Protease footprinting reveals a surface on transcription factor TFIIB that serves as an interface for activators and coactivators.

Transcriptional stimulation by the model activator GAL4-VP16 (a chimeric protein consisting of the DNA-binding domain of the yeast activator GAL4 and the acidic activation domain of the herpes simplex virus protein VP16) involves a series of poorly understood protein-protein interactions between the VP16 activation domain and components of the RNA polymerase II general transcription machinery. One of these interactions is the VP16-mediated binding and recruitment of transcription factor TFIIB. However, TATA box-binding protein (TBP)-associated factors (TAFs), or coactivators, are required for this interaction to culminate in productive transcription complex assembly, and one such TAF, Drosophila TAF40, reportedly forms a ternary complex with VP16 and TFIIB. Due to TFIIB's central role in gene activation, we sought to directly visualize the surfaces of this protein that mediate formation of the ternary complex. We developed an approach called protease footprinting in which the broad-specificity proteases chymotrypsin and alkaline protease were used to probe binding of 32P-end-labeled TFIIB to GAL4-VP16 or TAF40. Analysis of the cleavage products revealed two regions of TFIIB protected by VP16 from protease attack, one of which overlapped with a region protected by TAF40. The close proximity of the VP16 and TAF40 binding sites on the surface of TFIIB suggests that this region could act as a regulatory interface mediating the effects of activators and coactivators on transcription complex assembly.

Molecular approaches to smart materials via interface recognition and conformationally switchable cavitands

In this thesis the molecular level design of functional materials and systems is reported. In the first part, tetraphosphonate cavitand (Tiiii) recognition properties towards amino acids are studied both in the solid state, through single crystal X-ray diffraction, and in solution, via NMR and ITC experiments. The complexation ability of these supramolecular receptors is then applied to the detection of biologically remarkable N-methylated amino acids and peptides using complex dynamic emulsions-based sensing platforms. In the second part, a general supramolecular approach for surface decoration with single-molecule magnets (SMMs) is presented. The self-assembly of SMMs is achieved through the formation of a multiple hydrogen bonds architecture (UPy-NaPy complexation). Finally we explore the possibility to impart auxetic behavior to polymeric material through the introduction of conformationally switchable monomers, namely tetraquinoxaline cavitands (QxCav). Their interconversion from a closed vase conformation to an extended kite form is studied first in solution, then in polymeric matrixes via pH and tensile stimuli by UV-Vis spectroscopy.

Estudo fenomenológico e numérico do escoamento estratificado óleo-água ondulado e com mistura na interface

Escoamentos bifásicos estão presentes em diversos processos naturais e industriais, como na indústria de petróleo. Podem apresentar-se em diferentes configurações topológicas, ou, padrões de escoamento, entre eles o escoamento estratificado ondulado e o estratificado com mistura na interface. Os escoamentos bifásicos estratificados óleo-água têm sido utilizados como uma forma conveniente de evitar a formação de emulsões de água em óleo em oleodutos e possuem uma ocorrência comum em poços de petróleo direcionais. Quando a onda interfacial ultrapassa determinado limite geométrico e cinemático, surge o fenômeno do entranhamento de gotas, representado por misturas entre as fases junto à interface que promovem um aumento na queda de pressão. Modelos têm sido apresentados pela literatura na tentativa de descrever o fenômeno do entranhamento de gotas. Neste trabalho é apresentada uma nova proposta de modelagem matemática unidimensional para o entranhamento de gotas com o objetivo de melhorar a previsão dos parâmetros envolvidos, em especial, da fração volumétrica de óleo e da queda de pressão bifásica. Também foi utilizada simulação numérica computacional, CFD (Computational Fluid Dynamics), com o uso de software comercial para obtenção dos valores dos parâmetros do escoamento estratificado ondulado óleo-água (fração volumétrica de óleo, queda de pressão, amplitude e comprimento da onda interfacial). Os resultados da modelagem fenomenológica para entranhamento e os de CFD foram comparados com bancos de dados experimentais. Os resultados em CFD mostram concordância com os resultados experimentais, tanto na análise qualitativa das propriedades geométricas das ondas interfaciais, quanto na comparação direta com os dados para fração volumétrica e queda de pressão. Os resultados numéricos da modelagem fenomenológica para fatores de entranhamento apresentam boa concordância com dados da literatura.

