PubMed · 13778933
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M U UDABE. 1960-09-26. [The thermodynamic climogram].. https://pubmed.ncbi.nlm.nih.gov/13778933/
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MOTIVATION: Understanding how the genome encodes the regulatory logic of transcription is a main challenge of the post-genomic era, and can be overcome with the aid of customized computational tools. RESULTS: We report an automated framework for analyzing an ensemble of fits to data of a thermodynamics-based sequence-level model for transcriptional regulation. The fits are clustered accordingly with their intrinsic regulatory logic. A multiscale analysis enables visualization of quantitative features resulting from the deconvolution of the regulatory profile provided by multiple transcription factors interacting with the locus of a gene. Quantitative experimental data on reporters driven by the whole locus of the even-skipped gene in the blastoderm of Drosophila embryos was used for validating our approach. A few clusters of highly active DNA binding sites within the enhancers collectively modulate even-skipped gene transcription. Analysis of variable enhancers' length shows the importance of bound protein-protein interactions for transcriptional regulation. The interplay between activation and quenching enables function conservation of enhancers despite length variations. AVAILABILITY AND IMPLEMENTATION: The transcription factor level data used for performing the reported study is accessible in the input files in Zenodo and GitHub as well the full code. Additional data from formerly FlyEx database will be available under request.
Monolayers of amphiphilic melamine derivatives are good candidates for the formation of supramolecular structures by hydrogen-bonding of nonsurface active species dissolved in the aqueous subphase by molecular recognition. In the present work, the thermodynamic and structural properties of the Langmuir monolayers of a homologous series of a selected amphiphilic melamine-type are characterized. Good candidates for such studies are the decyl, undecyl, and dodecyl homologues of the 2,4-di(n-alkylamino)-6-amino-1,3,5-triazine (2CnH(2n+1)-melamine) monolayers because of their two-phase coexistence region in the accessible temperature range. The characterization of the structural and phase behavior is performed by a combination of surface pressure studies with Brewster angle microscopy (BAM) imaging and Grazing incidence X-ray diffraction (GIXD) measurements. A comprehensive thermodynamic analysis provides good agreement between the experimental surface pressure - area (Pi-A) isotherms and the theoretical curves that were calculated on the basis of equations of state for a large region of monolayer stages developed by us in J. Phys. Chem. 1999, 103, 145. Theoretical curves calculated by application of equations of state only for the fluid monolayer state proposed recently by Rusanov (J. Chem Phys. 2004, 120, 10736) are in good agreement with the experiments in a limited temperature range. A rigorous equation is derived and applied to the experimental results for the calculation of the enthalpy of two-dimensional phase transition. The combination of BAM and GIXD illustrates that the microscopic long range ordering of the condensed monolayer phases is related to the lattice structure of the condensed monolayer.
In solutions consisting of solvent water (component '1') and two solute components ('2' and '3'), various thermodynamic effects of differences between solute-solute and solute-solvent interactions are quantitatively characterized by state functions commonly called 'preferential interaction coefficients': gamma(mu(1),mu(3)) triple bond (delta(m3)/delta(m2))(T,mu(1),mu(3)) and gamma(mu(k)) triple bond (delta(m3)/delta(m2))(T,P,mu(k)), where k = 1,2 or 3. These different derivatives are not all directly accessible to experimental determination, nor are they entirely equivalent for analyses and interpretations of thermodynamic and molecular effects of preferential interactions. Consequently, various practical and theoretical considerations arise when, for a given system, different kinds of preferential interaction coefficients have significantly different numerical values. Previously we derived the exact relationship linking all three coefficients of the type gamma(mu(k), and hence identified the physical origins of the differences between gamma(mu(1)) and gamma(mu(3)) that have been experimentally determined for each of various common biochemical solutes interacting with a protein [J. Phys. Chem. B, 106 (2002) 418-433]. Continuing our investigation of exact thermodynamic linkages among different types of preferential interaction coefficients, we present here a generalized derivation of the relationship linking gamma(mu(1),mu(3)), gamma(mu(3)) and gamma(mu(1)), with no restrictions on m(2), m(3) or any physical characteristic of either solute component (such as partial molar volume). Hence, we show that (gamma(mu(1),mu(3)) - gamma(mu(3))) is related directly to (gamma(mu(3)) - gamma(mu(1))), for which the physical determinants have been considered in detail previously, and to a factor dependent on the ratio of the partial molar volumes V3/V1. Our generalized expression also provides a basis for calculating gamma(mu(1),mu(3)), even in situations where preferential interactions could not be investigated by equilibrium dialysis. To demonstrate this applicability, we analyze isopiestic distillation data for aqueous solutions containing urea and NaCl, two small solute components that cannot be selectively dialyzed.