Network regulation in biological metabolic networks and pathways. Medical search. Frequent questions

MicroRNA (miRNA) is a class of non-coding small RNAs, which post-transcriptionally regulate a large number of genes and are now known to be important regulators in a wide variety of biological processes including metabolism. (bvsalud.org)
Such extensive study will help in systematically elucidating the regulatory networks in metabolism of rice, which in turn can be utilised to devise strategies for crop improvement and novel cultivar development. (bvsalud.org)
Moreover, modulation of the proteins involved in cellular metal homeostasis may help in the regulation of metabolism, adaptability to a diverse range of environmental conditions, and biofortification. (frontiersin.org)
Despite decades of investigations into anaerobic microbiome metabolism, our ability to predict the interwoven metabolic networks driving organic matter conversion to bioproducts remains insufficient for bioengineering. (utoronto.ca)
Our main research objectives in this area are 1) quantitative understanding of microbiome metabolism remodeling during different feeding and operational strategies, 2) metabolic regulation in non-model anaerobic microorganisms involved in waste deconstruction and conversion, and 3) elucidating metabolic interactions and fluxes in anaerobic microbiomes. (utoronto.ca)
Created in 1995, the team "Engineering and Evolution of Metabolic Pathways in Prokaryotes" dedicates its fundamental research to i) the exhaustive analysis of bacterial central metabolism in order to improve our knowledge and to identify its regulation mechanisms and ii) the adaptive evolution of bacteria under metabolic constraints. (toulouse-biotechnology-institute.fr)
Based on the knowledge acquired on metabolic networks, the concept of microbial cellular factory is developed: new metabolic pathways are created and metabolism is rationally modified and reoriented, in order to maximize the substrate/product conversion yield for the biological production of synthons for chemistry and/or energy. (toulouse-biotechnology-institute.fr)
Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes. (biomedcentral.com)
With a minimalist model of metabolism, cell growth and transcriptional regulation in a microorganism, we explore how the interaction between environmental conditions and gene regulation set the growth rate of cells in the phase of exponential growth. (lu.se)
A very natural place to study gene detecting and metabolizing lactose, it is known that the overall regulation is in the metabolism of the cell, and then specifically in effect of expressing the lac genes in vain is a drop in the growth rate the regulation of genes that code for enzymes and transporter of as much as 5% [1,6]. (lu.se)

Protein-protein interactions (PPIs) play essential roles in many biological processes. (nature.com)
The construction of gene regulatory networks (GRNs) is vital for understanding the regulation of metabolic pathways, biological processes, and complex traits during plant growth and responses to environmental cues and stresses. (mtu.edu)
Most of the biological processes were associated with cellular processes, biological regulation, metabolic processes, and developmental processes. (bvsalud.org)
Gene ontology functional enrichment analysis revealed twenty eight biological processes and 10 molecular functions associated with cognitive impairment. (ijpsonline.com)
To analyze the brain cell grouping of PQ-infected mice and the biological processes involved in the subpopulation of PD-like changes cells by scRNA-seq, and to provide clues for revealing potential mechanisms of PQ-induced PD-like changes in mouse brains. (jeom.org)
Finally, GO and KEGG analyses were performed on the differential genes of PD-associated cell subsets between the PQ-treated group and the control group, and the biological processes in which these genes may participate were analyzed. (jeom.org)
While microbiome engineering has traditionally relied on selection (e.g. manipulation of environmental variables) to steer biological processes towards a desired function, this approach results in highly complex communities that offer little control over the specific products that can be made. (utoronto.ca)
GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. (biomedcentral.com)
A growing body of evidence shows that lncRNAs play important functional roles in diverse biological processes, such as epigenetic regulation, cell cycle regulation, cellular growth and differentiation, by regulating the level of target genes [ 3 , 4 ]. (biomedcentral.com)
The activation of multiple hormone signaling pathways after both light exclusion and re-exposure treatments was inconsistent with the changes in phenolic accumulation, indicating a limited role of plant hormones in mediating light/darkness-regulated phenolic biosynthesis processes. (biomedcentral.com)
Alterations of these biological processes may not only interfere with critical MEC functions impacting CSF and hence optic nerve homeostasis, but may likely alter SAS structure, thereby further impeding cerebrospinal fluid flow. (biomedcentral.com)
The behavioural and biological responses of a child to the obesogenic environment can be shaped by processes even before birth, placing an even greater number of children on the pathway to becoming obese when faced with an unhealthy diet and low physical activity. (who.int)

