Ultra-high resolution X-ray structure of orthorhombic bovine pancreatic Ribonuclease A at 100K

The crystal structure of orthorhombic Bovine Pancreatic Ribonuclease A has been determined to 0.85 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16000 keV (λ = 0.77 Å). This is the first ultra-high-resolution structure of a native form of Ribonuclease A to be reported. Refinement carried out with anisotropic displacement parameters, stereochemical restraints, inclusion of H atoms in calculated positions, five SO2−4 moieties, eleven ethanol molecules and 293 water molecules, converged with final R values of R1(Free) = 0.129 (4279 reflections) and R1 = 0.112 (85,346 reflections). The refined structure was deposited in the Protein Data Bank as structure 7p4r. Conserved waters, using four high resolution structures, have been investigated. Cluster analysis identified clusters of water molecules that are associated with the active site of Bovine Ribonuclease A. Particular attention has been paid to making detailed comparisons between the present structure and other high quality Bovine Pancreatic Ribonuclease A X-ray crystal structures with special reference to the deposited classic monoclinic structure 3RN3 Howlin et al. (Acta Crystallogr A 45:851–861, 1989). Detailed studies of various aspects of hydrogen bonding and conformation have been carried out with particular reference to active site residues Lys-1, Lys-7, Gln-11, His-12, Lys-41, Asn-44, Thr-45, Lys-66, His-119 and Ser-123. For the two histidine residues in the active site the initial electron density map gives a clear confirmation that the position of His-12 is very similar in the orthorhombic structure to that in 3RN3. In 3RN3 His-119 exhibited poor electron density which was modelled and refined as two distinct sites, A (65%) and B (35%) but with respect to His-119 in the present ultra-high resolution orthorhombic structure there is clear electron density which was modelled and refined as a single conformation distinct from either conformation A or B in 3RN3. Other points of interest include Serine-32 which is disordered at the end of the sidechain in the present orthorhombic form but has been modelled as a single form in 3RN3. Lysine-66: there is density indicating a possible conformation for this residue. However, the density is relatively weak, and the conformation is unclear. Three types of amino acid representation in the ultra-high resolution electron density are examined: (i) sharp with very clearly resolved features, for example Lys-37; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry, for example Tyr-76; (iii) poor density and difficult or impossible to model, an example is Lys-31 for which density is missing except for Cβ. The side chains of Gln-11, His-12, Lys-41, Thr-45 and His-119 are generally recognised as being closely involved in the enzyme activity. It has also been suggested that Lys-7, Asp-44, Lys-66, Phe-120, Asp-121 and Ser-123 may also have possible roles in this mechanism. A molecular dynamics study on both structures has investigated the conformations of His-119 which was modelled as two conformations in 3RN3 but is observed to have a single clearly defined conformation in the present orthorhombic structure. MD has also been used to investigate Lys-31, Lys-41 and Ser32. The form of the Ribonuclease A enzyme used in both the present study and in 3RN3 (Howlin et al. in Acta Crystallogr A 45:851–861, 1989) includes a sulphate anion which occupies approximately the same location as the PO2−4 phosphate group in protein nucleotide complexes (Borkakoti et al. in J Mol Biol 169:743–755, 1983). The present structure contains 5 SO2−4 groups SO41151–SO41155 two of which, SO41152 and SO41153 are disordered, SO41152 being in the active site, and 11 EtOH molecules, EOH A 201–EOH A 211 all of which have good geometry. H atoms were built into the EtOH molecules geometrically. Illustrations of these features in the present structure are included here. The sulphates are presumably present in the material purchased for use in the present study. 293 water molecules are included in the present structure compared to 134 in 3RN3 (Howlin et al. in Acta Crystallogr A 45:851–861, 1989)

Measurement of the gamma ray background in the Davis Cavern at the Sanford Underground Research Facility

Deep underground environments are ideal for low background searches due to the attenuation of cosmic rays by passage through the earth. However, they are affected by backgrounds from γ-rays emitted by 40K and the 238U and 232Th decay chains in the surrounding rock. The LUX-ZEPLIN (LZ) experiment will search for dark matter particle interactions with a liquid xenon TPC located within the Davis campus at the Sanford Underground Research Facility, Lead, South Dakota, at the 4,850-foot level. In order to characterise the cavern background, in-situ γ-ray measurements were taken with a sodium iodide detector in various locations and with lead shielding. The integral count rates (0--3300~keV) varied from 596~Hz to 1355~Hz for unshielded measurements, corresponding to a total flux in the cavern of 1.9±0.4~γ cm−2s−1. The resulting activity in the walls of the cavern can be characterised as 220±60~Bq/kg of 40K, 29±15~Bq/kg of 238U, and 13±3~Bq/kg of 232Th

Southern African perspectives on banning corporal punishment – a comparison of Namibia, Botswana, South Africa and Zimbabwe

