Putting the “rad” in “graduate student”: Becoming a runner!

At the beginning of this year, I gave myself a pretty straightforward yet daunting 2014 goal: become a “runner”. And not to toot my own horn or anything, but I think that I am kicking ass and taking names in this category thus far. Let’s reflect a bit on my progress, shall we?!

I’m going to just come out and say it: I have never been an athlete. Or anything close to an athlete for that matter. Well, I DID take a gymnastics class or two as a 4 year old, if that counts? As an adolescent, the closest I got to “sports” was a brief foray into horseback riding lessons. This lasted about 9 months until I decided that playing the flute was much more my style. (Plus, I’ve never been a big fan of getting dirty, and there are very few things that are dirtier than a horse barn). I’ve just never liked playing sports, nor have I ever been very good at them. My throwing arm leaves a lot to be desired and my eyesight is so terrible that it’s a miracle I have even once caught a ball. I’m also so competitive that I might have seriously injured someone on an opposing team if I lost, and assault charges as a 10 year old are usually frowned upon. Have I convinced you yet? Sports have just never been my thing.

But in the last three months, I’ve run nearly 150 miles.

150 MILES. That, my friend, is crazy town banana pants. Last month, I ran the Seahawks 12K (or a little under 8 miles for the nonmetric folk). This was the longest run I had ever attempted, even in practice. It turned out to be a blast, and while I didn’t set any land speed records, I finished! Last Sunday, I was in a crappy mood and didn’t feel like leaving my couch, but eventually ended up running for 10 miles! I don’t know who this person is that has become a quote unquote runner, but I’m not going to ask too many questions.

Ready to run the Seahawks 12K!

Ready to run the Seahawks 12K!

Over the last few months, I’ve learned that I am not a huge fan of a very strict running schedule. In fact, I very much detest it. This initially surprised me, as I’ve always considered myself a planner. However, upon further reflection, I think this is in some ways due to my experiences as a graduate student over the last 4 years. It is really hard for me to wake up in the morning and say “I MUST run 10 miles today”. Similarly, I also find it hard to say “I MUST sit at my desk today for ten hours and write 10 pages of this manuscript”. I am much more successful on a day-to-day basis by giving myself a bit of flexibility. Maybe, like this morning, I wake up on Monday and decide to write and edit a blog post. Did I plan on writing this today? Nope! But I knew what projects were on my to-do list, so I picked the task I felt most motivated to accomplish this morning. Similarly, I woke up that Sunday knowing I needed to accomplish SOME sort of run and ultimately felt motivated to run 10 miles. See, FLEXIBILITY!

Of course, flexibility isn’t always possible. When I’m in the middle of a time-sensitive experiment, there are days where I MUST get A,B and C completed. If a grant is due on Friday and I spend all of Monday on a blog post, then I most definitely deserve a kick in the pants. However, now that my life has entered into the writing, writing, writing phase of graduate school, I’m finding it fun, and most importantly productive, to be flexible.

I recently spent some time chatting in the hallway with a fellow MCB Incoming Class of 2010er. We both mentioned that one of the BIGGEST things that we have learned over the years is that graduate school isn’t a 9 to 5 job, nor is it the same for everyone. In fact, the path that we take through graduate school is RADICALLY different from one individual to the other, and making comparisons between your path and another’s is just plain silly, and frankly, potentially very harmful. Our path is molded by a combination of hundreds of variables: your boss, your personality, your home life, your career goals, the success of particular experiments, your work ethic, and so on. And that path is redesigned and full of detours and speed bumps over time. But one thing that is required for each and every individual’s success in graduate school (and running, for that matter) is self-motivation. No, I’m not in lab at 8 am every single day like some. In fact, some days it is nearly lunchtime and I am sitting at my dining room table working on blogs and conference abstracts (hint: that’s today). To be honest, I used to feel really guilty about not being at the bench every minute, and I have felt bad about not running as far as I would like on a particular day. However, my new found flexibility mixed with plenty of self-motivation means that I am not only just as productive as ever, but probably a bit happier too.

So, after quite a long tangent, my point is this: no, I am not a conventional runner. But I don’t really do many things by convention anymore. And that, my friends, is quite alright with me.

