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To better understand the factors facilitating or impeding the translation of “promising controversies” (Taylor & Snoddon, 2013, p. 439) of plurilingualism theory into meaningful practices, this article presents a synthesis of 30 empirical studies on plurilingual pedagogy as enacted and experienced by educators and learners in various global K–12 and postsecondary contexts. Informed by plurilingualism (Coste et al., 1997/2009; Council of Europe, 2020), this synthesis forefronts the key contributions of plurilingual pedagogy as it fosters: (a) students’ development of plurilingual (and pluri-/intercultural) competence, (b) evolution of language beliefs towards a positive orientation to plurality and hybridity, (c) affirmation of student and teacher identity and promotion of agency, and (d) language and literacy development. The perceived challenges, however, are related to the nature and practical issues of designing and implementing plurilingual pedagogy in the classroom which are interconnected with institutional policies and ideological discourses. The results illuminate the up-to-date progress as well as hurdles of promoting plurilingual pedagogies across different contexts and provide important implications for multiple stakeholders involved in pre-service teacher education, in-service professional development, curriculum improvement, and language policy making in Canada and other multicultural and multilingual societies and communities. Afin de mieux comprendre les facteurs facilitant ou entravant la traduction de « controverses prometteuses » (Taylor & Snoddon, 2013, p. 439) de la théorie du plurilinguisme en pratiques significatives, cet article présente une synthèse de 30 études empiriques sur la pédagogie plurilingue telle qu’adoptée et vécue par des éducateurs chevronnés et des apprenants dans divers contextes mondiaux de la maternelle à la 12e année et postsecondaires. Informée par le plurilinguisme (Coste et al., 1997/2009; Conseil de l’Europe, 2020), cette synthèse met en avant les contributions clés de la pédagogie plurilingue puisqu’elle favorise: (a) le développement des compétences plurilingues (et inter-/pluriculturelles) des étudiants, (b) l’évolution des croyances langagières vers une orientation positive envers la pluralité et l’hybridité, (c) l’affirmation de l’identité de l’étudiant et de l’enseignant ainsi que la promotion de l’autonomie et (d) le développement de la langue et de la littératie. Cependant, les défis perçus sont liés à la nature et aux problèmes pratiques de concevoir et de mettre en place une pédagogie plurilingue dans la salle de classe, ce qui rejoignent les politiques institutionnelles et les discours idéologiques. Les résultats mettent en lumière les progrès actualisés ainsi que les obstacles liés à la promotion du plurilinguisme dans différents contextes et fournissent des implications importantes pour les multiples parties prenantes impliquées dans le pré-service de la formation initiale des enseignants, ainsi que l’élaboration des politiques linguistiques au Canada et dans d’autres sociétés et communautés multilingues et multiculturelles.

Duoethnography is an emerging research methodology and tool for reflective practice in English language teaching (ELT). Duoethnography allows for people to become the sites of their own inquiry and investigate issues and phenomena of importance to them (Sawyer Norris, 2013). In duoethnography, participants engage in critical dialogue with one another as a way to challenge broader normative assumptions but also as a way to bring meaning to experiences and find solutions to immediate teaching issues. In this duoethnography, we examine the phenomenon of silence through our shared experiences as English language teachers and applied linguists but also from our diverging perspectives, cultures, and backgrounds. Data were gathered from online conversations, reflective notes, and memos between the two authors with emerging themes including 1) Shifting perspectives on silence, 2) Silence in the online classroom, and 3) Turn-taking and student/teacher discourse expectations. While specific to the authors, it is hoped that this duoethnography may resonate with readers and serve as a catalyst for further reflection on silence.

Les auteurs analysent l’incidence des niveaux autodéclarés de compétences langagières en anglais, des diplômes de formation à l’enseignement en langues, de l’identité linguistique (par exemple, celle d’enseignant non anglophone) et de l’expérience en enseignement sur le sentiment d’autoefficacité des enseignants de l’anglais. Ils conçoivent une nouvelle échelle d’autoefficacité des enseignants à partir de données provenant des enseignants de l’anglais en Ontario. Une analyse de régression multiple révèle que la compétence, l’identité linguistique et l’expérience en enseignement ont toutes une incidence sur l’autoefficacité des enseignants. Toutefois, pour ce groupe d’enseignants, un diplôme de maîtrise en formation à l’enseignement en langues n’a pas d’incidence marquée sur la confiance autodéclarée des enseignants. Ces résultats sont comparés à ceux des études antérieures, et des recommandations quant aux pistes de recherches futures sont mises de l’avant.

Duoethnography is an emerging methodology in English language teaching (ELT)/applied linguistics where two or more participants critically examine a shared phenomenon or experience as a way to challenge assumptions and develop new understandings of critical events (Lowe & Lawrence, 2020). It is a flexible tool with an emphasis on interaction, both between people, and people and various physical or digital artefacts (e.g., documents, academic literature). In this paper, we outline our duoethnography on our experience with the Certificate for English Language Teaching to Adults (CELTA) with a focus on how academic literature and social media pervaded our inquiry. We highlight how academic articles and social media were used as artefacts in our study and how their role as “co-participants” enhanced our investigation. La duoethnographie est une méthodologie émergeante dans l’enseignement de l’anglais (ELT)/en linguistique appliquée dans laquelle deux participants ou plus examinent de façon critique un phénomène ou une expérience partagée comme manière de remettre en question les hypothèses et de créer de nouvelles voies pour comprendre des évènements critiques (Lowe & Lawrence, 2020). Il s’agit d’un outil souple qui met l’emphase sur l’interaction, à la fois entre les personnes, ainsi qu’entre les personnes et divers artefacts physiques ou numériques (par exemple, des documents, des écrits universitaires). Dans cet article, nous exposons notre duoethnographie dans notre expérience du Certificat pour l’enseignement de l’anglais aux adultes (CELTA), en portant une attention particulière à la façon dont les écrits universitaires et les médias sociaux ont imprégné notre enquête. Nous soulignons la manière dont les articles universitaires et les médias sociaux ont été utilisés comme artefacts dans notre étude et de quelle façon leur rôle de « coparticipants » a mis notre enquête en valeur.

