Susan B. Anchovy: the story of a whitefish

When you study fish in Alaska, you may find yourself covered in slime. During one slime-intensive day, Duncan Green and his field assistant were wading in knee-deep ocean 200 feet offshore. They looked back to see a polar bear perched on the bed of the truck, sniffing around for helpless terrestrial mammals covered in delicious fish goo. In reality, the bear was probably just checking out the truck, but Duncan had to call for someone to drive out and scare the bear away before they could head back in. Just another day in the life of Duncan Green, fish biologist!

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At the end of an exciting 2017 field season, 220 fish, including the illustrious Susan B. Anchovy and Edgar Allen Cod, were live-shipped on ice from the North Slope to the University of Alaska Fairbanks campus. Duncan studies broad whitefish (Coregonus nasus), an Arctic Alaskan species that is an important subsistence food for coastal villages like Kaktovik, Nuiqsut, and Utqiaġvik. Although it is well known that the Arctic is warming faster than other parts of the planet, it is not well understood how ecosystems will respond to this change. To add one small piece to this big puzzle, Duncan is investigating how warming waters may influence whitefish growth rates. Will Susan and Edgar grow big and healthy in warmer waters? Or might they be stressed by an environment that’s just too hot, inhibiting growth? Time, and the data, will tell.

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Duncan is a well-rounded man. Beyond his identity as an aspiring fishy scientist, he is also a fat-tire biker (completed the White Mountains 100, a human-powered race through Alaska’s Interior), makes a mean pizza cake (fourteen layers of frozen pizza and pizza rolls, baked all together and topped with cream cheese frosting), and also ice fishes for fish for food. Itching to hear a classic cinematic monologue? Duncan delivers a moving recitation of Quint’s “Indianapolis” speech from the 1975 film Jaws. In short, Duncan is a most colorful person and adds a lot of life to any potluck, field expedition, or fish-naming production.

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P in streams

I work with some incredible grad students at the University of Alaska Fairbanks. Today, I’d like to highlight research led by Sophie Weaver, a student in the Biology & Wildlife department.

When asked about her research, Sophie likes to say she studies “P in streams.” Sophie is investigating how differences in nutrient availability might affect the growth of the organisms that make up the green scum, or microbial skins, that one slips on when crossing a stream. Besides phosphorus (the “P” in her descriptive quip), she also works with nitrate, ammonium, and acetate.

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Sophie with her little blue cups.

After adding various nutrients to little blue cups, she launches them in her research streams. Post-incubation, she collects the cups to measure the abundance of autotrophs (critters that produce their own energy) and heterotrophs (critters that, like us, consume delicious things to produce energy). The ratio of autotrophs to heterotrophs can tell her something about how nutrients impact green scum composition. This research is important because stream microorganisms directly influence water quality and ecosystem function.

Sophie conducts her research at the Caribou-Poker Creeks Research Watershed (CPCRW), a pristine watershed located about thirty-five miles northeast of Fairbanks. Rumor has it that Sophie and her labmates been known to pursue the other wonders of CPCRW besides what fuels green scum growth, from chilling ciders in wee arctic streams to stripping down, jumping in, and cooling off on a “hot” Alaskan summer day.

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To freeze or not to freeze: insect overwintering strategies

Perhaps winter hasn’t quite yet crawled up your windowpanes or stretched its fingers across your favorite pond, but it’s certainly making its presence known at latitude 64°N. I’ve been pulling out extra quilts, wrapping up in scarves for my morning bike commute, and making more baked goods to keep up with my hot chocolate habit.

As a graduate student, I study the molecular story behind arctic ground squirrel hibernation at the University of Alaska Fairbanks. I’m the first to admit I’m a mammal kind of gal⎯I gravitate towards the furry and fuzzy and revel in soft fur, large eyes, and squeaky-cute chirps. However, every now and then I step outside of my mammalian bias and remember that there is a world of tiny, crawling, wiggling creatures that are surviving the cold in ways that are equally as extraordinary as the strategies employed by my favorite hibernating rodent.

