The blue light signaling inhibitor 3-bromo-7-nitroindazole affects gene translation at the initial reception of blue light in young seedlings.

Initial light reception after germination is a dramatic life event when a seedling starts proper morphogenesis. Blue light contains a range of light wavelengths that plants can perceive. A previous report suggested that the chemical compound 3-bromo-7-nitroindazole (3B7N) inhibits blue light-mediated suppression of hypocotyl elongation by physically interacting with the blue light receptor Cryptochrome 1 (CRY1).

ARGONAUTE1-binding Tudor domain proteins function in small interfering RNA production for RNA-directed DNA methylation.

Transposable elements (TEs) contribute to plant evolution, development, and adaptation to environmental changes, but the regulatory mechanisms are largely unknown. RNA-directed DNA methylation (RdDM) is 1 TE regulatory mechanism in plants. Here, we identified that novel ARGONAUTE 1 (AGO1)-binding Tudor domain proteins Precocious dissociation of sisters C/E (PDS5C/E) are involved in 24-nt siRNA production to establish RdDM on TEs in Arabidopsis thaliana.

Translational activation of ribosome-related genes at initial photoreception is dependent on signals derived from both the nucleus and the chloroplasts in Arabidopsis thaliana.

Light is one of the indispensable elements that plants need in order to grow and develop. In particular, it is essential for inducing morphogenesis, such as suppression of hypocotyl elongation and cotyledon expansion, that plants undergo when they first emerge after germination. However, there is a lack of knowledge about the gene expression and, in particular, the translational levels that induce a response upon light exposure.

Intergenic splicing-stimulated transcriptional readthrough is suppressed by nonsense-mediated mRNA decay in Arabidopsis.

Recent emerging evidence has shown that readthrough transcripts (RTs), including polycistronic mRNAs, are also transcribed in eukaryotes. However, the post-transcriptional regulation for these remains to be elucidated. Here, we identify 271 polycistronic RT-producing loci in Arabidopsis.

Tracking metabolites at single-cell resolution reveals metabolic dynamics during plant mitosis.

Analyzing only one cell allows the changes and characteristics of intracellular metabolites during the chromosome segregation process to be precisely captured and mitotic sub-phases to be dissected at the metabolite level.

Analysis of the Effects of Electronic Medical Records and a Payment Scheme on the Length of Hospital Stay.

Objective: This study analyzed the effects of computerization of medical information systems and a hospital payment scheme on medical care outcomes. Specifically, we examined the effects of Electronic Medical Records (EMRs) and a diagnosis procedure combination/per-diem payment scheme (DPC/PDPS) on the average length of hospital stay (ALOS).

Methods: Post-intervention changes in the monthly ALOS were measured using an interrupted time-series analysis.

Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton.

Photoreceptors are conserved in green algae to land plants and regulate various developmental stages. In the ocean, blue light penetrates deeper than red light, and blue-light sensing is key to adapting to marine environments. Here, a search for blue-light photoreceptors in the marine metagenome uncover a chimeric gene composed of a phytochrome and a cryptochrome (Dualchrome1, DUC1) in a prasinophyte, Pycnococcus provasolii.

Method for Phenotypic Chemical Screening to Identify Cryptochrome Inhibitors.

After germination, plants determine their morphogenesis, such as hypocotyl elongation and cotyledon opening, by responding to various wavelengths of light (photomorphogenesis). Cryptochrome is a blue-light photoreceptor that controls de-etiolation, stomatal opening and closing, flowering time, and shade avoidance. Successful incorporation of these phenotypes as indicators into a chemical screening system results in faster selection of candidate compounds.

Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in .

Natural rubber is the main component of latex obtained from laticifer cells of . For improving rubber yield, it is essential to understand the genetic molecular mechanisms responsible for laticifer differentiation and rubber biosynthesis. Jasmonate enhances both secondary laticifer differentiation and rubber biosynthesis.

uORF Shuffling Fine-Tunes Gene Expression at a Deep Level of the Process.

Upstream open reading frames (uORFs) are present in the 5' leader sequences (or 5' untranslated regions) upstream of the protein-coding main ORFs (mORFs) in eukaryotic polycistronic mRNA. It is well known that a uORF negatively affects translation of the mORF. Emerging ribosome profiling approaches have revealed that uORFs themselves, as well as downstream mORFs, can be translated.

Time-Course Transcriptome Study Reveals Mode of bZIP Transcription Factors on Light Exposure in .

The etiolation process, which occurs after germination, is terminated once light is perceived and then de-etiolation commences. During the de-etiolation period, monochromatic lights (blue, red and far-red) induce differences in gene expression profiles and plant behavior through their respective photoreceptors. ELONGATED HYPOCOTYL 5 (HY5), a bZIP-type transcription factor (TF), regulates gene expression in the de-etiolation process, and other bZIP TFs are also involved in this regulation.

