Wednesday, December 28, 2011

New Year, New Vents

Exploration of new vent regions has yielded more exciting observations - especially in the Indian Ocean and along the Mid-Cayman Rise (see map). New species have been discovered on the SW Indian Ridge, including potentially new Yetti crabs (see Deep Sea News's coverage, and a step behind, BBC's story).

New species and a new cross roads has been discovered only this summer on the Mid-Cayman Rise. The deepest deep-sea vents made headlines last year and are set to make new headlines during the upcoming cruise, OASES - setting out at the dawn of the new year (Jan 6th). This summer, remotely operated vehicles, Institute for Exploration’s (IFE) Little Hercules ROV and NOAA’s Seirios camera sled, spotted an unusual sight - tubeworms and swarms of shrimp co-inhabiting. Shrimp swarming on vent chimneys are usually restricted to vents along the Mid-Atlantic Ridge and in the Indian Ocean; whereas clumps of brilliant tubeworms are usually restricted to vents in the Pacific Ocean. How these two ended up together is a mystery of plate movements, dispersal and evolution. The OASES expedition will start to provide some clues as they collect samples and explore the newly-discovered vents more closely. You can join them on the cruise to enjoy the discoveries in near-real time through their blog.

Tuesday, December 27, 2011

A happy holidays for the lab

Its been a busy time in the lab with everyone putting papers across the boss's desk. But the results so far are pretty good. My paper just came out in Nature Communications and a manuscript by three members of the lab and an undergraduate intern was just accepted by Science!  Congrats!! Hopefully, the remaining manuscripts fair as well in the new year.

Friday, December 23, 2011

Happy Holidays

Wishing you and yours all the best this holiday season.

Tuesday, December 20, 2011

Just out

NPG Press release:

Co-opting behavioural responses for development

Dopamine signaling prevents elongation of the feeding structure in sea urchin larvae, when food is abundant, reports a study published in Nature Communications this week. These findings suggest that sea urchin larvae may have appointed a pathway normally used for behavioural responses to instead alter their development.

Food or prey can act as a powerful stimulus to elicit metabolic, behavioural and developmental responses in organisms. Like many other prey-induced responses, the sea urchin larval response has been characterized as an offensive response, to increase food acquisition of the predator. Diane Adams and colleagues show that the food-induced dopamine signaling suppresses the developmental 'default' program operating in pre-feeding larvae to produce shorter feeding structures with lower food acquisition potential. The authors demonstrate that when food is abundant, sea urchin larvae protrude a shorter feeding arm and trade-off maximum food acquisition potential in order to conserve maternal resources and thus maximize fitness.

Nature Communications Featured Image 12/20
These findings suggest that dopamine signalling can be manipulated in order to rapidly alter development in response to food availability.


Rapid adaptation to food availability by a dopamine-mediated morphogenetic response

Diane K. Adams, Mary A. Sewell, Robert C. Angerer, Lynne M. Angerer
Published online: 20 December 2011 | doi 10.1038/ncomms1603
Abstract | Full text | PDF

Debris field

Its amazing and a bit sad how disasters spurs scientific innovation and opportunity. The introduction of 14C into the oceans by nuclear testing and attacks provided a marker to follow ocean overturning and circulation patterns. Large response teams, including scientists, were mobilized after the Deep Horizon blowout. The influx of funding has improved research efforts and our understanding of the Gulf Coast ecosystem from the shoreline to the deep sea.

NOAA has run OSCURS (Ocean Surface Current Simulator), a numeric model for ocean surface currents, to predict the movement of marine debris generated by the Japan tsunami over five years. The results are shown here. Year 1 = red; Year 2 = orange; Year 3 = yellow; Year 4 = light blue; Year 5 = violet.  The OCSURS model is used to measure the movement of surface currents over time, as well as the movement of what is in or on the water. Map courtesy of J. Churnside (NOAA OAR) and created through Google.
The opportunities from the devastating Japan earthquake and tsunami have been less publicized in the US (since it was not a national affair and had less commercial and political drama). Still, scientific resources have been mobilized here as well. While the goals have largely been to track the debris field and assess the radiation risk to humans and marine life, the work is also providing information and tools to help understand dispersal (how selfish of me). Debris tracks (click to see animated projections) are in many ways equivalent to, and thus can inform, dispersal trajectories.

More locally in Japan, the radiation spike introduced rare isotopes that will be taken up into biological material, including the shells and/or tissues of larvae. The concentration of the isotopes combined with an age estimate (possible for fish) of larvae collected at settlement or just after settlement would facilitate generating population matricies - the isotope concentration provides information about the home location and collection site is the final settlement site. Using isotopes and other geochemical tags is already being applied to population connectivity studies. However, the limiting factor is often geographic variation in isotopes. The radiation leak, while horrible, introduced an anthropogenic gradient in rare isotopes with variable half lives. Its an interesting opportunity... I hope someone is doing it!

Friday, December 16, 2011

Deep Sea News

Besides lacking a hyphen between deep and sea (can you tell that I've been nailed a few times for doing this myself), Deep Sea News is quickly becoming one of my favorite science blogs. It is probably no surprise given a nearly life-long fascination with strange marine life including that at deep-sea hydrothermal vents and a sincere appreciation for the mission and driving forces of the blog.

... I have always wanted DSN [Deep Sea News] to do that for our readers, that sense of awe, passion, novelty, and most of all participation in exploration.On the rollercoaster that is being a burgeoning professional academic, DSN is my daily reminder of why I do this. I enjoy the part of the day I set down at my computers and share with the readers the wonderment that is the environment that I have dedicated my life to. The readers reaffirm how blessed we are to be in this field–Craig McClain, Deep Sea News, editor-in-chief  full excerpt

This makes me reconsider my motivation and goals for this blog... and, more importantly for you, to share one of my favorite videos posted by Deep Sea News - a National Geographic clip Bioluminescence on Camera. The exceptional images remind me of the amazing things that life can do and of late nights in high school spent at the beach with good friends watching breaking waves fluoresce.