Enhancing the ratio of molecular ions to non-covalent compounds in the electrospray interface of LC-MS in quantitative analysis

A common problem encountered during the development of MS methods for the quantitation of small organic molecules by LGMS is the formation of non-covalently bound species or adducts in the electrospray interface. Often the population of the molecular ion is insignificant compared to those of all other forms of the analyte produced in the electrospray, making it difficult to obtain the sensitivity required for accurate quantitation. We have investigated the effects of the following variables: orifice potential, nebulizer gas flow, temperature, solvent composition and the sample pH on the relative distributions of ions of the types MH+, MNa+, MNH+, and 2MNa(+), where M represents a 4 small organic molecule: BAY 11-7082 ((E)-3-[4-methylphenylsulfonyl]-2-propenenitrile). Orifice potential, solvent composition and the sample pH had the greatest influence on the relative distributions of these ions, making these parameters the most useful for optimizing methods for the quantitation of small molecules.

Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface

Hydrophobins are small (similar to 100 aa) proteins that have an important role in the growth and development of mycelial fungi. They are surface active and, after secretion by the fungi, self-assemble into amphipathic membranes at hydrophobic/hydrophilic interfaces, reversing the hydrophobicity of the surface. In this study, molecular dynamics simulation techniques have been used to model the process by which a specific class I hydrophobin, SC3, binds to a range of hydrophobic/ hydrophilic interfaces. The structure of SC3 used in this investigation was modeled based on the crystal structure of the class II hydrophobin HFBII using the assumption that the disulfide pairings of the eight conserved cysteine residues are maintained. The proposed model for SC3 in aqueous solution is compact and globular containing primarily P-strand and coil structures. The behavior of this model of SC3 was investigated at an air/water, an oil/water, and a hydrophobic solid/water interface. It was found that SC3 preferentially binds to the interfaces via the loop region between the third and fourth cysteine residues and that binding is associated with an increase in a-helix formation in qualitative agreement with experiment. Based on a combination of the available experiment data and the current simulation studies, we propose a possible model for SC3 self-assembly on a hydrophobic solid/water interface.

Simulations of pendant drop formation of a viscoelastic liquid

A modified Volume-of-Fluid (VOF) numerical method is used to predict the dynamics of a liquid drop of a low viscosity dilute polymer solution, forming in air from a circular nozzle. Viscoelastic effects are represented using an Oldroyd-B model. Predicted drop shapes are compared with experimental observations. The main features, including the timing of the shape evolution and the bead-on-a-string effect, are well reproduced by the simulations. The results confirm published conclusions of the third author, that the deformation is effectively Newtonian until near the time of Newtonian pinch-off and that the elastic stress becomes large in the pinch region due to the higher extensional flow there.

Can an episodic approach to social identification account for identification as interaction between individual and collective identity work in an increasingly flexible and transient identity formation context?

A review of available literature suggests that social identification exists at the interface between individual and collective identity work. This poster proposes that it is the interaction between these two processes that leads a person to define themselves in terms of their membership of a particular social group. The poster suggests that identity work undertaken by the group (or ‘the creation of identities as widely understood signs with a set of rules and conventions for their use’, Schwalbe & Mason-Schrock, 1996, p.115), can be used by a person to inform their own individual identity work and, from this, the extent of alignment between their identity and the perceived identity of the group. In stable or internally-structured groups collective identity work may simply take the form of communication and preservation of dominant collective identities. However, in unstable, new or transitional groups, interaction between individual and collective identity work may be more dynamic, as both collective and individual identities are simultaneously codified, enacted and refined. To develop an understanding of social identification that is applicable in both stable and transitional social groups, it is useful to consider recent proposals that identification may occur cyclically as a series of discrete episodes (Ashforth, Harrison & Corley, 2008). This poster draws on the literature to present these suggestions in greater detail, outlining propositions for social identification that are relevant to transient as well as stable identity formation, supported by suggestion of how episodes of social identification may lead to a person identifying with a group.

