The Activity Coefficients of Amino Acids and Peptides in Aqueous Solutions Containing Guanidinium Chloride

Six systems of the type amino acid- or peptide-guanidinium chloride-water have been investigated over wide solute molality ranges using vapor pressure osmometry. The amino acids used were glycine and L-leucine, while the peptides were diglycine, triglycine, glycyl-L-leucine and L-leucyl-L-leucine. Equations for the ratios of the activity coefficients of these compounds in the salt solutions and water, respectively, were obtained in terms of the molalities of the solutes. The activity coefficient ratios for glycine are not much below one, whereas those for i.-leucine are considerably smaller reflecting the presence of the leucyl side chain. The activity coefficient ratios for the peptides are generally smaller than those for the amino acids which can be attributed to . the presence of the peptide group

The Activity Coefficients of Amino Acids and Peptides in Aqueous Solutions Containing Guanidinium Chloride

Six systems of the type amino acid- or peptide-guanidinium chloride-water have been investigated over wide solute molality ranges using vapor pressure osmometry. The amino acids used were glycine and L-leucine, while the peptides were diglycine, triglycine, glycyl-L-leucine and L-leucyl-L-leucine. Equations for the ratios of the activity coefficients of these compounds in the salt solutions and water, respectively, were obtained in terms of the molalities of the solutes. The activity coefficient ratios for glycine are not much below one, whereas those for i.-leucine are considerably smaller reflecting the presence of the leucyl side chain. The activity coefficient ratios for the peptides are generally smaller than those for the amino acids which can be attributed to . the presence of the peptide group

Aquifer Characterization and Monitoring by Active and Passive Seismic Surveys

AbstractA 3D active and passive seismic survey was carried over an aquifer in Italy. We used 1-component vertical receivers in a fine areal grid of 100x100 m. Furthermore, two orthogonal linear profiles were acquired with 3-component receivers, recording the signal of a directional vibrator in the x, y and z direction, so getting a 9-component wave field. The data allow studying the elastic propagation effects of seismic waves in the aquifer, getting independent measurements of direct P, SH and SV arrivals. The elastic parameters they provide allow exploiting the Rayleigh wave velocities obtained by passive seismic for aquifer monitoring

Osmometric Study of Aggregation in Dye Solutions

The osmotic coefficient of aqueous solutions of four different dyes was measured as a function of the concentration. From the results the dependence of the mean aggregation number of the dye on the concentration was determined. The calculations were based on the application of the spherical cell model of colloid solutions

DNA hybridization to mismatched templates: a chip study

High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from hybridizing the target RNA to two nearly identical templates: a perfect match (PM) and a single mismatch (MM) probe. It has been observed that a large fraction of MM probes repeatably bind targets better than the PMs, against the usual expectation from sequence-specific hybridization; this is difficult to interpret in terms of the underlying physics. We examine this problem via a statistical analysis of a large set of microarray experiments. We classify the probes according to their signal to noise ($S/N$) ratio, defined as the eccentricity of a (PM, MM) pair's `trajectory' across many experiments. Of those probes having large $S/N$ ($>3$) only a fraction behave consistently with the commonly assumed hybridization model. Our results imply that the physics of DNA hybridization in microarrays is more complex than expected, and they suggest new ways of constructing estimators for the target RNA concentration.Comment: 3 figures 1 tabl

Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations

Recently various pathways of human telomere (ht) DNA folding into G-quadruplexes and of ligand binding to these structures have been proposed. However, the key issue as to the nature of forces driving the folding and recognition processes remains unanswered. In this study, structural changes of 22-mer ht-DNA fragment (Tel22), induced by binding of ions (K(+), Na(+)) and specific bisquinolinium ligands, were monitored by calorimetric and spectroscopic methods and by gel electrophoresis. Using the global model analysis of a wide variety of experimental data, we were able to characterize the thermodynamic forces that govern the formation of stable Tel22 G-quadruplexes, folding intermediates, and ligand-quadruplex complexes, and then predict Tel22 behavior in aqueous solutions as a function of temperature, salt concentration, and ligand concentration. On the basis of the above, we believe that our work sets the framework for better understanding the heterogeneity of ht-DNA folding and binding pathways, and its structural polymorphism

Solving the riddle of the bright mismatches: hybridization in oligonucleotide arrays

HDONA technology is predicated on two ideas. First, the differential between high-affinity (perfect match, PM) and lower-affinity (mismatch, MM) probes is used to minimize cross-hybridization. Second, several short probes along the transcript are combined, introducing redundancy. Both ideas have shown problems in practice: MMs are often brighter than PMs, and it is hard to combine the pairs because their brightness often spans decades. Previous analysis suggested these problems were sequence-related; publication of the probe sequences has permitted us an in-depth study of this issue. Our results suggest that fluorescently labeling the nucleotides interferes with mRNA binding, causing a catch-22 since, to be detected, the target mRNA must both glow and stick to its probe: without labels it cannot be seen even if bound, while with too many it won't bind. We show that this conflict causes much of the complexity of HDONA raw data, suggesting that an accurate physical understanding of hybridization by incorporating sequence information is necessary to perfect microarray analysis.Comment: 4 figure

Adaptive regridding in 3D reflection tomography

3D reflection tomography allows the macro-model of complex geological structures to be reconstructed. In the usual approach, the spatial distribution of the velocity field is discretized by regular grids. This choice simplifies the development of the related software, but introduces two serious drawbacks: various domains of the model may be poorly covered, and a relevant mismatch between the grid and a complex velocity field may occur. So the tomographic inversion becomes unstable, unreliable and necessarily blurred. In this paper we introduce an algorithm to adapt the grid to the available ray paths and to the velocity field in sequence: so we get irregular grids with a locally variable resolution. We can guide the grid fitting procedure interactively, if we are going to introduce some geological a priori information; otherwise, we define a fully automatic approach, which exploits the Delauny triangles and Voronoi polygons