Tomatosphere and Epigenetics

Have you heard of Tomatosphere™? This is a really cool program operated in Canada through Let’s Talk Science. It is a free program offered to students from Kindergarten to Grade 12, where these students can study the effects of “space” on the germination of tomato seeds. Participating classes receive two packages of tomato seeds: one is a package of seeds from tomatoes that were sent into space or treated to space-simulation conditions, i.e., the experimental group; the second package contains seeds that spent time on plain old Earth, i.e., the control group. Students the study the germination of these two groups of seeds, expanding on the basic experiment depending on curriculum and grade level.

As a scientist and a gardener, I am in LOVE with this program. But I have a question for Tomatosphere™: I want to know if anyone is looking at the possibility of EPIGENETIC changes to the tomatoes. This begs the next question: what is epigenetics? That’s the question I am hoping to answer for you today.

Tomatospher Question

My tweet to Tomatosphere

 

To begin our understanding of epigenetics, let’s do a quick review of the central dogma of genetics and inheritance. The traits that make us a human (or a gorilla, or a tomato plant) are coded in our DNA. To express the trait, the DNA is transcribed into messenger RNA (mRNA), which is in turn translated into amino acids that are then put together to build the necessary proteins for each trait. We inherit these genes from our biological parents: one gene from the egg and one gene from the sperm. The trait that is expressed is the dominant gene. Differences in expression generally mean differences in the genes, or the specific DNA code.

For example, let’s look at blood types. Let’s say you inherit the “A gene” from your dad and the “O gene” from your mum. Your genotype will be AO. But since the A gene is dominant, you will only express this gene and you will have blood type A. This is called your phenotype. To change your blood type, you would need to change your genotype. That is the basics of inheritance.

Epigenetics throws a wrench into this understanding of genetics and inheritance. Epigenetics means “outside genetics”, and refers to changes in gene expression that are not a result of physical changes to the DNA sequence. In other words, changing our phenotype without changing our genotype. Epigenetic marks control the expression of genes, which ones are turned on, when, and how much. One of the most interesting things about epigenetics is that we can start to see how the environment plays a role in gene expression. Our lifestyles, our preferences, our exposures to certain environmental factors can all contribute to variations in how the same gene can be expressed across individuals. What’s more, is that it has been discovered that these changes in epigenetics can be inherited. What this means is that if you exposed to something in your environment that causes a change in how a gene in your DNA is expressed, this change could be passed on to your child, and even to your grandchild. This is referred to as transgenerational epigenetics. It is an emerging area of research and the exact mechanisms of how this works is being widely studied.

This brings us back to Tomatosphere™ and my question. In the experiment we have tomato seeds that were exposed to space conditions. These conditions may not have changed the gene sequence, the genotype, of the tomato, but they may have caused epigenetic changes. It has been shown that changes in the gene that controls ripening in tomatoes is impacted by epigenetics, so do we see changes in other factors with these space tomatoes? AND, what about the progeny? Do the tomato plants grown from the seeds of the space tomatoes also show epigenetic changes?

Epigenetic tomato experiment

A sketch of my proposed Tomatosphere experiment.

 

For more information on transgenerational epigenetics, check out this Nature article.  I also recommend the website What is Epigenetics for a more detailed description of epigenetics.

 

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What is a DNA Fingerprint?

Gel featuring DNA bands from three individuals compared to an unknown sample.

Gel featuring DNA bands from three individuals compared to an unknown sample.

Today in Kingston, ON, a man was arrested in connection with a kidnapping and sexual assault that took place in Calgary, AB, 20 years ago. The police were able to connect the suspect to the case by comparing his DNA to samples from the Calgary cold case.

I was asked to talk with the CTV reporter covering the story to explain DNA fingerprinting. RCMP forensics scientists-the real experts who made this type of arrest possible, aren’t available on Sundays. But if you happen to be a scientist and the sister of said reporter, you tend to be more available on Sundays.

One of the big questions from today’s interview was “how does this technology work?” Now, in the interview, my answer was pretty quick, because there wasn’t too much time to really explore the details-the story wasn’t about the science, or at least not ALL about the science. So here is a chance to go into a bit more detail.

The first thing to understand about DNA fingerprinting (the preferred term is actually genetic profiling) is that all of a person’s DNA (called the “whole genome“) is NOT sequenced. Only pieces of the DNA are sequenced. Your DNA contains TERABYTES of data. (The MacBook pro that I am writing this on has only 500 gigabytes of storage-it wouldn’t even hold the information that your DNA holds.) It would take a very long time to sift through the data from a whole genome, especially since 99.9% of our DNA is the same as everyone else. And thanks to evolution, we have a whole lot of junk DNA that we just kept with us as we climbed the evolutionary ladder.

What scientists use instead to build a DNA “fingerprint” are genetic markers called short tandem repeats (STR). These are areas of your DNA that present in every human, but are highly variable (polymorphic), meaning that they differ from person to person. There are typically 13 STR loci that forensic scientists use to create a genetic profile.

Simple overview of steps in DNA profiling.

Simple overview of steps in DNA profiling.

Steps:

1) DNA sample is collected: could be blood, hair, saliva

2) The DNA is then broken up into smaller pieces, using an enzyme that cleaves DNA at specific locations

3) The DNA markers are amplified by a technique called PCR (Polymerase Chain Reaction). This means that the original DNA sample can be quite small-maybe only 20 DNA containing cells.

4) The DNA pieces are then run through a technique called gel electrophoresis, where a high voltage current is applied to a gel that contains the DNA fragments. The fragments separate out based on size, with the smaller fragments travelling faster. The result is the band-like structure seen in the picture at the top.

The bands on a gel from the unknown sample will be compared to suspects (in the case of criminal DNA testing). If the unknown DNA is a match for a suspect, the bands on the unknown sample will exactly match. Take a look at the samples in the picture at the top. Can you identify which suspect is a match for the sample from the crime scene? (Answer at the bottom.)

Each of these STRs are independent, meaning that a particular sequence of one does not influence the other. In probability terms this means that each of these is an independent event. The result is a one in several trillion chance of two sequences from two individuals being identical. The notable exception being identical twins, who by definition have the same DNA.

Me, talking to CTV.

Me, talking to CTV.

What has changed since 1995?

Well, the techniques are better, we can use smaller samples of DNA. We can even now put together samples from degraded ancient DNA. We can’t quite use those samples to clone a velociraptor (a la Jurassic Park); however, we can use the sample to identify remains of those long dead. Analysis of mitochondrial DNA was how the remains of Richard III were unequivocally identified in 2013.

Better, faster, more sensitive techniques allow for identification that may not have been possible in 1995. Further, PCR was developed in 1991, meaning that 20 years ago, it was still relatively new. Today we are much more comfortable with DNA analysis, as is the legal system.

Check out the story on CTV:

http://calgary.ctvnews.ca/video?clipId=595358

*The unknown DNA sample in the top image is a match for suspect number 2