Structural basis for the binding of tryptophan-based motifs by δ-COP.

Coatomer consists of two subcomplexes: the membrane-targeting, ADP ribosylation factor 1 (Arf1):GTP-binding βγδζ-COP F-subcomplex, which is related to the adaptor protein (AP) clathrin adaptors, and the cargo-binding αβ'ε-COP B-subcomplex. We present the structure of the C-terminal μ-homology domain of the yeast δ-COP subunit in complex with the WxW motif from its binding partner, the endoplasmic reticulum-localized Dsl1 tether. The motif binds at a site distinct from that used by the homologous AP μ subunits to bind YxxΦ cargo motifs with its two tryptophan residues sitting in compatible pockets. We also show that the Saccharomyces cerevisiae Arf GTPase-activating protein (GAP) homolog Gcs1p uses a related WxxF motif at its extreme C terminus to bind to δ-COP at the same site in the same way. Mutations designed on the basis of the structure in conjunction with isothermal titration calorimetry confirm the mode of binding and show that mammalian δ-COP binds related tryptophan-based motifs such as that from ArfGAP1 in a similar manner. We conclude that δ-COP subunits bind Wxn(1-6)[WF] motifs within unstructured regions of proteins that influence the lifecycle of COPI-coated vesicles; this conclusion is supported by the observation that, in the context of a sensitizing domain deletion in Dsl1p, mutating the tryptophan-based motif-binding site in yeast causes defects in both growth and carboxypeptidase Y trafficking/processing.We should like to thank the beamline scientists at the Diamond Light Source and Mike Lewis (MRC LMB), Gerry Johnston (Dalhousie University), and Mark Rose (Princeton University) for helpful discussions and technical advice. RJS and DJO are funded by a Wellcome Trust fellowship to DJO (090909). PPP was funded by Canadian Institute of Health Research. RD acknowledges support from the DFG Excellence Cluster “Inflammation and Interfaces” (ECX306) and the University of Lübeck. SMT and FMH acknowledge support from NIH (GM071574). PRE is funded by MRC grant U105178845This is the author accepted manuscript. The final version is available from PNAS via http://dx.doi.org/10.1073/pnas.150618611

A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements, and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.Comment: Documents version 3 of the forma

A Spitzer c2d Legacy Survey to Identify and Characterize Disks with Inner Dust Holes

Understanding how disks dissipate is essential to studies of planet formation. However, identifying exactly how dust and gas dissipates is complicated due to difficulty in finding objects clearly in the transition of losing their surrounding material. We use Spitzer IRS spectra to examine 35 photometrically-selected candidate cold disks (disks with large inner dust holes). The infrared spectra are supplemented with optical spectra to determine stellar and accretion properties and 1.3mm photometry to measure disk masses. Based on detailed SED modeling, we identify 15 new cold disks. The remaining 20 objects have IRS spectra that are consistent with disks without holes, disks that are observed close to edge-on, or stars with background emission. Based on these results, we determine reliable criteria for identifying disks with inner holes from Spitzer photometry and examine criteria already in the literature. Applying these criteria to the c2d surveyed star-forming regions gives a frequency of such objects of at least 4% and most likely of order 12% of the YSO population identified by Spitzer. We also examine the properties of these new cold disks in combination with cold disks from the literature. Hole sizes in this sample are generally smaller than for previously discovered disks and reflect a distribution in better agreement with exoplanet orbit radii. We find correlations between hole size and both disk and stellar masses. Silicate features, including crystalline features, are present in the overwhelming majority of the sample although 10 micron feature strength above the continuum declines for holes with radii larger than ~7 AU. In contrast, PAHs are only detected in 2 out of 15 sources. Only a quarter of the cold disk sample shows no signs of accretion, making it unlikely that photoevaporation is the dominant hole forming process in most cases.Comment: 24 pages, 18 figures and 8 tables. Fixed a typo in Table

Measurements and Analysis of Secondary User Device Effects on Digital Television Receivers

This is the published version. Copyright © 2009 Newman et al.This article presents results from a study of the potential effects of secondary users operating in unoccupied television spectrum. Television spectrum is known within the wireless communications community as being underutilized, making it a prime candidate for dynamic spectrum access. The proposed use of this open spectrum has prompted questions concerning the quantity of available channel space that could be used without negative impact on consumers who view digital television broadcasts and the viability of secondary use of open channels immediately adjacent to a digital television broadcast channel. In this work, we investigate secondary device operation in the channels directly adjacent to a desired television channel, and the effects upon a selection of consumer digital television (DTV) receivers. Our observations strongly suggest that secondary users could operate "White Space Devices" (WSDs) in unoccupied channel bandwidth directly adjacent to a desired digital television (DTV) channel, with no observable adverse impact upon the reception of the desired channel content

Association of High-Sensitivity Troponin with Cardiac CT Angiography Evidence of Myocardial and Coronary Disease in a Primary Prevention Cohort of Men: Results from MACS.

