Physicochemical Signatures Research Articles

Use of physicochemical signatures to assess the sources of metals in urban road dust

Road deposited dust is a complex mixture of pollutants derived from a wide range of sources. Accurate identification of these sources is seminal for effective source-oriented control measures. A range of techniques such as enrichment factor analysis (EF), principal component analysis (PCA) and hierarchical cluster analysis (HCA) are available for identifying sources of complex mixtures. However, they have multiple deficiencies when applied individually. This study presents an approach for the effective utilisation of EF, PCA and HCA for source identification, so that their specific deficiencies on an individual basis are eliminated. EF analysis confirmed the non-soil origin of metals such as Na, Cu, Cd, Zn, Sn, K, Ca, Sb, Ba, Ti, Ni and Mo providing guidance in the identification of anthropogenic sources. PCA and HCA identified four sources, with soil and asphalt wear in combination being the most prominent sources. Other sources were tyre wear, brake wear and sea salt.

Pyrite as a proxy for the identification of former coastal lagoons in semiarid NE Brazil

This work aimed to test the suitability of pyrite (FeS2) as a proxy for reconstructing past marine environmental conditions along the semiarid coast of Brazil. Morphological description combined with physicochemical analyses including Fe partitioning were conducted for soil depth profiles (30 and 60 cm depths) at three sites in two contrasting lagoons of the state of Ceara: a suspected former lagoon that would have been transformed into a freshwater “lake” at a site vegetated by Juncus effusus (site P1), and another lagoon with connection to the sea at sites vegetated by J. effusus (site P2) or Portulaca oleracea (site P3). Soil samples were collected in September 2010. Site P3 had more reducing conditions, reaching Eh values of –132 mV in the surface layer (0–10 cm), whereas minimum values for the P1 and P2 sites were +219 and +85 mV, respectively. Lower pyritic Fe values were found at site P1, with a degree of pyritization (DOP) ranging from 10 to 13%. At sites P2 and P3, DOP ranged from 9 to 67% and from 55 to 72%, respectively. These results are consistent with an interruption of tidal channels by eolian dune migration inducing strong changes in the hydrodynamics and physicochemical characteristics (lower salinity, oxidizing conditions) of these sites, causing the dieback of suspected former mangroves and a succession to freshwater marshes with an intermediate salt marsh stage. Together with other physicochemical signatures, pyrite can evidently serve as a useful proxy in tracking environmental changes in such ecotones, with implications for coastal management.

Residue analysis and ornament suspension techniques in prehistory: cyprinid pharyngeal teeth beads from Late Mesolithic burials at Vlasac (Serbia)

The authors discuss Late Mesolithic ornament suspension techniques on the basis of their analysis of 288 cyprinid fish pharyngeal teeth appliqués found in an infant burial at the site of Vlasac in the Danube Gorges region of the north-central Balkans. Our interdisciplinary approach includes archaeozoological and taphonomic analyses of archaeological cyprinid teeth ornaments, experiments on modern reference specimens, and the identification of use-wear traces and morphological and physicochemical signatures of residues on archaeological as well as comparative ethnographic ornaments from a selection of traditional hunter–gatherer societies worldwide. While focusing on one particular case study, the paper aims to provide an analytical and methodological framework for archaeological cases dealing with the reconstruction of materials and techniques used in prehistoric systems of ornamentation. Finally, our findings are compared to a strikingly similar set of cyprinid pharyngeal teeth ornaments from broadly contemporaneous Mesolithic sites found in the Upper Danube region, and a discussion is provided that attempts to account for this similarity.

Physicochemical Signatures of Natural Sea Films from Middle Adriatic Stations

Monolayer studies and a force-area quantification approach, in combination with electrochemical methods, are applied for physicochemical characterization of surface active substances (SAS) of the sea surface microlayers (MLs) from Middle Adriatic stations. Higher primary production during late spring-early autumn was reflected in the presence of MLs of higher surfactant activity containing on average molecules of lower molecular masses (M(w) = 0.65 ± 0.27 kDa) and higher miscibility (y = 6.46 ± 1.33) and elasticity (E(isoth) = 18.33 ± 2.02 mN m(-1)) modulus in comparison to structural parameters (average M(w) = 2.15 ± 1.58 kDa; y = 3.51 ± 1.46; E(isoth) = 6.41 ± 1.97 mN m(-1)) obtained for MLs from a period of lower production. A higher inhibition effect on the reduction process of Cd(2+) was observed for SAS abundant MLs from a more productive period. This kind of distribution is explained as the consequence of competitive adsorption of hydrophobic lipid-like substances of lower M(w) that act as end-members, highly influencing the surface structural properties of the natural air-water interface forming there segregated surface films during more productive period.

