Tuesday, March 4, 2014

Grad Publication: Evan Fricke

      One of the big goals of ecology is to understand how ecosystems contain so many different species – in other words, to understand the mechanisms that maintain biodiversity. This is a particularly good question to ask for trees in the tropics both because forests there can have hundreds of tree species in just a single hectare and because trees use pretty much the same resources. How is it that one tree species doesn’t do slightly better than the rest at capturing light or using nutrients and crowd out the other species from the forest? One of our best explanations is that herbivores, predators, and pathogens keep individual tree species from becoming too abundant within the forest. The idea is that the more common a tree species is, the bigger target it becomes for specialized predators and pathogens. These ‘natural enemies’ limit the abundance of plant species, leaving room for other species to stay in the community. Ecologists see the signature of this occurring in tropical and temperate forests all over the world – plants experience distance- or density-dependent mortality, surviving better when away from members of the same species.

      Despite having so much evidence of distance-dependent mortality, we don’t have a great idea of the organisms that are the most important causes of it. The most likely players are probably insects, mammals, and fungi. Individual studies show that each of these natural enemy types contribute for certain plant species. In fact, the great majority of these studies show a role for fungi. This has led some folks to claim that fungal pathogens are the most important cause of the phenomenon.
It ain't easy being green
      
      So are fungi responsible for the extraordinary diversity of tropical forests? Well, using evidence from existing experiments might be misleading for a couple reasons. First, there have been way more studies targeting fungi than any other enemy type – other enemy types might seem more important if we looked harder at them too. Second, existing experiments that determine the cause of distance-dependent mortality have only targeted at single enemy type for the plant species – that sort of study can’t in principle tell us whether one enemy is more important than another for that plant species. To determine the relative importance of these natural enemy types, what we really need are studies that simultaneously manipulate multiple enemy types in the field.

      And that is what we did. Here is the link to the new paper in Ecology Letters. Using fungicide, insecticide, and mesh exclosures, we determined the source and severity of distance-dependent mortality for the seed and seedling stages of three tree species on the Pacific island of Saipan. We observed distance-dependent mortality in 5 of the 6 species-stages, with survival higher in areas away from adults of the same species. But surprisingly, these experiments did not show that fungal pathogens were most important. Instead, insects caused distance dependence in three species-stages, rodents in two, and fungal pathogens in just one species-stage. Our approach provides a way forward for tackling this question about the relative importance of enemy types, and the results show in particular that the importance of insects may have been overlooked. While this is a nice step in our basic understanding of this diversity promoting mechanism, these same data give us useful information for understanding the consequence of the loss of avian seed dispersers for these same tree species on the neighboring island of Guam. No seed dispersal on Guam is great news for the predators and pathogens that hang out under the trees – not so great for the trees though.

      In the interest of catching up Science Positive, I thought I would plug a paper that came out last summer while I was doing fieldwork in the Mariana Islands. Here’s the link to that paper. That work also concerns natural enemy attack and dispersal away from parent plants, and more specifically if there are benefits of dispersal when a plant can’t escape natural enemies.


      This is getting to be quite a long entry, and some other folks were kind enough to talk about this elsewhere, so I’ll just include some links. Here is a more academic perspective in the Journal of Experimental Biology and one from Science. Or if you’re looking for the spoken word, some popular science outlets made little radio spots too: Scientific American and PRI’s Living On Earth. To offer a bit more of a teaser, this study sort of involves bird poop - the more popular articles (especially Science) seem to focus heavily on the poop aspect.

Monday, February 24, 2014

Diggin' the South Lake Union Mammoth with Biology Grad Dave DeMar!

