Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development.

During the phylotypic period, embryos from different genera show similar gene expression patterns, implying common regulatory mechanisms. Here we set out to identify enhancers involved in the initial events of cardiogenesis, which occurs during the phylotypic period. We isolate early cardiac progenitor cells from zebrafish embryos and characterize 3838 open chromatin regions specific to this cell population. Of these regions, 162 overlap with conserved non-coding elements (CNEs) that also map to open chromatin regions in human. Most of the zebrafish conserved open chromatin elements tested drive gene expression in the developing heart. Despite modest sequence identity, human orthologous open chromatin regions recapitulate the spatial temporal expression patterns of the zebrafish sequence, potentially providing a basis for phylotypic gene expression patterns. Genome-wide, we discover 5598 zebrafish-human conserved open chromatin regions, suggesting that a diverse repertoire of ancient enhancers is established prior to organogenesis and the phylotypic period

A marker-free system for highly efficient construction of vaccinia virus vectors using CRISPR Cas9

© 2015 Official journal of the American Society of Gene & Cell Therapy The current method for creation of vaccinia virus (VACV) vectors involves using a selection and purification marker, however inclusion of a gene without therapeutic value in the resulting vector is not desirable for clinical use. The Cre-LoxP system has been used to make marker-free Poxviruses, but the efficiency was very low. To obtain a marker-free VACV vector, we developed marker gene excision systems to modify the thymidine kinase (TK) regi on and N1L regions using Cre-Loxp and Flp-FRET systems respectively. CRISPR-Cas9 system significantly resulted in a high efficiency (â¼90%) in generation of marker gene-positive TK-mutant VACV vector. The marker gene (RFP) could be excised from the recombinant virus using Cre recombinase. To make a marker-free VV vector with double gene deletions targeting the TK and N1L gene, we constructed a donor repair vector targeting the N1L gene, which can carry a therapeutic gene and the marker (RFP) that could be excised from the recombinant virus using Flp recombinase. The marker-free system developed here can be used to efficiently construct VACV vectors armed with any therapeutic genes in the TK region or N1L region without marker genes. Our marker-free system platform has significant potential for development of new marker-free VACV vectors for clinical application.Link_to_subscribed_fulltex

ELM of ELM-WD: An extremely low mass hot donor star discovered in LAMOST survey

The Extremely Low Mass White Dwarfs (ELM WDs) and pre-ELM WDs are helium core white dwarfs with mass $<\sim 0.3M_{\odot}$. They are formed in close binaries and have lost over half of their initial masses via Common Envelope (CE) ejection or stable Roche Lobe Over Flow (RLOF). Both evolution simulations and observations show that a lower mass limit for ELM WDs exists at $\approx0.14M_{\odot}$. Here we report the discovery of an extremely low mass ELM WD, ID70904216 in LAMOST survey, that may be lower than the ELM WD mass limit. Based on LAMOST and P200 spectroscopic observations, ID70904216 shows orbital period $P_{orb} =$ 0.219658 days and radial velocity semi-amplitude $K1=317.33km/s$, which gives the mass function of 0.73$M_{\odot}$, indicating the companion is a compact star. The low resolution spectra shows a F type star with $T_{\rm eff} \sim 7361K$ without emission features. The temperature is consistent with that derived from SED fitting($7440K$) and multi-color light curve solution($7400K$). The optical light curves, in ZTF g, r and i bands and Catalina V band, show ellipsoidal variability with amplitudes $\approx30\%$, suggesting that the visible companion is heavily tidal distorted. Combining with the distance from Gaia survey, the WD code modeling estimates that the mass of the visible star is $M1=0.08^{+0.06}_{-0.03}M_{\odot}$, and the mass of the invisible star is $M2=0.94^{+0.45}_{-0.10}M_{\odot}$. The radius of the visible donor is $R=0.29\pm0.01R_{\odot}$. The inclination angle is constrained between 60$^{\circ}$ and 90$^{\circ}$. The observations indicate the system is a pre-ELM WD + WD/NS binary system with an extremely low mass hot donor below the $0.14M_{\odot}$ theoretical limit.Comment: 16 pages, 10 figure

Photometric Variability in the CSTAR Field: Results From the 2008 Data Set

The Chinese Small Telescope ARray (CSTAR) is the first telescope facility built at Dome A, Antarctica. During the 2008 observing season, the installation provided long-baseline and high-cadence photometric observations in the i-band for 18,145 targets within 20 deg2 CSTAR field around the South Celestial Pole for the purpose of monitoring the astronomical observing quality of Dome A and detecting various types of photometric variability. Using sensitive and robust detection methods, we discover 274 potential variables from this data set, 83 of which are new discoveries. We characterize most of them, providing the periods, amplitudes and classes of variability. The catalog of all these variables is presented along with the discussion of their statistical properties.Comment: 38 pages, 11 figures, 4 tables; Accepted for publication in ApJ

Orbital parameters for an ELM white dwarf with a white dwarf companion: LAMOST J033847.06+413424.2

