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The molecular bases of Alzheimer's disease (AD) remain unclear. We used a lipidomic approach to identify lipid abnormalities in the brains of subjects with AD (N = 37) compared to age-matched controls (N = 17). The analyses revealed statistically detectable elevations in levels of non-esterified monounsaturated fatty acids (MUFAs) and mead acid (20:3n-9) in mid-frontal cortex, temporal cortex and hippocampus of AD patients. Further studies showed that brain mRNAs encoding for isoforms of the rate-limiting enzyme in MUFAs biosynthesis, stearoyl-CoA desaturase (SCD-1, SCD-5a and SCD-5b), were elevated in subjects with AD. The monounsaturated/saturated fatty acid ratio (‘desaturation index’) – displayed a strong negative correlation with measures of cognition: the Mini Mental State Examination test (r = −0.80; P = 0.0001) and the Boston Naming test (r = −0.57; P = 0.0071). Our results reveal a previously unrecognized role for the lipogenic enzyme SCD in AD.

The effect of relative humidity (RH) on the composition and concentrations of gas-phase products and secondary organic aerosol (SOA) generated from the photooxidation of isoprene under high-NOx conditions was investigated. Experiments were performed with hydrogen peroxide as the OH precursor and in the absence of seed aerosol. The relative yields of most gas-phase products were the same regardless of initial water vapor concentration with exception of hydroxyacetone and glycolaldehyde, which were considerably affected by RH. A significant change was observed in the SOA composition, with many unique condensed-phase products formed under humid (90% RH) vs. dry (< 2% RH) conditions, without any detectable effect on the rate and extent of the SOA mass growth. There is a 40% reduction in the number and relative abundance of distinct particle-phase nitrogen-containing organic compounds (NOC) detected by high resolution mass spectrometry. The suppression of condensation reactions, which produce water as a product, is the most important chemical effect of the increased RH. For example, the total signal from oligomeric esters of 2-methylglyceric acid was reduced by about 60% under humid conditions and the maximum oligomer chain lengths were reduced by 7-11 carbons. Oligomers formed by addition mechanisms, without direct involvement of water, also decreased at elevated RH but to a much smaller extent. The observed reduction in the extent of condensation-type oligomerization at high RH may have substantial impact on the phase characteristics and hygroscopicity of the isoprene aerosol. The reduction in the amount of organic nitrates in the particle phase has implications for understanding the budget of NOC compounds.

Exosomes are directly involved in governing physiological and pathological processes of an organism by horizontal transfer of functional molecules (proteins, microRNA, etc.) from producing to receiving cells. We explored the relationship of proteins from plasma exosomes, and exosomes from the total blood of healthy females (HFs) and breast cancer patients (BCPs), with crucial steps of tumor progression: EMT, cell proliferation, invasion, cell migration, stimulation of angiogenesis, and immune response. A proteomic analysis of exosomes isolated from samples using ultrafiltration and ultracentrifugation was performed. Their nature has been verified using cryo-electron microscopy and flow cytometry. Bioinformatics analysis showed that 84% of common exosomal proteins were of cytoplasmic and vesicle origin. They perform functions of protein binding and signaling receptor binding, and facilitated the processes of the regulated exocytosis and vesicle-mediated transport. Half of the identified exosomal proteins from blood of HFs and BCPs are involved in crucial steps of the tumor progression: EMT, cell proliferation, invasion, cell migration stimulation of angiogenesis, and immune response. Moreover, we found that protein cargo of exosomes from HF total blood was enriched with proteins inhibiting EMT, cell migration, and invasion. Tumor diagnostic/prognostic protein markers accounted for 47% of the total composition of cell-surface-associated exosomes (calculated as the difference between the total blood exosomes and plasma exosomes) from BCP blood. Breast cancer-associated proteins were equally represented in the blood cell-surface-associated exosomes and in the plasma exosomes from BCPs. However, hyper-expressed proteins predominate in the blood cell-surface-associated exosomes as compared to the plasma exosomes (64 vs. 14%). Using breast cancer proteins data from the Human Protein Atlas (HPA) (www.proteinatlas.org/), three favorable (SERPINA1, KRT6B, and SOCS3), and one unfavorable (IGF2R) prognostic protein markers were found in the BCP total blood exosomes. Identified exosomal proteins from BCP blood can be recommended for further testing as breast cancer diagnostic/prognostic biomarkers or novel therapeutic targets.

Like other RNA viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in host cells, continuously modulating the molecular environment. It encodes 28 multifunctional proteins that induce an imbalance in the metabolic and proteostatic homeostasis in infected cells. Recently, proteomic approaches have allowed the evaluation of the impact of SARS-CoV-2 infection in human cells. Here, we discuss the current use of proteomics in three major application areas: (i) virus-protein interactomics, (ii) differential proteotyping to map the virus-induced changes in different cell types, and (iii) diagnostic methods for coronavirus infectious disease 2019 (COVID-19). Since the nasal cavity is one of the entry sites for SARS-CoV-2, we will also discuss the potential application of olfactory proteomics to provide novel insights into the olfactory dysfunction triggered by SARS-CoV-2 in patients with COVID-19.

