IMPROvER : the Integral Membrane Protein Stability Selector

Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of alpha -helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/.Peer reviewe

Izolacija i sposobnost hvatanja slobodnih radikala cijanidin 3-O-glikozida iz plodova Ribes biebersteinii Berl.

The reversed-phase preparative high performance liquid chromatographic purification of the methanol extract of the fruits of Ribes biebersteinii Berl. (Grossulariaceae) afforded five cyanidin glycosides, 3-O-sambubiosyl-5-O-glucosyl cyanidin (1), cyanidin 3-O-sambubioside (2), cyanidin 3-O-glucoside (3), cyanidin 3-O-(2G-xylosyl)-rutinoside (4) and cyanidin 3-O-rutinoside (5). They showed considerable free-radical-scavenging properties in the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay with the RC50 values of 9.29 × 106, 9.33 × 106, 8.31 × 106, 8.96 × 106 and 9.55 × 106 mol L1, respectively. The structures of these compounds were elucidated by various chemical hydrolyses and spectroscopic means. The total anthocyanin content was 1.9 g per 100 g dried fruits on cyanidin 3-glucoside basis.Pet cijanidin glikozida, 3-O-sambubiozil-5-O-glukozil cijanidin (1), cijanidin 3-O-sambubiozid (2), cijanidin 3-O-glukozid (3), cijanidin 3-O-(2G-ksilozil)-rutinozid (4) i cijanidin 3-O-rutinosid (5) izolirani su iz metanolnog ekstrakta plodova Ribes biebersteinii Berl. (Grossulariaceae) koristeći reverzno-faznu preparativnu tekućinsku kromatografiju visoke učinkovitosti. Cijanidin glikozidi pokazali su sposobnost hvatanja slobodnih radikala u pokusu s 2,2-difenil-1-pikrilhidrazilom (DPPH). Dobivene su sljedeće RC50 vrijednosti: 9,29 × 106, 9,33 × 106, 8,31 × 106, 8,96 × 106, odnosno 9,55 × 106 mol L1. Strukture glikozida određene su kemijskom hidrolizom i spektroskopijom masa. Ukupni sadržaj antocijanina bio je 1,9 g na 100 g suhih plodova preračunato na cijanidin 3-glukozid

SimSpin v2.6.0 -- Constructing synthetic spectral IFU cubes for comparison with observational surveys

In this work, we present a methodology and a corresponding code-base for constructing mock integral field spectrograph (IFS) observations of simulated galaxies in a consistent and reproducible way. Such methods are necessary to improve the collaboration and comparison of observation and theory results, and accelerate our understanding of how the kinematics of galaxies evolve over time. This code, SimSpin, is an open-source package written in R, but also with an API interface such that the code can be interacted with in any coding language. Documentation and individual examples can be found at the open-source website connected to the online repository. SimSpin is already being utilised by international IFS collaborations, including SAMI and MAGPI, for generating comparable data sets from a diverse suite of cosmological hydrodynamical simulations.Comment: 20 pages, 15 figures, 2 tables. Accepted for publication in PASA. 30/08/2

Mangroves enhance the biomass of coral reef fish communities in the Caribbean

Mangrove forests are one of the world's most threatened tropical ecosystems with global loss exceeding 35% (ref. 1). Juvenile coral reef fish often inhabit mangroves, but the importance of these nurseries to reef fish population dynamics has not been quantified. Indeed, mangroves might be expected to have negligible influence on reef fish communities: juvenile fish can inhabit alternative habitats and fish populations may be regulated by other limiting factors such as larval supply or fishing. Here we show that mangroves are unexpectedly important, serving as an intermediate nursery habitat that may increase the survivorship of young fish. Mangroves in the Caribbean strongly influence the community structure of fish on neighbouring coral reefs. In addition, the biomass of several commercially important species is more than doubled when adult habitat is connected to mangroves. The largest herbivorous fish in the Atlantic, Scarus guacamaia, has a functional dependency on mangroves and has suffered local extinction after mangrove removal. Current rates of mangrove deforestation are likely to have severe deleterious consequences for the ecosystem function, fisheries productivity and resilience of reefs. Conservation efforts should protect connected corridors of mangroves, seagrass beds and coral reefs

Tropical coastal habitats as surrogates of fish community structure, grazing, and fisheries value

Habitat maps are frequently invoked as surrogates of biodiversity to aid the design of networks of marine reserves. Maps are used to maximize habitat heterogeneity in reserves because this is likely to maximize the number of species protected. However, the technique's efficacy is limited by intra-habitat variability in the species present and their abundances. Although communities are expected to vary among patches of the same habitat, this variability is poorly documented and rarely incorporated into reserve planning. To examine intra-habitat variability in coral-reef fishes, we generated a data set from eight tropical coastal habitats and six islands in the Bahamian archipelago using underwater visual censuses. Firstly, we provide further support for habitat heterogeneity as a surrogate of biodiversity as each predefined habitat type supported a distinct assemblage of fishes. Intrahabitat variability in fish community structure at scales of hundreds of kilometers (among islands) was significant in at least 75% of the habitats studied, depending on whether presence/absence, density, or biomass data were used. Intra-habitat variability was positively correlated with the mean number of species in that habitat when density and biomass data were used. Such relationships provide a proxy for the assessment of intra-habitat variability when detailed quantitative data are scarce. Intra-habitat variability was examined in more detail for one habitat (forereefs visually dominated by Montastraea corals). Variability in community structure among islands was driven by small, demersal families (e. g., territorial pomacentrid and labrid fishes). Finally, we examined the ecological and economic significance of intra-habitat variability in fish assemblages on Montastraea reefs by identifying how this variability affects the composition and abundances of fishes in different functional groups, the key ecosystem process of parrotfish grazing, and the ecosystem service of value of commercially important finfish. There were significant differences in a range of functional groups and grazing, but not fisheries value. Variability at the scale of tens of kilometers (among reefs around an island) was less than that among islands. Caribbean marine reserves should be replicated at scales of hundreds of kilometers, particularly for species-rich habitats, to capture important intra-habitat variability in community structure, function, and an ecosystem process

Predicting the Impact of Climate Change on Threatened Species in UK Waters

Global climate change is affecting the distribution of marine species and is thought to represent a threat to biodiversity. Previous studies project expansion of species range for some species and local extinction elsewhere under climate change. Such range shifts raise concern for species whose long-term persistence is already threatened by other human disturbances such as fishing. However, few studies have attempted to assess the effects of future climate change on threatened vertebrate marine species using a multi-model approach. There has also been a recent surge of interest in climate change impacts on protected areas. This study applies three species distribution models and two sets of climate model projections to explore the potential impacts of climate change on marine species by 2050. A set of species in the North Sea, including seven threatened and ten major commercial species were used as a case study. Changes in habitat suitability in selected candidate protected areas around the UK under future climatic scenarios were assessed for these species. Moreover, change in the degree of overlap between commercial and threatened species ranges was calculated as a proxy of the potential threat posed by overfishing through bycatch. The ensemble projections suggest northward shifts in species at an average rate of 27 km per decade, resulting in small average changes in range overlap between threatened and commercially exploited species. Furthermore, the adverse consequences of climate change on the habitat suitability of protected areas were projected to be small. Although the models show large variation in the predicted consequences of climate change, the multi-model approach helps identify the potential risk of increased exposure to human stressors of critically endangered species such as common skate (Dipturus batis) and angelshark (Squatina squatina)