The Columbian mammoth (Mammathus columbi) is
Washington's state fossil and had tusks up to 15 feet long.
 These mammoths ranged across North America (down to Honduras!)
until the last glacial retreat ~11,000 years ago. Art by Raul Martin. 
      On Tuesday, February 11, 2014, an employee of Transit Plumbing Inc. discovered a Columbian mammoth tusk at a South Lake Union construction site in Seattle. I had heard about its discovery that day but hadn’t given it much thought beyond thinking “you never know when or where fossil discoveries are going to turn up”. The following Thursday at around 8:30 a.m. I received a text message from Dr. Christian Sidor, University of Washington Associate Professor of Biology and Curator of Vertebrate Paleontology at the Burke Museum, asking if I would like to help excavate the mammoth tusk. I immediately responded “Sure!” thinking what an adventure it would be digging up an ice age animal in the middle of a city. Most fossil excavations that I have participated in involve much older deposits such as those from the age of dinosaurs (66 million year plus) and from places like the badlands of Montana and Wyoming. Later that day I met with Dr. Sidor at the Burke Museum along with Burke Museum Fossil Preparator Bruce Crowley and Research Associate of Paleontology Bax Barton to load up tools and collecting materials such as shovels, awls, paint brushes, burlap strips, and plaster before heading to the site to excavate the tusk. Upon arrival at around 3 p.m. we suited up for the construction site excavation by sporting safety vests, goggles, and hard hats. That wasn’t the first time I had worn such apparel while excavating a fossil. In September of 2006, while working for Uinta Paleontological Associates Inc., I helped excavate a Late Jurassic dinosaur bonebed from a pipeline construction site near Laramie, Wyoming. What I hadn’t encountered was the tremendous amount of news coverage the mammoth tusk would generate. Being in the spotlight was a little unnerving for me but luckily I managed to focus on excavating the tusk and by keeping my distance from the news teams as they interviewed Dr. Sidor and the Burke Museum’s Director Dr. Julie Stein.


Chief Preparator Bruce Crowley searches for the end of the tusk.
Photo courtesy of the Burke Museum.
      Our first objective during the excavation was to determine the length of the tusk by exposing its outer margins. We measured its total preserved length at 8.5 feet (2.6 m) which according to Bax is only about half the length of the largest tusks ever found! Dr. Sidor figured that bit of information would satisfy the news reporters during their early interviews until later developments of the dig transpired. As we continued to unearth the mammoth tusk helicopters hovered overhead while children off in the distance from the neighboring day care center yelled “dig it up, dig it up”. The tusk was waterlogged and soft meaning we would have to be even more careful not to damage it during its excavation.  The tusk was surrounded by loose stratified sand and rounded pebbles and cobbles sometimes as large as a softball. Above that coarse sediment was a thick layer of grayish clay which was deposited at the bottom of an ice age lake. As daylight turned to dusk the small ~12 x 12 ft. squared-off pit encompassing the tusk was bathed in light from two bright lamps provided by the construction crew. After shoveling what was likely more than a ton of wet rock from around the tusk we had it fully exposed and on a pedestal. Several zip ties were wrapped around the tusk to help prevent the enamel from delaminating during the drying process. Subsequently, we placed aluminum foil over the tusk and covered it with plaster soaked burlap strips. After the initial two layers of burlap were added we placed several wooden 2x4s at strategic points around the tusk and a final two layers of burlap for additional support. At that point, which was after midnight and approximately nine hours of intense labor, all we could do was wait for the plaster to dry before undercutting the rocky pedestal and flipping the specimen for extraction the following day.

Chris, Dave, Bruce, and Bax pose with their wrapped prize!
Photo courtesy of the Burke Museum.
      On the second and final day of the mammoth tusk excavation, we prepared for what we had hoped would be a successful extraction of the specimen. Ron Eng, Collections Manager at the Burke Museum, joined us that day at the construction site with a flatbed truck and metal palette for transport of the tusk back to the Burke Museum. Upon our arrival the construction crew and crane operator readied the crane lurking high above for removal of the tusk from out of the ~30 ft. deep pit and onto the flatbed truck. Two of the construction workers attached the palette resting on the flatbed truck to the crane via hooks and rigging and directed it up and over to the smaller pit surrounding the tusk. Once the palette was in place adjacent to the tusk, Dr. Sidor, Bruce, the two construction workers guiding the crane operator, and I readied the palette with blankets for cushioning and extra rigging for securing the tusk to the palette. We also created a makeshift ramp using 2x4s for guiding the tusk up and onto the palette from its pedestalled position. Our biggest concern during the tusk’s removal was that it would break apart as we separated it from its pedestal. Flipping jacketed fossil bones can be tricky as each situation is unique. Given the delicate nature, size, and spiraling shape of the waterlogged tusk we had to act fast yet gentle when flipping the tusk. The last thing we wanted was for the specimen to fall out of the bottom of the jacket, especially under the watchful eyes of the news crews and numerous excited spectators. As we prepared to flip the jacketed tusk, Bruce took the tip end while I took the root end. Dr. Sidor and the two construction workers readied the center of the tusk. On the count of three we swiftly flipped the specimen onto the makeshift ramp and pushed it up and onto the palette with relative ease. Thankfully, our major concern of it coming apart wasn’t realized as the specimen remained intact revealing nicely preserved ivory on its underside. Once the specimen was secured to the palette with a blanket on top for added protection, the palette was fastened to the rigging of the crane and hoisted out of the pit. As it slowly made its way up and out of the pit spectators from all around the construction site began cheering and whistling. Those of us at ground zero shared a sigh of relief and Dr. Sidor and I exchanged a welcomed handshake for its successful extraction. Dr. Sidor soon made his way out of the construction site to watch the tusk’s final descent onto the back of the flatbed truck and to meet the news teams for questions. 

