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

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

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

Case Report: SATB2-Associated Syndrome Overlapping With Clinical Mitochondrial Disease Presentation: Report of Two Cases

SATB2-associated syndrome (SAS) is an autosomal dominant neurogenetic multisystemic disorder. We describe two individuals with global developmental delay and hypotonia who underwent an extensive evaluation to rule out an underlying mitochondrial disorder before their eventual diagnosis of SAS. Although the strict application of the clinical mitochondrial disease score only led to the designation of “possible” mitochondrial disorder for these two individuals, other documented abnormalities included nonspecific neuroimaging findings on magnetic resonance imaging and magnetic resonance spectroscopy, decreased complex I activity on muscle biopsy for patient 2, and variation in the size and relative proportion of types of muscle fibers in the muscle biopsies that were aligned with mitochondrial diseases. SAS should be in the differential diagnoses of mitochondrial disorders, and broad-spectrum diagnostic tests such as exome sequencing need to be considered early in the evaluation process of undiagnosed neurodevelopmental disorders

Energetic signatures of single base bulges: thermodynamic consequences and biological implications

DNA bulges are biologically consequential defects that can arise from template-primer misalignments during replication and pose challenges to the cellular DNA repair machinery. Calorimetric and spectroscopic characterizations of defect-containing duplexes reveal systematic patterns of sequence-context dependent bulge-induced destabilizations. These distinguishing energetic signatures are manifest in three coupled characteristics, namely: the magnitude of the bulge-induced duplex destabilization (ΔΔGBulge); the thermodynamic origins of ΔΔGBulge (i.e. enthalpic versus entropic); and, the cooperativity of the duplex melting transition (i.e. two-state versus non-two state). We find moderately destabilized duplexes undergo two-state dissociation and exhibit ΔΔGBulge values consistent with localized, nearest neighbor perturbations arising from unfavorable entropic contributions. Conversely, strongly destabilized duplexes melt in a non-two-state manner and exhibit ΔΔGBulge values consistent with perturbations exceeding nearest-neighbor expectations that are enthalpic in origin. Significantly, our data reveal an intriguing correlation in which the energetic impact of a single bulge base centered in one strand portends the impact of the corresponding complementary bulge base embedded in the opposite strand. We discuss potential correlations between these bulge-specific differential energetic profiles and their overall biological implications in terms of DNA recognition, repair and replication

Surfaces engineering approaches for cell culture substrates using biomimetic Human Elastin-Like Polypeptides

Spatially controlled cell adhesion and multicellular organization is critical to many biomedical and tissue-engineering applications. Many efforts have therefore focused on the production of engineered surfaces that can promote, and possibly control, cell adhesion and growth. Here we present the characterization of these spontaneously formed patterns using HELP-fluoresceinated derivatives. The ability to support cell adhesion and growth of the HELP-based substrates is also explored