Selective separation and enrichment of peptides for MS analysis using the microspheres composed of Fe3O4@nSiO2 core and perpendicularly aligned mesoporous SiO2 shell

In this work, we report the development of a novel enrichment protocol for peptides by using the microspheres composed of Fe₃O₄@nSiO₂ Core and perpendicularly aligned mesoporous SiO₂ shell (designated Fe₃O₄@nSiO₂@mSiO₂). The Fe₃O₄@nSiO₂@mSiO₂ microspheres possess useful magnetic responsivity which makes the process of enrichment fast and convenient. The highly ordered nanoscale pores (2 nm) and high‐surface areas of the microspheres were demonstrated to have good size‐exclusion effect for the adsorption of peptides. An increase of S/N ratio over 100 times could be achieved by using the microspheres to enrich a standard peptide, and the application of the microspheres to enrich universal peptides was performed by using myoglobin tryptic digest solution. The enrichment efficiency of re‐used Fe₃O₄@nSiO₂@mSiO₂ microspheres was also studied. Large‐scale enrichment of endogenous peptides in rat brain extract was achieved by the microspheres. Automated nano‐LC‐ESI‐MS/MS was applied to analyze the sample after enrichment, and 60 unique peptides were identified in total. The facile and low‐cost synthesis as well as the convenient and efficient enrichment process of the novel Fe₃O₄@nSiO₂@mSiO₂ microspheres makes it a promising candidate for selectively isolation and enrichment of endogenous peptides from complex biological samples.     

Proteomics in the liver of gilthead sea bream (Sparus aurata) to elucidate the cellular response induced by the intake of maslinic acid

Maslinic acid (MA) is a pentacyclic triterpene used as a feed additive to stimulate growth, protein‐turnover rates, and hyperplasia in fish. To further our understanding of cellular mechanisms underlying the action of MA, we have used 2‐DE coupled with MS to identify proteins differentially expressed in the livers of juvenile gilthead sea bream (Sparus aurata) grown under fish‐farm conditions and fed with a 100 mg/kg MA‐enriched diet (MA₁₀₀). After the comparison of the protein profiles from MA₁₀₀ fed fish and from control, 49 protein spots were found to be altered in abundance (≥2‐fold). Analysis by MALDI‐TOF/TOF allowed the unambiguous identification of 29 spots, corresponding to 19 different proteins. These proteins were: phosphoglucomutase, phosphoglucose isomerase, S‐adenosyl methionine‐dependent methyltransferase class I, aldehyde dehydrogenase, catalase, 6‐phosphogluconate dehydrogenase, fumarylacetoacetate hydrolase, 4‐hydroxyphenylpyruvic dioxygenase, methylmalonate‐semialdehyde dehydrogenase, lysozyme, urate oxidase, elongation factor 2, 60 kDa heat‐shock protein, 58 kDa glucose‐regulated protein, cytokeratin E7, type‐II keratin, intermediate filament proteins, 17‐β‐hydroxysteroid dehydrogenase type 4, and kinase suppressor of Ras1. Western blot analysis of kinase suppressor of Ras1, glucose 6‐phosphate dehydrogenase, elongation factor 2, 60 kDa heat‐shock protein, and catalase supported the proteome evidence. Based on the changes found in the protein‐expression levels of these proteins, we proposed a cellular‐signalling pathway to explain the hepatic‐cell response to the intake of a diet containing MA.     

2-D DIGE analysis of the mitochondrial proteome from human skeletal muscle reveals time course-dependent remodelling in response to 14 consecutive days of endurance exercise training