The tusk is hoisted into the air and delivered
to a waiting flatbed truck. Photo courtesy of
the Burke Museum.
      During the two day tusk excavation I also aided Bax in digging an approximately two meter tall vertical trench for sediment samples and description of the lithology (rock types) and stratigraphy (rock layering) of the surrounding rocks. Those collected samples and data are critical for determining the depositional environment (e.g., lake versus stream deposits) that the tusk was buried in and for reconstructing the ancient landscape of the area the mammoth once roamed. To determine what plant types may have been around during the life of the mammoth, Bax and I collected 21 small sediment samples at every 10 cm interval for fossil pollen. We additionally collected bulk sediment from each of those 10 cm intervals for underwater screenwashing and sieving with hopes that at least part of the contemporaneous microfauna and flora was also preserved. We are somewhat optimistic in finding additional components of the microfauna and flora in those samples as we already discovered the fossilized remains of a partial insect carapace (likely a beetle) in the clay deposits of the ancient lake as well as plant debris.  Those samples including the Columbian mammoth tusk are now at the Burke Museum waiting preparation and study and the results hopefully will provide a better understanding of what Seattle was like 10’s of thousands of years ago.

Here are the rest of the Burke's photos, including those with excited children.

A tour of Cretaceous Montana with Dave
      As an added bonus to Dave’s experience at the South Lake Union mammoth site, check out this Jurassic Park themed video he initially created for his family entitled An Adventure 66 Million Years in the Making... Watch while Dave narrates and walks you through his 2012 dissertation research field season in northeastern Montana starting with the Wilson Lab’s base camp at Hell Creek State Park and later in the field in dinosaur-occupied deposits of the Hell Creek Formation. Dave and his field assistant and ex UW Biology student Bashira Chowdhury guide you through their discoveries and collection of the fossilized remains of animals that lived more than 66 million years ago; a time just before the extinction of non-avian dinosaurs and prior to the rise of mammals following the end-Cretaceous mass extinction. The first few minutes of the video are a bit windy but bear with it as the adventures had only just begun. The video is broken into seven major segments with times provided in parentheses for quick access to each major segment and shorter sub-segment:

1) Base Camp: Hell Creek State Park (00:25) and Base Camp Part II (03:01)
2) Preparing to work the From Mars locality (08:50)
3) Crossing Reid Coulee: The way down (10:25), At the bottom (11:47), and The other side (12:47)
4) The Journey to From Mars Parts I-V: Navigating the Landscape (13:52), Fossil Clams (15:00), Fossil Turtle (15:33), The Hill (16:40), and The Locality (17:34)
5) CMM & JPC Localities (19:55)
6) Kafir Locality (21:52)
7) Breakfast at Base Camp and Finale (23:57) and End Credits (24:58)



Tuesday, February 11, 2014

Bats, Bats, Bats!

      Both Santana lab grad students Leith Miller & Rochelle Kelly recently returned from La Selva in Costa Rica where they took part in an Organization for Tropical Studies (OTS) course entitled Introduction to Tropical Ecology. Enjoy Leith taking you on a very polished tour of their exploits!

Monday, February 3, 2014

Biology Graduate Student Retreat 2014

      The weekend of January 31st-February 2nd (immediately preceding a Superbowl massacre led by the Seahawks) was the annual graduate student retreat at Wallace Falls Lodge in Gold Bar. The weekend was spent hot tub stargazing, eating, skiing, gaming, DANCIN', hiking, chasing a gyrfalcon, and riding the Whip. It was yet another delightful weekend in the Cascades. See you in 2015!

