Silent moments in education Granger, Colette
Silent moments in education,
c2011, 20111210, 2011, 2011-01-01, 2011-12-10
eBook
Silent Moments in Educationcombines autoethnography with psychoanalytic theory and critical discourse analysis in a unique consideration of the relations teachers and learners forge with knowledge, ...with ideas, and with one another.
Absolute quantification of macromolecules in single cells is critical for understanding and modeling biological systems that feature cellular heterogeneity. Here we show extremely sensitive and ...absolute quantification of both proteins and mRNA in single mammalian cells by a very practical workflow that combines proximity ligation assay (PLA) and digital PCR. This digital PLA method has femtomolar sensitivity, which enables the quantification of very small protein concentration changes over its entire 3-log dynamic range, a quality necessary for accounting for single-cell heterogeneity. We counted both endogenous (CD147) and exogenously expressed (GFP-p65) proteins from hundreds of single cells and determined the correlation between CD147 mRNA and the protein it encodes. Using our data, a stochastic two-state model of the central dogma was constructed and verified using joint mRNA/protein distributions, allowing us to estimate transcription burst sizes and extrinsic noise strength and calculate the transcription and translation rate constants in single mammalian cells.
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•Digital PLA protocol allows ultrasensitive protein quantification from single cells•Combination with digital PCR allows joint single-cell protein and mRNA measurements•Absolute mRNA and protein abundances measured jointly from single mammalian cells•Joint mRNA-protein data was used to build a two-step model of gene expression
A single-protein counting method called digital PLA was developed, allowing ultrasensitive measurement of absolute protein and mRNA copy numbers from single mammalian cells. Joint single-cell mRNA/protein measurements were then used to construct and validate a stochastic two-state model for transcription and translation of the gene CD147.
Lateral organ position along roots and shoots largely determines plant architecture, and depends on auxin distribution patterns. Determination of the underlying patterning mechanisms has hitherto ...been complicated because they operate during growth and division. Here, we show by experiments and computational modeling that curvature of the Arabidopsis root influences cell sizes, which, together with tissue properties that determine auxin transport, induces higher auxin levels in the pericycle cells on the outside of the curve. The abundance and position of the auxin transporters restricts this response to the zone competent for lateral root formation. The auxin import facilitator, AUX1, is up-regulated by auxin, resulting in additional local auxin import, thus creating a new auxin maximum that triggers organ formation. Longitudinal spacing of lateral roots is modulated by PIN proteins that promote auxin efflux, and pin2,3,7 triple mutants show impaired lateral inhibition. Thus, lateral root patterning combines a trigger, such as cell size difference due to bending, with a self-organizing system that mediates alterations in auxin transport.
Embryogenesis is the beginning of plant development, yet the cell fate decisions and patterning steps that occur during this time are reiterated during development to build the post-embryonic ...architecture. In Arabidopsis, embryogenesis follows a simple and predictable pattern, making it an ideal model with which to understand how cellular and tissue developmental processes are controlled. Here, we review the early stages of Arabidopsis embryogenesis, focusing on the globular stage, during which time stem cells are first specified and all major tissues obtain their identities. We discuss four different aspects of development: the formation of outer versus inner layers; the specification of vascular and ground tissues; the determination of shoot and root domains; and the establishment of the first stem cells.
EURO-CORDEX is an international climate downscaling initiative that aims to provide high-resolution climate scenarios for Europe. Here an evaluation of the ERA-Interim-driven EURO-CORDEX regional ...climate model (RCM) ensemble is presented. The study documents the performance of the individual models in representing the basic spatiotemporal patterns of the European climate for the period 1989–2008. Model evaluation focuses on near-surface air temperature and precipitation, and uses the E-OBS data set as observational reference. The ensemble consists of 17 simulations carried out by seven different models at grid resolutions of 12 km (nine experiments) and 50 km (eight experiments). Several performance metrics computed from monthly and seasonal mean values are used to assess model performance over eight subdomains of the European continent. Results are compared to those for the ERA40-driven ENSEMBLES simulations. The analysis confirms the ability of RCMs to capture the basic features of the European climate, including its variability in space and time. But it also identifies nonnegligible deficiencies of the simulations for selected metrics, regions and seasons. Seasonally and regionally averaged temperature biases are mostly smaller than 1.5 °C, while precipitation biases are typically located in the ±40% range. Some bias characteristics, such as a predominant cold and wet bias in most seasons and over most parts of Europe and a warm and dry summer bias over southern and southeastern Europe reflect common model biases. For seasonal mean quantities averaged over large European subdomains, no clear benefit of an increased spatial resolution (12 vs. 50 km) can be identified. The bias ranges of the EURO-CORDEX ensemble mostly correspond to those of the ENSEMBLES simulations, but some improvements in model performance can be identified (e.g., a less pronounced southern European warm summer bias). The temperature bias spread across different configurations of one individual model can be of a similar magnitude as the spread across different models, demonstrating a strong influence of the specific choices in physical parameterizations and experimental setup on model performance. Based on a number of simply reproducible metrics, the present study quantifies the currently achievable accuracy of RCMs used for regional climate simulations over Europe and provides a quality standard for future model developments.
