MicroPhenoDB Associates Metagenomic Datawith Pathogenic Microbes,Microbial Core Genes,and Human Disease Phenotypes

Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching, and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available through http://www.liwzlab.cn/microphenodb and http://lilab2.sysu.edu.cn/microphenodb.     

Impact of genetic variants in IL-2RA and IL-2RB on breast cancer risk in Chinese Han women

The expression of IL-2RA and IL-2RB was correlated with breast cancer (BC) progression. However, there is no literature investigating the association of IL-2RA and IL-2RB polymorphisms with BC predisposition among Chinese Han Women. Seven SNPs in IL-2RA and IL-2RB were genotyped by Agena MassARRAY platform among 553 BC patients and 550 healthy controls. Odds ratios (OR) and 95% confidence interval (CI) adjusted for age were calculated for the effect of IL-2RA and IL-2RB variants on BC susceptibility. IL-2RA rs12722498 was a protective factor for BC occurrence (OR?=?0.70, p?=?0.019), especially in subjects with age?≤?52 years (OR?=?0.55, p?=?0.004). IL-2RA rs12569923 (OR?=?9.07, p?=?0.033), IL-2RB rs2281089 (OR?=?0.67, p?=?0.043) and rs9607418 (OR?=?0.59, p?=?0.012) were related to the incidence of estrogen receptor positive (ER?+) BC. IL-2RB rs3218264 (OR?=?1.38, p?=?0.010) and rs9607418 (OR?=?0.56, p?=?0.009) were associated with the risk of developing progesterone receptor positive (PR?+) BC. Rs2281089 (OR?=?1.54, p?=?0.012) and rs1573673 (OR?=?0.72, p?=?0.035) were correlated to Ki-67 level. Moreover, IL-2RB rs2281089 (OR?=?0.72, p?=?0.022) showed a reduced risk of BC metastasis, and IL-2RA rs12722498 (OR?=?0.54, p?=?0.030) had a lower frequency in BC patients with tumor size?>?2 cm. Our study identified the potential effect of genetic variations in IL-2RA and IL-2RB on BC susceptibility and/or BC clinicopathologic indicators among Chinese Han Women.

     

Breast milk contains probiotics with anti-infantile diarrhoea effects that may protect infants as they change to solid foods

Infants often experience complementary food-induced diarrhoea (CFID), which occurs when infants switch from breast milk to solid foods. The relative abundances of Prevotella and Rothia were higher in stools of infants with CFID, while the relative abundances of Enterococcus and Escherichia were higher in healthy infants. The abundance of Lactobacillus spp. normally found in breast milk fed to infants with CFID was significantly reduced, and Enterococcus spp. were less abundant when diarrhoea occurred. Furthermore, Lactobacillus and Enterococcus were present as shared bacteria in both mother and infant, and they were considered potential anti-CFID probiotics as their relative abundances in breast milk were negatively correlated to infant CFID. Kyoto encyclopedia of genes and genomes (KEGG) functional analysis showed that the function of amino acid metabolism differed between infants with CFID and healthy infants. Therefore, CFID might be related to the decomposition of proteins in food supplements. The screening revealed seven hydrolytic casein and five hydrolytic casein and rice protein isolates from 320 suspected Lactobacillus and Enterococcus isolates. The animal experiments demonstrated that a mixture of five isolates effectively hydrolysed the casein and rice protein and prevented diarrhoea in young rats. Thus, the occurrence of CFID was found to be closely related to the intestinal and breast milk microbiota, and bacteria that could assist in the digestion of cereal proteins were involved in CFID.     

Structural analysis of glycosaminoglycans from Colla corii asini by liquid chromatography-electrospray ion trap mass spectrometry

Glycoconjugate Journal - Colla corii asini (CCA) made from donkey-hide has been widely used as a traditional animal-based Chinese medicine. Chondroitin sulfate (CS), dermatan sulfate (DS) and...     

