scholarly journals Finding MEMo: Minimum sets of elementary flux modes

2019 ◽  
Author(s):  
Annika Röhl ◽  
Alexander Bockmayr
Keyword(s):  
Steady State ◽  
Metabolic Network ◽  
Metabolic Networks ◽  
Point Of View ◽  
Computational Systems Biology ◽  
Huge Number ◽  
Elementary Flux Modes ◽  
Practical Point ◽  
Generating Sets ◽  
Computational Systems

AbstractMetabolic network reconstructions are widely used in computational systems biology for in silico studies of cellular metabolism. A common approach to analyse these models are elementary flux modes (EFMs), which correspond to minimal functional units in the network. Already for medium-sized networks, it is often impossible to compute the set of all EFMs, due to their huge number. From a practical point of view, this might also not be necessary because a subset of EFMs may already be sufficient to answer relevant biological questions. In this article, we study MEMos or minimum sets of EFMs that can generate all possible steady-state behaviours of a metabolic network. The number of EFMs in a MEMo may be by several orders of magnitude smaller than the total number of EFMs. Using MEMos, we can compute generating sets of EFMs in metabolic networks where the whole set of EFMs is too large to be enumerated.

scholarly journals Phosphates as Energy Sources to Expand Metabolic Networks

Life ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 43 ◽  
Author(s):  
Tian Tian ◽  
Xin-Yi Chu ◽  
Yi Yang ◽  
Xuan Zhang ◽  
Ye-Mao Liu ◽  
...  
Keyword(s):  
Metabolic Network ◽  
Metabolic Networks ◽  
Energy Sources ◽  
Coding System ◽  
Computational Systems Biology ◽  
Origin And Evolution ◽  
Network Expansion ◽  
Evolution Of Metabolism ◽  
The Origin Of Life ◽  
Computational Systems

Phosphates are essential for modern metabolisms. A recent study reported a phosphate-free metabolic network and suggested that thioesters, rather than phosphates, could alleviate thermodynamic bottlenecks of network expansion. As a result, it was considered that a phosphorus-independent metabolism could exist before the phosphate-based genetic coding system. To explore the origin of phosphorus-dependent metabolism, the present study constructs a protometabolic network that contains phosphates prebiotically available using computational systems biology approaches. It is found that some primitive phosphorylated intermediates could greatly alleviate thermodynamic bottlenecks of network expansion. Moreover, the phosphorus-dependent metabolic network exhibits several ancient features. Taken together, it is concluded that phosphates played a role as important as that of thioesters during the origin and evolution of metabolism. Both phosphorus and sulfur are speculated to be critical to the origin of life.

Integration and virtual reality exploration of biomedical data with CmPI and VANTED

2017 ◽  
Vol 59 (4) ◽  
Author(s):  
Björn Sommer ◽  
Falk Schreiber
Keyword(s):  
Virtual Reality ◽  
Biological Networks ◽  
Metabolic Networks ◽  
Research Field ◽  
Biomedical Data ◽  
Computational Systems Biology ◽  
Metabolic Processes ◽  
Spatially Distributed ◽  
A Cell ◽  
Computational Systems

AbstractModelling and analysis of metabolic processes is an established research field in Computational Systems Biology and Medicine. There are many different approaches for modelling as well as for visualization, but often these methods ignore the subcellular localization of proteins, enzymes and transporters involved in the metabolic processes.Over the recent years, we developed two tools: CELLmicrocosmos 4 PathwayIntegration (CmPI) and VANTED. CmPI is used to analyse, visualize and explore potential subcellular localizations in a cell environment. CmPI provides import capabilities for metabolic pathways and simple visualization of directed networks showing the enzyme-compound relationships inside this environment in 2D as well as 3D. VANTED allows to analyse and visualize biological networks, to integrate data into these networks and simulate their dynamics.Here, we will discuss future perspectives of these approaches and how to extend the capabilities of CmPI's localization method to provide a) complex modelling, visualization and exploration of metabolic networks in combination with -omics data, and b) immersive analytics of the spatially distributed networks using different Virtual Reality-based technologies. We discuss the prototypic integration of CmPI with VANTED and the large display visualization framework Omegalib in combination with a semi-immersive monitor zSpace

scholarly journals Community standards to facilitate development and address challenges in metabolic modeling

