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.

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.

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.

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.

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.

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.

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.

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.

Proteomic analysis of the extracellular matrix in idiopathic pes equinovarus.

Idiopathic pes equinovarus is a congenital deformity of the foot and lower leg defined as a fixation of the foot in adduction, supination, and varus. Although the pathogenesis of clubfoot remains unclear, it has been suggested that fibroblasts and growth factors are involved. To directly analyze the protein composition of the extracellular matrix in contracted tissue of patients with clubfoot. A total of 13 infants with idiopathic clubfoot treated with the Ponseti method were included in the present study. Tissue samples were obtained from patients undergoing surgery for relapsed clubfeet. Contracted tissues were obtained from the medial aspect of the talonavicular joint. Protein was extracted after digestion and delipidation using zip-tip C18. Individual collagenous fractions were detected using a chemiluminescent assay. Amino acid analysis of tissue samples revealed a predominance of collagens, namely collagen types I, III, and VI. The high content of glycine and h-proline suggests a predominance of collagens I and III. A total of 19 extracellular matrix proteins were identified. The major result of the present study was the observation that the extracellular matrix in clubfoot is composed of an additional 16 proteins, including collagens V, VI, and XII, as well as the previously described collagen types I and III and transforming growth factor ß. The characterization of the general protein composition of the extracellular matrix in various regions of clubfoot may help in understanding the pathogenesis of this anomaly and, thus, contribute to the development of more efficacious therapeutic approaches.

Effects of mtDNA in SHR-mtF344 versus SHR conplastic strains on reduced OXPHOS enzyme levels, insulin resistance, cardiac hypertrophy, and systolic dysfunction.

Common inbred strains of the laboratory rat can be divided into four major mitochondrial DNA (mtDNA) haplotype groups represented by the BN, F344, LEW, and SHR strains. In the current study, we investigated the metabolic and hemodynamic effects of the SHR vs. F344 mtDNA by comparing the SHR vs. SHR-mt(F344) conplastic strains that are genetically identical except for their mitochondrial genomes. Altogether 13 amino acid substitutions in protein coding genes, seven single nucleotide polymorphisms in tRNA genes, and 12 single nucleotide changes in rRNA genes were detected in F344 mtDNA compared with SHR mtDNA. Analysis of oxidative phosphorylation system (OXPHOS) in heart left ventricles (LV), muscle, and liver revealed reduced activity and content of several respiratory chain complexes in SHR-mt(F344) conplastic rats compared with the SHR strain. Lower function of OXPHOS in LV of conplastic rats was associated with significantly increased relative ventricular mass and reduced fractional shortening that was independent of blood pressure. In addition, conplastic rats exhibited reduced sensitivity of skeletal muscles to insulin action and impaired glucose tolerance. These results provide evidence that inherited alterations in mitochondrial genome, in the absence of variation in the nuclear genome and other confounding factors, predispose to insulin resistance, cardiac hypertrophy and systolic dysfunction.

Mono-N-acyl-2,6-diaminopimelic acid derivatives: analysis by electromigration and spectroscopic methods and examination of enzyme inhibitory activity.

Thirteen mono-N-acyl derivatives of 2,6-diaminopimelic acid (DAP)-new potential inhibitors of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE; EC 3.5.1.18)-were analyzed and characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopies and two capillary electromigration methods: capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC). Structural features of DAP derivatives were characterized by IR and NMR spectroscopies, whereas CZE and MEKC were applied to evaluate their purity and to investigate their electromigration properties. Effective electrophoretic mobilities of these compounds were determined by CZE in acidic and alkaline background electrolytes (BGEs) and by MEKC in acidic and alkaline BGEs containing a pseudostationary phase of anionic detergent sodium dodecyl sulfate (SDS) or cationic detergent cetyltrimethylammonium bromide (CTAB). The best separation of DAP derivatives, including diastereomers of some of them, was achieved by MEKC in an acidic BGE (500 mM acetic acid [pH 2.54] and 60mM SDS). All DAP derivatives were examined for their ability to inhibit catalytic activity of DapE from Haemophilus influenzae (HiDapE) and ArgE from Escherichia coli (EcArgE). None of these DAP derivatives worked as an effective inhibitor of HiDapE, but one derivative-N-fumaryl, Me-ester-DAP-was found to be a moderate inhibitor of EcArgE, thereby providing a promising lead structure for further studies on ArgE inhibitors.

Proteomic analysis of chicken eggshell cuticle membrane layer.

