“Groundbreaking” ‘Duon’ Paper Only Continues Research From Prior Studies


There is a lot of chatter on the internets about the press release from the University of Washington about a paper published in the journal Science this week. One claim within the press release is that findings in the present study uncover a ‘hidden’ code within human DNA that scientists had no prior knowledge of. As many have written, this assumption is completely false and grossly exagerated.

After reading the paper (paywall), I can say the study does add a wealth of new information to an already known phenomenon. I recommend reading the article if one is in the molecular biology or human genetics fields. However, the press release about this study should be retracted for the amount of misleading claims raised within it.

In fact, the authors write in the final paragraph,

Our results indicate that simultaneous encoding of amino acid and regulatory information within exons is a major functional feature of complex genomes. The information architecture of the received genetic code is optimized for superimposition of additional information (3435), and this intrinsic flexibility has been extensively exploited by natural selection. Although TF binding within exons may serve multiple functional roles, our analyses above is agnostic to these roles, which may be complex (36).

Pay close attention to the parenthetical numbers within the quote. These indicate the statement is referencing a prior publication. 34 is reference to a paper from 2007 in Genome Research entitled, “The genetic code is nearly optimal for allowing additional information within protein-coding sequences.” and can be found here. 35 is a paper from 2010 also in Genome Research; “Overlapping codes within protein-coding sequences.” found here. And 36 is from Nature Genetics earlier this year entitled, “DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements” found here.

A question for UW Today,

If these authors uncovered an unknown, hidden code within DNA, how could they reference earlier studies that essentially elaborated upon these same ‘secrets’?

I’ll be waiting for an answer…

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Nanobiopsy: the beauty in the very small is a big deal


The ability to study the living without destroying it has been the goal of many scientists for decades. A new article in ACS Nano has paved the road towards noninvasive cellular-level examination. The only true way to study cellular dynamics is to study a single cell over time (temporally). The reason for this is the heterogeneous nature of any cell culture because no two cells are identical spatially and temporally. Each individual cell has its own set of experiences that has generated its current molecular inventory, ie. RNA molecules, metabolites, proteins, sugars, lipids, etc. Studying a community of cells gives rise to noise that makes finding significant differences incredibly difficult.

In the article entitled Compartmental Genomics in Living Cells Revealed by Single-Cell Nanobiopsy, the authors used a kind of microscopy called scanning ion conductance microscopy, or SICM, that allows for continuous sampling of a single cell over time. The authors used a nanopipette as part of the SICM and combined this with sensitive sequencing techniques resulting in a high resolution look at what genes are being expressed over time into RNA molecules. Furthermore, this technique was used to study the genomic information of individual mitochondria within a single cell without also studying the nuclear material. In other words, this new technique has resulted in the ability to not only study cellular dynamics, but go beyond that and study subcellular dynamics.

This breakthrough will have impacts across many fields from cancer biology to improving climate models.

Paolo Actis, Michelle M. Maalouf, Hyunsung John Kim, Akshar Lohith, Boaz Vilozny, R. Adam Seger, & Nader Pourmand (2013). Compartmental Genomics in Living Cells Revealed by Single-Cell Nanobiopsy ACS Nano DOI: 10.1021/nn405097u

The Tree of (the Study of) Life


American Renaisscience: Bioengineering stem cells for targeted drug delivery


mesenchymal stem cell, research, nature, science, biology, medicine

The field of stem cell research promises to deliver truly amazing medical breakthroughs in the coming decades. However, the fundamental research needed must first provide the proof-of-principle necessary for private industry to take note. That is happening according to a recent article published in the journal Blood. Researchers at Brigham and Women’s HospitalHarvard‘s Stem Cell Institute, in collaboration with MIT and Mass General have successfully reprogrammed a type of connective tissue stem cell line, known as mesenchymal stem cells, to produce specific surface proteins and the anti-inflammatory molecule interleukin-10.

To accomplish this, researchers injected a modified form of messenger RNA, the blueprint for protein synthesis in cells. The modified stem cells were injected into mice. Once in the mouse bloodstream, the stem cells successfully targeted sites of inflammation and reduced swelling.

This approach is promising because it targets the site in need of therapeutics and can deliver the needed drug at a level high enough to provide results. This approach is attracting attention from large pharmaceutical companies because of the capability to target the disease site itself.

Reference

Oren Levy, Weian Zhao, Luke J. Mortensen, Sarah LeBlanc, Kyle Tsang, Moyu Fu, Joseph A. Phillips, Vinay Sagar, Priya Anandakumaran, Jessica Ngai, Cheryl H. Cui, Peter Eimon, Matthew Angel, Charles P. Lin, Mehmet Fatih Yanik, & Jeffrey M. Karp (2013). mRNA-engineered mesenchymal stem cells for targeted delivery of interleukin-10 to sites of inflammation Blood DOI: 10.1182/blood-2013-04-495119
 

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A New Blog Series: Time for an American Renaisscience


A major reason Science does not have a more prevalent position in our society and government is the lack of understanding of what Science really is and can do for us. So, I have decided to use this blog as a starting point to hopefully explain some of the crazy, wild, innovative, creative, and science-fictionesque stories coming out about current research. I hope this will get more of the public excited or, at least, interested in what science and health research can accomplish.