Global analysis of binding sites of U2AF1 and ZRSR2 reveals RNA elements required for mutually exclusive splicing by the U2- and U12-type spliceosome.

Recurring mutations in genes encoding 3' splice-site recognition proteins, U2AF1 and ZRSR2 are associated with human cancers. Here, we determined binding sites of the proteins to reveal that U2-type and U12-type splice sites are recognized by U2AF1 and ZRSR2, respectively. However, some sites are spliced by both the U2-type and U12-type spliceosomes, indicating that well-conserved consensus motifs in some U12-type introns could be recognized by the U2-type spliceosome. Nucleotides flanking splice sites of U12-type introns are different from those flanking U2-type introns. Remarkably, the AG dinucleotide at the positions -1 and -2 of 5' splice sites of U12-type introns with GT-AG termini is not present. AG next to 5' splice site introduced by a single nucleotide substitution at the -2 position could convert a U12-type splice site to a U2-type site. The class switch of introns by a single mutation and the bias against G at the -1 position of U12-type 5' splice site support the notion that the identities of nucleotides in exonic regions adjacent to splice sites are fine-tuned to avoid recognition by the U2-type spliceosome. These findings may shed light on the mechanism of selectivity in U12-type intron splicing and the mutations that affect splicing.

Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1.

L1TD1 is a cytoplasmic RNA-binding protein specifically expressed in pluripotent stem cells and, unlike its mouse ortholog, is essential for the maintenance of stemness in human cells. Although L1TD1 is the only known protein-coding gene domesticated from a LINE-1 (L1) retroelement, the functional legacy of its ancestral protein, ORF1p of L1, and how it is manifested in L1TD1 are still unknown. Here, we determined RNAs associated with L1TD1 and found that, like ORF1p, L1TD1 binds L1 RNAs and localizes to high-density ribonucleoprotein (RNP) condensates. Unexpectedly, L1TD1 enhanced the translation of a subset of mRNAs enriched in the condensates. L1TD1 depletion promoted the formation of stress granules in embryonic stem cells. In HeLa cells, ectopically expressed L1TD1 facilitated the dissolution of stress granules and granules formed by pathological mutations of TDP-43 and FUS. The glutamate-rich domain and the ORF1-homology domain of L1TD1 facilitated dispersal of the RNPs and induced autophagy, respectively. These results provide insights into how L1TD1 regulates gene expression in pluripotent stem cells. We propose that the ability of L1TD1 to dissolve stress granules may provide novel opportunities for treatment of neurodegenerative diseases caused by disturbed stress granule dynamics.

Nuclear receptor-enhanced transcription requires motor- and LSD1-dependent gene networking in interchromatin granules.

While the transcriptional machinery has been extensively dissected at the molecular level, little is known about regulation of chromosomal organization in the three-dimensional space of the nucleus to achieve integrated transcriptional responses to diverse signaling events. Here, we report that ligand induces rapid interchromosomal interactions among subsets of estrogen receptor alpha-bound transcription units, with a dramatic reorganization of nuclear territories requiring nuclear actin/myosin-I transport machinery, dynein light chain 1 (DLC1), and a specific subset of transcriptional coactivators and chromatin remodeling complexes. We establish a requirement for the histone lysine demethylase, LSD1, in directing specific interchromosomal interaction loci to distinct interchromatin granules, long thought to be "storage" sites for splicing machinery, and demonstrate that these three-dimensional motor-dependent interactions are required to achieve enhanced transcription of specific estrogen-receptor target genes. These findings reveal roles for the modulation of nuclear architecture in orchestrating regulated gene-expression programs in the mammalian nucleus.

The conserved microRNA miR-8-3p coordinates the expression of V-ATPase subunits to regulate ecdysone biosynthesis for Drosophila metamorphosis.

