Mutation patterns of amino acid tandem repeats in the human proteome

Background: Amino acid tandem repeats are found in nearly one-fifth of human proteins. Abnormal expansion of these regions is associated with several human disorders. To gain further insight into the mutational mechanisms that operate in this type of sequence, we have analyzed a large number of mutation variants derived from human expressed sequence tags (ESTs).Results: We identified 137 polymorphic variants in 115 different amino acid tandem repeats. Of these, 77 contained amino acid substitutions and 60 contained gaps (expansions or contractions of the repeat unit). The analysis showed that at least about 21% of the repeats might be polymorphic in humans. We compared the mutations found in different types of amino acid repeats and in adjacent regions. Overall, repeats showed a five-fold increase in the number of gap mutations compared to adjacent regions, reflecting the action of slippage within the repetitive structures. Gap and substitution mutations were very differently distributed between different amino acid repeat types. Among repeats containing gap variants we identified several disease and candidate disease genes.Conclusion: This is the first report at a genome-wide scale of the types of mutations occurring in the amino acid repeat component of the human proteome. We show that the mutational dynamics of different amino acid repeat types are very diverse. We provide a list of loci with highly variable repeat structures, some of which may be potentially involved in disease.

Calling and career preparation: Investigating developmental patterns and temporal precedence

The presence of a calling and career development are assumed to be closely related. However, the nature of and reason for this relationship have not been thoroughly investigated. We hypothesized the existence of reciprocal effects between calling and three dimensions of career preparation and assessed the change of the presence of a calling, career planning, decidedness, and self-efficacy with three waves of a diverse sample of German university students (N = 846) over one year. Latent growth analyses revealed that the intercepts of calling showed a significant positive correlation with the intercepts of all career preparation measures. The slope of calling was positively related to those of decidedness and self-efficacy but not to planning. Cross-lagged analyses showed that calling predicted a subsequent increase in planning and self-efficacy. Planning and decidedness predicted an increase in the presence of a calling. The results suggest that calling and career preparation are related due to mutual effects but that effects differ for different career preparation dimensions.

Determination of the Enantiomers of Mianserin and its Metabolites in Plasma by Capillary Electrophoresis After Liquid-Liquid Extraction and On-Column Sample Preconcentration

Capillary electrophoresis has drawn considerable attention in the past few years, particularly in the field of chiral separations because of its high separation efficiency. However, its routine use in therapeutic drug monitoring is hampered by its low sensitivity due to a short optical path. We have developed a capillary zone electrophoresis (CZE) method using 2mM of hydroxypropyl-β-cyclodextrin as a chiral selector, which allows base-to-base separation of the enantiomers of mianserin (MIA), desmethylmianserin (DMIA), and 8-hydroxymianserin (OHMIA). Through the use of an on-column sample concentration step after liquid-liquid extraction from plasma and through the presence of an internal standard, the quantitation limits were found to be 5 ng/mL for each enantiomer of MIA and DMIA and 15 ng/mL for each enantiomer of OHMIA. To our knowledge, this is the first published CE method that allows its use for therapeutic monitoring of antidepressants due to its sensitivity down to the low nanogram range. The variability of the assays, as assessed by the coefficients of variation (CV) measured at two concentrations for each substance, ranged from 2 to 14% for the intraday (eight replicates) and from 5 to 14% for the interday (eight replicates) experiments. The deviations from the theoretical concentrations, which represent the accuracy of the method, were all within 12.5%. A linear response was obtained for all compounds within the range of concentrations used for the calibration curves (10-150 ng/mL for each enantiomer of MIA and DMIA and 20-300 ng/mL for each enantiomer of OHMIA). Good correlations were calculated between [(R) + (S)]-MIA and DMIA concentrations measured in plasma samples of 20 patients by a nonchiral gas chromatography method and CZE, and between the (R)- and (S)-concentrations of MIA and DMIA measured in plasma samples of 37 patients by a previously described chiral high-performance liquid chromatography method and CZE. Finally, no interference was noted from more than 20 other psychotropic drugs. Thus, this method, which is both sensitive and selective, can be routinely used for therapeutic monitoring of the enantiomers of MIA and its metabolites. It could be very useful due to the demonstrated interindividual variability of the stereoselective metabolism of MIA.

