Showing posts with label Grad Student Life. Show all posts
Showing posts with label Grad Student Life. Show all posts

Wednesday, January 14, 2015

Algae Met a Bear: Algae where you'd least expect them!

January 14, 2015 0
Polar bear! In the EVERGLADES?!?!
So how many of you know the poem "Algy"?

"Algy met a bear.
The bear met Algy.
The bear was bulgy.
The bulge was Algy."


I think my dad sang "Algy" to me when I was a little tyke, though in my 3-year-old wisdom I must have taken "Algy" as "Algae" and from then on aspired to become a phycologist. Now, some attribute this verse to Ogden Nash, while others chalk it up to Anonymous (that great and varied writer!). And while this verse may be humorous, it's not truly nonsense (though this sentence is). I've seen analysis of Algy and the bear as an allegory for existentialist being (what does it mean "to be"?), while others just say (spoiler alert) that the bear ate Algy. BUT, I think they're all wrong as a result of a translational error where "Algy" should be "Algae" as my 3-year-old self clearly realized. THEREFORE:

Looks a little green 'round the edges.
"Algae met a bear.
The bear met algae."

These lines are clearly discussing the cyanobacteria that grow in polar bear hair fibers! That's right - there's a type of cyanobacteria (blue-green algae) that lives in the hollow hairs of polar bears. This isn't a natural phenomenon, as the cold habitat of polar bears prevents algae from normally colonizing polar bear fur, but in warmer zoos algae find the hair follicles of the bears a cozy place to set up shop (and turn the polar bears what some think is a sickly "green around the edges").

"The bear was bulgy.
The bulge was algae."

All pictures are a different scale: 1. Polar bear hair (tiny dots are the algae), 2. Close-up of the tiny Aphanocapsa dots, 3. Super close-up of Aphanocapsa montana, aka "the bulge". From Lewin et al. 1981.
These lines are, likewise, clearly categorizing the specific type of the cyanobacteria in those hairs. Lewin et al. in 1981 found that the algae living in polar bear hair were cyanobacteria of the order Chroococcales, resembling the species Aphanocapsa montana. Individuals of this species are unicellular and spherical, described as globules and gelatinous. I think Anonymous added "bulgy" to that description!

Glad we cleared that up.

But from here we can go completely crazy. You know that greenish tinge of sloths? Algae. (This one's really quite cool, too. Sloth hairs have cracks that allow rain to saturate the follicle, which in turn allows algae to grow hydroponically - in this case a green alga named Trichophilus welckeri is most common.

There's a really quite hilarious and informative recent study by Pauli et al. 2014 and article that summarizes a very "crappy" pathway among sloths, moths, and algae - check it out and impress your friends! Make that one sloth-obsessive think twice about that love for adorable sloths. And even a new genus and species of red has been described from sloth hair!)
Cute obligatory sea otter.

I think I also promised a picture of a sea otter. You know what? Algae in their hair, too.

And if we look beyond hair, we see all sorts of epizoic algae (algae growing on animals): on shells, turtles, lizards, manatees! Moral of the story? Wash your hair. Algae are here to take over the world.

Oh? You don't see the relevance of this to graduate research in the Everglades? Well, I could attribute this to the strain of my M.S. research finally getting to me, propelling me into babbling analysis of children rhymes and my research project (I wonder if I could squeeze this into a chapter of interdisciplinary applications of the research...). But, really, I was thinking up ways of introducing those that need no introduction: ALGAE! Pop quiz for name recognition:

Agar, biofuels, harmful algal blooms, ice cream, Naked Juice, nori, oxygen, Spirulina.

This author's personal favorite. And,
yes, it does have carrageenan.
And apparently half the fat. Tasty algae.
If any of those sound familiar, you've likely come across algae in some way or another, either as a product using some algae extract (e.g., carrageenan, a thickening agent, is used in many ice creams and is extracted from the red alga Chondrus crispus) or some other basic function (e.g., algae produce over half of the oxygen in the atmosphere!). Sylvia Lee's already written about "What is algae?" so I won't elaborate beyond "the bulge" (as above). But, instead, what's the big deal about algae in the Everglades? Well, you're going to have to stay tuned for next week's (?) episode of Nick's Wonderful World of Algae. I see you all waiting as eagerly for it as for new episodes of The Walking Dead or Game of Thrones, etc. But what about The Walking Algae or Game of Cyanos?

