Subtle Chemical Variations Research Articles

Using subtle variations in groundwater geochemistry to identify the proximity of individual geological structures: a case study from the Grimsel Test Site (Switzerland)

Understanding groundwater flow and the evolution of groundwater chemistry in networks of fractures in crystalline rock is of fundamental interest for geothermal projects, nuclear waste disposal, and groundwater resources. Groundwater chemistry at a given location is typically conceived of being of a specific ‘type’ (e.g. meteoric, juvenile, connate, marine), with associated chemical types controlled through water–rock interactions. Minor chemical variations between groundwater sample locations with the same chemical type are generally considered as ‘noise’ in the geochemical data. Here, we argue that this noise contains useful information on the mineral phases encountered by the groundwater as it travels through specific flow pathways. We analyse the spatial variability of groundwater chemistry around the Grimsel Test Site (GTS), Switzerland, where groundwater is hosted in two lithologies: the Central Aar Granite and the Grimsel Granodiorite, where flow occurs predominantly in a fracture network created by brittle reactivation of ductile shear zones. Groundwater chemistry is analysed using principal component and hierarchical cluster analyses, which identify two groundwater types based on their chemistry. The primary control on groundwater type is the host rock lithology (granite/granodiorite). While the spatial variability of groundwater chemistry within each of the two lithologies is small, statistical analysis of the data shows similar groundwater chemistry in borehole intervals that are crosscut by similar geological structures, implying a structural control on groundwater chemistry. Our research shows that subtle chemical variations in groundwater provide information on fracture network connectivity and the proximity of geological features, that specific volumes of groundwater has interacted with.

Characterization of isomeric lipid A species from Pseudomonas aeruginosa PAO1 by non-aqueous capillary electrophoresis with positive and negative ion electrospray tandem mass spectrometry

Pseudomonas aeruginosa is a priority target pathogen for antibiotic research and development because of its high resistance to a wide range of antibiotics. Acquisition of resistance is sometimes associated with modifications of the lipid A component present in the outer membrane of most Gram-negative bacteria. For a deeper understanding of subtle chemical variations of lipid A in relation to biological properties, the structural elucidation of lipid A species within a bacterial strain is of crucial importance. However, the simultaneous presence of monophosphorylated positional isomers in naturally heterogeneous lipid A samples cannot easily be recognized with direct MS measurements or with conventional LC-MS strategies. Herein, we present the application of a non-aqueous capillary electrophoresis (NACE) method coupled to positive and negative ion electrospray tandem mass spectrometry with collision-induced dissociation (CID) activation technique for the in-depth analysis of the lipid A isolate of P. aeruginosa PAO1. The main advantage of our NACE strategy is its separation power regarding the site of phosphorylation of the lipid A structures, which makes it a good orthogonal technique to chromatographic characterizations of the bacterial lipid A composition, where the separation is mainly based on acylation differences of the species. Overall, the results of this electrophoretic approach revealed hitherto unreported isomeric monophosphorylated PAO1 lipid A constituents, including both phosphate and acyl chain positional isomers. The parallel fragmentation in the complementary positive and negative ion modes enabled the unequivocal assignment of the phosphorylation site and position of acyl chains in lipid A compounds of three acylation families ranging from tetra- to hexa-acylation. Moreover, C1-monophosphorylated lipid A species have been identified in P. aeruginosa for the first time.

Cuticular hydrocarbons as cues of caste and sex in the German wasp Vespula germanica

The complex system of communication used by social insects is responsible for their success on Earth. Cuticular hydrocarbons (CHCs) are considered the most commonly used form of communication among social insects. The best-known function of CHCs is to distinguish nestmates, providing cues to the whole colony to identify potential threats. In some species, CHCs function as queen pheromones, which contribute to the queens’ ability to regulate the reproductive division of labor. Additionally, differences of CHCs were described in castes and they are also important in sex recognition. Here, we reinvestigated the chemical composition on the cuticle of German wasp Vespula germanica and we found that proportions of linear alkanes were more abundant in the cuticle of queens than other castes. Chemical analysis between caste and sex, including data of virgin queens and males, showed that each group possesses different compositions on their cuticle, being mostly quantitative differences. Thus, individuals of V. germanica may recognize and discriminate caste and sex through subtle chemical variations, or alternatively, based on templates used in nestmate recognition. The chemical analysis provides correlative evidence of CHCs being used as cues in the chemical communication of this species.

Evaluation of rice varieties using LIBS and FTIR techniques associated with PCA and machine learning algorithms.