Learning to not feel guilty when this doesn't happen

Learning to not feel guilty when this doesn’t happen has been HARD

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Before I leave, it’s time to set my next short-term goal in my 2014 Killing the Bear goal. I guess I set this a while ago, but I haven’t announced it on my blog yet. Next month, I will be running my FIRST HALF MARATHON! I am officially registered for the 2014 Rock ‘N Roll Seattle Half Marathon on June 21st, 2014. 5 weeks to go! I’m feeling confident that I can finish the race, and that is HUGE progress from where I was 4 months ago. Will I be fast? Probably not… but that just means I’ll have another goal to set after June 21st!

Lessons learned: Giving a talk at NWDB 2014

Disclaimer: I’ve written the beginning of a new blog post about 5 separate times over the last few weeks. It always happens the same way: I jot down my thoughts, reread them, dislike them, save them in a “Blog drafts???” folder, and forget about them. This morning, I went back through those old “crap” blogs, and realized the content was not nearly as terrible as I thought. So here is the first of several posts this week (I PROMISE), which were actually written some time ago. This particular blog was drafted April 1st. I guess it is a very belated April Fools joke to post it a month and a half later. :)

Thoughts from Northwest Developmental Biology Meeting!

I did quite a bit of traveling around the Pacific Northwest in March. The first was my yearly pilgrimage to the Friday Harbor Laboratories on San Juan Island for the Northwest Developmental Biology Meeting! This was my FOURTH straight year attending, which makes me feel both old and excited at the same time. NWDB is the regional meeting of the Society for Developmental Biology, and it is by far one of my favorite meetings that I have ever attended. The setting is BEAUTIFUL, the audience is engaged and relaxed, and there is a mind-blowing amount of cool science. Think summer camp for scientists: AWESOME.

Apparently I only attend conferences in beautiful locales.

Apparently I only attend conferences in beautiful locales.

For the second year in a row, I submitted an abstract to present a short oral presentation, and was selected. I was scheduled to give the very first student talk of the meeting. This was pretty exciting for me, especially since I went last in 2013. That year, I spent the entire meeting worrying about my talk and didn’t get to totally appreciate the other speakers. I woke up at 6 am (yikes) to practice my talk a few times, and headed over to the conference hall around 8 to eat some breakfast and grab a seat before the hour-long plenary talk. However, I barely had time to finish my bagel when the moderator walked up to the microphone and said, “Due to a scheduling conflict, our plenary speaker will be moved to the end of this session. Please welcome your first speaker, Emily Fawcett”. Thankfully I am fully functional in the morning and one of the few scientists who doesn’t need a cup of coffee to be coherent before 9 am, but my initial response?

PANIC.

I even believe the first sentence I said when I got the microphone went something like “I am so not ready for this” followed by a nervous giggle. The best thing I’ve ever said into a microphone? Probably not. But did give me at least a second to compose myself? You betcha.

Now, when I give a talk, I have the benefit of studying a really cool but completely off-the-wall topic. Not many people think about stress memories and even fewer people think about hydrogen sulfide, so I’ve had a LOT of practice convincing people that it’s something worth studying. Just call me the used car salesman of H2S memory.

I’ve also recently started to overcome my “nervous talking equals talking at 1,000 mph” problem. There is nothing that confuses your audience more than rattling off unfamiliar science at the speed of an auctioneer.

My goal? Be more understandable than an auctioneer.

My goal? Be more understandable than an auctioneer.

10 or so minutes later, I had successfully (and at an adequate speed) navigated through my talk. And, importantly, I could even remember giving the talk after I had finished! This may sound trivial, but for the first year or two of public speaking, those 10 minutes would have been a huge black box that I would never fully remember.

Ok great, the talk is over and I think it went pretty well. But now? Now it’s time for…. dun dun dun… QUESTIONS.

I have always been irrationally afraid of the question section of scientific talks. I have never been particularly confident speaking on my toes, and so my nerves have often gotten the best of me. I’d say that I am just one of a huge number of grad students that experienced the dreaded Impostor Syndrome in graduate school. It is really hard to look around a room of scientists and think of yourself as a colleague, as opposed to an insignificant dummy that got into graduate school by mistake. It’s taken me 4 years, countless tears, several boxes of tissues to catch those tears, and a whole lot of grunt work to acquire the confidence necessary to not completely fall to pieces in front of a crowd.

