Many faces of survey equipment failures during marine research at sea-Risk analysis.

Research of the marine environment is still a huge challenge for humanity. Each survey campaign is a complex project, where research vessels and relevant survey equipment is used. One of the problems that limit the success of working at sea are failures of survey equipment.

On a risk of inhalation exposure during visits in Chernobyl exclusion zone.

In recent years Chernobyl exclusion zone has become a very popular tourist destination. Many people visiting power plant, Pripyat city or surrounding villages use different types of personal dosimeters to control external exposure, however very small group of tourist have opportunity to control internal contamination of respiratory tract using dedicated, high sensitive whole body counters. In this study 11 anti-dust masks collected from CEZ visitors and filters from one military MP-5 mask were analyzed using alpha, beta and gamma spectrometry to determine doses from actinides and fission products which can be inhaled without proper protective equipment.

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry.

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows.

Lead shielding efficiency from the gamma background measurements in the salt cavern of the Polkowice-Sieroszowice copper mine.

The studies of lead shielding efficiency from the gamma background measurements were performed in the salt cavern of the copper mine - a site considered for an underground laboratory. Within the energy range of 50-2700 keV, the measured gamma-ray count rates normalized to the mass of the high-purity detectors germanium crystal are 5.93 and 6.

Gamma emitters in atmospheric precipitation in Krakow (Southern Poland) during the years 2005-2015.

The results of the sum of dry and wet activity deposition for naturally occurring Be, Pb, K, Na and anthropogenic Cs radionuclides in Krakow (Southern Poland) for the samples collected over 10 years (from August 2005 to July 2015) are presented and discussed. The radionuclides were determined using low background gamma spectrometry with HPGe detectors. Additionally, in this paper there are shown the results of activity concentrations in water from air precipitation for Be, Pb, Na, K and Cs radioisotopes from the period of 7 years (from August 2008 to July 2015).

Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only).

All-atom crystal simulations of DNA and RNA duplexes.

Background: Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data.

Methods: We report simulations of DNA and RNA duplexes in their crystalline environment.

Evaluation of acridine orange, LysoTracker Red, and quinacrine as fluorescent probes for long-term tracking of acidic vesicles.

Acidic vesicles can be imaged and tracked in live cells after staining with several low molecular weight fluorescent probes, or with fluorescently labeled proteins. Three fluorescent dyes, acridine orange, LysoTracker Red DND-99, and quinacrine, were evaluated as acidic vesicle tracers for confocal fluorescence imaging and quantitative analysis. The stability of fluorescent signals, achievable image contrast, and phototoxicity were taken into consideration.

Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path.

The hairpin ribozyme accelerates a phosphoryl transfer reaction without catalytic participation of divalent metal ions. Residues A38 and G8 have been implicated as playing roles in general acid and base catalysis, respectively. Here we explore the structure and dynamics of key active site residues using more than 1 μs of molecular dynamics simulations of the hairpin ribozyme at different stages along the catalytic pathway.

Peptide crystal simulations reveal hidden dynamics.

Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in X-ray diffraction data. We present here 9.6 μs of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell.

Rationale for the real-time and dynamic cell death assays using propidium iodide.

We have recently reported an innovative approach to use charged fluorochromes such as propidium iodide (PI) in the real-time, dynamic cell viability assays. This study was designed to provide a mechanistic rationale for the kinetic assays using cell permeability markers. Uptake of PI by live cells, effect on the cell cycle, long-term proliferation capacity, DNA damage response, and pharmacologic interactions with anticancer drugs were studied using both laser scanning microscopy and laser scanning cytometry.