Thursday, December 15, 2011

Many hats

The business of science is an interesting one. A professor/scientist must be many things at once - a researcher, a teacher, a counselor, a storyteller, a writer, an orator, and even a publicist...not to mention life outside of work. I'm sure there are many more roles as well. I guess that's partly why I love doing science and why its so difficult. Its a constant juggling act, but it never gets boring.

This week, I've spent a chunk of time collecting images - not for a figure - but for cover spreads and media packets for three different manuscripts in press. Preparing media packets is especially interesting. There's a good deal of effort for a story that may or may not be picked up by the press. If you'd like a taste of the buffet of press releases each day, check out EurekAlert! Press interest always a mystery. I mean, how did deep-reaching eddies get into the Economist? I'm not complaining, but I would never have predicted the outcome. We'll see if anyone in the media is interested in my latest story about little sea urchin larvae due out next week.

Tuesday, December 13, 2011

IVF for marine larvae

There are a lot of sperm and embryos frozen in the DC metro area. Every morning on my drive into work, I hear an ad for one of the many local institutes that combat infertility to help couples "realize their dream of having a baby". It is also becoming popular (and somewhat controversial) for our soldiers to store sperm before deploying to war zones.

The National Zoo has another set of repositories for sperm and embryos, to instead combat declining biodiversity. One of their repositories specifically targets corals from the Great Barrier Reef. The idea is that embryos could be thawed, reared in the lab and then transferred onto the reef to add genetic diversity, help boost potentially dwindling numbers, or even reintroduce an extinct species. Similarly, sperm could be thawed to fertilize fresh eggs adding potentially extinct genotypes back into the wild population.

In theory, this sounds like a great insurance policy. However, this isn't just a seed bank for crops that humans have developed and selected for over thousands of years that will be sewn into a controlled field. We're talking about wild populations with some complex symbioses. Will evolving populations and a changing climate make the stored genotypes inferior?

Tuesday, December 6, 2011


My bag seems to be packed just in time for my kids to get home and attack. I'm off to an interview this evening. I'm super excited that all traces of laryngitis are finally gone... two weeks later. Two days of talking could have been harsh. The gash on my face (courtesy of my son excitedly pointing out my nose) is also almost healed. I have been having nightmares about going into the interview looking like a mute pirate. I wonder what I'll dream about tonight instead.

Wish me luck.

Wednesday, November 30, 2011

Failed Halloween

A month later, I've realized that I failed the wonderful holiday of Halloween with my post. Not that it wasn't interesting or witty, etc, but it wasn't very apropos for the occasion.

Science Sushi Blog did a much better job in capturing the spirit of Halloween with Your Average, Everyday Zombie - an entertaining and informative post about how creatures (often to fuel developing larvae or to increase dispersal) can take over and control their hosts. The neuroscience, behavior, developmental, and ecological questions are many fold, but really it comes down to being COOL. And a couple of days later, my family and I were privileged and horrified to see one of the examples, the parasitic wasp (see the section The Zombie, It Stings), on a stem of broccoli from our local organic farmer's market. It was definitely organic!

Back up with the other Atlantis?

Everyone can't be marine biologists? Now they tell me!
I've been on the Research Vessel Atlantis (ship) quite a few times now.  Maybe should I apply to the astronaut program as a back up? I'm a bit late to make it on the space shuttle Atlantis; but they're currently seeking candidates: USAJobs

Friday, November 25, 2011

"O Oysters, come and walk with us!"

"The time has come," the Walrus said,
"To talk of many things:
Of shoes--and ships--and sealing-wax--
Of cabbages--and kings--
And why the sea is boiling hot--
And whether pigs have wings."
   - Lewis Carroll
     The Walrus and The Carpenter

The little oysters on the west coast are rapidly disappearing. Not due to walruses or carpenters but due to climate change. The sea may be increasing in temperature, but is the increase in acidification (drop in pH due to higher levels of CO2) that is really doing the damage. There have been numerous lab experiments that have shown that increased CO2 in the atmosphere causes changes in larval development in many marine species. These changes can be positive, neutral or detrimental depending on the experimental set up and the species tested. These variable results may leave questions for policy
(c) VIMS
makers and the public about the effects of climate change or global warming on ocean life. However, now there is clear evidence of the detrimental effects to life and the economy from the real world - outside of the lab.

Thursday, November 24, 2011


This week was one of those weeks. It seemed like if it could go wrong, it did. But, as Bing Crosby sang, "Still, there's plenty to be thankful for." This has been a great and productive year. Two papers published in broad, high impact journals and two more manuscripts in the pipeline. I had a fabulous undergrad working with me over the summer to develop a new project. I feel like the hard work is paying off with good job prospects. I am thankful. Most importantly, I've accomplished a lot professionally while still spending a lot of time with my family and watching my kids grow. My son has gone from a crawling baby to a running toddler and my daughter is flourishing in her first year in preschool. Its been a good year and its not quite over yet.

Monday, November 21, 2011

"Career Intellect?"

I firmly decided I wanted to be a marine biologist when I was in 7th grade. I, of course, had no idea of what that entailed at the time. I still don't claim to have this job search thing figured out.  We'll see how this year turns out. Thus far, I've been invited for four interviews, so I'm maintaining my optimistically hopeful attitude. I've worked hard to get to a place where I'm competitive to reach that goal. Often as grad students and postdocs, we keep our heads down and work hard into the night on our myopic problems of interest. I found that there are some other things (in addition to hard work) that we must do to advance ourselves. Here are a couple of tips that I've found or thought hard about over the course of my job search (take 'em or leave 'em):

1. Get familiar with the process. 
2. Promote yourself.
3. Take the lead.
4. Remember the Big Picture.

Friday, November 11, 2011

A week in my life

This week was fun. Another 8 job applications in. One rejection email. One email invitation for an interview. A great new set of in situs. Final revisions for an accepted manuscript turned in. A set of positive reviews for another ms received. And half of a holiday to relax with the family.

