slide1
Download
Skip this Video
Download Presentation
Advanced Center for Genome Technology ACGT

Loading in 2 Seconds...

play fullscreen
1 / 14

Advanced Center for Genome Technology ACGT - PowerPoint PPT Presentation


  • 97 Views
  • Uploaded on

The UNIVERSITY of OKLAHOMA. Advanced Center for Genome Technology ACGT. T. C. A. G. Fares Z. Najar, Sandra W. Clifton, Tyrell Conway, and Bruce A. Roe. The UNIVERSITY of OKLAHOMA. Advanced Center for Genome Technology ACGT. Orphans & Orthologes. Project Goals.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Advanced Center for Genome Technology ACGT' - mercer


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
slide1

TheUNIVERSITY ofOKLAHOMA

Advanced Center for Genome Technology

ACGT

T

C

A

G

Fares Z. Najar, Sandra W. Clifton, Tyrell Conway, and Bruce A. Roe

slide2

TheUNIVERSITY ofOKLAHOMA

Advanced Center for Genome Technology

ACGT

Orphans & Orthologes

slide3

Project Goals

  • To define stucture and function of Predicted Hypothetical ORFs (orhtologoes and orphans) in genetically established microbial models.
  • To generate a database of indexed clones of Predicted Hypothetical ORFs (available for the scientific community).
  • Train all-level students (high school, undergraduate, and graduate) on bioinformatics and molecular tools.
slide4

ACGT profile

  • Part of the Human Chromosome 22 project.
  • Home to the Bioinformatics Core Facility (BCF) that houses the E. coli Community’s Gene Expression Database (GenExpDB).
  • Computational genomics facility for analysis of both DNA and gene expression.
  • Large scale DNA sequencing using both 454 massively parallel automated DNA sequencing and capillary sequencers (ABI 3730).
  • Robotic methods for DNA isolation and analysis.
  • Partnered with several departments at OU and other educational institutions within the state.
slide5

Eukaryotic Projects

Bacterial Genomes

Meta-’omics

Human

Chimp

Streptococcus oligofermentas

Mouse

Staph. aureus

Costarican Forest

Tall grass Priare

N. gonorrhoeae

Rat

A. actinomycetemcomitans

Desulfogleba alkanexidens

Oil

Strep. Pyogenes

Mouse Gut

Medicago

Tylorella equigenitalis.

Cow Rumen

Cotton

Soil

Xanthomonas vasicola

Soy

Vellionella atypica

Tomato

Manduca

Leptospira interrogans pomona

Leptospira interrogans Grippo

Screw worm

Spiroplasma kunkelii

Tick

ACGT profile

slide7

Characterization of the “PREDICTOMES”

  • Rationale:
  • About 30-40% of predicted proteins are “Hypotheticals Orthologes”.
  • About 5-20% orphan proteins that have no matches in the database (Hypothetical Orphans).
  • These putative ORFs represent a fertile ground for basic research and a great opportunity as an educational tool for the next generation scientist.
  • Goals:
  • Functional charcerization of the predictome.
  • Creating a clone library of predicted ORFs.
  • Train the next generation of scientists at all levels by creating student-specific tailored and balanced regimen of bioinformatics and wet-lab experiments.
  • Approach:
  • Define Criteria:
    • Hypothetical Orthologes in established genetic systems (e-value<=10-5.)
    • Hypothetical Orphans in established genetic systems.
  • Clone in E. coli.
  • Expression & Purification.
  • Generate mutant strains.
  • Crystallization.

23%

67%

4%

73%

100%

25%

8%

90%

80%

  • Meta-transcriptom

Hypothetical Orphans

Hypothetical Orthologes

70%

Functional prediction

60%

50%

40%

30%

20%

10%

0%

microbial Genomes

slide8

Life Sciences Knowledge

Sequence data

Coding

Non-coding

Enzymes

Non-enzymatic

Hypothetical

Orthologes

Structural

Regulatory

Hypothetical

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

slide9

Generating an Indexed Gene library of “predicted” proteins in Bacteria with Established Genetic System

Hypothetical Orphans

Hypothetical Orthologoes

Functional Hypotheticals

BLAST

COG

KEGG

GO

PSORT

PROSPECT

Cloning

Expression

Hypotheses

Purification

Mutations

Metabolomic

Crystal-lization

slide10

Preliminary Flowchart for Functional Genomics

ORF

Bioinformatics pipeline

Are there biological predictions?

Yes

No

Is the gene lethal ?

  • PCR
  • Clone in E. coli.

Yes

Store Data

  • Hypotheses
  • PCR
  • Clone in E. coli.

No

  • Express
  • Purify
  • Crystallize
  • Deletion mutations
slide11

Dynamics of Systems Biology’s Family

Professor

Student

Postdocs

Research scientists

Technicians

slide12

Dynamics of Systems Biology’s Family

Research scientists

Professor

Professor

Technicians

Student

Postdocs

Postdocs

Research scientists

Technicians

slide14

A map of Science:

How Scientific paradigms relate

  • Bioinformatics
  • Molecular Biology
  • Biochemistry
  • Microbiology

Nature (Dec. 2006, 444: 985)

ad