A day in the life of a biotechnologist

Like humans, trees also get sick. One of the diseases that trees suffer from is caused by a group of fungi called Botryosphaeria species. These fungi are parasites that can enter the tree through wounds caused by insect damage. If the tree experiences stressful conditions like a hailstorm or frost, the fungi pierce through, multiply in numbers, and cause symptoms on all parts of the tree.

Such fungi can also attack the roots of the tree and this can be seen easily by the cracks that develop in the roots. This affects water uptake by the roots to other parts of the plant. One of the symptoms of the disease is the development of brown to blackish spots on the leaves. This affects the most important functions of the plant, such as photosynthesis. If photosynthesis is affected, the plant does not get sufficient nutrients to survive; the leaves start wilting and eventually lose their lively greenish colour becoming a morose golden-brown. These symptoms can be so severe that the tree starts swelling. The tree swells until the stem cracks up, followed by a dark, slimy, gum-like sap called kino which oozes out as if the tree were bleeding. This leads to girdling where the fungus grows and covers the entire stem with lesions. Girdling affects the flow of nutrients and the uptake of water by regions at the top of the tree. The tree becomes weaker and weaker and it eventually dies.

Infected trees can be seen by the discolouration of the leaves.

As the tree swells, cracks appear and a black kino oozes out as if the tree were bleeding.

Thanks to the TPCP for use of images above

The production of food and fruit and fibres such as paper from crops and trees is important for our country's well-being and economy. How do we protect these resources against such attacks on trees? The good news is that similar to humans, trees also have "doctors", or rather scientists who study these diseases. In South Africa, we have an organization called FABI, short for the Forestry and Agricultural Biotechnology Institute where a number of scientists are doing just that. FABI is based at the University of Pretoria and conducts research in forestry and agriculture. Because it is based at a university, the institute is also involved in training young scientists in the field of biotechnology.

We wondered what exactly a young biotechnologist who studies tree diseases does each day. Armed with a camera, we followed Happy Maleme a first year Master of Science in biotechnology student at FABI for a day.

Happy comes from Klerksdorp where she is the eldest of five children. She completed her Bachelor of Science degree and her Honours degree at the University of Limpopo before coming to FABI at the University of Pretoria to do her Masters in Biotechnology.

A wide range of research is conducted at FABI. For example, some research groups look at developing better ways of growing trees and plants, others are developing ways of testing for plant diseases and also managing plant diseases. In Happy's research group they try to understand where pests and disease-causing pathogens come from. This will help them to understand how to reduce the damage caused by these pests to plants and trees.

Happy's research project is supported by the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) at FABI. This is one of the six Centres of Excellence in the country selected for long-term support by the Department of Science and Technology (DST) and the National Research Foundation (NRF). It is envisaged that such centres will stimulate sustained distinction in research while simultaneously generating highly qualified human resource capacity to impact meaningfully on key national and global areas of knowledge.

Because there are so many different areas of research at FABI, it is very important for the biotechnologists to talk to each other about their research. On this particular day when we visited Happy, part of the day was devoted to seminars. During seminars, one of the researchers presents their work in front of the rest of the group. This is a good opportunity for Happy to keep track of developments in biotechnology. It is also a good opportunity for the biotechnologist presenting their work to receive some valuable comments and constructive criticism. Many alternative ideas and solutions to problems originate here, and after all, two heads are better than one!

Now it is time for laboratory work. Happy's research project is based on the Botryosphaeria canker caused by the fungus mentioned in the beginning. This is one of the most important diseases of Eucalyptus trees in South Africa. Happy starts with making the necessary preparations. She knows that thorough planning of experiments is essential for success.

Here Happy collects leaves from experimental plants infected with the Botryosphaeria fungus. The plants are grown in plant growth chambers where conditions such as temperature are regulated and controlled.

Here Happy extracts DNA from the plant material using a special sequence of chemicals. Deoxyribonucleic acids, DNA for short, is the genetic material of a cell.

Once she has extracted the DNA, Happy needs to inspect the quality and the quantity of the DNA. She does this by running what is known as an agarose gel using a technique known as Agarose gel electrophoresis to separate fragments of DNA fragments. Read more about an agarose gel and agarose gel electrophoresis below.

After lunch, Happy is taught a new skill: how to sequence the DNA she has isolated. Nucleotides are the basic building blocks of DNA and consist of adenine, cytosine, guanine and thymine. The DNA sequencer machine will give Happy information on the order, or rather, sequence in which these four nucleotides are found. FABI is well equipped with the most modern technology and students receive training on all equipment before using it.

In biotechnology research, as in other scientific fields, the research supervisor plays a critical role in guiding research. Here Happy discusses the results of her research with her supervisor. Based on the results, together they decide on the next steps in Happy's research.

It's not all work. Happy has time for a cup of coffee and shares a joke with some of her colleagues.

As mentioned before, good planning skills are important. Before Happy leaves work, she uses what is known as an autoclave machine to sterilize the equipment she will need to use the following day. Autoclaves are pressurized machines which use steam to sterilize equipment.

Home time! Happy is pleased with the success of the day and heads home for dinner, friends and relaxation.

Just before bedtime, we catch Happy reading some scientific papers. Biotechnology is a fast developing field and keeping up to date with the literature in biotechnology is very important if one is to be successful at research. After her reading it's off to bed and we bid Happy a goodbye and a good night's sleep.

It's still early days for Happy and her research on tree diseases but with hard work, passion and determination, we have no doubt that Happy will make good progress. Watch this space!

Agarose gel

Agar is a compound that is found in the cell walls of some of the red algae such as seaweed. It provides a mechanical support, which prevents cells from collapsing. It is also used in the food industry as ingredient stabilizers of e.g. dessert jelly, which is popular. It has cross-links, and when the agar is heated, the gel melts and the cross-links are broken. When poured into a mould and cooled down, the cross-links reform and the gel sets in the shape of a mould.

Agarose gel electrophoresis for separation of DNA fragments

Theory: Fragments of DNA can be separated according to their size (length) by a method known as agarose gel electrophoresis. During this method, DNA (which is negatively charged) is loaded onto an agarose gel (in an aqueous buffer) over which an electrical current is then placed.

Method: Agarose is an expensive, non-toxic powder mixture, which is produced from seaweed. To make an agarose gel, this powder is dissolved in an aqueous buffer at a high temperature and allowed to cool down and set. Agarose gels are porous, and when DNA is loaded onto the gel and an electrical current placed over it, the negatively charged DNA fragments move to the positive pole. The DNA fragments are then separated from each other according to their size (their ability to move through these pores): larger fragments moving slower than shorter fragments.