81 research outputs found
Systematic genetic array analysis links the Saccharomyces cerevisiae SAGA/SLIK and NuA4 component Tra1 to multiple cellular processes
<p>Abstract</p> <p>Background</p> <p>Tra1 is an essential 437-kDa component of the <it>Saccharomyces cerevisiae </it>SAGA/SLIK and NuA4 histone acetyltransferase complexes. It is a member of a group of key signaling molecules that share a carboxyl-terminal domain related to phosphatidylinositol-3-kinase but unlike many family members, it lacks kinase activity. To identify genetic interactions for <it>TRA1 </it>and provide insight into its function we have performed a systematic genetic array analysis (SGA) on <it>tra1</it><sub><it>SRR</it>3413</sub>, an allele that is defective in transcriptional regulation.</p> <p>Results</p> <p>The SGA analysis revealed 114 synthetic slow growth/lethal (SSL) interactions for <it>tra1</it><sub><it>SRR</it>3413</sub>. The interacting genes are involved in a range of cellular processes including gene expression, mitochondrial function, and membrane sorting/protein trafficking. In addition many of the genes have roles in the cellular response to stress. A hierarchal cluster analysis revealed that the pattern of SSL interactions for <it>tra1</it><sub><it>SRR</it>3413 </sub>most closely resembles deletions of a group of regulatory GTPases required for membrane sorting/protein trafficking. Consistent with a role for Tra1 in cellular stress, the <it>tra1</it><sub><it>SRR</it>3413 </sub>strain was sensitive to rapamycin. In addition, calcofluor white sensitivity of the strain was enhanced by the protein kinase inhibitor staurosporine, a phenotype shared with the Ada components of the SAGA/SLIK complex. Through analysis of a GFP-Tra1 fusion we show that Tra1 is principally localized to the nucleus.</p> <p>Conclusion</p> <p>We have demonstrated a genetic association of Tra1 with nuclear, mitochondrial and membrane processes. The identity of the SSL genes also connects Tra1 with cellular stress, a result confirmed by the sensitivity of the <it>tra1</it><sub><it>SRR</it>3413 </sub>strain to a variety of stress conditions. Based upon the nuclear localization of GFP-Tra1 and the finding that deletion of the Ada components of the SAGA complex result in similar phenotypes as <it>tra1</it><sub><it>SRR</it>3413</sub>, we suggest that the effects of <it>tra1</it><sub><it>SRR</it>3413 </sub>are mediated, at least in part, through its role in the SAGA complex.</p
The Angular Correlation Function of K=19.5 Galaxies and the Detection of a Cluster at z=0.775
On five K-band Omega camera images, covering a total of 162.2 sq. arcmin to
K=19.5, we investigate (i) the clustering environment of 5 radio galaxies at
0.7<z<0.8 and (ii) the galaxy angular correlation function. We detect a cluster
of estimated Abell richness class 1 or 2, centred on the radio galaxy 5C6.75 at
z=0.775. Of the other radio galaxies, two appear to be in less rich groups or
structures, and two in field environments. The mean clustering environment of
all 5 is similar to that of radio galaxies at more moderate redshifts of
0.35<z<0.55. The angular correlation function of the galaxies, at limits
K=18.5--20.0, is most consistent with a luminosity evolution model in which
E/S0 galaxies are much more clustered than spirals (r_0=8.4 compared to 4.2 1/h
Mpc) and clustering is approximately stable (epsilon=0), although the
clustering may exceed the stable model at the highest (z>1.5) redshifts. We
also find a significant excess of 1.5--5.0 arcsec separation pairs of galaxies
compared to the expectation from the inward extrapolation of omega(theta). To
K=19.5, we estimate that 11.0\pm 3.4 per cent of galaxies are in close pairs in
excess of omega(theta). This can be explained if the local rate of galaxy
mergers and interactions increases with redshift as with
.Comment: 14 pages, latex, 8 figures, submitted to MNRA
The driver landscape of sporadic chordoma.
Chordoma is a malignant, often incurable bone tumour showing notochordal differentiation. Here, we defined the somatic driver landscape of 104 cases of sporadic chordoma. We reveal somatic duplications of the notochordal transcription factor brachyury (T) in up to 27% of cases. These variants recapitulate the rearrangement architecture of the pathogenic germline duplications of T that underlie familial chordoma. In addition, we find potentially clinically actionable PI3K signalling mutations in 16% of cases. Intriguingly, one of the most frequently altered genes, mutated exclusively by inactivating mutation, was LYST (10%), which may represent a novel cancer gene in chordoma.Chordoma is a rare often incurable malignant bone tumour. Here, the authors investigate driver mutations of sporadic chordoma in 104 cases, revealing duplications in notochordal transcription factor brachyury (T), PI3K signalling mutations, and mutations in LYST, a potential novel cancer gene in chordoma
Clustering of galaxies around radio quasars at 0.5 < z < 0.8
We have observed the galaxy environments around a sample of 21 radio-loud,
steep-spectrum quasars at 0.5<z<0.82, spanning several orders of magnitude in
radio luminosity. The observations also include background control fields used
to obtain the excess number of galaxies in each quasar field. The galaxy excess
was quantified using the spatial galaxy-quasar correlation amplitude, B_gq, and
an Abell-type measurement, N_0.5 (Hill & Lilly 1991). A few quasars are found
in relatively rich clusters, but on average, they seem to prefer galaxy groups
or clusters of approximately Abell class 0. We have combined our sample with
literature samples extending down to z=0.2 and covering the same range in radio
luminosity. By using Spearman statistic to disentangle redshift and luminosity
dependences, we detect a weak, but significant, positive correlation between
the richness of the quasar environment and the quasar's radio luminosity.
