Apple Cores

Lara P., Barnaby S-M., Tobi T., Joel P., Jessica K.

Approximately one billion people are currently at risk of dying of cyanide poisoning.  Most of the people at risk are completely unaware that they are poisoning themselves.  The staple food known most commonly as the Cassava plant can contain up to 200 ppm (parts per million) of cyanide in drought conditions, and with the World Health organization recognising 10 ppm being the safe consumption limit, this poses a massive risk to the people consuming it on a daily bases.

What is cyanide?

Cyanide is a chemical poison that acts rapidly once digested to bind to the haemoglobin (a protein that carries oxygen around our bodies) in red blood cells.  This prevents blood from correctly carrying oxygen around our body, which affects cellular respiration, the process that converts oxygen, ADP (depleted energy/ATP), and glucose (a form of sugar), into ATP (energy).

 

What is Cassava?

A commonly eaten plant mainly found in subtropical regions.  If untreated or eaten raw, the cyanide is sometimes strong enough to severely harm and permanently damage its consumers.  If eaten daily, it can cause a variety of side effects ranging from headaches to death, the most notable of which is Konzo, a horrific condition causing paralysis from the waist down.

Isolating DNA

On our first day of working with GTAC we isolated important DNA from mature and juvenile Sugar Gum, and sour plum leaves.  The gene we were attempting to isolate was the UGT gene, a key gene in the production of cyanide compounds in plants. We were separating it from the two different species of plants to find similarities, with the end product hopefully allowing us to understand the gene and possibly allow us to use the information to manipulate the growth of the gene.

 

Thermocycler

The thermocycler is basically a heat block with wells to store Eppendorf tubs in.  It changes temperature according to the different times and can be programmed to run for an allocated amount of time.  We used it to primarily replicate strands.  The process worked like this.

• Separating the purified DNA into two single helices instead of one double helix (A helix is half of the spiral shape that is DNA.)  This is done at 94 degrees Celsius.
• Annealing (When the primer, a short DNA sequence that acts like a starting point, attaches itself to the template/purified DNA.)  This is done at 62 degrees Celsius.
• Extension is next, which is when the DNA is extended by the Taq DNA polymerase (A short name for the enzyme from an underwater volcanic bacteria we use to assist the DNA in surviving the high temperatures.)  This is done at 72 degrees Celsius.

This process multiplies the DNA strand we’re looking for and allows use to separate the DNA we want from the DNA we don’t want.

Dark room

We then put our DNA through gel electrophoresis. We used electricity to draw the DNA and a dye that we added to it into a gel.  The small sized DNA was swept further than the large DNA, which gave us interesting results. DNA has a slightly negative charge, so that when a negative charge is put on one side and a positive charge is put on the other, the DNA is attracted to the positive and repulsed by the negative, so the DNA moves through the gel. The more segments, the harder it is for the strands to move through the gel, so the slower they go.  In the dark room, we use UV light to make the DNA glow, by adding a dye to it.  We can physically see the spacing, size and strength of the DNA bands.

Results

The results we got weren’t the ones that we were expecting.  Instead of finding the strands of large DNA we were looking for, we found many smaller DNA strands that multiplied in their place.  We repeated the last part of the experiment in case something went wrong.  The results were slightly different, but still similarly unexpected.

 

Extracting Cyanide from Cassava

We wanted to find out if cassava food products found in common supermarkets contained lethal doses of cyanide, or if they were well processed.  We ground down the specimens, which were

• Juvenile sugar gum fed nitrogen
• Juvenile sugar gum with low nitrogen
• Ground and frozen cassava tuber
• Cassava chips

To ground down the leaf specimens we use liquid nitrogen.  We would snap freeze it and then melt it, only to snap freeze it again.  By using liquid nitrogen, the water immediately became shards of ice, quickly enough that it tore through the leaf fibre.  Our results were interesting, with a couple being rather unpredictable.  When converted, the cassava chips were below the safe amount of cyanide by quite a lot, making them safe for consumption.  The ground tuber was almost double the safe amount, averaging at about 24, with the safe limit being 10.  This wasn’t too alarming, as, if eaten in proportion, it probably wouldn’t be lethal.  The two sugar gums were extremely over the limit, and the nitrogen high sugar gum had a surprisingly larger amount of cyanide in it than the low nitrogen sugar gum.  We guessed that this might be because nitrogen is part of cyanide, and it could have fuelled the production of cyanide in the leaves.  But we weren’t entirely sure.