Here, we report proteome profiling of peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cell (iPSC)-derived, lens-like organoids termed lentoid bodies at two differentiation time points. A small aliquot of the blood sample was ascertained to collect PBMCs that were reprogrammed to iPSCs. The PBMC-originated, iPSCs were differentiated to lentoid bodies employing the “fried egg” method. Quantitative real-time PCR (qRT-PCR) analysis revealed increased expression levels of lens-associated markers in lentoid bodies while transmission electron microscopy identified closely packed lens epithelial- and differentiating fiber-like cells in lentoid bodies. Total cellular protein was extracted from lentoid bodies at differentiation day 25 and mass spectrometry identified a total of 9,473 proteins. The low counts of crystallin proteins at differentiation day 25 prompted us to re-examine the proteome at differentiation day 35 as we reasoned that 10 additional days of differentiation will increase the crystallin count. However, we did not detect any substantial increase in crystallin protein counts at differentiation day 35. In conclusion, we report generation and proteome profiles of PBMC-originated, iPSC-derived lentoid bodies at multiple differentiation time points.

Herpes simplex virus 1 (HSV-1) and varicella-zoster virus (VZV) are two closely related human alphaherpesviruses that persistently infect most adults worldwide and cause a variety of clinically important diseases. Herpesviruses are extremely well adapted to their hosts and interact broadly with cellular proteins to regulate virus replication and spread. However, it is incompletely understood how HSV-1 and VZV interact with the host proteome during productive infection. This study determined the temporal changes in virus and host protein expression during productive HSV-1 and VZV infection in the same cell type. Results demonstrated the temporally coordinated expression of HSV-1 and VZV proteins in infected cells. Analysis of the host proteomes showed that both viruses affected extracellular matrix composition, transcription, RNA processing and cell division. Moreover, the prominent role of epidermal growth factor receptor (EGFR) signaling during productive HSV-1 and VZV infection was identified. Stimulation and inhibition of EGFR leads to increased and decreased virus replication, respectively. Collectively, the comparative temporal analysis of viral and host proteomes in productively HSV-1 and VZV-infected cells provides a valuable resource for future studies aimed to identify target(s) for antiviral therapy development.

Phosphatidylcholines (PC) are the main membrane lipid constituents comprising more than 50% of total glycerophospholipids. They coordinate a number of cell functions, particularly cell growth, homeostasis, secretion, recognition and communication. In basidial fungi PC are synthesized via the Kennedy pathway as well as through methylation of phosphatidylethanolamines (PE) and then undergo remodeling in Lands cycle that replaces fatty acids in PC molecules. The molecular profile of PC is determined by the genetic features that are characteristic for every species and depend on the environment. Here we present the results of ESI-MS based analyses of PC profiles of 38 species of basidiomycetes belonging to Agaricales (12), Polyporales (17), Russulales (5), Gleophyllales (2), Cantharellales (1), Auriculariales (1), Phallales (1). Although the variety of PC molecular species of basidiomycetes is rather diverse (20–38 molecular species in every profile), only 1–3 main molecular species represent 70–90% of total PC content. The most abundant of them are C36:4 and C36:3, followed by C34:1, C34:2, C36:5, C36:2. In the majority of basidiomycetes, C36:4 reaches up to 50–70% of total PC molecular species. Based on the results of hierarchical cluster analysis four main types of PC profiles which characterized the studied fungi independently from their taxonomic position, ecology, trophic status, and hyphal differentiation have been revealed. Comparative analyses of studied fungi using PCA method have shown that species of Polyporales differ from those of Agaricales by higher variability of PC profiles.

Metastasis is the primary cause of colorectal cancer (CRC) death. The liver and lung, besides adjacent lymph nodes, are the most common sites of metastasis. Here, we aimed to study the lymph nodes, liver, and lung CRC metastasis by quantitative spatial proteomics analysis using CRC cell-based models that recapitulate these metastases. The isogenic KM12 cell system composed of the non-metastatic KM12C cells, liver metastatic KM12SM cells, and liver and lung metastatic KM12L4a cells, and the isogenic non-metastatic SW480 and lymph nodes metastatic SW620 cells, were used. Cells were fractionated to study by proteomics five subcellular fractions corresponding to cytoplasm, membrane, nucleus, chromatin-bound proteins, and cytoskeletal proteins, and the secretome. Trypsin digested extracts were labeled with TMT 11-plex and fractionated prior to proteomics analysis on a Q Exactive. We provide data on protein abundance and localization of 4710 proteins in their different subcellular fractions, depicting dysregulation of proteins in abundance and/or localization in the most common sites of CRC metastasis. After bioinformatics, alterations in abundance and localization for selected proteins from diverse subcellular localizations were validated via WB, IF, IHC, and ELISA using CRC cells, patient tissues, and plasma samples. Results supported the relevance of the proteomics results in an actual CRC scenario. It was particularly relevant that the measurement of GLG1 in plasma showed diagnostic ability of advanced stages of the disease, and that the mislocalization of MUC5AC and BAIAP2 in the nucleus and membrane, respectively, was significantly associated with poor prognosis of CRC patients. Our results demonstrate that the analysis of cell extracts dilutes protein alterations in abundance in specific localizations that might only be observed studying specific subcellular fractions, as here observed for BAIAP2, GLG1, PHYHIPL, TNFRSF10A, or CDKN2AIP, which are interesting proteins that should be further analyzed in CRC metastasis.