Microplastics (MPs) have been found in all terrestrial, marine, and riparian environments, including remote regions. This implies that atmospheric transport is an important pathway when considering ...MP sources and global budgets. However, limited empirical data exist to aid in effective development and parameterization of MP atmospheric transport models. This study measured the atmospheric settling and horizontal drift velocities of various sizes and shapes of MPs in two specially designed settling columns using a laser Doppler anemometer. The settling velocities were generally lower than modeled values, while shape exerted the most significant influence on the rate of settling. Rather than conforming to well-established, power-law models, each class of MP exhibited a linear but different relationship between MP size and settling velocity, with markedly higher slopes for the spheres and cylinders as compared to the films and fibers. Shape also had a substantial influence on particle drift, with the fibers and films exhibiting the greatest horizontal motion, as suggestive of their changing orientation in response to particle interactions and fluid drag. As a consequence, microplastic particles identified within atmospheric deposition samples collected at a single point may derive from entirely different sources representing a wide range in transport distance.
Vascular calcification is associated with increased cardiovascular morbidity and mortality in patients with atherosclerosis, diabetes and chronic kidney disease. However, no viable treatments for ...this condition have been identified. This study aimed to determine whether farnesyl transferase inhibitors (FTIs) can reduce vascular calcification and the mechanism by which this reduction occurs.
We demonstrate that FTI-277 significantly inhibits phosphate-induced mineral deposition by vascular smooth muscle cells (VSMC) in vitro, prevents VSMC osteogenic differentiation, and increases mRNA expression of matrix Gla protein (MGP), an inhibitor of mineralization. FTI-277 increases Akt signaling in VSMC in short-term serum-stimulation assays and in long-term mineralization assays. In contrast, manumycin A has no effect on Akt signaling or mineralization. Co-incubation of VSMC with FTI-277 and SH6 (an Akt inhibitor) significantly reduces the inhibitory effect of FTI-277 on mineralization, demonstrating that FTI-277 inhibits calcification by activating Akt signaling. Over-expression of the constitutively active p110 sub-unit of PI3K in VSMC using adenovirus activates Akt, inhibits mineralization, suppresses VSMC differentiation and significantly enhances MGP mRNA expression. FTI-277 also inhibits phosphate-induced activation of caspase 3 and apoptosis of VSMC, and these effects are negated by co-incubation with SH6. Finally, using an ex vivo model of vascular calcification, we demonstrate that FTI-277 inhibits high phosphate-induced mineralization in aortic rings derived from rats with end-stage renal failure.
Together, these results demonstrate that FTI-277 inhibits VSMC mineral deposition by up-regulating PI3K/Akt signaling and preventing apoptosis, suggesting that targeting farnesylation, or Akt specifically, may have therapeutic potential for the prevention of vascular calcification.
A novel climate downscaling methodology that attempts to correct climate simulation biases is proposed. By combining an advanced statistical bias correction method with a dynamical downscaling it ...constitutes a hybrid technique that yields nearly unbiased, high‐resolution, physically consistent, three‐dimensional fields that can be used for climate impact studies. The method is based on a prior statistical distribution correction of large‐scale global climate model (GCM) 3‐dimensional output fields to be taken as boundary forcing of a dynamical regional climate model (RCM). GCM fields are corrected using meteorological reanalyses. We evaluate this methodology over a decadal experiment. The improvement in terms of spatial and temporal variability is discussed against observations for a past period. The biases of the downscaled fields are much lower using this hybrid technique, up to a factor 4 for the mean temperature bias compared to the dynamical downscaling alone without prior bias correction. Precipitation biases are subsequently improved hence offering optimistic perspectives for climate impact studies.
Key Points
Novel hybrid dynamical and statistical regional climate downscaling technique
Decreases substantially temperature and precipitation biases
Produces physically consistent unbiased 3D fields for climate impact models
Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including ...photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.
Tropospheric trace gas and aerosol pollutants have adverse effects on health, environment and climate. In order to quantify and mitigate such effects, a wide range of processes leading to the ...formation and transport of pollutants must be considered, understood and represented in numerical models. Regional scale pollution episodes result from the combination of several factors: high emissions (from anthropogenic or natural sources), stagnant meteorological conditions, kinetics and efficiency of the chemistry and the deposition. All these processes are highly variable in time and space, and their relative contribution to the pollutants budgets can be quantified with chemistry-transport models. The CHIMERE chemistry-transport model is dedicated to regional atmospheric pollution event studies. Since it has now reached a certain level a maturity, the new stable version, CHIMERE 2013, is described to provide a reference model paper. The successive developments of the model are reviewed on the basis of published investigations that are referenced in order to discuss the scientific choices and to provide an overview of the main results.
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