scholarly journals Dissecting the sugarcane expressed sequence tag (SUCEST) database: unraveling flower-specific genes

2001 ◽  
Vol 24 (1-4) ◽  
pp. 77-84 ◽  
Author(s):  
R.C. Figueiredo ◽  
M.S. Brito ◽  
L.H.M. Figueiredo ◽  
A.C. Quiapin ◽  
P.M. Vitorelli ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Tissue Expression ◽  
Reproductive Organs ◽  
Cdna Libraries ◽  
Computer Assisted ◽  
Transcript Accumulation ◽  
Gene Encoding ◽  
Assisted Analysis ◽  
Expressed Sequence ◽  
Different Tissues

There are almost 260,000 independent clones sequenced from the 5’ end in the Sugarcane Expressed Sequence Tag (SUCEST) database, which have been obtained from 37 cDNA libraries prepared from different tissues. This large number of expressed sequence tags (ESTs) provides an opportunity, unprecedented in plants, to perform ‘digital differential screening’ on selected cDNA libraries. In general, the frequency of a particular EST correlates with transcript accumulation in the tissues from which the cDNA libraries were constructed, so it is possible to compare the whole transcriptome from different tissues using computer-assisted analysis of an EST database. In our research we analyzed sugarcane ESTs according to tissue expression and identified more than 1,000 putative flower-specific genes. The fact that using this technique we were able to identify sugarcane homologues of several genes previously described as pollen-specific justifies this method of assessing tissue specificity. In addition, ESTs similar to genes specific to reproductive organs were detected e.g. a sugarcane gene encoding a meiotic protein essential for assembly of the synaptonemal complex and normal synapsis. This approach also allowed the identification of many flower-specific anonymous sequences that are good candidates for being novel genes involved in plant reproduction. This paper describes the analysis of the gene expression levels of 24 EST clusters during flower development using a ‘digital northern blot’ constructed from direct EST counts made on the non-normalized sugarcane cDNA libraries.

A comprehensive nonredundant expressed sequence tag collection for the developing Rattus norvegicus heart

2004 ◽  
Vol 17 (2) ◽  
pp. 245-252 ◽  
Author(s):  
Jennifer J.S. Laffin ◽  
Todd E. Scheetz ◽  
Maria de Fatima Bonaldo ◽  
Rebecca S. Reiter ◽  
Shereen Chang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expressed Sequence Tag ◽  
Heart Defects ◽  
The United States ◽  
Cdna Libraries ◽  
Tissue Samples ◽  
Rat Hearts ◽  
Subtracted Cdna Libraries ◽  
Gene Expression Studies ◽  
Expressed Sequence

Congenital heart defects affect ∼1,000,000 people in the United States, with 40,000 new births contributing to that number every year. A large percentage of these defects can be attributed to septal defects. We assembled a nonredundant collection of over 12,000 expressed sequence tags (ESTs) from a total of 30,000 ESTs, with the ultimate goal of identifying spatially and/or temporally regulated genes during heart septation. These ESTs were compiled from nonnormalized, normalized, and serially subtracted cDNA libraries derived from two sets of tissue samples. The first includes microdissected rat hearts from embryonic (E) days E13, E15, and E16.5–E18.5 and adult heart. The second includes hearts from embryonic days E17, E19, and E21 and postnatal (P) days P1, P12, P74, and P200. Over 6,000 novel ESTs were identified in the libraries derived from these two sets of tissues, all of which have been contributed to the NCBI rat UniGene collection. It is anticipated that such EST and cDNA clone resources will prove invaluable to gene expression studies aimed at the understanding of the molecular mechanisms underlying heart septation defects.

Analysis of expressed sequence tags from the ectoparasitic nematode Xiphinema index

Nematology ◽  
2005 ◽  
Vol 7 (1) ◽  
pp. 95-104 ◽  
Author(s):  
Cleber Furlanetto ◽  
Linda Cardle ◽  
Derek J.F. Brown ◽  
John T. Jones
Keyword(s):  
Expressed Sequence Tag ◽  
In Situ Hybridisation ◽  
Cdna Libraries ◽  
Small Scale ◽  
Xiphinema Index ◽  
Genes Encoding ◽  
Predicted Signal Peptide ◽  
Basal Bulb ◽  
Expressed Sequence

AbstractWe report the results of a small-scale expressed sequence tag project performed on the ectoparasitic nematode Xiphinema index. Approximately 1400 genes were sequenced, 70% from a cDNA library generated from dissected basal bulbs (containing the pharyngeal gland cells) and 30% from cDNA libraries generated from whole mixed stage nematodes. A large portion of the bulb library (48%) was composed of proteins with no matches in the database. Further analysis of these genes revealed that a total of 51 contigs were present, half of which encoded novel secreted proteins. By contrast, the whole nematode library contained more housekeeping and nematode-specific genes. Only one of the novel genes from the whole nematode library had a predicted signal peptide at the N-terminus. Genes encoding transthyretin-like proteins were abundant in the bulb library and in situ hybridisation confirmed that one of these is expressed in the basal bulb. Genes encoding a variety of proteases, which were shown using in situ hybridisation to be expressed in the gut, were also identified.

