Difference between revisions of "HughesLab:Academic Analytics"

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== Academic Analytics==
 
== Academic Analytics==
  
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== Discovery of circadian harmonics ==
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[[Image:SciTM_Figure1.jpg|left|thumb|'''Figure 1''': [http://www.ncbi.nlm.nih.gov/pubmed/20944088 Hughes et al. (2011)]<br>Social Networking Analysis of the Institute for Translational Medicine and Therapeutics.]]
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We profiled global gene expression over two full days using Affymetrix microarrays.  We identified rhythmic transcripts in the mouse liver and pituitary, as well as fibroblasts (NIH3T3) and osteosarcoma cells (U2OS).  These data have been made freely available on [http://bioinf.itmat.upenn.edu/circa CircaDB] as a resource to the field. To our surprise, we found several hundred genes cycling with period lengths much shorter than 24 hours (Fig. 1).  These ultradian rhythms had period lengths of ~8 and ~12 hours -- i.e., the second and third harmonics of 24 hour oscillations. </p>
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Subsequently, we have shown that these rhythms are found in tissues throughout the body.  Moreover, they are found in fruit flies as well, suggesting that circadian harmonics are a common feature of animal transcriptional rhythms.  At a mechanistic level, 12 hour rhythms require both a central and peripheral circadian oscillator, indicating that these rhythms are ultimately downstream of the conventional circadian clock.  Typically, they are involved in cellular responses to stress, suggesting that ultradian transcriptional rhythms respond to twice daily stresses.
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Revision as of 08:01, 6 August 2013

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Academic Analytics

Discovery of circadian harmonics

Figure 1: Hughes et al. (2011)
Social Networking Analysis of the Institute for Translational Medicine and Therapeutics.

We profiled global gene expression over two full days using Affymetrix microarrays. We identified rhythmic transcripts in the mouse liver and pituitary, as well as fibroblasts (NIH3T3) and osteosarcoma cells (U2OS). These data have been made freely available on CircaDB as a resource to the field. To our surprise, we found several hundred genes cycling with period lengths much shorter than 24 hours (Fig. 1). These ultradian rhythms had period lengths of ~8 and ~12 hours -- i.e., the second and third harmonics of 24 hour oscillations.

Subsequently, we have shown that these rhythms are found in tissues throughout the body. Moreover, they are found in fruit flies as well, suggesting that circadian harmonics are a common feature of animal transcriptional rhythms. At a mechanistic level, 12 hour rhythms require both a central and peripheral circadian oscillator, indicating that these rhythms are ultimately downstream of the conventional circadian clock. Typically, they are involved in cellular responses to stress, suggesting that ultradian transcriptional rhythms respond to twice daily stresses.




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Hughes Lab
Department of Biology
University of Missouri, St. Louis