DNA Binding in High Salt: Analysing the Salt Dependence of Replication Protein A3 from the Halophile Haloferax volcanii

Halophilic archaea maintain intracellular salt concentrations close to saturation to survive in high-salt environments and their cellular processes have adapted to function under these conditions. Little is known regarding halophilic adaptation of the DNA processing machinery, particularly intriguing since protein-DNA interactions are classically salt sensitive. To investigate such adaptation, we characterised the DNA-binding capabilities of recombinant RPA3 from Haloferax volcanii (HvRPA3). Under physiological salt conditions (3M KCl), HvRPA3 is monomeric, binding 18 nucleotide ssDNA with nanomolar affinity, demonstrating that RPAs containing the single OB-fold/zinc finger architecture bind with broadly comparable affinity to two OB-fold/zinc finger RPAs. Reducing the salt concentration to 1M KCl induces dimerisation of the protein, which retains its ability to bind DNA. On circular ssDNA, two concentration-dependent binding modes are observed. Conventionally, increased salt concentration adversely affects DNA binding but HvRPA3 does not bind DNA in 0.2M KCl, although multimerisation may occlude the binding site. The single N-terminal OB-fold is competent to bind DNA in the absence of the C-terminal zinc finger, albeit with reduced affinity. This study represents the first quantitative characterisation of DNA binding in a halophilic protein in extreme salt concentrations

Performance of Hollow Load Process Challenge Devices (HLPCDs) for the determination of air removal and steam penetration in porous load steam sterilization processes: Part 1 – The evolution of HLPCDs in standards and a review of the current supporting published evidence

Steam sterilization Process Challenge Devices (PCDs) are devices which present a defined challenge to a sterilization process. In part one of a two part series the authors review the published literature covering studies evaluating the removal of air and penetration of steam into hollow tubular devices and then discuss the relevance of the material in support of the current custom and practice of utilising simple tubular PCDs (Hollow Load Process Challenge Devices HLPCDs) as a means of monitoring production loads for adequacy of air removal and steam penetration. This review places such data in the context of the evolution of HLPCDs in the standards for small and large porous load steam sterilizers. With regard to the apparent acceptance of the HLPCD in EN 867-5 into custom and practice for batch monitoring the literature suggests this may be misleading. The literature review concludes that there is an urgent need for an International Standard which describes how a HLPCD can be developed and tested against real medical devices in a range of sterilization processes representing current state of the art in full load conditions

Transient analysis techniques in performing impact and crash dynamic studies

Because of the emphasis being placed on crashworthiness as a design requirement, increasing demands are being made by various organizations to analyze a wide range of complex structures that must perform safely when subjected to severe impact loads, such as those generated in a crash event. The ultimate goal of crashworthiness design and analysis is to produce vehicles with the ability to reduce the dynamic forces experienced by the occupants to specified levels, while maintaining a survivable envelope around them during a specified crash event. DYCAST is a nonlinear structural dynamic finite element computer code that started from the plans systems of a finite element program for static nonlinear structural analysis. The essential features of DYCAST are outlined

Higher Dimensional Effective Operators for Direct Dark Matter Detection

We discuss higher dimensional effective operators describing interactions between fermionic dark matter and Standard Model particles. They are typically suppressed compared to the leading order effective operators, which can explain why no conclusive direct dark matter detection has been made so far. The ultraviolet completions of the effective operators, which we systematically study, require new particles. These particles can potentially have masses at the TeV scale and can therefore be phenomenologically interesting for LHC physics. We demonstrate that the lowest order options require Higgs-portal interactions generated by dimension six operators. We list all possible tree-level completions with extra fermions and scalars, and we discuss the LHC phenomenology of a specific example with extra heavy fermion doublets.Comment: 27 pages, 11 figures, 3 table

Approximate Degradable Quantum Channels

Degradable quantum channels are an important class of completely positive trace-preserving maps. Among other properties, they offer a single-letter formula for the quantum and the private classical capacity and are characterized by the fact that a complementary channel can be obtained from the channel by applying a degrading channel. In this work we introduce the concept of approximate degradable channels, which satisfy this condition up to some finite $\varepsilon\geq0$. That is, there exists a degrading channel which upon composition with the channel is $\varepsilon$-close in the diamond norm to the complementary channel. We show that for any fixed channel the smallest such $\varepsilon$ can be efficiently determined via a semidefinite program. Moreover, these approximate degradable channels also approximately inherit all other properties of degradable channels. As an application, we derive improved upper bounds to the quantum and private classical capacity for certain channels of interest in quantum communication.Comment: v3: minor changes, published version. v2: 21 pages, 2 figures, improved bounds on the capacity for approximate degradable channels based on [arXiv:1507.07775], an author adde

Test of a simple and flexible molecule model for alpha-, beta- and gamma-S8 crystals

S8 is the most stable compound of elemental sulfur in solid and liquid phases, at ambient pressure and below 400K. Three crystalline phases of S8 have been clearly identified in this range of thermodynamic parameters, although no calculation of its phase diagram has been performed yet. alpha- and gamma-S8 are orientationally ordered crystals while beta-S8 is measured as orientationally disordered. In this paper we analyze the phase diagram of S8 crystals, as given by a simple and flexible molecule model, via a series of molecular dynamics (MD) simulations. The calculations are performed in the constant pressure- constant temperature ensemble, using an algorithm that is able to reproduce structural phase transitions.Comment: RevTex,7 pages, 5 figures,to appear in J. Chem. Phy

DYCAST: A finite element program for the crash analysis of structures

DYCAST is a nonlinear structural dynamic finite element computer code developed for crash simulation. The element library contains stringers, beams, membrane skin triangles, plate bending triangles and spring elements. Changing stiffnesses in the structure are accounted for by plasticity and very large deflections. Material nonlinearities are accommodated by one of three options: elastic-perfectly plastic, elastic-linear hardening plastic, or elastic-nonlinear hardening plastic of the Ramberg-Osgood type. Geometric nonlinearities are handled in an updated Lagrangian formulation by reforming the structure into its deformed shape after small time increments while accumulating deformations, strains, and forces. The nonlinearities due to combined loadings are maintained, and stiffness variation due to structural failures are computed. Numerical time integrators available are fixed-step central difference, modified Adams, Newmark-beta, and Wilson-theta. The last three have a variable time step capability, which is controlled internally by a solution convergence error measure. Other features include: multiple time-load history tables to subject the structure to time dependent loading; gravity loading; initial pitch, roll, yaw, and translation of the structural model with respect to the global system; a bandwidth optimizer as a pre-processor; and deformed plots and graphics as post-processors

Ultra-long-term follow-up of pediatric spinal deformity problems: 23 patients with a mean follow-up of 51 years

AbstractBackground.The aim of this study was to analyze the true outcomes of a unique cohort of patients with spinal deformities who were treated as children and followed for 40 or more years.Methods.Altogether, 23 patients were reviewed who had been originally treated in our community, whose original charts and radiographs were still available, and who had undergone recent evaluation.Results.The diagnoses were congenital deformity in eight, adolescent idiopathic scoliosis in four, poliomyelitis in three, infantile idiopathic scoliosis in two, spondylolisthesis in two, and one each of tuberculosis and dwarfism. Sixteen had undergone fusion surgery.Conclusions.Early spine fusion for deformity produced far better results than delayed fusion. A solid fusion at the end of growth remained unchanged. Degenerative changes outside the fusion area were rare and seldom required further surgery. In summary, 23 patients with a mean follow-up of 51 years after treatment are presented. Early fusion was far superior to delayed or nonsurgical treatment