Non-combinatorial library screening reveals subsite cooperativity and identifies new high-efficiency substrates for kallikrein-related peptidase 14

An array of substrates link the tryptic serine protease, kallikrein-related peptidase 14 (KLK14), to physiological functions including desquamation and activation of signaling molecules associated with inflammation and cancer. Recognition of protease cleavage sequences is driven by complementarity between exposed substrate motifs and the physicochemical signature of an enzyme's active site cleft. However, conventional substrate screening methods have generated conflicting subsite profiles for KLK14. This study utilizes a recently developed screening technique, the sparse matrix library, to identify five novel high-efficiency sequences for KLK14. The optimal sequence, YASR, was cleaved with higher efficiency (k(cat)/K(m)=3.81 ± 0.4 × 10(6) M(-1) s(-1)) than favored substrates from positional scanning and phage display by 2- and 10-fold, respectively. Binding site cooperativity was prominent among preferred sequences, which enabled optimal interaction at all subsites as indicated by predictive modeling of KLK14/substrate complexes. These simulations constitute the first molecular dynamics analysis of KLK14 and offer a structural rationale for the divergent subsite preferences evident between KLK14 and closely related KLKs, KLK4 and KLK5. Collectively, these findings highlight the importance of binding site cooperativity in protease substrate recognition, which has implications for discovery of optimal substrates and engineering highly effective protease inhibitors.

Rapid Probing of Biological Surfaces with a Sparse-Matrix Peptide Library

Finding unique peptides to target specific biological surfaces is crucial to basic research and technology development, though methods based on biological arrays or large libraries limit the speed and ease with which these necessary compounds can be found. We reasoned that because biological surfaces, such as cell surfaces, mineralized tissues, and various extracellular matrices have unique molecular compositions, they present unique physicochemical signatures to the surrounding medium which could be probed by peptides with appropriately corresponding physicochemical properties. To test this hypothesis, a naïve pilot library of 36 peptides, varying in their hydrophobicity and charge, was arranged in a two-dimensional matrix and screened against various biological surfaces. While the number of peptides in the matrix library was very small, we obtained “hits” against all biological surfaces probed. Sequence refinement of the “hits” led to peptides with markedly higher specificity and binding activity against screened biological surfaces. Genetic studies revealed that peptide binding to bacteria was mediated, at least in some cases, by specific cell-surface molecules, while examination of human tooth sections showed that this method can be used to derive peptides with highly specific binding to human tissue.

Structural conservation of druggable hot spots in protein–protein interfaces

Despite the growing number of examples of small-molecule inhibitors that disrupt protein-protein interactions (PPIs), the origin of druggability of such targets is poorly understood. To identify druggable sites in protein-protein interfaces we combine computational solvent mapping, which explores the protein surface using a variety of small "probe" molecules, with a conformer generator to account for side-chain flexibility. Applications to unliganded structures of 15 PPI target proteins show that the druggable sites comprise a cluster of binding hot spots, distinguishable from other regions of the protein due to their concave topology combined with a pattern of hydrophobic and polar functionality. This combination of properties confers on the hot spots a tendency to bind organic species possessing some polar groups decorating largely hydrophobic scaffolds. Thus, druggable sites at PPI are not simply sites that are complementary to particular organic functionality, but rather possess a general tendency to bind organic compounds with a variety of structures, including key side chains of the partner protein. Results also highlight the importance of conformational adaptivity at the binding site to allow the hot spots to expand to accommodate a ligand of drug-like dimensions. The critical components of this adaptivity are largely local, involving primarily low energy side-chain motions within 6 Å of a hot spot. The structural and physicochemical signature of druggable sites at PPI interfaces is sufficiently robust to be detectable from the structure of the unliganded protein, even when substantial conformational adaptation is required for optimal ligand binding.

Carrier-resolved technology for homogeneous and multiplexed DNA assays in a ‘one-pot reaction’

For clinical diagnosis, a small number of targets (2-10 biomarkers) are often all that is required for disease assessment and accurate early disease diagnosis. In the current paper we have developed novel, carrier-resolved, single-label-based multiplexed assays for the simultaneous detection and quantification of a limited number of DNA targets associated with breast cancer. In contrast to current encoding strategies, every hybridization signal for the corresponding DNA target in our protocol is uniquely immobilized onto one carrier vehicle with a unique and intrinsic physico-chemical signature. Moreover, a simple chemiluminescence setup is employed to read the carrier code instead of expensive and complicated flow-cytometer or imaging-systems commonly used for multiplexed assays. Herein we demonstrate a new protocol using three homogeneous carriers, i.e. thermo-sensitive poly(N-isopropylacrylamide) (PNIP), polystyrene beads, and magnetic beads respectively. This new methodology allowed for the simultaneous determination of three oligonucleotide sequences (60 bases in length) associated with the breast cancer gene (BRCA1) and showed high selectivity and attomolar-femtomolar sensitivity. The mixture of three different capture probe conjugates first hybridizes with three corresponding target sequences, sandwiches with three biotinylated DNAs, and then reacts with peroxidase-streptavidin polymer in a single vessel without any washing, leading to the development of a 'one-pot reaction system'. Only one washing step in our protocol is required prior to detection leading to our whole procedure being simple and efficient. The results show that the hybridization response to sample mixtures containing increasing levels of each target is proportional to the amount of corresponding DNA targets, indicating minimal cross-interferences. The work presented here validates the design and concept of a system for the detection of a limited number of DNA targets and provides the foundation for the development of highly sensitive techniques with increased multi-analyte capabilities.