One of my favorite pieces of advice about question sections that I’ve ever received was that questions are actually a good sign! It means that your audience not only understood what you’ve presented to them, but they have processed it and want to know more! I had to stop thinking of questions as confrontational but as simply inquisitive. Therefore, when I saw more than half a dozen hands shoot into the air at the end of my talk, I experienced a strange mix of fear and excitement. Apparently I was a bit under time, so my moderator let me continue to answer question after question after question. For some of the questions, I had concrete answers and for others I had not-so-concrete speculations. But I was at least answering them coherently. Woo!  It was then time for my last question. A man sitting front and center raised his hand and very quietly asked:

“How confident are you that your hypothesis is not completely wrong?”

Hmmm. Ok. This is a curve ball. Wasn’t most of my talk presenting evidence that my hypothesis was at least feasible? Did he not believe any of it? Oh no.

PANIC. PART TWO.

2 moments of panic in less than 15 minutes?! This was becoming quite unfortunate. However, since he had asked the question so quietly, I had the benefit of a few seconds to gather my composure before answering. I leaned up to the microphone, and slowly repeated the question verbatim. I will forever be grateful for the murmur of giggles that quickly swept around the room. A well-known P.I. in the front even yelled out with a huge smile on his face: “Oh, you know, I’d probably say about 50%?!”. Ok, everyone understands this is a tricky question to address.

Phew. Crisis averted.

I then took a deep breath, broke into a smile, and asked the man to clarify which part of the hypothesis he’d like me to address. It turned out that he had a totally valid concern which I quickly addressed and concluded my talk. Once again, I had survived a talk. SUCCESS!

I guess I went into so much detail about this short oral presentation because I think it highlights not only the terrifying inferiority complex we face as graduate students but also the progress I’ve made to tackle it in the last 4 years. Talks will never go exactly how I want them to go and there will always be things I want to fix about them, but they are lessons learned and baby steps in the right direction. That final question I received, which gave me the biggest amount of concern, has even become sort of a joke within my training grant. No one will ever listen to me speak again without being tempted to ask that question, and we’ve even all come up with our favorite “answers” in the event that we get that question again.

Overall, NWDB 2014 was another fabulous success. The science was incredible, the feedback I received was invaluable, and the friendship I strengthened with my training grant cohort and fellow graduate students is irreplaceable. Onto the next one! Next stop? Madison, WI!

Killing the bear (and other 2014 goals)

Hello friends! So… it’s been a while. It’d be a lie if I didn’t admit that I’m a bit embarrassed and quite disappointed in how long it has taken me to come back to this blog. Last year, when SciFund outreach ended, I made a promise to myself that I would blog at LEAST once a month. And, to put it bluntly, I failed miserably. And for those of you who know me, I’m not really one to accept failure. SO, it’s time to (wo)man up and get back on the right track with this blog! But in order for that to happen, I think it’s time to make some changes. BIG changes. So bring on the personal anecdotes and corny jokes because…

this blog is about to get personal.

In order to understand why I think I need to make changes, let’s take a look back to a lovely evening of sushi and cocktails that I had with my friend, colleague, and importantly, fellow blogger, last month. In between rounds of Jenga and lychee martinis, Albert asked me what sounded like a simple question:

So what happened to your blog?

I remember that I immediately responded with an excuse, something along the lines of, “it’s hard for me to think of good scientific content so frequently, I got busy, I traveled a lot… blah blah blah”. But it was then that I realized I didn’t have a good excuse. There’s no need for my blog to be scientific gold every entry. There’s no need to continuously come up with a fresh take on my research. I just need to WRITE. And write often. This week, Albert posted a new entry into his blog, and so shall I. Thanks for the motivation, Steak Sauce. I owe you one. Oh, and he’s a great blogger, check it out here.

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So I think I’ll start my blogs for 2014 with a quick review of my accomplishments in 2013, and a look ahead to my goals for 2014. I’ve decided to loosely structure my blog around these goals, both personal and professional, to hopefully encourage me to write informally and often.

2013 Accomplishment: Get involved with a nonprofit!

At the beginning of 2013, April, a post-doc in our lab (and a wonderful human being all around), asked me what I wanted to do after I got my Ph.D.. I told her the truth: I’m not exactly sure, but I am really passionate about the mission and motivation behind nonprofit organizations. So she challenged me to find a nonprofit organization in Seattle, and to get involved. REALLY involved. And so I did! For the last year, I have volunteered weekly (and sometimes a bit more), at the Seattle Cancer Care Alliance, where the mission is to offer world-class cancer treatment to the community while supporting the conduct of cutting-edge cancer research. I’ve spent most of my Saturday afternoons at Shine, a retail store housed in the Seattle Cancer Care Alliance house, which provides oncology-related goods, services and support to cancer patients, their families, and the community. While I think I will dedicate a future blog to my love for nonprofits and my experiences with the SCCA, I am proud to say that I have accomplished my 2013 goal of getting involved, and couldn’t be happier about it!

