Construction of full-length cDNA library from Antrodia cinnamomea mycelium and EST sequence analysis / 中草药

Objective: To excavate the terpenoid synthesis and metabolism-related gene function and screen the interaction protein and fingerprint analysis of Antrodia cinnamomea mycelium, a cDNA library from A. cinnamomea mycelia was constructed and the EST sequences were analyzed. Methods: The cDNA library from the A. cinnamomea mycelium was constructed by the Gateway technique. A part of EST sequences about the bioinformatics, functional annotation and EST-SSR were analyzed. Results: The cDNA library of the A. cinnamomea mycelium was constructed successfully. The recombinant rate of the cDNA library was 95%, the titer of the library was 6.1 × 106 cfu/mL, the total cloning number was 1.2 × 107 cfu, the length of cDNA was between 300-2 000 bp with an average length of 1 000 bp. The clones were randomly sequenced and 65 valid ESTs were obtained. After being compared in the Genbank database, 45 ESTs had a definite annotation, and 18 ESTs were unnamed and hypothetical protein. The results with GO functional annotation showed that the ESTs involved the cell composition, transport, catalytic activity, regulation functions and etc. It contained 271 SSRs of all the ESTs in total. The nucleotide repeats in A. cinnamomea were abundant, among which dinucleotide and trinucleotide repeat units were more common accounting for 94.23%. Conclusion: The cDNA library from the A. cinnamomea mycelium and its ESTs related biological information were preliminarily identified, which will provide a theoretical foundation for research the mycelium genomics of A. cinnamomea.

Construction of full-length cDNA library of Sarcandra glabra and sequences analysis on EST / 中草药

Objective: Sarcandra glabra was recognized as an important research material attributing to its high medicinal value and economic value. However, little information was known about its genomics and regulatory pathway participating in reproductive development. For the first step to understand the molecular basis and further explore genes which related to metabolism and resistance in S. glabra. Methods: A SMART full-length complementary DNA library from the leaves tissue was constructed and characterized to providing the experimental basis for discovery of functional genes of S. glabra. The assembly expressed sequence tag (EST) data were completed by ABI3730 DNA program. A high quality full-length cDNA library was constructed successfully from S. glabra leaves. Results: The titer of library was 1.14×107 pfu/mL and the average length of inserted fragments was 1 000 bp. A total of 221 clones were sequenced from the cDNA library and obtained 177 EST sequences. The EST sequences were assembled into 151 unigenes including 12 contigs and 119 singletons (79%). EST exhibited significant similarity with known putative functional nucleotide sequences in the GenBank database. These genes were mostly involved in cell development, signal transduction, protein synthesis, transcription, stress tolerance response, energy metabolism based on molecular function of GO annotation. Conclusion: This report constructs a full-length-cDNA library and analyzes the bioinformatics of the related EST sequences, and then offers a reference to genomic research of S. glabra.

Expression and Characterization of Genes by Expressed Sequence Tag Analysis in the Rat Thymus during Regeneration following Acute Thymic Involution Induced by Cyclophosphamide / 체질인류학회지

The thymus is the central lymphoid organ for the development of bone marrow-derived precursor cells into mature T-cells. Understanding the molecular mechanism of thymic involution and regeneration is critical to develop methods to normalize or improve host immunity from the decreased immune function caused by thymic involution. In this study, the regenerating thymus cDNA library was constructed in the rat from a model of thymic involution and regeneration induced by cyclophosphamide. Expressed sequence tags (ESTs) were obtained by partial sequencing of 700 randomly selected insert-containing clones. A total of 630 ESTs were analyzed, of which 486 ESTs (78%) matched to known genes and 125 ESTs (19%) matched to other ESTs (unknown genes). The 19 ESTs (3%) did not match with any known sequences. The ESTs were grouped into six main functional categories: metabolism (44%), signaling components (20%), membrane transport (7%), cytoskeleton (2%), cell division (2%) and defense (2%). As a result of RT-PCR analysis, expression of putative gene 01, putative E2IG2 gene, musculin and osteoactivin significantly increased in rat thymus during regeneration. The putative gene 01 showed complete homology with mitochondrial ribosomal protein S4 by homology search and multiple alignment of amino acid. These results provide the extensive molecular information on thymus regeneration and will be useful source to identify various genes which may play an important role in the thymus regeneration as well as to clone novel genes. Furthermore, the availability of these data will serve as a basis for further research to understand the molecular mechanism of thymus regeneration.