Predicting current and future spatial community patterns of plant functional traits

Community-level patterns of functional traits relate to community assembly and ecosystem functioning. By modelling the changes of different indices describing such patterns - trait means, extremes and diversity in communities - as a function of abiotic gradients, we could understand their drivers and build projections of the impact of global change on the functional components of biodiversity. We used five plant functional traits (vegetative height, specific leaf area, leaf dry matter content, leaf nitrogen content and seed mass) and non-woody vegetation plots to model several indices depicting community-level patterns of functional traits from a set of abiotic environmental variables (topographic, climatic and edaphic) over contrasting environmental conditions in a mountainous landscape. We performed a variation partitioning analysis to assess the relative importance of these variables for predicting patterns of functional traits in communities, and projected the best models under several climate change scenarios to examine future potential changes in vegetation functional properties. Not all indices of trait patterns within communities could be modelled with the same level of accuracy: the models for mean and extreme values of functional traits provided substantially better predictive accuracy than the models calibrated for diversity indices. Topographic and climatic factors were more important predictors of functional trait patterns within communities than edaphic predictors. Overall, model projections forecast an increase in mean vegetation height and in mean specific leaf area following climate warming. This trend was important at mid elevation particularly between 1000 and 2000 m asl. With this study we showed that topographic, climatic and edaphic variables can successfully model descriptors of community-level patterns of plant functional traits such as mean and extreme trait values. However, which factors determine the diversity of functional traits in plant communities remains unclear and requires more investigations.

Polyethylene glycol and polyvinylpirrolidone effect on bacterial rRNA extraction and hybridization from cells exposed to tannins

In order to detect fluctuations in ruminal microbial populations due to forage tannins using 16S ribosomal RNA (rRNA) probes, recovery of intact rRNA is required. The objective of this work was to evaluate the effect of polyethylene glycol (PEG) and polyvinylpirrolidone (PVP) on extraction of bacterial rRNA, in the presence of tannins from tropical legume forages and other sources, that hybridize with oligonucleotide probes. Ruminococcus albus 8 cells were exposed to 8 g/L tannic acid or 1 g/L condensed tannins extracted from Acacia angustissima, banana (Musa sp.) skin, Desmodium ovalifolium, red grape (Vitis vinifera) skin and Inga edulis, or no tannins. Cells were rinsed with Tris buffer pH 7 containing either 8% PEG or 6% PVP prior to cell lysis. Total RNA samples rinsed with either PEG or PVP migrated through denaturing agarose gels. The 16S rRNA bands successfully hybridized with a R. albus species-specific oligonucleotide probe, regardless of tannin source. The effect of rinsing buffers on the density of 16S rRNA bands, as well as on the hybridization signals was compared. There were significant effects (P<0.01) when the controls were compared to either buffer treatments due to tannin type, buffer used and the interaction of tannin type and buffer. The significant interaction indicates the influence of tannin type on the parameters evaluated.

Regional income inequality in Italy in the long run (1871–2001). Patterns and determinants

The chapter presents up-to-date estimates of Italy’s regional GDP, with the present borders, in ten-year benchmarks from 1871 to 2001, and proposes a new interpretative hypothesis based on long-lasting socio-institutional differences. The inverted U-shape of income inequality is confirmed: rising divergence until the midtwentieth century, then convergence. However, the latter was limited to the centrenorth: Italy was divided into three parts by the time regional inequality peaked, in 1951, and appears to have been split into two halves by 2001. As a consequence of the falling back of the south, from 1871 to 2001 we record σ-divergence across Italy’s regions, i.e. an increase in dispersion, and sluggish β-convergence. Geographical factors and the market size played a minor role: against them are both the evidence that most of the differences in GDP are due to employment rather than to productivity and the observed GDP patterns of many regions. The gradual converging of regional GDPs towards two equilibria instead follows social and institutional differences − in the political and economic institutions and in the levels of human and social capital – which originated in pre-unification states and did not die (but in part even increased) in postunification Italy.

