Characterization Of Structural Changes Research Articles

What Can Be Learned from the Partitioning Behavior of Proteins in Aqueous Two-Phase Systems?

This review covers the analytical applications of protein partitioning in aqueous two-phase systems (ATPSs). We review the advancements in the analytical application of protein partitioning in ATPSs that have been achieved over the last two decades. Multiple examples of different applications, such as the quality control of recombinant proteins, analysis of protein misfolding, characterization of structural changes as small as a single-point mutation, conformational changes upon binding of different ligands, detection of protein-protein interactions, and analysis of structurally different isoforms of a protein are presented. The new approach to discovering new drugs for a known target (e.g., a receptor) is described when one or more previous drugs are already available with well-characterized biological efficacy profiles.

Characterization of structural changes occurring in insulin at different time intervals at room temperature by surface-enhanced Raman spectroscopy

BackgroundInsulin storage above the temperature recommended by food and drug administration (FDA) causes decrease in its functional efficacy due to degradation and aggregation of its protein based active pharmaceutical ingredient (API) that results poor glycemic control in diabetic patients. The aggregation of protein causes serious neurodegenerative diseases such as type-2 diabetes, Huntington disease, Parkinson's disease, and Alzheimer's disease. Surface-enhanced Raman spectroscopy (SERS) has been employed for the denaturation study of many proteins at the temperature above the recommendations of food and drug administration (FDA) (above 30 °C) which indicates potential of technique for such studies. ObjectiveSERS along with multivariate discriminating analysis techniques-based analysis of degradation of liquid pharmaceutical insulin protein after regular intervals of time at room temperature to analyze the structural changes in this protein during the storage of insulin pharmaceutical at room temperature. MethodsSilver nanoparticles (Ag-NPs) prepared by chemical reduction method are used as SERS active substrate for the surface enhancement of the insulin spectral signal. SERS spectral measurements of insulin were collected from eight different samples of insulin in the time range of 7 pm to 7 am first at fridge temperature (5 °C), second after half hour and next six with the time difference of 2 h each time at room temperature. The acquired SERS spectral data was preprocessed and analyzed. SERS structural transformations detection and discrimination potential in insulin was further confirmed by applying multivariate discriminating analysis techniques including principal component analysis (PCA) and Partial least square regression analysis (PLSR). ResultsSERS significantly detects the structural changes produced in insulin even after 2 h of insulin placement at room temperature. PCA successfully differentiates the insulin spectral data obtained after regular intervals of time according to PC-1 (77 %) explained variance. Application of PLSR model provides quantitative confirmation of SERS efficiency, by providing insulin data regression coefficients plot, efficient prediction of time with calibration data set having 0.77 mean square absolute error of calibration (RMSAEC), validation data set with 0.80 mean square absolute error of prediction (RMSAEP) and 0.98 coefficient of determination (R2) for both calibration and validation data set. ConclusionSERS is proved as a highly sensitive and discriminating technique to detect and discriminate insulin structural changes after regular intervals of time at room temperature.

Production of oyster mushroom (Pleurotus ostreatus) from some waste lignocellulosic materials and FTIR characterization of structural changes

In this study, oyster (Pleurotus ostreatus) mushroom was cultivated from hazelnut branches (HB) (Corylus avellana L.), hazelnut husk (HH), wheat straw (WS), rice husk (RH) and spent coffee grounds (CG). Hazelnut branch waste was used for the first time in oyster mushroom cultivation. In the study, mushrooms were grown by preparing composts from 100 to 50% mixtures of each waste type. Yield, biological activity, spawn run time, total harvesting time and mushroom quality characteristics were determined from harvested mushroom caps. In addition, chemical analysis of lignocellulosic materials (extractive contents, holocellulose, α-cellulose, lignin and ash contents) were carried out as a result of mushroom production and their changes according to their initial amounts were examined. In addition, the changes in the structure of waste lignocellulosic materials were characterized by FTIR analysis. As a result of the study, 172 g/kg yield was found in wheat straw used as a control sample, while it was found as 255 g/kg in hazelnut branch pruning waste. The highest spawn run time (45 days) was determined in the compost prepared from the mixture of hazelnut husk and spent coffee ground wastes. This study showed that HB wastes can be used for the cultivation of oyster mushroom (P. ostreatus). After mushroom cultivation processes, holocelulose and α-cellulose content rates decreased while ash contents increased. FTIR spectroscopy indicated that significant changes occurred in the wavelengths regarding cellulose, hemicellulose and lignin components. Most significant changes occurred in 1735, 1625, 1510, 1322 and 1230 wavelengths.

