustainable energy production has attracted considerable attention. Life cycle assessment (LCA) is an effective tool for comparing environmental impacts. However, there are differences in the choice of LCA methods, detail sharing, and sensitivity analysis among different studies, making it difficult to compare results.
COMPUTERS & CHEMICAL ENGINEERING
(2024)
Article
Engineering, Chemical
Jesper Frandsen, Jakob K. Huusom, Krist V. Gernaey, Jens Abildskov
Summary: This paper presents a method for the design and verification of isocratic and gradient simulated moving bed (SMB) chromatography based on the triangle theory. The method is applicable to a wide range of isotherms and multicomponent systems, and explores the influence of modifier concentrations on gradient SMB performance.