66 posts · 21,376 views
To master molecular mechanisms we need to know how they works within the whole organism. My vision is that new developments in genetic engineering will branch new applications for reporter genes, not necessarily confined to report transcriptional regulation. In my blog I trend advances in such a 'reportergenomics', a discipline at the crossroad between synthetic and system biology.
96well
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- March 2, 2010
- 06:01 PM
- 59 views
A darwinian legacy OR Why we need fluorescent rabbits
by 96well in Reportergene
My post about fluorescent rabbits is gaining a momentum on the Flickr group 'Bunny Lovers Unite' and in the Rabbitmatch's blog. Most people ask itself: WHY making fluorescent bunnies? And others feel outraged.
Animal research is long debated, and my hope is that the development of new reporter probes would allow to reconsider current research protocols while increasing the scientific significance of the experiments done, this is the focus of my current research. Here, a take opportunity of this........ Read more »
Ciana, P., Raviscioni, M., Mussi, P., Vegeto, E., Que, I., Parker, M., Lowik, C., & Maggi, A. (2002) In vivo imaging of transcriptionally active estrogen receptors. Nature Medicine, 9(1), 82-86. DOI: 10.1038/nm809
Maggi A, & Rando G. (2009) Reporter mice for the study of intracellular receptor activity. Methods in molecular biology (Clifton, N.J.), 307-16. PMID: 19763513
- February 17, 2010
- 01:11 PM
- 63 views
Molecular surgery: playing with network edges
by 96well in Reportergene
Protein X interacts with protein Y, what are the phenotypic consequences? And what is the impact of the X-Y partnership in the whole protein-protein interaction network? To address this question, scientists often remove specific network nodes by eliminating (knock-out) or downregulating (knock-down) the gene encoding one protein product (i.e. X). This is a poor strategy, because usually X interacts not only with Y, but also with P, Q, R, S, T, U, V, W and Z. Thus, X-KO strategy is too much invas........ Read more »
Ear, P., & Michnick, S. (2009) A general life-death selection strategy for dissecting protein functions. Nature Methods, 6(11), 813-816. DOI: 10.1038/NMETH.1389
- February 11, 2010
- 01:43 PM
- 108 views
Are you a motivated labmate?
by 96well in Reportergene
I went through this little gift from Uri Alon: its essay appeared in Molecular Cell which aims to conjugate psychological principles to the every-day lab routine for improving motivation. How Uri Alon improves the motivation of his lab? He try to balance three fundamental needs of any scientist: competence, autonomy and social connectedness, for instance:I make our weekly group meeting an event that enhances social connectedness. The first half hour of the two hour meeting is devoted to nonscien........ Read more »
Alon, U. (2010) How to Build a Motivated Research Group. Molecular Cell, 37(2), 151-152. DOI: 10.1016/j.molcel.2010.01.011
- January 20, 2010
- 02:04 PM
- 118 views
Camel vs Jellyfish: a battle with green fluorescence
by 96well in Reportergene
Does the spectral properties of GFP can be modulated by antibody-derivatives? To explore this hypothesis, Axel Kirchhofer and colleagues from Munich Center for Advanced Photonics have designed a number of NanoBodies (NBs) to bind to GFP. (Nanobodies? They are small, antigen-binding, single-domain polypeptides derived from some camelid antibodies). The authors found NBs could increase or decrease GFP fluorescence: in fact, co-chystallization of GFP-NB complexes revealed NBs inducing subtle chan........ Read more »
Kirchhofer, A., Helma, J., Schmidthals, K., Frauer, C., Cui, S., Karcher, A., Pellis, M., Muyldermans, S., Casas-Delucchi, C., Cardoso, M.... (2009) Modulation of protein properties in living cells using nanobodies. Nature Structural , 17(1), 133-138. DOI: 10.1038/nsmb.1727
- January 19, 2010
- 11:00 PM
- 112 views
Green Fluorescent Rabbit
by 96well in Reportergene
A new study demonstrates the feasibility of using a lentiviral approaches to create transgenic rabbits with more efficiency than classical pronuclear injection transgenesis developed in rabbits two decades ago.