Bump time-frequency toolbox: a toolbox for time-frequency oscillatory bursts extraction in electrophysiological signals

Background: oscillatory activity, which can be separated in background and oscillatory burst pattern activities, is supposed to be representative of local synchronies of neural assemblies. Oscillatory burst events should consequently play a specific functional role, distinct from background EEG activity – especially for cognitive tasks (e.g. working memory tasks), binding mechanisms and perceptual dynamics (e.g. visual binding), or in clinical contexts (e.g. effects of brain disorders). However extracting oscillatory events in single trials, with a reliable and consistent method, is not a simple task. Results: in this work we propose a user-friendly stand-alone toolbox, which models in a reasonable time a bump time-frequency model from the wavelet representations of a set of signals. The software is provided with a Matlab toolbox which can compute wavelet representations before calling automatically the stand-alone application. Conclusion: The tool is publicly available as a freeware at the address: http:// www.bsp.brain.riken.jp/bumptoolbox/toolbox_home.html

Investigation of ICA algorithms for feature extraction of EEG signals in discrimination of Alzheimer disease

In this paper we present a quantitative comparisons of different independent component analysis (ICA) algorithms in order to investigate their potential use in preprocessing (such as noise reduction and feature extraction) the electroencephalogram (EEG) data for early detection of Alzhemier disease (AD) or discrimination between AD (or mild cognitive impairment, MCI) and age-match control subjects.

Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer.

The recognition that colorectal cancer (CRC) is a heterogeneous disease in terms of clinical behaviour and response to therapy translates into an urgent need for robust molecular disease subclassifiers that can explain this heterogeneity beyond current parameters (MSI, KRAS, BRAF). Attempts to fill this gap are emerging. The Cancer Genome Atlas (TGCA) reported two main CRC groups, based on the incidence and spectrum of mutated genes, and another paper reported an EMT expression signature defined subgroup. We performed a prior free analysis of CRC heterogeneity on 1113 CRC gene expression profiles and confronted our findings to established molecular determinants and clinical, histopathological and survival data. Unsupervised clustering based on gene modules allowed us to distinguish at least five different gene expression CRC subtypes, which we call surface crypt-like, lower crypt-like, CIMP-H-like, mesenchymal and mixed. A gene set enrichment analysis combined with literature search of gene module members identified distinct biological motifs in different subtypes. The subtypes, which were not derived based on outcome, nonetheless showed differences in prognosis. Known gene copy number variations and mutations in key cancer-associated genes differed between subtypes, but the subtypes provided molecular information beyond that contained in these variables. Morphological features significantly differed between subtypes. The objective existence of the subtypes and their clinical and molecular characteristics were validated in an independent set of 720 CRC expression profiles. Our subtypes provide a novel perspective on the heterogeneity of CRC. The proposed subtypes should be further explored retrospectively on existing clinical trial datasets and, when sufficiently robust, be prospectively assessed for clinical relevance in terms of prognosis and treatment response predictive capacity. Original microarray data were uploaded to the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/) under Accession Nos E-MTAB-990 and E-MTAB-1026. © 2013 Swiss Institute of Bioinformatics. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Auditory localisation and recognition after left inferior collicular lesion: effects of work load on cortical activation patterns (fMRI study)