Melt polycondensation of poly (butylene oxalate-co-succinate) with great potential in curbing marine plastic pollution

Marine plastic pollution, with annual emissions into the marine over 53 million metric tons, has been a major worldwide concern. Many of so-called “biodegradable” polymers degrade very slowly in seawater. Oxalate have attracted attention because the electron-withdrawing effect of adjacent ester bonds promotes their natural hydrolysis, particularly in the ocean. However, the low boiling point and poor thermal stability of oxalic acids severely limits their applications. The successful synthesis of light-colored poly(butylene oxalate-co-succinate) (PBOS), with weight average molecular weight higher than 1 × 105 g/mol, displays the breakthroughs in the melt polycondensation of oxalic acid-based copolyesters. The copolymerization of oxalic acid retains the crystallization rate of PBS, with minimum half-crystallization times from 16 s (PBO10S) to 48 s (PBO30S). PBO10S-PBO40S exhibit good mechanical properties with elastic modulus of 218–454 MPa, and tensile strength between 12 and 29 MPa, better than packaging materials such as biodegradable PBAT and non-degradable LLDPE. PBOS achieve rapid degradation in the marine environment, with a mass loss 8%− 45% after 35 days. The characterization of structural changes demonstrate that the introduced oxalic acid plays a key role in the process of seawater degradation. This new class of polymers therefore provide highly promising materials for sustainable packaging with unique seawater degradation properties.

Scanning Electron Microscopy and Raman Spectroscopy Characterization of Structural Changes Induced by Thermal Treatment in Innovative Bio-Based Polyamide Nanocomposites

A comprehensive Raman scattering-based characterization of a full bio-based polyamide loaded with graphene nanoplatelets or layered double hydroxides (LDH) was assessed. The potential of the Raman spectroscopy was used to reveal several particularities of the nanocomposite structures induced by thermal treatment. Thus, a complete morpho-structural picture was obtained in combination with scanning electron microscopy (SEM) analysis of the neat polyamide and polyamide nanocomposites exposed at different thermal conditions (room temperature, 80 °C, and 145 °C). The analysis of G, D and 2D Raman peaks and their relative intensity ratio ID/IG, revealed the fact that the presence of graphene in polyamide is suitable for improving the essential physical properties and is also responsible for the decrease in the defects’ occurrence in the graphene layers. The surface of nanocomposites based on full bio-based polyamide, with different 2D fillers (graphenic and non-graphenic structures), was carefully evaluated before and after the thermal treatment by employing SEM and Raman analyses. The two thermal treatments allowed different chain mobility of the polymer (first temperature being over the polymer Tg and second one close to the melting phase in the viscoelastic stage). The spectroscopic and microscopic investigation was used to determine the conformational changes in filler aggregates and polymer surface, respectively.

Gastrophysical and chemical characterization of structural changes in cooked squid mantle.

Squid (Loligo forbesii and Loligo vulgaris) mantles were cooked by sous vide cooking using different temperatures (46°C, 55°C, 77°C) and times (30 s, 2min, 15min, 1 h, 5h, 24h), including samples of raw tissue. Macroscopic textural properties were characterized by texture analysis (TA) conducted with Meullenet-Owens razor shear blade and compared to analysis results from differential scanning calorimetry. The collagen content of raw tissues of squid was quantified as amount of total hydroxyproline using ultra-high-performance liquid chromatography. Structural changes were monitored by Raman spectroscopy and small-angle X-ray scattering and visualized by second harmonic generation microscopy. Collagen in the squid tissue was found to be highest in arms (4.3% of total protein), then fins (3.0%), and lowest in the mantle (1.5%), the content of the mantle being very low compared to that of other species of squid. Collagen was found to be the major protein responsible for cooking loss, whereas both collagen and actin were found to be key to mechanical textural changes. A significant decreased amount of cooking loss was obtained using a lower cooking temperature of 55°C compared to 77°C, without yielding significant textural changes in most TA parameters, except for TA hardness which was significantly less reduced. An optimized sous vide cooking time and temperature around 55-77°C and 0.5-5h deserves further investigation, preferably coupled to sensory consumer evaluation. PRACTICAL APPLICATION: The study provides knowledge about structural changes during sous vide cooking of squid mantle. The results may be translated into gastronomic use, promoting the use of an underutilized resource of delicious and nutritious protein (Loligo vulgaris and Loligo forbesii).

