Communications Biophysics

Contains reports on two research projects.United States Air Force (Contract AF19(604)-4112

An Inversion Disrupting FAM134B Is Associated with Sensory Neuropathy in the Border Collie Dog Breed

Sensory neuropathy in the Border Collie is a severe neurological disorder caused by the degeneration of sensory and, to a lesser extent, motor nerve cells with clinical signs starting between 2 and 7 months of age. Using a genome-wide association study approach with three cases and 170 breed matched controls, a suggestive locus for sensory neuropathy was identified that was followed up using a genome sequencing approach. An inversion disrupting the candidate gene FAM134B was identified. Genotyping of additional cases and controls and RNAseq analysis provided strong evidence that the inversion is causal. Evidence of cryptic splicing resulting in novel exon transcription for FAM134B was identified by RNAseq experiments. This investigation demonstrates the identification of a novel sensory neuropathy associated mutation, by mapping using a minimal set of cases and subsequent genome sequencing. Through mutation screening, it should be possible to reduce the frequency of or completely eliminate this debilitating condition from the Border Collie breed population

Reversible Fluorination of Graphene: towards a Two-Dimensional Wide Bandgap Semiconductor

We report the synthesis and evidence of graphene fluoride, a two-dimensional wide bandgap semiconductor derived from graphene. Graphene fluoride exhibits hexagonal crystalline order and strongly insulating behavior with resistance exceeding 10 G$\Omega$ at room temperature. Electron transport in graphene fluoride is well described by variable-range hopping in two dimensions due to the presence of localized states in the band gap. Graphene obtained through the reduction of graphene fluoride is highly conductive, exhibiting a resistivity of less than 100 k$\Omega$ at room temperature. Our approach provides a new path to reversibly engineer the band structure and conductivity of graphene for electronic and optical applications.Comment: 7 pages, 5 figures, revtex, to appear in PR

A novel role for proline- and acid-rich basic region leucine zipper (PAR bZIP) proteins in the transcriptional regulation of a BH3-only proapoptotic gene.

Proline- and acid-rich (PAR) basic region leucine zipper (bZIP) proteins thyrotroph embryonic factor (TEF), D-site-binding protein (DBP), and hepatic leukemia factor have been involved in neurotransmitter homeostasis and amino acid metabolism. Here we demonstrate a novel role for these proteins in the transcriptional control of a BH3-only gene. PAR bZIP proteins are able to transactivate the promoter of bcl-gS. This promoter is particularly responsive to TEF activation and is silenced by NFIL3, a repressor that shares the consensus binding site with PAR bZIP proteins. Consistently, transfection of TEF induces the expression of endogenous bcl-gS in cancer cells, and this induction is independent of p53. A naturally occurring variant of DBP (tDBP), lacking the transactivation domain, has been identified and shown to impede the formation of active TEF dimers in a competitive manner and to reduce the TEF-dependent induction of bcl-gS. Of note, treatment of cancer cells with etoposide induces TEF activation and promotes the expression of bcl-gS. Furthermore, blockade of bcl-gS or TEF expression by a small interfering RNA strategy or transfection with tDBP significantly reduces the etoposide-mediated apoptotic cell death. These findings represent the first described role for PAR bZIP proteins in the regulation of a gene involved in the execution of apoptosis

Dynamic Provenance for SPARQL Update

While the Semantic Web currently can exhibit provenance information by using the W3C PROV standards, there is a "missing link" in connecting PROV to storing and querying for dynamic changes to RDF graphs using SPARQL. Solving this problem would be required for such clear use-cases as the creation of version control systems for RDF. While some provenance models and annotation techniques for storing and querying provenance data originally developed with databases or workflows in mind transfer readily to RDF and SPARQL, these techniques do not readily adapt to describing changes in dynamic RDF datasets over time. In this paper we explore how to adapt the dynamic copy-paste provenance model of Buneman et al. [2] to RDF datasets that change over time in response to SPARQL updates, how to represent the resulting provenance records themselves as RDF in a manner compatible with W3C PROV, and how the provenance information can be defined by reinterpreting SPARQL updates. The primary contribution of this paper is a semantic framework that enables the semantics of SPARQL Update to be used as the basis for a 'cut-and-paste' provenance model in a principled manner.Comment: Pre-publication version of ISWC 2014 pape

Themed project case study: Quadruple tanks control with PLCs^†

A themed project based on the control of a quadruple tank rig using PLCs has been successfully carried out as part of the MSc in Advanced Control and Systems Engineering at the University of Manchester. The themed project involves ten students who address a single multivariable control challenge under the supervision of two academics and four PhD students. As every student is required to write their own MSc dissertation, the key point is the possibility of using different control techniques to be implemented on different hardware platforms. </jats:p

The influence of natural flow regimes on macroinvertebrate assemblages in a semiarid Mediterranean basin

The investigation of flow-ecology relationships constitutes the basis for the development of environmental flow criteria. The need to understand hydrology-ecology linkages in natural systems has increased owing to the prospect of climate change and flow regime management, especially in water-scarce areas such as Mediterranean basins. Our research quantified the macroinvertebrate community response at family, genus and species level to natural flow regime dynamics in freshwater streams of a Mediterranean semiarid basin (Segura River, SE Spain) and identified the flow components that influence the composition and richness of biotic assemblages. Flow stability and minimum flows were the principal hydrological drivers of macroinvertebrate assemblages, whereas the magnitude of average and maximum flows had a limited effect. Perennial stable streams were characterized by flow sensitive lotic taxa (Ephemeroptera, Plecoptera and Trichoptera) and intermittent streams by predominately lentic taxa (Odonata, Coleoptera, Heteroptera and Diptera). Relatively minor biological changes were recorded for intermediate flow regime classes along a gradient of flow stability. Seasonal variation and minimum flows are key hydrological components that need to be considered for river management and environmental flows in the Segura River basin and other Mediterranean basins. The anthropogenic modification of these parameters, due to both human activities and climate change, would probably lead to significant changes in the structure and composition of communities in perennial stable streams. This would be characterized by a reduction of flow sensitive Ephemeroptera, Plecoptera and Trichoptera taxa and an increase in more resilient Odonata, Coleoptera, Heteroptera and Diptera taxa. © 2012 John Wiley & Sons, Ltd

Bilepton contributions to the neutrinoless double beta decay in the economical 3-3-1 model

Possible contributions of the bilepton to the neutrinoless double beta $(\beta\beta)_{0\nu}$ decay in the economical 3-3-1 model are discussed. We show that the $(\beta\beta)_{0\nu}$ decay in this model is due to both sources--Majorana $_{L}$ and Dirac $_{D}$ neutrino masses. If the mixing angle between charged gauge bosons, the standard model $W$ and bilepton $Y$, is in range of the ratio of neutrino masses $_{L}/< M_{\nu}>_{D}$, both the Majorana and Dirac masses simultaneously give contributions dominant to the decay. As results, constraints on the bilepton mass are also given.Comment: 9 pages, 6 figure