MSC in the News!
The local magazine, Northshore Magazine, gives props to our excellent science and outreach programs. Take a look at the story beginning on page 70!
http://www.mstand.com/publication/60293
Thermotaxis is better than incometaxis.
Note the chiller on one end, and the heater on the other. I hope to add section dividers and a light flow to establish a linear temperature gradient.
One topic that really interests me is thermoregulation, which is essentially an organisms ability to regulate its internal body temperature in spite of a changing environment. We see exhibits of thermoregulation all the time– such as a dog panting after exercise or in hot weather, or my collection of winter coats, snowpants, and hats that I need stay warm while skiing (or just to survive Boston winters). Thermoregulation is more difficult for animals that can’t internally regulate their body temperature, such as a turtle or a crab. In this case, we often see a phenomenon called ‘thermotaxis’, where the animal moves towards warmer or colder temperatures to regulate their body temperature. Right now I am building a tank with escalating temperature gradients to run some experiments on thermotaxis. Here is a sneak peek at my design!
Sea star sink surprise!
This morning I went to wash my hands and stumbled across this:
Oh it’s just a constellation of sea stars acclimating to some seawater before settling into their new home: a touch tank.
Touch tanks at the Marine Science Center are set up by the Outreach Program which runs a wide variety of classes, public lectures, and other events open to the public. More info can be found here.
On Thursday, I presented my research in poster form at the annual Northeastern Research Innovation and Scholarship Expo (RISE). After doing an oral presentation at Benthics (the conference that Kylla and Liz blogged about) presenting a poster was pretty fun and relaxing. Usually its a one on one interaction and you can explain your research in a more casual way than in an oral presentation. Also, its less commitment for someone to come ask you about your poster, than to attend an oral presentation, so you often get visitors to your poster who aren’t necessarily experts in your field of research. This is cool for two reasons: 1) you get to enlighten someone about a subject they might have previously known nothing about (stay tuned for fun story about this perk later), 2) you can get fresh insight about your project from someone who hasn’t already tired their brain out thinking it.
Judges circled around the many posters, stopping to hear the presenter’s “pitch”, a short 3-5 minute synopsis of your poster. This took a bit of preparation on my part: I could talk about my research forever! So 3-5 minutes was a challenge. Luckily, all the judges were very friendly. In fact, learning about my research brought back memories of SCUBA diving here at the MSC on Canoe Beach for one judge, and inspired a story of seasonal fluctuations creating algal blooms in a backyard pond for another.
In addition to the official judges, everyone attending was a judge, in some respect. All presenters and attendees of the expo received 3 research dollars to be distributed to whoever they thought had the best research idea that deserves additional funding. Whoever collected the most research dollars by the end of the expo won the “People’s Choice Award” and received actual dollars to fund their research.
The winner of the people’s choice award was a group of undergraduates who have designed a personal fitness tracking device that sends physiological information right to your smart phone/computer. My favorite part is the name: SQUID. Check it out in the video below:
Inverts & Extroverts: Presenting at Benthics
Our own Kylla presenting her fancy statistical modeling of intertidal algal ecosystem biodiversity.
Last week is now a blur – Benthics went by much too quickly. This was my second time attending the conference; the first time I went was two years ago when it was held at my alma mater (for my masters), UNC Wilmington. I gave an oral presentation both times – and although I felt a bit less nervous leading up to the presentation this year, by the time I got up to give my talk I had butterflies – and the presentation itself flew by. In fact, when I finished my talk, I was so shocked that I had not gone over my 15 minute time limit, I figured I must have forgotten to say a bunch of stuff. I was happy that I got a number of questions from the audience – but not having prepared answers in advance, that part did not go as well as I would have hoped. But, in the end I got some great feedback from people and made some new contacts, so it seems the other benthic ecologists were quite forgiving!
