Identification of a functional genetic variant driving racially dimorphic platelet gene expression of the thrombin receptor regulator, PCTP.

Platelet activation in response to stimulation of the Protease Activated Receptor 4 (PAR4) receptor differs by race. One factor that contributes to this difference is the expression level of Phosphatidylcholine Transfer Protein (PCTP), a regulator of platelet PAR4 function. We have conducted an expression Quantitative Trait Locus (eQTL) analysis that identifies single nucleotide polymorphisms (SNPs) linked to the expression level of platelet genes. This analysis revealed 26 SNPs associated with the expression level of PCTP at genome-wide significance (p \u3c 5×10(-8)). Using annotation from ENCODE and other public data we prioritised one of these SNPs, rs2912553, for functional testing. The allelic frequency of rs2912553 is racially-dimorphic, in concordance with the racially differential expression of PCTP. Reporter gene assays confirmed that the single nucleotide change caused by rs2912553 altered the transcriptional potency of the surrounding genomic locus. Electromobility shift assays, luciferase assays, and overexpression studies indicated a role for the megakaryocytic transcription factor GATA1. In summary, we have integrated multi-omic data to identify and functionalise an eQTL. This, along with the previously described relationship between PCTP and PAR4 function, allows us to characterise a genotype-phenotype relationship through the mechanism of gene expression

DEqMS : A Method for Accurate Variance Estimation in Differential Protein Expression Analysis

Quantitative proteomics by mass spectrometry is widely used in biomarker research and basic biology research for investigation of phenotype level cellular events. Despite the wide application, the methodology for statistical analysis of differentially expressed proteins has not been unified. Various methods such as t test, linear model and mixed effect models are used to define changes in proteomics experiments. However, none of these methods consider the specific structure of MS-data. Choices between methods, often originally developed for other types of data, are based on compromises between features such as statistical power, general applicability and user friendliness. Furthermore, whether to include proteins identified with one peptide in statistical analysis of differential protein expression varies between studies. Here we present DEqMS, a robust statistical method developed specifically for differential protein expression analysis in mass spectrometry data. In all data sets investigated there is a clear dependence of variance on the number of PSMs or peptides used for protein quantification. DEqMS takes this feature into account when assessing differential protein expression. This allows for a more accurate data-dependent estimation of protein variance and inclusion of single peptide identifications without increasing false discoveries. The method was tested in several data sets including E. coli proteome spike-in data, using both label-free and TMT-labeled quantification. Compared with previous statistical methods used in quantitative proteomics, DEqMS showed consistently better accuracy in detecting altered protein levels compared with other statistical methods in both label-free and labeled quantitative proteomics data. DEqMS is available as an R package in Bioconductor.Peer reviewe

Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors

Comparison of gene expression in normal and glaucomatous eyes from Caucasian American and African American donors reveals differences that might reflect different susceptibility to glaucoma

Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps

<p>Abstract</p> <p>Background</p> <p>Peptide Recognition Domains (PRDs) are commonly found in signaling proteins. They mediate protein-protein interactions by recognizing and binding short motifs in their ligands. Although a great deal is known about PRDs and their interactions, prediction of PRD specificities remains largely an unsolved problem.</p> <p>Results</p> <p>We present a novel approach to identifying these Specificity Determining Residues (SDRs). Our algorithm generalizes earlier information theoretic approaches to coevolution analysis, to become applicable to this problem. It leverages the growing wealth of binding data between PRDs and large numbers of random peptides, and searches for PRD residues that exhibit strong evolutionary covariation with some positions of the statistical profiles of bound peptides. The calculations involve only information from sequences, and thus can be applied to PRDs without crystal structures. We applied the approach to PDZ, SH3 and kinase domains, and evaluated the results using both residue proximity in co-crystal structures and verified binding specificity maps from mutagenesis studies.</p> <p>Discussion</p> <p>Our predictions were found to be strongly correlated with the physical proximity of residues, demonstrating the ability of our approach to detect physical interactions of the binding partners. Some high-scoring pairs were further confirmed to affect binding specificity using previous experimental results. Combining the covariation results also allowed us to predict binding profiles with higher reliability than two other methods that do not explicitly take residue covariation into account.</p> <p>Conclusions</p> <p>The general applicability of our approach to the three different domain families demonstrated in this paper suggests its potential in predicting binding targets and assisting the exploration of binding mechanisms.</p

