Functional interaction between the estrogen receptor and CTF1: analysis of the vitellogenin gene B1 promoter in yeast.

Eukaryotic gene expression depends on a complex interplay between the transcriptional apparatus and chromatin structure. We report here a yeast model system for investigating the functional interaction between the human estrogen receptor (hER) and CTF1, a member of the CTF/NFI transcription factor family. We show that a CTF1-fusion protein and the hER transactivate a synthetic promoter in yeast in a synergistic manner. This interaction requires the proline-rich transactivation domain of CTF1. When the natural estrogen-dependent vitellogenin B1 promoter is tested in yeast, CTF1 and CTF1-fusion proteins are unable to activate transcription, and no synergy is observed between hER, which activates the B1 promoter, and these factors. Chromatin structure analysis on this promoter reveals positioned nucleosomes at -430 to -270 (+/-20 bp) and at -270 to - 100 (+/-20 bp) relative to the start site of transcription. The positions of the nucleosomes remain unchanged upon hormone-dependent transcriptional activation of the promoter, and the more proximal nucleosome appears to mask the CTF/NFI site located at - 101 to -114. We conclude that a functional interaction of hER with the estrogen response element located upstream of a basal promoter occurs in yeast despite the nucleosomal organization of this promoter, whereas the interaction of CTF1 with its target site is apparently precluded by a nucleosome.

Interaction of a discrete breather with a lattice junction

We study the scattering of a moving discrete breather (DB) on a junction in a Fermi-Pasta-Ulam chain consisting of two segments with different masses of the particles. We consider four distinct cases: (i) a light-heavy (abrupt) junction in which the DB impinges on the junction from the segment with lighter mass, (ii) a heavy-light junction, (iii) an up mass ramp in which the mass in the heavier segment increases continuously as one moves away from the junction point, and (iv) a down mass ramp. Depending on the mass difference and DB characteristics (frequency and velocity), the DB can either reflect from, or transmit through, or get trapped at the junction or on the ramp. For the heavy-light junction, the DB can even split at the junction into a reflected and a transmitted DB. The latter is found to subsequently split into two or more DBs. For the down mass ramp the DB gets accelerated in several stages, with accompanying radiation (phonons). These results are rationalized by calculating the Peierls-Nabarro barrier for the various cases. We also point out implications of our results in realistic situations such as electron-phonon coupled chains.

LEVERAGING SANDBOX IMMERSIVE 3D VIRTUAL WORLDS TO DEVELOP DO-IT- YOURSELF TEACHING GAMES: IMPLEMENTATION TO MARKETING CASE STUDY TEACHING IN SECOND LIFE

Games are powerful and engaging. On average, one billion people spend at least 1 hour a day playing computer and videogames. This is even more true with the younger generations. Our students have become the < digital natives >, the < gamers >, the < virtual generation >. Research shows that those who are most at risk for failure in the traditional classroom setting, also spend more time than their counterparts, using video games. They might strive, given a different learning environment. Educators have the responsibility to align their teaching style to these younger generation learning styles. However, many academics resist the use of computer-assisted learning that has been "created elsewhere". This can be extrapolated to game-based teaching: even if educational games were more widely authored, their adoption would still be limited to the educators who feel a match between the authored games and their own beliefs and practices. Consequently, game-based teaching would be much more widespread if teachers could develop their own games, or at least customize them. Yet, the development and customization of teaching games are complex and costly. This research uses a design science methodology, leveraging gamification techniques, active and cooperative learning theories, as well as immersive sandbox 3D virtual worlds, to develop a method which allows management instructors to transform any off-the-shelf case study into an engaging collaborative gamified experience. This method is applied to marketing case studies, and uses the sandbox virtual world of Second Life. -- Les jeux sont puissants et motivants, En moyenne, un milliard de personnes passent au moins 1 heure par jour jouer à des jeux vidéo sur ordinateur. Ceci se vérifie encore plus avec les jeunes générations, Nos étudiants sont nés à l'ère du numérique, certains les appellent des < gamers >, d'autres la < génération virtuelle >. Les études montrent que les élèves qui se trouvent en échec scolaire dans les salles de classes traditionnelles, passent aussi plus de temps que leurs homologues à jouer à des jeux vidéo. lls pourraient potentiellement briller, si on leur proposait un autre environnement d'apprentissage. Les enseignants ont la responsabilité d'adapter leur style d'enseignement aux styles d'apprentissage de ces jeunes générations. Toutefois, de nombreux professeurs résistent lorsqu'il s'agit d'utiliser des contenus d'apprentissage assisté par ordinateur, développés par d'autres. Ceci peut être extrapolé à l'enseignement par les jeux : même si un plus grand nombre de jeux éducatifs était créé, leur adoption se limiterait tout de même aux éducateurs qui perçoivent une bonne adéquation entre ces jeux et leurs propres convictions et pratiques. Par conséquent, I'enseignement par les jeux serait bien plus répandu si les enseignants pouvaient développer leurs propres jeux, ou au moins les customiser. Mais le développement de jeux pédagogiques est complexe et coûteux. Cette recherche utilise une méthodologie Design Science pour développer, en s'appuyant sur des techniques de ludification, sur les théories de pédagogie active et d'apprentissage coopératif, ainsi que sur les mondes virtuels immersifs < bac à sable > en 3D, une méthode qui permet aux enseignants et formateurs de management, de transformer n'importe quelle étude de cas, provenant par exemple d'une centrale de cas, en une expérience ludique, collaborative et motivante. Cette méthode est appliquée aux études de cas Marketing dans le monde virtuel de Second Life.