Thank you to all of men and women who serve or have served our country.

Thursday, November 10, 2011

Crowning the Queen

The tale of the honeybee queen is a classic and popular example of developmental plasticity (aka changes in development in response to the environment). Although this is not a marine example, it is an elegant system for looking at the role of larval development in ecosystem function. Queens, worker bees and drones all have the same genome, but have very different final forms. The important determining factor in social class is eating like a queen. You are what you eat. A diet of Royal Jelly causes hormones to rage and a queen to develop. 

The role of Royal Jelly has been well established, but only now have the active ingredient(s) in the jelly and mechanism by which it works been revealed. M. Kamakura, apparently singlehandedly, discovered that a single protein, royalactin, was responsible for making a queen. Furthermore, he connected royalactin to changes in hormones through epithelial growth factor (EGF) signaling.

This work was a breakthrough in understanding the signaling mechanisms involved in drastically altering development. It identifies new players and seemingly disproved the involvement of another key player - insulin.

Monday, October 31, 2011


A common question in marine biology is how do life histories evolve?  Less common is how do life histories contribute to new evolutionary innovations?

Intermediate species with a bubble raft and egg masses (pink below the bubbles). photograph by Denis Riek
It has long been a wonder how snails walk on (or more accurately, under) the surface of water. These snails float in the neuston (at the air-water interface) on rafts made of bubbles resembling the bubble wrap you'll soon be pulling out of holiday packages. How the snails transitioned from a bottom dwelling lifestyle to one closer to the sun has remained a mystery. The key is determining how the bubble rafts evolved. Churchill and her colleagues unraveled the solution by using DNA evidence to piece together a family/evolutionary tree (phylogenetics). Like a court room, the DNA revealed the source of the commotion.  The bubble-rafting snails' closest relatives were bottom-dwelling snails which made egg masses encapsulated in mucus. Bubble-rafters have modified this mucus to be quick hardening in order to trap air for floats.  Intermediate species (see picture) have maintained both the bubble floats and egg masses; however some of the most derived snails have transitioned to brooding instead producing egg masses.

Reference: Females floated first in bubble-rafting snails. CKC Churchill, DO Fioghil, EE Strong and A Gittenberger. Current Biology. 2011.
also see coverage by National Geographic News

Sunday, October 23, 2011

Currents vs larval biology: The biology matters

Dr Shima at Victoria's Marine Lab reports that fish larvae can actively control their distribution in the ocean - not just vertically - and that where they grow up has a large effect on their chances of survival. I can't wait to see the publication(s), since these ideas are both counter to much prevailing dogma regarding marine larvae.

Larvae are small and generally believed to be weak swimmers with little to no capacity to counter the strong ocean currents. Fish larvae are more proficient swimmers than their invertebrate counterparts, but are still quite weak especially during early stages. Yet, Dr. Shima reports that fish larvae are preferentially found along the coast, rather than swept out to sea as current flow would predict. It is not clear how the larvae are accomplishing this feat, but it highlights the importance of considering biology in estimates of larval dispersal and population connectivity.

Although it really shouldn't be, the importance of WHERE larvae grow up may be even more revolutionary for considering population connectivity - which is in essence a network of lines connecting larval birth places with the location where they spend adulthood. There is no consideration of the planktonic trajectory in between - just beginning and end.  However, more and more experimental evidence and now field observations support the idea that larval quality which is a function of its experience in the water column has a profound effect on which larvae are successful once they settle. Dr Shima suggests that Wellington Harbor may act as a type of nursery habitat, increasing the success of triplefin larvae. For some (many?) species, it may not be enough that they simply get there, but that the larvae also experienced favorable environmental conditions for rapid growth and development to facilitate survival to adulthood.

It is likely these biological factors that can account for differences between observed or actual population connectivity and the output of oceanographic models.

Reference: More than chance determines future for baby fish,

Saturday, October 22, 2011

Tuesday, October 18, 2011


I didn't realize it would feel so good to get short-listed somewhere... I'm not telling where, but it would be a good fit for me and a good area for my husband to get a job. Here's hoping for more short lists and to move to the short-short list of candidates.  Is it too soon to feel optimistically hopeful about this year?

Wednesday, October 12, 2011

Sight for the blind?

Larvae across many phyla have distinct eye spots or eyes. Even 'primative' sponge larvae have a pigmented ring of cells that can sense light. This may not be surprising since light is pervasive in most environments and serves as an important cue for feeding and predator avoidance, amongst other things. (For additional gorgeous pictures and information about marine larvae check out the Friday Harbor Invertebrate Embryology Course Blog.

Yet, sea urchin larvae (below) seem to lack any discernible light sensing organs. There are pigment cells (red) scattered across the body and concentrated often at the tips of the arms.


However, a light sensing function has not (yet?) been assigned to these cells or regions. So why might sea urchin larvae have lost their ability to sense light?  Or do they have a way to sense light, possibly a novel way, that is yet to be discovered? 

Adult sea urchins do it in a strange, unique way (Ullrich-Luter et al 2011). Why not larvae too?  The entire adult sea urchin serves as a type of eye. Visual opsins are found in the tube feet all around the urchin, but there is no associated pigment. The test (shell) of the sea urchin serves as a 'shading pigment' to provide directional information about the ambient light. 