H-induced platelet and crack formation in hydrogenated epitaxial Si/Si0.98 B0.02 /Si structures

An approach to transfer a high-quality Si layer for the fabrication of silicon-on-insulator wafers has been proposed based on the investigation of platelet and crack formation in hydrogenated epitaxialSi/Si0.98B0.02/Si structures grown by molecular-beam epitaxy. H-related defect formation during hydrogenation was found to be very sensitive to the thickness of the buried Si0.98B0.02 layer. For hydrogenated Si containing a 130nm thick Si0.98B0.02 layer, no platelets or cracking were observed in the B-doped region. Upon reducing the thickness of the buried Si0.98B0.02 layer to 3nm, localized continuous cracking was observed along the interface between the Si and the B-doped layers. In the latter case, the strains at the interface are believed to facilitate the (100)-oriented platelet formation and (100)-oriented crack propagation.

Spectrum of morphological and visual changes due to vitreomacular interface disorders encountered in a large consecutive cohort of patients

Aim: Identify the incidence of vitreomacular traction (VMT) and frequency of reduced vision in the absence of other coexisting macular pathology using a pragmatic classification system for VMT in a population of patients referred to the hospital eye service. Methods: A detailed survey of consecutive optical coherence tomography (OCT) scans was done in a high-throughput ocular imaging service to ascertain cases of vitreomacular adhesion (VMA) and VMT using a departmental classification system. Analysis was done on the stages of traction, visual acuity, and association with other macular conditions. Results: In total, 4384 OCT scan episodes of 2223 patients were performed. Two hundred and fourteen eyes had VMA/VMT, with 112 eyes having coexisting macular pathology. Of 102 patients without coexisting pathology, 57 patients had VMT grade between 2 and 8, with a negative correlation between VMT grade and number of Snellen lines (r= -0.61717). There was a distinct cutoff in visual function when VMT grade was higher than 4 with the presence of cysts and sub retinal separation and breaks in the retinal layers. Conclusions: VMT is a common encounter often associated with other coexisting macular pathology. We estimated an incidence rate of 0.01% of VMT cases with reduced vision and without coexisting macular pathology that may potentially benefit from intervention. Grading of VMT to select eyes with cyst formation as well as hole formation may be useful for targeting patients who are at higher risk of visual loss from VMT.

Building better relationships workshop: An intervention fostering identity formation and interpersonal development in middle adolescents

The aim of this study was to further knowledge development concerning the formation of a sense of identity and intimacy. This study drew on the growing recognition by many researchers in the psychosocial development field of the need to target interventions at the interface of the development of identity and intimacy. The specific aim of the study was to address the question of whether it would be possible to develop intervention procedures for fostering identity and intimacy exploration and development. Using both qualitative and quantitative measurements, the results appeared to clearly support an affirmative answer to this question. A total of sixty-three middle adolescent students from an urban, public high school participated in this study. Twenty-nine participants in the treatment group and 34 participants in the comparison group were pre- and post tested on measures of identity and intimacy. Participants in this study consisted of multiethnic, urban youth that presented themselves for relationship counseling. Repeated measures analysis of variance's (RMANOVA's), used to evaluate the impact of the intervention on the quantitative measures of identity and intimacy exploration, clearly supported the efficacy of the intervention. In addition, the findings also provided tentative support for the view that the increase in exploration that results from entering a period of active exploration is associated with a “loosening” of commitment. Finally, the findings of this study also contributed to the empirical knowledge-base about procedures for intervening with respect to the process of intimacy development. More specifically, both the qualitative and quantitative findings of this study began to shed some light on the potential impact of exploration for interpersonal insight as that as a process for fostering intimacy development. ^

Ultrasonic measurement of anisotropic reflectivity from Water-Phenolic CE Interface