However, we do not find any epoch dependence in B_gq, as has previously been
reported for radio quasars and galaxies. We discuss the radio
luminosity-cluster richness link and possible explanations for the weak
correlation that is seen.Comment: 18 pages, 9 figures, submitted to MNRA
The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: measurements of the growth of structure and expansion rate at z=0.57 from anisotropic clustering
We analyze the anisotropic clustering of massive galaxies from the Sloan
Digital Sky Survey III Baryon Oscillation Spectroscopic Survey (BOSS) Data
Release 9 (DR9) sample, which consists of 264,283 galaxies in the redshift
range 0.43 < z < 0.7 spanning 3,275 square degrees. Both peculiar velocities
and errors in the assumed redshift-distance relation ("Alcock-Paczynski
effect") generate correlations between clustering amplitude and orientation
with respect to the line-of-sight. Together with the sharp baryon acoustic
oscillation (BAO) standard ruler, our measurements of the broadband shape of
the monopole and quadrupole correlation functions simultaneously constrain the
comoving angular diameter distance (2190 +/- 61 Mpc) to z=0.57, the Hubble
expansion rate at z=0.57 (92.4 +/- 4.5 km/s/Mpc), and the growth rate of
structure at that same redshift (d sigma8/d ln a = 0.43 +/- 0.069). Our
analysis provides the best current direct determination of both DA and H in
galaxy clustering data using this technique. If we further assume a LCDM
expansion history, our growth constraint tightens to d sigma8/d ln a = 0.415
+/- 0.034. In combination with the cosmic microwave background, our
measurements of DA, H, and growth all separately require dark energy at z >
0.57, and when combined imply \Omega_{\Lambda} = 0.74 +/- 0.016, independent of
the Universe's evolution at z<0.57. In our companion paper (Samushia et al.
prep), we explore further cosmological implications of these observations.Comment: 19 pages, 11 figures, submitted to MNRAS, comments welcom
CP Violation and Neutrino Oscillations
We review the basic mechanisms of neutrino mass generation and the
corresponding structure of the lepton mixing matrix. We summarize the status of
three-neutrino oscillation parameters as determined from current observations,
using state-of-the-art solar and atmospheric neutrino fluxes, as well as latest
experimental data as of September 2007. We also comment on recent attempts to
account for these results and to understand flavour from first principles. We
discuss extensively the prospects for probing the strength of CP violation in
two near term accelerator neutrino oscillation experiments, T2K and NOvA, as
well as possible extensions such as T2KK and a second large off-axis detector
near the NOvA detector. We also briefly discuss the possibility of probing the
effect of Majorana phases in future neutrinoless double beta decay searches and
discuss other implications of leptonic CP violation such as leptogenesis.
