利用EST序列构建Mascot本地数据库

对蛋白质质谱数据进行数据库比对和鉴定是蛋白质组学研究技术中的一个重要步骤。由于公共数据库蛋白质数据信息不全,有些蛋白质质谱数据无法得到有效的鉴定。而利用相关物种的EST序列构建专门的质谱数据库则可以增加鉴定未知蛋白的几率。本文介绍了利用EST序列构建Mascot本地数据库的具体方法和步骤,扩展了Mascot检索引擎对蛋白质质谱数据的鉴定范围,从数据库层面提高了对未知蛋白的鉴别几率,为蛋白质组学研究提供了一种较为实用的生物信息学分析技术。     

Exploiting a wheat EST database to assess genetic diversity

Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F₂ individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01.     

球毛壳菌(Chaetomium globosum)EST生物信息分析数据库的建立

用基因本体论（Cene Ontology,GO）中的相关的规范术语和BLAST分析结果来对球毛壳菌EST及CONTIG序列信息进行注释,利用GO的语义模型构建不同物种数据库之间的语义联接,在此基础上建立球毛壳菌EST生物信息分析数据库,在概念和联系层面上有效地解决了不同物种生物信息的整合问题,实现了对球毛壳菌生物信息学数据智能化的多重、复合和交叉检索。为球毛壳菌生物信息学的进一步研究奠定了坚实的基础。文中详细论述了基于GO的球毛壳菌EST生物信息学数据库的研究背景、建立过程、查询功能及其维护。     

Characterization and mapping of three new mammalian ATP-binding transporter genes from an EST database

Analysis of the human expressed sequence tag (EST) database identified four clones that contain sequences of previously uncharacterized genes, members of the ATP-binding cassette (ABC) superfamily. Two new ABC genes (EST20237, 31252) are located at Chromosome (Chr) 1q42 and 1q25 respectively in humans, as determined by FISH; at locations distinct from previously mapped genes of this superfamily. Two additional clones, EST 600 and EST 1596, were found to represent different ATP-binding domains of the same gene, ABC2. This gene was localized to 9q34 in humans by FISH and to the proximal region of Chr 2 in mice by linkage analysis. All genes display extensive diversity in sequence and expression pattern. We present several approaches to characterizing EST clones and demonstrate that the analysis of EST clones from different tissues is a powerful approach to identify new members of important gene families. Some drawbacks of using EST databases, including chimerism of cDNA clones, are discussed.     

Initial characterization of a recombinant kynureninase from Trypanosoma cruzi identified from an EST database

Kynureninase has been described in bacteria, fungi and animals as an enzyme involved in the catabolic degradation pathway of l-tryptophan. This pyridoxal 5′-phosphate (PLP)-dependent enzyme catalyzes the hydrolytic cleavage of l-kynurenine and 3-hydroxy-l-kynurenine to yield l-alanine and either anthranilic or 3-hydroxyanthranilic acid, respectively. We identified a putative kynureninase gene from a Trypanosoma cruzi project aiming at the structural and functional characterization of more than 100 proteins differentially expressed during metacyclogenesis. This gene encodes a protein similar in size and sequence to kynureninases from other sources. This open reading frame was cloned and the recombinant enzyme was overexpressed. Recombinant T. cruzi kynureninase was purified to homogeneity and its identity was confirmed by mass spectrometry. The apparent molecular mass of the native T. cruzi kynureninase was estimated by gel filtration, suggesting that the protein is a homodimer. Circular dichroism spectrum indicated a mixture of α-helix and β-sheet structure, expected for an aminotransferase fold. l-kynurenine, preferentially hydrolyzed by prokaryotic inducible kynureninases, and 3-hydroxy-l-kynurenine, the preferred substrate in fungi and vertebrates, are both catabolized equally well by T. cruzi kynureninase. Further experimental assays will be performed to fully understand the importance of this enzyme for T. cruzi metabolism.     

番红花EST资源的SSR信息分析

从NCBI公共数据库下载得到6745条番红花EST,通过前处理得到全长为612.01 kb的无冗余EST 1431条.在这些序列中搜索出108个SSR,分布于103条EST中,出现频率为7.55%.这些EST-SSR的平均分布距离是5.67 kb.二核苷酸重复和三核苷酸重复是番红花主要的重复类型,分别占总EST-SSR...     

