Pfam database

Pfam is a novel database that contains conserved proteins and domains, usually employed in proteome analyses or sequencing classification. In this database, proteins are classified into two groups: Pfam-A families are manually annotated and inserted into the database after overcoming strictly threshold, while Pfam-B families are automatically created and clustered through similar sequence regions not matched with Pfam-A. A further rearrangement divides Pfam-A families in clans in respect to a hierarchical classification. The proteome coverage of Pfam database is different among species: information about bacteria are the most complete. Coverage is defined as sequence or amino acid coverage. In the first case, the proportion of sequence with a match with at least one of Pfam-A family describes the grade of completeness of the information. In the second case, is the proportion of amino acid belonging to the Pfam-A family that corresponds to the coverage. In order to grow and increase the information contained in the database, authors affiliated to the Wellcome Trust Sanger Institute, require the contribution of all scientists working on proteome. They are looking for new alignments, annotations or references for novel families, and updates for the existing ones.

Data sharing in neuroscience

Data sharing is one of most important challenge in several scientific fields and it has already given good results in genomic and proteomic analysis. Also neuroscience should benefit from data sharing, in particular from functional magnetic resonance imaging (fMRI) data sharing. This technique is used to map functional region of brain that are monitored and recorded in resting or working state. The entire map of functionally tuned regions in the brain constitutes the connectome and it may help scientists to better understand brain physiology and functioning. Michael Milham and his group of psychiatry at the New York University propose to other scientists worldwide to share their images of functional magnetic resonance in order to dispose more samples to analyze and compare. Indeed, even if these images have been generated in uncoordinated manner and with different purposes, data sharing could be extremely useful. Thus, they proposed the 1000 Functional Connectomes Project in which they wanted to collect data from fMRI. More than 35 centers decided to have part in this project, shared the images of more than 1400 volunteers, and deposited them into an open access database. Applying analytic and computational methods to evaluate and aggregate shared data, Milham and coworkers demonstrated a universal architecture of functional connections in the resting human brain. Furthermore, they highlighted the consistent loci of variability between individuals and centers and the brain region for which age and gender emerged as significant determinants. This study was published on PNAS Journal in 2010. Other follow-up studies will be necessary to validate the results described here. For instance, the information collected in the Functional Connectomes database could be used to build normative maps of functional system in the brain, as well as to interpret laboratory test results, thus using this method for a clinical application. The Functional Connectomes project is continuously growing and their supporters and creators encourage all groups involved in neuroscience imaging to share their data. This collaborative effort will give important scientific result because of the synergistic effect of data sharing: indeed, data that are brought together can be much more than the sum of the parts. Based on that, data sharing could be crucial also in other medical disciplines where imaging may explain biological processes. Of course, specific software will be necessary to effectively manage the huge amount of data derived from data sharing and the computational biologist will be fundamental in the laboratory. In conclusion, sharing data and computational analysis have become milestones in several field of science, and we are sure that this collaboration will give a significant contribution in scientific advances.

Addgene, a tool to share reagents

Plasmids are the most important tool in molecular biology for many reasons. Firstly, they make possible to produce proteins or portions of proteins in whatever system, from bacteria to mammalian, by cloning techniques. In order to share vectors and plasmid a novel system has been set up. Addgene is a no profit repository in which is possible to deposit your plasmids, as well as to request what you are looking for. You need to be registered -for institutions is free- and you can have access to the database. There, you can find plasmids previously described in published paper with all the information required to use them –resistance, length, host- Otherwise, you can decide to share your plasmid and using such as a deposit allows you to save much time and money. Indeed, you can re-address scientists who ask you the reagent to Addgene, without loosing time in packaging and shipment. In the Addgene website you can also find some enthusiastic opinions from important scientists who decided to use this system. We hope that similar organization will arise for other reagents, for instance cellular lines or antibodies not yet available on the market, in order to maximize the scientific advances.

Imaging data sharing

Imaging technologies become every day more important in scientific world. Several times in this blog we have talked about the advances of microscopy, fluorescence detection and in general imaging. Now we would like to analyze some problems related to data sharing. In 2008, the Journal of Cell Biology started the JBC Data Viewer, an online repository for original images in life sciences. The novelty of this tool is the possibility to preserve and share some information about instruments used, acquisition settings, image size and resolution. All these information are important to critically evaluate the data published. Indeed, the JBC Data Viewer collects only images previously published in scientific literature. Of course, such as a tool is extremely useful also because JBC Data Viewer is free for charge and authors have access to original data for viewing, simple measurement and review. This system doesn’t allow the download of original data and sophisticated image analysis and querying tools are not included in this application.

