Thiocyanate as a Local Probe of Ultrafast Structure and Dynamics in Imidazolium-Based Ionic Liquids: Water-Induced Heterogeneity and Cation-Induced Ion Pairing

Ultrafast two-dimensional infrared spectroscopy (2D-IR) of thiocyanate ([SCN]⁻) in 1-butyl-3-methylimidazolium bis­(trifluoromethylsulfonyl)­imide ([C₄C₁im]­[NTf₂]) and 1-butyl-2,3-dimethylimidazolium bis­(trifluoromethylsulfonyl)­imide ([C₄C₁C₁²im]­[NTf₂]) ionic liquids probes local structure and dynamics as a function of the water content, solute counterion, and solute concentration. The 2D-IR spectra of the water-saturated ionic liquids resolve two distinct kinds of dynamics. This dynamical heterogeneity is explained as two subensembles, one with and one without a water molecule in the first solvation shell. When the countercation is K⁺, ion pairs between K⁺ and [SCN]⁻ that persist for >100 ps are detected by long-lasting vibrational frequency correlations. The observed dynamics are invariant to [SCN]⁻concentration, which indicates that the [SCN]⁻ does not cluster in ionic liquid solution. Taken together, these results are consistent with a picture of thiocyanate as a local probe that can interrogate ultrafast structure and dynamics at a small spatial scale in ionic liquids

Optimal transfection conditions.

<p>(A) Cell viability with siRNA and transfection reagent siRNA-Mate at different concentrations was assessed with the MTT assay. (B) qPCR was conducted to analyze the knockdown efficiency of transfecting different ratios of siRNA:siRNA-Mate/cm². Each sample was analyzed in triplicate, and data are expressed as the mean ± SEM. *<i>P</i><0.05 vs. virus control group. (C) FAM-tagged siRNA was transfected into Vero cells with a transfection ratio of 20 pmol siRNA:1 µl siRNA-Mate/cm². The transfection efficiency and durability of the siRNA were detected by fluorescence microscopy on days 1, 2 and 3 after transfection.</p

Joint inhibitory effects of siUL18 and siUL19 on different HSV strains.

<p>Vero cells were co-transfected with siUL18 and siUL19 each at a concentration of 10 pmol with 1 µl siRNA-Mate/cm². Inhibitory effects were evaluated by a plaque reduction assay. Cell cultures were infected with (A) HSV-1/F, (B) HSV-2/33, (C) HSV-2/106, (D) HSV-1/153 or (E) HSV-1/blue, and plaques were counted 72 h later. The relative survival rate of each group was compared with the virus control set at 100%. Each sample was analyzed in triplicate, and data are expressed as the mean ± SEM. *<i>P</i><0.05 vs. viral group.</p

Effect of siRNA on HSV-1 plaque formation and relative expression of capsid-related genes in HSV-1-infected Vero cells.

<p>(A–F) Effects of siRNA on relative mRNA expression levels of capsid genes (<i>UL18</i>, <i>UL19</i>, <i>UL26</i>, <i>UL26.5</i>, <i>UL35</i> and <i>UL38</i>, respectively) compared with the virus group were analyzed by qPCR. (a–f) Effects of siRNA against different capsid genes (<i>UL18</i>, <i>UL19</i>, <i>UL26</i>, <i>UL26.5</i>, <i>UL35</i> and <i>UL38</i>, respectively) on HSV-1 proliferation were evaluated by a plaque reduction assay. Vero cells were treated with different siRNAs. Cultures were infected with HSV-1, and plaques were counted 72 h later. The relative survival rate of each group was compared with the virus control set at 100%. Each sample was analyzed in triplicate, and data are expressed as the mean ± SEM. *<i>P</i><0.05 vs. viral group.</p

Effects of knockdown VP23 and VP5 on cellular viral genome load.

