Homologues of archaeal rhodopsins in plants, animals and fungi: structural and functional predications for a putative fungal chaperone protein

AbstractThe microbial rhodopsins (MR) are homologous to putative chaperone and retinal-binding proteins of fungi. These proteins comprise a coherent family that we have termed the MR family. We have used modeling techniques to predict the structure of one of the putative yeast chaperone proteins, YRO2, based on homology with bacteriorhodopsins (BR). Availability of the structure allowed depiction of conserved residues that are likely to be of functional significance. The results lead us to predict an extracellular protein folding function and a transmembrane proton transport pathway. We suggest that protein folding is energized by a novel mechanism involving the proton motive force. We further show that MR family proteins are distantly related to a family of fungal, animal and plant proteins that include the human lysosomal cystine transporter (LCT) of man (cystinosin), mutations in which cause cystinosis. Sequence and phylogenetic analyses of both the MR family and the LCT family are reported. Proteins in both families are of the same approximate size, exhibit seven putative transmembrane α-helical spanners (TMSs) and show limited sequence similarity. We show that the LCT family arose by an internal gene duplication event and that TMSs 1–3 are homologous to TMSs 5–7. Although the same could not be demonstrated statistically for MR family members, homology with the LCT family suggests (but does not prove) a common evolutionary pathway. Thus, TMSs 1–3 and 5–7 in both LCT and MR family members may share a common origin, accounting for their shared structural features

Flux Stabilization in 6 Dimensions: D-terms and Loop Corrections

We analyse D-terms induced by gauge theory fluxes in the context of 6-dimensional supergravity models. On the one hand, this is arguably the simplest concrete setting in which the controversial idea of `D-term uplifts' can be investigated. On the other hand, it is a very plausible intermediate step on the way from a 10d string theory model to 4d phenomenology. Our specific results include the flux-induced one-loop correction to the scalar potential coming from charged hypermultiplets. Furthermore, we comment on the interplay of gauge theory fluxes and gaugino condensation in the present context, demonstrate explicitly how the D-term arises from the gauging of one of the compactification moduli, and briefly discuss further ingredients that may be required for the construction of a phenomenologically viable model. In particular, we show how the 6d dilaton and volume moduli can be simultaneously stabilized, in the spirit of KKLT, by the combination of an R symmetry twist, a gaugino condensate, and a flux-induced D-term.Comment: 24 pages, 1 figure v2:minor correction

Granular discharge and clogging for tilted hoppers

We measure the flux of spherical glass beads through a hole as a systematic function of both tilt angle and hole diameter, for two different size beads. The discharge increases with hole diameter in accord with the Beverloo relation for both horizontal and vertical holes, but in the latter case with a larger small-hole cutoff. For large holes the flux decreases linearly in cosine of the tilt angle, vanishing smoothly somewhat below the angle of repose. For small holes it vanishes abruptly at a smaller angle. The conditions for zero flux are discussed in the context of a {\it clogging phase diagram} of flow state vs tilt angle and ratio of hole to grain size

Stimulant Medication and Reading Performance

The study examined the sustained effects of methylphenidate on reading performance in a sample of 42 boys, ages 8 to 11, with attention deficit-hyperactivity disorder (ADHD). Two subgroups were formed based on the presence or absence of co-occurring conduct disorders. Subjects were selected on the basis of their positive response to methylphenidate as determined in a series of original medication trials (Forness, Cantwell, Swanson, Hanna, & Youpa, 1991). For the purpose of this study, subjects were placed on their optimal dose of medication for a 6-week period and then tested on measures of oral reading and reading comprehension equivalent to those used in the original trials, retested after a week without medication (placebo), then tested again the following week after return to medication. Only the subgroup with conduct disorders responded, and this response was limited to reading comprehension improvement in only those subjects who also demonstrated improvement in oral reading on original trials. No response differences were found between subjects with or without learning disabilities.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68569/2/10.1177_002221949202500205.pd

An efficient adaptive multigrid algorithm for predicting thin film flow on surfaces containing localised topographic features

