Team:Alberta/project

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Latest revision as of 03:57, 28 October 2010

TEAM ALBERTA

Project Overview

GENOMIKON: an Educational Toolkit for Rapid Genetic Construction

Synthetic biology and gene manipulation have potential applications in many fields. Unfortunately, courses in this field are only taught to university students who have already chosen to specialize in genetics. Recognizing that many of the basic principles and methods are easily explained, the University of Alberta sought to make synthetic biology more accessible by creating GENOMIKON, a gene manipulation and synthetic biology kit designed to work in a high school environment. To construct the kit, we first created the BioBytes 2.0 assembly method so that the DNA in the kit could be ligated into plasmids quickly and efficiently. We then designed experiments for the kit with the aim of making them quick, reliable, and easy to perform even with minimal lab equipment. To make GENOMIKON useful as a classroom resource, an interactive lab manual was created to guide students through their experiments. We also developed a distribution plan for getting the kit into high schools across Canada. GENOMIKON's aim is to be a fun way of giving students an introduction to genetics and molecular biology, even before they enter post-secondary education. From our experience over the past six months, we believe it will be a success.

BioBytes Theory

The DNA components of the GENOMIKON kit will be provided in linear pieces called BioBytes. These Bytes have 5' overhangs, four bases long on both ends, which gives specificity to the Bytes that can neighbor them. BioBytes come in two formats: 'AB Bytes' and 'BA Bytes'. AB Bytes can only be ligated to BA Bytes and vice versa. This leads to a construct alternating in AB and BA Bytes. The bytes are bound to an anchor which specifies the order of alternation between AB and BA bytes.

The GENOMIKON Kit

The GENOMIKON kit was designed for use in a high school environment, however most high schools lack the lab equipment traditionally used to perform genetic experiments. Fortunately, the BioBytes 2.0 assembly method does not require centrifuges, thermocyclers or extreme accuracy with regards to volume and temperature. The only equipment a high school must supply is a hot plate and a beaker. Creating a sterile environment in a high school lab was another challenge that had to be addressed. The reagents in the kit are sent in individual sterilized packages along with everything that a high school would need to perform the transformations using synthetic parts.

GENOMIKON ONLINE

GENOMIKON.ca was created as a lab manual to accompany the GENOMIKON kit. It was designed to act as a teaching resource to give students background information for the experiments they design and to introduce them to the kit and its uses. Features include BioByte descriptions, an interactive plasmid construction tool where students can engineer their own plasmids by dragging and dropping different parts into sequence, a glossary and encyclopedia. Lastly, the teacher can coordinate the class experiments by working through the groups feature.