Physical-chemistry of “polygomer” surfaces through AFM force measurements

AFM microscope is used here as a surface forces apparatus at the nanometer scale. We show through several examples that the curves forces (nN) vs. distance (nm) obtained are the physico-chemical signature of the interacting surfaces. From such a curve, chemical, frictional (mobility) and mechanical top surface aspects can be studied.

Geochemical hydrocarbon exploration — a new/old exploration tool

The search for petroleum has evolved into a highly sophisticated technology where today almost every scientific discipline known is being brought to bear upon the endeavour. Yet, the use of geochemical hydrocarbon exploration remains a peripheral exploration tool. The trend toward scientific integration has led the petroleum explorationist to the point of being a specialist. It would seem that our petroleum scientists have focussed their interests mainly on the investigation of principles and less on their ultimate purpose of discovering new and larger oil and gas reserves. So, it is not by chance, that leading geochemists have been speaking more and more freely of the necessity to integrate our tools of exploration and thereby do a better job. The theoretical basis for hydrocarbon geochemistry is complex, and, as with all exploration tools, the problems and difficulties of interpreting the data will never be completely eliminated. This article considers the importance of using the ΔC method in geochemical hydrocarbon exploration which has been employed successfully for over 40 years. The addition of carbon-isotope ratios and trace-element analysis to this method has added a new dimension to geochemical hydrocarbon exploration. The theoretical basis of the ΔC method has been presented earlier by the author and will only be touched upon briefly here. Very simply, the basis of all geochemical hydrocarbon exploration is based on the much debated premise that the lighter hydrocarbon gases and their components migrate vertically from a trap through the overlying sedimentary pile to the surface. Upon reaching the surface, through oxidation, they leave their signatures in one form or another that can be detected by physicochemical methods. These physicochemical signatures are discernable as “geochemical haloes”. From soil samples, collected from 2–3 m deep, what is measured is the result of absorption and adsorption by soil particles that are altered to CO 2 by oxidation and form a unique, stable, carbonate system with the surface and near-surface material. This is unlike other carbonate systems and when subjected to a differential thermal technique, dissociates into CO 2 surface material is cumulative and indicates where maximum hydrocarbon leakage has taken place over the life span of the material sampled. It is durable and unaffected by pressure and temperature variation or recent hydrocarbon contamination. Values are expressed in terms of millivolts which are proportional to the CO 2 given off by the dissociation of the carbonate system under standard conditions. Frequency curves are constructed for all values for the determination of significant contour levels above the normal geochemical background for mapping. After significant ΔC anomalies are located, they can be further verified by use of carbon-isotope ratios. As methane migrates to the surface from underlying hydrocarbon accumulations, there is a progressive selection or fractionation that causes enrichment of the carbon-13 isotope. The methane, thus reaching the near-surface, is isotopically lighter. When oxidized in accordance with the equation CH 4 + 2O 2 → 2H 2O + CO 2, the carbon having been converted to carbon dioxide, is taken up in the pore-filling carbonate cements that are found in the near-surface soils and sediments. High carbon dioxide values (ΔC) in the geochemical halo are related the δ 13C carbon-isotope ratios from underlying hydrocarbon accumulations. This is observed over fields containing hydrocarbon accumulations where δ 13C values in the pore-filling carbonate cements become increasingly negative (lighter) toward the crests of traps (i.e. exhibiting lower ΔC values). This indicates enrichment of 12C relative to the PDB standard. Whereas, positive values of δ 13C indicate depletion in 12C or enrichment in 13C (i.e. exhibiting higher ΔC values away from the crests of the traps). The observed ΔC anomalies and δ 13C anomalies leave an indelible pattern in the near-surface sediments and soils which are herein referred to as geochemical hydrocarbon haloes. Trace-element associations, that form organometallic compounds, are found “haloed” or concentrated over or around underlying hydrocarbon reservoirs. These associations seem to have occurred from vertically migrating methane that has acted as a “carrier” sweeping up the trace elements on the pathways to the surface. Vanadium, nickel, chromium, iron, cobalt, copper, manganese, strontium, barium are various trace element ratios seen to also halo and indicate subsurface hydrocarbon accumulations. An example presented from the Ocho-Juan Field, a producing reef field, located in Scurry and Fisher Counties, Texas shows that the combination of ΔC, δ 13C and trace-element analysis from near-surface soil sampling is a significant step forward in improving geochemical hydrocarbon exploration methods.