110 research outputs found

    Supplement 1: Interacting photon pulses in a Rydberg medium

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    1 Originally published in Optica on 20 October 2016 (optica-3-10-1095

    Transgenic zebrafish study.

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    <p>(A) Schematic view of the Tol2 transposon-based plasmid carrying a 185 bp zebrafish <i>nphs2</i> promoter. (B-D) Transient GFP expression in zebrafish podocytes at 4 dpf. Lateral view (B), confocal image (C), and dorsal view (D). Pronephros and dorsal aorta are indicated by arrows and an arrowhead, respectively. (E) GFP expression rate in 4 dpf-embryos injected with different constructs. The plasmid without inserts was used as a control for the baseline. The HCS3-A or -C sequence was subcloned upstream of the promoter. They are schematically shown in left panel. The bar graph illustrates expression rate (%) and total number of G<sub>0</sub> embryos for assessment are indicated in parentheses.</p

    Genomic conservation analysis.

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    <p>The upper panel illustrates the physical map of the SNP rs1866813 and the four nearby genes. The 11-kb high LD block containing rs1866813 is indicated with a gray box. The VISTA plot displays that three human conserved sequences (HCS1-3) are highly conserved (score >90%) against mouse genome and one sequence is aligned with orthologous zebrafish region (score >75%). The position of three SNPs (rs62408925, rs9826507 and rs1866813) is indicated with vertical black bars. The lower panel illustrates generation of the constructs used for functional analyses. Open boxes denote PCR amplicons of HCS1-3 with SNPs and size of the amplicons is indicated in parenthesis. Three single HCSs were ligated together leading to two combined haplotype constructs, HCS123-TGC and -CAA, indicated with three long arrows.</p

    Luciferase activity.

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    <p>(A) Luciferase reporter constructs with different inserts were transiently transfected in HEK293 cells. (B) The construct with HCS3-C or HCS3-A was transiently transfected in HT1080 or HeLa cells. Relative luciferase activity was obtained by setting the relative luciferase activity of the empty plasmid (Luc-null) to be 1. Schematic illustration of luciferase constructs used for the assays are shown on the left side of the bar graph. A minimal promoter (minP) is indicated with an arrow.</p

    Glomerular expression analysis of four nearby genes.

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    <p>(A) Immunofluorescence staining of mouse kidney sections. Positive signals of staining and locations of glomeruli are indicated by arrows and arrowheads, respectively. (B) Positive and negative controls of mouse kidney immunofluorescence staining for IL-20rb. LPS-treated mouse kidney was used as a positive control. Staining without primary antibody to IL-20rb was used as a negative control. (C) Western blotting analysis. Nck1 and calnexin, an internal control, are shown in the left side. Stag1, Tmem22, IL-20rb and β-action, an internal control, are shown in the right side. Glo, the glomerular lysate; ROK, the rest of kidney, indicating lysates from kidney that lacks glomeruli fractions. Molecular weight is indicated by number of kDa. (D) Double immunostaining of mouse kidney sections with a podocyte marker nephrin (green) and Nck1 (red). Yellow color pointed by arrows indicates partial colocaliztion of staining of Nck1 and nephrin staining. (E) qPCR analysis. mRNA expression of four genes from isolated glomeruli of adult C57BL/6 mouse kidney was quantified using the TaqMan method.</p

    Differential expression of <i>NCK1</i> in humans and mice.

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    <p>(A) Correlation of <i>NCK1</i> expression with genotypes of the SNP rs1866813. Relative <i>NCK1</i> mRNA levels in three genotype groups are shown in open bars. Total RNA was extracted from immortalized lymphocytes derived from 25 diabetic patients with different rs1866813 genotypes and their numbers are indicated in parentheses. These cells were cultured under 5 mM glucose. (B) Differential expression of glomerular <i>Nck1</i> in mice with different strains. Relative <i>Nck1</i> mRNA levels in isolated glomeruli from four C57BL/6 mice and five mice with C57BL/6×129/Sv background are shown in a black bar. Bars represent mean ± s.e.m 2<sup>-ΔCt</sup>. *<i>P</i><0.05.</p

    mUbiSiDa: A Comprehensive Database for Protein Ubiquitination Sites in Mammals

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    <div><p>Motivation</p><p>Protein ubiquitination is one of the important post-translational modifications by attaching ubiquitin to specific lysine (K) residues in target proteins, and plays important regulatory roles in many cell processes. Recent studies indicated that abnormal protein ubiquitination have been implicated in many diseases by degradation of many key regulatory proteins including tumor suppressor, oncoprotein, and cell cycle regulator. The detailed information of protein ubiquitination sites is useful for scientists to investigate the mechanism of many cell activities and related diseases.</p><p>Results</p><p>In this study we established mUbiSida for mammalian Ubiquitination Site Database, which provides a scientific community with a comprehensive, freely and high-quality accessible resource of mammalian protein ubiquitination sites. In mUbiSida, we deposited about 35,494 experimentally validated ubiquitinated proteins with 110,976 ubiquitination sites from five species. The mUbiSiDa can also provide blast function to predict novel protein ubiquitination sites in other species by blast the query sequence in the deposit sequences in mUbiSiDa. The mUbiSiDa was designed to be a widely used tool for biologists and biomedical researchers with a user-friendly interface, and facilitate the further research of protein ubiquitination, biological networks and functional proteomics. The mUbiSiDa database is freely available at <a href="http://reprod.njmu.edu.cn/mUbiSiDa" target="_blank">http://reprod.njmu.edu.cn/mUbiSiDa</a>.</p></div

    Molecular Dynamics Study on the Nucleation Characteristics of Mixed Na<sub>2</sub>SO<sub>4</sub>/K<sub>2</sub>SO<sub>4</sub> Solution in Supercritical Water

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    Nucleation properties of mixed Na2SO4/K2SO4 solutions were investigated by molecular dynamics simulations. In the mixed solution, ions were attracted to each other and collided to form ion pairs or small clusters, and deposition occurred after further collisions up to a certain scale. The radial distribution function, hydrogen bonding, PMF curves, and coordination number indicated that K+ had a stronger ability to attract water molecules, and in the presence of K+, water molecules in the vicinity of Na+ were decreased, and the probability of collision between Na+ and SO42– ascended. This accelerated the deposition of Na2SO4. The deposition mechanism in the mixed solution was summarized based on the simulation results. It was also found that the nucleation of Na2SO4 was more sensitive to temperature and that of K2SO4 was more sensitive to concentration in the mixed solution

    Molecular Dynamics Study on the Nucleation Characteristics of Mixed Na<sub>2</sub>SO<sub>4</sub>/K<sub>2</sub>SO<sub>4</sub> Solution in Supercritical Water

    No full text
    Nucleation properties of mixed Na2SO4/K2SO4 solutions were investigated by molecular dynamics simulations. In the mixed solution, ions were attracted to each other and collided to form ion pairs or small clusters, and deposition occurred after further collisions up to a certain scale. The radial distribution function, hydrogen bonding, PMF curves, and coordination number indicated that K+ had a stronger ability to attract water molecules, and in the presence of K+, water molecules in the vicinity of Na+ were decreased, and the probability of collision between Na+ and SO42– ascended. This accelerated the deposition of Na2SO4. The deposition mechanism in the mixed solution was summarized based on the simulation results. It was also found that the nucleation of Na2SO4 was more sensitive to temperature and that of K2SO4 was more sensitive to concentration in the mixed solution
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