Deciphering the enigmatic PilY1 of Acidithiobacillus thiooxidans: An in silico analysis.

Thirty years since the first report on the PilY1 protein in bacteria, only the C-terminal domain has been crystallized; there is no study in which the N-terminal domain, let alone the complete protein, has been crystallized. In our laboratory, we are interested in characterizing the Type IV Pili (T4P) of Acidithiobacillus thiooxidans. We performed an in silico characterization of PilY1 and other pilins of the T4P of this acidophilic bacterium. In silico characterization is crucial for understanding how proteins adapt and function under extreme conditions. By analyzing the primary and secondary structures of proteins through computational methods, researchers can gain valuable insights into protein stability, key structural features, and unique amino acid compositions that contribute to resilience in harsh environments. Here, it is presented a description of the particularities of At. thiooxidans PilY1 through predictor software and homology data. Our results suggest that PilY1 from At. thiooxidans may have the same role as has been described for other PilY1 associated with T4P in neutrophilic bacteria; also, its C-terminal interacts (interface interaction) with the minor pilins PilX, PilW and PilV. The N-terminal region comprises domains such as the vWA and the MIDAS, involved in signaling, ligand-binding, and protein-protein interaction. In fact, the vWA domain has intrinsically disordered regions that enable it to maintain its structure over a wide pH range, not only at extreme acidity to which At. thiooxidans is adapted. The results obtained helped us design the correct methodology for its heterologous expression. This allowed us partially experimentally characterize it by obtaining the N-terminal domain recombinantly and evaluating its acid stability through fluorescence spectroscopy. The data suggest that it remains stable across pH changes. This work thus provides guidance for the characterization of extracellular proteins from extremophilic organisms.

Exploration of Free Energy Surface of the Au10 Nanocluster at Finite Temperature.

The first step in comprehending the properties of Au10 clusters is understanding the lowest energy structure at low and high temperatures. Functional materials operate at finite temperatures; however, energy computations employing density functional theory (DFT) methodology are typically carried out at zero temperature, leaving many properties unexplored. This study explored the potential and free energy surface of the neutral Au10 nanocluster at a finite temperature, employing a genetic algorithm coupled with DFT and nanothermodynamics. Furthermore, we computed the thermal population and infrared Boltzmann spectrum at a finite temperature and compared it with the validated experimental data. Moreover, we performed the chemical bonding analysis using the quantum theory of atoms in molecules (QTAIM) approach and the adaptive natural density partitioning method (AdNDP) to shed light on the bonding of Au atoms in the low-energy structures. In the calculations, we take into consideration the relativistic effects through the zero-order regular approximation (ZORA), the dispersion through Grimme's dispersion with Becke-Johnson damping (D3BJ), and we employed nanothermodynamics to consider temperature contributions. Small Au clusters prefer the planar shape, and the transition from 2D to 3D could take place at atomic clusters consisting of ten atoms, which could be affected by temperature, relativistic effects, and dispersion. We analyzed the energetic ordering of structures calculated using DFT with ZORA and single-point energy calculation employing the DLPNO-CCSD(T) methodology. Our findings indicate that the planar lowest energy structure computed with DFT is not the lowest energy structure computed at the DLPN0-CCSD(T) level of theory. The computed thermal population indicates that the 2D elongated hexagon configuration strongly dominates at a temperature range of 50-800 K. Based on the thermal population, at a temperature of 100 K, the computed IR Boltzmann spectrum agrees with the experimental IR spectrum. The chemical bonding analysis on the lowest energy structure indicates that the cluster bond is due only to the electrons of the 6 s orbital, and the Au d orbitals do not participate in the bonding of this system.

Biosynthesis of carotenoids in Azospirillum brasilense Cd is mediated via squalene (C30) route.

Azospirillum brasilense is a non-photosynthetic α-Proteobacteria, belongs to the family of Rhodospirillaceae and produces carotenoids to protect itself from photooxidative stress. In this study, we have used Resonance Raman Spectra to show similarity of bacterioruberins of Halobacterium salinarum to that of A. brasilense Cd. To navigate the role of genes involved in carotenoid biosynthesis, we used mutational analysis to inactivate putative genes predicted to be involved in carotenoid biosynthesis in A. brasilense Cd. We have shown that HpnCED enzymes are involved in the biosynthesis of squalene (C30), which is required for the synthesis of carotenoids in A. brasilense Cd. We also found that CrtI and CrtP desaturases were involved in the transformation of colorless squalene into the pink-pigmented carotenoids. This study elucidates role of some genes which constitute very pivotal role in biosynthetic pathway of carotenoid in A. brasilense Cd.

