Automatic non-proliferative diabetic retinopathy screening system based on color fundus image

Background

Non-proliferative diabetic retinopathy is the early stage of diabetic retinopathy. Automatic detection of non-proliferative diabetic retinopathy is significant for clinical diagnosis, early screening and course progression of patients.

Methods

This paper introduces the design and implementation of an automatic system for screening non-proliferative diabetic retinopathy based on color fundus images. Firstly, the fundus structures, including blood vessels, optic disc and macula, are extracted and located, respectively. In particular, a new optic disc localization method using parabolic fitting is proposed based on the physiological structure characteristics of optic disc and blood vessels. Then, early lesions, such as microaneurysms, hemorrhages and hard exudates, are detected based on their respective characteristics. An equivalent optical model simulating human eyes is designed based on the anatomical structure of retina. Main structures and early lesions are reconstructed in the 3D space for better visualization. Finally, the severity of each image is evaluated based on the international criteria of diabetic retinopathy.

Results

The system has been tested on public databases and images from hospitals. Experimental results demonstrate that the proposed system achieves high accuracy for main structures and early lesions detection. The results of severity classification for non-proliferative diabetic retinopathy are also accurate and suitable.

Conclusions

Our system can assist ophthalmologists for clinical diagnosis, automatic screening and course progression of patients.

     

Red/ET同源重组技术及其在微生物基因组挖掘中的应用进展

Red/ET同源重组技术(Red/ET recombineering)是由来源于大肠杆菌λ噬菌体的蛋白对Redα/Redβ或来源于Rac原噬菌体的蛋白对Rec E/Rec T所介导的基于短同源臂(40–50 bp)的同源重组技术,能对宿主DNA序列进行快速、高效、精确的修饰和操作。本文主要综述了2010年以来Red/ET同源重组技术在大肠杆菌及其他细菌中的研究进展,同时简要介绍了该技术在微生物基因组挖掘,尤其是在微生物基因簇的异源表达领域的应用进展。     

2016年度国家自然科学基金微生物学学科项目申请与资助概况分析

摘要:本文介绍了2016年度国家自然科学基金微生物学学科项目申请、受理和资助概况,分析了各分支学科和各项目类别申请的特点和存在的问题,并对今后微生物学学科资助方向进行了展望,希望能够为本学科科研人员今后的项目申请提供有益参考。     

Investigation of an “alternate water supply system” in enzymatic hydrolysis in the processive endocellulase Cel7A from Rasamsonia emersonii by molecular dynamics simulation

Cel7A from Rasamsonia emersonii is one of the processive endocellulases classified under family 7 glycoside hydrolase. Molecular dynamics simulations were carried out to obtain the optimized sliding and hydrolyzing conformations, in which the reducing ends of sugar chains are located on different sites. Hydrogen bonds are investigated to clarify the interactions between protein and substrate in either conformation. Nine hydrogen bonding interactions are identified in the sliding conformation, and six similar interactions are also found correspondingly in the hydrolyzing conformation. In addition, four strong hydrophobic interactions are also determined. The domain cross‐correlation map analysis shows movement correlation of protein including autocorrelation between residues. The root mean square fluctuations analysis represents the various flexibilities of different fragment in the two conformations. Comparing the two conformations reveals the water‐supply mechanism of selective hydrolysis of cellulose in Cel7A. The mechanism can be described as follow. When the reducing end of substrate slides from the unhydrolyzing site (sliding conformation) to the hydrolyzing site (hydrolyzing conformation), His225 is pushed down and rotated, the rotation leads to the movement of Glu209 with the interstrand hydrogen bonding in β‐sheet. It further makes Asp211 close to the hydrolysis center and provides a water molecule bounding on its carboxyl in the previous unhydrolyzing site. After the hydrolysis takes place and the product is excluded from the enzyme, the Asp211 comes back to its initial position. In summary, Asp211 acts as an elevator to transport outer water molecules into the hydrolysis site for every other glycosidic bond.     

