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

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

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

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

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

Failure of non-vacuum steam sterilization processes for dental handpieces

Background: Dental handpieces are used in critical and semi-critical operative interventions. Although a number of dental professional bodies recommend that dental handpieces are sterilized between patient use there is a lack of clarity and understanding of the effectiveness of different steam sterilization processes. The internal mechanisms of dental handpieces contain narrow lumens (0·8-2·3mm) which can impede the removal of air and ingress of saturated steam required to achieve sterilization conditions. Aim: To identify the extent of sterilization failure in dental handpieces using a non-vacuum process. Methods: In-vitro and in-vivo investigations were conducted on commonly used UK benchtop steam sterilizers and three different types of dental handpieces. The sterilization process was monitored inside the lumens of dental handpieces using thermometric (TM) methods (dataloggers), chemical indicators (CI) and biological indicators (BI). Findings: All three methods of assessing achievement of sterility within dental handpieces that had been exposed to non-vacuum sterilization conditions demonstrated a significant number of failures (CI=8/3,024(fails/n tests); BI=15/3,024; TM=56/56) compared to vacuum sterilization conditions (CI=2/1,944; BI=0/1,944; TM=0/36). The dental handpiece most likely to fail sterilization in the non-vacuum process was the surgical handpiece. Non-vacuum sterilizers located in general dental practice had a higher rate of sterilization failure (CI=25/1,620; BI=32/1,620; TM=56/56) with no failures in vacuum process. Conclusion: Non-vacuum downward/gravity displacement, type-N steam sterilizers are an unreliable method for sterilization of dental handpieces in general dental practice. The handpiece most likely to fail sterilization is the type most frequently used for surgical interventions

Investigating steam penetration using thermometric methods in dental handpieces with narrow internal lumens during sterilizing processes with non-vacuum or vacuum processes

Background: Dental handpieces are required to be sterilized between patient use. Vacuum steam sterilization processes with fractionated pre/post-vacuum phases or unique cycles for specified medical devices, are required for hollow instruments with internal lumens to assure successful air removal. Entrapped air will compromise achievement of required sterilization conditions. Many countries and professional organisations still advocate non-vacuum sterilization processes for these devices. Aim: To investigate non-vacuum downward/gravity displacement, type-N steam sterilization of dental handpieces, using thermometric methods to measure time to achieve sterilization temperature at different handpiece locations. Methods: Measurements at different positions within air turbines were undertaken with thermocouples and dataloggers. Two examples of commonly used UK benchtop steam sterilizers were tested; a non-vacuum benchtop sterilizer (Little Sister 3, Eschmann, UK) and a vacuum benchtop sterilizer (Lisa, W&H, Austria). Each sterilizer cycle was completed with three handpieces and each cycle in triplicate. Findings: A total of 140 measurements inside dental handpiece lumens were recorded. We demonstrate that the non-vacuum process fails (time range 0-150 seconds) to reliably achieve sterilization temperatures within the time limit specified by the International standard (15 seconds equilibration time). The measurement point at the base of the handpiece failed in all test runs (n=9) to meet the standard. No failures were detected with the vacuum steam sterilization type B process with fractionated pre-vacuum and post-vacuum phases. Conclusion: Non-vacuum downward/gravity displacement, type-N steam sterilization processes are unreliable in achieving sterilization conditions inside dental handpieces and the base of the handpiece is the site most likely to fail

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

Optical and X-ray Properties of the Swift BAT-detected AGN

The Swift Gamma-Ray Burst satellite has detected a largely unbiased towards absorption sample of local ($\approx 0.03$) AGN, based solely on their 14--195 keV flux. In the first 9 months of the survey, 153 AGN sources were detected. The X-ray properties in the 0.3--10 keV band have been compiled and presented based on analyses with XMM-Newton, Chandra, Suzaku, and the Swift XRT (Winter et al. 2009). Additionally, we have compiled a sub-sample of sources with medium resolution optical ground-based spectra from the SDSS or our own observations at KPNO. In this sample of 60 sources, we have classified the sources using standard emission line diagnostic plots, obtained masses for the broad line sources through measurement of the broad H$\beta$ emission line, and measured the [OIII] 5007\AA luminosity of this sample. Based on continuum fits to the intrinsic absorption features, we have obtained clues about the stellar populations of the host galaxies. We now present the highlights of our X-ray and optical studies of this unique sample of local AGNs, including a comparison of the 2--10 keV and 14--195 keV X-ray luminosities with the [OIII] 5007\AA luminosity and the implications of our results towards measurements of bolometric luminosities.Comment: 4 pages, 2 figures, to appear in proceedings for 'X-ray Astronomy 2009', Bologna 09/2009, AIP Conference Series, Eds. A. Comastri, M. Cappi, L. Angelin