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Yamano K Unuma T 《Comparative biochemistry and physiology. Part A, Molecular & integrative physiology》2006,143(2):155-161
We analyzed the expressed sequence tags (ESTs) obtained from a cDNA library of the eyestalk of the kuruma prawn, Marsupenaeus japonicus, to examine gene expression profile with special focus on female reproduction. The assembly of 1988 ESTs created 136 contigs from 738 ESTs; however 1250 ESTs remained singletons. Significant similarities (blast score > or = 50 bits) to the DNA sequences in the databank were found for only 16.7% of the 1386 sequences (136 contigs plus 1250 singletons), suggesting that the eyestalk library contains many unknown genes. Ribosomal RNA and mitochondrial respiration enzymes with significant similarities were found abundantly in the ESTs, whereas genes related to maturation or endocrine systems were scarce. Three ESTs were assumed to encode novel eyestalk hormones with marked similarities to pigment-dispersing hormone, molt-inhibiting hormone and crustacean hyperglycemic hormone. Sequences encoding a product highly homologous to farnesoic acid O-methyltransferase, an enzyme that produces methyl farnesoate, were also found. 相似文献
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Expressed sequence tags (ESTs) were obtained from the kidney and gill tissues of rainbow trout, Oncorhynchus mykiss, infected with infectious hematopoietic necrosis virus (IHNV). The results of single-pass sequencing of ESTs from 198 clones
(AU081027–AU081192) from kidney complementary DNA and 45 clones (AU081193–AU081236) from gill cDNA are reported herein. Sequences
of the cDNA clones were compared with sequences in the GenBank database. Fourteen clones (20%) appeared to be completely unknown
and may represent newly described genes, whereas 158 clones (80%) were identified on the basis of matches to sequences in
the database. Three of the unidentified sequences were isolated from both the kidney and the gill cDNA libraries. However,
no sequences were identical between kidney and gill clones.
Received December 7, 1999; accepted April 28, 2000. 相似文献
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Daniel L. Hartl 《BioEssays : news and reviews in molecular, cellular and developmental biology》1996,18(12):1021-1023
A recently published study(1) has identified a set of candidate genes for human diseases based on findings from Drosophila. Each human expressed sequence tag (EST) in a large database was compared with all known Drosophila genes. After eliminating matches between genes of already known function, the remaining sequences were mapped in the human genome. In each region, the phenotypes of all known human diseases were compared with the phenotypes of known Drosophila mutations in order to identify candidate genes for the human diseases. Are the correspondences real or coincidental? 相似文献
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Kiew-Lian Wan Saw-Peng Chong Szu-Ting Ng Martin W. Shirley Fiona M.Tomley Mohd. Sanusi Jangi 《International journal for parasitology》1999,29(12):29
A study of about 500 expressed sequence tags (ESTs), derived from a merozoite cDNA library, was initiated as an approach to generate a larger pool of gene information on Eimeria tenella. Of the ESTs, 47.7% had matches with entries in the databases, including ribosomal proteins, metabolic enzymes and proteins with other functions, of which 14.3% represented previously known E. tenella genes. Thus over 50% of the ESTs had no significant database matches. The E. tenella EST dataset contained a range of highly abundant genes comparable with that found in the EST dataset of T. gondii and may thus reflect the importance of such molecules in the biology of the apicomplexan organisms. However, comparison of the two datasets revealed very few homologies between sequences of apical organelle molecules, and provides evidence for sequence divergence between these closely-related parasites. The data presented underpin the potential value of the EST strategy for the discovery of novel genes and may allow for a more rapid increase in the knowledge and understanding of gene expression in the merozoite life cycle stage of Eimeria spp. 相似文献
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T. P. L. Smith S. C. Fahrenkrug G. A. Rohrer F. A. Simmen C. E. Rexroad III & J. W. Keele 《Animal genetics》2001,32(2):66-72
The goal of this study was to identify and map genes expressed during the elongation phase of embryogenesis in swine. Expressed sequence tags were analysed from a previously described porcine cDNA library prepared from elongating swine embryos. Average insert length of randomly selected clones was approximately 600 bp, with a range from < 100 to > 2500 bp. Single-pass, coding strand sequences from 1132 independent clones were compared with the GenBank non-redundant (nr) database via BLASTN analysis to identify potential porcine homologous of known genes. Among these sequences, 781 (69%) showed significant (score > 300) homology to non- mitochondrial sequences previously deposited in GenBank. Sequences matching interleucin 1 beta and thymosin beta 10 were most frequently observed (24 and 18 clones, respectively), in addition to matches with 310 other distinct genes. No significant match in the GenBank nr database was obtained for 303 sequences. Analysis demonstrated that 151 (50%) had open reading frames (ORF) extending at least 50 codons from the first base of the clone insert. Genetic markers were developed and used to map a subset of 17 genes, selected on the basis of function or of the ability to design primers that successfully amplified porcine genomic DNA, to 10 different porcine chromosomes, providing a set of mapped markers corresponding to genes expressed during conceptus elongation. 相似文献
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LIM5 and LIM13 are novel meiosis-associated genes isolated from Lilium longiflorum. The presence of a hydrophobic N-terminal region predicted from the amino acid sequence has suggested that they function
as extracellular structural components. However, both proteins also contain clusters of basic amino acids which may function
as nuclear localization signals. To investigate the cellular localization of the protein, we tagged the C-termini of LIM5
and LIM13 with a green fluorescent protein. Transient expression of fusion proteins in onion epidermal cells revealed nuclear
localization activity of both proteins. Mutational analysis indicated that amino acid sequences that constitute bipartite-type
nuclear localization signals are necessary and sufficient for the intracellular localization of both proteins.