Tracing Ruppy, the reporter-dog, the enhanced transgenic bunny carries a green fluorescent protein. Rabbits are still used as laboratory animals as they are genetically closer to primates and are large enough to allow safe and secure blood sampling compared to mice. Thus, transgenic rabb........ Read more »
Hiripi, L., Negre, D., Cosset, F., Kvell, K., Czömpöly, T., Baranyi, M., Gócza, E., Hoffmann, O., Bender, B., & Bősze, Z. (2010) Transgenic rabbit production with simian immunodeficiency virus-derived lentiviral vector. Transgenic Research. DOI: 10.1007/s11248-009-9356-y
- January 13, 2010
- 06:10 PM
- 149 views
EXTassays, toward maturity of RNA reporters
by 96well in Reportergene
I read with some interest a recent Nature Methods paper appeared this January. Anna Botvinnik and colleagues from Max Planck Institute, conceived a new reporter system able to measure receptor activation (receptor dimerization), downstream signaling (adapter recruitment) and subsequnent cis-regulatory responsive elements transactivation efficacies by...
...no, you don't need a 64-milion new-generation machine, you need Trizol!
As I reviewed in my first 2010 post, there is a trend to develop mu........ Read more »
Botvinnik, A., Wichert, S., Fischer, T., & Rossner, M. (2010) Integrated analysis of receptor activation and downstream signaling with EXTassays. Nature Methods, 7(1), 74-80. DOI: 10.1038/nmeth.1407
- January 4, 2010
- 12:00 AM
- 83 views
2010: luminometers OR sequencers?
by 96well in Reportergene
Next generation sequencing (solexa, illumina, 454) is offering a new opportunity for the design of multiplexed reporter assays. With the notable 2007 exception of Brainbow (in which however, it was not possible to discriminate the origin of the 90 or more observed fluorescent colors because they come from random recombination), simply the co-detection of more than three fluorescent proteins is very challenging in real life because of spectral overlapping and other shortcomings. Early in 2008, I ........ Read more »
Patwardhan, R., Lee, C., Litvin, O., Young, D., Pe'er, D., & Shendure, J. (2009) High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nature Biotechnology, 27(12), 1173-1175. DOI: 10.1038/nbt.1589
- December 23, 2009
- 08:11 AM
- 205 views
bacteria towing santa's wagon?
by 96well in Reportergene
Bacteria swim in water solution with a random movement resembling brownian motion. Imagine they while impacting randomly on a micro-gear. They will transfer some energy to the gear, but due to random movements the resultant will not provide any directed motion. However, you should remember from physics101 that a principle for the conservation of the force does NOT exist: imagine each tooth of the gear as a lever arm, and do design gears with asymmetric teeth. In this way, bacteria impacting on o........ Read more »
Sokolov, A., Apodaca, M., Grzybowski, B., & Aranson, I. (2009) Swimming bacteria power microscopic gears. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0913015107
- November 28, 2009
- 07:50 AM
- 26 views
Sorry, I'm experiencing a temporal drift toward metaphysics
by 96well in Reportergene
As we know it, our molecular life as individuals starts with a fusion between a female oocyte and a male sperm cell. When our mother was born, she got already in her ovary that small not-matured oocyte that than contributed to our first half cell at the time of ovulation several years later. Conversely, it is believed that our father at the time of conception, just donate our second half cell by means of a sperm cell (randomly) produced de novo.
