real time pcr
DESCRIPTION
FAM. TAMRA. Real Time PCR. Production at FIOCRUZ in GMP condition of Enzymes, Primers and Probes, Mater mix in ready to use format. Calibration System. FAM. Detection Sequence 5’ AGTATTCATCCACAATTTT A AAAGAAAAGGGGGGAT TGGGGGGT ACAGTGCAGGGGAAAGAAT 3’ Calibration Sequence - PowerPoint PPT PresentationTRANSCRIPT
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Real Time PCR
FAM TAMRA
Production at FIOCRUZ in GMP condition of Enzymes, Primers and Probes, Mater mix in ready to use format.
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Detection SequenceDetection Sequence5’ 5’ AGTATTCATCCACAATTTTAGTATTCATCCACAATTTTAAAAAGAAAAGGGGGGATAAAGAAAAGGGGGGATTGGGGGGTTGGGGGGTACAGTGCAGGGGAAAGAATACAGTGCAGGGGAAAGAAT 3’ 3’
Calibration Sequence Calibration Sequence 5’ 5’ AGTATTCATCCACAATTTTAGTATTCATCCACAATTTTAAAAAGAAAGGGGGAAAAGGGGAAAAGGATGGATTGGGGGGTTGGGGGGTACAGTGCAGGGGAAAGAAT ACAGTGCAGGGGAAAGAAT 3’3’
FAM
VIC
Calibration SystemCalibration System
HIV
VCAHCV
FAM
FAM
VIC
PET ou TAMRA
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ResultsResults
Calibrator Standart curve
FIOCRUZ - PATENTFIOCRUZ - PATENT
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FIOCRUZ NAT Platform FIOCRUZ NAT Platform Bio-Manguinhos/IBMPBio-Manguinhos/IBMP
•Extraction •PCR Setup •Detection
•HTP
•LTP
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Liquid Microarrays for Diagnosis
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Liquid Microarrays
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Liquid Microarrays
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Green laserReporterFluorescence
Red laserBeadFluorescence
Liquid Microarrays
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Pilot project multi-test
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Different Trypanosoma cruzi antigen preparations
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Trypanosoma cruzi ORFeome
• 23,083 “genes” (GenBank, Jul 2009)
• Highly redundant, estimated to be ~12,000 distinct gene loci
• Few gene families account for a large proportion of genes (6 families, 4967
“genes”, 21% of gene content)
• The repetitive nature of the genome makes assembly difficult. As a
consequence, the ORF definition is worse than for other organisms.
• Related organisms, as Leishmania sp. and T. brucei, have about 8,000 genes,
which is a good estimation for the lower limit of T. cruzi genes.
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Trypanosoma cruzi ORFeome Institute Carlos Chagas/FIOCRUZ
Organism Genome (ORFs)
Suitable Vector(Gateway)
ORFeome(all ORFs in a suitable vector)
ORFeome (Wikipedia)Orfeome is the totality of open reading frames(ORF) from one organism. ORFs are the most important genetic elements in genomes as they code for proteins
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1st step. PCR amplification2 PCRs per gene, US$3/gene
2nd step. PCR purificationMagnetic, US$1/gene
4th step. Bacterial transformation,Colony picking and Culture
Agar plates, 4 clones/gene, US$0.25/gene
3rd step. Gateway entryBP reaction, US$5/gene
Pre-processing
• Intense bioinformatics analysis, using all ORFs from Kinetoplastida genome projects, to better define the region to be amplified.
• Primers are 30mer in average, i.e., US$6/gene
5th step. Plasmid purificationMagnetic, US$1/gene
6th step. Plasmid verificationPCR, US$ 0,1/gene
Trypanosoma cruzi ORFeome Institute Carlos Chagas/FIOCRUZ
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Trypanosoma cruzi ORFeome ICC/FIOCRUZ
• 3,840 primer pairs designed and ordered.
• 1,920 genes amplified (~85% of them were positive).
• ~7,500 clones collected and certified by PCR.
Current state (v. 0.2)
40%
20%
20%
Completeness
• 7,680 primer pairs designed and ordered.
• Amplification of all analyzed genes.
• All clones (~30,000) collected and certified by PCR.
• All clones sequenced and certified ORFeome produced.
Future prospects (6 months, v. 1.0)
• Information from other T. cruzi strain will be added and used for covering more
ORFs that were excluded or not present in CL Brener.
Future prospects (12-18 months, v. 2.0)
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Trypanosoma cruzi ORFeome
Organism Genome (ORFs)
Suitable Vector(Gateway)
ORFeome(all ORFs in a suitable vector)
InteractomeLocalizome
HT protein expression Ag-Ab screening
Downstream Applications(among many others)
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Antonio G.P.Ferreira Bio-Manguinhos-FiocruzBruna P.F.Fonseca, Bio-Manguinhos-FiocruzEdimilson D.Silva, Bio-Manguinhos-FiocruzChristiane F.S.Marques Bio-Manguinhos –FiocruzAlexandre Costa IBMPViviane Goes IBMPCristiane Reinarch IBMP Cesar A.B. Duarte, ICC-FiocruzLeonardo Foti ICC-FiocruzChristian M.Probst ICC-FiocruzDaniela Parada Pavoni ICC-FiocruzSamuel Goldenberg, ICC-Fiocruz/IBMP
Marco Aurelio KriegerICC-Fiocruz/IBMP [email protected]