-
Novel applications of nanobodies
Posted on February 25th, 2010 No commentsCamelid derived single domain peptides are a novel form of antibody which maintain the same antigen binding properties but have greater stability and smaller size than traditional antibody. These molecules can be conjugate with several chromophores, for instance with green fluorescent protein for cellular imaging applications.
A group from the University of Munich (German) applied its deepen knowledge about GFP modifications to nanobodies, this is the name of camelid peptides. The result was an improvement in GFP brightness modulation. By performing a phage display screening, they found out seven different molecules able recognize GFP and enhance or minimize its fluorescent signal. To validate the system, they produced a GFP- tagged oestrogen receptor and a nuclear binding enhancer nanobody, in presence of hormone the receptor moved into the nucleus and GFP signal increased five- fold its brightness. Several applications can be thought for this tool. For instance, nanobodies for each cellular compartment can be useful to determine how the protein of interest tagged with GFP change their position inside the cells in response to specific stimuli. Alternatively, protein- protein interaction can be studied because nanobody can bind one protein and after interaction with the second protein fluorescent signal can be modulated, as well as it should be possible to evaluate the duration of interaction self. A novel and flexible tool is now available for biologists. -
The value of negative results
Posted on February 15th, 2010 No commentsNegative results are similarly important than positive results for science advances. Indeed, a large number if hypothesis could be excluded if we considered negative results from other studies. Unfortunately, negative results are not so easily accepted and published in peer reviewed journal, thus are not available for science community.
Scientists from the German Research Centre for Environmental Health and from the University of Munich spent their time to collect negative results from protein-protein interaction studies and built a database, called “negatome”. They used data from literature search and from structural information retrieved into Protein Data Bank and identified almost two thousand of not interacting pairs. The novelty is that the not-interaction is experimentally demonstrated and published, while in previous work not- interaction was determined from not co-localization: if two proteins are differentially located, they will not interact. This sentence could be true, but is not predictive of interaction, just co-localization. The Negatome can contain some false negative pairs, but in general it can be considered a useful tool to compare and confirm results from immunoprecipitation or two hybrid system or other techniques that usually generate some false positive. We hope that this example should be followed by other databases for negative results. -
Automation in High-throughput screening
Posted on February 5th, 2010 No commentsDrug discovery uses the major amount of its resources for the high throughput screening. Based on specific probabilistic calculation, large experiments in HTS are performed by pharmaceutical and biotech companies to identify some molecules that could become drug after further long analyses. Robots are usually used in this complex process. It’s important that all data are generated in reliable and accurate manner in order to obtain useful results.
Robots can execute some passages: from serial dilution to reaction buffer disposal. In each of these steps, errors could be generated and, giving the small volumes in which HTS is usually performed, robots must be well calibrated in order to exclude the possibility to have this kind of problems. A lot of data arises from an HTS. Data management and statistical analyses are other key- steps for the high throughput screening. Thus, IT systems have not only to control robots to correctly work, but also help scientists to produce meaningful results from raw data. This kind of experiments are highly expensive and can be repeated only strictly necessary times. However, it’s really important to plan the experiment in the correct way and set up robot ant other IT systems involved into the process to obtain more data as possible. -
Statistics in science
Posted on January 29th, 2010 No commentsA common English quote says that there are three kinds of lies: lies, damned lies and statistics. This sentence was wrongly attributed to Disraeli, whereas it was firstly published by Marc Twain. Even if it could seem true, statistics is the only tool available up to date to manage a large amount of data and to give their a mean. Several functions are usually used in statistical analysis; the most common are the average, standard deviation, frequency and also the number of observation is reported in scientific publications.
All these data are defined as descriptive statistics because of their direct characterization of the population of interest. In other cases more complex calculations must be done to find significance from the study. Linear or logistic regressions are models to identify the trend that better explain and summarize the collected data. From linear or logistic regression is possible to interpolate or extrapolate data in order to predict results into the studied range or outside the studied range, respectively. Furthermore, from statistical analyses prevalence, incidence, absolute risk, odd ratio and relative risk are determined. All of these parameters are so important that must be determined during clinical study and are subsequently used to compare different protocols, drugs and so on. Clinical studies are classified as experimental studies or observational studies. The main difference between these two classes is the presence of a treatment given to patients in the experimental studies, whereas in the observational studies none treatment is followed but the selected population is just observed to determine the parameters of interest. In both cases, given the high number of patients enrolled in order to obtain significant results, statistics is useful to compare treated cohort and placebo cohort, for example, as well as to evaluate the role of specific component of the study, namely called covariates.