So what do sea urchin larvae do to sense light? There are projects going on around the world that are starting to shed light on this question.  We've got a handful of genes that specifying putative (novel?) light-sensing cells. It will be a collaborative, international effort... and I hope a fruitful one.
Ullrich-Luter ME, Dupont S, Arboleda E, Hausen H, and Arnone MI. 2011. Unique system of photoreceptors in sea urchin tube feet. Proceedings of the National Academy of Sciences USA. 108(20):8367-72.

Jobs, jobs, and more jobs

My own dispersal depends on applying to jobs and hopefully getting one. At least this year there are lots of jobs to which to apply. There are even some 'dream jobs' on the list, including my Alma mater, UC Santa Barbara.

For anyone out there looking for ecology or evolution academic positions, check out the Ecology and Evolution Jobs Forum.  I probably shouldn't be sharing this because it will only increase the competition, but we all could use a little help in this job market.  Its not totally inclusive, but pretty darn good.

Good luck to everyone in their searches! Maybe I'll pass you in the airport on the way to an interview.

Thursday, September 22, 2011


Back to the science...
I thought I was finally getting developmental biology, and then I read about engrailed. Engrailed is a transcription factor that often represses expression of its target genes.  However, Layalle and colleagues show that engrailed can have another function - as a signaling molecule.  The authors use an elegant approach with single chain antibodies with a signal peptide to specifically knock-down extracellular function in Drosophila wings. This is then integrated in the powerful UAS-Gal system to drive expression of these antibodies in different regions to understand which part of the engrailed expression domain is involved in sending the signal and where the signal is received.  It was quite convincing and made me question or at least think about what a gene expression pattern, even of a transcription factor, means.  Engrailed is not the only transcription factor with known signaling functions, and there could be more yet to discover.

Reference: Layalle S, Volovitch M, Mugat B, Bonneaud N, Parmentier ML, Prochiantz A, Joliot A, Maschat F. (2011) Engrailed homeoprotein acts as a signaling molecule in the developing fly. Development. 138:2315-23.

Wednesday, August 31, 2011

Alas, a lack!

Ah... after a summer of interviewing and negotiating, the faculty position in the school of pharmacy fell through and I'm back on the job market - not that I ever really left completely.  In many ways, I'm bummed because I liked the people, it seemed like a supportive and collaborative environment, and I am tired of applying for jobs.  At least this happened now... its that season - academic job market season.  Full of wishful ads and piles of applications currently labeled 'TO DO'. The season seems to have started a little early this year.  Last year the deadlines huddled around October and November, the year before October to December. Now deadlines are well into September. 

My mentors all seem optimistic now that I've got a Science paper and it looks like I'll have a paper in press very soon in a Nature Publishing Group journal (in revision after good reviews but not yet accepted).  Optimism is a very nice luxury when its not you that has to wait to be weighed against a deep pool of candidates.  I do hope that they're right.  I guess here's to hoping.

Monday, August 8, 2011

Developmental Biology - Frog day

Sparked by journal club discussion today, I'm going to try to finish plugging the DMC Developmental Biology Workshop.  In case you're interested, we discussed a Science article on establishing anterior-posterior polarity when planarians regenerate ... in human-speak, how the a flatworm determines whether to make a new head or tail.  We were disappointed that in the end, they found a player in the mechanism but didn't actually find the way the heads or tail decision is made.  :-(   But... to come back to the workshop, my experience cutting and hacking at planarians to make a 2 headed worm helped me evaluate, understand and critique the paper.

So... Frog Day.  We had a preview of the slimy, squirmy critters the day before when we helped collect eggs and testes.  Frog day was dedicated to the frog embryo.  It was an amazing nod to the cutting-edge and to history.

32-cell stage frog embryos

First was a look forward. One can imagine that as the embryo cleaves, that you just pinch the existing membrane around the cytoplasm to get many new cells.  To test this, we inhibited the actin cytoskeleton during cleavage - the mechanism by which the membrane 'pinches' along the cleavage furrow.  Without actual cleavage and fascinating thing occurs - white stripes start appearing in the pigmented animal half.

What are these stripes - they're new membrane that is being laid down during cleavage.  So its not just a pinching.  New material must also be added.  Interestingly, as time continues, the orientation of the would-be cleavages are preserved.  This is most likely because the mitotic spindle orientations remain uninterrupted.

In the afternoon, we went back in time to revisit THE classic frog developmental biology experiment - the Spemann Organizer.  This is an embryo manipulation experiment in which pieces of embryos are transplanted.  I never in a million years thought I would recreate this landmark experiment.  Yet, some how I successfully excised a piece of the dorsal lip - through which cells invaginate during gastrulation.  Then transferred the piece of dorsal lip into a new embryo in an attempt to make a second access - a Siamese twin.  We also did a modification of this experiment with later stage neurula-stage embryos.  I did eight transplants hoping to have some survive and one actually twin.  Well, I got 3 to twin to varying degrees!!  One of them was even better than a twin.  I made a triplet.  The easiest way to count heads is to look for a black dot, called the cement gland - this helps the tadpole attach to the bottom until its able to swim.

Hall of fame from the class.  The one in the middle with 2 visible black dots is mine.

Twinned neurula (earlier stage).  Note that the future notochord (line down the middle) splits near the bottom.
 Successfully completing these experiments made the gift from the instructors even more amazing -- every participant got a Hans Spemann spider plant.  Spider plants constantly make new plants as offshoots that resemble spiders hanging on threads (thus the name).  I now have an offshoot of an offshoot of an offshoot, etc, originating from a spider plant in Hans Spemann's office.  An amazing legacy that I hope to continue with any developmental biology students that come to work in (hopefully) my future lab.  I've already started a lineage with an african violet which served as a thesis present for some of my best friends from graduate school.  For a marine biologist, I seem to have a soft spot for cloning plants.