Ellipsometric analysis of isothermally devitrified metallic glasses

Effects of devitrification in metallic glasses are of particular interest for their utilization in various applications as the phase transformation from amorphous to crystalline state is known to significantly change their properties. In this work, we study the effect of devitrification on the optical properties of metallic glasses using the spectroscopic ellipsometry technique. Ellipsometry measurements on isothermally crystallized samples at controlled temperatures between the glass transition temperature and the crystallization temperature revealed characteristic dependence of the complex index of refraction on the controlled devitrification temperature, suggesting an effective optical approach which can be prospectively used for characterization of structural changes during devitrification. The crystallinity of devitrified samples was verified using a combination of differential scanning calorimetry and X-ray diffraction measurements.

Structural properties of diluted alkali-soluble pectin from Pyrus communis L. in water and salt solutions

The self-assembly and gelation of low-methoxyl diluted alkali-soluble pectin (LM DASP) from pear fruit (Pyrus communis L. cv. Conference) was studied in water and salt solutions (NaCl and CaCl2, constant ionic strength) without pH adjustment at 20 °C. The samples at different LM DASP concentrations were characterized using rheological tests, Fourier-transform infrared spectroscopy, dual-angle dynamic light scattering and atomic force microscopy. LM DASP from pear fruit (Pyrus communis L.) showed gelling ability. The indices (aggregation index and shape factor) based on light scattering may be useful for the characterization of structural changes in polysaccharide suspension, particularly for the determination of a gel point. The results obtained may be important for the food, cosmetic and pharmaceutical industries where pectin is used as a texturizer, an encapsulating agent, a carrier of bioactive substances or a gelling agent.

Characterization of structural changes in modern and archaeological burnt bone: Implications for differential preservation bias.

Structural and thermodynamic factors which may influence burnt bone survivorship in archaeological contexts have not been fully described. A highly controlled experimental reference collection of fresh, modern bone burned in temperature increments 100-1200˚C is presented here to document the changes to bone tissue relevant to preservation using Fourier transform infrared spectroscopy and X-ray diffraction. Specific parameters investigated here include the rate of organic loss, amount of bone mineral recrystallization, and average growth in bone mineral crystallite size. An archaeological faunal assemblage ca. 30,000 years ago from Tolbor-17 (Mongolia) is additionally considered to confirm visibility of changes seen in the modern reference sample and to relate structural changes to commonly used zooarchaeological scales of burning intensity. The timing of our results indicates that the loss of organic components in both modern and archaeological bone burnt to temperatures up to 700˚C are not accompanied by growth changes in the average crystallite size of bone mineral bioapatite, leaving the small and reactive bioapatite crystals of charred and carbonized bone exposed to diagenetic agents in depositional contexts. For bones burnt to temperatures of 700˚C and above, two major increases in average crystallite size are noted which effectively decrease the available surface area of bone mineral crystals, decreasing reactivity and offering greater thermodynamic stability despite the mechanical fragility of calcined bone. We discuss the archaeological implications of these observations within the context of Tolbor-17 and the challenges of identifying anthropogenic fire.

X-ray Natural Circular Dichroism Imaging of Multiferroic Crystals

The polarizing spectroscopy techniques in visible range optics have been used since the beginning of the 20th century to study the anisotropy of crystals based on birefringence and optical activity phenomena. On the other hand, the phenomenon of X-ray optical activity has been demonstrated only relatively recently. It is a selective probe for the element-specific properties of individual atoms in non-centrosymmetric materials. We report the X-ray Natural Circular Dichroism (XNCD) imaging technique which enables spatially resolved mapping of X-ray optical activity in non-centrosymmetric materials. As an example, we present the results of combining micro-focusing X-ray optics with circularly polarized hard X-rays to make a map of enantiomorphous twinning in a multiferroic SmFe3(BO3)4 crystal. Our results demonstrate the utility and potential of polarization-contrast imaging with XNCD as a sensitive technique for multiferroic crystals where the local enantiomorphous properties are especially important. In perspective, this brings a novel high-performance method for the characterization of structural changes associated with phase transitions and identification of the size and spatial distribution of twin domains.

