Peptide analysis of tooth enamel - A sex estimation tool for archaeological, anthropological, or forensic research.

Proteomics has become an attractive method to study human and animal material, biological profile, and origin as an alternative to DNA analysis. It is limited by DNA amplification in ancient samples and its contamination, high cost, and limited preservation of nuclear DNA. Currently, three approaches are available to estimate sex-osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. Proteomics provides a new, seemingly simple, and relatively non-expensive way of sex estimation without the risk of contamination. Proteins can be preserved in hard teeth tissue (enamel) for tens of thousands of years. It uses two sexually distinct forms of the protein amelogenin in tooth enamel detectable by liquid chromatography-mass spectrometry; the protein amelogenin Y isoform is present in enamel dental tissue only in males, while amelogenin isoform X can be found in both sexes. From the point of view of archaeological, anthropological, and forensic research and applications, the reduced destruction of the methods used is essential, as well as the minimum requirements for sample size.

The chiral proteomic analysis applied to aging collagens by LC-MS: Amino acid racemization, post-translational modifications, and sequence degradations during the aging process.

Collagen is the most abundant protein in the animal and human bodies, and it is not exempt from this aging phenomenon. Some age-related changes may appear on collagen sequences, such as increased surface hydrophobicity, the appearance of post-translational modifications, and amino acids racemization. This study has shown that the protein hydrolysis under deuterium conditions is privileged to limit the natural racemization during the hydrolysis. Indeed, under the deuterium condition, the homochirality of recent collagens is preserved whose amino acids are found in their L-form. However, in aging collagen, a natural amino acid racemization was observed. These results confirmed that the % d-amino acids are progressive according to age. The collagen sequence is degraded over time, and a fifth of the sequence information is lost during aging. Post-translational modifications (PTMs) in aging collagens can be a hypothesis to explain the modification of the hydrophobicity of the protein with the decrease of hydrophilic groups and the increase of hydrophobic groups. Finally, the exact positions of d-amino acids and PTMs have been correlated and elucidated.

Reduced Graphene Oxide Aerogels Cartridges for Solid Phase Extraction of Benzotriazoles.

UV-benzotriazoles have been identified as water micropollutants that cause serious problems for human health and the environment. Their low concentration in water bodies complicates their detection by direct water analysis, slowing the corrective actions to avoid bioaccumulation. In this regard, the use of graphene-based materials with a high affinity for non-polar molecules has been demonstrated to be a potential tool for the optimal separation and concentration of this type of molecules in solid phase extraction (SPE) processes. This work evaluates the potential of novel reduced graphene oxide aerogels (rGO) as extractants of mixtures of three UV-benzotriazoles in water at low concentrations. These rGO aerogels incorporate graphenic domains into a tough structure of polymeric chains by adding graphene oxide during the synthesis of resorcinol-formaldehyde gels. Aerogels with a different content and ordering of graphenic domains were obtained and characterized using Raman, XRD, SEM and nitrogen adsorption isotherms (-196 °C). The rGO aerogels that performed better as solid phase extractants were those containing 60% rGO. Aerogels with lower rGO contents (40%) required a high-temperature (2000 °C) treatment to render competitive results. The SPE methodology using selected rGO aerogels was optimized by varying the elution solvent, elution time and volume. The best performances, i.e., recoveries of 80-100% and enrichment factors of 12.5-50, were accomplished when using 0.8 mL of tetrahydrofuran (THF) as an elution solvent. As a result, a fast (10 min) and simple extraction method of UV-benzotriazoles in water was attained, achieving a detection limit of 1 ng mL-1. Selected aerogels were finally tested for the SPE of spiked samples of river waters, showing a similar performance to that observed with synthetic mixtures.

New insights into the relationships between egg maternal components: the interplays between albumen steroid hormones, proteins and eggshell protoporphyrin.