基于BP神经网络与ETM+遥感数据的盐城滨海自然湿地覆被分类

高效而精确的湿地遥感分类是大范围湿地资源动态监测与管理的必要保障。本研究使用ETM 遥感数据,借助Matlab神经网络工具箱,构建了基于BP神经网络的滨海湿地覆被分类模型,并将其应用于江苏盐城沿海湿地珍禽国家级自然保护区的核心区的自然湿地覆被分类研究中。本研究选择3、4、7、8波段作为输入层变量,单隐藏层设为10个节点,输出层变量对应待划分的8种覆被类型,构建三层式BP神经网络滨海湿地覆被分类模型。结果显示,BP分类总精度为85.91%,Kappa系数为0.8328,与最小距离法和极大似然法的分类总精度相比,分别提高了7.99%和6.08%,Kappa系数也相比提高。研究结果表明,BP神经网络分类法是一种较为有效的湿地遥感影像分类技术,能够提高分类精度。     

木瓜籽毛油精炼条件筛选及其理化指标分析

以磷脂含量为指标对木瓜〔Chaenomeles sinensis ( Thouin) Koehne〕籽毛油水化脱胶过程中脱胶剂种类、脱胶剂添加量、脱胶时间、加水量和脱胶温度进行单因素实验,并在此基础上对脱胶时间、加水量和脱胶温度进行L9(33)正交实验;以酸价为指标对碱炼脱酸过程中的碱液(NaOH溶液)浓度、碱炼温度和超碱用量进行单因素实验和L9(33)正交实验;并比较了毛油、脱胶油、脱酸油和精炼油的主要理化指标变化。单因素实验和正交实验结果表明：在木瓜籽毛油水化脱胶过程中采用不同的脱胶剂种类(包括柠檬酸、草酸和蒸馏水)、脱胶剂添加量(质量分数0.1%~0.5%)、脱胶时间(10~70 min)、加水量(质量分数1%~6%)和脱胶温度(65℃~85℃),毛油中的磷脂含量均有明显差异;而碱炼脱酸过程中采用不同的碱液浓度(质量分数6%~14%)、碱炼温度(40℃~80℃)和超碱用量(质量分数0.15%~0.40%),毛油酸价也有明显变化。总体上看,木瓜籽毛油水化脱胶的适宜条件为添加质量分数0.2%柠檬酸为脱胶剂、脱胶温度75℃、加水量为质量分数4%、脱胶时间50 min;碱炼脱酸的适宜条件为碱液浓度为质量分数12%、碱炼温度80℃、超碱用量为质量分数0.30%。理化指标的测定结果表明：与毛油相比,脱胶油、脱酸油和精炼油的碘值略升高但差异不明显、过氧化值明显升高、磷脂含量和皂化值均明显下降,而脱酸油和精炼油的酸价也明显下降。研究结果显示：经过脱胶、脱酸、水洗干燥一系列过程后获得的木瓜籽精炼油的理化指标基本符合国家食用植物油卫生标准。     

Stathmin inhibits proliferation and differentiation of dental pulp stem cells via sonic hedgehog/Gli

The mineralization of dental pulp stem cells is an important factor in the tissue engineering of teeth, but the mechanism is not yet obvious. This study aimed to identify the effect of Stathmin on the proliferation and osteogenic/odontoblastic differentiation of human dental pulp stem cells (hDPSCs) and to explore whether the Shh signalling pathway was involved in this regulation. First, Stathmin was expressed in the cytoplasm and on the cell membranes of hDPSCs by cell immunofluorescence. Then, by constructing a lentiviral vector, the expression of Stathmin in hDPSCs was inhibited. Treatment with Stathmin shRNA (shRNA‐Stathmin group) inhibited the ability of hDPSCs to proliferate, as demonstrated by a CCK8 assay and flow cytometry analysis, and suppressed the osteogenic/odontoblastic differentiation ability, as demonstrated by alizarin red S staining and osteogenic/odontoblastic differentiation‐related gene (ALP, BSP, OCN, DSPP) activity, compared to that of hDPSCs from the control shRNA group. Molecular analyses showed that the Shh/GLI1 signalling pathway was inhibited when Stathmin was silenced, and purmorphamine, the Shh signalling pathway activator, was added to hDPSCs in the shRNA‐Stathmin group, real‐time PCR and Western blotting confirmed that expression of Shh and its downstream signalling molecules PTCH1, SMO and GLI1 increased significantly. After activating the Shh signalling pathway, the proliferation of hDPSCs increased markedly, as demonstrated by a CCK8 assay and flow cytometry analysis; osteogenic/odontoblastic differentiation‐related gene (ALP, BSP, OCN, DSPP) expression also increased significantly. Collectively, these findings firstly revealed that Stathmin‐Shh/GLI1 signalling pathway plays a positive role in hDPSC proliferation and osteogenic/odontoblastic differentiation.