The ensemble photometric variability of over 10510^5 quasars in the Dark Energy Camera Legacy Survey and the Sloan Digital Sky Survey

We present the ensemble variability analysis results of quasars using the Dark Energy Camera Legacy Survey (DECaLS) and the Sloan Digital Sky Survey (SDSS) quasar catalogs. Our dataset includes 119,305 quasars with redshifts up to 4.89. Combining the two datasets provides a 15-year baseline and permits analysis of the long timescale variability. Adopting a power-law form for the variability structure function, $V=A(t/1yr)^{\gamma}$, we use the multi-dimensional parametric fitting to explore the relationships between the quasar variability amplitude and a wide variety of quasar properties, including redshift (positive), bolometric luminosity (negative), rest-frame wavelength (negative), and black hole mass (uncertain). We also find that $\gamma$ can be also expressed as a function of redshift (negative), bolometric luminosity (positive), rest-frame wavelength (positive), and black hole mass (positive). Tests of the fitting significance with the bootstrap method show that, even with such a large quasar sample, some correlations are marginally significant. The typical value of $\gamma$ for the entire dataset is $\gtrsim 0.25$, consistent with the results in previous studies on both the quasar ensemble variability and the structure function. A significantly negative correlation between the variability amplitude and the Eddington ratio is found, which may be explained as an effect of accretion disk instability.Comment: 13 pages, 8 figures, 4 tables, accepted for publication in Ap

The First Data Release of the Beijing-Arizona Sky Survey

The Beijing-Arizona Sky Survey (BASS) is a new wide-field legacy imaging survey in the northern Galactic cap using the 2.3m Bok telescope. The survey will cover about 5400 deg$^2$ in the $g$ and $r$ bands, and the expected 5$\sigma$ depths (corrected for the Galactic extinction) in the two bands are 24.0 and 23.4 mag, respectively. BASS started observations in January 2015, and has completed about 41% of the whole area as of July 2016. The first data release contains both calibrated images and photometric catalogs obtained in 2015 and 2016. The depths of single-epoch images in the two bands are 23.4 and 22.9 mag, and the full depths of three epochs are about 24.1 and 23.5 mag, respectively.Comment: 16 pages, published by A

Systematical identification of splicing regulatory cis-elements and cognate trans-factors

The majority of human genes undergo alternative splicing to generate multiple isoforms with distinct functions. This process is generally controlled by cis-acting splicing regulatory elements (SREs) that recruit trans-acting factors to promote or inhibit the use of nearby splice sites. The growing interest in understanding the regulatory rules of splicing necessitates the systematic identification of these SREs and their cognate protein factors using experimental and computational approaches. Here we describe a strategy to identify and analyze both cis-acting SREs and trans-acting splicing factors. This strategy involves a cell-based screen to identify SREs from a random sequences library and a modified RNA affinity purification approach to unbiasedly identify the splicing factors. These methods can be adopted to identify splicing enhancers or silencers in both exons and introns, and can be extended to different cultured cells. The resulting SREs and splicing factors can be further analyzed with a series of computational and experimental approaches. This approach will help us to collect a molecular part-list for splicing regulation, providing a rich data source that enables a better understanding of the “splicing code”

Efficient backsplicing produces translatable circular mRNAs

While the human transcriptome contains a large number of circular RNAs (circRNAs), the functions of most circRNAs remain unclear. Sequence annotation suggests that most circRNAs are generated from splicing in reversed orders across exons. However, the mechanisms of this backsplicing are largely unknown. Here we constructed a single exon minigene containing split GFP, and found that the pre-mRNA indeed produces circRNA through efficient backsplicing in human and Drosophila cells. The backsplicing is enhanced by complementary introns that form double-stranded RNA structure to bring splice sites in proximity, but such structure is not required. Moreover, backsplicing is regulated by general splicing factors and cis-elements, but with regulatory rules distinct from canonical splicing. The resulting circRNA can be translated to generate functional proteins. Unlike linear mRNA, poly-adenosine or poly-thymidine in 3′ UTR can inhibit circular mRNA translation. This study revealed that backsplicing can occur efficiently in diverse eukaryotes to generate circular mRNAs

Discovery of 16 new z ∼ 5.5 quasars: filling in the redshift gap of quasar color selection