BackgroundHigh-sensitivity cardiac troponin (hs-cTn) elevations are associated with incident cardiovascular disease events in primary prevention samples. However, the mechanisms underlying this association remain unclear.MethodsWe studied 458 men without known cardiovascular disease who participated in the cardiovascular disease substudy of the Multicenter AIDS Cohort Study and had cardiac CT angiography. We used multivariable linear and logistic regression models to examine the cross-sectional associations between coronary artery stenosis, coronary artery plaque, indexed left ventricular mass (LVMi), and the outcome of hs-cTnI. We also evaluated the associations between HIV serostatus or use of highly active antiretroviral therapy (HAART) and hs-cTnI.ResultsThe mean age was 54 years, 54% were white, and 61% were HIV infected. In multivariable-adjusted logistic models, comparing the highest quartile of LVMi with the lowest quartile, the odds ratio (OR) of hs-cTnI ≥75th percentile was 2.59 (95% CI, 1.20-5.75). There was no significant association between coronary stenosis severity or plaque type and hs-cTnI in linear models; however, in logistic regression models, coronary artery stenosis ≥70% (8% of sample) was marginally associated with a higher likelihood (OR, 2.75 [95% CI, 1.03, 7.27]) of having hs-cTnI ≥75th percentile. There were no associations between HIV serostatus or HAART use and hs-cTnI in either linear or logistic models.ConclusionAmong primary prevention men with or at risk for HIV, hs-cTnI concentrations were strongly associated with LVMi but were not associated with HIV infection or treatment status or with coronary plaque type or stenosis until the extremes of severity (≥70% stenosis)

APP metabolism regulates tau proteostasis in human cerebral cortex neurons.

Accumulation of Aβ peptide fragments of the APP protein and neurofibrillary tangles of the microtubule-associated protein tau are the cellular hallmarks of Alzheimer's disease (AD). To investigate the relationship between APP metabolism and tau protein levels and phosphorylation, we studied human-stem-cell-derived forebrain neurons with genetic forms of AD, all of which increase the release of pathogenic Aβ peptides. We identified marked increases in intracellular tau in genetic forms of AD that either mutated APP or increased its dosage, suggesting that APP metabolism is coupled to changes in tau proteostasis. Manipulating APP metabolism by β-secretase and γ-secretase inhibition, as well as γ-secretase modulation, results in specific increases and decreases in tau protein levels. These data demonstrate that APP metabolism regulates tau proteostasis and suggest that the relationship between APP processing and tau is not mediated solely through extracellular Aβ signaling to neurons.This research was supported by grants from Alzheimer’s Research UK and the Wellcome Trust (to F.J.L.) and core funding to the Gurdon Trust from the Wellcome Trust and Cancer Research UK. N.S. was supported by a Woolf-Fisher Trust (NZ) PhD studentship. H.Z. was supported by the Wolfson Centre at UCL, and the UCLH Dementia BRU provided financial support for the collection of patient materials. F.J.L. is a Wellcome Trust Senior Investigator, K.B. is a Torsten So¨ derberg Academy Professor, and H.Z. is a Wallenberg Academy Fellow.This is the final version. It was first published by Elsevier at http://www.sciencedirect.com/science/article/pii/S2211124715003599

High Throughput In Situ XAFS Screening of Catalysts

We outline and demonstrate the feasibility of high-throughput (HT) in situ XAFS for synchrotron radiation studies. An XAS data acquisition and control system for the analysis of dynamic materials libraries under control of temperature and gaseous environments has been developed. The system is compatible with the 96-well industry standard and coupled to multi-stream quadrupole mass spectrometry (QMS) analysis of reactor effluents. An automated analytical workflow generates data quickly compared to traditional individual spectrum acquisition and analyses them in quasi-real time using an HT data analysis tool based on IFFEFIT. The system was used for the automated characterization of a library of 91 catalyst precursors containing ternary combinations of Cu, Pt, and Au on ?-Al2O3, and for the in situ characterization of Au catalysts supported on Al2O3 and TiO2