Recent studies have shown that the egg yolk maternal components, which are a mixture of substances that can affect the developing embryo, do not act separately but are interconnected and co-adapted. Surprisingly, no study to date has focused on the associations between maternally derived albumen steroids and albumen and eggshell compounds with pleiotropic effects. Eggshell pigment protoporphyrin (PROTO IX) should provide primary antimicrobial protection for eggs, but as a proven pro-oxidant, it may compromise female fitness. Abundant albumen proteins ovotransferrin (OVOTR) and lysozyme (LSM) have been shown to have antimicrobial, antioxidant, immunoregulatory and growth-regulatory roles. To investigate associations between albumen steroids and OVOTR, LSM and eggshell cuticle PROTO IX, we used chicken eggs with differently pigmented eggshells. We found that albumen steroid hormones were strongly intercorrelated. In addition, we revealed that albumen LSM and testosterone (T) were positively associated, while a negative association was found between albumen LSM and pregnenolone (P5). Eggshell cuticle PROTO IX was negatively associated with the concentration of albumen 17α-hydroxypregnenolone (17-OHP5). Finally, of all the hormones tested, only the concentration of albumen 17-OHP5 correlated negatively with egg volume and varied with eggshell colour and chicken breed. Although experimental evidence for the effect of maternal albumen steroids on avian developing embryo is still scarce, our study is the first to highlight co-variation and potential co-adjustment of maternally derived albumen steroids, proteins and eggshell cuticle pigment suggesting similar allocation mechanisms known for yolk maternal compounds with the potential to influence the avian embryo and offspring phenotype.

Application of Sol-Gels Modified with Natural Plants Extracts as Stationary Phases in Open-Tubular Capillary Electrochromatography.

Ethanol extracts of three widely growing plants were added to silica sol-gel solutions, which were subsequently applied as wall surface modifiers in inner quartz capillaries. Modified capillaries were used for open-tubular capillary electrochromatographic separation of nucleotides and amino groups containing biological compounds (neurotransmitters, amino acids and oligopeptides). The experiments were performed at physiological pH 7.40, and eventual changes of effective mobilities were calculated. Specific compounds characteristic for each plant were tested as sol-gel additives as well, and thus-modified capillaries were used for the separations of the same analytes under identical conditions. The aim of this study was to find out possible interactions between physiological compounds and extracts of freely available plants anchorded in the sol-gel stationary phase in the flowing system. Even though the amount of the modifier in each capillary is very small, basic statistical evaluation showed some not negligible changes in effective mobility of tested analytes. These changes were bigger than ±5% for separations of nucleotides in capillaries with curcuma, Moringa or the mixture of synthetic additives as the sol-gel aditive, and for separations of amino compounds where these changes varying by additive, analyte by analyte.

Arrested in Glass: Actin within Sophisticated Architectures of Biosilica in Sponges.

Actin is a fundamental member of an ancient superfamily of structural intracellular proteins and plays a crucial role in cytoskeleton dynamics, ciliogenesis, phagocytosis, and force generation in both prokaryotes and eukaryotes. It is shown that actin has another function in metazoans: patterning biosilica deposition, a role that has spanned over 500 million years. Species of glass sponges (Hexactinellida) and demosponges (Demospongiae), representatives of the first metazoans, with a broad diversity of skeletal structures with hierarchical architecture unchanged since the late Precambrian, are studied. By etching their skeletons, organic templates dominated by individual F-actin filaments, including branched fibers and the longest, thickest actin fiber bundles ever reported, are isolated. It is proposed that these actin-rich filaments are not the primary site of biosilicification, but this highly sophisticated and multi-scale form of biomineralization in metazoans is ptterned.

Open-tubular capillary electrochromatographic application of a sol-gel matrix with chilli peppers, garlic, or synthetic additives.

This article describes a possible combination of two promising fields of analytical chemistry-the preparation of sol-gel matrices with varying additives and their application in capillary electrochromatography. The inner surfaces of capillaries were coated with the sol-gel solution containing either pure synthetic chemical additive-alliin or capsaicin-or an extract of their natural sources-garlic and chilli pepper, respectively. The modified capillaries were tested for interaction with two neurotransmitters, oligopeptides and nucleotides under conditions of open-tubular capillary electrochromatography. Because both of the natural extracts also contain vitamin C and saccharose, the capillaries with sol-gel modifiers containing each of these substances were also tested. The obtained results from the perspective of changes in the electrochromatograms and the effective mobilities of analytes are discussed with respect to mild conditions both in the preparation process of the sol-gel matrix and during the separations.

Na+/K+-ATPase and lipid peroxidation in forebrain cortex and hippocampus of sleep-deprived rats treated with therapeutic lithium concentration for different periods of time.

