Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers

Wang, Yumeng,Xu, Xiaoyan,Yu, Shuangxing,Jeong, Kang Jin,Zhou, Zhicheng,Han, Leng,Tsang, Yiu Huen,Li, Jun,Chen, Hu,Mangala, Lingegowda S.,Yuan, Yuan,Eterovic, A. Karina,Lu, Yiling,Sood, Anil K.,Scott, Cold Spring Harbor Laboratory Press 2017 Genome research Vol.27 No.7

<P>RNA editing, a widespread post-transcriptional mechanism, has emerged as a new player in cancer biology. Recent studies have reported key roles for individual miRNA editing events, but a comprehensive picture of miRNA editing in human cancers remains largely unexplored. Here, we systematically characterized the miRNA editing profiles of 8595 samples across 20 cancer types from miRNA sequencing data of The Cancer Genome Atlas and identified 19 adenosine-to-inosine (A-to-I) RNA editing hotspots. We independently validated 15 of them by perturbation experiments in several cancer cell lines. These miRNA editing events show extensive correlations with key clinical variables (e.g., tumor subtype, disease stage, and patient survival time) and other molecular drivers. Focusing on the RNA editing hotspot in miR-200b, a key tumor metastasis suppressor, we found that the miR-200b editing level correlates with patient prognosis opposite to the pattern observed for the wild-type miR-200b expression. We further experimentally showed that, in contrast to wild-type miRNA, the edited miR-200b can promote cell invasion and migration through its impaired ability to inhibit <I>ZEB1/ZEB2</I> and acquired concomitant ability to repress new targets, including <I>LIFR</I>, a well-characterized metastasis suppressor. Our study highlights the importance of miRNA editing in gene regulation and suggests its potential as a biomarker for cancer prognosis and therapy.</P>

Effects of Tween 80 on In Vitro Fermentation of Silages and Interactive Effects of Tween 80, Monensin and Exogenous Fibrolytic Enzymes on Growth Performance by Feedlot Cattle

Wang, Y.,McAllister, T.A.,Baah, J.,Wilde, R.,Beauchemin, K.A.,Rode, L.M.,Shelford, J.A.,Kamande, G.M.,Cheng, K.J. Asian Australasian Association of Animal Productio 2003 Animal Bioscience Vol.16 No.7

The effects of monensin, Tween 80 and exogenous fibrolytic enzymes on ruminal fermentation and animal performance were studied in vitro and in vivo. In Expt 1, the effects of the surfactant Tween 80 (0.2% wt/wt, DM basis) on ruminal fermentation of alfalfa, corn and orchardgrass silages were investigated using in vitro gas production techniques. Tween 80 did not affect (p>0.05) cumulative gas production at 24 h, but it reduced (p<0.05) the lag in fermentation of all three silages. With corn silage and orchardgrass silage, gas production rates and concentrations of total volatile fatty acids (VFA) were increased (p<0.05) by Tween 80; with alfalfa silage, they were reduced (p<0.05). Tween 80 increased (p<0.05) the proportion of propionate in total VFA, and reduced (p<0.05) acetate to propionate ratios (A:P) with all three silages. In Expt 2, exogenous fibrolytic enzymes (E; at 0, 37.5 or 75 g/tonne DM), monensin (M; at 0 or 25 ppm and Tween 80 (T; at 0 or 2 L/tonne DM) were added alone or in combination to backgrounding and finishing diets fed to 320 crossbred steers in a feeding trial with a $3{\times}2{\times}$2 factorial arrangement of treatments. The backgrounding and finishing diets contained barley grain and barley silage in ratios of 57.8:42.2 and 93.5:6.5 (DM basis), respectively. Added alone, none of the additives affected DM intake (p>0.1) in the backgrounding or in the finishing period, but interactive $M{\times}T$ effects were observed in the finishing period (p=0.02) and overall (p=0.04). In the finishing period, T without M tended to reduce DM intake (p=0.11), but T with M increased (p=0.05) DM intake. Monensin increased average daily gain (ADG) during backgrounding (p=0.07) and finishing (p=0.01), and this ionophore also improved overall feed efficiency (p=0.02). Warm carcass weight was increased (p<0.001) by M, but dressing percentage was reduced (p=0.07). In the backgrounding period, T increased ADG by 7% (p=0.06). Enzymes increased (p=0.07) ADG by 5 and 6% (low and high application rates, respectively) during backgrounding, but did not affect (p>0.10) ADG during finishing, or overall feed efficiency. Whereas T enhanced the positive effects of M on ADG during backgrounding (p=0.04) and overall (p=0.05), it had no impact (p>0.1) on the effects of E. Interactions between M and T suggest that the surfactant may have potential for enhancing the positive effects of monensin on beef production, but this requires further research.