Finally we comment on the issue of robustness of the current oscillation
interpretation and possible ways of probing for non-standard neutrino
interactions in precision oscillation studies.Comment: 78 pages, 46 figures, minor misprint corrections, a few new
references and an acknowledgement to a funding agency. Review to be published
in Prog. Part. Nucl. Phy
Effectiveness of in planta control measures for Xylella fastidiosa
This opinion updates the information included in the previous EFSA Scientific Opinion concerning the
in planta control measures for Xylella fastidiosa, with a systematic review and critical analysis of
the potential treatment solutions that have been published against this pest so far. The output of this
opinion focuses on the application of chemical or biological treatments on living plants. In vitro studies,
hot water treatments, use of resistant varieties and vector control are excluded from the review. The
use of antibiotics is not considered due to the risk of antimicrobial resistance development. The use of
weakly virulent or avirulent strains of X. fastidiosa is covered in this review, although this organism is
an EU quarantine plant pest and its introduction in the EU territory is banned. Experiments were
recently conducted to assess the effect of application of zinc, copper, and citric acid biocomplex, of
N-acetylcysteine, and of âdiffusible signal factorâ (and of its homologs). Their results showed that these
control measures were sometimes able to reduce symptoms caused by X. fastidiosa. Recent
experiments also showed that several species of endophytic microorganisms, some bacteriophages and
inoculation of weakly virulent/avirulent strains of X. fastidiosa could offer some protection against the
Pierceâs disease. However, based on the reviewed results, the Panel concludes that, although several
published experiments show some effects in reducing symptoms development, the tested control
measures are not able to completely eliminate X. fastidiosa from diseased plants. The Panel confirms
as previously stated that there is currently no control measure available to eliminate the bacteria from
a diseased plant in open field conditions
The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe
The preponderance of matter over antimatter in the early Universe, the
dynamics of the supernova bursts that produced the heavy elements necessary for
life and whether protons eventually decay --- these mysteries at the forefront
of particle physics and astrophysics are key to understanding the early
evolution of our Universe, its current state and its eventual fate. The
Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed
plan for a world-class experiment dedicated to addressing these questions. LBNE
is conceived around three central components: (1) a new, high-intensity
neutrino source generated from a megawatt-class proton accelerator at Fermi
National Accelerator Laboratory, (2) a near neutrino detector just downstream
of the source, and (3) a massive liquid argon time-projection chamber deployed
as a far detector deep underground at the Sanford Underground Research
Facility. This facility, located at the site of the former Homestake Mine in
Lead, South Dakota, is approximately 1,300 km from the neutrino source at
Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino
charge-parity symmetry violation and mass ordering effects. This ambitious yet
cost-effective design incorporates scalability and flexibility and can
accommodate a variety of upgrades and contributions. With its exceptional
combination of experimental configuration, technical capabilities, and
potential for transformative discoveries, LBNE promises to be a vital facility
for the field of particle physics worldwide, providing physicists from around
the globe with opportunities to collaborate in a twenty to thirty year program
of exciting science. In this document we provide a comprehensive overview of
LBNE's scientific objectives, its place in the landscape of neutrino physics
worldwide, the technologies it will incorporate and the capabilities it will
possess.Comment: Major update of previous version. This is the reference document for
LBNE science program and current status. Chapters 1, 3, and 9 provide a
comprehensive overview of LBNE's scientific objectives, its place in the
landscape of neutrino physics worldwide, the technologies it will incorporate
and the capabilities it will possess. 288 pages, 116 figure
Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.
Messenger RNA encodes cellular function and phenotype. In the context of human cancer, it defines the identities of malignant cells and the diversity of tumor tissue. We studied 72,501 single-cell transcriptomes of human renal tumors and normal tissue from fetal, pediatric, and adult kidneys. We matched childhood Wilms tumor with specific fetal cell types, thus providing evidence for the hypothesis that Wilms tumor cells are aberrant fetal cells. In adult renal cell carcinoma, we identified a canonical cancer transcriptome that matched a little-known subtype of proximal convoluted tubular cell. Analyses of the tumor composition defined cancer-associated normal cells and delineated a complex vascular endothelial growth factor (VEGF) signaling circuit. Our findings reveal the precise cellular identities and compositions of human kidney tumors
The MassiveBlack-II simulation: the evolution of haloes and galaxies to z 0
(Abridged for arXiv)We investigate the properties of halos, galaxies and
blackholes to z=0 in the high resolution hydrodynamical simulation
MassiveBlack-II (MBII) which evolves a LCDM cosmology in a comoving volume
Vbox=100(Mpc/h)^3. MBII is the highest resolution simulation of this size which
includes a self-consistent model for star formation, black hole accretion and
associated feedback. We provide a simulation browser web application which
enables interactive search and tagging of halos, subhalos and their properties
and publicly release our galaxy catalogs. Our analysis of the halo mass
function (MF) in MBII reveals that baryons have strong effects, with changes in
the halo abundance of 20-35% below the knee of the MF (Mhalo < 10^13.2 Msun/h
at z=0) when compared to fits based on dark matter only simulations. We provide
a fitting function for the halo MF out to redshift z=11 and discuss how the
onset of non-universality in the MF limits the accuracy of our fit. We study
the halo occupation distribution and clustering of galaxies, in particular the
evolution and scale dependence of stochasticity and bias finding reasonable
agreement with observational data. The shape of the cosmic spectral energy
distribution predicted by MBII is consistent with observations, but lower in
amplitude. The Galaxy Stellar Mass Function (GSMF) function is broadly
consistent with observations at z>=2. At z<2, the population of passive low
mass (for M*<10^9 Msun) galaxies in MBII makes the GSMF too steep compared to
observations whereas at the high mass end (M*>10^11 Msun) galaxies hosting
bright AGNs make significant contributions to the GSMF. The quasar bolometric
luminosity function is also largely consistent with observations. We note
however that more efficient AGN feedback (beyond simple thermal coupling used
here) is likely necessary for the largest, rarest objects/clusters at low
redshifts.Comment: 26 pages, 25 figures. Submitted to MNRAS. High-resolution version and
MBII galaxy catalogs can be found at http://mbii.phys.cmu.edu/data
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