Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans

The International Mouse Phenotyping Consortium (IMPC) (http://www.mousephenotype.org) will reveal the pleiotropic functions of every gene in the mouse genome and uncover the wider role of genetic loci within diverse biological systems. Comprehensive informatics solutions are vital to ensuring that this vast array of data is captured in a standardised manner and made accessible to the scientific community for interrogation and analysis. Here we review the existing EuroPhenome and WTSI phenotype informatics systems and the IKMC portal, and present plans for extending these systems and lessons learned to the development of a robust IMPC informatics infrastructure.     

Pidotimod: the state of art

Despite the use of antibiotics and vaccines, the frequency of respiratory tract infections is still high and these infections interest a wide range of patients, from children to aged people, including in particular these extreme categories because of the deficiency of their immune system, due to immaturity in the former case and to “immunosenescence” in the latter. For that reason immunostimulant drugs are getting more important to prevent and to attenuate infections. Pidotimod (3-L-pyroglutamyl-L-thiazolidine-4carboxylic acid) is a synthetic dipeptide with immunomodulatory properties. We reviewed studies conducted on different categories of patients, with particular attention on children and senile patients suffering from recurrent respiratory tract infections, associated, or not, with asthma or COPD. The outcomes considered are both clinical and laboratory parameters. The common end-point of these studies is that Pidotimod has an immunomodulatory activity which is able both to improve the clinical conditions of patients and to enhance and stimulate their immunity cells (lymphocytes but not only) functions acting on adaptive and innate immunity. Pidotimod is also able to increase the concentration of salivary IgA directed against bacteria; furthermore, it can modulate airway epithelial cells functions up-regulating the expression of toll-like receptors and acting on adhesion molecules. According to studies conducted on patients with atopic asthma, it seems that Pidotimod could affect T-lymphocytes balance with a possible addictional anti-allergic activity. Furthermore, it has been demonstrated an improvement of FEV1 and PEF in asthmatic patients treated with Pidotimod. Main clinical outcomes are the reduction of the number of infectious episodes, lesser severity of signs and symptoms and, consequently, a reduction in use of antibiotics and symptomatic drugs, less working and school days lost, less mortality and morbidity. The studies considered give positive results, confirming Pidotimod’s efficacy. Furthermore, many studies show a good safety profile of the drug, without recording serious adverse events and mutagenic potential, and a very low incidence of side effects. Pidotimod is also a more safe solution in patients subjected to vaccination, if compared to lyophilized polibacterial, which can’t be administered for thirty days before vaccination.     

Enzyme stabilization: state of the art

Enzyme stabilization is one of the most important fields in basic and applied enzymology. In basic enzymology, it is of particular relevance to understand enzyme stabilization principles first elucidating how and why the enzymes lose their biological activity and then deriving structure-stability relationships existing in enzymatic molecules. In applied enzymology, the most significant goal is to achieve useful compounds by biocatalysis. Enzymes are good catalysts in terms of high catalytic and specific activity with ability to function under mild conditions. However, they are not always ideal catalysts for practical applications because they are generally unstable and they inactivate rapidly through several mechanisms. In order to enhance enzyme stability, many strategies have been pursued in recent years. The present article is an attempt to provide detailed information about these strategies.     

Artificial insemination: the state of the art

The history of research into artificial insemination (AI) is over two centuries old and its commercial application now spans 75 years. It is appropriate to reflect on the contribution of this powerful method of gene dispersal. AI remains as one of the most important assisted reproductive technologies. The three cornerstones for its application are: it is simple, economical and successful. The importance of AI will be challenged in the next few decades. The remarkable progress made in other assisted reproductive technologies does have the potential to rapidly generate offspring. The challenge for any of these reproductive technologies to attain widespread use is to match AI in being simple, economical and successful. This review aims at capturing the salient advances in AI, the comparisons with natural mating and other reproductive technologies, and, whether the future of AI will be challenged. It predicts what the new horizon looks like and the role that AI will play in the overall reproductive technologies landscape.     