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Arctic ground squirrel hibernating in the lab. So cute. Copyright © 2013 Øivind Tøien/Institute of Arctic Biology.

I don’t think I’m alone in my mammalian predisposition. It can be easy to overlook insects, especially the more inconspicuous and less flashy species. However, during the Alaskan spring and summer, it is impossible to ignore the state’s most infamous insect: the mosquito.

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Mosquito (Culex quinquefasciatus) larva. Image courtesy of the CDC.

Growing up in Alaska, I never thought about what happened to mosquitoes during the winter. Perhaps I was simply happy they were gone, or maybe my gravitation towards the furry was present from a tender age. In any case, it wasn’t until I was in my late twenties that I learned there are two general types of Alaskan mosquitoes. One variety⎯affectionately called “snow mosquitoes”⎯overwinter in adult form. When temperatures start to drop, they tuck away in tree bark or bury themselves in the leaf litter and begin the process of supercooling.

You may have heard of supercooling, the process by which a liquid can remain liquid below its usual freezing point. A supercooled liquid must remain completely free of any impurity, as even a speck of dust can serve as a nucleation point for ice crystals to form. After snow mosquitoes rid their blood of impurities, they are able to survive winter temperatures as low as -31°C.

The adults of the other variety of mosquito lay their eggs in the fall. After depositing the next generation of blood-sucking babes, the adults do not attempt to make it through the chilly winter ahead and die an unmourned death. Their progeny hatch in the spring and are considered much more voracious biters than their cousins. (Interested in mosquito matters? Refer to the seminal 1949 book The Natural History of Mosquitoes by Marston Bates.)

(Quick mammalian aside: Arctic ground squirrels are the only known mammal to supercool. Similar to mosquitoes, they are also thought to remove their blood of impurities that would otherwise encourage ice growth. Arctic ground squirrels can lower their body temperature to -2.9°C, an incredible feat for an endotherm.)

Supercooling is an example of a freeze-avoidant strategy, in which an animal shifts its physiology to avoid the buildup of ice crystals in its blood. Yellowjacket queens living in subarctic Alaska also supercool. To avoid touching snow or ice, which can disturb a supercooled insect and promote instantaneous freezing, the queens hang by their mandibles from a twig or leaf stem in the leaf litter. The hollow space occupied by their hanging body creates a buffer of air between them and any dangerous frozen water.

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Vespula vulgaris, or common wasp, or yellowjacket. Image courtesy of JL Boyer.

Another equally impressive strategy employed by overwintering insects is freeze tolerance. Instead of preventing the formation of internal ice, these insects embrace it. There are various means of becoming an insect icicle, and most involve promoting crystallization extracellularly. Encouraging ice to form outside of cells protects the delicate machinery within cells, which carries clear benefits to the animal. One exception to this rule is found in the alpine cockroach (Celatoblatta quinquemaculata), which can survive temperatures down to -9°C and allows for the formation of ice crystals within its gut cells. It isn’t entirely clear how they achieve this feat, but it could be via thermal hysteresis proteins (also known as antifreeze proteins). These proteins widen the gap between water’s melting point and freezing point by shaping ice into protein-sheathed, faceted ice crystals. Employing a thermal hysteresis strategy decreases the insect’s lower lethal temperature. Other freeze-tolerant insects include the Isabella tiger moth (Pyrrharctia isabella) and the flightless midge (Belgica antarctica).

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The mechanism of thermal hysteresis via antifreeze proteins. Figure courtesy of Davies 2014.

It’s incredible to think about anything staying warm during a Fairbanks winter, much less a tiny mosquito or a wee wasp queen. To maintain my own endothermic heat through Alaska’s longest season, I use a variety of items and strategies, including down jackets, mittens, extra socks, toe warmers, heating oil, gasoline, wood stoves, hot chocolate, soup, quilts, and dog snuggles. Not nearly as efficient as some of my insect friends, but they will have to do.

Dynamic telomeres and the aging process

My name is Sara Wilbur. I’m a third-year masters student in biology at the University of Alaska Fairbanks.

