AU-rich transient response transcripts in the human genome: expressed sequence tag clustering and gene discovery approach

Genomics ◽  
2005 ◽  
Vol 85 (2) ◽  
pp. 165-175 ◽  
Author(s):  
Khalid S.A. Khabar ◽  
Tala Bakheet ◽  
Bryan R.G. Williams
Genome ◽  
2008 ◽  
Vol 51 (11) ◽  
pp. 888-896 ◽  
Author(s):  
Rong Li ◽  
Matthew G. Links ◽  
Branimir Gjetvaj ◽  
Andrew Sharpe ◽  
Abdelali Hannoufa

Expressed sequence tag (EST) libraries are a powerful tool for gene discovery in plants with genomes that are not fully sequenced. Adonis aestivalis (Ranunculaceae) is unusual among higher plants in that it accumulates large amounts of the valuable red ketocarotenoid astaxanthin in the flower petals, in addition to other carotenoids, and should therefore be a rich source of transcripts involved in carotenoid biosynthesis. To create a resource for gene discovery and increase our understanding of ketocarotenoid biosynthesis in plants, we sequenced 4189 cloned cDNAs from the floral tissues of A. aestivalis. The EST collection was annotated using sequence homology searches comparing the A. aestivalis ESTs with reference databases. ESTs involved in carotenoid biosynthesis were identified based on sequence homology to published sequences and by functional prediction using InterProScan. This study identified expressed transcripts for most of the known genes involved in the carotenoid pathway. Using an Escherichia coli functional expression system, two candidate transcripts from the A. aestivalis cDNA library were functionally characterized and identified as a novel β-carotene 3-hydroxylase (CrtH2) and a β-carotene monooxygenase. The expanded use of this EST collection combined with the E. coli expression system as presented here will greatly facilitate the cloning and characterization of candidate genes involved in carotenoid biosynthesis in plants.


1997 ◽  
Vol 92 (5) ◽  
pp. 625-629 ◽  
Author(s):  
Élida ML Rabelo ◽  
Glória R Franco ◽  
Vasco AC Azevedo ◽  
Heloisa B Pena ◽  
Túlio M Santos ◽  
...  

2000 ◽  
Vol 68 (6) ◽  
pp. 3491-3501 ◽  
Author(s):  
Michelle Lizotte-Waniewski ◽  
Wilson Tawe ◽  
David B. Guiliano ◽  
Wenhong Lu ◽  
Jing Liu ◽  
...  

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.


AAPS PharmSci ◽  
2003 ◽  
Vol 5 (1) ◽  
pp. 1-18 ◽  
Author(s):  
Shoshana Brown ◽  
Jean l. Chang ◽  
Wolfgang Sadee ◽  
Patricia C. Babbitt

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