Predicting MicroRNA Biomarkers for Cancer Using Phylogenetic Tree and Microarray Analysis

MicroRNAs (miRNAs) are shown to be involved in the initiation and progression of cancers in the literature, and the expression of miRNAs is used as an important cancer prognostic tool. The aim of this study is to predict high-confidence miRNA biomarkers for cancer. We adopt a method that combines miRNA phylogenetic structure and miRNA microarray data analysis to discover high-confidence miRNA biomarkers for colon, prostate, pancreatic, lung, breast, bladder and kidney cancers. There are 53 miRNAs selected through this method that either have potential to involve a single cancer’s development or to involve several cancers’ development. These miRNAs can be used as high-confidence miRNA biomarkers of these seven investigated cancers for further experiment validation. miR-17, miR-20, miR-106a, miR-106b, miR-92, miR-25, miR-16, miR-195 and miR-143 are selected to involve a single cancer’s development in these seven cancers. They have the potential to be useful miRNA biomarkers when the result can be confirmed by experiments.     

柯萨奇B4病毒jlu06株基因序列及遗传进化分析

目的对柯萨奇B4病毒(CVB4)jlu06株进行基因序列及遗传进化分析,并探讨其与致病相关的分子基础。方法Trizol法提取病毒RNA,RT-PCR扩增目的基因片段,测定基因组全序列,并进行序列同源性及遗传进化分析。结果CVB4 jlu06株基因组全长7 395个核苷酸,编码2 183个氨基酸,与其他CVB4株的同源性较高,且发生了10个氨基酸的变异,与HumanCB4和POLG_CXB4亲缘关系较近,与CXB2亲缘关系较远;CVB4 jlu06株与具有潜在致糖尿病性病毒株,在非结构蛋白3A区4个位点有共同的氨基酸,与非致病毒株不同。结论CVB4 jlu06株具有典型的CVB4基因组特征,在非结构蛋白3A区发生的核苷酸和氨基酸变异可能与其致病性相关。     

豆壳过氧化物酶的序列联配、二级结构预测及疏水性分析

利用生物大分子数据库和软件技术对豆壳过氧化物酶 (Soybeanhullperoxidase ,SHP ,EC 1 .1 1 .1 .7)进行了序列联配、二级结构预测及疏水性分析 ,通过与其它来源过氧化物酶的比较研究 ,分析了结构保守性与功能域的关系 ,从分子水平探讨了过氧化物酶活性位点结构特征。     

The Complete Analysis of Wood Polysaccharides Using HPLC

The paper describes an analytical method whereby the chemical composition of the polysaccharide fraction of woody materials, including the uronic acids and carbohydrate acid degradation products, can be completely determined. Sealed vessels, termed bombs, are used during the high temperature acid hydrolysis of the materials to retain volatile constituents that would otherwise be lost. High-Performance Liquid Chromatography (HPLC) is used for all of the analyses. The sample preparation procedures are simple and easily adopted into a routine. To demonstrate the reproducibility of the method, triplicate samples of Quaking aspen ( Populus tremuloides ) and White fir ( Abies concolor ) were analyzed. No significant peaks in the chromatograms were left unidentified.     

Complete Genome Sequence Analysis of Bacillus subtilis Bbv57, a Promising Biocontrol Agent against Phytopathogens

Plant growth-promoting rhizobacteria (PGPR) are a group of root-associated beneficial bacteria emerging as one of the powerful agents in sustainable plant disease management. Among the PGPR, Bacillus sp. has become a popular biocontrol agent for controlling pests and the diseases of several crops of agricultural and horticultural importance. Understanding the molecular basis of the plant growth-promoting and biocontrol abilities of Bacillus spp. will allow us to develop multifunctional microbial consortia for sustainable agriculture. In our study, we attempted to unravel the genome complexity of the potential biocontrol agent Bacillus subtilis Bbv57 (isolated from the betelvine’s rhizosphere), available at TNAU, Coimbatore. A WGS analysis generated 26 million reads, and a de novo assembly resulted in the generation of 4,302,465 bp genome of Bacillus subtilis Bbv57 containing 4363 coding sequences (CDS), of which 4281 were functionally annotated. An analysis of 16S rRNA revealed its 100% identity to Bacillus subtilis IAM 12118. A detailed data analysis identified the presence of >100 CAZymes and nine gene clusters involved in the production of secondary metabolites that exhibited antimicrobial properties. Further, Bbv57 was found to harbor 282 unique genes in comparison with 19 other Bacillus strains, requiring further exploration.     