Most English language teachers around the world speak English as an additional language, and their level of English proficiency is often a matter of concern for them and their employers who associate higher levels of language proficiency with more effective teaching skills. To this end, several studies have examined the relationship between language proficiency and teachers’ beliefs about their pedagogical capabilities, commonly known as self-efficacy. While generally studies show a positive relationship between language proficiency and self-perceived teaching ability, findings regarding the strength of the relationship, the role of specific language skills (e.g. speaking, listening), and how they interact with different teaching abilities (e.g. classroom management) are inconsistent. By combining data from 19 studies, this meta-analytic study examined the relationship between language proficiency and teaching self-efficacy and analysed the role of various moderators such as teaching degree, teaching experience, and type of self-efficacy/proficiency measures. Findings reveal a moderate relationship ( r = .37) between language proficiency and teaching self-efficacy, with some moderator variables showing significant differences across correlations. The results indicate that only a small percentage of the variance in self-efficacy can be accounted for by teachers’ language proficiency, suggesting that while language proficiency is important, there is more to self-efficacy than just language proficiency.

Sample preparation for mass-spectrometry-based proteomic analyses usually requires intricate, multistep workflows that are often limited in capacity or suffer from sample loss. Here, we introduce a lean adsorption-based protocol (ABP) for the extraction of proteins from fresh cell lysates that enables us to modify and tag protein samples under harsh conditions, such as organic solvents, high salt concentrations, or low pH values. This offers high versatility while also reducing the required steps in the preparation process significantly. Protein identifications are slightly increased compared to traditional acetone precipitation followed by an in-solution digestion (AP/IS) or filter aided sample preparation (FASP) and proved complementary to both methods regarding proteome coverage. When combined with ArgC-like digestion, this approach delivered 5386 uniquely identified proteins, a substantial increase of 18.27% over tryptic digestion (4554), while decreasing spectra complexity due to a lower number of peptide to spectra matches per protein and the number of missed cleaved peptides. In addition, an increased number of identified membrane proteins and histones as well as improved fragmentation and intensity coverage were observed through comprehensive data analysis.

We show an easy and fast method for improved detection of lipophilic peptides with MALDI-MS utilizing the nonionic detergents n-octylglucoside and n-dodecylmaltoside (laurylmaltoside). Investigations comprised on-plate digestion of proteins with trypsin, detergent effects on the protease trypsin, and the changes in MALDI matrix crystallization. Investigations also exhibited a higher tryptic activity in trypsin activity assay of 139% when using laurylmaltoside as supplement. Crystallization changed toward a more homogeneous crystal distribution and especially trypsinized insulin spectra recorded with MALDI-MS showed improved detectability of lipophilic peptides.

The American copyright act from 1976 has drawn much attention in the literature, however it has received little consideration by economists. We contribute to this literature by taking up the assumption that publishers may internalize the harm from termination decisions and illuminate the consequences for the contractual relationship between authors and publishers. We provide a bargaining model, the results of which offer new insights and provide a benchmark for future research. We identify differences in contract structures between terminating and non-terminating authors and introduce some key principles for contractual designs. A risk analysis reveals that, contrary to the view in the literature, a termination option does not necessarily force authors into lotteries. In addition, we analyze the limits of the law with respect to complementary institutional regulations and current norms in creative industries.

The NADH:ubiquinone oxidoreductase (complex I) is the first enzyme of the respiratory chain and the entry point for most electrons. Generally, the bacterial complex I consists of 14 core subunits, homologues of which are also found in complex I of mitochondria. In complex I preparations from the hyperthermophilic bacterium Aquifex aeolicus we have identified 20 partially homologous subunits by combining MALDI-TOF and LILBID mass spectrometry methods. The subunits could be assigned to two different complex I isoforms, named NQOR1 and NQOR2. NQOR1 consists of subunits NuoA(2), NuoB, NuoD(2), NuoE, NuoF, NuoG, Nuol(1), NuoH(1), NuoJ(1), NuoL(1), NuoM(1) and NuoN(1), with an entire mass of 504.17 kDa. NQOR2 comprises subunits NuoA(1), NuoB, NuoD(1), NuoE, NuoF, NuoG, NuoH(2), NuoI(2), NuoJ(1), NuoK(1), NuoL(2), NuoM(2) and NuoN(2), with a total mass of 523.99 kDa. Three Fe-S clusters could be identified by EPR spectroscopy in a preparation containing predominantly NQOR1. These were tentatively assigned to a binuclear center N1, and two tetranuclear centers, N2 and N4. The redox midpoint potentials of N1 and N2 are 273 mV and 184 mV, respectively. Specific activity assays indicated that NQOR1 from cells grown under low concentrations of oxygen was the more active form. Increasing the concentration of oxygen in the bacterial cultures induced formation of NQOR2 showing the lower specific activity.

