Hi-Meth：特定位点DNA甲基化高通量检测平台

胞嘧啶甲基化是DNA表观遗传修饰的主要类型之一,在维持正常细胞功能和调控基因表达中具有重要作用。重亚硫酸盐测序法(bisulfite sequencing PCR,BSP)是特异性位点DNA甲基化检测的通用方法,能明确目的片段中每一个CpG位点的甲基化状态,但此方法需要大量的单克隆测序,操作过程较繁琐、成本昂贵。因此,开发准确、高效、便捷的DNA甲基化检测技术对提升表观遗传研究效率具有重要意义。基于本课题组开发的高通量突变类型检测平台Hi-TOM (high-throughput tracking of mutations),我们进一步建立了特定位点DNA甲基化高通量检测平台Hi-Meth (high-throughput detection of DNA methylation)。DNA样品通过重亚硫酸盐处理之后,仅需一轮PCR扩增即可通过Hi-Meth平台获得特定位点DNA甲基化分析结果。利用Hi-Meth平台,对水稻不同基因启动子区域进行了DNA甲基化检测分析,并与基于BSP方法获得的结果进行了比较。结果表明,Hi-Meth策略与BSP策略检测结果基本一致。而且通过Hi-Meth平台可以更准确、便捷地获得特异性位点DNA甲基化分析结果。综上所述,Hi-Meth为特定DNA区域提供了重要的甲基化检测平台,对表观遗传研究具有重要意义。     

AoP-LSE: Antioxidant Proteins Classification Using Deep Latent Space Encoding of Sequence Features

It is of utmost importance to develop a computational method for accurate prediction of antioxidants, as they play a vital role in the prevention of several diseases caused by oxidative stress. In this correspondence, we present an effective computational methodology based on the notion of deep latent space encoding. A deep neural network classifier fused with an auto-encoder learns class labels in a pruned latent space. This strategy has eliminated the need to separately develop classifier and the feature selection model, allowing the standalone model to effectively harness discriminating feature space and perform improved predictions. A thorough analytical study has been presented alongwith the PCA/tSNE visualization and PCA-GCNR scores to show the discriminating power of the proposed method. The proposed method showed a high MCC value of 0.43 and a balanced accuracy of 76.2%, which is superior to the existing models. The model has been evaluated on an independent dataset during which it outperformed the contemporary methods by correctly identifying the novel proteins with an accuracy of 95%.     

Advanced Glycation End Products Increase Salivary Gland Hypofunction in d-Galactose-Induced Aging Rats and Its Prevention by Physical Exercise

A declined salivary gland function is commonly observed in elderly people. Advanced glycation end products (AGEs) are believed to contribute to the pathogenesis of aging. Although physical exercise is shown to increase various organ functions in human and experimental models, it is not known whether it has a similar effect in the salivary glands. In the present study, we evaluated the AGEs burden in the salivary gland in the aging process and the protective effect of physical exercise on age-related salivary hypofunction. To accelerate the aging process, rats were peritoneally injected with D-galactose for 6 weeks. Young control rats and d-galactose-induced aging rats in the old group were not exercised. The rats in the physical exercise group ran on a treadmill (12 m/min, 60 min/day, 3 days/week for 6 weeks). The results showed that the salivary flow rate and total protein levels in the saliva of the d-galactose-induced aging rats were reduced compared to those of the young control rats. Circulating AGEs in serum and secreted AGEs in saliva increased with d-galactose-induced aging. AGEs also accumulated in the salivary glands of these aging rats. The salivary gland of aging rats showed increased reactive oxygen species (ROS) generation, loss of acinar cells, and apoptosis compared to young control mice. However, physical exercise suppressed all of these age-related salivary changes. Overall, physical exercise could provide a beneficial option for age-related salivary hypofunction.     

Renal Cell Carcinoma-Infiltrating CD3low Vγ9Vδ1 T Cells Represent Potentially Novel Anti-Tumor Immune Players

Due to the highly immunogenic nature of renal cell carcinoma (RCC), the tumor microenvironment (TME) is enriched with various innate and adaptive immune subsets. In particular, gamma-delta (γδ) T cells can act as potent attractive mediators of adoptive cell transfer immunotherapy because of their unique properties such as non-reliance on major histocompatibility complex expression, their ability to infiltrate human tumors and recognize tumor antigens, relative insensitivity to immune checkpoint molecules, and broad tumor cytotoxicity. Therefore, it is now critical to better characterize human γδ T-cell subsets and their mechanisms in RCCs, especially the stage of differentiation. In this study, we aimed to identify γδ T cells that might have adaptive responses against RCC progression. We characterized γδ T cells in peripheral blood and tumor-infiltrating lymphocytes (TILs) in freshly resected tumor specimens from 20 RCC patients. Furthermore, we performed a gene set enrichment analysis on RNA-sequencing data from The Cancer Genome Atlas (TCGA) derived from normal kidneys and RCC tumors to ascertain the association between γδ T-cell infiltration and anti-cancer immune activity. Notably, RCC-infiltrating CD3^low Vγ9Vδ1 T cells with a terminally differentiated effector memory phenotype with up-regulated activation/exhaustion molecules were newly detected as predominant TILs, and the cytotoxic activity of these cells against RCC was confirmed in vitro. In an additional analysis of the TCGA RCC dataset, γδ T-cell enrichment scores correlated strongly with those for CTLs, Th1 cells, “exhausted” T cells, and M1 macrophages, suggesting active involvement of γδ T cells in anti-tumor rather than pro-tumor activity, and Vδ1 cells were more abundant than Vδ2 or Vδ3 cells in RCC tumor samples. Thus, we posit that Vγ9Vδ1 T cells may represent an excellent candidate for adoptive immunotherapy in RCC patients with a high risk of relapse after surgery.     

