Genome-Wide Identification and Characterization of the CC-NBS-LRR Gene Family in Cucumber (Cucumis sativus L.)

The NBS-LRR (NLR) gene family plays a pivotal role in regulating disease defense response in plants. Cucumber is one of the most important vegetable crops in the world, and various plant diseases, including powdery mildew (PM), cause severe losses in both cucumber productivity and quality annually. To characterize and understand the role of the CC-NBS-LRR(CNL) family of genes in disease defense response in cucumber plants, we performed bioinformatical analysis to characterize these genes systematically. We identified 33 members of the CNL gene family in cucumber plants, and they are distributed on each chromosome with chromosome 4 harboring the largest cluster of five different genes. The corresponding CNL family member varies in the number of amino acids and exons, molecular weight, theoretical isoelectric point (pI) and subcellular localization. Cis-acting element analysis of the CNL genes reveals the presence of multiple phytohormone, abiotic and biotic responsive elements in their promoters, suggesting that these genes might be responsive to plant hormones and stress. Phylogenetic and synteny analysis indicated that the CNL proteins are conserved evolutionarily in different plant species, and they can be divided into four subfamilies based on their conserved domains. MEME analysis and multiple sequence alignment showed that conserved motifs exist in the sequence of CNLs. Further DNA sequence analysis suggests that CsCNL genes might be subject to the regulation of different miRNAs upon PM infection. By mining available RNA-seq data followed by real-time quantitative PCR (qRT-PCR) analysis, we characterized expression patterns of the CNL genes, and found that those genes exhibit a temporospatial expression pattern, and their expression is also responsive to PM infection, ethylene, salicylic acid, and methyl jasmonate treatment in cucumber plants. Finally, the CNL genes targeted by miRNAs were predicted in cucumber plants. Our results in this study provided some basic information for further study of the functions of the CNL gene family in cucumber plants.     

A typology of different development and testing options for symbolic regression modelling of measured and calculated datasets

Data-driven modelling is used to develop two alternative types of predictive environmental model: a simulator, a model of a real-world process developed from either a conceptual understanding of physical relations and/or using measured records, and an emulator, an imitator of some other model developed on predicted outputs calculated by that source model. A simple four-way typology called Emulation Simulation Typology (EST) is proposed that distinguishes between (i) model type and (ii) different uses of model development period and model test period datasets. To address the question of to what extent simulator and emulator solutions might be considered interchangeable i.e. provide similar levels of output accuracy when tested on data different from that used in their development, a pair of counterpart pan evaporation models was created using symbolic regression. Each model type delivered similar levels of predictive skill to that other of published solutions. Input–output sensitivity analysis of the two different model types likewise confirmed two very similar underlying response functions. This study demonstrates that the type and quality of data on which a model is tested, has a greater influence on model accuracy assessment, than the type and quality of data on which a model is developed, providing that the development record is sufficiently representative of the conceptual underpinnings of the system being examined. Thus, previously reported substantial disparities occurring in goodness-of-fit statistics for pan evaporation models are most likely explained by the use of either measured or calculated data to test particular models, where lower scores do not necessarily represent major deficiencies in the solution itself.     

Consideration of the BDNF gene in relation to two phenotypes: Hoarding and obesity.

The gene coding for the brain derived neurotrophic factor (BDNF) has emerged as an interesting candidate for multiple brain and brain disorder-related phenomena. The primary aim of the present investigation was to consider the relationship between the BDNF Val66Met variant and two phenotypes: compulsive hoarding as a symptom dimension of obsessive–compulsive disorder (OCD), and body mass index (BMI). We examined the BDNF gene in a large (N = 301) clinical sample of probands with OCD. Participants were classified as hoarding or nonhoarding using a strict, multimeasure grouping approach. Results revealed that the Val/Val genotype was linked with hoarding classification and more severe hoarding behaviors, as well as greater BMI levels. Hoarding status was also associated with greater BMI scores, with individuals in the hoarding group being far more likely to be classified as obese compared with the nonhoarding group. Our findings may provide a distinct avenue through which hoarding and BMI could be linked. These findings are suggestive of a complex gene, body weight, and psychopathology relationship wherein a primitive, survival “thrifty gene” strategy may be conserved and represented in a subgroup of humans manifesting severe hoarding symptoms. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

基于邻域粗糙集的加权KNN肿瘤基因表达谱分类算法

肿瘤亚型的准确判别对肿瘤的治疗具有重要意义,对肿瘤的不同亚型进行准确判别是当前生物信息学研究的重要课题．本文首先利用Relief算法排序基因并选出初始的肿瘤信息基因子集,然后利用向基于邻域粗糙集模型的向前属性约减算法FARNeM来计算加权基因集合,最后用加权KNN算法对肿瘤对这些数据进行分析,从而发现有差异的基因表达。实验结果表明了上述方法的可行性和有效性。     

基于基因表达式编码算法的红外图像轮廓提取

针对红外图像轮廓特征信息提取的特点,提出基因表达式编码算法.首先建立基因表达式编码规则,求出最大的基因编码空间以及基因编码个数;接着把红外图像像素集合与染色体基因序列构建映射关系,不同的基因编码则代表不同的像素值,适应度函数大的基因参与数据优化,最后给出了红外图像轮廓特征信息提取评价函数以及算法过程.实验仿真得出基因表达式编码提取的红外图像轮廓没有伪吉斯效应,时效性快,边缘点保持指数接近理想状态.     

基于Gabor滤波的表情动态特征提取方法

针对目前动态特征提取方法在提取序列表情特征时人脸外貌特征也一起被提取的缺陷,提出了一种基于Gabor滤波的表情动态特征提取方法。利用Gabor滤波器在频率和方向上的选择特性,在提取表情特征时较好地抑制了人脸外貌特征的提取,从而减少了表情特征中人脸外貌特征的含量。在Cohn-Kanade和CMU-AMP人脸库上的表情识别实验表明,本文方法获得的表情动态特征对表情识别更有效。     

基于动态交互数值组件的设计与实现

在嵌入式程序设计中,需要使用数值表达式计算数值组件,以解决动态交互的数值计算问题,介绍了一种通过对数值表达式进行解释和计算来设计和实现数值组件。     

混合模拟退火算法解决VLSI布局问题

VLSI布局问题是集成电路物理设计过程中的关键步骤，它直接影响整个设计的成败。Slicing结构是一种简单而高效的布局表示方法，采用正则波兰表达式编码，将模拟退火与禁忌搜索算法结合形成了一种以模拟退火算法为基础的混合算法进行求解，用MCNC benchmarks进行实验，结果表明：文章提出的混合算法比模拟退火算法在求解效率和质量上都有较大的提高。