A teaser: I mentioned algae on manatees. Dr. Tom Frankovich from FIU has actually looked into diatoms that live on manatees 'round these parts - super cool stuff. You may have noticed manatees that look a bit mossy. Let's amend that to "algae-y" and start singing, "Algae met a manatee. The manatee met algae." And they lived happily ever after.
D'aww. From: Fish and Wildlife Service
Tags # Algae # Carbon # climate change Continue Reading
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Thursday, September 11, 2014

Okeechobee or Okoboji? An Everglades Student’s Corny Tale

September 11, 2014 0

This post was written by Nick Schulte, a Master's student in Evelyn Gaiser's lab at Florida International University. 

So where would you go to study how Everglades algae respond to increased nutrients from sea level rise? The Florida Everglades, right? That’s what I thought. But I went to Iowa.


Iowa Lakeside Laboratory, more specifically, on the shores of Lake Okoboji (yes, I still confuse it with that big lake in the northern ‘Glades). A bit clearer but still unhelpful? This summer I attended two courses at Lakeside: Ecology and Systematics of Diatoms and Ecology and Systematics of Freshwater Algae. In that order – specific to general, that’s how it’s normally done, right? Start looking at the fineries of a specific group of algae (“the algae that live in glass houses”, or diatoms) and then see how they fit into the bigger picture of general phycology (“phykos” for “seaweed”). It actually makes a lot sense, especially when my research pays particular attention to the changes among the diatoms within algae communities in the Everglades (now I’m finally getting to the point). And it just so happens that the place to learn about diatoms is 1,800 miles from South Florida (or a 26-hour car drive, but who counted?). So while many of my peers were up to their knees in peat or swarmed by mosquitoes in the mangroves of the Everglades this summer field season, I was swarmed by mosquitoes by the lake, up to my knees in what many would call “lake scum”, and up to my eyes in diatoms in Iowa. And it was excellent.

Life at a biological field station is an experience completely its own, and as such it’ll get its own blog post! But suffice it to say, here, that it facilitates connections that are hard-pressed to forge elsewhere – connections to the research, to faculty, to peers, to the community, to nature. And it is my good fortune that Gene Stoermer established a “Diatom Clinic” at Lakeside in 1963 and that this course has persisted for 52 years, taught by Gene, Charlie Reimer, Gene again, and now Mark Edlund and Sarah Spaulding – all rock stars in diatom science committed to grooming new generations of diatomists. And the intrigue and utility of diatoms (boy, what a boring book title – we’ll have to think of something better) is such that students from all over the world – literally – come to this Great Lakes region of Iowa each summer to gain a proper education and exposure to the wonderful world of diatoms (getting there. But, really, “Great Lakes region of Iowa”?! Whoever heard of such a thing? Sounded like science fiction to me.). The class is capped at ten students per summer (one four-week session), and this year we came from Miami, Delaware, Colorado, Utah, MinnesOta, Montana, Ontario, and Colombia – with some old class T.A.s who can’t get enough from Arkansas and Macedonia. In short, students and professionals come from all over for a very focused class on a very focused group of algae that many people probably don’t know exist.

But, why? Why diatoms? If you can’t even see these microalgae, why even care? Why not care more about the cursed algae causing that green scum layer on my mom’s supposed-to-be-blue pool? Or those algae being used to solve our fossil fuel dependency? Well, we do care about those – I think cf. Thomas jeffersonii is keyed out as having “all algae are created equal” in its striae pattern (who wants to erect that genus?!) – but some pay particular attention to diatoms for a variety of reasons. And you can see diatoms – but few with the unaided eye. But when a bunch of 10 µm cells (1/1000thof a millimeter) hold a party they can be seen collectively (but only if you want to be seen as a party crasher). If you’ve ever fallen ungracefully into a lake because you slipped on those muddy rocks, don’t curse the mud but the diatoms and the mucilage they produce. Actually, I wouldn’t curse them – maybe reprimand them for their slippery inconvenience – but get to know them (especially now that you’re intimately acquainted, having fallen face first into a nice community [biofilm] of them). When you get to know them you realize that diatoms. are. awesome.