This chapter reviews recent judicial and legislative developments concerning steps towards – and against – the abolition of corporal punishment in four closely connected southern African jurisdictions: South Africa, Namibia, Botswana and Zimbabwe. Not only are these countries neighbours, they share a common legal heritage as recipients of a blend of Roman Dutch law and English law and, in the case of Namibia, the country was, until independence in 1990, a protectorate of South Africa with laws and institutions in common. Hence, all countries under discussion inherited from English law the “reasonable chastisement” defence available to parents utilising physical force against their children. In short, this meant that charges of assault could be countered with the common law defence that the parent was merely exercising legitimate parental authority. Although the scope of the application of the defence did narrow to exclude the most egregious forms of abuse in recent decades, in the face of mounting evidence of child abuse and changing social norms, it remained intact. This was the case even in the face of developing legislative measures to counter child abuse in various welfare and protection statutes in all of the four countries at defined points in the 20th century

Survey Spectroscopy in the Submillimeter and Millimeter, from the CSO to CCAT

I outline some results from the Z-Spec instrument at the CSO and present a concept for CCAT survey spectrometer

Mountain roads and non-native species modify elevational patterns of plant diversity

Aim: We investigated patterns of species richness and community dissimilarity along elevation gradients using globally replicated, standardized surveys of vascular plants. We asked how these patterns of diversity are influenced by anthropogenic pressures (road construction and non-native species). Location: Global. Time period: 2008-2015. Major taxa studied: Vascular plants. Methods: Native and non-native vascular plant species were recorded in 943 plots along 25 elevation gradients, in nine mountain regions, on four continents. Sampling took place in plots along and away from roads. We analysed the effects of elevation and distance from road on species richness patterns and community dissimilarity (beta-diversity), and assessed how non-native species modified such elevational diversity patterns. Results: Globally, native and total species richness showed a unimodal relationship with elevation that peaked at lower-mid elevations, but these patterns were altered along roads and due to non-native species. Differences in elevational species richness patterns between regions disappeared along roadsides, and non-native species changed the patterns' character in all study regions. Community dissimilarity was reduced along roadsides and through non-native species. We also found a significant elevational decay of beta-diversity, which however was not affected by roads or non-native species. Main conclusions: Idiosyncratic native species richness patterns in plots away from roads implicate region-specific mechanisms underlying these patterns. However, along roadsides a clearer elevational signal emerged and species richness mostly peaked at mid-elevations. We conclude that both roads and non-native species lead to a homogenization of species richness patterns and plant communities in mountains

Mountain roads shift native and non-native plant species ranges

Roads are known to act as corridors for dispersal of plant species. With their variable microclimate, role as corridors for species movement and reoccurring disturbance events, they show several characteristics that might influence range dynamics of both native and non-native species. Previous research on plant species ranges in mountains however seldom included the effects of roads. To study how ranges of native and non-native species differ between roads and adjacent vegetation, we used a global dataset of plant species composition along mountain roads. We compared average elevation and range width of species, and used generalized linear mixed models (GLMMs) to compile their range optimum and amplitude. We then explored differences between roadside and adjacent plots based on a species? origin (native vs non-native) and nitrogen and temperature affinity. Most non-native species had on average higher elevational ranges and broader amplitudes in roadsides. Higher optima for non-native species were associated with high nitrogen and temperature affinity. While lowland native species showed patterns comparable to those in non-native species, highland native species had significantly lower elevational ranges in roadsides compared to the adjacent vegetation. We conclude that roadsides indeed change the elevational ranges of a variety of species. These changes are not limited to the expansion of non-native species along mountain roads, but also include both upward and downward changes in ranges of native species. Roadsides may thus facilitate upward range shifts, for instance related to climate change, and they could serve as corridors to facilitate migration of alpine species between adjacent high-elevation areas. We recommend including the effects of mountain roads in species distribution models to fine-tune the predictions of range changes in a warming climate.Fil: Lembrechts, Jonas. Universiteit Antwerp; BélgicaFil: Alexander, Jake. Swiss Federal Institute of Technology Zurich; SuizaFil: Cavieres, Lohengrin. Universidad de Concepción; ChileFil: Haider, Sylvia. Martin-Luther Universität Halle-Wittenberg; Alemania. German Centre For Integrative Biodiversity Research.; AlemaniaFil: Lenoir, Jonathan. Université de Picardie Jules Verne; FranciaFil: Kueffer, Christoph. Swiss Federal Institute of Technology Zurich; SuizaFil: McDougall, Keith. La Trobe University; AustraliaFil: Naylor, Bridgett. United States Department of Agriculture; Estados UnidosFil: Nuñez, Martin Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Pauchard, Aníbal. Universidad de Concepción; ChileFil: Rew, Lisa. State University of Montana; Estados UnidosFil: Nijs, Ivan. Universiteit Antwerp; BélgicaFil: Milbau, Ann. Universidad de Umea; Suecia. Research Institute for Nature and Forest; Bélgic