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Me and my dog Junie biking the White Mountains trail. Photo credit: Jason Clark.

I’ve written for NiB before, about work-life balance in academia, and yesterday I was introduced as the newest contributor to NiB. I’m very excited to write for this wonderful project! You can expect future articles to focus on telomeres, arctic ground squirrels/hibernation, and scientific life in Alaska.

Aging, DNA structure, and the dynamic telomere

The mind simplifies difficult concepts to support graspability. One example of this tendency is found in our attempts to define the aging process. Aging is complex, nuanced, and expressed differently across individuals. It would be quite useful if there was a quantifiable “thing” in the body that indicated how long an organism had left to live. In the mid-1970s, a discovery came that presented itself as a solution to the problem of measuring age: protective, terminal chromosome sequences known as telomeres.

2930423615_5320362dea_o.jpgAging is complex and nuanced. Photo credit: Flickr.

As is widely understood, DNA provides the molecular “blueprint” for all organisms, influencing what they look like and how they behave. The particular nucleic acid sequences (the Ts, As, Gs, and Cs) of an individual’s DNA codes for specific proteins, which are involved in virtually every cellular process. However, of all the DNA you have, only 1% of DNA contains coding sections. Initially considered “junk DNA,” the remaining 99% of noncoding DNA fulfills many important functions, including transcriptional regulation (turning genes “up” to make more of a particular protein or “down” to lessen protein production) and DNA protection, a duty fulfilled by the dynamic telomere.

Telomeric duties

Telomeres have two main purposes. One is to maintain chromosome integrity. If you’re a molecule of DNA, a double-strand break is cause for alarm. Fortunately, DNA repair enzymes are recruited to double-strand breaks, allowing DNA to replicate properly and be transcribed faithfully. However, if you think about it, a chromosome end could be seen as a double-strand break. What prevents chromosome ends from being unnecessarily repaired? It turns out that telomeres aren’t simply naked DNA sequences, but are instead intimately associated with several proteins in a complex known as shelterin. Shelterin proteins help the telomere fold back and associate with itself. This forms a “t-loop” to essentially hide and protect the chromosome end.

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Telomeric structure and associated proteins. Figure credit: Blackburn et al. 2015.

Perhaps more famously, telomeres also act as a buffer to prevent coding DNA erosion during cell replication. An important consequence of the evolution of linear chromosomes (found in all eukaryotes, from yeast to elephants) is that a few nucleotides are lost with each round of cell division. The DNA replication machinery cannot fully replace the outermost nucleotides, so the DNA strand gets shorter over time. As it is the telomere sequence that caps chromosomes, it is these sequences—rather than the DNA in between—that take the hit.

How are telomeres implicated in the aging process?

Telomere shortening over time is thought contribute to the aging process. Before I describe why this might be, let’s explore a more fundamental idea: what is aging, anyway? Basically, it’s a loss of physiological—or bodily—function. A proposed root case of declining functionality in the body is cellular senescence, or when a cell ceases dividing; a buildup of these cells within a tissue is associated with aging. Telomere shortening is one cause of cellular senescence: when telomeres reach a critically short length, cells cease to divide. This is a mechanism to prevent cells from becoming cancerous. However, there is a tradeoff: a buildup of senescent cells that can no longer induce tumor growth could be driving the aging process.

Telomere length does change with time, but shortening is also influenced by lifestyle and genetics. Some species have “mega-telomeres” (including mice, which are a common model for in vivo telomere length research), which have a different biology than more run-of-the-mill telomeres (as we humans possess). To further complicate matters, some species possess the enzyme telomerase in their body cells. This enzyme replaces lost nucleotides, essentially preserving telomere length over time. However, telomerase isn’t the answer to short telomere’s prayers: 80 to 90% of all cancers are associated with over-active telomerase activity.

