Tuesday, October 13, 2015

Ada Lovelace Day: Celebrating rad science women!

Today is Ada Lovelace Day, and we are joining in the 7th annual world celebration of the contributions made by women to STEM fields. Named in honor of one of the pioneers of computer programming, this day affords us the opportunity to highlight the accomplishments of women who we admire in these fields. Here, biograds introduce and discuss women who have been important to their pursuit of science. 

Barbara McClintock 

(by Marie Clifford)

Barbara McClintock, giving her Nobel lecture (note demographics of attendees)

An amazing, tenacious woman scientist who discovered movable genetic elements called transposons in the 1940s. She was basically ignored and left to do more awesome genetics research in corn, her model system, for 40 years while people thought that (1) she was crazy and (2) that genes were totally static. And then it came to light that actually transposons are found in pretty much every living thing and she won a Nobel Prize for Physiology or Medicine in 1983. (P.S. Nobel prizes for people doing plant science are almost non-existent, even when people discover important things in plants first like RNAi or gaseous hormones or whatever ... so this is kind of a big deal.) Beyond being super interesting from an academic perspective, transposons are super important in medicine: transposons are the elements that often convey antibiotic resistance from one bacterium to another, and can be mutagens, so have been implicated in cancer. They have also been used as an important tool for understanding how particular genes work in many organisms, with applications for plant genetics, cancer genetics, and beyond. [Ed: She is also the only woman to receive an unshared Nobel in Phys/Med]

Terry Root 

(by Leander Anderegg)

Photo: http://www.upfsi.org/members/#Root
I'm not sure that I would be a biologist, perhaps a scientist of any sort, if it weren't for Dr. Terry Root. Terry is a scientific bigwig. She's a world renowned ecologist (her most cited paper on the ecological fingerprints of climate change has been cited over 3,000 times). She's a brilliant scientific mind, a co-recipient of a Nobel Peace Prize (she was a lead author of the Prize winning IPCC's Fourth Assessment Report on climate change), and an inspiring public speaker (even on depressing topics). And yet Terry is also one of the most dedicated science educators I have ever met. 

When I met Terry, she was a Stanford Professor who was so busy that one had to email her, call her, and then camp outside her office for 1-2 days to get hold of her. I was a wide-eyed freshman, straight from the lovely hamlet of Cortez, CO (a town of 8,500 people four hours from the nearest city), who was chagrined to learn that somehow all 2000 of my classmates were smarter, more well read, funnier, and better groomed than I was. I began working for her as a research assistant because she was nice, and because my brother had gotten me the job, and because she had awesome pictures of birds in her office. By the end of the year, Terry had not only convinced me to become an ecologist, but had taught me more about science and how it is performed than four years of classes possibly could.

As a graduate student in the 80s, Terry was a rare female scientist in a generation of primarily male ecologists. Perhaps because of this, she is a first rate meta-scientist who taught me that science cannot be separated from the human factors (social interactions, intrinsic gender and racial bias, implicit world views). Sure, Terry taught me a lot of practical things. Terry taught me that if you can't draw a graph of your expected results before you start a project, it's probably not worth doing. She taught me how to make a powerpoint presentation that will keep >50% of an audience engaged and >75% awake. She taught me that most other scientists don't really know what they're doing most of the time either. But Terry also taught me that science is a fundamentally human endeavor, and should be viewed and analyzed as such.

Nina Sandlin 

(by Meera Lee Sethi)

Nina Sandlin. Photo: Field Museum
Nina Sandlin works as a communications strategist and technology wizard in Chicago (need help with Perl? Nina’s your girl!). She earned a Masters degree in history, not a Ph.D. in biology or paleontology or computer science. Nina isn’t, at least not officially, a professional scientist. So why am I celebrating her on Ada Lovelace Day? Well, I—like many of you, probably—am a big fan of spiders, museum collections, and taxonomy. And for the last 17 years, Nina has made it her life’s mission to help museum curators figure out what they’re looking at, when they’re looking at some of the most difficult-to-identify spiders in North America. She’s creating a photographic key to genus for the only Nearctic spiders that don’t yet have one: female erigonine "dwarf spiders” belonging to the family Linyphiidae. Why don’t they already have a key? You’ll have to read my profile of Nina and her work to find out. It involves cat whiskers, sweater fibers, and that old “too many elbows for the photograph” problem.

I’ve heard people say, “Science is what scientists do”; but that’s not true, today or any other day. Science is the process of making knowledge. Nina is doing exactly that.

For more on Nina Sandlin: 

Jane Lubchenco

(by Hilary Hayford)

Jane Lubchenco with P. ochraceus and quadrat.
Photo: SciFun.org
One of the many women in science that I greatly admire is Dr. Jane Lubchenco. I admire Dr. Lubchenco not only for her rigorous science, but for the leadership roles she’s taken in applied conservation, improving science communication, and promoting women and families in academic science.