Adaptation of skeletal muscle to repeated bouts of endurance exercise increases aerobic capacity and improves mitochondrial function. However, the adaptation of human skeletal muscle mitochondrial proteome to short‐term endurance exercise training has not been investigated. Eight sedentary males cycled for 60 min at 80% of peak oxygen consumption (VO_2peak) each day for 14 consecutive days, resulting in an increase in VO_2peak of 17.5±3.8% (p<0.01). Mitochondria‐enriched protein fractions from skeletal muscle biopsies taken from m. vastus lateralis at baseline, and on the morning following the 7th and 14th training sessions were subjected to 2‐D DIGE analysis with subsequent MS followed by database interrogation to identify the proteins of interest. Thirty‐one protein spots were differentially expressed after either 7 or 14 days of training (ANOVA, p<0.05). These proteins included subunits of the electron transport chain, enzymes of the tricarboxylic acid cycle, phosphotransfer enzymes, and regulatory factors in mitochondrial protein synthesis, oxygen transport, and antioxidant capacity. Several proteins demonstrated a time course‐dependent induction during training. Our results illustrate the phenomenon of skeletal muscle plasticity with the extensive remodelling of the mitochondrial proteome occurring after just 7 days of exercise training suggestive of enhanced capacity for adenosine triphosphate generation at a cellular level.     

Evaluation of VITEK matrix‐assisted laser desorption ionization–time of flight mass spectrometry for identification of anaerobes

Rapid and adequate identification of anaerobic bacterial species still presents a challenge for most diagnostic laboratories, hindering the selection of appropriate therapy. In this study, the identification capacity of 16S rRNA sequence analysis, VITEK 2 (BioMérieux, Lyon, France) compact analysis and VITEK MS‐mediated identification for anaerobic bacterial species was compared. Eighty‐five anaerobic bacterial isolates from 11 provinces in China belonging to 14 genera were identified by these three methods. Differences in identification between these three methods were compared. Consistent identification results were obtained for 54 (54/85, 63.5%) isolates by all three methods, the most discordant results being concentrated in Clostridium XI (n = 8) and Bacteroides fragilis (n = 9) clusters. Using the VITEK MS system, 74 (74/90, 82.2%) isolates were identified as single species consistent with 16S rRNA sequence analysis, which was significantly better than the results obtained with VITEK 2 Compact (P < 0.01). Misidentifications by the Vitek 2 Compact and Vitek MS systems were mainly observed in the Clostridium XI (n = 8)and B. fragilis clusters (n = 9). VITEK MS identified anaerobic bacteria even after they had been exposed to oxygen for a week. Identification by the Vitek MS system was more consistent with 16S rRNA sequence analysis than identification by Vitek 2 Compact. Continuous expansion of the VITEK MS database with rare described anaerobic species is warranted to improve both the efficiency and accuracy of VITEK MS identification in routine diagnostic microbiology.     

Molecular characterization of heat shock proteins 90 (HSP83?) and 70 in tropical strains of Bombyx mori

Following the concept of whole organism, we have extracted total protein from the Bombyx mori for the identification and analysis of HSPs. Expression of 90 kDa HSP in first, second and third instars, 84 kDa in fourth instar and 90‐, 84‐, 62‐, 60‐, 52‐ and 33‐kDa HSPs in fifth instar larvae of tropical polyvoltine and bivoltine silkworm strains were obvious. Further, we have combined single and 2‐DE with MALDI‐TOF for analysis of BmHSPs. Ninety kilodalton band excised from 1‐DE gel was identified as HSP83 by MALDI‐TOF‐MS. The immunoblot analysis confirmed the expression of HSP90 in all the instars larvae of B. mori. Heat shock‐induced protein spots were excised from 2‐DE gels for MALDI‐TOF‐MS analysis. The Mascot search results are for HSP68, HSC70‐1 and HSP70Ba in Pure Mysore, and major HSP70Bbb, HSP68, HSC‐3 and HSP83 in NB₄D₂. Multiple sequence alignment explicit the variations in amino acid sequence between Pure Mysore and NB₄D₂. Notably, the PMF of spot 2 matched the coding sequence of B. mori and its gene annotation was determined on chromosome 9. With this novel approach, expression of BmHSP90 was confirmed in all the instars and uncovered isoforms of BmHSP70, which provided unequivocal insight to analyze and understand the biological significance in B. mori.     