Conic snails are slow-moving carnivorous that use a very powerful venom to hunt. This venom is a combination of different toxins from the family of conototoxins. This research was carried out to identify a marine Cone snail, Conus pennaceus quasimagnificus in Shibderaz Cost, South of Qeshm Island. After sampling the venom was isolated using a buffer and centrifuge. Then the lethal dose (LD50) on mice was analyzed and various conotoxins were identified. For the first time, the presence of a conotoxin called “alpha-conotoxin-like” of the A-superfamily was found in the venom of the collected specimens. This peptide was tested for its anti-bacterial activity after being synthesized. Analysis of the isolated DNA showed that the species studied was C. pennaceus and phylogenetical studies showed the closest distance to the C. pennaceus quasimagnificus subspecies. The venom of this cone snake showed the LD50 of 500 mg kg-1. This peptide showed no effect on different strains of bacteria, however, given the strong inhibitory effect of venom on nicotine acetylcholine receptors (nAChR), it can be further studied for its pain relief effect.

We have developed an automated data analysis method for atmospheric particles using scanning transmission X-ray microscopy coupled with near edge X-ray fine structure spectroscopy (STXM/NEXAFS). This method is applied to complex internally mixed submicrometer particles containing organic and inorganic material. Several algorithms were developed to exploit NEXAFS spectral features in the energy range from 278 to 320 eV for quantitative mapping of the spatial distribution of elemental carbon, organic carbon, potassium, and noncarbonaceous elements in particles of mixed composition. This energy range encompasses the carbon K-edge and potassium L2 and L3 edges. STXM/NEXAFS maps of different chemical components were complemented with a subsequent analysis using elemental maps obtained by scanning electron microscopy coupled with energy dispersive X-ray analysis (SEM/EDX). We demonstrate the application of the automated mapping algorithms for data analysis and the statistical classification of particles.

Topicality. To date, one third of medicines are derived from medicinal plant raw materials and every year the medicinal plants continue to cause increasing interest among doctors. Phytopreparations are attracted by the fact that their use is accompanied by a minimum of side effects, they do not interact with other medicines, they help restore and normalize vital processes, provide the body with the necessary minerals and vitamins, maintain a certain level of metabolism and are successfully used in many chronic diseases. Aim. The purpose of the study was to study the composition of BAS in dense extracts from immature walnut fruit and clarify their role in the restoration and normalization of vital processes in the human body. Materials and methods. Dense aqueous extract and thick water-alcohol extracts with an extractant concentration of 30 % ethyl alcohol, 70 % and 96 % were obtained on the basis of the NPAU under the guidance of Professor V.A. Georgiyants, by means of complex processing of immature fruits of milk-wax ripeness of walnut. Determination of the content of BAS in the thick extracts studied was carried out by chromatography-mass spectrometry. Results. In the study of extracts by chromatography-mass spectrometry, 23 substances were found in the aqueous extract; in water-alcoholic with concentration of extractant - ethyl alcohol 30%, 70% and 96% - 16 34 and 39 compounds, respectively. Conclusions. By the method of chromatography-mass spectrometry in an aqueous extract of immature walnut fruit 23 substances were detected, in water-alcoholic (30, 70 and 96%) – 16 34 and 39, respectively. Among these compounds we paid attention to 1,4-naphthoquinone, 1-hydroxy-anthraquinone, lilac and lauric acids, diethyl oxalate, eugenol, squalene, juglone - substances with various pharmacological properties.

Background. Multiple myeloma (MM) is a hematologic malignancy of plasma cells. The microenvironment plays a key role in MM cell survival and drug resistance through release of soluble factors, expression of adhesion molecules and release of exosomes (EXs). The role that EXs, released by MM cells have in cell-to-cell communication and signaling in the bone marrow is currently unknown. EXs as a source of markers for MM diagnostics are also not studied.Objective: to use proteomic profiling of EXs as a tool to identify circulating tumor associated markers in MM patients.Results. The proteome composition of EXs obtained from plasma of patients with MM and multiple sclerosis was studied for the first time. nano-HPLC–MS/MS analysis identified a total of 332 proteins in the EXs of both groups of patients and determined the proximity of their qualitative composition. For the first time, 12 differentially expressed proteins were detected, the levels of which were significantly increased in EXs from patients with MM. This allowed us to consider them as potential markers of the disease.Conclusion. Proteomic analysis of EXs obtained from plasma of patients with MM is an important method for finding disease markers.

Applicability of isotope-ratio mass spectrometry of light elements (C, N, О, H) has been assessed for identification of geographical origin of Russian milk collected in different parts of the Russian Federation (235 sample of whole milk). Quantitative assessment was carried out in a series of statistical tests based on nonparametric dispersion analysis.

The article is devoted to the problem of quality assurance of medicinal products, namely the determination of elemental impurity concentration compared to permitted daily exposures for and the correct choice analytical methods that are adequate to the formulated tasks. The paper goal is to compare characteristics of four analytical methods recommended by the Pharmacopoeia of various countries to control the content of elemental impurities in medicines, including medicinal plant raw materials and herbal medicines. Both advantages and disadvantages were described for atomic absorption spectroscopy with various atomising techniques, as well as atomic emission spectroscopy and mass spectrometry with inductively coupled plasma. The choice of the most rational analysis method depends on a research task and is reasoned from the viewpoint of analytical objectives, possible complications, performance attributes, and economic considerations. The methods of ICP-MS and GFAAS were shown to provide the greatest potential for determining the low and ultra-low concentrations of chemical elements in medicinal plants and herbal medicinal products. The other two methods, FAAS and ICP-AES, are limited to the analysis of the main essential elements and the largest impurities. The ICP-MS is the most efficient method for determining ultra-low concentrations. However, the interference of mass peaks is typical for ICP-MS. It is formed not only by impurities but also by polyatomic ions with the participation of argon, as well as atoms of gases from the air (C, N and O) or matrices (O, N, H, P, S and Cl). Therefore, a correct sample preparation, which guarantees minimisation of impurity contamination and loss of analytes becomes the most crucial stage of analytical applications of ICP-MS. The detections limits for some chemical elements, which content is regulated in modern Pharmacopoeia, were estimated for each method and analysis conditions of medicinal plant raw materials and herbal medicinal products.

