Moving Forward: Update on Work in the Lab


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The blog has fell silent for a number of months, mainly because my work and other endeavors has consumed all of my time. The work in the lab has taken on new dimensions, with our staff significantly expanded at the beginning of the semester. This has translated into a lot more time spent training and managing, rather than directly generating data. But I also spend a significant amount of time pushing some of my own projects forward.

On the professional development front I have been working on expanding my skill sets in statistics and programming, which mostly involves taking some courses (university, online, and books) and just putting in a lot of time getting my hands dirty with R. My work in the lab has started to shift to this area and I’ve spent many hours getting comfortable with a whole new set of tools.

One nice part with Dr. S is that even though I lack a PhD., I’m not treated any differently than those that have more degrees. So as one of the people in the lab with the most hands-on experience with a number of important protocols and experiments, it is often necessary to make recommendations and help with troubleshooting, as well as offer advice based on past experience. It’s been a nice challenge in shifting to a job that includes a lot of project management instead of primarily generating data.

Also, when I get a chance I keep up on a number of blogs in the science area, which mostly includes a lot of young PI’s, postdocs, and graduate students. It’s always interesting to hear how your experiences in science in compare with people at other universities and companies.

PLoS ONE: Why I Changed My Mind


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Longtime readers may remember a couple years ago when I did a post subtly criticizing the relatively new journal PLoS ONE, saying that it was not much more than a repository for rejected papers from the more selective PLoS journals, such as PLoS Biology and PLoS Genetics.  Immediately after, I took flack some of the more senior people in the lab, saying I was probably premature to cast judgment on such a young journal.  And furthermore, some people suggested that I should keep my big mouth shut, as I was a lowly undergrad and, furthermore, this is how things work in academia.

I’m not about to take back what I wrote back then, because I think it was spot on at the time and was a reflection of what the journal’s product was at the time.  But that doesn’t mean that it necessarily holds true today.

PLoS ONE has gained remarkable popularity in such a short time because they avoid one of the major issues that costs many researchers a ton of time and, in many cases, grants: reviewer bias.  I’ve seen it many times in the short time that I’ve been a part of the lab here at WSU, and I’ve come to realize how much of an impact that it has on the ability of a researcher to get a reasonably justified and supported article published (and included with a grant submittal).

In addition, I’ve seen other researchers starting to understand the advantages of publishing in PLoS ONE, and as a result I think the article quality overall has gone up.

Last year I recommended to my lab that they take a look at the journal as a possibility for a future article submission, as it has the tremendous advantages of quick turnaround times for publication (which can be of tangible importance during close grant deadlines) and open access for wider dissemination of your work.

This comes up now as PLoS ONE last week launched a new blog, everyONE, where they’ll be highlighting articles from the journal and trying to stimulate more conversations around their core content.

And I hope they continue to grow, as it provides a nice template for future academic journals to follow their lead with a more interactive approach.

Newsweek: Transgenerational epigenetics is “the new Lamarckism”


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A recent article in Newsweek from science writer Sharon Begley reports on “the new Lamarckism,” citing studies from epigenetics researchers, including Emma Whitelaw. The article seems to be all about transgenerational epigenetics, but rather than ever use the word “epigenetics,” the favored term is “the new Lamarckism.” Link

But evidence for the new Lamarckism is strong enough to say the last word on inheritance and evolution has not been written.

My guess is that Begley was intent on building up controversy in her opening that seemed to be criticizing evolution during Darwin’s big 200/150 year. And in that regard, she piqued the interest of one of the most popular science bloggers, PZ Myers, who criticized the article in a post on his blog–sending tons of traffic to Newsweek.

It’s very cool stuff, but evolutionary biologists are about as shocked by this as they are by the idea that malnourished mothers have underweight babies. That environmental influences can have multi-generational effects, and that developmental programs can cue off of the history of the germ line, is not a new idea, especially among developmental biologists.

