Interplay of Mre11 Nuclease with Dna2 plus Sgs1 in Rad51-Dependent Recombinational Repair

The Mre11/Rad50/Xrs2 complex initiates IR repair by binding to the end of a double-strand break, resulting in 5′ to 3′ exonuclease degradation creating a single-stranded 3′ overhang competent for strand invasion into the unbroken chromosome. The nuclease(s) involved are not well understood. Mre11 encodes a nuclease, but it has 3′ to 5′, rather than 5′ to 3′ activity. Furthermore, mutations that inactivate only the nuclease activity of Mre11 but not its other repair functions, mre11-D56N and mre11-H125N, are resistant to IR. This suggests that another nuclease can catalyze 5′ to 3′ degradation. One candidate nuclease that has not been tested to date because it is encoded by an essential gene is the Dna2 helicase/nuclease. We recently reported the ability to suppress the lethality of a dna2Δ with a pif1Δ. The dna2Δ pif1Δ mutant is IR-resistant. We have determined that dna2Δ pif1Δ mre11-D56N and dna2Δ pif1Δ mre11-H125N strains are equally as sensitive to IR as mre11Δ strains, suggesting that in the absence of Dna2, Mre11 nuclease carries out repair. The dna2Δ pif1Δ mre11-D56N triple mutant is complemented by plasmids expressing Mre11, Dna2 or dna2K1080E, a mutant with defective helicase and functional nuclease, demonstrating that the nuclease of Dna2 compensates for the absence of Mre11 nuclease in IR repair, presumably in 5′ to 3′ degradation at DSB ends. We further show that sgs1Δ mre11-H125N, but not sgs1Δ, is very sensitive to IR, implicating the Sgs1 helicase in the Dna2-mediated pathway

On the Solution of Convection-Diffusion Boundary Value Problems Using Equidistributed Grids

The effect of using grid adaptation on the numerical solution of model convection-diffusion equations with a conservation form is studied. The grid adaptation technique studied is based on moving a fixed number of mesh points to equidistribute a generalization of the arc-length of the solution. In particular, a parameter-dependent monitor function is introduced which incorporates fixed meshes, approximate arc-length equidistribution, and equidistribution of the absolute value of the solution, in a single framework. Thus the resulting numerical method is a coupled nonlinear system of equations for the mesh spacings and the nodal values. A class of singularly perturbed problems, including Burgers's equation in the limit of small viscosity, is studied. Singular perturbation and bifurcation techniques are used to analyze the solution of the discretized equations, and numerical results are compared with the results from the analysis. Computation of the bifurcation diagram of the system is performed numerically using a continuation method and the results are used to illustrate the theory. It is shown that equidistribution does not remove spurious solutions present on a fixed mesh and that, furthermore, the spurious solutions can be stable for an appropriate moving mesh method

Fast three dimensional r-adaptive mesh redistribution

This paper describes a fast and reliable method for redistributing a computational mesh in three dimensions which can generate a complex three dimensional mesh without any problems due to mesh tangling. The method relies on a three dimensional implementation of the parabolic Monge–Ampère (PMA) technique, for finding an optimally transported mesh. The method for implementing PMA is described in detail and applied to both static and dynamic mesh redistribution problems, studying both the convergence and the computational cost of the algorithm. The algorithm is applied to a series of problems of increasing complexity. In particular very regular meshes are generated to resolve real meteorological features (derived from a weather forecasting model covering the UK area) in grids with over 2×107 degrees of freedom. The PMA method computes these grids in times commensurate with those required for operational weather forecasting

A heat transfer with a source: the complete set of invariant difference schemes

In this letter we present the set of invariant difference equations and meshes which preserve the Lie group symmetries of the equation u_{t}=(K(u)u_{x})_{x}+Q(u). All special cases of K(u) and Q(u) that extend the symmetry group admitted by the differential equation are considered. This paper completes the paper [J. Phys. A: Math. Gen. 30, no. 23 (1997) 8139-8155], where a few invariant models for heat transfer equations were presented.Comment: arxiv version is already officia

Use of Clumped-Isotope Thermometry To Constrain the Crystallization Temperature of Diagenetic Calcite

We describe an approach to estimating the crystallization temperatures of diagenetic calcites using clumped-isotope thermometry, a paleothermometer based on the ^(13)C–^(18)O-bond enrichment in carbonates. Application of this thermometer to calcified gastropod shells and calcite cements in an early Eocene limestone from the Colorado Plateau reveals a record of calcite precipitation and replacement at temperatures varying from 14 to 123°C. The early Eocene host sediments were never deeply buried, but they experienced a significant thermal pulse associated with the emplacement of a late Miocene basalt flow. The combination of independent constraints on thermal history with clumped-isotope thermometry, petrographic (including cathodoluminescence) observations, and oxygen isotopic data provides an improved basis for estimation of the temperature and timing of diagenetic events and fluid sources. The petrography and calcite δ^(18)O values, taken alone, suggest that the aragonite-to-calcite transformation of gastropod shell material occurred simultaneously with early formation of cements and lithification of the matrix in the same sample. However, addition of clumped-isotope thermometry demonstrates that this phase transformation of shell material occurred at temperatures of 94–123°C in a highly rock-buffered microenvironment (i.e., with the isotopic composition of fluid buffered by coexisting carbonate), millions of years after lithification of the matrix and formation of initial low-temperature (14–19°C) calcite cements within shell body cavities. Clumped-isotope temperatures in excess of reasonable Earth-surface conditions recorded by later-formed cements demand that cement growth occurred in association with the lava emplacement. Our results illustrate the potential for clumped-isotope thermometry to constrain conditions of diagenesis and guide interpretations that would not be possible on the basis of conventional stable-isotopic and petrographic data alone, and demonstrate how petrographic characterization of clumped-isotope thermometry samples can benefit paleoclimate studies

Aesthetics and literature : a problematic relation?