scholarly journals Confirming Single Nucleotide Polymorphisms from Expressed Sequence Tag Datasets Derived from Three Cattle cDNA Libraries

BMB Reports ◽  
2006 ◽  
Vol 39 (2) ◽  
pp. 183-188 ◽  
Author(s):  
Seung-Hwan Lee ◽  
Eung-Woo Park ◽  
Yong-Min Cho ◽  
Ji-Woong Lee ◽  
Hyoung-Yong Kim ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tag ◽  
Cdna Libraries ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence

scholarly journals Parasitic helminth genomics

Parasitology ◽  
1999 ◽  
Vol 118 (7) ◽  
pp. 39-51 ◽  
Author(s):  
M. BLAXTER ◽  
M. ASLETT ◽  
D. GUILIANO ◽  
J. DAUB ◽  
THE FILARIAL GENOME PROJECT
Keyword(s):  
Drug Targets ◽  
Expressed Sequence Tag ◽  
Genome Project ◽  
Cdna Libraries ◽  
Quality Of Data ◽  
C Elegans ◽  
Medical Importance ◽  
Expressed Sequence ◽  
Genome Projects

The initiation of genome projects on helminths of medical importance promises to yield new drug targets and vaccine candidates in unprecedented numbers. In order to exploit this emerging data it is essential that the user community is aware of the scope and quality of data available, and that the genome projects provide analyses of the raw data to highlight potential genes of interest. Core bioinformatics support for the parasite genome projects has promoted these approaches. In the Brugia genome project, a combination of expressed sequence tag sequencing from multiple cDNA libraries representing the complete filarial nematode lifecycle, and comparative analysis of the sequence dataset, particularly using the complete genome sequence of the model nematode C. elegans, has proved very effective in gene discovery.

scholarly journals PNG1, a Yeast Gene Encoding a Highly Conserved Peptide:N-Glycanase

2000 ◽  
Vol 149 (5) ◽  
pp. 1039-1052 ◽  
Author(s):  
Tadashi Suzuki ◽  
Hangil Park ◽  
Nancy M. Hollingsworth ◽  
Rolf Sternglanz ◽  
William J. Lennarz
Keyword(s):  
Biological Function ◽  
Expressed Sequence Tag ◽  
Yeast Gene ◽  
Gene Encoding ◽  
Reading Frame ◽  
Cell Extracts ◽  
Lack Of Information ◽  
Defective Mutant ◽  
Expressed Sequence ◽  
Insight Into

It has been proposed that cytoplasmic peptide:N-glycanase (PNGase) may be involved in the proteasome-dependent quality control machinery used to degrade newly synthesized glycoproteins that do not correctly fold in the ER. However, a lack of information about the structure of the enzyme has limited our ability to obtain insight into its precise biological function. A PNGase-defective mutant (png1-1) was identified by screening a collection of mutagenized strains for the absence of PNGase activity in cell extracts. The PNG1 gene was mapped to the left arm of chromosome XVI by genetic approaches and its open reading frame was identified. PNG1 encodes a soluble protein that, when expressed in Escherichia coli, exhibited PNGase activity. PNG1 may be required for efficient proteasome-mediated degradation of a misfolded glycoprotein. Subcellular localization studies indicate that Png1p is present in the nucleus as well as the cytosol. Sequencing of expressed sequence tag clones revealed that Png1p is highly conserved in a wide variety of eukaryotes including mammals, suggesting that the enzyme has an important function.

scholarly journals Identification and characterization of GSTT3, a third murine Theta class glutathione transferase

2002 ◽  
Vol 366 (1) ◽  
pp. 323-332 ◽  
Author(s):  
Marjorie COGGAN ◽  
Jack U. FLANAGAN ◽  
Michael W. PARKER ◽  
Vanicha VICHAI ◽  
William R. PEARSON ◽  
...  
Keyword(s):  
Glutathione Transferase ◽  
Expressed Sequence Tag ◽  
Molecular Model ◽  
Binding Pocket ◽  
Gene Encoding ◽  
Hydrophobic Substrate ◽  
Intron Structure ◽  
Identification And Characterization ◽  
Expressed Sequence

A novel Theta class glutathione transferase (GST) isoenzyme from mouse termed mGSTT3 has been identified by analysis of the expressed sequence tag database. The gene encoding mGSTT3 is clustered with the mGSTT1 and mGSTT2 genes on chromosome 10 and has an exon/intron structure that is similar to that of the other Theta class genes. mGSTT3 is expressed strongly in the liver and to a decreasing extent in the kidney and testis. Recombinant mGSTT3-3 expressed in Escherichia coli had a substrate-specificity profile that differed significantly from that of GSTT1-1 and GSTT2-2 isoenzymes. A molecular model of mGSTT3 suggested that, in comparison with GSTT2, a decrease in volume of the hydrophobic substrate-binding site and the loss of the sulphate-binding pocket prevents its use of the GSTT2 substrate 1-menaphthyl sulphate.