The eggshell is a barrier that plays an important role in the defense of the egg against microbial and other infections; it protects the developing bird against unfavorable impacts of the environment and is essential for the reproduction of birds. The avian eggshell is a complex structure that is formed during movement along the oviduct by producing a multilayered mineral-organic composite. The extractable proteins of avian eggshells have been studied extensively and many of them identified, however, the insoluble (non-extractable) proteins have been sparsely studied. We studied the EDTA-insoluble proteinaceous film from the cuticle layer of eggshell. This film consists of three main areas: spots (cca 300 µm diameter), blotches (small spots with diameter only tens of µm), and the surroundings (i.e., the area without spots and blotches) where spots contain a visible accumulation of pigment. These areas were cut out of the membrane by laser microdissection, proteins were cleavaged by trypsin, and the peptides were analyzed by nLC/MS (Q-TOF). This study has identified 29 proteins and a further eight were determined by less specific "cleavage" with semitrypsin. The relative abundances of these proteins were determined using the exponentially modified protein abundance index (emPAI) where the most dominant proteins were eggshell-specific ones, such as ovocleidin-17 and ovocleidin-116. Individual areas of the cuticle membrane differ in their relative proportions of 14 proteins, where significant differences between the three quantification criteria (direct, after normalization to ovocledin-17, or to ovocledin-116) were observed in four proteins.

Early life stress shapes female reproductive strategy through eggshell pigmentation in Japanese quail.

Physiological constraints on colouration have been widely reported; especially in birds, which trade-off antioxidant responses against colourful costly signals. One female extended phenotypic trait, which might also highlight important physiological trade-offs, is the pigmentation of their eggshells. In ground-nesting species, producing eggs that are visually undetectable by predators is the best camouflage strategy. However, the condition-dependence of eggshell pigmentation, and the pigments role in oxidative stress, may constrain females to trade-off between their antioxidant capacity and maximising the camouflage of their eggs when they deposit eggshell pigments. Developmental stress is one factor that influences female antioxidant capacity, and could lead to variations in eggshell pigmentation that might have crucial consequences on individual fitness if egg crypsis is compromised especially under stressful conditions. We investigated the interaction between developmental and breeding conditions with respect to eggshell pigmentation in Japanese quail. We studied 30 females that bred under both control and stressful conditions, and were exposed to pre- and/or post-natal stress, or neither. Pre- and post-natal stress independently influenced eggshell pigmentation strategies under stressful breeding conditions. Under stressful reproduction, eggshell protoporphyrin concentration and maculation were affected by pre-natal stress, whereas eggshell reflectance and biliverdin concentration were influenced by post-natal stress. These changes may reflect potential adaptive strategies shaped by developmental stress, but additional data on the benefit of egg crypsis in quail, combined with studies on the role of both pigments on chick survival, will help to clarify whether early life stress can enhance fitness through eggshell pigmentation when developmental and reproductive environments match.

Monotopic modifications derived from in vitro glycation of albumin with ribose.

Post-translational modifications are significant reactions that occur to proteins. One of these modifications is a non-enzymatic reaction between the oxo-group(s) of sugars and amino-group(s) of protein - glycation. This reaction plays an important role in the chronic complications of diabetes mellitus, or in the aging process of organisms, that is, it has an important role in the pathophysiology and "normal" physiology of animals. In the work presented here, we studied the glycation of albumins (HSA and BSA). Methodologically, we used nano-LC coupled to a QTOF mass spectrometer. In vitro-modified proteins were cleaved by trypsin and the arising peptides were separated on a C(18) nano column with a trap-column. Peptides and their modifications were analysed with a high-resolution QTOF mass spectrometer with a mass determination precision of better than 5 ppm. Non-enzymatic in vitro reaction products between albumin and ribose were identified. Besides well-known carboxymethyl lysine, new modifications were determined - creating mass shifts of 78 and 218. The origin of the first modification is discussed and its possible structure is presented. In addition, a mass shift of 132 belonging to a Schiff base was also identified. The location of all the modifications within the structure of the proteins was determined and their reactivity to various oxo-compounds was also examined.

Condition-dependent strategies of eggshell pigmentation: an experimental study of Japanese quail (Coturnix coturnix japonica).