Birch pollen allergy is diagnosed and treated with aqueous extracts from birch pollen, which contain a mixture of allergens and nonallergenic proteins, including large numbers of closely related sequence variants, so-called iso-allergens of the major allergen, Bet v 1. The quality of therapeutic and diagnostic allergen products largely depends on the allergen and iso-allergen composition. Several biochemical methods are currently applied to detect and quantify allergens and to record protein profiles without differentiating between iso-allergens. Mass spectrometry (MS) may entirely replace these technologies, as it allows sequence specific identification and quantification of proteins and protein profiles including sequence variants in one run. However, the protein inference problem still hampers the automatic assignment of peptide sequences to proteins, consequently impeding the quantification of sequence variants. Therefore, the aim of the study was to set up semitargeted analyses of label-free MS data that allow unambiguous identification and quantification of birch pollen allergens and nonallergenic proteins. We combined data independent acquisition with manual assignment of predefined target sequences for quantification of iso-allergens and automatic quantification of other allergens and nonallergenic proteins. The quantitative data for birch pollen allergens and sequence variants of Bet v 1 were further confirmed by multiple reaction monitoring.

A commercially available digestion chamber (SunDigest, SunChrom) is used for on-target digestion of proteins for subsequent direct MALDI-MS analysis. Temperature and humidity in the chamber can be controlled and kept constant during the reactions. For the first time, not only the tryptic digestion but also reduction and alkylation were performed in only one μL of sample directly on the MALDI sample plate. Each reaction step was optimized with regard to reactant concentration, temperature and time. Under optimized conditions a significant increase in sequence coverage is obtained. Proteins such as BSA and Apo-transferrin give best results when all reaction steps are performed at 50 °C, which results in a considerably reduced total time of 65 min compared to in-solution digests. Moreover, the on-target protocol is not only faster, but also superior with respect to the required protein amount; at the tested lower limit for PMF-analysis of 100 fmol the on-target procedure exhibits strongly superior sequence coverage and identification scores. Using lower protein amounts (10–50 fmol) an identification with MS/MS-analysis is possible. This newly developed protocol combines the benefits of the programmable SunDigest humidity chamber with a time-saving on-plate reduction, alkylation and digestion workflow for protein identification.

This article provides a review and analysis of current research examining the connection between teacher language proficiency and their self-reported beliefs about their pedagogical abilities. Generally speaking, (English) language teachers require an advanced level of proficiency in order to be successful language teachers, but pedagogical skills are also necessary for effective instruction. However, examining the relationship between language proficiency and pedagogical skills is not straightforward given the nature of language teaching in which language is both the content and medium of instruction, issues with defining language proficiency (for teaching), and disagreement regarding effective teaching skills in different social contexts. One approach has been to focus on teachers’ self-efficacy beliefs about their abilities to enact specific classroom tasks in certain contexts and potential relationships with teachers’ reported language proficiency. The analysis provided in this article highlights how these constructs have been measured in the literature and if/how they are connected to one another across different studies. Overall, teachers’ self-efficacy beliefs regarding their pedagogical abilities do correlate with language proficiency, but results are at times weak and/or inconclusive with inconsistent results across studies and contexts.

5‐Lipoxygenase (5‐LO) is the initial enzyme in the biosynthesis of leukotrienes, which are mediators involved in pathophysiological conditions such as asthma and certain cancer types. Knowledge of proteins involved in 5‐LO pathway regulation, including gene regulatory proteins, is needed to evaluate all options for therapeutic intervention in these diseases. Here, we present a mass spectrometric screening of ALOX5 promoter‐interacting proteins, obtained by DNA pulldown and label‐free quantitative mass spectrometry. Protein preparations from myeloid and B‐lymphocytic cell lines were screened for promoter DNA interactors. Through statistical analysis, 66 proteins were identified as specific ALOX5 promotor binding proteins. Among those, the 15 most likely candidates for a prominent role in ALOX5 gene regulation are the known ALOX5 interactors Sp1 and Sp3, the related factor Sp2, two Krüppel‐like factors (KLF13 and KLF16) and six other zinc finger proteins (MAZ, PRDM10, VEZF1, ZBTB7A, ZNF281 and ZNF579). Intriguingly, we also identified two helicases (BLM and DHX36) and the proteins hnRNPD and hnRNPK, which are, together with the protein MAZ, known to interact with DNA G‐quadruplex structures. As G‐quadruplexes are implicated in gene regulation, spectroscopic and antibody‐based methods were used to confirm their presence within the GC‐rich sequence of the ALOX5 promoter. In summary, we have systematically characterized the interactome of the ALOX5 promoter, identifying several zinc finger proteins as novel potential ALOX5 gene regulators. Further, we have shown that the ALOX5 promoter can form DNA G‐quadruplex structures, which may play a functional role in ALOX5 gene regulation.

Enzymatic digestion of complex protein samples is often performed by use of multiple proteases to improve protein identification and characterization. Combining trypsin with ArgC is one option to enhance sequence coverage in bottom-up proteomics. However, the low selectivity of this endoprotease derogates from the benefit of the combination. Our approach here is to mimic ArgC digestion by chemically modifying all lysine residues in proteins so that trypsin can only cleave C-terminal to arginine. Four different amine modifications, dimethylation, acetylation, propionylation, and carbethoxylation, were tested, and the protocols were optimized. A nearly complete conversion of the primary amines was achieved for all modifications. Tryptic digestion of Escherichia coli lysate proteins after acylation of lysine residues shows the most significant improvement compared with data received from ArgC digest. After propionylation, 9216 unique peptides identified 1439 proteins, which, compared with a conventional tryptic digestion, represents the identification of 150 additional proteins due to a reasonable reduction of the sample complexity and higher fragmentation efficiencies of the peptides. It is therefore concluded that the Arg-C like digestion should no longer be regarded as a complementary approach but forms a viable and superior alternative to the conventional trypsin digestion.