2014 Goal: Kill the bear

Two weeks ago, during dinner with the fantastic Dr. Alex Schier, my training grant cohort asked if he had any advice for young scientists. His advice was simply to “kill the bear”. And, while it didn’t make too much sense at first, I think this advice makes for a GREAT 2014 goal. Let me elaborate…

As scientists, our research isn’t doing anyone any good sitting in notebooks. There are always more experiments we could do, always another question that could be answered. However, we need to stop trying to teach our proverbial “bear” new tricks. Don’t feed our bear any more treats. Don’t pet the bear.

JUST KILL THE BEAR.

And so, my professional goal for 2014 is to publish more! I have two pretty advanced drafts that have been collecting electronic dust on my computer, but I find myself starting new experiments instead of polishing these manuscripts. It’s time to make publishing my number one goal… it’s time to kill the bear!

He may be cute, but it's time to kill the bear!

He may be cute, but it’s time to kill the bear!

I’ll also be working towards killing the bear in my personal life. I’ve come to really enjoy running in the past year or so, but last October, while training for the Dawg Dash 10K, I got a stress fracture in the arch of my foot.  I ended up in a cast for about 2 months, and had to stay away from running until the New Year. Let me promise you, that was NOT FUN. However, I did learn that it is still possible to dress up a cast for a formal function, jump around in the ECS section at a Sounders game, and that the cast can even improve your Halloween costume (at least when you go as Buzz Lightyear, as I did).

Walking casts, despite the name, make walking a bit of a challenge.

Walking casts, despite the name, make walking a bit of a challenge.

Even though I’ve always talked about setting running goals, to this day, I’ve never run a race longer than a 5K. So, it’s time to kill the bear! I’m signed up to run the 12th Man 12K (GO HAWKS!) in early April, and am slowly but surely getting back into running shape after my injury. I have some other BIG plans that I’m not quite ready to share with the world yet, but watch out 2014… I’m going to be running circles around you!!!

I hope you guys are excited as I am for Emily’s blog version 2.0. Will there be science? You bet. But will there be a bit more of me? Yeah, I think so. So get ready for many adventures (and some misadventures) as I try to figure out what the HELL I am doing. Toodles!

Top 5 Highlights from WORM2013!

I will always remember June 2013 as a whirlwind month of airports, poster sessions, and far too little sleep. On final count, I took 10 flights out of 8 different airports through 11 states, 4 time zones, and 2 countries! After giving myself a bit of July to recover, I am glad to report that June was a marvelous success, inspiring me with new research ideas and lighting a fire under me to get to writing! I believe my next blog may be a photo tour of June 2013, but until then… let’s talk worms!

My last stop for the month was the 19th International C. elegans Meeting at UCLA in Los Angeles, California! In many ways, this trip was reminiscent of my trip to Cancun (discussed here).

For one, the temperatures were similar:

photo

And secondly, another beautiful location:

photo (4)

While roaming through the rows and rows of posters, it was easy to identify the “unreasonably tan” colleagues who had also attended the ICDB conference in Cancun the previous week. Think of it as Where’s Waldo:

photo (5)

And just like Cancun, I learned a lot about really cool science at WORM2013! So, in the spirit of my last blog post, here are my top 5 highlights from my week in LA at WORM2013:

#1: The hot topic: chromatin remodeling during stress!

I remain a bit partial to this topic, as it is the focus of my own research, but I was extremely excited to see so many fabulous talks and posters focusing on the relationship between chromatin remodeling and stress response! In particular, Christian Riedel from Gary Ruvkun’s lab demonstrated that the SWI/SNF chromatin-remodeling complex is required for DAF-16 (FOXO) gene-activation, and ultimately DAF-16 dependent longevity. This work was recently published in Nature Cell Biology and can be found here. Excitingly, David Fay also described a role for SWI/SNF in stress response, as a mediator of the ethanol and stress-response element (ESRE) pathway. These talks, along with multiple posters (including mine!), really begin to illustrate the critical requirement for chromatin remodeling in a multitude of stress response pathways.

