Combination Of Hydrophobicity Research Articles

Use of soil moisture dynamics and patterns at different spatio-temporal scales for the investigation of subsurface flow processes

Abstract. Spatial patterns as well as temporal dynamics of soil moisture have a major influence on runoff generation. The investigation of these dynamics and patterns can thus yield valuable information on hydrological processes, especially in data scarce or previously ungauged catchments. The combination of spatially scarce but temporally high resolution soil moisture profiles with episodic and thus temporally scarce moisture profiles at additional locations provides information on spatial as well as temporal patterns of soil moisture at the hillslope transect scale. This approach is better suited to difficult terrain (dense forest, steep slopes) than geophysical techniques and at the same time less cost-intensive than a high resolution grid of continuously measuring sensors. Rainfall simulation experiments with dye tracers while continuously monitoring soil moisture response allows for visualization of flow processes in the unsaturated zone at these locations. Data was analyzed at different spacio-temporal scales using various graphical methods, such as space-time colour maps (for the event and plot scale) and binary indicator maps (for the long-term and hillslope scale). Annual dynamics of soil moisture and decimeter-scale variability were also investigated. The proposed approach proved to be successful in the investigation of flow processes in the unsaturated zone and showed the importance of preferential flow in the Malalcahuello Catchment, a data-scarce catchment in the Andes of Southern Chile. Fast response times of stream flow indicate that preferential flow observed at the plot scale might also be of importance at the hillslope or catchment scale. Flow patterns were highly variable in space but persistent in time. The most likely explanation for preferential flow in this catchment is a combination of hydrophobicity, small scale heterogeneity in rainfall due to redistribution in the canopy and strong gradients in unsaturated conductivities leading to self-reinforcing flow paths.

Transmembrane helix prediction in proteins using hydrophobicity properties and higher-order statistics

Prediction of the transmembrane (TM) helices is important in the study of membrane proteins. A novel method to predict the location and length of both single and multiple TM helices in human proteins is presented. The proposed method is based on a combination of hydrophobicity and higher-order statistics, resulting in a TM prediction tool, namely K 4 HTM . A training dataset of 117 human single TM proteins and two test-datasets containing 499 and 484 human single and multiple TM proteins, respectively, were drawn from the SWISS-PROT public database and used for the optimisation and evaluation of K 4 HTM . Validation results showed that K 4 HTM correctly predicts the entire topology for 99.68% and 93.08% of the sequences in the single and multiple test-datasets, respectively. These results compare favourably with existing methods, such as SPLIT4, TMHMM2, WAVETM and SOSUI, constituting an alternative approach to the TM helix prediction problem.

Application of polycarboxylic acid sodium salt in the dyeing of cotton fabric with reactive dyes

AbstractIn this study, the effects of polycarboxylic acid sodium salt on the dyeing of cotton with reactive dyes were evaluated by measuring and comparing the K/S values and dyeing fastnesses of the dyed cotton fabric samples. Results showed that the K/S value and dyeing fastness of cotton fabrics dyed with polycarboxylic acid sodium salt, substituting inorganic salts as exhausting agent were close to that of with sodium chloride when dip‐dyeing process was used. While, in pad‐dry dyeing, the K/S value of cotton fabric samples dyed with polyacid salts as exhausting agent was higher than that of with sodium sulfate, and the dyeing fastnesses of these samples were nearly the same. The dyeing mechanism of cotton fabric with reactive dye, using polycarboxylic acid sodium salt as exhausting agent was analyzed. The dyeing exhausting mechanism of reactive dye seems different when the inorganic salt and polycarboxylic acid sodium salt were used as exhausting agent in the dyeing of cotton fabric with reactive dye. The polycarboxylic acid sodium salt, as weak electrolyte, increased the dye‐uptake of reactive dye on cotton fabric not only by screening negative charges on cotton surface, but also by the effect of salting‐out or hydrophobic combination. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007

Predicting the Toxicity of Substituted Phenols to Aquatic Species and Its Changes in the Stream and Effluent Waters