Caracterización molecular de los genes pr1 y tpt1 en especies y variedades cubanas de tabaco (Nicotiana tabacum L. ) / Molecular characterization of pr1 and tpt1 proteins in cuban tobacco species and varieties (Nicoatiana tabacum L. )

La identificación de genes nuevos relacionados con la respuesta de Nicotiana tabacum L. al estrés biótico y abiótico contribuye al mejoramiento genético del cultivo del tabaco en todo el mundo. El objetivo de este trabajo fue detectar la presencia de los genes tpt1 y pr1 en el genoma de algunas especies y variedades cubanas de tabaco. Se identificaron 265 etiquetas de secuencias expresadas (ESTs-expressed sequences tags) que nunca se habían informado con anterioridad en especies vegetales, y el gen que codifica para la proteí­na tumoral controlada durante la transcripción (Transcriptional Controlled Tumor Protein) (tpt1) nunca se había informado en N. tabacum, pues los estudios del mismo se han centrado en su mayoría en animales y humanos. Los resultados del microarreglo se confirmaron utilizando la RT-PCR cuantitativa en tiempo real. Los genes tpt1 y proteí­na relacionada con la patogénesis (pr1) se utilizaron para diseñar cebadores para la caracterización molecular de algunas especies y variedades de tabaco cubano. El gen tpt1 solamente se expresó en dos especies (N. glutinosa y N. tomentosiformis) y el pr1, después de la digestión, mostró diferentes bandas entre las variedades susceptibles y resistentes. La presencia de estos genes en una parte del germoplasma analizado constituye un paso inicial para la utilización de este conocimiento en el mejoramiento genético del tabaco.

The identification of new genes related with Nicotiana tabacum L. response to biotic and abiotic stress contribute to the genetic improvement of tobacco plants around the world. The aim of this research was to identify tpt1 and pr1 genes in the genomic of some cuban tobacco varieties and species. The microarray technology has been used with ESTs for the construction of a cDNA library. 265 expressed sequences tags (ESTs) that have never been reported before in vegetables species were identified and the gene that codified for the Transcriptional Controlled Tumor Protein (tpt1), has never been reported before in N. tabacum, with the studies about this gene being focused on human and animals mostly. The microarray results were confirmed using quantitative RT- PCR. TCTP and pathogenesis-related protein 1 (PR-1) ESTs were used to design primers for the molecular characterization of some species and cuban tobacco varieties. The tpt1 gene was only expressed in two species (N. glutinosa y N. tomentosiformis) and pr1 gen, after a digestion, exhibited different bands for susceptible and resistant varieties. The detection of these genes in some species and cuban tobacco varieties represents one step to go deeply in the molecular characterization of cuban germoplasm.

Characterization of novel genic SSR markers in Linum usitatissimum (L. ) and their transferability across eleven Linum species

Little is known about the evolutionary relationships among Linum species, basically because of the lack of transferable molecular markers. Currently, expressed sequence tags available in public databases provide an opportunity for the rapid and inexpensive development of simple sequence repeat (SSR) markers in wild flax species. In this regard, fifty expressed sequence tag-derived microsatellite markers (EST-SSRs) were evaluated for polymorphism and transferability in 50 Linum usitatissimum cultivars/accessions and 11 Linum species. Among them 23 EST-SSRs were polymorphic in L. usitatissimum, while 2-4 alleles were detected (average 2.26 per locus). The polymorphism information content value ranged from 0.08 to 0.55 (average 0.38). Forty one genic markers (95.3 percent) produced strong amplicons in at least two of the 11 Linum species. The percentage of cross amplification ranged from 34.1 percent to 92.7 percent in L. tauricum and L. bienne, respectively. Moreover, the rate of transferability was associated positively with the botanical section. Our results suggest that the high degree of EST-SSRs transferability to Linum species can be a useful enhancement of the current database of SSR markers for future genetic and evolutionary studies.

