Thoughts on Science
Since the semester ended, I've spent a much larger portion of my time at the microscope sorting and identifying aquatic invertebrates. Here are a few photos of what I've been seeing in the microscope. With the exception on the scud (Gammarus minus), these are some of the animals I've not seen very often. Enjoy!
You may have noticed my absence from blogging in December (or, maybe not). I wish I could attribute this to an overwhelming abundance of festivities and merry-making, but that is not the case. Don't get me wrong, there were festivities, but that did not delay my blogging; it takes more than a few parties to keep me away from my adoring reader. (See you on Tuesday, mom!)
The Biology Department at Saint Louis University was displaced about 18 months ago by a fire. Nobody was hurt - unless you count the tears and heartache of years of lost work for some faculty and grad students. Anyway, we've been in temporary dwellings across campus while Macelwane Hall was repaired and renovated....until December. About half of the department, including yours truly, were moved back into the newly renovated space last month, so we spent the first part of December packing our desks and lab spaces. That, and running one last toxicity experiment before the upheaval.
Megan and I finished the last of our packing and prepared to take a last look to make sure everything was properly labeled for the move. Fortunately, we were only responsible for the packing and unpacking (still to come). A couple of companies were hired to actually move the boxes and furniture from place to place.
Our newly renovated biology building is fantastic! Well, it will be when they finish getting the kinks out. My shared office space has no functioning outlets, the air lines and water treatment system for the aquatics lab are not installed yet, and the shelving units in the lab are missing some parts. While we wait for the details to come together, I've been fairly productive in my temporary home office. I have to share the space (see photo), but my table-mate is generally quiet and well-behaved (although at the moment she is playing with a bit of caulk she removed from the bathroom, but that's another story).
But the new building... when it is done, it will be great!! There is a lot of natural lighting on the three upper floors and even in the windowless basement, the fixtures make it feel like daylight. The lab space for our group is bigger than before with separate spaces for our GIS work and wet-lab efforts. The aquatics lab has a huge sink with an industrial sprayer and will be equipped with a high-quality water filtration system. The mud room for our field gear is spacious and has room to both clean and store gear. There is a new space for biological collections, something that was distinctly lacking before. The graduate student offices are near their labs (often with windows into the lab space) and are equipped with printers, refrigerators, and (coming soon) coffee makers. All in all, it is a state-of-the-art building that will serve the department well in the coming years. I can't wait to tell you all about it!
The lab I work in has been a very busy place for the past few weeks, especially for my lab-mate, Megan Pagliaro. She is studying how fish from streams and lakes respond to long-term increases in water temperatures. The expectation or hypothesis is that fish living in places where summer water temperature is warmer will be able to survive higher peak temperatures better than fish from places where where summer temperatures are more moderate. This is kind of like saying that someone from Oregon will be better suited to a Texas summer than someone from Alaska. Megan is using the existence of the urban heat island effect in St. Louis as the source of the temperature difference.
Over the summer, Megan captured fish from sites in about 16 lakes and 14 streams. Each of these sites has also been home to a temperature logger that has recorded hourly temperatures. The expectation is that the lakes and streams that are closer to the city will generally be warmer than those that are farther from the city; factors like lake size and the presence of springs in some streams may influence the water temperature and mute the urban heat island effect. The data from the temperature loggers will help Megan place the sites on the heat island temperature gradient and relate the fish responses to the actual conditions in their home waters.
So how does one go about testing the temperature tolerance of the fish? With a test of the Critical Thermal Maximum (or CTMax). I can share the basics of how Megan did it. First, she acclimated all of the fish to the same moderate temperature. Then she put some of them (11 or 12 at a time) in individual small containers in an aquarium so that all of the fish in the aquarium would experience the same rate of temperature change. Water was pumped through a heater and back into the aquarium to gradually increase the temperature. She would then watch the fish until they experienced a loss of equilibrium (this means that they couldn't stay right-side-up anymore). The temperature when each fish lost equilibrium is the CTMax for that fish. Megan then repeated the test on additional groups of fish. Each test took 2-3 hours, so this process went on for a couple of days.