The changes in the acute toxicity of 16 phenols toward Selenastrum capricornutum and Daphnia magna were examined as a function of their physical/chemical properties. The results demonstrated that phenols with a higher octanol-water partition coefficient (K(ow)) had a higher toxicity toward aquatic organisms. The toxicity of phenols was closely related to the log K(ow) values, with correlation coefficients of 0.93 (except for the nitrophenols) and 0.89 for S. capricornutum and D. magna, respectively. The changes in the phenols toxicities in the site waters (i.e., stream and effluent waters) were investigated by calculating the water effect ratios (WER) from the results of the toxicity tests in the site waters using D. magna. The results showed that the degree of ionization for each phenolic compound was altered by the differences in the dissociation constant (pK(a)), and the change in the toxicity could be predicted. Therefore, the WER should be considered when the toxicity of phenolic compounds is estimated in site waters. The quantitative structure-activity relationships (QSAR) study showed that the toxicity of the phenols to D. magna could be predicted by the hydrophobicity (log K(ow)) alone and by combining the log K(ow) with pK(a), while the toxicity to S. capricornutum was predicted by a combination of hydrophobicity (log K(ow)) and E(LUMO) (or pK(a)).

Purification of two peroxidase isoenzymes of Aloe barbadensis which oxidize p-coumaric acid

Using a combination of hydrophobicity and ion-exchange chromatography methods, one cationic (p I 9.0) and one anionic (p I 4.5) peroxidase (donor: hydrogen-peroxide oxidoreductase; EC 1.11.1.7) isoenzymes of Aloe barbadensis have been purified (the cationic peroxidase to homogeneity as judged by SDS-PAGE analysis and microsequencing). This allowed us to initiate the investigation of individual catalytic properties to be related to their respective functions in vivo. The two peroxidases have an optimal activity at pH 6.0. Apparent affinities for H 2O 2 range between 0.01 and 0.14 mM depending on the phenolic substrate and the isoenzyme. The apparent K m values for the phenolics ( p-coumaric acid and hydroquinone) are some 25-fold lower in the anionic (around 0.02 mM) than in the cationic (around 0.77 and 0.34 mM, respectively) isoenzyme. The possible functions of the activities are discussed.

TM Finder: a prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales.

Based on the principle of dual prediction by segment hydrophobicity and nonpolar phase helicity, in concert with imposed threshold values of these two parameters, we developed the automated prediction program TM Finder that can successfully locate most transmembrane (TM) segments in proteins. The program uses the results of experiments on a series of host-guest TM segment mimic peptides of prototypic sequence KK AAAXAAAAAXAAWAAXAAAKKKK-amide (where X = each of the 20 commonly occurring amino acids) through which an HPLC-derived hydropathy scale, a hydrophobicity threshold for spontaneous membrane insertion, and a nonpolar phase helical propensity scale were determined. Using these scales, the optimized prediction algorithm of TM Finder defines TM segments by first searching for competent core segments using the combination of hydrophobicity and helicity scales, and then performs a gap-joining operation, which minimizes prediction bias caused by local hydrophilic residues and/or the choice of window size. In addition, the hydrophobicity threshold requirement enables TM Finder to distinguish reliably between membrane proteins and globular proteins, thereby adding an important dimension to the program. A full web version of the TM Finder program can be accessed at http://www.bioinformatics-canada.org/TM/.

The influence of dissolved gas on the interactions between surfaces of different hydrophobicity in aqueous media Part I. Measurement of interaction forces

An atomic force microscope (AFM) was used to directly measure the symmetric interaction forces between solid surfaces in dilute aqueous electrolyte solutions as the type and concentration of dissolved gas were varied. The gases studied were air, argon and carbon dioxide. The amount of dissolved gas was reduced by degassing the electrolyte solutions. The solid surfaces studied were silica, hydrophobised by either dehydroxylation or methylation. The approach of methylated surfaces in electrolyte solutions was typically characterised by a jump into contact from separations sufficiently large so as to not be attributed to van der Waals forces. The range of these attractive jumps was quite reproducible for a given pair of interacting surfaces. However the jump distance was found to vary dramatically (between 5 and 75 nm) for differing pairs of interacting surfaces, albeit prepared in an identical maner. For surfaces with large jump distances (>25 nm), degassing of the electrolyte solution caused a significant reduction in the jump distance. When smaller jump distances were measured, whether involved methylated or dehydroxylated surfaces, degassing had no significant effect on the jump distance. The effect of gas type on jump distance was examined for both types of surfaces. For dehydroxylated silica surfaces interacting in CO2 saturated electrolyte solutions, the jump distances were significantly greater than in the presence of air or argon. Overall this interaction behaviour may be explained by the presence of gas bubbles formed on hydrophobic solid surfaces. The gas bubbles are stabilised by a combination of hydrophobicity and chemical heterogeneity.