One of the problems with calling epigenetics “the new Lamarckism” is that it can have the connotation that the field is going the way of Lamarckism, or that geneticists are unable to account for (or are afraid of acknowledging) these strange phenomena. In truth, geneticists are aware of these phenomena, and are eager to see what mechanism is at play in the inheritance of these traits across generations–whether it be methylation, small RNAs, or a host of other possibilities.

But no one in science is crying over the fact that epigenetics is uncovering more details about how disease is acquired or traits inherited.

Happy New Year!


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I was just reminded that I have been neglecting my duties as a blogger when I read this post from Alex Palazzo at The Daily Transcript.  Ironically, Alex does a great job reflecting why I have been neglecting those duties, concluding, “This is why I’m in science.”

My results had arrived! Before anyone was up, I looked over the list and realized what I had stumbled into. I couldn’t believe my eyes. It’s obviously the answer. Obvious. I should have gone fishing earlier. Now all that is missing is the last piece of the puzzle. That last factor that must link all the bits together.

This is why I haven’t been blogging. This is why it’s 10:01PM and I’m in the lab. This is why I’ve been totally obsessed with my work.

In short, I have also been chasing some loose ends that have had me completely mesmorized. And transitioning from undergraduate/part-time research work to full-time research work has had its share of challenges, but I feel like I am getting my feet under me and making significant contributions to not only the overall arc of the research but also to the productivity of the other lab members. This makes me very happy.

And with that, happy new year to all of the (loyal) readers!

Lab Atmosphere: Good, Bad, or Indifferent?


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One of the labs that I visited during my job interviews had the most amazing atmosphere of any lab that I have been in during my work thus far. Undeniably, it didn’t hurt that everything was clean and equipment was mostly boxed up, which meant there was no clutter to make the space less appealing. But the open sky windows and big glass windows didn’t hurt either, as well as the high, raised ceilings and plenty of space in between benchtops. Also, the adjacent lab was separated by an unclosed wall, which had the effect of making the space seem even larger. I was really looking forward to the chance to work there, knowing how much a working environment can affect your mood and, ultimately, productivity.

The lab that I’m in now has no windows, although I have plenty of benchtop and desk areas, and there’s very few people around to make noise or provide distraction, which can be a good or bad thing depending on how you want to to look at it. My question is: what is your lab environment like? Do you feel like it helps you be more productive, or could there definitely be some improvments that would make it much better?

Intro to Epigenetics


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University of Minnesota-Morris biologist PZ Myers has written an introduction to epigenetics at Pharyngula, with some nice illustrations of some of the basic concepts and mechanisms that are generally grouped under the heading of “epigenetics.” It’s a great way to bring yourself up to speed if you don’t know much about epigenetics and want a single article to give you the basics. I’ve come to realize that the majority of the readers here are not in that crowd, as many are working in research labs and companies that have some connection to the area of epigenetics and want to keep up on the very latest developments in epigenetics. So for those are you that are not part of that group, I highly recommend that you head over to this article and read about the basics of epigenetics. Link

One of the questions brought up in the article, which has been covered here before, is what all falls under the umbrella of epigenetics? I think that this is largely an issue of semantics, with some established researchers having an interest in restricting the use of the word in literature, and many others expanding the reach of the word to greater and greater lengths. As I’ve mentioned before, I think this trend is largely a result of the funding opportunities available, and the general trend in recent years as epigenetics becoming one of the “hot new” areas of science.

7 Random Things About A Meme Newbie


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Sandra Porter at Discovering Biology in a Digital World (excellent blog) has decided to tag Epigenetics News with a meme. With this being the first meme at the site, I should probably explain what a meme is. From Wikipedia:

A meme, as defined within memetic theory, constitutes a theoretical unit of cultural information, the building block of cultural evolution or diffusion that propagates from one mind to another analogously to the way in which a gene propagates from one organism to another as a unit of genetic information and of biological evolution.

Yes, that definition should explain everything for our audience at Epigenetics News.

If you’re still confused, a meme might be best described as the bloggers’ equivalent of an e-mail chain letter, perhaps with a little more purpose in extracting useful information from a number of people with shared interests.