From spatially explicit ecological models to mean-field dynamics: The state of the art and perspectives

In this paper, we provide a brief review of the well-known methods of reducing spatially structured population models to mean-field models. First, we discuss the terminology of mean-field approximation which is used in the ecological modelling literature and show that the various existing interpretations of the mean-field concept can imply different meanings. Then we classify and compare various methods of reducing spatially explicit models to mean-field models: spatial moment approximation, aggregation techniques and the mean-field limit of IBMs. We emphasize the importance of spatial scales in the reduction of spatially explicit models and briefly consider the inverse problem of scaling up local ecological interactions from microscales to macroscales. Then we discuss the current challenges and limitations for construction of mean-field population models. We emphasize the need for developing mixed methods based on a combination of various reduction techniques to cope with the spatio-temporal complexity of real ecosystems including processes taking place on multiple time and space scales. Finally, we argue that the construction of analytically tractable mean-field models is becoming a key issue to provide an insight into the major mechanisms of ecosystem functioning. We complete this review by introducing the contributions to the current special issue of Ecological Complexity.     

The state of the art

Graphical representation of molecular and cellular features is a key form of communication in structural biology in which abstract symbols of an economical and visually appropriate kind, pseudo-color coding, and dynamic animations all play their parts. Accordingly, it should not be surprising that many structural biologists--like traditional biologists before them--are talented artists who also express themselves on "non-scientific" topics. This article illustrates the approaches of and pictures by several practicing scientist-artists-mainly, in this sampling, electron microscopists.     

Oscillating chemiluminescence systems: state of the art

Oscillating chemiluminescence (CL) was reported for the first time about 30 years ago. Since then several systems based on addition of a chemiluminescent reagent to a known oscillator system or based on the light emitting features of one component of the oscillating system, have been described. This information, scattered in the scientific literature, is compiled in the present paper. Several oscillating CL systems, including those based on Belousov–Zhabotinskii and Orban oscillators, or horseradish peroxidase‐catalyzed reactions, among others, are critically presented. The application of this type of oscillatory systems is also discussed, in analytical chemistry and for educational purposes. Copyright © 2010 John Wiley & Sons, Ltd.     

Phytosterol oxidation products: state of the art

This editorial gives an overview of the current status of the research on the phytosterol oxidation products. The most relevant studies on their in vivo origin, biological effects and analysis in foodstuffs and biological samples are critically reviewed, in order to give concluding remarks on and to establish the future research needs in this field.     

Structure prediction: The state of the art

A recent meeting to evaluate the state of the art of protein structure prediction saw progress on all fronts; for prediction methods based on comparative modeling or fold recognition, the progress was incremental, but in the case of ab initio structure prediction, some surprising successes were reported.     

Systematics of prokaryotes: the state of the art

The term taxonomy is often used synonymously with systematics but it should be regarded more as a specific part of the latter and comprises the orderly arrangements of (defined) units in addition to the nomenclature, i.e. labelling of these units defined by classification, and also identification of these units defined by classification and labeled by nomenclature. Similar to all biological disciplines, taxonomic approaches in microbiology aim at the establishment of a system that mirrors the “order in nature” as closely as possible with the ultimate goal to describe the whole evolutionary order back to the origin of life. With the recognition of molecular markers present in all organisms (here in particular the small subunit rRNAs, ssRNSs), the achievement of this goal has become more and more feasible and the generation of gene and increasing numbers of genome sequences allow nowadays the generation of large amounts of data and often a very detailed insight into the genetic potential of prokaryotes. The possibility to generate whole genome sequences in a very short period of time leads to a strong tendency to base the taxonomic system more and more on sequence data. However, a comprehensive understanding of all the information behind sequence data is lagging far behind their accumulation. Genes and genomes may (or may not) function only in a given “environment”, with the cell as basic entity for the display of this potential. Prokaryotic taxonomy still has its focus on the whole organism. In this context, natural selection drives evolution selecting the existing phenotypes and it is the phenotype that “exhibits” this process both in a given cellular and also environmental context. The term polyphasic taxonomy, which was coined almost 40 years ago and aimed at the integration of many levels of information (from molecular to ecological data) thereby allowing a more holistic view, should be revisited in the light of the enormous potential of the novel information associated with large data sets.