Single Molecule Studies Of Spliceosomal Snrnas U2-U6

Spliceosomes catalyze the maturation of precursor mRNAs in organisms ranging from yeast to humans. Their catalytic core comprises three small nuclear RNAs (U2, U5 and U6) involved in substrate positioning and catalysis. It has been postulated, but never shown experimentally, that the U2-U6 complex adopts at least two conformations that reflect different activation states. We have used single-molecule fluorescence to probe the structural dynamics of a protein-free RNA complex modeling U2-U6 from yeast and mutants of highly conserved regions of U2-U6. Our data show the presence of at least three distinct conformations in equilibrium. The minimal folding pathway consists of a two-step process with an obligatory intermediate. The first step is strongly magnesium dependent, and we provide evidence suggesting that the second step corresponds to the formation of the genetically conserved helix IB. Site-specific mutations in the highly conserved AGC triad and the U80 base in U6 suggest that the observed conformational dynamics correlate with residues that have an important role in splicing. We also report the first direct structural evidence that supports the existence of the base triples in the spliceosomal snRNA U2/U6. These interactions were proposed according to a corresponding set of base triple interactions discovered in the recent published crystal structure of the self-splicing group II intron.19-16, 24b-17, 48 We proposed that these base triples existing in the spliceosomal RNA U2/U6 complex are in the same family of the ones found in crystal structure of the self-splicing group II intron given the extensive similarities between the spliceosome and the group II intron. Our data agree very well with the hypothesis. There are a large number of proteins in the spliceosome that play vital structural and catalytic roles3,36. RNA Chaperones, like Prp24, help the structural rearrangements of spliceosomal snRNAs. We report single molecule FRET data showing that spliceosomal protein Prp24 can induce a conformational change in U2/U6 complex. This RNA:protein interaction is Mg2+ and protein concentration dependent and inhibits the binding of Mg2+ to U2/U6

Identification of LncRNA Linc00513 Containing Lupus-Associated Genetic Variants as a Novel Regulator of Interferon Signaling Pathway

Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by augmented type I interferon signaling. High-throughput technologies have identified plenty of SLE susceptibility single-nucleotide polymorphisms (SNPs) yet the exact roles of most of them are still unknown. Functional studies are principally focused on SNPs in the coding regions, with limited attention paid to the SNPs in non-coding regions. Long non-coding RNAs (lncRNAs) are important players in shaping the immune response and show relationship to autoimmune diseases. In order to reveal the role of SNPs located near SLE related lncRNAs, we performed a transcriptome profiling of SLE patients and identified linc00513 as a significantly over expressed lncRNA containing functional SLE susceptibility loci in the promoter region. The risk-associated G allele of rs205764 and A allele of rs547311 enhanced linc00513 promoter activity and related to increased expression of linc00513 in SLE. We also identified linc00513 to be a novel positive regulator of type I interferon pathway by promoting the phosphorylation of STAT1 and STAT2. Elevated linc00513 expression positively correlated with IFN score in SLE patients. Linc00513 expression was higher in active disease patients than those inactive ones. In conclusion, our data identify two functional promoter variants of linc00513 that contribute to increased level of linc00513 and confer susceptibility on SLE. The study provides new insights into the genetics of SLE and extends the role of lncRNAs in the pathogenesis of SLE

Identification of Renal Long Non-coding RNA RP11-2B6.2 as a Positive Regulator of Type I Interferon Signaling Pathway in Lupus Nephritis

Objective: Lupus nephritis (LN) is one of the most serious complications of systemic lupus erythematosus (SLE). Type I interferon (IFN-I) is associated with the pathogenesis of LN. Long non-coding RNAs (lncRNAs) have been implicated in the pathogenesis of SLE, however, the roles of lncRNAs in LN are still poorly understood. Here, we identified and investigated the function of LN-associated lncRNA RP11-2B6.2 in regulating IFN-I signaling pathway.Methods: RNA sequencing was used to analyze the expression of lncRNAs in kidney biopsies from LN patients and controls. Antisense oligonucleotides and CRISPRi system or overexpression plasmids and CRISPRa system were used to perform loss or gain of function experiments. In situ hybridization, imaging flow cytometry, dual-luciferase reporter assay, and ATAC sequencing were used to study the functions of lncRNA RP11-2B6.2. RT-qPCR, ELISA, and western blotting were done to detect RNA and protein levels of specific genes.Results: Elevated lncRNA RP11-2B6.2 was observed in kidney biopsies from LN patients and positively correlated with disease activity and IFN scores. Knockdown of lncRNA RP11-2B6.2 in renal cells inhibited the expression of IFN stimulated genes (ISGs), while overexpression of lncRNA RP11-2B6.2 enhanced ISG expression. Knockdown of LncRNA RP11-2B6.2 inhibited the phosphorylation of JAK1, TYK2, and STAT1 in IFN-I pathway, while promoted the chromatin accessibility and the transcription of SOCS1.Conclusion: The expression of lncRNAs is abnormal in the kidney of LN. LncRNA RP11-2B6.2 is a novel positive regulator of IFN-I pathway through epigenetic inhibition of SOCS1, which provides a new therapeutic target to alleviate over-activated IFN-I signaling in LN

