Targeted Metabolomics for Biomarker Discovery

Metabolomics is a truly interdisciplinary field of science, which combines analytical chemistry, platform technology, mass spectrometry, and NMR spectroscopy with sophisticated data analysis. Applied to biomarker discovery, it includes aspects of pathobiochemistry, systems biology/medicine, and molecular diagnostics and requires bioinformatics and multivariate statistics. While successfully established in the screening of inborn errors in neonates, metabolomics is now widely used in the characterization and diagnostic research of an ever increasing number of diseases. In this Review we highlight important technical prerequisites as well as recent developments in metabolomics and metabolomics data analysis with special emphasis on their utility in biomarker identification and qualification, as well as targeted metabolomics by employing high‐throughput mass spectrometry.     

Modification of tricine–SDS–PAGE for online and offline analysis of phosphoproteins by ICP-MS

This study describes a modification to tricine sodium dodecyl sulphate polyacrylamide gel electrophoresis to make it more effective for the separation of low molecular mass proteins and for coupling with inductively coupled plasma mass spectrometry (ICP-MS). The modified method employs low-percentage polyacrylamide gels (7–10%) (w/v) and low reagent concentrations that provide efficient separations, good quantitation and low matrix levels that are compatible with ICP-MS. Using phosphopeptides as a model system, and offline analysis, we obtained recoveries of 73% (w/v) in a 9% gel compared with 55% in a conventional 16% gel. Online coupling was achieved by modification of a standard commercially available gel electroelution apparatus and casting of the gel into a 7.3-cm-long tube. Online separation of a digest of β-casein was demonstrated with recovery of the mono- and tetraphosphopeptides, which were identified by comparison with peptide standards. A mass balance study with the standards yielded recoveries of 95% for tetraphosphopeptides and 48% for monophosphopeptides. The factors affecting the separations and recoveries are discussed in detail. The detection limits for 10-μL samples of the mono- and tetraphosphopeptides were 0.7 μM (7 pmol) and 0.2 μM (2 pmol) respectively.     

Electron capture dissociation mass spectrometry of tyrosine nitrated peptides

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification. Here, we have investigated the electron capture dissociation (ECD) and collision-induced dissociation (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains.     

Chemical composition and antimicrobial activity of essential oils from Centaurea pannonica and C. jacea

The chemical composition and antimicrobial activity of the essential oils obtained by hydrodistillation from Centaurea pannonica (Heufel) Simonkai and C. jacea L. (Asteraceae), were investigated. The essential oils were analyzed by GC and GC-MS. Forty five and twenty nine compounds were identified in the two oils, respectively. C. pannonica oil was rich in fatty acids (43.7%), with 9-octadecanoic acid (34.0%) and (Z,Z)-9,12-octadecadienoic acid (8.6%) as the major compounds. In contrast, the essential oil of C. jacea was dominated by oxygenated sesquiterpenes (43.2%), among which caryophyllene oxide (23.5%) and spathulenol (8.9%) were the major constituents. However, the oil was also characterized by an important fatty acid fraction (15.5%), with 9-octadecanoic acid (8.9%) and hexadecanoic acid (6.6%) being the main components. The antimicrobial activities of the essential oils were evaluated by the microdilution method against three Gram-positive and three Gram-negative bacteria, and one yeast. Both oils exhibited significant antimicrobial activity, especially against Gram-positive bacteria.     

Rapid synthesis of carbohydrate derivatives, including mimetics of C-linked disaccharides and C-linked aza disaccharides, using the hetero-Diels-Alder reaction

In this work we demonstrate the value of performing a hetero-Diels-Alder reaction (HDAR) between Danishefsky's diene and a range of aldehydes or imines, under microwave irradiation. By using a range of aldehydes and imines, including those derived from carbohydrates, access to functionalized 2,3-dihydro-4H-pyran-4-ones or 2,3-dihydro-4-pyridinones in good to excellent synthetic yields is possible. A particular strength of the methodology is its ability to access mimetics of C-linked disaccharides and C-linked aza disaccharides, targets of current therapeutic interest, in a rapid, convenient, and diastereoselective manner. The effect of high pressure on the HDARs involving carbohydrate-derived aldehydes and imines is also explored, with enhancement in yields occurring for the aldehyde substrates. Finally, HDARs using carbohydrate derived ketones, enones, and enals are described under a range of conditions. Optimum results were obtained under high-pressure conditions, with highly functionalized carbohydrate derivatives being afforded, in good yields, in this way.     

Determination of anthelmintic drug residues in milk using ultra high performance liquid chromatography–tandem mass spectrometry with rapid polarity switching

A new UHPLC–MS/MS (ultra high performance liquid chromatography coupled to tandem mass spectrometry) method was developed and validated to detect 38 anthelmintic drug residues, consisting of benzimidazoles, avermectins and flukicides. A modified QuEChERS-type extraction method was developed with an added concentration step to detect most of the analytes at <1 μg kg⁻¹ levels in milk. Anthelmintic residues were extracted into acetonitrile using magnesium sulphate and sodium chloride to induce liquid–liquid partitioning followed by dispersive solid phase extraction for cleanup. The extract was concentrated into dimethyl sulphoxide, which was used as a keeper to ensure analytes remain in solution. Using rapid polarity switching in electrospray ionisation, a single injection was capable of detecting both positively and negatively charged ions in a 13 min run time. The method was validated at two levels: the unapproved use level and at the maximum residue level (MRL) according to Commission Decision (CD) 2002/657/EC criteria. The decision limit (CCα) of the method was in the range of 0.14–1.9 and 11–123 μg kg⁻¹ for drugs validated at unapproved and MRL levels, respectively. The performance of the method was successfully verified for benzimidazoles and levamisole by participating in a proficiency study.     