The steroid hormone ecdysone is the central regulator of insect metamorphosis, during which a growing, immature larva is remodeled, through pupal stages, to a reproductive adult. However, the underlying mechanisms of ecdysone-mediated metamorphosis remain to be fully elucidated. Here, we identified metamorphosis-associated microRNAs (miRNAs) and their potential targets by cross-linking immunoprecipitation coupled with deep sequencing of endogenous Argonaute 1 protein in Drosophila. Interestingly, miR-8-3p targeted five Vha genes encoding distinct subunits of vacuolar H+ -ATPase (V-ATPase), which has a vital role in the organellar acidification. The expression of ecdysone-responsive miR-8-3p is normally downregulated during Drosophila metamorphosis, but temporary overexpression of miR-8-3p in the whole body at the end of larval development led to defects in metamorphosis and survival, hallmarks of aberrant ecdysone signaling. In addition, miR-8-3p was expressed in the prothoracic gland (PG), which produces and releases ecdysone in response to prothoracicotropic hormone (PTTH). Notably, overexpression of miR-8-3p or knockdown of its Vha targets in the PG resulted in larger than normal, ecdysone-deficient larvae that failed to develop into the pupal stage but could be rescued by ecdysone feeding. Moreover, these animals showed defective PTTH signaling with a concomitant decrease in the expression of ecdysone biosynthetic genes. We also demonstrated that the regulatory network between the conserved miR-8-3p/miR-200 family and V-ATPase was functional in human cells. Consequently, our data indicate that the coordinated regulation of V-ATPase subunits by miR-8-3p is involved in Drosophila metamorphosis by controlling the ecdysone biosynthesis.

Ecdysone-responsive microRNA-252-5p controls the cell cycle by targeting Abi in Drosophila.

The steroid hormone ecdysone has a central role in the developmental transitions of insects through its control of responsive protein-coding and microRNA (miRNA) gene expression. However, the complete regulatory network controlling the expression of these genes remains to be elucidated. In this study, we performed cross-linking immunoprecipitation coupled with deep sequencing of endogenous Argonaute 1 (Ago1) protein, the core effector of the miRNA pathway, in Drosophila S2 cells. We found that regulatory interactions between miRNAs and their cognate targets were substantially altered by Ago1 in response to ecdysone signaling. Additionally, during the larva-to-adult metamorphosis, miR-252-5p was up-regulated via the canonical ecdysone-signaling pathway. Moreover, we provide evidence that miR-252-5p targets Abelson interacting protein ( Abi) to decrease the protein levels of cyclins A and B, controlling the cell cycle. Overall, our data suggest a potential role for the ecdysone/miR-252-5p/Abi regulatory axis partly in cell-cycle control during metamorphosis in Drosophila.-Lim, D.-H., Lee, S., Han, J. Y., Choi, M.-S., Hong, J.-S., Seong, Y., Kwon, Y.-S., Lee, Y. S. Ecdysone-responsive microR-252-5p controls the cell cycle by targeting Abi in Drosophila.

Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping.

Recent transcriptome analysis indicates that > 90% of human genes undergo alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract-binding protein PTB is a well-characterized splicing repressor, but PTB knockdown causes both exon inclusion and skipping. Genome-wide mapping of PTB-RNA interactions and construction of a functional RNA map now reveal that dominant PTB binding near a competing constitutive splice site generally induces exon inclusion, whereas prevalent binding close to an alternative site often causes exon skipping. This positional effect was further demonstrated by disrupting or creating a PTB-binding site on minigene constructs and testing their responses to PTB knockdown or overexpression. These findings suggest a mechanism for PTB to modulate splice site competition to produce opposite functional consequences, which may be generally applicable to RNA-binding splicing factors to positively or negatively regulate alternative splicing in mammalian cells.

Hybrid Structure White Organic Light Emitting Diode for Enhanced Efficiency by Varied Doping Rate.

Novel materials based on Zn(HPB)2 and Ir-complexes were synthesized as blue or red emitters, respectively. White organic light emitting diodes were fabricated using the Zn(HPB)2 as a blue emitting layer, Ir-complexes as a red emitting layer and Alq3 as a green emitting layer. The obtained experimental results, were based on white OLEDs fabricated using double emission layers of Zn(HPB)2 and Alq3:Ir-complexes. The doping rate of the Ir-complexes was varied at 0.4%, 0.6%, 0.8% and 1.0%. When the doping rate of the Alq3:Ir-complexes was 0.6%, a white emission was achieved. The Commission Internationale de l'Eclairage coordinates of the device's white emission were (0.316, 0.331) at an applied voltage of 10.75 V.

Global identification of target recognition and cleavage by the Microprocessor in human ES cells.

