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  • Klionsky, Daniel J., et al. (författare)
  • Guidelines for the use and interpretation of assays for monitoring autophagy
  • 2012
  • Ingår i: Autophagy. - : Landes Bioscience. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
  • Forskningsöversikt (refereegranskat)abstract
    • In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
  • Bentley, Amy R., et al. (författare)
  • Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids
  • 2019
  • Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:4, s. 636-
  • Tidskriftsartikel (refereegranskat)abstract
    • The concentrations of high- and low-density-lipoprotein cholesterol and triglycerides are influenced by smoking, but it is unknown whether genetic associations with lipids may be modified by smoking. We conducted a multi-ancestry genome-wide gene-smoking interaction study in 133,805 individuals with follow-up in an additional 253,467 individuals. Combined meta-analyses identified 13 new loci associated with lipids, some of which were detected only because association differed by smoking status. Additionally, we demonstrate the importance of including diverse populations, particularly in studies of interactions with lifestyle factors, where genomic and lifestyle differences by ancestry may contribute to novel findings.
  • de Vries, Paul S., et al. (författare)
  • Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions
  • 2019
  • Ingår i: American Journal of Epidemiology. - : Oxford University Press. - 0002-9262 .- 1476-6256. ; 188:6, s. 1033-1054
  • Tidskriftsartikel (refereegranskat)abstract
    • A person's lipid profile is influenced by genetic variants and alcohol consumption, but the contribution of interactions between these exposures has not been studied. We therefore incorporated gene-alcohol interactions into a multiancestry genome-wide association study of levels of high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. We included 45 studies in stage 1 (genome-wide discovery) and 66 studies in stage 2 (focused follow-up), for a total of 394,584 individuals from 5 ancestry groups. Analyses covered the period July 2014-November 2017. Genetic main effects and interaction effects were jointly assessed by means of a 2-degrees-of-freedom (df) test, and a 1-df test was used to assess the interaction effects alone. Variants at 495 loci were at least suggestively associated (P < 1 x 10(-6)) with lipid levels in stage 1 and were evaluated in stage 2, followed by combined analyses of stage 1 and stage 2. In the combined analysis of stages 1 and 2, a total of 147 independent loci were associated with lipid levels at P < 5 x 10(-8) using 2-df tests, of which 18 were novel. No genome-wide-significant associations were found testing the interaction effect alone. The novel loci included several genes (proprotein convertase subtilisin/kexin type 5 (PCSK5), vascular endothelial growth factor B (VEGFB), and apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1) complementation factor (A1CF)) that have a putative role in lipid metabolism on the basis of existing evidence from cellular and experimental models.
  • Feitosa, Mary F., et al. (författare)
  • Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries
  • 2018
  • Ingår i: PLoS ONE. - : Public library science. - 1932-6203. ; 13:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Heavy alcohol consumption is an established risk factor for hypertension; the mechanism by which alcohol consumption impact blood pressure (BP) regulation remains unknown. We hypothesized that a genome-wide association study accounting for gene-alcohol consumption interaction for BP might identify additional BP loci and contribute to the understanding of alcohol-related BP regulation. We conducted a large two-stage investigation incorporating joint testing of main genetic effects and single nucleotide variant (SNV)-alcohol consumption interactions. In Stage 1, genome-wide discovery meta-analyses in approximate to 131 K individuals across several ancestry groups yielded 3,514 SNVs (245 loci) with suggestive evidence of association (P <1.0 x 10(-5)). In Stage 2, these SNVs were tested for independent external replication in individuals across multiple ancestries. We identified and replicated (at Bonferroni correction threshold) five novel BP loci (380 SNVs in 21 genes) and 49 previously reported BP loci (2,159 SNVs in 109 genes) in European ancestry, and in multi-ancestry meta-analyses (P < 5.0 x 10(-8)). For African ancestry samples, we detected 18 potentially novel BP loci (P< 5.0 x 10(-8)) in Stage 1 that warrant further replication. Additionally, correlated meta-analysis identified eight novel BP loci (11 genes). Several genes in these loci (e.g., PINX1, GATA4, BLK, FTO and GABBR2 have been previously reported to be associated with alcohol consumption. These findings provide insights into the role of alcohol consumption in the genetic architecture of hypertension.
  • Aad, G., et al. (författare)
  • Charged-particle multiplicities in pp interactions at root s=900 GeV measured with the ATLAS detector at the LHC ATLAS Collaboration
  • 2010
  • Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier. - 0370-2693 .- 1873-2445. ; 688:1, s. 21-42
  • Tidskriftsartikel (refereegranskat)abstract
    • The first measurements from proton-proton collisions recorded with the ATLAS detector at the LHC are presented. Data were collected in December 2009 using a minimum-bias trigger during collisions at a centre-of-mass energy of 900 GeV. The charged-particle multiplicity, its dependence on transverse momentum and pseudorapidity, and the relationship between mean transverse momentum and charged-particle multiplicity are measured for events with at least one charged particle in the kinematic range vertical bar eta vertical bar < 2.5 and p(T) > 500 MeV. The measurements are compared to Monte Carlo models of proton-proton collisions and to results from other experiments at the same centre-of-mass energy. The charged-particle multiplicity per event and unit of pseudorapidity eta = 0 is measured to be 1.333 +/- 0.003(stat.) +/- 0.040(syst.), which is 5-15% higher than the Monte Carlo models predict. 2010 Published by Elsevier B.V.