A relationship has been suggested between eggshell colour and female body condition based on the opposing antioxidant properties of the two main eggshell pigments: the antioxidant biliverdin (blue-green) and the pro-oxidant protoporphyrin (brown). We hypothesized that experimentally food-restricted females with low antioxidant capacity would deposit more protoporphyrin and less biliverdin in their eggshells, resulting in eggshells of reduced brightness but increased colour intensity. Two eggs were collected at the beginning and two at the end of a 2 week period from each of 24 female Japanese quails that were either food restricted or receiving ad libitum food (i.e. controls) during that time. Reflectance spectra were recorded and analysed using spectral shape descriptors, chromatic and achromatic contrasts were computed accounting for avian visual sensitivities, and eggshell pigments were quantified. We examined both spot and background pigmentation and found no significant effect of food restriction on eggshell reflectance. However, food-restricted females in lower body condition increased the deposition of protoporphyrin and decreased the amount of biliverdin invested in their eggshells. We hypothesize that in species laying brown-spotted eggshells, females modulate eggshell pigment investment in response to their body condition. According to this hypothesis, we predict that females maintain eggshell colour to limit visible changes that could be detected by predators and thereby conceal their eggs, although this work has yet to be conducted. We suggest that further experimental work on egg camouflage under different environmental conditions will elaborate on the process of pigment deposition and the physiological costs to females of laying heavily pigmented eggshells.

Serine protease from midgut of Bombus terrestris males.

A serine protease was isolated from midguts of the bumblebee male Bombus terrestris by a combination of precipitation procedures with column chromatography. The purified enzyme exhibited two bands with molecular masses of 25 and 26 kDa as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis. These bands showed a proteolytic activity in zymography assay. Midgut enzymes showed optimum proteolytic activity at pH 9 and 35°C using N-succinyl-L-alanyl-L-alanyl-L-prolyl-L-phenyl-alanine 4-nitroanilide as a substrate. The Michaelis constant (Km) and maximum reaction rate (Vmax) were 0.55±0.042 mM and 0.714±0.056 µmol p-nitroalanine produced min(-1) mg protein(-1) , respectively. Inhibition was affected by trypsin inhibitor, but not by phenylmethylsulfonyl fluoride and N-tosyl-L-phenylalanine chloromethyl ketone, which indicated the trypsin-like but not chymotrypsin-like specificity. The identity of the serine protease was confirmed by nanoliquid-tandem mass spectrometry. Eleven unique peptides of the B. terrestris serine protease were found. It shows high homology to a previously reported B. ignitus serine protease covering more than 65% of the protein amino acid sequence.

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.

Nonsynonymous variants in mt-Nd2, mt-Nd4, and mt-Nd5 are linked to effects on oxidative phosphorylation and insulin sensitivity in rat conplastic strains.

Common inbred strains of the laboratory rat can be divided into four different mitochondrial DNA haplotype groups represented by the SHR, BN, LEW, and F344 strains. In the current study, we investigated the metabolic and hemodynamic effects of the SHR vs. LEW mitochondrial genomes by comparing the SHR to a new SHR conplastic strain, SHR-mt(LEW); these strains are genetically identical except for their mitochondrial genomes. Complete mitochondrial DNA (mtDNA) sequence analysis comparing the SHR and LEW strains revealed gene variants encoding amino acid substitutions limited to a single mitochondrial enzyme complex, NADH dehydrogenase (complex I), affecting subunits 2, 4, and 5. Two of the variants in the mt-Nd4 subunit gene are located close to variants known to be associated with exercise intolerance and diabetes mellitus in humans. No variants were found in tRNA or rRNA genes. These variants in mt-Nd2, mt-Nd4, and mt-Nd5 in the SHR-mt(LEW) conplastic strain were linked to reductions in oxidative and nonoxidative glucose metabolism in skeletal muscle. In addition, SHR-mt(LEW) conplastic rats showed increased serum nonesterified fatty acid levels and resistance to insulin stimulated incorporation of glucose into adipose tissue lipids. These results provide evidence that inherited variation in mitochondrial genes encoding respiratory chain complex I subunits, in the absence of variation in the nuclear genome and other confounding factors, can influence glucose and lipid metabolism when expressed on the nuclear genetic background of the SHR strain.

Analysis of drugs of forensic interest with capillary zone electrophoresis/time-of-flight mass spectrometry based on the use of non-volatile buffers.

The present work is aimed at investigating the influence of the background electrolyte composition and concentration on the separation efficiency and resolution and mass spectrometric detection of illicit drugs in a capillary zone electrophoresis-electrospray ionization-time of flight mass spectrometry (CZE-ESI-TOF MS) system. The effect of phosphate, borate and Tris buffers on the separation and mass spectrometry response of a mixture of 3,4-methylenedioxyamphetamine, 3,4-methylenedioxymethamphetamine, methadone, cocaine, morphine, codeine and 6-monoacetylmorphine was studied, in comparison with a reference ammonium formate separation buffer. Inorganic non-volatile borate and Tris buffers proved hardly suitable for capillary electrophoresis-mass spectrometry (CE-MS) analysis, but quite unexpectedly ammonium phosphate buffers showed good separation and ionization performances for all the analytes tested. Applications of this method to real samples of hair from drug addicts are also provided.