Lithium (Li) is a typical mood stabilizer and the first choice for treatment of bipolar disorder (BD). Despite an extensive clinical use of Li, its mechanisms of action remain widely different and debated. In this work, we studied the time-course of the therapeutic Li effects on ouabain-sensitive Na+/K+-ATPase in forebrain cortex and hippocampus of rats exposed to 3-day sleep deprivation (SD). We also monitored lipid peroxidation as malondialdehyde (MDA) production. In samples of plasma collected from all experimental groups of animals, Li concentrations were followed by ICP-MS. The acute (1 day), short-term (7 days) and chronic (28 days) treatment of rats with Li resulted in large decrease of Na+/K+-ATPase activity in both brain parts. At the same time, SD of control, Li-untreated rats increased Na+/K+-ATPase along with increased production of MDA. The SD-induced increase of Na+/K+-ATPase and MDA was attenuated in Li-treated rats. While SD results in a positive change of Na+/K+-ATPase, the inhibitory effect of Li treatment may be interpreted as a pharmacological mechanism causing a normalization of the stress-induced shift and return the Na+/K+-ATPase back to control level. We conclude that SD alone up-regulates Na+/K+-ATPase together with increased peroxidative damage of lipids. Chronic treatment of rats with Li before SD, protects the brain tissue against this type of damage and decreases Na+/K+-ATPase level back to control level.

Concentration of egg white antimicrobial and immunomodulatory proteins is related to eggshell pigmentation across traditional chicken breeds.

Eggshell colour, quality, and biosafety of table eggs are of significant commercial interest. To date, there have been few studies investigating the relationship between eggshell pigmentation and internal egg quality in commercially bred birds. Moreover, the genetic basis and mechanisms behind the effects of extrinsic factors on deposition of antimicrobial compounds in egg white and eggshell pigments are not fully understood. In the present study, we evaluate the effect of chicken breed identity, eggshell pigmentation and the role of extrinsic factors (year and breeder identity) on variability in the concentrations of 2 major egg white antimicrobial proteins (AMPs), lysozyme (LSM), and ovotransferrin (OVOTR), across 23 traditional chicken breeds. We found that chicken breed identity and eggshell pigmentation explained most variability in the concentration of egg white LSM and OVOTR. Year and breeder identity were also significant predictors of egg white LSM and OVOTR variability, and showed selective effects on the deposition of both AMPs in egg white. We also documented a positive correlation between concentration of egg white LSM and eggshell cuticle protoporphyrin in tinted and dark brown eggs, but not in brown, white, and blue eggs. We assume that a combination of both intrinsic genetic and hormonally regulated extrinsic factors is responsible for this relationship and for the variability in egg white AMPs. In this study, we demonstrate the existence of a relationship between eggshell pigmentation and egg white AMPs content in the eggs of traditional chicken breeds that may advertise the egg's antimicrobial potential and biosafety. These findings provide novel insights into the relationship between eggshell pigmentation and egg internal quality and may stimulate the recovery and exploitation of traditional chicken breeds for egg production, where the demands for egg quality and biosafety, in conjunction with animal welfare, are a priority.

Identification of short-chain poly-3-hydroxybutyrates in Saiga horn extracts using LC-MS/MS.

Saiga horn extracts were analyzed with the goal of obtaining new information about compounds present in it. The purpose of this study is to find synthetic alternatives to Saiga horn extract, which is used in traditional Chinese medicine, by identifying potentially biologically active compounds in the extracts. Using high-performance liquid chromatography coupled with high-resolution mass spectrometry, we have been able to identify a series of short-chain polyhydroxybutyrates in alcoholic extracts of Saiga horn. Optimized high-performance liquid chromatography coupled with tandem mass spectrometry methods for analysis of short-chain poly-3-hydroxybutyrates were developed and subsequently applied to investigate Saiga horn extract for the presence of these compounds, which might explain its biological actions, particularly for its antipyretic and procoagulant properties.

Novel contribution to clubfoot pathogenesis: The possible role of extracellular matrix proteins.

Idiopathic pes equinovarus (clubfoot) is a congenital deformity of the feet and lower legs. Clubfoot belongs to a group of fibro-proliferative disorders but its origin remains unknown. Our study aimed to achieve the first complex proteomic comparison of clubfoot contracted tissue of the foot (medial side; n = 16), with non-contracted tissue (lateral side; n = 13). We used label-free mass spectrometry quantification and immunohistochemistry. Seven proteins were observed to be significantly upregulated in the medial side (asporin, collagen type III, V, and VI, versican, tenascin-C, and transforming growth factor beta induced protein) and four in the lateral side (collagen types XII and XIV, fibromodulin, and cartilage intermediate layer protein 2) of the clubfoot. Comparison of control samples from cadavers brought only two different protein concentrations (collagen types I and VI). We also revealed pathological calcification and intracellular positivity of transforming growth factor beta only in the contracted tissue of clubfoot. Most of the 11 differently expressed proteins are strongly related to the extracellular matrix architecture and we assume that they may play specific roles in the pathogenesis of this deformity. These proteins seem to be promising targets for future investigations and treatment of this disease. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res.

Coupling of CE-MS for protein and peptide analysis.