#2: Transdifferentiation… is awesome.

As a trainee in developmental biology, and after recently listening to John Gordun discussing the challenges in transdifferentiation at ISDB2013, Joel Rothman’s talk blew me away. While Gordun’s talk emphasized how removal of chromatin marks specific to differentiated cells is one of the most difficult aspects of transdifferentiation, Rothman described a phenomenon in worms in which this process is not even necessary!  Expressing a single transcription factor, elt-7, resulted in the conversion of differentiated pharynx into endoderm, even in the absence of cell division. This talk was definitely one of the “THAT IS SO COOL” moments of WORM2013 for me.

#3: Memorable talks about teeth, exercise, and sex

Based on the conference twitter feed and the chatter buzzing about the crowd, the next 3 talks were some of the most memorable, as well as the most unique! Mary Ann Royal of the Driscoll lab showed that 30 minutes of swimming a day results in increased pharyngeal pumping later in life, suggesting that “exercising” has health benefits even in worms! Eric Ragsdale of the Sommer lab wowed the crowd with a gruesome video of P. pacificus chowing down on an unsuspecting C. elegans. His talk then went on to focus on the genetic control of a developmental teeth dimorphism in P. pacificus by a sulfatase encoded by eud-1. Finally, Cheng Shi of the Murphy lab pointed out a phenomenon we all felt we should have noticed previously: N2 worms shrink up to 30% after mating! These animals, in addition to a reduction in size, also are less attractive to other males, and live shorter lives. As male seminal fluid contributes to this phenomenon, it may represent an example of male influence on hermaphrodites to maximize their own reproductive success. Overall, Mary Ann, Eric, and Cheng definitely win the “most memorable” superlatives of WORM2013.

#4: More disease models in C. elegans

As a scientist working in model organisms, I am always excited to hear about disease models in C. elegans, as it is a great way to study the genetic basis of human disease. Susana Garcia from the Ruvkun lab introduced a worm model designed to investigate the toxicity of CUG repeat-containing RNA, which is commonly associated with the human disease myotonic dystrophy. Garcia discovered that the nonsense mediated decay pathway normally functions to clear these toxic repeats, suggesting that it may be a good target for future myotonic dystrophy research.

Emery-Dreifuss muscular dystrophy is due to mutation in the lamin protein. A.  Mattout from the Gasser lab demonstrated that this mutation, in worms, leads to failed tissue-specific release of heterochromatin and disrupted muscle function. By restoring chromatin organization through genetic manipulation, Mattout was able to fully rescue muscle function in these animals, suggesting that chromatin mislocalization may be of particular importance in human laminopathies.

#5: New insight into everyone’s favorite topic, insulin-like signaling!

It wouldn’t be a worm meeting without several dozen talks and posters about the FOXO transcription factor DAF-16. This year was no exception, but it was great to see some really remarkable new discoveries in a field that has garnered so much interest in the worm community! To highlight just a few, Adrian Wolstenholme from the University of Bath demonstrated the discovery of the sole glutamate transporter in worms, FGT-1! Additionally, Ronald Tepper from the Bussemaker lab at Columbia gave a great talk on the identification of PQM-1, the main regulator of the class II growth and development genes originally thought to be directly activated by DAF-16.

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As you can tell from the sheer number of talks I’ve mentioned, there was a huge amount of elegant science and interesting discoveries at WORM2013. Visit the meeting’s website for full abstracts and dates of future WORM events!

Top 5 Highlights from ICDB 2013!

It seems that I have neglected my blog a bit this month, but thankfully this is due to an exciting (and exhausting!) month of travel! As of June 1st, I have been to 10 states, 4 time zones, and 2 countries!

I began my whirlwind month in Maryland visiting my family and attending Alumni Weekend at my undergraduate institution, St. Mary’s College of Maryland. This trip was full of crabs, sunshine, and reminiscing with old friends. All in all, it was a great way to get reenergized for conference season!

Speaking of conferences…

A few months ago, I gave a talk at the Northwest Regional Society for Developmental Biology (SDB) meeting, and was beyond excited to win a travel award to attend SDB’s national meeting! Excitingly, this year the national SDB collaborated with other international societies to host the 17th International Congress of Developmental Biology!

The conference was fabulous, and I could blog for hours about all of the amazing science that I got to hear about at the conference. But to save us all some time, here are my top 5 highlights of my trip to ICDB 2013!!