Discovery and Characterization of a Baeyer-Villiger Monooxygenase Using Sequence Similarity Network Analysis

Baeyer-Villiger monooxygenases (BVMOs) are important flavin-dependent enzymes which perform oxygen insertion reactions leading to valuable products. As reported in many studies, BVMOs are usually unstable during application, preventing a wider usage in biocatalysis. Here, we discovered a novel NADPH-dependent BVMO which originates from Halopolyspora algeriensis using sequence similarity networks (SSNs). The enzyme is stable at temperatures between 10 °C to 30 °C up to five days after the purification, and yields the normal ester product. In this study, the substrate scope was investigated for a broad range of aliphatic ketones and the enzyme was biochemically characterized to identify optimum reaction conditions. The best substrate (86 % conversion) was 2-dodecanone using purified enzyme. This novel BVMO could potentially be applied as part of an enzymatic cascade or in bioprocesses which utilize aliphatic alkanes as feedstock.     

A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications

The production of biochemicals requires the use of microbial strains with efficient substrate conversion and excellent environmental robustness, such as Weizmannia coagulans species. So far, the genomes of 47 strains have been sequenced. Herein, we report a comparative genomic analysis of nine strains on the full repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms to environmental challenges. Moreover, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immune system along with CRISPR-associated (Cas) genes, was also analyzed. Overall, this study expands our understanding of the strain’s genomic diversity of W. coagulans to fully exploit its potential in biotechnological applications.     

雪腐核盘菌的ITS序列分析

首次对来自日本和我国神农架且不同寄主的3株雪腐核盘菌（Sclerotinia nivalis Saito）的核糖体基因转录间隔区（ITS）DNA序列进行了测定,并与GenBank中的同源序列进行比较,没有发现序列完全相同的真菌种类,已将雪腐核盘菌中国分离物Let-19的ITS序列在GenBank进行了注册,登陆号为DQ234388。通过软件DNAStar比对分析,发现菌株Let-19与日本的2个雪腐核盘菌菌株AGT和C-1-2的ITS序列没有差异性。说明不同地域、不同寄主来源的雪腐核盘菌的ITS序列非常保守。     

无须常规维修的长输液氨管道的设计和管理

长输液氨管道的维修,由于受多种因素的制约,其困难非同一般。采用现代技术和科学管理相结合的办法,通过精心设计、严格施工、法制化管理,可保证管道在使用年限内（10～30年）长期不维修或大修,秦皇岛长输液氨管道运行10年的经验,值得借鉴。     

Phenotypic and Safety Assessment of the Cheese Strain Lactiplantibacillus plantarum LL441, and Sequence Analysis of its Complete Genome and Plasmidome

This work describes the phenotypic typing and complete genome analysis of LL441, a dairy Lactiplantibacillus plantarum strain. LL441 utilized a large range of carbohydrates and showed strong activity of some carbohydrate-degrading enzymes. The strain grew slowly in milk and produced acids and ketones along with other volatile compounds. The genome of LL441 included eight circular molecules, the bacterial chromosome, and seven plasmids (pLL441-1 through pLL441-7), ranging in size from 8.7 to 53.3 kbp. Genome analysis revealed vast arrays of genes involved in carbohydrate utilization and flavor formation in milk, as well as genes providing acid and bile resistance. No genes coding for virulence traits or pathogenicity factors were detected. Chromosome and plasmids were packed with insertion sequence (IS) elements. Plasmids were also abundant in genes encoding heavy metal resistance traits and plasmid maintenance functions. Technologically relevant phenotypes linked to plasmids, such as the production of plantaricin C (pLL441-1), lactose utilization (pLL441-2), and bacteriophage resistance (pLL441-4), were also identified. The absence of acquired antibiotic resistance and of phenotypes and genes of concern suggests L. plantarum LL441 be safe. The strain might therefore have a use as a starter or starter component in dairy and other food fermentations or as a probiotic.     

Repetitive Sequence Barcode Probe for Karyotype Analysis in Tripidium arundinaceum

The barcode probe is a convenient and efficient tool for molecular cytogenetics. Tripidium arundinaceum, as a polyploid wild allied genus of Saccharum, is a useful genetic resource that confers biotic and abiotic stress resistance for sugarcane breeding. Unfortunately, the basic cytogenetic information is still unclear due to the complex genome. We constructed the Cot-20 library for screening moderately and highly repetitive sequences from T. arundinaceum, and the chromosomal distribution of these repetitive sequences was explored. We used the barcode of repetitive sequence probes to distinguish the ten chromosome types of T. arundinaceum by fluorescence in situ hybridization (FISH) with Ea-0907, Ea-0098, and 45S rDNA. Furthermore, the distinction among homology chromosomes based on repetitive sequences was constructed in T. arundinaceum by the repeated FISH using the barcode probes including Ea-0663, Ea-0267, EaCent, 5S rDNA, Ea-0265, Ea-0070, and 45S rDNA. We combined these probes to distinguish 37 different chromosome types, suggesting that the repetitive sequences may have different distributions on homologous chromosomes of T. arundinaceum. In summary, this method provide a basis for the development of similar applications for cytogenetic analysis in other species.     

Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns

Nucleosomes are basic units of DNA packing in eukaryotes. Their structure is well conserved from yeast to human and consists of the histone octamer core and 147 bp DNA wrapped around it. Nucleosomes are bound to a majority of the eukaryotic genomic DNA, including its regulatory regions. Hence, they also play a major role in gene regulation. For the latter, their precise positioning on DNA is essential. In the present paper, we describe Galaxy dnpatterntools—software package for nucleosome DNA sequence analysis and mapping. This software will be useful for computational biologists practitioners to conduct more profound studies of gene regulatory mechanisms.     

利用标准等温线分析活性炭的完全孔分布

利用我们从标准等温线性质发展的孔分布计算两个新方法——完全无模型孔分布计算法和改进的微孔分析法对有代表性的九个活性炭样品进行了完全孔分布分析.用吸附仪测量样品的低温氮吸附等温线,用Pickett方程关联了这些吸附等温线,发现n值在1.1—1.4之间.因常数C值在100—300之间,选用标准等温线n_2作为完全孔分布分析的依据.获得了总表面积、微孔的表面积和体积、非微孔的表面积和体积以及平均微孔水力半径等主要孔结构参数,并获得了所有样品的完全孔分布.两个比值SR和VR在0.9—1.1之间,结果是令人满意的.分析结果指出,DX-09-1-1,7S及J三个样品基本上全是微孔,而其余的炭毡及BPL炭样品都有相当数量的非微孔.这些结果说明,利用标准等温线进行活性炭样品的完全孔分布分析是实用的.     

长输石油管道盗孔修复强度分析

在众多管道失效形式中,长输石油管道盗孔现象尤为普遍。这些被打孔盗油的管道需要修复或者更换。尽管目前管道修复提倡采用非焊接的方法,但这类非焊接的修复方法只适用于管壁未穿透的缺陷。在管壁被穿透的情况下,只能采用焊接的方法修复。现场焊接修复打孔管道的方式有两种：接管和补板。运用ANSYS软件对两种修复方法进行有限元分析,结果表明,接管或补板的存在使管道修复结构应力分布不均匀,出现了一定的应力集中;两种修复结构整体的极限裁荷相近。文章给出了两种修复结构中,不同结构尺寸对于修复结果的影响,并且提出了修复建议,对于实际打孔管道修复有一定的参考价值。     

喷涂距离对涂料利用率的影响分析

通过不同生产线之间喷涂参数的对比分析,对汽车自动化喷涂生产线的喷涂程序进行优化。经过对喷涂距离等参数进行调整,提高了涂料利用率,并达到了节约生产成本和减少环境污染的目的。     

Discovering Biomarkers for Non-Alcoholic Steatohepatitis Patients with and without Hepatocellular Carcinoma Using Fecal Metaproteomics

High-calorie diets lead to hepatic steatosis and to the development of non-alcoholic fatty liver disease (NAFLD), which can evolve over many years into the inflammatory form of non-alcoholic steatohepatitis (NASH), posing a risk for the development of hepatocellular carcinoma (HCC). Due to diet and liver alteration, the axis between liver and gut is disturbed, resulting in gut microbiome alterations. Consequently, detecting these gut microbiome alterations represents a promising strategy for early NASH and HCC detection. We analyzed medical parameters and the fecal metaproteome of 19 healthy controls, 32 NASH patients, and 29 HCC patients, targeting the discovery of diagnostic biomarkers. Here, NASH and HCC resulted in increased inflammation status and shifts within the composition of the gut microbiome. An increased abundance of kielin/chordin, E3 ubiquitin ligase, and nucleophosmin 1 represented valuable fecal biomarkers, indicating disease-related changes in the liver. Although a single biomarker failed to separate NASH and HCC, machine learning-based classification algorithms provided an 86% accuracy in distinguishing between controls, NASH, and HCC. Fecal metaproteomics enables early detection of NASH and HCC by providing single biomarkers and machine learning-based metaprotein panels.     

Complete Mitochondrial Genome Sequence and Identification of a Candidate Gene Responsible for Cytoplasmic Male Sterility in Celery (Apium graveolens L.)

