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.

The binary expression system Q

The binary expression system is a strategy to finely tune the tragene expression in a model organism. One example of this kind of system is the GAL4- UAS in which the GAL4 gene is under control of the promoter of interest. GAL 4 activates a second exogenous gene bearing the upstream activating sequence. A possible alternative to the GAL 4- UAS system is the Q system. In this case the transcriptional activator QF binds to a specific sequence Q- UAS, as well as its repressor QS. QS in turn can be regulated by the addition of quinic acid into the medium and a further level of control can be added. A common application for this kind of systems is the generation of mosaic animals through the MARCM, the mosaic analysis with a repressible cell marker. In MARCM cell division is coupled to the repression of the gene of interest in one of daughter cells, allowing to study at the same time the effects of knock down in comparison to the normal cells. The Q system works in mammal cells but further improvements are necessary to use this tool for generating transgenic mice or for some application to zebrafish and worm, rather than flies.

The Baculovirus expression system

The Baculovirus expression system provides a versatile and reliable system for the production of recombinant proteins in insect cells. Although many different viruses belong to the Baculovirus family, the most widely used is Autographa Californica multiple capsid nucleopolyhedrovirus (AcMNPV) which can be propagated in Spodoptera Frugiperda (Sf), Trichoplusia Ni (Tn) insect cell lines.Virus genes are expressed in early, late and very late phases of infection: the early and late genes are largely related to the production of viral particles which then bud from the infected cell thus spreading infection to other cells. The very late genes that encode for polyhedrin and p10 are required for the production of the occlusion bodies containing the virus particle in the nucleus of the host cell. Both of these genes are under the control of strong promoter, but can be deleted from the virus genome without interfering with the production of infectious virus particles. As consequence, foreign genes can substitute the polyhedrin and p10 sequences to derive expression vector. This system has been largely used to express mammalian proteins because it guarantees, even if with some limitation, to obtain a correct folding. This capability is extremely important when active enzymes must be synthesized. Further advances in this techniques allow the production of all challenging proteins.

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.

Cellular role of chloride movement

The movement of ions inside or outside the cellular membrane is crucial to maintain pH homeostasis, the membrane potential and in some cases they may regulate also the entrance of drugs, glucose and so on. The chloride ion moves into the cells through the intracellular member of the chloride channels family. Chloride moves into the organelle lumen toward a positive electrical potential firstly generated by the activity of proton pump. This movement destroys the electrical potential and allows vesicle acidification. In contrast, it has been recently hypostasized and demonstrated that cells exploit proton gradient to concentrate the chloride ions inside the endosomes and other vesicles. A similar activity has been described in plants to accumulate the nitrate. Animal models that present knock out CLC proteins show kidneys symptoms or osteopetrosis, like in human disorders. These genetic alterations uncouple the chloride channels from proton exchangers. Therefore, the main characteristic of chloride movement is the coupling to proton movement. In yeast, chloride- proton coupling is related to multicopper oxidase synthesis, and a problem at ion movement levels generates immature oxidases. In conclusion, ions movement is functional not only for hydrolytes balance, but also to metabolism and biogenesis. Next works will clarify better these processes.

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.

The transcription factors map

Transcription factors are key regulator of gene expressing and are crucial for determining tissues and cells properties. Of course the transcription factors can accomplish their functions only when they are included into a well organized network. Thus, the scientific interest is now switched on the relationship and interaction between transcription factors. A recent paper published in Cell Journal describes the effort of a big international collaboration to generate a comprehensive map of physical interaction between mammal transcription factors. The transcription factors dataset were analyzed by the same strategies previously used to study for network alignment or biomarker discovery. Indeed, if we consider the key role of transcription factors into tissue regulation, they might be useful as a predictive tool of certain diseases, for instance tumors. In order to achieve this important goal, scientists classified the transcription factors expression profile from several human tissues. They used information from quantitative mRNAs analysis and the physical interaction network. They excluded all the interactions that were not highly correlated in one tissue; in this way they could classify tissue type according to embryonic germ layer. The next step will be the comparison between disease transcription networks and the normal ones in order to identify novel target for therapeutic approach.

The peer reviewed process

The peer review process is the current procedure to publish scientific papers. Scientists usually submit their work to the journal of choice and the editor in chief sends the manuscripts to a series of expert reviewers, able to critically judge the draft. This process should guarantee the goodness of science, but it doesn’t always correctly work.
Indeed, few months ago a group of scientists, studying stem cells, wrote an open letter tho major scientific journals, such as Science and Nature for instance. They complained the delay of data publications in their field. It seemed that some reviewers of rival institutions suggested long and useless experiments to scientists who submitted their paper, with the final aim of blocking publication and be able to publish as first. This behavior is partially explained by the financial interest related to stem cells research, because this topic is continuously funded by governmental institutions. Anyway, reviewers must be scientifically honest and this misconduct must be condemned.

In their open letter, scientists proposed to publish reviewers’ comment in the supplementary materials in order to guarantee the transparency of the process, but the main journals deny the allegations. Competition between journals is another aspect that has to be kept in account. Editors in chief are usually informed of the misconduct of reviewers – that is not limited to stem cells field, but is also present in other branches of research- but don’t want to loose the opportunity to get published the papers of reviewers self, that of course, before being reviewers, are important scientist.
An auspicable solution of this problem is more professionalism from editors and scientists, in oder to save science integrity. A second solution has been published on Plos Medicine journal: it may be possible to modify the impact factor criterion to evaluate the scientific value of a paper. Currently, the impact factor is considered when scientists choose the journal to whom submit the paper, or when job promotion has to be assigned. The impact factor is calculated on the number of citations that an article has gained: this indicates the visibility of the work in the scientific community. Dr Walker in her paper published on Plos Medicine proposed the article metrics as an alternative to impact factor criterion. The article metrics calculates how many times the article has been cited in other articles, reviews or blogs and how many times it has been viewed and downloaded. In this way, it shows the overall interest that the paper has created in the scientific community and not only the number of citations. Article metrics should make more transparent the publication process. In conclusion, for scientific advance it should be reasonable to set up the best system to conduct the publication process.

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.

Studying chemistry

Chemistry is an amazing and interesting subject, but a lot of students have big problem to learn it. In particular, some difficulties arise from abstract concepts that hardly can be applied to all days life. Scientists from the University of Pittsburg set up a digital library of virtual activities in order to teach general chemistry and engage students in problem solving. The Chemcollective collects a list of information for both teachers and students. In teacher section there are activities based on fundamental concepts of general chemistry, such as stoichiometry, acid- basis, molarity and so on, and some free courses on stoichiometry. The special feature is the application of knowledge on real world problems: the arsenic contamination in Bangladesh may cause water pollution. Students have to determine how various powders absorb arsenic, or whether water is safe to drink. Based on this principle, students are engaged and stimulated to find out practical chemical solutions to proposed issues. In student section, a deepen tutorial summarizes the most important chemical concepts with simple and clear definitions. Simulations of experiments are also available in this section. In summary, this project allows students to love chemistry and better understand its peculiarity.