5-Lipoxygenase (5-LO, EC1.13.11.34) has been implicated in the pathogenesis of inflammatory and immune diseases. Recently, aminothiazole comprising inhibitors have been discovered for this valuable target. Yet, the molecular mode of action of this class of substances is only poorly understood. Here, we present the detailed molecular mechanism of action of the compound class and the in vitro pharmacological profile of two lead compounds ST-1853 and ST-1906. Mechanistic studies with recombinant proteins as well as intact cell assays enabled us to define this class as a novel type of 5-LO inhibitors with unique characteristics. The parent compounds herein presented a certain reactivity concerning oxidation and thiol binding: Unsubstituted aminophenols bound covalently to C159 and C418 of human 5-LO. Yet, dimethyl substitution of the aminophenol prevented this reactivity and slowed down phase II metabolism. Both ST-1853 and ST-1906 confirmed their lead likeness by retaining their high potency in physiologically relevant 5-LO activity assays, high metabolic stability, high specificity and non-cytotoxicity.

This study investigates turn-taking and silent learning during teacher-fronted open class discussions. Drawing on classroom observations and interview data, the study tracks the turn-taking habits of an advanced level EAP class in Ontario, Canada, and investigates how students use their non-verbal time during class discussions to enhance language learning. The participants use a variety of turn-taking mechanisms in order to enter classroom conversation, but many of the speaking turns are short and participation is unequal. For some, their lack of verbal contribution is due to various internal and external causes of reticence. However, the interview data reveal a variety of ways that some of these L2 learners silently engage with the discussion and enhance their language learning. Silent learning strategies, the impact of different cultural learning practices, and potential pedagogical suggestions are all discussed.

Summary 5-Lipoxygenase (5-LO) initiates the biosynthesis of pro-inflammatory leukotrienes from arachidonic acid, which requires the nuclear membrane-bound 5-LO-activating protein (FLAP) for substrate transfer. Here, we identified human 5-LO as a molecular target of melleolides from honey mushroom (Armillaria mellea). Melleolides inhibit 5-LO via an α,β-unsaturated aldehyde serving as Michael acceptor for surface cysteines at the substrate entrance that are revealed as molecular determinants for 5-LO activity. Experiments with 5-LO mutants, where select cysteines had been replaced by serine, indicated that the investigated melleolides suppress 5-LO product formation via two distinct modes of action: (1) by direct interference with 5-LO activity involving two or more of the cysteines 159, 300, 416, and 418, and (2) by preventing 5-LO/FLAP assemblies involving selectively Cys159 in 5-LO. Interestingly, replacement of Cys159 by serine prevented 5-LO/FLAP assemblies as well, implying Cys159 as determinant for 5-LO/FLAP complex formation at the nuclear membrane required for leukotriene biosynthesis.

Aberrant neuronal network activity associated with neuronal hyperexcitability seems to be an important cause of cognitive decline in aging and Alzheimer’s disease (AD). Out of many antiepileptics, only levetiracetam improved cognitive dysfunction in AD patients and AD animal models by reducing hyperexcitability. As impaired inhibitory interneuronal function, rather than overactive neurons, seems to be the underlying cause, improving impaired neuronal function rather than quieting overactive neurons might be relevant in explaining the lack of activity of the other antiepileptics. Interestingly, improvement of cognitive deficits by levetiracetam caused by small levels of soluble Aβ was accompanied by improvement of synaptic function and plasticity. As the negative effects of Aβ on synaptic plasticity strongly correlate with mitochondrial dysfunction, wehypothesized that the effect of levetiracetam on synaptic activity might be raised by an improved mitochondrial function. Accordingly, we investigated possible effects of levetiracetam on neuronal deficits associated with mitochondrial dysfunction linked to aging and AD. Levetiracetam improved several aspects of mitochondrial dysfunction including alterations of fission and fusion balance in a cell model for aging and early late-onset AD. We demonstrate for the first time, using immunohistochemistry and proteomics, that the synaptic vesicle protein 2A (SV2a), the molecular target of levetiracetam, is expressed in mitochondria. In addition, levetiracetam shows significant effect on the opening of the mitochondrial permeability transition pore. Importantly, the effects of levetiracetam were significantly abolished when SV2a was knockdown using siRNA. In conclusion, interfering with the SV2a protein at the mitochondrial level and thereby improving mitochondrial function might represent an additional therapeutic effect of levetiracetam to improve symptoms of late-onset AD.

Multiple eukaryotic Hsp70 typically localized in the cytoplasm are also distributed to the intermembrane space of chloroplasts and might thereby represent the missing link in energizing protein translocation. Protein translocation into organelles is a central cellular process that is tightly regulated. It depends on signals within the preprotein and on molecular machines catalyzing the process. Molecular chaperones participate in transport and translocation of preproteins into organelles to control folding and to provide energy for the individual steps. While most of the processes are explored and the components are identified, the transfer of preproteins into and across the intermembrane space of chloroplasts is not yet understood. The existence of an energy source in this compartment is discussed, because the required transit peptide length for successful translocation into chloroplasts is shorter than that found for mitochondria where energy is provided exclusively by matrix chaperones. Furthermore, a cytosolic-type Hsp70 homologue was proposed as component of the chloroplast translocon in the intermembrane space energizing the initial translocation. The molecular identity of such intermembrane space localized Hsp70 remained unknown, which led to a controversy concerning its existence. We identified multiple cytosolic Hsp70s by mass spectrometry on isolated, thermolysin-treated Medicago sativa chloroplasts. The localization of these Hsp70s of M. sativa or Arabidopsis thaliana in the intermembrane space was confirmed by a self-assembly GFP-based in vivo system. The localization of cytosolic Hsp70s in the stroma of chloroplasts or different mitochondrial compartments could not be observed. Similarly, we could not identify any cytosolic Hsp90 in the intermembrane space of chloroplast. With respect to our results we discuss the possible targeting and function of the Hsp70 found in the intermembrane space.

