An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia

BACKGROUND: Only one spliceosomal-type intron has previously been identified in the unicellular eukaryotic parasite, Giardia lamblia (a diplomonad). This intron is only 35 nucleotides in length and is unusual in possessing a non-canonical 5' intron boundary sequence, CT, instead of GT. RESULTS: We have identified a second spliceosomal-type intron in G. lamblia, in the ribosomal protein L7a gene (Rpl7a), that possesses a canonical GT 5' intron boundary sequence. A comparison of the two known Giardia intron sequences revealed extensive nucleotide identity at both the 5' and 3' intron boundaries, similar to the conserved sequence motifs recently identified at the boundaries of spliceosomal-type introns in Trichomonas vaginalis (a parabasalid). Based on these observations, we searched the partial G. lamblia genome sequence for these conserved features and identified a third spliceosomal intron, in an unassigned open reading frame. Our comprehensive analysis of the Rpl7a intron in other eukaryotic taxa demonstrates that it is evolutionarily conserved and is an ancient eukaryotic intron. CONCLUSION: An analysis of the phylogenetic distribution and properties of the Rpl7a intron suggests its utility as a phylogenetic marker to evaluate particular eukaryotic groupings. Additionally, analysis of the G. lamblia introns has provided further insight into some of the conserved and unique features possessed by the recently identified spliceosomal introns in related organisms such as T. vaginalis and Carpediemonas membranifera

A Family Showing No Evidence of Linkage Between the Ataxia Telangiectasia Gene and Chromosome

We have studied an inbred family in which two cousins presented with the same clinical features of ataxia telangiectasia (AT). Both patients are still ambulatory at ages 25 and 20. Cellular features of both patients are typical of AT and include increased radiosensitivity and an increased level of spontaneously occurring chromosome aberrations in peripheral blood lymphocytes. Linkage studies and haplotype analysis show no clear evidence that the gene for AT in this family is on chromosome 11q22-23. As previously reported AT families from complementation groups AB, C, and D have all shown linkage to this region of 11q22-23. Our study is of importance in suggesting additional locus heterogeneity

Exclusion limits on the WIMP-nucleon cross-section from the Cryogenic Dark Matter Search

The Cryogenic Dark Matter Search (CDMS) employs low-temperature Ge and Si detectors to search for Weakly Interacting Massive Particles (WIMPs) via their elastic-scattering interactions with nuclei while discriminating against interactions of background particles. For recoil energies above 10 keV, events due to background photons are rejected with >99.9% efficiency, and surface events are rejected with >95% efficiency. The estimate of the background due to neutrons is based primarily on the observation of multiple-scatter events that should all be neutrons. Data selection is determined primarily by examining calibration data and vetoed events. Resulting efficiencies should be accurate to about 10%. Results of CDMS data from 1998 and 1999 with a relaxed fiducial-volume cut (resulting in 15.8 kg-days exposure on Ge) are consistent with an earlier analysis with a more restrictive fiducial-volume cut. Twenty-three WIMP candidate events are observed, but these events are consistent with a background from neutrons in all ways tested. Resulting limits on the spin-independent WIMP-nucleon elastic-scattering cross-section exclude unexplored parameter space for WIMPs with masses between 10-70 GeV c^{-2}. These limits border, but do not exclude, parameter space allowed by supersymmetry models and accelerator constraints. Results are compatible with some regions reported as allowed at 3-sigma by the annual-modulation measurement of the DAMA collaboration. However, under the assumptions of standard WIMP interactions and a standard halo, the results are incompatible with the DAMA most likely value at >99.9% CL, and are incompatible with the model-independent annual-modulation signal of DAMA at 99.99% CL in the asymptotic limit.Comment: 40 pages, 49 figures (4 in color), submitted to Phys. Rev. D; v.2:clarified conclusions, added content and references based on referee's and readers' comments; v.3: clarified introductory sections, added figure based on referee's comment

Model-Independent Comparison of Direct vs. Indirect Detection of Supersymmetric Dark Matter