Absorption spectra of p-nitroaniline derivatives: charge transfer effects and the role of substituents.

CONTEXT: Push-pull compounds are model systems and have numerous applications. By changing their substituents, properties are modified and new molecules for different applications can be designed. The work investigates the gas-phase electronic absorption spectra of 15 derivatives of push-pull para-nitroaniline (pNA). This molecule has applications in pharmaceuticals, azo dyes, corrosion inhibitors, and optoelectronics. Both electron-donor and electron-withdrawing groups were investigated. Employing machine learning-derived Hammett's constants σm, σm0, σR, and σI, correlations between substituents and electronic properties were obtained. Overall, the σm0 constants presented the best correlation with HOMO and LUMO energies, whereas the σR constants best agreed with the transition energy of the first band and HOMO-LUMO energy gap. Electron-donors, which have lower σR values, redshift the absorption spectrum and reduce the HOMO-LUMO energy gap. Conversely, electron-withdrawing groups (higher σR's) blueshift the spectrum and increase the energy gap. The second band maximum energies, studied here for the first time, showed no correlation with σ but tended to increase with σ. A comprehensive charge transfer (CT) analysis of the main transition of all systems was also carried out. We found that donors (lower σ's) slightly enhance the CT character of the unsubstituted pNA, whereas acceptors (higher σ's) decrease it, leading to increased local excitations within the aromatic ring. The overall CT variation is not large, except for pNA-SO2H, which considerably decreases the total CT value. We found that the strong electron donors pNA-OH, pNA-OCH3, and pNA-NH2, which have the smallest HOMO-LUMO energy gaps and lowest σ's, have potential for optoelectronic applications. The results show that none of the studied molecules is fluorescent in the gas phase. However, pNA-NH2 and pNA-COOH in cyclohexane and water reveal fluorescence upon solvation. METHODS: We investigated theoretically employing the second-order algebraic diagrammatic construction (ADC(2)) ab initio wave function and time-dependent density functional theory (TDDFT) the gas-phase electronic absorption spectra of 15 derivatives of p-nitroaniline (pNA). The investigated substituents include both electron-donor (C6H5, CCH, CH3, NH2, OCH3, and OH,) and electron-withdrawing (Br, CCl3, CF3, Cl, CN, COOH, F, NO2, and SO2H) substituents.

Red Dragon Fruit Peels: Effect of Two Species Ratio and Particle Size on Fibre Quality and Its Application in Reduced-Fat Alpaca-Based Sausages.

This research aimed to assess the influence of red dragon fruit peels ratio (RDF-PR) from two species, Hylocereus hybridum (HH) and Hylocereus undatus (HU), and particle size (PS) on quality parameters of red dragon fruit peel powder (RDF-PP) and its further application in emulsified alpaca-based sausages as partial substitutes of pork-back fat. A three-level full factorial design (nine treatments) was employed to evaluate the effect of RDF-PR (HH(0%):HU(100%), HH(50%):HU(50%), and HH(100%):HU(0%)) and PS (499-297, 296-177, and <177 µm) on the dependent variables: L*, a*, b*, C, h°, water-holding capacity, oil-holding capacity, swelling capacity, pectin yield, degree of esterification (analysed through FT-IR), and crude fibre content. The data analysed through a response surface methodology showed that treatment one (T1) is the best with the optimised conditions at 100% HU RDF-PR and PS of <177 µm. The statistical validation of T1 exhibited the highest water-holding capacity (32.1 g/g peel), oil-holding capacity (2.20 g oil/g peel), and pectin yield (27.1%). A completely randomised design (four formulations) was then used to assess the effect of partial replacement of pork-back fat by T1 in emulsified alpaca-based sausages on the colourimetric, physicochemical, and texture properties (hardness, chewiness, cohesiveness, springiness, adhesiveness, and adhesive force). Likewise, a sensory hedonic scale was employed to evaluate the appearance, colour, odour, flavour, texture, and overall acceptability of sausages. The results revealed that 65.7% of pork-back fat content was successfully replaced compared with a control formulation. Additionally, F3 showed significantly (p < 0.05) better colourimetric, physicochemical, and textural characteristics, such as lower hardness (34.8 N) and chewiness (21.7 N) and higher redness (a* = 19.3) and C (22.9), compared to a control formulation. This research presents RDF-PP as a promising fat substitute for developing healthier, reduced-fat meat products using fibre-rich agroindustry by-products.