Double white dwarf systems are of great astrophysical importance in the field of gravitational wave and Type Ia supernova. While the binary fraction of CO core white dwarf is about a few percents, the extremely low mass white dwarfs are all thought to be within binary systems. In this work, we report the orbital solution of a double degenerate system: J033847.06+413424.24, an extremely low mass He core white dwarf orbiting a CO core white dwarf. With LAMOST and P200, time domain spectroscopic observations have been made and spectral atmosphere parameters are estimated to be $T_{\rm eff}\sim22500$ K and log $g\sim5.6$ dex. Combining Gaia parallax, 3D extinction, and evolution tracks, we estimate a radius of $\sim0.12$ $R_{\odot}$ and a mass of $\sim0.22$ $M_{\odot}$. With the 37 single exposure spectra, the radial velocities are measured and the orbital parameters are estimated to be $P=0.1253132(1)$ days, $K1=289\pm4$ km/s and $V_{sys}=-41\pm3$ km/s. The radial velocity based system ephemeris is also provided. The light curves from several photometric surveys show no orbital modulation. The orbital solution suggests that the invisible companion has a minimum mass of about 0.60 $M_{\odot}$ and is $\sim0.79$ $M_{\odot}$ for an inclination of $60.0^{\circ}$, indicating most probably a CO core white dwarf. The system is expected to merge in about 1 Gyr. With present period and distance ($\sim596$ pc) it can not irradiate strong enough gravitational wave for LISA. More double degenerate systems are expected to be discovered and parameterized as the LAMOST survey goes on.Comment: 12 pages, 11 figure

Photometry of Variable Stars from Dome A, Antarctica

Dome A on the Antarctic plateau is likely one of the best observing sites on Earth thanks to the excellent atmospheric conditions present at the site during the long polar winter night. We present high-cadence time-series aperture photometry of 10,000 stars with i<14.5 mag located in a 23 square-degree region centered on the south celestial pole. The photometry was obtained with one of the CSTAR telescopes during 128 days of the 2008 Antarctic winter. We used this photometric data set to derive site statistics for Dome A and to search for variable stars. Thanks to the nearly-uninterrupted synoptic coverage, we find 6 times as many variables as previous surveys with similar magnitude limits. We detected 157 variable stars, of which 55% are unclassified, 27% are likely binaries and 17% are likely pulsating stars. The latter category includes delta Scuti, gamma Doradus and RR Lyrae variables. One variable may be a transiting exoplanet.Comment: Accepted for publication in the Astronomical Journal. PDF version with high-resolution figures available at http://faculty.physics.tamu.edu/lmacri/papers/wang11.pd

Identification of differentially expressed genes of blood leukocytes for Schizophrenia

BackgroundSchizophrenia (SCZ) is a severe neurodevelopmental disorder with brain dysfunction. This study aimed to use bioinformatic analysis to identify candidate blood biomarkers for SCZ.MethodsThe study collected peripheral blood leukocyte samples of 9 SCZ patients and 20 healthy controls for RNA sequencing analysis. Bioinformatic analyses included differentially expressed genes (DEGs) analysis, pathway enrichment analysis, and weighted gene co-expression network analysis (WGCNA).ResultsThis study identified 1,205 statistically significant DEGs, of which 623 genes were upregulated and 582 genes were downregulated. Functional enrichment analysis showed that DEGs were mainly enriched in cell chemotaxis, cell surface, and serine peptidase activity, as well as involved in Natural killer cell-mediated cytotoxicity. WGCNA identified 16 gene co-expression modules, and five modules were significantly correlated with SCZ (p &lt; 0.05). There were 106 upregulated genes and 90 downregulated genes in the five modules. The top ten genes sorted by the Degree algorithm were RPS28, BRD4, FUS, PABPC1, PCBP1, PCBP2, RPL27A, RPS21, RAG1, and RPL27. RAG1 and the other nine genes belonged to the turquoise and pink module respectively. Pathway enrichment analysis indicated that these 10 genes were mainly involved in processes such as Ribosome, cytoplasmic translation, RNA binding, and protein binding.ConclusionThis study finds that the gene functions in key modules and related enrichment pathways may help to elucidate the molecular pathogenesis of SCZ, and the potential of key genes to become blood biomarkers for SCZ warrants further validation

The First Release of the CSTAR Point Source Catalog from Dome A, Antarctica

In 2008 January the 24th Chinese expedition team successfully deployed the Chinese Small Telescope ARray (CSTAR) to DomeA, the highest point on the Antarctic plateau. CSTAR consists of four 14.5cm optical telescopes, each with a different filter (g, r, i and open) and has a 4.5degree x 4.5degree field of view (FOV). It operates robotically as part of the Plateau Observatory, PLATO, with each telescope taking an image every 30 seconds throughout the year whenever it is dark. During 2008, CSTAR #1 performed almost flawlessly, acquiring more than 0.3 million i-band images for a total integration time of 1728 hours during 158 days of observations. For each image taken under good sky conditions, more than 10,000 sources down to 16 mag could be detected. We performed aperture photometry on all the sources in the field to create the catalog described herein. Since CSTAR has a fixed pointing centered on the South Celestial Pole (Dec =-90 degree), all the sources within the FOV of CSTAR were monitored continuously for several months. The photometric catalog can be used for studying any variability in these sources, and for the discovery of transient sources such as supernovae, gamma-ray bursts and minor planets.Comment: 1 latex file and 9 figures The paper is accepted by PAS