With that said, here are the rules of this meme:

  1. Link to the person that tagged you andpost the rules on your blog.
  2. Share 7 random or weird things about yourself.
  3. Tag 7 random people at the end of your post and include links to their blogs.
  4. Let each person know that they have been tagged by leaving a comment on their blog.

Seven Random Things About Me

Random thing #1: Science was my worst subject in high school.

Random thing #2: I started writing this blog before I had taken an introductory genetics course.

Random thing #3: I have been employed as a lab research assistant, wheat genetics field crew, newspaper circulation district manager, computer technician, staff writer, senior news editor, and oyster picker.

Random thing #4: I have been paid to play video games.

Random thing #5: I don’t play video games much anymore, unless it’s with my 13 year-old stepson.

Random thing #6: I attended the University of Southern California for a semester in 1997.

Random thing #7: I was covering Macworld Expo San Francisco as a staff writer when the first iPod was introduced.

Tag 7 Other Bloggers

Migrations
Sex Determination Research
Adventures in Ethics and Science
Eye on DNA
ScienceRoll
Omics! Omics!
ESI Blog

Tags:

Bringing Your Research Lab’s Web Site into the 21st Century


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I have been asked by enough people for advice on making their lab web site “better” for various reasons, so I decided to put together a list of things that will have a tremendous impact on a researcher’s ability to provide readers with the information they’re looking for, convey a professional effort in its appearance, and keep journalists, students, and others coming back regularly for updates. With that said, here are my top 5 tips for bringing your research lab’s web site into the 21st century:

1. Offer RSS feeds for your own papers or papers within your specific speciality. An RSS feed is a simple and effective way for anyone to keep updated with your work without constantly checking your web site. They are easily set up and maintained, and can be added to any type of web site, including your lab’s home on the web.

2. Make an XML sitemap and submit it to Google. If you don’t want your research (probably publicly funded) to be widely disseminated, why are you doing it in the first place? One of the best ways to help people find your site is to get it in the search engines. The best way to do that? Make an XML sitemap and submit it Google using their handy webmaster tools. They’ll then know where each of your site’s pages are, and will check them regularly for updates. That means your pages will appear more quickly in search results, meaning your research will be easily found, and more likely to be cited in other papers. See XML-Sitemaps.com for more information.

3. Provide PDF reprints of your latest papers. Let’s face it: not everyone has the luxury of an institutional subscription for access to hundreds of journals. Why not offer simple PDF reprints of your latest papers right from your site? This not only makes your work more widely available (and more likely to be cited), it also makes it dead simple for prospective graduate students, for instance, to see what you’re actually working on right now. (Of course, this tip would be negated if all of your work was available in open access journals, but that’s not very likely.)

4. Update the site regularly. This tip may seem simple, but most researchers are “too busy” to follow it. How many lab web sites have you been to with the latest paper shown is 2 or 3 years old, yet they have 10-15 papers published over the last couple years? I’ve seen dozens of sites just like this, and I’m hoping it’s not yours. Just taking the time and effort to keep your site reflective of your lab’s current work is a step in the right direction.

5. Take the web site seriously. A large majority of the lab web sites that I have seen in recent years are absolute jokes in terms of their utility. Students, journalists, fellow researchers — they would all be equally dissatisfied with the experience. We’re talking about the way in which hundreds of thousands of people will be able to judge your life’s work, and you put up a simple page with a generic research outline (probably outdated based on your current work) and a CV and call it good? This is not good enough for today’s researchers. In fact, it wasn’t good enough five years ago either.I have heard grumblings from some professors that go something like, “I’m too busy to constantly update my web site,” or “I don’t know enough about that technical stuff to do it right.” I’m sorry, but these excuses just don’t float when a simple job like this can be contracted for $500 or less — an amount you probably spend on pipette tips in a month. Remember, this is your contact point for telling the world about your life’s work. Isn’t that important enough to make a solid effort?Now maybe if you do your web site well enough, and people can clearly understand the relevance and importance of your work, you will also be nominated for 2007 Time Person of the Year, just like epigenetics and imprinting researcher Dr. Randy Jirtle was. (See Dr. Jirtle’s site, Geneimprint.org, for a site done right.)