Exosomes are directly involved in governing physiological and pathological processes of an organism by horizontal transfer of functional molecules (proteins, microRNA, etc.) from producing to receiving cells. We explored the relationship of proteins from plasma exosomes, and exosomes from the total blood of healthy females (HFs) and breast cancer patients (BCPs), with crucial steps of tumor progression: EMT, cell proliferation, invasion, cell migration, stimulation of angiogenesis, and immune response. A proteomic analysis of exosomes isolated from samples using ultrafiltration and ultracentrifugation was performed. Their nature has been verified using cryo-electron microscopy and flow cytometry. Bioinformatics analysis showed that 84% of common exosomal proteins were of cytoplasmic and vesicle origin. They perform functions of protein binding and signaling receptor binding, and facilitated the processes of the regulated exocytosis and vesicle-mediated transport. Half of the identified exosomal proteins from blood of HFs and BCPs are involved in crucial steps of the tumor progression: EMT, cell proliferation, invasion, cell migration stimulation of angiogenesis, and immune response. Moreover, we found that protein cargo of exosomes from HF total blood was enriched with proteins inhibiting EMT, cell migration, and invasion. Tumor diagnostic/prognostic protein markers accounted for 47% of the total composition of cell-surface-associated exosomes (calculated as the difference between the total blood exosomes and plasma exosomes) from BCP blood. Breast cancer-associated proteins were equally represented in the blood cell-surface-associated exosomes and in the plasma exosomes from BCPs. However, hyper-expressed proteins predominate in the blood cell-surface-associated exosomes as compared to the plasma exosomes (64 vs. 14%). Using breast cancer proteins data from the Human Protein Atlas (HPA) (www.proteinatlas.org/), three favorable (SERPINA1, KRT6B, and SOCS3), and one unfavorable (IGF2R) prognostic protein markers were found in the BCP total blood exosomes. Identified exosomal proteins from BCP blood can be recommended for further testing as breast cancer diagnostic/prognostic biomarkers or novel therapeutic targets. [ABSTRACT FROM AUTHOR]

Like other RNA viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in host cells, continuously modulating the molecular environment. It encodes 28 multifunctional proteins that induce an imbalance in the metabolic and proteostatic homeostasis in infected cells. Recently, proteomic approaches have allowed the evaluation of the impact of SARS-CoV-2 infection in human cells. Here, we discuss the current use of proteomics in three major application areas: (i) virus-protein interactomics, (ii) differential proteotyping to map the virus-induced changes in different cell types, and (iii) diagnostic methods for coronavirus infectious disease 2019 (COVID-19). Since the nasal cavity is one of the entry sites for SARS-CoV-2, we will also discuss the potential application of olfactory proteomics to provide novel insights into the olfactory dysfunction triggered by SARS-CoV-2 in patients with COVID-19. [ABSTRACT FROM AUTHOR]

In the present article a spatial confinement of microobjects were explored in the radiofrequency Paul trap at normal pressure. Spores of Lycopodium Clavatum, 33 μm in diameter, and CdSe/ZnS (core/shell) quantum dots conglomerates with size of 2–7 μm were used as such microobjects. Zero-crossing orbits of these objects were observed for the first time what indicates the nonlinear nature of dynamics of these particles in localization area. Mathematical description of particle dynamics in a viscous is presented. It is shown that friction value depends on the radius of microobjects and dynamic viscosity. Moreover, zero-crossing orbits of charged particles in the radiofrequency Paul trap were numerically simulated. A new method of comparative analysis of the morphology of microparticles is proposed. [ABSTRACT FROM AUTHOR]

• Temperature dependence of nine clinically available insulin were assessed using DLS. • Insulin Detemir showed significant reduction in size with increased temperature. • Size reduction was dependent on expiration and direction of temperature change. • Sedimentation velocity probed the stoichiometric/quaternary structure of Detemir. • Viscometry and Mass Spectrometry were also employed to investigate the phenomenon. Insulin, in typical use, undergoes multiple changes in temperature; from refrigerator, to room temperature, to body temperature. Although long-term storage temperature has been well-studied, the short term changes to insulin are yet to be determined. Insulin detemir (IDet) is a clinically available, slow-acting, synthetic analogue characterised by the conjugation of a C14 fatty acid. The function of this modification is to cause the insulin to form multi-hexameric species, thus retarding the pharmacokinetic rate of action. In this investigation, the temperature dependence properties of this synthetic analogue is probed, as well as expiration. Dynamic light scattering (DLS) and viscometry were employed to assess the effect of temperature upon IDet. Mass spectrometry was also used to probe the impact of shelf-life and the presence of certain excipients. IDet was compared with eight other insulins, including human recombinant, three fast-acting analogues and two other slow-acting analogues. Of all nine insulins, IDet was the only analogue to show temperature dependent behaviour, between 20 °C and 37 °C, when probed with non-invasive backscatter dynamic light scattering. Upon further investigation, IDet observed significant changes in size related to temperature, direction of temperature (heated/cooled) and expiration with cross-correlation observed amongst all 4 parameters. These findings are critical to our understanding of the behaviour of this particular clinically relevant drug, as it will allow the development of future generations of peptide-based therapies with greater clinical efficacy. [ABSTRACT FROM AUTHOR]