  

Thursday, January 30, 2014

Grad Publication: Stephanie Crofts

      There is an arms race between hard-shelled prey and their predators, an arms race that has been going on for quite some time now.  Most of the work that has been done on this system has focused on how shelled organisms avoid being eaten: they invade new niches, they grow spines, and overall just make themselves unappetizing.  But what about the predators?

      In the paper that my advisor, Adam Summers, and I just published, we asked the question: why are durophagous teeth (teeth that crush hard-prey items) shaped the way they are?   You would think this would be pretty straightforward, especially looking through the literature where most hard-prey crushing teeth are described in generally similar terms. They’re molariform, or rounded, or bulbous--but that doesn’t really get at the diversity.  In fact, crushing teeth can also be flat, concave, or even cusped!  So, to see if some teeth break shells better than others, we made aluminum tooth models and used them to crush some very special shells. 

      Instead of using actual snail shells, which come in different sizes, can have different material properties, and usually come with a snail inside them, we used a 3D printer to make our shells.  Modeled on local intertidal snails from Friday Harbor Labs, the 3D printed shells allowed us to eliminate variation due to natural history, while still maintaining all of the external and internal shell anatomy.  It also allowed us to make two very differently sized snails the same size.  Then we used a materials testing machine to crush the 3D printed shells and measured the force different theoretical tooth shapes needed to break them.   We found that flat teeth and cupped teeth aren’t as good at breaking hard prey as pointier teeth are.  But, pointed teeth are at a greater risk of being broken by the prey. 


      Unfortunately, we don’t see many hard-prey crushing teeth with long pointy cusps… they break!  Next step: figure out which shapes break less than others.

      Check out the video to see the crush in action! (Be patient...)

And here's the paper!

Monday, January 20, 2014

Fresh Insights into UW Biology: Part 2

      Enjoy round 2 of getting to know our current 1st year graduate students. Thanks due again to Melissa Steele-Ogus.

      Fabio Berzaghi studies conservation and wildlife ecology in lab of Sam Wasser, focusing on combining spatial and physiological ecology to study community dynamics where conservation and management actions are needed. He chose to come to the UW because he feels the University provides great foundations for learning and research. He has found graduate school to be intense, but filled with learning. he has been having great interactions, both within and outside the department, saying "The Department provides a lot of support and a great research community."

   
     Leonard Jones joined Adam Leaché's lab as he is interested in the evolutionary biology of reptiles and amphibians, specifically in the evolution of viviparous/oviparous/ovoviviparous reproductive strategies in pit vipers. During his interviews, he found the enthusiasm of current students and the strong diversity among UW Bio faculty research interests appealing. His experiences at the UW have been challenging (but in a good way), and he feels the department fosters an atmosphere of equality, treating its grad students both as students and as colleagues.

      Camila Crifo is in Caroline Stromberg's lab, studying paleobotany. What Camila finds most intriguing about plants is how they have had to adopt different and extraordinary solutions to overcome adverse climate conditions, predation, and competition, as well as reproduce and exploit resources. She came to UW for the collaborative and interdisciplinary approach of the Biology Department. Camila is happy to have survived her first quarter, and finds the department to be a very stimulating environment; people know how to be outstanding scientists, while remaining friendly and relaxed.

      Dave Slager's general research interests include phylogenetics, phylogeography, and population genetics in birds. He was attracted to UW and John Klicka's lab by the friendly atmosphere and many resources available at the Burke Museum, as well as the strong, supportive, and interdisciplinary research environment within the Biology Department. He says that his first quarter was action-packed, with TAing, courses, research, and many social activities with other grads. He is "very happy so far" with his decision to come to UW Bio!



Spotlight on Katrina van Raay
      Katrina is amazed at how you can watch microbes evolve "right before your eyes," and plans to study evolution in microbial systems with Ben Kerr. She is fascinated by everything that the world of microbes can demonstrate about evolution, from how organisms respond to changing environments and how cooperative behavior evolves, to the evolution of host-parasite relationships, or how microbes develop resistance to antibiotics.
      Katrina came to the UW because of how impressed she was with both the faculty and the graduate students. During her interview, she had such interesting conversations with faculty members that she was genuinely disappointed each time an interview session ended. She found all of the research to be so exciting that she says, "I was tempted to change my research focus after every conversation."
      Similarly, all of the graduate students seemed happy and enthusiastic about their work. The wide range of research areas also appealed to Katrina, as she likes the idea of being in a diverse department where students can learn about areas of biology outside of their immediate research focus.
      Katrina is very happy to be at the UW. She says that her experiences so far have been "great!" and that, "Everyone in the department is amazing." She has been particularly impressed by the staff, who "can seemingly solve any problem" and the faculty who are "surprisingly approachable." She has also found her fellow grads to be smart, supportive, and fun. One particular point of interest for Katrina is the opportunities for collaboration, and the wide range of outreach oppotunities, from elementary schools, to prisons, the Burke Museum, and blogging.

