Uracil–DNA glycosylases SMUG1 and UNG2 coordinate the initial steps of base excision repair by distinct mechanisms

DNA glycosylases UNG and SMUG1 excise uracil from DNA and belong to the same protein superfamily. Vertebrates contain both SMUG1 and UNG, but their distinct roles in base excision repair (BER) of deaminated cytosine (U:G) are still not fully defined. Here we have examined the ability of human SMUG1 and UNG2 (nuclear UNG) to initiate and coordinate repair of U:G mismatches. When expressed in Escherichia coli cells, human UNG2 initiates complete repair of deaminated cytosine, while SMUG1 inhibits cell proliferation. In vitro, we show that SMUG1 binds tightly to AP-sites and inhibits AP-site cleavage by AP-endonucleases. Furthermore, a specific motif important for the AP-site product binding has been identified. Mutations in this motif increase catalytic turnover due to reduced product binding. In contrast, the highly efficient UNG2 lacks product-binding capacity and stimulates AP-site cleavage by APE1, facilitating the two first steps in BER. In summary, this work reveals that SMUG1 and UNG2 coordinate the initial steps of BER by distinct mechanisms. UNG2 is apparently adapted to rapid and highly coordinated repair of uracil (U:G and U:A) in replicating DNA, while the less efficient SMUG1 may be more important in repair of deaminated cytosine (U:G) in non-replicating chromatin

Toward a More Comprehensive Understanding of organizational influences On Implementation: the organization theory For Implementation Science Framework

INTRODUCTION: Implementation is influenced by factors beyond individual clinical settings. Nevertheless, implementation research often focuses on factors related to individual providers and practices, potentially due to limitations of available frameworks. Extant frameworks do not adequately capture the myriad organizational influences on implementation. Organization theories capture diverse organizational influences but remain underused in implementation science. to advance their use among implementation scientists, we distilled 70 constructs from nine organization theories identified in our previous work into theoretical domains in the Organization Theory for Implementation Science (OTIS) framework. METHODS: The process of distilling organization theory constructs into domains involved concept mapping and iterative consensus-building. First, we recruited organization and implementation scientists to participate in an online concept mapping exercise in which they sorted organization theory constructs into domains representing similar theoretical concepts. Multidimensional scaling and hierarchical cluster analyses were used to produce visual representations (clusters) of the relationships among constructs in concept maps. Second, to interpret concept maps, we engaged members of the Cancer Prevention and Control Research Network (CPCRN) OTIS workgroup in consensus-building discussions. RESULTS: Twenty-four experts participated in concept mapping. Based on resulting construct groupings\u27 coherence, OTIS workgroup members selected the 10-cluster solution (from options of 7-13 clusters) and then reorganized clusters in consensus-building discussions to increase coherence. This process yielded six final OTIS domains: organizational characteristics (e.g., size; age); governance and operations (e.g., organizational and social subsystems); tasks and processes (e.g., technology cycles; excess capacity); knowledge and learning (e.g., tacit knowledge; sense making); characteristics of a population of organizations (e.g., isomorphism; selection pressure); and interorganizational relationships (e.g., dominance; interdependence). DISCUSSION: Organizational influences on implementation are poorly understood, in part due to the limitations of extant frameworks. to improve understanding of organizational influences on implementation, we distilled 70 constructs from nine organization theories into six domains. Applications of the OTIS framework will enhance understanding of organizational influences on implementation, promote theory-driven strategies for organizational change, improve understanding of mechanisms underlying relationships between OTIS constructs and implementation, and allow for framework refinement. Next steps include testing the OTIS framework in implementation research and adapting it for use among policymakers and practitioners

Increasing Access to Organization Theories for Implementation Science

Background Organization theories offer numerous existing, highly relevant, yet largely untapped explanations of the organizational dynamics underlying evidence-based intervention (EBI) implementation. Rooted in ideas regarding power, autonomy, and control, organization theories can explain how and why organizations adopt, implement, and sustain EBI use. Although they have gained visibility, organization theories remain underused in implementation research, perhaps due to their inaccessibility to implementation scientists. To improve access to organization theory among implementation scientists, we summarized organization theories with relevance to implementation science. Methods Led by the Cancer Prevention and Control Research Network (CPCRN) Organization Theory for Implementation Science workgroup, we employed a modified Delphi process to reach a consensus among 18 experts at the intersection of organization and implementation science regarding organization theories with relevance to implementation science. From texts that described the organization theories, using standardized abstraction forms, two investigators independently abstracted information regarding constructs, propositions regarding how or why constructs might influence implementation, the potential relevance of organization theories' propositions for implementation, and overviews of each theory. The investigators then reconciled discrepancies until reaching consensus. A third investigator reviewed reconciled abstraction forms for accuracy, coherence, and completeness. Findings We identified nine organization theories with relevance to implementation science: contingency, complexity, institutional, network, organizational learning, resource dependence, sociotechnical, and transaction cost economics. From the theories, we abstracted 70 constructs and 65 propositions. An example proposition from institutional theory is: “Coercive, mimetic, and normative pressures contribute to organizations…within an organizational field [becoming increasingly similar].” These propositions can be operationalized as levers to facilitate EBI implementation. Conclusions To increase use in the field, organization theories must be made more accessible to implementation scientists. The abstraction forms developed in this study are now publicly available on the CPCRN website with the goal of increasing access to organization theories among an interdisciplinary audience of implementation scientists through the CPCRN Scholars program and other venues. Next steps include consolidating organization theory constructs into domains and translating the resulting framework for use among researchers, policymakers and practitioners, aiding them in accounting for a comprehensive set of organization theory constructs thought to influence EBI implementation

