HLA typing from 1000 genomes whole genome and whole exome illumina data.

Specific HLA genotypes are known to be linked to either resistance or susceptibility to certain diseases or sensitivity to certain drugs. In addition, high accuracy HLA typing is crucial for organ and bone marrow transplantation. The most widespread high resolution HLA typing method used to date is Sanger sequencing based typing (SBT), and next generation sequencing (NGS) based HLA typing is just starting to be adopted as a higher throughput, lower cost alternative. By HLA typing the HapMap subset of the public 1000 Genomes paired Illumina data, we demonstrate that HLA-A, B and C typing is possible from exome sequencing samples with higher than 90% accuracy. The older 1000 Genomes whole genome sequencing read sets are less reliable and generally unsuitable for the purpose of HLA typing. We also propose using coverage % (the extent of exons covered) as a quality check (QC) measure to increase reliability.

In situ biodosimetric experiment for space applications.

This paper presents the principles and application of DNA based biological UV dosimeters, as developed by Research Group for Biophysics (RGB). These dosimeters are used for assessing the biological hazard of living systems on the Earth's surface and in different waters (rivers, lakes, seas, etc.). The UV dosimetry system has also been used in the space. In dosimeters a bacterial virus, bacteriophage T7 and polycrystalline uracil thin layers have been used as biological detectors. On the Earth's surface the UV radiation induces dimer formation in phage T7 and in the uracil detector, which was evaluated by loss of viability of the phage particles and by the decrease of the characteristic optical density (OD) of uracil thin layers. Recently the development of human space activities has also increased the need to measure the biological effect of extraterrestrial solar radiation, too. The evaluation of the space samples occurred on ground, thus only the starting and the final state were taken into account. A new improved, automated method is presented below which makes data collection more efficient and also makes the dynamics of the process observable.

Evaluation of drug-human serum albumin binding interactions with support vector machine aided online automated docking.

MOTIVATION: Human serum albumin (HSA), the most abundant plasma protein is well known for its extraordinary binding capacity for both endogenous and exogenous substances, including a wide range of drugs. Interaction with the two principal binding sites of HSA in subdomain IIA (site 1) and in subdomain IIIA (site 2) controls the free, active concentration of a drug, provides a reservoir for a long duration of action and ultimately affects the ADME (absorption, distribution, metabolism, and excretion) profile. Due to the continuous demand to investigate HSA binding properties of novel drugs, drug candidates and drug-like compounds, a support vector machine (SVM) model was developed that efficiently predicts albumin binding. Our SVM model was integrated to a free, web-based prediction platform (http://albumin.althotas.com). Automated molecular docking calculations for prediction of complex geometry are also integrated into the web service. The platform enables the users (i) to predict if albumin binds the query ligand, (ii) to determine the probable ligand binding site (site 1 or site 2), (iii) to select the albumin X-ray structure which is complexed with the most similar ligand and (iv) to calculate complex geometry using molecular docking calculations. Our SVM model and the potential offered by the combined use of in silico calculation methods and experimental binding data is illustrated.

Investigating the effects of simulated martian ultraviolet radiation on Halococcus dombrowskii and other extremely halophilic archaebacteria.

The isolation of viable extremely halophilic archaea from 250-million-year-old rock salt suggests the possibility of their long-term survival under desiccation. Since halite has been found on Mars and in meteorites, haloarchaeal survival of martian surface conditions is being explored. Halococcus dombrowskii H4 DSM 14522(T) was exposed to UV doses over a wavelength range of 200-400 nm to simulate martian UV flux. Cells embedded in a thin layer of laboratory-grown halite were found to accumulate preferentially within fluid inclusions. Survival was assessed by staining with the LIVE/DEAD kit dyes, determining colony-forming units, and using growth tests. Halite-embedded cells showed no loss of viability after exposure to about 21 kJ/m(2), and they resumed growth in liquid medium with lag phases of 12 days or more after exposure up to 148 kJ/m(2). The estimated D(37) (dose of 37 % survival) for Hcc. dombrowskii was > or = 400 kJ/m(2). However, exposure of cells to UV flux while in liquid culture reduced D(37) by 2 orders of magnitude (to about 1 kJ/m(2)); similar results were obtained with Halobacterium salinarum NRC-1 and Haloarcula japonica. The absorption of incoming light of shorter wavelength by color centers resulting from defects in the halite crystal structure likely contributed to these results. Under natural conditions, haloarchaeal cells become embedded in salt upon evaporation; therefore, dispersal of potential microscopic life within small crystals, perhaps in dust, on the surface of Mars could resist damage by UV radiation.