Putting the "Re” in Research


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Long-time readers may remember a time at which I mentioned that I was working on writing my first peer-reviewed research publication. Since then, I don’t think that I’ve mentioned it again. Well, to make a long story short, that work was put on the back burner, but is about to begin again, after repeating a series of experiments that was required after a previous result called for it.

All of this means that I won’t get to accomplish as much as I would have liked to as an undergraduate researcher, but it provides a much needed lesson for a researcher in training: this is how you can expect it to go. One of the former postdocs in the lab liked to say, “That’s the ‘re’ in research,” which isn’t the best thing to hear right after you learn that you’ll be repeating the experiment you just completed after months of work. Nevertheless, I can imagine that learning and accepting this reality even before I begin my graduate research will be a tremendous benefit in my future endeavors.
On a brighter note, shortly after arriving in the Skinner lab in 2004, I was involved in another project that now looks to be published in the next 3-4 months. That will be my first authorship in a peer-reviewed journal, and since it doesn’t relate to epigenetics, I doubt I will acknowledge it here when it finally does hit the press. But it does represent a major milestone in what I hope will be a future career in research, and at the very least, for that I can feel some sense of accomplishment.

5 Tips for Getting the Most Out of Undergraduate Research Positions


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While in the past I’ve provided some tips for getting into a good lab as an undergraduate, and ways to save time once you’re working at the bench, I haven’t yet described the best things to focus on during those few years that you have before heading on to graduate school or your professional career. Here’s five tips for taking full advantage of the hours spent in the lab as an undergraduate:

1. Learn good lab techniques from postdoctoral fellows and lab managers. It’s important to use time in the lab to get exposure to performing many different assays so that you’ll have a leg up when it comes time to using them for your own research. It gets easier to pick up new assays once you have good technique down, so that later you can get a protocol from literature and be able to perform it as described without supervision. While it’s easy for your supervisor in the lab to teach you one thing and then have you do that for 3-4 years, don’t let them off the hook that easily. Ask to learn new techniques or watch them do something else, and let them know that you’d like to get exposed to more than just one or two assays.

2. Not all advice is good advice. As an undergraduate, you might assume that everyone around you in the lab (more experienced undergraduates, postdocs, technicians, research associates, PI, etc.) has all the right answers. Well, guess what? They don’t. They may act like they do, and they may confidently answer your questions and requests for advice, but most will be faking it at least some of the time. Consider the source of the information. If you’re asking a graduate student or PhD research associate for advice on going to graduate school, do you think you’ll be getting an unbiased answer? On the other hand, if you’re asking for advice on an assay from a research associate with 20 years of experience, that’s probably a safe bet. Double check things and consider your sources before making final decisions.

3. Take advantage of opportunities to make poster presentations. Hopefully, you’ll have the opportunity to get involved directly in a research project and will be able to present your work at a conference or poster competition as an undergraduate. These are great opportunities to meet and talk with other scientists outside of your lab, make new contacts, and get experienced advice on your poster, presentation skills, and ideas for future experiments.

4. Your classes always come before the research. It’s easy to get caught up in the excitement of working in the lab as a researcher and making steady progress with your experiments, but the coursework has to come first. The classes provide the framework for everything that you’ll do now and in your future research career, so skipping classes and focusing more time and energy in the lab doesn’t make a lot of sense. Focus on studying your coursework and stick to a strict schedule for time spent working in the lab.

5. Be involved in as many areas as possible in the lab. When someone in the lab asks for a volunteer undergraduate to help them with an experiment, do it! This is a great way to learn new techniques as well as learn conceptually why the experiment is being performed. This is where the lab experience will really pay off: you may get exposed to a concept and technique months or years before you come across it duirng your coursework, and then you’ll be that much ahead of the game when it comes to exams. And the concept will probably stick better after you’ve done the assay yourself, rather then trying to memorize and understand how a technique works from a lecture and textbook.

Hopefully these tips will help you make the most of your time as an undergraduate researcher.

