基于PC/Linux的核酸序列分析系统的构建及其应用

基于PC机和Linux操作系统, 利用Phred/Phrap/Consed软件和Blast软件, 构建了核酸序列大规模自动分析系统. 该套系统可自动完成从测序峰图向核酸序列的转化、载体序列去除、序列自动拼接、重复序列鉴定以及序列的相似性分析, 可加速对大规模测序数据的分析和利用.     

蛋白质序列复杂性简化与非比对序列分析

非比对序列分析是最新发展的一种序列分析方法,具有计算效率高并适用于分析低相似性的序列,已成功用于DNA的序列分析中.但是由于蛋白质序列的复杂性,非比对序列分析对于蛋白质序列分析的准确度却不高.用将20种天然氨基酸残基归类的方法,简化了蛋白质序列的复杂性,并运用到对蛋白质的非比对序列分析中,有效地提高了序列分析的准确性.     

基于Linux的cDNA文库序列分析平台的构建与应用

本研究构建了基于Linux的cDNA文库序列分析平台,该分析平台可大批量自动处理测序后的序列,包括载体序列的去除、序列格式的转换、序列的自动拼接、序列对数据库的相似性搜索及全长ORF的预测等,可加速对大规模测序数据的分析和利用。用该平台对构建的野生大豆盐胁迫全长cDNA文库部分测序结果进行分析和利用。用该平台对构建的野生大豆盐胁迫全长cDNA文库部分测序结果进行分析,获得了较好的结果,已得到多个具有潜在价值的新基因序列。     

基于Windows的核酸序列分析软件的开发

随着基因组计划的发展和基因分离技术的不断提高,大量的DNA序列需要进行分析以获得有用的生物学信息。然而当前开发的大多数序列分析软件或者使用功能比较单一,或者价格比较昂贵,不能很好的满足日常工作的需要。利用流行的Visual Basic语言进行核酸序列分析软件的开发,编制的BioXM软件能够满足包括翻译、ORF查找、序列联配、酶切位点分析、引物辅助设计、序列排列格式化、序列格式转换、载体序列去除等需要,达到了满意的应用效果。     

MATLAB 7.X 生物信息工具箱的应用-- 专用分析工具（ 六）*

序列分析可以获取蕴藏在简单序列中的生物信息,是生物信息分析的基础。通过生物大分子序列差异分析构建的系统树则可为我们提供可视化的物种间的进化关系。MATLAB7.X生物信息工具箱包含了几个图形用户界面设计的专用分析工具,这些专用分析工具交互性好,易于使用。借助于这些分析工具,用户不仅可以对基因序列进行分析查看并能进行相对应的氨基酸序列分析,还可以方便快捷地构建系统发育树。即使用户不会编程也可以进行序列分析和系统发育分析的研究,大大地提高了分析的效率。本文详细介绍了序列分析工具Seqtool和系统发育分析工具Phytreetool在序列分析及系统发育树构建方面的应用,所有操作方便快捷,分析结果可视化程度高。     

一个基于Blast程序的多重序列对齐程序——Mblast

核酸序列和蛋白质序列的相似性分析日益成为生物信息学研究的核心内容.NCBI的Blast程序是进行此类分析的最有力工具.虽然它提供了初步的将多条序列进行综合对齐的分析方案,但是实际效果却很不理想.在对Blast程序的输出结果进行仔细分析的基础上,基于“求同存异”的思想,我们编制了一个多重序列对齐程序Mblast.该程序与目前流行的序列多重对齐程序相比,更容易检出序列的同源区.     

DNA序列分析技术的进展

近几年来,DNA序列分析技术有了很大发展,可以说,分子生物学突飞猛进的发展与DNA序列分析技术的不断改善是分不开的。虽然Wat(?)on与Crick早在1953年就测出了DNA的双螺旋结构,然而直到六十年代末还没有人能对DNA进行序列分析。值得注意的是,人们在六十年代中期就能够进行RNA序列分析。第一个被测出完整     

球毛壳菌循环肽HC-毒素基因的序列分析

为了验证Phrap软件是否适合在EST分析中应用,对球毛壳菌循环肽HC-毒素基因进行了序列分析。根据EST分析的结果,从cDNA文库中挑取循环肽HC-毒素基因的克隆进行了测序并序列分析。结果表明cDNA文库中循环肽HC-毒素基因的克隆插入片断大小为1217bp;用Phrap软件拼接出来的循环肽HC-毒素的表达序列标签拼接序列与实际序列不完全一致,因此Phrap软件不适合在EST分析中应用。     

基于Linux平台的林木EST序列分析系统的构建及应用

利用Phred/Phrap/Consed、cross.match、RepeatMasker、Blast等软件和自主开发程序,基于Linux操作系统,构建了林木EST序列分析系统,完成了从测序峰图向核酸序列的转化、载体序列的去除、重复序列鉴定、EST序列分类和组装、EST序列功能注释与功能分类以及SSR、SNP的发掘。并通过使用Perl语言结合bioperl模块写的脚本程序使分析过程自动化,从而可以快速地对大批林木EST数据进行分析,为林木的功能基因组学研究提供有用的信息。     