Dr. Lubchenco is considered “royalty” in the field of marine ecology, but if you keep up on alums you know she was a UW grad student of Bob Paine, earning a Master’s in Zoology (1971) for work on sea star competition. (Never fear, botany faithful, her dissertation at Harvard (1975) was greatly focused on seaweeds and herbivory). Her body of work targets interactions between humans and the marine environment, particularly marine reserves and sustainable fisheries.

Dr. Lubchenco is most well known as the first woman to be appointed as Undersecretary of Commerce for Oceans and Atmosphere and Administrator of the National Oceanic and Atmospheric Association (NOAA), serving 2009-2013. President Obama selected her to lead the country in marine issues. During her tenure she faced such challenges as the BP/Deepwater Horizon Oil Spill and the Tohoku Earthquake/Tsunami. In another example of her leadership, Dr. Lubchenco co-founded the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO), a long-term research and monitoring program studying the California Current Large Marine Ecosystem. A collaboration of four universities receiving nearly $90 million of funding in its first 10 years, PISCO was unprecedented in the field of marine ecology in its scale, scope, and budget.

Dr. Lubchenco has served as President of the American Association for the Advancement of Science (AAAS) and the Ecological Society of America (ESA), received the Mac Arthur Genius Award and 18 honorary doctorates, is an elected member of the National Academy of Sciences, the Royal Society… the list of accolades is very, very long. Despite this legacy of outstanding accomplishments, she has consistently taken time to mentor and support developing scientists. She has advocated for effective science communication (co-Founder of COMPASS) and participated in numerous panels/seminars on women in STEM. Dr. Lubchenco and her husband inspired a new approach to the struggle of academia and family by negotiating a novel arrangement with Oregon State University: splitting a full-time, tenure-track professorship, with each scientist working 50% time until their sons were grown.

Rachel Carson

Official US Fish and Wildlife photo of Rachel Carson
When I think of women in STEM, the name Rachel Carson always comes to my mind. While most know that her writings helped spur the global environmental movement of the 1960s, few are probably aware that she was an also an accomplished scientist. Raised in rural Pennsylvania, she developed a love for nature by exploring the forests and streams surrounding her family’s farm. In 1929, she graduated with a Bachelors degree in biology from the Pennsylvania College for Women and was subsequently awarded a scholarship to pursue a Masters degree in zoology and genetics at Johns Hopkins University, a remarkable accomplishment for a woman at that time. After completing her studies, she became an aquatic biologist for the U.S. Bureau of Fisheries, where she analyzed and reported data on fish populations, as well as communicated her work to the public via both brochures for the Bureau as well as articles in The Baltimore Sun. After publishing her first book, Under the Sea Wind, Carson transitioned to science writing full time. Her second book, The Sea Around Us, was an enormous success, remaining on the New York Times Bestseller list for 86 weeks. However, her most famous work stemmed from experiences she had while still associated with the Bureau. Carson was disturbed by the increased use of synthetic pesticides after World War II and their effects on marine wildlife. After several years of research on the subject, Carson warned the public about the long-term effects of misusing pesticides, especially DDT, in the classic book Silent Spring. This seminal work contains a detailed investigation on the effects of insecticides and pesticides on songbird populations in the U.S., whose declining numbers yielded the silence to which her title speaks. The publication of this text sparked a wave of environmental legislation, including the banning of DDT, and galvanized the ecological movement still alive today.

Rachel Carson’s life inspires and motivates me in so many ways. She broke the status quo by studying science and pursuing professional degrees at a time when it was uncommon for women to do so. She was also courageous to write about a controversial subject knowing that the backlash she would receive from the pesticide industry and similar entities would be far less harmful than the effects of these chemicals on both the environment and public health. Lastly, her work demonstrates that it is possible to start a global movement by wielding just your ideas and voice, and it reminds me of the importance of communicating my research and scientific ideas to the public.

Friday, October 2, 2015

Welcome, new BioGrads! See you at DISorientation

Welcome First YearsCongrats on finishing the first week of classes in the 2015-2016 Academic Year at UW (#quartersystem). Just this time last year the rising second years were in your shoes. With the past year fresh in their minds, a few second years, Meg Whitney (Sidor Lab), Ethan Linck (Klicka Lab), and Will King (Sebens Lab) have teamed up to share some thoughts on the first year as a grad student. 

TLDR: [Good for you! You're already prioritizing like a grad student!] GO TO DISORIENTATION!

1. What is the key to succeeding during your first year?

Will King taking his own advice for success.
Will King: Take breaks! Work at a sustainable pace.

Meg Whitney: The best advice and when things really clicked for me was when an older grad student told me that there was no right way to be a grad student and that you can make your grad school experience whatever you want it to be. When I stopped comparing myself to not only other first years but also older grad students, I felt much more at ease with being a grad student.

Ethan Linck: Define "success" as a series of tangible benchmarks (e.g., finish up that paper from your undergrad thesis, submit the GRFP application) rather than aiming for some sort of imprecise and unreachable standard of competence.