The Microprocessor plays an essential role in canonical miRNA biogenesis by facilitating cleavage of stem-loop structures in primary transcripts to yield pre-miRNAs. Although miRNA biogenesis has been extensively studied through biochemical and molecular genetic approaches, it has yet to be addressed to what extent the current miRNA biogenesis models hold true in intact cells. To address the issues of in vivo recognition and cleavage by the Microprocessor, we investigate RNAs that are associated with DGCR8 and Drosha by using immunoprecipitation coupled with next-generation sequencing. Here, we present global protein-RNA interactions with unprecedented sensitivity and specificity. Our data indicate that precursors of canonical miRNAs and miRNA-like hairpins are the major substrates of the Microprocessor. As a result of specific enrichment of nascent cleavage products, we are able to pinpoint the Microprocessor-mediated cleavage sites per se at single-nucleotide resolution. Unexpectedly, a 2-nt 3' overhang invariably exists at the ends of cleaved bases instead of nascent pre-miRNAs. Besides canonical miRNA precursors, we find that two novel miRNA-like structures embedded in mRNAs are cleaved to yield pre-miRNA-like hairpins, uncoupled from miRNA maturation. Our data provide a framework for in vivo Microprocessor-mediated cleavage and a foundation for experimental and computational studies on miRNA biogenesis in living cells.

Ornithodoros sawaii (Ixodida: Argasidae) Larvae Collected from Hydrobates monorhis on Sogugul and Gaerin Islands, Jeollanam-do (Province), Republic of Korea.

The 65th Medical Brigade and Public Health Command District-Korea, in collaboration with the Migratory Bird Research Center, National Park Research Institute, conducted migratory bird tick surveillance at Sogugul and Gaerin Islands (small rocky bird nesting sites), Jeollanam-do (Province), Republic of Korea (ROK), on 30 July and 1 August 2009. Breeding seabirds captured by hands in their nesting burrows were banded, identified to species, and carefully examined for ticks during the nesting season. A total of 9 Ornithodoros sawaii larvae were removed from 4 adult Hydrobates monorhis (Swinhoe's storm petrel). The identification of the larvae of O. sawaii collected from migratory seabirds were molecularly confirmed using mitochondrial 16S rDNA primer sets.

SRSF2 promotes splicing and transcription of exon 11 included isoform in Ron proto-oncogene.

The product of proto-oncogene Ron is a human receptor for the macrophage-stimulating protein (MSP). Upon activation, Ron is able to induce cell dissociation, migration and matrix invasion. Exon 11 skipping of Ron pre-mRNA produces Ron△165 protein that is constitutively active even in the absence of its ligand. Here we show that knockdown of SRSF2 promotes the decrease of exon 11 inclusion, whereas overexpression of SRSF2 promotes exon 11 inclusion. We demonstrate that SRSF2 promotes exon 11 inclusion through splicing and transcription procedure. We also present evidence that reduced expression of SRSF2 induces a decrease in the splicing of both introns 10 and 11; by contrast, overexpression of SRSF2 induces an increase in the splicing of introns 10 and 11. Through mutation analysis, we show that SRSF2 functionally targets and physically interacts with CGAG sequence on exon 11. In addition, we reveal that the weak strength of splice sites of exon 11 is not required for the function of SRSF2 on the splicing of Ron exon 11. Our results indicate that SRSF2 promotes exon 11 inclusion of Ron proto-oncogene through targeting exon 11. Our study provides a novel mechanism by which Ron is expressed.

Cell cycle-dependent regulation of Aurora kinase B mRNA by the Microprocessor complex.

Aurora kinase B regulates the segregation of chromosomes and the spindle checkpoint during mitosis. In this study, we showed that the Microprocessor complex, which is responsible for the processing of the primary transcripts during the generation of microRNAs, destabilizes the mRNA of Aurora kinase B in human cells. The Microprocessor-mediated cleavage kept Aurora kinase B at a low level and prevented premature entrance into mitosis. The cleavage was reduced during mitosis leading to the accumulation of Aurora kinase B mRNA and protein. In addition to Aurora kinase B mRNA, the processing of other primary transcripts of miRNAs were also decreased during mitosis. We found that the cleavage was dependent on an RNA helicase, DDX5, and the association of DDX5 and DDX17 with the Microprocessor was reduced during mitosis. Thus, we propose a novel mechanism by which the Microprocessor complex regulates stability of Aurora kinase B mRNA and cell cycle progression.

Electrical characterization of organic monolayers at a nanoscale.

