BioBuilding: Synthetic Biology for Students: Lab 5: Difference between revisions
No edit summary |
No edit summary |
||
Line 15: | Line 15: | ||
* Compare two engineering solutions to a given problem (redundancy vs kill switches) | * Compare two engineering solutions to a given problem (redundancy vs kill switches) | ||
==Introduction== | ==Introduction== | ||
One goal in the synthetic biology community is to convert scientific discoveries into practical solutions that meet real world needs. The world’s needs are many -- our population is aging, we’re putting increased pressures on our environment and there are widening economic inequalities -- but biology is a challenging material to work with. Our understanding nature is incomplete and evolving. Our tools for engineering it are primitive. | One goal in the synthetic biology community is to convert scientific discoveries into practical solutions that meet real world needs. The world’s needs are many -- our population is aging, we’re putting increased pressures on our environment and there are widening economic inequalities -- but biology is a challenging material to work with. Our understanding of nature is incomplete and evolving. Our tools for engineering it are primitive. Biology is not perfectly predictable. And as a society we’re often awkward or misguided when we interface with emerging technologies. We’d like to use our powers for good, to benefit all people and the planet, but what a complex challenge that is! | ||
===Background on Vitamin A production=== | ===Background on Vitamin A production=== | ||
"Nature is a masterful and prolific chemist" [[http://mmbr.asm.org/content/69/1/51.short| doi: 10.1128/MMBR.69.1.51-78.2005]] and many laboratories work hard to mimic even the smallest bit of nature's range and skill. In this experiment we'll examine the biosynthesis of a carotenoid, a member of the isoprenoid family of chemicals that is responsible for many of the vibrant colors seen in plants and animals. Nature makes it look easy! There are more than 600 natural carotenoids, playing important roles in harvesting light for photosynthesis, as anti-oxidants to detoxify reactive species, and as regulators of membrane fluidity. The color of the carotenoids is directly related to their structure, in particular the number of conjugated double bonds. A minimum of 7 conjugated bonds is needed for any color so cis-phytoene with only 3 is colorless while trans-neurosporene with 9 is yellow, and lycopene with 11 is red. The structure of carotenoids makes them lipophilic so in the lab they're more soluble in organic solvents like acetone than they are in water. We'll exploit this fact when we measure the beta-carotene in a collection of cells that we'll grow. <br> | "Nature is a masterful and prolific chemist" [[http://mmbr.asm.org/content/69/1/51.short| doi: 10.1128/MMBR.69.1.51-78.2005]] and many laboratories work hard to mimic even the smallest bit of nature's range and skill. In this experiment we'll examine the biosynthesis of a carotenoid, a member of the isoprenoid family of chemicals that is responsible for many of the vibrant colors seen in plants and animals. Nature makes it look easy! There are more than 600 natural carotenoids, playing important roles in harvesting light for photosynthesis, as anti-oxidants to detoxify reactive species, and as regulators of membrane fluidity. The color of the carotenoids is directly related to their structure, in particular the number of conjugated double bonds. A minimum of 7 conjugated bonds is needed for any color so cis-phytoene with only 3 is colorless while trans-neurosporene with 9 is yellow, and lycopene with 11 is red. The structure of carotenoids makes them lipophilic so in the lab they're more soluble in organic solvents like acetone than they are in water. We'll exploit this fact when we measure the beta-carotene in a collection of cells that we'll grow. <br> | ||
[[Image:P103b.gif|thumb| | [[Image:P103b.gif|thumb|350px | chemical structure of two carotenoids]] Plants can make their own carotenoids from scratch, but animals can't so we must eat all we need. Think of the bright orange color of carrots and you're thinking of the isoprenoid they make called beta-carotene. Cut beta-carotene in half and add a water molecule and you have Vitamin A ---which is why parents tell their kids to eat their vegetables. And why developing countries that have limited food supplies have high incidents of disease due to vitamin deficiencies. For example, between at least 250,000 children in the developing world go blind each year due to Vitamin A deficiency. It's a huge problem but not a new one. As we start this "Golden Bread" module, you may want to consider existing biotechnology approaches to this issue, including the story of "golden rice" and the social impact of GMOs in the US and in Europe. <br> | ||
===The Science and Engineering of Golden Bread=== | |||
[[Image:Xyanthopylomycese to Sacchromyces.png|thumb| 350px]] Xanthophyllomyces dendrorhous is a naturally red fungi that grows on tree stumps and other places. It's red because it can make its own carotenoids but it's not a particularly useful fungi in the lab or in industry. A much more useful yeast is Saccharomyces cerevisiae. That's the fungi also known as baker's yeast since it can be used to bake bread or brew beer. Based on how much Wonderbread and Budweiser is made each year, it seems like this S. cerevisiae would be a better chassis choice for large scale production efforts. So the reasonably simple idea to move the genes over was first published by van Ooyen in 2007 [[Media:Beta carotene Yeast AppEnvMicro 07.pdf| pdf is here]] and then developed further by the 2011 iGEM team from Jef Boeke's lab at Johns Hopkins, [http://2011.igem.org/Team:Johns_Hopkins iGEM 2011 project]. The goal was to transfer the genes that make carotenoids from the red fungi, Xyanthophylomyces, into the strain that we know how to work with, namely S. cerevisiae. <br> | |||