Leading up to a meeting, it’s my natural instinct to think, “do a poster!” After all, you still get to go to the meeting, interact with the other scientists, and get some feedback – with the bonus that it is a more informal presentation format. The idea of presenting a talk and getting up in front of a group of scientists (of unknown backgrounds with unpredictable questions) and presenting your work (a very personal endeavor) can be quite scary. At the conference, it was apparent that many faculty, who have been doing this for years, are at ease and animated in front of a large audience (at least, they make it look easy). I am nowhere near that stage, but while it is intimidating, giving presentations is an important step towards confronting the fear of public speaking. What you may learn is that you can have some slip ups and in the end, not only do you survive, but some people might even come up to you and share their excitement about your work. I figure, do that enough and eventually messing up a little isn’t something you need to spend your time worrying about. Looking back at the questions I wish I had answered better, I like to think of it as a learning experience so that I can better prepare for sharing my research in the future.
Rasit (my husband) armed and ready to put up his poster on phylogeography of decapod crustaceans in the Mediterranean and Black Sea.
The major benefit of giving a talk is the ability to share your work with a broader audience. This means it’s more likely that people who know something about what you do can give you some feedback, and people interested in working with you can approach you with ideas. Whether you decide to give a talk or present a poster, the most important thing is getting out there and talking with other people. The people who know a lot about your field can help you with analyses and keep you up-to-date on how other researchers are approaching similar questions, and the people who are not familiar with your subject are great for providing a real-world perspective and for learning how to explain the importance of your research to others. The MSC had an impressive showing at Benthics this year with about ten excellent talks and posters by students, our postdoc, faculty and collaborating students who did their fieldwork at Nahant. At the banquet on the final day of the conference, it was announced that next year’s meeting will be held in Savannah at Georgia Southern University. Hope to see you presenting your research there!
In 2010, the Benthic Ecology Meeting started a new tradition of hosting a film festival of ocean-themed short movies that range from light-hearted music videos to hard-hitting in-your-face documentation of anthropogenic threats to our oceans. The increase in quality and artistry of the films in just two short years is amazing! Props to all the film makers that presented this year!
Here are a few that I think are a must see by my self-imposed categories, enjoy!
Movies with a message
Plastic Future: The Midway Story
High Cuteness Factor
Are Some Weddell Seal Pups Couch Potatoes?
Just for Fun
Science explained via art
Trophic Cascades of the Purple Marsh Crab (disclaimer – this was my favorite!!!!)
Reporting from the Road: MSCers @ BEM 2012
Hello from the South!
I and six other MSC grads are at the Benthic Ecology Meeting in Norfolk, VA!
This year we decided to be adventurous and drive all the way from Nahant; the highlight of the trip was crossing the 20-mile Chesapeake Bay Bridge-Tunnel complete with dolphin and cool bird sightings.
I’ve been enjoying catching up with old friends, colleagues, and advisors (my undergrad, MS, and PhD advisors all under one roof -yay!) and hearing about exciting, current research from students and faculty. Some highlights of talks I really enjoyed so far…
Dr. Sarah Henkel is doing the ground work (conducting baseline surveys) to look at possible community effects of setting up buoy systems for wave energy development off the coast of the Pacific Northwest by identifying how infaunal communities vary over depth, longitudinal and habitat type (sediment/grain type). Dr. Henkel put the potential impact of these buoys in perspective – the anchors are roughly the size of a standard two-story house and the buoy is about the size of a small high rise building. Once an array is established you’ve got yourself a small city and suburb underwater! These baseline community surveys will be essential for making informed decisions about where to establish such technology.
Justin Campbell, a student in Dr. Fourqurean’s Lab of FIU, did an in situ ocean acidification study for an entire year (!) using a pretty nifty experimental design to pump CO2 onto seagrass beds to look at OA effects on the seagrass epiphyte community. Justin found that CO2, but not nutrients (eutrophication), had negative effects on calcifying epiphytes but positive effects on fleshy epiphytes causing a change in the epiphyte community structure with ocean acidification.
