Unbiased Selective Isolation of Protein N-terminal Peptides from Complex Proteome Samples Using Phospho Tagging (PTAG) and TiO2-based Depletion

A positional proteomics strategy for global N-proteome analysis is presented based on phospho tagging (PTAG) of internal peptides followed by depletion by titanium dioxide (TiO(2)) affinity chromatography. Therefore, N-terminal and lysine amino groups are initially completely dimethylated with formaldehyde at the protein level, after which the proteins are digested and the newly formed internal peptides modified with the PTAG reagent glyceraldhyde-3-phosphate in nearly perfect yields (> 99%). The resulting phosphopeptides are depleted through binding onto TiO(2), keeping exclusively a set of N-acetylated and/or N-dimethylated terminal peptides for analysis by liquid chromatography-tandem MS. Analysis of peptides derivatized with differentially labeled isotopic analogs of the PTAG reagent revealed a high depletion efficiency (> 95%). The method enabled identification of 753 unique N-terminal peptides (428 proteins) in N. meningitidis and 928 unique N-terminal peptides (572 proteins) in S. cerevisiae. These included verified neo-N termini from subcellular-relocalized membrane and mitochondrial proteins. The presented PTAG approach is therefore a novel, versatile, and robust method for mass spectrometry-based N-proteome analysis and identification of protease-generated cleavage products.     

Temporal Expectation and Attention Jointly Modulate Auditory Oscillatory Activity in the Beta Band

The neural response to a stimulus is influenced by endogenous factors such as expectation and attention. Current research suggests that expectation and attention exert their effects in opposite directions, where expectation decreases neural activity in sensory areas, while attention increases it. However, expectation and attention are usually studied either in isolation or confounded with each other. A recent study suggests that expectation and attention may act jointly on sensory processing, by increasing the neural response to expected events when they are attended, but decreasing it when they are unattended. Here we test this hypothesis in an auditory temporal cueing paradigm using magnetoencephalography in humans. In our study participants attended to, or away from, tones that could arrive at expected or unexpected moments. We found a decrease in auditory beta band synchrony to expected (versus unexpected) tones if they were unattended, but no difference if they were attended. Modulations in beta power were already evident prior to the expected onset times of the tones. These findings suggest that expectation and attention jointly modulate sensory processing.     

A comparative study of byssogenesis on zebra and quagga mussels: the effects of water temperature, salinity and light-dark cycle

The quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (Dreissena polymorpha) are invasive freshwater bivalves in Europe and North America. The distribution range of both Dreissena species is still expanding and both species cause major biofouling and ecological effects, in particular when they invade new areas. In order to assess the effect of temperature, salinity and light on the initial byssogenesis of both species, 24 h re-attachment experiments in standing water were conducted. At a water temperature of 25°C and a salinity of 0.2 psu, the rate of byssogenesis of D. polymorpha was significantly higher than that of D. rostriformis bugensis. In addition, byssal thread production by the latter levelled out between 15°C and 25°C. The rate of byssogenesis at temperatures<25°C was similar for both species. Neither species produced any byssal threads at salinities of 4 psu or higher. At a salinity of 1 psu and a water temperature of 15°C, D. polymorpha produced significantly more byssal threads than D. rostriformis bugensis. There was no significant effect of the length of illumination on the byssogenesis of either species. Overall, D. polymorpha produced slightly more byssal threads than D. rostriformis bugensis at almost all experimental conditions in 24 h re-attachment experiments, but both species had essentially similar initial re-attachment abilities. The data imply that D. rostriformis bugensis causes biofouling problems identical to those of D. polymorpha.     

Changes in lipid, protein and pigment concentrations in nitrogen-stressed Chlorella minutissima cultures

Many changes occur in the biochemical composition of microalgae in response to stress conditions. In the present study, two nitrogen-stressed Chlorella minutissima strains (MACC 360 and 452) were placed in media containing a range of nitrogen concentrations (7–700?mg?L^?1 N). Biomass, chlorophyll a and b, carotenoid, protein and lipid concentrations were monitored over 15?days. There was lower biomass accumulation in nitrogen-deficient treatments while lipid yields increased to 40–46% DW in response to nitrogen deficiency. Chlorophyll concentrations initially recovered in response to the nitrogen spike with maximum concentrations recorded on days?6–8 and decreased thereafter as nitrogen became limiting. In comparison, proteins recovered faster with maximum concentrations recorded on day?4. Carotenoid concentrations did not increase in response to the nitrogen spike.     

Estimation of shadow prices of soil organic carbon depletion and freshwater depletion for use in LCA

The International Journal of Life Cycle Assessment - The interpretation of differences between alternative systems in life cycle assessment (LCA) can be problematic when different impact categories...     

Finding a most parsimonious or likely tree in a network with respect to an alignment

Journal of Mathematical Biology - Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore...     

Applying a socio-ecological green network framework to Xi’an City,China

Landscape and Ecological Engineering - Green–blue space loss and fragmentation are particularly acute in Chinese cities due to rapid urbanization, large ring-road system and the following...     

Prevalence of Alzheimer's disease and vascular dementia: association with education. The Rotterdam study.

OBJECTIVE--To estimate the prevalence of dementia and its subtypes in the general population and examine the relation of the disease to education. DESIGN--Population based cross sectional study. SETTING--Ommoord, a suburb of Rotterdam. SUBJECTS--7528 participants of the Rotterdam study aged 55-106 years. RESULTS--474 cases of dementia were detected, giving an overall prevalence of 6.3%. Prevalence ranged from 0.4% (5/1181 subjects) at age 55-59 years to 43.2% (19/44) at 95 years and over. Alzheimer''s disease was the main subdiagnosis (339 cases; 72%); it was also the main cause of the pronounced increase in dementia with age. The relative proportion of vascular dementia (76 cases; 16%), Parkinson''s disease dementia (30; 6%), and other dementias (24; 5%) decreased with age. A substantially higher prevalence of dementia was found in subjects with a low level of education. The association with education was not due to confounding by cardiovascular disease. CONCLUSIONS--The prevalence of dementia increases exponentially with age. About one third of the population aged 85 and over has dementia. Three quarters of all dementia is due to Alzheimer''s disease. In this study an inverse dose-response relation was found between education and dementia--in particular, Alzheimer''s disease.     

Coexistence of Banksia species in southwestern Australia: the role of regional and local processes

Abstract. 60 of the 75 Banksia species are confined to southwestern Australia where five or six species often coexist. We explored the role of regional species richness, niche differentiation, and habitat specialization in structuring banksia assemblages. The diversity of growth forms and categories of seed production and response to fire were assessed in actual assemblages at 40 sites throughout southwestern Australia. Diversity indices at each site were compared with those from null communities assembled on the basis of the abundance and sociability of taxa in regional species pools. The relationship between local and regional species richness suggests that processes at the scale of 100-m² quadrats limit local richness and therefore coexistence. However, there was no consistent evidence that taxa are differentiated by growth form or regeneration strategy. No particular biological profile makes a banksia adept at coexisting with a wide range of other taxa. Habitat specialization is an important factor contributing to lower local richness than would be predicted from niche differentiation of taxa in regional pools. There is recent empirical evidence of several mechanisms whereby the number of coexisting banksias is increased beyond the limits suggested by simple niche theories. Variability in the fire regime also provides a mechanism for maintaining local species richness because different fires favour recruitment of different taxa.