Preparation of antimicrobial agar/banana powder blend films reinforced with silver nanoparticles

Orsuwan, A.,Shankar, S.,Wang, L.F.,Sothornvit, R.,Rhim, J.W. IRL Press ; Elsevier Science Ltd 2016 Food hydrocolloids Vol.60 No.-

<P>Binary blend films of agar and banana powder (A/B) and A/B composite films reinforced with silver nanoparticles (A/B/AgNPs) were prepared using a solution casting method and their properties were characterized. The SEM micrographs and FT-IR results confirmed the formation of physical interactions between polymer matrices and nanofillers. Apparent surface color and transmittance of the composite film were greatly influenced not only by the mixing of banana powder with agar but also by the incorporation of AgNPs. The UV light absorption, water vapor barrier properties, and antioxidant activity of A/B blend films increased with the increase in the concentration of the banana powder, while the mechanical properties decreased. The A/B/AgNPs composite film exhibited distinctive antimicrobial activity against food-borne pathogenic bacteria, Escherichia coli and Listeria monocytogenes with stronger antibacterial activity against Gram-negative bacteria than Gram-positive bacteria. The binary blend of A/B films are expected to be used for the edible film or coating of foods and their nanocomposite films with antimicrobial activity have a potential to be used as food packaging material for maintaining the safety and extending the shelf life of packaged food. (C) 2016 Elsevier Ltd. All rights reserved.</P>

Inhibition of TGFβ cell signaling for limbal explant culture in serumless, defined xeno-free conditions

Zamudio, A.,Wang, Z.,Chung, S.H.,Wolosin, J.M. Academic Press 2016 Experimental eye research Vol.145 No.-

Outgrowths of limbal epithelium by explant culture are used to treat limbal stem cell deficiency (LSCD). The explant culture medium is always complemented with serum, a complex solution which includes TGFβ. Since TGFβ is a cytostatic effector for epithelial proliferation we examined its effect on these cultures. Limbal biopsies were set on explant culture in DMEM/F12 with 5 ng/ml EGF and cholera toxin (ChT), ITS, and 5% FBS, henceforth SHEM or a) SHEMSB=SHEM plus SB431542 an inhibitor of TGFβ signaling; b) sfSHEM = SHEM with FBS replaced by 0.05% Albumax II; and c) sfSHEMSB and sfSHEMA83 = sfSHEM plus, respectively, SB431542 or A-83-01, another TGFβ inhibitor. After the initial outgrowths reached 3 cm in diameter, the limbal biopsies were serially transferred up to six times onto new inserts. Biopsy explant outgrowths were trypsinized and cell yield, morphology and stem-cell related JC-1 exclusion (IOVS, 52:4330) were determined by flow cytometry. Cells we plated at low density seeding to compare relative clonal proliferative activity. The expression of three proteins whose levels are associated with growth and differentiation states, Krt3, connexin 43 and p63 were determined by immunohistology and/or Western blot. Cell yield in rabbit, relative to SHEM (in %) were, SHEMSB, 104 +/- 13 (p > 0.95); sfSHEM: 5 +/- 3; and sfSHEMSB, 94 +/- 18 (p > 0.95). Cell size and morphology, JC1 dye exclusion, Krt3, p63 and connexin 43 content, proliferation efficiency and the preservation of extended proliferative potential of the serially cultured biopsies were similar for SHEM, SHEMSB and sfSHEMSB. The only differences observed where reduced expression of Krt3 and increased preservation of p63 in the FBS-free medium. Removal of EGF from sfSHEMSB reduced yield by 92 +/- 6% (p < 0.05). Removal of Albumax and ChT to establish a xeno-free medium caused a small, non-statistical decrease in growth rates. Equivalent results were observed in a preliminary experiment in human. These results suggest that in the absence serum endogenously generated TGFβ act as an autocrine cytostatic agent and that TGFβ inhibitors allow explant culture in xeno-free, chemically defined medium. Furthermore, the pro-growth effect of serum in limbal explant cultures may result exclusively from neutralization of the TGFβ cytostatic effect.