The identification of disease-causing genes is the first and most important step toward understanding the biological mechanisms underlying a disease. (bvsalud.org)
To better understand the function of the altered genes, gene ontology and pathway analysis are performed. (bvsalud.org)
Further, regulatory networks were constructed by the DEGs which are also co-expressed and the hub genes were identified. (bvsalud.org)
A genome-scale miRNA-miRNA co-functional network (MFSN) is constructed based on co-regulatory interactions among the miRNAs and common target genes by applying transformational procedures. (bvsalud.org)
The pathways that are probably regulated by the identified plant phytoconstituents were analyzed using Kyoto encyclopedia of genes and genomes. (ijpsonline.com)
Kyoto encyclopedia of genes and genomes pathway identified eight pathways that are directly related to cognitive impairment. (ijpsonline.com)
With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. (biomedcentral.com)
Han Y , He X , Lee S , Mao Y , Liu X , Sun H , Jin M , Kwon T , . Network analysis for the identification of hub genes and related molecules as potential biomarkers associated with the differentiation of bone marrow-derived stem cells into hepatocytes. (aging-us.com)
Cell segmentation was performed according to gene expression characteristics of different cell types, PD-related cell subsets were screened by bioinformatics tools, and gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), gene set enrichment analysis (GSEA), protein interaction network analysis, and transcription factor prediction were performed on their characteristic genes. (jeom.org)
Enriched expression of genes in LRECb was associated with stem cell attributes and identified WNT, TGF-β, and MAPK pathways of self renewal and proliferation. (frontiersin.org)
Genes expressed in LRECe revealed retention of some stem-like properties along with up-regulation of differentiation factors. (frontiersin.org)
Revolutionary advances in systems and synthetic biology are positioned to make these innovations possible, as breakthroughs in metagenomic sequencing, high-resolution mass spectrometry, and genome editing have opened a window into the metabolic and regulatory networks driving microbial community ("microbiome") functions, extending from single genes to whole ecosystems. (utoronto.ca)
Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes. (biomedcentral.com)
Transcriptional regulation of the genes in metabolic pathways is a highly successful strategy, which is virtually universal in microorganisms. (lu.se)
INTRODUCTION broken, which in realistic situations can severly constrain the Transcriptional regulation of effector genes is a highly successful regulatory options. (lu.se)
Here, the function of regulation is quite clear: expressing energy and carbon, that a number around 0.2% would be the right genes at the right time will enable the cell to make the expected, and that the difference is more or less specific to the lac most of the resources within its reach, by maximizing the uptake operon [7]. (lu.se)

PPIs are essential for individual protein functions, forming various cellular pathways, and are also involved in the development of diseases. (nature.com)
The storage and distribution of these minerals in various cellular organelles is strictly regulated to ensure optimal metabolic rates. (frontiersin.org)
Different subcellular compartments are suggested to be linked through complex retrograde signaling networks to regulate cellular metal homeostasis. (frontiersin.org)
Fe readily changes its oxidative state, which allows participation in cellular functions, and its regulation is extremely important to avoid cellular toxicity. (frontiersin.org)
Fe participates in cellular respiration, synthesis, and stabilization of chlorophyll, photosynthetic electron transport, and various other metabolic functions ( Grotz and Guerinot, 2006 ). (frontiersin.org)

The KEGG suggested that PI3K-AKT, Estrogen, FoxO, MAPK, HIF-1 signaling pathway may play a significant role in treating asthma. (researchsquare.com)

We first identified 51 active compounds from SZT and their 81 potential molecular targets by high-throughput computational analysis, from which we identified 4 major pathways including Th17 cell differentiation, metabolic pathways, pathways in cancer, and the PI3K-Akt signaling pathway. (hindawi.com)

Flux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of genome-scale metabolic networks. (biomedcentral.com)
As a consequence, FCA of genome-scale metabolic networks can now be performed in a routine manner. (biomedcentral.com)
We propose F2C2 as a fast tool for the computation of flux coupling in genome-scale metabolic networks. (biomedcentral.com)
We show that FCA can now be quickly performed even for very large genome-scale metabolic networks. (biomedcentral.com)

