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Lab 5: Golden Bread

Engineering reliability into an unstable genetic system may or may not make it a robust and profitable food source.

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 country

Objectives

By the conclusion of this laboratory investigation, the student will be able to:

Define and properly use synthetic biology terms: chassis, system, device, redundancy
Define and properly use molecular genetics terms: PCR, gene expression, codon shuffling.
Explain the role of redundancy in synthetic biology and engineering.
Conduct PCR and TLC and interpret the results each.
Compare two engineering solutions to a given problem (redundancy vs kill switches)

Introduction

Background

"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.

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.

Procedure

Part 1: Testing Genetic Variability

Yeast will arrive on a YPD plate to grow at 30°C or room temp and stored at room temp or in the fridge.
Identify color variants and restreak onto fresh YPD. Are there differences in the stability of the phenotypes? Are there growth conditions that make the colors more or less stable?

How to restreak cells

A video showing you how to restreak cells is here.

Label your new petri dish with your initials, today’s date, the kind of media in the petri dish and the strain that you’ll be restreaking onto it.
Start by dabbing the flat end of a toothpick onto a colony of yeast or bacteria that you want to restreak. The colony should be well isolated from the others and uniform in appearance.
Transfer the cells from that toothpick by lightlying touch the toothpick to a spot on the new petri dish that you’d like to grow. Note: you should not break the surface of the agar with any of this procedure, but the results will still be OK, even if you do.
With the flat end of a new toothpick, spread out the cells in the dab you made on the new petri dish by drawing your toothpick back and forth through the dab and then along the media in the dish. Do not back up as you draw since you are trying to spread out the cells that are on the toothpick from your one pass through the original dab of cells.
With a new toothpick, spread out the cells still further, drawing from the ending line you made with the second toothpick. Again, do not back up as you draw with this third toothpick and try not to break the surface of the media.
Replace the lid of the petri dish and incubate the plate media-side UP in an incubator (ideally 37° overnight for bacteria, 30° 2 days for yeast).

Part 2: PCR

Move Edvotek PCR bead to tube that fits in your PCR machine (or don't move the bead if the tube it comes in fits just fine)
Thaw primer pair NO302 and NO303. These amplify the crtYB gene ORF.
Prepare lysate: scoop a small colony you'd like to study into 50 ul H2O and microwave for 15 seconds with the lid of the eppendorf closed. Prepare lysate for any yeast you'd like to study.
To the bead that's in the PCR tube add
- 20 ul H2O and then vortex the sample
- 1 ul of each primer
- 2 ul of lysed yeast cells or + control DNA that carries crtYB on a plasmid
PCR cycle:
- 95° 2 minutes
- 95° 20 seconds
- 50° 20 seconds
- 72° 2.5 minutes
- repeat steps 2-4 a total of 35X
- 72° 10 minutes
- 4° hold
Add 5 ul loading dye to each sample
Run 25 ul on a 1% TAE gel with a stain to visualize the bands (Ethidium Bromide or CyberSafe). The gel could run for 20 minutes at 120V. Be sure to load a molecular weight marker on the gel with bands that range from 1 kb to 5 or 8 kb.

Part 3: Yeast Transformation

Part 4: Measuring Vitamin A

Part 5: Baking Bread

Next day

In 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 Report

I. Introduction

Provide a brief introduction describing the field of synthetic biology.
What is a ___? How does this ___work? How might ____ be useful?
Briefly describe the purpose of the lab. What are we trying to do here? Presume that a reader of your lab report has not read the assignment.
What is the role of the redundancy?
How does redundancy affect the expression of a genetic system?
How might synthetic biologists ___?
Why is it important to engineer a ___?
What are the advantages/concerns of engineering ___?
How might we test for the differences that the redundancy that may affect a genetic system?

II. Methods

You do not have to rewrite the procedure.
Explain why you did each step of the protocol.

III. Results

Present the data tables in clear format.
Present drawings of each slide.
Describe the results: Describe the appearance of the gel and the TLC plate. Are the bands and spots different?

IV. Discussion

Draw a conclusion: Do the ____ produce the same results in different chassis? Justify your answer.
Analyze the data: Be sure to discuss how each part of the experiment and results adds to your conclusion.
Are we sure that the transformation worked? What do the controls that lacked plasmid tell us?
Discuss errors and other reasons for data variability.
Use your results to explain why it is important for synthetic biologists to fully characterize the chassis used in an engineered system.

@@ Line 16: / Line 16: @@
 ==Introduction==
 ===Background===
-"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 carotenoids, a chemical family in the isoprenoid family that's responsible for many of the vibrant colors seen in plants and animals. Nature makes it look easy! Think of the bright orange color of carrots and you're thinking of the carotenoid they make called beta-carotene. 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 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>
-Plants can make their own carotenoids from scratch, but animals can't so we must eat all we need. That can lead to vitamin deficiencies. In cultures that can't grow many vitamin-rich plants, individuals can develop illnesses related to vitamin deficiency. You may want to consider biotechnology approaches to this issue, including the story of "golden rice" and the social impact of GMOs in the US and in Europe. <br>
+[[Image:P103b.gif|thumb|200px | 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>

BioBuilding: Synthetic Biology for Students: Lab 5