Tuesday, September 9, 2014

Sonia Singhal: Exploding Bacteria!

 "…very small living creatures in rain water."

The evolution course I took as an undergraduate was co-taught by two professors, one who studied butterflies and the other (my advisor at the time) who studied viral ecology and evolution. For one of the classes, the butterfly professor brought in models and pinned specimens to show off their beautiful patterns. My advisor decided he couldn’t be one-upped. “I had organism envy,” he explained to us as he passed around Petri dishes on which some viruses had been grown.

The organisms we study are all interesting and dynamic, but that can be easy to forget when they’re things that are not publicly “charismatic”, not bright and colorful or cute and cuddly, or just too small to see. For example, I only see bacteria when there are millions of them in one place, enough to turn liquid turbid or form a small, moist-looking dab on a Petri dish. At this scale, it can seem as though things are fairly static. The liquid only becomes so turbid. The moist dab only grows to a certain circumference. 

But during a synthetic biology course from Eric Klavins (UW Electrical Engineering), I had a chance to see my bacteria as individuals, rather than a collective. We decided that we wanted to characterize how individual bacterial cells were growing, so we turned to microscopy. Looking through the microscope, where little oblong cells zipped about or turned abstractedly in circles, was like discovering an entire new world. Oh—this is what my organism looks like! This is how it behaves! Then we added antibiotics and watched the cells explode, which was ay more fun than it should have been.

Video credit: Sonia Singhal, Rashmi Ravichandran, Gregory Rowe, Rob Egbert
Time series taken over 16 hours, with one hour of growth preceding the addition of antibiotic (ampicillin). Original (and larger) video here.

Wednesday, September 3, 2014

Grad Publication: Emily Bain, Anna McCann, Larissa Patterson

Pigment pattern is a defining characteristic of many animals that is more than just beautiful to look at; stripes, spots, and bright colors function in many behaviors such as warning coloration, mate recognition, and camouflage. Even among closely related species, pigment patterns can be stunningly diverse. In the Parichy lab, we use the pigment pattern of the adult zebrafish, Danio rerio, to study molecular and cellular mechanisms of pattern formation and how these processes evolve between species.

The stripes on a zebrafish are composed of three different cell types: black melanophores, yellow orange xanthophores, and iridescent iridophores. We know from previous work that interactions between pigment cells are crucial for stripe formation, but cues from the environment tell the pigment cells when and where to show up.
In this paper, we discuss the role of thyroid hormone in the development of different pigment cell lineages and metamorphosis using genetic mutants as well as a new technique to ablate the thyroid follicles in living fish. We find that no thyroid hormone results in no xanthophores, more melanophores, and a host of other developmental delays. On the other hand, too much thyroid hormone in the opallus mutant yields many more xanthophores, fewer melanophores, and other heterochronies in developmental milestones. Interestingly, the pigment pattern and anatomical features of the opallus mutant resemble D. albolineatus, a species that is closely related to D. rerio suggesting that the thyroid hormone pathway is involved in the divergence of these danios. By ablating the thyroid follicles in the other species, we learned that D. albolineatus have evolved a distinct pigment cell population that is independent of thyroid hormone while other functions of the hormone remain conserved.

These are just a few of the exciting new findings in this jam-packed report. Be sure to check it out (even if it’s just for the stellar pictures)!


Read the paper here!

Monday, August 25, 2014

Grad Publication: Edith Pierre-Jerome

The plant hormone auxin is involved in almost every aspect of plant growth and development.  Auxin has been studied for well over a century and while many aspects of its function have been elucidated, the details of how this one molecule can coordinate so many critical responses have remained a mystery.  A large facet of auxin function has been tied to its regulation of gene expression through a signaling pathway composed of only a handful of key components, each of which belongs to a large gene family. One attractive hypothesis for the diversity of auxin signaling responses is that functional divergence between signaling component family members could provide variation in response to a generic auxin signal.  Thus, different component family members can be used in combination to elicit distinct responses depending on the cellular complement of components. (For more details, see the review I co-authored that was published last summer). However, this pathway is complicated by genetic redundancy and co-expression of signaling component family members, auxin trafficking, and feedback that buffer perturbations to the pathway.

To simplify matters, I worked as part of a collaborative team between the Nemhauser (Biology) and Klavins (Electrical Engineering) labs to introduce all of the components of the auxin response pathway from the plant Arabidopsis thaliana to the fungus Saccharomyces cerevisiae (Baker's yeast).  In this way, we could test and expand our understanding of how auxin signaling components work together to generate diverse responses to auxin.  In our recent publication, we were an;e to show that the core auxin signaling components can reproduce auxin-induced gene expression in yeast - a feat possible thanks to the remarkable conservation of cellular machinery in eukaryotes. By applying the tenets of synthetic biology to recapitulate auxin signalling in yeast, we could systematically incorporate and vary individual components and component family members to precisely quantify the timing and performance of auxin signaling circuits. As a result, we were able to generate a new suite of tools for engineering complex synthetic systems and also gained unexpected insights into why plants can use auxin so effectively.