  • Aad, G., et al. (författare)
  • Drift Time Measurement in the ATLAS Liquid Argon Electromagnetic Calorimeter using Cosmic Muons
  • 2010
  • Ingår i: European Physical Journal C. Particles and Fields. - : Springer. - 1434-6044 .- 1434-6052. ; 70:3, s. 755-785
  • Tidskriftsartikel (refereegranskat)abstract
    • The ionization signals in the liquid argon of the ATLAS electromagnetic calorimeter are studied in detail using cosmic muons. In particular, the drift time of the ionization electrons is measured and used to assess the intrinsic uniformity of the calorimeter gaps and estimate its impact on the constant term of the energy resolution. The drift times of electrons in the cells of the second layer of the calorimeter are uniform at the level of 1.3% in the barrel and 2.8% in the endcaps. This leads to an estimated contribution to the constant term of (0.29(-0.04)(+0.05))% in the barrel and (0.54(-0.04)(+0.06))% in the endcaps. The same data are used to measure the drift velocity of ionization electrons in liquid argon, which is found to be 4.61 +/- 0.07 mm/mu s at 88.5 K and 1 kV/mm.
  • Aad, G., et al. (författare)
  • Measurement of inclusive jet and dijet cross sections in proton-proton collisions at 7 TeV centre-of-mass energy with the ATLAS detector
  • 2011
  • Ingår i: European Physical Journal C. Particles and Fields. - : Springer. - 1434-6044 .- 1434-6052. ; 71:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Jet cross sections have been measured for the first time in proton-proton collisions at a centre-of-mass energy of 7 TeV using the ATLAS detector. The measurement uses an integrated luminosity of 17 nb(-1) recorded at the Large Hadron Collider. The anti-k(t) algorithm is used to identify jets, with two jet resolution parameters, R = 0.4 and 0.6. The dominant uncertainty comes from the jet energy scale, which is determined to within 7% for central jets above 60 GeV transverse momentum. Inclusive single-jet differential cross sections are presented as functions of jet transverse momentum and rapidity. Dijet cross sections are presented as functions of dijet mass and the angular variable chi. The results are compared to expectations based on next-to-leading-order QCD, which agree with the data, providing a validation of the theory in a new kinematic regime.
  • Aad, G., et al. (författare)
  • Measurement of the W -> lv and Z/gamma* -> ll production cross sections in proton-proton collisions at root s=7 TeV with the ATLAS detector
  • 2010
  • Ingår i: Journal of High Energy Physics. - : Springer. - 1029-8479 .- 1126-6708. ; :12
  • Tidskriftsartikel (refereegranskat)abstract
    • First measurements of the W -> lv and Z/gamma* -> ll (l = e; mu) production cross sections in proton-proton collisions at root s = 7 TeV are presented using data recorded by the ATLAS experiment at the LHC. The results are based on 2250 W -> lv and 179 Z/gamma* -> ll candidate events selected from a data set corresponding to an integrated luminosity of approximately 320 nb(-1). The measured total W and Z/gamma*-boson production cross sections times the respective leptonic branching ratios for the combined electron and muon channels are sigma(tot)(W) center dot BR(W -> lv) = 9.96 +/- 0.23(stat) +/- 0.50(syst) +/- 1.10(lumi) nb and sigma(tot)(Z) center dot BR(Z/gamma* -> ll) = 0.82 +/- 0.06 (stat) +/- 0.05 (syst) +/- 0.09 (lumi) nb (within the invariant mass window 66 < m(ll) < 116 GeV). The W/Z cross-section ratio is measured to be 11.7 +/- 0.9(stat) +/- 0.4(syst). In addition, measurements of the W+ and W- production cross sections and of the lepton charge asymmetry are reported. Theoretical predictions based on NNLO QCD calculations are found to agree with the measurements.
  • Aad, G., et al. (författare)
  • Performance of the ATLAS detector using first collision data
  • 2010
  • Ingår i: Journal of High Energy Physics. - : Springer. - 1029-8479 .- 1126-6708. ; 56:9
  • Tidskriftsartikel (refereegranskat)abstract
    • More than half a million minimum-bias events of LHC collision data were collected by the ATLAS experiment in December 2009 at centre-of-mass energies of 0.9 TeV and 2.36 TeV. This paper reports on studies of the initial performance of the ATLAS detector from these data. Comparisons between data and Monte Carlo predictions are shown for distributions of several track- and calorimeter-based quantities. The good performance of the ATLAS detector in these first data gives confidence for successful running at higher energies.
  • Aad, G., et al. (författare)
  • Readiness of the ATLAS liquid argon calorimeter for LHC collisions
  • 2010
  • Ingår i: European Physical Journal C. Particles and Fields. - : Springer. - 1434-6044 .- 1434-6052. ; 70:3, s. 723-753
  • Tidskriftsartikel (refereegranskat)abstract
    • The ATLAS liquid argon calorimeter has been operating continuously since August 2006. At this time, only part of the calorimeter was readout, but since the beginning of 2008, all calorimeter cells have been connected to the ATLAS readout system in preparation for LHC collisions. This paper gives an overview of the liquid argon calorimeter performance measured in situ with random triggers, calibration data, cosmic muons, and LHC beam splash events. Results on the detector operation, timing performance, electronics noise, and gain stability are presented. High energy deposits from radiative cosmic muons and beam splash events allow to check the intrinsic constant term of the energy resolution. The uniformity of the electromagnetic barrel calorimeter response along eta (averaged over phi) is measured at the percent level using minimum ionizing cosmic muons. Finally, studies of electromagnetic showers from radiative muons have been used to cross-check the Monte Carlo simulation. The performance results obtained using the ATLAS readout, data acquisition, and reconstruction software indicate that the liquid argon calorimeter is well-prepared for collisions at the dawn of the LHC era.
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