Evidence from neuropsychological and activation studies (Clarke et al., 2oo0, Maeder et al., 2000) suggests that sound recognitionand localisation are processed by two anatomically and functionally distinct cortical networks. We report here on a case of a patientthat had an interruption of auditory information and we show: i) the effects of this interruption on cortical auditory processing; ii)the effect of the workload on activation pattern.A 36 year old man suffered from a small left mesencephalic haemotrhage, due to cavernous angioma; the let% inferior colliculuswas resected in the surgical approach of the vascular malformation. In the acute stage, the patient complained of auditoryhallucinations and of auditory loss in right ear, while tonal audiometry was normal. At 12 months, auditory recognition, auditorylocalisation (assessed by lTD and IID cues) and auditory motion perception were normal (Clarke et al., 2000), while verbal dichoticlistening was deficient on the right side.Sound recognition and sound localisation activation patterns were investigated with fMRI, using a passive and an activeparadigm. In normal subjects, distinct cortical networks were involved in sound recognition and localisation, both in passive andactive paradigm (Maeder et al., 2OOOa, 2000b).Passive listening of environmental and spatial stimuli as compared to rest strongly activated right auditory cortex, but failed toactivate left primary auditory cortex. The specialised networks for sound recognition and localisation could not be visual&d onthe right and only minimally on the left convexity. A very different activation pattern was obtained in the active condition wherea motor response was required. Workload not only increased the activation of the right auditory cortex, but also allowed theactivation of the left primary auditory cortex. The specialised networks for sound recognition and localisation were almostcompletely present in both hemispheres.These results show that increasing the workload can i) help to recruit cortical region in the auditory deafferented hemisphere;and ii) lead to processing auditory information within specific cortical networks.References:Clarke et al. (2000). Neuropsychologia 38: 797-807.Mae.der et al. (2OOOa), Neuroimage 11: S52.Maeder et al. (2OOOb), Neuroimage 11: S33

High-throughput and sensitive quantitation of plasma catecholamines by ultraperformance liquid chromatography-tandem mass spectrometry using a solid phase microwell extraction plate.

Plasma catecholamines provide a reliable biomarker of sympathetic activity. The low circulating concentrations of catecholamines and analytical interferences require tedious sample preparation and long chromatographic runs to ensure their accurate quantification by HPLC with electrochemical detection. Published or commercially available methods relying on solid phase extraction technology lack sensitivity or require derivatization of catecholamine by hazardous reagents prior to tandem mass spectrometry (MS) analysis. Here, we manufactured a novel 96-well microplate device specifically designed to extract plasma catecholamines prior to their quantification by a new and highly sensitive ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. Processing time, which included sample purification on activated aluminum oxide and elution, is less than 1 h per 96-well microplate. The UPLC-MS/MS analysis run time is 2.0 min per sample. This UPLC-MS/MS method does not require a derivatization step, reduces the turnaround time by 10-fold compared to conventional methods used for routine application, and allows catecholamine quantification in reduced plasma sample volumes (50-250 μL, e.g., from children and mice).

The birth of the Rheic Ocean - Early Palaeozoic subsidence patterns and subsequent tectonic plate scenarios

New plate-tectonic reconstructions of the Gondwana margin suggest that the location of Gondwana-derived terranes should not only be guided by the models, but should also consider the possible detrital input from some Asian blocks (Hunia), supposed to have been located along the Cambrian Gondwana margin, and accreted in the Silurian to the North-Chinese block. Consequently, the Gondwana margin has to be subdivided into a more western domain, where the future Avalonian blocks will be separated from Gondwana by the opening Rheic Ocean, whereas in its eastern continuation, hosting the future basement areas of Central Europe, different periods of crustal extension should be distinguished. Instead of applying a rather cylindrical model, it is supposed that crustal extension follows a much more complex pattern, where local back-arcs or intra-continental rifts are involved. Guided by the age data of magmatic rocks and the pattern of subsidence curves, the following extensional events can be distinguished: During the early to middle Cambrian, a back-arc setting guided the evolution at the Gondwana margin. Contemporaneous intra-continental rift basins developed at other places related to a general post-PanAfrican extensional phase affecting Africa Upper Cambrian formation of oceanic crust is manifested in the Chamrousse area, and may have lateral cryptic relics preserved in other places. This is regarded as the oceanisation of some marginal basins in a context of back-arc rifting. These basins were closed in a mid-Ordovician tectonic phase, related to the subduction of buoyant material (mid-ocean ridge?) Since the Early Ordovician, a new phase of extension is observed, accompanied by a large-scale volcanic activity, erosion of the rift shoulders generated detritus (Armorican Quartzite) and the rift basins collected detrital zircons from a wide hinterland. This phase heralded the opening of Palaeotethys, but it failed due to the Silurian collision (Eo-Variscan phase) of an intra-oceanic arc with the Gondwana margin. During this time period, at the eastern wing of the Gondwana margin begins the drift of the future Hunia microcontinents, through the opening of an eastern prolongation of the already existing Rheic Ocean. The passive margin of the remaining Gondwana was composed of the Galatian superterranes, constituents of the future Variscan basement areas. Remaining under the influence of crustal extension, they will start their drift to Laurussia since the earliest Devonian during the opening of the Palaeotethys Ocean. (C) 2008 Elsevier B.V. All rights reserved.

