Probing the denatured state ensemble with fluorescence

To understand protein stability and the mechanism of protein folding, it is essential that we gain a better understanding of the ensemble of conformations that make up the denatured state of a protein. The primary goal of the research described here was to see what we might learn about the denatured state using fluorescence. To this end, tryptophan was introduced at five sites in Ribonuclease Sa (RNase Sa): D1W, Y52W, Y55W, T76W, and Y81W. The fluorescent properties of the denatured states of these five proteins were studied and compared to the fluorescent properties of eight model compounds: N-acetyl-tryptophan-amide (NATA), N-acetyl-Ala-Trp-Ala-amide (AWA), N-acetyl-Ala-Ala-Trp-Ala-Ala-amide (AAWAA), and five pentapeptides based on the sequence around the original tryptophan substitutions in RNase Sa. Regardless of the denaturant, λmax for the proteins and model compounds differed very little, 349.3 ± 1.2 nm. However, significant differences were observed in the fluorescence intensity at λmax (IF), suggesting that IF is more sensitive to the immediate environment than λmax. The differences in IF are due in part to quenching by neighboring side chains. More importantly, IF was always significantly greater in the protein than in its corresponding pentapeptide, indicating that the protein exerts an effect on the tryptophan, which cannot be mimicked by the pentapeptide models. Acrylamide and iodide quenching experiments were also performed on the model compounds and proteins. Significant differences in the Stern-Volmer quenching constant (KSV) were also observed between the proteins and between the proteins and their corresponding pentapeptides. Importantly, the KSV for the protein was always less than in its corresponding pentapeptide. These data along with the IF data show that non-local structure in the unfolded state influences tryptophan fluorescence and accessibility. In summary, these and our other studies show that fluorescence can be used to gain a better understanding of the denatured states of proteins

City of clones: Facsimiles and governance in Sao Paulo, Brazil

São Paulo is a megacity defined by formal and informal patterns of urbanization. Informally urbanized spaces are not absent of state intent, despite appearances. Grassroots-led social and spatial practices for survival, agency and self-governance contribute to the reproduction of urban political order in surprisingly unoriginal and routinely recognizable ways. This article argues that these unexceptional informal practices can be understood as ‘facsimiles’ of their formal institutional originals. Using the example of cloned cars the article shows that the facsimile and the original are the same in form and function. Facsimiles do not exist outside of political authority, but are a byproduct and a component of it. They are indistinguishable in their bureaucratic deployment, recognition and acceptance as part of social and spatial order. This is the author accepted manuscript. The final version is available from Sage via https://doi.org/10.1177/001139211665729

UK national ecosystem assessment follow-on: cultural ecosystem services and indicators

No description supplie

A Quantum Exactly Solvable Nonlinear Oscillator with quasi-Harmonic Behaviour

The quantum version of a non-linear oscillator, previouly analyzed at the classical level, is studied. This is a problem of quantization of a system with position-dependent mass of the form $m={(1+\lambda x^2)}^{-1}$ and with a \la-dependent nonpolynomial rational potential. This \la-dependent system can be considered as a deformation of the harmonic oscillator in the sense that for \la\to 0 all the characteristics of the linear oscillator are recovered. Firstly, the \la-dependent Schr\"odinger equation is exactly solved as a Sturm-Liouville problem and the \la-dependent eigenenergies and eigenfunctions are obtained for both \la>0 and \la<0. The \la-dependent wave functions appear as related with a family of orthogonal polynomials that can be considered as \la-deformations of the standard Hermite polynomials. In the second part, the \la-dependent Schr\"odinger equation is solved by using the Schr\"odinger factorization method, the theory of intertwined Hamiltonians and the property of shape invariance as an approach. Finally, the new family of orthogonal polynomials is studied. We prove the existence of a \la-dependent Rodrigues formula, a generating function and \la-dependent recursion relations between polynomials of different orders.Comment: 29 pages, 4 figure

Similarities in butterfly emergence dates among populations suggest local adaptation to climate

Phenology shifts are the most widely cited examples of the biological impact of climate change, yet there are few assessments of potential effects on the fitness of individual organisms or the persistence of populations. Despite extensive evidence of climate-driven advances in phenological events over recent decades, comparable patterns across species' geographic ranges have seldom been described. Even fewer studies have quantified concurrent spatial gradients and temporal trends between phenology and climate. Here we analyse a large data set (~129 000 phenology measures) over 37 years across the UK to provide the first phylogenetic comparative analysis of the relative roles of plasticity and local adaptation in generating spatial and temporal patterns in butterfly mean flight dates. Although populations of all species exhibit a plastic response to temperature, with adult emergence dates earlier in warmer years by an average of 6.4 days per °C, among-population differences are significantly lower on average, at 4.3 days per °C. Emergence dates of most species are more synchronised over their geographic range than is predicted by their relationship between mean flight date and temperature over time, suggesting local adaptation. Biological traits of species only weakly explained the variation in differences between space-temperature and time-temperature phenological responses, suggesting that multiple mechanisms may operate to maintain local adaptation. As niche models assume constant relationships between occurrence and environmental conditions across a species' entire range, an important implication of the temperature-mediated local adaptation detected here is that populations of insects are much more sensitive to future climate changes than current projections suggest