Fall Semester and the Hunt for Graduate School Begin


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It has been a very busy and hectic late summer, and the blog activity reflects that.

On a brighter note, I just started my final year of undergraduate work at Washington State University. This semester I am taking Biochemistry, Perspectives in Biotechnology, Bioinformatics, and Human Genetics. The course load is about average, and after attending the first class sessions for each I am very excited about some and nervous about others.

I spent a lot of the summer considering my options for graduate work and concluded that I am most definitely interested in epigenetics research. I haven’t had the opportunity to discuss my research at larger conferences and meetings, or even here on the blog, but I can certainly wiling to divulge that information to labs looking for a graduate student for next fall.

As most readers know, I work in the laboratory of Dr. Michael Skinner, and am working on an aspect of the project investigating the transgenerational effects of endocrine disruptors on male fertility. The work has been both challenging and rewarding, and it will continue until graduation. But I am not going to restrict my future research to this area of exploration, and other areas of epigenetics research have especially piqued my interest. Histone modifications are probably at the top of my list, but I am excited about many areas of epigenetics research, and even staying in the area of environmental epigenomics is a distinct possibility.

If there are any labs doing epigenetics-related research in the U.S. that are seeking a hard-working graduate student for next fall, please drop me a line at admin AT epigeneticsnews dot com. I’m willing to discuss possibilities with any PIs in epigenetics, but preferably those in the northwest.

Summer Vacation in the Canadian Rockies


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The week-long trip to British Columbia, Canada is now complete. The family and I had a great time sightseeing, kayaking, and spotting black bears, elk, and plenty of deer.

In the meantime, it looks like I missed plenty of new epigenetics research that was published over the past week or two. I’ll be trying to catch up over the course of the week.

Unfortunately the guest blogger idea never panned out. Perhaps next time I’ll have the common sense to schedule posts to occur over the course of the time that I’m away. 

Black Bear
     

Odd Ways to Find Us Through a Search Engine


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I am always amazed when I browse through the statistics package for Epigenetics News and see the long list of keyphrases that were used to reach the site. There’s always the obvious ones, like “epigenetics” and “what is epigenetics”, but there’s also plenty of unusual ones that I can hardly remember ever writing. I figured it might be fun to share some of the weird search phrases that people have used to find this blog:

weird pictures – This search term came up from the blog post “Those Weird Pictures in the Sidebar.” I can only assume that people looking for “weird pictures” are going to be disappointed when they come to this site. Ironically, the aforementioned pictures in the sidebar have since been removed, largely because I have a hard time doing leisure reading when course textbooks are higher on the priority list.

ways to save panda – As most people know, this blog does not focus on conservation of any species, so saving the panda isn’t really our forte either. I’m assuming that “ways to save” came up from the half-jokingly made post from March 2007, “10 Best Ways to Save Time at the Lab Bench.”

fat as – I wonder if someone was searching for something else and had a typo. This search returns the post, “Liposuctioned Fat as a Source of Stem Cells.”

college students assays about why they want to work with children – So if you’re going to pass off someone else’s essay as your own, wouldn’t it be better to spell “essay” correctly? I suppose this is a good illustration of why this person doesn’t want their own writing to be judged. This search result points to “Scientists in Training: The Experience Dilemma.”

is trevor s disease passed genetically – In fact, yes, it is.

Top 5 Ways to Get Fired Up at Work


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Everyone knows that after weeks, months, and years of the same old, same old at your job, it tends to get repetitive and boring, and it gets difficult to remain as highly motivated as you were when you first started.

So, you’ve got to give yourself a boost to get you going again. Whether it’s in a lab, office cubicle, or construction work, there’s got to be ways to get yourself going again.

With that said, here are my top 5 ways to get fired up at work:

1. Make it a competition. Sports are very competitive, so why not your workplace? There’s nothing more motivating than beating your co-worker, boss, or friends at something they claim to be a professional at. Turn every minute task into a competition and you’ll be more excited about doing it than ever.