2. What was unexpected about your own experience?

WK: The extent to which I now cherish an hour of sunlight in winter. The importance of email brevity (cut in half, then half again). The beauty of Seattle.

MW: I was not expecting to have as much freedom with my own research. Pretty much from week 1 my advisor gave me a lot of encouragement to get going on my research which was awesome.

EL: Being a TA while attempting to navigate your first year of grad school is not so much a problem of time management (although that can certainly be an issue if you overcommit elsewhere) as it is a problem of energy management. Turns out teaching can be uniquely exhausting, even in short doses, and it's best to approach scheduling your own research, classwork, and learning with a healthy respect for this fact.

Ethan Linck balancing his teaching/research/classwork workload

3. What was the best advice you received?

WK: "Take agency of your grad school experience." As in: expect not only to take the reins, but also to build the carriage. Might have to find wood for it first. Also, you're the horse pulling the carriage.

EL: From our post-doc, after I became too comfortable writing from neighborhood cafés: Even if there's no particular reason for you to be in lab (e.g., you aren't working on a lab project), make a point of spending regular, consistent hours there. The simple act of being present exposes you to the countless little interactions (both professional and social) with colleagues that do wonders on both your academic progression and your general morale.

MW: [See #1]

4. What changed for you this year and what might you have done differently?

Meg Whitney in the field.
MW: It's a steep learning curve which is awesome. I feel like I have learned more in the past year than I did in two years of undergrad. It feels terrifying, but if someone had told me it is like that for everyone and that during that time you're actually learning a TON, I would have felt less worried. 

EL: I'm hoping to spend more time reading papers. I wish I had read more consistently than I did.

WK: Acing coursework is no longer a top priority nor a regular source of sweet, sweet validation. Avoid overloading on classes... It's tempting to try to learn everything.

5. Which was the must-attend BioGrad social event?

MW: Disorientation and bio grad retreat.

EL: Disorientation, no question.

WK: Do get to know your fellow grad students. They have diverse backgrounds, interesting passions, and, on occasions when the effort of sustaining friendships actually pays off, food to share.

Thank you Meg, Ethan, and Will! Well there you have it, First Years, everything you need to know! If we missed anything, additional good advice can be found here

Happy Researching!

Tuesday, September 29, 2015

Annual Departmental Retreat: It's a thing of beauty

This weekend, the department participated in the annual tradition of retreating to the San Juan Islands before the start of the academic year. Faculty, grads, and postdocs reunite after a summer spent scattered across the globe in pursuit of knowledge, to catch up on what everyone has been doing and get revved up about the coming year. 

Friday Harbor Labs is an idyllic setting and the weather couldn't have been better. Check out these photos from grads:


One of the favorite past times of being at the labs is exploring the world renowned marine diversity, you basically can't walk two feet without tripping over it. Here were some finds from this weekend:


If you thought that bucket of inverts was cool, you're absolutely right - check them out in motion here (from Yasmeen Hussain):


And there were even some human activities at this thing too! Highlights include Katie Dobkowski winning the prize for best grad student talk and Myles Fenske winning for best grad student poster. 


Until next year...

Tuesday, September 15, 2015

Grad Publication: Ethan Linck

Ethan Linck (Klicka Lab) explores the interaction of countervailing evolutionary forces in island biogeographic theory in a new paper in Molecular Phylogenetics and Evolution. Reposted from Beyond the Ranges.

Scientists often assume species living on oceanic islands have strong dispersal ability, surmising that colonizing these isolated, far-flung land masses in the first place would have required the ability to travel vast distances. Oceanic islands are also often known for their endemic species — organisms that are found nowhere else. Taken together, these two statements constitute a famous paradox in the field of island biogeography, a scientific discipline focused on studying the distributions of island organisms. The paradox goes: If island species are able to cover the great distances required to colonize their homes, shouldn’t this ability also maintain sufficient gene flow (the process of migrants from one population interbreeding with another, which tends to make both more similar) to outweigh the processes of evolution that give rise to unique, endemic species?

Supertramp Zosterops griseotinctus. Photo: E. Linck
In a paper my coauthors (Dr. Sarah Schaack and Dr. Jack Dumbacher) and I published this month in the journal Molecular Phylogenetics and Evolution, we investigated this paradox by examining patterns of genetic variation in a small songbird distributed on offshore islands in Papua New Guinea, the Louisiade White-eye (Zosterops griseotinctus). The Louisiade White-eye is a member of a family of birds (the White-eyes; Zosteropidae) known for their rapid speciation, with a large number of islands across the Pacific and Indian Oceans featuring an endemic species. But unusual for the White-eyes as a whole, the Louisiade White-eye is what Jared Diamond termed a “supertramp species:” an organism highly specialized for overwater dispersal. 

