Computing labs and Technology Classroom (ClTC) Initiative: A Model for Distributed Support

DePauw University is a small, liberal arts institution with 2200 undergraduate residential students and 222 faculty members, located in Greencastle, Indiana The challenges of supporting a campus with multiple and diverse facilities are further amplified by limited staff support resources. One of the strategies for addressing these challenges led to the formation of the Computing Labs and Technology Classrooms (CLTC) initiative. The CLTC recognizes and draws on the strengths of support specialists with a wide variety of professional training and experience, who regularly collaborate in the support and management of campus-wide labs and technology classrooms

Critical Casimir effect in classical binary liquid mixtures

If a fluctuating medium is confined, the ensuing perturbation of its fluctuation spectrum generates Casimir-like effective forces acting on its confining surfaces. Near a continuous phase transition of such a medium the corresponding order parameter fluctuations occur on all length scales and therefore close to the critical point this effect acquires a universal character, i.e., to a large extent it is independent of the microscopic details of the actual system. Accordingly it can be calculated theoretically by studying suitable representative model systems. We report on the direct measurement of critical Casimir forces by total internal reflection microscopy (TIRM), with femto-Newton resolution. The corresponding potentials are determined for individual colloidal particles floating above a substrate under the action of the critical thermal noise in the solvent medium, constituted by a binary liquid mixture of water and 2,6-lutidine near its lower consolute point. Depending on the relative adsorption preferences of the colloid and substrate surfaces with respect to the two components of the binary liquid mixture, we observe that, upon approaching the critical point of the solvent, attractive or repulsive forces emerge and supersede those prevailing away from it. Based on the knowledge of the critical Casimir forces acting in film geometries within the Ising universality class and with equal or opposing boundary conditions, we provide the corresponding theoretical predictions for the sphere-planar wall geometry of the experiment. The experimental data for the effective potential can be interpreted consistently in terms of these predictions and a remarkable quantitative agreement is observed.Comment: 30 pages, 17 figure

Leaf litter degradation in highly turbid transitional waters: preliminary results from litter-bag experiments in the Gironde Estuary

The rates of decomposition of oak (Quercus robur) leaves have been examined using litter bags in a very high turbidity macrotidal estuary, the Gironde Estuary (S.W. France). The first experiments show a marked decrease in the decomposition rate of oak leaves at the water-sediment interface (mud-contact: anoxic conditions, reduced physical fragmentation) in comparison to the water column. The results point out the impact of hydrodynamic conditions on leaf litter degradation in such fluvio-estuarine systems. Regarding the aquatic-terrestrial linkage, our observations suggest direct changes in leaf decomposition kinetics and then, a potential delay on the recycling and transport processes of coarse particulate organic matter, especially in a context of modification of the natural water flow, due to global and land use changes

Critical Casimir forces and adsorption profiles in the presence of a chemically structured substrate

Motivated by recent experiments with confined binary liquid mixtures near demixing, we study the universal critical properties of a system, which belongs to the Ising universality class, in the film geometry. We employ periodic boundary conditions in the two lateral directions and fixed boundary conditions on the two confining surfaces, such that one of them has a spatially homogeneous adsorption preference while the other one exhibits a laterally alternating adsorption preference, resembling locally a single chemical step. By means of Monte Carlo simulations of an improved Hamiltonian, so that the leading scaling corrections are suppressed, numerical integration, and finite-size scaling analysis we determine the critical Casimir force and its universal scaling function for various values of the aspect ratio of the film. In the limit of a vanishing aspect ratio the critical Casimir force of this system reduces to the mean value of the critical Casimir force for laterally homogeneous ++ and +- boundary conditions, corresponding to the surface spins on the two surfaces being fixed to equal and opposite values, respectively. We show that the universal scaling function of the critical Casimir force for small but finite aspect ratios displays a linear dependence on the aspect ratio which is solely due to the presence of the lateral inhomogeneity. We also analyze the order-parameter profiles at criticality and their universal scaling function which allows us to probe theoretical predictions and to compare with experimental data.Comment: revised version, section 5.2 expanded; 53 pages, 12 figures, iopart clas

