Whole genome sequencing-based mapping and candidate identification of mutations from fixed zebrafish tissue

As forward genetic screens in zebrafish become more common, the number of mutants that cannot be identified by gross morphology or through transgenic approaches, such as many nervous system defects, has also increased. Screening for these difficult-to-visualize phenotypes demands techniques such as whole-mount in situ hybridization (WISH) or antibody staining, which require tissue fixation. To date, fixed tissue has not been amenable for generating libraries for whole genome sequencing (WGS). Here, we describe a method for using genomic DNA from fixed tissue and a bioinformatics suite for WGS-based mapping of zebrafish mutants. We tested our protocol using two known zebrafish mutant alleles, gpr126st49 and egr2bfh227, both of which cause myelin defects. As further proof of concept we mapped a novel mutation, stl64, identified in a zebrafish WISH screen for myelination defects. We linked stl64 to chromosome 1 and identified a candidate nonsense mutation in the F-box and WD repeat domain containing 7 (fbxw7) gene. Importantly, stl64 mutants phenocopy previously described fbxw7vu56 mutants, and knockdown of fbxw7 in wild-type animals produced similar defects, demonstrating that stl64 disrupts fbxw7. Together, these data show that our mapping protocol can map and identify causative lesions in mutant screens that require tissue fixation for phenotypic analysis

Cutting edges at random in large recursive trees

We comment on old and new results related to the destruction of a random recursive tree (RRT), in which its edges are cut one after the other in a uniform random order. In particular, we study the number of steps needed to isolate or disconnect certain distinguished vertices when the size of the tree tends to infinity. New probabilistic explanations are given in terms of the so-called cut-tree and the tree of component sizes, which both encode different aspects of the destruction process. Finally, we establish the connection to Bernoulli bond percolation on large RRT's and present recent results on the cluster sizes in the supercritical regime.Comment: 29 pages, 3 figure

The ATLAS tile calorimeter digitizer

The ATLAS Tile Calorimeter digitizer system samples photomultiplier signals from the scintillating tiles of the hadronic calorimeter. For each channel a pair of 10-bit ADCs digitize high and low gain signals at 40.08 MHz to provide the necessary 16-bit dynamic range. The sampled data is temporarily stored in digital pipelines for up to 6.375 \mu­s, awaiting a level-1 accept. For each accept received, the corresponding sampled pulse is transferred to a derandomizer buffer for subsequent readout to the data acquisition system (DAQ). The main functionality of the digitizer is implemented in radiation tolerant ASICs, using a fault tolerant architecture to minimize the consequences of radiation induced faults

MAPfastR: Quantitative Trait Loci Mapping in Outbred Line Crosses

MAPfastR is a software package developed to analyze quantitative trait loci data from inbred and outbred line-crosses. The package includes a number of modules for fast and accurate quantitative trait loci analyses. It has been developed in the R language for fast and comprehensive analyses of large datasets. MAPfastR is freely available at: http://www.computationalgenetics.se/?page_id=7.Swedish Foundation for Strategic Research (Future Research Leader program), European Science Foundation (EURYI Award)

Paradoxical roles of antioxidant enzymes:Basic mechanisms and health implications

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from aerobic metabolism, as a result of accidental electron leakage as well as regulated enzymatic processes. Because ROS/RNS can induce oxidative injury and act in redox signaling, enzymes metabolizing them will inherently promote either health or disease, depending on the physiological context. It is thus misleading to consider conventionally called antioxidant enzymes to be largely, if not exclusively, health protective. Because such a notion is nonetheless common, we herein attempt to rationalize why this simplistic view should be avoided. First we give an updated summary of physiological phenotypes triggered in mouse models of overexpression or knockout of major antioxidant enzymes. Subsequently, we focus on a series of striking cases that demonstrate “paradoxical” outcomes, i.e., increased fitness upon deletion of antioxidant enzymes or disease triggered by their overexpression. We elaborate mechanisms by which these phenotypes are mediated via chemical, biological, and metabolic interactions of the antioxidant enzymes with their substrates, downstream events, and cellular context. Furthermore, we propose that novel treatments of antioxidant enzyme-related human diseases may be enabled by deliberate targeting of dual roles of the pertaining enzymes. We also discuss the potential of “antioxidant” nutrients and phytochemicals, via regulating the expression or function of antioxidant enzymes, in preventing, treating, or aggravating chronic diseases. We conclude that “paradoxical” roles of antioxidant enzymes in physiology, health, and disease derive from sophisticated molecular mechanisms of redox biology and metabolic homeostasis. Simply viewing antioxidant enzymes as always being beneficial is not only conceptually misleading but also clinically hazardous if such notions underpin medical treatment protocols based on modulation of redox pathways

Analysis of the low-energy electron-recoil spectrum of the CDMS experiment

We report on the analysis of the low-energy electron-recoil spectrum from the CDMS II experiment using data with an exposure of 443.2 kg-days. The analysis provides details on the observed counting rate and possible background sources in the energy range of 2 - 8.5 keV. We find no significant excess in the counting rate above background, and compare this observation to the recent DAMA results. In the framework of a conversion of a dark matter particle into electromagnetic energy, our 90% confidence level upper limit of 0.246 events/kg/day at 3.15 keV is lower than the total rate above background observed by DAMA by 8.9$\sigma$. In absence of any specific particle physics model to provide the scaling in cross section between NaI and Ge, we assume a Z^2 scaling. With this assumption the observed rate in DAMA differs from the upper limit in CDMS by 6.8$\sigma$. Under the conservative assumption that the modulation amplitude is 6% of the total rate we obtain upper limits on the modulation amplitude a factor of ~2 less than observed by DAMA, constraining some possible interpretations of this modulation.Comment: 4 pages, 3 figure

Search for inelastic dark matter with the CDMS II experiment

Results are presented from a reanalysis of the entire five-tower data set acquired with the Cryogenic Dark Matter Search (CDMS II) experiment at the Soudan Underground Laboratory, with an exposure of 969 kg-days. The analysis window was extended to a recoil energy of 150 keV, and an improved surface-event background-rejection cut was defined to increase the sensitivity of the experiment to the inelastic dark matter (iDM) model. Three dark matter candidates were found between 25 keV and 150 keV. The probability to observe three or more background events in this energy range is 11%. Because of the occurrence of these events the constraints on the iDM parameter space are slightly less stringent than those from our previous analysis, which used an energy window of 10-100 keV.Comment: 10 pages, 10 figures, minor changes to match published version, conclusion unchange

Results from a Low-Energy Analysis of the CDMS II Germanium Data

We report results from a reanalysis of data from the Cryogenic Dark Matter Search (CDMS II) experiment at the Soudan Underground Laboratory. Data taken between October 2006 and September 2008 using eight germanium detectors are reanalyzed with a lowered, 2 keV recoil-energy threshold, to give increased sensitivity to interactions from Weakly Interacting Massive Particles (WIMPs) with masses below ~10 GeV/c^2. This analysis provides stronger constraints than previous CDMS II results for WIMP masses below 9 GeV/c^2 and excludes parameter space associated with possible low-mass WIMP signals from the DAMA/LIBRA and CoGeNT experiments.Comment: 9 pages, 8 figures. Supplemental material included as ancillary files. v3) Added appendix with additional details regarding energy scale and background