In this contribution, we experimentally test the effects of azimuth and tilt angle on the acoustic reflectivity of a liquid- anisotropic solid interface. For this study, we are using a large source transducer, and acquired data for samples with different tilt angles. We use Phenolic CE material, which is known to have orthorhombic symmetry. Our results show that changes of the tilt angle produce important variations on the reflectivity that are larger as the tilt increases. The most remarkable feature is the change of the critical angle with the azimuth, which shows a larger spread for larger tilts. The spectral components of the acquired waveforms also show characteristic features linked to the location of the critical angle, we particularly observed a drop in the peak frequency. These observations suggest that care must be taken about the interpretation and inversion of observed incidence and azimuth dependent seismic reflectivities and critical angles in obtaining information on a formation's anisotropy. Zip archive contains four segy files: - LAB_TI00, is not tilted sample in contact with water, - LAB_TI30, is 30degrees tilted sample in contact with water, - LAB_TI45, is 45 degrees tilted sample in contact with water, - LAB_TI90, is 90 degrees tilted sample in contact with water.

Nanoporous InP: anodic formation and growth mechanism in aqueous electrolytes

Porous layers can be formed electrochemically on (100) oriented n-InP substrates in aqueous KOH. A nanoporous layer is obtained underneath a dense near-surface layer and the pores appear to propagate from holes through the near-surface layer. In the early stages of the anodization transmission electron microscopy (TEM) clearly shows individual porous domains that appear to have a square-based pyramidal shape. Each domain appears to develop from an individual surface pit which forms a channel through this near-surface layer. We suggest that the pyramidal structure arises as a result of preferential pore propagation along the <100> directions. AFM measurements show that the density of surface pits increases with time. Each of these pits acts as a source for a pyramidal porous domain. When the domains grow, the current density increases correspondingly. Eventually the domains meet, forming a continuous porous layer, the interface between the porous and bulk InP becomes relatively flat and its total effective surface area decreases resulting in a decrease in the current density. Current-time curves at constant potential exhibit a peak and porous layers are observed to form beneath the electrode surface. The density of pits formed on the surface increases with time and approaches a plateau value. Porous layers are also observed in highly doped InP but are not observed in wafers with doping densities below ~5 × 1017 cm-3. Numerical models of this process have been developed invoking a mechanism of directional selectivity of pore growth preferentially along the <100> lattice directions. Manipulation of the parameters controlling these curves shows that the fall-off in current is controlled by the rate of diffusion of electrolyte through the pore structure with the final decline in current being caused by the termination of growth at the pore tips through the formation of passivating films or some other irreversible modification of the pore tips.

AuxAg1-x alloy seeds: A way to control growth, morphology and defect formation in Ge nanowires

Germanium (Ge) nanowires are of current research interest for high speed nanoelectronic devices due to the lower band gap and high carrier mobility compatible with high K-dielectrics and larger excitonic Bohr radius ensuing a more pronounced quantum confinement effect [1-6]. A general way for the growth of Ge nanowires is to use liquid or a solid growth promoters in a bottom-up approach which allow control of the aspect ratio, diameter, and structure of 1D crystals via external parameters, such as precursor feedstock, temperature, operating pressure, precursor flow rate etc [3, 7-11]. The Solid-phase seeding is preferred for more control processing of the nanomaterials and potential suppression of the unintentional incorporation of high dopant concentrations in semiconductor nanowires and unrequired compositional tailing of the seed-nanowire interface [2, 5, 9, 12]. There are therefore distinct features of the solid phase seeding mechanism that potentially offer opportunities for the controlled processing of nanomaterials with new physical properties. A superior control over the growth kinetics of nanowires could be achieved by controlling the inherent growth constraints instead of external parameters which always account for instrumental inaccuracy. The high dopant concentrations in semiconductor nanowires can result from unintentional incorporation of atoms from the metal seed material, as described for the Al catalyzed VLS growth of Si nanowires [13] which can in turn be depressed by solid-phase seeding. In addition, the creation of very sharp interfaces between group IV semiconductor segments has been achieved by solid seeds [14], whereas the traditionally used liquid Au particles often leads to compositional tailing of the interface [15] . Korgel et al. also described the superior size retention of metal seeds in a SFSS nanowire growth process, when compared to a SFLS process using Au colloids [12]. Here in this work we have used silver and alloy seed particle with different compositions to manipulate the growth of nanowires in sub-eutectic regime. The solid seeding approach also gives an opportunity to influence the crystallinity of the nanowires independent of the substrate. Taking advantage of the readily formation of stacking faults in metal nanoparticles, lamellar twins in nanowires could be formed.

Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite

Most ice in nature forms because of impurities which boost the exceedingly low nucleation rate of pure supercooled water. However, the microscopic details of ice nucleation on these substances remain largely unknown. Here, we have unraveled the molecular mechanism and the kinetics of ice formation on kaolinite, a clay mineral playing a key role in climate science. We find that the formation of ice at strong supercooling in the presence of this clay is about 20 orders of magnitude faster than homogeneous freezing. The critical nucleus is substantially smaller than that found for homogeneous nucleation and, in contrast to the predictions of classical nucleation theory (CNT), it has a strong two-dimensional character. Nonetheless, we show that CNT describes correctly the formation of ice at this complex interface. Kaolinite also promotes the exclusive nucleation of hexagonal ice, as opposed to homogeneous freezing where a mixture of cubic and hexagonal polytypes is observed.

Étude exploratoire auprès de médecins des effets perçus d’une formation corps / esprit fondée sur les pratiques du Sensible

Résumé: Les pratiques du Sensible sont des pratiques d’accompagnement formatives et soignantes. Elles permettent d’apprendre comment l’expérience du corps et de son mouvement interne conduit au développement de la conscience et de la présence à soi ainsi qu’à l’autre, des qualités enviables pour des professionnelles et professionnels de la relation d’aide du secteur de la santé. Dans ces pratiques, le corps joue un rôle central à travers quatre types d’intervention : la thérapie manuelle, la gymnastique sensorielle, l’introspection sensorielle et l’entretien verbal à propos de l’expérience corporelle. Selon Large (2009), une qualité de présence particulière se construit chez les participantes et le participant aux pratiques du Sensible. Selon lui, ceux-ci se rapprochent de leur intériorité, parviennent à verbaliser à autrui ce qu’ils ressentent et en arrivent à poser des actions qui expriment ce qu’ils deviennent. Large (2009) constate qu’ils acquièrent de la stabilité, de l’adaptabilité et de l’autonomie. À la fois plus affirmatifs, ils gagnent aussi en proximité à l’autre. Bois (2007) note un changement de représentation lié aux idées, aux valeurs, à l’image de soi et au rapport perceptif à soi. Une chercheure et des chercheurs constatent un changement de conception de la santé (Duval, 2010; Laemmlin-Cencig et Humpich, 2009). À notre connaissance, il n’y a pas eu d’étude antérieure concernant l’influence des pratiques du Sensible auprès de médecins. Nous avons exploré, le cas échéant, comment une formation aux pratiques du Sensible, suivie par des médecins, a modifié leur rapport à leur corps, à leur propre santé, à leur conception de la santé, à la qualité de leur présence à eux-mêmes, aux autres professionnelles et professionnels et aux patientes et patients. Des entretiens semi-structurés d’une durée de 90 à 105 minutes ont été effectués auprès de six médecins français (cinq femmes et un homme) ayant été formés aux pratiques du Sensible entre 2005 et 2012. Deux types d’entretiens à visée compréhensive (Kaufmann, 2011) et d’explicitation (Vermersch, 2010; 2012) ont été réalisés. Des informations ont aussi été recueillies sur la formation et les activités professionnelles des participantes et du participant. Deux démarches d’analyse ont été utilisées, entre autres pour vérifier la cohérence des résultats et augmenter la rigueur de notre projet. Notre première démarche d’analyse a été conçue à partir de deux méthodes : au départ avec l’analyse thématique et par la suite une analyse avec les catégories conceptualisantes afin de déboucher sur une théorisation ancrée. La deuxième démarche d’analyse a consisté