Translational Landscape of Protein-Coding and Non-Protein-Coding RNAs upon Light Exposure in Arabidopsis.

Light is one of the most essential environmental clues for plant growth and morphogenesis. Exposure to blue monochromatic light from darkness is a turning point for plant biological activity, and as a result dramatic changes in gene expression occur. To understand the translational impacts of blue light, we have performed ribosome profiling analysis and called translated open reading frames (ORFs) de novo within not only mRNAs but also non-coding RNAs (ncRNAs).

Inhibition of Pre-mRNA Splicing Promotes Root Hair Development in Arabidopsis thaliana.

Root hairs protruding from epidermal cells increase the surface area for water absorption and nutrient uptake. Various environmental factors including light, oxygen concentration, carbon dioxide concentration, calcium and mycorrhizal associations promote root hair formation in Arabidopsis thaliana. Light regulates the expression of a large number of genes at the transcriptional and post-transcriptional levels; however, there is little information linking the light response to root hair development.

SnRK1 Kinase and the NAC Transcription Factor SOG1 Are Components of a Novel Signaling Pathway Mediating the Low Energy Response Triggered by ATP Depletion.

Plant growth is strictly controlled by cell division, elongation, and differentiation for which adequate supplies of intracellular ATP are required. However, it is unclear how changes in the amount of intracellular ATP affect cell division and growth. To reveal the specific pathway dependent on ATP concentration, we performed analyses on the mitochondria mutation .

The Plant Translatome Surveyed by Ribosome Profiling.

Although transcriptome changes have long been recognized as a mechanism to induce tentative substitution of expressed genes in diverse biological processes in plants, the regulation of translation-the final step of the central dogma of molecular biology-emerged as an alternative and prominent layer in defining the output of genes. Despite these demands, the genome-wide analysis of protein synthesis has posed technical challenges, resulting in the plant translatome being poorly understood. The development of ribosome profiling promises to address the hidden aspects of translation, and its application to plants is revolutionizing our knowledge of the translatome.

Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in .

Plants adapt to alterations in light conditions by controlling their gene expression profiles. Expression of light-inducible genes is transcriptionally induced by transcription factors such as HY5. However, few detailed analyses have been carried out on the control of transcription start sites (TSSs).

A Method for Deriving Quasi-healthy Cohorts From Clinical Data.

We evaluated quasi-healthy cohorts (model cohorts), derived from clinical data, to determine how well they simulated control cohorts. Control cohorts comprised individuals extracted from a public checkup database in Japan, under the condition that their values for 3 basic laboratory tests fall within specific reference ranges (3Ts condition). Model cohorts comprised outpatients, extracted from a clinical database at a hospital, under the 3Ts condition or under the condition that their values for 4 laboratory tests fall within specific reference ranges (4Ts condition).

Evaluation of the Anonymity and Utility of De-Identified Clinical Data Based on Japanese Anonymization Criteria.

We analyze the deterioration of clinical data quality due to anonymization. The result shows that data quality remained high with micro-aggregation and also verify the availability of noise addition to prevent illegal re-identification by matching another personal data.

Chemical-Induced Inhibition of Blue Light-Mediated Seedling Development Caused by Disruption of Upstream Signal Transduction Involving Cryptochromes in Arabidopsis thaliana.

Plants have a remarkable ability to perceive and respond to various wavelengths of light and initiate regulation of different cascades of light signaling and molecular components. While the perception of red light and the mechanisms of its signaling involving phytochromes are largely known, knowledge of the mechanisms of blue light signaling is still limited. Chemical genetics involves the use of diverse small active or synthetic molecules to evaluate biological processes.

Activity and roles of Arabidopsis thaliana XRN family exoribonucleases in noncoding RNA pathways.

RNA metabolism is mediated by several sophisticated exo- or endo- ribonucleases. XRN family proteins are the conserved 5'-3' exoribonucleases in eukaryotes. A.

Modification of plant cell wall structure accompanied by enhancement of saccharification efficiency using a chemical, lasalocid sodium.

The cell wall is one major determinant of plant cell morphology, and is an attractive bioresource. Here, we report a novel strategy to modify plant cell wall property by small molecules. Lasalocid sodium (LS) was isolated by chemical screening to identify molecules that affect the cell morphology of tobacco BY-2 cells.

The Inequality of Patient Profile Information in Japanese Hospitals.

A model dataset of patient profile information was created based on the items used at five Japanese university hospitals, the patient information data elements in Health Level 7 (HL7) v2.5, and the standard datasets for medical information exchange used in Japan. In order to check the validity of the model dataset, a cross-sectional survey was performed.