Jeremy Long, invoking the wisdom of Missy Elliott, explained how snails answer the question “is it worth it?”, when choosing between avoidance of predators or foraging, depends on traits of the plants they are feeding on.
All the MSCers that have presented so far have done an awesome job! Looking forward to seeing the rest of my colleagues show off their research!
Who Doesn’t Love Strawberries and DNA?
Today, I had a fantastic visit with the girls at Girls Inc. in Lynn, where our outreach fellow, Sarah, runs the Beach Sister Program. The program is dedicated to teaching girls about marine biology and environmental issues, but it’s also about introducing them to scientists and showing them that they can do science too. I brought some photos of my fieldwork with corals and then we talked about DNA and did a strawberry DNA extraction using household products. In all honesty, I had no idea how excited they would be about DNA and doing the extraction. It was awesome!
I mean, DNA is cool – as we all know from CSI – but the concept of DNA can be a bit elusive. It’s in our cells and the cells of all living things, but it can be hard to visualize, and this simple project can make it more tangible. Even when you work with DNA in a molecular biology lab, you may only see DNA as a little white dot at the bottom of a tube, or as a band fluorescing with ethidium bromide on a gel, or see the evidence of it as a list of As, Cs, Gs and Ts in a computer file. DNA is small by our standards, but there is actually quite a lot of it in our bodies and in the living things we see all around us, and yes, it’s in the things we eat.
Extracting DNA from a fruit, like a banana, or some strawberries, is quite easy and can be done with common household ingredients (a list with links to protocols and demonstrations is at the bottom of this post). Strawberries are good because they are fun, colorful, AND octoploid (they have eight sets of chromosomes), which means they have lots of DNA. However, the girls could not come to a consensus on whether the strawberry/DNA extraction buffer mixture smelled ‘good’ or ‘gross’. If you want to get more personal, you can do a very similar procedure to extract your own DNA from epithelial cells in your mouth… Although, that little clump of DNA has nothing on the snotty gob of DNA you will get from the strawberries. But, that’s up to you… why not try them both?
Tomorrow I am heading to Norfolk, VA for Benthics (aka, the Benthic Ecology Meeting), and I hope the audience for my talk there is as excited as my audience today. Since my talk is on Saturday, close to the end of the conference when everyone will be worn out from two and a half days of powerpoint presentations, maybe I should stock up on some household DNA extraction materials, just in case.
All you need is:
- Your fruit of choice
- A ziplock bag, a clear cup, and a measuring spoon & cup
- Water
- Dish soap, or hand soap, or shampoo
- Table salt
- A strainer, or a coffee filter, or cheese cloth, or a (paper)towel
- Isopropanol, or ethanol (these will work best when chilled)
- A popsicle stick or stirrer
Protocols & Demonstrations for the Strawberry DNA Extraction:
Spring Break Experimentation
Last week was Northeastern Spring Break! Woohoo! This meant I had no class, and no TAing and therefore more time for research! I saw this as the perfect opportunity to do experiments, uninterrupted by the usual commitments of the week.
I study seasonal nutrient cycling in coastal ecosystems and based on data I have collected over the past couple years, I know that this time of year is the time when essential nutrients like nitrogen are most abundant in coastal waters. This means that seaweeds can take up more nutrients, and store these in their tissues, to prepare for the summer when there will be limited amounts of these essential nutrients.
Work by other scientists (and some of my own previous experiments) shows that snails and other animals that eat seaweed might choose to eat different seaweed based on a variety of things, including the amount of nutrients they can get from the seaweed. Also seaweeds living at different places on the beach have different access to nutrients because they spend different amounts of time underwater when they can absorb nutrients.So a seaweed living low on the shore might be more tasty to a snail because it has more time to absorb nutrients and therefore has more nutrients in its tissues. Finally, seaweed might be more tasty to snails depending on whether the seaweed it is an adult or a baby.