Post-mortem correlates of Virchow-Robin spaces detected on in vivo MRI

The purpose of our study is to quantify the extent to which Virchow-Robin spaces (VRS) detected on in vivo MRI are reproducible by post-mortem MRI.Double Echo Steady State 3T MRIs were acquired post-mortem in 49 double- and 32 single-hemispheric formalin-fixed brain sections from 12 patients, who underwent conventional diagnostic 1.5 or 3T MRI in median 22 days prior to death (25% to 75%: 12 to 134 days). The overlap of in vivo and post-mortem VRS segmentations was determined accounting for potential confounding factors.The reproducibility of VRS found on in vivo MRI by post-mortem MRI, in the supratentorial white matter was in median 80% (25% to 75%: 60 to 100). A lower reproducibility was present in the basal ganglia, with a median of 47% (25% to 75%: 30 to 50).VRS segmentations were histologically confirmed in one double hemispheric section.Overall, the majority of VRS found on in vivo MRI was stable throughout death and formalin fixation, emphasizing the translational potential of post-mortem VRS studies

Silicon quantum dot devices with a self-aligned second gate layer

We implement silicon quantum dot devices with two layers of gate electrodes using a self-alignment technique, which allows for ultra-small gate lengths and intrinsically perfect layer-to-layer alignment. In a double quantum dot system, we investigate hole transport and observe current rectification due to Pauli spin blockade. Magnetic field measurements indicate that hole spin relaxation is dominated by spin-orbit interaction, and enable us to determine the effective hole $g$-factor $\simeq1.6$. From an avoided singlet-triplet crossing, occurring at high magnetic field, the spin-orbit coupling strength $\simeq0.27$meV is obtained, promising fast and all-electrical spin control

Online 13C and 14C gas measurements by EA-IRMS–AMS at ETH Zürich

Studies using carbon isotopes to understand the global carbon cycle are critical to identify and quantify sources, sinks, and processes and how humans may impact them. 13C and 14C are routinely measured individually; however, there is a need to develop instrumentation that can perform concurrent online analyses that can generate rich data sets conveniently and efficiently. To satisfy these requirements, we coupled an elemental analyzer to a stable isotope mass spectrometer and an accelerator mass spectrometer system fitted with a gas ion source. We first tested the system with standard materials and then reanalyzed a sediment core from the Bay of Bengal that had been analyzed for 14C by conventional methods. The system was able to produce %C, 13C, and 14C data that were accurate and precise, and suitable for the purposes of our biogeochemistry group. The system was compact and convenient and is appropriate for use in a range of fields of research

Exploiting the fungal highway: development of a novel tool for the in situ isolation of bacteria migrating along fungal mycelium

Fungi and bacteria form various associations that are central to numerous environmental processes. In the so-called fungal highway, bacteria disperse along fungal mycelium. We developed a novel tool for the in situ isolation of bacteria moving along fungal hyphae as well as for the recovery of fungi potentially involved in dispersal, both of which are attracted towards a target culture medium. We present the validation and the results of the first in situ test. Couples of fungi and bacteria were isolated from soil. Amongst the enriched organisms, we identified several species of fast-growing fungi (Fusarium sp. and Chaetomium sp.), as well as various potentially associated bacterial groups, including Variovorax soli, Olivibacter soli, Acinetobacter calcoaceticus, and several species of the genera Stenotrophomonas, Achromobacter and Ochrobactrum. Migration of bacteria along fungal hyphae across a discontinuous medium was confirmed in most of the cases. Although the majority of the bacteria for which migration was confirmed were also positive for flagellar motility, not all motile bacteria dispersed using their potential fungal partner. In addition, the importance of hydrophobicity of the fungal mycelial surface was confirmed. Future applications of the columns include targeting different types of microorganisms and their interactions, either by enrichment or by state of the art molecular biological method