Macroscopic Structural and Connectome Mapping of the Mouse Brain Using Diffusion Magnetic Resonance Imaging.

Translational work in rodents elucidates basic mechanisms that drive complex behaviors relevant to psychiatric and neurological conditions. Nonetheless, numerous promising studies in rodents later fail in clinical trials, highlighting the need for improving the translational utility of preclinical studies in rodents. Imaging of small rodents provides an important strategy to address this challenge, as it enables a whole-brain unbiased search for structural and dynamic changes that can be directly compared to human imaging. The functional significance of structural changes identified using imaging can then be further investigated using molecular and genetic tools available for the mouse. Here, we describe a pipeline for unbiased search and characterization of structural changes and network properties, based on diffusion MRI data covering the entire mouse brain at an isotropic resolution of 100 µm. We first used unbiased whole-brain voxel-based analyses to identify volumetric and microstructural alterations in the brain of adult mice exposed to unpredictable postnatal stress (UPS), which is a mouse model of complex early life stress (ELS). Brain regions showing structural abnormalities were used as nodes to generate a grid for assessing structural connectivity and network properties based on graph theory. The technique described here can be broadly applied to understand brain connectivity in other mouse models of human disorders, as well as in genetically modified mouse strains. Graphic abstract: Pipeline for characterizing structural connectome in the mouse brain using diffusion magnetic resonance imaging. Scale bar = 1 mm.

A NOVEL METHOD FOR ESTIMATION OF STRUCTURAL CHANGES IN POTATO CROPS FROM UAV-BASED DIGITAL SURFACE MODELS

Abstract. Climate change is arising challenges in potato crop production. More robust clones and cultivars adapted to climate change and resistant to pests and diseases, need to be developed. Several phenotyping approaches are being explored for a quick and affordable characterization of structural changes of crop varieties in real-world conditions. However, conventional methods present several problems. Field work in remote areas is time-consuming or difficult to carry out because of physical barriers. Satellite images lack the temporal resolution needed to monitor small changes in plant structure. Unmanned aerial vehicles (UAVs) provide high-resolution images which can give a better understanding of vegetation changes. Recent UAV-based studies have demonstrated the potential of the Normalized Difference Elevation Index (NDEI) to map centimeter-level changes in topography in different environments. This paper explores the potential of NDEI for identifying structural changes in experimental potato crops. In particular, it proposes an automatic method for estimation of volume changes in potato crop canopy. NDEI values were obtained by multi-temporal analysis of digital elevation models generated from UAV images using structure-from-motion (SfM) and multivision-stereo (MVS) techniques. The main components of the proposed method are: i) Image data capture from UAVs, ii) Data pre-processing, iii) NDEI calculation, and iv) Data processing and analysis. The results suggest that changes in surface elevation values, normalized using the NDEI index, are useful for rapid assessment of volume change in potato crop canopy. The NDEI reveals as an affordable technique to field measurement of phenotypic traits in potato breeding programs.

Avances y perspectivas en la modelación aplicada a la planeación forestal en México

En el ámbito forestal existe una larga historia en la parametrización y uso de modelos para cuantificar y predecir el crecimiento y rendimiento de las masas forestales, como un requisito fundamental para optimizar la aplicación de la silvicultura y el manejo forestal sustentable. La situación en México en el uso y generación de modelos ha avanzado de manera importante en los últimos años, lo que ha resultado en la constante generación de herramientas biométricas para la implementación de sistemas de planeación y ejecución de programas de manejo forestal. Sin embargo, aún existe la necesidad apremiante de generar herramientas biométricas para optimizar los procesos de planeación y aprovechamiento de los recursos forestales. Actualmente, se tiene un acervo importante de modelos para fines diversos, desde modelos de volumen, modelos de ahusamiento, sistemas compatibles ahusamiento-volumen, modelos de altura-diámetro, de clasificación de la productividad de terrenos forestales, de biomasa, carbono y contenido nutrimental de ecosistemas, de control de la densidad, de totalidad del rodal, de distribución diamétrica y de árbol individual. Dado el entorno dinámico que implica modelar procesos fisiológicos relacionados con el crecimiento forestal que involucran variables biológicamente más realistas, aún queda mucho por hacer en la modelación forestal. Sin embargo, se han dado pasos importantes en el establecimiento de sitios permanentes para la medición periódica del crecimiento y cambios estructurales de los rodales forestales, y aunado a la formación de especialistas en biometría y diseminados a lo largo del país, hacen que para un futuro cercano se pronostiquen avances importantes en esta área.

