Mission Antarctica: What We Do In the Lab

Part I

A very brief introduction to Molecular Biology

Nucleic Acids

DNA IllustrationNucleic acids are biological macromolecules (molecules that are big) necessary for any form of life. They include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) and are named after their initial discovery in the nucleus of cells. Both types of nucleic acids are found in abundance in every living thing except certain viruses that contain only RNA and no DNA. But in general all life - archaea, bacteria, eukaryotes and viruses are filled with RNA and DNA.

DNA is the medium for long-term storage of genetic information needed to construct other components of cells, such as proteins and RNA molecules and is used to pass on information from lineage to lineage. The content of DNA in an organism is refered to as the genome. The role of RNA is to transmit information stored in DNA into amino acid sequence of proteins (mRNA – messenger RNA), form a component of ribosomes (rRNA – ribosomal RNA), carry molecules of amino acids to be used in protein synthesis (tRNA – transfer RNA) as well as other functions. So think of RNA as something short lived that gives you a snap shot of what the cell is doing at the time you extract the RNA. This is called the transcriptome. The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells. Our main goal in Antarctica is to capture the transcriptome of phytoplankton cells as they adapt from winter to spring and summer conditions. Unlike the genome, which is roughly fixed for a given cell line (excluding mutations), the variation of the transcriptome with external environmental conditions tells us a lot about cells. (Similar methods are used to study infection, human disease, how to make better corn, tomatoes, etc.)

Our Project

Phytoplankton illustrationA part of our project is to characterize the transcriptome of marine phytoplankton community during the seasonal succession from late austral winter to austral spring. We anticipate seeing many changes in the RNA expression that will shed light on activity of individual genes as well as elucidating individual strategies that allow the organisms to adapt to extreme environments. 

How is it done?

To characterize the transcriptome, we need to extract total RNA from the samples collected from seawater. The samples are collected in several different ways: either sea water is pumped in the aquarium, or if weather and ice conditions allow, the scientists go boating (fig. 1, Scientists boating) and use either a pump, or a plankton net with a very small size pores to capture the organisms  (fig. 2, Plankton net). Our net sizes are 200, 63 and 5 μM. For reference, the width of a human hair is approximately 100μM.

The collected water is then brought into a cold room, further filtered and/or concentrated into a pellet (fig. 3, Phytoplankton pellet). Most of the phytoplankton we are finding in the water at this time are diatoms - a major group of phytoplankton responsible for about ½ of the primary production in the ocean and generate a lot of the oxygen we breathe. One of the many cool aspects of diatoms besides sustaining the atmosphere we breathe is that they are encased in beautifully elaborate silica cases called frustules.

Once we have lots of phytoplankton biomass from concentrating, filtering and centrifuging the cells are placed into a tube with zirconia/silica beads (diameter 0.1 mm) and denaturation solution. Then they are “bead beaten” in a machine called a bead beater (fig. 4, Bead beater), which violently shakes the tube to break the rigid frustule open.  Once the cells are open, we can take a break and freeze the samples in -80 °C or we can proceed with the extraction of total RNA.

Click images to enlarge
Scientists boating Plankton Net Close up Phytoplankton pellet
Fig. 1 Scientists boating
Fig. 2 Plankton net
Fig. 3a. Phytoplankton
Fig. 3b Phytoplankton pellet
Bead beater
Fig. 4 Bead beater

Next week we will detail the extraction, visualization and quantification of RNA!

Stay Tuned!