336 research outputs found
Development of a new application of the comet assay to assess levels of O6-methylguanine in genomic DNA (CoMeth)
O6-methylguanine (O6meG) is one of the most premutagenic, precarcinogenic, and precytotoxic DNA lesions formed by alkylating agents. Repair of this DNA damage is achieved by the protein MGMT, which transfers the alkyl groups from the O6 position of guanine to a cysteine residue in its active center. Because O6meG repair by MGMT is a stoichiometric reaction that irreversibly inactivates MGMT, which is subsequently degraded, the repair capacity of O6meG lesions is dependent on existing active MGMT molecules. In the absence of active MGMT, O6meG is not repaired, and during replication, O6meG:T mispairs are formed. The MMR system recognizes these mispairs and introduces a gap into the strand. If O6meG remains in one of the template strands the futile MMR repair process will be repeated, generating more strand breaks (SBs). The toxicity of O6meG is, therefore, dependent on MMR and DNA SB induction of cell death. MGMT, on the other hand, protects against O6meG toxicity by removing the methyl residue from the guanine. Although removal of O6meG makes MGMT an important anticarcinogenic mechanism of DNA repair, its activity significantly decreases the efficacy of cancer chemotherapeutic drugs that aim at achieving cell death through the action of the MMR system on unrepaired O6meG lesions. Here, we report on a modification of the comet assay (CoMeth) that allows the qualitative assessment of O6meG lesions after their conversion to strand breaks in proliferating MMR-proficient cells after MGMT inhibition. This functional assay allows the testing of compounds with effects on O6meG levels, as well as on MGMT or MMR activity, in a proliferating cell system. The expression of MGMT and MMR genes is often altered by promoter methylation, and new epigenetically active compounds are being designed to increase chemotherapeutic efficacy. The CoMeth assay allows the testing of compounds with effects on O6meG, MGMT, or MMR activity. This proliferating cell system complements other methodologies that look at effects on these parameters individually through analytical chemistry or in vitro assays with recombinant proteins.We thank the COST Action TD0905 âEpigenetics: From Bench to Bedsideâ for financial support. A.A. Ramos and D. Pedro are supported by the Foundation for Science and Technology, Portugal, Grant SFRH/BD/35672/2007 and SFRH/BD/64817/2009, respectively.
The work was supported by FCT research grant PEst-C/BIA/UI4050/2011, which is co-funded by the program COMPETE from QREN with co-participation from the European Community fund FEDER
Recommended from our members
Synthesis and Properties of a Compositional Series of MIL-53(Al) Metal-Organic Framework Crystal-Glass Composites
Metal-organic framework crystal-glass composites (MOF-CGCs) are materials in which a crystalline MOF is dispersed within a MOF glass. In this work, we explore the room temperature stabilization of the open-pore form of MIL-53(Al), usually observed at high-temperature, which occurs upon encapsulation within a ZIF-62(Zn) MOF glass matrix. A series of MOF-CGCs containing different loadings of MIL-53(Al) were synthesized and characterized using X-ray diffraction and nuclear magnetic resonance spectroscopy. An upper limit of MIL-53(Al) that can be stabilized in the composite was determined for the first time. The nanostructure of the composites was probed using pair distribution function analysis and scanning transmission electron microscopy. Notably, the distribution and integrity of the crystalline compo-nent in a sample series was determined, and these findings related to the MOF-CGC gas adsorption capacity in order to identify the optimal loading necessary for maximum CO2 sorption capacity.TDB would like to thank both the Royal Society for a University Research Fellowship (UF150021) and the Royal Society for a Research Grant (RG94426). CWA would like to thank the Royal Society for a PhD studentship (RG160498), and the Commonwealth Scientific and Industrial Research Council for additional support (C2017/3108). Both JH and TDB gratefully acknowledge the EPSRC (EP/R015481/1). AFS acknowledges EPSRC for a studentship award under the Doctoral Training Programme. AMB acknowledges the Royal Society for funding (RGF\EA\180092), as well as the Cambridge Trust for a Vice Chancellorâs Award (304253100). We extend our gratitude to Diamond Light Source, Rutherford Appleton Laboratory, UK, for access to Beamline I15-1 (EE20038-1) and access and support in the use of the electron Physical Science Imaging Centre (EM20195). SMC acknowledges the Henslow Research Fellowship at Girton College, Cambridge. PAM thanks the EPSRC for financial support under grant number EP/R025517/1
Wave 2 strains of atypical Vibrio cholerae El Tor caused the 2009-2011 cholera outbreak in Papua New Guinea
Vibrio cholerae is the causative agent of cholera, a globally important human disease for at least 200âyears. In 2009-2011, the first recorded cholera outbreak in Papua New Guinea (PNG) occurred. We conducted genetic and phenotypic characterization of 21 isolates of V. cholerae, with whole-genome sequencing conducted on 2 representative isolates. The PNG outbreak was caused by an atypical El Tor strain harbouring a tandem repeat of the CTX prophage on chromosome II. Whole-genome sequence data, prophage structural analysis and the absence of the SXT integrative conjugative element was indicative that the PNG isolates were most closely related to strains previously isolated in South-East and East Asia with affiliations to global wave 2 strains. This finding suggests that the cholera outbreak in PNG was caused by an exotic (non-endemic) strain of V. cholerae that originated in South-East Asia
Wave 2 strains of atypical Vibrio cholerae El Tor caused the 2009-2011 cholera outbreak in Papua New Guinea.