Check out a review here and read the most recent paper here!

Tuesday, July 1, 2014

Summer Plans: How can you not want to be a scientist?

      The grads of UW Biology will be spending the next few months diving into their research and soaking up some of that delicious and outrageous Seattle sunshine.

Brandon Peecook: "I'll be land-cruisin' around Africa collecting 1/4 billion year old fossils, discerning patterns of extinction and recovery, and trying to not be eaten by several known man-eaters."

(Dr.) Kelsey Byers: "I'll be traipsing around the Alps collecting floral scent and tissue from alpine orchids!"

Jack Cerchiara: "I'll be spending my summer studying the physiology of aging in Magellanic penguins."

Jake Cooper: "I'll be modeling how sex with neighbors is different from sex with randos."

Yasmeen Hussain: "I'll be watching sperm swim and making (urchin) babies."

Michael Dorrity: "I'll be pitting millions of yeast against each other in fiercely competitive agar-digging tournaments."

Stephanie Crofts: "I'll be playing with fish and finding new ways to crush shells."

David DeMar Jr.: "I'll be the field crew chief in northeastern Montana for the Hell Creek III project with hopes of finding a Tyrannosaurus rex skeleton for the UW Burke Museum."

Melissa Eng: "I'll be collecting time lapse images of developing fruit fly larvae to understand what contributes to maintained distinction between axons and dendrites (transmitters and receivers of information)."

Derek Smith: "I'll be following up on 2300-year-old benthic settlement experiments started by ancient Greek and Roman sailors when their ships and artifacts went down throughout the Mediterranean Sea."

Joshua Swore: "I'll be looking at and comparing babies... baby invertebrates found in the Puget Sound while they develop."

Leander Love-Anderegg: "I'll be exploring how Rocky Mountain forests deal with drought by shooting trees with a shotgun."

Stephanie Smith: "I am going to dig up some tiny fossil teeth and help Dave find that T. rex that he wants so much. "

Casey Self: "Defending, then starting a project measuring cranial suture patency in adult humans"

Jennifer Day: "I'll be watching digital critters make babies."

Jonathan Calede: "I'll be spending part of my summer digging up western Montana for fossil mammals and another part of it looking at gopher skulls. Lots of burrowing and burrowers!"

Emily Grason: "I'll be trying to guess what snails are thinking, and cleaning up lots of crab poop - and maybe doing some hiking."

Myles Fenske: "I'm spending my summer making petunias glow in the dark--to a rhythm!"

Emily Bain: "I'll be checking out expression of pigment cell genes in zebrafish and drinking lots of beer on a boat on Lake Washington."

Sweta Agrawal: "Seducing flies with magnets wasn't enough -- this summer, I'll be adding lasers to my system, so I can start to CONTROL FLY MINDS."

Matthew George: "I'll be yanking critters off of rocks."

Shawn Luttrell: "I'll be here on campus doing a ton of in situ hybridization and staining of neural tissue in regenerating hemichordates."

Katrina van Raay: "I'll be watching one of the world's smallest animals eat tiny multicellular algae from the inside out."

Charles Beightol: "I'll be in Zambia hunting prehistoric big game therapsids, and then finish off the summer at Petrified Forest National Park, AZ searching for lost croc relatives!"

Ian Breckheimer: “I’ll be torturing alpine plants on Mt. Rainier, where only the strong survive!”

Laura Newcomb: "I'll be pulling mussels off of aquaculture lines on board a mussel harvesting boat to help me understand how elevated temperature and ocean acidification may weaken mussel attachment strength."

Lauren Debey: "I'll be taking undergraduate students and K-12 teachers to Montana to dig for dinosaurs."

Lauren Vandepas: "I'll be subjecting the ctenophore Pleurobrachia bachei to immune challenges to characterize the innate immune system of a basal animal group and enjoying the gorgeousness that is summer at Friday Harbor Labs."

Jiae Lee: "I'll be zapping the fly neuron with a laser to find out what happens inside them with overcoming the pain and struggling to grow back."

Melissa Steele-Ogus: "I'm going to be indoctrinating undergrads in assisting me in my nefarious schemes to take over the world! Er, I mean, I'm going to quietly work on my research and not plot any sort of mad science."

Alexander Lowe: "I'll be recording eelgrass and oysters (De-?)acidifying the ocean."

Rochelle Kelly: "I'll be studying bat ecology on the San Juan Islands this summer."