Laser-induced breakdown spectroscopy (LIBS) for atomic multi-elementary analyses, and Fourier transform infrared spectroscopy (FTIR) for molecular identification, are often suggested as the most versatile spectroscopic techniques. The present work aimed to evaluate the performance of both techniques, LIBS and FTIR, combined with principal component analysis (PCA) and machine learning (ML) algorithms in the detection of the composition analysis and differentiation of four different types of rice, white, brown, black, and red. The two techniques were primarily used to obtain the elemental and molecular qualitative characterization of rice samples. Then, LIBS and FTIR data sets were subjected to PCA and supervised ML analysis to investigate which main chemical features were responsible for nutritional differences for the white (milled) and colored rice samples. In particular, PCA data analysis suggested that protein, fatty acids, and magnesium were the highest contributors to the sample's differentiation. The ML analysis based on this information yielded a 100% level of accuracy, sensitivity, and specificity on sample classification. In conclusion, LIBS and FTIR coupled with multivariate analysis were confirmed as promising tools alternative to traditional analytical techniques for composition analysis and differentiation when subtle chemical variations were observed.

Subtle Chemical Variations with Strong Ecological Significance: Stereoselective Responses of Male Orchid Bees to Stereoisomers of Carvone Epoxide.

Different enantiomers of chiral compounds within floral perfumes usually trigger distinct responses in insects; however, this has frequently been neglected in studies investigating semiochemicals in plant-pollinator interactions. Approximately 1000 neotropical plants produce floral perfumes as the only reward for pollinators, i.e. male euglossine bees. The chiral compound carvone epoxide is a key component of the scent bouquet of many perfume-rewarding plants that are pollinated by males of Eulaema. Here, we tested the biological activity of the four carvone epoxide stereoisomers to four Eulaema species occurring in the Atlantic Rainforest of NE-Brazil. We determined the stereochemistry of carvone epoxide in the floral scent of several Catasetum species, tested whether the antennae of bees respond differentially to these stereoisomers and investigated if there is a behavioural preference for any of the stereoisomers. We found that 1) Catasetum species emit only the (-)-trans-stereoisomer of carvone epoxide, 2) for E. atleticana and E. niveofasciata antennal responses to the (-)-trans-carvone epoxide were significantly stronger than those to (-)-cis-carvone epoxide, 3) the strength and pattern of antennal responses to all 4 stereoisomers (separately tested) did not differ among Eulaema species, and 4) there were significant differences in attractiveness of the four stereoisomers to the bees species with the (-)-trans-stereoisomer being particularly attractive. We assume (-)-trans-carvone epoxide to be the dominant isomer in perfume-rewarding plants pollinated by Eulaema. The universal occurrence of carvone epoxide in Catasetum species pollinated by Eulaema, suggests that this compound has evolved in perfume-rewarding as a specific attractant for Eulaema bees as pollinators.

Feasibility Study of Ore Classification Using Active Hyperspectral LiDAR

Recently, a major effort has been made to develop methods or tools for rock characterization and mineral content mapping. Light detection and ranging (LiDAR) is an efficient active remote sensing technique for collecting geometry information about rock surfaces. However, traditional LiDAR sensors work with a single-wavelength laser source, and it is unfeasible to obtain spectral information using one LiDAR sensor. The combination of hyperspectral imaging and LiDAR techniques is an emerging method for acquiring spatial and spectral information simultaneously that allows remote mapping of high-resolution mineral content and distributions and identifies subtle chemical variations. Unfortunately, spatial and spectral data registration, which introduces additional complicated data processing, is an inevitable and essential issue for this method. In this letter, first, we investigate the feasibility of ore classification applications with hyperspectral LiDAR (HSL). HSL consists of 17 spectral channels covering the visible–shortwave infrared (SWIR) spectral range. Spatial and spectral information about seven different ore samples is obtained under a controlled laboratory environment using HSL. The standard deviation of the distance measurements is less than 1.1 cm for different spectral channels, and the classification accuracy can reach 100% if all 17 spectral measurements are used. To optimize the system design with lower cost and system complexity, a spectral band selection criterion is built based on the feature contribution degree (FCD), which is calculated using the normalized variance of the reflectance values for different ore samples at each wavelength. Two different strategies of FCD selection are tested to generate vectors: ascending sequences and descending sequences. Feature vectors with descending sequences have better classification accuracy. In addition, the results show that the classification accuracy can reach 100% with the feature vector of the seven largest FCD values compared to 59.57% for the feature vector with the seven smallest FCD values. Moreover, we find that the channels with high FCD values are primarily centered in SWIR bands. This result could be a reference for optimizing the hardware design of HSL for ore classification or mineral identification.