Copper complex molecules as dye-sensitizers: Hybrid MetaGGA and standard + van der Waals functionals.

This study focuses on the use of Density Functional Theory calculations with two main approaches: computational chemistry and computational physics. The following three cases were considered for the derivation: (I) computational chemistry using the M06 hybrid functional, (II) computational chemistry using the standard PBE functional including vdW interactions, and (III) computational physics using the standard PBE functional including vdW interactions and periodic boundary conditions. Since the approximation using hybrid functionals M06 has been extensively validated, this method was used as a reference. The second and third methods are less expensive, it is ideal for use to extend large systems. From the sensitized molecules are found in the gas phase and include solvent effects through the integral equation formalism polarizable continuum model. In a systematic analysis of 15 Cu complex molecules, a complete characterization for DSSCs has been carried out and molecular geometry, electronic and optical measurements have been reported.

Lignin Analysis by HPLC and FTIR: Spectra Deconvolution and S/G Ratio Determination.

Fourier transform infrared spectroscopy (FTIR) is a simple nondestructive technique that allows the user to obtain quick and accurate information about the structure of the constituents of wood. Spectra deconvolution is a computational technique, complementary to FTIR analysis, which improves the resolution of overlapped or unobserved bands in the raw spectra. High performance liquid chromatography (HPLC) is an analytical technique useful to determine the ratio of the lignin monomers obtained by the alkaline nitrobenzene oxidation method. Furthermore, lignin content has been commonly determined by wet chemical methods; Klason lignin determination is a quick and accessible method. Here, we detail the procedures for chemical analysis of the wood lignin using these techniques. Additionally, the deconvolution process of FTIR spectra for the determination of the S/G ratio, in lignin isolated by this or other methods, is explained in detail.

New Tricholomalides D-G from the Mushroom Tricholoma ustaloides Grown in an Italian Beech Wood.

Four novel seconeodolastane diterpenoids, named tricholomalides D-G, were isolated, together with the known tricholomalide C, from the fruiting bodies of Tricholoma ustaloides Romagn., a species belonging to the large Tricholoma genus of higher mushrooms (Basidiomycota, family Tricholomataceae). They were isolated through multiple chromatographic separations, and the structures, including the absolute configuration, were established through a detailed analysis of MS, NMR, and CD spectral data and comparison with related compounds reported in the literature, which has been thoroughly revised.

Structural and Electromagnetic Signatures of Anatase and Rutile NTs and Sheets in Three Different Water Models under Different Temperature Conditions.

Experimental studies of TiO2 nanotubes have been conducted for nearly three decades and have revealed the remarkable advantages of this material. Research based on computer simulations is much rarer, with research using density functional theory (DFT) being the most significant in this field. It should be noted, however, that this approach has significant limitations when studying the macroscopic properties of nanostructures such as nanosheets and nanotubes. An alternative with great potential has emerged: classical molecular dynamics simulations (MD). MD Simulations offer the possibility to study macroscopic properties such as the density of phonon states (PDOS), power spectra, infrared spectrum, water absorption and others. From this point of view, the present study focuses on the distinction between the phases of anatase and rutile TiO2. The LAMMPS package is used to study both the structural properties by applying the radial distribution function (RDF) and the electromagnetic properties of these phases. Our efforts are focused on exploring the effect of temperature on the vibrational properties of TiO2 anatase nanotubes and an in-depth analysis of how the phononic softening phenomenon affects TiO2 nanostructures to improve the fundamental understanding in different dimensions and morphological configurations. A careful evaluation of the stability of TiO2 nanolamines and nanotubes at different temperatures is performed, as well as the adsorption of water on the nanosurface of TiO2, using three different water models.

