Team:Alberta/project

From 2010.igem.org

(Difference between revisions)

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}}
-[[Image:Alberta Plate highschool.jpg|center|frame|Bryce Stewart, a high school student shows off his colonies transformed with his plasmid constructed with GENOMIKON.]]
+[[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.]]
 {{Team:Alberta/endRightSideBar}}
@@ Line 16: / Line 16: @@
 ''GENOMIKON: an Educational Toolkit for Rapid Genetic Construction''
-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, which exposes young minds to genetic technology.  To construct the kit, known as GENOMIKON, we first optimized the BioBytes 2.0 assembly method created by the University of Alberta 2009 team. The experiments of the kit were then designed 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 through their experiments. Lastly, we looked at how best to distribute this kit into students’ 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 and functional technology, even before they enter post-secondary education.
+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.
 ==[[Team:Alberta/biobyte2 |BioBytes Theory]]==
-The DNA components of the GENOMIKON kit will be provided in linear pieces called 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: 'AB Bytes' and 'BA Bytes', which are defined by the composition of the overhangs it has. The result is that AB Bytes can only be ligated to BA Bytes and vice versa. This leads to a construct alternating in AB and BA Bytes.  The specificity in absolute order of a construct is given by an anchor, which restricts ligation to only one side.
+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.
 ==[[Team:Alberta/Kit |The GENOMIKON Kit]]==
-The GENOMIKON kit was designed for a high school environment. The major challenge facing the GENOMIKON kit was that high schools lack most lab equipment traditionally needed for molecular biology. Creating a sterile environment to avoid contamination was another challenge that had to be overcome. Fortunately, the BioByte 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 then is a hot plate, thermometer, and a beaker.  The issue of sterility is addressed by sending reagents in individual 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.
 ==[[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.ca. Features include: descriptions of the different parts used to construct a plasmid, a toolkit where students can engineer their own creative expressions by dragging and dropping different parts into sequence to automatically generate a protocol to follow. Students can also do predetermined experiments outlined and collect background information by 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}}