<p>(A) Vero cells were transfected with different siRNAs and infected with HSV-1/F at the multiplicity of infection (MOI) at 1. At the indicated times post-infection, the cellular viral genome DNA was extracted and assayed by quantitative real-time PCR. The results were expressed compared with the genome copies of viral group at 6 hours. (B) The vero cells were transfected with indicated siRNAs and infected with HSV-1/F at different multiplicity of infection (MOI = 1 and MOI = 10). At 18 h post-infection the viral genome of each group was extracted and the genome copy number was quantified. The results were expressed compared with the genome copies of viral group at MOI = 1. Data are expressed as the mean ± SEM. *<i>P<0.05</i> vs. viral group.</p

Insights from ENCODE on Missing Proteins: Why β‑Defensin Expression Is Scarcely Detected

β-Defensins (DEFBs) have a variety of functions. The majority of these proteins were not identified in a recent proteome survey. Neither protein detection nor the analysis of transcriptomic data based on RNA-seq data for three liver cancer cell lines identified any expression products. Extensive investigation into DEFB transcripts in over 70 cell lines offered similar results. This fact naturally begs the questionWhy are DEFB genes scarcely expressed? After examining DEFB gene annotation and the physicochemical properties of its protein products, we postulated that regulatory elements could play a key role in the resultant poor transcription of DEFB genes. Four regions containing DEFB genes and six adjacent regions on chromosomes 6, 8, and 20 were carefully investigated using The Encyclopedia of DNA Elements (ENCODE) information, such as that of DNase I hypersensitive sites (DHSs), transcription factors (TFs), and histone modifications. The results revealed that the intensities of these ENCODE features were globally weaker than those in the adjacent regions. Impressively, DEFB-related regions on chromosomes 6 and 8 containing several non-DEFB genes had lower ENCODE feature intensities, indicating that the absence of DEFB mRNAs might not depend on the gene family but may be reliant upon gene location and chromatin structure

siRNAs targeting HSV-1 capsid proteins.

<p>siRNAs targeting HSV-1 capsid proteins.</p

Election microscopy of infected cells.

<p>Electron microscopic images of (A) cell control group, (B) viral group, (C) siN.C-treated group, (D) siUL18-3 treated group and (E) siUL19-1 treated group. Black arrows indicate viral particles. Bar, 500 nm. (F) The numbers of particles in each group were counted from six fields and the mean particles per field were calculated. Data are expressed as the mean ± SEM. *<i>P</i><0.05 vs. viral group.</p

Effect of siUL19 on plaque formation and relative <i>UL19</i> gene expression of acyclovir-resistant HSV-1 strains and HSV-2 333.

<p>(A–D) Effects of siUL19 on relative mRNA expression level of the <i>UL19</i> gene were analyzed by qPCR compared with the viral group (HSV-2/33, HSV-2/106, HSV-1/153 and HSV-1/Blue, respectively). (a–d) Effects of siUL19 on proliferation of acyclovir-resistant HSV-1 and HSV-2 333 were evaluated by a plaque reduction assay. Cells were treated with siUL19 and infected with each virus (HSV-2/33, HSV-2/106, HSV-1/153 and HSV-1/blue, respectively). Plaques were counted 72 h later, and the relative survival rate of each group was compared with virus control set at 100%. Each sample was analyzed in triplicate, and data are expressed as the mean ± SEM. *<i>P</i><0.05 vs. viral group.</p

Appraisal of the Missing Proteins Based on the mRNAs Bound to Ribosomes

Considering the technical limitations of mass spectrometry in protein identification, the mRNAs bound to ribosomes (RNC-mRNA) are assumed to reflect the mRNAs participating in the translational process. The RNC-mRNA data are reasoned to be useful for appraising the missing proteins. A set of the multiomics data including free-mRNAs, RNC-mRNAs, and proteomes was acquired from three liver cancer cell lines. On the basis of the missing proteins in neXtProt (release 2014-09-19), the bioinformatics analysis was carried out in three phases: (1) finding how many neXtProt missing proteins have or do not have RNA-seq and/or MS/MS evidence, (2) analyzing specific physicochemical and biological properties of the missing proteins that lack both RNA-seq and MS/MS evidence, and (3) analyzing the combined properties of these missing proteins. Total of 1501 missing proteins were found by neither RNC-mRNA nor MS/MS in the three liver cancer cell lines. For these missing proteins, some are expected higher hydrophobicity, unsuitable detection, or sensory functions as properties at the protein level, while some are predicted to have nonexpressing chromatin structures on the corresponding gene level. With further integrated analysis, we could attribute 93% of them (1391/1501) to these causal factors, which result in the expression products scarcely detected by RNA-seq or MS/MS