Citation: Troein C, Ahre´n D, Krogh M, Peterson C (2007) Is Transcriptional Regulation of Metabolic Pathways an Optimal Strategy for Fitness? (lu.se)

Employing transfer learning techniques, this study has also successfully transferred the known knowledge of gene regulation from one species to another, substantially improving performance and manifesting the viability of cross-species learning using deep learning-based approaches. (mtu.edu)
An especially uncharted territory is the integration of statistical and network-based approaches for studying global lipidome changes. (mdpi.com)
Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. (biomedcentral.com)
This is because existing approaches fail to establish quantitative and causal links between feedstock chemistry, process rates and conditions, and in situ activity (i.e. fluxes) of microbiome metabolic networks. (utoronto.ca)
Our lab will focus on the systems-level analysis of metabolic regulation in anaerobic microbiomes and associated anaerobic microorganisms involved in converting wastes into bioproducts, using state-of-the-art metabolomic and metaproteomic approaches coupled to isotope tracing and quantitative metabolic modeling. (utoronto.ca)

Plants have evolved numerous adaptive developmental and metabolic responses to cope with growth under phosphate-limited conditions, and these responses include modifying the root system architecture (RSA), increasing acid phosphatase activity (APA), and the release of low-molecular-weight organic acids [ 20 ]. (biomedcentral.com)

The BioVis aims to educate, inspire, and engage bioinformatics and biology researchers in state-of-the-art visualization research and visualization researchers in problems in biological data visualization. (iscb.org)

The DEGs were further analysed for their gene ontologies (GO), pathway, protein-protein interactions and co-expression. (bvsalud.org)
In this study, we aimed to understand the significance of synergistic miRNA-miRNA interactions in rice by constructing and analysing metabolic networks. (bvsalud.org)
This technique provides not only a systematic representation of both the presence and abundance of biological molecules, but also displays the relationships or interactions between them. (biomedcentral.com)
It is impossible to fully understand biological systems without understanding the 3D structure of their constituting parts and their interactions. (iscb.org)
We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. (researchgate.net)
In addition, it can be used to predict genetic interactions [3] by comparing the sensitivity value of a double gene mutation from the value predicted from single mutations, and reveal the network intervention [4] by applying the state-flip mutation subject to a single gene. (researchgate.net)

To explore the possible dynamic behavior of metabolic networks in cases of lacking or incomplete enzyme-kinetic information, we present a computational approach based on structural kinetic modeling. (mpg.de)
We think that the proposed method represents an important intermediate step on the long way from topological network analysis to detailed kinetic modeling of complex metabolic networks. (mpg.de)

Our main objectives in this area are 1) systematic assembly and analysis of synthetic anaerobic microbiomes to produce valuable chemicals and 2) metabolic engineering of diverse non-model anaerobic microorganisms to optimize flux through microbiome metabolic networks. (utoronto.ca)
A number of studies have explored how regulation of generally, and at least to a first approximation, it is obvious that metabolic pathways affects the growth rate of microorganisms, gene regulation only is useful if the environmental conditions vary both in the steady state and in response to changes in the local with time. (lu.se)

On the one hand, this can help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions is in agreement with the experimental findings. (biomedcentral.com)

The best-performing hybrid models achieved over 95% accuracy on holdout test datasets, surpassing traditional ML and ANN models and also showed good accuracy on lignin biosynthesis pathway analysis. (mtu.edu)

Advances in lipidomics allow identification of hundreds of lipid species from biological samples. (mdpi.com)

We are testing the hypothesis that specific transcription factors form regulatory networks to execute gene expression programs important for SSC fate decisions (self-renewal and differentiation), and ultimately, spermatogenesis. (utsa.edu)

Submissions are encouraged to report on advances in algorithm development and optimization , data structures , data visualization, artificial intelligence/machine learning , text mining , statistical inference, database and ontology development , image analysis , citizen and open science, etc . to analyze all types of biological data. (iscb.org)