What are the main problems associated to the generation of a common repository of images? Every new platform must solve the basic problem of accessing the data contained in PFFs. Many commercially available microscope formats store their data in common formats, such as TIFF, DF5 or other formats that most software tools can read. In contrast, there is not an agreement about the metadata files and often data produced from competing companies are not compatible between them. For this reason, the standardization is required by all scientific community. Standards for biological imaging must be supported and developed, and once they are valuable for scientific discovery and data sharing, the community must demand the support of these formats in the commercial platforms.The challenge for software manufacturers is to find out an universal format that makes possible a data sharing in real time. It should be important to share not only final and published data but also the original images in order to better understand what has been the process to produce and correct the images self. The repository must be public and free for charges as in the case of JBC Data Viewer and the action must be concerted between public institutions, funding bodies and manufacturers. The final goal is quite easy to understand: scientific data founded by public money of non profit charities must be publicly available. Thus, in conclusion we hope that this repository will be soon available in order to continue the scientific advances also in the imaging field.

Online peer review

Last year, a scientist from the Ecole Polytechnique Federale de Lausanne (Swiss) proposed and patented a computerized method to perform online revision process for publications. This system allows an interactive peer review: authors submit their paper and automatically the best peer reviewers are contacted in order to immediately evaluate the work with high competence. Then, authors and reviewers can discuss and talk as in an on- line forum. Referees still are anonymous during this change, but their names will be appeared in the final publication. Thus, major transparency is guaranteed and also scientific quality is improved. All papers that have been positively judged by referees should be published, and readers should give their feedback. Indeed, the number of downloads and visits of the paper is calculated and the article metrics is the parameter used to determine the interest associated with a novel publication. Authors of the best rated works on primary research are invited to submit a follow up publication for broader public. This novel online revision process will be speed the procedure to publish and will solve at least in part the impact factor problem, that often interferes and delays the scientific advance.

Novel nomenclature system in botanic

The general rule to assign a name to novel plant species is to publish the name self on printed journal, in order to guarantee the immutability of the publication. In the modern era, electronic journals make possible a faster data sharing between scientists and also botanic must use these systems. Thus, for the first time four novel plants have been named and described in an article appeared in the Plos One journal, available only on-line.
The, authors printed 10 copies and distributed them to some libraries around the world in order to correctly follow the rule of the international code of botanical nomenclature and get their paper published. Even if the overall story is not so revolutionary, for the first time it has been possible a tempestive communication of data to other scientists. Furthermore, all scientists have been able to reach this paper, because it’s more probable that institutes buy an electronic journal rather the printed one. After the botanical example, also the international commission of zoological nomenclature started an updating process and positively considered the opportunity to open to the electronic journals. In all cases, we are sure that “verba volant, scripta manent” and printed copies allowed us reading experiments performed hundreds years ago.

Electronic Lab Notebook

An Electronic Lab Notebook (ELN) is a software program designed to substitute paper lab books. Scientists and technicians to note their experimental results, protocols, observations and so on use such tool. What is the advantage despite using paper notebooks, currently broadly diffused in research labs?
ELN has been studied, as an interface in which is possible to collect huge amount of data, derived from several instruments. It’s possible to manage chromatograms, spectra, calculations, and statistics by using only one software. To this purpose, ELN must to be flexible and have an out of the box configuration in order to be customized in respect to scientific exigencies of scientists. Several scientists can simultaneously use the same ELN and all lab members can add their data; thus, a broad vision of overall laboratory workflow is always updated. This point is really important for big groups, where more than ten people work together and data sharing is not so easy for different reasons, such as failure of communications or lack of time. ELN may help scientists at this point, allowing better communications between them and facilitating data traceability inside the laboratory.

