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  • 1
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    Lensing measurements of the mass distribution in SDSS voids (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-22
    Description: We measure weak lensing mass profiles of voids from a volume-limited sample of SDSS Luminous Red Galaxies (LRGs). We find voids using an algorithm designed to maximize the lensing signal by dividing the survey volume into 2D slices, and then finding holes in this 2D distribution of LRGs. We perform a stacked shear measurement on about 20 000 voids with radii between 15 and 55 Mpc h –1 , and redshifts between 0.16 and 0.37. We measure the characteristic radial shear signal of voids with a signal to noise of 7. The mass profile corresponds to a fractional underdensity of about –0.4 inside the void radius and a slow approach to the mean density indicating a partially compensated void structure. We compare our measured shape and amplitude with the predictions of Krause et al. Voids in the galaxy distribution have been extensively modelled using simulations and measured in the SDSS. We discuss how the addition of void mass profiles can enable studies of galaxy formation and cosmology.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Lensing measurements of the ellipticity of luminous red galaxies dark matter haloes (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-03
    Description: Lensing measurements of the shapes of dark matter haloes can provide tests of gravity theories and possible dark matter interactions. We measure the quadrupole weak lensing signal from the elliptical haloes of 70 000 Sloan Digital Sky Survey luminous red galaxies. We use a new estimator that nulls the spherical halo lensing signal, isolating the shear due to anisotropy in the dark matter distribution. One of the two Cartesian components of our estimator is insensitive to the primary systematic, a spurious alignment of lens and source ellipticities, allowing us to make robust measurements of halo ellipticity. Our best-fitting value for the ellipticity of the surface mass density is 0.24 ± 0.06, which translates to an axis ratio of 0.78. We rule out the hypothesis of no ellipticity at the 4 confidence level, and ellipticity 〈0.12 (axis ratio 〉0.89) at the 2 level. We discuss how our measurements of halo ellipticity are revised to higher values using estimates of the misalignment of mass and light from simulations. Finally, we apply the same techniques to a smaller sample of redMaPPer galaxy clusters and obtain a 3 measurement of cluster ellipticity. We discuss how the improved signal-to-noise ratio properties of our estimator can enable studies of halo shapes for different galaxy populations with upcoming surveys.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Identification and characterization of a functional mitochondrial angiotensin system [Cell Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-09-07
    Description: The renin-angiotensin (Ang) system regulates multiple physiological functions through Ang II type 1 and type 2 receptors. Prior studies suggest an intracellular pool of Ang II that may be released in an autocrine manner upon stretch to activate surface membrane Ang receptors. Alternatively, an intracellular renin-Ang system has been proposed, with a primary focus on nuclear Ang receptors. A mitochondrial Ang system has not been previously described. Here we report that functional Ang II type 2 receptors are present on mitochondrial inner membranes and are colocalized with endogenous Ang. We demonstrate that activation of the mitochondrial Ang system is coupled to mitochondrial nitric oxide production and can modulate respiration. In addition, we present evidence of age-related changes in mitochondrial Ang receptor expression, i.e., increased mitochondrial Ang II type 1 receptor and decreased type 2 receptor density that is reversed by chronic treatment with the Ang II type 1 receptor blocker losartan. The presence of a functional Ang system in human mitochondria provides a foundation for understanding the interaction between mitochondria and chronic disease states and reveals potential therapeutic targets for optimizing mitochondrial function and decreasing chronic disease burden with aging.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    New tools provide a second look at HDV ribozyme structure, dynamics and cleavage (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-12
    Description: The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.
