Search results for "alignment"
showing 10 items of 627 documents
Self-healing, an intrinsic property of biomineralization processes
2013
The sponge siliceous spicules are formed enzymatically via silicatein, in contrast to other siliceous biominerals. Originally, silicatein had been described as a major structural protein of the spicules that has the property to allow a specific deposition of silica onto their surface. More recently, it had been unequivocally demonstrated that silicatein displays a genuine enzyme activity, initiating and maintaining silica biopolycondensation at low precursor concentrations (<2 mM). Even more, as silicatein becomes embedded into the biosilica polymer, formed by the enzyme, it retains its functionality to enable a controlled biosilica deposition. The protection of silicatein through the biosi…
Applications of alignment-free methods in epigenomics
2013
Epigenetic mechanisms play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have supported a role of DNA sequences in recruitment of epigenetic regulators. Alignment-free methods have been applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles. Here, we review recent advances in such applications, including the methods to map DNA sequence to feature space, sequence comparison and prediction models. Computational studies using these methods have provided important insights into the epigenetic reg…
Phobalysin, a Small β-Pore-Forming Toxin of Photobacterium damselae subsp. damselae
2015
ABSTRACT Photobacterium damselae subsp. damselae , an important pathogen of marine animals, may also cause septicemia or hyperaggressive necrotizing fasciitis in humans. We previously showed that hemolysin genes are critical for virulence of this organism in mice and fish. In the present study, we characterized the hlyA gene product, a putative small β-pore-forming toxin, and termed it phobalysin P (PhlyP), for “photobacterial lysin encoded on a plasmid.” PhlyP formed stable oligomers and small membrane pores, causing efflux of K + , with no significant leakage of lactate dehydrogenase but entry of vital dyes. The latter feature distinguished PhlyP from the related Vibrio cholerae cytolysin…
The evolutionary history of the rediscovered Austrian population of the giant centipede Scolopendra cingulata Latreille 1829 (Chilopoda, Scolopendrom…
2014
The thermophilous giant centipede Scolopendra cingulata is a voracious terrestrial predator, which uses its modified first leg pair and potent venom to capture prey. The highly variable species is the most common of the genus in Europe, occurring from Portugal in the west to Iran in the east. The northernmost occurrences are in Hungary and Romania, where it abides in small isolated fringe populations. We report the rediscovery of an isolated Austrian population of Scolopendra cingulata with the first explicit specimen records for more than 80 years and provide insights into the evolutionary history of the northernmost populations utilizing fragments of two mitochondrial genes, COI and 16S, …
EST sequencing of Onychophora and phylogenomic analysis of Metazoa
2007
Onychophora (velvet worms) represent a small animal taxon considered to be related to Euarthropoda. We have obtained 1873 5' cDNA sequences (expressed sequence tags, ESTs) from the velvet worm Epiperipatus sp., which were assembled into 833 contigs. BLAST similarity searches revealed that 51.9% of the contigs had matches in the protein databases with expectation values lower than 10(-4). Most ESTs had the best hit with proteins from either Chordata or Arthropoda (approximately 40% respectively). The ESTs included sequences of 27 ribosomal proteins. The orthologous sequences from 28 other species of a broad range of phyla were obtained from the databases, including other EST projects. A conc…
AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation
2020
Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not only makes them challenging to understand and extend, but also difficult to port to other platforms. We present AnySeq - a novel library for computing different types of pairwise alignments of DNA sequences. Our approach combines high performance with an intuitively understandable implementation, which is achieved through the concept of partial evaluation. Using the AnyDSL compiler framework, AnySeq enables the compilation of algorithmic variants that ar…
Ultrafast ionization and rotational dynamics of molecules in strong laser fields
2021
The investigation of ultrafast molecular dynamics is of great importance towards the understanding of a variety of natural phenomena in physical and chemical sciences. With the rapid development of femtosecond laser systems and precision detection technologies, it is possible now to visualize and steer the motion of molecules in matter as well as the ultrafast dynamics of electrons and nuclei in molecules on a microscopic timescale. When a molecule is exposed to a strong laser field, its electrons can be freed or excited, which often triggers a rapid dissociation of the system, in which the released electrons and nuclei exhibit a strong correlation, while the electronic motion on attosecond…
Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analys…
2007
[Background] The phosphoenolpyruvate phosphotransferase system (PTS) plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. The PTS couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (PEP) and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme II complexes which catalyze the uptake and phosphorylation of solutes. Previous studies have suggested that the evolution of the constituents of the enzyme II complexes has been driven largely by horizontal gene transfer whereas vertical inheritance has been prevalent in the general phosphoryl transfer proteins in some bacter…
Characterization of PAMP/PRR interactions in European eel (Anguilla anguilla) macrophage-like primary cell cultures
2013
The eel (Anguilla anguilla) has been identified as a vulnerable species with stocks dramatically declining over the past decade. In an effort to support the species from overfishing of wild stocks increased interest in eel aquaculture has been notable. In order to expand the scarce knowledge concerning the biology of this species significant research efforts are required in several fields of biology. The development of cell culture systems to study the immune response is a key step towards an increased understanding of the immune response and to develop resources to support further study in this threatened species. Macrophages are one of the most important effector cells of the innate immun…
Implications of cysteine metabolism in the heavy metal response in Trichoderma harzianum and in three Fusarium species
2009
We studied the ability of four different fungal species, Trichoderma harzianum, Fusarium antophyllum, Fusarium compactum and Fusarium phyllophilum, to grow in the presence of heavy metals, and monitored their cysteine and glutathione content and the activity of O-acetylserine(thiol)lyase (OASTL), which is involved in cysteine biosynthesis. Zn and Pb did not affect fungal growth or sporulation at the concentrations used, whereas Cd and Hg did. In most cases, cysteine and glutathione content was higher when fungi were grown in the presence of toxic metals. As T. harzianum and F. phyllophilum presented the best growth rate on Cd and Hg, they were selected to further analyse the accumulation of…