The major part of software that help to collect and manage data from a clinical study have also some algorithms to calculate standard statistical parameters during the data collection self. Revision and further elaboration must be done by professionals in order to correctly consider study results. Statistics is important not only in clinical trials, but also in all experiments performed in science. Indeed, to be sure to have obtained a result as a consequence of certain conditions and not due to serendipity, all experiments are usually repeated three or more times. Data presentation normally comprises average and standard deviation or confidence interval and significance is determined by a series of tests that should be described in material and methods section of the publication. In conclusion scientists must have some basis of statistics because this discipline confers value to their experiments and make them shareable and comparable with scientific community. Even if statistics is considered as a lie in some cases, it will be useful for science advances. -
The pediatric knowledge base
Posted on January 25th, 2010 No commentsThe pediatric knowledge base (PKB) is an IT system developed at the Pediatric Pharmacology Unit of the Children’s Philadelphia Hospital. This project involved professionals from several disciplines, such as medicine, pharmacology, statistics, bioinformatics. They built a model in which clinical data from patient were combined with electronic medical records and drug profiling, in order to obtain an IT tool able to continuously learn information about the patients self.
PKB helps physicians to choose the better pharmacological therapy in terms of dose, agent performance, collateral effects and drug combination. Based on the profile of three common drugs, such as vancomycin, methotrexate and tacrolimus considered as prototype, PKB monitors the drug use and helps to predict the outcomes in children patients that are often more difficult to treat. PKB is updated by numerous hospital members, in this way deep knowledge about clinical adverse events or clinical advantages as well as innovative protocol can be shortly acquired with great benefits for patients. Furthermore, PKB is web based and it could be shared between hospitals of different countries. A consortium is planning to be created to coordinate PKB implementation across the world. Using PKB as a model, it could be possible to set up similar dashboard for other class of patients in the next future. -
IT system protection
Posted on January 15th, 2010 No commentsThe broad diffusion of technologies such as computers, databases, mobile phones and so on, has determined a considerable change in our life. We usually use this kind of instruments at the work or school, at home and in other situations of everyday life.
It’s really important that the global IT system would be safe and protected from hacking attacks. Last year, an important mobile phone manufacturer company found vulnerability in its system and phone calls could be listen by everyone knew this failure. This first episode started an intensive research on security system in order to preserve IT and our privacy. Scientists were called to identify flaws into algorithms, acting like legal hackers, and were invited to share their skills and experiences with the community. So, manufactures changed their habits to reject the possibility to reveal flaws in their systems and choose an ethic approach to improve the worldwide knowledge. Also manufacturers that produce IT systems for pharmaceutical companies must consider the opportunity to look for new devices to protect all sensible data regarding the clinical study. Indeed, personal details of patients contained in clinical study are usually shared between centres involved in the trial and become more sensitive of possible attacks. Thus, it’s ethic that these data should be preserved. -
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. -
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! -
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! -
Challenging in food safety
Posted on October 26th, 2009 No commentsFood safety is one of most important challenge in our countries. Indeed, adulteration and poising food are often described in newspapers. FDA and ESFA are the organisations issued to guarantee food safety in U.S and Europe, respectively. Which are the most common problems that determine food adulteration. The first cause of this kind of problem is the bacterial contamination: indeed bacteria can provoke food spoilage as well as they are pathogen in some cases.
To decrease the possibility of food spoilage, numerous testing must be performed in food processing company. The safety ideal “from farm to fork” created by FDA can be reached only through an attentive analysis of raw materials, processing and packing procedures in order to assure maximal sterility in each step. Furthermore, some laboratories are specialised in bacterial, toxin and sterility testing: the common goal is to provide consumers with safe and wholesome food at least for all shelf-life of food self. These laboratories usually offer a broad range of services and usually communicate with their clients through LIMS system. LIMS systems, indeed, are able to collect large number of data analysis, reports and general forms and rapidly make them available to clients.
Sponsors
