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Happy New Year!Jan 6, 2009 commentary, site news Leave a comment 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!E-mailCommentDel.icio.usDiggRedditTechnoratiFurl Recent Entries Epigenetics & Chromatin: Epigenetics Goes Open AccessNov 19, 2008 news links, research articles Comments Off  While Landes Bioscience made headway by debuting a journal devoted solely to epigenetics (Epigenetics), BMC has really opened the door to epigenetics research by debuting the first open-access journal devoted to epigenetics. Epigenetics & Chromatin is a new open-access option for researchers wanting to make their research available to a wider audience. The co-editors, Steven Henikoff and Frank Grosveld, are open to a wide range of topic areas:Epigenetics & Chromatin will publish articles aimed at understanding how gene and chromosomal elements are regulated and their activities maintained during cell division, self-renewal, differentiation and environmental alteration. Epigenetic research encompasses studies that use model systems to discover and investigate epigenetic mechanisms, as well as studies aimed at combating diseases that involve epigenetic processes. Topics include, but are not limited to, gene activation, silencing and imprinting, cellular reprogramming, nucleosome modification, assembly and remodeling, DNA methylation, chromatin structure and dynamics, chromosomal maintenance elements, dosage compensation, intra- and inter-chromosomal interactions and prion inheritance. Approaches that apply cutting-edge technologies to problems in the field are especially welcome.>A publication fee of US$1800 is pretty standard fare for an open-access journal, and I’ve heard that many scientists are willing to pay the fee if it means increased awareness (and citations) of their work. I have to believe that with an increased focus on the field from a diverse arrange of disciplines, Epigenetics & Chromatin will be a popular and high impact journal. Link Lab Atmosphere: Good, Bad, or Indifferent?Nov 14, 2008 commentary Comments Off 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? Constellation Pharmaceuticals Aims to Develop Epigenetic DrugsSep 2, 2008 news links Comments Off One of the news items that was missed in April during the brief hiatus was about a new biotech outfit (Constellation Pharmaceuticals) that had raised $32 million in a series A round of funding. The company immediately drew my attention not because they were planning to develop epigenetic drug therapies for cancer, but because of their founders: David Allis, Yang Shi, and Danny Reinberg are all well-respected scientists in the epigenetics field, and their founding of the company brings an immediate legitimacy to the organization, which was no doubt helpful in the round of funding. Additionally, it probably didn’t hurt gaining the attention of Mark Levin of Third Rock Ventures, the former cofounder of Millenium Pharmaceuticals, who is now the interim CEO of Constellation.The young company’s web site is full of promising publicity talk about the potential of epigenetic therapies, but little of material value. However, the company is quite young and it will likely take awhile before any promising candidates emerge. As a side note, if you’re a BS/MS-level graduate in molecular biology looking for work, Constellation is hiring in the Boston area.For more information about Constellation, see this article from the Boston Globe. Getting a Research Associate PositionAug 25, 2008 careers, news links 1 Comment I was able to secure an offer for continued employment as a Research Associate at Washington State University. I will be working in the lab of Dr. Skinner, who many know that I had also been working with during my undergraduate years. He has several NIH grants and recently secured new funding from the Department of Defense for a project that I will be closely involved in.The job hunting was exciting early on, but quickly moved into the frustrating stage and finally the depressing stage. The fact is there are a lot of unemployed M.S. and PhD scientists around here, and they are all in need of income, which means that they had been forced to settle for research technician jobs that are normally taken by B.S. graduates like myself. My 5+ years of research experience had a favorable impact on getting into final candidate lists, but I was only able to secure two offers from a list of 8 or 9 jobs. The rest were largely taken by those with advanced degrees. I was fortunate to have an hourly position to keep the bills paid during the process, which I know from experience could have been far more than depressing.In the lab, my “unnamed” project, which I have been working on since 2005, should be coming to the point of publication soon. For the longtime readers this is something they have probably heard before, and I should have learned my lesson long ago and just not make any predictions about it. Nonetheless, all the added data accrued during this time has been extremely productive, and should make for an interesting paper when it finally gets to that point.As for my writing here, as you can see it hasn’t been consistent. Our family was able to take a couple trips over the summer, including one a week ago to the Newport, Oregon area, which is a spot my family regularly went to growing up. It was good to share that experience with my wife and stepson.Hopefully now that the summer is coming to a close (classes start today here at WSU) the blog updates will be more consistent and often. Intro to EpigeneticsJul 22, 2008 commentary, news links Comments Off 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. LinkOne 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. Merging Blogging with the Pursuit of Academic TenureJul 21, 2008 careers, news links Comments Off John Hawks, who has maintained a popular blog focused on his field of expertise in paleoanthropology, has begun a series of posts discussing some of the pros and cons of blogging during the early years of a tenure-track position, and how he was able to successfully