High-fidelity correction of genomic uracil by human mismatch repair activities

<p>Abstract</p> <p>Background</p> <p>Deamination of cytosine to produce uracil is a common and potentially mutagenic lesion in genomic DNA. U•G mismatches occur spontaneously throughout the genome, where they are repaired by factors associated with the base excision repair pathway. U•G mismatches are also the initiating lesion in immunoglobulin gene diversification, where they undergo mutagenic processing by redundant pathways, one dependent upon uracil excision and the other upon mismatch recognition by MutSα. While UNG is well known to initiate repair of uracil in DNA, the ability of MutSα to direct correction of this base has not been directly demonstrated.</p> <p>Results</p> <p>Using a biochemical assay for mismatch repair, we show that MutSα can promote efficient and faithful repair of U•G mismatches, but does not repair U•A pairs in DNA. This contrasts with UNG, which readily excises U opposite either A or G. Repair of U•G by MutSα depends upon DNA polymerase δ (pol δ), ATP, and proliferating cell nuclear antigen (PCNA), all properties of canonical mismatch repair.</p> <p>Conclusion</p> <p>These results show that faithful repair of U•G can be carried out by either the mismatch repair or base excision repair pathways. Thus, the redundant functions of these pathways in immunoglobulin gene diversification reflect their redundant functions in faithful repair. Faithful repair by either pathway is comparably efficient, suggesting that mismatch repair and base excision repair share the task of faithful repair of genomic uracil.</p

Repression of human activation induced cytidine deaminase by miR-93 and miR-155

BACKGROUND: Activation Induced cytidine Deaminase (AID) targets the immunoglobulin genes of activated B cells, where it converts cytidine to uracil to induce mutagenesis and recombination. While essential for immunoglobulin gene diversification, AID misregulation can result in genomic instability and oncogenic transformation. This is classically illustrated in Burkitt's lymphoma, which is characterized by AID-induced mutation and reciprocal translocation of the c-MYC oncogene with the IgH loci. Originally thought to be B cell-specific, AID now appears to be misexpressed in several epithelial cancers, raising the specter that AID may also participate in non-B cell carcinogenesis. METHODS: The mutagenic potential of AID argues for the existence of cellular regulators capable of repressing inappropriate AID expression. MicroRNAs (miRs) have this capacity, and we have examined the publically available human AID EST dataset for miR complementarities to the human AID 3'UTR. In this work, we have evaluated the capacity of two candidate miRs to repress human AID expression in MCF-7 breast carcinoma cells. RESULTS: We have discovered moderate miR-155 and pronounced miR-93 complementary target sites encoded within the human AID mRNA. Luciferase reporter assays indicate that both miR-93 and miR-155 can interact with the 3'UTR of AID to block expression. In addition, over-expression of either miR in MCF-7 cells reduces endogenous AID protein, but not mRNA, levels. Similarly indicative of AID translational regulation, depletion of either miR in MCF-7 cells increases AID protein levels without concurrent increases in AID mRNA. CONCLUSIONS: Together, our findings demonstrate that miR-93 and miR-155 constitutively suppress AID translation in MCF-7 cells, suggesting widespread roles for these miRs in preventing genome cytidine deaminations, mutagenesis, and oncogenic transformation. In addition, our characterization of an obscured miR-93 target site located within the AID 3'UTR supports the recent suggestion that many miR regulations have been overlooked due to the prevalence of truncated 3'UTR annotations

Admittance measurement for tuning bi-ventricular pacemakers

An apparatus for treating a heart of a patient includes a first lead and at least a second lead for pacing the heart adapted to be in electrical communication with the heart. The apparatus includes a microcontroller in communication with the first and second leads which triggers the first lead at either different times or the same time from when the microcontroller triggers the second lead. Alternatively, the apparatus includes a microcontroller in communication with the first and second leads that determines heart volume, including stroke volume, end-systolic volume, and calculated values including ejection fraction, from admittance from signals from the first and second leads and uses the admittance as feedback to control heart volume ejected, as measured by stroke volume, calculated values such as ejection fraction, and control end-systolic volume, with respect to the first and second leads. A method for treating the heart of a patient.Board of Regents, University of Texas Syste

The Resolved Properties of Extragalactic Giant Molecular Clouds

We use high spatial resolution observations of CO to systematically measure the resolved size-line width, luminosity-line width, luminosity-size, and the mass-luminosity relations of Giant Molecular Clouds (GMCs) in a variety of extragalactic systems. Although the data are heterogeneous we analyze them in a consistent manner to remove the biases introduced by limited sensitivity and resolution, thus obtaining reliable sizes, velocity dispersions, and luminosities. We compare the results obtained in dwarf galaxies with those from the Local Group spiral galaxies. We find that extragalactic GMC properties measured across a wide range of environments are very much compatible with those in the Galaxy. We use these results to investigate metallicity trends in the cloud average column density and virial CO-to-H2 factor. We find that these measurements do not accord with simple predictions from photoionization-regulated star formation theory, although this could be due to the fact that we do not sample small enough spatial scales or the full gravitational potential of the molecular cloud. We also find that the virial CO-to-H2 conversion factor in CO-bright GMCs is very similar to Galactic, and that the excursions do not show a measurable metallicity trend. We contrast these results with estimates of molecular mass based on far-infrared measurements obtained for the Small Magellanic Cloud, which systematically yield larger masses, and interpret this discrepancy as arising from large H2 envelopes that surround the CO-bright cores. We conclude that GMCs identified on the basis of their CO emission are a unique class of object that exhibit a remarkably uniform set of properties from galaxy to galaxy (abridged).Comment: 21 pages, 7 figures, 4 tables (one of them electronic). The Astrophysical Journal, accepted. Revised to reflect changes made to proof