Rapid synthesis of titanium(IV)‐immobilized magnetic mesoporous silica nanoparticles for endogenous phosphopeptides enrichment

The MALDI‐TOF MS has already been a main platform for phosphoproteome analysis. However, there are some weaknesses in direct analysis of endogenous phosphopeptides by MALDI‐TOF MS because of the serious suppression effect and poor ionization efficiency, which is brought by the excess of nonphosphopeptides and protein. It is essential to enrich endogenous phosphopeptides from complex biosamples efficiently prior to MALDI‐TOF MS analysis. Herein, we present a time‐saving and detailed protocol for the synthesis of titanium(iv)‐immobilized magnetic mesoporous silica nanoparticles (denoted as Fe₃O₄@mSiO₂‐Ti⁴⁺), the subsequent enrichment process, and MALDI‐TOF MS analysis. We tested the LOD, size‐exclusive effect, reproducibility, and stability of Fe₃O₄@mSiO₂‐Ti⁴⁺ nanoparticles. Furthermore, the ability of this protocol for identifying endogenous phosphopeptides in healthy human serum and saliva was investigated.     

Hypoxia Impairs Muscle Function and Reduces Myotube Size in Tissue Engineered Skeletal Muscle

Contemporary tissue engineered skeletal muscle models display a high degree of physiological accuracy compared with native tissue, and therefore may be excellent platforms to understand how various pathologies affect skeletal muscle. Chronic obstructive pulmonary disease (COPD) is a lung disease which causes tissue hypoxia and is characterized by muscle fiber atrophy and impaired muscle function. In the present study we exposed engineered skeletal muscle to varying levels of oxygen (O₂; 21–1%) for 24 h in order to see if a COPD like muscle phenotype could be recreated in vitro, and if so, at what degree of hypoxia this occurred. Maximal contractile force was attenuated in hypoxia compared to 21% O₂; with culture at 5% and 1% O₂ causing the most pronounced effects with 62% and 56% decrements in force, respectively. Furthermore at these levels of O₂, myotubes within the engineered muscles displayed significant atrophy which was not seen at higher O₂ levels. At the molecular level we observed increases in mRNA expression of MuRF‐1 only at 1% O₂ whereas MAFbx expression was elevated at 10%, 5%, and 1% O₂. In addition, p70S6 kinase phosphorylation (a downstream effector of mTORC1) was reduced when engineered muscle was cultured at 1% O₂, with no significant changes seen above this O₂ level. Overall, these data suggest that engineered muscle exposed to O₂ levels of ≤5% adapts in a manner similar to that seen in COPD patients, and thus may provide a novel model for further understanding muscle wasting associated with tissue hypoxia. J. Cell. Biochem. 118: 2599–2605, 2017. © 2017 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.     

Graphene‐amplified electrogenerated chemiluminescence of CdTe quantum dots for H2O2 sensing

Electrogenerated chemiluminescence (ECL) of thiol‐capped CdTe quantum dots (QDs) in aqueous solution was greatly enhanced by PDDA‐protected graphene (P‐GR) film that were used for the sensitive detection of H₂O₂. When the potential was cycled between 0 and ?2.3 V, two ECL peaks were observed at ?1.1 (ECL‐1) and ?1.4 V (ECL‐2) in pH 11.0, 0.1 M phosphate buffer solution (PBS), respectively. The electron‐transfer reaction between individual electrochemically‐reduced CdTe nanocrystal species and oxidant coreactants (H₂O₂ or reduced dissolved oxygen) led to the production of ECL‐1. While mass nanocrystals packed densely in the film were reduced electrochemically, assembly of reduced nanocrystal species reacted with coreactants to produce an ECL‐2 signal. ECL‐1 showed higher sensitivity for the detection of H₂O₂ concentrations than that of ECL‐2. Further, P‐GR film not only enhanced ECL intensity of CdTe QDs but also decreased its onset potential. Thus, a novel CdTe QDs ECL sensor was developed for sensing H₂O₂. Light intensity was linearly proportional to the concentration of H₂O₂ between 1.0 × 10^?5 and 2.0 x 10^‐7 mol L^?1 with a detection limit of 9.8 x 10^?8 mol L^?1. The P‐GR thin‐film modified glassy carbon electrode (GCE) displayed acceptable reproducibility and long‐term stability. Copyright © 2012 John Wiley & Sons, Ltd.     