Wednesday, August 3, 2011

the waiting game part 2

Science is often a game of rush, work, rush, work, then wait...  Get proposals in, then wait months to hear if you got money to do more science.  For deep-sea research, you plan for months, get on a ship, throw instruments in the water and wait... hoping the instruments will be there and have worked when you return to pick them up.  If all went well, at the end of all that waiting, you'll have a brilliant data set to write up for an article.  Submit the manuscript and then wait... wait to hear from the editor, wait to hear from the reviewers... wait to hear from the reviewers again... Well, part two of the publishing waiting game is over.  I got the first round of reviews back. Overall... I'm quite happy. Great reviews - text edits and maybe one minor experiment.  As a co-author said, especially "positive in today's era of vicious reviewing."

Side note on vicious reviewing.  A couple of articles have popped up recently addressing the state of scientific review. But they're not harping on author misconduct or missing a technical flaw.  Instead the articles have a new perspective - a reviewer's job is advance science, not to tear it down, not to write the ms yourself, and not to advance your own career.  But it is so much easier to "destroy than to construct."

A quick guide to writing a solid peer review (Co-author is Kimberly A. Nicholas, DISCCRS V) – EOS – July 12, 2011 -

Friday, July 29, 2011

side note - job?

I know I've still got a couple more days to fill in from the developmental biology workshop, but its been quite busy.  Somehow I've ended up in an interview process for a faculty position.  I'm still not sure exactly what happened as it started with going to a friend's sister's house for a birthday and now I think I'm in negotiations for a tenure-track position in a school of pharmacy.  There's still a ways to go to make sure its a good fit for both parties, but its kind of exciting to have a good prospect.

The unfortunate part is that it takes a lot of time to interview, prepare materials, etc.  The good part is that I've got a great summer undergraduate in the lab, so the science is still moving forward.  We'll see how this all works out... but its interesting!

Tuesday, July 12, 2011

DMC DB Workshop - Day 2 urchins & chicks

Ah, urchins.  I study these and still I learned quite a bit.  We did what I consider more cell biology than developmental biology... but still I guess cells must divide to develop. I was amazed at what a cheap antibody from the Hybridoma bank and DAPI could accomplish.  It was more beautiful than anything they showed me in college and much more informative than the cartoon drawings of chromosomes moving around.  Admittedly, the class lost quite a few embryos in the washing, but I was intrigued to know that you didn't need to remove the fertilization envelope to stain.  Interesting...

Three spindles (green) due to the maternal contribution and that of 2 sperm... polyspermy
We got a brief introduction to frogs as Steve Black, a special guest instructor, started preparations for "Frog Day!"  The frogs looked very very squirmy - poor patients for injecting hormones.

And then it was time to cut more.  This time we zoomed up the evolutionary ladder to chickens.  I was hesitant about chickens.  The last time I 'explored' a chick embryo was in third grade.  I didn't like my third grade teacher to begin with (I was vehemently opposed to wearing a sign for weeks that said ILAC - I am Lovable and Capable) and after that lesson I refused to eat eggs for 2 years.  My mother thanks you. Excuse my digression.  This lesson was FAR better... and proved that my third grade teacher was WRONG.

The embryo is NOT the white things on the side.  It is the white swirl in the middle or if its old enough and has made blood it is in the center of the red area (see picture above).  By three days you can see the heart beat and move the blood around.  Very cool.

It was the heart that we went after for our chick experiment.  First we had to remove the embryo from the yolk and perform the surgery - a simple nick to the region of the future heart.  This nick causes the region to separate and form two twin hearts as the chick grows in culture.

3 somite chick at initial isolation in culture and post-surgery.

48 hours later the chick has grown in culture and developed twin hearts. Both hearts were observed to beat.

Monday, July 11, 2011

DMC DB Workshop - Day 1 cut it up

To ease us in to the workshop, we started by learning a couple of tricks on the microscope.  We made our own darkfield filters and reinhart filters.  Quick and easy arts and crafts time.  Reinhart filters were more fun than anything else - instant pop art!  Make a yellow embryo on a red background... Andy Warhol would have been proud.  Unfortunately, I didn't figure out how to use my camera with the microscope until later in the course... arg.  We used some beautiful ciliates to demonstrate the power of the filters and then looked at some sand dollar plutei.

After cutting up filters, we dove right into cutting up organisms.  (The theme of cutting continued throughout the course.)  We chopped planarians, brown and green hydra, and lumbricus worms all in the cause of understanding regeneration... and all in rapid fire, within ~ an hour or two before dinner.

By the end of the course, I had a camera-shy two headed planarian.

After dinner with a glass of wine, we had an introduction to sea urchin larvae - fertilization and first cleavages. I think they actually looked better in pop art than the ciliates, but I might be partial to urchins.

Thursday, June 30, 2011

DMC Developmental Biology Teaching Workshop

I'm in the gorgeous woods of Maine right now, hanging out with my good friend Rhian at the Darling Marine Center.  I'm here for a workshop in teaching Developmental Biology.  Its a 12 hour a day workshop... and we've done some crazy things during our time already - two headed planaria, mini sea urchin larvae, a chick embryo with two hearts, and hopefully by tomorrow a twinned frog.  We've still got a day and a half and flies and worms to go!  I'm a bit 'knackered' so I'll fill you in on all of the details with day by day highlights and pictures when I get back.  In the meantime, here's a picture of the rocky shores of Maine.

Sunday, June 19, 2011


In all things in life, you should have a plan B (and if you're a super anal-retentive control freak, a plan C and D).  I'm in the midst of writing an application for a postdoctoral fellowship at the University of Queensland, Australia.  I'm admittedly not super excited about another post-doc... but if I've got to do one, Australia and this lab in particular is looking pretty good! I could do worse. The lab fully integrates molecular biology, genomics and larval ecology... the closest thing I've ever seen to my own research interests.