#1: The meeting was held in CANCUN, MEXICO!

Here’s a photograph from my hotel room: IMG_5125

And another from my favorite beach chair:

IMG_5134

Need I say more? The location was absolutely incredible, with a very quick walk to the convention center, seen here across the street from my hotel:

IMG_5177

Located on the top floor of the Cancun Convention Center, the meeting was held in one large room that was easily separated into 3 concurrent sessions for some of the afternoons. The layout of the meeting made it really easy to bounce between rooms, so you could catch talks in all sorts of topics and disciplines. Additionally, posters were constantly on display in the break room, giving attendees plenty of time to scour the 600 excellent posters!

#2: Enhancers play a role in human disease, evolution… and just about everything you could imagine.

Enhancers really stole the show at this year’s meeting. Many of the talks, a large number of posters, and a lot of coffee break chatter surrounded some fascinating studies into the role of these noncoding regions of DNA in development.

For my developmental biology novices, let’s quickly define enhancers. Our genome consists of long sequences of DNA, in which some regions code for functional proteins, and some regions do not. Enhancers are found within this noncoding region of DNA and are thought to modulate the activity of proteins transcribed from nearby regions of coding DNA.

Schematic of enhancers (green), found upstream of effected genes (blue) (Photo credit: Wikipedia)

Schematic of enhancers (green), found upstream of effected genes (blue) (Photo credit: Wikipedia)

How do we identify enhancers? Chicks are often the best tool for identifying conserved enhancers, as their genome is compact and conserved noncoding regions are likely to contain important regulatory information.

Scientists have long been confused about how mutations in noncoding regions of DNA lead to human disease, but as described at ICDB 2013, many of these mutations are starting to be identified as being located within enhancer regions.

One of my favorite talks of the week was from Harvard’s Cliff Tabin. Many human traits seem to have regressed from the traits found in monkeys (less body hair, shorter fingers, etc.). Regressive traits often come from loss of enhancers upstream of trait-determining genes. Cliff’s lab has demonstrated that the human genome is enriched for deletions in transcription start sites and enhancer regions, suggesting that loss of enhancers did in fact contribute to our regressive loss of monkey-like traits.

For more information on the ICDB enhancer talks, check out the lab websites of Cliff TabinMarianne Bronner, and Alvaro Iglesias!

#3: There was a WHOLE SESSION on how the environment impacts development! 

My particular interest in developmental biology focuses around the long-term impact of environmental stress on phenotype and physiology. I was pleasantly surprised to find an entire session of talks dedicated to this topic!

While many human diseases can be attributed to genetic predisposition, environmental conditions can exaggerate these disease phenotypes.  Sally Dunwoodie gave a great talk discussing how low oxygen conditions (hypoxia) during early development increases the penetrance of genetically heritable scoliosis. Teiya Kijimoto demonstrated that genes involved in classical developmental decisions, including Hedgehog signaling, also control environmentally induced traits, such as horn size in dung beetles!

#4: Improving undergraduate interest in research with projects designed straight from the headlines!

The education section of ICDB 2013 focused on how we can interest students with research projects on current hot topics in the media.  I think this a great idea, as it is so much easier to get excited about science when you know that you are contributing to a relevant and important cause.

Barresi lab uses Deepwater Horizion oil spill as inspiration for undergraduate research (Photo credit: Wikipedia)

Barresi lab uses Deepwater Horizion oil spill as inspiration for undergraduate research (Photo credit: Wikipedia)

For example, Michael Barresi described the upper division research course he designed to investigate the effects of the Deepwater Horizon Oil spill on the development of fish in the Gulf of Mexico. Tyrone Hayes gave an eye-opening talk on the impact of the pesticide atrazine on the sexual behavior and fertility of frogs. Additionally, Tyrone showed correlations between his research on frogs and the decline in fertility of men in close contact with pesticides.

#5: Alternative model organisms are awesome!

As a scientist who works in a commonly used model organism, I am always impressed by the amount of work that goes into the implementation of new and alternative model organisms. This meeting did not disappoint, as I got to hear some really great talks about using tunicates, frogs, and honeybees for scientific research. Many of these tools are being developed to overcome the shortcomings of our current model systems and allow us to address questions that are currently unanswerable.

Nanette Nascone-Yoder introduced the Budgett’s frog- a giant cannibalistic Xenopus alternative that allows for higher resolution of frog development!