This study investigates the electrical properties of viologen derivatives at a nanoscale and analyzes it using a scanning tunneling microscopy (STM) in order to apply viologen molecules that represent a function in electron transfer mediators as a molecular electronic device. In addition, we measure conformational changes in the viologen molecular protrusions using STM and investigate changes in the width and height of the alkyl group that are due to the change in the polarity of viologen molecules by electron charges. In this experiment, high peak current is observed, such as a rectification at +1.14 V. Thus, according to the results of this experiment the rectification ratio [RR = J (at +2.5 V)/J (at -2.5 V)] of the viologen is found by 4.47 (HSC8VC8SH). Similar results are also obtained in some other cases of viologen derivatives.

White organic light-emitting diodes with Zn-complexes.

This paper reviews OLEDs fabricated using Zn-complexes. Zn(HPB)2, Zn(HPB)q, and Zn(phen)q were synthesized as new electroluminescence materials. The electron affinity (EA) and ionization potential (IP) of Zn complexes were also determined and devices were characterized. Zn complexes such as Zn(HPB)2, Zn(HPB)q, and Zn(phen)q were found to exhibit blue and yellow emissions with wavelengths of 455, 532, and 535 nm, respectively. On the other hand, Zn(HPB)2 and Zn(HPB)q were applied as hole-blocking materials. As a result, the OLED efficiency by using Zn(HPB)2 as a hole-blocking material was improved. In particular, the OLED property of Zn(HPB)2 was found to be better than that of Zn(HPB)q. Moreover, Zn(phen)q was used as an electron-transporting material and compared with Alq3. The performance of the device with Zn(phen)q as an electron-transporting material was improved compared with Alq3-based devices. The Zn complexes can possibly be used as hole-blocking and electron-transporting materials in OLED devices. A white emission was ultimately realized from the OLED devices using Zn-complexes as inter-layer components.

Synthesis and electroluminescent properties of a novel electroluminescence material of bis-2-(4-(diphenylphosphino)phenyl)benzo[d]oxazole (DPB).

A new light-emissive material, bis-2-(4-(diphenylphosphino)phenyl)benzo[d]oxazole (DPB), has been synthesized and characterized by FT-NMR, FT-IR, UV-Vis and elemental analysis. DPB has the band gap of 4.3 eV between HOMO and LUMO levels. The photoluminescence (PL) of DPB was measured at 410 nm from the chloroform solution. The electroluminescent (EL) devices with structures of ITO/NPB/DPB/LiF/Al and ITO/NPB/DPB/Alq3/LiF/Al were constructed and showed maximum emission at 540 nm. The device using DPB as emitting material showed the luminance of 1000 cd/m2 at 11 V. The CIE chromaticity of the device showed near the region of white color emission.

Fabrication of a polymer-metal combined atomic force microscopy probe for coarse food surface imaging.

We fabricated a polymer-metal combined atomic force microscopy (AFM) probe by two steps; a polymeric resin was used at first step, and a metal-ion was used at second step which needs more fabricating time than the resin. At first step, we fabricated a cylindrical base on to a commercial cantilever. At second step, we fabricated a conical probe on to the fabricated cylindrical base. To make the conical probe composed with silver, a 0.2 M aqueous solution of silver nitrate (AgNO3) was used. A 50 microm length polymeric-metallic hybrid tip has been fabricated to observe large bio and food samples. Generally, the AFM images of bio/food samples show cliff-like sharp patters in vertical. However, the AFM image by fabricated long tip shows clear structure of each brown rice flours. As most of commercial tips have three-angular pyramidal, the scanned results should be influenced by the lateral face of the three-angular pyramid, which results in cliff-like images. Because the sample size is large, the side area of the sample was adversely affected by the pyramidal structure during imaging. This problem may be resolved by designing conical structure tips. As the conical structure has no edge, the AFM image becomes clear. The fabricated tip has conical structure, and a clear AFM image was achieved.

Toxoplasma gondii and Rickettsia spp. in ticks collected from migratory birds in the Republic of Korea.

