A metabolic model of human erythrocytes: practical application of the E-Cell Simulation Environment.

Journal of Biomedicine & Biotechnology
Ayako Yachie-KinoshitaMasaru Tomita

Abstract

The human red blood cell (RBC) has long been used for modeling of complex biological networks, for elucidation of a wide variety of dynamic phenomena, and for understanding the fundamental topology of metabolic pathways. Here, we introduce our recent work on an RBC metabolic model using the E-Cell Simulation Environment. The model is sufficiently detailed to predict the temporal hypoxic response of each metabolite and, at the same time, successfully integrates modulation of metabolism and of the oxygen transporting capacity of hemoglobin. The model includes the mechanisms of RBC maintenance as a single cell system and the functioning of RBCs as components of a higher order system. Modeling of RBC metabolism is now approaching a fully mature stage of realistic predictions at the molecular level and will be useful for predicting conditions in biotechnological applications such as long-term cold storage of RBCs.

References

Dec 19, 1989·Journal of Theoretical Biology·A Joshi, B O Palsson
Dec 19, 1989·Journal of Theoretical Biology·A Joshi, B O Palsson
Mar 1, 1987·Journal of Biochemistry·A TsuneshigeI Tyuma
Aug 1, 1970·Journal of Biochemistry·N HamasakiS Minakami
Jan 1, 1971·The Journal of Clinical Investigation·H S Hsieh, E R Jaffé
Dec 1, 1968·The Journal of Clinical Investigation·C LenfantJ Faura
Jun 1, 1982·The Journal of General Physiology·J C Ellory, J S Willis
Jan 1, 1984·Bio Systems·M Brumen, R Heinrich
Oct 17, 1998·The Journal of Biological Chemistry·J W Vince, R A Reithmeier
Mar 9, 1999·Bioinformatics·M TomitaC A Hutchison
Apr 11, 2001·Bioinformatics·N JamshidiB O Palsson
May 18, 2001·Trends in Biotechnology·M Tomita
Nov 15, 2002·Nature·Hiroaki Kitano
Sep 1, 1960·The Journal of General Physiology·D C TOSTESON, J F HOFFMAN
Oct 25, 2003·Journal of Theoretical Biology·Nathan D PriceBernhard O Palsson
Dec 20, 2003·Omics : a Journal of Integrative Biology·Herbert M SauroHiroaki Kitano
Apr 17, 2004·American Journal of Physiology. Regulatory, Integrative and Comparative Physiology·Roy E WeberPhilip S Low
Sep 17, 2004·Cell·Jörg StellingJohn Doyle
Feb 3, 2005·Annals of Biomedical Engineering·Ranjan K Dash, James B Bassingthwaighte
Feb 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·M Estela CampanellaPhilip S Low
May 11, 2005·Theoretical Biology & Medical Modelling·Yoichi NakayamaMasaru Tomita
Jun 10, 2006·Nature Biotechnology·Rui AlvesArmindo Salvador
Jun 13, 2006·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·James B BassingthwaighteThomas R Bukowski
Jun 16, 2006·Annals of Biomedical Engineering·Ranjan K Dash, James B Bassingthwaighte
Jul 14, 2006·The Biochemical Journal·Haiyan Chu, Philip S Low
Aug 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Ralf SteuerBernd Blasius
Sep 22, 2006·Antioxidants & Redox Signaling·Kazuhiro SuganumaMakoto Suematsu
Oct 7, 2006·Nature·Barbara Di VenturaLuis Serrano
Oct 13, 2006·Bioinformatics·Stefan HoopsUrsula Kummer
Nov 23, 2007·Journal of Theoretical Biology·F B du PreezJ L Snoep
Aug 12, 2008·American Journal of Physiology. Heart and Circulatory Physiology·Julia C ArcieroTimothy W Secomb
Sep 13, 2008·PLoS Computational Biology·Neema Jamshidi, Bernhard Ø Palsson
Dec 3, 2008·IET Systems Biology·I I MoraruL M Loew

❮ Previous
Next ❯

Citations

Jun 22, 2011·Biochimie·David FangeMåns Ehrenberg
Dec 15, 2015·Transfusion·Travis NemkovAngelo D'Alessandro
Sep 5, 2014·Biophysical Journal·Johannes SchönebergFrank Noé
Jun 6, 2015·PLoS Computational Biology·Hanae ShimoKoichi Takahashi
Sep 21, 2016·Journal of Proteome Research·Angelo D'AlessandroRobert C Roach
Feb 9, 2017·Journal of Proteome Research·Anubhav SrivastavaDarren J Creek
Oct 4, 2018·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Carla R AngelaniPablo J Schwarzbaum
Jan 19, 2019·Expert Review of Proteomics·Angelo D'Alessandro
Jan 1, 2014·BMC Biophysics·Johannes SchönebergFrank Noé

❮ Previous
Next ❯

Methods Mentioned

BETA
NMR
electrophoresis

Software Mentioned

Cell
Cell IDE ( Integrated Development Environment )
Virtual Cell
- Cell
DBSolve
Cell IDE
Python
Cell System
Copasi
Cell Simulation Environment

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.