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RFID to easily identify frozen samples
Posted on November 30th, 2009 No commentsRFID means radio-frequency identification and is used to define tagged object that can be recognized through radio-waves. This system is composed by two part: the first one is an integrated circuit in which is possible to store and process information and modulate and de-modulated radio frequency; the second part is usually an antenna required for receiving and transmitting the signal. The first use of RFID was during the II World War when allies used this system to distinguish their planes from those of enemy; then in 1973 it was US patented by Mario Cardullo with a business plan showing uses in transportation, banking, security and medical. Now, RFID technology is currently used for several application: from passport to animal identification, from race timing to transportations payments.
In healthcare RFID are undergone to severe regulation to defence the privacy of consumers. In 2006, Food and Drug Administration highlighted the importance to do not include information about consumers, health practitioners or other uses of the product out of label. The RFID tag may be covered with a seal containing a logo, a message unrelated to product and an unique serial number and, mostly important, the tag will not substitute the traditional labelling process. This point wasn’t observed by GSK when they used RFID tag to control HIV treatment capsules and for this reason a violation was signalled. Another important use in scientific world is the tracking of nuclear substances during both storage and transportation. Indeed, scientists from the Department of Energy Argonne National Laboratory set up a system in order to gain information about the nuclear materials in real time, allowing the constant monitoring of the materials self. Moreover, some RFID devices have been added to notebooks to streamline information management and retrieval. This tool could be useful in big pharma, or big institutions in order to correctly manage all information without loosing time.
Sample identification is another important application in the scientific laboratory; for instance, it could be really useful to recognize frozen samples –cells, proteins and RNAs- without opening the box. The great advantage of this system is the perfect preservation of biological materials, indeed everyone knows that continuous and repeated extraction from liquid nitrogen seriously damage biological samples. Furthermore, RFID allows to immediately control the box status and find if vials are missing. In quality control system this system is strongly recommended because it makes transparent audit process. Modern RFID technology is miniaturized and cheap, so it could be applied on each cryovials through self-adhesive cryo safe labels. Using RFID tags has a lot of advantages specially if the freezing service is centralized or common for several laboratories: not only box contents are always well described, but also operators’ mistakes can be immediately repaired without loosing precious materials. Also in small scale laboratories this system could have some applications to manage samples during years specially if there is a quick turnover of workers, as usually happens in academic labs. RFID system is a modern tool to facilitate scientific job. -
iRNA in yeast
Posted on November 27th, 2009 No commentsiRNA is a tool currently used in molecular biology to define the function of a gene: indeed scientists block mRNA transcription of specific gene and observe the cellular response. This technique is extremely potent and specific and allows to study one protein at time. In yeast, certain strains lack the normal RNA interference machinery and have alternative enzyme variants which can be transplanted into truly deficient species. iRNA is specially useful to study budding yeast, but this model lacks the Dicer enzyme, responsible for processing the double stranded RNAs into small interfering RNAs.
Scientists from the Whitehead Institute identified many proteins that show hallmarks of Dicer- mediated cleavage; they moved these proteins into new strains in order to reconstitute the iRNA machinery and they observed the complete silencing of all gene of interest. Thus, no limitations were found to study genes and proteins involved in yeast biology. Moreover, transposons are efficiently silenced without interfering with other genes. The system is greatly specific. Based on this positive result, scientists want to apply this finding to pathogenic yeast Candida Albicans in order to better understand the behaviour of this organism and identify some pharmacological target. -
Databases
Posted on November 20th, 2009 No commentsTwo main databases are now available: the EMBL-EBI and the NCBI for Europe and US, respectively. These two databases are connected and all the information present are available in both systems. Another database is provided by a Japanese laboratory and is online at genome.jp.
Main databases contain information about DNA sequence, two examples are EMBL datalibrary and GenBank; all other databases regarding RNA, proteins and polymorphisms or rare diseases are connected to these two ones. Databases are usually checked by operators or software: the difference between these two control systems could be observed in the redundancy because manual control is usually more systematic than these performed by software. About proteins, three secondary databases are currently used: Swiss-Prot, TrEMBL and PIR. In these websites several bioinformatic tools are available to align sequences, predict primary and secondary structure of proteins or determine the isoelectric point, all these information are important especially at the beginning of the study. Other databases like PDB or Modbase offer three-dimensional structures of proteins and prediction of three-dimensional structures, respectively. As well as PROSITE collects information about protein motifs, functional domains and so on. Last but not least, Genome.jp is preparing a new tool, KEGG pathway, useful to retrieve information about enzymes and metabolic pathway. Good work! -
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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Pharmacological profile of Marijuana
Posted on November 16th, 2009 No commentsAncient Romains knew some pharmacological effect of Marijuana and have used it in their medicine. In the last time other positive effects have been identified for this plant. Unfortunately cannabis is often used out of medical control and is considered as a drug.