Luminescence Enhancement from Silica-Coated Gold Nanoparticle Agglomerates Following Multi-photon Excitation

Multi-photon absorption induced luminescence (MAIL) from bare gold nanoparticles, silica-coated particles, as well as silica-coated agglomerated gold nanoparticles suspended in aqueous solution was studied by using time-resolved and steady-state luminescence spectroscopy. The nanoparticles were excited by femtosecond pulses of wavelengths ranging from 630 nm to 900 nm. The luminescence from the particles exhibits a broad spectrum in the UV and VIS region. The time-resolved measurements indicate a luminescence lifetime of a few ps, limited by the response of the experimental system. The studied dependence of the MAIL efficiency on the excitation wavelength showed that the luminescence from silica-coated agglomerates was enhanced over the whole range of excitation wavelengths, when compared to the luminescence from individual gold nanoparticles. The agglomerates show an almost excitation wavelength independent efficiency of the MAIL, while for individual nanoparticles a rapid decrease of the MAIL efficiency was observed with increasing excitation wavelength. The observed enhancement of the MAIL from the agglomerated nanostructures can be attributed to the presence of localized surface plasmon resonances in the spectral region corresponding to the excitation wavelengths. The high MAIL efficiency from the agglomerated nanoparticle structures in the near-infrared could be an advantage in the expanding field of luminescence-based-imaging, as well as in biosensor technology.     

Qualities of examples in learning and teaching

In this paper, we theorise about the different kinds of relationship between examples and the classes of mathematical objects that they exemplify as they arise in mathematical activity and teaching. We ground our theorising in direct experience of creating a polynomial that fits certain constraints to develop our understanding of engagement with examples. We then relate insights about exemplification arising from this experience to a sequence of lessons. Through these cases, we indicate the variety of fluent uses of examples made by mathematicians and experienced teachers. Following Thompson’s concept of “didactic object” (Symbolizing, modeling, and tool use in mathematics education. Kluwer, Dordrecht, The Netherlands, pp 191–212, 2002), we talk about “didacticising” an example and observe that the nature of students’ engagement is important, as well as the teacher’s intentions and actions (Thompson avoids using a verb with the root “didact”. We use the verb “didacticise” but without implying any connection to particular theoretical approaches which use the same verb.). The qualities of examples depend as much on human agency, such as pedagogical intent or mathematical curiosity or what is noticed, as on their mathematical relation to generalities.     

The hydrological response of heavy clay grassland soils to rainfall in south‐west England using δ2H

Stable isotopes of water have been previously used in catchment studies to separate rain‐event water from pre‐event groundwater. However, there are a lack of studies at the smaller scale looking at the separation of event water from pre‐event water. This is particularly relevant for heavy clay soil systems through which the movement of water is uncertain but is thought to be rainwater‐dominated. The data presented here were collected at a rural site in the south‐west of England. The historic rainfall at the site was isotopically varied but similar to the global meteoric water line, with annual weighted means of ?37‰ for δ²H and ?5.7‰ for δ¹⁸O and with no seasonal variation. Drainage was sampled from the inter‐flow (surface runoff + lateral through‐flow) and drain‐flow (55 cm deep mole drains) pathways of two 1 ha lysimeters during two rainfall events, which had δ²H values of ?68‰ and ?92‰, respectively. The δ²H values of the lysimeter drainage water suggest that there was no contribution of event water during the first, small discharge (Q) event; however, the second larger event did show isotopic variation in δ²H values negatively related to Q indicating that rainwater was contributing to Q. A hydrograph separation indicated that only 49–58% of the inter‐flow and 18–25% of the drain‐flow consisted of event water. This was surprising given that these soil types are considered retentive of soil water. More work is needed on heavy clay soils to understand better the nature of water movement from these systems. Copyright © 2010 John Wiley & Sons, Ltd.     

Scheduling of frequently communicating tasks

Gang scheduling is an efficient resource management scheme for distributed systems which combines elements of time sharing and space sharing. It is a suitable technique particularly in the case when parallel tasks have to be running concurrently to make progress in communication. This paper studies the impact on scheduling performance when dynamically generated sequential gangs exist in the workload. In the case of sequential gangs, a subsequent gang can be dynamically generated after the execution of the initial gang based on affinity information which resides on the caches of the previously seized processors. The performance of different gang‐scheduling algorithms is examined for various cases of workload compositions which range from cases with a low demand for dynamically generated gangs to cases with a high ratio of sequential gangs to solitary gangs. A simulation model is implemented to address associated performance issues. Copyright © 2011 John Wiley & Sons, Ltd.