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Biology

So Long, and Thanks for All the Fish!

 

Many Hats

Graduate students (academics in general) wear a multitude of hats on any given day.  In fact, most days it feels like they’re perched so precariously that a whispered word could send them all tumbling to the ground.  What do I mean by this?  Well, of course, I’m a researcher.  That’s the fedora I put on every day when I walk into the lab.  I have an obligation – to my advisor, mostly, but also to myself – to produce high quality research that gets published in high impact journals.  As a researcher, I spend my days designing and executing various experiments, maintaining the fish breeding stocks, analyzing data, writing and editing manuscripts and grants, and making pretty figures that show off my data.  But I’m also a teacher, and that means putting on a baseball cap and getting out there to educate students.  With this hat on, I need to create lesson plans, perfect lectures, grade, and field questions from my students.  Then there’s the student hat – I’m still learning my craft, and so I slip on an ascot and meet with my adviser and committee members, take classes, and read lots and lots of papers from my field.  Beyond those three, I’m also a mentor to undergraduate researchers, a peer and colleague for the other students in my program and my lab, a science communicator…and, of course, a daughter, a sister, a friend, and a person.  Those last few often get ignored or pushed to the side, but they are just as important as any of the others.  After all, if I don’t function as a person, I’m not going to be able to function as a teacher or a researcher.

Graduate school: the great balancing act! (Source: abmichaels.com)

Graduate school: the great balancing act! (Source: abmichaels.com)

Exploring the Research Fedora

Research is arguably the scariest/most important hat for graduate students.  Every scientist I interact with over the next forty years will be judging me by the quality of this hat.  We have to live and breathe in this fedora – it’s on our minds as we’re falling asleep each night and the moment we wake up in the morning.  Given how important it is, I thought I’d dedicate the rest of this post to telling you more about what mine looks like, and we can probably drop the metaphor now and switch back to describing my life in scientific terms.  For the past four years, I’ve spent most of my time trying to figure out the genetic and environmental factors that influence variation in fin shape in a group of fish called African cichlids.

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African cichlids in an aquarium. (Source: Aquarium Domain)

Over 3000 species of cichlids exist throughout the world; many of them can be found in the three major African rift lakes of Victoria, Tanganyika, and Malawi.  The ones I study come from Malawi.  These are common aquarium imports – if you go to any Petco or Petsmart you will find a plethora of brightly-colored aquarium-bred cichlids for sale.  In fact, they are Malawi’s main export – so they don’t love it when foreign scientists want to come and sample them from their lake! That being said, we work with the main exporter of these fish from Malawi in order to get the live fish that we need to use in our developmental and genetic experiments.

Faces and bodies and fins, oh my!

Lakes aren’t homogenous environments; that is, the “landscape” of a lake varies depending on the depth, nutrient availability, and other physical or ecological factors.  There are different zones within a lake.  Two of the most important ones (at least from a fish’s perspective) are the benthic zone, which is the area closest to the bottom of the lake, including the shallows near the water’s edge, and the pelagic zone, which is the open water column.

Diagramming an aquatic habitat. (Source: Pearson Education)

Diagramming an aquatic habitat. (Source: Pearson Education)

Fish foraging in the benthic zone must behave very differently than fish hunting in the pelagic zone.  Benthic fish are struggling against the current to stay in one spot so that they can forage efficiently from above while pelagic fish must be agile in order to hunt down active or drifting prey.  Fish that are specialized to these different habitats also look quite different from one another; there are sweeping changes that occur in their facial shape, body shape, and fin shape.  Some cichlid species live primarily in the benthic zone while others are typically pelagic hunters; still others can move from one feeding mode to another with ease.  My research, and that of my advisor, tries to tease out the relative influence of diet and genetics on cichlid shape (my advisor mostly cares about their faces while my research has focused on their fins and body shape).

Benthic and pelagic species or forms of various types of fish, including cichlids.

Benthic and pelagic species or forms of various types of fish, including cichlids.

Using a technique called QTL analysis, which crosses two species that look different and then looks for an association between their physical traits and different areas of their genome, I was able to find two areas of the genome that were significantly associated with the number of fin rays, or bony structural elements underlying the fin pad.  I then looked at which genes were in those areas and found one in each that, based on what we already know about them, might influence that trait.  I figured out that one of those genes was expressed in the developing fins of the species that had more fin rays but wasn’t expressed in the fins of species that had fewer fin rays.  Using small molecules, I manipulated the expression of that gene in a single species and found that fish which over-expressed the gene had more fin rays than the control fish while fish that under-expressed the gene had fewer.

Number of fin rays in fish that have had my favorite gene manipulated (A and C, controls; B, expression increased; D, expression decreased). (Source: Navon et al. 2016)

Number of fin rays in fish that have had my favorite gene manipulated (A and C, controls; B, expression increased; D, expression decreased). (Source: Navon et al. 2016)

Teasing apart the relative influence of genes and the environment on an organism’s shape can be tricky, but as our environment rapidly changes, it’s going to become increasingly important to understand all of the many ways in which life can respond.  And since our own limbs evolved  from the fins of our fish-like ancestors millions of years ago, my research into the genetic underpinnings of fin shape may prove fruitful for those trying to understand genetic diseases that impact human limbs.  Of course, this is only a small slice of my research.  But I hope you’ve enjoyed hearing about it and reading my posts over the past year and a half!

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