Expressed Sequence Tag Analysis of the Erythrocytic Stage of Plasmodium berghei

Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploiting the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clusters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene Ontology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presently-collected ESTs and its bioinformatic analysis will be useful resources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.

EST Knowledge Integrated Systems (EKIS): An Integrated Database of EST Information for Research Application

The EST Knowledge Integrated System, EKIS (http://ekis.kribb.re.kr), was established as a part of Korea's Ministry of Education, Science and Technology initiative for genome sequencing and application research of the biological model organisms (GEAR) project. The goals of the EKIS are to collect EST information from GEAR projects and make an integrated database to provide transcriptomic and metabolomic information for biological scientists. The EKIS constitutes five independent categories and several retrieval systems in each category for incorporating massive EST data from high-throughput sequencing of 65 different species. Through the EKIS database, scientists can freely access information including BLAST functional annotation as well as Genechip and pathway information for KEGG. By integrating complex data into a framework of existing EST knowledge information, the EKIS provides new insights into specialized metabolic pathway information for an applied industrial material.

Identification of citrus expressed sequence tags (ESTs) encoding pleiotropic drug resistance (PDR)-like proteins

Pleiotropic drug resistance (PDR) proteins, a subfamily of the ATP-binding cassette (ABC) transporters, have been recently shown to play a role in plant defense against biotic and abiotic stresses. However, nothing is known about their expression in citrus. To investigate the occurrence of PDR homologues in citrus species, we have surveyed EST sequences from different tissues and conditions of the Citrus Expressed Sequence Tags (CitEST) database, through sequence similarity search analyses and inspections for characteristic PDR domains. Multiple sequence alignments, prediction of transmembrane topology and phylogenetic analysis of PDR-like proteins were additionally performed. This study allowed the identification of nine putative proteins showing characteristic PDR features in citrus species under various conditions, which may indicate a potential correlation between PDRs and stress and metabolism of citrus plants. Moreover, a tissue-specific putative PDR-like protein was found in sweet orange fruits. To our knowledge, this is the first report regarding the identification of citrus ESTs encoding PDR-like proteins as well as the first to identify a putative full ABC transporter with specific expression in fruits.

Clinical relevance of alternative splicing.

The unique phenomenon of alternative splicing is gathering concern due to its promising therapeutic potential. The human genome sequencing project suggests approximately 20,000-25,000 genes. Among these, about 35-60% of genes generate multiple mRNAs by alternative splicing mechanism and contribute to the diversity of the proteomic world. This 'gene shortfall' has ignited considerable interest in alternative RNA splicing. This process leads to expression of a single gene responsible for the transcription of different mRNA isoforms that might have multiple biological functions. The disruption of splicing pattern can produce aberrant splice variants, which are implicated in more than 50% of genetic disorders including cancer. Altered splice sites in neoplastic cell contribute to the development, progression and/or maintenance of tumorous growth. The repertoire of tumor-specific variant represents a potential marker in pharmacogenomic diagnostic relevance. Alternative splice isoforms have been analyzed serendipitously by qualitative gene profiling with in silico gene prediction software. Computational approach in identifying exonic splicing enhancers in genomic DNA and focus on microarray technology will elucidate differential expression of alternative splice variants. The antisense oligonucleotides modulate alternative splicing and engender the production of therapeutic gene products. Oligonucleotides have the potential to silence the mutations caused by aberrant splicing. The efficacy of the antisense oligonucleotides lies in the chemical configuration, affinity and delivery strategies. Hence the therapeutic potential of antisense oligonucleotides as modulators of aberrant alternative splicing would be a major challenge to the upcoming proteomic era.

