A collection of inducible transcription factor-glucocorticoid receptor fusion lines for functional analyses in Arabidopsis thaliana.

Arabidopsis possesses approximately 2000 transcription factors (TFs) in its genome. They play pivotal roles in various biological processes but analysis of their function has been hampered by the overlapping nature of their activities. To uncover clues to their function, we generated inducible TF lines using glucocorticoid receptor (GR) fusion techniques in Arabidopsis. These TF-GR lines each express one of 1255 TFs as a fusion with the GR gene. An average 14 lines of T2 transgenic TF-GR lines were generated for each TF to monitor their function. To evaluate these transcription lines, we induced the TF-GR lines of phytochrome-interacting factor 4, which controls photomorphogenesis, with synthetic glucocorticoid dexamethasone. These phytochrome-interacting factor 4-GR lines showed the phenotype described in a previous report. We performed screening of the other TF-GR lines for TFs involved in light signaling under blue and far-red light conditions and identified 13 novel TF candidates. Among these, we found two lines showing higher anthocyanin accumulation under light conditions and we examined the regulating genes. These results indicate that the TF-GR lines can be used to dissect functionally redundant genes in plants and demonstrate that the TF-GR line collection can be used as an effective tool for functional analysis of TFs.

MOROKOSHI: transcriptome database in Sorghum bicolor.

In transcriptome analysis, accurate annotation of each transcriptional unit and its expression profile is essential. A full-length cDNA (FL-cDNA) collection facilitates the refinement of transcriptional annotation, and accurate transcription start sites help to unravel transcriptional regulation. We constructed a normalized FL-cDNA library from eight growth stages of aerial tissues in Sorghum bicolor and isolated 37,607 clones. These clones were Sanger sequenced from the 5' and/or 3' ends and in total 38,981 high-quality expressed sequence tags (ESTs) were obtained. About one-third of the transcripts of known genes were captured as FL-cDNA clone resources. In addition to these, we also annotated 272 novel genes, 323 antisense transcripts and 1,672 candidate isoforms. These clones are available from the RIKEN Bioresource Center. After obtaining accurate annotation of transcriptional units, we performed expression profile analysis. We carried out spikelet-, seed- and stem-specific RNA sequencing (RNA-Seq) analysis and confirmed the expression of 70.6% of the newly identified genes. We also downloaded 23 sorghum RNA-Seq samples that are publicly available and these are shown on a genome browser together with our original FL-cDNA and RNA-Seq data. Using our original and publicly available data, we made an expression profile of each gene and identified the top 20 genes with the most similar expression. In addition, we visualized their relationships in gene co-expression networks. Users can access and compare various transcriptome data from S, bicolor at http://sorghum.riken.jp.

Background Factors Affecting the Radiation Exposure of the Lens of the Eye among Nurses in Interventional Radiology: A Quantitative Observational Study.

With the International Commission on Radiological Protection's (ICRP) reduction in the radiation dose threshold for cataracts, evaluating and preventing radiation exposure to the lens of the eye among interventional radiology (IR) staff have become urgent tasks. In this study, we focused on differences in lens-equivalent dose (HT Lens) to which IR nurses in three hospitals were exposed and aimed to identify factors underlying these differences. According to analyses of time-, distance-, and shielding-related factors, the magnitude of the HT Lens dose to which IR nurses were exposed could be explained not by time or shielding but by the distance between the X-ray exposure field and the location of the IR nurse. This distance tended to be shorter in hospitals with fewer staff. The most effective means of reducing the exposure of the lenses of IR nurses' eyes to radiation is to position them at least two meters from the radiation source during angiography procedures. However, some hospitals must provide IR departments with comparatively few staff. In work environments where it is infeasible to reduce exposure by increasing distance, interventions to reduce time by managing working practices and investment in shielding equipment are also important. This study was not registered.

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. Increased accumulation of RTs is detected in the nonsense-mediated mRNA decay (NMD)-deficient mutants compared with wild type, and the second open reading frames (ORFs) of bicistronic mRNAs are rarely translated in contrast to the first ORFs. Intergenic splicing (IS) events which occur between first and second genes are seen in 158 RTs. Splicing inhibition assays suggest that IS eliminates the chance of transcription termination at the polyadenylation sites of the first gene and promotes accumulation of RTs. These results indicate that RTs arise from genes whose transcription termination is relatively weak or attenuated by IS, but NMD selectively degrades them. Ultimately, this report presents a eukaryotic strategy for RNA metabolism.

