Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements.

Background: Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated. Results: Here we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes. Conclusions: Our findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architectur

Variable Levels Of Drift In Tunicate Cardiopharyngeal Gene Regulatory Elements

Background: Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated. Results: Here we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes. Conclusions: Our findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architecture

A model for the interaction between hydrophilic and hydrophobic solutes. A calorimetric study of the aqueous solutions containing alkylureas and urea at 298.15 K.

The heats of dilution of ternary aqueous solutions of urea and alkylureas and of ternary aqueous solution of mono, di and tetra alkylureas have been determined calorimetrically at 298.15 K. Pairwise cross interaction coefficients of the virial expansion of the excess enthalpies were determined. The behaviour of these systems was interpreted in terms of preferential interactions between hydrophilic domains and of repulsive interactions between hydrophobic and hydrophilic domains

Molecular recognition: A thermodynamic study of non bonded interactions in aqueous solutions of iminoacids. Effects of steric and geometric isomerism

Enthalpies of dilution of binary and ternary aqueous solutions containing L- and D-proline, cis-L- and cis-D-4-hydroxy proline, trans-L-4-hydroxy proline, have been determined by flow calorimetry at 25°C. Pairwise self- and cross-interaction coefficients of the virial expansion of the excess enthalpies were evaluated. They are positive for solutions of unsubstituted prolines. On the contrary, upon the introduction of a hydroxy group, they become negative, reaching the largest value for the cis-L-/cis-D-4-hydroxy proline system. The results are interpreted in terms of preferential configurations, stabilized by interactions between the hydrophilic groups

On the role of the functional group in determining the strength of hydrophobic interactions in aqueous solutions of α-amino acid derivatives

Calonmetric measurements were carried out at 25°C on binary aqueous solutions containing N-acetyl derivatives of the following α-amino acids: glycine, alanine, valine, leucine, norleucine, aspartic acid, glutamic acid, phenylalanine, methionine, asparagine, glutamine, cysteine, histidine, serine. The N-acetyl derivative of the α-amino acid proline was also studied. The results obtained have been used to calculate the pairwise enthalpic interaction coefficients and these are compared with results reported in the literature concerning free α-amino acids, and their acetylamide derivatives. The coefficients largely increase passing from free amino acids to N-acetyl derivatives. The derivatives of α-amino acids bearing unsubstituted alkyl chains present an increased cooperativity of hydrophobic interactions

A model for the interactions involving hydrophilic structure maker solutes: A thermodynamic study of ternary aqueous solutions of glucose and hydroxylated substances

Enthalpies of dilution of ternary aqueous solutions containing glucose and alkan-1-ols, alkan-1,2-diols and alkan-m,n-diols were determined at 298.15 K by flow microcalorimetry. The pair-wise cross interaction coefficients of the virial expansion of the excess enthalpies were evaluated: they are positive and depend in a complex manner on the length of the alkyl chain of the alkanols. The behaviour of these systems is interpreted in terms of preferential interactions between the hydrophilic groups of the alkanols and the destructured domain present on glucose. © 1996 Akadémiai Kiadó

Dependence of the cooperativity of hydrophobic interactions on the nature of functional groups. A microcalorimetric study of binary aqueous solutions of α,ω-difunctional compounds at 298.15 K

Enthalpies of dilution of binary aqueous solutions containing α,ω-amino acids, α,ω-dicarboxylic acids, α,ω-diamines and α,ω-diols have been determined at 298.15 K by flow microcalorimetry. The pairwise enthalpic coefficients of the virial expansion of the excess enthalpies were evaluated. These coefficients show that the investigated substances differ greatly in the cooperativity of their hydrophobic interactions, depending on the nature of the functional group. The diamines show the highest cooperativity among the solutes studied to date. The coefficients were interpreted using the 'preferential configuration' model and compared with the results obtained from a statistical approach

Preferential configurations in solution: Calorimetric study of ternary aqueous systems containing a destructuring agent and derivatives of α-amino acids at 298 K

Enthalpies of dilution of ternary aqueous solutions containing α-amino acids or their N-acetyl or N-acetylamide derivatives and urea, glycine, N-acetylglycine and N-acetylglycinamide have been determined by flow microcalorimetry at 298.15 K. Pairwise cross-interaction coefficients of the virial expansion of the excess enthalpies were evaluated. The behaviour of these systems seems to be determined by a balance between favourable hydrophilic-hydrophilic and repulsive hydrophilic-hydrophobic interactions. A common behaviour was shown by every studied series of substances, independently of the nature of the destructuring agent. The pairwise cross-interaction coefficients increase with increasing length of the alkyl side chains until a plateau is attained. This seems to be a general rule when homologous series of solutes having hydrophobic domains interact with a structure-breaker solute

COMPLEXATION OF MODIFIED CYCLODEXTRINS WITH HYDROXYLATED SUBSTANCES IN AQUEOUS SOLUTIONS. CALORIMETRIC STUDIES AT 298 K

The formation of complexes between hydroxypropyl-beta-cyclodextrin or methyl-beta-cyclodextrin and 1-alkanols or cycloalkanols has been studied calorimetrically at 298 K in water and in concentrated aqueous solutions of ethanol with the aim of understanding the effects of the solvent medium on the association process. When a complex is formed, calorimetry enables the calculation of both the enthalpy and the association constant, from which the free energy and the entropy of the process can be obtained. The forces involved in the association process are discussed in the light of the signs and values of the thermodynamic parameters obtained. The most important conclusions from this study are: (i) for linear alkanols, hydrophobic interactions are largely the forces acting in the complexation. That is detected by the small enthalpies and by the high and always positive entropies. For cycloalkanols, entropies are positive or negative-an indication that other forces act in the complexation. (ii) In concentrated aqueous solutions of cosolvent, complexation is characterized by enthalpy and entropy changes which depend on the extent of alteration induced by the cosolvent on the structure of water and on the hydration shells of the interacting substances. (iii) A linear correlation exists between enthalpy and entropy of complexation, thus indicating that inclusion is a process dominated by aquation phenomena and ascribed to the modifications experienced by the solvent in the hydration shells of the interacting substances

Molecular recognition and effects of steric and geometric isomerism: Thermodynamic study of non-bonding interactions in aqueous solutions of cycloalkanols

Enthalpies of dilution of binary and ternary aqueous solutions containing cyclobutanol, cyclopentanol, cyclohexanol, cycloheptanol, cyclooctanol, (1R,2R)-trans-cyclohexane-1,2-diol, (1S,2S)-trans-cyclohexane-1,2-diol, (1R,2S)-cis-cyclohexane-1,2-diol, (1R,2R)-trans-cyclopentane-1,2-diol, (1S,2S)-trans-cyclopentane-1,2-diol, (1R,2S)-cis-pentane-1,2-diol, cis-cyclooctane-1,2-diol, cis-cyclooctane-1,4-diol, cis-cyclooctane-1,5-diol, cis,cis-cyclohexane-1,3,5-triol and myo-inositol were determined by microcalorimetry at 298.15 K. Pairwise self- and cross-interaction coefficients of the virial expansion of the excess enthalpies were evaluated. The values of these coefficients are positive, depending in a very complex manner on the number of the hydroxy groups on the cyclic molecule and on steric and geometric isomerism. They have been interpreted according to an interaction model which indicates a preferential configuration between two hydrated interacting molecules, stabilized by the simultaneous juxtaposition of groups having the same action on water structure