Protein Kinase A Regulates ATP Hydrolysis and Dimerization by a CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) Domain

Gating of the CFTRCl− channel is associated with ATP hydrolysis at the nucleotide-binding domains (NBD1, NBD2) and requires PKA (protein kinase A) phosphorylation of the R domain. The manner in which the NBD1, NBD2 and R domains of CFTR (cystic fibrosis transmembrane conductance regulator) interact to achieve a properly regulated ion channel is largely unknown. In this study we used bacterially expressed recombinant proteins to examine interactions between these soluble domains of CFTR in vitro. PKA phosphorylated a fusion protein containing NBD1 and R (NBD1–R–GST) on CFTR residues Ser-660, Ser-700, Ser- 712, Ser-737, Ser-768, Ser-795 and Ser-813. Phosphorylation of these serine residues regulated ATP hydrolysis by NBD1–R–GST by increasing the apparent Km for ATP (from 70 to 250 μM) and the Hill coefficient (from 1 to 1.7) without changing the Vmax. When fusion proteins were photolabelled with 8-azido- [α-32P]ATP, PKA phosphorylation increased the apparent kd for nucleotide binding and it caused binding to become co-operative. PKA phosphorylation also resulted in dimerization of NBD1– R–GST but not of R–GST, a related fusion protein lacking the NBD1 domain. Finally, an MBP (maltose-binding protein) fusion protein containing the NBD2 domain (NBD2–MBP) associated with and regulated the ATPase activity of PKA-phosphorylated NBD1–R–GST. Thus when the R domain in NBD1–R–GST is phosphorylated by PKA,ATP binding and hydrolysis becomes cooperative and NBD dimerization occurs. These findings suggest that during the activation of native CFTR, phosphorylation of the R domain by PKA can control the ability of the NBD1 domain to hydrolyse ATP and to interact with other NBD domains

Multivariate Operator-Self-Similar Random Fields

Multivariate random fields whose distributions are invariant under operator-scalings in both time-domain and state space are studied. Such random fields are called operator-self-similar random fields and their scaling operators are characterized. Two classes of operator-self-similar stable random fields $X=\{X(t), t \in \R^d\}$ with values in $\R^m$ are constructed by utilizing homogeneous functions and stochastic integral representations.Comment: 27 page

Infinite factorization of multiple non-parametric views

Combined analysis of multiple data sources has increasing application interest, in particular for distinguishing shared and source-specific aspects. We extend this rationale of classical canonical correlation analysis into a flexible, generative and non-parametric clustering setting, by introducing a novel non-parametric hierarchical mixture model. The lower level of the model describes each source with a flexible non-parametric mixture, and the top level combines these to describe commonalities of the sources. The lower-level clusters arise from hierarchical Dirichlet Processes, inducing an infinite-dimensional contingency table between the views. The commonalities between the sources are modeled by an infinite block model of the contingency table, interpretable as non-negative factorization of infinite matrices, or as a prior for infinite contingency tables. With Gaussian mixture components plugged in for continuous measurements, the model is applied to two views of genes, mRNA expression and abundance of the produced proteins, to expose groups of genes that are co-regulated in either or both of the views. Cluster analysis of co-expression is a standard simple way of screening for co-regulation, and the two-view analysis extends the approach to distinguishing between pre- and post-translational regulation

‘It Takes Two Hands to Clap’: How Gaddi Shepherds in the Indian Himalayas Negotiate Access to Grazing

This article examines the effects of state intervention on the workings of informal institutions that coordinate the communal use and management of natural resources. Specifically it focuses on the case of the nomadic Gaddi shepherds and official attempts to regulate their access to grazing pastures in the Indian Himalayas. It is often predicted that the increased presence of the modern state critically undermines locally appropriate and community-based resource management arrangements. Drawing on the work of Pauline Peters and Francis Cleaver, I identify key instances of socially embedded ‘common’ management institutions and explain the evolution of these arrangements through dynamic interactions between individuals, communities and the agents of the state. Through describing the ‘living space’ of Gaddi shepherds across the annual cycle of nomadic migration with their flocks I explore the ways in which they have been able to creatively reinterpret external interventions, and suggest how contemporary arrangements for accessing pasture at different moments of the annual cycle involve complex combinations of the formal and the informal, the ‘traditional’ and the ‘modern’

Otto coupling to a transverse-electric-polarized mode on a metamaterial surface

publication-status: Publishedtypes: ArticleAlastair P. Hibbins, Matthew J. Lockyear and J. Roy Sambles, Physical Review B, Vol. 84, article 115130 (2011). Copyright © 2011 by the American Physical Society.Using the Otto geometry, prism coupling of microwave radiation to a metamaterial surface that supports a bound transverse-electric-polarized surface mode is demonstrated. The dispersion of this surface mode is characterised experimentally for incident radiation beyond the critical angle of the prism, and its resonant fields are explored using a numerical model

