Synthetic Gene DataBase
 

Synthetic Gene 64


 
  Welcome, Guest!

Field NameNatural GeneSynthetic Gene
SGDB Gene ID5664
GenBank AccessionL20587AY936879
GenBank GI46305761197041
Gene Namenefnef
Gene Length (bp)642621
Specieshuman immunodeficiency virus (HIV1)Homo sapiens
StrainsType 1EBV-transformed lymphoblastoid cell line (BLCL) B157
CDSatgggaaacgcattgagaaaaggtaaatttgagggatgggcagcagtaagagaaagaatg
agaagaactagaactttccctgagtctgaaccatgcgcacctggagtaggacagatctcc
agggaattagcagctagaggagggataccaagttcccatactcctcaaaacaatgcagcc
cttgcattcctagaaagtcaccaagaggaagaagtaggttttccagtagcacctcaagtg
cctctaaggccaatgacctataaaggagcatttgacctcagcttctttttaaaagaaaag
ggaggactggaagggttaatttactcccataaaagagcagaaatcctggatctttgggtg
tataacactcagggattcttccctgattggcagaactacacaccaggaccaggaaccagg
ttcccactgacatttggatggttgtttaaactagtaccagtgtcagaagaagaggcagaa
agactaggaaatacatgtgagagggctaatctcctgcatccagcatgtgcccatggattt
gaagatacacataaagaaatactgatgtggaagtttgatagatctctaggcaacacccat
gttgctatgataactcacccagagctcttccagaaggactaa
atggccggcaagtggagcaagagaagcgtggtgggctggcctacagtgagggagaggatg
agaagagccgagcctgccgccgacggagtgggcgccgtgtccagagacctggagaagcac
ggcgccatcaccagcagcaacaccgccgccaacaacgccgactgcgcctggctggaggcc
caggaggaggaggaagtgggcttccctgtgagacctcaggtgcccctgagacccatgacc
tacaaggccgccgtggacctgagccacttcctgaaggagaagggcggcctggagggcctg
atctacagccagaagcggcaggacatcctggacctgtgggtgtaccacacccagggctac
ttccctgactggcagaactacacccctggccctggcatcagataccctctgaccttcggc
tggtgcttcaagctggtgcctgtggagcctgagaaggtggaggaggccaacgagggcgag
aacaactctgccgcccaccctatgagcctgcacggcatggacgaccctgagagagaggtg
ctggtgtggaagttcgacagcaggctggccttccaccacatggccagagagctgcacccc
gagtactacaaagatctgtga
5' End
3' End
NotesNo information on the natural nef gene was given so the nef from HIV1 genome (L20587) was given for reference.mutant inactivated for MHC class I downregulation
Expression VectornapEGFP-N1
Assay MethodsnaFluorescence dection
ResultsNot reportedNot reported
Protein Functionprotein binding
Recoding PurposeTo improve expression
Synthesized ByGeneArt
Recoding MethodCodon usage optimized for human
Publication Author(s)van Baalen CA, Kwa D, Verschuren EJ, Reedijk ML, Boon AC, de Mutsert G, Rimmelzwaan GF, Osterhaus AD, Gruters RA.
Corresponding AuthorAlbert D.M.E. Osterhaus
Corresponding AddressDepartment of Virology, Erasmus MC, University Medical Center and Postgraduate School of Molecular Medicine, Rotterdam, The Netherlands.
Publication Year2005
Publication TitleFluorescent antigen-transfected target cell cytotoxic T lymphocyte assay for ex vivo detection of antigen-specific cell-mediated cytotoxicity.
AbstractEx vivo detection of virus-specific cytotoxic T lymphocyte (CTL) responses is limited to the use of methods assessing cytokine production, degranulation, or perforin contents of antigen-specific CD8+ T cells. Generally, their cytotoxic activity is detectable only after cultivation. We describe the fluorescent antigentransfected target cellCTL (FATT-CTL) assay, which measures antigen-specific cytotoxicity ex vivo. Target cells were generated by nucleofection with DNA vectors encoding antigengreen fluorescent protein (GFP) fusion proteins. After coculture at various effector : target (E : T) cell ratios, viable and dead GFP-positive cells were quantified by flow cytometry, and antigen-specific target-cell elimination was calculated. The assay was validated with human immunodeficiency virus (HIV) and influenza virusspecific CTL clones and revealed cytotoxicity at lower E : T cell ratios than standard 51Cr-release assays. Moreover, antigen-specific cytotoxicity was detected ex vivo within 1 day in peripheral blood mononuclear cells from HIV-infected individuals. The FATT-CTL assay provides a versatile tool that will advance our understanding of cell-mediated immunity.
JournalJ Infect Dis.. 192(7): 1183-90.
SummaryFour HIV1 genes were codon optimized for human (by GeneArt) and conjugated with GFP to act as markers in ex vivo dection of virus-specific cytotoxic T lymphocyte (CTL) response. They appeared to work well as expected.
Comments
Discussion http://www.evolvingcode.net/forum/viewtopic.php?t=513
PubMed ID16136460
Submitter NameWu, Gang
Submitter AddressDepartment of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
Entry ConfirmationNo
 
 

Copyright 2004 the Freeland Bioinformatics Lab, All Rights Reserved. | Contact Us | About this site