61 research outputs found
Calibration and Characterization of the IceCube Photomultiplier Tube
Over 5,000 PMTs are being deployed at the South Pole to compose the IceCube
neutrino observatory. Many are placed deep in the ice to detect Cherenkov light
emitted by the products of high-energy neutrino interactions, and others are
frozen into tanks on the surface to detect particles from atmospheric cosmic
ray showers. IceCube is using the 10-inch diameter R7081-02 made by Hamamatsu
Photonics. This paper describes the laboratory characterization and calibration
of these PMTs before deployment. PMTs were illuminated with pulses ranging from
single photons to saturation level. Parameterizations are given for the single
photoelectron charge spectrum and the saturation behavior. Time resolution,
late pulses and afterpulses are characterized. Because the PMTs are relatively
large, the cathode sensitivity uniformity was measured. The absolute photon
detection efficiency was calibrated using Rayleigh-scattered photons from a
nitrogen laser. Measured characteristics are discussed in the context of their
relevance to IceCube event reconstruction and simulation efforts.Comment: 40 pages, 12 figure
Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used theMonodelphis domestica (gray short-tailed opossum) sequence to construct the first map of a marsupial major histocompatibility complex (MHC). The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral “immune supercomplex” that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes
Specific Recognition of p53 Tetramers by Peptides Derived from p53 Interacting Proteins
Oligomerization plays a major role in regulating the activity of many proteins, and in modulating their interactions. p53 is a homotetrameric transcription factor that has a pivotal role in tumor suppression. Its tetramerization domain is contained within its C-terminal domain, which is a site for numerous protein-protein interactions. Those can either depend on or regulate p53 oligomerization. Here we screened an array of peptides derived from proteins known to bind the tetrameric p53 C-terminal domain (p53CTD) and identified ten binding peptides. We quantitatively characterized their binding to p53CTD using fluorescence anisotropy. The peptides bound tetrameric p53CTD with micromolar affinities. Despite the high charge of the binding peptides, electrostatics contributed only mildly to the interactions. NMR studies indicated that the peptides bound p53CTD at defined sites. The most significant chemical shift deviations were observed for the peptides WS100B(81–92), which bound directly to the p53 tetramerization domain, and PKCα(281–295), which stabilized p53CTD in circular dichroism thermal denaturation studies. Using analytical ultracentrifugation, we found that several of the peptides bound preferentially to p53 tetramers. Our results indicate that the protein-protein interactions of p53 are dependent on the oligomerization state of p53. We conclude that peptides may be used to regulate the oligomerization of p53
Measurement of acoustic attenuation in South Pole ice
Using the South Pole Acoustic Test Setup (SPATS) and a retrievable transmitter deployed in holes drilled for the IceCube experiment, we have measured the attenuation of acoustic signals by South Pole ice at depths between 190 m and 500 m. Three data sets, using different acoustic sources, have been analyzed and give consistent results. The method with the smallest systematic uncertainties yields an amplitude attenuation coefficient α = 3.20 ± 0.57 km−1 between 10 and 30 kHz, considerably larger than previous theoretical estimates. Expressed as an attenuation length, the analyses give a consistent result for λ ≡ 1/α of ∼300 m with 20% uncertainty. No significant depth or frequency dependence has been found
Solar Energetic Particle Spectrum on 13 December 2006 Determined by IceTop
On 13 December 2006 the IceTop air shower array at the South Pole detected a
major solar particle event. By numerically simulating the response of the
IceTop tanks, which are thick Cherenkov detectors with multiple thresholds
deployed at high altitude with no geomagnetic cut-off, we determined the
particle energy spectrum in the energy range 0.6 to 7.6 GeV. This is the first
such spectral measurement using a single instrument with a well defined viewing
direction. We compare the IceTop spectrum and its time evolution with
previously published results and outline plans for improved resolution of
future solar particle spectra.Comment: To appear in Astrophysical Journal Letters, 6 pages, 4 figure
The IceCube Data Acquisition System: Signal Capture, Digitization, and Timestamping
IceCube is a km-scale neutrino observatory under construction at the South
Pole with sensors both in the deep ice (InIce) and on the surface (IceTop). The
sensors, called Digital Optical Modules (DOMs), detect, digitize and timestamp
the signals from optical Cherenkov-radiation photons. The DOM Main Board (MB)
data acquisition subsystem is connected to the central DAQ in the IceCube
Laboratory (ICL) by a single twisted copper wire-pair and transmits packetized
data on demand. Time calibration is maintained throughout the array by regular
transmission to the DOMs of precisely timed analog signals, synchronized to a
central GPS-disciplined clock. The design goals and consequent features,
functional capabilities, and initial performance of the DOM MB, and the
operation of a combined array of DOMs as a system, are described here.
Experience with the first InIce strings and the IceTop stations indicates that
the system design and performance goals have been achieved.Comment: 42 pages, 20 figures, submitted to Nuclear Instruments and Methods
Tumor cell killing mechanisms of epidermal growth factor receptor (EGFR) antibodies are not affected by lung cancer-associated EGFR kinase mutations.
The Ras inhibitor farnesylthiosalicyclic acid (FTS) prevents nodule formation and development of preneoplastic foci of altered hepatocytes in rats.
BACKGROUND: Aberrant activation of oncogenes, such as Ras, likely contributes to the development of hepatocarcinoma (HCC). AIMS/METHODS: We evaluated in vivo the effect of intraperitoneal injections of the Ras inhibitor S-trans, trans-farnesylthiosalicyclic acid (FTS) on Ras activation and the development of preneoplastic liver lesions in rats receiving weekly diethylnitrosamine (DEN) injections for 16weeks. Western blotting, quantitative PCR, immunohistochemistry, Tunel and caspase activity assays were used. RESULTS: FTS prevents liver nodule formation and reduces foci expressing the tumour marker GSTp. FTS abrogates DEN-induced Ras membrane activity, increases Tunel positive cells in transformed, GSTp-expressing hepatocytes, up-regulates caspase 3 and 8 activity, induces Fas, Fas ligand and JNK phosphorylation that occurs independently of TNFalpha and Trail. Cytochrome C release, Bax, Bcl2, Bcl-xl, Ki67 and nuclear cyclin D expression is not affected by FTS. CONCLUSIONS: FTS inhibits Ras activation and prevents preneoplastic liver nodule development by inducing apoptosis in transformed hepatocytes through activation of the Fas/Fas ligand system. FTS might be new molecule for HCC treatment
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