Affinity Seeks Epigenomics Scientist in San Diego, CA


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Affinity Scientific, a scientific staffing and recruitment firm, is seeking qualified candidates for a scientist in research and development with epigenomics experience.

The following is a reprint of the position information as supplied by Affinity Scientific.

Scientist – Epigenomics

POSITION PURPOSE:

The position requires responsibility for planning and executing research and development projects and collaborations in the Molecular Applications department. Candidates will be applying biochemical and molecular biological methods for the development of novel methods for genotyping, loss-of-heterozygocity (LOH) analysis and elucidation of epigenetic changes, in particular cytosine methylation, and other applications in the field of cancer research. A prerequisite for the position is a profound scientific background in molecular biology, biochemistry, design of experiments (DOE). Experience in statistical data analysis and data analysis tools like Excel and MatLab or R is preferred. Expertise in mass spectrometry and a medical background with a focus in cancer research are highly advantageous.

ESSENTIAL DUTIES AND RESPONSIBILITIES:

  • Responsible for planning, implementing and executing research and development projects within the Molecular Applications Department
  • Serves as a Molecular Biology and Cancer Research subject matter expert that is a resource within the company
  • Develops next versions of the company‚Äôs methods for analysis of epigenetic changes as well as inception and development of novel genotyping and comparative sequence analysis applications including methods such as ultrasensitive detection of methylation and detection of mutations in circulating tumor DNA.
  • Works on problems of diverse scope where experimental setup requires DOEs (Design of Experiment) and where analysis of data requires computational capabilities in Excel and MatLab or R.
  • Is able to select appropriate model systems and clinical samples for proof-of-concept of the developed methods
  • Strives to achieve objectives as set forth by supervisor and/or project lead
  • Executes laboratory research, and is responsible for ensuring projects and tasks are completed within the established time frame
  • Determines & develops approach to solutions exercising judgment within generally defined practices and policies in selecting methods and techniques for obtaining solutions. Works under limited direction
  • Expected to maintain a broad knowledge of and high degree of competence in the field by staying abreast of state-of-the-art principles and theories along with high technical visibility throughout the functional area
  • Responsible for programming and usage of liquid handling equipment
  • Tunes and calibrates laboratory instruments
  • Assists in projects requiring collaborations with other research development personnel within the Molecular Applications Department, inter-departmental Projects, as well as collaborations with external partners.

MINIMUM EDUCATION & PREVIOUS EXPERIENCE REQUIRED:

  • MD and/or PhD in Molecular Biology/Biochemistry, or closely related field, with 2-5 years experience in a research and/or development environment. Postdoctoral may serve as experience.
  • Experience in statistical data analysis and data analysis tools.

KNOWLEDGE, SKILLS & ABILITIES:

  • Requires hands-on experience with advanced molecular biology and biochemistry of nucleic acids and DNA preparation from various sample sources.
  • Hands-on experience with high-throughput genotyping and sequencing technologies is a plus
  • Proven track record in molecular biology research, cancer research and product and/or technology development
  • Expertise in DOE and statistical data analysis tools like Excel, MatLab or R
  • Consistently meeting critical deadlines
  • Ability to work in a team environment
  • Demonstrated technical proficiency, effective problem solving and critical thinking skills required
  • Proficient computer literacy in Microsoft Office
  • Excellent communication, interpersonal and organizational skills

To apply please send electronic copy of CV to mwells@affinityscientific.com.

Margaux Wells
Affinity Scientific, LLC
4660 La Jolla Village Drive
Suite 500
San Diego, CA 92122
(858) 535-4874
www.affinityscientific.com

USC Expands Epigenetics Research Space with New Tower


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The University of Southern California in Los Angeles has just opened a new 10-story, 172,440 square foot facility dedicated exclusively to the study of epigenetics, the Harlyne J. Norris Cancer Research Tower. The tower will host five floors of basic research, two floors of preventative medicine research, the Hinderstein Family Meditation Garden, a 200-seat auditorium, one floor for the new Epigenome Center led by Dr. Peter Jones, and a temporary home for the Center for Stem Cell and Regenerative Medicine. Link

DNA Methylation Affects Nuclear Organization and Histone Modifications


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In a paper recently published in the Journal of Cell Biology, Gilbert et. al. use mutant mouse embryonic stem cells lacking DNA methylation to show that DNA methylation affects nuclear organization and nucleosome structure, but not chromatin compaction.

DNA methylation has been implicated in chromatin condensation and nuclear organization, especially at sites of constitutive heterochromatin. How this is mediated has not been clear. In this study, using mutant mouse embryonic stem cells completely lacking in DNA methylation, we show that DNA methylation affects nuclear organization and nucleosome structure but not chromatin compaction. In the absence of DNA methylation, there is increased nuclear clustering of pericentric heterochromatin and extensive changes in primary chromatin structure. Global levels of histone H3 methylation and acetylation are altered, and there is a decrease in the mobility of linker histones. However, the compaction of both bulk chromatin and heterochromatin, as assayed by nuclease digestion and sucrose gradient sedimentation, is unaltered by the loss of DNA methylation. This study shows how the complete loss of a major epigenetic mark can have an impact on unexpected levels of chromatin structure and nuclear organization and provides evidence for a novel link between DNA methylation and linker histones in the regulation of chromatin structure.

