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:

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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:

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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!

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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!

 

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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:

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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.

Peer-Review-Nick-Kim-cartoon3-resize (1)

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?

Hydrogen sulfide: A smelly, deadly gas… but could it save lives?

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Take a moment and imagine a street in Paris in the 18th century, much like this depiction of “Place du Havre, Paris, Rain” by Camille Pissarro. The first things you’ll notice: it’s beautiful, romantic, bustling. But what you might not notice is that is also very, VERY smelly.

Back then, sewer systems were extremely unsophisticated, and the smell of rotten eggs spilled into the streets. Even more, if a person were to go too far below ground, they would likely find themselves dead in minutes. The culprit? Hydrogen sulfide, a gas that smells of rotten eggs and is produced when bacteria breakdown the organic material found in sewage.

Thankfully for us, modern-day sewers have come a long way since the 18th century, but so has our understanding of this smelly, toxic gas. In the last 10-15 years, scientists have found that hydrogen sulfide is important for cell-to-cell communication in our bodies. Additionally, exposure to low levels of hydrogen sulfide has beneficial effects on many different organisms. For example, plants exposed to hydrogen sulfide grow  better, and worms grown in hydrogen sulfide are long-lived! Remarkably, in rats and mice, treatment with hydrogen sulfide also protects against damage from devastating injuries including stroke, heart attack, and severe blood loss. With so many recent discoveries highlighting the benefits of hydrogen sulfide, you may be asking yourself:

How can something that is so deadly also be beneficial?

The answer lies in the dosage. While scientists are still working on understanding HOW the gas functions in the body, we do know that hydrogen sulfide has beneficial effects at low levels, but toxic effects at high levels. The importance of dosage on human health is not just specific to smelly hydrogen sulfide. In fact, just about every substance that we come in contact with throughout the day has different effects depending on the dosage: even drinking water can be harmful if you consume too much! (Water intoxication: it’s a real thing! Read about it here.)

An easy way to think about dosage effects is the common saying (and the Kelly Clarkson pop hit):

What Doesn't Kill You, Makes You Stronger

In other words, exposure to low doses can activate cellular responses that provide protection to the cell, making it “stronger”. However, these cellular responses may be insufficient at higher doses, ultimately resulting in damage and death. 

There is a lot to learn about hydrogen sulfide before we begin using it regularly as a therapeutic. For those who work in environments where hydrogen sulfide poses a serious occupational threat, utilizing the gas for medical treatment still sounds extremely dangerous and irresponsible. By improving our understanding of the cellular effects of hydrogen sulfide at different doses, scientists can minimize potential dangers of hydrogen sulfide as a therapeutic. Ultimately, the potential benefits of hydrogen sulfide in agriculture and human health make it an important and exciting research field for the future.

If you’re interested in learning more about hydrogen sulfide, you can visit our lab’s website here!

This blog post originated as an exercise for my SciFund Challenge Outreach course, but I liked it so much that I thought it’d make a great first blog post! Let me know what you think!