Fertility, Living Arrangements, Care and Mobility

There are four main interconnecting themes around which the contributions in this book are based. This introductory chapter aims to establish the broad context for the chapters that follow by discussing each of the themes. It does so by setting these themes within the overarching demographic challenge of the twenty-first century – demographic ageing. Each chapter is introduced in the context of the specific theme to which it primarily relates and there is a summary of the data sets used by the contributors to illustrate the wide range of cross-sectional and longitudinal data analysed

Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway

The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al

Critical adsorption on curved objects

A systematic fieldtheoretic description of critical adsorption on curved objects such as spherical or rodlike colloidal particles immersed in a fluid near criticality is presented. The temperature dependence of the corresponding order parameter profiles and of the excess adsorption are calculated explicitly. Critical adsorption on elongated rods is substantially more pronounced than on spherical particles. It turns out that, within the context of critical phenomena in confined geometries, critical adsorption on a microscopically thin `needle' represents a distinct universality class of its own. Under favorable conditions the results are relevant for the flocculation of colloidal particles.Comment: 52 pages, 10 figure

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones

The versatile functions of the heat shock protein 70 (Hsp70) family of molecular chaperones rely on allosteric interactions between their nucleotide-binding and substrate-binding domains, NBD and SBD. Understanding the mechanism of interdomain allostery is essential to rational design of Hsp70 modulators. Yet, despite significant progress in recent years, how the two Hsp70 domains regulate each other's activity remains elusive. Covariance data from experiments and computations emerged in recent years as valuable sources of information towards gaining insights into the molecular events that mediate allostery. In the present study, conservation and covariance properties derived from both sequence and structural dynamics data are integrated with results from Perturbation Response Scanning and in vivo functional assays, so as to establish the dynamical basis of interdomain signal transduction in Hsp70s. Our study highlights the critical roles of SBD residues D481 and T417 in mediating the coupled motions of the two domains, as well as that of G506 in enabling the movements of the α-helical lid with respect to the β-sandwich. It also draws attention to the distinctive role of the NBD subdomains: Subdomain IA acts as a key mediator of signal transduction between the ATP- and substrate-binding sites, this function being achieved by a cascade of interactions predominantly involving conserved residues such as V139, D148, R167 and K155. Subdomain IIA, on the other hand, is distinguished by strong coevolutionary signals (with the SBD) exhibited by a series of residues (D211, E217, L219, T383) implicated in DnaJ recognition. The occurrence of coevolving residues at the DnaJ recognition region parallels the behavior recently observed at the nucleotide-exchange-factor recognition region of subdomain IIB. These findings suggest that Hsp70 tends to adapt to co-chaperone recognition and activity via coevolving residues, whereas interdomain allostery, critical to chaperoning, is robustly enabled by conserved interactions. © 2014 General et al

Identification and validation of a QTL influencing bitter pit symptoms in apple (Malus x domestica)

Bitter pit is one of the most economically important physiological disorders affecting apple fruit production, causing soft discrete pitting of the cortical flesh of the apple fruits which renders them unmarketable. The disorder is heritable; however, the environment and cultural practices play a major role in expression of symptoms. Bitter pit has been shown to be controllable to a certain extent using calcium sprays and dips; however, their use does not entirely prevent the incidence of the disorder. Previously, bitter pit has been shown to be controlled by two dominant genes, and markers on linkage group 16 of the apple genome were identified that were significantly associated with the expression of bitter pit symptoms in a genome-wide association study. In this investigation, we identified a major QTL for bitter pit defined by two microsatellite (SSR) markers. The association of the SSRs with the bitter pit locus, and their ability to predict severe symptom expression, was confirmed through screening of individuals with stable phenotypic expression from an additional mapping progeny. The data generated in this current study suggest a two gene model could account for the control of bitter pit symptom expression; however, only one of the loci was detectable, most likely due to dominance of alleles carried by both parents of the mapping progeny used. The SSR markers identified are cost-effective, robust and multi-allelic and thus should prove useful for the identification of seedlings with resistance to bitter pit using marker-assisted selection in apple breeding programs