Lepidobatrachus_laevis

Budgett’s Frog (Photo credit: wikipedia)

Robert Drewell discussed how DNA methylation in the eusocial honeybee is a new example of genomic imprinting!

Honeybees (Photo credit: NJDEP)

Honeybees (Photo credit: NJDEP)

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To summarize, the ICDB 2013 meeting was a great experience!

Tomorrow, I am off to the International Caenorhabditis elegans meeting at UCLA! Follow me on twitter @em_fawcett and look for my live tweets with #worm2013!

And look forward to another top 5 blog post next week!

 

You work with WHAT?! Common misconceptions about studying nematodes

We are all worms, but I do believe I am a glow-worm”- Winston Churchill

Well, if Mr. Churchill is right, and we are all worms, I am most definitely a nematode.

Now you may be thinking, “Emily, you’ve lost it. A nematode? A toad is most definitely NOT a worm”.  Don’t worry; I haven’t totally lost it (in this instance, anyways). Nematode is another name for the roundworm, which account for over 80% of the individual animals on the planet! In our lab at the University of Washington and at labs all around the world, the nematode is very close to our hearts. This is because we study one particular species of nematode called Caenorhabditis elegans. Scientific names can often be a mouthful, so most shorten it to simply C. elegans.

When I tell people that I work on worms, I usually get a look of disgust, confusion, or skepticism.  But let’s get something straight- C. elegans are not what you are picturing. They don’t look like this:

Source: fir0002 | flagstaffotos.com.au

Source: fir0002 | flagstaffotos.com.au

Or this:

100toys76

And unfortunately, they don’t look like this either:

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In fact, C. elegans are very hard to see without a microscope. Adults are only about 1 millimeter long. To put that into perspective, a single C. elegans worm could be picked up by a single eyelash! Having a hard time picturing it? Here are a couple of views of C. elegans:

Crawling C. elegans hermaphrodite worm

Crawling C. elegans hermaphrodite worm (Photo credit: Wikipedia)

Caenorhabditis elegans

Caenorhabditis elegans (Photo credit: AJC1)

Ok, ok… but who in their right mind decided studying these tiny worms was a good idea?

Well, studying diseases in larger animals like mice and rats isn’t easy: they take a long time to develop and grow, are expensive to maintain, and are complicated in design. In the 1960’s, a scientist named Sydney Brenner suggested that studying C. elegans would improve on a lot of these problems: C. elegans only live for a few weeks in the lab, are cheap and easy to maintain, and it is easy to manipulate their genes! To put the simplicity of C. elegans into perspective, while the human body has trillions of cells, C. elegans only have around 1000 cells! Today, along with fruit flies, C. elegans is frequently used as a model organism for studying disease and cellular processes.

In the 40+ years that C. elegans have been used in scientific research, they have greatly contributed to the advancement of science, particularly in the study of aging. Many genes that make C. elegans live longer in the laboratory have been identified as important in the aging process in humans and other mammals. Additionally, C. elegans are a great model  for studying human disease, as more than half of the genes known to be involved in human disease are also found in C. elegans. For example, models of neurodegenerative diseases including Parkinson’s and Alzheimer’s have been developed, and are currently being utilized to better understand and development treatments for these diseases.

In the last 15 years, THREE Nobel Prizes have been awarded to scientists for their work in C. elegans!

Hopefully, the next time that you hear a scientist mention that they study worms, you will not necessarily picture them digging around in the dirt and looking at earthworms. While we have all been known to dig in the dirt from time to time, C. elegans researchers are tackling tough research problems from behind a microscope, using this tractable and inexpensive model organism!

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And now for some great references to find out more about C. elegans!

A Short History of C. elegans Research

Worms in SPACE?!

Wormatlas: A bit dense for the nonscientist, but great images!

Introduction to C. elegans

 

When peer review meets the press

How do scientific ideas progress from being a project at my lab bench to being the headline story on your nightly news? The process, while all-too-familiar to research scientists, can be a bit of a black box to everyone else. In the last few weeks, this process has reached the front-page news more than once, so let’s talk about the scientific process (and some of its’ flaws)!

The first thing to realize? Science takes a very, very long time. The grant review process, the actual science, the publication process: all are notoriously slow, albeit crucial, steps in the world of science.