integrate his blogging activity into his tenure application (Hawks was granted tenure last month). The first segment (How to blog, get tenure and prosper: Starting the blog) is both insightful and honest, which is just the sort of writing I’ve come to expect from John Hawks. A Professor and a Graduate Student Mull Over EpigeneticsJul 20, 2008 news links Comments Off PZ Myers (Pharyngula), an associate professor in developmental biology, and Abigail Smith (erv), a graduate student studying retoroviral evolution, talk about a number of topics in a bloggingheads.tv exchange, including epigenetics. The segment of the video discussing epigenetics is embedded below. Epigenetics News ReturnsJun 18, 2008 site news 4 Comments In February 2008, I made the decision to shut down this blog in order to spend more time focusing on completing my degree and pushing my research project forward. Last month I completed my B.S. in Genetics and Cell Biology at Washington State University after an extremely stressful four years in which I tried to balance responsibilities as a full-time student, undergraduate researcher, husband, father, and blogger, among many other pursuits. This year, something had to give as my class schedule was extremely demanding and lab courses required a much larger share of my time. In addition, I had decided not to attend graduate school right away and was turning my attention to finding a research technician position in the area. That search is still ongoing, and I have applied for and interviewed with a number of research labs at WSU.It’s amazing how quickly you learn about other research programs under way when you begin to interview for positions. Many of the PIs hiring are working on newly funded grants that have not yet been publicly disclosed, and being able to get a glimpse of the work being done in a wide range of research areas has been a great educational opportunity. I have been working on a particular project for the last 3+ years (still ongoing), and it’s easy to become so immersed in your research that you forget about what others are doing around you. The job search has been a refreshing change of pace and I am looking forward to the next stage in my research career, whatever that may be.With that said, epigenetics research has continued to capture my attention over the past four months. This area of research has produced dramatic advances in our understanding of stem cells, cloning, cancer, development, nutrition, toxicology, and many other areas. With one educational milestone completed, it has opened up a space to continue to highlight important advances in epigenetics research at Epigenetics News. With some additional time available — and my newly acquired knowledge of important concepts and techniques critical to interpreting current research — I hope to make this project more of what I originally envisioned and present a more coherent view of the epigenetics research landscape.Thank you to all of you who offered your encouragement and support for this project, and especially to those that stuck around as RSS or newsletter subscribers while the site displayed abstracts. Welcome back! Histone lysine methyltransferases and demethylases in Plasmodium falciparum.Jun 4, 2008 research articles Comments Off Cui L, Fan Q, Cui L, Miao JInt J Parasitol (Aug 2008)Dynamic histone lysine methylation, regulated by methyltransferases and demethylases, plays fundamental roles in chromatin structure and gene expression in a wide range of eukaryotic organisms. A large number of SET-domain-containing proteins make up the histone lysine methyltransferase (HKMT) family, which catalyses the methylation of different lysine residues with relatively high substrate specificities. Another large family of Jumonji C (JmjC)-domain-containing histone lysine demethylases (JHDMs) reverses histone lysine methylation with both lysine site and methyl-state specificities. Through bioinformatic analysis, at least nine SET-domain-containing genes were found in the malaria parasite Plasmodium falciparum and its sibling species. Phylogenetic analysis separated these putative HKMTs into five subfamilies with different putative substrate specificities. Consistent with the phylogenetic subdivision, methyl marks were found on K4, K9 and K36 of histone H3 and K20 of histone H4 by site-specific methyl-lysine antibodies. In addition, most SET-domain genes and histone methyl-lysine marks displayed dynamic changes during the parasite asexual erythrocytic cycle, suggesting that they constitute an important epigenetic mechanism of gene regulation in malaria parasites. Furthermore, the malaria parasite and other apicomplexan genomes also encode JmjC-domain-containing proteins that may serve as histone lysine demethylases. Whereas prokaryotic expression of putative active domains of four P. falciparum SET proteins did not yield detectable HKMT activity towards recombinant P. falciparum histones, two protein domains expressed in vitro in a eukaryotic system showed HKMT activities towards H3 and H4, respectively. With the discovery of these Plasmodium SET- and JmjC-domain genes in the malaria parasite genomes, future efforts will be directed towards elucidation of their substrate specificities and functions in various cellular processes of the parasites. The mechanism of myoblast deformation in response to cyclic strain - A cytomechanical study.Jun 4, 2008 research articles Comments Off Zheng L, Song J, Li Z, Fan Y, Zhao Z, Chen Y, Deng F, Hu YCell Biol Int (Jul 2008)Mechanical strain is one of the important epigenetic factors that cause deformation and differentiation of skeletal muscles. This research was designed to investigate how myoblast deformation occurs after cyclic strain loading. Myoblasts were passaged three times and harvested; various cyclic strains (2.5kPa, 5kPa and 10kPa) were then loaded using a pulsatile mechanical system. The adaptive response of the myoblasts was observed at different time points (0.5h, 1h, 6h and 12h) post-loading. At the early stage of cyclic strain loading ( |
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