Evaluation of data analysis strategies for improved mass spectrometry-based phosphoproteomics

Here we describe a set of enhanced data processing and filtering methods to improve significance and coverage of phosphopeptide identifications by mass spectrometry. We demonstrate that for samples of limited complexity, spectra-based estimation of false discovery rates will lead to overprediction of confidently identified phosphorylated peptides due to a bias caused by multiple fragmentation of highly abundant peptide species. We further provide evidence that fragmentation of abundant peptides at the tails of their chromatographic peaks is a major source for false positive peptide matches and that overall confidence in phosphopeptide identifications can be improved by a chromatographic peak-based aggregation scheme, intensity rank-based neutral loss and optimized mass error filters. When replicate runs of a standard sample were performed using different fragmentation techniques on an Orbitrap mass spectrometer we observed improvements of 7-31% in phosphopeptide coverage depending on the fragmentation method and the desired false discovery rate.     

Monolithic silica-based capillary reversed-phase liquid chromatography/electrospray mass spectrometry for plant metabolomics

Application of C18 monolithic silica capillary columns in HPLC coupled to ion trap mass spectrometry detection was studied for probing the metabolome of the model plant Arabidopsis thaliana. It could be shown that the use of a long capillary column is an easy and effective approach to reduce ionization suppression by enhanced chromatographic resolution. Several hundred peaks could be detected using a 90-cm capillary column for LC separation and a noise reduction and automatic peak alignment software, which outperformed manual inspection or commercially available mass spectral deconvolution software.     

General microarray technique for immobilization and screening of natural glycans

We here present a printed covalent glycan microarray for protein-binding studies, using low-femtomole quantities of glycans. Glycans, either natural glycans, which were released from glycoproteins and glycolipids from natural sources, or synthetic glycans, were labeled with common fluorescent labels (e.g., 2-aminobenzamide or 2-aminobenzoic acid) by reductive amination and purified by HPLC. The purified glycoconjugates were covalently immobilized on commercial epoxide-activated glass slides via the secondary amine group that links the glycan moiety with the fluorescent tag. This immobilization procedure is generally applicable to reductively aminated glycans with different established fluorescent labels and allows the spatial arrangement of oligosaccharides. The microarray comprised a variety of natural glycans from various biological sources and synthetic glycans and provided informative binding fingerprints for the lectin concanavalin A as well as 14 monoclonal antibodies. Recognized glycans were characterized by tandem mass spectrometry revealing binding motifs. This natural glycan array allowed the characterization of the specificity of carbohydrate-binding proteins for oligosaccharide ligands from sparse biological sources. Moreover, it was applied for the characterization of the microarray glycans by using known carbohydrate-binding proteins.     

Tenant Empowerment Through Innovative Tenures: An Analysis of Woonbron–Maasoevers’ Client's Choice Programme

According to the recent Housing Memorandum (MVROM, 2000 MVROM 2000 Mensen-Wensen-Wonen: wonen in de 21e eeuw [What people want, where people live: housing in the 21st century] The Hague Ministry of Housing, Spatial Planning and the Environment  [Google Scholar] ), Dutch housing associations are expected to actively improve the control of tenants over their dwellings and their living environment and offer them more possibilities to choose their own type of tenure. Before the publication of the Memorandum, associations had already developed various innovative types of tenure, for example fixed rent contracts, tenant maintenance programmes and different forms of sale with discounts and risk-reducing conditions. With the introduction of these tenures, associations aim to contribute to their social objectives by improving tenants' satisfaction with their dwellings and to improve the market position of their stock as well. Our paper discusses innovative types of tenure that have been developed by the Dutch housing associations and their benefits and risks for tenant and landlord. We focus on the ‘Client's Choice’ programme that has been developed by the association WoonbronMaasoevers, which is recognised as a front-runner in offering households a wide range of choice in tenure and which is also illustrative of many of the benefits and risks of the innovative tenures.

We conclude that many of the innovative tenures, including the Client's Choice programme, can contribute to tenant empowerment and freedom of choice. However, low-income households will mostly have to keep relying on (social) rented housing and other forms of empowerment. For the landlord, the Client's Choice programme has the benefit of increasing cash flow, which can be used for (social) housing investments. However, there are also substantial financial risks, concerning the rate of sales, the development of market values and the potential costs of having to buy back all the dwellings at the end of their economic lifespan. Thus, the implementation of the Client's Choice programme on a large scale should be accompanied by measures to control or provide for these risks.     