Diamond’s concept of a supertramp draws mainly on patterns of distribution in South Pacific birds he observed during his extensive fieldwork in the region. Noting that some species were only found on low-lying, resource poor islands, and never on adjacent larger, higher-elevation islands, he hypothesized supertramps were skilled colonists and ecological generalists that competed poorly against more specialized species in richer habitats. He holds that the dispersal ability of supertramps is also an asset in providing the ability to move on to new habitat when resources were overexploited or otherwise became insufficient, and in escaping disturbances from cyclones, sea level rise, and volcanic eruptions. Intriguingly, in the few rare exceptions where supertramps were found on higher-elevation islands, there was evidence of shifts in their ecological niche towards more specialization.

If this change is accompanied by a reduction in dispersal, it might help explain the famous paradox mentioned above. Imagine a scenario in which a supertramp species arrives at a decently-sized, higher-elevation island lacking the kind of competitor species that have previously kept it to lower, smaller islands. On this new island, size and height mean disturbance is less prevalent and resource levels are less prone to catastrophic crashes. Dispersal ability therefore is less advantageous, and more individuals stay put and breed exclusively on their new home. As they more sedentary, gene flow is reduced to the point that populations are sufficiently isolated for long enough that processes such as natural selection and genetic drift become new species.

In our study, we examined the plausibility of this scenario using on a large number of samples of Louisiade White-eye tissue my coauthor Jack Dumbacher and his team collected via sailboat in 2009 and 2011. Jack focused on sampling small, coral atolls that had previously been overlooked by scientists. To represent the rare larger, taller islands where no collections had been made for nearly a century, we sampled tissues from toe-pads on specimens housed the American Museum of Natural History, originating from the seminal Whitney South Seas Expedition. Using a special technique known as ‘ancient’ DNA extraction, we were able to obtain DNA sequence from birds shot in the 1920s, perhaps the greatest “oh-s**t-science-is-cool” moment of the research project. Coupled with sequenced DNA from the modern samples, we ran analyses to reconstruct the evolutionary relationships of the different island populations of the Louisiade White-eye (building a phylogeny), and assessed relative levels of divergence. 

Ginetu Island Photo: J. Dumbaucher
We were particularly interested in learning 1) whether there was genetic evidence for the supertramp idea, e.g., a signature of significant interbreeding among different island populations; and 2) whether there was genetic evidence for the loss-of-dispersal-ability explanation for the ‘famous paradox’, which would show significant divergence on the few high-elevation islands in our sampling. While our data lacked the resolution to come to unequivocal conclusions, our results provide preliminary support for both these hypotheses, which, of course, only lead to more questions. How frequently are migrants exchanged between populations, and where do they go? How do shifts in dispersal ability occur?

It’s been a lot to chew on as I ponder future research, but in the mean time, you can read more of our conclusions and questions in the publication here.

Tuesday, August 18, 2015

Grad Publication: Myles Fenske

A paper by Myles Fenske (Imaizumi Lab) and colleagues recently was featured on the cover of PNAS. Read more about their research on the timing of Petunia fragrance below.

Myles Fenske et al. make the cover of PNAS!
August 4, 2015. vol. 12 no. 131
When most people think of circadian clocks, they think of jet lag, and… well, just jet lag1. Circadian clocks are in need of an awareness campaign. Even accomplished life scientists are guilty of asking the question: “plants have clocks?2”. Indeed they do, as does most every organism on Earth. Yes, even bacteria.

Turns out, being able to synchronize internal and external physiology with the rotation of the Earth is kind of a big deal. The early bird gets the worm, and to be the early bird, you gotta have an alarm clock.

Clocks are incredibly effective at timing behavior because of how pervasive they are in regulating physiology. A recent study showed that upwards of 30% of the plant genome (specifically Arabidopsis) is under circadian clock control3. Clocks don’t just regulate physiology at a single point of contact, they exert an influence over the entire organism.

There are some pretty interesting behaviors that the clock regulates; you may have seen the famous sun-tracking sunflower video. Back in the summer of 2011, I was reading Stacey Harmer’s excellent review of the plant circadian clock4, when I came across a paragraph listing a few other outputs of the clock: “photosynthesis, stem growth, and scent emission”. Scent emission, huh?

In fact, many flowering plants emit scent only at specific times of day, which corresponds with the activity of their most helpful pollinators. Our study organism, the common garden Petunia (Petunia hybrida), emits scent at night. Petunia hybrida’s parent, and “wild analog5”, Petunia axillaris, also emits scent at night, which attracts the attention of the large hawkmoth Manduca sexta.

While scent emission was already known to exhibit circadian rhythms, virtually nothing was known about the circadian clock’s connection to scent emission.

To make a long story short, in this paper, we identify Petunia hybrida’s LHY, the first identified clock gene in Petunia, and we then change its temporal expression pattern, and examine how that change in expression affects scent emission. When LHY is expressed constantly (during both day AND night) scent emission completely ceases! If you look at the underlying gene expression, many of the scent metabolic genes are repressed to the point that they no longer have evening peaks.

When we shifted the expression of LHY from its usual morning peak to the early afternoon, we saw a corresponding shift in scent emission, as well as seeing a shift in scent gene expression from the evening to the early afternoon. We also showed that LHY protein is able to directly bind to scent gene promoter sequences in vitro.