The antimicrobial peptide LL-37 is the sole member of the human cathelicidin family with immune system-modulating properties and roles in autoimmune disease development. Small molecules able to interact with LL-37 and to modulate its functions have not been described yet. Boswellic acids (BAs) are pentacyclic triterpene acids that are bioactive principles of frankincense extracts used as anti-inflammatory remedies. Although various anti-inflammatory modes of action have been proposed for BAs, the pharmacological profile of these compounds is still incompletely understood. Here, we describe the identification of human LL-37 as functional target of BAs. In unbiased target fishing experiments using immobilized BAs as bait and human neutrophils as target source, LL-37 was identified as binding partner assisted by MALDI-TOF mass spectrometry. Thermal stability experiments using circular dichroism spectroscopy confirm direct interaction between BAs and LL-37. Of interest, this binding of BAs resulted in an inhibition of the functionality of LL-37. Thus, the LPS-neutralizing properties of isolated LL-37 were inhibited by 3-O-acetyl-β-BA (Aβ-BA) and 3-O-acetyl-11-keto-β-BA (AKβ-BA) in a cell-free limulus amoebocyte lysate assay with EC50=0.2 and 0.8 μM, respectively. Also, LL-37 activity was inhibited by these BAs in LL-37-enriched supernatants of stimulated neutrophils or human plasma derived from stimulated human whole blood. Together, we reveal BAs as inhibitors of LL-37, which might be a relevant mechanism underlying the anti-inflammatory properties of BAs and suggests BAs as suitable chemical tools or potential agents for intervention with LL-37 and related disorders.

This study presents a simple and sensitive high-throughput matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-MS/MS) method for ex vivo quantification of methylphenidate (MPH) in rat plasma and brain. The common MALDI matrix alpha-cyano-4-hydroxycinnamic acid was used to obtain an optimal dried droplet preparation. For method validation, standards diluted in plasma and brain homogenate prepared from untreated (control) rats were used. MPH was quantified within a concentration range of 0.1-40 ng/ml in plasma and 0.4-40 ng/ml in brain homogenate with an excellent linearity (R2 ≥ 0.9997) and good precision. The intra-day and inter-day accuracies fulfilled the FDA's ±15/20 critera. The recovery of MPH ranged from 93.8 to 98.5% and 87.2 to 99.8% in plasma and homogenate, respectively. We show that MPH is successfully quantified in plasma and brain homogenate of rats pre-treated with this drug using the internal standard calibration method. By means of this method, a linear correlation between plasma and brain concentration of MPH in rodents pre-treated with MPH was detected. The simple sample preparation based on liquid-liquid extraction and MALDI-MS/MS measurement requires approximately 10 s per sample, and this significantly reduces analysis time compared with other analytical methods. To the best of our knowledge, this is the first MALDI-MS/MS method for quantification of MPH in rat plasma and brain. Copyright © 2015 John Wiley & Sons, Ltd.

The mitochondrial acyl carrier protein (ACPM/NDUFAB1) is a central element of the mitochondrial fatty acid synthesis type II machinery. Originally ACPM was detected as a subunit of respiratory complex I but the reason for the association with the large enzyme complex remained elusive. Complex I from the aerobic yeast Yarrowia lipolytica comprises two different ACPMs, ACPM1 and ACPM2. They are anchored to the protein complex by LYR (leucine-tyrosine-arginine) motif containing protein (LYRM) subunits LYRM3 (NDUFB9) and LYRM6 (NDUFA6). The ACPM1-LYRM6 and ACPM2-LYRM3 modules are essential for complex I activity and assembly/stability, respectively. We show that in addition to the complex I bound fraction, ACPM1 is present as a free matrix protein and in complex with the soluble LYRM4(ISD11)/NFS1 complex implicated in Fe-S cluster biogenesis. We show that the presence of a long acyl chain bound to the phosphopantetheine cofactor is important for docking ACPMs to protein complexes and we propose that association of ACPMs and LYRMs is universally based on a new protein-protein interaction motif.

Background Microdialysis is an established technique for collecting small molecular weight substances (e.g. neurotransmitter and energy metabolites) from the extracellular space. The major element of microdialysis is the probe which contains a semi-permeable membrane and is exposed to the interstitial space. As the microdialysis technique has major advantages, e.g. versatility and use in awake animals, commercially produced probes are in great demand. New method We here present the design of a probe assembly step by step which will enable researchers to build custom-made probes. Probe recoveries of substances with different molecular weight (ranging from 100 to 1600 Da) were compared for three different probes (CMA 12 Elite probe, custom-made 10 kDa and 30 kDa probes). Recoveries of glucose, lactate, acetylcholine, choline, ATP and the neuropeptides angiotensin II, substance P and somatostatin are presented. Results We found that the 10 kDa probe is only useful for compounds up to 1000 Da while recoveries of the CMA-12 Elite Probe are variable and apparently dependent on ionic charges of analytes. The recovery of the custom-made 30 kDa probe is highest and evidently not influenced by physicochemical parameters of analytes. In a further optimization step, we describe the use of ZipTip® μC-18 collection tips to replace the outlet tubing when purifying the dialysate for MALDI-MS measurements of neuropeptides. Comparison with existing methods The results show that self-built microdialysis probes can be equally or more effective than commercially available probes. Conclusions Self-built microdialysis probes with large pore-membranes are capable of dialyzing ATP and neuropeptides.

