Freedom of robots

A Science letter by Robert Stevenson focused my attention on the eventual patentability of new "automated" discoveries. This is of course a letter in response to the "automation of science" previously reviewed. Apparently, it should be legally difficult to patent any invention made by a robot: the American patent law strictly refer to the inventor as "a person", while the European law seems more broad. Thus, supposing a brilliant robot scientist is ever build, no man might protect/deserve those inventions for its proprietary benefit. Legacy is not considered: A invents robot/algorythm B, B invents drug C, but C is not patentable. Honestly, once developed such a robot, it should take no longer to develop a second robot mimicking human creativity (i.e., writing good and bad dates and results on a paper lab-book). Are we so close to Singularity? Interestingly, in a previous Science paper, Debra Meloso from the italian Bocconi University has modeled the patent system and proposed a better way to promote intellectual discovery (maybe including generation of robot-scientists) that should be based on a sort of 2.0 trading of discoveries. Might a machine sell a product? Ask to lawyer Crawford.

Stevenson, R., Murphy, J., & Clare, T. (2009). Robot Inventors: Patently Impossible? Science, 324 (5930), 1014-1014 DOI: 10.1126/science.324_1014a

Meloso, D., Copic, J., & Bossaerts, P. (2009). Promoting Intellectual Discovery: Patents Versus Markets Science, 323 (5919), 1335-1339 DOI: 10.1126/science.1158624

the infrared fluorescence protein war

In vivo optical imaging of deep tissues in animals is most feasible between 650 and 900 nm because such wavelengths minimize the absorbance by hemoglobin, water, and lipids, as well as light-scattering. Roger Tsien, last year's Nobel Prize in chemistry for his research on fluorescent proteins, introduced in a Science report, a modified version of the Deinococcus radiodurans phytochrome turned to be a infrared fluorescent protein (IFP). Carrying IFP into the mouse liver through an adenovirus-vector, the infrared fluorescence performed better than mKate a red fluorescent protein as imaged by a Maestro spectral imager. More background info available at Brainwindows.

Actually, this advance makes me a little gloomy, since I spoke about mKate in my first post. It was September 2007, does it takes only two years for a reporter gene to be outperformed? It is dramatic: it takes roughly two years to make a transgenic reporter mice, and another two-three years to get data with him! Once you start, you know that you will be outdated at half of your journey.

Update 2011

The infrared war continues: two years later, IFP1.4 is outdated and we probably have a brighter infrared fluorescent protein with emission maxima at 713 nm. The new IFP, called iRFP comes out in Nature Biotechnology from the laboratory of Vladislav Verkhusha and does not require exogeneous substrates like biliverdin. Luckily, now new zinc-finger transgenesis approaches are making faster the generation of transgenic mice.

Shu, X., Royant, A., Lin, M., Aguilera, T., Lev-Ram, V., Steinbach, P., & Tsien, R. (2009). Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome Science, 324 (5928), 804-807 DOI: 10.1126/science.1168683

Filonov GS, Piatkevich KD, Ting LM, Zhang Z, Kim K & Verkhusha VV (2011).
Bright and stable near-infrared fluorescent protein for in vivo imaging
Nature Biotechnology, 29, 757–761 DOI: 10.1038/nbt.1918

Is Reportergene a Google's Blog of Note?

Darwin and Mendel mainly worked with mere observation, and now it is possible to do it at molecular level. To support RG, you can contribute diffusing the concept that molecular biology can be studied in living, healthy life species (i.e., fluorescent dogs). Please, candidate Reportergene at Google's Blog of Note until May the 14th. It is just a matter of one click. Click it!

Top 15 in Researchblogging.org

Reportergene results 14th in the top Researchblogging contributors with 60 posted articles and >12500 views. Interestingly I'm aware of only 54 posts (as you can see on my left sidebar). ResearchBlogging, scroll me down! I'm not so productive :-)

DNA actively directs transcription itself

Traditionally, responsive promoter sequences on DNA have been considered only passive docking sites for a pletora of DNA-binding proteins supposed to play the active hard role of gene expression. Several proteins have been pulled-down according to their ability to bind DNA sequences (i.e., far western blotting) and lot of plasmids were generated carrying any responsive DNA element upstream of a reporter gene to mainly study the activity of such proteins (i.e., transcription factors) and eventually discover new drugs. In other words, reporter assay data have been mainly queried to address gene expression from the protein stand-point (trans-action).

It is worth to note, that protein activity is longly known to be allosterically regulated by the binding of ligands or cofactors outside the protein’s active site. Now, Sebastian Meijsing and colleagues from the Yamamoto Lab, are shifting the balance toward cis-acting factors (the DNA itself). They propose in a Science report that DNA is a sequence-specific allosteric ligand for the nuclear receptor GR (glucocorticoid receptor). GR may be considered a ligand-activated transcription factor (i.e., it is activated by cortisol or dexametasone). The Yamamoto group exploited a classic luciferase assay to test the activity resulting from the interaction between GR (protein) on its GREs (DNA) during dexametasone stimulation.

Molecular gymnast by:Elio Abbondanzieri

Interestingly, odd differences were found in their elegant 2x2 experimental scheme in which either single-poing mutations on the receptor or on the responsive elements were combinatorially tested to finally postulate that DNA topology actively directs transcription similarly to an allosteric regulator. Gene expression , crystallographic, gel-shift and ChIP assays corroborate this intuition. Pay attention to your plasmids: DNA is more than a passive docking site.

Meijsing, S., Pufall, M., So, A., Bates, D., Chen, L., & Yamamoto, K. (2009). DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity Science, 324 (5925), 407-410 DOI: 10.1126/science.1164265