Audrey Ragsac: "I'll be taking a course on tropical botany in Miami."

Leith Miller: "I'll be microCT scanning bat nose leaves and ears, as well as getting elbow deep in mammal masticatory muscles."

Aric Rininger: "I'm going to spend this summer watching weeds grow and taping leaves to microscope slides."

Edith Pierre-Jerome: "This summer I will be be gene cloning, gene cloning, and maybe do some more gene cloning."

Itzue Caviedes Solis: "I will spend my summer under the stars walking along the rivers looking for frogs in Mexican forest!"

Matthew McElroy: "This summer I'll be sequencing DNA from Puerto Rican lizards in order to study physiology and population differentiation."

CJ Battey: "I'm in Mexico surveying the avian biodiversity of the mountains of southeastern Nuevo León."  

Frazer Meacham: "I'll be speculating on some problems in fields only vaguely related to biology, while using some math."

William Hardin: "I'll be taking movies of reproducing Giardia, while listening to Pandora."

Eliza Heery: "I'll be sorting through worms, clams, snails and more in sediment samples from an experiment I'm running off of Alki Beach."

Jared Grummer: "I'll be collecting and analyzing genomic data of western North American lizards and frogs, while preparing for and subsequently presenting at the Joint Meeting of Ichthyologists and Herpetologists in Tennessee!"

Monday, June 23, 2014

Course Evaluation and Grad Publication: Hannah Jordt

Filling in that bubble sheet: An evaluation of a course you should have taken

Evaluator’s note to her fellow biograds:  Just as twelve of us were taught to do in Bio 505B this past quarter, I’m going to start off by stating my educational objectives up front. The goals of this blog post are 1) to inform N-12 of you that you missed out on a great class last quarter, 2) to convince you to accommodate it in your schedule next spring when it’s offered again, and 3) to fit in a slightly retroactive grad publication post.

Course: Bio 505B: Problems in Biological Instruction

Instructors: Scott Freeman, also featuring Mary Pat Wenderoth

Q1: What aspects of the course contributed most to your learning?

Short Answer: Active learning and peer instruction (take this course so you can role your eyes at the obviousness of this statement).

Longer answer: I admit that I’m fairly biased in how much importance I give to teaching and to having an understanding of evidence based teaching practices.  But we’re biologists. We all like evidence and critiquing design flaws for not flushing out those alternative hypotheses. We like admiring a well-designed experiment that gives us information about something relevant to our lives. In Bio 505B we spent one morning a week gathered around a table over coffee and scones, doing just this. We read papers regarding student demographics and mindsets, the best way to design a course or classroom, and various teaching techniques. We shared them with our peers in groups and then had lively debates about the merits of each, and about how we could use the results to shape our own teaching practices. There is evidence out there about what works and what doesn’t. Being exposed to this evidence through these discussions, and realizing that this knowledge will actually help you become a better teacher are the best parts of this class.

Q2: Did the instructor(s) seem knowledgeable about the material presented?

While I know we’re all pretty well aware of how great of a scientific research department UW Biology is, we’re also at the forefront of cutting-edge biology education research.  Members of the department’s Biology Education Research Group (BERG) regularly publish research articles, some of which include the #2 and #3 most cited papers in Life Sciences Education and publications in Science and PNAS. Scott and Mary Pat are two of the pillars of this group and being able to discuss biology education with them for a quarter is an opportunity you don’t want to miss out on. They are great guides to the current literature, and as you would expect from two people who have devoted their lives to improving biology education, excellent instructors. 

Q3: Do you have any recommendations for improving the course?

Advertise it more. Convince everyone to take it. Make it a mandatory graduate student requirement. Any or all of the above. As biologists and graduate students, teaching is relevant to all of us, and we can become so much better at it simply by being aware of the best ways (backed up with evidence!) to teach and communicate science. Plus, it’s fun! Trust me, grads, you want to take this class.

Q4: Do you have any additional comments?

Here’s the part where I subtly slip in a grad publication post and hope you all don’t realize it’s several weeks late. However, we were so excited about the results I wanted to encourage you all to take a look at it anyway. In our paper, “Active learning increases student performance in science, engineering, and mathematics” (Freeman et al. 2014), we meta-analyzed 225 studies that compared active learning to traditional lecturing and found that active learning reduces failure rates and increases student performance on exams. We’re hoping this paper helps put to rest the long-held debate on whether active learning or traditional lecturing is more effective, so that education researchers can turn their focus to 2nd generation research, i.e., exploring which forms of active learning are best, and how to optimally incorporate them in the classroom.

The paper can be found here!

A follow up commentary published in PNAS is here.

And UW Today’s take on it is here. 