[[Image:Metabolic Pathway for b-carotene.png| thumb| 350px]] There are three enzymes that the red fungi makes which allow it to convert simple molecules into beta-carotene. The genes that encode the enzymes are called crtE, crtI and crtYB. One of the enzymes, encoded by crtE is already made by baker's yeast from the native BTS1 gene. The other genes are needed in a couple of places on the metabolic path from starting material (Farnesyl-PP) to beta-carotene. <br> | |||
[[Image:Metabolic Pathway for b-carotene.png]] | |||
If synthetic biology is successful, then it will be possible to quickly and easily build biological technologies that improve health, provide sustainable energy or ensure a reliable global supply of food and water. | If synthetic biology is successful, then it will be possible to quickly and easily build biological technologies that improve health, provide sustainable energy or ensure a reliable global supply of food and water. | ||
==Procedure== | ==Procedure== |
Revision as of 09:12, 23 February 2013
Eau That Smell Lab |
Lab 5: Golden Bread
Acknowledgments: This lab was developed with materials from the Johns Hopkins 2011 iGEM team, as well as guidance and technical insights from BioBuilder teachers around the countryObjectivesBy the conclusion of this laboratory investigation, the student will be able to:
IntroductionOne goal in the synthetic biology community is to convert scientific discoveries into practical solutions that meet real world needs. The world’s needs are many -- our population is aging, we’re putting increased pressures on our environment and there are widening economic inequalities -- but biology is a challenging material to work with. Our understanding of nature is incomplete and evolving. Our tools for engineering it are primitive. Biology is not perfectly predictable. And as a society we’re often awkward or misguided when we interface with emerging technologies. We’d like to use our powers for good, to benefit all people and the planet, but what a complex challenge that is! Background on Vitamin A production"Nature is a masterful and prolific chemist" [doi: 10.1128/MMBR.69.1.51-78.2005] and many laboratories work hard to mimic even the smallest bit of nature's range and skill. In this experiment we'll examine the biosynthesis of a carotenoid, a member of the isoprenoid family of chemicals that is responsible for many of the vibrant colors seen in plants and animals. Nature makes it look easy! There are more than 600 natural carotenoids, playing important roles in harvesting light for photosynthesis, as anti-oxidants to detoxify reactive species, and as regulators of membrane fluidity. The color of the carotenoids is directly related to their structure, in particular the number of conjugated double bonds. A minimum of 7 conjugated bonds is needed for any color so cis-phytoene with only 3 is colorless while trans-neurosporene with 9 is yellow, and lycopene with 11 is red. The structure of carotenoids makes them lipophilic so in the lab they're more soluble in organic solvents like acetone than they are in water. We'll exploit this fact when we measure the beta-carotene in a collection of cells that we'll grow. The Science and Engineering of Golden BreadXanthophyllomyces dendrorhous is a naturally red fungi that grows on tree stumps and other places. It's red because it can make its own carotenoids but it's not a particularly useful fungi in the lab or in industry. A much more useful yeast is Saccharomyces cerevisiae. That's the fungi also known as baker's yeast since it can be used to bake bread or brew beer. Based on how much Wonderbread and Budweiser is made each year, it seems like this S. cerevisiae would be a better chassis choice for large scale production efforts. So the reasonably simple idea to move the genes over was first published by van Ooyen in 2007 pdf is here and then developed further by the 2011 iGEM team from Jef Boeke's lab at Johns Hopkins, iGEM 2011 project. The goal was to transfer the genes that make carotenoids from the red fungi, Xyanthophylomyces, into the strain that we know how to work with, namely S. cerevisiae.There are three enzymes that the red fungi makes which allow it to convert simple molecules into beta-carotene. The genes that encode the enzymes are called crtE, crtI and crtYB. One of the enzymes, encoded by crtE is already made by baker's yeast from the native BTS1 gene. The other genes are needed in a couple of places on the metabolic path from starting material (Farnesyl-PP) to beta-carotene. If synthetic biology is successful, then it will be possible to quickly and easily build biological technologies that improve health, provide sustainable energy or ensure a reliable global supply of food and water. ProcedurePart 1: Testing Genetic Variability
How to restreak cellsA video showing you how to restreak cells is here.
Part 2: PCR
Part 3: Yeast TransformationPart 4: Measuring Vitamin APart 5: Baking BreadNext dayIn your lab notebook, you will need to construct a data table as shown below. These may be provided. Also be sure to share your data with the BioBuilder community here. Lab ReportI. Introduction
II. Methods
III. Results
IV. Discussion
|