Interestingly, joining this lab was my plan A coming out of graduate school, but I didn't get the NSF International Postdoctoral Fellowship that I applied for.  So no money = no Australia.  I have no complaints though.  I've enjoyed my time and been productive at NIH.  Its interesting that this opportunity came up again.  I got an email out of the blue congratulating me on the Science paper and asking me if I was still interested.  Well here I am editing the fellowship application and pointing to Australia on the world map for my daughter.  I could still magically get a faculty position... or I could be bouncing with kangaroos on the beach... you never know whats next.

Thursday, June 16, 2011


Earlier this month marine scientists, real estate agents, neuroscientists, meditation practitioners, physicologists, surf shop owners and many others convened for the first BlueMind Summit.  These people may seem like an odd grouping but they all share the common lure of the ocean's sounds and sights.  BlueMind was a first step to understanding why people are drawn to and comforted by the ocean.  Instead of asking questions about how the ocean works, the summit pondered questions like:  Why do people pay a high premium for ocean views?  Why is the sound of the ocean so soothing - the most common sound in calming machines and sleep aids?  Why do we flock to the ocean for vacations?

Not surprisingly, I have always been inexplicably drawn to the ocean. Throughout my teens and twenties, the first place I would go when I was stressed or sought to be alone was the ocean.  The sound of the waves calmed me, the blue ripples soothed me, the vast horizon reminded me how small I and my troubles really were.  Interestingly though, the Pacific Ocean has a far more powerful pull on me than any other ocean.  But why?

Interesting theories came out of the summit from the chemical composition of the brain (saltwater) to evolution to perceived societal value.  Since all living things evolved from life in the ocean, it makes sense that we would have a connection.  But this doesn't explain the nature of the connection.  Others suggest that the ocean represents a safe place where vision is not obstructed - a perfect horizon from which any threats could be easily seen.  Thus our connection to the ocean would boil down to a behavioral choice to reduce predation risk.  This was probably my least favorite explanation having seen the threats, risks, and unknown lurking in the ocean.  I would instead argue that the ocean hides and conceals rather than provides uncluttered sight.

My favorite hypothesis from the summit that I've read about thus far came from a real estate agent.  The expanse of the ocean represents limitless opportunity.  Maybe I prefer this because my chosen profession is studying the process of the ocean but either way, I like it.  Because the ocean conceals its mysteries, one is open to imagine the adventures and treasures below.  Because the ocean is nearly 3/4 of the planet, it has control over the Earth - power- and we can't even comprehend the expanse - limitless, though we know there are limits. The power, mystery, and adventure of the smooth horizon can invoke fear, imagination, creativity, calm... pretty much any emotion... but it always invokes some feeling...

Though I hope we can come to understand humanity's draw to the ocean, I am currently satisfied with knowing that I always will be drawn to the ocean.

Wednesday, May 25, 2011

Scientific American stirs the pot

An online article in Scientific American showcases our work recently published in Science. 
Massive Ocean Eddies Stir Up Life around Deep-sea Vents

My favorite line: "It's not Kansas down there, but the new research suggests that powerful deep-sea cyclones—the whirling underbellies of eddies—sweep through these communities on a seasonal basis, transporting vent products to far-off waters."

Saturday, April 30, 2011

Sea Urchin XX

I'm on the Peter Pan bus heading up to Boston after a long but very good and productive Developmental Biology of the Sea Urchin Meeting XX.  Its always nice to be in Woods Hole - see old friends, the ocean, my old home.  But this was better than usual.  The conference was wonderful.  It had a much broader representation of what you can do with a sea urchin than usual.  There was the usual hardcore developmental biology, but there was also more integration outside of the norm -- immunology, circadian rhythms, 3 sessions of evolution & development -- even the field's fearless leader incorporated and acknowledged the world outside of cis-regulation of development.  This was especially rewarding for me -- since my interests are how the environment and development interact.

This new tone, or may be just coincidence, meant that there were numerous opportunities for collaboration that arose during the meeting.  Of course, that means I've got a long To Do list for when I get home.

Half of the new, larger personnel sphere being made.  (c) WHOI
The trip was also fruitful outside of the meeting.  It started with a fortuitous meeting with the head of the submersible Alvin retrofit and my old friend, who, as always, told great stories over dinner and a few beers. Then I got a tour of the Alvin mock up - full sized and with 2 more windows than before.  It should be nice!  I just hope I can get out to sea to take the real one for a test spin sooner than later!  A couple lunches at the Fishmonger and trips the Captain Kidd allowed me to catch up with great friends and also develop new project ideas.  I may have said something stupid and landed myself on a cruise in the near future as well.

All and all, a great trip.  I miss the Hole already... though admittedly, I don't miss the wooden chairs in Lillie Auditorium.

Friday, April 29, 2011


After a whirlwind of phone calls with reporters, traveling, and anticipation, the Science paper came out today!  Check it out.  (If you don't have access to Science, you can get the article from the pdf link found here.) There was also some pretty good press associated with the article.  There are too many to include here, but they can be found by clicking the tab "In the news" above.

Thank you to all of you for your emails and facebook messages of congrats!  I must say that its strange spending days working with the press and Science Magazine to promote your work.  I know a lot more people, oceanographers, scientists and non-scientists, will learn about this work.  I hope they and you like it.... or if you don't, I hope it makes you think of another experiment to test the work and push the field forward.

Tuesday, March 29, 2011

Shot of life

I received a shot of life yesterday... well actually I'm living pretty well, it was more my science career that might have been heading for trouble.  Science accepted my paper!  Wohoo!!