Wednesday, January 15, 2014

Grad Publication: Katrina van Raay

One of the awesome research experiences I had as an undergrad involved working with Dr. Jennifer Ruesink and Dr. Alan Trimble at their field station on Willapa Bay, located in southwest Washington. Willapa Bay, the second largest estuary on the west coast, is separated from the Pacific Ocean by a 28-mile long peninsula aptly named Long Beach Peninsula (and dubbed the “World’s Longest Beach”). Willapa Bay boasts an oyster and clam fishery, elusive seven-gill sharks (not be confused with friendly Puget Sound locals, the six-gill shark), sturgeon, and a myriad of migrating birds yearlong.  With the Pacific Ocean on one side, the Willapa Hills on the other, bald eagles flying overhead and great blue herons poised to catch fish as the tide goes out; it is truly a beautiful place.
We were interested in finding out what the distribution and recruitment of the nonnative Manila clam, Ruditapes philippinarum, looked like in Willapa Bay, both spatially and over time. Manila clams, which are now commercially harvested in Willapa Bay, likely hitchhiked their way into the bay on Pacific oysters that were introduced from Japan in the 1940’s.
Since Manila clams have a larval stage, it can be difficult to untangle what affects where they settle. Are they attracted to areas where there are lots of adult clams? Do they prefer areas that have more freshwater input from rivers, or places closer to the mouth of the bay? Or are they just going with the flow and letting the tide and currents determine their settling grounds?
To get at these questions, we made and put out lots of “clam bags” (mesh bags with gravel) on PVC poles onto tide flats all along the bay to measure recruitment, took sediment cores to determine recruit density, and took lots of plankton tows via boat to measure larval abundance.
What did we learn? Well read the paper to find out!

Here's the paper!
Willapa Bay, southwest Washington

Thursday, January 2, 2014

Fresh Insights into UW Biology: Part 1

This post is the first in a series featuring our current 1st-year Grads. These blurbs are meant to better introduce our department's newest members and allow them to share their thoughts on the Biology Department and UW thus far. In each post one grad is given a more in-depth feature. Thanks are owed to 1st year Melissa Steele-Ogus for putting this all together!
~Brandon

      Alex Lowe was lured to UW Biology by the long history of great ecologists in the department as well as the diversity of research within, which he finds "gives you access to tools and information far beyond your specific research needs." He says that, "the collaborative nature of the department ensures that you can take advantage of those tools in ways that expand your research." Since arriving, he has found that he is constantly challenged to improve, while still being inspired by faculty members and the other grads. Alex is currently rotating in Jennifer Ruesink's lab, focusing on the environmental and biological factors that can change the amount of food available to consumers in food webs, and the causes and consequences of this variability in marine ecosystems.

      Rochelle Kelly's research interests can be summed up in one word: bats! Specifically she is interested in the functional, behavioral, and community ecology of these winged mammals. She came to the University of Washington to work with Sharlene Santana, but says that the integrative and collaborative environment in the bio department really won her over. Thus far, Rochelle has found her first year of grad school to be challenging and intense, but "in a good way." She feels that the department is well run and welcoming, providing excellent academic and professional resources for their graduate students.

   



CJ Battey is interested in the ecological and geographic mechanisms that lead to speciation. The strong history of population genetics and genomics research in the Biology Department and Burke Museum fist attracted CJ to UW. He has found the department to be mostly hands-off, but "really supportive when they need to be." CJ is currently working on inferring the evolutionary history of a paraphyletic "species" of new-world blackbird (Quiscalus mexicanus/major) from mitochondrial DNA sequences in the lab of John Klicka.
   