Secretion of proteins is a central strategy of bacteria to influence and respond to their environment. Until now, there has been very few discoveries regarding the cyanobacterial secrotome or the secretion machineries involved. For a mutant of the outer membrane channel TolC-homologue HgdD of Anabaena sp. PCC 7120, a filamentous and heterocyst-forming cyanobacterium, an altered secretome profile was reported. To define the role of HgdD in protein secretion, we have developed a method to isolate extracellular proteins of Anabaena sp. PCC 7120 wild type and an hgdD loss-of-function mutant. We identified 51 proteins of which the majority is predicted to have an extracellular secretion signal, while few seem to be localized in the periplasmic space. Eight proteins were exclusively identified in the secretome of wild-type cells, which coincides with the distribution of type I secretion signal. We selected three candidates and generated hemagglutinin-tagged fusion proteins which could be exclusively detected in the extracellular protein fraction. However, these proteins are not secreted in the hgdD-mutant background, where they are rapidly degraded. This confirms a direct function of HgdD in protein secretion and points to the existence of a quality control mechanism at least for proteins secreted in an HgdD-dependent pathway.

The enzyme 5-lipoxygenase (5-LO) catalyzes the first reactions in the biosynthesis of leukotrienes, powerful lipid mediators that are involved in several physiological and pathological processes. 5-LO activity is tightly regulated by several factors, including post translational modifications (PTMs). Phosphorylations of 5-LO by the kinases extracellular signal-regulated kinase 2 (Erk2), mitogen-activated protein kinase activated protein kinase 2 (MK2) and protein kinase A (PKA) have been described to regulate 5-LO activity. Furthermore, 5-LO phosphorylation is considered a determinant of drug candidate potency. However, no evidence on a molecular level, as can be provided by MS, has as yet been presented for these PTMs. Here, we employ a workflow including different proteolytic cleavages and phosphopeptide enrichment for detection of 5-LO phosphorylation by MALDI-MS. Proof for the known phosphorylation sites of MK2 (Ser271) and PKA (Ser523) was provided by MS after in vitro phosphorylation, but not for the postulated Erk2 site (Ser663). Detection limits have been determined for all three sites. Moreover, we identified novel tyrosine kinase target sites within 5-LO using in silico and in vitro methods. Tyr42, Tyr53 and either Tyr94 or Tyr445 were phosphorylated by the Src kinases Fgr, hematopoietic cell kinase (HCK) and Yes. To analyze the phosphorylation state in the cellular context, we created stably 5-LO-transduced Mono Mac 6 cells. Here, we only detected phospho-Ser271 by MS, whereas immunoblot analysis indicated tyrosine phosphorylation, phospho-Ser271 and phospho-Ser663. Unexpectedly, phospho-Ser271 occurred independent of cell stimulation. Taken together, we describe a method for the molecular analysis of 5-LO phosphorylation, provide insights regarding the occurrence of known phosphorylation sites partly in contrast to earlier studies and present first evidence on novel phosphosites.

The discovery of PTMs in proteins by MS requires nearly complete sequence coverage of the detected proteolytic peptides. Unfortunately, mass spectrometric analysis of the desired sequence fragments is often impeded due to low ionization efficiency and/or signal suppression in complex samples. When several lysine residues are in close proximity tryptic peptides may be too short for mass analysis. Moreover, modified peptides often appear in low stoichiometry and need to be enriched before analysis. We present here how the use of sulfo-NHS-SS-biotin derivatization of lysine side chain can help to detect PTMs in lysine-rich proteins. This label leads to a mass shift which can be adjusted by reduction of the SS bridge and alkylation with different reagents. Low intensity peptides can be enriched by use of streptavidin beads. Using this method, the functionally relevant protein kinase A phosphorylation site in 5-lipoxygenase was detected for the first time by MS. Additionally, methylation and acetylation could be unambiguously determined in histones.

Neurotransmitter release as well as the structural and functional dynamics of the presynaptic active zone is controlled by proteinaceous components. Here we describe for the first time an experimental approach for the isolation of the presynaptic active zone from individual mouse brains, a prerequisite for understanding the functional inventory of the presynaptic protein network and for the later analysis of changes occurring in mutant mice. Using a monoclonal antibody against the ubiquitous synaptic vesicle protein SV2 we immunopurified synaptic vesicles docked to the presynaptic plasma membrane. Enrichment studies by means of Western blot analysis and mass spectrometry identified 485 proteins belonging to an impressive variety of functional categories. Our data suggest that presynaptic active zones represent focal hot spots that are not only involved in the regulation of neurotransmitter release but also in multiple structural and functional alterations the adult nerve terminal undergoes during neural activity in adult CNS. They furthermore open new avenues for characterizing alterations in the active zone proteome of mutant mice and their corresponding controls, including the various mouse models of neurological diseases.

The concept of rationally designing MALDI matrices has been extended to the next "whole sample" level. These studies have revealed some unexpected and exploitable insights in improving MALDI sensitivity. It is shown that (i) additives which only provide additional laser energy absorption are best to be avoided; (ii) the addition of proton donors in the form of protonated weak bases can be highly beneficial; (iii) the addition of glycerol for coating crystalline samples is highly recommended. Overall, analytical sensitivity has been significantly increased compared to the current "gold" standards in MALDI MS, and new insights into the mechanisms and processes of MALDI have been gained.

The biodistribution of nanoparticles is significantly influenced by their interaction with plasma proteins. In order to optimize and possibly monitor the delivery of drugs bound to nanoparticles across the blood–brain barrier (BBB), the protein adsorption pattern of uncoated poly(lactic-co-glycolic acid) (PLGA) nanoparticles after their incubation in human plasma was studied by mass spectrometry. After washing of the particles with water, the proteins were directly digested on the nanoparticle surface using trypsin and then analyzed by nLC MALDI-TOF/TOF. Up to now, the standard method for investigation into the plasma protein adsorption to the particles was 2D gel electrophoresis (2D-PAGE), in certain cases followed by mass spectrometry. The non-gel-based method proposed in the present study provides novel insights into the protein corona surrounding the nanoparticles. The proteins adsorbed on the PLGA nanoparticles after incubation that gave the best signal in terms of quality (high MASCOT score) in human plasma were apolipoprotein E, vitronectin, histidine-rich glycoprotein and kininogen-1. These proteins also are constituents of HDL.

