Hi, Just a short note to first of all say thank you, I've find this very helpful to know albeit I can't point to a direct application. Secondly however, I do wonder: Why & how come you neglected to - in either an inclusionary or exclusionary manner - address any potential epigenetic mechanisms?
Kind regards, Arthur On 20 April 2018 at 19:32, Sungchul Ji <s...@pharmacy.rutgers.edu> wrote: > Hi, > > > I am forwarding a slightly modified version of my previous post with the > same title which was rejected by the FIS list due to the heavy attachments. > The most significant addition is written in green. The removed attachments > are now replaced by their web addresses from which they can be downloaded > free of charge. > > > Best. > > > Sung > > ________________________________ > From: Sungchul Ji > Sent: Thursday, April 19, 2018 11:02 AM > To: FIS FIS > Cc: Sergey Petoukhov; dani...@shirasawa-acl.net; John Stuart Reid; sayer ji; > sji.confor...@gmail.com; x...@chemistry.harvard.edu; > sbur...@proteomics.rutgers.edu; n...@princeton.edu > Subject: The 'Shirasawa phenomenon' or the 'Shirasawa effect" > > > Hi FISers, > > > In 2003, Takuji Shirasawa and his coworkers  found that mutating certain > amino acids in the hemoglobin molecule (Hb) in mice produced the following > effects: > > (1) increase O_2 consumption and CO_2 production, > > (2) the conversion of the muscle histology from a fast glycolytic to a fast > oxidative type, > > (3) a mild anemia, and > > (4) faster running speed. > > > In other words, Shirasawa et al provided a concrete example of molecular > changes (e.g., amino acid mutations in Hb) leading to (or associated with) > macroscopic physiological changes in whole animals (e.g., anemia, running > behavior, etc.). For the convenience of discussions, I am taking the > liberty of referring to this finding as the "Shirasawa et al. > phenomenon/effect" or, more briefly, the "Shirasawa phenomenon/effect" which > may be viewed as the macroscopic version of the Bohr effect . > > > The 'Shirasawa phenomenon/effect' is not limited to hemoglobin. There are > now many similar phenomena found in the fields of voltage-gated ion > channels, i.e., molecular changes in the amino acid sequences of ion channel > proteins leading to (or associated with) macroscopic effects on the human > body called diseases . > > > Although the current tendency among practicing molecular biologists and > biophysicists would be to explain away what is here called the Shirasawa > phenomenon in terms of the microscopic changes "causing" the macroscopic > phenomenon in a 1:1 basis, another possibility is that the microscopic > changes "cause" a set of other microscopic changes at the DNA molecular > level which in turn cause a set of macroscopic changes", in a many-to-many > fashion. > > > Current trend: Microscopic change (Hb mutation) ---------> Macroscopic > change 1 (Oxygen affinity change of blood) ---------> Macroscopic change 2 > (O_2 metabolism, anemia, running behavior) > > > > Althernative mechanism: Microscopic change 1 (Hb mutation) -------> > Microscopic change 2 (Changes in the standing waves in DNA) -------> > Multiple macroscopic changes (O_2 metabolism, anemia, muscle cell > histological changes). > > > The alternative mechanism proposed here seems to me to be more consistent > with the newly emerging models of molecular genetics  and single-molecule > enzymology [5, 6]. > > > > Since the 'Shirasawa phenomenon/effect' evidently implicates information > transfer from the microscale to the macroscale, it may be of interest to > many information theoreticians in this group. If you have any questions, > comments, or suggestions, please let me know. > > > All the best. > > > Sung > > > > References: > >  Shirasawa, T., et al. (2003). Oxygen Affinity of Hemoglboin > Regulaters O_2 Comsumtion, Metabolism, and Physical Activity. J. Biol. > Chem. 278(7): 5035-5043. PDF at > http://www.jbc.org/content/278/7/5035.full.pdf > >  The Bohr effect. https://en.wikipedia.org/wiki/Bohr_effect >  Huang W, Liu M, S Yan F, Yan N. (2017). Structure-based assessment > of disease-related mutations in human voltage-gated sodium channels. Protein > Cell. 8(6):401-438. PDF at https://www.ncbi.nlm.nih.gov/pubmed/28150151 > >  Petoukhov, S. V. (2016). The system-resonance approach in modeling > genetic structures. BioSystems 139: 1–11. PDF at > https://www.sciencedirect.com/science/article/pii/S0303264715001732 > >  Lu, H. P., Xun, L. and Xie, X. S. (1998) Single-Molecule Enzymatic > Dynamics. Science 282:1877-1882. PDF at > http://www.jbc.org/content/274/23/15967.short >  Ji, S. (2017). RASER Model of Single-Molecule Enzyme Catalysis and > Its Application to the Ribosome Structure and Function. Arch Mol. Med & Gen > 1:104. PDF at http://hendun.org/journals/AMMG/PDF/AMMG-18-1-104.pdf > > > > > > > > > _______________________________________________ > Fis mailing list > Fis@listas.unizar.es > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > _______________________________________________ Fis mailing list Fis@listas.unizar.es http://listas.unizar.es/cgi-bin/mailman/listinfo/fis