 

Melbourne University School of Botany (Faculty of Biosciences)

 

On the afternoon of fourth day, we visited the Melbourne University School of Botany. We had a look at the wide variety of pressed plants in their Herbarium and the microscopes. Their collection of microscopes included a very expensive SEM scanning microscope that could take images of things at a molecular level.

Questions

-          What more could be researched in this field?

There’s a lot, we only did a handful of tests on a small scale for a week.  The tests could be replicated to assure our results were correct for a start.

-          Why did we do this research?

Because of the potential impacts on humans consuming cassava plants.  In the long term it would be to find a way to reduce the cyanide in the cassava plant, or find a way to allow humans to safely break down the cyanide in the staple food.

-          Why do plants produce cyanide?

Plants produce cyanide to protect themselves from predators, when they are under stressful scenarios such as a drought.  Unfortunately, they are also more likely to be eaten during a drought.

-          Cyanide and other food

Cyanide is found in apple seeds and stone fruits.  As long the seeds aren’t eaten in a bulk amount, they remain safe for human consumption, as we have a means to break them down to a degree.

GTAC Reflections

Jessica K

In the lead up to this week, I was incredibly excited. I really enjoy doing practical work, and going in-depth on scientific topics. Completing the program, I can now say that I enjoyed myself even more than I expected to. We have been looking into the DNA of cyanogenic plants, the effects of cyanogenic plants on society, and the variables that affect cyanide production in the same plant species. Learning about different scientific processes, going into the specifics of plants and genetics, and working in the lab has been so interesting that I have actually decided to take Biology for VCE.

Lara P

I didn’t know much about this program when I started, but I was really excited to learn that we were primarily working with plants.  In school, I found plant cells particularly interesting, and I knew very little about cyanide, which left me with a lot to learn.  I was super impressed with the numerous tools and machines we used throughout the week, and I think that the small insight the program provides shows of a more realistic view of science than simply hearing about it in a classroom.  I’m much more interested in a career in science than I was previously.

Joel P

I personally really enjoyed the GTAC experience. As someone who is really passionate about science I jumped at the opportunity to participate in proper research. While I learned an incredible amount, my biggest takeaway was learning how to operate in a workplace environment. Meeting the people, learning the protocols and taking on new responsibilities was a great journey. I never thought I would be sorting DNA, operating an SEM or visiting one of the oldest herbariums in Australia. The GTAC team was very welcoming and all in all SIRE was an amazing experience that I would love to repeat.

Tobi T

Before the SIRE program began, I didn’t know much about what was going to happen, I only had a brief idea of what was going on. At school I enjoyed biology a lot, so I thought that this program would be interesting, and it was. I enjoyed learning new things about plants that I didn’t know much about, and how everyday foods and plants can contain deadly chemicals like cyanide. My favourite parts of the program was doing the experiments, like extracting the DNA and trying to find the gene that create cyonagenes. I also enjoyed looking through the SEM microscope. Overall, this program has made me more interested in biology.

Barnaby S-M

I have very much enjoyed my time at GTAC. I have learnt a great deal, ranging from how dangerous many people’s food is around the world to how we know it’s dangerous and what makes it dangerous. I have operated machines that I might never operate and met people I might never have met. I have used methods I might not use again for a long time, and I have learnt and seen things I might never have learnt and seen otherwise.