    Keywords: Nucleic acid structure
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    NIR regulates early lymphocyte development [Immunology and Inflammation] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-09-24
    Description: Novel inhibitor of histone acetyltransferase repressor (NIR) is a transcriptional corepressor with inhibitor of histone acetyltransferase activity and is a potent suppressor of p53. Although NIR deficiency in mice leads to early embryonic lethality, lymphoid-restricted deletion resulted in the absence of double-positive CD4+CD8+ thymocytes, whereas bone-marrow-derived B cells were arrested...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Isolation of the cyclosporin-sensitive T cell transcription factor NFATp (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-10-29
    Description: Nuclear factor of activated T cells (NFAT) is a transcription factor that regulates expression of the cytokine interleukin-2 (IL-2) in activated T cells. The DNA-binding specificity of NFAT is conferred by NFATp, a phosphoprotein that is a target for the immunosuppressive compounds cyclosporin A and FK506. Here, the purification of NFATp from murine T cells and the isolation of a complementary DNA clone encoding NFATp are reported. A truncated form of NFATp, expressed as a recombinant protein in bacteria, binds specifically to the NFAT site of the murine IL-2 promoter and forms a transcriptionally active complex with recombinant protein fragment react with T cell NFATp. The molecular cloning of NFATp should allow detailed analysis of a T cell transcription factor that is central to initiation of the immune response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCaffrey, P G -- Luo, C -- Kerppola, T K -- Jain, J -- Badalian, T M -- Ho, A M -- Burgeon, E -- Lane, W S -- Lambert, J N -- Curran, T -- CA42471/CA/NCI NIH HHS/ -- GM46227/GM/NIGMS NIH HHS/ -- NS25078/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1993 Oct 29;262(5134):750-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Tumor Virology, Dana-Farber Cancer Institute, Boston, MA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8235597" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; DNA, Complementary ; DNA-Binding Proteins/genetics/*isolation & purification/physiology ; Immunosuppressive Agents/pharmacology ; Interleukin-2/genetics ; Mice ; Molecular Sequence Data ; NFATC Transcription Factors ; *Nuclear Proteins ; Phosphoproteins/genetics/isolation & purification/physiology ; Promoter Regions, Genetic ; Proto-Oncogene Proteins c-fos/physiology ; Proto-Oncogene Proteins c-jun/physiology ; RNA, Messenger/analysis ; Recombinant Proteins ; T-Lymphocytes/*chemistry ; Transcription Factors/genetics/*isolation & purification/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    TWEAK is implicated in antibody deficiency [Immunology] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-03-27
    Description: Mutations in the TNF family of proteins have been associated with inherited forms of immune deficiency. Using an array-based sequencing assay, we identified an autosomal-dominant deficiency in TNF-like weak inducer of apoptosis (TWEAK; TNFSF12) in a kindred with recurrent infection and impaired antibody responses to protein and polysaccharide vaccines. This...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Clustering and bias measurements of SDSS voids (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-17
    Description: Using a void catalogue from the Sloan Digital Sky Survey, we present the first measurements of void clustering and the corresponding void bias. Over the range 30–200 Mpc h –1 , the void autocorrelation is detected at 5 significance for voids of radius 15–20 Mpc h –1 . We also measure the void–galaxy cross-correlation at higher signal to noise and compare the inferred void bias with the autocorrelation results. Void bias is constant with scale for voids of a given size, but its value falls from 5.6 ± 1.0 to below zero as the void radius increases from 15 to 30 Mpc h –1 . The comparison of our measurements with carefully matched galaxy mock catalogues, with no free parameters related to the voids, shows that model predictions can be reliably made for void correlations. We study the dependence of void bias on tracer density and void size with a view to future applications. In combination with our previous lensing measurements of void mass profiles, these clustering measurements provide another step towards using voids as cosmological tracers.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    The ellipticity of galaxy cluster haloes from satellite galaxies and weak lensing (2018)
    Oxford University Press
    Details
    Publication Date: 2018-03-06
    Description: We study the ellipticity of galaxy cluster haloes as characterized by the distribution of cluster galaxies and as measured with weak lensing. We use Monte Carlo simulations of elliptical cluster density profiles to estimate and correct for Poisson noise bias, edge bias and projection effects. We apply our methodology to 10 428 Sloan Digital Sky Survey clusters identified by the redMaPPer algorithm with richness above 20. We find a mean ellipticity =0.271 ± 0.002 (stat) ±0.031 (sys) corresponding to an axis ratio = 0.573 ± 0.002 (stat) ±0.039 (sys). We compare this ellipticity of the satellites to the halo shape, through a stacked lensing measurement using optimal estimators of the lensing quadrupole based on Clampitt and Jain ( 2016 ). We find a best-fitting axis ratio of 0.56 ± 0.09 (stat) ±0.03 (sys), consistent with the ellipticity of the satellite distribution. Thus, cluster galaxies trace the shape of the dark matter halo to within our estimated uncertainties. Finally, we restack the satellite and lensing ellipticity measurements along the major axis of the cluster central galaxy's light distribution. From the lensing measurements, we infer a misalignment angle with an root-mean-square of 30° ± 10° when stacking on the central galaxy. We discuss applications of halo shape measurements to test the effects of the baryonic gas and active galactic nucleus feedback, as well as dark matter and gravity. The major improvements in signal-to-noise ratio expected with the ongoing Dark Energy Survey and future surveys from Large Synoptic Survey Telescope, Euclid, and Wide Field Infrared Survey Telescope will make halo shapes a useful probe of these effects.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Origins of lymphatic and distant metastases in human colorectal cancer (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-07-07
    Description: The spread of cancer cells from primary tumors to regional lymph nodes is often associated with reduced survival. One prevailing model to explain this association posits that fatal, distant metastases are seeded by lymph node metastases. This view provides a mechanistic basis for the TNM staging system and is the rationale for surgical resection of tumor-draining lymph nodes. Here we examine the evolutionary relationship between primary tumor, lymph node, and distant metastases in human colorectal cancer. Studying 213 archival biopsy samples from 17 patients, we used somatic variants in hypermutable DNA regions to reconstruct high-confidence phylogenetic trees. We found that in 65% of cases, lymphatic and distant metastases arose from independent subclones in the primary tumor, whereas in 35% of cases they shared common subclonal origin. Therefore, two different lineage relationships between lymphatic and distant metastases exist in colorectal cancer.
    Keywords: Medicine, Diseases
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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