Potential of Core-Collapse Supernova Neutrino Detection at JUNO

JUNO is an underground neutrino observatory under construction in Jiangmen, China. It uses 20kton liquid scintillator as target, which enables it to detect supernova burst neutrinos of a large statistics for the next galactic core-collapse supernova (CCSN) and also pre-supernova neutrinos from the nearby CCSN progenitors. All flavors of supernova burst neutrinos can be detected by JUNO via several interaction channels, including inverse beta decay, elastic scattering on electron and proton, interactions on C12 nuclei, etc. This retains the possibility for JUNO to reconstruct the energy spectra of supernova burst neutrinos of all flavors. The real time monitoring systems based on FPGA and DAQ are under development in JUNO, which allow prompt alert and trigger-less data acquisition of CCSN events. The alert performances of both monitoring systems have been thoroughly studied using simulations. Moreover, once a CCSN is tagged, the system can give fast characterizations, such as directionality and light curve

Detection of the Diffuse Supernova Neutrino Background with JUNO

As an underground multi-purpose neutrino detector with 20 kton liquid scintillator, Jiangmen Underground Neutrino Observatory (JUNO) is competitive with and complementary to the water-Cherenkov detectors on the search for the diffuse supernova neutrino background (DSNB). Typical supernova models predict 2-4 events per year within the optimal observation window in the JUNO detector. The dominant background is from the neutral-current (NC) interaction of atmospheric neutrinos with 12C nuclei, which surpasses the DSNB by more than one order of magnitude. We evaluated the systematic uncertainty of NC background from the spread of a variety of data-driven models and further developed a method to determine NC background within 15\% with {\it{in}} {\it{situ}} measurements after ten years of running. Besides, the NC-like backgrounds can be effectively suppressed by the intrinsic pulse-shape discrimination (PSD) capabilities of liquid scintillators. In this talk, I will present in detail the improvements on NC background uncertainty evaluation, PSD discriminator development, and finally, the potential of DSNB sensitivity in JUNO

Real-time Monitoring for the Next Core-Collapse Supernova in JUNO

Core-collapse supernova (CCSN) is one of the most energetic astrophysical events in the Universe. The early and prompt detection of neutrinos before (pre-SN) and during the SN burst is a unique opportunity to realize the multi-messenger observation of the CCSN events. In this work, we describe the monitoring concept and present the sensitivity of the system to the pre-SN and SN neutrinos at the Jiangmen Underground Neutrino Observatory (JUNO), which is a 20 kton liquid scintillator detector under construction in South China. The real-time monitoring system is designed with both the prompt monitors on the electronic board and online monitors at the data acquisition stage, in order to ensure both the alert speed and alert coverage of progenitor stars. By assuming a false alert rate of 1 per year, this monitoring system can be sensitive to the pre-SN neutrinos up to the distance of about 1.6 (0.9) kpc and SN neutrinos up to about 370 (360) kpc for a progenitor mass of 30$M_{\odot}$ for the case of normal (inverted) mass ordering. The pointing ability of the CCSN is evaluated by using the accumulated event anisotropy of the inverse beta decay interactions from pre-SN or SN neutrinos, which, along with the early alert, can play important roles for the followup multi-messenger observations of the next Galactic or nearby extragalactic CCSN.Comment: 24 pages, 9 figure

Full-Length Transcriptomics Reveal the Gene Expression Profiles of Reef-Building Coral Pocillopora damicornis and Symbiont Zooxanthellae

Since the last century, episodes of coral reef bleaching and mortality have occurred almost annually in tropical or subtropical seas. When the temperature exceeds the tolerant limit of a coral–zooxanthellae holobiont, it induces physiological stress and disrupts the vulnerable fine-tuned balance between the two partners, leading to bleaching. The gene expression profiles of a scleractinian coral and its symbiotic zooxanthellae can offer important information with which to decipher this balanced relationship at the functional level of genes. Here, we sequence a full-length transcriptome of a well-known, common and frequently dominant reef-building coral, Pocillopora damicornis, to acquire gene expression information for the coral–zooxanthellae holobiont. To this end, we identify 21,926 and 465 unique genes in the coral and algal symbiont, respectively, and examine the functional enrichment among these genes based on GO (gene ontology) terms and KEGG (the Kyoto Encyclopedia of Genes and Genomes) pathways. The results show that the zooxanthellae provide for their coral host through energy and nutrition metabolism by photosynthesis, and that both the coral host and zooxanthellae have an anti-stress molecular mechanism, though the two parties have independent abilities to survive in the short term. This work sheds light on the valuable gene expression profile of a coral–zooxanthellae holobiont and provides grounds for further molecular biological research to support ecological protection work

Rational Fabrication of Defect-Rich and Hierarchically Porous Fe-N-C Nanosheets as Highly Efficient Oxygen Reduction Electrocatalysts for Zinc-Air Battery

The rational design of morphology and structure for oxygen reduction reaction (ORR) catalysts still remains a critical challenge. Herein, we successfully construct defect-rich and hierarchically porous Fe-N-C nanosheets (Fe-N-CNSs), by taking advantage of metal-organic complexation and a mesoporous template. Benefiting from the advantages of high density of active sites, fast mass transfer channels, and sufficient reaction area, the optimal Fe-N-CNSs demonstrate satisfactory ORR activity with an excellent half-wave potential of up to 0.87 V, desirable durability, and robust methanol tolerance. Noteworthy, the Fe-N-CNSs based zinc–air battery shows significant performance with a peak power density of 128.20 mW cm−2 and open circuit voltage of 1.53 V, which reveals that the Fe-N-CNSs catalysts present promising practical application prospects. Therefore, we believe that this research will provide guidance for the optimization of Fe-N-C materials

Full-Length Transcriptome Sequencing of the Scleractinian Coral <i>Montipora foliosa</i> Reveals the Gene Expression Profile of Coral–Zooxanthellae Holobiont

Coral–zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral–zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa. Our results provide better material for studying coral symbiosis