Effect of coix on plasma, liver, and fecal lipid components in the rat fed on lard- or soybean oil-cholesterol diet

To determine the influence of dietary coix on lipid metabolism, the effect of coix on plasma, liver, and fecal lipid components was studied using Sprague-Dawley male rats. All rats were divided into four groups, and the rats of each group were fed the coix-lard diet, coix-soybean oil diet, or the respective control diets (containing 1% cholesterol each) for 27 days. Plasma and liver cholesterol levels in the coix-lard diet group significantly decreased as compared with those in the control group, whereas there was no effect on the fecal excretion of cholesterol. The decreases in the concentrated liver triglyceride and the increases in the fecal excretion of triglyceride were found in coix-soybean oil diet group. Moreover, liver and fecal phospholipid levels in both coix diet groups significantly increased. But there were no significant changes in plasma and fecal bile acids in either coix diet group. These results suggest the possibilities that coix may have an inhibitory action on cholesterol synthesis in liver, a facilitating effect on biliary excretion of triglyceride, and an acceleratory action on phospholipid synthesis in liver.     

口腔内金属材料对磁共振检查的影响

检测口腔内常用金属材料在磁共振检查时是否有伪影和伪影的严重程度。对２１种口腔内常用金属材料做了磁共振成像测试,磁共振仪磁场强度为１．５Ｔ,所用序列是梯度回波。铸金片、银汞合金、银尖等９种材料无伪影;钛合金和金属烤瓷成品有轻度伪影;牙用固位钉、椿钉等１０种材料有严重伪影。部分口腔内金属材料会引起严重伪影,影响图象质量,所以在做口腔颌面部和服部磁共振成像时,须引起重视。     

Phloem Exudate Collected via Scale Insect Stylets for the CAM Species Opuntia ficus-indica under Current and Doubled CO2 Concentrations

A method was devised for collecting phloem sap from the CAMspecies Opuntia ficus-indica using severed stylets of a scaleinsect (Dactylopius opuntiae), for which exudation could continuefor up to 5 d. For both basal (planted) cladodes and first-orderdaughter cladodes, the concentrations of sucrose and total aminoacids in the phloem exudate were virtually constant over 24-hperiods whereas the chlorenchyma osmolality had sizeable increasesduring the night under both current and doubled atmosphericCO₂ concentrations. Sucrose, total amino acids, and potassiumaccounted for 56, 21, and 9%, respectively, of the osmolalityof the phloem exudate, which was about 350 mOsm at the two CO₂concentrations; valine, isoleucine, leucine, tyrosine, glutamine,and lysine accounted for about 70% of the total amino acids.Doubling the CO₂ concentration led to approx. 5% more sucrose,560% more mannose and 17% less amino acids in the phloem exudateand also significantly increased mannose, starch and glucomannanin the chlorenchyma. Atmospheric CO₂ concentrations thus affectedvarious solute properties in the phloem and the chlorenchymaof O. ficus-indica.Copyright 1995, 1999 Academic Press Dactylopius opuntiae, Opuntia ficus-indica, cladode, CO₂ concentrations, Crassulacean acid metabolism, phloem exudate     

Microtubular response to colchicine in adult and fetal rat hepatocytes

1. Colchicine and related anti-microtubular drugs impair plasma protein secretion from adult rat liver explants 2-3-fold more than from fetal tissue. 2. Indirect immunofluorescence microscopy of cultured adult and fetal hepatocytes demonstrated that hepatocytes of both ages contain large numbers of densely packed microtubules which are equally disassembled by 10 microM colchicine. 3. Colchicine (10 microM) reduced secretion of [14C]leucine-labelled proteins from cultured adult hepatocytes by about 50% but did not significantly impede fetal secretion. 4. These results confirmed that plasma protein secretion can proceed without an intact microtubular system in fetal hepatocytes.     

Identification of highly selective type II kinase inhibitors with chiral peptidomimetic tails

Identification of highly selective type II kinase inhibitors is described. Two different chiral peptidomimetic scaffolds were introduced on the tail region of non-selective type II kinase inhibitor GNF-7 to enhance the selectivity. Kinome-wide selectivity profiling analysis showed that type II kinase inhibitor 7a potently inhibited Lck kinase with great selectivity (IC₅₀ of 23.0 nM). It was found that 7a and its derivatives possessed high selectivity for Lck over even structurally conserved all Src family kinases. We also observed that 7a inhibited Lck activation in Jurkat T cells. Moreover, 7a was found to alleviate clinical symptoms in DSS-induced colitis mice. This study provides a novel insight into the design of selective type II kinase inhibitors by adopting chiral peptidomimetic moieties on the tail region.