Development of High-Current Sheet Beam Cathodes for Terahertz Sources

Lili Li,Yiman Wang,Wei Liu,Yanchun Wang,Jinshu Wang,Srivastava, A.,Jin-Kyu So,Gun-Sik Park IEEE 2009 IEEE transactions on electron devices Vol.56 No.5

<P>Generation of a sheet beam directly from a scandia-doped dispenser cathode has been investigated and optimized by means of beam-profile simulations and measurements. Rectangular beams 600 mum wide and 100 mum thick with current densities over 50 A/cm<SUP>2</SUP> have been generated. The beams are stable for at least several hundred hours with the cathodes operating at 950degC<SUB>b</SUB>, making them promising candidates for application in the next generation of terahertz vacuum electron devices such as a 0.5-THz superradiant Smith-Purcell radiation source.</P>

Electron Emission from Nano-Structured Carbon Composite Materials and Fabrication of High-Quality Electron Emitters by Using Plasma Technology

H. Hiraki,A. Hiraki,H. X. Wang,N. Jiang 한국물리학회 2006 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.49 No.3

Many trials have been done to fabricate high-quality electron-emitters from nano-composite carbon materials (such as nano-diamond, carbon nano tubes and others) by means of a variety of plasma chemical-vapor-deposition (CVD) techniques. Based upon the mechanism of electron emission, we have proposed several strategic guide lines for the fabrication of good emitters. Then, following these lines, several types of emitters were tried. One of the emitters has shown a worldclass, top ranking for fabricating very bright lamps: namely, a low turn-on voltage (0.5 1 V/µm to induce 10 µA/cm2 emission current) to emit a 1 mA/cm2 current at 3 V/µm and 100 mA/cm2 current at a slightly higher applied voltage. The bright lamps are Mercury-free fluorescence lamps to exhibit brightness of 105 cd/m2 with high eciency of 100 lm/w.

The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation

Itsathitphaisarn, O.,Wing, Richard A.,Eliason, William K.,Wang, J.,Steitz, Thomas A. Cell Press ; MIT Press 2012 Cell Vol.151 No.2

DNA polymerases can only synthesize nascent DNA from single-stranded DNA (ssDNA) templates. In bacteria, the unwinding of parental duplex DNA is carried out by the replicative DNA helicase (DnaB) that couples NTP hydrolysis to 5' to 3' translocation. The crystal structure of the DnaB hexamer in complex with GDP-AlF<SUB>4</SUB> and ssDNA reported here reveals that DnaB adopts a closed spiral staircase quaternary structure around an A-form ssDNA with each C-terminal domain coordinating two nucleotides of ssDNA. The structure not only provides structural insights into the translocation mechanism of superfamily IV helicases but also suggests that members of this superfamily employ a translocation mechanism that is distinct from other helicase superfamilies. We propose a hand-over-hand mechanism in which sequential hydrolysis of NTP causes a sequential 5' to 3' movement of the subunits along the helical axis of the staircase, resulting in the unwinding of two nucleotides per subunit.

Variation of cassiicolin genes among Chinese isolates of Corynespora cassiicola

Jun Wu,Xue-Wen Xie,Yan-Xia Shi,A-Li Chai,Qi Wang,Bao-ju Li 한국미생물학회 2018 The journal of microbiology Vol.56 No.9

Corynespora cassiicola is a species of fungus that is a plant pathogen of many agricultural crop plants, including severe target spot disease on cucumber. Cassiicolin is an important effector of pathogenicity of this fungus. In this study, we collected 141 Corynespora isolates from eighteen hosts, and the casscolin gene was detected in 82 C. cassiicola strains. The deduced protein sequences revealed that 72 isolates contained the Cas2 gene, two strains from Gynura bicolor harboured the Cas2.2 gene, and 59 isolates without a cassiicolin gene were classified as Cas0. Phylogenetic analyses was performed for the 141 isolates using four loci (ITS, ga4, caa5, and act1) and revealed two genetic clusters. Cluster A is composed of four subclades: subcluster A1 includes all Cas2 isolates plus 18 Cas0 strains, subcluster A2 includes the eight Cas5 isolates and one Cas0 isolate, and subclusters A3 and A4 contain Cas0 strains. Cluster B consists of 21 Cas0 isolates. Twenty-two C. cassiicola strains from different toxin classes showed varying degrees of virulence against cucumber. Cas0 or Cas2 strains induced diverse responses on cucumber, from no symptoms to symptoms of moderate or severe infection, but all Cas5 isolates exhibited avirulence on cucumber.

