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Explore the Advanced Center for Genome Technology (ACGT) at OU, focusing on large-scale DNA sequencing, robotic methods, computational genomics, and training the next generation of scientists. The project aims to characterize predicted ORFs and orphan genes through various approaches. Discover how this initiative bridges education and basic research, generating new knowledge and hypotheses in life sciences.
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Advanced Center for Genome Technology ACGT T C A G Fares Z. Najar & Sandra W. Clifton
1000000 900 300000 800bp 100000 800 100000 30000 10000 700 10000 600bp 600bp 600 500bp 1000 500 1000 500 Mbase/run (Log scale) 100 Read length (bp) 100 350bp 30 400 10 250bp 300 200bp 1 1 200 100bp 0.2 75bp 0.1 35bp 26bp 100 0.04 0.01 0 FLX FLX-Ti FLX+ SoliD GS20 ABI370 Helicose ABI3700 ABI3730 Illumina polonator Sequencer platform A Brief History of Long Read Automated DNA Sequencing Instruments at OU Other Next- Generation Platforms 2 0 0 5 - Present 1994-2004
Advanced Center for Genome Technology ACGT • Human Chromosome 22 • Home to the Bioinformatics Core Facility • Large scale DNA sequencing • Partnered with several departments at OU and other educational institutions within the state • Maintain and inplements both 454 massively parallel automated DNA sequencing and capillary sequencers • Robotic methods for DNA isolation and analysis • Computational genomics facility for analysis of both DNA and gene expression
Characterizatino of Predicted ORFs. • Goals • The immediate goal of this project is to train the next generation of scientists at all levels by creating a student-specific tailored and balanced regiment of bioinformatics and wet-lab experiments. • Rationale: • from all sequencing data available that an average of 30-40% of the predicted proteins are hypotheticals that match other hypothetical proteins with about 15-20% orphan proteins that have no matches in the database. • But it also represents a very fertile ground for basic research and a great opportunity as an educational tool for the next generation scientist. • Approach: • To focus the effort, we will be looking at genes that have orthologes in prokaryotes with established genetic systems . • interrogate the genes individually using standard molecular biology techniques such as generating specific deletions and observation of resulting phenotypes and/or change in the transcription pattern • Putative orphan proteins will be cloned, validated, and made available for the scientific community.
Life Sciences Knowledge Sequence data Proteins Non-protein Enzymes Non-enzymatic Unknowns Structural Regulatory Orphans Cell Biology Virology Molecular Biology Anatomy Microbiology Biochemistry Predictions (pathways, regulatory network….etc) Generating Hypothesis Neuroscience Anthropology Physiology Genetics Botany Zoology Testing Hypothesis -- Generating new knowledge
Generating an Indexed Gene library of “predicted” proteins in Bacteria with Established Genetic System Orphan Genes Unknowns/Hypotheticals Predicted functional ORF BLASTP/y COG No Results Developing Testable Hypothesis KEGG GO PSORT PROSPECT • Clonning • Expression • Deletion • Clonning • Expression Protein isolation Protein Crystallization
Preliminary Flowchart for Functional Genomics ORF Bioinformatics pipeline Are there biological predictions? Yes No Is the gene lethal ? • PCR • Clone in E. coli. Yes Generate Hypothesis Store Data Are there orthologesin genetically-established bacterium? No No Yes • Express • Purify • Crystallize Other tests? Generate Deletion mutation
Dynamics of system biology’s family Student / Professor Generating Hypothesis Student / Professor / Postdocs and research scientists Experimental approach Student / Professor(s) / Postdocs and research scientists / Technicians