The two-conformer hypothesis: 2,3,4,6-tetra-O-methyl-mannopyranosyl and -glucopyranosyl oxacarbenium ions.

Computational chemistry can give information about the probable conformations of reactive intermediates that are difficult to determine experimentally. Based on density functional theory (DFT) calculations of tetra-O-methyl-D-mannopyranosyl and -glucopyranosyl oxacarbenium ions, two families of conformations, which we call B0 and B1, were found. For the manno configuration, a 4H3 and 3E almost isoenergetic pair were found, whereas for the gluco-configuration a 4H3 and 5S1 pair favouring 4H3 were calculated. These results corroborate earlier results and suggest that this two or more conformer hypothesis is general. Nucleophilic attack on these pairs of cations was modelled with methanol and led to four cases to consider namely alpha- or beta-attack on B0 or B1. The resulting complexes (G0, G1 and F0, F1) demonstrate facial selectivity. The relative energies of these complexes are dominated by intramolecular hydrogen bonding and the conformational consequences to the pyranose ring of changes in the C-5-O-5-C-1-C-2 torsion angle. Constrained variation of the nucleophilic oxygen (methanol) to C-1 distance shows that these ion dipole complexes are the only minima with this constraint.

Conformational pathways of saturated six-membered rings. A static and dynamical density functional study.

The conformation of the six-membered ring of pyranosyl sugars has pronounced effects on the physical and chemical properties of carbohydrates. We present a method to determine key features of the potential energy surfaces, such as transition states associated with the inversion pathways of the model compounds cyclohexane, tetrahydropyran, p-dioxane, m-dioxane, s-trioxane, and 2-oxanol. Finally, we make the first determination of the pathways for inversion of penta-O-methyl-alpha-D-glucopyranose and penta-O-methyl-beta-D-glucopyranose. For both anomers, a transition state with five coplanar atoms with appreciable (O)E character was found. The method is based on constrained Car-Parrinello ab initio molecular dynamics, as implemented in the projector augmented-wave (PAW) method. The constraints are derived from the normal modes of six-membered rings and are described in terms of the canonical conformations (1)C(4) chair, (1,4)B boat, and (O)S(2) skew-boat. The PAW derived trajectories are in agreement with previous suggestions in the literature that pseudorotation is an important feature of such conformational interconversions. The dynamic nature as well as the internal coordinate-based constraints provide a method which can reliably accommodate pseudorotation. To determine semiquantitative energies, we recalculate key conformations using standard quantum mechanical calculations while keeping the ring dihedral angles frozen at their values found in the dynamics. In all cases where experimental barriers are known, our results are in excellent agreement.

Efficacy of different UV-emitting light sources in the induction of T-cell apoptosis.

Ultraviolet B (UV-B) radiation is a modality widely used for the treatment of different skin diseases. One of the major mechanisms of UV-B immunosuppression in this treatment modality is thought to be an apoptosis-inducing effect on T cells infiltrating the skin. We examined the T-cell apoptosis-induction capacities of four different UV light sources, with and without UV filters. The xenon chloride (XeCl) laser proved to be the strongest apoptosis inducer. The use of a phtalic acid filter eliminated UV radiation almost completely below 300 nm, which resulted in a severe decrease in the apoptosis-inducing capacity of different UV-B sources. Using the results of the measurements with polychromatic UV light sources, the wavelength dependence of UV-B light for the induction of T-cell apoptosis was also determined. The regression line of the action spectrum demonstrated a continuous decrease from 290 to 311 nm. The apoptosis-inducing capacity of the XeCl laser was almost four times higher than the calculated value according to the action spectrum, which might be attributed to the high irradiance of the laser as compared with nonlaser light sources.

Solar UV irradiation conditions on the surface of Mars.