基于非线性方法的DNA序列分析

以人类DNA序列为原始数据,对其进行数字编码。在利用功率谱分析编码DNA序列的基础上,利用Hurst指数进一步分析序列的自相似性。从分析结果看出,DNA序列中的确存在长程相关现象,而且这种长程相关现象与DNA的组成结构有关,表现为它的结构基团的Hurst指数大于其功能基团的Hurst指数。同时,从内含子含量的角度分析序列的长程相关程度,结果表明,同一序列中,内含子含量与不同的化学基团具有不同的关系。这表明不同的化学结构对DNA序列特征具有不同的贡献。这些结论从非线性方法的角度对DNA序列的分析提供了新的思路。     

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

正Dear Editor,In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19) in Wuhan, Hubei, China(Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases     

Inquiry-based laboratory course improves students' ability to design experiments and interpret data

We redesigned our intermediate-level organismal physiology laboratory course to center on student-designed experiments in plant and human physiology. Our primary goals were to improve the ability of students to design experiments and analyze data. We assessed these abilities at the beginning and end of the semester by giving students an evaluation tool consisting of an experimental scenario, data, and four questions of increasing complexity. To control for nontreatment influences, the improvement scores (final minus initial score for each question) of students taking both the laboratory and the companion lecture course were compared with those of students taking the lecture course only. The laboratory + lecture group improved more than the lecture-only group for the most challenging question. This evidence suggests that our inquiry-based curriculum is achieving its primary goals. The evaluation tool that we developed may be useful to others interested in measuring experimental analysis abilities in their students.     

SNP array analysis in constitutional and cancer genome diagnostics--copy number variants, genotyping and quality control

Array-based comparative genomic hybridization analysis of genomic DNA was first applied in postnatal diagnosis for patients with intellectual disability (ID) and/or congenital anomalies (CA). Genome-wide single-nucleotide polymorphism (SNP) array analysis was subsequently implemented as the first line diagnostic test for ID/CA patients in our laboratory in 2009, because its diagnostic yield is significantly higher than that of routine cytogenetic analysis. In addition to the detection of copy number variations, the genotype information obtained with SNP array analysis enables the detection of stretches of homozygosity and thereby the possible identification of recessive disease genes, mosaic aneuploidy, or uniparental disomy. Patient-parent (trio) information analysis is used to screen for the presence of any form of uniparental disomy in the patient and can determine the parental origin of a de novo copy number variation. Moreover, the outcome of a genotype analysis is used as a final quality control by ruling out potential sample mismatches due to non-paternity or sample mix-up. SNP array analysis is now also used in our laboratory for patients with disorders for which locus heterogeneity is known (homozygosity pre-screening), in prenatal diagnosis in case of structural ultrasound anomalies, and for patients with leukemia. In this report, we summarize our array findings and experiences in the various diagnostic applications and demonstrate the power of a SNP-based array platform for molecular karyotyping, because it not only significantly improves the diagnostic yield in both constitutional and cancer genome diagnostics, but it also enhances the quality of the diagnostic laboratory workflow.     

Microbe-I: fungal biota analyses of the Japanese experimental module KIBO of the International Space Station before launch and after being in orbit for about 460 days

In addition to the crew, microbes also find their way aboard the International Space Station (ISS). Therefore, microbial monitoring is necessary for the health and safety of the crew and for general maintenance of the facilities of this station. Samples were collected from three sites in the Japanese experimental module KIBO on the ISS (air diffuser, handrail, and surfaces) for analysis of fungal biota approximately 1 year after this module had docked with the ISS. Samples taken from KIBO before launch and from our laboratory were used as controls. In the case of KIBO, both microbe detection sheet (MDS) and swab culture tests of orbital samples were negative. The MDS were also examined by field emission-scanning electron microscopy; no microbial structures were detected. However, fungal DNAs were detected by real-time PCR and analyzed by the clone library method; Alternaria sp. and Malassezia spp. were the dominant species before launch and in space, respectively. The dominant species found in specimens from the air conditioner diffuser, lab bench, door push panel, and facility surfaces on our laboratory (ground controls) were Inonotus sp., Cladosporium sp., Malassezia spp., and Pezicula sp., respectively. The fungi in the KIBO were probably derived from contamination due to humans, while those in our laboratory came from the environment (e.g., the soil). In conclusion, the cleanliness in KIBO was equivalent to that in a clean room environment on the ground.     

