Assessment of sample preparation bias in mass spectrometry-based proteomics

For mass spectrometry-based proteomics, the selected sample preparation strategy is a key determinant for information that will be obtained. However, the corresponding selection is often not based on a fit-for-purpose evaluation. Here we report a comparison of in-gel (IGD), in-solution (ISD), on-filter (OFD), and on-pellet digestion (OPD) workflows on the basis of targeted (QconCAT-multiple reaction monitoring (MRM) method for mitochondrial proteins) and discovery proteomics (data dependent acquisition, DDA) analyses using three different human head and neck tissues (i.e. nasal polyps, parotid gland, and palatine tonsils). Our study reveals differences between the sample preparation methods, for example with respect to protein and peptide losses, quantification variability, protocol-induced methionine oxidation and asparagine/glutamine deamidation as well as identification of cysteine containing peptides. However, none of the methods performed best for all types of tissues, which argues against the existence of a universal sample preparation method for proteome analysis

An Upper Limit on the Albedo of HD 209458b: Direct Imaging Photometry with the MOST Satellite

We present space-based photometry of the transiting exoplanetary system HD 209458 obtained with the MOST (Microvariablity and Oscillations of STars) satellite, spanning 14 days and covering 4 transits and 4 secondary eclipses. The HD 209458 photometry was obtained in MOST's lower-precision Direct Imaging mode, which is used for targets in the brightness range $6.5 < V < 13$. We describe the photometric reduction techniques for this mode of observing, in particular the corrections for stray Earthshine. We do not detect the secondary eclipse in the MOST data, to a limit in depth of 0.053 mmag (1 \sigma). We set a 1 \sigma upper limit on the planet-star flux ratio of 4.88 x 10^-5 corresponding to a geometric albedo upper limit in the MOST bandpass (400 to 700 nm) of 0.25. The corresponding numbers at the 3 \sigma level are 1.34 x 10^-4 and 0.68 respectively. HD 209458b is half as bright as Jupiter in the MOST bandpass. This low geometric albedo value is an important constraint for theoretical models of the HD209458b atmosphere, in particular ruling out the presence of reflective clouds. A second MOST campaign on HD 209458 is expected to be sensitive to an exoplanet albedo as low as 0.13 (1 sigma), if the star does not become more intrinsically variable in the meantime.Comment: 29 pages, 9 figures. Accepted for publication in the Astrophysical Journal (July 2006, v645n1

The effect of activity and novelty on response frequency in a two-choice learning situation.

Originally published in Optics Express on 23 March 2015 (oe-23-6-7734

The Very Low Albedo of an Extrasolar Planet: MOST Spacebased Photometry of HD 209458

Measuring the albedo of an extrasolar planet provides insights into its atmospheric composition and its global thermal properties, including heat dissipation and weather patterns. Such a measurement requires very precise photometry of a transiting system sampling fully many phases of the secondary eclipse. Spacebased optical photometry of the transiting system HD 209458 from the MOST (Microvariablity and Oscillations of STars) satellite, spanning 14 and 44 days in 2004 and 2005 respectively, allows us to set a sensitive limit on the optical eclipse of the hot exosolar giant planet in this system. Our best fit to the observations yields a flux ratio of the planet and star of 7 $\pm$ 9 ppm (parts per million), which corresponds to a geometric albedo through the MOST bandpass (400-700 nm) of $A_g$ = 0.038 $\pm$ 0.045. This gives a 1$\sigma$ upper limit of 0.08 for the geometric albedo and a 3$\sigma$ upper limit of 0.17. HD 209458b is significantly less reflective than Jupiter (for which $A_g$ would be about 0.5). This low geometric albedo rules out the presence of bright reflective clouds in this exoplanet's atmosphere. We determine refined parameters for the star and exoplanet in the HD 209458 system based on a model fit to the MOST light curve.Comment: 23 pages, 8 figures, accepted to the ApJ. v2: minor changes to mirror accepted ApJ versio

Yersinia enterocolitica exploits different pathways to accomplish adhesion and toxin injection into host cells.

The current paradigm suggests that Yersinia enterocolitica (Ye) adheres to host cells via the outer membrane proteins Yersinia adhesin A (YadA) or invasin (Inv) to facilitate injection of Yops by the type III secretion system. In this process Inv binds directly to β1 integrins of host cells while YadA may bind indirectly via extracellular matrix proteins to β1 integrins. Here we challenged this paradigm and investigated the requirements for Yop injection. We demonstrate that Inv- but not YadA-mediated adhesion depends on β1 integrin binding and activation, and that tight adhesion is a prerequisite for Yop injection. By means of novel transgenic cell lines, shRNA approaches and RGD peptides, we found that YadA, in contrast to Inv, may use a broad host cell receptor repertoire for host cell adhesion. In the absence of β1 integrins, YadA mediates Yop injection by interaction with αV integrins in cooperation with yet unknown cofactors expressed by epithelial cells, but not fibroblasts. Electron microscopic and flow chamber studies revealed that a defined intimate contact area between Ye and host cells resulting in adhesion forces resisting shear stress is required for Yop injection. Thus, the indirect binding of YadA to a broad extracellular matrix (ECM) binding host cell receptor repertoire of different cell types makes YadA a versatile tool to ensure Yop injection. In conclusion, given the differential expression of the outer membrane proteins Inv and YadA in the course of Ye infection and differential expression of integrins by various host cell populations, the data demonstrate that Ye is flexibly armed to accomplish Yop injection in different host cell types, a central event in its immune evasion strategy

COL4A2 is associated with lacunar ischemic stroke and deep ICH: Meta-analyses among 21,500 cases and 40,600 controls

Objective: To determine whether common variants in familial cerebral small vessel disease (SVD) genes confer risk of sporadic cerebral SVD. Methods: We meta-analyzed genotype data from individuals of European ancestry to determine associations of common single nucleotide polymorphisms (SNPs) in 6 familial cerebral SVD genes (COL4A1, COL4A2, NOTCH3, HTRA1, TREX1, and CECR1) with intracerebral hemorrhage (ICH) (deep, lobar, all; 1,878 cases, 2,830 controls) and ischemic stroke (IS) (lacunar, cardioembolic, large vessel disease, all; 19,569 cases, 37,853 controls). We applied data quality filters and set statistical significance thresholds accounting for linkage disequilibrium and multiple testing. Results: A locus in COL4A2 was associated (significance threshold p , 3.5 3 1024) with both lacunar IS (lead SNP rs9515201: odds ratio [OR] 1.17, 95%confidence interval [CI] 1.11-1.24, p 56.62 31028) and deep ICH (lead SNP rs4771674: OR 1.28, 95%CI 1.13-1.44, p 55.76 3 1025). A SNP in HTRA1 was associated (significance threshold p , 5.5 3 1024) with lacunar IS (rs79043147: OR 1.23, 95%CI 1.10-1.37, p 5 1.90 3 1024) and less robustly with deep ICH. There was no clear evidence for association of common variants in either COL4A2 or HTRA1 with non-SVD strokes or in any of the other genes with any stroke phenotype