The Effect of Pre-Operative Verbal Confirmation for Interventional Radiology Physicians on Their Use of Personal Dosimeters and Personal Protective Equipment.

Interventional radiology (IR) physicians must be equipped with personal passive dosimeters and personal protective equipment (PPE); however, they are inconsistently used. Therefore, we aimed to explore practical measures to increase PPE usage and ascertain whether these measures could lead to an actual decrease in exposure doses to IR physicians. Dosimeters and PPE were visually inspected. Then, a pre-operative briefing was conducted as a direct intervention, and the use of dosimeters and PPE was verbally confirmed. Finally, the intervention effect was verified by measuring the use rates and individual exposure doses. Because of the intervention, the use rate markedly improved and was almost 100%. However, both the effective dose rate (effective dose/fluoroscopy time) and the lens equivalent dose rate (lens equivalent dose/fluoroscopy time) showed that the intervention led to a statistically significant increase in exposure (effective dose rate: p = 0.033; lens equivalent dose rate: p = 0.003). In conclusion, the proper use of dosimeters and PPE raised the radiation exposure values for IR physicians immediately after the intervention, which was hypothesized to be due to the inclusion of exposure overlooked to date and the changes in the dosimeter management method from a single- to a double-dosimeter approach.

Granulocyte and monocyte apheresis therapy for patients with active ulcerative colitis associated with COVID-19: a case report.

Coronavirus disease 2019 (COVID-19), caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is now a pandemic. Although several treatment guidelines have been proposed for patients who have both inflammatory bowel disease and COVID-19, immunosuppressive therapy is essentially not recommended, and the treatment options are limited. Even in the COVID-19 pandemic, adjuvant adsorptive granulocyte and monocyte apheresis may safely bring ulcerative colitis (UC) into remission by removing activated myeloid cells without the use of immunosuppressive therapy. Our patient was a 25-year-old Japanese male with UC and COVID-19. This is the first case report of the induction of UC remission with granulocyte and monocyte apheresis treatment for active UC associated with COVID-19.

Strategy to Reduce the Collective Equivalent Dose for the Lens of the Physician's Eye Using Short Radiation Protection Curtains to Prevent Cataracts.

A short curtain that improves on the low versatility of existing long curtains was developed as a dedicated radiation protective device for the over-table tube fluorographic imaging units. The effect of this short curtain in preventing cataracts was then examined. First, the physician lens dose reduction rate was obtained at the position of the lens. Next, the reduction rate in the collective equivalent dose for the lens of the physician's eye was estimated. The results showed that lens dose reduction rates with the long curtain and the short curtain were 88.9% (literature-based value) and 17.6%, respectively, higher with the long curtain. In our hospital, the reduction rate in the collective equivalent dose for the lens of the physician's eye was 9.8% and 17.6% with a procedures mixture, using the long curtain where technically possible and no curtain in all other procedures, and the short curtain in all procedures, respectively, higher with the short curtain. Moreover, a best available for curtains raised the reduction rate in the collective equivalent dose for the lens of the physician's eye a maximum of 25.5%. By introducing the short curtain, it can be expected to have an effect in preventing cataracts in medical staff.

Development and assessment of an educational application for the proper use of ceiling-suspended radiation shielding screens in angiography rooms using augmented reality technology.

PURPOSE: An augmented reality (AR) application to help medical staff involved in interventional radiology (IR) learn how to properly use ceiling-suspended radiation shielding screens was created, and its utility was tested from the perspective of learner motivation. METHOD: The distribution of scattered radiation in an angiography room was visualized with an AR application in three settings: when a ceiling-suspended radiation shielding screen is not used (incorrect); when there is a gap between the bottom edge of the shielding screen and the patient's torso (incorrect); and when there is no gap between the bottom edge of the shielding screen and the patient's torso (correct). This AR application was used by 33 medical staff, after which an Instructional Materials Motivation Survey (IMMS) based on the John Keller's ARCS (four categories of Attention, Relevance, Confidence, and Satisfaction) Motivation Model, consisting of 36-items with responses on a 5-point (1-5) Likert scale, was conducted. RESULTS: The overall score was a high 4.67 ± 0.30 (mean ± standard deviation). Physician's scores tended to be lower than those of other medical staff in the categories of Attention, Relevance, and Satisfaction (not statistically significant). CONCLUSIONS: The AR application to learn how to properly use ceiling-suspended radiation shielding screens was highly rated from the perspective of learner motivation.