Although the extraction of intact proteins from polyacrylamide gels followed by mass spectrometric molecular mass determination has been shown to be efficient, there is room for alternative approaches. Our study evaluates ethylene glycol diacrylate, a cleavable cross-linking agent used for a new type of dissolvable gels. It attains an ester linkage that can be hydrolyzed in alkali conditions. The separation performance of the new gel system was tested by 1D and 2D SDS-PAGE using the outer chloroplast envelope of Pisum sativum as well as a soluble protein fraction of human lymphocytes, respectively. Gel spot staining (CBB), dissolving, and extracting were conducted using a custom-developed workflow. It includes protein extraction with an ammonia-SDS buffer followed by methanol treatment to remove acrylamide filaments. Necessary purification for MALDI-TOF analysis was implemented using methanol-chloroform precipitation and perfusion HPLC. Both cleaning procedures were applied to several standard proteins of different molecular weight as well as 'real' biological samples (8-75 kDa). The protein amounts, which had to be loaded on the gel to detect a peak in MALDI-TOF MS, were in the range of 0.1 to 5 μg, and the required amount increased with increasing mass.

Although less specific proteases have been established in proteomics, resulting peptides are often disadvantaged in mass spectrometric analysis compared to tryptic peptides. This is due to the high number of theoretically possible peptides as well as their relatively inefficient ionization and fragmentation. One possibility to improve the performance of less specific digests is to employ amine reactive, basic labels such as tandem mass tags (TMT) for the N-terminal derivatization of peptides. This study uses elastase and thermolysin digestion of cytosolic extracts with and without the use of TMT labeling for analysis via nanoflow high-performance liquid chromatography (nLC) coupled to an electrospray ionization quadrupole orthogonal acceleration time-of-flight (ESI-QoTOF) mass spectrometer. Differences between tryptic and less specific digests and their behavior during chromatographic separation and tandem mass spectrometric (MS/MS) analysis are highlighted. Furthermore, this work shows how the tandem mass spectrometric analysis of less specific digests can be optimized with reference to peptide ionization and fragmentation. The effect of TMT labeling on the number and characteristics of identified peptides as well as peptide fragmentation behavior is examined. Taking all these factors into consideration, this work constitutes an optimized strategy for the analysis of less specific digests via nLC–ESI-QoTOF-MS/MS.

Synaptic release sites are characterized by exocytosis-competent synaptic vesicles tightly anchored to the presynaptic active zone (PAZ) whose proteome orchestrates the fast signaling events involved in synaptic vesicle cycle and plasticity. Allocation of the amyloid precursor protein (APP) to the PAZ proteome implicated a functional impact of APP in neuronal communication. In this study, we combined state-of-the-art proteomics, electrophysiology and bioinformatics to address protein abundance and functional changes at the native hippocampal PAZ in young and old APP-KO mice. We evaluated if APP deletion has an impact on the metabolic activity of presynaptic mitochondria. Furthermore, we quantified differences in the phosphorylation status after long-term-potentiation (LTP) induction at the purified native PAZ. We observed an increase in the phosphorylation of the signaling enzyme calmodulin-dependent kinase II (CaMKII) only in old APP-KO mice. During aging APP deletion is accompanied by a severe decrease in metabolic activity and hyperphosphorylation of CaMKII. This attributes an essential functional role to APP at hippocampal PAZ and putative molecular mechanisms underlying the age-dependent impairments in learning and memory in APP-KO mice.

Recently, we published that nitro-fatty acids (NFA) are potent electrophilic molecules which inhibit 5-lipoxygenase (5-LO) by interacting with catalytically cysteine residues next to a substrate entry channel. The electrophilicity is derived from an intramolecular Michael acceptor moiety consisting of an electron-withdrawing group in close proximity to a double bond. The potential of the Michael acceptor moiety to interact with functionally relevant cysteines of proteins potentially renders them effective and sustained enzyme activity modulators. We screened a large library of naturally derived and synthetic electrophilic compounds to investigate whether other types of Michael acceptor containing drugs suppress 5-LO enzyme activity. The activity was measured by assessing the effect on the 5-LO product formation of intact human polymorphonuclear leukocytes. We demonstrated that a number of structurally different compounds were suppressive in the activity assays and showed that Michael acceptors of the quinone and nitro-alkene group produced the strongest inhibition of 5-LO product formation. Reactivity with the catalytically relevant cysteines 416 and 418 was confirmed using mutated recombinant 5-LO and mass spectrometric analysis (MALDI-MS). In the present study, we show for the first time that a number of well-recognized naturally occurring or synthetic anti-inflammatory compounds carrying a Michael acceptor, such as thymoquinone (TQ), the paracetamol metabolite NAPQI, the 5-LO inhibitor AA-861, and bardoxolone methyl (also known as "RTA 402", "CDDO-methyl ester") are direct covalent 5-LO enzyme inhibitors that target the catalytically relevant cysteines 416 and 418.

A novel type of peptide standard is introduced that consists of two peptides combined in one synthetic molecule and separated by a proteolytic cleavage site. Upon enzymatic digestion, the two peptides are released in a molar one-to-one ratio. This method enables the generation of exact equimolar mixtures of two peptides of any nature and origin, thereby providing a valuable tool for the investigation of fundamental phenomena in MS. The applicability of the method is exemplified by the analysis of the effect of peptide sequence variations on the relative ionization efficiency in ESI- and MALDI-MS.