              E Pleurosira Unum? Creepy.

Diatoms are generically and specifically diverse (see what I did there?), widespread, productive, and tasty; they throw great house parties (just don’t throw rocks – their cell walls are glass after all); and they keep on giving after they’ve stopped living. They’re the algae you want to get to know at a party, the ones that always have your back and will give you good guidance in times of trouble (just like Mother Mary). They’re your best friends in the algae world.

Want to know why? Why choose diatoms over beautiful kelp forests or tasty nori (Porphyra, a red alga ‘seaweed’) or nutritious Spirulina (cyanobacteria)? Will Nick be held accountable for such a preposterous claim (after all, who 
doesn’t love sea otters?!)? Will we ever get to the “wonder” in the Wonderful World of Diatoms? Tune in next week for even more humorless asides and frustrating skirting around the facts (we are in a bit of a political lull, though!). Tune in next week for these answers and more!

(In all seriousness, thanks for reading this far, and I really do hope you’ll continue with this series!)




Tags # Algae # Diatoms # Ecology Continue Reading
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Monday, June 17, 2013

Florida Coastal Everglades in the Classroom

June 17, 2013 0
PhD students at FIU are required to teach a lab for two semesters.  So, for the past two semesters I have been a teaching assistant (TA) for Ecology lab and have thoroughly enjoyed the experience.  A typical ecology lab consists of a large majority of pre-professional students (pre -med, -dental, -vet, etc.) who need an upper-level elective.  Translation:  many students are enrolled in Ecology because they have to.  I don't expect my students to change their career paths and become ecologists; I simply want them to understand why ecology is important.  Memorizing terminology and examples, while they have their place, are not as useful in the long-term – it’s the experiences and hands-on activities we remember.   I am an ecologist and all I remember from my undergraduate ecology class is going out to my university’s nature preserve looking at species abundances and distributions.  If a student who is preparing for a career in ecology and research doesn’t remember that she (or he!) learned about Trophic Cascades as a 19 year-old biology major, how can we expect students preparing for a career in medicine to remember similar concepts?

Sorting through a seine sample for our Marine Ecological Processes lab (Texas A&M Univ- Corpus Christi).

Throughout the semester we investigate many topics, such as sampling techniques, species distributions, life tables, species interactions, and ecosystem metabolism around FIU’s campus and in the FIU nature preserve.  We also take a trip to Fairchild Tropical Botanic garden where we discuss the importance of Botanic gardens to conservation and education programs.

Photo of Ecology Lab students being photographed interacting with a volunteer at FTBG!




Our lab culminates in a trip to Everglades National Park where we visit different habitats such as, Taylor & Shark River Sloughs, hardwood hammocks, pine rocklands, mangrove lakes, cypress domes, and Florida Bay.  During this trip we discuss all the topics discussed in lab as a way to bring the concepts to reality.  We also emphasize the importance of ecosystem conservation, restoration, and habitat connectivity.
Ecology Lab students exploring and learning about Cypress Domes.
Most importantly, through the field trips and field exercises students get the hands-on experiences necessary for them to truly appreciate ecology and the complicated processes at play in each individual system.  
Tags # Education and Outreach # Everglades restoration # Field work Continue Reading
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Thursday, February 21, 2013

4 Things I Wish I Knew Before Starting Grad School

February 21, 2013 0

Gastric bypass- a wonderful alternative to graduate school

'Tis the season of grad school acceptances and major life choices. Two years ago (!) I was an overly confident undergrad preparing to become a graduate researcher. Late night Googling of "how to prepare for grad school" further assured me I was ready. Have experience in a research lab? Check. Know I may have weird hours? Check. Secured some kind of TA/RA funding? Check. Today, reflecting upon this time of year, I wish someone would have told me about a few aspects of grad school that seem to never be highlighted on those "What to Know about Grad School" websites:


1. Yes, being successful in grad school is about working hard, but it’s even more about being creative.

Probably in your undergrad studies, the more time spent on homework or a project was directly proportional to your grades or success. I assumed that since I was a hard worker and previously worked in a research lab, I would be a great grad student. However, once you enter a graduate program, you are likely designing your own study and teaching yourself research methods. In other words, your success is entirely dependent on your creativity. If your plan is to research whales in the Antarctic, for example, you will have to figure out HOW you are getting to the Antarctic, HOW many whales you are tagging, HOW you are tagging the whales, and most importantly, HOW you are paying for it- not your advisor, not your department, not your best friend- YOU. Also, you will have to go way beyond the idea of “I want to study whales in the Antarctic.” You will have to come up with testable hypotheses, such as “Using complicated organic chemistry, I will show that the number of female whales in January positively correlates with annual apple harvests in United States- here’s how I will experimentally prove it…”

2. Often in the sciences there is not a specific timeline for graduation.

Many students entering grad school enter with the belief that getting a master’s degree will be completed in exactly 2 years while a PhD takes 4 years to complete. Most people are familiar with the undergrad concept of schooling: when you earn X number of credits, which should take Y years to complete, you get your degree. The timeline of your graduation, however, is ENTIRELY dependent on your thesis/dissertation progress. Have your class credits out of the way? GREAT! Experiments not working- well, you’re staying here another 3 years.

3. Be prepared for the fact that no one will respect your “flexible” schedule.

Because you likely aren’t confined to a 9-5 schedule, your friends with "real jobs" will assume you are always available to talk on the phone, pick them up from the airport, help them move, do their weekly grocery shopping, groom their monitor lizard, etc. Additionally, when they are free from work, they assume you are as well. “Hey, I got tickets to Soviet Russia the Musical without consulting you; you can write your thesis some other time.” The best way to deal with this is to simply lie: “I teach 9 classes and no one can replace me.”

4. Unless you clone yourself, someone will see you as a bad grad student.

Many times you will have an obligation to be in 3 or 4 places at once.  Tomorrow, for example, I have boat crew training, which is required for my field work.  This time spent on training, however, means I'm not working on my thesis writing, not working on homework, not available for makeup labs with my students, and not attending the weekly grad seminar.  Somewhere along this line, a student of mine, a professor in my department, one of my committee members, or my neglected dog will wonder where I am and why I am a horrible person.  And why did I spend so much time writing this blog post?
Tags # Amber Kiger # Data # Field work Continue Reading
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Tuesday, November 20, 2012

Helpful Websites - My Parting Gift to You

November 20, 2012 0
As I sit here struggling to write my very last blog post, I wonder "What can I leave people that they'll find useful in any way?"  I could provide meaningful insight on what it was like being a graduate student in my lab, but my thesis sucked all the meaning out of my brain and suddenly I can't even manage to put two sentences together that make sense.  So instead, the most useful thing(s) I can leave you all, is (are) my bookmarks!  Those that know me know how incredibly organized (read: obsessive compulsive) I am, so over the last 2.5 years I've collected quite a bit of useful internet knowledge and organized it into various categories on my computer.   So, as my parting gift to you, I leave you these helpful links on everything from job sites, to SAS codes, to data portals, and most importantly, sites for procrastination.  I can't promise these links will stay active forever, but last I checked they worked.  So enjoy!
  1. GIS DATA
    2. From here.
    • FIU GIS Center has some helpful tips/links: http://gis.fiu.edu/maps-data/finding-guides/
    • Everywhere
      • http://datagateway.nrcs.usda.gov/GDGOrder.aspx
      • http://glovis.usgs.gov/
      • http://earthexplorer.usgs.gov/
      • http://data.labins.org/2003/
    • Florida
      • http://www.fgdl.org/metadataexplorer/explorer.jsp
      • http://www.sfwmd.gov/portal/page/portal/levelthree/GIS
      • http://fcelter.fiu.edu/data/GIS/interactive_map/
      • http://sofia.usgs.gov/eden/stationlist-area.php?area=ENP
  2. SAS Codes
    3. From here.
    • A long list of codes: http://core.ecu.edu/psyc/wuenschk/SAS/SAS-Programs.htm
    • Various info on stat methods with SAS examples: http://www.uvm.edu/~dhowell/StatPages/StatHomePage.html
    • Not sure which test to run?  Check this handy dandy table out: http://www.ats.ucla.edu/stat/mult_pkg/whatstat/choosestat.html
    • Poisson: http://www.ats.ucla.edu/stat/sas/dae/poissonreg.htm
    • Repeated Meaures ANOVA: http://www.ats.ucla.edu/stat/sas/library/repeated_ut.htm
    • Linear Models from Littell et al. 2002: http://faculty.ucr.edu/~hanneman/linear_models/c8.html
  3. Job Sites
    4. From here.
    • http://wfscjobs.tamu.edu/job-board/
    • http://fisheries.org/jobs
    • http://www.sws.org/jobs/
    • http://www.erf.org/taxonomy/term/2
    • http://esa.org/careers_certification/jobLists.php
    • http://www.conbio.org/professional-development/scb-job-board/
    • http://www.aslo.org/jobs.html
    • https://careers.nature.org/
    • http://www.nwf.org/About/Jobs-at-NWF.aspx
    • http://www.oceanconservancy.org/who-we-are/about-employment.html
    • http://www.edf.org/jobs
  4. Procrastinate!
    5. From here.
    • http://whatshouldwecallgradschool.tumblr.com/
    • http://www.phdcomics.com/comics.php
    • http://www.mcsweeneys.net/articles/back-from-yet-another-globetrotting-adventure-indiana-jones-checks-his-mail-and-discovers-that-his-bid-for-tenure-has-been-denied
    • http://www.mcsweeneys.net/articles/faq-the-snake-fight-portion-of-your-thesis-defense
    • Cook this cajun dish and thank me later: http://www.nola.com/food/index.ssf/2008/05/lorin_gaudins_crawfish_etouffe.html
Tags # Data # Grad Student Life # Jobs Continue Reading
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Wednesday, October 24, 2012