Biochemical characterization of primary bilateral macronodular adrenocortical hyperplasia (PBMAH) by distinct plasma steroid profiles and its putative correlation to disease has not been previously studied. LC-MS/MS--based steroid profiling of 16 plasma steroids was applied to 36 subjects (22 females, 14 males) with PBMAH, 19 subjects (16 females, 3 males) with other forms of adrenal Cushing's syn drome (ACS), and an age and sex-matched control group. Germline ARMC5 sequencing was performed in all PBMAH cases. Compared to controls, PBMAH showed increased plasma 11-deoxycortisol, corticosterone, 11-deoxycorticosterone, 18-hydroxycortisol, and aldosterone, but lower progesterone, DHEA, and DHEA-S with distinct differences in subjects with and without pathogenic variants in ARMC5. Steroids that showed isolated differences included cortisol and 18-oxocortisol with higher (P < 0.05) concentrations in ACS than in controls and aldosterone with higher concentrations in PBMAH when compared to controls. Larger differences in PBMAH than with ACS were most clear for co rticosterone, but there were also trends in this direction for 18-hydroxycortisol and aldosterone. Logistic regression analysis indicated four steroids -- DHEA, 11-deoxycortisol, 18-oxocortisol, and corticosterone -- with the most power for distinguishing the groups. Discriminant analyses with step-wise variable selection indicated correct classification of 95.2% of all subjects of the four groups using a panel of nine steroids; correct classification of subjects with and without germline variants in ARMC5 was achieved in 91.7% of subjects with PBMAH. Subjects with PBMAH show distinctive plasma steroid profiles that may offer a supplementary single-test alternative for screening purposes. [ABSTRACT FROM AUTHOR]

Herpes simplex virus 1 (HSV-1) and varicella-zoster virus (VZV) are two closely related human alphaherpesviruses that persistently infect most adults worldwide and cause a variety of clinically important diseases. Herpesviruses are extremely well adapted to their hosts and interact broadly with cellular proteins to regulate virus replication and spread. However, it is incompletely understood how HSV-1 and VZV interact with the host proteome during productive infection. This study determined the temporal changes in virus and host protein expression during productive HSV-1 and VZV infection in the same cell type. Results demonstrated the temporally coordinated expression of HSV-1 and VZV proteins in infected cells. Analysis of the host proteomes showed that both viruses affected extracellular matrix composition, transcription, RNA processing and cell division. Moreover, the prominent role of epidermal growth factor receptor (EGFR) signaling during productive HSV-1 and VZV infection was identified. Stimulation and inhibition of EGFR leads to increased and decreased virus replication, respectively. Collectively, the comparative temporal analysis of viral and host proteomes in productively HSV-1 and VZV-infected cells provides a valuable resource for future studies aimed to identify target(s) for antiviral therapy development. [ABSTRACT FROM AUTHOR]

Background: Aquaculture is a fast-growing industry and therefore welfare and environmental impact have become of utmost importance. Preventing stress associated to common aquaculture practices and optimizing the fish stress response by quantification of the stress level, are important steps towards the improvement of welfare standards. Stress is characterized by a cascade of physiological responses that, in-turn, induce further changes at the whole-animal level. These can either increase fitness or impair welfare. Nevertheless, monitorization of this dynamic process has, up until now, relied on indicators that are only a snapshot of the stress level experienced. Promising technological tools, such as proteomics, allow an unbiased approach for the discovery of potential biomarkers for stress monitoring. Within this scope, using Gilthead seabream (Sparus aurata) as a model, three chronic stress conditions, namely overcrowding, handling and hypoxia, were employed to evaluate the potential of the fish protein-based adaptations as reliable signatures of chronic stress, in contrast with the commonly used hormonal and metabolic indicators. Results: A broad spectrum of biological variation regarding cortisol and glucose levels was observed, the values of which rose higher in net-handled fish. In this sense, a potential pattern of stressor-specificity was clear, as the level of response varied markedly between a persistent (crowding) and a repetitive stressor (handling). Gel-based proteomics analysis of the plasma proteome also revealed that net-handled fish had the highest number of differential proteins, compared to the other trials. Mass spectrometric analysis, followed by gene ontology enrichment and protein-protein interaction analyses, characterized those as humoral components of the innate immune system and key elements of the response to stimulus. Conclusions: Overall, this study represents the first screening of more reliable signatures of physiological adaptation to chronic stress in fish, allowing the future development of novel biomarker models to monitor fish welfare. [ABSTRACT FROM AUTHOR]