The Role of Carbohydrates in the Lipopolysaccharide (LPS)/Toll-Like Receptor 4 (TLR4) Signalling.

The interactions between sugar-containing molecules from the bacteria cell wall and pattern recognition receptors (PRR) on the plasma membrane or cytosol of specialized host cells are the first molecular events required for the activation of higher animal’s immune response and inflammation. This review focuses on the role of carbohydrates of bacterial endotoxin (lipopolysaccharide, LPS, lipooligosaccharide, LOS, and lipid A), in the interaction with the host Toll-like receptor 4/myeloid differentiation factor 2 (TLR4/MD-2) complex. The lipid chains and the phosphorylated disaccharide core of lipid A moiety are responsible for the TLR4 agonist action of LPS, and the specific interaction between MD-2, TLR4, and lipid A are key to the formation of the activated complex (TLR4/MD-2/LPS)2, which starts intracellular signalling leading to nuclear factors activation and to production of inflammatory cytokines. Subtle chemical variations in the lipid and sugar parts of lipid A cause dramatic changes in endotoxin activity and are also responsible for the switch from TLR4 agonism to antagonism. While the lipid A pharmacophore has been studied in detail and its structure-activity relationship is known, the contribution of core saccharides 3-deoxy-d-manno-octulosonic acid (Kdo) and heptosyl-2-keto-3-deoxy-octulosonate (Hep) to TLR4/MD-2 binding and activation by LPS and LOS has been investigated less extensively. This review focuses on the role of lipid A, but also of Kdo and Hep sugars in LPS/TLR4 signalling.

The mitochondrial VDAC of bean seeds recruits phosphatidylethanolamine lipids for its proper functioning

The voltage-dependent anion-selective channel (VDAC) is the main pathway for inorganic ions and metabolites through the mitochondrial outer membrane. Studies recently demonstrated that membrane lipids regulate its function. It remains, however, unclear how this regulation takes place. In this study, we show that phospholipids are key regulators of Phaseolus VDAC function and, furthermore, that the salt concentration modulates this regulation. Both selectivity and voltage dependence of Phaseolus VDAC are very sensitive to a change in the lipid polar head from PC to PE. Interestingly enough, this dependence is observed only at low salt concentration. Furthermore, significant changes in VDAC functional properties also occur with the gradual methylation of the PE group pointing to the role of subtle chemical variations in the lipid head group. The dependence of PcVDAC gating upon the introduction of a small mole fraction of PE in a PC bilayer has prompted us to propose the existence of a specific interaction site for PE on the outer surface of PcVDAC.Eventually, comparative modeling and molecular dynamics simulations suggest a potential mechanism to get insight into the anion selectivity enhancement of PcVDAC observed in PE relative to PC.

Mechanisms of Ligand-Protein Interaction in Sec-14-like Transporters Investigated by Computer Simulations.

We review our recent work on protein-ligand interactions in vitamin transporters of the Sec-14-like protein. Our studies focused on the cellular-retinaldehyde binding protein (CRALBP) and the α-tocopherol transfer protein (α-TTP). CRALBP is responsible for mobilisation and photo-protection of short-chain cis-retinoids in the dim-light visual cycle or rod photoreceptors. α-TTP is a key protein responsible for selection and retention of RRR-α-tocopherol, the most active isoform of vitamin E in superior animals. Our simulation studies evidence how subtle chemical variations in the substrate can lead to significant distortion in the structure of the complex, and how these changes can either lead to new protein function, or be used to model engineered protein variants with tailored properties. Finally, we show how integration of computational and experimental results can contribute in synergy to the understanding of fundamental processes at the biomolecular scale.

A double effect molecular switch leads to a novel potent negative allosteric modulator of metabotropic glutamate receptor 5

Compounds that modulate the function of G-protein-coupled receptors (GPCRs) by binding to their allosteric sites are of potential interest for the treatment of multiple CNS and non-CNS disorders. Allosteric ligands can act either as positive (PAM), negative (NAM), or silent (SAM) receptor modulators and have numerous advantages over classic orthosteric compounds, including improved GPCR-subtype selectivity; the capacity to adapt to physiological conditions; and better safety profiles. Despite these benefits, allosteric modulators are difficult to design and optimize and are often prone to “molecular switching”: a structural phenomenon by which very subtle chemical variations in the ligand result in unexpected changes in selectivity profiles or pharmacology, changing PAMs to NAMs or vice versa. Here, we report the discovery of a nanomolar and subtype selective NAM of metabotropic glutamate receptor 5 (mGlu5) through a targeted “double effect molecular switch” of a potent mGlu4 PAM, and suggests a promising approach towards the discovery of novel mGluR allosteric modulators.