Admittedly, I have joked with my colleagues about the science tabloids - Science, Nature and Cell - when another manuscript got flat out rejected.  But when it comes down to it, I read those journals as much and sometimes more than other specialty journals; the quality of the research is generally higher though the interpretations are sometimes more tenacious; and its really good for an early career researcher to have those names on your CV.  So the joking was out of envy.  I'm ecstatic that my paper got in!  Last night we broke open a bottle of wine that we've been saving for a special occasion to celebrate.

... now, waiting on Current Biology to hear about another submission and time to start working on a new manuscript.  It never ends.  Publish or perish - true at any stage of your career.  At least, now I'm enjoying writing and telling stories.

Friday, March 18, 2011

Flies in Heat Part 1: Hot vs Cold

One of the themes of my research interests is understanding how organisms sense and adaptively respond to their environment.  While I am mainly interested in marine larvae, because their responses can have effects on dispersal and thus population connectivity and dynamics, these are not model organisms where the bulk of the progress is occurring.  So it is useful to keep up with some of the fascinating research that is being done on animals like flies, plants (see previous post) and worms (sorry Palin).

Two recent articles uncover some of the secrets of how flies sense temperature.  I'll comment on one article in this post and the second article in Part 2.

Zuker and colleages show that flies have separate neurons in their antennae to sense hot or cold.  The hot neurons and cold neurons project onto distinct but neighboring regions in the fly 'brain' to process this information.  So while hot and cold sensation are related, both use TRP channel receptors and project onto the same part of the brain, they have dedicated machinery (neurons) and processing areas.

While this work on the adult flies is fascinating and provides new mechanistic insight into the neural processing of temperature, it also leaves room for thought on how changes in ambient temperature (e.g. climate change) affect thermosensation.  Before learning anything on the subject, I would have guessed that temperature was sensed as a continuous variable - one set of one neuron type that sensed all temperatures (from hot to cold).  With a division of the work between hot neurons and cold neurons, I can't help but to wonder how the two temperature regimes are divided.  One organism's hot could be another's cold.  Ambient or optimal temperature should lie, I would hope, between the two temperature regimes.

What happens when ambient temperature shifts?  How is ambient temperature sensed? (Part 2 may have some clues to this second question.) Logic would then assume that there are then three types of neurons for temperature sensation - Hot, Cold, and Ambient.  Hot and Cold may be detected like pain stimuli (TRP channels are also involved in pain sensation), whereas Ambient may be more similar to my naive idea of a detecting a continuous gradient.  This would mean that now THREE sensory pathways must be selected upon to adapt to new environmental temperature regimes (climate change).  A tall order indeed.

Gallio, M., T.A. Ofstad, L.J. Macpherson, J.W. Wang, and C.S. Zuker. (2011) The Coding of Temperature in the Drosophila Brain. Cell. 144(4): 614-624.DOI 10.1016/j.cell.2011.01.028

Friday, March 11, 2011

Power of the Ocean

Once again we're reminded of the dangers that lie beneath and the power of the ocean.  Our thoughts and prayers go out to all of our friends, colleagues, and everyone in Japan. 

Wednesday, March 2, 2011

Feeling the Heat - climate change and development

Climate change or no climate change, organisms respond to changes in temperature on a regular basis.  Heat shock proteins are notorious for being up-regulated during periods of temperature shock.  Plants and animals time their reproduction to seasonal variation in temperatures.  We determine our wardrobe choices (at least partially) based on the temperature outside.   Internal clocks are partially set by daily changes in temperature.  But how is temperature sensed?  There isn't a photon or chemical odor to be received. 

Kumar and Wigge have uncovered that chromatin changes mediated by the alternative histone H2A.Z are responsible for sensing temperature in Arabidopsis (a member of the cabbage or mustard family).  Plants without H2A.Z mimic plants grown in warm temperatures - e.g. faster development, fewer leaves and shorter time to flowering.  The idea is that H2A.Z histones are incorporated into the DNA in the promoters of temperature sensitive genes (such as heat shock proteins). The H2A.Z histones change the way the DNA is wrapped to prevent transcription or interfere with repressors.  As the temperature increases, H2A.Z releases the DNA allowing for activator or repressor transcription factors to bind and/or work to rapidly change gene expression. 

With the threat of global warming looming in the not so distant future, understanding the mechanisms by which organisms sense and respond to temperature is increasingly important.  Kumar and Wigge (2010) found that yeast also use H2A.Z to sense temperature.  It will be interesting to see if animals also use H2A.Z in this fashion.  H2A.Z is highly conserved across metazoa, however there could be small changes in the protein that shed light on differential responses to temperature.  When do H2A.Z leave the DNA? 1 degree change, 10 degree change?  Also, perturbation of H2A.Z would reveal the species-specific molecular consequences of increasing temperature.  How does this pathway feed into developmental gene regulatory networks?

Friday, February 25, 2011

Pink Slips?

While Congress has been on recess, we've been going through contingency plans regarding a government shut down.  That means no new experiments that longer than a week... arg.

That's pretty much what it comes down to... arg.  Social security workers will continue to cut checks, but NIH will be nearly barren with millions of dollars of experiments going to waste.  What a waste...

Friday, February 18, 2011

Friday Feature: parasitic pearls

Its been a while since I've posted a Friday Feature on larval related news.  Finally, I'm back at home with a break in traveling and the holidays over (though my daughter wishes otherwise)... so its time.

Larvae can develop under many different conditions - in the open ocean (planktonic), brooded within/on a parent, and snuggled in an egg capsule.  These types of development have very different consequences for maternal investment (how much energy the mother spends on reproduction rather than her own metabolism and growth), survival, and dispersal.  Broadcast spawning eggs and sperm into the ocean results in 'wastage' due to the high mortality rates for larvae in the open water.  Brooding and encapsulating the larvae protects the larvae and thus reduces mortality, but this usually comes at an energetic cost and reduces dispersal potential.  Brooding entails parental care during development. Parents often leave egg capsules once laid, reducing the cost of actively caring for them, but there is still a cost associated with making the egg capsules themselves and providing sufficient nutrients to fuel development within the capsules (rather than from feeding in the water column).  There are always trade offs.