Slow dynamis in the 3D gonihedric model

We provide analytical evidence of stochastic resonance in polarization switching vertical-cavity surface-emitting lasers (VCSELs). We describe the VCSEL by a two-mode stochastic rate equation model and apply a multiple time-scale analysis. We were able to reduce the dynamical description to a single stochastic differential equation, which is the starting point of the analytical study of stochastic resonance. We confront our results with numerical simulations on the original rate equations, validating the use of a multiple time-scale analysis on stochastic equations as an analytical tool.

Relativistic mean-field interaction with density-dependent meson-nucleon vertices based on microscopical calculations

Although ab initio calculations of relativistic Brueckner theory lead to large scalar isovector fields in nuclear matter, at present, successful versions of covariant density functional theory neglect the interactions in this channel. A new high-precision density functional DD-MEδ is presented which includes four mesons, σ, ω, δ, and ρ, with density-dependent meson-nucleon couplings. It is based to a large extent on microscopic ab initiocalculations in nuclear matter. Only four of its parameters are determined by adjusting to binding energies and charge radii of finite nuclei. The other parameters, in particular the density dependence of the meson-nucleon vertices, are adjusted to nonrelativistic and relativistic Brueckner calculations of symmetric and asymmetric nuclear matter. The isovector effective mass mp*−mn* derived from relativistic Brueckner theory is used to determine the coupling strength of the δ meson and its density dependence.

Charged-particle interaction with liquids: Ripplon excitations

We calculate the ripplon field contribution to the self-energy of an electron exterior to a liquid for planar and spherical geometries. We compare the full dielectric calculation of the electron-liquid interaction with the simpler alternative method consisting of integrating the electron-atom static-induced-dipolar potential through the whole liquid volume. We obtain good agreement between both methods for a nonpolar liquid such as 4He but differences up to 40% for a polar liquid such as water. We study the conditions under which the ripplon contribution to the self-energy is a perturbation. For an electron moving parallel to a planar liquid surface, we calculate the ripplon contribution to its stopping power. For this dynamical case, we conclude that the alternative method is a good approximation even for polar liquids.

TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.

A fast 3D approach for coronary MRA.

Two-dimensional (2D)-breath-hold coronary magnetic resonance angiography (MRA) has been shown to be a fast and reliable method to depict the proximal coronary arteries. Recent developments, however, allow for free-breathing navigator gated and navigator corrected three-dimensional (3D) coronary MRA. These 3D approaches have potential for improved signal-to-noise ratio (SNR) and allow for the acquisition of adjacent thin slices without the misregistration problems known from 2D approaches. Still, a major impediment of a 3D acquisition is the increased scan time. The purpose of this study was the implementation of a free-breathing navigator gated and corrected ultra-fast 3D coronary MRA technique, which allows for scan times of less than 5 minutes. Twelve healthy adult subjects were examined in the supine position using a navigator gated and corrected ECG triggered ultra-fast 3D interleaved gradient echo planar imaging sequence (TFE-EPI). A 3D slab, consisting of 20 slices with a reconstructed slice thickness of 1.5 mm, was acquired with free-breathing. The diastolic TFE-EPI acquisition block was preceded by a T2prep pre-pulse, a diaphragmatic navigator pulse, and a fat suppression pre-pulse. With a TR of 19 ms and an effective TE of 5.4 ms, the duration of the data acquisition window duration was 38 ms. The in-plane spatial resolution was 1.0-1.3 mm*1.5-1.9 mm. In all cases, the entire left main (LM) and extensive portions of the left anterior descending (LAD) and right coronary artery (RCA) could be visualized with an average scan time for the entire 3D-volume data set of 2:57 +/- 0:51 minutes. Average contiguous vessel length visualized was 53 +/- 11 mm (range: 42 to 75 mm) for the LAD and 84 +/- 14 mm (range: 62 to 112 mm) for the RCA. Contrast-to-noise between coronary blood and myocardium was 5.0 +/- 2.3 for the LM/LAD and 8.0 +/- 2.9 for the RCA, resulting in an excellent suppression of myocardium. We present a new approach for free-breathing 3D coronary MRA, which allows for scan times superior to corresponding 2D coronary MRA approaches, and which takes advantage of the enhanced SNR of 3D acquisitions and the post-processing benefits of thin adjacent slices. The robust image quality and the short average scanning time suggest that this approach may be useful for screening the major coronary arteries or identification of anomalous coronary arteries. J. Magn. Reson. Imaging 1999;10:821-825.