Terrestrial lidar and hyperspectral data fusion products for geological outcrop analysis

Close-range hyperspectral imaging is an emerging technique for remotely mapping mineral content and distributions in inaccessible geological outcrop surfaces, allowing subtle chemical variations to be identified with high resolution and accuracy. Terrestrial laser scanning (lidar) is an established method for rapidly obtaining three-dimensional geometry, with unparalleled point density and precision. The combination of these highly complementary data types – 3D topography and surface properties – enables the production of value-added photorealistic outcrop models, adding new information that can be used for solving geological problems. This paper assesses the benefits of merging lidar and hyperspectral imaging, and presents qualitative and quantitative means of analysing the fused datasets. The integration requires an accurate co-registration, so that the 2D hyperspectral classification products can be given real measurement units. This stage is reliant on using a model that correctly describes the imaging geometry of the hyperspectral instrument, allowing image pixels and 3D points in the lidar model to be related. Increased quantitative analysis is then possible, as areas and spatial relationships can be examined by projecting classified material boundaries into 3D space. The combined data can be interpreted in a very visual manner, by colouring and texturing the lidar geometry with hyperspectral mineral maps. Because hyperspectral processing often results in several image products and classifications, these can be difficult to analyse simultaneously. A novel visualisation method is presented, where photorealistic lidar models are superimposed with multiple texture-mapped layers, allowing blending between conventional and hyperspectral imaging products to assist with interpretation and validation. The advantages and potential of the data fusion are illustrated with example outcrop data.

Unravelling carbonatite–silicate magma interaction dynamics: A case study from the Velay province (Massif Central, France)

Mechanisms of interaction between a carbonatite magma and a silicate magma are inferred on the basis of the textural and geochemical features of a carbonate-bearing tuff from the Massif Central, characterized by the presence of carbonatite globules within a silicate glass matrix. A two-fluid dynamical model is proposed in order to constrain the formation of the carbonatite globules that underwent no geochemical re-equilibration with the trachyte magma due to rapid thermal re-equilibration and crystallization of dolomite. It is suggested that a viscous fingering instability occurred simultaneously with the injection of a carbonatite magma into a chamber filled with a more viscous trachytic magma. Instantaneous fragmentation of the fingers, induced by the action of gradient stresses, resulted in the formation of a magmatic emulsion. The replenishment event triggered immediate evacuation of the magma chamber such that interaction between the two magmas occurred over a short time scale and large-scale mixing was prevented. The exsolution of volatiles, perhaps as a consequence of the recharge event shortly before the eruption, drove a metasomatic event that produced the subtle chemical variations observed at the interface between carbonatite globules and silicate matrix.

Solid State Phosphorus‐31 Magnetic Resonance Imaging of Bone Mineral

Chemically selective solid state phosphorus-31 nuclear magnetic resonance (NMR) imaging of the mineral phase of bone and synthetic calcium phosphate models for bone mineral is demonstrated with microscopy-scale (about 5 mm field of view) apparatus at 6.0 T magnetic field strength. Pixel-by-pixel linear combination of image data from multiple radio frequency (RF) pulse sequences, chosen to develop contrast between chemical constituents of interest in the mineral, generates derived images showing the distribution of individual constituents. The technique combines the noninvasive character of magnetic resonance imaging (MRI) with the ability of solid state NMR spectroscopy to characterize subtle chemical variations in bone mineral, as well as to measure the amount of mineral. These methods are, in principle, extensible to larger dimensional scales suitable for live animal subjects or human limbs.

ChemInform Abstract: Chemical Aspects of Selenium as a Photoreceptor.

Abstract Selenium has been a prime material choice for use as a photoreceptor in xerographic machines because of its high conversion efficiency of visible radiation to charge carriers, its excellent charge transport and its immunity to change during use. Impacts to these properties have been ascribed to structural and chemical variations. The current status is reviewed and new data is presented implicitly demonstrating the subtle chemical variations which have important impacts on trapping kinetics. The role of arsenic and chlorine alloying upon these kinetics is introduced.

CHEMICAL ASPECTS OF SELENIUM AS A PHOTORECEPTOR

Abstract Selenium has been a prime material choice for use as a photoreceptor in xerographic machines because of its high conversion efficiency of visible radiation to charge carriers, its excellent charge transport and its immunity to change during use. Impacts to these properties have been ascribed to structural and chemical variations. The current status is reviewed and new data is presented implicitly demonstrating the subtle chemical variations which have important impacts on trapping kinetics. The role of arsenic and chlorine alloying upon these kinetics is introduced.