The UV radiation environment on planetary surfaces and within atmospheres is of importance in a wide range of scientific disciplines. Solar UV radiation is a driving force of chemical and organic evolution and serves also as a constraint in biological evolution. In this work we modeled the transmission of present and early solar UV radiation from 200 to 400 nm through the present-day and early (3.5 Gyr ago) Martian atmosphere for a variety of possible cases, including dust loading, observed and modeled O3 concentrations. The UV stress on microorganisms and/or molecules essential for life was estimated by using DNA damaging effects (specifically bacteriophage T7 killing and uracil dimerization) for various irradiation conditions on the present and ancient Martian surface. Our study suggests that the UV irradiance on the early Martian surface 3.5 Gyr ago may have been comparable with that of present-day Earth, and though the current Martian UV environment is still quite severe from a biological viewpoint, we show that substantial protection can still be afforded under dust and ice.

Can the stereochemical outcome of glycosylation reactions be controlled by the conformational preferences of the glycosyl donor?

Previous static and dynamical density functional theory studies of the 2,6-di-O-acetyl-3,4-O-isopropylidene-D-galactopyranosyl cations and their methanol adducts has led to an hypothesis that these cations exist in two families of conformers characterized as (2)S(O) and B(2,5), respectively. These families differ by ring inversion, each with its own reactivity. New calculations on the 2,6-di-O-acetyl-3,4-di-O-methyl-D-galactopyranosyl cation confirmed these trends. Removing the isopropylidene group allows more flexibility, but two families of conformers can be discerned with the monocyclic oxocarbenium ions in the E(3) conformation and the bicyclic dioxolenium ions in the (4)H(5) conformation. Attack on the beta-face of these monocyclic cations is favored by hydrogen bonding and the anomeric effect. The experimentally observed high beta-stereoselectivity of mannopyranosyl donors and high alpha-stereoselectivity of glucopyranosyl donors with the 4,6-O-benzylidene protecting groups can be rationalized assuming that the trans-fused 1,3-dioxane ring allows population of only one family of conformers. The combination of hydrogen bonding and conformational changes of the pyranose ring in response to the C-5[bond]O-5[bond]C-1[bond]C-2 torsion angle changes are identified as key factors in stereoselectivity. Based on these observations a strategy to design face discriminated glycosyl donors that exist predominantly in only one family of conformers is proposed.

Ligand Effects in the Models and Mimics of Oxyhemocyanin and Oxytyrosinase. A Density Functional Study of Reversible Dioxygen Binding and Reversible O-O Bond Cleavage.

We studied the energetics of dioxygen binding and the core isomerization between the Cu(2)(&mgr;-eta(2):eta(2)-O(2)) and Cu(2)(&mgr;-O)(2) core structures of {[LCu](2)O(2)}(2+), L = 1,4,7-triazacyclononane (1) and L = hydrotris(pyrazolyl)borate (2), by gradient-corrected density functional methods. N-Substituted derivatives of 1 and 2 are synthetic inorganic mimics of oxyhemocyanin with similar physical and spectroscopic properties but different chemical behavior. The calculated dioxygen binding energies of 1 and 2 are -60 and -184 kJ/mol, respectively, in line with the observation that 1 binds oxygen reversibly and 2 does so irreversibly. Bond energy decomposition showed that orbital interactions contribute equally to the binding energy of 1 and 2, which explains the similarities in their spectral properties. Electrostatic interactions due to the negatively charged ligand are responsible for stronger binding in 2. The core isomerization energies for isomerization from the Cu(2)(&mgr;-eta(2):eta(2)-O(2)) to the Cu(2)(&mgr;-O)(2) isomers of 1 and 2 are +1 and +12 kJ/mol, respectively. The barrier heights of the core isomerizations of 1 and 2 relative to the Cu(2)(&mgr;-eta(2):eta(2)-O(2)) isomer are 33 and 37 kJ/mol, respectively. The results on 1 are in line with the experimentally observed fast and reversible interconversion between the two isomers while these data on 2 suggest that the observation of 2 in the (&mgr;-O)(2) isomer was only prevented by its thermal instability. We also considered a purely theoretical model compound, {[(NH(3))(3)Cu](2)O(2)}(2+) (3). Calculations on 3 show that this model is clearly inadequate even for qualitative energetic modeling of dioxygen binding while it is successful in describing spectral, structural, and magnetic properties. Calculations show that the isomerization of 3 is endoergic by 49 kJ/mol, and there is essentially no energy barrier relative to the higher energy (&mgr;-O)(2) isomer. The dioxygen binding energy of 3 is endoergic by 160 kJ/mol as opposed to the exoergic binding in both 1 and 2.