De novo assembly and characterization of the transcriptome of the newly described dinoflagellate Ansanella granifera: Spotlight on flagellum-associated genes.

Many dinoflagellates are known to cause red tides and often outgrow non-motile diatoms and motile small flagellates through active vertical migration between well-lit surface and eutrophic deep waters and/or by locating and ingesting prey cells. Their flagella play important roles in these two critical behaviors. However, the structural and functional genes of dinoflagellate flagella are very little known.

Whole genome sequence and genome annotation of Colletotrichum acutatum, causal agent of anthracnose in pepper plants in South Korea.

Colletotrichum acutatum is a destructive fungal pathogen which causes anthracnose in a wide range of crops. Here we report the whole genome sequence and annotation of C. acutatum strain KC05, isolated from an infected pepper in Kangwon, South Korea.

A library of TAL effector nucleases spanning the human genome.

Transcription activator-like (TAL) effector nucleases (TALENs) can be readily engineered to bind specific genomic loci, enabling the introduction of precise genetic modifications such as gene knockouts and additions. Here we present a genome-scale collection of TALENs for efficient and scalable gene targeting in human cells. We chose target sites that did not have highly similar sequences elsewhere in the genome to avoid off-target mutations and assembled TALEN plasmids for 18,740 protein-coding genes using a high-throughput Golden-Gate cloning system.

Flexible alignment of small molecules using the penalty method.

An efficient flexible alignment method using the penalty method, called FAP, is described. FAP is a pairwise alignment algorithm that matches a flexible sample to a rigid template. It is a pure atom-based 3D method that utilizes the modified SEAL similarity index combined with an energy penalty term.

Conformational flexibility in mammalian 15S-lipoxygenase: Reinterpretation of the crystallographic data.

Lipoxygenases (LOXs) are a family of nonheme iron dioxygenases that catalyze the regioselective and stereospecific hydroperoxidation of polyunsaturated fatty acids, and are involved in a variety of inflammatory diseases and cancers. The crystal structure of rabbit 15S-LOX1 that was reported by Gillmor et al. in 1997 has played key roles for understanding the properties of mammalian LOXs.