Search results for "CLU"
showing 10 items of 14395 documents
Inhabiting plant roots, nematodes, and truffles—polyphilus, a new helotialean genus with two globally distributed species
2018
Fungal root endophytes, including the common group of dark septate endophytes (DSEs), represent different taxonomic groups and potentially diverse life strategies. In this study, we investigated two unidentified helotialean lineages found previously in a study of DSE fungi of semiarid grasslands, from several other sites, and collected recently from a pezizalean truffle ascoma and eggs of the cereal cyst nematode Heterodera filipjevi. The taxonomic positions and phylogenetic relationships of 21 isolates with different hosts and geographic origins were studied in detail. Four loci, namely, nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS]), partial 28S nuc rDNA (28S), partial 18S nu…
Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs
2017
Detecting higher-order epistatic interactions in Genome-Wide Association Studies (GWAS) remains a challenging task in the fields of genetic epidemiology and computer science. A number of algorithms have recently been proposed for epistasis discovery. However, they suffer from a high computational cost since statistical measures have to be evaluated for each possible combination of markers. Hence, many algorithms use additional filtering stages discarding potentially non-interacting markers in order to reduce the overall number of combinations to be examined. Among others, Mutual Information Clustering (MIC) is a common pre-processing filter for grouping markers into partitions using K-Means…
Long-term genomic coevolution of host-parasite interaction in the natural environment
2017
Antagonistic coevolution of parasite infectivity and host resistance may alter the biological functionality of species, yet these dynamics in nature are still poorly understood. Here we show the molecular details of a long-term phage–bacterium arms race in the environment. Bacteria (Flavobacterium columnare) are generally resistant to phages from the past and susceptible to phages isolated in years after bacterial isolation. Bacterial resistance selects for increased phage infectivity and host range, which is also associated with expansion of phage genome size. We identified two CRISPR loci in the bacterial host: a type II-C locus and a type VI-B locus. While maintaining a core set of conse…
Exosome-mediated drug resistance in cancer: the near future is here.
2016
Drug resistance exerts a crucial role in several cancer treatments. Understanding the resistance mechanisms against different therapeutic agents can be helpful to determine the prognosis, but remains a tricky task. In this context, tumor-derived exosomes (TDEs) may give crucial answers about these resistance mechanisms. Exosomes are biological nanovesicles with an average size around 30–100 nm of diameter (Figure 1) that originate from the endocytic pathway by the inward budding of multivesicular bodies (MVB), and they function as cell-free messengers, involved in the cell–cell communication [Kowal et al. 2014]. It has been demonstrated that both cells in physiological and pathological cond…
Iron-loaded transferrin (Tf) is detrimental whereas iron-free Tf confers protection against brain ischemia by modifying blood Tf saturation and subse…
2018
Despite transferrin being the main circulating carrier of iron in body fluids, and iron overload conditions being known to worsen stroke outcome through reactive oxygen species (ROS)-induced damage, the contribution of blood transferrin saturation (TSAT) to stroke brain damage is unknown. The objective of this study was to obtain evidence on whether TSAT determines the impact of experimental ischemic stroke on brain damage and whether iron-free transferrin (apotransferrin, ATf)-induced reduction of TSAT is neuroprotective. We found that experimental ischemic stroke promoted an early extravasation of circulating iron-loaded transferrin (holotransferrin, HTf) to the ischemic brain parenchyma.…
Prospects and challenges for computer simulations of monolayer-protected metal clusters
2021
Precise knowledge of chemical composition and atomic structure of functional nanosized systems, such as metal clusters stabilized by an organic molecular layer, allows for detailed computational work to investigate structure-property relations. Here, we discuss selected recent examples of computational work that has advanced understanding of how these clusters work in catalysis, how they interact with biological systems, and how they can make self-assembled, macroscopic materials. A growing challenge is to develop effective new simulation methods that take into account the cluster-environment interactions. These new hybrid methods are likely to contain components from electronic structure t…
Transfer Free Energies of Test Proteins Into Crowded Protein Solutions Have Simple Dependence on Crowder Concentration
2019
The effects of macromolecular crowding on the thermodynamic properties of test proteins are determined by the latter's transfer free energies from a dilute solution to a crowded solution. The transfer free energies in turn are determined by effective protein-crowder interactions. When these interactions are modeled at the all-atom level, the transfer free energies may defy simple predictions. Here we investigated the dependence of the transfer free energy (Δμ) on crowder concentration. We represented both the test protein and the crowder proteins atomistically, and used a general interaction potential consisting of hard-core repulsion, non-polar attraction, and solvent-screened electrostati…
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
2016
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…
Interaction of C 60 fullerenes with asymmetric and curved lipid membranes: a molecular dynamics study
2015
Interaction of fullerenes with asymmetric and curved DOPC/DOPS bicelles is studied by means of coarse-grained molecular dynamics simulations. The effects caused by asymmetric lipid composition of the membrane leaflets and the curvature of the membrane are analyzed. It is shown that the aggregates of fullerenes prefer to penetrate into the membrane in the regions of the moderately positive mean curvature. Upon penetration into the hydrophobic core of the membrane fullerenes avoid the regions of the extreme positive or the negative curvature. Fullerenes increase the ordering of lipid tails, which are in direct contact with them, but do not influence other lipids significantly. Our data sugges…
The essentials of marine biotechnology
2021
Coastal countries have traditionally relied on the existing marine resources (e.g., fishing, food, transport, recreation, and tourism) as well as tried to support new economic endeavors (ocean energy, desalination for water supply, and seabed mining). Modern societies and lifestyle resulted in an increased demand for dietary diversity, better health and well-being, new biomedicines, natural cosmeceuticals, environmental conservation, and sustainable energy sources. These societal needs stimulated the interest of researchers on the diverse and underexplored marine environments as promising and sustainable sources of biomolecules and biomass, and they are addressed by the emerging field of ma…