Integration of string and de Bruijn graphs for genome assembly.

MOTIVATION: String and de Bruijn graphs are two graph models used by most genome assemblers. At present, none of the existing assemblers clearly outperforms the others across all datasets. We found that although a string graph can make use of entire reads for resolving repeats, de Bruijn graphs can naturally assemble through regions that are error-prone due to sequencing bias. RESULTS: We developed a novel assembler called StriDe that has advantages of both string and de Bruijn graphs. First, the reads are decomposed adaptively only in error-prone regions. Second, each paired-end read is extended into a long read directly using an FM-index. The decomposed and extended reads are used to build an assembly graph. In addition, several essential components of an assembler were designed or improved. The resulting assembler was fully parallelized, tested and compared with state-of-the-art assemblers using benchmark datasets. The results indicate that contiguity of StriDe is comparable with top assemblers on both short-read and long-read datasets, and the assembly accuracy is high in comparison with the others. AVAILABILITY AND IMPLEMENTATION: https://github.com/ythuang0522/StriDe CONTACT: : ythuang@cs.ccu.edu.tw SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family.

The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast (cp) genomes. However, ndh genes are truncated or deleted in some autotrophic Epidendroideae orchid cp genomes. To determine the evolutionary timing of the gene deletions and the genomic locations of the various ndh genes in orchids, the cp genomes of Vanilla planifolia, Paphiopedilum armeniacum, Paphiopedilum niveum, Cypripedium formosanum, Habenaria longidenticulata, Goodyera fumata and Masdevallia picturata were sequenced; these genomes represent Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae subfamilies. Four orchid cp genome sequences were found to contain a complete set of ndh genes. In other genomes, ndh deletions did not correlate to known taxonomic or evolutionary relationships and deletions occurred independently after the orchid family split into different subfamilies. In orchids lacking cp encoded ndh genes, non cp localized ndh sequences were identified. In Erycina pusilla, at least 10 truncated ndh gene fragments were found transferred to the mitochondrial (mt) genome. The phenomenon of orchid ndh transfer to the mt genome existed in ndh-deleted orchids and also in ndh containing species.

Controlled rupture of magnetic polyelectrolyte microcapsules for drug delivery.

In this study, a magnetic-sensitive microcapsule was prepared using Fe 3O 4/poly(allylamine) (Fe 3O 4/PAH) polyelectrolyte to construct the shell. Structural integrity, microstructural evolution, and corresponding release behaviors of fluorescence dyes and doxorubicin were systematically investigated. Experimental observations showed that the presence of the magnetic nanoparticles in the shell structure allowed the shell structure to evolve from nanocavity development to final rupture of the shell under a given magnetic stimulus of different time durations. Such a microstructural evolution of the magnetic sensitive shell structure explained a corresponding variation of the drug release profile, from relatively slow release to burst-like behavior at different stages of stimulus. It has proposed that the presence of magnetic nanoparticles produced heat, due to magnetic energy dissipation (as Brown and Neel relaxations), and mechanical vibration and motion that induced stress development in the thin shell. Both mechanisms significantly accelerated the relaxation of the shell structure, causing such a microstructural evolution. With such a controllable microstructural evolution of the magnetic-sensitive shell structure, active substances can be well-regulated in a manageable manner with a designable profile according to the time duration under magnetic field. A cell culture study also indicated that the magnetic-sensitive microcapsules allowed a rapid uptake by the A549 cell line, a cancerous cell line, suggesting that the magnetic-sensitive microcapsule with controllable rupturing behavior of the shell offers a potential and effective drug carrier for anticancer applications.