Celery (Apium graveolens L.) is an important leafy vegetable worldwide. The development of F₁ hybrids in celery is highly dependent on cytoplasmic male sterility (CMS) because emasculation is difficult. In this study, we first report a celery CMS, which was found in a high-generation inbred line population of the Chinese celery “tanzhixiangqin”. Comparative analysis, following sequencing and assembly of the complete mitochondrial genome sequences for this celery CMS line and its maintainer line, revealed that there are 21 unique regions in the celery CMS line and these unique regions contain 15 ORFs. Among these ORFs, only orf768a is a chimeric gene, consisting of 1497 bp sequences of the cox1 gene and 810 bp unidentified sequences located in the unique region, and the predicted protein product of orf768a possesses 11 transmembrane domains. In summary, the results of this study indicate that orf768a is likely to be a strong candidate gene for CMS induction in celery. In addition, orf768a can be a co-segregate marker, which can be used to screen CMS in celery.     

Genetic Analysis of Hexaploid Wheat (Triticum aestivum L.) Using the Complete Sequencing of Chloroplast DNA and Haplotype Analysis of the Wknox1 Gene

The aim of the presented study is a genetic characterization of the hexaploid wheat Triticum aestivum L. Two approaches were used for the genealogical study of hexaploid wheats—the complete sequencing of chloroplast DNA and PCR-based haplotype analysis of the fourth intron of Wknox1d and of the fifth-to-sixth-exon region of Wknox1b. The complete chloroplast DNA sequences of 13 hexaploid wheat samples were determined: Free-threshing—T. aestivum subsp. aestivum, one sample; T. aestivum subsp. compactum, two samples; T. aestivum subsp. sphaerococcum, one sample; T. aestivum subsp. carthlicoides, four samples. Hulled—T. aestivum subsp. spelta, three samples; T. aestivum subsp. vavilovii jakubz., two samples. The comparative analysis of complete cpDNA sequences of 20 hexaploid wheat samples (13 samples in this article plus 7 samples sequenced in this laboratory in 2018) was carried out. PCR-based haplotype analysis of the fourth intron of Wknox1d and of the fifth-to-sixth exon region of Wknox1b of all 20 hexaploid wheat samples was carried out. The 20 hexaploid wheat samples (13 samples in this article plus 7 samples in 2018) can be divided into two groups—T. aestivum subsp. spelta, three samples and T. aestivum subsp. vavilovii collected in Armenia, and the remaining 16 samples, including T. aestivum subsp. vavilovii collected in Europe (Sweden). If we take the cpDNA of Chinese Spring as a reference, 25 SNPs can be identified. Furthermore, 13–14 SNPs can be identified in T. aestivum subsp. spelta and subsp. vavilovii (Vav1). In the other samples up to 11 SNPs were detected. 22 SNPs are found in the intergenic regions, 2 found in introns, and 10 SNPs were found in the genes, of which seven are synonymous. PCR-based haplotype analysis of the fourth intron of Wknox1d and the fifth-to-sixth-exon region of Wknox1b provides an opportunity to make an assumption that hexaploid wheats T. aestivum subsp. macha var. palaeocolchicum and var. letshckumicum differ from other macha samples by the absence of a 42 bp insertion in the fourth intron of Wknox1d. One possible explanation for this observation would be that two Aegilops tauschii Coss. (A) and (B) participated in the formation of hexaploids through the D genome: Ae. tauschii (A)—macha (1–5, 7, 8, 10–12), and Ae. tauschii (B)—macha M6, M9, T. aestivum subsp. aestivum cv. ‘Chinese Spring’ and cv. ‘Red Doly’.     

初始内压和帘线间距对膜式空气弹簧横向刚度特性影响的有限元分析

运用ABAQUS分析软件建立膜式空气弹簧的有限元模型,通过仿真计算获得负荷-横向位移曲线,研究初始内压和帘线间距对膜式空气弹簧横向刚度的影响。结果表明,空气弹簧的横向刚度随着初始内压的提高而增大,同时由于空气弹簧膨胀造成帘线间距增大,引起横向刚度降低。本研究为膜式空气弹簧设计中合理选择初始内压和帘线间距提供了参考。     

一种基于层序分析的相对深度校正方法

本文提出一种基于地层层序分析的相对深度校正方法：它利用活度分析法将不同次下井测得的两条测井曲线进行地层界面划分;根据地层层序不变的原则利用局部相关分析的方法确定这两条曲线的匹配关系;然后分析这两条曲线各个配对层位的顶、底界面深度,对其中一条曲线进行深度校正。这种深度校正方法计算量小,而且精度较高。