Shape, Microstructure, and Chemical Composition of Pearls from the Freshwater Clam Diplodon chilensis Native to South America.

The capability to produce pearls is widespread in the phylum Mollusca, including bivalves of the superfamily Unionoidea. Here, we identified and characterized natural pearls formed by Diplodon chilensis, a freshwater clam native to southern South America, using samples obtained from two lakes located in the Chilean Patagonia. Pearls were studied using light and scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), Fourier transform infrared spectroscopy (FTIR), and Raman spectroscopy. Naturally formed pearls were found in both male and female D. chilensis specimens. Pearls are produced in different shapes, including spherical, ellipsoidal, buttoned, and bumpy, ranging in size from 200 µm to 1.9 mm. The internal microstructure is composed of irregular polygonal tablets, about 0.40 to 0.55 µm in thickness. EDX analysis showed that pearls are composed of calcium carbonate. FTIR and Raman spectra recorded several peaks attributable to the aragonite in pearls of this species, as has been shown in other mollusks. In addition to these results, pearls of different colors are illustrated.

Phenotypic Analysis of Fourier-Transform Infrared Milk Spectra in Dairy Goats.

The infrared spectrum of bovine milk is used to predict many interesting traits, whereas there have been few studies on goat milk in this regard. The objective of this study was to characterize the major sources of variation in the absorbance of the infrared spectrum in caprine milk samples. A total of 657 goats belonging to 6 breeds and reared on 20 farms under traditional and modern dairy systems were milk-sampled once. Fourier-transform infrared (FTIR) spectra were taken (2 replicates per sample, 1314 spectra), and each spectrum contained absorbance values at 1060 different wavenumbers (5000 to 930 × cm-1), which were treated as a response variable and analyzed one at a time (i.e., 1060 runs). A mixed model, including the random effects of sample/goat, breed, flock, parity, stage of lactation, and the residual, was used. The pattern and variability of the FTIR spectrum of caprine milk was similar to those of bovine milk. The major sources of variation in the entire spectrum were as follows: sample/goat (33% of the total variance); flock (21%); breed (15%); lactation stage (11%); parity (9%); and the residual unexplained variation (10%). The entire spectrum was segmented into five relatively homogeneous regions. Two of them exhibited very large variations, especially the residual variation. These regions are known to be affected by the absorbance of water, although they also exhibited wide variations in the other sources of variation. The average repeatability of these two regions were 45% and 75%, whereas for the other three regions it was about 99%. The FTIR spectrum of caprine milk could probably be used to predict several traits and to authenticate the origin of goat milk.

Selectivity of soil constituents by termites in the construction of Brazilian termite mounds

Termites can create structures that alter the physical and chemical properties of soils. In this process, termites are selective about the soil constituents they will use to construct their mounds. Considering the common occurrence of termite mounds in Brazilian soils, this study aimed to investigate the selective action of termites in the mound building process. Samples were collected from six termite mounds and control soils (at a distance of 15 to 30 m from the termite mound) in different regions in Brazil to analyze the fine earth fraction. The content of clay fraction, organic C and Fe in pedogenic iron oxides increased in the mounds resulting in specific surface area increments. X-ray diffraction indicated a selectivity of termites by clay-sized particles such as kaolinite, gibbsite and iron oxides (hematite and goethite) rather than larger particles such as quartz. The proportion of low-crystalline iron oxides and the maghemite amount decreased in the mounds. The change of color parameters in the termite mounds was due to a combination of increase in clay fraction, organic carbon and iron oxides. The techniques used were sensitive, indicating changes and similarities between the control soils and the termite mounds.(AU)

First report of chemical composition and cytotoxicity evaluation of Foraminispora rugosa basidiomata from Brazil.

BACKGROUND: Foraminispora rugosa is a species reported from Brazil, Venezuela, French Guiana, Costa Rica and Cuba. It is a basidiomycete in the Ganodermataceae family. In this study, both chemical composition and cytotoxicity of the ethanolic extract of F. rugosa were investigated for the first time. RESULTS: Phylogenetic analysis confirmed the identification of the specimens, and the results of cytotoxicity assays showed that at concentrations of 7.8-500.0 µg/mL the ethanolic extract displayed weak cytotoxicity against the tested cell lines. Five oxylipins were identified by ultra high performance liquid chromatography coupled with quadrupole time-of-flight and mass spectrometry (UHPLC-QTOF-MS). CONCLUSIONS: This study provides new insights into the current knowledge of bioactive compounds produced by macrofungi, and provides data for future biological assays with relative selectivity and safety.