How to Hate Ecology and Still Write a Thesis

October 24, 2012 0
How to Hate Ecology and Still Write a Thesis
During my first year as a graduate student, a week didn't go by where someone didn't ask me "So what's your research question?"  I hated that question more than anything.  I had combed the literature, searching for research ideas, only to discover everything I was interested in had already been done a hundred times over.  All of the mysteries of the environment had been answered and there wasn't anything left to be studied.  "Why am I even here and why are any of us doing science," I frequently asked myself.  "Ecology is stupid.  Ecology is hard.  I hate Ecology!" were also common chants I shouted in my office (and by office, I mean the spare lab next door that was used for storage and sleeping quarters for homeless grad students).  Then, one day, it suddenly all made sense.  I realized I was being punished by my adviser, because he was punished by his adviser, and his adviser's adviser punished him, etc. etc....


Then I stopped blaming the world, sucked it up, and read some more literature.  Every idea I had, I wrote down.  I carried around a notebook to every meeting, every class, and any time something came to me, I wrote it down.  Alot of them were bad, very bad.  But I wrote it down anyway.  It fostered more ideas which led to even better ideas which then led to terrible ideas, and so on and so forth.  I shared them with fellow labmates and post-docs who helped me refine them.  I had meeting after meeting and exchanged numerous emails with my adviser, who dismissed many of my ideas and forced me to use my brain more than I ever had.  Eventually, I figured it out.  Ecology didn't seem so stupid anymore.  It was still hard...very hard.  But it wasn't stupid and I didn't hate it, at least not as much as I once did.  

And so my lesson to you, boys and girls, is that it's o.k. to hate ecology.  Spit on it, kick it, throw it in the trash for a week and ignore it.  It doesn't mind.  It will still be there waiting for you to explore its insides.  Although often times it's hard to see this, there are still plenty of mysteries to be solved.  Heck, you may even find a new species of monkey or discover millions of microscopic marine life.  

That's my story and I'm sticking to it.
Tags # Ann Hijuelos # Ecology # Grad Student Life Continue Reading
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Thursday, October 11, 2012

Toto, I don’t think we’re in Kansas anymore!

October 11, 2012 0

Guest post today from a new member of the FCE community!
--------------------------------------------------------------------------------------------------------------------------
Howdy ya’ll! I’m one of the newest members of the Trexler lab, here all the way from Houston, Texas. I finished my Masters in May, which focused on reproductive life histories of small stream fishes. In addition to working in some amazing clear water East Texas streams, I have a love/hate relationship with springs in the beautiful West Texas Chihuahuan desert. But, life hasn’t all been unicorns and butterflies; I’ve worked in my share of dumpy freshwater sites. However, nothing prepared me for what I was to endure in the Everglades. 


