Results 91 to 100 of about 508,394 (292)

Comprehensive Review of Models and Methods for Inferences in Bio-Chemical Reaction Networks [PDF]

Frontiers in Genetics, 2019
Key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their non-linear dynamics.
Loskot, P., Atitey, K., Mihaylova, L.
openaire   +7 more sources

pH‐mediated activation of the lysosomal arginine sensor SLC38A9

FEBS Letters, EarlyView.
Cells monitor nutrient levels via the lysosomal transporter SLC38A9 to activate the mechanistic target of rapamycin complex 1 (mTORC1). This study reveals that SLC38A9 function is regulated by pH. We identified histidine 544 as a critical pH sensor that undergoes conformational changes to control amino acid efflux from lysosomes; therefore, it ...
Xuelang Mu, Ampon Sae Her, Tamir Gonen
wiley   +1 more source

Transcriptional network analysis of PTEN‐protein‐deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication

Molecular Oncology, EarlyView.
Combining PTEN protein assessment and transcriptomic profiling of prostate tumors, we uncovered a network enriched in senescence and extracellular matrix (ECM) programs associated with PTEN loss and conserved in a mouse model. We show that PTEN‐deficient cells trigger paracrine remodeling of the surrounding stroma and this information could help ...
Ivana Rondon‐Lorefice, Jose I. Lopez, Aitziber Ugalde‐Olano, Maite Zufiaurre, Ianire Astobiza, Natalia Martin‐Martin, Laura Bozal‐Basterra, Saioa Garcia‐Longarte, Amaia Zabala‐Letona, Sofia Rey, Aida Santos‐Martin, Miguel Unda, Ana Loizaga‐Iriarte, Mariona Graupera, Paolo Nuciforo, Arkaitz Carracedo, Isabel Mendizabal   +16 more
wiley   +1 more source

Construction and analysis of the model of energy metabolism in E. coli. [PDF]

PLoS ONE, 2013
Genome-scale models of metabolism have only been analyzed with the constraint-based modelling philosophy and there have been several genome-scale gene-protein-reaction models. But research on the modelling for energy metabolism of organisms just began in
Zixiang Xu, Xiao Sun, Jibin Sun
doaj   +1 more source

Kinetic Intersections as a Source of Information on Rate Coefficients [PDF]

, 2017
C
Branco Pinto, Daniel, Constales, Denis, Marin, Guy, Yablonsky, Grigoriy   +3 more
core   +1 more source

Potential therapeutic targeting of BKCa channels in glioblastoma treatment

Molecular Oncology, EarlyView.
This review summarizes current insights into the role of BKCa and mitoBKCa channels in glioblastoma biology, their potential classification as oncochannels, and the emerging pharmacological strategies targeting these channels, emphasizing the translational challenges in developing BKCa‐directed therapies for glioblastoma treatment.
Kamila Maliszewska‐Olejniczak, Karolina Pytlak, Sandra Jaworowska, Bogusz Kulawiak, Piotr Bednarczyk   +4 more
wiley   +1 more source

The Nondeterministic Waiting Time Algorithm: A Review

, 2009
We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for ...
A. Funahashi, A. Funahashi, A. V. Hill, Andrei Păun, Bianca Truthe, C. M. Guldberg, C. M. Guldberg, C. V. Rao, C. Zandron, D. A. McQuarrie, D. T. Gillespie, D. T. Gillespie, E. L. Haseltine, E. S. Lander et al., E. W. Montroll, F. Hua, G. Lahav, G. Paun, Giovanni Pighizzini, H. A. Kramers, J. Jack, J. Jack, J. Jack, J. Jack, J. M. G. Vilar, John Jack, Jürgen Dassow, K. Oda, L. M. Adleman, L. Wilhelmy, M. A. Gibson, M. Hucka et al., N. Selliah, P. Waage, R. L. Bar-Or, S. Cheruku   +35 more
core   +2 more sources

Dammarenediol II enhances etoposide‐induced apoptosis by targeting O‐GlcNAc transferase and Akt/GSK3β/mTOR signaling in liver cancer

Molecular Oncology, EarlyView.
Etoposide induces DNA damage, activating p53‐dependent apoptosis via caspase‐3/7, which cleaves PARP1. Dammarenediol II enhances this apoptotic pathway by suppressing O‐GlcNAc transferase activity, further decreasing O‐GlcNAcylation. The reduction in O‐GlcNAc levels boosts p53‐driven apoptosis and influences the Akt/GSK3β/mTOR signaling pathway ...
Jaehoon Lee, Byung‐Cheol Han, Gi‐Bang Koo, Jihye Park, Mijin Kwon, Young Bin Park, Jae‐Mun Choi, Seung‐Ho Lee, Sangho Roh   +8 more
wiley   +1 more source

Interpretation of chemical reaction yields with graph neural additive network

Machine Learning: Science and Technology
Prediction of chemical yields is crucial for exploring untapped chemical reactions and optimizing synthetic pathways for targeted compounds. Recently, graph neural networks have proven successful in achieving high predictive accuracy.
Youngchun Kwon, Yongsik Jung, Youn-Suk Choi, Seokho Kang   +3 more
doaj   +1 more source

Scaling limits of spatial compartment models for chemical reaction networks

The Annals of Applied Probability, 2015
We study the effects of fast spatial movement of molecules on the dynamics of chemical species in a spatially heterogeneous chemical reaction network using a compartment model. The reaction networks we consider are either single- or multi-scale.
Pfaffelhuber, Peter, Popovic, Lea
openaire   +5 more sources