Error-tolerant EST database searches by tandem mass spectrometry and multiTag software

The MultiTag method (Sunyaev et al., Anal. Chem. 2003 15, 1307-1315) employs multiple error-tolerant searches with peptide sequence tags (Mann and Wilm, Anal. Chem. 1994, 66, 4390-4399) for the identification of proteins from organisms with unsequenced genomes. Here we demonstrate that the error-tolerant capabilities of MultiTag increased the number of peptide alignments and improved the confidence of identifications in an EST database. The MultiTag outperformed conventional database searching software that only utilizes stringent matching of tandem mass spectra to nucleotide sequences of ESTs.     

GoSh: a web-based database for goat and sheep EST sequences

The GoSh database is a collection of 58 990 Capra hircus and Ovis aries expressed sequence tags. A perl pipeline was prepared to process sequences, and data were collected in a MySQL database. A PHP-based web interface allows browsing and querying the database. Putative single nucleotide polymorphism (SNP) detection, as well as search to repeats were performed, and links to external related resources were provided. Sequences were annotated against three different databases and an algorithm was implemented to create statistics of the distribution of retrieved homologous ontologies in the Gene Ontology categories. The GoSh database is a repository of data and links related to goat and sheep expressed genes. AVAILABILITY: The GoSh database is available at http://www.itb.cnr.it/gosh/     

Somatic embryogenesis from stigmas and styles of grapevine

Summary An in vitro protocol has been developed for callus indiction, somatic embryogenesis, and plant regeneration from stigma-style culture of grapevine. Four different grapevine cultivars (Vitis vinifera L.: cvs. ‘Bombino Nero’, ‘Greco di Tufo’, ‘Merlot’, and ‘Sangiovese’) were tested. Exlants were cultured on Nitsch and Nitsch medium (NN) supplemented with various combinations of 6-benzylaminopurine (BA: 4.5 and 9.0 μM) and β-naphthoxyacetic acid (NOA; 5.0 and 9.9 μM). Sucrose (88 mM) was used as the carbon source. Somatic embryogenesis was induced within 3–7 mo. after culture initiation. Even though explants of different origin (unfertilized ovules and anthers) regenerated somatic embryos, the higher embryogenic potential was observed in stigma and style explants, with the exception of ‘Merlot’, which regenerated somatic embryos only from unfertilized ovules. The percentages of stigma-style explants producing somatic embryos was 7% in ‘Bombino Nero’ (cultured on NN medium supplemented 9.0 μM BA and 9.9 μM NOA). 14% in ‘Greco di Tufo’ (4.5 μM BA and 9.9 μM NOA), and 8% in ‘Sangiovese’ (9.0 μM BA and 9.9 μM NOA). The presence of growth regulators (BA and NOA) in the medium was essential for induction of somatic embryogenesis. Plants were regenerated on hormone-free NN medium containing 88 mM sucrose.     

Eleven polymorphic simple sequence repeat markers from expressed sequence tags of Pacific oyster Crassostrea gigas EST database

Oyster (Crassostrea gigas) is widely distributed in coastal areas of world. We developed and evaluated simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) of C. gigas and to amplify EST-SSR in C. gigas. Characteristics of 11 EST-SSR loci were investigated using 45 C. gigas individuals. The number of alleles per locus ranged from two to thirteen. The observed heterozygosity (H _o) ranged from 0.0889 to 0.7333 and the expected heterozygosity (H _e) ranged from 0.0859 to 0.8981. Because of their high level of polymorphism, our 11 single-locus EST-SSR markers will be valuable tools for research on mating system, population genetics and systemic evolution of oyster in the future.     

Unix下EST数据库本地化更新及序列预处理分析

利用FreeBSD操作系统的文本过滤命令将NCBI的Genbank数据库的EST序列实现本地化导入到MySQL数据库中并能够进行更新,这利于对不同物种不同组织器官基因表达的分析。以水稻EST数据为例,对EST序列两端出现的polyA/T和载体序列亦进行了鉴别及去除,经过预处理的EST序列数据将为进一步进行EST聚类及基因表达分析提供可靠的保证。     

GarlicESTdb: an online database and mining tool for garlic EST sequences

Background  

Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression.     

Pscroph,a parasitic plant EST database enriched for parasite associated transcripts

Background  

Parasitic plants in the Orobanchaceae develop invasive root haustoria upon contact with host roots or root factors. The development of haustoria can be visually monitored and is rapid, highly synchronous, and strongly dependent on host factor exposure; therefore it provides a tractable system for studying chemical communications between roots of different plants.