Mathematical models of the cellular metabolism have become an essential tool for the optimization of biotechnological processes. They help to obtain a systemic understanding of the metabolic processes in the used microorganisms and to find suitable genetic modifications maximizing the production performance. In particular, methods of stoichiometric and constraint-based modeling are frequently used in the context of metabolic and bioprocess engineering. Since metabolic networks can be complex and comprise hundreds or even thousands of metabolites and reactions, dedicated software tools are required for an efficient analysis. One such software suite is CellNetAnalyzer, a MATLAB package providing, among others, various methods for analyzing stoichiometric and constraint-based metabolic models. CellNetAnalyzer can be used via command-line based operations or via a graphical user interface with embedded network visualizations. Herein we will present key functionalities of CellNetAnalyzer for applications in biotechnology and metabolic engineering and thereby review constraint-based modeling techniques such as metabolic flux analysis, flux balance analysis, flux variability analysis, metabolic pathway analysis (elementary flux modes) and methods for computational strain design.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.jbiotec.2017.05.001 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Potential roles of mitochondrial carrier proteins in plant responses to abiotic stress.
J Exp Bot
January 2025
National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, Minas Gerais, Brazil.
The transport of metabolites across the inner mitochondrial membrane (IMM) is crucial for maintaining energy balance and efficient distribution of metabolic intermediates between cellular compartments. Under abiotic stress, mitochondrial function becomes particularly critical, activating complex signaling pathways essential for plant stress responses. These pathways modulate stress-responsive gene expression, influencing key physiological processes such as cell respiration and senescence, helping plants adapt to stress.
View Article and Find Full Text PDFProtocol for investigating astrocytic mitochondria in neurons of adult mice using two-photon microscopy.
STAR Protoc
January 2025
Department of Neurosurgery, the First Affiliated Hospital of Jinan University, Guangzhou, China; Department of Neurosurgery, the Affiliated Hospital, Southwest Medical University, Luzhou 646000, China; Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital, Southwest Medical University, Luzhou 646000, China. Electronic address:
Under pathological conditions, astrocytes can transfer mitochondria to neurons, where they exert neuroprotective effects. In this context, we present a protocol for capturing astrocytic mitochondria in neurons of adult mice using a two-photon microscope. We describe an approach for constructing a mouse model with combined labeling of astrocytic mitochondria and neurons.
View Article and Find Full Text PDFShould adrenal incidentaloma patients be evaluated for muscle mass, function, and quality? A cross-sectional study.
Endocrine
January 2025
Department of Endocrinology and Metabolic Diseases, Manisa Celal Bayar University Hospital, Manisa, Turkey.
Purpose: Our study evaluated skeletal muscle mass, function and quality among mild autonomous cortisol secretion (MACS) patients and non-functioning adrenal incidentaloma (NFAI) patients in comparison with the control group without adrenal mass.
Methods: 63 NFAI (49 female, 14 male) and 31 MACS (24 female, 7 male) patients were included in the study. As the control group, 44 patients (31 women, 13 men) who were known to have no radiological adrenal pathology on computed tomography or magnetic resonance imaging performed for other reasons were selected.
[Body composition assessment methods in clinical practice].
Orv Hetil
January 2025
1 Semmelweis Egyetem, Általános Orvostudományi Kar, Belgyógyászati és Onkológiai Klinika Budapest, Korányi S. u. 2/A, 1083 Magyarország.
18F-Sodium Fluoride PET/CT as a Tool to Assess Enthesopathies in X-Linked Hypophosphatemia.
Calcif Tissue Int
January 2025
Endocrinology Department, School of Medicine, Pontificia Universidad Católica de Chile, Av. Diagonal Paraguay 262, Cuarto Piso, Santiago, Chile.
X-linked hypophosphatemia (XLH) is a rare metabolic disorder characterized by elevated FGF23 and chronic hypophosphatemia, leading to impaired skeletal mineralization and enthesopathies that are associated with pain, stiffness, and diminished quality of life. The natural history of enthesopathies in XLH remains poorly defined, partly due to absence of a sensitive quantitative tool for assessment and monitoring. This study investigates the utility of 18F-NaF PET/CT scans in characterizing enthesopathies in XLH subjects.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!