It appears that LHY primarily contributes to the timing of scent emission not by regulating the expression of enzymes directly responsible for producing scent, but those responsible for producing the precursor substrates.

Check out our paper and some of the press links (ranging from Nature to creationist bloggers6!) at:


  1. Or Taco Time®.
  2. First hand experiences
  3. Covington MF, et al. (2008) Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9(8):R130
  4. Harmer SL. (2009) The circadian system in higher plants. Annu Rev Plant Biol 60:357–377.
  5. I may have made up this term. The research model for the common garden petunia, P. hybrida, is a cultivar named “Mitchell”. It’s a hybrid of P. axillaris and P. integrifolia. P. axillaris has large white flowers with long and narrow corolla tubes (which require long proboscises, unless you’re a nectar robber) and is largely pollinated at night when it emits a strong bouquet of scent. P. integrifolia has purple flowers with short and wide corolla tubes (which facilitate bumble bee visitation during the daytime). P. hybrida most closely resembles P. axillaris, with white flowers emitting a P. axillaris-like scent profile at night, and is readily pollinated by Manduca sexta in Tom Daniel’s windtunnel. Why not do this study in P. axillaris? Because the metabolic pathways were characterized in P. hybrida, the economically significant species.
  6. This is why you don’t move the phylogeny to the supplement.

Wednesday, August 12, 2015

Alex Lowe: Ecology Between and Below Pacific Tides: a new field course adds a twist to a classic theme.

Field trips, travel to beautiful places, and new friends: Summer as a grad student can be a lot like summer camp as a kid, only nerdier. Several UW Biograds have had amazing opportunities to take advantage of different types of training and research during the summer. Biograd Alex Lowe discusses his participation in creating a new field course at Friday Harbor Labs.

In 1939, Ed Ricketts and Jack Calvin published Between Pacific Tides, a guide to the common and conspicuous organisms inhabiting the intertidal zone along the Pacific Coast of North America. The book is a must-have for ecologists (marine or otherwise) and enthusiasts alike; John Steinbeck even contributed the foreword to an early edition, so you know it’s good. Since that time, the field of intertidal ecology has transitioned from natural history observations to experimental manipulations and spread like an encrusting Halichondria into the subtidal, using SCUBA as a method of research. UW Biology has been a major player in the development of the field thanks to research from Bob Paine and his students working along the Pacific Coast, as well as many other prominent researchers. And now the tradition continues in a new field course being taught at the Friday Harbor Labs.

UW Biograd Katie Dobkowski (@KatieDobkowski) shows the 
EBBPT class how to conduct intertidal algal surveys at 
Cattle Point, San Juan Island.
Traditionally, intertidal and subtidal ecologists live in separate worlds - the air-sea interface apparently impenetrable, methodologically speaking. These habitat zones, though often just feet apart, are accessed in different ways. Intertidal ecologists often walk down from the shore during low tides, but subtidal ecologists use SCUBA to swim up underwater. While originally proposed as two separate courses, thus perpetuating the stereotype, the evolution of the Ecology Between and Below Pacific Tides course (follow us on Twitter and Facebook at #EBBPT15) led to a joint "omnitidal" experiment in field-based science education. The course combines the intertidal experience of Tiffany Stephens (University of Otago; @tiffanybot) and Megan Dethier (UW) with the subtidal experience of Aaron Galloway (Oregon Institute of Marine Biology; @awegalloway), David Duggins (UW), Pema Kitaeff (FHL Dive safety office; @pemarami) and myself, Alex Lowe (UW; @h2_Lo). A group of good friends who are also colleagues - a stellar staff by any measure.

The subtidal methods aspect of the course introduces another novel twist for a field course: EBBPT is a for-credit class offering AmericanAcademy for Underwater Sciences scientific diving certification. AAUS certification training is required for all scientific diving operations occurring at US universities, but has been primarily a specialty course offered at a few institutions at high cost. This was a major issue I was determined to address when Pema, Robin Elahi (@elahi_r; recent UW Ph.D. from the Sebens Lab and original co-creator of the course) and I were developing the course a couple years ago. As soon as students can get credit for AAUS certification, they can get financial aid, which opens this opportunity to a broader range of people. I once missed the opportunity to conduct research using SCUBA on sea ice-associated communities along the western Antarctic Peninsula owing to the prohibitive cost of the scientific diving course. I’ll be damned if that happens again!
Group photo of the dive team during our rescue session in the San Juan Island Sherrif's pool. Author center.
The Ecology Between and Below Pacific Tides course takes advantage of the resources only available at a marine field station, and the Friday Harbor Labs in particular. All students are trained in marine identification with living organisms, first aid, field rescue techniques, snorkeling or SCUBA diving, and boat handling. In their independent research and limited spare time they have been interacting with visiting professors and grad students about ongoing research and marine ecological methods. Their course-related work affords them full-time access to faculty, TAs and experienced volunteers (but seriously, FULL TIME. Like, 9 hours a day. Try that on a college campus…).