2. Work like you’re being considered for a promotion. That’s right, it’s promotion time any time of the year. Making your mark on a project or being an outspoken leader in a group can get you noticed, will bring you more professional opportunities and will set you apart as the one to move up the ranks faster than those who lay low and wait for the time to come.

3. Own your project. Don’t let the fact that you’re working on a piece of someone else’s larger project get you down. This piece of the project is yours. Everyone will know that you did it, so it better be your best possible work and not the halfway effort that you’ve been giving lately. Put everything you’ve got into it and you’ll feel more satisfied with the end product. Plus, other people will notice how hard you worked to make it great.

4. Take a minute to remember why you’re here. Are you working to make a quick buck, or are you looking to move on to bigger and better things? If you’re like most people, you’re in the latter group. Take some time to remind yourself of what your ultimate goals are and keep striving to reach them.

5. Stop wishing it was Friday. Yeah, it’s great to kick back on the porch, throw some burgers on the grill and hang out with friends and family for a Saturday barbecue. But that’s for the weekend. While you’re staring at your computer screen dreaming about the weekend, your co-worker across the lab is coming up with a great idea for an experiment. Stop dreaming about the future and make right now what you’re all about.

This post is part of the ProBlogger Group Writing project – Top 5.

How Often is the Word ‘Epigenetics’ Used? More Than Ever.


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There has been some discussion as of late concerning the increasing use of the words “epigenetic” and “epigenetics.” For starters, amnestic at Gene Expression wrote an excellent two-part series on epigenetics and memory (part 1, part 2) that included a review of definitions of epigenetics and some discussion concerning use of the word.Earlier this month, Mark Ptashne of the Sloan Kettering Institute in New York wrote an essay in the journal Current Biology on the use of the word “epigenetic.” Link

Over the past few years we have seen an odd change, or extension, in the use of the word ‘epigenetic’ when describing matters of gene regulation in eukaryotes. Although it may generally be that it is not worth arguing over definitions, this is true only insofar as the participants in the discussion know what each other means. I believe the altered use of the term carries baggage from the standard definition that can have misleading implications. Here I wish to probe our use of language in this way, and to show how such a discussion leads to some more general considerations concerning gene regulation.

The essay goes on to describe how certain regulators of gene expression now commonly referred to as “epigenetic modifications” are perhaps improperly labelled because these changes are not heritable.I went ahead and did a review of the publications listed at PubMed tha contain the word “epigenetics” from 2000 to 2006. Here are the results:Epigenetics Publications by YearThe results show that there is clearly a significant increase in use of the word “epigenetics” in scientific publications over the past 7 years. Here are a few factors that I believe are the most likely contributors in an increase in use of the word, although I suspect that long-time researchers within the field may have a better grasp of other trends that have also contributed to its increasing popularity.

  • Advances in technologies to study epigenetic mechanisms.There have been considerable advances in technology that allow for the study of the influence that epigenetics has on many different areas of research. This is a great positive feedback loop: as better technology becomes available, more research is done, which drives development of better tools for researchers to use.
  • New insights into the link between epigenetics and cancer. Epigenetics (i.e. DNA methylation) has offered new hope for understanding how cancer develops and finding new ways to detect and diagnose it.
  • Surprising discoveries bring new researchers into the field. Some researchers stumbled into epigenetics research when their own, unrelated research led them down this path. Again, advances in technology to study epigenetics have largely made this possible.

The increase in the popularity of epigenetics has emerged earlier this year in the form of two high impact journals, Cell and Nature Reviews Genetics, publishing special editions solely on new topics in the epigenetics field. And last year an entire textbook on epigenetics was published by Cold Spring Harbor Press, indicating that the field has grown to a level that warrants such special attention.It’s also important to note that stem cell researchers are increasingly becoming interested in how epigenetics may hold the key for critical advances in their understanding of these unique cell types. And epigenetics is now clearly important in improving the efficiency of cloning (somatic cell nuclear transfer), which will be tremendously beneficial to a wide spectrum of researchers and most importantly, to public health.With all of these high profile and highly funded areas becoming closely associated with epigenetics, is it any surprise that more researchers are finding ways to include their focus as part of “epigenetics”?