Validation of a multiplex reverse transcription and pre-amplification method using TaqMan(®) MicroRNA assays.

Since the discovery of microRNAs (miRNAs), different approaches have been developed to label, amplify and quantify miRNAs. The TaqMan(®) technology, provided by Applied Biosystems (ABIs), uses a stem-loop reverse transcription primer system to reverse transcribe the RNA and amplify the cDNA. This method is widely used to identify global differences between the expression of 100s of miRNAs across comparative samples. This technique also allows the quantification of the expression of targeted miRNAs to validate observations determined by whole-genome screening or to analyze few specific miRNAs on a large number of samples. Here, we describe the validation of a method published by ABIs on their web site allowing to reverse transcribe and pre-amplify multiple miRNAs and snoRNAs simultaneously. The validation of this protocol was performed on human muscle and plasma samples. Fast and cost efficient, this method achieves an easy and convenient way to screen a relatively large number of miRNAs in parallel

A Comparative Analysis of Genistein and Daidzein in Affecting Lipid Metabolism in Rat Liver

Effects of soy isoflavones, genistein and daidzein, on the hepatic gene expression profile and indices for lipid metabolism were compared in rats. In the first experiment (Expt. 1), animals were fed diets containing 2 g/kg of either genistein or daidzein, or a control diet free of isoflavone for 14 days. In the second experiment (Expt. 2), rats were fed diets containing 1 or 2 g/kg of genistein, or an isoflavone-free diet for 16 days. Genistein at a dietary level of 2 g/kg reduced serum triacylglycerol concentrations in both experiments, and serum concentrations of cholesterol in Expt. 2. However, daidzein at 2 g/kg did not decrease serum lipid concentrations in Expt. 1. A DNA microarray analysis in Expt. 1 showed that genistein was stronger than daidzein in affecting gene expression in liver, targeting many genes involved in lipid and carbohydrate metabolism. Detailed analyses indicated that alterations in the expression of genes related to lipogenesis are primarily responsible for the serum lipid-lowering effect of genistein. This notion was supported by analyses of the activity of enzymes involved in lipogenesis in Expt. 2

The Photon Dispersion as an Indicator for New Physics ?

We first comment on the search for a deviation from the linear photon dispersion relation, in particular based on cosmic photons from Gamma Ray Bursts. Then we consider the non-commutative space as a theoretical concept that could lead to such a deviation, which would be a manifestation of Lorentz Invariance Violation. In particular we review a numerical study of pure U(1) gauge theory in a 4d non-commutative space. Starting from a finite lattice, we explore the phase diagram and the extrapolation to the continuum and infinite volume. These simultaneous limits - taken at fixed non-commutativity - lead to a phase of broken Poincare symmetry, where the photon appears to be IR stable, despite a negative IR divergence to one loop.Comment: 8 pages, 4 figures, talk presented at the VI International Workshop on the Dark Side of the Universe, Leon (Mexico), June 1-6, 2010. References adde

Expression of microRNAs and target proteins in skeletal muscle of rats selectively bred for high and low running capacity

Impairments in mitochondrial function and substrate metabolism are implicated in the etiology of obesity and Type 2 diabetes. MicroRNAs (miRNAs) can degrade mRNA or repress protein translation and have been implicated in the development of such disorders. We used a contrasting rat model system of selectively bred high- (HCR) or low- (LCR) intrinsic running capacity with established differences in metabolic health to investigate the molecular mechanisms through which miRNAs regulate target proteins mediating mitochondrial function and substrate oxidation processes. Quantification of select miRNAs using the rat miFinder miRNA PCR array revealed differential expression of 15 skeletal muscles (musculus tibialis anterior) miRNAs between HCR and LCR rats (14 with higher expression in LCR; P < 0.05). Ingenuity Pathway Analysis predicted these altered miRNAs to collectively target multiple proteins implicated in mitochondrial dysfunction and energy substrate metabolism. Total protein abundance of citrate synthase (CS; miR-19 target) and voltage-dependent anion channel 1 (miR-7a target) were higher in HCR compared with LCR cohorts (~57 and ~26%, respectively; P < 0.05). A negative correlation was observed for miR-19a-3p and CS (r = 0.32, P = 0.015) protein expression. To determine whether miR-19a-3p can regulate CS in vitro, we performed luciferase reporter and transfection assays in C2C12 myotubes. MiR-19a-3p binding to the CS untranslated region did not change luciferase reporter activity; however, miR-19a-3p transfection decreased CS protein expression (∼70%; P < 0.05). The differential miRNA expression targeting proteins implicated in mitochondrial dysfunction and energy substrate metabolism may contribute to the molecular basis, mediating the divergent metabolic health profiles of LCR and HCR rat

The prospective kindergarten and elementary school teachers’ understanding of the ratio concept