Marine bacterial exopolysaccharide EPS11 inhibits migration and invasion of liver cancer cells by directly targeting collagen I

Many natural polysaccharides have significant anticancer activity with low toxicity, but the complex chemical structures make in-depth studies of the involved mechanisms extremely difficult. The purpose of this study was to investigate the effect of the marine bacterial exopolysaccharide (exopolysaccharide 11 [EPS11]) on liver cancer metastasis to explore the underlying target protein and molecular mechanism. We found that EPS11 significantly suppressed cell adhesion, migration, and invasion in liver cancer cells. Proteomic analysis showed that EPS11 induced downregulation of proteins related to the extracellular matrix–receptor interaction signaling pathway. In addition, the direct pharmacological target of EPS11 was identified as collagen I using cellular thermal shift assays. Surface plasmon resonance and pull-down assays further confirmed the specific binding of EPS11 to collagen I. Moreover, EPS11 was shown to inhibit tumor metastasis by directly modulating collagen I activity via the β1-integrin–mediated signaling pathway. Collectively, our study demonstrated for the first time that collagen I could be a direct pharmacological target of polysaccharide drugs. Moreover, directly targeting collagen I may be a promising strategy for finding novel carbohydrate-based drugs.     

基于线粒体D-loop 区比较分析野生与养殖斜带髭鲷种群的遗传多样性

采集广东省深圳市南澳区野生斜带髭鲷Hapalogenys nitens (Richardson)和养殖斜带髭鲷各25 个样本。通过设计特异性引物, 采用PCR 技术对该50 个个体的mtDNA D-loop 区全序列进行扩增, 测序得到的序列进行比对, 发现该50 个序列长度变异较小, 均在788-790 bp 之间, 野生型和养殖型区别不大。采用MEGA(version 4.0)和DnaSP(version 4.0)软件对序列进行分析, 结果显示: 50 条序列中T、C、A 和G 碱基平均含量分别为29.9%、21.5%、35.2%和13.5%, 其中A+T 的含量(65.1%)显著高于G+C 含量(34.9%), 表现了明显的碱基偏倚。50 个个体表现为26 种单倍型, 包括91 个多态位点, 单倍型间平均遗传距离为0.024, 单倍型多态性(h)为0.958, 核苷酸多态性()值为0.02277。研究表明, mtDNA D-loop 区可以作为检测野生与养殖斜带髭鲷群体遗传多样性的有效分子标记, 而广东省深圳市南澳区野生斜带髭鲷种群遗传多样性已经下降至中等水平。研究提示野生斜带髭鲷种群遗传多样性不容乐观, 资源调查、种质维护与遗传评价有待深入。       

喀斯特峰丛洼地不同退耕模式土壤微生物多样性

利用变性梯度凝胶电泳和Biolog_Eco生态培养平板技术,调查了喀斯特自然退耕(NT,撂荒)、人工种植经济林(CM,木豆-板栗)、免耕(PI,牧草-任豆)和传统耕作(MB,玉米-大豆)4种退耕模式下的土壤微生物遗传分类和土壤细菌代谢功能多样性.结果表明:退耕模式显著影响了土壤微生物群落结构和细菌代谢模式, 其中真菌群落更依赖于退耕模式,而细菌群落对季节变迁更敏感;短时期(6～7年)不同退耕模式下土壤中细菌遗传分类多样性没有显著性差异(P>0.05),经济林与牧草地土壤真菌遗传分类多样性显著高于撂荒和传统耕作地(P<0.05);免耕牧草地土壤细菌代谢功能多样性显著低于其他模式(P<0.05).因此,真菌遗传多样性和细菌代谢多样性较细菌遗传多样性对退耕模式响应更敏感;土壤细菌群落对季节的变化比真菌敏感;木豆 板栗经济林对维持土壤微生物遗传和细菌代谢功能多样性具有优势,是较好的退耕模式.     