Vibrio cholerae is the causative agent of cholera, a globally important human disease for at least 200âyears. In 2009-2011, the first recorded cholera outbreak in Papua New Guinea (PNG) occurred. We conducted genetic and phenotypic characterization of 21 isolates of V. cholerae, with whole-genome sequencing conducted on 2 representative isolates. The PNG outbreak was caused by an atypical El Tor strain harbouring a tandem repeat of the CTX prophage on chromosome II. Whole-genome sequence data, prophage structural analysis and the absence of the SXT integrative conjugative element was indicative that the PNG isolates were most closely related to strains previously isolated in South-East and East Asia with affiliations to global wave 2 strains. This finding suggests that the cholera outbreak in PNG was caused by an exotic (non-endemic) strain of V. cholerae that originated in South-East Asia
The Astropy Problem
The Astropy Project (http://astropy.org) is, in its own words, "a community
effort to develop a single core package for Astronomy in Python and foster
interoperability between Python astronomy packages." For five years this
project has been managed, written, and operated as a grassroots,
self-organized, almost entirely volunteer effort while the software is used by
the majority of the astronomical community. Despite this, the project has
always been and remains to this day effectively unfunded. Further, contributors
receive little or no formal recognition for creating and supporting what is now
critical software. This paper explores the problem in detail, outlines possible
solutions to correct this, and presents a few suggestions on how to address the
sustainability of general purpose astronomical software
Measurement of Ï c1 and Ï c2 production with sâ = 7 TeV pp collisions at ATLAS
The prompt and non-prompt production cross-sections for the Ï c1 and Ï c2 charmonium states are measured in pp collisions at sâ = 7 TeV with the ATLAS detector at the LHC using 4.5 fbâ1 of integrated luminosity. The Ï c states are reconstructed through the radiative decay Ï c â J/ÏÎł (with J/Ï â ÎŒ + ÎŒ â) where photons are reconstructed from Îł â e + e â conversions. The production rate of the Ï c2 state relative to the Ï c1 state is measured for prompt and non-prompt Ï c as a function of J/Ï transverse momentum. The prompt Ï c cross-sections are combined with existing measurements of prompt J/Ï production to derive the fraction of prompt J/Ï produced in feed-down from Ï c decays. The fractions of Ï c1 and Ï c2 produced in b-hadron decays are also measured
Hundreds of variants clustered in genomic loci and biological pathways affect human height
Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (Pâ<â0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
Effects of Impact and Target Parameters on the Results of a Kinetic Impactor: Predictions for the Double Asteroid Redirection Test (DART) Mission
The Double Asteroid Redirection Test (DART) spacecraft will impact into the asteroid Dimorphos on 2022 September 26 as a test of the kinetic impactor technique for planetary defense. The efficiency of the deflection following a kinetic impactor can be represented using the momentum enhancement factor, ÎČ, which is dependent on factors such as impact geometry and the specific target material properties. Currently, very little is known about Dimorphos and its material properties, which introduces uncertainty in the results of the deflection efficiency observables, including crater formation, ejecta distribution, and ÎČ. The DART Impact Modeling Working Group (IWG) is responsible for using impact simulations to better understand the results of the DART impact. Pre-impact simulation studies also provide considerable insight into how different properties and impact scenarios affect momentum enhancement following a kinetic impact. This insight provides a basis for predicting the effects of the DART impact and the first understanding of how to interpret results following the encounter. Following the DART impact, the knowledge gained from these studies will inform the initial simulations that will recreate the impact conditions, including providing estimates for potential material properties of Dimorphos and ÎČ resulting from DARTâs impact. This paper summarizes, at a high level, what has been learned from the IWG simulations and experiments in preparation for the DART impact. While unknown, estimates for reasonable potential material properties of Dimorphos provide predictions for ÎČ of 1â5, depending on end-member cases in the strength regime
Proton-Nucleus Collisions at the LHC: Scientific Opportunities and Requirements
Proton-nucleus (p+A) collisions have long been recognized as a crucial
component of the physics programme with nuclear beams at high energies, in
particular for their reference role to interpret and understand nucleus-nucleus
data as well as for their potential to elucidate the partonic structure of
matter at low parton fractional momenta (small-x). Here, we summarize the main
motivations that make a proton-nucleus run a decisive ingredient for a
successful heavy-ion programme at the Large Hadron Collider (LHC) and we
present unique scientific opportunities arising from these collisions. We also
review the status of ongoing discussions about operation plans for the p+A mode
at the LHC.Comment: 33 pages, 15 Figure
- âŠ