Analysis of slipped sequences in EST projects

Slippage is an important sequencing problem that can occur in EST projects. However, very few studies have addressed this. We propose three new methods to detect slippage artifacts: arithmetic mean method, geometric mean method, and echo coverage method. Each method is simple and has two different strategies for processing sequences: suffix and subsequence. Using the 291,689 EST sequences produced in the SUCEST project, we performed comparative tests between our proposed methods and the SUCEST method. The subsequence strategy is better than the suffix strategy, because it is not anchored at the end of the sequence, so it is more flexible to find slippage at the beginning of the EST. In a comparison with the SUCEST method, the advantage of our methods is that they do not discard the majority of the sequences marked as slippage, but instead only remove the slipped artifact from the sequence. Based on our tests the echo coverage method with subsequence strategy shows the best compromise between slippage detection and ease of calibration.

Identification of a Novel Gene by EST Clustering and its Expression in Mouse Ovary and Testis / 대한불임학회지

OBJECTIVE: Identification of the regulatory mechanism for arrest and initiation of primordial follicular growth is crucial for female fertility. Previously, we found 15 expressed sequence tags (ESTs) that were specifically abundant in the day-5-subtracted cDNA library and that the B357 clone was novel. The present study was conducted to obtain the whole sequence of the novel gene including B357 and to characterize its mRNA and protein expression in mouse ovary and testis. METHODS: The extended sequence of the 2,965-bp cDNA fragment for the clone B357 was named 5-day-ovary-specific gene-1 (5DOS1) and submitted to GenBank (accession number AY751521). Expression of 5DOS1 was characterized in both female and male gonads at various developmental stages by Northern blotting, real-time RT-PCR, in situ hybridization, Western blotting, and immunohistochemistry. RESULTS: The 5DOS1 transcript was highly expressed in the adult testis, brain, and muscle as compared to the other tissues. In the ovary, the 5DOS1 transcript was detected in all oocytes from primordial to antral follicles, and highly expressed at day 5 after birth and decreased thereafter. In contrast, expression of 5DOS1 showed a gradual increase during testicular development and its expression was limited to various stages of male germ cells except spermatogonia. CONCLUSIONS: This is the first report on the expression and characterization of the 5DOS1 gene in the mouse gonads. Further functional analysis of the 5DOS1 protein will be required to predict its role in gametogenesis.

Paracoccidioides brasiliensis RNA biogenesis apparatus revealed by functional genome analysis

The RNA biogenesis machinery of Paracoccidioides brasiliensis was assessed by comparative analyses of PbAESTs (P. brasiliensis assembled expressed sequence tags (ESTs)) with sequences from Saccharomyces cerevisiae MIPS database. PbAESTs related to almost all categories of S. cerevisiae RNA biogenesis were found. Two of the 12 S. cerevisiae RNA Pol II core subunits, Rpb3 and Rpb7, were found, probably reflecting the growth phase from which the cDNA libraries used in ESTs generation were constructed, as well as the low abundance of some of these transcripts. We have also found orthologs to TATA-box-binding protein (TBP), and at least one subunit of each TBP-associated factors (TFII) in P. brasiliensis transcriptome, except TFIIB. Genes associated to the chromatin remodeling complex, as well as transcription factors probably involved in the control of genes associated to a sexual cycle and virulence, were also identified. With respect to the pre-mRNA processing, 65 PbAEST orthologs to S. cerevisiae basal splicing machinery and 21 orthologs of 5'- and 3'-end formation processes were found. Components involved in RNA interference were detected, suggesting that this gene expression regulation mechanism is probably used by P. brasiliensis. Twelve PbAESTs related to Pol I and Pol III machineries were assigned as S. cerevisiae orthologs. Finally, 25 and 10 PbAESTs associated to rRNA and tRNA processing, respectively, were detected. Taken together, our results enable us to depict, for the first time, a global view of transcription and RNA processing in P. brasiliensis.

