Oxidative DNA damage bypass in Arabidopsis thaliana requires DNA polymerase λ and proliferating cell nuclear antigen 2

The oxidized base 7,8-oxoguanine (8-oxo-G) is the most common DNA lesion generated by reactive oxygen species. This lesion is highly mutagenic due to the frequent misincorporation of A opposite 8-oxo-G during DNA replication. In mammalian cells, the DNA polymerase (pol) family X enzyme DNA pol l catalyzes the correct incorporation of C opposite 8-oxo-G, together with the auxiliary factor proliferating cell nuclear antigen (PCNA). Here, we show that Arabidopsis thaliana DNA pol l, the only member of the X family in plants, is as efficient in performing error-free translesion synthesis past 8-oxo-G as its mammalian homolog. Arabidopsis, in contrast with animal cells, possesses two genes for PCNA. Using in vitro and in vivo approaches, we observed that PCNA2, but not PCNA1, physically interacts with DNA pol l, enhancing its fidelity and efficiency in translesion synthesis. The levels of DNA pol l in transgenic plantlets characterized by overexpression or silencing of Arabidopsis POLL correlate with the ability of cell extracts to perform error-free translesion synthesis. The important role of DNA pol l is corroborated by the observation that the promoter of POLL is activated by UV and that both overexpressing and silenced plants show altered growth phenotypes

The structure of optimal parameters for image restoration problems

We study the qualitative properties of optimal regularisation parameters in variational models for image restoration. The parameters are solutions of bilevel optimisation problems with the image restoration problem as constraint. A general type of regulariser is considered, which encompasses total variation (TV), total generalized variation (TGV) and infimal-convolution total variation (ICTV). We prove that under certain conditions on the given data optimal parameters derived by bilevel optimisation problems exist. A crucial point in the existence proof turns out to be the boundedness of the optimal parameters away from 0 which we prove in this paper. The analysis is done on the original -- in image restoration typically non-smooth variational problem -- as well as on a smoothed approximation set in Hilbert space which is the one considered in numerical computations. For the smoothed bilevel problem we also prove that it Γ converges to the original problem as the smoothing vanishes. All analysis is done in function spaces rather than on the discretised learning problem.In Cambridge, this project has been supported by King Abdullah University of Science and Technology (KAUST) Award No. KUK-I1-007-43, EPSRC grants Nr. EP/J009539/1 “Sparse & Higher-order Image Restoration”, and Nr. EP/M00483X/1 “Efficient computational tools for inverse imaging problems”. In Quito, the project has been supported by the Escuela Politécnica Nacional de Quito under award PIS 12-14 and the MATHAmSud project SOCDE “Sparse Optimal Control of Differential Equations”. When in Quito, T. Valkonen was moreover supported by a Prometeo scholarship of the Senescyt (Ecuadorian Ministry of Science, Technology, Education, and Innovation).This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.jmaa.2015.09.02

A combined first and second order variational approach for image reconstruction

In this paper we study a variational problem in the space of functions of bounded Hessian. Our model constitutes a straightforward higher-order extension of the well known ROF functional (total variation minimisation) to which we add a non-smooth second order regulariser. It combines convex functions of the total variation and the total variation of the first derivatives. In what follows, we prove existence and uniqueness of minimisers of the combined model and present the numerical solution of the corresponding discretised problem by employing the split Bregman method. The paper is furnished with applications of our model to image denoising, deblurring as well as image inpainting. The obtained numerical results are compared with results obtained from total generalised variation (TGV), infimal convolution and Euler's elastica, three other state of the art higher-order models. The numerical discussion confirms that the proposed higher-order model competes with models of its kind in avoiding the creation of undesirable artifacts and blocky-like structures in the reconstructed images -- a known disadvantage of the ROF model -- while being simple and efficiently numerically solvable.Comment: 34 pages, 89 figure

Role of the Polymerase ϵ sub-unit DPB2 in DNA replication, cell cycle regulation and DNA damage response in Arabidopsis

Faithful DNA replication maintains genome stability in dividing cells and from one generation to the next. This is particularly important in plants because the whole plant body and reproductive cells originate from meristematic cells that retain their proliferative capacity throughout the life cycle of the organism. DNA replication involves large sets of proteins whose activity is strictly regulated, and is tightly linked to the DNA damage response to detect and respond to replication errors or defects. Central to this interconnection is the replicative polymerase DNA Polymerase ϵ (Pol ϵ) which participates in DNA replication per se, as well as replication stress response in animals and in yeast. Surprisingly, its function has to date been little explored in plants, and notably its relationship with DNA Damage Response (DDR) has not been investigated. Here, we have studied the role of the largest regulatory sub-unit of Arabidopsis DNA Pol ϵ DPB2, using an over-expression strategy. We demonstrate that excess accumulation of the protein impairs DNA replication and causes endogenous DNA stress. Furthermore, we show that Pol ϵ dysfunction has contrasting outcomes in vegetative and reproductive cells and leads to the activation of distinct DDR pathways in the two cell types. © 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research

Finite Element Methods for Elliptic Distributed Optimal Control Problems with Pointwise State Constraints

Finite element methods for a model elliptic distributed optimal control problem with pointwise state constraints are considered from the perspective of fourth order boundary value problems

A review of the fossil record of turtles of the clade Pan-Carettochelys

Turtles of the total clade Pan-Carettochelys have a relatively poor fossil record that extends from the Early Cretaceous. The clade is only found in Asia during the Cretaceous, but spreads to Europe and North America during the Eocene. Neogene finds are restricted to Europe, Africa and Australia, whereas the only surviving species, Carettochelys insculpta, lives in New Guinea and the Northern Territories of Australia. The ecology of fossil pan-carettochelyids appears similar to that of the extant C. insculpta, although more primitive representatives were likely less adapted to brackish water. Current phylogenies only recognize three internested clades: Pan- Carettochelys, Carettochelyidae and Carettochelyinae. A taxonomic review of the group concludes that of 25 named taxa, 13 are nomina valida, 7 are nomina invalida, 3 are nomina dubia, and 2 are nomina nuda