Purified Mesenchymal Stem Cells Are an Efficient Source for iPS Cell Induction

Induced pluripotent stem (iPS) cells are generated from mouse and human somatic cells by the forced expression of defined transcription factors. Although most somatic cells are capable of acquiring pluripotency with minimal gene transduction, the poor efficiency of cell reprogramming and the uneven quality of iPS cells are still important problems. In particular, the choice of cell type most suitable for inducing high-quality iPS cells remains unclear.Here, we generated iPS cells from PDGFRα+ Sca-1+ (PαS) adult mouse mesenchymal stem cells (MSCs) and PDGFRα⁻ Sca-1⁻ osteo-progenitors (OP cells), and compared the induction efficiency and quality of individual iPS clones. MSCs had a higher reprogramming efficiency compared with OP cells and Tail Tip Fibroblasts (TTFs). The iPS cells induced from MSCs by Oct3/4, Sox2, and Klf4 appeared to be the closest equivalent to ES cells by DNA microarray gene profile and germline-transmission efficiency.Our findings suggest that a purified source of undifferentiated cells from adult tissue can produce high-quality iPS cells. In this context, prospectively enriched MSCs are a promising candidate for the efficient generation of high-quality iPS cells

KAGRA: 2.5 Generation Interferometric Gravitational Wave Detector

The recent detections of gravitational waves (GWs) reported by LIGO/Virgocollaborations have made significant impact on physics and astronomy. A globalnetwork of GW detectors will play a key role to solve the unknown nature of thesources in coordinated observations with astronomical telescopes and detectors.Here we introduce KAGRA (former name LCGT; Large-scale Cryogenic Gravitationalwave Telescope), a new GW detector with two 3-km baseline arms arranged in theshape of an "L", located inside the Mt. Ikenoyama, Kamioka, Gifu, Japan.KAGRA's design is similar to those of the second generations such as AdvancedLIGO/Virgo, but it will be operating at the cryogenic temperature with sapphiremirrors. This low temperature feature is advantageous for improving thesensitivity around 100 Hz and is considered as an important feature for thethird generation GW detector concept (e.g. Einstein Telescope of Europe orCosmic Explorer of USA). Hence, KAGRA is often called as a 2.5 generation GWdetector based on laser interferometry. The installation and commissioning ofKAGRA is underway and its cryogenic systems have been successfully tested inMay, 2018. KAGRA's first observation run is scheduled in late 2019, aiming tojoin the third observation run (O3) of the advanced LIGO/Virgo network. In thiswork, we describe a brief history of KAGRA and highlights of main feature. Wealso discuss the prospects of GW observation with KAGRA in the era of O3. Whenoperating along with the existing GW detectors, KAGRA will be helpful to locatea GW source more accurately and to determine the source parameters with higherprecision, providing information for follow-up observations of a GW triggercandidate

Application of independent component analysis to the iKAGRA data

We apply independent component analysis (ICA) to real data from a gravitational wave detector for the first time. Specifically, we use the iKAGRA data taken in April 2016, and calculate the correlations between the gravitational wave strain channel and 35 physical environmental channels. Using a couple of seismic channels which are found to be strongly correlated with the strain, we perform ICA. Injecting a sinusoidal continuous signal in the strain channel, we find that ICA recovers correct parameters with enhanced signal-to-noise ratio, which demonstrates the usefulness of this method. Among the two implementations of ICA used here, we find the correlation method yields the optimal results for the case of environmental noise acting on the strain channel linearly

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

First cryogenic test operation of underground km-scale gravitational-wave observatory KAGRA

KAGRA is a second-generation interferometric gravitational-wave detector with 3 km arms constructed at Kamioka, Gifu, Japan. It is now in its final installation phase, which we call bKAGRA (baseline KAGRA), with scientific observations expected to begin in late 2019. One of the advantages of KAGRA is its underground location of at least 200 m below the ground surface, which reduces seismic motion at low frequencies and increases the stability of the detector. Another advantage is that it cools down the sapphire test mass mirrors to cryogenic temperatures to reduce thermal noise. In April-May 2018, we operated a 3 km Michelson interferometer with a cryogenic test mass for 10 d, which was the first time that km-scale interferometer was operated at cryogenic temperatures. In this article, we report the results of this 'bKAGRA Phase 1' operation. We have demonstrated the feasibility of 3 km interferometer alignment and control with cryogenic mirrors

Construction of KAGRA: An underground gravitational-wave observatory

The major construction and initial-phase operation of a second-generation gravitational-wave detector, KAGRA, has been completed. The entire 3 km detector is installed underground in a mine in order to be isolated from background seismic vibrations on the surface. This allows us to achieve a good sensitivity at low frequencies and high stability of the detector. Bare-bones equipment for the interferometer operation has been installed and the first test run was accomplished in March and April of 2016 with a rather simple configuration. The initial configuration of KAGRA is called iKAGRA. In this paper, we summarize the construction of KAGRA, including a study of the advantages and challenges of building an underground detector, and the operation of the iKAGRA interferometer together with the geophysics interferometer that has been constructed in the same tunnel. © The Author(s) 2018. Published by Oxford University Press on behalf of the Physical Society of Japan

Application of independent component analysis to the iKAGRA data

We apply independent component analysis (ICA) to real data from a gravitational wave detector for the first time. Specifically, we use the iKAGRA data taken in April 2016, and calculate the correlations between the gravitational wave strain channel and 35 physical environmental channels. Using a couple of seismic channels which are found to be strongly correlated with the strain, we perform ICA. Injecting a sinusoidal continuous signal in the strain channel, we find that ICA recovers correct parameters with enhanced signal-to-noise ratio, which demonstrates the usefulness of this method. Among the two implementations of ICA used here, we find the correlation method yields the optimal results for the case of environmental noise acting on the strain channel linearly