Three Generations of Bile Acid Sequestrants

AbstractCholestyramine, the first bile acid sequestrant to be marketed, has been in use for over 20 years. Despite its low potency, requiring 16-24 g of polymer to achieve 20% LDL cholesterol reduction in hypercholesterolemic individuals, only one other sequestrant, colestipol, has come to market in the ensuing period. GelTex Pharmaceuticals has been involved for over six years in the discovery and development of new, more potent polymeric sequestrants. Two binding mechanisms are presented — one that operates via an aggregate binding structure and one that is effective via a defined site binding structure. These two binding mechanisms are compared and contrasted through bile acid binding isotherms. The best of these new sequestrants bind bile acids through a combination of hydrophobicity and ion exchange. Optimization and balancing of each of these interactions led us to more potent materials. The first of these, colesevelam hydrochloride is expected to be three to four times more potent than cholestyramine. A third generation product is still in research at GelTex. With another twofold increase in potency possible, single tablet therapy may become a reality.

Selective lysis of bacteria but not mammalian cells by diastereomers of melittin: structure-function study.

Studies on lipid-peptide interactions of cytolytic polypeptides tend to emphasize the importance of the amphipathic alpha-helical structure for their cytolytic activity. In this study, diasetereomers of the bee venom melittin (26 a.a.), a non-cell-selective cytolysin, were synthesized and investigated for their structure and cytolytic activity toward bacteria and mammalian cells. Similarly to the findings with the diastereomers of the less cytolytic peptide pardaxin (33 a.a.) (Shai & Oren. 1996), the melittin diastereomer, lest their alpha-helical structure, which abrogated their hemolytic activity toward human erythrocytes. However, they retained their antibacterial activity and completely lysed both Gram-positive and Gram-negative bacteria, as revealed by transmission electron microscopy. To understand the molecular mechanism underlying this selectivity, binding experiments utilizing the intrinsic tryptophan of melittin, tryptophan quenching experiments using brominated phospholipids, and membrane destabilization studies were done. The data revealed that the melittin diastereomers bound to and destabilized only negatively-charged phospholipid vesicles, in contrast to native melittin, which binds strongly to both negatively-charged and zwitterionic phospholipids. However, the partition coefficient, the depth of penetration into the membrane, and the membrane-permeating activity of the diastereomers with negatively-charged phospholipids were similar to those obtained with melittin. The results obtained do not support the formation of transmembrane pores as the mode of action of the diastereomers, but rather suggest that these peptides bind to the surface of the bacterial membrane, cover it in a "carpet-like" manner, and dissolve it like a detergent. The results presented here together with those obtained with the cytolytic peptide pardaxin suggest that the combination of hydrophobicity and net positive charge may be sufficient in the design of potent diastereomers of antibacterial polypeptides for the treatment of infectious diseases.

Structural distribution of dipeptides that are identified to be determinants of intracellular protein stability.

The dipeptides that had been previously implicated as determinants of in vivo protein stability (Guruprasad, K., Reddy, B.V.B. and Pandit, M.W., 1990. Protein Eng. 4, 155-161) have been reassessed on a latest data set and about 25% dipeptide combinations (102 dipeptides) were found to play significant role in determining the intracellular protein stability. These were classified as stabilizing dipeptides (Stb), destabilizing dipeptides (Dst) and normal dipeptides (Nor). By different theoretical approaches we have investigated the global localization of these dipeptides in a set of 303 best resolved (< or = 2.0A) non-homologous X-ray defined protein structures. The Dst dipeptides are found to be more of hydrophilic combinations where as Stb dipeptides are more of hydrophobic combinations. We observed a significant difference in overall frequency of occurrence of Stb and Dst dipeptides in different secondary structural regions. The sensitive dipeptides (Stb + Dst) are less in beta-strands and more in coils. A high frequency of occurrence of Stb are observed in the regions closer to the molecular surface compared to the Dst and Nor dipeptides. A significantly high dipole interactions are observed in the Dst dipeptides. The studies indicate that though the Dst dipeptides are more of hydrophilic nature they are localized significantly more in the buried regions of protein structures, on the other hand Stb are more of hydrophobic nature but relatively more accessible to the solvent. These dipeptides therefore increasing sensitivity of the protein to external environment, any alteration in their occurrence in the sequence could increase or decrease intracellular stability of the protein. These observations are useful to select mutations to alter intracellular stability of a given protein and therefore have implications in protein engineering.