We present initial results from the first systematic survey of luminous z ∼ 5.5 quasars. Quasars at z ∼ 5.5, the post-reionization epoch, are crucial tools to explore the evolution of intergalactic medium, quasar evolution, and the early super-massive black hole growth. However, it has been very challenging to select quasars at redshifts 5.3 ≤ z ≤ 5.7 using conventional color selections, due to their similar optical colors to late-type stars, especially M dwarfs, resulting in a glaring redshift gap in quasar redshift distributions. We develop a new selection technique for z ∼ 5.5 quasars based on optical, near-IR, and mid-IR photometric data from Sloan Digital Sky Survey (SDSS), UKIRT InfraRed Deep Sky Surveys—Large Area Survey (ULAS), VISTA Hemisphere Survey (VHS), and Wide Field Infrared Survey Explorer. From our pilot observations in the SDSS-ULAS/VHS area, we have discovered 15 new quasars at 5.3 ≤ z ≤ 5.7 and 6 new lower redshift quasars, with SDSS z band magnitude brighter than 20.5. Including other two z ∼ 5.5 quasars already published in our previous work, we now construct a uniform quasar sample at 5.3 ≤ z ≤ 5.7, with 17 quasars in a ∼4800 square degree survey area. For further application in a larger survey area, we apply our selection pipeline to do a test selection by using the new wide field J-band photometric data from a preliminary version of the UKIRT Hemisphere Survey (UHS). We successfully discover the first UHS selected z ∼ 5.5 quasar

Evidence for acquisition of virulence effectors in pathogenic chytrids

Background The decline in amphibian populations across the world is frequently linked to the infection of the chytrid fungus Batrachochytrium dendrobatidis (Bd). This is particularly perplexing because Bd was only recently discovered in 1999 and no chytrid fungus had previously been identified as a vertebrate pathogen. Results In this study, we show that two large families of known virulence effector genes, crinkler (CRN) proteins and serine peptidases, were acquired by Bd from oomycete pathogens and bacteria, respectively. These two families have been duplicated after their acquisition by Bd. Additional selection analyses indicate that both families evolved under strong positive selection, suggesting that they are involved in the adaptation of Bd to its hosts. Conclusions We propose that the acquisition of virulence effectors, in combination with habitat disruption and climate change, may have driven the Bd epidemics and the decline in amphibian populations. This finding provides a starting point for biochemical investigations of chytridiomycosis

An extensive program of periodic alternative splicing linked to cell cycle progression

Progression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1300 genes with cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose level undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control

Engineered proteins with Pumilio/ fem-3 mRNA binding factor scaffold to manipulate RNA metabolism

Pumilio/fem-3 mRNA binding factor (FBF) proteins are characterized by a sequence-specific RNA-binding domain. This unique single-stranded RNA recognition module, whose sequence specificity can be reprogrammed, has been fused with functional modules to engineer protein factors with various functions. Here we summarize the advancement in developing RNA regulatory tools and opportunities for the future

Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus

Marine phages play an important role in marine biogeochemical cycles by regulating the death, physiological metabolism, and evolutionary trajectory of bacteria. The Roseobacter group is an abundant and important heterotrophic bacterial group in the ocean, and plays an important role in carbon, nitrogen, sulfur and phosphorus cycling. The CHAB-I-5 lineage is one of the most dominant Roseobacter lineages, but remains largely uncultured. Phages infecting CHAB-I-5 bacteria have not yet been investigated due to the lack of culturable CHAB-I-5 strains. In this study, we isolated and sequenced two new phages (CRP-901 and CRP-902) infecting the CHAB-I-5 strain FZCC0083. We applied metagenomic data mining, comparative genomics, phylogenetic analysis, and metagenomic read-mapping to investigate the diversity, evolution, taxonomy, and biogeography of the phage group represented by the two phages. The two phages are highly similar, with an average nucleotide identity of 89.17%, and sharing 77% of their open reading frames. We identified several genes involved in DNA replication and metabolism, virion structure, DNA packing, and host lysis from their genomes. Metagenomic mining identified 24 metagenomic viral genomes closely related to CRP-901 and CRP-902. Genomic comparison and phylogenetic analysis demonstrated that these phages are distinct from other known viruses, representing a novel genus-level phage group (CRP-901-type). The CRP-901-type phages do not contain DNA primase and DNA polymerase genes, but possess a novel bifunctional DNA primase-polymerase gene with both primase and polymerase activities. Read-mapping analysis showed that the CRP-901-type phages are widespread across the world’s oceans and are most abundant in estuarine and polar waters. Their abundance is generally higher than other known roseophages and even higher than most pelagiphages in the polar region. In summary, this study has greatly expanded our understanding of the genetic diversity, evolution, and distribution of roseophages. Our analysis suggests that the CRP-901-type phage is an important and novel marine phage group that plays important roles in the physiology and ecology of roseobacters