As a developing educator, a field course like EBBPT offers me an incredible teaching experience where “Teachable moments” abound. I’m verklempt just thinking about it. This course is particularly valuable to me since I have been part of every step of the development, from lectures to field activities as well as the student research projects.

The first two weeks of class were saturated with group experiments spanning the supralittoral to subtidal. By planting kelp detritus at different tidal elevations, putting out settling plates and surveying the diverse habitats around San Juan Island, the students gained experience in natural history observation and experimental techniques that guided them into their independent research. We intentionally spanned mean lower low water to stretch our students’ concept of an ecosystem and to compare and contrast important processes driving ecosystem structure in these connected habitats. You can follow our natural history observations in the class organism ID wiki here.

University of Wisconsin-Madison student Allie Brown instructs Dr. Megan Dethier 
to, "clear all of the Ulva out of the plot." After three weeks of training, the students 
are now the researchers. Allie is interested in the influence of green algae 
blooms on cobble communities.
Three weeks into the course, our students, who are from all over the country, are hard at work on independent projects. The roles have been flipped; the instructors are now the technicians and the students the researchers. It’s a rare experience for a student to tell the associate director of a marine lab to put on her gloves and start shoveling seaweed for you. The diverse interests of the students have paired impeccably well with the diverse habitats of the San Juan Islands. Projects include work in soft sediment and rocky reef seagrass beds (studying wasting disease in intertidal and subtidal Zostera marina and influence of epiphyte load on epifaunal community in Phyllospadix beds), tide flats (effects of Ulva blooms on cobble communities), shallow rocky reefs (influence of hydrodynamics and blade morphology on Nereocystis luetkeana growth and survival and a study investigating plasticity of encrusting sponges across a intertidal-subtidal depth gradient), and large scale rocky reef habitat (the role of Mesocentrotus franciscanus in the detrital kelp food web). The students will present their research in written reports and oral presentations at the end of the quarter. Keep an eye on twitter (#EBBPT15) for updates on projects and news about ways to follow the presentations.

From Summer Camp,

Alex Lowe
EBBPT15 Students

Monday, August 3, 2015

Beautiful Monsters

UW Grad Students participate in many different forms of outreach. John Chau, who studies evolutionary relationships among members of the genus Buddleia (Butterfly Bush), writes about "local color" for a popular neighborhood blog the Capitol Hill Seattle Blog. He contributes to the Pikes/Pines series, providing a natural history context for the urban jungle.

Read his recent post on Beautiful Monsters describing the genetic horrorshow that is the cultivated roses. 

YOU MONSTER! John explains the double rose in his Pikes/Pines post. Credit: J. Chau.

Friday, July 24, 2015

Ain't nothin better than the summer in the northwest

Our unusually warm weather this year brought all sorts of crazy phenomena: massive siphonophore strandings on the coast, Dungeness crab molting frenzies, algal blooms (also some things happened on land maybe?), but it also meant an early arrival of weather we typically don't get until July 5th, starting during a month locally renamed "Junuary".

Summer means we grad students don't get to keep as close of tabs on each other, often heading out to field sites, or into the lab for many hours straight. What are UW Biograds up to this summer?

Octavio Campos: I have already defended, so I have my "D"; now this summer I just have to work on finishing my written dissertation so that I can get my "r" to officially become... a Dr.

Jake Cooper: I'll be tracking evolution in my simulated populations, some of which can have sex and some of which can't.

Marie Clifford: This summer I am writing up my paper on floral scent so that the scientific community can WITNESS the convergent chemical evolution between plants with the same pollinator.

Marie's Passiflora Valhalla awaits...

Myles Fenske: Many plants require insects to facilitate their lovemaking, I'll be watching bugs in a windtunnel decide which plants they want to third-wheel for.

Emily Grason: Mud-truckin' again this summer, this time all over Puget Sound looking [hopefully in vain] for invasive European green crab - Carcinus maenas.

Jared Grummer: I am going to be doing a lot of genomic sequencing of frogs, lizards, and caiman, while writing manuscripts and preparing to be in Argentina for 5 months!

Hilary Hayford: I am sharing everything I know about invertebrates with a dedicated group of students, writing about radio-tracking marine snails, piecing together data on behavior, temperature, and performance to evaluate snail "decision-making," and letting my bike get some time in the sun.

Eliza Heery: I'm figuring out why sea urchins are currently taking over Seattle and studying the community of worms, clams, snails, and crustaceans that inhabit soft sediment habitats in the urban subtidal.

Yasmeen Hussain: This summer, I'll be banging on a keyboard and filling glass tubes with charcoal and alcohol. [aaah, science...]

Will King: This summer, I contemplate the metaphorical links between intertidal barnacle zonation on San Juan Island and my ever deepening tan lines.

Alex Lowe: I'm figuring out which marine adhesive is best for gluing oysters (thousands of oysters) to tile.