2019 ◽  
Author(s):  
Maureen A. Carey ◽  
Andreas Dräger ◽  
Jason A. Papin ◽  
James T. Yurkovich
Keyword(s):  
Systems Biology ◽  
Metabolic Network ◽  
Gold Standard ◽  
Metabolic Modeling ◽  
Computational Systems Biology ◽  
High Quality ◽  
Metabolic Network Reconstruction ◽  
Computational Systems ◽  
Content Annotation

ABSTRACTStandardization of data and models facilitates effective communication, especially in computational systems biology. However, both the development and consistent use of standards and resources remains challenging. As a result, the amount, quality, and format of the information contained within systems biology models are not consistent and therefore present challenges for widespread use and communication. Here, we focused on these standards, resources, and challenges in the field of metabolic modeling by conducting a community-wide survey. We used this feedback to (1) outline the major challenges that our field faces and to propose solutions and (2) identify a set of features that defines what a “gold standard” metabolic network reconstruction looks like concerning content, annotation, and simulation capabilities. We anticipate that this community-driven outline will help the long-term development of community-inspired resources as well as produce high-quality, accessible models. More broadly, we hope that these efforts can serve as blueprints for other computational modeling communities to ensure continued development of both practical, usable standards and reproducible, knowledge-rich models.

Tertiary Nitrification Pilot Plants on Parisian Waste Water

1990 ◽  
Vol 22 (1-2) ◽  
pp. 347-352 ◽  
Author(s):  
C. Paffoni ◽  
B. Védry ◽  
M. Gousailles
Keyword(s):  
Waste Water ◽  
Metropolitan Area ◽  
Fixed Bed ◽  
Point Of View ◽  
Operating Conditions ◽  
Research Center ◽  
Daily Output ◽  
Practical Point ◽  
Fixed Bed Reactors

The Paris Metropolitan area, which contains over eight million inhabitants, has a daily output of about 3 M cu.meters of wastewater, the purification of which is achieved by SIAAP (Paris Metropolitan Area Sewage Service) in both Achères and Valenton plants. The carbon pollution is eliminated from over 2 M cu.m/day at Achères. In order to improve the quality of output water, its tertiary nitrification in fixed-bed reactors has been contemplated. The BIOFOR (Degremont) and BIOCARBONE (OTV) processes could be tested in semi-industrial pilot reactors at the CRITER research center of SIAAP. At a reference temperature of 13°C, the removed load is approximately 0.5 kg N NH4/m3.day. From a practical point of view, it may be asserted that in such operating conditions as should be at the Achères plant, one cubic meter of filter can handle the tertiary nitification of one cubic meter of purified water per hour at an effluent temperature of 13°C.

Differential Drug Target Selection in Blood Coagulation: What can we get from Computational Systems Biology Models?

2020 ◽  
Vol 26 (18) ◽  
pp. 2109-2115 ◽  
Author(s):  
Mikhail A. Panteleev ◽  
Anna A. Andreeva ◽  
Alexey I. Lobanov
Keyword(s):  
Blood Coagulation ◽  
Biological Network ◽  
Target Selection ◽  
Anticoagulation Therapy ◽  
Differential Regulation ◽  
Coagulation Cascade ◽  
Computational Systems Biology ◽  
Analysis Strategies ◽  
Optimal Target ◽  
Computational Systems

