visions in gene targeting

In a recent interview on the new journal "Disease and Model Mechanisms", Mario Capecchi, Nobel prize and pionier in mouse transgenesis visions about the problems to overcame in gene targeting:

With current conditional mutagenesis protocols, we can readily perform processes that occur in a day, but we cannot operate within minutes, seconds or milliseconds. [...] A recent development is the ability to activate genes with light [...] in addition to rapid switches, the capture time for signals (i.e. reporter genes) will also have to be increased enormously

Priceless

Reportergene poll

Dear 15% returning visitors, please, I'm offering a poll in the side column for you.

(I'm wondering about the "taste" of this site)

• How do you wish reading from Reportergene in the near future?
• More day-by-day conversations or more balanced news about assay technology?
• How do you read Reportergene?

It is a blog or a magazine?

Please vote and then come back again!

omics for protein stability

A new genetic technology has been developed at Harvard HHMI that allow tracking the stability of individual proteins within a complex (omics) mixture. Sherry Yen and colleagues, introduced in Science magazine the Global Protein Stability (GPS), a parallel multiplexing strategy to simultaneously measure the half-lives of thousands of proteins in mammalian cells. Of course, the core is based on two fluorescent reporters (DsRed and EGFP), so we can provocatively name it reportergenomics. How does it works?

Take a strong promoter like CMV and make a library coding the first reporter (DsRed)alone and the second one (EGFP) fused in frame within one of the >8000 human proteins X (take the X library from the hORFeome cDNA library). Of course, you need viral IRES to let the ribosome translate two protein from the same mRNA. Then, express the library in your favourite cell line. Once protein X is degradated, if you "believe" also EGFP will be degradated, then you can FACS the EGFP/dsRED ratio obtaining 7 population of cells containing only stable-->unstable proteins in your vector. Make 7 microarrays opportunely designed to find the DNA of your vector and identify which proteins (ORF) are stable/unstable. Give the results to a team of bioinformatics/system biologists and mine the dataset to find correlation between protein stability and roles/pathways/amino acid composition/astrological signs and what else you can get statistically significant. Submit the manuscript to Science.

Take care! It would be possible that the EGFP fusion with X protein, generates a protease site. In that case, the EGFP/dsRED ratio may not be a reliable readout of protein stability. If you don't want to take such risk, hire a PhD student and ask him to made 8000 western blots with 8000 working antibodies. Then, submit the manuscript to Reportergene*

* in 2019, when your PhD student will give you the results, Reportergene will have the biggest impact factor.

H.-C. S. Yen, Q. Xu, D. M. Chou, Z. Zhao, S. J. Elledge (2008). Global Protein Stability Profiling in Mammalian Cells Science, 322 (5903), 918-923 DOI: 10.1126/science.1160489

how to don't start the working week

I never received a refuse so sharp and still engaging (in love affairs). My dear, in future you will weep me.

Because your manuscript was not given a high priority rating during the initial screening process, we will not be able to send it out for in-depth review. Your analysis is interesting and our decision is not necessarily a reflection of the quality of your research but rather of our stringent space limitations.

importance of a journal to its field

For some strange reasons, lot of visitors found this site while they were looking for the impact factor of Genes and Development magazine. Of course, I wish to help them but actually I can not disclosure any real IF, since Journal Impact Factor is copyrighted from Journal Citation Report (JCR), a product of Thomson ISI.

OK guys, if it's enough for you, just mind that Genes & Development IF is roughly half of Nature IF, and roughly the double of Development.

Do you think a blogger can influence the impact of scientific papers? I had some thougths here, and here.

how to do a reporter assay

One year ago I posted a joke about reporter gene ABC, and that page was read by hundreds of visitor searching basic information about reporter assays. If you are one of them, and you are looking something more serious, at Promega you will find a simple flash animation describing how to design and perform reporter assay. Of course, if you wish shaking me to post more advanced tutorials, slides, excel sheet templates or what else, give your feedback in the comment section.

If you teach molecular biology, you own didactic material, and you want to exploit Reportergene as a 2.0 tool for your students, write me at info@reportergene.com, I'll grant you some space and your intellectual property will be always acknowledged.

FDA starts planning transgenic GE animal commercial use

Genetically engineered (GE) animals are those modified by recombinant DNA (rDNA) techniques. After a decade of delays and procrastination, the US Food and Drug Administration (FDA) has finally issued a draft guidance (http://www.fda.gov/cvm/GEAnimals.htm) describing how it plans to regulate the commercial use of genetically engineered (GE) animals. The guidance document is being distributed for comment purposes only and not yet for implementations.

Accorging to FDA's opinion, GE animals currently being developed can be divided into six broad classes based on the intended purpose of the genetic modification:

1. to enhance food quality or agronomic traits (e.g., pigs with less environmentally deleterious wastes, faster growing fish);
2. to improve animal health (e.g., disease resistance);
3. to produce products intended for human therapeutic use (e.g., pharmaceutical products or tissues for transplantation; these GE animals are sometimes referred to as “biopharm” animals);
4. to enrich or enhance the animals’ interactions with humans (e.g., hypo-allergenic pets);
5. to develop animal models for human diseases (e.g., pigs as models for cardiovascular diseases); and
6. to produce industrial or consumer products (e.g., fibers for multiple uses).

Although commercial reporter mice can partially belong to the point 5, my first feelings are that there is still lot of work pending in order to fully understand, and then regulate, recombinant life engineering.

RG is popular on Nature Blogs

Yes, today Reportergene was in the NatureBlogs top ten (popularity).

Why you don't contribute to the race toward reportergenomics by becaming a featured RG blogger? Or, if you are only a reader, by sharing/backlinking this blog...

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