Ejection dynamics of a ring polymer out of a nanochannel

We investigate the ejection dynamics of a ring polymer out of a cylindrical nanochannel using both theoretical analysis and three dimensional Langevin dynamics simulations. The ejection dynamics for ring polymers shows two regimes like for linear polymers, depending on the relative length of the chain compared with the channel. For long chains with length $N$ larger than the critical chain length $N_{c}$, at which the chain just fully occupies the nanochannel, the ejection for ring polymers is faster compared with linear chains of identical length due to a larger entropic pulling force; while for short chains ($N<N_c$), it takes longer time for ring polymers to eject out of the channel due to a longer distance to be diffused to reach the exit of the channel before experiencing the entropic pulling force. These results can help understand many biological processes, such as bacterial chromosome segregation.Comment: 8 pages, 10 figures. To appear in Soft Matte

A System of Photocatalysis for NAD+ Regeneration of Product of (S)-1-Pheylethanol by Enzymic Catalysis

In this study, a system of photocatalysis for NAD+ regeneration of enzymatic catalysis was constructed. The optimal conditions for the coupling reaction of photocatalysis and biocatalysis were explored. Blue light was chosen for the efficient reaction and the optimal concentration of VB2 (vitamin B2, riboflavin) was determined. NAD+-dependent (R)-1-phenylethanol dehydrogenase was used in the reaction for transforming (R)-1-phenylethanol to acetophenone. The byproducts of the reaction were just H2O and O2 by means of catalase. The coupling reaction of catalysis and photocatalysis can be used for obtaining (S)-1-phenylethanol through racemization of 1-phenylethanol. Copyright © 2019 BCREC Group. All rights reserve

Association of eNOS Polymorphisms with Anterior Chamber Depth in Han Chinese: Jiangsu Eye Study

Recently, a study reported that single nucleotide polymorphisms (SNP) in endothelial nitric oxide synthase (eNOS) were associated with primary angle closure glaucoma (PACG) in Australian cohort. In this study, we aimed to investigate whether those eNOS SNPs are associated with primary angle closure (PAC) or ocular biometric characteristics such as axial length (AL), anterior chamber depth (ACD), and diopter of spherical power (DS) in Han Chinese. The samples consisted of 232 PAC subjects and 306 controls collected from a population-based prevalence survey conducted in Funing County of Jiangsu, China. The rs3793342 and rs11771443 in eNOS were genotyped by TaqMan-MGB probe using the RT-PCR system. Our data did not identify any association of the eNOS SNPs with PAC. However, the analysis on the quantitative traits of ocular biometrics showed that the ACD of rs11771443 AA and GA carriers is significantly deeper than that of rs11771443 GG carriers (P = 0.0025), even though the AL and DS are not associated with rs11771443 genotypes. Rs3793342 was not associated with any biometric parameters including ACD, AL and DS. In summary, our data indicates that eNOS rs11771443 is associated with ACD and its role in the pathogenesis of PACG warranted further study

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3-prime untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3-prime polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental dataComment: 44 pages, 9 figure

Fast Green FCF Attenuates Lipopolysaccharide-Induced Depressive-Like Behavior and Downregulates TLR4/Myd88/NF-κB Signal Pathway in the Mouse Hippocampus

Depression is a common neuropsychiatric disorder and new anti-depressive treatments are still in urgent demand. Fast Green FCF, a safe biocompatible color additive, has been suggested to mitigate chronic pain. However, Fast green FCF’s effect on depression is unknown. We aimed to investigate Fast green FCF’s effect on lipopolysaccharide (LPS)-induced depressive-like behavior and the underlying mechanisms. Pretreatment of Fast green FCF (100 mg/kg, i.p. daily for 7 days) alleviated depressive-like behavior in LPS-treated mice. Fast green FCF suppressed the LPS-induced microglial and astrocyte activation in the hippocampus. Fast green FCF decreased the mRNA and protein levels of Toll-like receptor 4 (TLR4) and Myeloid differentiation primary response 88 (Myd88) and suppressed the phosphorylation of nuclear factor-κB (NF-κB) in the hippocampus of LPS-treated mice. Fast green FCF also downregulated hippocampal tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6, but did not alter the level of the brain-derived neurotrophic factor (BDNF) in the hippocampus of LPS-treated mice. The molecular docking simulation predicts that Fast green FCF may interact with TLR4 and interrupt the formation of the TLR4-MD2 complex. In conclusion, the anti-depressive action of Fast green FCF in LPS-treated mice may involve the suppression of neuroinflammation and the downregulation of TLR4/Myd88/NF-κB signal pathway in mouse hippocampus. Our findings indicate the potential of Fast green FCF for controlling depressive symptoms

EpCAM-Positive Hepatocellular Carcinoma Cells Are Tumor-Initiating Cells With Stem/Progenitor Cell Features

Cancer progression/metastases and embryonic development share many properties including cellular plasticity, dynamic cell motility, and integral interaction with the microenvironment. We hypothesized that the heterogeneous nature of hepatocellular carcinoma (HCC) may be, in part, due to the presence of hepatic cancer cells with stem/progenitor features

Identification of microRNA-181 by genome-wide screening as a critical player in EpCAM-positive hepatic cancer stem cells

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that regulate gene expression with functional links to tumorigenesis. Hepatocellular carcinoma (HCC) is the most common type of liver cancer and it is heterogeneous in clinical outcomes and biological activities. Recently, we have identified a subset of highly invasive EpCAM+ HCC cells from AFP+ tumors with cancer stem/progenitor cell features, i.e., the abilities to self-renew, differentiate and initiate aggressive tumors in vivo. Here, using a global microarray-based microRNA profiling approach followed by validation with quantitative reverse transcription polymerase chain reaction, we have demonstrated that conserved miR-181 family members were upregulated in EpCAM+AFP+ HCCs and in EpCAM+ HCC cells isolated from AFP+ tumors. Moreover, miR-181 family members were highly expressed in embryonic livers and in isolated hepatic stem cells. Importantly, inhibition of miR-181 led to a reduction in EpCAM+ HCC cell quantity and tumor initiating ability, while exogenous miR-181 expression in HCC cells resulted in an enrichment of EpCAM+ HCC cells. We have found that miR-181 could directly target hepatic transcriptional regulators of differentiation (i.e., CDX2 and GATA6) and an inhibitor of wnt/β-catenin signaling (i.e., NLK). Taken together, our results define a novel regulatory link between miR-181s and human EpCAM+ liver cancer stem/progenitor cells and imply that molecular targeting of miR-181 may eradicate HCC