An experimental evaluation of a loop versus a reference design for two-channel microarrays

Motivation: Despite theoretical arguments that socalled "loop designs" of two-channel DNA microarray experiments are more efficient, biologists keep on using "reference designs". We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicor). In each case, both a loop and a reference design were performed using the same RNA preparations with the aim to study their relative efficiency. Results: The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example by taking log-ratios or including spot-effects, then the model will perform poorly. The first result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice

Activation of P2X(7) receptors stimulates the expression of P2Y(2) receptor mRNA in astrocytes cultured from rat brain.

Under pathological conditions brain cells release ATP at concentrations reported to activate P2X7 ionotropic receptor subtypes expressed in both neuronal and glial cells. In the present study we report that the most potent P2X7 receptor agonist BzATP stimulates the expression of the metabotropic ATP receptor P2Y2 in cultured rat brain astrocytes. In other cell types several kinds of stimulation, including stress or injury, induce P2Y2 expression that, in turn, is involved in different cell reactions. Similarly, it has recently been found that in astrocytes and astrocytoma cells P2Y2 sites can trigger neuroprotective pathways through the activation of several mechanisms, including the induction of genes for antiapoptotic factors, neurotrophins, growth factors and neuropeptides. Here we present evidence that P2Y2 mRNA expression in cultured astrocytes peaks 6 h after BzATP exposure and returns to basal levels after 24 h. This effect was mimicked by high ATP concentrations (1 mM) and was abolished by P2X7-antagonists oATP and BBG. The BzATP-evoked P2Y2 receptor up-regulation in cultured astrocytes was coupled to an increased UTP-mediated intracellular calcium response. This effect was inhibited by oATP and BBG and by P2Y2siRNA, thus supporting evidence of increased P2Y2 activity. To further investigate the mechanisms by which P2X7 receptors mediated the P2Y2 mRNA up-regulation, the cells were pre-treated with the chelating agent EGTA, or with inhibitors of mitogen-activated kinase (MAPK) (PD98059) or protein kinase C, (GF109203X). Each inhibitor significantly reduced the extent to which BzATP induced P2Y2 mRNA. Both BzATP and ATP (1 mM) increased ERK1/2 activation. P2X7-induced ERK1/2 phosphorylation was unaffected by pre-treatment of astrocytes with EGTA whereas it was inhibited by GF109203X. Phorbol-12-myristate-13-acetate (PMA), an activator of PKCs, rapidly increased ERK1/2 activation. We conclude that activation of P2X7 receptors in astrocytes enhances P2Y2 mRNA expression by a mechanism involving both calcium influx and PKC/MAPK signalling pathways

Le Elezioni Politiche 2013

Le elezioni politiche del 24 e 25 febbraio 2013 hanno sancito un forte cambiamento della struttura del sistema partitico italiano. In un contesto di altissima volatilità elettorale e di accelerato declino della partecipazione al voto, il sistema è divenuto sostanzialmente tripolare, dopo vent’anni di strutturazione e tenuta del bipolarismo. A questo esito hanno concorso da un lato l’erosione dei principali schieramenti politici che a partire dal novembre 2011 avevano sostenuto l’esperienza del governo Monti (nonché la deludente prova elettorale dello stesso Presidente del Consiglio uscente), e dall’altro lo straordinario successo del Movimento 5 stelle. Quest’ultimo, al primo test elettorale di livello nazionale, ha raccolto un risultato sorprendente, giungendo ad oltre un quarto dei voti validi. Siamo di fronte ad una parentesi momentanea dovuta all’effetto combinato di crisi economica e crisi politica, oppure le contraddizioni interne alla Seconda Repubblica l’hanno condotta effettivamente al suo crepuscolo? Come uscirà il sistema partitico italiano da questa nuova fase di destabilizzazione? Questo quarto Dossier CISE, che raccoglie contributi apparsi sul sito web del Cise prima e dopo le elezioni, fornisce una prima analisi del voto, presentando elaborazioni su dati aggregati, stime dei flussi elettorali, alcune prime analisi su dati di sondaggio, nonché una panoramica dei nuovi eletti e un’appendice ricca di tabelle e mappe riassuntive del risultato elettorale. Come i precedenti Dossier, si tratta di uno strumento prodotto rapidamente all’indomani del voto, con l’intento di suggerire primi spunti di interpretazione da approfondire in seguito, cercando di contribuire alla lettura di un risultato elettorale cruciale, in una delicata fase di cambiamento del sistema partitico italiano

A Spatial Analysis of the Italian Second Republic

Published in Journal of Legislative Studies, 2013, 19 (3), 328-350. https://doi.org/10.1080/13572334.2013.812342</p

Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue

<p>Abstract</p> <p>Background</p> <p>Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Particularly, faithful visualization methods are beneficial for revealing interesting gene expression patterns and functional relationships of coexpressed genes. Such screening helps to gain deeper insights into regulatory behavior and cellular responses, as will be discussed for expression data of developing barley endosperm tissue. For that purpose, high-throughput multidimensional scaling (HiT-MDS), a recent method for similarity-preserving data embedding, is substantially refined and used for (a) assessing the quality and reliability of centroid gene expression patterns, and for (b) derivation of functional relationships of coexpressed genes of endosperm tissue during barley grain development (0–26 days after flowering).</p> <p>Results</p> <p>Temporal expression profiles of 4824 genes at 14 time points are faithfully embedded into two-dimensional displays. Thereby, similar shapes of coexpressed genes get closely grouped by a correlation-based similarity measure. As a main result, by using power transformation of correlation terms, a characteristic cloud of points with bipolar sandglass shape is obtained that is inherently connected to expression patterns of pre-storage, intermediate and storage phase of endosperm development.</p> <p>Conclusion</p> <p>The new HiT-MDS-2 method helps to create global views of expression patterns and to validate centroids obtained from clustering programs. Furthermore, functional gene annotation for developing endosperm barley tissue is successfully mapped to the visualization, making easy localization of major centroids of enriched functional categories possible.</p

Isolation and characterization of canine perivascular stem/stromal cells for bone tissue engineering

For over 15 years, human subcutaneous adipose tissue has been recognized as a rich source of tissue resident mesenchymal stem/stromal cells (MSC). The isolation of perivascular progenitor cells from human adipose tissue by a cell sorting strategy was first published in 2008. Since this time, the interest in using pericytes and related perivascular stem/stromal cell (PSC) populations for tissue engineering has significantly increased. Here, we describe a set of experiments identifying, isolating and characterizing PSC from canine tissue (N = 12 canine adipose tissue samples). Results showed that the same antibodies used for human PSC identification and isolation are cross-reactive with canine tissue (CD45, CD146, CD34). Like their human correlate, canine PSC demonstrate characteristics of MSC including cell surface marker expression, colony forming unit-fibroblast (CFU-F) inclusion, and osteogenic differentiation potential. As well, canine PSC respond to osteoinductive signals in a similar fashion as do human PSC, such as the secreted differentiation factor NEL-Like Molecule-1 (NELL-1). Nevertheless, important differences exist between human and canine PSC, including differences in baseline osteogenic potential. In summary, canine PSC represent a multipotent mesenchymogenic cell source for future translational efforts in tissue engineering

Chi è arrivato primo?

2nonenoneR. D'ALIMONTE; VASSALLO SD'Alimonte, Roberto; Vassallo, S