Now, Zhuoru Wu and her colleagues at the Universi........ Read more »
Wu, Z., Luby-Phelps, K., Bugde, A., Molyneux, L., Denard, B., Li, W., Suel, G., & Garbers, D. (2009) Capacity for stochastic self-renewal and differentiation in mammalian spermatogonial stem cells. The Journal of Cell Biology, 187(4), 513-524. DOI: 10.1083/jcb.200907047
- November 25, 2009
- 08:27 AM
- 286 views
Malaria in 3D: bioluminescence imaging
by 96well in Reportergene
In a recent Plos One paper, Ploemen and colleagues (Nijmegen Medical Centre) use previously generated luciferase-bearing malaria parasites (PbGFP-Luccon) to study the spatio-temporal development of malaria infection in liver of living infected mice. The final aim of the paper is to propose 3D-imaging to explore the effect of drug and vaccines on P. falciparum infection without surgery and other invasive methodologies in the mouse. Interestingly, they report good tri-dimensional plasmodium tracki........ Read more »
Ploemen, I., Prudêncio, M., Douradinha, B., Ramesar, J., Fonager, J., van Gemert, G., Luty, A., Hermsen, C., Sauerwein, R., Baptista, F.... (2009) Visualisation and Quantitative Analysis of the Rodent Malaria Liver Stage by Real Time Imaging. PLoS ONE, 4(11). DOI: 10.1371/journal.pone.0007881
- October 28, 2009
- 01:35 PM
- 273 views
Chromophores, a new class of reporters
by 96well in Reportergene
A new Nature letter has the potential to abnormally extend (until extinction) the whole spectrum of reporter genes. So far, "reporters" were those genes coding for an easily detectable product (i.e., those coding for fluorescent or luminescent proteins). Wei Min and other Harvard's colleagues introduced a new technique, namely stimulated emission microscopy, that seems able to turn into mini-lasers any non-fluorescent light-absorbing molecule. It means that several chromophores, such as haemog........ Read more »
Min, W., Lu, S., Chong, S., Roy, R., Holtom, G., & Xie, X. (2009) Imaging chromophores with undetectable fluorescence by stimulated emission microscopy. Nature, 461(7267), 1105-1109. DOI: 10.1038/nature08438
- September 11, 2009
- 01:15 PM
- 413 views
engineering photo-activable proteins
by 96well in Reportergene
Plants contain proteins subjected to conformational changes in direct response to light irradiation. Moieties of those proteins, like the LOV2 domain from the Avena sativa Phototropin1 can be used to introduce light-operated switches onto other functional proteins. In a recent letter to Nature, Yi Wu and colleagues (Carolina University) poked at the Stratagene Quickchange kit to obtain a constitutive active Rac protein that was coupled to the vegetable LOV2 light switch using an overlapping PC........ Read more »
Wu, Y., Frey, D., Lungu, O., Jaehrig, A., Schlichting, I., Kuhlman, B., & Hahn, K. (2009) A genetically encoded photoactivatable Rac controls the motility of living cells. Nature, 461(7260), 104-108. DOI: 10.1038/nature08241
- August 28, 2009
- 08:08 AM
- 364 views
[150th post!] GPCR receptor hidden life
by 96well in Reportergene
hidden life of GPCR receptors unveiled with reporter approaches Two recent studies exploited reporter genes to unveil hidden secrets of GPCR signaling which is apparently harder to die than expected. From the cell surface, G-Protein Coupled Receptors are activated by the intended ligand. According to the current feed-back dogma, excessive stimulation results in de-activation (de-sensitization) of the receptor and subsequent internalization.With a genetically-encoded FRET sensor, Païkan Marcag........ Read more »
Marcaggi, P., Mutoh, H., Dimitrov, D., Beato, M., & Knopfel, T. (2009) Optical measurement of mGluR1 conformational changes reveals fast activation, slow deactivation, and sensitization. Proceedings of the National Academy of Sciences, 106(27), 11388-11393. DOI: 10.1073/pnas.0901290106
Calebiro, D., Nikolaev, V., Gagliani, M., de Filippis, T., Dees, C., Tacchetti, C., Persani, L., & Lohse, M. (2009) Persistent cAMP-Signals Triggered by Internalized G-Protein–Coupled Receptors. PLoS Biology, 7(8). DOI: 10.1371/journal.pbio.1000172
- June 14, 2009
- 09:15 AM
- 411 views
Sensitive imaging of T-cells with Gaussia reporter
