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.

NIH Challenge Grants Include Bait for Epigenetics Researchers


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Yesterday the National Institutes of Health (NIH) released the Request for Applications (RFA) for the NIH Challenge Grants in Health and Science Research. The omnibus includes a list of 15 topic areas for proposals:

1. Behavior, Behavior Change, and Prevention
2. Bioethics
3. Biomarker Discovery and Validation
4. Clinical Research
5. Comparative Effectiveness Research (CER)
6. Enabling Technologies
7. Enhancing Clinical Trials
8. Genomics
9. Health Disparities
10. Information Technology for Processing Health Care Data
11. Regenerative Medicine
12. Science, Technology, Engineering and Mathematics Education
13. Smart Biomaterials – Theranostics
14. Stem Cells
15. Translational Science

The omnibus PDF (link, 1.7 MB) also includes specific topic areas of interest, as well as topics that are considered the highest priority by individual centers.

Among the specific topic areas are several that could be applicable to researchers within the broad spectrum of epigenetics research:

01-DA-111 Approaches to study the interactions among individual behaviors, social and physical environments, and genetic/epigenetic processes during critical developmental periods. NIDA is soliciting research that integrates environmental and developmental variables with genotypic information in order to permit comprehensive model-building and hypothesis testing for determining genetic, environmental, and developmental contributions to substance abuse and related phenotypes.

01-OD(OBSSR)-102* Methods for studying the interactions among behaviors, environments, and genetic/epigenetic processes. Research is needed to develop analytic methods, systems science approaches, or computational models designed to address the interactions among individual behaviors, social and physical environments and genetic/epigenetic processes during critical developmental periods and over time. This research is essential to incorporating the dynamic complexity of behavior and environments in the study of gene-environment interactions in health.

02-DK-101 Ethical issues related to genetic and epigenetic information. Genotype and genome-wide association studies, as well as the large databases containing this information for many individuals create a series of challenging ethical issues. In genome wide epigenetic studies have the potential to identify specific environmental exposures linked to genotyped individuals. Relevant studies will address issues such as recontact, return of research results and incidental findings, informed consent in the context of possible identifiability, and implications for related individuals for diseases that fall within the scope of the NIDDK mission.

02-OD-101 Bioethical concerns unique to epigenomic research. Emerging evidence suggests that epigenetic changes may have an important role in a variety of diseases. Although our understanding of the bioethics of genomic studies is mature, our understanding of the bioethics of epigenomic studies is very much in its infancy. Specific environmental exposures (use of illicit drugs or alcohol, HIV infection, psychosocial stress, etc) or disease states (depression, HIV infection status, etc) may be correlated with specific epigenomic changes. Thus epigenomic research may lead to unique and unanticipated bioethical challenges that must be overcome. Studies exploring bioethical concerns unique to epigenomic research would identify unanticipated ethical problems and help identify appropriate solutions to be sure human subjects involved in epigenomic research are properly protected.

03-OD-101 Use of epigenetic signatures in blood cells to predict disease. Although epigenomic changes appear to be important in many diseases, disease diagnosis may be quite challenging if epigenomic analysis of tissues that are not readily accessible (brain, heart, etc) is required. Blood cells are readily accessible and could serve as powerful “sentinels” or biomarkers for a variety of complex diseases. Characterization of epigenomic signatures in blood cells in a variety of disease situations could lead to the development of entirely new non-invasive diagnostic strategies.

06-AR-103 Systems Biology for Skin and Rheumatic Diseases. Expansion of Merck’s proposed Integrative Bionetwork Community to include skin biology and diseases and rheumatic diseases. Merck has proposed to make their database of phenotypic data and genetics available to the public. While it is not clear what this database currently contains, in the area of skin biology/diseases and rheumatic diseases, there are already efforts by several NIAMS-supported research groups to identify the genetic basis of several diseases (e.g. psoriasis, vitiligo, and alopecia areata) through GWAS and to link expression data with the genetics. Similar efforts are ongoing in rheumatic diseases. It would be useful to extend the dataset by the addition of genome-wide epigenetics data and a catalogue of microRNAs identified by high throughput sequencing technologies. The data could also be extended through the addition of more diseases as well as the effects of treatment. There may also be some benefit to include stages of skin development and epidermal differentiation.

06-DA-103 Identification of chemical modulators of epigenetic regulators. There are a limited number of pharmacological agents available to manipulate the in vivo activity of most epigenetic modifying enzymes, effector molecules, etc. High-throughput small- molecule screening strategies targeted at specific epigenetic regulatory molecules could identify chemical reagents targeting a broad range of epigenetic regulatory molecules. These high impact reagents have the potential to transform the way epigeneticists conduct in vivo disease research.

06-HL-108 Develop new informatics techniques for integrative analysis of genomic and epigenomic data. Much of the complex interplay between genetic and environmental risk factors for disease likely occurs through the interactive regulation of gene expression by both genotype and epigenetic markings of the genome. Epigenetic tags such as cytosine methylation and histone tail modifications, which modulate chromatin structure and function thereby affecting gene expression, are associated with environmental toxicities and are well documented. An integrated analysis of gene expression regulation, with simultaneous consideration of both genetic and epigenetic characteristics and of the interactions between these factors, is essential for understanding the complex pathobiology of chronic heart, lung, and blood diseases. New computational and informatics techniques are needed to allow such analyses.

06-NS-105 Importing important technologies into neuroscience. The challenge is to capitalize on existing knowledge and technologies from other scientific disciplines (e.g. applied physics, nanotechnology, cancer biology, and immunology) to catalyze progress in basic and clinical neuroscience (e.g. cell signaling or cell cycle control mechanisms in neurodegeneration, inflammation in neurological disease, epigenetics in neural development, etc.). Proposals will also be considered that seek to validate, in neurological systems, technologies originally developed for use in other biological systems.

There are also many more topics listed that are very applicable for epigenetics researchers. So, if you have some time to crank out a grant proposal, you have 53 days and counting…

(HT: DrugMonkey)