Histone H2A and H2B Are Monoubiquitinated at AID-Targeted Loci

Background: Somatic hypermutation introduces base substitutions into the rearranged and expressed immunoglobulin (Ig) variable regions to promote immunity. This pathway requires and is initiated by the Activation Induced Deaminase (AID) protein, which deaminates cytidine to produce uracils and UG mismatches at the Ig genes. Subsequent processing of uracil by mismatch repair and base excision repair factors contributes to mutagenesis. While selective for certain genomic targets, the chromatin modifications which distinguish hypermutating from non-hypermutating loci are not defined. Methodology/Principal Findings: Here, we show that AID-targeted loci in mammalian B cells contain ubiquitinated chromatin. Chromatin immunoprecipitation (ChIP) analysis of a constitutively hypermutating Burkitt\u27s B cell line, Ramos, revealed the presence of monoubiquitinated forms of both histone H2A and H2B at two AID-associated loci, but not at control loci which are expressed but not hypermutated. Similar analysis using LPS activated primary murine splenocytes showed enrichment of the expressed V(H) and S gamma 3 switch regions upon ChIP with antibody specific to AID and to monoubiquitinated H2A and H2B. In the mechanism of mammalian hypermutation, AID may interact with ubiquitinated chromatin because confocal immunofluorescence microscopy visualized AID colocalized with monoubiquitinated H2B within discrete nuclear foci. Conclusions/Significance: Our results indicate that monoubiquitinated histones accompany active somatic hypermutation, revealing part of the histone code marking AID-targeted loci. This expands the current view of the chromatin state during hypermutation by identifying a specific nucleosome architecture associated with somatic hypermutation

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD

Differential limit on the extremely-high-energy cosmic neutrino flux in the presence of astrophysical background from nine years of IceCube data

We report a quasi-differential upper limit on the extremely-high-energy (EHE) neutrino flux above $5\times 10^{6}$ GeV based on an analysis of nine years of IceCube data. The astrophysical neutrino flux measured by IceCube extends to PeV energies, and it is a background flux when searching for an independent signal flux at higher energies, such as the cosmogenic neutrino signal. We have developed a new method to place robust limits on the EHE neutrino flux in the presence of an astrophysical background, whose spectrum has yet to be understood with high precision at PeV energies. A distinct event with a deposited energy above $10^{6}$ GeV was found in the new two-year sample, in addition to the one event previously found in the seven-year EHE neutrino search. These two events represent a neutrino flux that is incompatible with predictions for a cosmogenic neutrino flux and are considered to be an astrophysical background in the current study. The obtained limit is the most stringent to date in the energy range between $5 \times 10^{6}$ and $5 \times 10^{10}$ GeV. This result constrains neutrino models predicting a three-flavor neutrino flux of $E_\nu^2\phi_{\nu_e+\nu_\mu+\nu_\tau}\simeq2\times 10^{-8}\ {\rm GeV}/{\rm cm}^2\ \sec\ {\rm sr}$at$10^9\ {\rm GeV}$. A significant part of the parameter-space for EHE neutrino production scenarios assuming a proton-dominated composition of ultra-high-energy cosmic rays is excluded.Comment: The version accepted for publication in Physical Review

A Two-Component Probability Distribution Function Describes the mid-IR Emission from the Disks of Star-Forming Galaxies

High-resolution JWST-MIRI images of nearby spiral galaxies reveal emission with complex substructures that trace dust heated both by massive young stars and the diffuse interstellar radiation field. We present high angular (0."85) and physical resolution (20-80 pc) measurements of the probability distribution function (PDF) of mid-infrared (mid-IR) emission (7.7-21 $\mu$m) from 19 nearby star-forming galaxies from the PHANGS-JWST Cycle-1 Treasury. The PDFs of mid-IR emission from the disks of all 19 galaxies consistently show two distinct components: an approximately log-normal distribution at lower intensities and a high-intensity power-law component. These two components only emerge once individual star-forming regions are resolved. Comparing with locations of HII regions identified from VLT/MUSE H$\alpha$-mapping, we infer that the power-law component arises from star-forming regions and thus primarily traces dust heated by young stars. In the continuum-dominated 21 $\mu$m band, the power-law is more prominent and contains roughly half of the total flux. At 7.7-11.3 $\mu$m, the power-law is suppressed by the destruction of small grains (including PAHs) close to HII regions while the log-normal component tracing the dust column in diffuse regions appears more prominent. The width and shape of the log-normal diffuse emission PDFs in galactic disks remain consistent across our sample, implying a log-normal gas column density $N$(H)$\approx10^{21}$cm$^{-2}$ shaped by supersonic turbulence with typical (isothermal) turbulent Mach numbers $\approx5-15$. Finally, we describe how the PDFs of galactic disks are assembled from dusty HII regions and diffuse gas, and discuss how the measured PDF parameters correlate with global properties such as star-formation rate and gas surface density.Comment: 30 pages without appendix, 17 figures, (with appendix images of full sample: 56 pages, 39 figures), accepted in A