The future of telomere research

The initial excitement surrounding telomeres’ discovery forty years ago and the potential for its use as a simple biomarker of aging and disease are still with us today. However, like any biological process, telomere dynamics are much more complicated than we first thought. For instance, while there is overwhelming evidence from the past few decades that telomeres do decline with age across species, it is still unclear if telomere length can accurately predict calendar age. The future of telomere research will continue to evolve away from cell culture work into living systems, and from common laboratory animals to a wider species diversity, including ectotherms (“cold-blooded” animals), plants, and hibernators. Stay tuned for more on telomere dynamics in these “non-traditional” organisms!

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What’s happening in hibernator telomeres? Juvenile arctic ground squirrel hiding in some willows. Photo credit: the author.

Are you my advisor?

Ok, great news!  You’ve figured out you want to go to graduate school (thanks to this post here) and you have decided on your degree (MS vs PhD).

Now the question is: who will you work with? Graduate school is different from undergraduate in that where you go isn’t nearly as important as who you work with.

A good advisor will increase your number of publications, assist you in avoiding going too far into debt, and generally make your life better. So before you sign up for this person to be a critical, and intrusive part of your life for the next 4-10 years  (there are many people who spend a really long time in graduate school), here are some things to consider.

  1. Do you want a big lab or a small lab? A big lab means your advisor will be splitting his/her time between you and the 10+ other graduate students and postdocs in the lab. This can mean that you’ll have a good community of peers (and suffering together makes your bonds closer, remember), and you might get more help overall. Conversely, a small lab means your advisor spends more time with you. If you want a lot of attention and time from your advisor, fewer other people in the lab might be ideal.  But if you’ve got a problem with authority, or are nervous in front of your advisor,  this might result in problems. There is no right answer to this question, it really is personal preference. But it’s something you need to think through before you seek out an advisor.
  2. What is the funding situation? This is one of those things you need to ask up front, and means more than YOUR funding situation. If you are not independently wealthy, and are seeking financial assistance to complete graduation school, you need to gather critical information.  Are you going to have to teach every semester? If you love teaching and want to inspire young minds, this might be good, but keep in mind, every hour prepping for class, teaching class, and having student office hours is time not doing your primary research. So teaching at lot will likely affect how long it will take you to get your PhD. Are you going to get paid during the summer? Are there opportunities for you to get funded (grants in progress), or does your advisor already have money (multi-year research grant)? Not only are these important for your PhD (having to take a second job really cuts into your PhD time) but also for your future (being in debt forever really sucks).
  3. Are the current and former students of the advisor happy/satisfied/graduated? This one is key. If you want to know what an advisor is like, ask his students. Don’t limit yourself to just the students currently in the lab (especially if they are new), but ask the older students. And the recently graduated. Honestly, towards the end of my PhD, my friend Bobbi and I stopped being invited to the recruitment events… because the department wasn’t wild about the new students seeing how much we were suffering. But these are the people you want to talk to. They will give you the honest opinion on the things the advisor is bad at. And here’s an important point: EVERY ADVISOR IS BAD AT SOMETHING. You need to figure out if their “bad something” is a thing you don’t care about, or things that you actually like/require in an advisor.

Pick someone who is right for you. There are a lot of advisor-advisee interactions that make a  graduate student successful.  An advisor that someone else had difficulty with may be ideal for you, your personality, your interests, and your work ethic.  That’s why the big lab vs. small lab, and the qualities of the advisor are so important. Picking a person who is a really good scientist, but not a good fit for you is going to end up difficult for everyone involved.

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Should I go to grad school?

I have spent the majority of my life as a student. Not too many 33 year olds can say that.  If you include college, people who haven’t spent time in graduate school will now be reaching the break even point on the school/no school ratio, unlike us fools who went to graduate school.

As a result, I get asked “should I go back to school” A LOT. It’s almost always from friends who have been out in the workforce and are thinking of coming back to get a graduate degree. Luckily, since I’ve had to answer this question so many times, I have a well formatted/throughly thought out response.

