基于知识图谱的肿瘤MDT研究可视化分析

目的 梳理肿瘤多学科诊疗团队研究关键主题,分析研究热点和趋势。方法 应用CiteSpace对肿瘤多学科诊疗团队研究进行可视化分析。结果 相关文献共2 160篇,关键文献10篇,主要主题聚类15个,突现术语29个。结论 肿瘤MDT研究主要集中于多学科诊疗团队的构建及运行、推行情况、效果评价,研究前沿如提高实施效率、成本—效果分析、随机对照研究等,为中国肿瘤多学科诊疗团队研究和发展提供了新视角。     

寡氧单胞菌中CRISPR位点的分析

对寡氧单胞菌基因组中的CRISPR位点进行生物信息学分析。CRISPRdb数据库中公布的和NCBI上下载的共26株寡氧单胞菌的基因组序列,分析其CRISPR位点的分布情况、重复序列、间隔序列以及间隔序列和噬菌体序列数量之间的关系。共发现15个确定的CRISPR结构和132个可疑的CRISPR,不同菌株CRISPR结构中的重复序列具有较强的保守性。间隔序列的靶向基因主要来自细菌的基因组,说明寡氧单胞菌CRISPR的的进化与其他细菌基因有关。此外,间隔序列与前噬菌体数量之间的负相关关系,说明CRISPR能阻止噬菌体的入侵。寡氧单胞菌CRISPR位点的分析为进一步研究耐药性及基因组稳定性奠定了基础。     

基于CRISPR/dCas9技术活细胞成像基因组位点的研究进展

基因组的三维空间组织在调节其功能、维持表观遗传和稳定性方面起着重要作用.虽然基于荧光原位杂交的标记技术或单细胞显微观察等方法对此进行了广泛研究,但是细胞内部的时空动态在很大程度上仍难以捉摸.目前标记和观察活细胞中特定内源基因组位点的方法操作难度大且对生物的侵入性伤害较大.CRISPR的发现彻底改变了基因组工程领域.除了...     

基于CRISPR/Cas9系统对干酪乳杆菌进行红色荧光蛋白标记

本实验利用CRISPR/Cas9系统对干酪乳杆菌(Lactobacillus casei) LC2W进行红色荧光蛋白(red fluorescent protein,RFP)标记,用于研究干酪乳杆菌在肠道内的分布和定植状况,评价其作为益生菌的功能。首先,基于本实验室已有的干酪乳杆菌CRISPR/Cas9编辑质粒pLCNICK-1628构建重组质粒pLCNICK-1628-RFP,电转入干酪乳杆菌LC2W感受态细胞中,使干酪乳杆菌基因组中的LC2W-1628基因被红色荧光蛋白基因替换,从而使干酪乳杆菌LC2W能表达出红色荧光蛋白。得到红色荧光标记的干酪乳杆菌LC2W突变株后,测定了其荧光强度-OD600标准曲线,发现RFP在干酪乳杆菌LC2W中能稳定表达。     

基于CRISPR/Cas9的基因分析方法研究进展

自2012年首次证明了CRISPR/Cas9可以在体外进行DNA切割试验以来,CRISPR技术逐渐在基因编辑研究中获得了迅速的发展,除了应用于基因编辑领域之外,它在基因表达调控、基因成像、基因分析等方面也展现出了巨大的应用潜力。尤其在基因分析领域,CRISPR技术由于其精确的基因识别、室温的反应条件、易设计性和操作性等特色,使得一系列新型的基因检测技术得以发展,并取得了超越常规技术的一些检测参数。本文以Cas9蛋白为对象,综述了近些年来在该领域取得的研究进展。主要论述Cas9蛋白的功能、改造、引导RNA(sgRNA)的设计及其在基因分析方法上的应用。     