Monday, June 2, 2014

Grad Publication: Jared Grummer

This just in: there aren’t enough lizards in the world!

      As of February 2014, the TIGR Reptile Database reports the existence of 5,914 lizard species (9,372 if you include the highly specialized lizards we call snakes).  Well, TIGR, as of May 2015, tally up one more! My collaborator, Rob Bryson Jr., and I have recently described a new species of Mexican lizard (genus Sceloporus) based on extensive DNA and morphological analyses. The title of this post is in response to an article from the Irish Times referencing a new species of horned lizard my advisor Dr. Adam Leaché (and collaborators) recently described, “As if there weren't enough lizards in the world..."
Jared wrangles a Sceloporus.
      I began my Master’s thesis in 2008 at San Diego State University under the guidance of Dr. Tod Reeder. As academic incest would have it, I am now a PhD candidate in the lab of Dr. Adam Leaché, who also got his MSc from Dr. Reeder, but ~10 years before me. Anyways, my Master’s project was initially focused on studying genetics amongst various populations in Arizona and New Mexico of the bunchgrass lizard Sceloporus slevini, a member of the Sceloporus scalaris species group. Ten species existed in this group before I began my research, all of which are distributed across mid- to high-elevation mountains in Mexico and the U.S. southwest. This group of lizards is cool, despite their drab grey-brown appearance, because one species has evolved viviparity, or the act of giving live birth. This attribute, along with a unique montane distribution, attracted the attention of many biologists in the 1990s to figure out the relationships and “species limits” amongst members of this group.
      Since the 1990s, sequencing and analytical techniques have substantially progressed. Most importantly, for population geneticists and systematists, researchers have embraced the use of multi-locus nuclear DNA when inferring the species-level history of organisms. Similarly, multi-locus species delimitation has become a popular subject in the past 5-10 years. Many methods and programs that delimit species have been devised by a variety of researchers, each with their own strengths and weaknesses. Myself, under the guidance of my Master’s thesis advisor, along with collaborator Rob Bryson Jr., have developed another method for delimiting species. In doing so, we also discovered and described a new species of Sceloporus in Mexico.
Habitat of the new species.
      Our new method of species delimitation takes advantage of the fact that many species tree inference programs require the user to assign individuals to lineages (a.k.a. “species”) before analysis. In this sense, the researcher can determine the best configuration of populations into species, given a particular dataset. For instance, based on the most current data, we know that the closest living relative to humans is the chimpanzee, and that humans and chimps together are closest related to the gorilla, and that the three of these are all equally related to orangutans. To a phylogeneticist, this “tree”, or set of evolutionary relationships, can be expressed as (Orangutan, (Gorilla, (Human, Chimp))).
Now let’s say that we sequence individuals from multiple populations of each “species” of great ape, so that we have DNA from multiple individuals for each species.  Using our method, our first hypothesis would assign every chimp individual to the species “chimp”, every human individual to the species “human”, etc. A phylogenetic tree would be constructed with these assignments, generating a likelihood score that we can now use to rank this model of species limits against other such models. In our toy example, a second model of species limits we could create would have all human individuals assigned to the “chimp” species, just to ruffle those creationist feathers. After inferring the species-level phylogeny with these species limits, we would see that the score of this model is worse because the data do not support this relationship (the creationists can now rejoice, we are indeed a different species from the chimpanzee). Although the outcome is obvious in this example, identifying species limits with drab tropical lizards is not quite so simple.
In this exact same way, my co-authors and I tested many models of species limits amongst 12+ populations of lizards in the Sceloporus scalaris group using multi-locus nuclear DNA. This method identified and validated a “cryptic” species within the group, meaning that it is morphologically indistinguishable from other close relatives (except for some males who brandish an orange belly during the breeding season). Although not overly sophisticated, our method was published in the journal Systematic Biology at the end of 2013. Our article has been viewed over 1,200 times and used by 4 other research groups so far in their scientific publications.
Our research highlights the need for in-depth genetic analyses of widely distributed species, especially those in the tropics. Central America in particular is a geologically complex region that has generated a large number of species, many of which are endemic to very isolated regions. The new species of lizard we discovered, Scleoporus aurantius (aurantius owing to the orange sides discovered in breeding males), exists in southwestern Mexico in the states of Jalisco and Aguascalientes, but we are currently uncertain of its exact geographic extent.
The holotype of Sceloporus aurantius
We are excited to discover a new species of vertebrate amongst an era marked by habitat destruction and global species declines. But maybe more importantly, we are very excited to present a method to the scientific community that we hope many researchers will use in their studies and aid in the discovery of new species in the future.

If you would like a copy of any of these articles, please email me at grummer@uw.edu.

New species description (preview): http://www.mapress.com/zootaxa/2014/f/z03790p450f.pdf