slide1 n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Aims PowerPoint Presentation
Download Presentation
Aims

Loading in 2 Seconds...

play fullscreen
1 / 46

Aims - PowerPoint PPT Presentation


  • 95 Views
  • Uploaded on

Aims. How to implement elementary computations? How to form a more complex one?. Concrete Example. Gates: NAND, NOR, NOT gates, 2 levels Wires: 3 wires, which can cross and branch off I/O: 2 inputs and 2 outputs. Concrete Example. Gates: NAND, NOR, NOT gates, 2 levels

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 'Aims' - iolana


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
slide2
Aims
  • How to implement elementary computations?
  • How to form a more complex one?
concrete example
Concrete Example
  • Gates: NAND, NOR, NOT gates, 2 levels
  • Wires: 3 wires, which can cross and branch off
  • I/O: 2 inputs and 2 outputs
concrete example1
Concrete Example
  • Gates: NAND, NOR, NOT gates, 2 levels
  • Wires: 3 wires, which can cross and branch off
  • I/O: 2 inputs and 2 outputs
objectives
Objectives
  • Transcriptional Regulation can be utilized to implement NAND, NOR, NOT gates in E.coli.
  • Transcriptional Factors can transmit message from one component to another.
repression model
Repression Model

Bintu, L. et al. Transcriptional regulation by the numbers: models. Curr

Opin Genet Dev (2005)

repression model1
Repression Model

Bintu, L. et al. Transcriptional regulation by the numbers: models. Curr

Opin Genet Dev (2005)

constructions and measurements
Constructions and Measurements

PCR Construction

Solo-Repression Assay

Co-Repression Assay

77 Promoter Synthesized

~ 400 Quantitative Assays

dna looping
DNA-Looping

[1] Müller, J., et al. Repression of lac promoter as a function of distance,

phase and quality of an auxiliary lac operator. J. Mol. Bio. (1996)

[2] Saiz, L. and Vilar, J. M. G. DNA looping: the consequences and its

control., Curr Opin Struct Biol (2006)

directed evolution
Directed Evolution
  • Select Target Sites
  • Mutagenesis by PCR
  • Screen on Plates
  • Quality Control
  • Quantitative Measurements
  • Result Analysis
directed evolution1
Directed Evolution
  • Select Target Sites
  • Mutagenesis by PCR
  • Screen on Plates
  • Quality Control
  • Quantitative Measurements
  • Result Analysis
directed evolution2
Directed Evolution
  • Select Target Sites
  • Mutagenesis by PCR
  • Screen on Plates
  • Quality Control
  • Quantitative Measurements
  • Result Analysis

5000 colonies screened

3 artificial operators

400 candidates per operator

11 novel artificial repressors

directed evolution3
Directed Evolution
  • Select Target Sites
  • Mutagenesis by PCR
  • Screen on Plates
  • Quality Control
  • Quantitative Measurements
  • Result Analysis
directed evolution4
Directed Evolution
  • Select Target Sites
  • Mutagenesis by PCR
  • Screen on Plates
  • Quality Control
  • Quantitative Measurements
  • Result Analysis
directed evolution5
Directed Evolution
  • Select Target Sites
  • Mutagenesis by PCR
  • Screen on Plates
  • Quality Control
  • Quantitative Measurements
  • Result Analysis

Repression Matrix

Diagonal Repression Matrix

repressor evolution in silico
Repressor Evolution in Silico

Side chain conformation optimization

Sequence evaluation

Test the results in vivo

Selection of target ligand

and variable positions

repressor evolution in silico1
Repressor Evolution in Silico

Side chain conformation optimization

Selection of target ligand

and variable positions

Sequence evaluation

Test the results in vivo

diagonal repression matrix
Diagonal Repression Matrix

9 Repressors vs. 4 Operators

6 repressors bind to only 1 operator

3 repressors bind to 2 operators

3x3 array for the demo system

slide39

What we have done:

Patterns for NAND, NOR, NOT gates

Highly-specific artificial repressors

A demonstration system

123 Parts Submitted

247 Part Sequences

77 Synthesized Promoters

11 Novel Artificial Repressors

~ 350 New Strains

~ 130 DNA Strands Sequenced

> 5000 Colonies Screened

~ 400 Quantitative Assays

Extensible Logic Circuit in Bacteria

USTC iGEM 2007

cis acting logic gates
Cis-acting Logic Gates

Promoters with Cis-acting Elements

  • Work in vivo
  • Can be systematically constructed
  • Small in scale
    • About 2.0nm in width
    • 20 - 70nm in length
  • Can be cascaded to implement complex combinational logic computation
wires without interference
Wires without Interference

Highly-Specific Artificial Repressor

  • The number can grow
  • Do not interrupt natural signaling network
  • Do not interrupt each other
  • Provide supports for cis-acting logic gates
    • DNA Recognition
    • Dimerization
    • Tetramerization
what we plan to do
What We Plan To Do
  • Further Optimization
    • Size of the Wires
    • Response Time
    • More Input Signals
    • Better NOR pattern
  • Conductance Adjusting
    • Using different RBS
    • Using different operators
further more
Further More

The First Transistor

1947

The First Integrated Circuit

1958

ustc igem 2007
USTC iGEM 2007
  • Graduates
    • Zhan Jian
    • Ding Bo
    • Ma Rui
    • Ma Xiaoyu
  • Undergrads
    • Liu Ziqing
    • Su Xiaofeng
    • Zhao Yun
  • Advisors
    • Prof. HY Liu
    • Prof. JR Wu
    • Prof. ZH Hou
acknowledgments
Acknowledgments

We are sponsored by:

Univ. of Sci. and Tech. of China

NNSFC

HHTech Co. Ltd.