Don’t get me wrong, I am in no way suggesting that the Everglades are “dumpy,” but rather mysterious and frankly, comedic. This past summer I was lucky enough to (literally) get my feet wet in the Everglades. I was excited, yet terrified. In Texas, alligators eat people… or so the story goes. I envisioned myself on this amazing airboat ride, only to get my calf taken out by a man-eating reptile. My first trip to the glades was with Mike Bush, who suggested I “shuffle my feet” to avoid gators. Seriously Bush?! I doubt “shuffling my feet” is going to keep a gator from eating me!! Anyway, he may or may not have been right, but I did not encounter nor become the dinner of an alligator. Day two was much more eventful; it was pouring rain and I had no rain gear. We were setting up drift fences made of 32 lbs of rebar (this may be a slight exaggeration) and I somehow managed to step in every chin-deep hole in the Gap (area between Water Conservation Areas 3A and 3B) while carrying these fences. My waders were filled with water/mud, the rain was freezing and I had a soggy pb&j for lunch. If you can believe it, I came back for thirds. 

Setting up drift fences.  Photo courtesy of Eric Fortman.


After a couple of interesting trips, I discovered the beauty and elegance of this system. In particular, Shark River Slough and Taylor Slough were some of the most amazing sites I've seen to date. The sheer size of this ecosystem is astonishing and the more I learn about its flora, fauna and ecology, the more intrigued I become; I have even learned to befriend (but respect) the gators! I am extremely lucky to have the opportunity to work in the country’s most prized restoration project. I guess Marjory Stoneman Douglas had it right- “it reveals its secrets slowly…” After traveling to almost every corner of this amazingly diverse ecosystem, I came to a couple of conclusions: 1) The Everglades are amazing, and 2) The Gap must be part of the ‘Truman Show’ and Mike Bush is the main star. 

Photo courtesy of Eric Fortman.



Jessica Sanchez
Doctoral Student
Florida International University
Department of Biological Sciences
jsanc318@fiu.edu
Tags # Alligator # Grad Student Life # Guests Continue Reading
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Friday, September 21, 2012

Epiphanies in Ecology

September 21, 2012 0

For Long-Term Ecological Research (LTER) research in the Seagrass Ecosystems Lab, we venture out into Florida Bay every two months to do a survey of the submerged aquatic vegetation (seagrasses and macroalgae).  As I mentioned in my last post (Florida Bay:  Beneath the Surface) Florida Bay is a honeycomb of basins, which creates different habitat types.  These different habitats, specifically the type and density of vegetation on the floor and sediment type (and many other factors that are beyond the scope of this post), attribute to the color of the water.  In a single LTER trip, we see water ranging from deep blue to teal, green, and even brown!   After 2 years of running the LTER project for our lab, I am still amazed by the dynamic nature of Florida Bay on the surface and below.

Darker blue waters as we travel to Sprigger Bank.
At Sprigger Bank:  notice the greenish patch to the left.  There is sparse shoal grass (Halodule wrightii) in that patch.  The darker areas have turtle grass (Thalassia testudinum) and manatee grass (Syringodium filiforme).
Milky teal waters of Duck Key.
Duck Key on a different day.  
Little Madiera a week after TS Isaac passed through.  Little Madiera is located near mainland Florida and receives a lot of freshwater input, especially after a major storm like Isaac.   
 During my first year as a PhD student, these LTER trips were pivotal in maintaining my sanity and reminding me of the reasons I became an ecologist.  As I have developed as a scientist, these trips have become more of a gateway for the development of research questions to test different theoretical concepts that we have studied in depth in our classes.  I’m a very visual person and being outside helps me to connect the dots between theory and the development of research questions.  I guess you could say, nature is my muse (sorry for the cliché but I really couldn't resist!).  For the most part, major discoveries in science have been made rather serendipitously.  I have come up with many research questions while being on the LTER and, needless to say, I am not the only scientist who does this.  See a great example of what may have started as an ecological epiphany in Science Magazine.  I can only hope that when I grow up my epiphanies will be published in such high-impact journals as Science or Nature!  Until then...
Tags # Florida Bay # Grad Student Life # Jenn Sweatman Continue Reading
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