Results 91 to 100 of about 450,408 (297)

Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws [PDF]

, 2014
In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions.
Cercignani C., De Donder T., Hill T. L., Massimiliano Esposito, Matteo Polettini, Nicolis G., Prigogine I., Schrodinger E., Tolman R. C., Voet D.   +9 more
core   +2 more sources

Interplay between circadian and other transcription factors—Implications for cycling transcriptome reprogramming

FEBS Letters, EarlyView.
This perspective highlights emerging insights into how the circadian transcription factor CLOCK:BMAL1 regulates chromatin architecture, cooperates with other transcription factors, and coordinates enhancer dynamics. We propose an updated framework for how circadian transcription factors operate within dynamic and multifactorial chromatin landscapes ...
Xinyu Y. Nie, Jerome S. Menet
wiley   +1 more source

GEMsembler: consensus model assembly and structural comparison of genome-scale metabolic models across tools improve functional performance

mSystems
Genome-scale metabolic models (GEMs) are widely used in systems biology to investigate metabolism and predict perturbation responses. Automatic GEM reconstruction tools generate GEMs with different properties and predictive capacities for the same ...
Elena K. Matveishina, Bartosz J. Bartmanski, Sara Benito-Vaquerizo, Maria Zimmermann-Kogadeeva   +3 more
doaj   +1 more source

Ensemble Modeling of Metabolic Networks [PDF]

Biophysical Journal, 2008
Complete modeling of metabolic networks is desirable, but it is difficult to accomplish because of the lack of kinetics. As a step toward this goal, we have developed an approach to build an ensemble of dynamic models that reach the same steady state.
Tran, Linh M., Rizk, Matthew L., Liao, James C.   +2 more
openaire   +2 more sources

Real‐time assay of ribonucleotide reductase activity with a fluorescent RNA aptamer

FEBS Letters, EarlyView.
Ribonucleotide reductases (RNR) synthesize DNA building blocks de novo, making them crucial in DNA replication and drug targeting. FLARE introduces the first single‐tube real‐time coupled RNR assay, which enables isothermal tracking of RNR activity at nanomolar enzyme levels and allows the reconstruction of allosteric regulatory patterns and rapid ...
Jacopo De Capitani, Noemi E. Nwosu, Viktoria Gocke, Müge Kasanmascheff, Hannes Mutschler   +4 more
wiley   +1 more source

Systems biology in animal sciences [PDF]

, 2011
Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract ...
Bannink, A., Pas, M.F.W., te, Smits, M.A., Veerkamp, R.F., Woelders, H.   +4 more
core   +3 more sources

Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation

FEBS Letters, EarlyView.
Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe, Tanmay Kumar Mohanty, Rashna Bhandari, Dorothea Fiedler   +3 more
wiley   +1 more source

In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer’s disease

Gut Microbes Reports
The gut microbiome has become increasingly recognized for its role in the pathogenesis of Alzheimer’s disease (AD) and is thought to influence AD pathogenesis via metabolic crosstalk with the host.
Tim Hensen, Shahzad Ahmad, Gabi Kastenmüller, Robert Kraaij, Mohsen Ghanbari, Arfan Ikram, Rima Kaddurah-Daouk, Ines Thiele   +7 more
doaj   +1 more source

The role of histone modifications in transcription regulation upon DNA damage

FEBS Letters, EarlyView.
This review discusses the critical role of histone modifications in regulating gene expression during the DNA damage response (DDR). By modulating chromatin structure and recruiting repair factors, these post‐translational modifications fine‐tune transcriptional programmes to maintain genomic stability.
Angelina Job Kolady, Siyao Wang
wiley   +1 more source

Metabolic remodeling of microorganisms by mobile genetic elements alters mutualistic community composition

mSystems
Mobile genetic elements (MGEs) are ubiquitous in prokaryotes and exert significant influence on microbial communities, in part through their effects on host metabolism. While some MGEs directly alter host metabolism by introducing novel enzymes, all MGEs
Ave T. Bisesi, Ross P. Carlson, Lachlan Cotner, William R. Harcombe   +3 more
doaj   +1 more source