以Ca-Ca距离为基础的构象空间的可视化研究

蛋白质结构构象呈现明显的规律,研究其在特定构象空间的分布对蛋白质结构预测和模拟具有重要意义。本文以449个非冗余的高分辨串蛋白质结构为材料,以Ga-Ga距离向量代表蛋白质片段。然后利用主成分分析方法,建立蛋白质片段构象空间的可视化构图,并且单个蛋白质分子可以映射到该空间形成一个顺序连接的路径。从而,可以很直观的分析各长度片段（4-9个残基的片段）的分布情况及其内在的连接关系。图形显示了明显的聚集性,以及各种类型片段与二级结构明显的对应关系。     

糙皮侧耳(Pleurotus ostreatus)的AFLP指纹图谱分析

在对糙皮侧耳(Pleurotus ostreatus)的AFLP分析条件进行优化的基础上,利用该技术建立了14株产自不同地区的糙皮侧耳：DNA指纹图谱,并进行了数据分析。结果表明,在合成的14条引物的不同组合中,引物对E-3／M-3可以产生较多的DNA多态片段,E-AGC／M-CAT引物对的扩增效果最好,共获得184条DNA扩增带,其中多态性条带i101条,占54．89％。利用UPGMA法对所获数据进行聚类分析,计算得到糙皮侧耳菌株之间的遗传距离,发现不同品种间遗传距离差异较大,从0．192到0．754,说明糙皮侧耳的遗传多样性比较丰富。绘制的指纹分析树状图表明,14个糙皮侧耳菌株被分为6个组群,其中P17和杂3的相似性系数最高,达到了81．2％,而侧5与其他菌株的亲缘关系相对最远。     

Dynamical Analysis and Visualization of Tornadoes Time Series

In this paper we analyze the behavior of tornado time-series in the U.S. from the perspective of dynamical systems. A tornado is a violently rotating column of air extending from a cumulonimbus cloud down to the ground. Such phenomena reveal features that are well described by power law functions and unveil characteristics found in systems with long range memory effects. Tornado time series are viewed as the output of a complex system and are interpreted as a manifestation of its dynamics. Tornadoes are modeled as sequences of Dirac impulses with amplitude proportional to the events size. First, a collection of time series involving 64 years is analyzed in the frequency domain by means of the Fourier transform. The amplitude spectra are approximated by power law functions and their parameters are read as an underlying signature of the system dynamics. Second, it is adopted the concept of circular time and the collective behavior of tornadoes analyzed. Clustering techniques are then adopted to identify and visualize the emerging patterns.     

Dynamic Analysis and Pattern Visualization of Forest Fires

This paper analyses forest fires in the perspective of dynamical systems. Forest fires exhibit complex correlations in size, space and time, revealing features often present in complex systems, such as the absence of a characteristic length-scale, or the emergence of long range correlations and persistent memory. This study addresses a public domain forest fires catalogue, containing information of events for Portugal, during the period from 1980 up to 2012. The data is analysed in an annual basis, modelling the occurrences as sequences of Dirac impulses with amplitude proportional to the burnt area. First, we consider mutual information to correlate annual patterns. We use visualization trees, generated by hierarchical clustering algorithms, in order to compare and to extract relationships among the data. Second, we adopt the Multidimensional Scaling (MDS) visualization tool. MDS generates maps where each object corresponds to a point. Objects that are perceived to be similar to each other are placed on the map forming clusters. The results are analysed in order to extract relationships among the data and to identify forest fire patterns.     