Comparing the backfilling of mesoporous titania thin films with hole conductors of different sizes sharing the same mass density.

Efficient infiltration of a mesoporous titania matrix with conducting organic polymers or small molecules is one key challenge to overcome for hybrid photovoltaic devices. A quantitative analysis of the backfilling efficiency with time-of-flight grazing incidence small-angle neutron scattering (ToF-GISANS) and scanning electron microscopy (SEM) measurements is presented. Differences in the morphology due to the backfilling of mesoporous titania thin films are compared for the macromolecule poly[4,8-bis-(5-(2-ethyl-hexyl)-thio-phen-2-yl)benzo[1,2-b;4,5-b']di-thio-phene-2,6-diyl-alt-(4-(2-ethyl-hexyl)-3-fluoro-thieno[3,4-b]thio-phene-)-2-carboxyl-ate-2-6-diyl)] (PTB7-Th) and the heavy-element containing small molecule 2-pinacol-boronate-3-phenyl-phen-anthro[9,10-b]telluro-phene (PhenTe-BPinPh). Hence, a 1.7 times higher backfilling efficiency of almost 70% is achieved for the small molecule PhenTe-BPinPh compared with the polymer PTB7-Th despite sharing the same volumetric mass density. The precise characterization of structural changes due to backfilling reveals that the volumetric density of backfilled materials plays a minor role in obtaining good backfilling efficiencies and interfaces with large surface contact.

Structural heterogeneity of epileptic foci in local drug-resistant epilepsy

To study etiopathogenesis is one of the most important tasks of modern neurology. Various types of structural changes occur in drug-resistant epilepsy (DRE); however, they are described as distinct phenomena. To provide a comprehensive characterization of structural changes in the cortex and adjacent white matter in the electrophysiological activity zone (in the epileptic focus) in patients undergoing surgery for DRE. Biopsy material of fragments of the temporal lobe and hippocampus from 16 patients aged 21 to 54 years (mean age, 25 years) with DRE were intraoperatively obtained at the Prof. A.L. Polenov Russian Research Institute of Neurosurgery. The investigators studied histological sections stained with H&E, toluidine blue according to the Nissl method and the Spielmeyer method, as well as the results of immunohistochemical reactions with glial fibrillary acidic protein (GFAP), vimentin, and neurofilaments (NF) (Dako antibodies, Denmark). Histological examination revealed a set of heterogeneous changes, reflecting the complex pathogenetic interactions that developed during the formation of an epileptic focus. Structural brain damage involved both gray and white matter. Focal cortical dysplasia was diagnosed in 14 (87.5%) cases; white matter neuronal heterotopia in 100%; neuronal reactive and destructive changes in 100%; epileptic leukoencephalopathy (vascular demyelination, microcysts, sclerosis and dystonia, gliosis) in 100%, cortical atrophy in 12.5%, and hippocampal sclerosis in 20% (in 2 out of the 10 examinees). The morphopathological heterogeneity in the structure of epileptic foci reflects the complexity of etiopathogenetic interactions, the polymorphism of epileptic manifestations, and the individual nature of formation of the epileptic system, which requires an integral approach to understanding the pathogenesis and morphogenesis of formation of the epileptic system and provides a direction for a personalized approach to epilepsy treatment.