Biolog微生物鉴定系统中接种液的替代

目的：采用市售试剂自行配制Biolog菌种鉴定接种液,代替Biolog公司的原装接种液,用以降低菌种鉴定成本。方法：用实验室自行配制的接种液和Biolog公司的接种液,对120株细菌和50株丝状真菌进行Biolog微生物系统鉴定,对比鉴定结果。结果：用2种接种液进行菌种鉴定时,鉴定板上部分孔的颜色反应不同,但鉴定结果一致。结论：自行配制的接种液可以满足菌株鉴定的要求,具有推广意义。     

Chromosome studies on cells cultured from serous effusions. Use in routine cytologic practice

Cytogenetic analysis was used to supplement the cytologic diagnosis of malignancy in serous effusions. Current methods of analysis involve immediate preparation, but our study showed that prior culture of the cells is a more practical approach to the use of chromosome analysis in the routine cytology laboratory. This method permits the retrospective selection of specimens for chromosome analysis from patients in whom there is a strong clinical suspicion of malignant disease but who have negative or equivocal cytology reports. The preparative technique and the recognition of structural and numerical chromosome anomalies can be readily learned by the cytotechnologist and incorporated into the routine cytology laboratory.     

Prebiotic Organic Microstructures

Micro- and sub-micrometer spheres, tubules and fiber-filament soft structures have been synthesized in our experiments conducted with 3?MeV proton irradiations of a mixture of simple inorganic constituents, CO, N(2) and H(2)O. We analysed the irradiation products, with scanning electron microscopy (SEM) and atomic force microscopy (AFM). These laboratory organic structures produced a wide variety of proteinaceous and non-proteinaceous amino acids after HCl hydrolysis. The enantiomer analysis for D,L-alanine confirmed that the amino acids were abiotically synthesized during the laboratory experiment. We discuss the presence of CO(2) and the production of H(2) during exothermic processes of serpentinization and consequently we discuss the production of hydrothermal CO in a ferromagnesian silicate mineral environment. We also discuss the low intensity of the Earth's magnetic field during the Paleoarchaean Era and consequently we conclude that excitation sources arising from cosmic radiation were much more abundant during this Era. We then show that our laboratory prebiotic microstructures might be synthesized during the Archaean Eon, as a product of the serpentinization process of the rocks and of their mineral contents.     

Detection of an unusual combination of mutations in the HFE gene for hemochromatosis

In the present paper, we describe an individual, found as part of a screening study, being homozygous for the C282Y mutation and at the same time heterozygous for the H63D mutation in the HFE gene. Identical results were obtained by three different methods, i.e., by PCR-RFLP, by sequencing, and by melting curve analysis. Thus, the common conception that the C282Y and the H63D mutations are mutually exclusive is not valid. Clinical symptoms and laboratory data on the individual were similar to hemochromatosis patients homozygous for the C282Y mutation. The implications of our finding for diagnostic analytical laboratory procedures are briefly discussed.     

rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity

Contemporary microbial community analysis frequently involves PCR-amplified sequences of the 16S rRNA gene (rDNA). However, this technology carries the inherent problem of heterogeneity between copies of the 16S rDNA in many species. As an alternative to 16S rDNA sequences in community analysis, we employed the gene for the RNA polymerase beta subunit (rpoB), which appears to exist in one copy only in bacteria. In the present study, the frequency of 16S rDNA heterogeneity in bacteria isolated from the marine environment was assessed using bacterial isolates from the red alga Delisea pulchra and from the surface of a marine rock. Ten strains commonly used in our laboratory were also assessed for the degree of heterogeneity between the copies of 16S rDNA and were used to illustrate the effect of this heterogeneity on microbial community pattern analysis. The rock isolates and the laboratory strains were also used to confirm nonheterogeneity of rpoB, as well as to investigate the versatility of the primers. In addition, a comparison between 16S rDNA and rpoB PCR-DGGE (denaturing gradient gel electrophoresis)-based community analyses was performed using a DNA mixture of nine isolates from D. pulchra. Eight out of 14 isolates from D. pulchra, all rock isolates, and 6 of 10 laboratory strains displayed multiple bands for 16S rDNA when analyzed by DGGE. There was no indication of heterogeneity for either the rock isolates or the laboratory strains when rpoB was used for PCR-DGGE analysis. Microbial community pattern analysis using 16S rDNA PCR-DGGE showed an overestimation of the number of laboratory strains in the sample, while some strains were not represented. Therefore, the 16S rDNA PCR-DGGE-based community analysis was proven to be severely limited by 16S rDNA heterogeneity. The mixture of isolates from D. pulchra proved to be more accurately described using rpoB, compared to the 16S rDNA-based PCR-DGGE.     

中国特有两栖动物研究1.山东半岛林蛙的生活史

生活史的研究可以为系统发育研究和珍稀濒危物种的保护和管理对策的制定提供参考资料。林蛙是我国分布比较广泛而复杂多样的一个类群,在山东半岛的昆嵛山和崂山,分别分布有昆嵛林蛙（Rana kunyuensis）和中国林蛙（R．chensinensis）。本文报道我们从1997年到2006年,对这两种林蛙在山东半岛的地理分布、繁殖习性、蝌蚪特征和生长发育以及冬眠等方面的调查和观察研究结果。结果表明昆嵛林蛙和分布于崂山的中国林蛙尽管在栖息地生境方面比较相似,但在生活史方面表现出较大的不同。