Attention-gated reinforcement learning of internal representations for classification

Animal learning is associated with changes in the efficacy of connections between neurons. The rules that govern this plasticity can be tested in neural networks. Rules that train neural networks to map stimuli onto outputs are given by supervised learning and reinforcement learning theories. Supervised learning is efficient but biologically implausible. In contrast, reinforcement learning is biologically plausible but comparatively inefficient. It lacks a mechanism that can identify units at early processing levels that play a decisive role in the stimulus-response mapping. Here we show that this so-called credit assignment problem can be solved by a new role for attention in learning. There are two factors in our new learning scheme that determine synaptic plasticity: (1) a reinforcement signal that is homogeneous across the network and depends on the amount of reward obtained after a trial, and (2) an attentional feedback signal from the output layer that limits plasticity to those units at earlier processing levels that are crucial for the stimulus-response mapping. The new scheme is called attention-gated reinforcement learning (AGREL). We show that it is as efficient as supervised learning in classification tasks. AGREL is biologically realistic and integrates the role of feedback connections, attention effects, synaptic plasticity, and reinforcement learning signals into a coherent framework.     

Effects of Quantitative Variation in Allelochemicals in <Emphasis Type="Italic">Plantago lanceolata</Emphasis> on Development of a Generalist and a Specialist Herbivore and their Endoparasitoids

Studies in crop species show that the effect of plant allelochemicals is not necessarily restricted to herbivores, but can extend to (positive as well as negative) effects on performance at higher trophic levels, including the predators and parasitoids of herbivores. We examined how quantitative variation in allelochemicals (iridoid glycosides) in ribwort plantain, Plantago lanceolata, affects the development of a specialist and a generalist herbivore and their respective specialist and generalist endoparasitoids. Plants were grown from two selection lines that differed ca. 5-fold in the concentration of leaf iridoid glycosides. Development time of the specialist herbivore, Melitaea cinxia, and its solitary endoparasitoid, Hyposoter horticola, proceeded most rapidly when reared on the high iridoid line, whereas pupal mass in M. cinxia and adult mass in H. horticola were unaffected by plant line. Cotesia melitaearum, a gregarious endoparasitoid of M. cinxia, performed equally well on hosts feeding on the two lines of P. lanceolata. In contrast, the pupal mass of the generalist herbivore, Spodoptera exigua, and the emerging adult mass of its solitary endoparasitoid, C. marginiventris, were significantly lower when reared on the high line, whereas development time was unaffected. The results are discussed with regards to (1) differences between specialist and generalist herbivores and their natural enemies to quantitative variation in plant secondary chemistry, and (2) potentially differing selection pressures on plant defense.     

Constrained tGAP for generalization between scales: The case of Dutch topographic data

This article presents the results of integrating large- and medium-scale data into a unified data structure. This structure can be used as a single non-redundant representation for the input data, which can be queried at any arbitrary scale between the source scales. The solution is based on the constrained topological Generalized Area Partition (tGAP), which stores the results of a generalization process applied to the large-scale dataset, and is controlled by the objects of the medium-scale dataset, which act as constraints on the large-scale objects. The result contains the accurate geometry of the large-scale objects enriched with the generalization knowledge of the medium-scale data, stored as references in the constraint tGAP structure. The advantage of this constrained approach over the original tGAP is the higher quality of the aggregated maps. The idea was implemented with real topographic datasets from The Netherlands for the large- (1:1000) and medium-scale (1:10,000) data. The approach is expected to be equally valid for any categorical map and for other scales as well.     

A multi-angular mass spectrometric view at cyclic nucleotide dependent protein kinases: in vivo characterization and structure/function relationships

Mass spectrometry has evolved in recent years to a well-accepted and increasingly important complementary technique in molecular and structural biology. Here we review the many contributions mass spectrometry based studies have made in recent years in our understanding of the important cyclic nucleotide activated protein kinase A (PKA) and protein kinase G (PKG). We both describe the characterization of kinase isozymes, substrate phosphorylation, binding partners and post-translational modifications by proteomics based methodologies as well as their structural and functional properties as revealed by native mass spectrometry, H/D exchange MS and ion mobility. Combining all these mass spectrometry based data with other biophysical and biochemical data has been of great help to unravel the intricate regulation of kinase function in the cell in all its magnificent complexity.     

Water conservation through trade: the case of Kenya

This study quantifies and maps the water footprint of Kenya from both production and consumption perspectives and estimates the country’s virtual water export and import. Kenya’s virtual water export related to trade in agricultural products was 4.1 km³/y; its virtual water import was 4.0 km³/y. The average export earning per unit of water consumed or polluted in producing agricultural export products was USD 0.25/m³, while the average expenditure on imported commodities per unit of virtual water imported was USD 0.10/m³. In addition to increasing water productivity in crop production, Kenya can mitigate its water scarcity by increasing imports of water-intensive products such as cereals and exports of high-value products such as cut flowers, vegetables, spices and tea.