The review is focused on the latest developments in the analysis of proteins and peptides by capillary electrophoresis techniques coupled to mass spectrometry. First, the methodology and instrumentation are overviewed. In this section, recent progress in capillary electrophoresis with mass spectrometry interfaces and capillary electrophoresis with matrix-assisted laser desorption/ionization is mentioned, as well as separation tasks. The second part is devoted to applications-mainly bottom-up and top-down proteomics. It is obvious that capillary electrophoresis with mass spectrometry methods are well suited for peptide and protein analysis (proteomic research) and it is described how these techniques are complementary and not competitive with the often used liquid chromatography with mass spectrometry methods.

Proteomic analysis of dentin-enamel junction and adjacent protein-containing enamel matrix layer of healthy human molar teeth.

The dentin-enamel junction (DEJ) is the border where two different mineralized structures - enamel and dentin - meet. The protein-rich DEJ, together with the inner enamel region of mature teeth, is known to exhibit higher fracture toughness and crack growth resistance than bulk phase enamel. However, an explanation for this behavior has been hampered by the lack of compositional information for the DEJ and the adjacent enamel organic matrix (EOM). We studied proteomes of the DEJ and EOM of healthy human molars and compared them with dentin and enamel proteomes from the same teeth. These tissues were cut out of tooth sections by laser capture microdissection, proteins were extracted and cleaved by trypsin, then processed by liquid chromatography coupled to tandem mass spectrometry to analyze the proteome profiles of these tissues. This study identified 46 proteins in DEJ and EOM. The proteins identified have a variety of functions, including calcium ion-binding, formation of extracellular matrix, formation of cytoskeleton, cytoskeletal protein binding, cell adhesion, and transport. Collagens were identified as the most dominant proteins. Tissue-specific proteins, such as ameloblastin and amelogenin, were also detected. Our findings reveal new insight into proteomics of DEJ and EOM, highly mineralized tissues that are obviously difficult to analyze.

Social defeat stimulates local glucocorticoid regeneration in lymphoid organs.

Stress is an important risk factors for human diseases. It activates the hypothalamic-pituitary-adrenal (HPA) axis and increases plasma glucocorticoids, which are powerful regulators of immune system. The response of the target cells to glucocorticoids depends not only on the plasma concentrations of cortisol and corticosterone but also on their local metabolism. This metabolism is catalyzed by 11ß-hydroxysteroid dehydrogenases type 1 and 2, which interconvert glucocorticoid hormones cortisol and corticosterone and their 11-oxo metabolites cortisone and 11-dehydrocorticosterone. The goal of this study was to determine whether stress modulates glucocorticoid metabolism within lymphoid organs - the structures where immune cells undergo development and activation. Using the resident-intruder paradigm, we studied the effect of social stress on glucocorticoid metabolism in primary and secondary lymphoid organs of Fisher 344 (F344) and Lewis (LEW) rats, which exhibit marked differences in their HPA axis response to social stressors and inflammation. We show that repeated social defeat increased the regeneration of corticosterone from 11-dehydrocorticosterone in the thymus, spleen and mesenteric lymphatic nodes (MLN). Compared with the F344 strain, LEW rats showed higher corticosterone regeneration in splenocytes of unstressed rats and in thymic and MLN mobile cells after stress but corticosterone regeneration in the stroma of all lymphoid organs was similar in both strains. Inactivation of corticosterone to 11-dehydrocorticosterone was found only in the stroma of lymphoid organs but not in mobile lymphoid cells and was not upregulated by stress. Together, our findings demonstrate the tissue- and strain-dependent regeneration of glucocorticoids following social stress.

Investigation of hydride generation from arsenosugars - Is it feasible for speciation analysis?

Hydride generation (HG) from arsenosugars (dimethylarsinoylribosides) in batch and flow injection modes was studied. Its efficiency was found higher in H2SO4 medium than in HCl and higher in the batch mode than in the flow injection mode. To increase the efficiency in the flow injection mode a new generator with two inlets of NaBH4 solution was designed. This modified generator was interfaced between a HPLC column and an atomic fluorescence detector. The arsenosugars studied yielded HG efficiencies in the range 13-30% most probably due to a complicated mechanism of HG. While the mechanism included a formation of two structures of the analyte-borane-complexes, only one of them can lead to a formation of volatile arsanes (dimethylarsane, methylarsane, and arsane were identified).

Proteomic analysis of cardiac ventricles: baso-apical differences.