miR‐516a‐3p inhibits breast cancer cell growth and EMT by blocking the Pygo2/Wnt signalling pathway

miR‐516a‐3p has been reported to play a suppressive role in several types of human tumours. However, the expression level, biological function and fundamental mechanisms of miR‐516a‐3p in breast cancer remain unclear. In the present study, we found that miR‐516a‐3p expression was down‐regulated and Pygopus2 (Pygo2) expression was up‐regulated in human breast cancer tissues and cells. Through analysing the clinicopathological characteristics, we demonstrated that low miR‐516a‐3p expression or positive Pygo2 expression was a predictor of poor prognosis for patients with breast cancer. The results of a dual luciferase reporter assay and Western blot analysis indicated that Pygo2 was a target gene of miR‐516a‐3p. Moreover, overexpression of miR‐516a‐3p inhibited cell growth, migration and invasion as well as epithelial‐mesenchymal transition (EMT) of breast cancer cells, whereas reduced miR‐516a‐3p expression promoted breast cancer cell growth, migration, invasion and EMT. Furthermore, we showed that miR‐516a‐3p suppressed cell proliferation, metastasis and EMT of breast cancer cells by inhibiting Pygo2 expression. We confirmed that miR‐516a‐3p exerted an anti‐tumour effect by inhibiting the activation of the Wnt/β‐catenin pathway. Finally, xenograft tumour models were used to show that miR‐516a‐3p inhibited breast cancer cell growth and EMT via suppressing the Pygo2/Wnt signalling pathway. Taken together, these results show that miR‐516a‐3p inhibits breast cancer cell growth, metastasis and EMT by blocking the Pygo2/ Wnt/β‐catenin pathway.     

丙型肝炎病毒核心蛋白基因表达致人肝细胞恶性转化的研究

丙型肝炎病毒核心（HCV-C）蛋白是维持丙型肝炎病毒结构的重要蛋白质,由于参与调节细胞的生长与凋亡,被认为与HCV感染所致的肝硬化及肝细胞癌的发生有关.为了进一步探索HCV-C蛋白与肝细胞癌发生的关系,首先构建了表达HCV-C蛋白的真核表达载体,脂质体介导转染Chang-liver人肝细胞株,建立表达HCV-C蛋白的人肝细胞模型,RT-PCR方法检测HCV-C基因在人肝细胞内的表达,蛋白质印迹和免疫细胞化学方法鉴定Chang-liver肝细胞内HCV-C蛋白及其在细胞内的分布情况.表达HCV-C蛋白的Chang-liver人肝细胞培养20代以后,与对照组细胞相比,细胞的形态出现长梭形样改变,生长速度显著加快,细胞内DNA含量的均一性变差.接种表达HCV-C蛋白的Chang-liver人肝细胞的6只裸鼠在第20天时全部有肿瘤长出,且肿瘤组织结构符合肝细胞癌病理形态特点,对照组裸鼠未见肿瘤生长.上述结果表明HCV-C基因表达可导致Chang-liver人肝细胞发生恶性转化,提示HCV-C蛋白与HCV感染所致肝细胞癌的发生有直接关系.     

三种盐胁迫对互花米草和芦苇光合作用的影响北大核心CSCD

互花米草(Spartina alterniflora)的入侵给海岸带盐沼生态系统的结构和功能带来了显著影响。互花米草盐沼中的硫含量高于附近的土著芦苇(Phragmites australis)盐沼。为探讨硫元素对互花米草和芦苇竞争过程的可能影响及其作用机制,以50mmol·L–1的Na2SO4和Na2S对互花米草和芦苇进行处理,分析处理前后5天内两种植物光合气体交换和叶绿素荧光指标变化的差异,实验另设等Na+浓度的Na Cl处理作为比较。研究发现:Na2S对互花米草和芦苇光合作用影响的差异最大,Na Cl次之,Na2SO4最小。Na2S处理后,互花米草净光合速率(Pn)出现显著上升,芦苇Pn值大幅度下降。互花米草的光饱和点(Isat)上升而芦苇的Isat值无变化。表明Na2S处理对互花米草的光合能力有促进作用,但对芦苇的光合能力有抑制作用。Na Cl处理后互花米草Pn值也出现小幅上升,而芦苇Pn值略有下降。Na2SO4处理对互花米草和芦苇的Pn值均无显著影响。除Na2SO4处理的互花米草外,不同盐处理后的互花米草和芦苇非光化学淬灭(NPQ)均出现上升趋势。研究结果表明互花米草对环境硫胁迫的适应能力显著高于芦苇,暗示盐沼高硫环境尤其是硫化物有助于互花米草相对于芦苇的竞争,也很可能是其形成单一植被的重要原因之一。