Physical Fitness and Other Individual Factors Relating to the Shiftwork Tolerance of Women

Maximal oxygen consumption (V˙O₂max), muscle strength (MS) and physical activity were compared to age, shiftwork experience, morningness, personality traits and social factors intervening in the shiftwork tolerance of 128 women. The subjects were nurses and nursing aids working irregular shifts in a hospital. Neuroticism was the most powerful negative factor connected to higher fatigue and various symptoms of the subjects. High V˙O₂max and good MS were, on the other hand, the most important positive factors connected to lower fatigue and musculoskeletal symptoms and better sleep quality of the subjects. In different shifts, fatigue, sleep length and quality were influenced most by morningness. It is concluded that physical fitness is an important individual factor explaining the variations of shiftwork tolerance in women.     

Advanced Electrolytes for Fast‐Charging High‐Voltage Lithium‐Ion Batteries in Wide‐Temperature Range

LiNi_xMn_yCo_1?x?yO₂ (NMC) cathode materials with Ni ≥ 0.8 have attracted great interest for high energy‐density lithium‐ion batteries (LIBs) but their practical applications under high charge voltages (e.g., 4.4 V and above) still face significant challenges due to severe capacity fading by the unstable cathode/electrolyte interface. Here, an advanced electrolyte is developed that has a high oxidation potential over 4.9 V and enables NMC811‐based LIBs to achieve excellent cycling stability in 2.5–4.4 V at room temperature and 60 °C, good rate capabilities under fast charging and discharging up to 3C rate (1C = 2.8 mA cm^?2), and superior low‐temperature discharge performance down to ?30 °C with a capacity retention of 85.6% at C/5 rate. It is also demonstrated that the electrode/electrolyte interfaces, not the electrolyte conductivity and viscosity, govern the LIB performance. This work sheds light on a very promising strategy to develop new electrolytes for fast‐charging high‐energy LIBs in a wide‐temperature range.     

Proteomics reveals lowering oxygen alters cytoskeletal and endoplasmatic stress proteins in human endothelial cells

A proteomic approach was applied to explore the signalling pathways elicited by lowering O₂ in endothelial cells. Endothelial cells isolated from native umbilical cords were subjected to 21, 5, or 1% O₂ for 24 h. 2‐D PAGE was performed and candidate proteins were identified using LC‐MS/MS. Lowering of O₂ from 21 to 5% induced upregulation of cofilin‐1, cyclophilin A, tubulin and tubulin fragments, a fragment of glucose‐regulated protein 78 (Grp78) and calmodulin. The upregulation of Grp78 suggested that ER stress proteins were altered and indeed Grp94 and caspase 12 expression were increased in cells exposed to 5% O₂. The presence of ER stress is also supported by findings of blunted caffeine‐evoked ER calcium release in cells exposed to 5 and 1% O₂. Exposure to 1% O₂ caused increases in cofilin‐1, cyclophilin A, and caspase 12 as well as a decrease of β‐actin, but it did not alter the expression of calmodulin, tubulin, Grp78, and Grp94. Incubation with CoCl₂, a stabilizer of the hypoxia‐inducible factor, increased the expression of several of the proteins. The present investigations reveal that lowering O₂, probably in part through hypoxia‐inducible factor, alter the expression of a series of proteins mainly involved in cytoskeletal changes (e.g. cofilin‐1, tubulin, and β‐actin) and in ER stress/apoptosis (e.g. Grp78/94, caspase 12, and cyclophilin A).     

Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis

While Listeria monocytogenes is responsible for listeriosis, it is also a saprophytic species with exceptional survival aptitudes. Secreted proteins are one of the main tools used by bacteria to interact with their environment. In order to take into account the biodiversity of L. monocytogenes species, exoproteomic analysis was carried out on 12 representative strains. Following 2‐DE and MALDI‐TOF MS, a total of 151 spots were identified and corresponded to 60 non‐orthologous proteins. To categorize and analyze these proteomic data, a rational bioinformatic approach predicting final subcellular localization was carried out. Fifty‐two out of the 60 proteins identified (86.7%) were indeed predicted as localized in the extracellular milieu (gene ontology (GO): 0005576). Most of them (65.4%) were actually predicted as secreted via the Sec translocon. Comparative analysis allowed for proteins found in all or only in a subset of L. monocytogenes strains to be defined. While the core exoproteome included most proteins related to bacterial virulence, cell wall biogenesis, as well as proteins secreted by unknown pathways, a slight variation in the protein members of these categories were observed and constituted the variant exoproteome. This investigation resulted in the first definition of the core and variant exoproteomes of L. monocytogenes where corollaries on bacterial physiology are further discussed.     

