In part I of the NextBio tutorials, we explain how and why NextBio helps explore data relevant to a gene query
A single gene can be studied in many ways- genome-wide analysis for associations with diseases, experimental studies of function in cell lines or animal models, or pharmaceutical research as a potential drug target. At NextBio, we aggregate these diverse kinds of data, normalize and integrate them on a common platform, coalescing diffuse “data clouds” to address focused research questions.
In the first of our NextBio Public tutorials, we explain how to use simple NextBio functions to find this aggregated data relevant to a gene, beginning with GWAS associations, to descriptions of tissues and cell lines and results from pharmacological experiments, all in a matter of minutes.
From the lab to scientific publishing to clinical solutions, the Open Access movement is changing the way science advances
(Guest post by Joseph Jackson)
The 2nd Open Science Summit is the weekend of October 22-23, 2011 at the Computer History Museum in Mountain View, just before the 2011 Open Access (OA) week, which runs October 24th-28th. Open Science evokes different associations for different people, depending on which part of the scientific process they most regularly engage with. One critical component focuses on access to scientific literature. The OA movement has made great strides in the last ten years with the creation and maturation of journals and publishers like PLoS and Biomed Central.
But the most critical shifts toward Open Science arguably are happening in the life sciences. The technological revolution underway in next generation sequencing is enabling, but also requiring bold new collaborative approaches to manage increasing complexity and accelerate the translation of scientific discoveries into desperately needed therapies.
Sirtuin 2 may suppress tumor formation in mice and humans
Sirtuins are a family of proteins that have been implicated in processes ranging from aging and tumor formation to obesity and cerebral ischemia. Seven sirtuin proteins are known to exist in mammals, two of which (SIRT1 and SIRT3), are known tumor suppressor genes. The function of sirtuin 2 (SIRT2) remained unclear however, until recent research from scientists at the National Institute of Health, Vanderbilt University and the University of Texas, Dallas discovered that SIRT2 could play an important role in preventing cancer. In a paper published in Cancer Cell this week, the researchers describe the role of SIRT2 in maintaining genomic stability in cells, a function critical in aging and cancer-related processes.
Interns at NextBio learn to set the stage for a unique kind of data exploration
At NextBio, genomic data snakes through the hands of scientific teams and the automated pipelines they design, connecting people intellectually and socially. Each department is responsible for their own piece of the NextBio puzzle as well as helping new team members cultivate their skills.
The data curation team at NextBio mimics the work of a heart, channeling in the public genomic data that’s essential to the NextBio platform. Beatrice Chiu, who graduated from the Molecular and Cell biology program at UC Berkeley, began her journey at NextBio as a Web Product intern, conducting usability tests to optimize the NextBio user interface. She switched over to the curation team earlier this year to help with a large scale GWAS (genome-wide association study) tagging project. As Beatrice explains, “All studies in the NextBio database usually have a minimum of a biodesign tag, like disease vs. normal, response to a drug, etc. and then a more specific phenotype tag, say for a disease. GWAS studies can also get classified using case-control or other association tags.”
Increases in Dicer gene expression improve some cancers and worsen others
Some of the tiniest players on the field, microRNAs (miRNAs) are short strands of RNA that work to control gene expression in several pathways. Though they don’t encode any proteins, miRNAs regulate genes involved in embryonic growth, cell differentiation, angiogenesis and other cellular processes. They have also gained steady prominence in cancer research, with several studies connecting abnormal miRNA regulation to cancer progression and metastasis in cell lines, animal models and samples from patients.
The potential diagnostic and therapeutic value of miRNAs has also turned attention to the molecules involved in making miRNAs in cells, particularly the enzyme Dicer. A recent study by Zhihai Ma and colleagues in PLoS One reports that higher Dicer expression correlates to more advanced stages of cutaneous melanoma, characterized by increased metastatic potential, tumor mitotic index, and other stages (as defined by the American Joint Committee on Cancer) .