31 August 2008

no more press releases please

Researchblogging.org strives to identify serious academic blog posts about peer-reviewed research with a brand new 2.0 aggregation site still launched.


Member from January 2008, Reportergene helps the community in finding posts related to development of new reporter assays. Altough still in its infancy, this way to broadcast scientific news, promises to be an effective alternative to boring press releases.

Read also: Does a blogger increase impact factor?

30 August 2008

poisonous mushrooms? use real-time PCR!

Boletus edulis or Amanita muscaria? Species-specific identification of the major cooked and fresh poisonous mushrooms in Japan was performed using a real-time PCR system, as reviewed by Elio at Small thing considered. Don't forget the thermocycler into your wild mushrooming trails!

27 August 2008

Diagrammatic notation of celluler processes standardized

Via systems-biology.org I have been acquainted with the first specification for Process Diagrams of the Systems Biology Graphical Notation (SBGN) announced yesterday. The goal of SBGN is to standardise the graphical representation of essential biochemical and cellular processes. Standardising graphical notations for describing biological interactions is an important step towards the efficient communication of biological knowledge between different communities. More information on SBGN and SBGN Process Diagram Level 1 can be found here http://www.sbgn.org/

In september, after the august truce, there is a burst in standardization (according to google trends)

24 August 2008

Science bloggers meet in London

Nature Network, in collaboration with the Royal Institution, is pleased to announce its inaugural science blogging conference:

Science Blogging 2008: London
30 August 2008, Royal Institution, London, UK

The science blogging community is growing rapidly and reaching larger audiences. At Science Blogging 2008, science bloggers from around the world will have the opportunity to meet and discuss the pressing issues in science, science communication, publishing and education. What can science bloggers do to maximise their impact? Can blogging contribute to scientific research and careers? How can blogs be used to help educate the public about science? What other emerging online tools will play a role in science? Readers and writers of science blogs, those who follow trends in online scientific communication and anyone else interested in learning more about science blogging will benefit from the discussions.

20 August 2008

Cherry-picking from Nature Methods

The august issue of Nature Methods seems very appetizing for any reporter-genomist. The following is only a personal cherry-picking from the table of contents.

A time stamp for proteins (doi:10.1038/nmeth0808-662a)
  • A new protein tag simplifies labeling and visualization of newly synthesized target proteins in tissue and whole animals.
Improving membrane voltage measurements using FRET with new fluorescent proteins (doi:10.1038/nmeth.1235)
  • Designing fluorescent protein-based sensors that display large changes in fluorescence resonance energy transfer (FRET) is challenging. Redesign of a FRET-based voltage sensor using new fluorescent proteins increased the sensor response to changes in membrane voltage and measurements at warmer temperatures displayed faster kinetics comparable to action potentials.
Detection of heteromerization of more than two proteins by sequential BRET-FRET (doi:10.1038/nmeth.1229)
  • Many proteins, including G protein–coupled receptors (GPCRs), interact to form oligomers at the cell surface. A combination of bioluminescence resonance energy transfer (BRET) and fluorescence resonance energy transfer (FRET) in a technique called sequential resonance energy transfer (SRET) extends these methods to study higher-order oligomers of GPCRs or other proteins.
!!!If you wish to find reviews of any paper in the next Reportergene posts, just suggest it in the comments or in the submit page.

15 August 2008

wiki for reporter assay?

According to my referrals, these are the keywords most searched in the last period (wordle elaboration). Lot of people is looking for a wiki of reporter genes (top left), does this resource eventually be useful for you? I'll think about it at the seaside. Holidays!

4 August 2008

Nuclear Magnetic Reporters

With the advantage of tomographical data set and detailed anatomical information, magnetic resonance imaging (MRI) features an unsurpassed space resolution (micrometers!) in the field of in vivo imaging. Conversely, imaging of optical reporters like luciferase and GFP, still suffers from short-sighted resolution, often requiring longer post-mortem analysis (i.e. microscopy-slides) to identify and deconvolve photon emission sources from in vivo datasets. From this "topological" standpoint it is easy to understand the growing awareness and demand of new 'super-paramagnetic"'' reporter genes to be detected according to their 'relaxivity'. NMR gene expression strategies thus far introduced in recent literature include:
  • detection of beta-galactosidase activity;
  • targeting of amide protons of expressed proteins;
  • expression of natural iron homeostasis proteins such as transferrin, ferritin, MagA.
Nonetheless, those "magnetic" papers had very low followup, and a transgenic paramagnetic reporter mouse still doesn't exists. MRI reporters classically suffer from low sensitivity (lot of reporter need to be expressed in order to be detected) and low dynamic range (the detection doesn't discriminate very well different reporter concentrations). It is possible to conceive a reporter gene with high space/time resolution, high sensitivity and high linear range? With multimodality imaging a super reporter mouse can harbor a vector containing more than one reporter (for different imaging modalities). This is very attractive for lab leaders in imaging techs, and lot of cut and paste have been made with reporter sequences. Do you know any super-mouse?

2 August 2008

Reduce, Refine and Replace

As a perspective, with in vivo imaging this one will be the last dissected rat.

Image by Natalie Zee Drieu (Craftzine.com)