define: reporter gene

In 2008 I directly blogged about ~50 peer-reviewed research articles. My readings clearly highlight the need to revise the current definition of "reporter gene". Although it is clear that a reporter gene can be used to study gene expression, and in 2008 new advances were from the profiling of multiple transcription factors to the ability to characterize intron-delayed transcriptional clocks, a genetically-encoded assay can be designed to study more than gene expression. I learnt that reporters can be adopted to study cell microchimerism, cell fusion, membrane biogenesis, while different assays were aimed at understanding protein interaction. Reporter assays were exploited not only to address basic biology questions, but also to help solving related problems, like heavy metal detection, DNA sequencing, or to faithfully report conditional transgenesis. Again, some authors suggested reporter genes for the preparative chemist, and FDA finally started to deal with glowing-pets for our children.

From my PhD, I mainly learnt that transgenic reporter mice may open the window to the full spectrum of molecular mechanism assessment in a whole-body context, now that I'm looking for a system-biology postdoc, I'm happy to realize that my experience with reporter mice can be so widely turned in different fields. Happy 2009, and thanks for reading.

The site is not dead

I didn't wrote any update about reporters in the last 15 days, because I did not update myself. I did not update myself because I have been quite busy in defending my PhD thesis. To date, I got a PhD in Pharmacology! In those winter holydays I'm skimming and reading most papers related to new advances in reportergenomics, I'll wrote a cumulative post very soon.

Reporter models for physiology

A hybrid mouse obtained by morulae aggregation of two different reporter mice (GFP and lacZ) allowed Francesca Faggioli and colleagues from the Italian National Research Council to obtain a model in which single cells may be marked differentially with GFP or bgal. So, by finding single cells expressing both reporters (immuno-histochemistry and single-cell PCR), the italian researchers found that cell fusion is a physiological process not only in muscle, throphoblast and osteoclasts, but also in adult mouse liver. This results finally answers long-lived questions about the origins of hepatic polyploidy, that was believed to occur only following DNA duplication and aborted cytokinesis. The two mechanisms aren't mutually exclusive, but Francesca showed us that reporter mice can shed light also on the physiology, because actually they may be considered physiology-respectful models respect to other hard settings (irradiation/ablation regimens, chronic liver damage) used to understand plasticity and cell fusion, with consequent difficulties in discerning whether the results have any physiologic significance or are largely artificial. Of course, the introduction of a foreign gene (the reporter) in any genomic locus, raises questions about the real physiological status of any transgenic organism, however research is in progress to find appropriate reporters with minimal toxicity, and this has a major impact on research community, as recently showed by Rita Stack and Daniel Strongin (University of Chicago) with the development of a safer DsRed protein.

Francesca Faggioli, Maria Grazia Sacco, Lucia Susani, Cristina Montagna, Paolo Vezzoni (2008). Cell fusion is a physiological process in mouse liver Hepatology, 48 (5), 1655-1664 DOI: 10.1002/hep.22488

Rita L Strack, Daniel E Strongin, Dibyendu Bhattacharyya, Wen Tao, Allison Berman, Hal E Broxmeyer, Robert J Keenan, Benjamin S Glick (2008). A noncytotoxic DsRed variant for whole-cell labeling Nature Methods, 5 (11), 955-957 DOI: 10.1038/nmeth.1264

google hit list (last 6 months)

In the last 6 months, visitors from google were looking for...
title="Wordle: reportergene hit list"> src="http://www.wordle.net/thumb/wrdl/357277/reportergene_hit_list"
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Compared to the last period, less people is looking for a wiki of reporter genes, now they ask more for assays, and their are catched by luciferase.

I'm wondering if they are happy about their findings: actually in the last period, according to the feed, I speaked about title="Wordle: reportergene feed"> src="http://www.wordle.net/thumb/wrdl/357295/reportergene_feed"
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So I roughly tried to normalize the referrals according to the time visitors have been spent on reading me. According to this analysis, the TREND in reportergene development of the last six months is title="Wordle: interesting pages on reportergene"> src="http://www.wordle.net/thumb/wrdl/357308/interesting_pages_on_reportergene"
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I got why Big Pharmas are in trouble

Selective Progestin Receptor Modulators (SPERMs) are a class of new contraceptives. Yes, there is a crisis in the pharma market, and the causes are quite evident in my humble opinion.

microfluidics, fluorescent reporters and synthethic/system biology for dummies

Getting the first name on Nature it isn't so frequent, but getting it two times in a year (2008) by using a nobelized reporter gene is very impressive, and Matthew Bennet got it. In the group of Jeff Hasty at the University of California, those guys used a microfluidics platform in combination with fluorescence microscopy to look at:

1. the loops of a synthethic dual-feedback circuit forming positive and negative tunable feedback loops on yemGFP expression in E. coli;
2. the response of the galactose-utilization network in the yeast to sinusoidal changes in glucose concentration over a steady galactose background.

It comes to mind Jacobs and Monod with their petri dishes, but time changes. According to Jeff:

increasingly, there are microfluidics people in every department.

In my department, there are people who are still scared about multichannel pipettors and 96well plates. Neanderthal biologists!

Matthew R. Bennett, Wyming Lee Pang, Natalie A. Ostroff, Bridget L. Baumgartner, Sujata Nayak, Lev S. Tsimring, Jeff Hasty (2008). Metabolic gene regulation in a dynamically changing environment Nature, 454 (7208), 1119-1122 DOI: 10.1038/nature07211

Jesse Stricker, Scott Cookson, Matthew R. Bennett, William H. Mather, Lev S. Tsimring, Jeff Hasty (2008). A fast, robust and tunable synthetic gene oscillator Nature, 456 (7221), 516-519 DOI: 10.1038/nature07389

the system biology boundary

We have to stop to use omics technologies to turn biology (and system biology) in an exact science. Our vision of "exactiness" is inside the problem: we are organisms and our point of view, our cognitive brain, evolved together with the system we are trying to hack. We only need models in biology to getting things done, that's it. Stop packing biology in our stupid packages, let it work the model.

Fuzziness is not simply the manifestation of methodological limitations, but is also inherent in many biological problems and our reductionist approaches to them

Monika Fuxreiter, Peter Tompa (2008). Fuzzy interactome: the limitations of models in molecular biology Trends in Biochemical Sciences DOI: 10.1016/j.tibs.2008.10.006