Simulated nitrogen deposition induces shifts in growth and resource-use strategies during range expansion of an invasive plant

Biological Invasions - An appropriate resource-use strategy contributes to the invasion success of exotic plants. During range expansion, population density and nitrogen availability are two...     

Weighted double deep Q-network based reinforcement learning for bi-objective multi-workflow scheduling in the cloud

Cluster Computing - As a promising distributed paradigm, cloud computing provides a cost-effective deploying environment for hosting scientific applications due to its provisioning elastic,...     

Identification of the three subtypes and the prognostic characteristics of stomach adenocarcinoma: analysis of the hypoxia-related long non-coding RNAs

Functional & Integrative Genomics - Stomach adenocarcinoma (STAD) is one of the most commonly diagnosed cancers. This study analyzed the subtypes and characteristics of STAD subtypes by...     

A facile fluorescence turn-on biosensor customized for monitoring of protein kinase activity based on carboxylic carbon nanoparticle–peptide complexes

In this study, we present a facile and low-cost approach for detecting protein kinase A (PKA) by assembling a purpose-designed carboxyfluorescein (FAM)-labelled peptide with carboxylic carbon nanoparticles (CNPs). Fluorescence of the FAM-labelled peptide gradually decreases to a low background signal as a result of the electron transfer from CNPs to FAM-labelled peptide via the peptide, which acts as a bridge. The reaction in the sensor in the presence of adenosine 5′-triphosphate and PKA phosphorylates the substrate peptide and disrupts the electrostatic repulsive force between the CNPs and the peptide, therefore altering the spectroscopic signal of the system. The change in fluorescence signal was directly proportional to the PKA concentration in the range 0–1.8 U/ml with a detection limit of 0.04 U/ml. These results suggest that PKA activity can be effectively measured using the developed PKA biosensor. Moreover, the fluorescence biosensor was successfully used in the investigation of PKA in spiked human embryonic kidney (HEK) 293 cells lysates, indicating its potential applications in protein kinase-related biochemical fundamental research.     

A prostate cancer tissue specific spectral library for targeted proteomic analysis

Prostate cancer is the most common cancer in males worldwide. Mass spectrometry-based targeted proteomics has demonstrated great potential in quantifying proteins from formalin-fixed paraffin-embedded (FFPE) and (fresh) frozen biopsy tissues. Here we provide a comprehensive tissue-specific spectral library for targeted proteomic analysis of prostate tissue samples. Benign and malignant FFPE prostate tissue samples were processed into peptide samples by pressure cycling technology (PCT)-assisted sample preparation, and fractionated with high-pH reversed phase liquid chromatography (RPLC). Based on data-dependent acquisition (DDA) MS analysis using a TripleTOF 6600, we built a library containing 108,533 precursors, 84,198 peptides and 9384 unique proteins (1% FDR). The applicability of the library was demonstrated in prostate specimens.     

Mathematical modeling of shear-activated targeted nanoparticle drug delivery for the treatment of aortic diseases

Biomechanics and Modeling in Mechanobiology - The human aorta is a high-risk area for vascular diseases, which are commonly restored by thoracic endovascular aortic repair. In this paper, we report...     

楸树CbuATX1，CbuATX1-like和CbuATX2基因克隆及生物信息学分析

开花是高等植物内部遗传因素和外界环境因素共同调节完成的复杂生命过程,是植物进入生殖生长从而具备遗传能力和繁殖能力的象征。使用PCR技术,以楸树（Catalpa bungei）混合芽cDNA为模板分别克隆CbuATX1,CbuATX1-like和CbuATX2 3个基因,并利用相关生物信息学软件对这3个基因编码的蛋白质结构进行预测,同时对基因的启动子序列进行顺式作用元件分析,通过qRT-PCR技术检测3个基因在楸树混合芽不同发育时期的表达量。结果表明：CbuATX1的CDS全长为726 bp,编码241个氨基酸,存在跨膜运输结构,属于HMA蛋白家族,与芝麻（Sesamum indicum）、甜菜（Beta vulgaris）亲缘关系较近。CbuATX1-like的CDS全长为801 bp,编码266个氨基酸,存在跨膜运输结构,属于HMA蛋白家族,与胡萝卜（Daucus carota）、欧洲橄榄（Olea europaea）亲缘关系较近。CbuATX2的CDS全长为1 554 bp,编码517个氨基酸,不存在跨膜运输结构,属于PWWP蛋白家族,与马尾草（Erythranthe guttatus）亲缘关系较近。这3个基因启动子均含有多个真核生物启动子的基本元件,如CAAT-box和TATA-box等,此外,还含有光响应、低温响应、生长素响应,以及与干旱诱导相关的MYB结合位点等3个基因与光响应密切相关,还可能参与外界环境胁迫响应等过程。qRT-PCR结果显示,上述3个基因在1年生普通楸树无性系9-1和突变株系-百日花楸树不同发育时期的表达量呈现显著差异。通过以上研究以期能够进一步阐述百日花楸树开花的性状,为楸树开花机制的研究和楸树的定向遗传改良提供理论支持。     