Este artigo centra-se na compreensão que futuros educadores e professores dos primeiros anos de escolaridade evidenciam do conceito de razão. No estudo participaram 81 estudantes do 2º ano da Licenciatura em Educação Básica, de uma universidade portuguesa, aos quais foi aplicado um questionário, incidindo em quatro dimensões: significado de razão; usos do conceito de razão; representação simbólica de razão; e representações para explicação do conceito de razão. Em termos de resultados, as maiores frequências foram obtidas para a: ideia de razão como comparação/relação entre grandezas; crença em que o conceito de razão pode ser usado em contextos diversificados; crença em que pode ser representado através de operações envolvendo letras, números ou apenas os sinais das operações, quando é pedida a sua representação simbólica, e através de diagramas e representações gráficas, quando é solicitada a descrição da sua explicação. Estes resultados revelam fragilidades no conhecimento matemático dos estudantes, sobretudo no que se refere à definição do conceito de razão e às suas representações.This paper focuses on the prospective kindergarten and elementary school teachers’ understanding of the ratio concept. Eighty-one undergraduates preparing to become kindergarten and primary school teachers, in a Portuguese university, participated in the study. They answered to a questionnaire aiming at evaluating their understanding of the ratio concept based on four dimensions: meaning of ratio; use of the ratio concept; symbolic representations of ratio; and representations for explaining the ratio concept. As far as results are concerned, the highest frequencies were obtained for: the idea of ratio as a comparison/relationship between two magnitudes; the belief that this concept is used in several contexts; the belief that it can be represented through operations with letters, figures or operation signals, as in symbolic representations; and through diagrams and graphical representations, as in representations for explaining the ratio concept. The results show weaknesses in prospective teachers’ mathematical knowledge of ratio, namely with regard to its definition and representations.Este trabalho contou com o apoio de Fundos Nacionais através da FCT – Fundação para a Ciência e a Tecnologia no âmbito do projecto PEst-OE/CED/UI1661/2014 do CIEd-UM.info:eu-repo/semantics/publishedVersio

Stringy Space-Time Foam and High-Energy Cosmic Photons

In this review, I discuss briefly stringent tests of Lorentz-violating quantum space-time foam models inspired from String/Brane theories, provided by studies of high energy Photons from intense celestial sources, such as Active Galactic Nuclei or Gamma Ray Bursts. The theoretical models predict modifications to the radiation dispersion relations, which are quadratically suppressed by the string mass scale, and time delays in the arrival times of photons (assumed to be emitted more or less simultaneously from the source), which are proportional to the photon energy, so that the more energetic photons arrive later. Although the astrophysics at the source of these energetic photons is still not understood, and such non simultaneous arrivals, that have been observed recently, might well be due to non simultaneous emission as a result of conventional physics effects, nevertheless, rather surprisingly, the observed time delays can also fit excellently the stringy space-time foam scenarios, provided the space-time defect foam is inhomogeneous. The key features of the model, that allow it to evade a plethora of astrophysical constraints on Lorentz violation, in sharp contrast to other field-theoretic Lorentz-violating models of quantum gravity, are: (i) transparency of the foam to electrons and in general charged matter, (ii) absence of birefringence effects and (iii) a breakdown of the local effective lagrangian formalism.Comment: 26 pages Latex, 4 figures, uses special macros. Keynote Lecture in the International Conference "Recent Developments in Gravity" (NEB14), Ioannina (Greece) June 8-11 201

Prospective, Multicenter Phase II Trial of Non-Pegylated Liposomal Doxorubicin Combined with Ifosfamide in First-Line Treatment of Advanced/Metastatic Soft Tissue Sarcomas

Doxorubicin is a widely used anticancer agent as a first-line treatment for various tumor types, including sarcomas. Its use is hampered by adverse events, among which is the risk of dose dependence. The potential cardiotoxicity, which increases with higher doses, poses a significant challenge to its safe and effective application. To try to overcome these undesired effects, encapsulation of doxorubicin in liposomes has been proposed. Caelyx and Myocet are different formulations of pegylated (PLD) and non-pegylated liposomal doxorubicin (NPLD), respectively. Both PLD and NPLD have shown similar activity compared with free drugs but with reduced cardiotoxicity. While the hand–foot syndrome exhibits a high occurrence among patients treated with PLD, its frequency is notably reduced in those receiving NPLD. In this prospective, multicenter, one-stage, single-arm phase II trial, we assessed the combination of NPLD and ifosfamide as first-line treatment for advanced/metastatic soft tissue sarcoma (STS). Patients received six cycles of NPLD (50 mg/m2) on day 1 along with ifosfamide (3000 mg/m2 on days 1, 2, and 3 with equidose MESNA) administered every 3 weeks. The overall response rate, yielding 40% (95% CI: 0.29–0.51), resulted in statistical significance; the disease control rate stood at 81% (95% CI: 0.73—0.90), while only 16% (95% CI: 0.08–0.24) of patients experienced a progressive disease. These findings indicate that the combination of NPLD and ifosfamide yields a statistically significant response rate in advanced/metastatic STS with limited toxicity