The classification and management of limestone pavements : an endangered habitat

This thesis describes an in-depth study of limestone pavements across North West England and North Wales. The aim was to combine elements of geodiversity and biodiversity in order to create a holistic limestone pavement classification to inform future management. A field-based research protocol was used to assess a stratified random sample (46 pavements), accounting for approximately 10% of the limestone pavements in the geographical area. Detailed analyses of key elements are presented, along with important issues that continue to pose threats to this Annex One Priority Habitat. This research resulted in a comprehensive classification, using TWINSPAN analysis and Nonmetric Multidimensional Scaling, identifying six distinct holistic functional groups. The prime factors driving limestone pavement morphology, and hence the classification, were established to be lithology, proximity to structural fault, altitude and human intervention, particularly in terms of grazing intensity. Three upland, open limestone pavement classes were formed. Of these, the richest in terms of geodiversity and biodiversity was the group with the thickest bedding planes and hence the deepest grikes, typically greater than 1m. The class that was most species-poor was "at the highest altitude (above 450m), formed on the thin limestones of the Yoredales. These were characterised by shallow, wide grikes. The third upland limestone pavement group had mid-range grikes, generally 0.5-1m in depth, and small clints. Two wooded classes were identified. One was a lowland 'classic' wooded limestone pavement group with deep, narrow grikes and shallow soils. Indicator species included Juniperus communis and Taxus baccata. The second wooded group was situated proximal to a major structural fault. In this group the pavement dip ranged between 10°-40° with well-runnelled clints that were heavily moss-covered. The sixth group was low altitude, proximal to the coast, characterised by low moss growth, un-vegetated clints and the presence of Ulex europaeus. Conservation management was identified as key to the quality of the limestone pavement habitat and this thesis identifies best management practises and links these to the holistic limestone pavement classification. Finally, as a sample case study, this thesis presents mollusc species and diversity from eleven of the Yorkshire limestone pavements. Analysis establishes significant links between geodiversity and mollusc populations, with key drivers for mollusc communities echoing those of plant species on limestone pavement.EThOS - Electronic Theses Online ServiceYorkshire Dales National ParkUniversity of ChesterGBUnited Kingdo

Depth sensitive X-ray diffraction as a probe of buried half-metallic inclusions

The ferromagnetic material MnSb can exist in two polymorphs in epitaxial thin-film form, namely niccolite n-MnSb and cubic c-MnSb. We investigate the behavior of these polymorphs using grazing incidence depth-dependent in-plane X-ray diffraction. The in-plane lattice parameter evolution of a nominal 3000 Å thin film reveals a small near-surface compression of math formula0.1% in the majority n-MnSb component. A similar effect is also observed for the cubic polymorph, suggesting that the local strain environment of these crystallites is dominated by the n-MnSb matrix

Galileo dust data from the jovian system: 2000 to 2003

The Galileo spacecraft was orbiting Jupiter between Dec 1995 and Sep 2003. The Galileo dust detector monitored the jovian dust environment between about 2 and 370 R_J (jovian radius R_J = 71492 km). We present data from the Galileo dust instrument for the period January 2000 to September 2003. We report on the data of 5389 particles measured between 2000 and the end of the mission in 2003. The majority of the 21250 particles for which the full set of measured impact parameters (impact time, impact direction, charge rise times, charge amplitudes, etc.) was transmitted to Earth were tiny grains (about 10 nm in radius), most of them originating from Jupiter's innermost Galilean moon Io. Their impact rates frequently exceeded 10 min^-1. Surprisingly large impact rates up to 100 min^-1 occurred in Aug/Sep 2000 when Galileo was at about 280 R_J from Jupiter. This peak in dust emission appears to coincide with strong changes in the release of neutral gas from the Io torus. Strong variability in the Io dust flux was measured on timescales of days to weeks, indicating large variations in the dust release from Io or the Io torus or both on such short timescales. Galileo has detected a large number of bigger micron-sized particles mostly in the region between the Galilean moons. A surprisingly large number of such bigger grains was measured in March 2003 within a 4-day interval when Galileo was outside Jupiter's magnetosphere at approximately 350 R_J jovicentric distance. Two passages of Jupiter's gossamer rings in 2002 and 2003 provided the first actual comparison of in-situ dust data from a planetary ring with the results inferred from inverting optical images.Comment: 59 pages, 13 figures, 6 tables, submitted to Planetary and Space Scienc