Discovery and selection of the potential targets are some of the important issues in pharmacology. Even when all the reactions and the proteins in a biological network are known, how does one choose the optimal target? Here, we review and discuss the application of the computational methods to address this problem using the blood coagulation cascade as an example. The problem of correct antithrombotic targeting is critical for this system because, although several anticoagulants are currently available, all of them are associated with bleeding risks. The advantages and the drawbacks of different sensitivity analysis strategies are considered, focusing on the approaches that emphasize: 1) the functional modularity and the multi-tasking nature of this biological network; and 2) the need to normalize hemostasis during the anticoagulation therapy rather than completely suppress it. To illustrate this effect, we show the possibility of the differential regulation of lag time and endogenous thrombin potential in the thrombin generation. These methods allow to identify the elements in the blood coagulation cascade that may serve as the targets for the differential regulation of this system.

scholarly journals On the Design of Outdoor Leader-Follower UAV-Formation Controllers from a Practical Point of View

IEEE Access ◽  
2021 ◽  
pp. 1-1
Author(s):  
Lucas Vago Santana ◽  
Alexandre Santos Brandao ◽  
Mario Sarcinelli-Filho
Keyword(s):  
Point Of View ◽  
Practical Point

scholarly journals Metabolic Reprogramming of Fibroblasts as Therapeutic Target in Rheumatoid Arthritis and Cancer: Deciphering Key Mechanisms Using Computational Systems Biology Approaches

Cancers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 35
Author(s):  
Sahar Aghakhani ◽  
Naouel Zerrouk ◽  
Anna Niarakis
Keyword(s):  
Rheumatoid Arthritis ◽  
Extracellular Matrix ◽  
Systems Biology ◽  
Healing Process ◽  
Metabolic Reprogramming ◽  
Critical Event ◽  
Wound Healing Process ◽  
Computational Systems Biology ◽  
Structural Framework ◽  
Computational Systems

Fibroblasts, the most abundant cells in the connective tissue, are key modulators of the extracellular matrix (ECM) composition. These spindle-shaped cells are capable of synthesizing various extracellular matrix proteins and collagen. They also provide the structural framework (stroma) for tissues and play a pivotal role in the wound healing process. While they are maintainers of the ECM turnover and regulate several physiological processes, they can also undergo transformations responding to certain stimuli and display aggressive phenotypes that contribute to disease pathophysiology. In this review, we focus on the metabolic pathways of glucose and highlight metabolic reprogramming as a critical event that contributes to the transition of fibroblasts from quiescent to activated and aggressive cells. We also cover the emerging evidence that allows us to draw parallels between fibroblasts in autoimmune disorders and more specifically in rheumatoid arthritis and cancer. We link the metabolic changes of fibroblasts to the toxic environment created by the disease condition and discuss how targeting of metabolic reprogramming could be employed in the treatment of such diseases. Lastly, we discuss Systems Biology approaches, and more specifically, computational modeling, as a means to elucidate pathogenetic mechanisms and accelerate the identification of novel therapeutic targets.

scholarly journals The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Metabolites ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Julia Koblitz ◽  
Sabine Will ◽  
S. Riemer ◽  
Thomas Ulas ◽  
Meina Neumann-Schaal ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Point Of View ◽  
Use Cases ◽  
Mathematical Methods ◽  
State Behavior ◽  
Web Based ◽  
Research Fields ◽  
Balance Analysis ◽  
Metabolic Models ◽  
User Friendly

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (Metano Modeling Toolbox), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.

Systematic Investigation of Mouse Models of Parkinson’s Disease by Transcriptome Mapping on a Brain-Specific Genome-Scale Metabolic Network

2021 ◽  
Author(s):  
Ecehan Abdik ◽  
Tunahan Cakir
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Metabolic Network ◽  
Mouse Models ◽  
Mus Musculus ◽  
Metabolic Networks ◽  
Systematic Investigation ◽  
Omics Data ◽  
Metabolic Alterations ◽  
Genome Scale

Genome-scale metabolic networks enable systemic investigation of metabolic alterations caused by diseases by providing interpretation of omics data. Although Mus musculus (mouse) is one of the most commonly used model...

Sign in / Sign up

Export Citation Format

Share Document