谷子SSR分子图谱的构建及主要农艺性状QTL定位

试验拟对谷子重要农艺性状进行数量性状位点QTL分析。以表型差异较大的沈3/晋谷20F2作图群体为材料,观测其株高、穗长等性状,选用SSR做分子标记,利用完备区间作图法(BASTEN C J)进行QTL分析。结果显示,表型数据在作图群体中呈现连续分布,表现为多基因控制的数量性状,被整合的54个SSR标记构建10个连锁群,LOD阈值设置为2.0,检测到与株高相关的主效QTL2个,联合贡献率45.9637%,穗长主效QTL1个,贡献率14.9647%,与穗重、粒重相关的主效QTL为同一位点,贡献率分别为11.9601%和10.1879%。有6组QTL位点之间存在基因互作效应,大小范围为-0.4986-16.6407,对性状的贡献率在2.2716％至6.7478％之间。谷子表型控制复杂,相关QTL的检测受环境影响较大,不同连锁群QTL间互作明显。     

组蛋白去乙酰化酶抑制剂(HDACi)对小麦基因编辑效率的影响及转录组学分析

主要研究组蛋白去乙酰化酶抑制剂(HDACi)与染色质状态以及CRISPR/Cas9的编辑效率之间的关系。利用不同浓度的尼克酰胺(0,2.5和5 mmol/L)和丁酸钠(0,5和10 mmol/L)对小麦幼苗处理7 d和14 d,结果显示丁酸钠处理会抑制幼苗的生长,而尼克酰胺对幼苗影响较小。对尼克酰胺处理的小麦幼苗进行转录组测序,发现了一些有利于促进染色质状态开放的基因:6个甲基转移酶合成通路基因。此外对未发生编辑的TaAGO4a基因编辑转基因小麦材料的T2代进行尼克酰胺处理,结果显示5 mmol/L处理14 d时检测到1株3A和3B基因组均杂合编辑的植株,编辑效率从0提高到8.3%,其它处理组和对照组均没有检测到编辑。本研究证明尼克酰胺确实可以提高小麦基因编辑效率,为提高小麦基因编辑效率提供了一种新策略。     

基于文献计量学的《中国医院管理》文献可视化分析

目的 通过文献计量学方法,探索《中国医院管理》的发展脉络及医院管理领域近年来的科研合作演进过程。方法 利用信息可视化分析软件CiteSpace,对近10年（2006—2015年）间刊发在《中国医院管理》的科学文献进行文献计量学分析（共有4 169篇文献纳入）。结果 其中高产作者有方鹏骞、薛迪、吴群红等,分别达到56篇、51篇、22篇。高产单位有华中科技大学同济医学院医药卫生管理学院、哈尔滨医科大学附属第一医院和首都医科大学卫生管理与教育学院,合作频次分别达到187次、96次和56次。其中“公立医院”“医院管理”“医疗质量”等关键词共现率较高均超过100次。2013年后“医药分开”“患者安全”“合理用药”和“县级公立医院等”等内容逐渐成为研究热点。结论 《中国医院管理》杂志是广大读者了解和学习医院管理领域研究热点和重大成果的重要平台。     

Leptin gene-targeted editing in ob/ob mouse adipose tissue based on the CRISPR/Cas9 system

Gene therapy has become the most effective treatment for monogenic diseases. Congenital LEPTIN deficiency is a rare autosomal recessive monogenic obesity syndrome caused by mutations in the Leptin gene. Ob/ob mouse is a monogenic obesity model, which carries a homozygous point mutation of C to T in Exon 2 of the Leptin gene. Here, we attempted to edit the mutated Leptin gene in ob/ob mice preadipocytes and inguinal adipose tissues using CRISPR/Cas9 to correct the C to T mutation and restore the production of LEPTIN protein by adipocytes. The edited preadipocytes exhibit a correction of 5.5% of Leptin alleles and produce normal LEPTIN protein when differentiated into mature adipocytes. The ob/ob mice display correction of 1.67% of Leptin alleles, which is sufficient to restore the production and physiological functions of LEPTIN protein, such as suppressing appetite and alleviating insulin resistance. Our study suggests CRISPR/Cas9-mediated in situ genome editing as a feasible therapeutic strategy for human monogenic diseases, and paves the way for further research on efficient delivery system in potential future clinical application.     