Multivariate strategy for identifying and quantifying jet fuel contaminants by MCR-ALS/PLS models coupled to combined MIR/NIR spectra.

The investigation and control of jet fuel contamination for private aircrafts has gained attention due to the softer monitoring in comparison to commercial aviation. The possible contamination with kerosene solvent (KS) makes this investigation more challenging, since it has physicochemical similarities with jet fuel. To help solve this problem, a chemometric methodology was applied in this research combining multivariate curve resolution with alternating least squares (MCR-ALS) and partial least squares (PLS) models coupled to near- and mid-infrared spectroscopies (MIR/NIR) in order to detect and quantify KS in blends with JET-A1 using 23 samples (5-60% v/v). Additionally, 98 samples were stored for 60 days, and principal component analysis, genetic algorithm, and successive projections algorithm were coupled to linear discriminant analysis (PCA-LDA, GA-LDA, and SPA-LDA) in order to classify the blends according to the bands assigned to oxidation products, such as phenols and carboxylic acids. GA-LDA and SPA-LDA models were accurate and reached 100% sensitivity and specificity. Physicochemical analysis was not able to detect the presence of KS in contaminated jet fuel samples, even in high concentrations. The use of MIR-NIR combined spectra improved the quantification results, thus decreasing the experimental error from 5.22% (using only NIR) to 1.64%. PLS regression quantified the content of KS with high accuracy (RMSEP < 1.64%, R2 > 0.995). The MCR-ALS model stood out for recovering the spectral profile of kerosene solvent by segregating it from jet fuel spectra. The development of models using chemometric tools contributed to a fast, low-cost, and efficient process for quality control that can be applied in the fuel industry.

Estimation of Soluble Solids for Stone Fruit Varieties Based on Near-Infrared Spectra Using Machine Learning Techniques.

The quality control for fruit maturity inspection is a key issue in fruit packaging and international trade. The quantification of Soluble Solids (SS) in fruits gives a good approximation of the total sugar concentration at the ripe stage, and on the other hand, SS alone or in combination with acidity is highly related to the acceptability of the fruit by consumers. The non-destructive analysis based on Visible (VIS) and Near-Infrared (NIR) spectroscopy has become a popular technique for the assessment of fruit quality. To improve the accuracy of fruit maturity inspection, VIS−NIR spectra models based on machine learning techniques are proposed for the non-destructive evaluation of soluble solids in considering a range of variations associated with varieties of stones fruit species (peach, nectarine, and plum). In this work, we propose a novel approach based on a Convolutional Neural Network (CNN) for the classification of the fruits into species and then a Feedforward Neural Network (FNN) to extract the information of VIS−NIR spectra to estimate the SS content of the fruit associated to several varieties. A classification accuracy of 98.9% was obtained for the CNN classification model and a correlation coefficient of Rc>0.7109 for the SS estimation of the FNN models was obtained. The results reported show the potential of this method for a fast and on-line classification of fruits and estimation of SS concentration.

Micellar entanglement and its relation to the elastic behavior of wormlike micelle fluids.

HYPOTHESIS: The elastic contribution to the fluid dynamics of wormlike micellar solutions makes these fluids unique due to the distinctive self-assembled micellar network formed by tubular micelles. Measured mesoscopic scales of the micellar network related to the degree of entanglement can give guidelines for understanding the origin of elastic forces and their effect on rheological response. EXPERIMENTS: Different experiments were made as flow curves, rotating the internal or external cylinder in a Couette geometry, small and large oscillatory shear tests, and linear shear banding observations, all of them to determine how elastic forces modify the rheological behavior in systems made of different ratios of hexadecyltrimethylammonium bromide (CTAB)/sodium salicylate (NaSal) and different ratios of CTAB/NaNO3. Diffusive wave spectroscopy micro-rheology was also performed to measure the mean square displacements of microspheres embedded in the micellar fluids to obtain their high-frequency viscoelastic spectra. With this information, the entanglement index κ, the ratio of the total contour of the micelles to the entanglement length, was estimated and correlated with the rheological behavior. FINDINGS: The entanglement index is a valuable piece of information to understand the origin of the contribution of the elastic forces from a molecular point of view on the fluid dynamics of wormlike micelle solutions.

