Projective superspace and hyperkahler sigma models on cotangent bundles of Hermitian symmetric spaces

We review the projective-superspace construction of four-dimensional N=2 supersymmetric sigma models on (co)tangent bundles of the classical Hermitian symmetric spaces.Comment: 4 pages. Contribution to the proceedings of PASCOS-07, 2-7 July 2007, Imperial College, Londo

A longitudinal study of the human oropharynx microbiota over time reveals a common core and significant variations with self-reported disease

Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean=204.55 OTUs, sd=35.64), evenness (19.83, sd=9.74) and high temporal stability (mean Pearson’s correlation between samples of 0.52, sd=0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modelling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics

Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement

A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein–protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein–protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation–condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs

Dynamics, Conformational Entropy, and Frustration in Protein–Protein Interactions Involving an Intrinsically Disordered Protein Domain

Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of subnanosecond dynamics and the conformational entropy that it represents in protein–protein interactions involving IDPs. Using nuclear magnetic resonance side chain and backbone relaxation, stopped-flow kinetics, isothermal titration calorimetry, and computational studies, we have characterized the interaction between the globular TAZ1 domain of the CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2). We show that the TAZ1/TAD-STAT2 complex retains considerable subnanosecond motions, with TAD-STAT2 undergoing only a partial disorder-to-order transition. We report here the first experimental determination of the conformational entropy change for both binding partners in an IDP binding interaction and find that the total change even exceeds in magnitude the binding enthalpy and is comparable to the contribution from the hydrophobic effect, demonstrating its importance in the binding energetics. Furthermore, we show that the conformational entropy change for TAZ1 is also instrumental in maintaining a biologically meaningful binding affinity. Strikingly, a spatial clustering of very high amplitude motions and a cluster of more rigid sites in the complex exist, which through computational studies we found to overlap with regions that experience energetic frustration and are less frustrated, respectively. Thus, the residual dynamics in the bound state could be necessary for faster dissociation, which is important for proteins that interact with multiple binding partners

Intersubjectivity in action: studies in language and social interaction/ edited by Jan Lindström, Ritva Laury, Anssi Peräkylä, Marja-Leena Sorjonen.

Includes bibliographical references and index."Intersubjectivity is a precondition for human life - for social organization as well as for individual development and well-being. Through empirical examination of social interactions in everyday and institutional settings, the authors in this volume explore the achievement and maintenance of intersubjectivity. The contributions show how language codes and creates intersubjectivity, how interactants move towards shared understanding in interaction, how intersubjectivity is central to phenomena and experiences often considered merely individual, and how intersubjectivity evolves through learning. While the core methodology of the studies is Conversation Analysis, the volume highlights the advantages of using several methods to tackle intersubjectivity"--Intersubjectivity in action : an introduction / Marja-Leena Sorjonen, Anssi Peräkylä, Ritva Laury and Jan Lindström -- Organizing the "we" in interaction / Marja Etelämäki -- Definitely indefinite : negotiating intersubjective common group in everyday interaction in Finnish / Ritva Laury -- Directive turn design and intersubjectivity / Elizabeth Couper-Kuhlen, Marja Etelämäki and Marja-Leena Sorjonen -- On agency and affiliation in second assessments : German and Swedish opinion verbs in talk-in-interaction / Peter Auer and Jan Lindström -- Mirror-like address practice in Arabic-medium classroom interaction : managing social relations and intersubjectivity / Irina Piippo -- Brokering co-participants' volition in request and offer sequences / Katriina Harjunpää -- Decision-making in salesperson-customer interaction : establishing a common ground for obtaining commitment / Jarkko Niemi, Ellen Pullins and Timo Kaski -- Building an intersubjective understanding of the patient's mental suffering / Elina Weiste -- Shared understandings of the human-nature relationship in encounters with small wildlife / Mirka Rauniomaa, Tiina Keisanen and Pauliina Siitonen -- Extending sequences of other-initiated repair in Finnish conversation / Markku Haakana, Salla Kurhila, Niina Lilja and Marjo Savijärvi -- Co-presence during lapses : on "comfortable silences" in Finnish every day interaction / Anna Vatanen -- Achieving the intersubjectivity of sensorial practices : body, language, and the senses in tasting activities / Lorenza Mondada -- Emotion, psychophysiology, and intersubjectivity / Anssi Perakyla, Liisa Voutilainen, Melisa Stevanovic, Pentti Henttonen, Mikko Kahri, Maari Kivioja, Emmi Koskinen, Mikko Sams, and Niklas Ravaja -- Movement synchrony as a topic of empirical social interaction research / Melisa Stevanovic and Tommi Himberg -- Learning to request in interaction : intersubjective development of children's requesting between one and give years / Minna Laakso -- How an improvised scene emerges in theatre rehearsal : constructing coherence by recycling / Marjo Savijärvi and Laura Ihalainen -- Interactional reciprocity in human-dog interaction / Mika Simonen and Hannes Lohi.1 online resource