How to minimise the effect of tumour cell content in detection of aberrant genetic markers in neuroblastoma

Background:Clinical heterogeneity reflects the complexity of genetic events associated with neuroblastoma (NB). To identify the status of all described genetic loci with possible prognostic interest, high-throughput approaches have been used, but only with tumour cell content >60%. In some tumours, necrotic, haemorrhagic and/or calcification areas influence the low amount of neuroblasts. We evaluated the effect of tumour cell content in the detection of relevant aberrant genetic markers (AGM) diagnosed by fluorescence in situ hybridisation (FISH) on tissue microarrays (TMA) in NB.Methods:Two hundred and thirty-three MYCN non-amplified primary NB included in 12 TMAs were analysed.Results:Presence of AGM reduced event-free survival (EFS) (P=0.004) as well as overall survival (OS) (P=0.004) of patients in the whole cohort. There were no differences in prognostic impact of presence of AGM according to tumour cell content.Conclusion:We propose the use of FISH to diagnose AGM of all NB samples having the above-mentioned areas to determine patient risk

Haloes gone MAD: The Halo-Finder Comparison Project

[abridged] We present a detailed comparison of fundamental dark matter halo properties retrieved by a substantial number of different halo finders. These codes span a wide range of techniques including friends-of-friends (FOF), spherical-overdensity (SO) and phase-space based algorithms. We further introduce a robust (and publicly available) suite of test scenarios that allows halo finder developers to compare the performance of their codes against those presented here. This set includes mock haloes containing various levels and distributions of substructure at a range of resolutions as well as a cosmological simulation of the large-scale structure of the universe. All the halo finding codes tested could successfully recover the spatial location of our mock haloes. They further returned lists of particles (potentially) belonging to the object that led to coinciding values for the maximum of the circular velocity profile and the radius where it is reached. All the finders based in configuration space struggled to recover substructure that was located close to the centre of the host halo and the radial dependence of the mass recovered varies from finder to finder. Those finders based in phase space could resolve central substructure although they found difficulties in accurately recovering its properties. Via a resolution study we found that most of the finders could not reliably recover substructure containing fewer than 30-40 particles. However, also here the phase space finders excelled by resolving substructure down to 10-20 particles. By comparing the halo finders using a high resolution cosmological volume we found that they agree remarkably well on fundamental properties of astrophysical significance (e.g. mass, position, velocity, and peak of the rotation curve).Comment: 27 interesting pages, 20 beautiful figures, and 4 informative tables accepted for publication in MNRAS. The high-resolution version of the paper as well as all the test cases and analysis can be found at the web site http://popia.ft.uam.es/HaloesGoingMA

Initiating and continuing participation in citizen science for natural history

Background: Natural history has a long tradition in the UK, dating back to before Charles Darwin. Developing from a principally amateur pursuit, natural history continues to attract both amateur and professional involvement. Within the context of citizen science and public engagement, we examine the motivations behind citizen participation in the national survey activities of the Open Air Laboratories (OPAL) programme, looking at: people’s experiences of the surveys as ‘project-baed leisure’; their motivations for taking part and barriers to continued participation; where they feature on our continuum of engagement; and whether participation in an OPAL survey facilitated their movement between categories along this continuum. The paper focuses on a less-expected but very significant outcome regarding the participation of already-engaged amateur naturalists in citizen science. Methods: The paper draws upon research conducted by the authors (a sociologist of science and a cultural geographer) over a five-year period, who followed the development and implementation of the OPAL surveys. The authors engaged with members of the public and natural history enthusiasts to understand how and why people engaged with the OPAL surveys, seeking to explore the motivations and barriers they faced to any further engagement with natural history. This involved carrying out interviews and focus groups with willing participants. Results: Our main findings relate to: first, how committed amateur naturalists (already-engaged) have also enjoyed contributing to OPAL and the need to respect and work with their interest to encourage broader and deeper involvement; and second, how new (previously-unengaged) and relatively new participants (casually-engaged) have gained confidence, renewed their interests, refocussed their activities and/or gained validation from participation in OPAL. Overall, we argue that engagement with and enthusiasm for the scientific process is a motivation shared by citizens who, prior to participating in the OPAL surveys, were previously-unengaged, casually-engaged or already-engaged in natural history activities. Conclusions: Citizen science has largely been written about by professional scientists for professional scientists interested in developing a project of their own. This study offers a qualitative example of how citizen science can be meaningful to participants beyond what might appear to be a public engagement data collection exercise