Molecular structures of two copper complexes with the pharmaceuticals norfloxacin and tinidazole, when powder X-ray diffraction assists multi-domain single-crystal X-ray diffraction.

The crystal structures of bis[1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-ium-4-yl)-1,4-dihydroquinoline-3-carboxylato]copper(II) sulfate heptahydrate, [Cu(C16H18FN3O3)2]SO4·7H2O or [Cu(nor)2]SO4·7H2O (nor is norfloxacin), and bis{1-[2-(ethylsulfonyl)ethyl]-2-methyl-5-nitroimide}dinitratocopper(II), [Cu(NO3)2(C8H13N3O4S)2] or [Cu(NO3)2(tnz)2] (tnz is tinidazole), were solved by X-ray diffraction. Both complexes crystallize in the space group P21/c, with Z = 4 (for nor) and Z = 2 (for ntz) molecules per unit cell. In [Cu(nor)2]SO4·7H2O, the CuII ion is at the centre of a square-planar environment, trans coordinated to two independent norfloxacin molecules in the zwitterionic form acting as bidentate ligands through one of the carboxyl (cbx) and the carbonyl (cb) O atoms. The solid is further stabilized by an extensive network of N-H...O(sulfate), N-H...O(cbx), N-H...OW, OW-H...O(sulfate) and OW-H...OW hydrogen bonds. The [Cu(NO3)2(tnz)2] complex is centrosymmetric, with the CuII ion in a square planar environment, coordinated to a tinidazole molecule acting as a monodentate ligand through its imidazole N atom and to one nitrate O atom. The vibrational FT-IR absorption spectra and thermal behaviour of the complexes were also studied and are briefly discussed based on the crystal structures.

Investigation of the influence of clathrate hydrate crystals on the structuring of homeopathic high dilutions

High dilutions (HD) of drugs used in homeopathy are mostly too dilute to contain original drug molecules. But evidences support their specific biological and therapeutic effects. The reason behind this is thought to be water structure characteristic of the original drug. Spectroscopic studies indicate that the specific water structure in HDs can be resolved into free water molecules, hydrogen bonding strength of water hydroxyl, number of hydrogen bonds and clathrate hydrate crystals (CHC). HDs are prepared in EtOH water solution by serial dilution and mechanical agitation, and are called potencies. The objective of the present study is to further confirm the presence of CHCs in the two potencies of three drugs. Electronic spectra of the HDs of the potencies indicate two broad peaks and marked difference in intensities of absorption. Furior Transform Infrared (FT-IR) spectra of the test potencies and their control show difference in intensity shift and contour shape of OH stretching and bending bands. All the experimental data indicate the presence of CHCs in varying amounts in the test potencies.

Blue Titania: The Outcome of Defects, Crystalline-Disordered Core-Shell Structure, and Hydrophilicity Change.

In this research, changes in several characteristics of partially reduced titania were studied. The reduction process used made it possible to gradually observe changes in the material depending on the amount of reducing agent used. We used NaBH4 to impregnate commercial TiO2 with isopropyl alcohol. Impregnated TiO2 nanoparticles were dried and thermally treated in a nitrogen flow to obtain blue titania samples. Thorough spectroscopic characterization showed that oxygen atoms from hydroxyl groups, as well as from the surface, and the lattice of TiO2 was consumed. This caused changes in the surface and even in the bulk of TiO2 when the amount of reducing agent used was increased. Structural, optical, superficial, and textural characteristics were studied using XRD, Raman, DRS UV-Vis-NIR, Mid-DRIFT, XPS, and nitrogen adsorption/desorption isotherms. A photocatalytic test of the degradation of methylene blue dye was performed. Among different effects on the mentioned characteristics, we found evidence of changes in the surface properties of the blue titania samples and their probable effect on the photocatalytic properties. The reduction process implied a preponderant decrease in the surface hydrophilicity of the reduced samples, an effect shown for the first time in this type of material.