Received: 9 February 1998 / Revision received: 9 March 1999 / Accepted: 22 March 1999 相似文献
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Naxin Huo Yong Q Gu Gerard R Lazo John P Vogel Devin Coleman-Derr Ming-Cheng Luo Roger Thilmony David F Garvin Olin D Anderson 《Génome》2006,49(9):1099-1108
Brachypodium is well suited as a model system for temperate grasses because of its compact genome and a range of biological features. In an effort to develop resources for genome research in this emerging model species, we constructed 2 bacterial artificial chromosome (BAC) libraries from an inbred diploid Brachypodium distachyon line, Bd21, using restriction enzymes HindIII and BamHI. A total of 73,728 clones (36,864 per BAC library) were picked and arrayed in 192,384-well plates. The average insert size for the BamHI and HindIII libraries is estimated to be 100 and 105 kb, respectively, and inserts of chloroplast origin account for 4.4% and 2.4%, respectively. The libraries individually represent 9.4- and 9.9-fold haploid genome equivalents with combined 19.3-fold genome coverage, based on a genome size of 355 Mb reported for the diploid Brachypodium, implying a 99.99% probability that any given specific sequence will be present in each library. Hybridization of the libraries with 8 starch biosynthesis genes was used to empirically evaluate this theoretical genome coverage; the frequency at which these genes were present in the library clones gave an estimated coverage of 11.6- and 19.6-fold genome equivalents. To obtain a first view of the sequence composition of the Brachypodium genome, 2185 BAC end sequences (BES) representing 1.3 Mb of random genomic sequence were compared with the NCBI GenBank database and the GIRI repeat database. Using a cutoff expectation value of E<10-10, only 3.3% of the BESs showed similarity to repetitive sequences in the existing database, whereas 40.0% had matches to the sequences in the EST database, suggesting that a considerable portion of the Brachypodium genome is likely transcribed. When the BESs were compared with individual EST databases, more matches hit wheat than maize, although their EST collections are of a similar size, further supporting the close relationship between Brachypodium and the Triticeae. Moreover, 122 BESs have significant matches to wheat ESTs mapped to individual chromosome bin positions. These BACs represent colinear regions containing the mapped wheat ESTs and would be useful in identifying additional markers for specific wheat chromosome regions. 相似文献
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Expressed sequence tags (ESTs) are partial sequences of cDNAs, and can be used to characterize gene expression in organisms
or tissues. We have constructed a 200-sequence EST database from vegetative thalli of Gracilaria gracilis, the first ESTs
reported from any alga. This database contains recognizable ESTs corresponding to genes of carbohydrate metabolism (seven),
amino acid metabolism (three), photosynthesis (five), nucleic acid synthesis, repair and processing (three), protein synthesis
(14), protein degradation (six), cellular maintenance and stress response (three), other identifiable protein-coding genes
(13) and 146 sequences for which significant matches were not found in existing sequence databases. We have already used this
EST database to recover genes of carbohydrate biosynthesis from G. gracilis.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
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为进一步分析腺瘤相对正常SSH文库(A-N)的差异表达候选基因的表达谱,结合通用的生物信息学软件,自行开发、搭建包括核酸自动分析平台及GetUNi软件包的生物信息学平台,实现了将A-N文库109个差异克隆序列与本地下载的非冗余核酸数据库、人UniGene数据库比对、聚类,至获取差异表达候选基因的自动化分析。对这些基因进行GOTM(GOTree Machine)初步生物信息学分析及RT-PCR验证。结果共发现62个候选基因,包括6个核糖体蛋白成员,6个免疫相关基因。Reg4和FAM46A两个基因出现频次最高,分别为13次和4次,半定量RT-PCR显示这两个基因分别在10/10和9/10例腺瘤相对正常黏膜表达上调。对于这些差异表达候选基因的进一步分析和研究将有助于揭示结肠腺瘤发生的分子机制。 相似文献
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Caggese C Ragone G Perrini B Moschetti R De Pinto V Caizzi R Barsanti P 《Molecular & general genetics : MGG》1999,261(1):64-70
As a first step towards using cross-species comparison to complete the inventory of the nuclear genes that encode mitochondrial
polypeptides, and ultimately to understand their function through systematic molecular and genetic analysis in a model organism
of choice, we report here the characterization of 41 Drosophila melanogaster cDNAs. These cDNAs were isolated by screening an ovarian expression library with antibodies against mitochondrial proteins
and identify 17 novel Drosophila genes. The deduced amino acid sequences encoded by the majority of these cDNAs turned out to show significant homology to
mitochondrial proteins previously identified in other species. Among others, ORFs putatively encoding six different subunits
of ATP synthase and three NADH:ubiquinone reductase subunits were detected. By in situ hybridization, all cDNAs were mapped
to single bands on polytene chromosomes, thus identifying candidate Drosophila genes required for mitochondrial biogenesis and maintenance. A search of the Human Gene Index database made it possible in
most cases to align the entire Drosophila coding sequence with a human consensus sequence, suggesting that the cDNAs originate from insect counterparts of expressed
mammalian genes. Our experimental strategy represents an efficient approach to the identification and interspecies comparison
of genes encoding products targeted to the mitochondrion.
Received: 13 July 1998 / Accepted: 12 October 1998 相似文献