Nondestructive characterization of structural changes during in vitro gastric digestion of apples using 3D time-series micro-computed tomography

An in-depth understanding of food structural breakdown during gastric digestion is paramount for development of health-promoting foods. This study presents a novel application of nondestructive time-series micro-computed tomography (micro-CT) to study structural breakdown during in vitro gastric digestion of apples (var. Granny Smith). Data collected from micro-CT images were compared with results from destructive analyses of apple tissue hardness (texture analysis) and moisture uptake during soaking in gastric juice or deionized water. Apples in gastric juice showed similar trends in intensity change (from micro-CT images) and hardness decrease (from texture analysis) over time compared with apples in water (p < 0.001). Apples in gastric juice or water exhibited similar changes in porosity and showed similar moisture uptake (p > 0.05). Overall, micro-CT imaging allows for assessment of changes along with detailed structural characterization of solid foods during in vitro gastric digestion.

Focus on lasers, imaging, and microscopy

Focus on lasers, imaging, and microscopy

Characterization of peptides self-assembly by low frequency Raman spectroscopy.

Low Frequency Vibrational (LFV) modes of peptides and proteins are attributed to the lattice vibrations and are dependent on their structural organization and self-assembly. Studies taken in order to assign specific absorption bands in the low frequency range to self-assembly behavior of peptides and proteins have been challenging. Here we used a single stage Low Frequency Raman (LF-Raman) spectrometer to study a series of diastereomeric analogue peptides to investigate the effect of peptides self-assembly on the LF-Raman modes. The structural variation of the diastereomeric analogues resulted in distinct self-assembly groups, as confirmed by transmission electron microscopy (TEM) and dynamic light scattering (DLS) data. Using LF-Raman spectroscopy, we consistently observed discrete peaks for each of the self-assembly groups. The correlation between the spectral features and structural morphologies was further supported by principal component analysis (PCA). The LFV modes provide further information on the degrees of freedom of the entire peptide within the higher order organization, reflecting the different arrangement of its hydrogen bonding and hydrophobic interactions. Thus, our approach provides a simple and robust complementary method to structural characterization of peptides assemblies.

In vivo characterization of structural changes after topical application of glucocorticoids in healthy human skin.

Topical glucocorticoids (GC) are known to induce changes in human skin with the potential to develop skin atrophy. Here, atrophogenic effects and subsequent structural changes in the skin after topical application of GC were investigated in vivo. Sixteen healthy volunteers were topically treated daily on the forearms with clobetasol propionate, betamethasone dipropionate, and the petrolatum vehicle for 4 weeks. All treated skin areas and a nontreated control area were examined by ultrasound, optical coherence tomography, confocal laser scanning microscopy, multiphoton tomography (MPT), and resonance Raman spectroscopy at baseline 1 day after last application and 1 week after last application. Investigated parameters included stratum corneum thickness, epidermal, and full skin thickness, keratinocyte size and density, keratinocyte nucleus-to-cytoplasm ratio, skin surface classification, relative collagen and elastin signal intensity, second-harmonic generation-to-autofluorescence aging index of dermis (SAAID), and the antioxidant status of the skin. A reduction in epidermal and dermal skin thickness was observed in GC treated as well as in vehicle-treated and untreated skin areas on the volar forearm. MPT analysis showed an increased epidermal cell density and reduced cell size and nucleus-to-cytoplasm ratio and a significant increase of SAAID after GC treatment indicating a restructuring or compression of collagen fibers clinically being observed as atrophic changes.

Dynamic characterization of structural changes in vapochromic compounds by pair distribution function

Two examples of anionic complexes having vapochromic behavior are investigated: [K(H2O)][Pt(ppy)(CN)2] “Pt(ppy)” and [K(H2O)][Pt(bzq)(CN)2] “Pt(bzq)”, where ppy = 2-phenylpyridinate and bzq = 7,8-benzoquinolate. These monohydrate-potassium salts exhibit a change in color from purple to yellow [Pt(ppy)] and from red to yellow [Pt(bzq)] upon heating to 110 °C, and they transform back into the original color upon absorption of water molecules from the environment. Available only in the form of polycrystalline samples, no structural information on such compounds is accessible, due to highly overlapping peaks in powder diffraction profiles. We use in situ Pair Distribution Function measurements on powder samples to investigate the dynamics of the structural changes induced by temperature variations. By means of a multivariate approach, we were able to extract dynamic structural information from collected profiles without using prior knowledge on the static crystal structure of the compounds. The critical temperature and the characteristics of the vapochromic transition have been identified, as well as the main structural changes causing it.