Saab Symmetry, by South Africa's Saab Systems Grintek, is a generic analysis tool for determining interoperability between nodes on a tactical network. (wikipedia.org)
Through network analysis of the compound-target pathway, we identified hub molecular targets within these pathways including carbonic anhydrase II (CA2), peroxisome proliferator activated receptor γ (PPAR γ ), retinoid X receptor α (RXRA), and vitamin D receptor (VDR). (hindawi.com)
However, a systems biological analysis of the lipidome, by incorporating pathway information remains challenging, leaving lipidomics behind compared to other omics disciplines. (mdpi.com)
The results of GO analysis showed that the biological function of this subpopulation mainly enriched neurotransmitter transport and regulation. (jeom.org)
The results of GSEA analysis showed that the tyrosine metabolic pathway and the ligand-receptor interaction pathway of neural activity in brain tissues were significantly enriched. (jeom.org)
Constraint-based analysis is based on the application of a series of constraints that govern the operation of a metabolic network at steady state. (biomedcentral.com)
Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress. (biomedcentral.com)
Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation. (who.int)

This includes the stoichiometric and thermodynamic constraints, which limit the range of possible behaviors of the metabolic network, corresponding to different metabolic phenotypes. (biomedcentral.com)
The flux cone contains the full range of achievable behaviors of the metabolic network at steady state. (biomedcentral.com)

Moreover, our approach allows to differentiate quantitatively between metabolic states related to senescence and metabolic collapse of the human erythrocyte. (mpg.de)

We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)
To address this issue, we developed RMut, which is an R package to analyze the Boolean network-based sensitivity by efficiently employing not only many well-known node-based and edgetic mutations but also novel user-defined mutations. (researchgate.net)
RMut can be used to analyze large-scale networks because it is implemented in a parallel algorithm using the OpenCL library. (researchgate.net)

FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state. (biomedcentral.com)

The stoichiometric and thermodynamic constraints not only determine all possible steady-state flux distributions over a network, they also induce coupling relations between the reactions. (biomedcentral.com)

CSF not only provides important cushioning, but is also essential for central nervous system homeostasis, sustaining nutrient supply to neuronal-glial networks, mediating transportation of signaling molecules and removing toxic metabolites [ 1 ]. (biomedcentral.com)
When a second nutrient and its metabolic pathway are introduced, the system must further decide whether and how to activate both pathways. (lu.se)
Even the crudest transcriptional network is shown to substantially increase the fitness of the organism, and this effect persists even when the range of nutrient levels is kept very narrow. (lu.se)
We show that maximal growth is achieved when pathway activation is a more or less steeply graded function of the nutrient concentration. (lu.se)

Mazza A1, Gat-Viks I, Sharan R. Elucidating Influenza Inhibition Pathways via Network Reconstruction. (tau.ac.il)

The construction of the network involves target gene prediction of experimentally verified miRNAs of rice and then appending associated metabolic pathways to the network. (bvsalud.org)
Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (researchgate.net)

Network representation is frequently used to capture the presence of these molecules as well as their relationship. (biomedcentral.com)
What if we produced, by a biological and renewable way, molecules of interest that serve the chemical industry? (toulouse-biotechnology-institute.fr)

The dynamic behavior of metabolic networks is governed by numerous regulatory mechanisms, such as reversible phosphorylation, binding of allosteric effectors or temporal gene expression, by which the activity of the participating enzymes can be adjusted to the functional requirements of the cell. (mpg.de)
And due to the multi-component, multi-target, and multi-pathway of Traditional Chinese medicine, it is difficult to understand the molecular mechanisms by conventional research methods. (researchsquare.com)

Gat-Viks I, Meller R, Kupiec M, Shamir R: Understanding gene sequence variation in the context of transcription regulation in yeast. (tau.ac.il)
Thus, for better understanding these complex biological networks, and to derive their significance and inter-dependency, a systems biology approach enables us to explore and draw vital insights into these molecular network architectures. (bvsalud.org)
In this review, we aim to improve the understanding of challenges in biomedical research and establish a common ground between clinicians and systems biologists to further promote the application of network biology in translational medicine. (biomedcentral.com)