Brandon Peecook: I'll be an American in Paris (and Tübingen and Cambridge) scampering around in museum basements before returning to the US of A to dig up some OLD (and hopefully a few new) friends in the Petrified Forest of Arizona. "Je suis un paléontologue, uh huh huh".

Elli Theobald: I'll be looking into my crystal ball to look at what flowers will do in the future. I'm taking advantage of the early summer weather to explore what future climate conditions might mean for flowers and pollinators on Mt. Rainier. This summer, flower phenology is already 4-6 weeks earlier than usual, mimicking conditions predicted for the year 2080! Already we are seeing signs of community reassembly that we had predicted from climate models.

Katrina van Raay: This summer, I'll be evolving virus and bacteria mutants, and taking some breaks from lab to traipse around the beautiful Pacific Northwest.

Lauren Vandepas: I will be alternating between demanding that anemones reveal the secrets of their stinging cell harpoons and trying to watch jellies poop, in between sessions of sitting in an inner tube on a lake wearing a big floppy sun hat.

So that's the summer life of Biograds in a nutshell.  Hope your summer is just as ... interesting.

Thursday, July 16, 2015

Grad Publication: Ann Wen-Yang Lin

Ann (Parrish Lab) just had a paper published in Genes and Development about pathetic mutants! Below she describes the impetus and context for the paper, as well as the results.

The link to the full paper is found here.

A central question in growth control of multicellular organisms is how growing organisms maintain proportionality. For example, as animals grow, dendrite arbors of many neurons must expand proportionally to sustain proper connectivity and maintain coverage of their receptive field. However, different types of neurons have different growth requirements, depending on the size and complexity of their dendrite (and axon) arbors. We have been working to identify the cellular machinery that supports neuron growth with a focus on understanding whether neurons with large arbors have specialized mechanisms to support their extreme growth requirements.

From a genetic screen, we identified a mutant that selectively affects dendrite growth in neurons with large dendrite arbors without affecting dendrite growth in neurons with small dendrite arbors or the animal overall. This mutant disrupts a putative amino acid transporter, Pathetic (Path), that localizes to the cell surface and endolysosomal compartments in neurons. Although Path is broadly expressed in neurons and non-neuronal cells, mutation of path impinges on nutrient responses and protein homeostasis specifically in neurons with large dendrite arbors but not in other cells. Altogether, our results demonstrate that specialized molecular mechanisms exist to support growth demands in neurons with large dendrite arbors and define Path as a founding member of this growth program.
Figure 1: Role of the SLC36 Pathetic in
supporting extreme dendrite growth.

Shown here (Figure 1) is a confocal image of Drosophila Class IV da neurons (labeled by ppk-CD4-tdTomato) in a pathetic zygotic null mutant 3rd instar larva. Dendrite growth arrests at a fixed limit in pathetic mutant sensory neurons (cyan neurons), but in very rare cases (<0.5% of neu- rons), persistent maternal Pathetic protein rescue the mutant phenotype (red neuron), demonstrating that low levels of Pathetic are sufficient to support extreme dendrite growth in these neurons. Pathetic supports dendrite growth in part by increasing translational output, but is dispensable for growth and patterning of other larval tissues.
Figure 2: Specialized requirements for growth in neurons with large dendrite arbors. 

Shown here (Figure 2) are confocal images of Drosophila Class I (magenta) and Class IV da neurons (red), labeled by 98b-Gal4, UAS-CD4-tdGFP and ppk-CD4- tdTomato, respectively, in pathetic mutant (left) or wild type (right) 2nd instar larva (cyan). Dendrites of Drosophila dendrite arborization neurons grow continuously during larval development to maintain proportional body wall coverage, but Class IV da neurons have much larger and more elaborate dendrite arbors than Class I da neurons. Mutation of pathetic selectively affects dendrite growth in neurons with large dendrite arbors, including Class IV da neurons, doing so by affecting translational output of neurons. By contrast, pathetic is dispensable for dendrite growth in neurons with small dendrite arbors or the animal overall, demonstrating that growth of large dendrite arbors entails specialized molecular mechanisms.

Thursday, July 9, 2015

Laura Newcomb: Spidermen of the Sea

Washington State is a fantastic place to study shellfish – not only are they plentiful to study, the state is home to a productive shellfish industry which has enabled me to apply my results in the lab to real life problems.

This piece was originally prepared for FHL's Tide Bites:

As you walk past the Kings Market seafood aisle in Friday Harbor or browse at Costco, chances are that you will see fresh mussels harvested locally from Penn Cove Shellfish on Whidbey Island, WA. These mussels have been cleaned and washed to look enticing to buy, cook, and eat. What you do not see when you look at these mussels is one of the most important parts: the byssal threads that attached the mussels to the lines they grew on (Figure 1), enabling them to then progress from the ocean to your plate.