Characterization of E. coli-induced Genes in Bombyx mori Fatbody using Expressed Sequence Tags Analysis

To accelerate the molecular analysis of specifically induced antibacterial peptide against pathogen (E. coli), cDNA library prepared from the larvae fatbody of Bombyx mori was examined by the expressed sequence tag (EST) analysis. In a total of 722 clones, 653 clones were unique genes. Of 653 unique genes, 43.2% (282/653 ESTs) was identified as characterized genes, 38.1% (249/653 ESTs) as uncharacterized genes, and 18.7% (122/653 ESTs) as novel ESTs. According to the functional categorization of the characterized genes, 36.2% (102/282 ESTs) was antibacterial proteins. The highest expressed peptides, 78.4% of all the expressed antibacterial proteins (80/102 ESTs), belonged to the cecropin family. The antibacterial effect of selected clones representing novel ESTs based on a phylogenetic analysis was examined against various bacterial strains. None of the clones showed significant inhibitory effect to the bacteria tested. These results suggested that most of the novel molecules induced by E. coli may not act as immune-induced antibacterial peptides in the fatbody.

SCREENING OF THE DIFFERENTIALLY EXPRESSED GENES IN LEFT OPTIC TECTA OF PIGEONS WITH THEIR LEFT-RETINA REMOVED / 解剖学报

Objective To screen the differentially expressed genes in optic tecta of pigeon with monooccular deprivation. Methods Using suppression subtractive hybridization technique,the differentially expressed cDNA library for the left optic tecta of pigeons was constructed;recombinant clones were sequenced randomly and further proved to be the true positive by reverse Northern blot analysis. Results 150 of EST (expressed sequence tags) were sequenced and 16 of them proved true positive,which included those homologous to known genes and those having no matches.138 of ESTs were assigned Accession Number by Genbank.Conclusion\ Our data provided to be the useful clues for studying the development of visual system and the molecular construction of vision center system.

Data mining for simple sequence repeats in expressed sequence tags from Saruma henryi / 中草药

Objective To analyze the simple sequence repeat(SSR)information in expressed sequence tag(EST)resource of Saruma henryi and lay a solid foundation for the development of EST-SSR markers in this species.Methods ESTs of S.henryi were downloaded from GenBank and used to perform the contig assembly using Sequencher 4.8.Uni-ESTs were obtained and screened for SSR-containing unigenes using SciRoKo 3.4.The distributing frequency of the EST-SSRs and the basic characteristics of motifs were analyzed.Results A total of 10 274 ESTs of S.henryi were retrieved and were assembled into 6 643 non-redundant Uni-ESTs with a total length of 5.11?106 bp.In all,the data mining yielded 1 408 SSR loci,which corresponded to 1 232 Uni-ESTs(18.55%).On average,EST-SSRs spanned 22.30 bp,and occurred every 3.63 kb in length.In S.henryi,mononucleotide repeats predominated with an occurrence frequency of 12.24%.Dinucleotide repeats followed with a frequency of 5.01%.The most frequent one was A/T among all the repeat motifs,then followed by AG/CT.Conclusion SSRs in ESTs of S.henryi display a relatively high level of occurrence frequency and show abundance of types.

Expressed Sequence Tags(ESTs) Analysis of Angiostrongylus cantonensis / 中国寄生虫学与寄生虫病杂志

A total of 1 277 ESTs of Angiostrongylus cantonensis were downloaded from GenBank and analyzed with BlastX.SignalP V3.0 analysis was applied to predict potential putative antigen or allergen relative proteins with N-terminal secreted signal peptides or signal anchors.BlastX analysis showed that there were 614 ESTs scored more than 100, of which 14 were identical with A.cantonensis, 60 ESTs did not match any proteins in the databases.The identified 614 ESTs could be grouped into 10 categories, 80 ESTs expressed 22 antigen or allergen relative proteins, in which 12 had N-terminal secreted signal peptides and 3 had signal anchors.