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Cellular transfection
Posted on May 17th, 2010 No commentsExperimental research uses modern and old cellular biology techniques for an high number of applications. For this reason, cellular biology shows great advances in last decades. Improvement in cell culture media allows propagating cell lines that was not possible to culture just few years ago. For instance, stem cells are now available and can be maintained in plate without loosing their stemness. Despite these advances in cell culturing, the method of transfection, most widely used, still is the calcium phosphate method. Indeed, either adherent and in suspension cells can be treated with this technique and can be successfully transfected.
The general protocol requires the direct addition of calcium phosphate DNA complex to cell medium, at least for six hours. Nevertheless, some modifications have been proposed in order to increase transfection. It could be possible to pre-treat cells with chloroquine, that is able to produce pores into cellular membranes. Otherwise, it’s also possible to shock cells with glycerol for less than two minutes. After glycerol treatment, it’s fundamental to accurately rinse cells with sterile PBS in order to completely remove the glycerol self. The calcium phosphate method is also inexpensive because all reagents can be produced in house, by using salts and powders usually present in research lab. -
The IntOGen interface
Posted on March 23rd, 2010 No commentsSometimes, there is a gap between experimental biology and clinical medicine while a continuous interchange would be auspicial to well direct experiments and keep updated the therapies. An interesting tool has been developed at the Barcelona Medical Research Park (Spain).
IntOGen is a frame work that collects, integrates and manages data derived from genome- wide experiments on large scale projects such as the Cancer Genome Atlas and the International Cancer Genome Consortium. Scientists manually annotate all samples by using the International Classification of Disease for Oncology vocabulary, in terms of tumour topography and morphology. Furthermore, they apply statistical methods to identify the most relevant alterations, by analyzing multiple studies on the same kind of tumour. Finally, they consider the role of whole biological modules, such as a pathway, to demonstrate the involvement of a single gene altered. The website www.intogen.org is available for free and allows to know modules and genes important in cancer, share experiments and analyze data in the context of cancer. This interface has been built to fill the gap between medicine and molecular biology. Similar tools should be really useful not only for cancer but also for other kind of diseases, such as neurodegenerative disorders. -
New challenges for synthetic biology
Posted on February 1st, 2010 No commentsSynthetic biology is a modern discipline that tries to manipulate cells and program them to perform some activities useful for us. Different products or services may be provided by cells, for instance production of biofuel or toxin identification into a body as well as controlled insulin release. Synthetic biology requires a strict control of the system, but many parts involved into the process have not been known yet.
For instance, DNA sequence in the promoter region is not always well characterized and this is a crucial point to increase cell productivity. So, the first point to be clarified to obtain results from synthetic biology is the knowledge of expression system. Furthermore, it’s important to understand how all parts can work together. This is another challenge for synthetic biology because of the complexity of regulation mechanism into the cells. Circuits can work in an unpredictable manner and results are often few understandable. Finally, even if the circuit seems to work very well, the system could not be reliable in all situations and it could fall because of genetic mutations which could arise in any time. In summary, synthetic biology is an important challenge for scientists for the next future. Biofuel, toxin detection and insulin release are only three of different purposes for which this discipline must be applied. -
What is bioinformatics?
Posted on November 18th, 2009 No commentsBioinformatics is a modern scientific discipline which wants to apply mathematical model to biology in particular to cellular and molecular biology and biochemistry. Even if in the last years important projects, such as the Genome or the Proteome project, have required a large use of bioinformatic tools, a lot of work will be done to exactly correlate biological results to in silico models. Bioinformatics is useful to create statistical model to explain biological experiments and identify significant trends. Moreover, it’s possible to generate models to compare sequences of DNA, RNA and proteins to identify relevant sequences for the evolution or for biomolecule functions. These tools are usually available for free in several websites – Expasy for instance-, are user friendly and are currently used by all scientists, even without special skills in bioinformatics. By contrast, more complex processes, like creating network with data, require great competences on biology, biochemistry, mathematics and bioinformatics. For this reason, the crucial point to obtain useful results from bioinformatics is to have a tight collaboration with other professionals in order to evaluate all the results in the right way. One big challenge of bioinformatics is to try to rationalize the biological system, overcoming the unexplainable phenomena which are often encountered.
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