Specially young people prefers Marijuana to other drug, because the most recognized effect on central nervous system is an unusual happiness and appreciation of music, art and in general pleasure; furthermore it gives a relaxing sensation. The pharmacological reason for these effects is the distribution of cannabioidis receptors that are located in brain area involved in tension control, movement control and in the nucleus accumbens that is the pleasure centre of the brain. Marijuana is usually smoked and through this way it’s almost impossible to reach dangerous or lethal dosed from a pharmacological point of view. Of course the abuse of this substance causes a decreased attention that could be really dangerous if you drive. Other collateral effects are nausea and cardiovascular problems specially if it is assumed in presence of other drugs, such as cocaine. No correlation between marijuana and the use of other drugs has been identified, thus marijuana can not be considered as a passage- drug. -
Animal model for Parkinson’s disease
Posted on November 11th, 2009 No commentsAt the moment no animal models are available for human Parkinson’s disease. Everyone knows the importance to have right model to study a disease or test drug to care it; this lack must be rapidly overcome, giving the high number of people that suffers for this disease.
Michael J Fox Foundation and Sigma Aldrich set up a rat model in which it was possible to measure neurological damages and show symptomatically what is seen in Parkinson’s disease. Scientists knocked down five genes involved in the disease: leucine-rich repeat kinase 2 (LRRK2), α-synuclein (SNCA), DJ-1 (PARK7), Parkin (PARK2) and PTEN induced putative kinase 1 (PINK1). In this way only genes ownregulated in the disease can be studied, but this is the first step to build more accurate and useful models. They applied the Zinc Finger Nuclease to insert mutations in DNA of one day old rat embryo, then transplanted the embryos into pseudo-pregnant rat and obtain KO offspring. With ZFN technique is possible to eliminate the necessity to bred heterozygous chimeric mice to obtain KO animals. Genetically manipulated rats are now commercially available also for Parkinson’s disease and this opens new challenging opportunities to care this disease. -
Tools to manage the bibliography
Posted on November 9th, 2009 No commentsBibliography is a fundamental part of every scientific publication, from PhD thesis to review and experimental paper, as well as pharmaceutical reports or clinician case reports. Each journal has specific requirements and before starting writing any documents it could be useful know about bibliography rule.
In particular, in scientific paper every sentence must refer to other publications in order to prove that the work has been founded on scientifically accepted basis. References can be managed through several software, for instance EndNote. Nature website proposes a new tool to manage references, called Connotea. This tool allows saving links to web pages or PubMed entry numbers or Amazon pages for a book. Because Connotea it web-based, it’s not necessary to download references and bibliography is always available in each computer. Furthermore, it’s also possible to share references with colleagues or everyone is interested, and there are no limitations about the number of persons with which share these information or about the number of link saved. To use Connotea you must subscribe for free and you will get your space in which you can tag your reference and easily recognize them. Knowing literature is the first step to produce significant data in science! -
One odd and dramatic case in medicine
Posted on November 5th, 2009 No commentsIn 2007 a young Japanese woman gave birth to her child and after only one month died for leukaemia, ABL-BRC positive. During her pregnancy she didn’t know to be sick and also doctors didn’t diagnose the disease. After eleven months, also the baby showed a tumour into his cheek. Physicians excluded a possible sarcoma and diagnosed also in this case leukaemia, ABL-BCR positive, the same mother’s disease. Further analyses demonstrated that no genetic material from the father was present in baby’s tumour, this means that cancer cells derived only form the mother and escaped the foetal barrier into uterus. Scientist has suspected that some forms of cancers, such as leukaemia and melanoma that are prompt to metastasize, could move form mother to fetus and this unfortunate story gave the genetic proof. Cancer cells can escape our immune system and also foetal barrier, knowing molecular basis of this mechanism could help us to better understand cancer biology and find new strategies for therapeutic intervention. Fortunately, there are few possibilities that the case of Japanese woman can repeat and we can learn a lot from odd examples like this. A positive note to conclude this post: the baby was successfully cared and is still alive.
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Gene therapy to restore sight
Posted on November 2nd, 2009 No commentsLeber’s congenital amaurosis is a pathology that affects 3000 people in USA and causes loss of sight from birth until reaching complete blindness at about 40 years. This disease interests a gene, RPE65 that helps in rhodopsin synthesis. If this gene is mutated, as occurs in the disease, photoreceptor cells into the retina will die.
During an important study carried out at the University of Pennsylvania, gene therapy was applied to blind dog to restore the activity of RPE65 gene and restore sight, as a consequence. Then, a small- scale study in human started in 2007, to ascertain the safety and efficacy of using virus to carry the RPE65 gene. First results showed that four of six young adults with Leber’s congenital amaurosis, had an improvement in their sight. Nevertheless, researchers knew that children with an intact retina –not already compromised by the disease- could have major benefits from this therapy. Thus, they performed the same study including four children for 8 to 11 years old and obtained great results in terms of increased light sensitivity. This work has been published in Lancet Journal in October, 2009. As all therapies that can improve the life quality of children, this work offers an hope for families that have so serious problems.
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