Migratory birds disperse ticks and associated tick-borne pathogens along their migratory routes. Four selected pathogens of medical importance (Coxiella burnetii, Rickettsia spp., Francisella tularensis, and Toxoplasma gondii) were targeted for detection in 804 ticks (365 pools) collected from migratory birds at Hong and Heuksan Islands in the Republic of Korea (ROK) from 2010 to 2011 and 2016. Toxoplasma gondii and Rickettsia spp., were detected in 1/365 (0.27%) and 34/365 (9.32%) pools of ticks, respectively. T. gondii and five rickettsial species were recorded in ticks collected from migratory birds for the first time in ROK. The five rickettsial species (R. monacensis, Candidatus Rickettsia longicornii, R. japonica, R. raoultii, and R. tamurae) were identified using sequence and phylogenetic analysis using ompA and gltA gene fragments. Rickettsia spp. are important pathogens that cause rickettsiosis in humans, with cases recorded in the ROK. These results provide important evidence for the potential role of migratory birds in the introduction and dispersal of T. gondii and Rickettsia spp. along their migratory routes and raise awareness of potential transmission of zoonotic tick-borne pathogens associated with migratory birds in the ROK.

Highly efficient blue organic light-emitting diodes based on 2-(diphenylamino)fluoren-7-ylvinylarene derivatives that bear a tert-butyl group.

Blue fluorescent materials with a 2-(diphenylamino)fluoren-7-ylvinylarene emitting unit and tert-butyl-based blocking units were synthesized. The photophysical properties of these materials, including UV/Vis absorption, photoluminescent properties, and HOMO-LUMO energy levels, were characterized and rationalized with quantum-mechanical DFT calculations. The electroluminescent properties of these molecules were examined through the fabrication of multilayer devices with a structure of indium-tin oxide, 4,4'-bis{N-[4-(N,N-di-m-tolylamino)phenyl]-N-phenylamino}biphenyl, 4'-bis[N-(1-naphthyl)-N-phenylamino]biphenyl, and blue materials doped in 2-methyl-9,10-di(2-naphthyl)anthracene/tris(8-quinolinolato)aluminum/LiF/Al. All devices exhibit highly efficient blue electroluminescence with high external quantum efficiency (3.20-7.72 % at 20 mA cm(-2)). A deep-blue device with Commission Internationale de l'Eclairage (CIE) coordinates of (0.15, 0.11) that uses 7-[2-(3',5'-di-tert-butylbiphenyl-4-yl)vinyl]-9,9-diethyl-2-N-(3,5-di-tert-butylphenyl)-2,4-difluorobenzenamino-9H-fluorene as a dopant in the emitting layer showed a luminous efficiency and external quantum efficiency of 3.95 cd A(-1) and 4.23 % at 20 mA cm(-2), respectively. Furthermore, a highly efficient sky-blue device that uses the dopant 7-{2-[2-(3,5-di-tert-butylphenyl)-9,9'-spirobifluorene-7-yl]vinyl}-9,9-diethyl-2-N,N-diphenylamino-9H-fluorene exhibited a luminous efficiency and high quantum efficiency of 10.3 cd A(-1) and 7.7 % at 20 mA cm(-2), respectively, with CIE coordinates of (0.15, 0.20).

Electroluminescent properties of an electrochemically cross-linkable carbazole peripheral poly(benzyl ether) dendrimer.

The electroluminescent (EL) properties of a cross-linkable carbazole-terminated poly(benzyl ether) dendrimer, G(3)-cbz DN, doped into a PVK:PBD host matrix with a double-layer device configuration are investigated. Different concentrations of the guest material can control device efficiency, related to chromaticity of white emission and the origin of excited-state complexes occurring between hole-transporting carbazole units (PVK or G(3)-cbz DN) and electron-transporting oxadiazole (PBD). Two excited states (exciplex and electroplex) generated at the interfaces of PVK/G(3)-cbz DN and PBD result in competitive emission, exhibiting a broad band in the EL spectra.

Thermodynamic control over the competitive anchoring of N719 dye on nanocrystalline TiO2 for improving photoinduced electron generation.

TiO(2) electrodes, sensitized with the N719 dye at high immersion temperatures during the sensitization process, were found to have large fractions of weakly bound N719 on the electrode surface, which resulted in dye aggregation and decreased device longevity. These disadvantages were ameliorated using a low-temperature stearic acid (SA)-assisted anchoring method described here. The activation energy (ΔE(NS)(++)) and relative fraction of strongly bound N719 were twice as large as the respective values obtained without the use of SA. Slowing of adsorption, both by thermal means and through SA-mediated processes, effectively controlled the binding mode of N719 on the surface of TiO(2). The resulting sensitized electrodes displayed enhanced device longevity and improved generation of photoinduced electrons.