Megan just collected the last of the dataloggers from the lakes last week and some of the ones in streams are still in the field. I hope to share her results in the future, so be sure to check back in the coming months!
A few weeks ago, Dr. Jason Knouft, the PI of the lab where I work, was busily setting up a microscope and a variety of sterilized tools. Most of the readers of this post will not appreciate how unusual this is. While I'm spending much of my time these days at a microscope to identify the many aquatic invertebrates I've collected, Jason's research efforts are generally spent either collecting fish in rivers or analyzing data using GIS (for my non-tech/science readers, we'll say fancy mapping).
While many wise graduate students would run and hide when such unusual activities begin in the lab, I elected to observe quietly to see where the day would lead. Soon the lab bench held not only the microscope and tools, but also a container of live fish and a cooler with liquid nitrogen. At this point, I knew I would be witnessing an interesting event. Jason was going to be collecting fish tissue for some baseline genomic work.
Soon, Dr. Warren from Washington University arrived and the tissue collection began. I grabbed my phone and started taking pictures to document the process. The fish were anesthetized before being sacrificed to expand our knowledge of fish genetics. Next, brain tissue was removed, packaged, and frozen to preserve the DNA. Since these little fish have small brains, extra muscle tissue was collected and frozen, just in case. All in all, the dissection and tissue collection from 3 fish only took about 20 minutes. The work to read the DNA of these fish will take quite a bit longer.
Scientists do many things. At any given time, a scientist may be planning new studies, grant writing, and collecting data; reading, writing, and revising; compiling, analyzing, and presenting; learning, teaching, and mentoring. And there is waiting: waiting for projects to be funded, waiting for purchased resources to arrive, waiting for feedback, waiting for data to be collected, waiting for collaborators to contribute the next piece, waiting for journals to decide if your work is worthy of their publication, waiting for inspiration... Fortunately, there is so much to do as a scientist that when you are waiting to be able to continue with one task, there are at least four or five urgent tasks that you should be working on. Multitasking has always been a way of life for me, but working on my PhD is taking it to a whole new level.
Currently, I am working on two grant-funded projects. The first is an EPA funded project looking at the transport of road salt in urban stormwater. The funding of this grant has not been impacted by political events; I'm crossing my fingers that this will continue. At this point, I am mostly in the data collection phase of this project: downloading data each month from field equipment and checking to make sure everything is still in place after storms. But there is much more than just data collection going on. In order to fulfill our contract with EPA, I need to generate quarterly reports, plan and carry out public meetings, communicate my work to the general public (I'll be at St. Louis Earth Day in Forest Park if you'd like to say hi!), and make sure the results of my study are shared with the right people to make a difference (ie, publish my work). In order to generate a publication based on the data I am gathering right now, I need to become familiar with a large amount of previous work completed along the same lines as my work. This includes reports on methods of data analysis that I may use, documents that provide guidance to municipal stormwater managers, and many other scientific papers. There is a lot to do!
My second project was funded by the Webster Groves Nature Study Society, a nonprofit group established in 1920 that works to stimulate interest in nature study and observation in the St. Louis area. They graciously provided funding for me to collect and identify the aquatic macroinvertebrates (small water critters) that are living in 20 streams in St. Louis County. I collected my first set of 60 samples (three from each stream) last September and October. Each of these samples included at least 3 types of critters, but many held 10 or more. Each sample also had a large amount of non-critter debris: leaves, small sticks, sand, silt, small gravel, seeds, glass and anything else you can imagine finding in an urban, suburban, or rural stream. Just yesterday, I finished sorting through those 60 samples that I collected almost 6 months ago to separate the critters from the debris and to group the critters in individual containers (mostly by order or family). I will eventually try to identify each to its species, but that will have to wait; for the next few weeks I will be heading back to those locations to collect 60 more samples to sort and identify! In the meantime I will at least make the time to count the number of types of critters I found in each location and see how that compares to the road salt measurements that have been made. Check back soon for that info!