The paper argues that there is a proper place for literature within aesthetics but that care must be taken in identifying just what the relation is. In characterising aesthetic pleasure associated with literature it is all too easy to fall into reductive accounts, for example, of literature as merely "fine writing". Belleslettrist or formalistic accounts of literature are rejected, as are two other kinds of reduction, to pure meaning properties and to a kind of narrative realism. The idea is developed that literature-both poetry and prose fiction-invites its own distinctive kind of aesthetic appreciation which far from being at odds with critical practice, in fact chimes well with it

Singular and regular solutions of a non-linear parabolic system

We study a dissipative nonlinear equation modelling certain features of the Navier-Stokes equations. We prove that the evolution of radially symmetric compactly supported initial data does not lead to singularities in dimensions $n\leq 4$. For dimensions $n>4$ we present strong numerical evidence supporting existence of blow-up solutions. Moreover, using the same techniques we numerically confirm a conjecture of Lepin regarding existence of self-similar singular solutions to a semi-linear heat equation.Comment: 16 page

Long-term effects of ocean temperature rise on the deep sea

The Comprehensive Nuclear Test Ban Treaty Organization operates a global International Monitoring System, with 11 hydroacoustic stations around the globe located in the deep-sea sound channel. Continuous measurements provide up to 20 years of sound pressures at frequencies of up to 100 Hz, depending on when each station was installed. These relatively long timescales allow investigating the effects of climate over that period. This presentation will show data from CTBT stations H11 (Wake Island, in the North Pacific) and H01 (Cape Leeuwin, in the Indian Ocean). Multiscale aggregations of 1-minute power spectral density (PSD) levels and sound energy measures over several days are used to show their correlation with sea surface temperature (SST) measurements at different timescales. In particular, we can detect seasonal changes in the SST as well as longer term climatic variations. The spectral analysis also shows periodic features in PSD levels around 15 to 31 Hz. The Intergovernmental Panel on Climate Change concluded in 2014 that the increase in temperature has mostly affected the upper (0 - 700 m) ocean while assessing the impact of climate change in the deep sea (> 1000 m) is a challenging task due to the difficulty of gathering long-term comprehensive data. This link between sound pressure levels at 1-km depths and the surface temperature of the ocean is particularly important. Sound is an Essential Ocean Variable, and a key factor to better understand the Earth’s climate system

PIM-1 membranes containing POSS - graphene oxide for CO2 separation

PIM-1 mixed matrix membranes (MMMs) were fabricated with polyhedral oligomeric silsesquioxane (POSS) and graphene oxide (GO) functionalized with POSS (GO-POSS), and tested for CO2/N2 (single gas) and CO2/CH4 (1:1, v:v gas mixture). The CO2 permeability of the best performing fresh MMM (containing 0.05 wt% GO-POSS) was ~ 12000 Barrer, which is 69% higher than that of the neat PIM-1 membrane, with about the same selectivity (CO2/CH4 selectivity ~ 12 and CO2/N2 selectivity ~ 20). In both cases, the gas separation data surpass the 2008 Robeson upper bound. In addition to the initial CO2 permeability enhancement, the use of GO-POSS is an efficient strategy to slow down physical aging. The MMM at a filler loading of 0.75 wt% showed less than half of the reduction in CO2 permeability than the neat PIM-1 membrane 160 days after preparation (26% for the MMM vs 58% for the purely polymeric one). © 2022 The Author(s

DNA end resection by Dna2–Sgs1–RPA and its stimulation by Top3–Rmi1 and Mre11–Rad50–Xrs2

The repair of DNA double-strand breaks (DSBs) by homologous recombination requires processing of broken ends. For repair to start, the DSB must first be resected to generate a 3′-single-stranded DNA (ssDNA) overhang, which becomes a substrate for the DNA strand exchange protein, Rad51 (ref. 1). Genetic studies have implicated a multitude of proteins in the process, including helicases, nucleases and topoisomerases. Here we biochemically reconstitute elements of the resection process and reveal that it requires the nuclease Dna2, the RecQ-family helicase Sgs1 and the ssDNA-binding protein replication protein-A (RPA). We establish that Dna2, Sgs1 and RPA constitute a minimal protein complex capable of DNA resection in vitro. Sgs1 helicase unwinds the DNA to produce an intermediate that is digested by Dna2, and RPA stimulates DNA unwinding by Sgs1 in a species-specific manner. Interestingly, RPA is also required both to direct Dna2 nucleolytic activity to the 5′-terminated strand of the DNA break and to inhibit 3′ to 5′ degradation by Dna2, actions that generate and protect the 3′-ssDNA overhang, respectively. In addition to this core machinery, we establish that both the topoisomerase 3 (Top3) and Rmi1 complex and the Mre11–Rad50–Xrs2 complex (MRX) have important roles as stimulatory components. Stimulation of end resection by the Top3–Rmi1 heterodimer and the MRX proteins is by complex formation with Sgs1 (refs 5, 6), which unexpectedly stimulates DNA unwinding. We suggest that Top3–Rmi1 and MRX are important for recruitment of the Sgs1–Dna2 complex to DSBs. Our experiments provide a mechanistic framework for understanding the initial steps of recombinational DNA repair in eukaryotes