The analysis of amino acid coevolution has emerged as a practical method for protein structural modeling by providing structural contact information from alignments of amino acid sequences. In parallel, chemical cross‐linking/mass spectrometry (XLMS) has gained attention as a universally applicable method for obtaining low‐resolution distance constraints to model the quaternary arrangements of proteins, and more recently even protein tertiary structures. Here, we show that the structural information obtained by XLMS and coevolutionary analysis are effectively complementary: the distance constraints obtained by each method are almost exclusively associated with non‐coincident pairs of residues, and modeling results obtained by the combination of both sets are improved relative to considering the same total number of constraints of a single type. The structural rationale behind the complementarity of the distance constraints is discussed and illustrated for a representative set of proteins with different sizes and folds. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMPs) are natural antagonistic tools of many bacteria and are considered as attractive antimicrobial agents for the treatment of bacteria with multidrug resistance. Lactic acid bacteria from the gastrointestinal tract of animals and human produce various AMPs inhibiting the growth of pathogens. Here we report the isolation and identification of novel Lactobacillus fermentum strain HF-D1 from the human gut producing AMPs which prevents the growth of P. aeruginosa and S. marcescens. The active fraction of peptides was obtained from the culture liquid by precipitation at 80% saturation of ammonium sulphate. For peptides identification, the precipitate was treated with guanidine hydrochloride to desorb from proteins, separated with ultrafiltration on spin columns with 10,000 MWCO, desalted with a reversed-phase chromatography and subjected to LC–MS/MS analysis. The in silico analysis of the identified 1111 peptides by using ADAM, CAMPR3 and AMPA prediction servers led to identification of the linear peptide with highly probable antimicrobial activity and further investigation of its antibacterial activity mechanism is promising. By using the dereplication algorithm, the peptide highly similar to non-ribosomal cyclic AMPs originally isolated from Staphylococcus epidermidis has been identified. This indicates that L. fermentum HF-D1 represents a novel strain producing antimicrobial peptides targeting P. aeruginosa and S. marcescens. [ABSTRACT FROM AUTHOR]

The post-translational protein modification via lysine residues can significantly alter its function. α2-antiplasmin, a key inhibitor of fibrinolysis, contains 19 lysine residues. We sought to identify sites of glycation and acetylation in human α2-antiplasmin and test whether the competition might occur on the lysine residues of α2-antiplasmin. We analyzed human α2-antiplasmin (1) untreated; (2) incubated with increasing concentrations of β- d -glucose (0, 5, 10, 50 mM); (3) incubated with 1.6 mM acetylsalicylic acid (ASA) and (4) incubated with 1.6 mM ASA and 50 mM β- d -glucose, using the ultraperformance liquid chromatography system coupled to mass spectrometer. Eleven glycation sites and 10 acetylation sites were found in α2-antiplasmin. Incubation with β- d -glucose was associated with glycation of 4 (K-418, K-427, K-434, K-441) out of 6 lysine residues, known to be important for mediating the interaction with plasmin. Glycation and acetylation overlapped at 9 sites in samples incubated with β- d -glucose or ASA. Incubation with concomitant ASA and β- d -glucose was associated with the decreased acetylation at all sites overlapping with glycation sites. At K-182 and K-448, decreased acetylation was associated with increased glycation when compared with α2-antiplasmin incubated with 50 mM β- d -glucose alone. Although K-24 located in the proximity of the α2-antiplasmin cleavage site, was found to be only acetylated, incubation with ASA and 50 mM β- d -glucose was associated the absence of acetylation at that site. Human α2-antiplasmin is glycated and acetylated at several sites, with the possible competition between acetylation and glycation at K-182 and K-448. Our finding suggests possibly relevant alterations to α2-antiplasmin function at high glycemia and during aspirin use. • There are 11 glycation sites and 10 acetylation sites in α2-antiplasmin. • Four out of 6 lysine residues involved in interaction with plasmin are glycated. • Acetylated lysine residue 24 is in the proximity from α2-antiplasmin cleavage site. • Acetylation overlappes with glycation at 9 lysine residues. • Possible competition between acetylation and glycation occurs at site 182 and 448. [ABSTRACT FROM AUTHOR]

Measurements of hydroxyl ( OH) and hydroperoxy (HO2) radicals were made during the Mexico City Metropolitan Area (MCMA) field campaign as part of the MILAGRO (Megacity Initiative: Local and Global Research Observations) project during March 2006. These measurements provide a unique opportunity to test current models of atmospheric ROx (OH + HO2 + RO2) photochemistry under polluted conditions. A zero-dimensional box model based on the Regional Atmospheric Chemical Mechanism (RACM) was constrained by 10-min averages of 24 J-values and the concentrations of 97 chemical species. Several issues related to the ROx chemistry under polluted conditions are highlighted in this study: (i) Measured concentrations of both OH and HO2 were underpredicted during morning hours on a median campaign basis, suggesting a significant source of radicals is missing from current atmospheric models under polluted conditions, consistent with previous urban field campaigns. (ii) The model-predicted HO2/OH ratios underestimate the measurements for NO mixing ratios higher than 5 ppb, also consistent with previous urban field campaigns. This suggests that under high NOx conditions, the HO2 to OH propagation rate may be overestimated by the model or a process converting OH into HO2 may be missing from the chemical mechanism. On a daily basis ( 08: 40 a. m.-06: 40 p. m.), an analysis of the radical budget indicates that HONO photolysis, HCHO photolysis, O-3-alkene reactions and dicarbonyls photolysis are the main radical sources. O-3 photolysis contributes to less than 6% of the total radical production.

