Science Update
We have finished our sampling in this area of the Drake Passage and are heading towards another sampling station. While underway, the science team is collecting final samples on Incubation 1. The science team refers to this process as 'crashing the bottles'. Final samples for 30 bottles will be filtered throughout the day. This large amount of sampling means long hours for most of the science team. It is a privilege to work with such a hard-working group of people! Each member of the team understands the importance of all-day sampling event - especially with only 2 weeks left before we begin our trek across the Drake Passage towards Chile - and they all pitch in to help in any way possible.
Filter Frenzy
In the journal Filters, I discussed some of the different types of filters in use during this research cruise. Filtering is an important part of the research process because it allows the science team to collect biomass or biological material from the seawater. Most of the biomass in these seawater samples is microscopic, so the filters allow the science team to filter large volumes of water to collect enough microscopic biomass to study in future analyses and experiment. I recently spent time in 'Big Antarctica' (a large walk-in cooler set at 4C/37F) to work with Kim Powell from Old Dominion University (ODU) as she extracts biomass samples for DNA and RNA analysis. Kim is the lab manager in Dr. Dreux Chappell's lab at ODU. She has worked at ODU for 2 years and has worked on another of oceanographic cruise with Dr. Chappell, but this is her first to Antarctica. Before we get to the science, Kim has a special message to send: I'm very Lucky to have two amazing children, Ben and Lily. Today is Lily's birthday, so... Happy 10th Birthday, to my daughter, Lily!!!! I wish I could be there, but I'm so proud of her!!!
Kim Powell, lab manager for Dr. Chappell at ODU, has the primary responsibility of filtering DNA and RNA samples during this research cruise.
DNA and RNA
DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are biological molecules that store genetic information. All organisms have genetic material that controls the cell and oversees the production of proteins (along with other functions).
Ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) are important molecules in all living things. This diagram shows the general structure of each molecule. Image icensed with Cc-by-sa-3.0, Cc-by-sa-3.0,2.5,2.0,1.0, GFDL
Scientists from ODU and the University of Rhode Island (URI) filter large quantities of seawater to collect biomass samples of diatoms and bacteria in the Southern Ocean. Analysis of the DNA can help with identifying specific species of diatoms and bacteria. Analysis of the RNA can tell us more about the physiological changes that happen as the diatoms experience different conditions. For instance, during the incubation experiments, diatoms are exposed to different treatments of nutrients. The RNA analysis can help determine how the genetic instructions of diatoms may change in response to these different concentrations and mixtures of nutrients. In other words, do the diatoms make different molecules in response to change? The same RNA analysis can be done for other types of environmental changes such as temperature, salinity, oxygen levels, etc. depending on the interests of the scientists. RNA can degrade (break down) quickly, so sampling in cold temperatures is important. In addition, it is important to keep the diatoms in stable temperatures to mimic their natural setting. A large change in temperature may cause the diatoms to begin production of RNA molecules that are not normally produced, unless during temperature changes. Care is taken to keep the temperature similar to the ambient (natural) temperature until the DNA and RNA samples can be frozen for future use. So - let's go to Big Antarctica and see how Kim collects these important samples.
Big Antarctica
As water is collected from incubation bottles or during station sampling with the conventional CTD rosette, large quantities of seawater are delivered to Kim in the cold room. Inside this walk-in cooler, Kim has a lab station with equipment including a peristaltic pump, graduated cylinders, lots of tubing and lots and lots of filters.
Kim Powell prepares to stop the peristaltic pump for an incubation sample. This pump helps to push seawater through fine filters in order to catch biomass (biological samples) from Southern Ocean water. Kim wears her red 'puffy' parka to help stay warm inside the cold room.
One end of the pump is placed in the seawater sample while the other end is attached to a filter or a filter set. For most of the sampling, Kim uses a 3 micron and a .2 micron filter set. Water from the samples is forced past the filters due to the pressure created by the pump. As the water passes through the filters, the sea water collects in the large graduated cylinders while the biomass collects on the filters. This is very similar to using a strainer to drain noodles. The only difference is the use of the filter to help move a larger volume of water.
As the peristalsis pump pushed water through the filter rig, the biomass collects on the filters housed inside. The filtered water collects in a graduated cylinder so that water volumes can be recorded.
After approximately 45 minutes (more or less depending on the sample size), Kim begins to take apart the filter rig in order to collect the filters and preserve the biomass for later use. First, she uses a large syringe to remove the remaining drops of water from the filter rig.
Kim Powell uses a large syringe to push the remaining seawater out of the filter.
Next, Kim takes apart the filter rigs and begins to remove the filters from the holder. At the beginning of the research cruise, most of the filters only showed a slight change in color, indicating a small amount of biomass. Three weeks into the cruise, however, the same volume of water is leaving behind more biomass. This may be an indication that the diatoms are reacting to the increased light of springtime and starting to grow.
The tan color on the normally clear filter is the biomass. Large amounts of phytoplankton and bacteria discolor the filter as they stay on one side of the filter and the sea water exits the other side.
Kim carefully removes the filters from the holders and places each filter into an individual cryovial. These vials are used because they are made for cold temperature storage (cryo is Greek for ice cold).
Filters containing biomass are inserted into a buffer solution for storage. These small cryo-vials will be flash frozen for storage and eventual transport to Dr. Chappell's lab at ODU.
Finally, the cryovials are transferred to a dewar filled with liquid nitrogen. The liquid nitrogen flash freezes the samples to ensure the preservation of the DNA and RNA at the time of filtration. These samples are stored in a large freezer on the RVIB Palmer for the duration of the cruise. Shipping to ODU and URI will be expedited upon our return to Punta Arenas in a little over two weeks. Upon arrival at the labs, these samples will be used for molecular analysis of the RNA and DNA codes.
cryovials are transported to the liquid nitrogen dewar. The liquid nitrogen will flash freeze the samples to minimize changes to the DNA and RNA in each cell.
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