基于卷积神经网络的大肠杆菌启动子预测

目的 基于位点特异性打分矩阵（position-specific scoring matrices,PSSM）的预测模型已经取得了良好的效果,基于PSSM的各种优化方法也在不断发展,但准确率相对较低,为了进一步提高预测准确率,本文基于卷积神经网络（convolutional neural networks,CNN）算法做了进一步研究。方法 采用PSSM将启动子序列处理成数值矩阵,通过CNN算法进行分类。大肠杆菌K-12（Escherichia coli K-12,E.coli K-12,下文简称大肠杆菌）的Sigma38、Sigma54和Sigma70 3种启动子序列被作为正集,编码（Coding）区和非编码（Non-coding）区的序列为负集。结果 在预测大肠杆菌启动子的二分类中,准确率达到99%,启动子预测的成功率接近100%;在对Sigma38、Sigma54、Sigma70 3种启动子的三分类中,预测准确率为98%,并且针对每一种序列的预测准确率均可以达到98%以上。最后,本文以Sigma38、Sigma54、Sigma70 3种启动子分别和Coding区或者Non-coding区序列做四分类,预测得到的准确性为0.98,对3种Sigma启动子均衡样本的十交叉检验预测精度均可以达到0.95以上,海明距离为0.016,Kappa系数为0.97。结论 相较于支持向量机（support vector machine,SVM）等其他分类算法,CNN分类算法更具优势,并且基于CNN的分类优势,编码方式亦可以得到简化。     

桃Pp4CL2基因的克隆及抗寒功能验证

基于‘丁家坝李光桃’抗寒转录组数据,采用RT PCR技术克隆桃4 香豆酸辅酶A连接酶基因(Pp4CL2),并对其进行生物信息学及转化模式植物拟南芥和烟草的抗寒分析,以解析‘丁家坝李光桃’的抗寒机制。结果显示：(1)成功克隆获得桃Pp4CL2基因(登录号：LOC18792923),其cDNA序列为1 635 bp,编码544个氨基酸残基,具有4CL基因家族保守结构域。(2)二级结构分析显示,Pp4CL2蛋白由4种状态的二级结构组成,其中α螺旋占30.51%、β 折叠占7.35%、不规则卷曲及延伸链分别占41.54%和20.59%。(3)顺式作用元件分析发现,Pp4CL2基因上游启动子区含有光、低温以及多种激素响应元件。(4)序列系统进化分析显示,桃Pp4CL2与杏(Prunus armeniaca)、欧洲甜樱桃(Prunus avium)和梅(Prunus mume)的蛋白相似性最高,分别为99.08%、97.98%和96.14%。(5)成功构建转化载体Pp4CL2 pRI101,对拟南芥和烟草进行遗传转化并通过PCR鉴定获得转基因拟南芥和烟草。(6)与野生型相比,低温胁迫下转基因拟南芥和烟草的Pp4CL2基因相对表达量高,受冷害程度轻,具有更高的渗透调节物质含量和抗氧化酶活性,对低温具有更强的耐受性。研究表明,过表达Pp4CL2基因可增强植物对低温的耐受性,推测Pp4CL2基因在‘丁家坝李光桃’响应低温胁迫过程中具有重要作用。     

四川格西沟国家级自然保护区鸟类多样性初探

鸟类多样性研究是国家级自然保护区的重要工作。2020年6月—2021年5月,采用样线法和样点法,调查了四川格西沟国家级自然保护区的鸟类多样性。结果显示:结合历史文献资料,保护区共有鸟类19目56科249种。其中,国家一级重点保护动物10种,国家二级重点保护动物35种,中国特有种11种。居留型以留鸟为主,共156种(62.65%),其次是夏候鸟60种(24.10%)、旅鸟19种(7.63%)、冬候鸟14种(5.62%)。区系组成以东洋界为主,共116种(46.59%),古北界103种(41.37%)、广布种30种(12.04%)。各生态系统中森林和灌丛生态系统Shannon-Wiener指数最高,其他生态系统最低,森林和灌丛生态系统的Sorenson相似性指数最高;夏、秋季的Shannon-Wiener指数和Pielou均匀度指数最高,冬季最低。建议保护区建立长期监测体系,并持续开展鸟类保护宣传活动,加大巡护和管控力度,降低保护区内的人为干扰,同时注重鸟类所利用栖息地的保护。