We compare the rate for elastic scattering of neutralinos from various nuclei with the flux of upward muons induced by energetic neutrinos from neutralino annihilation in the Sun and Earth. We consider both scalar and axial-vector interactions of neutralinos with nuclei. We find that the event rate in a kg of germanium is roughly equivalent to that in a $10^5$- to $10^7$-m$^2$ muon detector for a neutralino with primarily scalar coupling to nuclei. For an axially coupled neutralino, the event rate in a 50-gram hydrogen detector is roughly the same as that in a 10- to 500-m$^2$ muon detector. Expected experimental backgrounds favor forthcoming elastic-scattering detectors for scalar couplings while the neutrino detectors have the advantage for axial-vector couplings.Comment: 10 pages, self-unpacking uuencoded PostScript fil

Indirect Detection of a Light Higgsino Motivated by Collider Data

Kane and Wells recently argued that collider data point to a Higgsino-like lightest supersymmetric partner which would explain the dark matter in our Galactic halo. They discuss direct detection of such dark-matter particles in laboratory detectors. Here, we argue that such a particle, if it is indeed the dark matter, might alternatively be accessible in experiments which search for energetic neutrinos from dark-matter annihilation in the Sun. We provide accurate analytic estimates for the rates which take into account all relevant physical effects. Currently, the predicted signal falls roughly one to three orders of magnitude below experimental bounds, depending on the mass and coupling of the particle; however, detectors such as MACRO, super-Kamiokande, and AMANDA will continue to take data and should be able to rule out or confirm an interesting portion of the possible mass range for such a dark-matter particle within the next five years.Comment: 10 pages, RevTe

Nuclear Shell Model Calculations of Neutralino-Nucleus Cross Sections for Silicon 29 and Germanium 73

We present the results of detailed nuclear shell model calculations of the spin-dependent elastic cross section for neutralinos scattering from \si29 and \ge73. The calculations were performed in large model spaces which adequately describe the configuration mixing in these two nuclei. As tests of the computed nuclear wave functions, we have calculated several nuclear observables and compared them with the measured values and found good agreement. In the limit of zero momentum transfer, we find scattering matrix elements in agreement with previous estimates for \si29 but significantly different than previous work for \ge73. A modest quenching, in accord with shell model studies of other heavy nuclei, has been included to bring agreement between the measured and calculated values of the magnetic moment for \ge73. Even with this quenching, the calculated scattering rate is roughly a factor of 2 higher than the best previous estimates; without quenching, the rate is a factor of 4 higher. This implies a higher sensitivity for germanium dark matter detectors. We also investigate the role of finite momentum transfer upon the scattering response for both nuclei and find that this can significantly change the expected rates. We close with a brief discussion of the effects of some of the non-nuclear uncertainties upon the matrix elements.Comment: 31 pages, figures avaiable on request, UCRL-JC-11408

Exclusion Limits on the WIMP-Nucleon Cross-Section from the First Run of the Cryogenic Dark Matter Search in the Soudan Underground Lab

The Cryogenic Dark Matter Search (CDMS-II) employs low-temperature Ge and Si detectors to seek Weakly Interacting Massive Particles (WIMPs) via their elastic scattering interactions with nuclei. Simultaneous measurements of both ionization and phonon energy provide discrimination against interactions of background particles. For recoil energies above 10 keV, events due to background photons are rejected with >99.99% efficiency. Electromagnetic events very near the detector surface can mimic nuclear recoils because of reduced charge collection, but these surface events are rejected with >96% efficiency by using additional information from the phonon pulse shape. Efficient use of active and passive shielding, combined with the the 2090 m.w.e. overburden at the experimental site in the Soudan mine, makes the background from neutrons negligible for this first exposure. All cuts are determined in a blind manner from in situ calibrations with external radioactive sources without any prior knowledge of the event distribution in the signal region. Resulting efficiencies are known to ~10%. A single event with a recoil of 64 keV passes all of the cuts and is consistent with the expected misidentification rate of surface-electron recoils. Under the assumptions for a standard dark matter halo, these data exclude previously unexplored parameter space for both spin-independent and spin-dependent WIMP-nucleon elastic scattering. The resulting limit on the spin-independent WIMP-nucleon elastic-scattering cross-section has a minimum of 4x10^-43 cm^2 at a WIMP mass of 60 GeV/c^2. The minimum of the limit for the spin-dependent WIMP-neutron elastic-scattering cross-section is 2x10^-37 cm^2 at a WIMP mass of 50 GeV/c^2.Comment: 37 pages, 42 figure