The limitations of heart rate as a predictor of metabolic rate in fish

Although telemetered heart rate (f_H) has been used as a physiological correlate to predict the metabolic rate (as oxygen consumption, V?O₂) of fish in the field, it is our contention that the method has not been validated adequately for fish. If f_H in fish is to be used to estimate V?O₂, a single linear (or log-linear) relationship must be established for each species between the two variables which allows V?O₂ to be predicted accurately under all environmentally relevant conditions. Our analyses of existing data indicate that while a good linear (or log-linear) relationship can be established between f_H and V?O₂, the conditions under which the relationship applies may be quite restricted. Physiological states and environmental factors affect the relationship between f_H and V?O₂ significantly such that several curves can exist for a single species. In addition, there are situations in which f_H and V?O₂ do not covary in a significant manner. In some situations f_H can vary over much of its physiological range while V?O₂ remains constant; in others V?O₂ may vary while f_H is invariate. The theoretical basis for this variability is examined to explain why the use of telemetered f_H in predicting V?O₂ of fish may be limited to certain specified applications.     

Genetic changes in muscle protein following hybridization between Haliotis diversicolor reeve Japan and Taiwan populations revealed using a proteomic approach

Protein expression patterns were compared in a Japan and Taiwan population of Haliotis diversicolor and in a hybrid between them using 2DE and MALDI‐TOF‐TOF analyses. Using the software PDQuest, 924 ± 7 protein spots were detected in the Japan population (RR), 861 ± 11 in the Taiwan population (TT), and 882 ± 9 in the F₁ hybrid (TR). RR and TR were clustered together, but the distance between RR and TT was the maximum using hierarchical cluster analysis. A total of 46 gel spots were identified and a total of 15 spots matched with abalone proteins (a 33.6% identification rate). Hybrid exhibiting additivity or overdominance accounted for 73.9% of these 46 identified proteins. The 46 differentially expressed proteins were shown to be involved in major biological processes, including muscle contraction and regulation, energy metabolism, and stress response. The proteins involved in energy metabolism included adenosine triphosphate (ATP) synthase β subunit, fructose 1, 6‐bisphosphate aldolase, triosephosphate isomerase, enolase, arginine kinase, and tauropine dehydrogenase. These proteins exhibited additivity in their offspring. The proteins involved in stress responses included HSP Hsp70 (exhibiting overdominance in the offspring) and Cu/Zn‐superoxide dismutase (exhibiting additivity). These results suggested that proteomic approach is suitable for analysis of heterosis and functional prediction of abalone hybridization.     

Characterization of lacrimal proline‐rich protein 4 (PRR4) in human tear proteome

This study was initiated considering the lack of comprehensive characteristics profile of PRR4 in tears of healthy subjects. Therefore, detailed characterizations of PRR4 from basal tears employing in‐gel and in‐solution digestions for MS systems are presented herein. First, pooled tear samples (n = 10) were utilized to identify PRR4‐rich region/spots in 1DE/2DE gels employing LC‐MALDI‐MS and 1DE‐LC‐ESI‐LTQ‐Orbitrap‐MS systems. PRR4‐rich region and ten spots with vast polymorphisms (M_r: 17–30 kDa, pI: 3.0–6.6) were identified in 1DE and 2DE gels, respectively. In addition, combinations of four types of PTMs, which are methylation, acetylation, oxidation, and pyroglutamate formation, were identified in these ten PRR4 spots. Furthermore, a targeted data‐acquisition approach was utilized to identify PRR4 isoforms in individual tear samples (n = 61) by in‐solution digestion combined with a LC‐ESI‐LTQ‐Orbitrap‐MS system. Importantly, a new PRR4 isoform designated as PRR4‐N3 in addition to PRR4 (gi154448886) and pHL E1F1 (gi1050983) was identified. Moreover, different combinations of these three PRR4 isoforms identified in the individual tear samples could be categorized into six distinguished groups. Conclusively, these findings provide fundamental insight into the complex characteristics profile of PRR4 isoforms and their PTMs in tears of healthy individuals.     

