miRNomics

Recent studies demonstrate an increased importance of miRNA in regulating cell function, in particular in stem cells or during embryo development, otherwise deregulated expression of miRNA often causes diseases, such as cancer. miRNAs have been identified in viruses, plants and animals and regulate protein expression by inducing degradation of mRNA target.
miRNA are short RNA sequences that recognize from ten to hundred mRNA targets, usually identified by computational analysis. Several software based on homology search and/or other parameters (free energy of folding, length of symmetric stem, A C G U content) allow us to identify mRNA targets and recognize miRNA sequence inside the genome. In April 2009 (Curr Biol. 2009 Apr 15) Dr Hervè Seitz form the University of Massachusetts Medical School proposes a new role of messenger, target of miRNA.

He wrote: “Many computationally identified miRNA targets may actually be competitive inhibitors of miRNA function, preventing miRNAs from binding their authentic targets by sequestering them”. He proposed a new model to explain the regulation of miRNA activity, based on expression of mRNA target and not on expression of miRNA itself. Once again, it’s fundamental the synergy between biological experiments and computational analysis to obtain straightforward data and enrich our knowledge of miRNome.

Expression of infrared fluorescent proteins

On May 2009 in Science Magazine one really interesting novelty has been presented: infrared fluorescent proteins. A team of the University of California (San Diego) produced a monomeric version of batteriophytochrome (Deinococcus radiodurans) that spontaneously incorporates biliverdin. Phytochromes are bacterial proteins that absorb deep red light in visible spectrum and use this energy to induce expression of peculiar genes. Scientists modified the protein sequence and eliminated all portions responsible of biochemical signalling, but preserving the capability to absorb energy.

This energy was used to produce infrared emission, by using biliverdin as chromophore. The sequence of infrared fluorescent proteins were inserted in Adenoviruses in order to infect mammalian cells and whole animals. Comparing to visible light (fluorescence), infrared rays can more easily penetrate tissues and allow to trace single proteins in animals. This technique makes possible a lot of experiments, for instance the real time analysis of protein expression after external stimuli visualizing where proteins are expressed, as well as following disease progression at molecular level.
Infrared proteins offer new perspectives to imaging technology and can be further improved because other bacterial strains rather than Deinococcus radiodurans present proteins similar to phytochromes.

Event: A novel journal about translational medicine

“From bench to bedside” is the expression currently use to refer translational medicine. This branch of medicine builds on basic research advances to develop new therapies or medical procedures. Indeed, biological studies using cells or animals as model, furnish important results that can be easily translated into current medical approaches.

For example, DNA sequencing in patients affected by myeloid chronic leukaemia allows to choose the better therapy and in presence of Abl-Bcr fusion gene is possible to use Imatinib that potently inhibits deregulated ABL activity. This is only an example of how knowledge derived from biochemical analysis of a protein and biological studies on cells have a direct impact on health care, several other studies are reported in literature.

For both, medical doctors and scientists becomes necessary to have an inter-disciplinary preparation in order to make possible and useful the communication between “lab and hospital”. Furthermore, development and use of software is also crucial to correctly manage data derived from cells, animals and patients.
Science group will publish a new journal about translational medicine within few next months: the goal would be help scientists to access and apply new findings from many different fields, as B. Alberts, Science’s Editor-In-Chief, explained. Good reading!

How to manage genome-wide high-throughput data

Today, we would like to propose you an important tool to manage genome-wide high-throughput data, available in the website of the University of California Santa Cruz. The UCSC Cancer Genomic Browser allows scientists to integrate and interactively display analysis of cancer genomic and clinical data. Genome heatmaps display copy number abnormality in samples of interest and chromosome or gene set visualizations are available. For each data sets, clinical data ( for instance for breast cancer: ER expression, PR, Her2, TP53 level, age, tissue source) are reported again in heatmaps.

Thus, in one page it’s possible to compare different studies or different kind of cancers and save the result of your analysis. Literature references are linked and standard statistical tools provide quantitative analysis of subsets of genome data. Then, in Genome Browser you can find out biological, genetic and biochemical information about the chromosomal portion or gene datasets of your choice.
Indeed, with this tool user-defined gene sets can be filter and this is really useful to facilitate the analysis. In conclusion, the main goal of UCSC is to provide a platform to present data in an integrated system not only for cancer researchers but also for broader scientific community.

Event: 100th AACR Annual Meeting

Last April, AACR (American Association for Cancer Research) held its 100th Annual Meeting in Denver. This association offers a wide educational program since 1907, when its first president Dr James Edwing said: “Modern cancer research fills a urgent needs without which progress would be handicapped”.

Even if a lot of progress and new knowledge have been accomplished in this field of medicine, cancer research still be a challenge for academy or industry scientists. Based on recent evidences, tailored therapies are now available (for instance therapy with small molecule inhibitors) and represent a good example of collaboration between academic scientists, clinicians and pharmaceutical industries. This therapies are one of the first important goal of translational research, which needs a synergy between basic biological laboratories, engineering, mathematics and physics to be productive. As a consequence, modern scientists must have an inter-disciplinary preparation and a really open mind in order to make possible this thigh collaboration.
AACR launched meetings and workshops, to help scientist to fill the gap and continuously offers fellowship. Qualified information can be also retrieved in blogs and scientific forums. In 2009, dear scientist, you must be creative (and critical, as usual) when you are looking for sources!