The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition

The degradation of the poly(A) tail is crucial for posttranscriptional gene regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN) is one of the major mammalian 3′ specific exo-ribonucleases involved in the degradation of the mRNA poly(A) tail, and it is also involved in the regulation of translation in early embryonic development. The interaction between PARN and the m7GpppG cap of mRNA plays a key role in stimulating the rate of deadenylation. Here we report the solution structures of the cap-binding domain of mouse PARN with and without the m7GpppG cap analog. The structure of the cap-binding domain adopts the RNA recognition motif (RRM) with a characteristic α-helical extension at its C-terminus, which covers the β-sheet surface (hereafter referred to as PARN RRM). In the complex structure of PARN RRM with the cap analog, the base of the N7-methyl guanosine (m7G) of the cap analog stacks with the solvent-exposed aromatic side chain of the distinctive tryptophan residue 468, located at the C-terminal end of the second β-strand. These unique structural features in PARN RRM reveal a novel cap-binding mode, which is distinct from the nucleotide recognition mode of the canonical RRM domains

One-Step Detection of the 2009 Pandemic Influenza A(H1N1) Virus by the RT-SmartAmp Assay and Its Clinical Validation

<div><h3>Background</h3><p>In 2009, a pandemic (pdm) influenza A(H1N1) virus infection quickly circulated globally resulting in about 18,000 deaths around the world. In Japan, infected patients accounted for 16% of the total population. The possibility of human-to-human transmission of highly pathogenic novel influenza viruses is becoming a fear for human health and society.</p> <h3>Methodology</h3><p>To address the clinical need for rapid diagnosis, we have developed a new method, the “RT-SmartAmp assay”, to rapidly detect the 2009 pandemic influenza A(H1N1) virus from patient swab samples. The RT-SmartAmp assay comprises both reverse transcriptase (RT) and isothermal DNA amplification reactions in one step, where RNA extraction and PCR reaction are not required. We used an exciton-controlled hybridization-sensitive fluorescent primer to specifically detect the HA segment of the 2009 pdm influenza A(H1N1) virus within 40 minutes without cross-reacting with the seasonal A(H1N1), A(H3N2), or B-type (Victoria) viruses.</p> <h3>Results and Conclusions</h3><p>We evaluated the RT-SmartAmp method in clinical research carried out in Japan during a pandemic period of October 2009 to January 2010. A total of 255 swab samples were collected from outpatients with influenza-like illness at three hospitals and eleven clinics located in the Tokyo and Chiba areas in Japan. The 2009 pdm influenza A(H1N1) virus was detected by the RT-SmartAmp assay, and the detection results were subsequently compared with data of current influenza diagnostic tests (lateral flow immuno-chromatographic tests) and viral genome sequence analysis. In conclusion, by the RT-SmartAmp assay we could detect the 2009 pdm influenza A(H1N1) virus in patients' swab samples even in early stages after the initial onset of influenza symptoms. Thus, the RT-SmartAmp assay is considered to provide a simple and practical tool to rapidly detect the 2009 pdm influenza A(H1N1) virus.</p> </div

LuminantCube: Omnidirectional and Auto-stereoscopic 3D Display using Diffusion of Laser-light within a Micro Region

STSS(International Symposium on Socially and Technically Symbiotic Systems)/ISSNP(International Symposium on Symbiotic Nuclear Power Systems) 2015: August 25-28, Main Campus of Kyoto University.Standard flat screen 3D displays such as 3D-televisions use parallax to replicate spatial effect within the plane. However, such types require wearing special glass-like equipment and both viewing angle and total number of viewers are very limited. Thus, the present paper proposes a new 3 dimensional display named “LuminantCube”, which is able to provide omnidirectional and auto-stereoscopic views. LuminantCube, consisted of a glass cuboid and laser pico-projectors, uses diffusion of lights projected from the projectors, caused within a volumetrically arranged micro voids processed numerously and randomly inside the glass. LuminantCube will be able to achieve high resolution and contrast ratio by optimizing the algorithm of converting projector pixel to display pixel for multiple projectors for the former and overlapping multiple light rays from multiple projectors for each individual micro voids for the latter

Development of automatic matching and image quality improving methods for scattering 3D display

Up to this day, many types of 3D displays have been developed. However, there remain some challenges in the displays, for example, restriction of view points and vergence-accommodation conflict. A 3D display was proposed in the past using light diffusion within 3-dimensionally positioned micro voids processed in a crystal glass cuboid. It is able to present 3D objects to any number of simultaneous viewers at any viewpoint, without wearing any kind of special glass-like equipments. However, in order to successfully present 3D objects, the projection must be adjusted precisely for each individual micro void by investigating the correspondence between each projector pixel and micro voids. This process not only requires a great amount of user's effort but also consumes a lot of time. Hence, for this research, pixel-to-void matching methods which can automatically find out correspondence between each projector pixel and micro voids by using a camera were developed. These methods were verified in the experimental systems to be able to perform such matching procedure automatically and accurately. In addition, using multiple projectors, brightness and resolution of the display was improved. Two types of the displays were developed, one aimed to improve especially its brightness and the other aimed to improve especially its resolution. While the latter one resulted in higher resolution but in subjective evaluation experiment no improvement of visibilities was verified, the former one resulted in higher brightness and it was verified to have improved visibilities in subjective evaluation experiment

Development and Evaluation of Calibration Methods for an Autoscopic 3D Display using Light Diffusion within Micro Regions

[The 16th International Meeting on Information Display (IMID 2016)] Date: August 23-26, 2016/Location: ICC Jeju, Jeju, Kore

Investigation of cystine as differential diagnostic biomarker between astrocytomas and oligodendrogliomas based on global- and targeted analysis using liquid chromatography/tandem mass spectrometric analysis

Astrocytoma and oligodendroglioma are primary brain tumors classified as gliomas. Because there is difference in the prognostic significance of the extent of resection between IDH-mutant astrocytoma and oligodendroglioma, intraoperative differential diagnosis between them provides important information for optimal extent of resection. Although the characteristics of genetic mutations and chromosomal aberrations in both tumors have been reported, there is no molecular diagnostic methods that is able to be used quickly and simply for differentiate the two tumors. Therefore, we aimed to search for biomarker candidates for differentiating them with metabolome analysis using liquid chromatography/tandem mass spectrometry and develop a molecular diagnostic method based on quantitative analysis.We searched for peaks that differed in two types of gliomas using global metabolomics. Next, we identified five biomarker candidates as hypoxanthine, inosine, cystine, proline and uric acid, respectively. Next, we developed an LC/MS/MS analytical method for five biomarker candidates and quantified them in brain tumors. Cystine had significantly lower amounts in astrocytomas than in oligodendrogliomas. We developed two prediction models for differentiation of the two gliomas and validated them using the separated two dataset. The logistic regression model with only cystine provided the best prediction performance. It was suggested that mass spectrometric analysis of cystine in surgery might be useful for differentiating astrocytoma and oligodendroglioma with 91.7% positive prediction value and 80.0% specificity whereas negative predictive value and sensitivity was lesser than 70%, so that further exploration for unknown metabolite is mandatory