Understanding the cellular mechanism of recovery from freeze–thaw injury in spinach: possible role of aquaporins,heat shock proteins,dehydrin and antioxidant system

Recovery from reversible freeze–thaw injury in plants is a critical component of ultimate frost survival. However, little is known about this aspect at the cellular level. To explore possible cellular mechanism(s) for post‐thaw recovery (REC), we used Spinacia oleracea L. cv. Bloomsdale leaves to first determine the reversible freeze–thaw injury point. Freeze (–4.5°C)–thaw‐injured tissues (32% injury vs <3% in unfrozen control) fully recovered during post‐thaw, as assessed by an ion leakage‐based method. Our data indicate that photosystem II efficiency (Fv/Fm) was compromised in injured tissues but recovered during post‐thaw. Similarly, the reactive oxygen species (O₂^?? and H₂O₂) accumulated in injured tissues but dissipated during recovery, paralleled by the repression and restoration, respectively, of activities of antioxidant enzymes, superoxide dismutase (SOD) (EC. 1.14.1.1), and catalase (CAT) (EC.1.11.1.6) and ascorbate peroxidase (APX) (EC.1.11.1.11). Restoration of CAT and APX activities during recovery was slower than SOD, concomitant with a slower depletion of H₂O₂ compared to O₂^??. A hypothesis was also tested that the REC is accompanied by changes in the expression of water channels [aquaporines (AQPs)] likely needed for re‐absorption of thawed extracellular water. Indeed, the expression of two spinach AQPs, SoPIP2;1 and SoδTIP, was downregulated in injured tissues and restored during recovery. Additionally, a notion that molecular chaperones [heat shock protein of 70 kDa (HSP70s)] and putative membrane stabilizers [dehydrins (DHNs)] are recruited during recovery to restore cellular homeostasis was also tested. We noted that, after an initial repression in injured tissues, the expression of three HSP70s (cytosolic, endoplasmic reticulum and mitochondrial) and a spinach DHN (CAP85) was significantly restored during the REC.     

Adenosinergic Modulation of Ventilation in Obese Zucker Rats

Objectives: The goal of our study was to determine whether altered adenosinergic mechanisms contribute to the depressed ventilatory response observed in obese Zucker rats. Research Methods and Procedures: Eight lean and eight obese Zucker rats were studied at 7 to 8 weeks of age. Ventilation (V˙_E) during room air, during 5‐minute hypercapnic (7% CO₂, balance O₂), and during 30‐minute sustained hypoxic (10% O₂) exposures were sequentially measured by the barometric method on three separate occasions after the randomized blinded administration of equal volumes of either saline (control), 8‐(p‐sulfophenyl)‐theophylline (8‐PST, 7 mg/kg, peripheral adenosine antagonist), or aminophylline (AMPH, 15 mg/kg, peripheral and central adenosine antagonist). Results: During room air and hypercapnic exposures, AMPH (but not 8‐PST) significantly (p < 0.05) increased V˙_E in both lean and obese rats. During acute (2 minute) hypoxic exposure, 8‐PST (but not AMPH) significantly depressed V˙_E in lean rats. In contrast, AMPH (but not 8‐PST) selectively increased V˙_E in obese rats. During sustained (10 to 30 minutes) hypoxic exposure, neither AMPH nor 8‐PST administration altered V˙_E in lean rats. In contrast, AMPH (but not 8‐PST) selectively increased V˙_E during the late response in obese rats. Discussion: Our findings indicate that obese rats possess altered adenosinergic modulation of ventilatory responses to acute and sustained hypoxia in two opposite ways. We conclude that the reduced hypoxic ventilatory response observed in obese Zucker rats is attributed to depressed adenosinergic peripheral excitatory mechanisms and to enhanced adenosinergic central depression mechanisms, both of which contribute to the blunted ventilatory response in obesity.