Over the past few decades, in addition to advances in biological treatment research, molecular biology, cell bioengineering, and the stem cell research, stem cell therapy has emerged as an economic and feasible liver disease treatment for the end-stage liver disease [ 3 ], particularly decompensated cirrhosis liver failure and advanced liver cancer, and offers an effective strategy with no limit of supply and demand [ 3 ]. (aging-us.com)
Genetic Regulation of DNA Methylation Yields Novel Discoveries in GWAS of Colorectal Cancer. (who.int)

Recent advances in biological technologies, such as tiling arrays and RNA deep sequencing (RNA-seq), have made it possible to survey the transcriptomes of many organisms to an unprecedented degree [ 6 ]. (biomedcentral.com)

Traditional Chinese Medicine (TCM) has demonstrated significant success in treating complex diseases by regulating multiple pathways working to return dysfunctional organ systems back to normal [ 8 ]. (hindawi.com)

Other studies believe that IDD is closely related to hormone regulation, especially the decrease of estrogen level in menopausal women may lead to the occurrence of IDD [ 8 ]. (hindawi.com)

Nonetheless, our results demonstrate that hybrid models integrating ML and artificial neural network (ANN) techniques significantly outperformed traditional methods in predicting gene regulatory relationships. (mtu.edu)

Therefore, a network pharmacology and molecular docking technology were used to uncover the active compounds and pharmacological mechanism of XQLD on asthma. (researchsquare.com)

Conception d'un consortium synthétique stable pour la conversion de cellulose en n-butanol soutenance prévue fin 2023 Ecole doctorale SEVAB. (toulouse-biotechnology-institute.fr)

From the clinicians' point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world's major diseases. (biomedcentral.com)

Over evolutionary time scales, regulation must provide a fitness benefit that offsets the costs of maintaining the regulatory system. (lu.se)

Lipids play an important role in biological systems and have the potential to serve as biomarkers in medical applications. (mdpi.com)
Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. (biomedcentral.com)
Therefore, the search for early biological markers of IDD can not only better maintain the biological function of the patient's intervertebral disc but also reduce the probability of the possible occurrence of back pain, which has important clinical significance. (hindawi.com)
We hope for two days of important lectures and discussion, but also networking and a good social atmosphere. (lu.se)

Mazza A, Gat-Viks I, Farhan H, Sharan R. A minimum-labeling approach for reconstructing protein networks across multiple conditions. (tau.ac.il)

A PPI network provides crucial information on how biological pathways are structured and coordinated from individual protein functions. (nature.com)

In the past two decades, large-scale PPI networks of a handful of organisms were determined by experimental techniques. (nature.com)
Network representations have been widely used in physics and social science for decades, and are now among the most frequently used tools in systems biology. (biomedcentral.com)

In unicellular organisms like E. coli and yeast, the benefits of between potential cost and benefit, regulation can make the most a well-adapted regulatory system are readily quantified, as the difference to the long-term growth rate if the resource in question fitness of an individual can be estimated by its growth rate in is only available a similarly small fraction of the time. (lu.se)

There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. (researchgate.net)

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. (ntu.edu.sg)

Our findings show that allosteric enzyme regulation significantly enhances the stability of the network and extends its potential dynamic behavior. (mpg.de)

Anatomy7

Organisms17

Diseases1

Chemicals and Drugs20

Analytical, Diagnostic and Therapeutic Techniques and Equipment33

Phenomena and Processes67

Disciplines and Occupations12

Anthropology, Education, Sociology and Social Phenomena2

Technology, Industry, Agriculture4

Humanities1

Information Science32

Health Care12

Metabolism10

Processes12

Genes16

Cellular5

MAPK1

PI3K-Akt1

Genome-scale4

Transcriptional regulation1

Approaches5

Phosphate1

Bioinformatics1

Interactions6

Kinetic2

Microorganisms2

Curation1

Biosynthesis1

Lipid1

Regulatory networks1

Visualization1

Analysis8

Behaviors2

Quantitatively1

Analyze3

Fluxes1

Constraints1

Nutrient4

Reconstruction1

Experimentally2

Molecules2

Mechanisms2

Understanding3

Cancer2

Advances in biological1

Complex1

Hormone1

Predicting1

Pharmacology1

20231

Diseases1

Evolutionary1

Important4

Multiple1

Functions1

Decades2

Yeast1

Investigate1

Nitrogen1

Significantly1