References:

Gilbert N, Thomson I, Boyle S, Allan J, Ramsahoye B, Bickmore WA. 2007. DNA methylation affects nuclear organization, histone modifications, and linker histone binding but not chromatin compaction. Journal of Cell Biology 177(3):401-411.
doi:10.1083/jcb.200607133

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.

Global Epigenomics Market to Reach $4.1 Billion by 2012


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“$4.1 Billion by 2012″ is the major finding of a market report on the global epigenomics market published by BCC Research. The report identified three key market segments that will be commercially important in the field of epigenomics in the next 5 years: research tools, cancer diagnostics, and cancer therapeutics.

There are three major highlights from the report (which I have not read in its entirety due to its cost):


  • The global market for epigenomics was $161.8 million in 2005 and $263.2 million in 2006. The market will cross $385 million by 2007 and at a compound annual growth rate (CAGR) of 60.4% will reach nearly $4.1 billion by 2012.
  • Drug applications for epigenetics are by far the largest sector of the market. These drugs will hold 61% of the total global market in 2007 and will grow to over a 65% market share by 2012.
  • Epigenetic diagnostics has the most potential for growth through the forecast period. In 2006 and 2007 its applications were negligible, but by 2012 this booming sector will be worth over $947 million.

The full market report is available for US$4,850. Link

The DNA Network: Group of Genetics Bloggers


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Hsien Lei of Eye on DNA and Rick Vidal of My Biotech Life have spearheaded an effort to start a FeedBurner network: The DNA Network. This provides a handy aggregate feed and summary page for fans of genetics to get a quick summary of some of the best genetics writing from around the blogosphere. It has alsp provided an opportunity for some of us genetics bloggers to open an avenue of communication that hasn’t been there in the past.

They invited me to the network, and I couldn’t see any reason not to have Epigenetics News be a part of it, so I said “yes.” The DNA Network currently consists of the following blogs:

Hopefully the aggregate feed will be something useful for consuming a wider range of genetics topics.

Tangled Bank #79


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Over the past two weeks, dozens of writers in their own shabby huts across the globe have toiled for countless hours to share their unique perspective on issues affecting all areas of science. Now you’re being given an opportunity to read all of that hard work, in one simple place.

Welcome to the 79th edition of the Tangled Bank.

Before we get started, I would like to welcome all of the new visitors to Epigenetics News. I encourage you to check out what this newfangled “epigenetics” thing is all about — maybe hit the “random post” link over to the right a few times to get an idea.

Evolution

The evolution of wings, based on an accumulation of evidence from dinosaur fossils, is reviewed in an excellent post at Duo Quartunciae, a new blog from “Sylas” on science, mathematics, and unbelief.

Mary Hrovat of The Thinking Meat Project provides a synopsis of a two-day symposium on brain evolution in “I think I can feel my brain evolving.”

Sarda Sahney of Fish Feet asks and answers the question, “Why does a platypus lay eggs anyway?

John Beetham of A DC Birding Blog summarizes the latest research into the evolution of duck phalluses and other strange genitalia.

Monado of Science Notes provides a nice history lesson (with excellent illustrations from Charles Darwin’s own handwritten notebooks) on Darwin and punctuated equilibrium.

And in a different sort of evolution, Coturnix of A Blog Around the Clock goes above and beyond to explain the evolution of the modern chronobiology field and reviews a recent seminal paper that provides conclusive evidence that a pacemaker is a network.

Medicine

A drug now in clinical trials offers hope for treating hundreds of diseases caused by nonsense mutations, including cystic fibrosis and muscular dystrophy, reports Orac at Respectful Insolence.

GrrlScientist of Living the Scientific Life (Scientist, Interrupted) provides a glimpse of the groundbreaking research in regenerative medicine, which allowed researchers to give paralyzed mice the chance to walk again.

Dan Rhoads of Migrations points out a review and primary article on hypoxia-inducible cancers and selections for malignancy in tumor masses.

The long shadow of smallpox from Tara C. Smith of Aetiology describes the recent phenomena of contact transmission of the vaccinia virus following vaccinations given to service men and women.

Conservation

Jeremy Bruno at The Voltage Gate is questioning the sincerity of evangelical environmentalists after reviewing the conservation book: Serve God, Save the Planet: A Christian Call to Action by J. Matthew Sleeth.

Tim Abbott of Walking the Berkshires takes some time to review the evolution of The Nature Conservancy logo and reflects on how each logo change coincided with remarkable transformations in the organization over its recent history.

Jennifer Forman Orth of Invasive Species remarks on the impact that certain invasive species of fish may have on the sport fishing industry at Lake Michigan.

The tactics of companies using the heightened awareness of consumers to global conservation in designing product marketing is the topic of discussion at _Paddy K_.

Mike Bergin of 10,000 Birds writes convincingly about the “eerie, sinister, unnaturally still” bird, the night heron.

Miscellaneous

A brief review of research into erectile dysfunction that aims to better define the force needed to collapse an “apparatus” is the topic of discussion by Mark A. Rayner at the skwib.

