Pipeline for macro- and microarray analyses

The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA.61561

Influence of coil geometry, supply conditions and nanoparticle heating properties on magnetic hyperthermia in mouse models

For in vivo magnetic hyperthermia tests, which are typically conducted on small animal models, one of the objectives is the design of alternating current (AC) magnetic field applicators able to guarantee an effective activation of magnetic nanoparticles (MNPs). During therapy application, it is critical to optimize heat deposition due to MNPs and minimize side effects in healthy tissues. For an accurate treatment planning, it is required to carefully select the geometry of the applicator coils and their location with respect to the body, as a function of the position and size of the tumour target region. Additionally, one should preliminary estimate the impact of experimental conditions on the MNP heating efficiency and thus on their capability to induce a temperature increase in tissues. Biophysical constraints have also to be taken into account in the choice of AC magnetic field parameters (frequency and amplitude), to avoid eddy current effects as much as possible. In this study, we present realistic simulations of preclinical tests on a mouse model, evaluating thermal response under various experimental conditions. We investigate different field applicator configurations, including helical, Helmholtz and pancake coils, while also analysing the role of the amplitude and frequency of the supply current, as well as of the type and administered dose of MNPs. The temperature increase in tissues, resulting from the heating effects due to AC magnetic field exposure and MNP activation, is calculated by means of in-house finite element models that solve the low -frequency electromagnetic field problem and the bioheat transfer equation. This in silico approach, which is applicable to any type of field applicators and MNPs, has been demonstrated to provide useful insights for the optimization of in vivo experiments, enabling the design of safer and more effective treatments

An Overview on ERAP Roles in Infectious Diseases

Endoplasmic reticulum (ER) aminopeptidases ERAP1 and ERAP2 (ERAPs) are crucial enzymes shaping the major histocompatibility complex I (MHC I) immunopeptidome. In the ER, these enzymes cooperate in trimming the N-terminal residues from precursors peptides, so as to generate optimal-length antigens to fit into the MHC class I groove. Alteration or loss of ERAPs function significantly modify the repertoire of antigens presented by MHC I molecules, severely affecting the activation of both NK and CD8+ T cells. It is, therefore, conceivable that variations affecting the presentation of pathogen-derived antigens might result in an inadequate immune response and onset of disease. After the first evidence showing that ERAP1-deficient mice are not able to control Toxoplasma gondii infection, a number of studies have demonstrated that ERAPs are control factors for several infectious organisms. In this review we describe how susceptibility, development, and progression of some infectious diseases may be affected by different ERAPs variants, whose mechanism of action could be exploited for the setting of specific therapeutic approaches

Changes in the bacterial community of soil from a neutral mine drainage channel

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments95CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP550240/2010-12012/05429-

Characterization of the core microbiota of the drainage and surrounding soil of a brazilian copper mine

The core microbiota of a neutral mine drainage and the surrounding high heavy metal content soil at a Brazilian copper mine were characterized by 16S rDNA pyrosequencing. The core microbiota of the drainage was dominated by the generalist genus Meiothermus. The soil samples contained a more heterogeneous bacterial community, with the presence of both generalist and specialist bacteria. Both environments supported mainly heterotrophic bacteria, including organisms resistant to heavy metals, although many of the bacterial groups identified remain poorly characterized. The results contribute to the understanding of bacterial communities in soils impacted by neutral mine drainage, for which information is scarce, and demonstrate that heavy metals can play an important role in shaping the microbial communities in mine environments384484489CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP550240/2010-12012/05429-

Le conoscenze in Física all'inizio dei corsi universitari in Italia

The article reports the results of an investigation on Italian university students concerning physics knowledge related to common sense schemes at the beginning of the university courses. The results of the diagnosis were communicated both to the students and to the teachers of the courses. The communication enabled the teachers, in the didactical practice, to pinpoint and discuss with the students the discrepancies between the scientific newtonian scheme and common sense scheme. A posttest, given at the end of the course, gives the indication that this practice is effective in inducing a change in the students ideas, notwithstanding the fact that no complete understanding of the scientific viewpoint is teached by the majority of students