What Hinders Electron Transfer Dissociation (ETD) of DNA Cations?

Radical activation methods, such as electron transfer dissociation (ETD), produce structural information complementary to collision-induced dissociation. Herein, electron transfer dissociation of 3-fold protonated DNA hexamers was studied to gain insight into the fragmentation mechanism. The fragmentation patterns of a large set of DNA hexamers confirm cytosine as the primary target of electron transfer. The reported data reveal backbone cleavage by internal electron transfer from the nucleobase to the phosphate linker leading either to a?/w or d/z? ion pairs. This reaction pathway contrasts with previous findings on the dissociation processes after electron capture by DNA cations, suggesting multiple, parallel dissociation channels. However, all these channels merely result in partial fragmentation of the precursor ion because the charge-reduced DNA radical cations are quite stable. Two hypotheses are put forward to explain the low dissociation yield of DNA radical cations: it is either attributed to non-covalent interactions between complementary fragments or to the stabilization of the unpaired electron in stacked nucleobases. MS³ experiments suggest that the charge-reduced species is the intact oligonucleotide. Moreover, introducing abasic sites significantly increases the dissociation yield of DNA cations. Consequently, the stabilization of the unpaired electron by π–π-stacking provides an appropriate rationale for the high intensity of DNA radical cations after electron transfer.

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Flavin Adenine Dinucleotide and N5,N10‐Methenyltetrahydrofolate are the in planta Cofactors of Arabidopsis thaliana Cryptochrome 3

Members of the cryptochrome/photolyase family (CPF) of proteins utilize noncovalently bound light‐absorbing cofactors for their biological function. Usually, the identity of these cofactors is determined after expression in heterologous systems leaving the question unanswered whether these cofactors are identical to the indigenous ones. Here, cryptochrome 3 from Arabidopsis thaliana was expressed as a fusion with the green fluorescent protein in Arabidopsis plants. Besides the confirmation of the earlier report of its localization in chloroplasts, our data indicate that fractions of the fusion protein are present in the stroma and associated with thylakoids, respectively. Furthermore, it is shown that the fusion protein expressed in planta contains the same cofactors as the His₆‐tagged protein expressed in Escherichia coli, that is, flavin adenine dinucleotide and N⁵,N¹⁰‐methenyltetrahydrofolate. This demonstrates that the heterologously expressed cryptochrome 3, characterized in a number of previous studies, is a valid surrogate of the corresponding protein expressed in plants. To our knowledge, this is also a first conclusive analysis of cofactors bound to an Arabidopsis protein belonging to the CPF and purified from plant tissue.     

CsSc3F6[SeO3]2: A New Rare‐Earth Metal(III) Fluoride Oxoselenate(IV) With Sections Of The ReO3‐Type Structure

A new representative of rare‐earth metal(III) fluoride oxoselenates(IV) derivatized with alkali metals could be synthesized via solid‐state reactions. Colorless single crystals of CsSc₃F₆[SeO₃]₂ were obtained through the reaction of Sc₂O₃, ScF₃, and SeO₂ (molar ratio 1:1:3) with CsBr as reactant and fluxing agent. For this purpose, corundum crucibles embedded as liners into evacuated silica ampoules were applied as containers for these reactions at 700 °C for seven days. The new quintenary compound crystallizes in the trigonal space group P3m1 with a = 565.34(4) and c = 1069.87(8) pm (c/a = 1.892) for Z = 1. The crystal structure of CsSc₃F₆[SeO₃]₂ contains two crystallographically different Sc³⁺ cations. Each (Sc1)³⁺ is surrounded by six fluoride anions as octahedron, while the octahedra about (Sc2)³⁺ are formed by three fluoride anions and three oxygen atoms from three terminal [SeO₃]^2– anions. The [(Sc1)F₆]^3– octahedra link via common F^– vertices to six fac‐[(Sc2)F₃O₃]^6– octahedra forming ²_∞{[Sc₃F₆O₆]^9–} layers parallel to (001). These layers are separated by oxygen‐coordinated Cs⁺ cations (C.N. = 12), arranging for the charge compensation, while Se⁴⁺ cations within the layers surrounded by three oxygen atoms as ψ¹‐tetrahedral [SeO₃]^2– units complete the structure. EDX measurements confirmed the composition of the title compound and single‐crystal Raman studies showed the typical vibrational modes of isolated [SeO₃]^2– anions with ideal C_3v symmetry.     