Martin Rundkvist of Aardvarchaeology discusses the impact of essentialism on archaeological interpretation.

Obligatory Administrative Details

The next Tangled Bank will be available on May 23, 2007 at geek counterpoint. To submit a post, e-mail host@tangledbank.net.

Short Commercial Break and Some Random Post


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I wanted to take a moment to thank all of the sponsors that have helped support the ongoing activities of Epigenetics News: Medical Software Associates, CalculateMe.com, Red Apple Living, Surgeon’s Advisor, HealthTalk, ShoXX.com, Asbestos Mesothelioma Lawyers and Drugs.MD.

In addition, some readers may have noticed a link added to the top of the right sidebar: Click here for a random post. It will direct you to a random post from the Epigenetics News archives, allowing new readers to get a quick taste of some of what this site tends to cover. I hope that it’s both useful and fun for old and new readers alike.

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.

Mendel’s Garden #14


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Welcome to the fourteenth edition of Mendel’s Garden, a blog carnival devoted to everything that has to do with the discipline of genetics. It’s ironic that it’s being hosted on a blog devoted entirely to showing that classical genetics isn’t what it’s all about — epigenetics is, in some ways, challenging the classical assumptions of Mendelian inheritance. But we couldn’t have learned anything about epigenetics until a multitude of genetic mechanisms were clearly established. And many are yet to be uncovered.

With that said, Rich at evolgen has succinctly summarized the newly discovered in the area of sex chromosomes in the pufferfish, cat, and mouse. The research centers mainly on sex determination, natural selection, and nucleotide diversity.

Hsien Lei at the newly minted blog Eye on DNA recently covered an interesting finding from deCODE Genetics showing an association between a single nucleotide polymorphism (SNP) and increased risk of heart attack and cardiovascular disease.

p-ter at Gene Expression has given his take on the recent paper describing positive selection between chimps and humans, “More genes underwent positive selection in chimpanzee evolution than in human evolution.”

From this blog, I wrote from my perspective on the increasing use of the word ‘epigenetics’ in response to an essay postulating that the word was being improperly used.

Song and Plumage Evolution in New World Orioles is the topic of choice at Living the Scientific Life (Scientist, Interrupted).

And Carl Zimmer, the science writer often appearing in the New York Times, has done just that with his recent article on evolution and duck phalluses.

That’s all for this edition. If you would like to host the next Mendel’s Garden, details are at the carnival’s home page.

Moving Towards Better Mapping of CpG Islands


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A new research paper available as an early online release in the journal PLoS Compitational Biology helps provide some new insight into how the definition and mapping of CpG islands could be improved.

CpG islands were originally identified by epigenetic and functional properties, namely absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (i) reliance on arbitrary threshold parameters which bear little biological justification; (ii) failure to account for widespread heterogeneity among CpG islands; and (iii) apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of “CpG island strength”, which incorporates epigenetic and functional aspects, can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human chromosomes 21 and 22 we identify informative DNA attributes that correlate with open and compact chromatin structures, respectively. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features we estimate the inherent CpG island strength for each CpG island in the human genome, i.e. its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted “bona fide CpG islands”. The mapping of CpG islands by epigenome prediction is conceptually superior to widely used CpG island criteria since it links CpG island detection to their characteristic epigenetic and functional states. And it is superior to purely experimental epigenome mapping for CpG island detection since it abstracts from specific properties that are limited to a single cell type or tissue. In addition, using computational epigenetics methods we could identify strong correlation between the epigenome and characteristics of the DNA sequence, which emphasizes the need for a better understanding of the mechanistic links between genome and epigenome.

Link

Launch of Eye on DNA and Call for Submissions


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One of the first established genetics/health bloggers to give some link love to Epigenetics News after its launch in March 2006 was Dr. Hsien-Hsien Lei, formerly of the b5 media blog Genetics and Health. Just recently, she announced that she is breaking out on her own with a new blog devoted entirely to genetics, Eye on DNA. The site is just getting going, but Hsien-Hsien has always impressed me with her overall knowledge of genetics issues and her ability to convey some complex and controversial topics to a general audience. I have no doubt that Eye on DNA will be an excellent source of unique information and perspectives from a veteran genetics blogger.

Tangled Bank and Mendel’s Garden

On another note, as some people may have now realized, Epigenetics News will be host to two blog carnivals next week, Mendel’s Garden (May 8) and Tangled Bank (May 10). The alignment of these two science link festivals at this blog was a complete coincidence on the part of the separate scheduling parties, but since they fall on the week after finals, I’ll have so much time on my hands that hosting two carnivals in one week will be like shooting a pipette tip from the corner of the lab, banking off a stack of histology slide boxes and into the tall trash receptacle next to the door. (Translation: Easy.)

So, if you’d like to submit a bit of genetics goodness or any science-related blog writing over the past 2-4 weeks, go ahead and submit to admin AT epigeneticsnews DOT com. I’ll be sure to include everything that has some connection to either genetics or science in general.

Until then, anyone have any last-minute pieces of advice on memorizing cell signaling pathways?