Formation of isoprene nitrates (INs) is an important free radical chain termination step ending production of ozone and possibly affecting formation of secondary organic aerosol. Isoprene nitrates also represent a potentially large, unmeasured contribution to OH reactivity and are a major pathway for the removal of nitrogen oxides from the atmosphere. Current assessments indicate that formation rates of isoprene nitrates are uncertain to a factor of 2-3 and the subsequent fate of isoprene nitrates remains largely unconstrained by laboratory, field or modeling studies. Measurements of total alkyl and multifunctional nitrates (Sigma ANs), NO2, total peroxy nitrates (Sigma PNs), HNO3, CH2O, isoprene and other VOC were obtained from the NASA DC-8 aircraft during summer 2004 over the continental US during the INTEX-NA campaign. These observations represent the first characterization of Sigma ANs over a wide range of land surface types and in the lower free troposphere. Sigma ANs were a significant, 12-20%, fraction of NOy throughout the experimental domain and Sigma ANs were more abundant when isoprene was high. We use the observed hydrocarbon species to calculate the relative contributions of Sigma AN precursors to their production. These calculations indicate that isoprene represents at least three quarters of the Sigma AN source in the summertime continental boundary layer of the US. An observed correlation between Sigma ANs and CH2O is used to place constraints on nitrate yields from isoprene oxidation, atmospheric lifetimes of the resulting nitrates and recycling efficiencies of nitrates during subsequent oxidation. We find reasonable fits to the data using sets of production rates, lifetimes and recycling efficiencies of INs as follows (4.4%, 16 h, 97%), (8%, 2.5h, 79%) and (12%, 95 min, 67%). The analysis indicates that the lifetime of Sigma ANs as a pool of compounds is considerably longer than the lifetime of the individual isoprene nitrates to reaction with OH, implying that the organic nitrate functionality is at least partially maintained through a second oxidation cycle.

Introduction: Dengue virus (DENV), a mosquito-borne flavivirus, continues to be a major public health threat in many countries and there are no antiviral therapeutics available. Limited protective efficacy across four dengue serotypes of the current available DENGVAXIA and QDENGA vaccine prompt the need to search for alternative. Methods: In this work, we discovered a sulfonyl anthranilic acid (SAA) derivative of the 2,1-benzothiazine 2,2-dioxide core that was previously used to develop DENV NS5 polymerase inhibitors. Dose-response inhibition experiment of SAA against DENV was performed to determine the EC50 and CC50 values. Time-of-drug-addition assay (TODA) was carried out to investigate the mechanism of action of the most potent compound - FlaR18, followed by quantification of viral RNA level and viral protein production. The efficacy of FlaR18 is also evaluated in different cell lines. Thermal proteome profiling (TPP) was performed to investigate the binding target of FlaR18. Results: Of the 38 SAA derivatives, several exhibited potent anti-DENV-2 activity in the cell-based inhibition assay, but surprisingly did not inhibit DENV NS5 polymerase activity. Notably, compound FlaR18 showed EC50 values in the range of 0.3 to 0.6 µM against the four dengue serotypes (DENV-1-4) and different RNA viruses. Time of addition assay revealed that analogue FlaR18 is a post-entry replication inhibitor that appears to be specific for cells of primate origin, implicating a host target. We have taken a high throughput proteomic approach, Cellular Thermal Shift Assay coupled to Mass Spec (MS-CETSA), to identify potential host targets that are currently being validated in gene knock out assays to elucidate the mechanism of action for compound FlaR18. Conclusion: Compound FlaR18 could serve as a lead for more potent inhibitors against the target since it also shows similar antiviral efficacy against other RNA viruses that have been tested. [ABSTRACT FROM AUTHOR]

Trypanosoma theileri maintains a long-term extracellular infection with a low parasitaemia in bovids. The surface of this parasite is predicted to be decorated with several surface molecules including membrane surface proteases (MSPs), trans-sialidases and T. theileri putative surface proteins (TTPSPs). However, there are no experimental data to verify this hypothesis. Here, we have purified and partially characterized the surface glycoconjugates of T. theileri using biochemical and mass spectrometry-based approaches. The glycoconjugates fall into two classes: glycoproteins and glycolipids. Proteomic analysis of the glycoprotein fraction demonstrated the presence of MSPs and abundant mucin-like TTPSPs, with most predicted to be GPI-anchored. Mass spectrometric characterization of the glycolipid fraction showed that these are mannose- and galactose-containing glycoinositolphospholipids (GIPLs) that are larger and more diverse than those of its phylogenetic relative T. cru z i , containing up to 10 hexose residues and carrying either alkylacyl-phosphatidylinositol or inositol-phospho-ceramide (IPC) lipid components. [Display omitted] • The surface of Trypanosoma theileri is heavily glycosylated and like that of Trypanosoma cruzi. • Many T. theileri putative surface proteins (TTPSPs) are expressed in T. theileri cultured cells. • Most expressed TTPSPs are glycosylphosphatidylinositol (GPI)-anchored proteins. • T. theileri cultured cells express abundant and relatively large glycoinositolphospholipids (GIPLs). [ABSTRACT FROM AUTHOR]