Positive impact of inhibitory Ly49 receptor-MHC class I interaction on NK cell development.

NK cells can kill MHC-different or MHC-deficient but not syngeneic MHC-expressing target cells. This MHC class I-specific tolerance is acquired during NK cell development. MHC recognition by murine NK cells largely depends on clonally distributed Ly49 family receptors, which inhibit NK cell function upon ligand engagement. We investigated whether these receptors play a role for the development of NK cells and provide evidence that the expression of a Ly49 receptor transgene on developing NK cells endowed these cells with a significant developmental advantage over NK cells lacking such a receptor, but only if the relevant MHC ligand was present in the environment. The data suggest that the transgenic Ly49 receptor accelerates and/or rescues the development of NK cells which would otherwise fail to acquire sufficient numbers of self-MHC-specific receptors. Interestingly, the positive effect on NK cell development is most prominent when the MHC ligand is simultaneously present on both hemopoietic and nonhemopoietic cells. These findings correlate with functional data showing that MHC class I ligand on all cells is required to generate functionally mature NK cells capable of reacting to cells lacking the respective MHC ligand. We conclude that the engagement of inhibitory MHC receptors during NK cell development provides signals that are important for further NK cell differentiation and/or maturation.

Sugarcane trash management assessed by the interaction of yield with soil properties

Currently, sugarcane plays an important global role, particularly with a view to alternative energy sources. Thus, in a sugarcane field of the mill Vale do Paraná S/A Álcool e Açúcar, Rubineia, São Paulo State, managed under two green cane harvest systems (cane trash left on and cane trash removed from the soil), Pearson and spatial correlations between the sugarcane yield (variety RB855035 in the third cut) and soil physical and chemical properties were studied to identify the property best correlated with stalk yield and the best harvest method. For this purpose, two geostatistical grids (121 sampling points on 1.30 ha) were installed on a eutrophic Red Argisol (homogeneous slope of 0.065 m m-1), in 2011, to determine the properties: stalk yield and sugarcane plant population, and soil resistance to penetration, gravimetric moisture, bulk density, and carbon stock, in the layers 0-0.20 and 0.20-0.40 m. The data were analyzed by descriptive, linear correlation and geostatistical analysis. In both treatments, the property stand density was best correlated with sugarcane yield (r = 0.725 in the trash mulching treatment - TM and r = 0.769 in the trash removal treatment - TR). However, in relation to the soil properties, bulk density (0-0.20 m) was best correlated (r = 0.305 in TM, r = 0.211 in TR). Similarly, from the spatial point of view, stand density was the property that best explained the sugarcane yield. However, in the TM treatment the density (0.20-0.40 m) was the only soil property spatially correlated with stalk yield. The carbon stock in the soil of the TM was 11.5 % higher than in the TR treatment. Results of the TM treatment were best, also with regard to soil management and conservation.

Real-time motion correction in navigator-gated free-breathing double-oblique submillimeter 3D right coronary artery magnetic resonance angiography.

RATIONALE AND OBJECTIVES: The purpose of this study was the investigation of the impact of real-time adaptive motion correction on image quality in navigator-gated, free-breathing, double-oblique three-dimensional (3D) submillimeter right coronary magnetic resonance angiography (MRA). MATERIALS AND METHODS: Free-breathing 3D right coronary MRA with real-time navigator technology was performed in 10 healthy adult subjects with an in-plane spatial resolution of 700 x 700 microm. Identical double-oblique coronary MR-angiograms were performed with navigator gating alone and combined navigator gating and real-time adaptive motion correction. Quantitative objective parameters of contrast-to-noise ratio (CNR) and vessel sharpness and subjective image quality scores were compared. RESULTS: Superior vessel sharpness, increased CNR, and superior image quality scores were found with combined navigator gating and real-time adaptive motion correction (vs. navigator gating alone; P < 0.01 for all comparisons). CONCLUSION: Real-time adaptive motion correction objectively and subjectively improves image quality in 3D navigator-gated free-breathing double-oblique submillimeter right coronary MRA.

Sensitivity of temperate grassland species to elevated atmospheric CO2 and the interaction with temperature and water stress

Selostus: Kohonneen hiilidioksidipitoisuuden, lämpötilan ja kuivuuden vaikutus nurmikasveihin