Figure 1. Mussels attached to each other by byssal threads.
Mussels are the Spidermen of the sea: they mold byssal threads to attach to a variety of surfaces, from rocks to aquaculture lines. These threads act as stretchy tethers to keep a mussel in place (Bell and Gosline 1996). The mussel aquaculture industry takes advantage of this characteristic in their farming practices. Adult mussels living along the shores of Penn Cove release egg and sperm into the water column, a process known as mass spawning. When egg and sperm collide, the egg is fertilized and the larva begins to grow. During this phase, larvae swim around in the currents, feeding and looking for a good home to settle and attach with their first adult byssal threads. Penn Cove Shellfish puts out collector lines in early spring (April May) to catch this mussel “seed.” Mussels then grow right on these collector lines for about one year, until they reach harvestable size (Figures 2 and 3).
Figure 2. Penn Cove Shellfish mussel harvesting boat tied up to a mussel raft.

Figure 3. Mussel aquaculture lines hanging in the water at Penn Cove.
The problem arises when the mussels fall off, leaving the lines bare. Mussel fall-off due to seasonally weak attachment and increased storm action is a process mussels encounter on rocky shores (Paine and Levin 1981). A mussel becomes weakly attached when it produces fewer or poor quality individual byssal threads, making the animal more likely to dislodge under waves and currents. Mussel fall-off cuts into a grower’s yield at harvest and is a problem for the industry worldwide.

With funding support from Washington Sea Grant and the National Science Foundation, a team led by Dr. Emily Carrington and including Dr. Carolyn Friedman, Dr. Michael (Moose) O’Donnell, Penn Cove Shellfish General Manager Ian Jefferds, Matt George, Molly Roberts, and myself have set out to address this problem. Our work seeks to identify what environmental factors may trigger weakened mussel attachment in farmed mussels. We started in the laboratory by identifying two potential culprits, ocean acidification and ocean warming, that weaken mussel byssal threads. Using controlled experimental mesocosms (aka fancy Igloo coolers) in Friday Harbor Laboratories’ Ocean Acidification Environmental Laboratory (FHL OAEL), we exposed mussels to a range of conditions to identify the threshold values for weakening: pH below 7.6 (O'Donnell et al. 2013) and temperature above 19˚C (66˚F). We also learned that elevated temperature reduces the number of threads a mussel makes, further weakening whole mussel attachment.

With the lab experiments identifying pH and temperature as possible weakening agents, we moved out to a mussel farm to ask if mussels ever encounter these threshold conditions and if so, do these events coincide with weak mussel attachment?

Partnering with Penn Cove Shellfish (the oldest and largest mussel farm in the nation), we installed multi-parameter instruments in Penn Cove on Whidbey Island to log hourly measurements of seawater temperature and pH, as well as salinity, dissolved oxygen, and chlorophyll. These data are uploaded onto the internet in real time (http://nvs.nanoos.org/Explorer) so that we (and anyone else) can check in to see what the conditions are like at any time (Figure 4).

Figure 4. Grad Laura Newcomb with solar powered
telemetry units on a mussel harvesting raft.  Water
temperature and pH measurements are uploaded
to NVS and publicly available.
Growers hang mussel lines vertically in the water at depths from 1 to 7m, so we placed our sensor arrays at those depths to capture conditions throughout the water column. This equipment has been in place and logging since late summer 2014. So far, we have found summer water temperatures at 1m can surpass the 19˚C (66˚F) threshold for a few hours on warm days and pH dips below the threshold of 7.6, with especially prolonged periods from October February at both 1 and 7m. These measurements tell us that mussels do experience conditions that can weaken their attachment, and our concern is that these conditions are projected to get worse over the next 100 years.

At this point in the study, we don’t quite have enough monthly measurements of mussel attachment at 1 and 7m to fully evaluate how pH and high temperature may be affecting mussels in the field. However, we have observed that mussels are weaker in the months when the maximum temperature exceeds 18˚C. This observation suggests temperature may act as an environmental trigger for weak attachment. We are continuing to measure mussels and water conditions and will soon be able to firm up our conclusions about the effects of temperature and pH on mussels at the farm.

Moving our research from the lab to the field has allowed us to extend our results to an industry that stands to be affected by changing ocean conditions. By installing sensors that monitor the water in real time, we hope to give mussel farmers an early warning system for conditions that could threaten their mussels. Recently we have expanded our studies to include Penn Cove Shellfish’s farm in Quilcene Bay, WA, made possible by our partnership with Washington State Department of Natural Resources. We are excited our collaborative research can contribute to sustaining a culturally and economically important resource for Washington State and keep this popular seafood in grocery stores for years to come (Figure 5).

Figure 5. Biology Professor Emily Carrington meets with Governer Jay Inslee
to discuss the effects of ocean acidification.

Works Cited:
Bell E., and J. Gosline. 1996. Mechanical design of mussel byssus: material yield enhances attachment strength. Journal Exp Biol 199:10051017 (link)

Paine R.T., and S.A. Levin. 1981. Intertidal Landscapes: Disturbance and the Dynamics of Pattern. Ecol Monographs 51:145 (link)

O'Donnell M.J., George M. N., and E. Carrington. 2013. Mussel byssus attachment weakened by ocean acidification. Nature Climate Change 3:14 (link)