@@ Line 7: / Line 7: @@
 {{Team:Alberta/beginRightSideBar}}
-== WWW.GENOMIKON.CA ==
+[[Image:Alberta Plate highschool.jpg|center|frame|Bryce Stewart, a grade 10 student shows off colonies transformed with a plasmid constructed using the GENOMIKON kit.]]
-This is the online lab manual and educational resource for the Genomikon Kit
 {{Team:Alberta/endRightSideBar}}
@@ Line 14: / Line 13: @@
 ==Project Overview==
+<div id="horiz-line"></div>
+''GENOMIKON: an Educational Toolkit for Rapid Genetic Construction''
-''Genomikon: an Educational Toolkit for the Rapid Assembly of Plasmids''
+Synthetic biology and gene manipulation have potential applications in many fields. Unfortunately, courses in this field are only taught to university students who have already chosen to specialize in genetics. Recognizing that many of the basic principles and methods are easily explained, the University of Alberta sought to make synthetic biology more accessible by creating GENOMIKON, a gene manipulation and synthetic biology kit designed to work in a high school environment.  To construct the kit, we first created the BioBytes 2.0 assembly method so that the DNA in the kit could be ligated into plasmids quickly and efficiently. We then designed experiments for the kit with the aim of making them quick, reliable, and easy to perform even with minimal lab equipment.  To make GENOMIKON useful as a classroom resource, an interactive lab manual was created to guide students through their experiments. We also developed a distribution plan for getting the kit into high schools across Canada.  GENOMIKON's aim is to be a fun way of giving students an introduction to genetics and molecular biology, even before they enter post-secondary education.  From our experience over the past six months, we believe it will be a success.
-Genetic manipulation using synthetic biology is a technology with unlimited potential. Unfortunately its teaching is currently confined to universities where students have chosen to specialize in science. Recognizing that many of the basic principles and methods are easily explained the University of Alberta sought to expand the accessibility of synthetic biology by creating a teaching package capable of working within a high school environment. This kit exposes young minds to genetic technology before they enter university.  To construct the kit known as GENOMIKON we first made it functional by optimizing the biobyte assembly method created by the University of Alberta 2009 team. The experiments of the kit were then designed to be able to be done quickly reliably and with very limited equipment.  To make GENOMIKON useful as a classroom resource an interactive lab manual was created to guide students though their experiments. Lastly we looked at how best to bring this kit to the market and into student’s hands.  GENOMIKON is a major advancement for synthetic biology because it shows the next generation of students how biology can work as an engineering discipline even before they enter university.
+==[[Team:Alberta/biobyte2 |BioBytes Theory]]==
-==BioByte Theory==
+The DNA components of the GENOMIKON kit will be provided in linear pieces called BioBytes.  These Bytes have 5' overhangs, four bases long on both ends, which gives specificity to the Bytes that can neighbor them. BioBytes come in two formats: 'AB Bytes' and 'BA Bytes'. AB Bytes can only be ligated to BA Bytes and vice versa. This leads to a construct alternating in AB and BA Bytes. The bytes are bound to an anchor which specifies the order of alternation between AB and BA bytes.
-The DNA components of the Genomikon kit will be provided in linear pieces named BioBytes.  These Bytes have 4 base 5' overhangs on both ends which gives specificity to the bytes that can neighbor it. BioBytes come in two flavors: A bytes and B bytes, which are defined by the composition of the overhangs it has. The result is that A bytes can only be ligated to B bytes and vise versa leading to a construct alternating in A and B bytes.  The specificity in absolute order of a construct is given by an anchor which restricts ligation to only one side.
-[[Image:Team-Alberta-Alberta2010kaTheoryimage.jpg]]
-==The Genomikon Kit==
+==[[Team:Alberta/Kit |The GENOMIKON Kit]]==
-The GENOMIKON kit was designed for a high school environment. The major challenge then facing the GENOMIKON kit was that high schools lack lab most equipment traditionally needed for molecular biology experiments. Further creating a sterile environment to avoid contamination was another challenge that had to be overcome. Fortunately the biobyte assembly method does not require centrifuges, thermocyclers or extreme accuracy with regards to volume and temperature. The only equipment a high school must supply then is a hot plate thermometer and a beaker.  The issue of sterility is addressed by sending all the parts necessary to be sterile in sterilized packages. The kit sends everything that a high school would need to perform the transformations using synthetic parts.
+The GENOMIKON kit was designed for use in a high school environment, however most high schools lack the lab equipment traditionally used to perform genetic experiments.  Fortunately, the BioBytes 2.0 assembly method does not require centrifuges, thermocyclers or extreme accuracy with regards to volume and temperature. The only equipment a high school must supply is a hot plate and a beaker.  Creating a sterile environment in a high school lab was another challenge that had to be addressed.  The reagents in the kit are sent in individual sterilized packages along with everything that a high school would need to perform the transformations using synthetic parts.
-==Genomikon Online==
+==[[Team:Alberta/Software |GENOMIKON ONLINE]]==
-For the GENOMIKON kit to be functional students and teachers need access to a lab manual that can accommodate the many different experiments possible.  The GENOMIKON lab manual was designed to act as a teaching resource giving students background information for the experiments they design.  GENOMIKON ONLINE was created as the lab manual complementary to the GENOMIKON kit. GENOMIKON ONLINE is found at the website www.genomikon.com. Features include: descriptions of the different parts used to construct a plasmid, a toolkit where student’s can engineer their own creative expressions by dragging and dropping different parts into sequence automatically generating a protocol to follow. Students can also do predetermined experiments outlined and collect background information reading articles. Lastly the teacher can coordinate the class experiments by working through the groups feature.
+GENOMIKON.ca was created as a lab manual to accompany the GENOMIKON kit.  It was designed to act as a teaching resource to give students background information for the experiments they design and to introduce them to the kit and its uses. Features include BioByte descriptions, an interactive plasmid construction tool where students can engineer their own plasmids by dragging and dropping different parts into sequence, a glossary and encyclopedia. Lastly, the teacher can coordinate the class experiments by working through the groups feature.
 {{Team:Alberta/endMainContent}}