Solving the robust two-stage capacitated facility location problem with uncertain transportation costs

In this study, we start from a multi-source variant of the two-stage capacitated facility location problem (TSCFLP) and propose a robust optimization model of the problem that involves the uncertainty of transportation costs. Since large dimensions of the robust TSCFLP could not be solved to optimality, we design a memetic algorithm (MA), which represents a combination of an evolutionary algorithm (EA) and a modified simulated annealing heuristic (SA) that uses a short-term memory of undesirable moves from previous iterations. A set of computational experiments is conducted to examine the impact of different protection levels on the deviation of the objective function value. We also investigate the impact of variations of transportation costs that may occur on both transhipment stages on the total cost for a fixed protection level. The obtained results may help in identifying a sustainable and efficient strategy for designing a two stage capacitated transportation network with uncertain transportation costs, and may be applicable in the design and management of similar transportation networks.     

Dijkstra meets Steiner: a fast exact goal-oriented Steiner tree algorithm

We present a new exact algorithm for the Steiner tree problem in edge-weighted graphs. Our algorithm improves the classical dynamic programming approach by Dreyfus and Wagner. We achieve a significantly better practical performance via pruning and future costs, a generalization of a well-known concept to speed up shortest path computations. Our algorithm matches the best known worst-case run time and has a fast, often superior, practical performance: on some large instances originating from VLSI design, previous best run times are improved upon by orders of magnitudes. We are also able to solve larger instances of the d-dimensional rectilinear Steiner tree problem for \(d \in \{3, 4, 5\}\), whose Hanan grids contain up to several millions of edges.     

Shortest Paths with Shortest Detours

This paper is concerned with a biobjective routing problem, called the shortest path with shortest detour problem, in which the length of a route is minimized as one criterion and, as second, the maximal length of a detour route if the chosen route is blocked is minimized. Furthermore, the relation to robust optimization is pointed out, and we present a new polynomial time algorithm, which computes a minimal complete set of efficient paths for the shortest path with shortest detour problem. Moreover, we show that the number of nondominated points is bounded by the number of arcs in the graph.     

A heuristic approach for dividing graphs into bi-connected components with a size constraint

In this paper we propose a new problem of finding the maximal bi-connected partitioning of a graph with a size constraint (MBCPG-SC). With the goal of finding approximate solutions for the MBCPG-SC, a heuristic method is developed based on the open ear decomposition of graphs. Its essential part is an adaptation of the breadth first search which makes it possible to grow bi-connected subgraphs. The proposed randomized algorithm consists of growing several subgraphs in parallel. The quality of solutions generated in this way is further improved using a local search which exploits neighboring relations between the subgraphs. In order to evaluate the performance of the method, an algorithm for generating pseudo-random unit disc graphs with known optimal solutions is created. Computational experiments have also been conducted on graphs representing electrical distribution systems for the real-world problem of dividing them into a system of fault tolerant interconnected microgrids. The experiments show that the proposed method frequently manages to find optimal solutions and has an average error of only a few percent to known optimal solutions. Further, it manages to find high quality approximate solutions for graphs having up to 10,000 nodes in reasonable time.     

Semi-Markov Modelling for Multi-State Systems

In this work we focus on multi state systems that we model by means of semi-Markov processes. The sojourn times are seen to be independent not identically distributed random variables and assumed to belong to a general class of distributions that includes several popular reliability distributions like the exponential, Weibull, and Pareto. We obtain maximum likelihood estimators of the parameters of interest and investigate their asymptotic properties. Plug-in type estimators are furnished for various quantities related to the system under study.     

An optimal reinsurance problem in the Cramér–Lundberg model

In this article we consider the surplus process of an insurance company within the Cramér–Lundberg framework with the intention of controlling its performance by means of dynamic reinsurance. Our aim is to find a general dynamic reinsurance strategy that maximizes the expected discounted surplus level integrated over time. Using analytical methods we identify the value function as a particular solution to the associated Hamilton–Jacobi–Bellman equation. This approach leads to an implementable numerical method for approximating the value function and optimal reinsurance strategy. Furthermore we give some examples illustrating the applicability of this method for proportional and XL-reinsurance treaties.