Potato Expressed Sequence Tag Generation and Analysis using Standard and Unique cDNA Libraries

2005 ◽  
Vol 59 (3) ◽  
pp. 407-433 ◽  
Author(s):  
Barry Flinn ◽  
Charlotte Rothwell ◽  
Rebecca Griffiths ◽  
Martin Lägue ◽  
David DeKoeyer ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Cdna Libraries ◽  
Expressed Sequence

scholarly journals In silico characterization and expression analyses of sugarcane putative sucrose non-fermenting-1 (SNF1) related kinases

2001 ◽  
Vol 24 (1-4) ◽  
pp. 35-41 ◽  
Author(s):  
Dirce Maria Carraro ◽  
Marcio R. Lambais ◽  
Helaine Carrer
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Protein Kinases ◽  
Catalytic Domain ◽  
Expressed Sequence Tag ◽  
Higher Plants ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Cdna Libraries ◽  
Expressed Sequence

Sucrose non-fermenting-1-related protein kinases (SnRKs) may play a major role in regulating gene expression in plant cells. This family of regulatory proteins is represented by sucrose non-fermenting-1 (SNF1) protein kinase in Saccharomyces cerevisiae, AMP-activated protein kinases (AMPKs) in mammals and SnRKs in higher plants. The SnRK family has been reorganized into three subfamilies according to the evolutionary relationships of their amino acid sequences. Members of the SnRK subfamily have been identified in several plants. There is evidence that they are involved in the nutritional and/or environmental stress response, although their roles are not yet well understood. We have identified at least 22 sugarcane expressed sequence tag (EST) contigs encoding putative SnRKs. The amino acid sequence alignment of both putative sugarcane SnRKs and known SnRKs revealed a highly conserved N-terminal catalytic domain. Our results indicated that sugarcane has at least one member of each SnRK subfamily. Expression pattern analysis of sugarcane EST-contigs encoding putative SnRKs in 26 selected cDNA libraries from the sugarcane expressed sequence tag SUCEST database has indicated that members of this family are expressed throughout the plant. Members of the same subfamily showed no specific expression patterns, suggesting that their functions are not related to their phylogenic relationships based on N-terminal amino acid sequence phylogenetic relationships.

scholarly journals Identification of Potential Vaccine and Drug Target Candidates by Expressed Sequence Tag Analysis and Immunoscreening of Onchocerca volvulus Larval cDNA Libraries

2000 ◽  
Vol 68 (6) ◽  
pp. 3491-3501 ◽  
Author(s):  
Michelle Lizotte-Waniewski ◽  
Wilson Tawe ◽  
David B. Guiliano ◽  
Wenhong Lu ◽  
Jing Liu ◽  
...  
Keyword(s):  
Drug Targets ◽  
Expressed Sequence Tag ◽  
Proteinase Inhibitors ◽  
Gene Discovery ◽  
Onchocerca Volvulus ◽  
Detoxification Enzymes ◽  
Cdna Libraries ◽  
Cdna Clones ◽  
Expressed Sequence Tag Analysis ◽  
Expressed Sequence

ABSTRACT The search for appropriate vaccine candidates and drug targets against onchocerciasis has so far been confronted with several limitations due to the unavailability of biological material, appropriate molecular resources, and knowledge of the parasite biology. To identify targets for vaccine or chemotherapy development we have undertaken two approaches. First, cDNA expression libraries were constructed from life cycle stages that are critical for establishment of Onchocerca volvulus infection, the third-stage larvae (L3) and the molting L3. A gene discovery effort was then initiated by random expressed sequence tag analysis of 5,506 cDNA clones. Cluster analyses showed that many of the transcripts were up-regulated and/or stage specific in either one or both of the cDNA libraries when compared to the microfilariae, L2, and both adult stages of the parasite. Homology searches against the GenBank database facilitated the identification of several genes of interest, such as proteinases, proteinase inhibitors, antioxidant or detoxification enzymes, and neurotransmitter receptors, as well as structural and housekeeping genes. Other O. volvulus genes showed homology only to predicted genes from the free-living nematode Caenorhabditis elegans or were entirely novel. Some of the novel proteins contain potential secretory leaders. Secondly, by immunoscreening the molting L3 cDNA library with a pool of human sera from putatively immune individuals, we identified six novel immunogenic proteins that otherwise would not have been identified as potential vaccinogens using the gene discovery effort. This study lays a solid foundation for a better understanding of the biology of O. volvulus as well as for the identification of novel targets for filaricidal agents and/or vaccines against onchocerciasis based on immunological and rational hypothesis-driven research.

Sign in / Sign up

Export Citation Format

Share Document