Effectiveness of Electrochemical Chloride Extraction for the Iowa Avenue Pedestrian Bridge, TR-499, 2005

The main objective of this study is to determine the effectiveness of the Electrochemical Chloride Extraction (ECE) technique on a bridge deck with very high concentrations of chloride. This ECE technique was used during the summer of 2003 to reverse the effects of corrosion, which had occurred in the reinforcing steel embedded in the pedestrian bridge deck over Highway 6, along Iowa Avenue, in Iowa City, Iowa, USA. First, the half cell potential was measured to determine the existing corrosion level in the field. The half-cell potential values were in the indecisive range of corrosion (between -200 mV and -350 mV). The ECE technique was then applied to remove the chloride from the bridge deck. The chloride content in the deck was significantly reduced from 25 lb/cy to 4.96 lb/cy in 8 weeks. Concrete cores obtained from the deck were measured for their compressive strengths and there was no reduction in strength due to the ECE technique. Laboratory tests were also performed to demonstrate the effectiveness of the ECE process. In order to simulate the corrosion in the bridge deck, two reinforced slabs and 12 reinforced beams were prepared. First, the half-cell potentials were measured from the test specimens and they all ranged below -200 mV. Upon introduction of 3% salt solution, the potential reached up to -500 mV. This potential was maintained while a salt solution was being added for six months. The ECE technique was then applied to the test specimens in order to remove the chloride from them. Half-cell potential was measured to determine if the ECE technique can effectively reduce the level of corrosion.

Estimating traveltimes and groundwater flow patterns using 3D time-lapse crosshole ERT imaging of electrical resistivity fluctuations induced by infiltrating river water

The infiltration of river water into aquifers is of high relevance to drinking-water production and is a key driver of biogeochemical processes in the hyporheic and riparian zone, but the distribution and quantification of the infiltrating water are difficult to determine using conventional hydrological methods (e.g., borehole logging and tracer tests). By time-lapse inverting crosshole ERT (electrical resistivity tomography) monitoring data, we imaged groundwater flow patterns driven by river water infiltrating a perialpine gravel aquifer in northeastern Switzerland. This was possible because the electrical resistivity of the infiltrating water changed during rainfall-runoff events. Our time-lapse resistivity models indicated rather complex flow patterns as a result of spatially heterogeneous bank filtration and aquifer heterogeneity. The upper part of the aquifer was most affected by the river infiltrate, and the highest groundwater velocities and possible preferential flow occurred at shallow to intermediate depths. Time series of the reconstructed resistivity models matched groundwater electrical resistivity data recorded on borehole loggers in the upper and middle parts of the aquifer, whereas the resistivity models displayed smaller variations and delayed responses with respect to the logging data. in the lower part. This study demonstrated that crosshole ERT monitoring of natural electrical resistivity variations of river infiltrate could be used to image and quantify 3D bank filtration and aquifer dynamics at a high spatial resolution.