An immediate advantage of this global vision ensured by ELN is the perfect planning and managing of experiments: what has been already done is always updated and what still to be done may be recorded, saving money and time. ELN allows scientists sharing experimental information and raw data, even if they work in different places around the world. Real time data sharing is fundamental to collaborate in a productive and efficient manner. Of course, in this context security is a must. ELN has been set up in order to satisfy all requirements to prevent unauthorized changes without substantial collusion of otherwise independent personnel. Furthermore, giving their use in pharmaceutical industry ELN is expected to comply FDA regulation about software validation.
In particular, FDA is concerned with system integrity and falsification avoidance to guarantee correctness of scientific and pharmaceutical production. Good laboratory procedures and Good manufacturing procedure may require ELN to store and classify data, making ELN a fundamental tool also in quality control assurance. Indeed, ELN may be directly connected to instruments, such as pHmeter, refrigerator or balances and record calibration data. In this way, validation sheets are directly filled without further work of scientists.
Last but not least, ELN allows saving space, because it is paperless. Traditional lab notebooks and files folders need a lot of space to be stored, while it is really easier to back up an IT notebook. What are some of the best ELNs on the market today? Check out Sciency ELN at www.ruro.com/sciency. In conclusion, ELN will be an essential tool in all labs within few years and global science will be a reality!

Ten years after the Human Genome Project

The Human Genome Project started ten years ago, with the challenging promise to sequence the whole genome and definitively understand all genetic secrets.
Two astonishing –but also scientifically interesting- surprises were presented to scientists of all countries: firstly only few genes are present in the genome, and this number -20000- is not so different from those of other species; secondarily, the major portion of DNA has regulatory functions rather than encoding significance. Thus, human genome sequencing has generated a lot of further questions about the mechanism of expression tuning. In 1960s Jacob and Monod demonstrated the presence of gene regulator in prokaryotic organisms, such as E. Coli; only few years ago we obtained the confirmation of this presence also in the human genome and numerous gaps have to be filled to reach a comprehensive understanding of molecular mechanism in cells. Epigenetic studies, microRNAs identification and gene expression analysis will help to gain a complete overview of human genome regulation, in addition to gene sequencing. Moreover, the Proteome Project will continue to clarify how proteins are involved in cellular life. Fortunately, a lot of open questions still be unsolved, and a lot of work has to be done by scientists worldwide.

The IntOGen interface

Sometimes, 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.

Application of molecular biology to medicine

Modern medicine is based on evidence. Despite few years ago, physicians based their diagnosis and therapies on their previous experiences, now clinical trials, approved protocols and worldwide accepted treatment help physicians to make the better choice for their patients. To reach this important goal, molecular medicine gave a big contribution. Molecular medicine is a novel branch of medicine in which molecular biology or biochemistry techniques are usually used to accomplish exams and screening or diagnose the diseases. Molecular biology labs have worked as research and development department to improve protocols or set up novel methodologies at the beginning just to be used for research purposes, then applied to diagnosis. For instance, we could focus our attention on the polymerase chain reaction, namely the PCR.
This techniques has been developed to produce DNA portion in vitro and has quickly revolutionized molecular biology, allowing cloning, sequencing and in general gene manipulation. The improved type of PCR, the real time PCR is now currently used in modern hospital to detect certain diseases, such as recidivate leukemia in patients’ blood or gene signature in familial diseases. Other important tools which have found a good application in diagnosis are the monoclonal/ polyclonal antibodies. Several techniques employed antibodies to detect proteins in cellular lysates through western blotting, or directly in whole cells, through the immuno-chemistry and molecular imaging. As well as, it’s also possible to purify small amount of native protein through immuno-precipitation and so on. Antibodies are really largely used in biochemistry labs and some techniques are applied also in diagnostic labs.
For instance, we can talk about the ELISA assay, normally used to quantify serum proteins or cell sorting analysis, in which some antibodies that specifically recognize surface proteins are used to separate different kind of cells. Finally, also cellular biology gave important results in modern medicine. The capability to culture in vitro cellular populations changes the therapeutic opportunity for a lot of diseases. For instance, now it’s possible to select healthy cellular population in leukemic patient, propagate it in vitro and then draft it, reducing in this way several problems of rejection and immuno-suppressive events. We can continue to talk about other examples of molecular, biochemical or cellular protocols that have found a great application in clinics. This overview strongly confirms how scientific advances are important because they have an immediate benefit on modern medicine and as a consequence on the human life. It’s important to remember that not only good protocols, but also good quality of science and good data management and reporting are two further parameters to improve modern medicine, but this is the topic for another post!!!