Gravity-driven continuous thin film flow over a plane, containing well-defined single and grouped topographic features, is modelled as a Stokes flow using lubrication theory. The associated time dependent, nonlinear, coupled set of governing equations are solved using a Full Approximation Storage (FAS) Multigrid algorithm by employing automatic mesh adaptivity, the power efficiency and accuracy of which is demonstrated by comparing the results with corresponding global fine-mesh solutions.. These show that automatic grid refinement effectively restricts the use of find grids to regions of rapid flow development which, for flow over the topographies considered, includes the topography itself, the upstream Capillary ridge, downstream sure region, and the characteristic bow wave. It is shown that for the accurate solution of such flow problems, adaptive Multigridding offers increased flexibility together with a significant reduction in memory requirement. This is further demonstrated by solving the problem of transient flow over a trench topography, generated by a sinusoidally varying inlet condition

"The extreme penalty of the law": mercy and the death penalty as aspects of state power in colonial Nyasaland, c. 1903-47

Open access article.Capital punishment was the pinnacle of the colonial judicial system and its use of state violence, but has previously been neglected as a topic of historical research in Africa. This article is based on the case files and legal records of over 800 capital trials – predominantly for murder – dating between 1900 and 1947. It outlines the functioning of the legal system in Nyasaland and the tensions between “violence” and “humanitarianism” in the use and reform of the death penalty. Capital punishment was a political penalty as much as a judicial punishment, with both didactic and deterrent functions: it operated through mercy and the sparing of condemned lives as well as through executions. Mercy in Nyasaland was consistent with colonial political objectives and cultural values: it was decided not only on the facts of cases, but according to British conceptions of “justice”, “order”, “criminality”, and “African” behaviour. This article analyses the use of mercy in Nyasaland to provide a lens on the nature of colonial governance, and the tensions between African and colonial understandings of violence.Arts and Humanities Research Council (UK) and the Beit Fund, University of Oxfor

Grain Surface Models and Data for Astrochemistry

AbstractThe cross-disciplinary field of astrochemistry exists to understand the formation, destruction, and survival of molecules in astrophysical environments. Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. A broad consensus has been reached in the astrochemistry community on how to suitably treat gas-phase processes in models, and also on how to present the necessary reaction data in databases; however, no such consensus has yet been reached for grain-surface processes. A team of ∼25 experts covering observational, laboratory and theoretical (astro)chemistry met in summer of 2014 at the Lorentz Center in Leiden with the aim to provide solutions for this problem and to review the current state-of-the-art of grain surface models, both in terms of technical implementation into models as well as the most up-to-date information available from experiments and chemical computations. This review builds on the results of this workshop and gives an outlook for future directions

Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis

Pantoea ananatis is a highly versatile enterobacterium isolated from diverse environmental sources. The ecological diversity of this species may be attributed, in part, to the acquisition of mobile genetic elements. One such element is an Integrative and Conjugative Element (ICE). By means of in silico analyses the ICE elements belonging to a novel family, ICEPan, were identified in the genome sequences of five P. ananatis strains and characterized. PCR screening showed that ICEPan is prevalent among P. ananatis strains isolated from different environmental sources and geographic locations. Members of the ICEPan family share a common origin with ICEs of other enterobacteria, as well as conjugative plasmids of Erwinia spp. Aside from core modules for ICEPan integration, maintenance and dissemination, the ICEPan contain extensive non-conserved islands coding for proteins that may contribute toward various phenotypes such as stress response and antibiosis, and the highly diverse ICEPan thus plays a major role in the diversification of P. ananatis. An island is furthermore integrated within an ICEPan DNA repair-encoding locus umuDC and we postulate its role in stress-induced dissemination and/or expression of the genes on this island.This study was partially supported by the University of Pretoria Postdoctoral Fellowship Fund, National Research Foundation (NRF), the Tree Protection Co-operative Programme (TPCP), the NRF/Dept. of Science and Technology Centre of Excellence in Tree Health Biotechnology (CTHB), and the THRIP support program of the Department of Trade and Industry, South Africa, the department of Life Sciences and Facility Management of ZHAW, the Swiss Federal Office for Agriculture (BLW Fire Blight Research – Achilles), and the Swiss Secretariat for Education and Research (SBF C07.0038).http://www.frontiersin.org/Microbiologyam2016Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog