Dissection of GTPase activating proteins reveals functional asymmetry in the COPI coat of budding yeast.

The Arf GTPase controls formation of the COPI vesicle coat. Recent structural models of COPI revealed the positioning of two Arf1 molecules in contrasting molecular environments. Each of these pockets for Arf1 is expected to also accommodate an Arf GTPase-activating protein (ArfGAP). Structural evidence and protein interactions observed between isolated domains indirectly suggests that each niche may preferentially recruit one of the two ArfGAPs known to affect COPI, Gcs1/ArfGAP1 and Glo3/ArfGAP2/3, although only partial structures are available. The functional role of the unique non-catalytic domain of either ArfGAP has not been integrated into the current COPI structural model. Here, we delineate key differences in the consequences of triggering GTP hydrolysis via the activity of one versus the other ArfGAP. We demonstrate that Glo3/ArfGAP2/3 specifically triggers Arf1 GTP hydrolysis impinging on the stability of the COPI coat. We show that the yeast homologue of AMP kinase, Snf1, phosphorylates the region of Glo3 that is critical for this effect and thereby regulates its function in the COPI-vesicle cycle. Our results revise the model of ArfGAP function in the molecular context of COPI

Fundamental parameters of 16 late-type stars derived from their angular diameter measured with VLTI/AMBER

Thanks to their large angular dimension and brightness, red giants and supergiants are privileged targets for optical long-baseline interferometers. Sixteen red giants and supergiants have been observed with the VLTI/AMBER facility over a two-years period, at medium spectral resolution (R=1500) in the K band. The limb-darkened angular diameters are derived from fits of stellar atmospheric models on the visibility and the triple product data. The angular diameters do not show any significant temporal variation, except for one target: TX Psc, which shows a variation of 4% using visibility data. For the eight targets previously measured by Long-Baseline Interferometry (LBI) in the same spectral range, the difference between our diameters and the literature values is less than 5%, except for TX Psc, which shows a difference of 11%. For the 8 other targets, the present angular diameters are the first measured from LBI. Angular diameters are then used to determine several fundamental stellar parameters, and to locate these targets in the Hertzsprung-Russell Diagram (HRD). Except for the enigmatic Tc-poor low-mass carbon star W Ori, the location of Tc-rich stars in the HRD matches remarkably well the thermally-pulsating AGB, as it is predicted by the stellar-evolution models. For pulsating stars with periods available, we compute the pulsation constant and locate the stars along the various sequences in the Period -- Luminosity diagram. We confirm the increase in mass along the pulsation sequences, as predicted by the theory, except for W Ori which, despite being less massive, appears to have a longer period than T Cet along the first-overtone sequence.Comment: 15 pages, 9 figures, 6 table

In vitro invasion of small-cell lung cancer cell lines correlates with expression of epidermal growth factor receptor.

Formation of metastasis is a multistep process involving attachment to the basement membrane, local proteolysis and migration into surrounding tissues, lymph or bloodstream. In the present study, we have analysed the correlation between in vitro invasion and presence of the epidermal growth factor receptor (EGFR) in a panel of 21 small-cell lung cancer (SCLC) cell lines. We have previously reported that ten of these cell lines expressed EGFR protein detected by radioreceptor and affinity labelling assays. In 11 small-cell lung cancer (SCLC) cell lines, EGFR mRNA was detected by Northern blot analysis. In vitro invasion in a Boyden chamber assay was found in all EGFR-positive cell lines, whereas no invasion was detected in the EGFR-negative cell lines. Quantification of the in vitro invasion in 12 selected SCLC cell lines demonstrated that, in the EGFR-positive cell lines, between 5% and 16% of the cells added to the upper chamber were able to traverse the Matrigel membrane. Expression of several matrix metalloproteases (MMP), of tissue inhibitor of MMP (TIMP) and of cathepsin B was evaluated by immunoprecipitation, Western blot analysis and reverse transcriptase polymerase chain reaction (RT-PCR). However, in vitro invasive SCLC cell lines could not be distinguished from non-invasive cell lines based on the expression pattern of these molecules. In six SCLC cell lines, in vitro invasion was also determined in the presence of the EGFR-neutralizing monoclonal antibody mAb528. The addition of this antibody resulted in a significant reduction of the in vitro invasion in three selected EGFR-positive cell lines. Our results show that only EGFR-positive SCLC cell lines had the in vitro invasive phenotype, and it is therefore suggested that the EGFR might play an important role for the invasion potential of SCLC cell lines

NDC1: a crucial membrane-integral nucleoporin of metazoan nuclear pore complexes

POM121 and gp210 were, until this point, the only known membrane-integral nucleoporins (Nups) of vertebrates and, thus, the only candidate anchors for nuclear pore complexes (NPCs) within the nuclear membrane. In an accompanying study (see Stavru et al. on p. 477 of this issue), we provided evidence that NPCs can exist independently of POM121 and gp210, and we predicted that vertebrate NPCs contain additional membrane-integral constituents. We identify such an additional membrane protein in the NPCs of mammals, frogs, insects, and nematodes as the orthologue to yeast Ndc1p/Cut11p. Human NDC1 (hNDC1) likely possesses six transmembrane segments, and it is located at the nuclear pore wall. Depletion of hNDC1 from human HeLa cells interferes with the assembly of phenylalanine-glycine repeat Nups into NPCs. The loss of NDC1 function in Caenorhabditis elegans also causes severe NPC defects and very high larval and embryonic mortality. However, it is not ultimately lethal. Instead, homozygous NDC1-deficient worms can be propagated. This indicates that none of the membrane-integral Nups is universally essential for NPC assembly, and suggests that NPC biogenesis is an extremely fault-tolerant process

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We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a small number of individual patient samples. From this Phase-1 data a panel of marker genes is derived. In Phase-2, the expression values of these marker panel genes are measured for a large group of patients and a predictive classification model is learned from this data. Phase-2 does not require the use of expensive whole genome microarrays, thus making EMPD a cost efficient alternative for current trials. The expected performance loss of EMPD is compared to designs which use genome-wide microarrays for all patients. We also examine the trade-off between the number of patients included in Phase-1 and the number of marker genes required in Phase-2. By analysis of five published datasets we find that in Phase-1 already 16 patients per group are sufficient to determine a suitable marker panel of 10 genes, and that this early decision compromises the final performance only marginally

Imaging simulations of selected science with the Magdalena Ridge Observatory Interferometer

We present simulated observations of surface features on Red Supergiant (RSG) stars and clumpy dust structures surrounding Active Galactic Nuclei (AGN) with the Magdalena Ridge Observatory Interferometer (MROI). These represent two of the classes of astrophysical targets enumerated in the MROI Key Science Mission that are typical of the types of complex astrophysical phenomena that the MROI has been designed to image. The simulations are based on source structures derived from recent theoretical models and include both random and systematic noise on the measured Fourier data (visibility amplitudes and closure phases) consistent with our expectations for typical such targets observed with the MROI. Image reconstructions, obtained using the BSMEM imaging package, are presented for 4-, 6- and 8- telescope implementations of the array. Although a rudimentary imaging capability is demonstrated with only 4 telescopes, the detailed features of targets are only reliably determined when at least 6 telescopes are present. By the tine 8 telescope are used, the reconstructed images are sufficiently faithful to allow the discrimination between competing models, confirming the design goal of the MROI, i.e. to offer model-independent near-infrared imaging on sub-milliarcsecond scales

A silicate disk in the heart of the Ant

We aim at getting high spatial resolution information on the dusty core of bipolar planetary nebulae to directly constrain the shaping process. Methods: We present observations of the dusty core of the extreme bipolar planetary nebula Menzel 3 (Mz 3, Hen 2-154, the Ant) taken with the mid-infrared interferometer MIDI/VLTI and the adaptive optics NACO/VLT. The core of Mz 3 is clearly resolved with MIDI in the interferometric mode, whereas it is unresolved from the Ks to the N bands with single dish 8.2 m observations on a scale ranging from 60 to 250 mas. A striking dependence of the dust core size with the PA angle of the baselines is observed, that is highly suggestive of an edge-on disk whose major axis is perpendicular to the axis of the bipolar lobes. The MIDI spectrum and the visibilities of Mz 3 exhibit a clear signature of amorphous silicate, in contrast to the signatures of crystalline silicates detected in binary post-AGB systems, suggesting that the disk might be relatively young. We used radiative-transfer Monte Carlo simulations of a passive disk to constrain its geometrical and physical parameters. Its inclination (74 degrees $\pm$ 3 degrees) and position angle (5 degrees $\pm$ 5 degrees) are in accordance with the values derived from the study of the lobes. The inner radius is 9$\pm$ 1 AU and the disk is relatively flat. The dust mass stored in the disk, estimated as 1 x 10-5Msun, represents only a small fraction of the dust mass found in the lobes and might be a kind of relic of an essentially polar ejection process

Building Bridges with Boats: Preserving Community History through Intra- and Inter-Institutional Collaboration

This chapter discusses Launching through the Surf: The Dory Fleet of Pacific City, a project which documents the historical and contemporary role of dory fishers in the life of the coastal village of Pacific City, Oregon, U.S. Linfield College’s Department of Theatre and Communication Arts, its Jereld R. Nicholson Library, the Pacific City Arts Association, the Pacific City Dorymen\u27s Association, and the Linfield Center for the Northwest joined forces to engage in a collaborative college and community venture to preserve this important facet of Oregon’s history. Using ethnography as a theoretical grounding and oral history as a method, the project utilized artifacts from the dory fleet to augment interview data, and faculty/student teams created a searchable digital archive available via open access. The chapter draws on the authors’ experiences to identify a philosophy of strategic collaboration. Topics include project development and management, assessment, and the role of serendipity. In an era of value-added services where libraries need to continue to prove their worth, partnering with internal and external entities to create content is one way for academic libraries to remain relevant to agencies that do not have direct connections to higher education. This project not only developed a positive “town and gown” relationship with a regional community, it also benefited partner organizations as they sought to fulfill their missions. The project also serves as a potential model for intra- and inter-agency collaboration for all types of libraries