Freshwater pearl mussels (not marine, I know, but pretty cool... so we'll go with it) seem to have found way around some of the costs associated with brooding or encapsulation.  Mussel larvae are released into the water but instead of drifting in the streams for months, they attach themselves to fish gills.  The arvae will develop attached to trout or salmon gills until they are old enough to drop off into the gravel where they will spend the rest of their lives. 

A parasitic strategy provides some of the benefits of brooding and of planktonic development.  The fish provide protection for the larvae, but at a lower/no cost to the mussel parent.  Movements of the fish will contribute to larval dispersal, but will prevent being washed away to inhospitable locations. 

Despite this ingenious strategy for larval development, the freshwater pearl mussel is endangered.  Overfishing of the mussel to obtain freshwater pearls and river pollution have drastically diminished it abundance and distribution.  Fishing of the fish hosts also poses a threat.

Breeding programs are finally becoming successful.  The complex life cycle posed challenges, but it appears that there may be new hope for restocking freshwater pearl mussels and preventing their extinction.

BBC news: Freshwater pearl mussels breeding in Northumberland

Tuesday, February 15, 2011

Tick tock

Another intriguing piece of advice that I received recently - follow the time line.  Assuming that you do secure that illusive assistant professor position, how do you achieve the next illusive position - tenure?  Follow the time line.  With 6 to max 8 years on the tenure clock, its not graduate students who will get you tenure.  It takes 6 years to complete a program these days, so even you can attract a top notch graduate student in your first year, they'll just be getting their best stuff out in your last year before or just after your tenure clock goes off. Postdocs are good but expensive and difficult to attract as a young, unproven assistant professor.  Undergraduates are well great to train but aren't likely to generate cutting edge work that will get you to the next step.  So who or what will get you that tenure? .... something to think about....

Friday, February 4, 2011


I'd like to share some advice that I got today that I really like.  There is one key thing you must master at each stage of your career to really make it.

Undergraduate School -- hardwork
Graduate School -- creativity
Postdoctoral Fellowship -- marketing
Assistant Professor -- organization

I think I made it out of the first two quite successfully.  I'm still working on marketing myself though.  I think self-marketing is one of those activities that has a gender bias.  Males seem to be much better at this than females.  I'm trying though.  My mini-tour was really for self-promotion, networking, initiating possible collaborations, and getting feedback on my work.  I really do enjoy giving talks and talking to people, so it was also fun. I got to interact with some brilliant people and talk science.  When it comes down to it -- it was marketing. Maybe I will get it right in the end...

Monday, January 24, 2011

Shameless self promotion

Scripps Pier and the gorgeous Pacific Ocean... ahh...
I'm head out in a few days to do a little self promotion on the west coast.  I was kindly invited to give a seminar at Scripps Institution of Oceanography in La Jolla, Ca almost a year and a half ago.  Budgets being the way they are, travel for out-of-towners has been one of the first things cut at institutions across the country.

I decided to take things into my own hands.  Sunny California sounds quite nice this time of year (high today in DC 30 F, in La Jolla 75 F) and I could use the practice and promotion.  Think the tickets are tax deductible? So, I'm packing up the kids and heading to grandma's house in LA for a mini-speaking tour.  I'll also be giving seminars at USC and Cal State LA.

Wednesday, January 5, 2011

Leaky pipeline

The movement to increase female representation in the academic workforce has identified and been (partially) perplexed by a leaky pipeline.  There are currently a large fraction of females attending undergraduate programs in STEM fields but the proportion in faculty positions, especially more senior positions, remains low.  While, I am sure that there are LOTS of reasons for this, I'd like to ponder some of the challenges facing women pursuing this career path that occur particularly at the postdoctoral stage. (Note that this is my based on my own experiences and does not represent any quantitative analysis of postdoctoral experiences.)

Tuesday, January 4, 2011

SICB Meeting

I think I may have found my new favorite scientific meeting.   While other meetings often have more friends at them, I feel like the Society for Integrative and Comparative Biology (SICB) embodies my scientific approach and is more accepting of my genre of work at the boundaries of multiple fields.  So intellectually, this has been a really interesting meeting and I'm only through part of the first full day.

So far my two favorite talks were on the effects of ocean acidification on sand dollar larvae and on brain and sensory development in Malawi fish.  Very different talks which each play to a more disciplinary aspect of my work - larval ecology or development respectively.  Since this blog is dedicated to larvae and scientists adrift, I'll provide a brief summary of the talk by Karen Chan of the University of Washington on ocean acidification and sand dollar larvae.

Many effects of ocean acidification (that is a drop in the pH of the ocean due to higher CO2 levels in the atmosphere) are non-lethal.  This is often the case for echinoderm larvae and some bivalve larvae which become smaller.  The consequences for fitness have been inferred and guessed, but only recently being explicitly tested.  Shorter arms for echinoderm plutei likely would affect swimming stability (based on models) and feeding potential.  Karen and her colleagues empirically tested in the lab both stability and, indirectly, feeding ability.  While one would predict a decrease in stability due to shorter arms, this was not observed.  Instead, a concurrent change in the angle of the arms compensated to maintain normal stability.  Unfortunately, there did not seem to be a compensation mechanism for the predicted decrease in feeding ability.  Larvae exposed to ocean acidification conditions had smaller stomachs, suggesting reduced feeding.

Chan, KYK, D Grunbaum and MJ O'Donnell. Effects of ocean acidification on swimming performance in larval sand dollars.  Presented at SICB Jan 2011.