Cowpea seed protein hydrolysates (CPH) were output from cowpea seeds applying alcalase® from Bacillus licheniformis. CPH with an elevated level of hydrolysis was fractionated by size exclusion chromatography (SEC). Both CPH and SEC-portions showed to contain antimicrobial peptides (AMPs) as they inhibited both Gram-positive bacteria, such as Listeria monocytogenes LMG10470 (L. monocytogenes), Listeria innocua. LMG11387 (L. innocua), Staphylococcus aureus ATCC25923 (S.aureus), and Streptococcus pyogenes ATCC19615 (St.pyogenes), and Gram-negative bacteria, such as Klebsiella pnemoniae ATCC43816 (K. pnemoniae), Pseudomonas aeroginosa ATCC26853 (P. aeroginosa), Escherichia coli ATCC25468) (E.coli) and Salmonella typhimurium ATCC14028 (S. typhimurium).The data exhibited that both CPH and size exclusion chromatography-fraction 1 (SEC-F1) showed high antibacterial efficiency versus almost all the assessed bacteria. The MIC of the AMPs within SEC-F1 and CPHs were (25 µg/mL) against P. aeruginosa, E.coli and St. pyogenes. However, higher MICsof approximately 100–150 µg/mL showed for both CPHs and SEC-F1 against both S. aureus and L. innocua; it was 50 µg/mL of CPH against S.aureus. The Electro-spray-ionization-mass-spectrometry (ESI-MS) of fraction (1) revealed 10 dipeptides with a molecular masses arranged from 184 Da to 364 Da and one Penta peptide with a molecular mass of approximately 659 Da inthe case of positive ions. While the negative ions showed 4 dipeptides with the molecular masses that arranged from 330 Da to 373 Da. Transmission electron microscope (TEM) demonstrated that the SEC-F1 induced changes in the bacterial cells affected. Thus, the results suggested that the hydrolysis of cowpea seed proteins by Alcalase is an uncomplicated appliance to intensify its antibacterial efficiency.

In vitro produced (IVP) embryos show large metabolic variability induced by breed, culture conditions, embryonic stage and sex and gamete donors. We hypothesized that the birth potential could be accurately predicted by UHPLC-MS/MS in culture medium (CM) with the discrimination of factors inducing metabolic variation. Day-6 embryos were developed in single CM (modified synthetic oviduct fluid) for 24 h and transferred to recipients as fresh (28 ETs) or frozen/thawed (58 ETs) Day-7 blastocysts. Variability was induced with seven bulls, slaughterhouse oocyte donors, culture conditions (serum + Bovine Serum Albumin [BSA] or BSA alone) prior to single culture embryonic stage records (Day-6: morula, early blastocyst, blastocyst; Day-7: expanding blastocyst; fully expanded blastocysts) and cryopreservation. Retained metabolite signals (6111) were analyzed as a function of pregnancy at Day-40, Day-62 and birth in a combinatorial block study with all fixed factors. We identified 34 accumulated metabolites through 511 blocks, 198 for birth, 166 for Day-62 and 147 for Day-40. The relative abundance of metabolites was higher within blocks from non-pregnant (460) than from pregnant (51) embryos. Taxonomy classified lipids (12 fatty acids and derivatives; 224 blocks), amino acids (12) and derivatives (3) (186 blocks), benzenoids (4; 58 blocks), tri-carboxylic acids (2; 41 blocks) and 5-Hydroxy-l-tryptophan (2 blocks). Some metabolites were effective as single biomarkers in 95 blocks (Receiver Operating Characteristic – Area Under the Curve [ROC-AUC]: 0.700–1.000). In contrast, more accurate predictions within the largest data sets were obtained with combinations of 2, 3 and 4 single metabolites in 206 blocks (ROC-AUC = 0.800–1.000). Pregnancy-prone embryos consumed more amino acids and citric acid, and depleted less lipids and cis-aconitic acid. Big metabolic differences between embryos support efficient pregnancy and birth prediction when analyzed in discriminant conditions.

Background. The transforming growth factor beta 1 (TGF-β1) is one of the most important tissue factors secreted by the development of epithelial tumors. Increased expression of TGF-β1 in lung tumors promotes cancer cells survival enhancing their growth, migration, invasion, angiogenesis, immune system suppression.Objective: to study molecular mechanisms of TGF-β1 action on A549 human lung adenocarcinoma cells by means of proteomic high-resolution mass spectrometry. Results. Intracellular signaling pathways responsible for the involvement of TGF-β1 in the oncogenesis of non-small cell lung cancer have been found, which include the differential expressed proteins of the families of cullin, ETS oncogenes, histone diacelases, cyclin-dependent kinases, and the signaling pathway phosphatidylinositol 3-kinase (PI3K).Conclusions. Important patterns are determined that could be used for the development of new approaches for detection of lung cancer metastasis candidate markers and potential therapy targets of this decease.

Aim. Study taxonomic belonging of collection strains of tularemia causative agent based on proteomic and molecular-genetic methods of identification. Materials and methods. 23 strains of tularemia were used in the study, isolated from Krasnoyarsk region and Altai Republic from 1950 to 2015. FT-agar was used for the cultivation. Spectra for time-of-flight mass-spectrometry were collected using Microflex LT (Bruker Daltonics, Germany) and analyzed compared with previously collected enhanced database of MALDI Biotyper 3.0. PC R with specific primers was carried out with electrophoretic visualization of results in real time. Results. F. tularensis strains isolated from south of western Siberia from 1950 to 2010 were established to belong to subspecies holarctica, and 56.3% of those - erythromycin sensitive (1 biovar Erys), the rest - erythromycin-resistant (II biovar EryR). 7 strains isolated after 2011 by citrulline ureidase activity, cleavage of glycerin and presence of pdpA and pdpD fragments of pathogenicity island (FP1) were determined as Central Asian subspecies. Conclusion. Results of a retrospective study of biological properties of tularensis strains isolated from south Siberia have shown the lack of Central Asian subspecies tularemia causative agent in the collection of Irkutsk Institute for Plague Control before 2011. Detection of this subspecies in Russian Federation gives evidence on the necessity to study and analyze problems of epidemiology, ecology and epizootology of Central Asian subspecies tularemia causative agent as well as determination of borders of its spread.