     Hannah Jordt attended UW for her undergraduate education, and choose to stay for graduate school because of the collaborative and collegial atmosphere in the department, and says that "even as an undergraduate" she was treated more as a colleague than a student. She says she "could not be happier with UW Biology" and has found the department to be extremely supportive and full of opportunities for collaboration, outreach, and exploration of "anything you can dream up." Hannah is in Ben Kerr's lab, where she is using microbial systems to study altruism evolution, how antibiotic resistance develops, and biofuels.

Spotlight on Foen Peng
      Foen originally hails from Hunan Province in central China, and attended East China Normal University in Shanghai. He had never visited the United States before moving to Seattle to attend UW. While the transition has been somewhat challenging, he considers it an adventure. Foen says he enjoys "the process to independently find solutions and overcome difficulties" in respect to living in a completely different culture than what he's used to. Although he spent a good deal of time in lab this quarter and hasn't yet had many opportunities to explore, he has found Seattle to be a fun city, filled with friendly people. In particular he likes the Burke-Gilman trail, Suzzalo library, and the many city parks. 
      Foen first became interested in biology in high school, finding both the diversity of life and the common underlying mechanisms of diversity particularly amazing. In college he wanted to "explore a wider spectrum of [his] interests and expand [his] scope of knowledge" and chose to study Urban Planning as it contained a number of sub-disciplines, including: geography, ecology, and economics. However, he found that nothing got him "happy and excited" quite like biology, so he switched back to his true passion. Foen now studies evolutionary biology, conducting research on the genetic basis of floral traits in the laboratory of Toby Bradshaw

Monday, November 25, 2013

Grad Publication: Dave DeMar

The earliest crown group frog, Prosalirus, from the Early Jurassic
Kayenta Formation of Arizona. Prosalirus retains some tell tale
features of its shared ancestry with salamanders.
(From Shubin & Jenkins, 1995)
        A paper coauthored by UW Biology graduate student Dave DeMar was recently published online in the journal Palaeobiodiversity and Palaeoenvironments. Dave's paper with coauthor James (Jim) Gardner of the Royal Tyrrell Museum of Palaeontology stemmed from a symposium entitled "Insights from the Fossil Record into the Evolution of Extant Amphibians and Reptiles", which was part of the Seventh World Congress of Herpetology held in August 2012 in Vancouver, British Columbia. Jim and Dave's paper is a comprehensive chronological review of fossil lissamphibians (frogs, salamanders, caecilians, and albanerpetontids) from North America that lived during the age of dinosaurs (Mesozoic) and the first epoch (Paleocene) following the demise of non-avian dinosaurs at the end of the Cretaceous. Their review, which is based on more than 400 published and unpublished accounts from 61 geological formations, is complemented by two plates illustrating several impressive lissamphibian fossils and a series of maps, time scales, and annotated faunal lists supplemented by several online appendices to aid in summarizing the geographic and stratigraphic distributions of fossil localities and the lissamphibian taxa found within them.
The earliest stem member of the odd clade of living amphibians,
the caecilians. Eocaecilia is also from the Early Jurassic Kayenta
of Arizona. Illustration by N. Tamura.
        Several of those published accounts derive from Dave's undergraduate research while at the University of Wyoming and his ongoing dissertation project here at UW with Dr. Gregory Wilson. Those accounts include his recent description of the fossil proteid salamander Paranecturus garbanii (see Science Positive post from May 8, 2013), geographic range extensions of some rare and poorly known Late Cretaceous frogs (e.g., Theatonius lancensis), and recognition of several undescribed new salamander species, all from the Upper Cretaceous Hell Creek Formation of Montana.        

Jim and Dave highlight the importance of the North American lissamphibian fossil record as it documents the origins, radiations, and extinctions prior to the establishment of the more modern aspect of the clade and the initial phases of that modernization on the continent during the Late Cretaceous and into the Neogene. For example, the North American record includes the oldest global occurrence of a crown frog (Prosalirus) and a stem caecilian (Eocaecilia), both from the Early Jurassic of Arizona. From the fossil occurrence data compiled in their study Jim and Dave created the first species richness curve for North American lissamphibians from the Mesozoic and Paleocene. Their plots demonstrate a general increase in species richness leading up to the Cretaceous-Paleogene boundary (~66 million years ago) and a decline thereafter, but caution that the curves are highly influenced by factors such as research bias and uneven temporal sampling. Jim and Dave end their review by stating:

"While compiling this review, it became glaringly obvious to us that we have barely scratched the surface of the North American Mesozoic and Palaeocene lissamphibian record. If the surge of new localities, specimens, taxa, and ideas that have come to light in the last five decades since Estes' (1964) monograph on non-mammalian vertebrates from the Lance Formation is any indication, the future holds many exciting new opportunities for the study of Mesozoic and Paleocene lissamphibians in North America."

