Inducible Expression of the Restriction Enzyme Uncovered Genome-Wide Distribution and Dynamic Behavior of Histones H4K16ac and H2A.Z at DNA Double-Strand Breaks in Arabidopsis.

DNA double-strand breaks (DSBs) are among the most serious types of DNA damage, causing mutations and chromosomal rearrangements. In eukaryotes, DSBs are immediately repaired in coordination with chromatin remodeling for the deposition of DSB-related histone modifications and variants. To elucidate the details of DSB-dependent chromatin remodeling throughout the genome, artificial DSBs need to be reproducibly induced at various genomic loci.

Cryptic promoter activation occurs by at least two different mechanisms in the Arabidopsis genome.

In gene-trap screening of plant genomes, promoterless reporter constructs are often expressed without trapping of annotated gene promoters. The molecular basis of this phenomenon, which has been interpreted as the trapping of cryptic promoters, is poorly understood. Here, we found that cryptic promoter activation occurs by at least two different mechanisms using Arabidopsis gene-trap lines in which a firefly luciferase (LUC) open reading frame (ORF) without an apparent promoter sequence was expressed from intergenic regions: one mechanism is 'cryptic promoter capturing', in which the LUC ORF captured pre-existing promoter-like chromatin marked by H3K4me3 and H2A.

Preculture in an enriched nutrient medium greatly enhances the -mediated transformation efficiency in T87 cultured cells.

The T87 cell line has been widely used in both basic and biotechnological plant sciences. -mediated transformation of this cell line was reported to be highly efficient when precultured in Gamborg's B5 medium for a few days. However, because we could not obtain the expected efficiency in our laboratory, we further examined the preculture conditions of T87 cells in the -mediated transformation.

De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome.

The manner in which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines.

Kozak Sequence Acts as a Negative Regulator for De Novo Transcription Initiation of Newborn Coding Sequences in the Plant Genome.

The manner in which newborn coding sequences and their transcriptional competency emerge during the process of gene evolution remains unclear. Here, we experimentally simulated eukaryotic gene origination processes by mimicking horizontal gene transfer events in the plant genome. We mapped the precise position of the transcription start sites (TSSs) of hundreds of newly introduced promoterless firefly luciferase (LUC) coding sequences in the genome of Arabidopsis thaliana cultured cells.

Treatment of tetracycline antibiotics by laccase in the presence of 1-hydroxybenzotriazole.

Tetracycline antibiotics are widely used in human and veterinary medicine; however, residual amounts of these antibiotics in the environment are of concern since they could contribute to selection of resistant bacteria. In this study, tetracycline (TC), chlortetracycline (CTC), doxycycline (DC) and oxytetracycline (OTC) were treated with laccase from the white rot fungus Trametes versicolor in the presence of the redox mediator 1-hydroxybenzotriazole (HBT). High performance liquid chromatography demonstrated that DC and CTC were completely eliminated after 15 min, while TC and CTC were eliminated after 1 h.

Elimination of carbamazepine by repeated treatment with laccase in the presence of 1-hydroxybenzotriazole.

Carbamazepine (CBZP) is used as an antiepileptic drug and is highly persistent. In this study, CBZP was treated with laccase from white rot fungus Trametes versicolor in the presence of a redox mediator 1-hydroxybenzotriazole (HBT). A single treatment with laccase and HBT eliminated CBZP by about 22% after 24h, and repeated treatments with laccase and HBT, which were added to the reaction mixture every 8h, helped eliminate about 60% of CBZP after 48h.

Elimination and detoxification of triclosan by manganese peroxidase from white rot fungus.

The antimicrobial and preservative agent triclosan (TCS) is an emerging and persistent pollutant with a ubiquitous presence in the aquatic environment. Thus, TCS was treated with manganese peroxidase (MnP), laccase and the laccase-mediator system with 1-hydroxybenzotriazole. MnP was most effective in eliminating TCS among the three enzymatic treatments, with TCS concentration being reduced by about 94% after 30 min following treatment with 0.

Removal of diclofenac and mefenamic acid by the white rot fungus Phanerochaete sordida YK-624 and identification of their metabolites after fungal transformation.

The non-steroidal anti-inflammatory drugs diclofenac (DCF) and mefenamic acid (MFA) were treated with the white rot fungus Phanerochaete sordida YK-624. DCF completely disappeared and MFA decreased by about 90% after 6 days of treatment. It was also confirmed that the fungus almost completely removed the acute lethal toxicity of DCF and MFA towards the freshwater crustacean Thamnocephalus platyurus after 6 days of treatment.