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. DUC1 detects light within the orange/far-red and blue spectra, and acts as a dual photoreceptor. Analyses of its genome reveal the possible mechanisms of light adaptation. Genes for the light-harvesting complex (LHC) are duplicated and transcriptionally regulated under monochromatic orange/blue light, suggesting P. provasolii has acquired environmental adaptability to a wide range of light spectra and intensities.

Systematic approaches to using the FOX hunting system to identify useful rice genes.

Ectopic gene expression, or the gain-of-function approach, has the advantage that once the function of a gene is known the gene can be transferred to many different plants by transformation. We previously reported a method, called FOX hunting, that involves ectopic expression of Arabidopsis full-length cDNAs in Arabidopsis to systematically generate gain-of-function mutants. This technology is most beneficial for generating a heterologous gene resource for analysis of useful plant gene functions. As an initial model we generated more than 23,000 independent Arabidopsis transgenic lines that expressed rice fl-cDNAs (Rice FOX Arabidopsis lines). The short generation time and rapid and efficient transformation frequency of Arabidopsis enabled the functions of the rice genes to be analyzed rapidly. We screened rice FOX Arabidopsis lines for alterations in morphology, photosynthesis, element accumulation, pigment accumulation, hormone profiles, secondary metabolites, pathogen resistance, salt tolerance, UV signaling, high light tolerance, and heat stress tolerance. Some of the mutant phenotypes displayed by rice FOX Arabidopsis lines resulted from the expression of rice genes that had no homologs in Arabidopsis. This result demonstrated that rice fl-cDNAs could be used to introduce new gene functions in Arabidopsis. Furthermore, these findings showed that rice gene function could be analyzed by employing Arabidopsis as a heterologous host. This technology provides a framework for the analysis of plant gene function in a heterologous host and of plant improvement by using heterologous gene resources.

A novel rat model of inflammatory bowel disease developed using a device created with a 3D printer.

OBJECTIVE: Inflammatory bowel disease (IBD) is an intractable condition. Existing models of experimental IBD are limited by their inability to create consistent ulcers between animals. The aim of this study was to develop a novel model of experimental colitis with ulcers of reproducible size. DESIGN: We used a 3D printer to fabricate a novel device containing a small window (10 × 10 mm) that could be inserted rectally to facilitate the creation of a localized ulcer in the rat intestinal mucosa. The mucosa within the window of the device was exposed to 2,4,6-trinitrobenzene sulfonic acid (TNBS) to generate ulceration. We evaluated the effects of conventional drug therapies (mesalazine and prednisolone) and local transplantation of allogeneic adipose-derived mesenchymal stem cells (ASCs) on ulcer size (measured from photographic images using image analysis software) and degree of inflammation (assessed histologically). RESULTS: The novel method produced localized, circular or elliptical ulcers that were highly reproducible in terms of size and depth. The pathological characteristics of the lesions were similar to those reported previously for conventional models of TNBS-induced colitis that show greater variation in ulcer size. Ulcer area was significantly reduced by the administration of mesalazine or prednisolone as an enema or localized injection of ASCs. CONCLUSION: The new model of TNBS-induced colitis, made with the aid of a device fabricated by 3D printing, generated ulcers that were reproducible in size. We anticipate that our new model of colitis will provide more reliable measures of treatment effects and prove useful in future studies of IBD therapies.

The AtXTH28 gene, a xyloglucan endotransglucosylase/hydrolase, is involved in automatic self-pollination in Arabidopsis thaliana.

Successful automatic self-pollination in flowering plants is dependent on the correct development of reproductive organs. In the stamen, the appropriate growth of the filament, which largely depends on the mechanical properties of the cell wall, is required to position the anther correctly close to the stigma at the pollination stage. Xyloglucan endotransglucosylase/hydrolases (XTHs) are a family of enzymes that mediate the construction and restructuring of xyloglucan cross-links, thereby controlling the extensibility or mechanical properties of the cell wall in a wide variety of plant tissues. Our reverse genetic analysis has revealed that a loss-of-function mutation of an Arabidopsis XTH family gene, AtXTH28, led to a decrease in capability for self-pollination, probably due to inhibition of stamen filament growth. Our results also suggest that the role of AtXTH28 in the development of the stamen is not functionally redundant with its closest paralog, AtXTH27. Thus, our finding indicates that AtXTH28 is specifically involved in the growth of stamen filaments, and is required for successful automatic self-pollination in certain flowers in Arabidopsis thaliana.