Advanced single-cell pooled CRISPR screening identifies C19orf53 required for cell proliferation based on mTORC1 regulators

Cell Biology and Toxicology - Multiplexed single-cell CRISPR screening has accelerated the systematic dissection of biological discoveries; however, the efficiency of CRISPR-based gene knockout has...     

Centromere-Linkage Analysis and Consolidation of the Zebrafish Genetic Map

The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.     

拟南芥黄心突变体yh基因的图位克隆及分析

在研究光合作用相关基因的过程中,获得了一个叶片为黄心(yellow heart,yh)的突变株,与野生型拟南芥(Col 0)相比,其新生叶片发黄,突变表型由隐性单基因控制。采用图位克隆及其精细定位技术,将yh突变基因定位在1号染色体的INS1_55_342与INS1_56_34区间,物理距离约为676 kb。通过测序得知yh在At1g64790第44个内含子剪接处有4个碱基的缺失,导致内含子剪切位点的变化。RT PCR分析显示,该基因表达降低,是At1g64790基因的一个新等位突变。研究表明,yh突变体与叶绿体的发育相关,可为进一步探究植物叶绿体和叶片发育机制提供新的遗传材料。     

Visualization of UV exposure of the human body based on data from a scanning UV-measuring system

In general, measurements of UV radition are related to horizontal surfaces, as in the case of the internationally standardized and applied UV index, for example. In order to obtain more relevant information on UV exposure of humans the new measuring system ASCARATIS (Angle SCAnning RAdiometer for determination of erythemally weighted irradiance on TIlted Surfaces) was developed and built. Three systems of ASCARATIS have been in operation at different locations in Bavaria for 3 years, providing erythemally weighted UV irradiation data for 27 differently inclined surfaces every 2 min. On the basis of these data virtual three-dimensional models of the human body surface consisting of about 20,000 triangles could be created and each of these triangles coloured according to its UV irradiation. This allowed the UV exposure of the human body to be visualized for any kind of body posture and spatial orientation on the basis of real measuring data. The results of the UV measurements on inclined surfaces have shown that measuring UV radiation on horizontal surfaces, as done routinely worldwide, often underestimates the UV exposure of the human skin. Especially at times of the day or year with low solar elevations the UV exposure of parts of the human skin can be many times higher than that of the horizontal surface. Examples of three-dimensional modelling of the human UV irradiation are shown for different times of the day and year, altitudes above sea level, body postures and genders. In these examples the UV hotspots can be detected and, among other things, used to inform and educate the public about UV radiation.     

Impact of Perfusion Map Analysis on Early Survival Prediction Accuracy in Glioma Patients

Studies investigating dynamic susceptibility contrast magnetic resonance imaging-determined relative cerebral blood volume (rCBV) maps as a metric of treatment response assessment have generated conflicting results. We evaluated the potential of various analytical techniques to predict survival of patients with glioma treated with chemoradiation. rCBV maps were acquired in patients with high-grade gliomas at 0, 1, and 3 weeks into chemoradiation therapy. Various analytical techniques were applied to the same cohort of serial rCBV data for early assessment of survival. Three different methodologies were investigated: 1) percentage change of whole tumor statistics (i.e., mean, median, and percentiles), 2) physiological segmentation (low rCBV, medium rCBV, or high rCBV), and 3) a voxel-based approach, parametric response mapping (PRM). All analyses were performed using the same tumor contours, which were determined using contrast-enhanced T1-weighted and fluid attenuated inversion recovery images. The predictive potential of each response metric was assessed at 1-year and overall survival. PRM was the only analytical approach found to generate a response metric significantly predictive of patient 1-year survival. Time of acquisition and contour volume were not found to alter the sensitivity of the PRM approach for predicting overall survival. We have demonstrated the importance of the analytical approach in early response assessment using serial rCBV maps. The PRM analysis shows promise as a unified early and robust imaging biomarker of treatment response in patients diagnosed with high-grade gliomas.