Team:SUSTC-Shenzhen-B/introduction

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<p>the secondary structure of terminator</p>
<p>the secondary structure of terminator</p>
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<p>Measurment</p>
<p>Measurment</p>

Revision as of 03:50, 23 September 2012

SUSTC iGEM Theme - Free CSS Template

SUSTC iGEM Theme - Free CSS Template

Introduction

Transcription:

The transcription stage, the reading of genetic information from DNA, is composed of promoter binding and the activation of RNA polymerase, RNA transcript initiation and promoter escape, RNA transcript elongation, and transcript termination, and release.


What is terminator?

Terminators are genetic parts that usually occur at the end of a gene or operon and cause transcription to stop. In prokaryotes, terminators usually fall into two categories (1) rho-independent terminators and (2) rho-dependent terminators.

Rho-independent terminators are generally composed of palindromic sequence that forms a stem loop rich in G-C base pairs followed by several T bases. The conventional model of transcriptional termination is that the stem loop causes RNA polymerase to pause and transcription of the poly-A tail causes the RNA:DNA duplex to unwind and dissociate from RNA polymerase.


Terminator Efficiency:

Although terminators are positioned at the ends of genes, they also play irreplaceable roles. It is important that transcription is imperfectly terminated at some terminator so that the ratio of the amount of the mRNA transcribed from upstream and that from downstream of the terminator is controlled. This regulation is qualified by the termination efficiency.


Brief idea to calculate efficiency:

The fluorescence produced by the characterization devices are then measured using flow cytometry to calculate the termination efficiency of the terminators.

E=S/(S+F)

E: Terminator efficiency

S: The number of cells that have been terminated successfully

F: Number of cells that haven’t been terminated successfully.

Tools

Because we are a software producer, we need to use different tools to write our software. First, our algorithm were written using c# in vs2010, in order to get the aim that the software can run in the back of the user interface. Second, the software user interface was wrote in vs2010 using WPF directly which we thought is the easiest and most beautiful technology for windows software. The first and second version of the website was made by three software: Photoshop, which was used for getting great picture, Dreamwaver, which was used for making the structure of the interface, and vs2010, which was used for connecting the UI with our algorithm. When everything was done, we applied our own realm name and server to achieve the dream of building the website. Although the processes of debugging and building the server were very hard, we make our software successfully.

Brief Flow Chart

Online Tool

The process of transcription


the secondary structure of terminator








Measurment


This is the address of our “transcriptional terminator efficiency calculator” website.


acknowledgements

This is the first time that we join this competition, we got many help from some companies and other teams. thanks for their help and supports!