My short answer is usually, “no”. But here’s why. There are only two reasons you should pursue a graduate degree:

  1. You wake up every morning thinking about the thing you want to study. You are frighteningly passionate about mantis shrimp! You can’t imagine not wanting to know more about the diet of grizzly bears! You wonder about the processes that change organisms over time and can’t help but wonder what parameters affect these processes! In your SPARE TIME you pursue these questions, whether out in nature or on wikipedia. If this is true, then go to graduate school. It’s a number of years (sometimes too many) where you get to study what you want, and answer the questions you find interesting. You will be stimulated by people who are also frighteningly passionate about studying similar questions, and they understand your desires to learn more. If you’re really lucky, you get to teach undergraduates and inspire young and impressionable minds to be as passionate about what you’re passionate about. Go for it – grad school is made for people like you.
  2. You are facing a serious glass ceiling at your current job and getting that graduate degree will allow you to earn SUBSTANTIALLY  more. The first category of people aren’t motivated by money (because despite what you’ve heard, there’s no money in academia, we’re all broke), but if you are, don’t be embarrassed.  Earning a good income and having money is nice, and if getting that masters degree immediately allows you to have greater earning potential, go for it. Get that degree, check those boxes, and get that raise, you deserve it!

If one of these two reasons is not true for you, then you should probably not go to graduate school. There are moments when graduate school is awesome, but there are also long periods when it takes everything out of you. This is true for every graduate student I have ever met. We all look back fondly on those wonderful moments where we bonded or stayed up late studying/working together (some of my favorite memories). But the truth is that you get paid very little or not at all, to do a job that requires all of your time. You’ll always feel like you’re behind, imposter syndrome is a real thing, and it is HARD to get through a graduate degree. But if one of the two bullet points above are true, then you might have enough passion and perseverance to get through. And you might even look back at it fondly.

However, if one of those two doesn’t apply, then I urge you to consider if you’re wasting your time and money.  It is important to be realistic – graduate school years are marked by low pay, and high cost (tuition and living expenses).  Student debt is a national problem, but manifested in your own life, it is a significant mortgage on your future and the choices you will be able to make.  If the reasons below apply to your consideration of graduate study, then you might want to think about a different career trajectory:

  1. You remember college fondly, wouldn’t it be fun to do that more? -Grad school isn’t college. It’s not all football games and frat parties. If you thought you had good time management skills in undergrad, you ain’t seen nothing yet. It is a 60-80 hour a week job, it is meant to grind you down and rebuild you into something better, it is a slog through massive amounts of thankless work. It is not keg stands and afternoon naps.
  2. You don’t know what to do next with your life. – That sucks and I’m sorry. The economy is hard,  and getting a meaningful, professionally satisfying job is difficult. Entry jobs are rarely glamorous or exciting, and “paying your dues” looks (and is) a long and painful process.  None of this will change if you go to grad school. Unlike undergraduate schooling, you have to start grad school having some idea of what you want to do, otherwise you’re just going to leave with more debt, and still not have that job described above. Sorry.

I have had this conversation with dozens of people, and I don’t want to discourage people who are passionate from pursuing their passion. Go for it! The work is hard, but it is sometimes rewarding. The people around you all understand the difficulty of what you are going through, because they are going through it too. Like any group that suffers together, this will make you infinitely closer and build stronger bonds. The friends I have from graduate school are “lifetime” friends, and I still talk to most of them every week. But you need to be sure that you’re going for the right reasons.

What do you think? What were your reasons for going? Do you have regrets?

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My PhD cohort: Roxanna Hickey, Genevive Metzger, Hannah Marx, Tim McGinn, Matt Singer and Tyler Heather. I honestly wouldn’t have made it through without their support.

 

Should you go to graduate school?

I’ve come to the realization that I’ve been doing this academia thing for long enough that younger scientists have started asking for my advice (“starting” is the wrong word, this has been going on for awhile…).

And while I’m by no means wildly successful, I have been around long enough that I have advice to offer.

So I’m going to start a weekly series called “When I grow up” going through the different stages of the academic ladder and how to approach them/succeed.

I’m going to start with undergraduate research, but until next week (Stay tuned) I’m going to leave this article here.

More soon.

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