In order to fund, perform, and publish scientific research, scientists rely on one very important group: our peers. First, a panel of other scientists reviews our grant proposals. Once the grant is funded, collaborations are critical for the success of a research project. Finally, when the research is completed and submitted for publication, our colleagues review the manuscript for content and clarity. Involving our peers in every step of the process, in theory, ensures the funding of only the best grants and the publication of only the best scientific papers.

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Peer review can be a long, hard road for any scientist                                               (Cartoon credit: Nick D Kim, strange-matter.net)

As the title of my post suggests, the peer review process has come under scrutiny as of late. Let’s do a quick rundown of the recent headlines about the scientific process!

1) The battle over open access

If I were to give you a list of 10 influential scientific articles from the last 20 years and ask you to find full versions of them, you would have a very hard time. In fact, when you reach the website of the appropriate journal, you’d probably be asked to pay the reasonable fee of only 50-100 dollars to view the article.

Wait… $100 to read ONE article?!

The reason? Most research journals charge steep subscription fees to access their articles (current or archived). However, as a large number of these articles are from publicly funded research labs, many believe that this research should be free for anyone to read.

The good news? We have seen a rise in the number of journals with “open access” policies over the last few years. As of 2011, 12% of articles were available open access, with this number rising all the time. The availability of academic research to the public is increasing, and this is definitely a good thing!

Read more: Nature News tackles the topic of Open Access 

2) Is the peer review process in grant selection unsatisfactory?

The National Science Foundation (NSF) is a government agency that provides a large amount of funding to science and engineering research. NSF grants are selected, you guessed it, through a peer review process. After an intensive review of grants that received funding from the NSF over the last few years, some lawmakers believe that the selected grants are not always “groundbreaking” research.

To “fix” this apparent problem, Representative Lamar Smith (R-TX) drafted a bill last month to implement Congress-selected funding criteria on the grant selection process. Many scientists believe that this funding criteria, which requires grants to “answer questions or solve problems that are of utmost importance to society at large”, undermines the peer review process and would negatively impact the advancement of basic research.  Basic research, as opposed to being aimed at curing a particular disease or illness, focuses on understanding the fundamental principles of the world. While this work may not directly “advance the national health, prosperity, or welfare”, it is important an building block for our understanding of the human world. The bill, which has not been formally introduced to Congress, has sparked a large amount of debate within the scientific and political realm. How should we decide who gets funded, when the amount of funding keeps dwindling?

Read more: Science Insider on the NSF Grant Bill

3) Are timeliness and thoroughness in peer review mutually exclusive?

When something BIG happens in science, the authors want to get it out fast with as big of a splash as possible. But where do we find the balance between rushing to publish big results and allowing the peer review process to be effective?

One of those BIG things in science happened this month: Shoukhrat Mitalipov, a US researcher, reported that he had cloned human stem cells from skin cells. The research was published in the journal Cell, a prestigious journal in the scientific community. In the last few days, concerns from anonymous readers began pouring in on potential errors  in the publication. Figures were labeled incorrectly, and an image was duplicated and reused in a different section of the paper. These are the type of errors that are usually caught during the tedious peer review process. So why weren’t they corrected before the publication of such a big story?

To put it simply, this paper went through review at an incomprehensibly fast rate. To give you a framework, a case study of 2,000 manuscripts submitted to a journal in 2010 reported that the average submission took 6.8 weeks from submission to editorial decision. Mitalipov’s submission was reviewed and accepted in only 3 days. Additionally, the paper was published just 12 days after acceptance.

Cell went on to defend the speediness of their review process, stating: “It is a misrepresentation to equate slow peer review with thoroughness or rigor or to use timely peer review as a justification for sloppiness in manuscript preparation”. Thankfully, it appears that the errors in the manuscript do not impact the findings of the research. However, the negative publicity from these errors certainly detracts from the impressive and innovative science performed by Mitalipov and colleagues.

Read more: Nature News: “Human stem cells created by cloning

Read more: Nature News on Errors in Mitalipov Stem Cell Paper

Read more: 2010 Case Study on average length of peer review

Conclusions

In summary, these three stories have brought the scientific process and peer review into the spotlight. Peer review has a lot of benefits, improving the caliber of the science we deliver to the public and lowering the rate of publication of unethical scientific practices. However, the question now remains: how do we improve the peer review process to keep up with the rapid speed of scientific discovery while still yielding the high quality publications we expect?

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Some suggested reading for more information:

Nature tackles the Peer Review Debate

Nature: How are funded grants chosen?