BACE1 activity impairs neuronal glucose oxidation:rescue by beta-hydroxybutyrate and lipoic acid

Glucose hypometabolism and impaired mitochondrial function in neurons have been suggested to play early and perhaps causative roles in Alzheimer's disease (AD) pathogenesis. Activity of the aspartic acid protease, beta-site amyloid precursor protein (APP) cleaving enzyme 1 (BACE1), responsible for beta amyloid peptide generation, has recently been demonstrated to modify glucose metabolism. We therefore examined, using a human neuroblastoma (SH-SY5Y) cell line, whether increased BACE1 activity is responsible for a reduction in cellular glucose metabolism. Overexpression of active BACE1, but not a protease-dead mutant BACE1, protein in SH-SY5Y cells reduced glucose oxidation and the basal oxygen consumption rate, which was associated with a compensatory increase in glycolysis. Increased BACE1 activity had no effect on the mitochondrial electron transfer process but was found to diminish substrate delivery to the mitochondria by inhibition of key mitochondrial decarboxylation reaction enzymes. This BACE1 activity-dependent deficit in glucose oxidation was alleviated by the presence of beta hydroxybutyrate or α-lipoic acid. Consequently our data indicate that raised cellular BACE1 activity drives reduced glucose oxidation in a human neuronal cell line through impairments in the activity of specific tricarboxylic acid cycle enzymes. Because this bioenergetic deficit is recoverable by neutraceutical compounds we suggest that such agents, perhaps in conjunction with BACE1 inhibitors, may be an effective therapeutic strategy in the early-stage management or treatment of AD

Nondestructive assessment of freshness in packaged sliced chicken breasts using SW-NIR spectroscopy

A technique was developed to predict the freshness of packaged sliced chicken breast employing a nondestructive visible and short-wavelength near-infrared (SW-NIR) spectroscopy method. Spectra were recorded at 0, 7 and 14days using a camera, spectral filter (400-1000nm) and a halogen flood lighting system which were developed and calibrated for the purpose. Physicochemical, biochemical and microbiological properties such as moisture (x w), water activity (a w), pH, total volatile basic nitrogen (TVB-N), ATP breakdown compounds (K 1 values) and mesophilic bacteria (cfu g -1) were determined to predict freshness degradation. The spectra obtained were related to the storage time of the samples. The best wavelengths for modeling freshness were 413, 426, 449, 460, 473, 480, 499, 638, 942, 946, 967, 970 and 982nm. A linear correlation was found between the visible and SW-NIR spectroscopy and parameters such as microbiological counts, K 1 and T-VBN indexes. © 2010 Elsevier Ltd.We wish to thank the Polytechnic University of Valencia and Generalitat Valenciana for the financial support they provided through the PAID-06-08-3251 and GVPRE/2008/170 Projects, respectively.Grau Meló, R.; Sánchez Salmerón, AJ.; Girón Hernández, LJ.; Ivorra Martínez, E.; Fuentes López, A.; Barat Baviera, JM. (2011). Nondestructive assessment of freshness in packaged sliced chicken breasts using SW-NIR spectroscopy. Food Research International. 44:331-337. doi:10.1016/j.foodres.2010.10.011S3313374

Uracil DNA N-Glycosylase Promotes Assembly of Human Centromere Protein A

Uracil is removed from DNA by the conserved enzyme Uracil DNA N-glycosylase (UNG). Previously, we observed that inhibiting UNG in Xenopus egg extracts blocked assembly of CENP-A, a histone H3 variant. CENP-A is an essential protein in all species, since it is required for chromosome segregation during mitosis. Thus, the implication of UNG in CENP-A assembly implies that UNG would also be essential, but UNG mutants lacking catalytic activity are viable in all species. In this paper, we present evidence that UNG2 colocalizes with CENP-A and H2AX phosphorylation at centromeres in normally cycling cells. Reduction of UNG2 in human cells blocks CENP-A assembly, and results in reduced cell proliferation, associated with increased frequencies of mitotic abnormalities and rapid cell death. Overexpression of UNG2 induces high levels of CENP-A assembly in human cells. Using a multiphoton laser approach, we demonstrate that UNG2 is rapidly recruited to sites of DNA damage. Taken together, our data are consistent with a model in which the N-terminus of UNG2 interacts with the active site of the enzyme and with chromatin

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results