Here's the link!
For a pdf of the paper (and its impressive figures) contact Dave!

Tuesday, October 29, 2013

Grad Publication: Melissa Eng

        This is my first blog post but I hope to contribute more in the future (about my work on dendrite maintenance in the Parrish laboratory). Today’s post is about the work I did prior to starting graduate school at UW.
        Once upon a time I joined Amin Ghabrial's laboratory at the University of Pennsylvania as a technician. Before that, I honestly had not given much thought to tubes. I remember the first time a straw failed me (it had a hole in it), and I remember feeling rather betrayed. Luckily straws are replaceable; the tubes running through our bodies though are not, therefore we better learn about and take good care of the ones we have.

        Some of the most important tubes in the human body are the capillary tubes that allow for separation of blood and brain fluid (known as the blood-brain barrier). In Cerebral Cavernous Malformation, a hereditary disorder that causes migraines, seizures, and even stroke-induced death, this barrier is compromised as a result of dilated and leaky capillary tubes[1]. The thinnest capillary tubes are often of seamless nature, and are difficult to study by default because of their small size and physical inaccessibility. Luckily we can use model organisms to explore tube formation and maintenance. To the right is a schematic of tracheal cells representing two ways that a single cell can make a tube.

       During my two years in the Ghabrial laboratory studying tracheal system development in Drosophila melanogaster I became ever more thankful that the tubes I use to breathe, pump blood, and poo all work. At the same time, I learned to love the fruit fly as a model organism and to marvel at the power of molecular genetics as tools for biological inquiry. Thanks to translucent larvae, high-powered microscopy, and techniques for mosaic analysis, we can look at the effect of one gene’s misexpression on one cell or a small subset of cells in a healthy live animal. This way we can get at cell specific mechanisms of action. I mean come on! If that’s not cool I don’t know what is.
        Mutation of the gene CCM3 is one way CCM can manifest, and I studied the effect of this and a few other genes’ misexpression in fruit fly trachea. I had the great pleasure of working closely with Yanjun Song and Amin on this project, and I am so grateful they included me as 2nd author on this paper. Our work, "Focal Defects in Single-Celled Tubes Mutant for Cerebral Cavernous Malformation 3, GCKIII, or NSF2”, was published in the June 10, 2013 issue of Developmental Cell.
        We showed that CCM3 and GCKIII, also referred to as wheezy in the paper (a line recovered from Amin’s mutant screen at Stanford, no relation to Lil Wayne) genetically interact. As shown here (inset), wild type tracheal cells should be of uniform diameter and have specific morphology.


          Tracheal cells missing GCKIII and tracheal cells missing CCM3 display a large tubular dilation. To say that two genes “interact” means that misexpression of both together cause a more severe defect (in this case frequency of dilations) than that seen by loss of either gene alone. We did see this relationship between CCM3 and GCKIII. Yanjun also goes on to show several different ways that re-supplying these proteins in only the trachea reduce dilations, and that loss of apical and septate junction proteins can also repress tube dilation.
        Excitingly these results can now be tested in vertebrate and mammalian systems, and hopefully CCM patients can benefit from this research someday. I certainly have benefited from doing this research; I gained some good Leica microscopy skills, I learned how to make knockout mutants using P-element mobilization, learned how to survive minor existential crises when data turn out weird or scoopage is a possibility, but most importantly I learned that sharing science is extremely important. I was lucky to have great mentors and feel encouraged to ask questions when learning about diverse research. Seamlessly now that I’m at UW I feel that same strong sense of scientific community. So NB to my fellow grads: I may go MIA for several weeks at a time, but it’s because I am working hard and the clouds can make me forget how to socialize, but trust me when I say: UW Biology rocks and I am so happy to be here! Flygirl out.

-Melissa Eng

And here's the paper!




[1] Haasdijk et al. European Journal of Human Genetics (2012) 20, 134–140; doi:10.1038/ejhg.2011.155