by 96well in Reportergene
Gaussia luciferase (GLuc) holds the promise to became a great reporter. In the native form, GLuc is secreted. This feature gives additional advantages, but markedly attenuates its application for in vivo imaging. At MSKCC.org, Elmer Santos and colleagues recently described on Nature Medicine a membrane anchored external GLuc (termed extGluc) genetically engineered through the addition of a CD8 transmembrane domain to the carboxy terminus of the enzyme. The strategy to put the reporter outside th........ Read more »
Santos, E., Yeh, R., Lee, J., Nikhamin, Y., Punzalan, B., Punzalan, B., Perle, K., Larson, S., Sadelain, M., & Brentjens, R. (2009) Sensitive in vivo imaging of T cells using a membrane-bound Gaussia princeps luciferase. Nature Medicine, 15(3), 338-344. DOI: 10.1038/nm.1930
- May 25, 2009
- 04:53 PM
- 489 views
Freedom of robots
by 96well in Reportergene
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 ........ Read more »
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
- May 11, 2009
- 11:04 AM
- 503 views
introducing infrared fluorescence protein IFP
by 96well in Reportergene
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-vect........ Read more »
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
- May 4, 2009
- 05:23 PM
- 459 views
DNA actively directs transcription itself
by 96well in Reportergene
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 eventual........ Read more »
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
- April 11, 2009
- 04:03 PM
- 668 views
Might a machine win a Nobel prize?
by 96well in Reportergene
In 1997, the IBM computer Deep Blue wins a chess-game vs Garry Kasparov. This is considered a milestone in Artificial Intelligence research. Now, a second milestone dates April the 3rd, 2009 with Science publishing two reports on automating science. In the first one, Schmidt and Lipson (Cornell) propose a computational approach for detecting physical laws from experimentally collected data. As a principle for the identification on non-triviality, they first numerically calculate partial derivati........ Read more »
Schmidt, M., & Lipson, H. (2009) Distilling Free-Form Natural Laws from Experimental Data. Science, 324(5923), 81-85. DOI: 10.1126/science.1165893
King, R., Rowland, J., Oliver, S., Young, M., Aubrey, W., Byrne, E., Liakata, M., Markham, M., Pir, P., Soldatova, L.... (2009) The Automation of Science. Science, 324(5923), 85-89. DOI: 10.1126/science.1165620
- April 9, 2009
- 11:27 AM
- 579 views
Ruppy, the first fluorescent-dog
by 96well in Reportergene
A Korean team report the generation of a RFP-transgenic beagle. Dogs exhibits 224 genetic diseases similar to those found in humans making them one of the closest known models for various human hereditary diseases. However, experimentation with animal -which should be at the service of the whole mankind - raises strong and acute ethical challenges, particularly if the experimental model is a pet. Although still prototypical, the concept of "reporter animal" arguments toward a new use of a........ Read more »
Hong, S., Kim, M., Jang, G., Oh, H., Park, J., Kang, J., Koo, O., Kim, T., Kwon, M., Koo, B.... (2009) Generation of red fluorescent protein transgenic dogs. genesis. DOI: 10.1002/dvg.20504
- March 25, 2009
- 02:02 PM
- 541 views
optogenetic control of intracellular signaling
by 96well in Reportergene
Pharmacokinetics and pharmacodynamics should include in future opto-kinetic and opto-dynamic disciplines. At Stanford, Raag Airan and colleagues developed opsin-receptor chimaeras (the optoXR family) as a new class of retinal-based tools. In a Nature letter, they show that the class of OptoXRs can be functionally expressed in vivo, to permit differential photoactivable control of intracellular cascades with significant impact on the phenotype (i.e., behavior when light was targeted in brain via ........ Read more »
Airan, R., Thompson, K., Fenno, L., Bernstein, H., & Deisseroth, K. (2009) Temporally precise in vivo control of intracellular signalling. Nature. DOI: 10.1038/nature07926
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