Simple construction of plant RNAi vectors using long oligonucleotides.

RNA interference (RNAi) is one of the most important technologies currently available for the analysis of gene function. However, despite the development of various methods, it is still difficult to construct RNAi vectors for plants with the appropriate inverted repeat fragments to produce double-stranded RNA for knockdown experiments. To solve this problem we have developed an easy and simple method to make RNAi constructs using two long oligonucleotides consisting of partially complementary sequences without the need for PCR amplification and multiple cloning steps. CHS RNAi plants generated using this method showed yellow seed color and a decrease in antocyanin content--phenotypes typically observed in CHS loss-of-function mutants. Moreover, we demonstrated specific knockdown of both the PHYA and PHYB genes using a tandem RNAi construct. This method thus represents a powerful tool for gene knockdown in plants.

Improvement of Agrobacterium-mediated transformation for tannin-producing sorghum.

Sorghum (Sorghum bicolor L.) ranks as the fifth most widely planted cereal in the world and is used for food as well as a biomass plant for ethanol production. Use of the TX430 non-tannin sorghum variety has enhanced Agrobacterium-mediated sorghum transformation. These protocols could not be applied, however, to other tannin producing sorghum varieties such as the BTx623 model cultivar for sorghum with full genome information of sorghum. Here we report an improved protocol for Agrobacterium-mediated genetic transformation of tannin-producing sorghum variety BTx623. We successfully developed modification of root regeneration condition for generation of transgenic plant of BTx623. We inoculated immature embryos with Agrobacterium tumefaciens strain EHA105 harboring pMDC32-35S-GFP to generate transgenic plants. In the root regeneration step, we found that regeneration from transformed calli was affected by tannin. For root regeneration, shoots that appeared were not transferred to agar plate, but instead transferred to vermiculite in a plastic pod. Direct planting of regenerated shoots into vermiculite prevented the toxic effect of tannin. Root regeneration efficiency from calli emerged shoots in vermiculite was 78.57%. Presence of sGFP transgene in the genome of transgenic plants was confirmed by PCR and sGFP expression was confirmed in transgenic plants. This improved protocol of Agrobacterium-mediated transformation for tannin-producing sorghum BTx623 could be a useful tool for functional genomics using this plant.

Establishment and characterization of transplantable tumor line (KB) and cell lines (KB-P and KB-D8) from a rat thymus-derived dendritic cell sarcoma.

A transplantable tumor line (KB) was established in syngeneic rats from a naturally occurring sarcoma that had arisen in the thymus of a 24-month-old male F344 rat. Further, a cell line (KB-P) was induced from KB and a cloned cell line (KB-D8) was isolated from KB-P. The primary thymic tumor and KB tumors showed heterogeneous histological growth patterns such as sheet-like, ill-defined bundle, fascicular and interwoven fashions, consisting of spindle cells, oval cells and histiocytic large round cells. Immunohistochemically, neoplastic cells in KB tumors and KB-P and KB-D8 cultures reacted to vimentin and were labeled with antibodies of OX6 (for rat major histocompatibility complex class-II antigens), ED5 (for rat follicular dendritic cells; FDCs) and RED-1 (for interdigitating dendritic cells) in varying degrees, indicating that neoplastic cells exhibited the immunophenotypes of rat dendritic cells. In addition, neoplastic cells were immunoreactive to ED1 (for rat monocytes/macrophages) and ED2 (for rat tissue macrophages), and also showed positive reactions to histiocytic lysosomal enzymes such as acid phosphatase and non-specific esterase. Ultrastructurally, neoplastic cells had cell surface projections, cisterna-like structures and variously developed lysosomes in the cytoplasm. Based on these findings, the present tumor was regarded as dendritic cell-derived sarcoma capable of expressing macrophage-like and histiocytic nature. A reverse-transcription polymerase chain reaction method revealed that the addition of lipopolysaccharide dose dependently increased the expression of mRNA of transforming growth factor-beta1, a proinflammatory factor, in KB-D8 cells. The transplantable line (KB) and cell lines (KB-P and KB-D8) may become useful tools for studying the histogenesis and pathobiological functions of dendritic cells.