Pig H3K4me3,H3K27ac,and gene expression profiles reveal reproductive tissue-specific activity of transposable elements

Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species;however,their roles in gene transcription,especially tissue-specific expression,remain largely unknown.Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations.Here,we conducted an integrated analysis using H3K27ac ChIP-seq,H3K4me3 ChIP-seq,and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs.We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages.Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity,results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3.Furthermore,1.45%of TEs overlapped with either the H3K27ac or H3K4me3 peaks,with the majority displaying tissue-specific activity.Notably,a TE subfamily(LTR4C_SS),containing binding motifs for SIX1 and SIX4,showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries.RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes,including 4688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression.Of note,1967 TE-containing transcripts were enriched in the testes.We identified a long terminal repeat(LTR),MLT1F1,acting as a testis-specific alternative promoter in SRPK2(a cell cycle-related protein kinase)in our pig dataset.This element was also conserved in humans and mice,suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns.Collectively,our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions,particularly in the reproductive organs.

The THU-NAOC transient survey: the performance and results from the first year

The Tsinghua University-National Astronomical Observatories, Chinese Academy of Sciences （NAOC） Transient Survey is an automatic survey that conducts a systematic exploration of optical transients. This project utilizes a 60/90 cm Schmidt telescope at the Xinglong Station of NAOC. This survey repeatedly covers - 1000 square degrees of the northern sky with a cadence of 34 d. With an exposure of 60 s, the survey reaches a limiting unfiltered magnitude of about 19.5 mag, which enables us to discover supernovae in their relatively young stages. We describe the overall performance of our survey during the first year and present some preliminary results.

South Galactic Cap u-band Sky Survey(SCUSS):Project Overview

The South Galactic Cap u-band Sky Survey （SCUSS） was established in 2009 in order to provide a photometric input catalog for target selection of the Large Sky Area Multi-Object Fiber Spectroscopic Telescope （LAMOST） project. SCUSS is an international cooperative project between National Astronomical Observatories, Chinese Academy of Sciences, and Steward Observatory at the University of Arizona, using the 90 inch （2.3 m） Bok telescope on Kitt Peak. The telescope is equipped with a prime focus camera that is composed of a mosaic of four 4096 × 4096 CCDs and has a field of view of about 1 deg2. From 2009 to 2013, SCUSS performed a sky survey of an approximately 5000 deg2 field of the South Galactic Cap in u band, including the Galactic anticenter area and the SDSS-IV extended imaging area. The limiting magnitude of SCUSS is deeper than 23 mag （at a signal-to-noise ratio of 5）. In this paper, we briefly describe the goals of this project, method of observations and data reduction, and we also introduce current and potential scientific activities related to the SCUSS project.

Metallicity and star formation activities of the interacting system Arp 86 from observations with MOS on the Xinglong 2.16m telescope

We present an analysis of the metallicity and star formation activities of H II regions in the interacting system Arp 86, based on the first scientific observations using mulri-object spectroscopy with the 2.16 m telescope at the Xinglong Observing Station. We find that the oxygen abundance gradient in Arp 86 is flatter than that in normal disk galaxies, which confirms that gas inflows caused by tidal forces during encounters can flatten the metallicity distributions in galaxies. The companion galaxy NGC 7752 is currently experiencing a galaxy-wide starburst with a higher star for- marion rate surface density than the main galaxy NGC 7753, which can be explained in that the companion galaxy is more susceptible to the effects of interaction than the primary. We also find that the galaxy 2MASX J23470758＋2926531 has similar abun- dance and star formation properties to NGC 7753, and may be a part of the Arp 86 system.

Far-Infrared and submillimeter properties of SDSS galaxies in the Herschel ATLAS science demonstration phase field

Using the Herschel ATLAS science demonstration phase data cross- identified with SDSS DR7 spectra, we select 297 galaxies with F250μm 〉 5σ. The sample galaxies are classified into five morphological types, and more than 40% of the galaxies are peculiar/compact galaxies. The peculiar galaxies show higher far- infrared/submillimeter luminosity-to-mass ratios than the other types. We perform and analyze the correlations of far-infrared/submillimeter and Hα luminosities for differ- ent morphological types and different spectral types. The Spearman rank coefficient decreases and the scatter increases with the wavelength increasing from 100 μm to 500 μm. We conclude that a single Herschel SPIRE band is not good for tracing star formation activities in galaxies. AGNs contribute less to the far-infrared/submillimeter luminosities and do not show a difference from star-forming galaxies. However, the earlier type galaxies present significant deviations from the best fit of star-forming galaxies.

Star formation properties in barred galaxies (SFB) Ⅱ. NGC 2903 and NGC 7080

Stellar bars are important for the secular evolution of disk galaxies because they can drive gas into the galactic central regions. To investigate the star formation properties in barred galaxies, we presented a multi-wavelength study of two barred galaxies： NGC 2903 and NGC 7080. We performed the three-component bulge-diskbar decomposition using the 3.6 μm images, and identified the bulges in the two galaxies as pseudobulges. Based on the narrowband Hα images, the star formation clumps were identified and analyzed. The clumps in the bulge regions have the highest surface densities of star formation rates in both galaxies, while the star formation activities in the bar of NGC 2903 are more intense than those in the bar of NGC 7080. Finally, we compared our results with the scenario of bar-driven secular evolution in previous studies, and discussed the possible evolutionary stages of the two galaxies.

Analysis of Spherical Polyelectrolyte Brushes by Small Angle X-ray Scattering

Spherical polyelectrolyte brushes （SPBs） with PS core and poly（acrylic acid） （PAA） brushes were prepared and analyzed by SAXS in this article. A radial electron density profile of SPB was brought up, which fits well with the SAXS result and shows a core-shell structure. The effect of pH on SPB form was represented by SAXS and it proves that the chains of SPB will stretch in response to increased pH owning to the increased electrostatic repulsion. SPBs immobilized with magnetic nanoparticles or bovine serum albumin （BSA） were prepared and analyzed by SAXS as well. SAXS could characterize the changes of electron density inside brushes of SPBs due to the immobilization of magnetic nanoparticles or BSA. This provides significant supports for further application of immobilized metal nanoparticles or proteins.

Parallelized deformable part models with effective hypothesis pruning

As a typical machine-learning based detection technique, deformable part models(DPM)achieve great success in detecting complex object categories. The heavy computational burden of DPM,however, severely restricts their utilization in many real world applications. In this work, we accelerate DPM via parallelization and hypothesis pruning. Firstly,we implement the original DPM approach on a GPU platform and parallelize it, making it 136 times faster than DPM release 5 without loss of detection accuracy.Furthermore, we use a mixture root template as a prefilter for hypothesis pruning, and achieve more than 200 times speedup over DPM release 5, apparently the fastest implementation of DPM yet. The performance of our method has been validated on the Pascal VOC2007 and INRIA pedestrian datasets, and compared to other state-of-the-art techniques.