Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)

Solving the structure of protein-protein complexes is one of the most important tasks in structural biology. Even though there has been great progress in recent years there still a small number of protein complexes structures deposited in the Protein Data Bank in comparison to isolated partners. In this sense, the computational prediction of protein complexes starting from the unbound structures, protein-protein Docking algorithms, has emerged as a reasonable alternative. Many docking programs employ Fast Fourier Transform (FFT) correlations as an efficient search strategy. We describe an implementation of a protein-protein docking program based on FFT surface complementarity that runs entirely on a Graphics Processing Unit (GPU), including grid generation, rotation and scoring. We evaluate its performance, and show that it can be up to 13 times faster than conventional CPU based implementations.Sociedad Argentina de Informática e Investigación Operativ

An Analysis of Nasal Irritation Thresholds Using a New Solvation Equation

In the present paper we have developed a quantitative structure-activity relationship (QSAR) equation for nasal pungency caused by nonreactive volatile organic compounds (VOCs). Our QSAR was developed upon previously published nasal pungency thresholds in anosmics, i.e., patients lacking a sense of smell and thus responding only to sensory irritation evoked by trigeminal nerve stimulation. The reported solvation equation, which fits the data with considerable precision, describes sensory potency in terms of interaction via electron pairs, dipolarity/polarizability, hydrogen bond acidity and basicity, and hydrophobicity. It correspondingly suggests relevant physicochemical properties of the biophase where the sensory response is brought about. The equation implies that in the range of molecular size where nonreactive VOCs can produce any pungency, transport from the air to the biophase strictly determines potency. In this respect, the potency of nasal pungency shares characteristics with the ability of VOCs to cause narcosis and anesthesia

An Analysis of Nasal Irritation Thresholds Using a New Solvation Equation

In the present paper we have developed a quantitative structure-activity relationship (QSAR) equation for nasal pungency caused by nonreactive volatile organic compounds (VOCs). Our QSAR was developed upon previously published nasal pungency thresholds in anosmics, i.e., patients lacking a sense of smell and thus responding only to sensory irritation evoked by trigeminal nerve stimulation. The reported solvation equation, which fits the data with considerable precision, describes sensory potency in terms of interaction via electron pairs, dipolarity/polarizability, hydrogen bond acidity and basicity, and hydrophobicity. It correspondingly suggests relevant physicochemical properties of the biophase where the sensory response is brought about. The equation implies that in the range of molecular size where nonreactive VOCs can produce any pungency, transport from the air to the biophase strictly determines potency. In this respect, the potency of nasal pungency shares characteristics with the ability of VOCs to cause narcosis and anesthesia

Softlithography in Chemical Sensing – Analytes from Molecules to Cells

Imprinting is a flexible and straightforward technique to generate selective sensormaterials e.g. for mass-sensitive detection. Inherently, the strategy suits both molecularanalytes and entire micro organisms or cells. Imprinted polyurethanes e.g. are capable ofdistinguishing the different xylene isomers with very appreciable selectivity factors.Combining imprinted titanates with surface transverse wave resonators (STW) leads to apowerful tool for detecting engine oil degradation, which is an excellent example foroxidative deterioration processes in a highly complex matrix. Surface imprints withgeometrically equal cavities exhibit clear chemical selectivity, as can e.g. be seen throughthe example of different human rhinovirus (HRV) serotypes. Another example is a bloodgroup-selective sensor prepared by templating with erythrocyte ghosts. Both the bloodgroupA and B imprinted material selectively distinguish between blood groups A, B and O,whereas no difference in sensor signal has been observed for AB, where both blood groupantigen types are present on the cell surface

Ontogeny of embryogenic callus in Medicago truncatula: the fate of the pluripotent and totipotent stem cells

Background and Aims: Understanding the fate and dynamics of cells during callus formation is essential to understanding totipotency and the mechanisms of somatic embryogenesis. Here, the fate of leaf explant cells during the development of embryogenic callus was investigated in the model legume Medicago truncatula. Methods: Callus development was examined from cultured leaf explants of the highly regenerable genotype Jemalong 2HA (2HA) and from mesophyll protoplasts of 2HA and wild-type Jemalong. Callus development was studied by histology, manipulation of the culture system, detection of early production of reactive oxygen species and visualization of SERK1 (SOMATIC EMBRYO RECEPTOR KINASE1) gene expression. Key Results: Callus formation in leaf explants initiates at the cut surface and within veins of the explant. The ontogeny of callus development is dominated by the division and differentiation of cells derived from pluripotent procambial cells and from dedifferentiated mesophyll cells. Procambium-derived cells differentiated into vascular tissue and rarely formed somatic embryos, whereas dedifferentiated mesophyll cells were competent to form somatic embryos. Interestingly, explants incubated adaxial-side down had substantially less cell proliferation associated with veins yet produced similar numbers of somatic embryos to explants incubated abaxial-side down. Somatic embryos mostly formed on the explant surface originally in contact with the medium, while in protoplast microcalli, somatic embryos only fully developed once at the surface of the callus. Mesophyll protoplasts of 2HA formed embryogenic callus while Jemalong mesophyll protoplasts produced callus rich in vasculature. Conclusions: The ontogeny of embryogenic callus in M. truncatula relates to explant orientation and is driven by the dynamics of pluripotent procambial cells, which proliferate and differentiate into vasculature. The ontogeny is also related to de-differentiated mesophyll cells that acquire totipotency and form the majority of embryos. This contrasts with other species where totipotent embryo-forming initials mostly originate from procambial cells