Graphite as MALDI matrix or in combination with other substances has been reported in recent years. Here, we demonstrate that graphite can be used as target coating supporting the crystallization of the α-cyano-4-hydroxycinnamic acid matrix. A conventional dried-droplet preparation of matrix and analyte solution on a graphite-coated metal target leads to a thin, uniform layer of cubic crystals with about 1 μm edge length. Commercially available graphite powder of 1-2 μm particle size is gently wiped over the target using a cotton Q-tip, leading to an ultra-thin, not-visible film. This surface modification considerably improves analysis of peptides and proteins for MALDI MS using conventional dried-droplet preparation. Compared with untreated targets, the signal intensities of standard peptides are up to eight times higher when using the graphite supported crystallization. The relative standard deviation in peak area of angiotensin II for sample amounts between 1 and 50 fmol is reduced to about 15 % compared with 45 % for untreated sample holders. For a quantification of 1 fmol of the peptide using an internal standard the coefficient of variation is reduced to 3.5 % from 8 %. The new graphite supported preparation (GSP) protocol is very simple and does not require any technical nor manual skills. All standard solvents for peptides and proteins can be used.

Although sharing a certain degree of structural uniformity, natural product classes exhibit variable functionalities such as different amino acid or acyl residues. During collision induced dissociation, some natural products exhibit a conserved fragmentation pattern close to the precursor ion. The observed fragments result from a shared set of neutral losses, creating a unique fragmentation pattern, which can be used as a fingerprint for members of these natural product classes. The culture supernatants of 69 strains of the entomopathogenic bacteria Photorhabdus and Xenorhabdus were analyzed by MALDI-MS(2), and a database comprising MS(2) data from each strain was established. This database was scanned for concordant fragmentation patterns of different compounds using a customized software, focusing on relative mass differences of the fragment ions to their precursor ion. A novel group of related natural products comprising 25 different arginine-rich peptides from 16 different strains was identified due to its characteristic neutral loss fragmentation pattern, and the structures of eight compounds were elucidated. Two biosynthesis gene clusters encoding nonribosomal peptide synthetases were identified, emphasizing the possibility to identify a group of structurally and biosynthetically related natural products based on their neutral loss fragmentation pattern.

Stable isotope dilution-based quantitative proteomics with intact labeled proteins as internal standards in combination with a bottom-up approach, i.e., with quantification on the peptide level, is an established method. To explore the technical precision of this approach, calmodulin-like protein 3 was prepared in non-labeled (light) and SILAC-type labeled (heavy) form by cell-free synthesis, mixed, digested with trypsin, and analyzed by UPLC-ESI-MS. In total, 16 light/heavy peptide pair ratios were determined. Pair-wise comparison of ratios of 12 peptides selected according to S/N ratios >50 revealed that the majority exhibited ratios, which were different at a high level of statistical significance (p < 0.001). HPLC-MALDI-MS ratio data confirmed this observation, thus excluding the ionization method as a source of the observed ratio differences. Variation of the digestion time from 0.25 to 4 h showed that the light/heavy ratios of most peptides decrease with time, indicating a kinetic isotope effect leading to preferred cleavage of light calmodulin-like protein 3. The subset of peptides with statistically identical ratios resulted in an average ratio with a RSD of 1.0 %. The light/heavy ratio calculated on the basis of these peptides probably provides the most accurate molar protein ratio.

tRNAs from all three kingdoms of life contain a variety of modified nucleotides required for their stability, proper folding, and accurate decoding. One prominent example is the eponymous ribothymidine (rT) modification at position 54 in the T-arm of eukaryotic and bacterial tRNAs. In contrast, in most archaea this position is occupied by another hypermodified nucleotide: the isosteric N1-methylated pseudouridine. While the enzyme catalyzing pseudouridine formation at this position is known, the pseudouridine N1-specific methyltransferase responsible for this modification has not yet been experimentally identified. Here, we present biochemical and genetic evidence that the two homologous proteins, Mja_1640 (COG 1901, Pfam DUF358) and Hvo_1989 (Pfam DUF358) from Methanocaldococcus jannaschii and Haloferax volcanii, respectively, are representatives of the methyltransferase responsible for this modification. However, the in-frame deletion of the pseudouridine N1-methyltransferase gene in H. volcanii did not result in a discernable phenotype in line with similar observations for knockouts of other T-arm methylating enzymes.

Secondary ion mass spectrometry (SIMS) is a desorption/ionization method in which ions are generated by the impact of a primary ion beam on a sample. Classic matrix assisted laser desorption and ionization (MALDI) matrices can be used to increase secondary ion yields and decrease fragmentation in a SIMS experiment, which is referred to as matrix enhanced SIMS (ME-SIMS). Contrary to MALDI, the choice of matrices for ME-SIMS is not constrained by their photon absorption characteristics. This implies that matrix compounds that exhibit an insufficient photon absorption coefficient have the potential of working well with ME-SIMS. Here, we evaluate a set of novel derivatives of the classical MALDI matrices α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) for usability in ME-SIMS. This evaluation was carried out using peptide mixtures of different complexity and demonstrates significant improvements in signal intensity for several compounds with insufficient UV absorption at the standard MALDI laser wavelengths. Our study confirms that the gas-phase proton affinity of a matrix compound is a key physicochemical characteristic that determines its performance in a ME-SIMS experiment. As a result, these novel matrices improve the performance of matrix enhanced secondary ion mass spectrometry experiments on complex peptide mixtures.