The heart is characterized by a remarkable degree of heterogeneity. Since different cardiac pathologies affect different cardiac regions, it is important to understand molecular mechanisms by which these parts respond to pathological stimuli. In addition to already described left ventricular (LV)/right ventricular (RV) and transmural differences, possible baso-apical heterogeneity has to be taken into consideration. The aim of our study has been, therefore, to compare proteomes in the apical and basal parts of the rat RV and LV. Two-dimensional electrophoresis was used for the proteomic analysis. The major result of this study has revealed for the first time significant baso-apical differences in concentration of several proteins, both in the LV and RV. As far as the LV is concerned, five proteins had higher concentration in the apical compared to basal part of the ventricle. Three of them are mitochondrial and belong to the "metabolism and energy pathways" (myofibrillar creatine kinase M-type, L-lactate dehydrogenase, dihydrolipoamide dehydrogenase). Myosin light chain 3 is a contractile protein and HSP60 belongs to heat shock proteins. In the RV, higher concentration in the apical part was observed in two mitochondrial proteins (creatine kinase S-type and proton pumping NADH:ubiquinone oxidoreductase). The described changes were more pronounced in the LV, which is subjected to higher workload. However, in both chambers was the concentration of proteins markedly higher in the apical than that in basal part, which corresponds to the higher energetic demand and contractile activity of these segments of both ventricles.

Analysis of Siamese Crocodile (Crocodylus siamensis) Eggshell Proteome.

The proteins and pigment of the eggshell of the Siamese crocodile (Crocodylus siamensis) were analysed. For proteomic analysis, various decalcification methods were used when the two main surface layers were analyzed. These layers are important for antimicrobial defense of egg (particularly the cuticle). We found 58 proteins in both layers, of which 4 were specific for the cuticle and 26 for the palisade (honeycomb) layer. Substantial differences between proteins in the eggshell of crocodile and previously described birds' eggshells exist (both in terms of quality and quantity), however, the entire proteome of Crocodilians has not been described yet. The most abundant protein was thyroglobulin. The role of determined proteins in the eggshell of the Siamese crocodile is discussed. For the first time, the presence of porphyrin pigment is reported in a crocodilian eggshell, albeit in a small amount (about 2 to 3 orders of magnitude lower than white avian eggs).

Separation of oligopeptides, nucleobases, nucleosides and nucleotides using capillary electrophoresis/electrochromatography with sol-gel modified inner capillary wall.

The aim of this article is to study the modification of an inner capillary wall with sol-gel coating (pure silica sol-gel or silica sol-gel containing porphyrin-brucine conjugate) and determine its influence on the separation process using capillary electrophoresis/electrochromatography method. After modification of the inner capillary surface the separation of analytes was performed using two different phosphate buffers (pH 2.5 and 9.0) and finally the changes in electrophoretic mobilities of various samples were calculated. To confirm that the modification of the inner capillary surface was successful, the parts of the inner surfaces of capillaries were observed using scanning electron microscopy. The analytes used as testing samples were oligopeptides, nucleosides, nucleobases and finally nucleotides.

Eggshell coloration and its importance in postmating sexual selection.

Avian eggshell color seems to fulfill multiple functions, some of them being structural and others signaling. In this study, we tested whether or not eggshell coloration may play a role in sexual selection of Tree Sparrows (Passer montanus). According to the "Sexually selected eggshell coloration" hypothesis, eggshell coloration signals female, egg or chick quality and males adjust parental investment according to this signal. Eggs of this species are covered with brown spots and patches, and variation between clutches is high. We found that eggshell coloration correlates with both protoporphyrin and biliverdin, but protoporphyrin concentrations are ten times higher. Eggshell coloration reflects egg and offspring quality, but not female quality. Thus, eggshell coloration may signal female postmating investment in offspring rather than female quality. Furthermore, differential allocation in terms of maternal investment is supported by the fact that females lay more pigmented clutches when mated to males with bigger melanin-based ornaments relative to their own. Moreover, males invested proportionally more to chicks that hatched from more pigmented clutches. Our correlative results thus seem to support a role of sexual selection in the evolution of eggshell coloration in birds laying brown eggs, pigmented mainly by protoporphyrin.

Capillary electrochromatography of proteins and peptides (2006-2015).

This review summarizes the development and the applications of capillary electrochromatographic techniques pertinent to the analysis of proteins and peptides, which took place over the last 10 years (2006-mid-2016). This "hybrid" technique is useful for the analysis of a broad spectrum of proteins and peptides and is an approach that is complementary to the liquid chromatographic and the capillary electrophoretic analysis. All modes of capillary electrochromatography are described here, which includes particle-packed columns, monolithic stationary phases, and open-tubular capillary electrochromatography.