Implementing virtual collaborative inquiry practises in a middle-school context

The aim of the present study was to investigate the challenges that relate to the implementation of virtual inquiry practises in middle school. The case was a school course in which a group of Finnish students (N = 14) and teachers (N = 7) completed group inquiries through virtual collaboration, using a web-based learning environment. The task was to accomplish a cross-disciplinary inquiry into cultural issues. The students worked mainly at home and took much responsibility for their course achievements. The investigators analysed the pedagogical design of the course and the content of the participants' interaction patterns in the web-based environment, using qualitative content analysis and social network analysis. The findings suggest that the students succeeded in producing distinctive cultural products, and both the students and the teachers adopted novel roles during the inquiry. The web-based learning environment was used more as a coordination tool for organizing the collaborative work than as a forum for epistemic inquiry. The tension between the school curriculum and the inquiry practises was manifest in the participants' discussions of the assessment criteria of the course.The aim of the present study was to investigate the challenges that relate to the implementation of virtual inquiry practises in middle school. The case was a school course in which a group of Finnish students (N = 14) and teachers (N = 7) completed group inquiries through virtual collaboration, using a web-based learning environment. The task was to accomplish a cross-disciplinary inquiry into cultural issues. The students worked mainly at home and took much responsibility for their course achievements. The investigators analysed the pedagogical design of the course and the content of the participants' interaction patterns in the web-based environment, using qualitative content analysis and social network analysis. The findings suggest that the students succeeded in producing distinctive cultural products, and both the students and the teachers adopted novel roles during the inquiry. The web-based learning environment was used more as a coordination tool for organizing the collaborative work than as a forum for epistemic inquiry. The tension between the school curriculum and the inquiry practises was manifest in the participants' discussions of the assessment criteria of the course.The aim of the present study was to investigate the challenges that relate to the implementation of virtual inquiry practises in middle school. The case was a school course in which a group of Finnish students (N = 14) and teachers (N = 7) completed group inquiries through virtual collaboration, using a web-based learning environment. The task was to accomplish a cross-disciplinary inquiry into cultural issues. The students worked mainly at home and took much responsibility for their course achievements. The investigators analysed the pedagogical design of the course and the content of the participants' interaction patterns in the web-based environment, using qualitative content analysis and social network analysis. The findings suggest that the students succeeded in producing distinctive cultural products, and both the students and the teachers adopted novel roles during the inquiry. The web-based learning environment was used more as a coordination tool for organizing the collaborative work than as a forum for epistemic inquiry. The tension between the school curriculum and the inquiry practises was manifest in the participants' discussions of the assessment criteria of the course.Peer reviewe

Discharge–calcium concentration relationships in streams of the Amazon and Cerrado of Brazil : soil or land use controlled

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of springer for personal use, not for redistribution. The definitive version was published in Biogeochemistry 105 (2011): 19-35, doi:10.1007/s10533-011-9574-2.Stream discharge-concentration relationships are indicators of terrestrial ecosystem function. Throughout the Amazon and Cerrado regions of Brazil rapid changes in land use and land cover may be altering these hydrochemical relationships. The current analysis focuses on factors controlling the discharge-calcium (Ca) concentration relationship since previous research in these regions has demonstrated both positive and negative slopes in linear log10discharge-log10Ca concentration regressions. The objective of the current study was to evaluate factors controlling stream discharge-Ca concentration relationships including year, season, stream order, vegetation cover, land use, and soil classification. It was hypothesized that land use and soil class are the most critical attributes controlling discharge-Ca concentration relationships. A multilevel, linear regression approach was utilized with data from 28 streams throughout Brazil. These streams come from three distinct regions and varied broadly in watershed size (106 ha) and discharge (10-5.7 to 103.2 m3 sec-1). Linear regressions of log10Ca versus log10discharge in 13 streams have a preponderance of negative slopes with only two streams having significant positive slopes. An ANOVA decomposition suggests the effect of discharge on Ca concentration is large but variable. Vegetation cover, which incorporates aspects of land use, explains the largest proportion of the variance in the effect of discharge on Ca followed by season and year. In contrast, stream order, land use, and soil class explain most of the variation in stream Ca concentration. In the current data set, soil class, which is related to lithology, has an important effect on Ca concentration but land use, likely through its effect on runoff concentration and hydrology, has a greater effect on discharge-concentration relationships.This research was supported by grant #’s NCC5-686 and NNG06GE88A of NASA’s Terrestrial Ecology Program as part of the Large-scale Biosphere-Atmosphere Experiment in Amazonia (LBA-ECO) project