à créer une liste de vingt-six phénomènes présents pour la majorité des entretiens suite à des discussions tenues avec notre équipe de direction. Selon nos résultats, suite à la formation aux pratiques du Sensible, les cinq participantes témoignent d’une plus grande proximité et attention à leur corps et d’une meilleure écoute de celui-ci. Cet ancrage corporel de leur présence les informe davantage sur leur mode de vie et d’existence. Il en ressort ainsi des prises de conscience importantes grâce auxquelles les participantes font des choix nouveaux pour une vie plus cohérente et recentrée sur leur intériorité. Par le fait même, elles récupèrent leur pouvoir sur leur vie comme sur leur santé. En outre, parmi les six médecins, quatre ont modifié leur conception de la santé. Celle-ci s’est en effet élargie pour inclure de nouveaux éléments, dont la qualité du rapport à soi et l’accordage entre le corps et la pensée. Le corps semble être une voie souterraine à partir de laquelle se sont réalisées des transformations dans la personne, comme si le corps devenait une interface ayant des effets sur plusieurs facettes de la personne. Ces transformations semblent avoir une influence sur la manière dont celle-ci exerce sa profession, comme si un savoir-être renouvelé de la personne transformait son savoir-faire au sein de sa pratique. Au plan de la qualité de la présence aux autres, il est rapporté que les relations professionnelles se sont améliorées pour la majorité des participantes. Des transformations personnelles semblent avoir eu des effets sur leurs relations professionnelles. Par exemple, tous témoignent d’une meilleure qualité de présence et de disponibilité aux patientes et patients. La plupart signalent l’apprentissage d’une juste distance thérapeutique et, en même temps, d’une relation plus singulière avec chaque patiente et patient. Nous constatons par notre analyse que la relation aux patientes et patients est modifiée aux plans de la communication, du toucher et de l’écoute. Le parcours de formation des étudiantes et étudiants en médecine semble créer des conditions favorisant l’épuisement (Brazeau, Schroeder, Rovi et Boyd, 2010; Colombat, Altmeyer, Barruel, Bauchetet, Blanchard, Colombat et al., 2011; Ishak, Nikravesh, Lederer, Perry, Ogunyemi et Bernstein, 2013; Llera et Durante, 2014; Rodrigues, Albiges et Blanchard, 2012). Certaines interventions de type corps / esprit semblent pouvoir minimiser cet impact (Elder, Rakel, Heitkemper, Hustedde, Harazduk, Gerik et al., 2007; Hewson, Copeland, Mascha, Arrigain, Topol et Fox, 2006; Irving, Park-Saltzman, Fitzpatrick, Dobkin, Chen et Hutchinson, 2014; Maclaughlin, Wang, Noone, Liu, Harazduk, Lumpkin et al., 2011; Motz, Graves, Gross, Saunders, Amri, Harazduk et al., 2012; Rosenzweig, Reibel, Greeson, Brainard et Hojat, 2003; Saunders, Tractenberg, Chaterji, Amri, Harazduk, Gordon et al., 2007). Notre recherche démontre chez nos participantes et notre participant que la formation aux pratiques du Sensible leur a permis de faire plusieurs gains pour leur propre santé. Il semble qu’en amont des apprentissages liés à la profession médicale, une qualité de savoir-être puisse solidifier la personne, ses apprentissages et sa future pratique médicale. Les étudiantes et étudiants en médecine seraient ainsi mieux outillés pour traverser ce cursus de formation exigent et épuisant. Il serait intéressant de reprendre la recherche auprès d’un plus grand nombre de médecins ou d’étudiantes et étudiants en médecine afin d’y observer les éléments de théorisation répétitifs inclus dans la théorisation ancrée de notre étude exploratoire. Ainsi, selon les résultats, il serait alors plus aisé de promouvoir l’apprentissage expérientiel d’approches de type corps / esprit (dont les PS) dans les cursus universitaires en médecine.