Yummm seaweed!
The experiment that I did tested these factors that might change the way that snails and seaweeds interact. I chose to do the experiment in March, because I have done similar experiments in April and June and I want to see how the interactions I observe change with season. For the experiment, I put seaweeds and snails in “mesocosms” (fancy word for reusable plastic containers – see photo) to see which seaweeds snails like to eat: seaweed living high or low on the shore, and seaweed that is an adult or baby. I let snails choose between all combinations of these types of seaweeds, and weighed the seaweed before and after the three-day experiment to see how much of each seaweed the snails ate.
Snails escaping from mesocosm!
My favorite part of this experiment is that it also allows me to test the positive effects of the snails on the seaweed. So, I know right now your asking“What? Positive? I thought the snails were eating the seaweed?!”, but in addition to eating seaweed, snails can also benefit them by excreting ammonium AKA snail pee! The ammonium can be an important source of nitrogen for the seaweeds – facilitation! The experiment is set up so that I can measure how the seaweed grows when it’s being eaten, when it’s benefiting from extra nutrients via snail pee and when no snails are around at all. Positive interactions are neat, and understudied in the field of ecology, because negative interactions are much more obvious. Its easy to see a lion eat a gazelle, but much harder to see a snail pee on a seaweed, increasing its growth.
Season, snails and seaweeds mediate nutrient cycling on rocky shores
Why do you care about which seaweeds snails eat, you might ask. Well, these seaweeds and snails provide important nutrients to the whole community of organisms living on a rocky beach, so learning more about how they interact, and how those interactions can change with season, is essential to predicting how the whole rocky shore ecosystem might be affected by human impacts like pollution and climate change.
This experiment was very labor intensive – I weighed 480 pieces of seaweed, twice! But luckily I had some help from an awesome high school student volunteering in our lab – thanks Hannah! Also, I’m sure the neat results will make all the hard work worth it. So get excited for ground-breaking conclusions about seasonal, tide height and seaweed life-stage impacts on seaweed-herbivore interactions and rocky shore nutrient cycling – once I analyze the data!
BEM and the Art of Heat Maps
Sample heat map showing expression of 6 genes (listed down the side) for three samples from each of two treatments (A & B; labeled along the top).
The Benthic Ecology Meeting is coming up in a couple of weeks – which means I am trying to get my presentation finished up. I study gene expression in corals, comparing how genes are expressed differently in different parts of the colony. The best visual way that I know of to present gene expression data is through heat maps. Basically, these consist of a list of genes (transcripts) with the amount of expression in each of your samples – where the relative value of expression is color coded (usually red is high expression and blue is low expression).The example on the right shows how 6 genes from 3 different functional processes could be expressed. Genes 1 & 2 are consistently expressed more in in the A samples than the B samples. Both genes 1 & 2 are associated with one functional process, so this suggests that Process 1 is upregulated in treatment A. Genes 3 & 4 show the opposite pattern for genes in Process 2 [I should add that increased expression of an inhibitor would actually mean downregulation of a process... so it can be complicated]. Whereas genes 5 & 6 show no consistent pattern of expression among the two treatment groups. A functional process could be something like a signaling pathway involved in development, or a synthesis pathway involved in producing structural molecules.
Heat Map Eye Candy. This should probably be marine themed, but... well, feel free to imagine it is a spiny fish...
You can make heat maps in the program R, but the Broad Institute has a couple of relatively user-friendly programs that are more straight-forward and don’t require any coding. The one I just started to use is called GENE-E, and for my purposes it has some major benefits over the program that I used to use, GenePattern. I made a bunch of heat maps for my data, and it definitely helps me to see the data expressed this way in order to pick out patterns. But, all the tiny blue and red squares are making me a bit cross-eyed. So, on my nerd-break I crafted this… porcupine (in soothing fenerbahce colors).
Looking forward to finishing up this presentation and sharing my data with the world (of benthic ecologists) soon!