Comparison of Carcass and Meat Quality Traits among Three Rabbit Breeds

Wang, Jie,Su, Yuan,Elzo, Mauricio A.,Jia, Xianbo,Chen, Shiyi,Lai, Songjia Korean Society for Food Science of Animal Resource 2016 한국축산식품학회지 Vol.36 No.1

The objective of this study was to compare carcass composition and meat quality traits in the longissimus dorsi and biceps femoris muscles in the Hyla, Champagne and Tianfu Black rabbit breeds. Tianfu Black rabbits had the heaviest head, skin, thoracic viscera and commercial carcass percentage (p<0.05). In addition, Tianfu Black had the highest pH_{0 h} value, followed by the Champagne and Hyla breeds (p<0.01) in the longissimus dorsi and biceps femoris muscles. Tianfu Black had a higher a* (0 h and 24 h) than the other two breeds in both longissimus dorsi and biceps femoris muscles (p<0.05). The Hyla, Champagne, and Tianfu Black breeds showed a similar pattern of differences for meat quality traits (pH, L*, a* and b*) measured in fresh meat (0 h) and meat stored for 24 h. Hyla had the highest IMF values of the three breeds (p<0.01). The lower intramuscular fat of Tianfu Black and Champagne rabbits gives them an advantage over Hyla rabbits among most consumers seeking lean rabbit meat.

Sensitivity of Escherichia coli to Seaweed (Ascophyllum nodosum) Phlorotannins and Terrestrial Tannins

Wang, Yuxi,Xu, Z.,Bach, S.J.,McAllister, T.A. Asian Australasian Association of Animal Productio 2009 Animal Bioscience Vol.22 No.2

Pure culture experiments were conducted to assess the bacteriostatic and bactericidal effects of phlorotannins (PT) isolated from Ascophyllum nodosum (brown seaweed) on Escherichia coli O157:H7. In Exp. 1, one non-O157:H7 strain (25922) and three strains of E. coli O157:H7 (3081, EDL933 and E318N) were cultured in M9 medium with PT included at 0 (control), 25, 50 or $100{\mu}g/ml$ (n = 3). Bacterial growth was monitored by $OD_{600}$ at 0, 4, 6, 12 and 24 h, and by dilution plating at 0, 4, 6 and 24 h. All strains were inhibited (p<0.001) by PT to varying degrees. At 50 or $100{\mu}g/ml$, PT prevented growth of all four strains. At $25{\mu}g\;PT/ml$, growth of 25922, 3081, E318N and EDL933 was inhibited for 6, 12 and 24 h, respectively, but 25922 and 3081 resumed growth by 12 and 24 h. Direct plating confirmed bactericidal effects of PT on all four strains at $100{\mu}g/ml$, and on EDL933 and E318N at $50{\mu}g/ml$. In Exp. 2, strains 25922 and 3081 were incubated with no tannins or with $50{\mu}g/ml$ of PT, purified condensed tannins (CT) from Quebracho (Schinopsis balansaei), or purified tannic acid from Rhus semialata (Anacardiaceae) as hydrolysable tannins (HT). Strain 3081 was unaffected by HT or CT, but was completely inhibited (p<0.001) by PT at 4, 6 and 24 h. Strain 25922 was unaffected by HT, slightly inhibited by CT, and almost eradicated by PT at 4 and 6 h. Transmission electron microscopy revealed tannin-mediated alterations to bacterial cell walls. Phlorotannins from A. nodosum exhibit growth-inhibiting and bactericidal effects in vitro against the strains of E. coli O157:H7 investigated. Anti-E. coli efficacy of A. nodosum PT is superior to that of terrestrial tannins purified from Quebracho and from Rhus semialata.