Energy landscapes of a hairpin peptide including NMR chemical shift restraints.

Methods recently introduced to improve the efficiency of protein structure prediction simulations by adding a restraint potential to a molecular mechanics force field introduce additional input parameters that can affect the performance. Here we investigate the changes in the energy landscape as the relative weight of the two contributions, force field and restraint potential, is systematically altered, for restraint functions constructed from calculated nuclear magnetic resonance chemical shifts. Benchmarking calculations were performed on a 12-residue peptide, tryptophan zipper 1, which features both secondary structure (a β-hairpin) and specific packing of tryptophan sidechains. Basin-hopping global optimization was performed to assess the efficiency with which lowest-energy structures are located, and the discrete path sampling approach was employed to survey the energy landscapes between unfolded and folded structures. We find that inclusion of the chemical shift restraints improves the efficiency of structure prediction because the energy landscape becomes more funnelled and the proportion of local minima classified as native increases. However, the funnelling nature of the landscape is reduced as the relative contribution of the chemical shift restraint potential is increased past an optimal value.This research was supported by the EPSRC and the ERC.This is the final version of the article. It first appeared from the Royal Society of Chemistry via http://dx.doi.org/10.1039/C5CP01259

Energy landscapes and persistent minima.

We consider a coarse-graining of high-dimensional potential energy landscapes based upon persistences, which correspond to lowest barrier heights to lower-energy minima. Persistences can be calculated efficiently for local minima in kinetic transition networks that are based on stationary points of the prevailing energy landscape. The networks studied here represent peptides, proteins, nucleic acids, an atomic cluster, and a glassy system. Minima with high persistence values are likely to represent some form of alternative structural morphology, which, if appreciably populated at the prevailing temperature, could compete with the global minimum (defined as infinitely persistent). Threshold values on persistences (and in some cases equilibrium occupation probabilities) have therefore been used in this work to select subsets of minima, which were then analysed to see how well they can represent features of the full network. Simplified disconnectivity graphs showing only the selected minima can convey the funnelling (including any multiple-funnel) characteristics of the corresponding full graphs. The effect of the choice of persistence threshold on the reduced disconnectivity graphs was considered for a system with a hierarchical, glassy landscape. Sets of persistent minima were also found to be useful in comparing networks for the same system sampled under different conditions, using minimum oriented spanning forests.D.J.W and J.M.C gratefully acknowledge funding from the European Research Council [267369].This is the author accepted manuscript. The final version is available at http://scitation.aip.org/content/aip/journal/jcp/144/5/10.1063/1.4941052

Histopathologic and Biochemical Responses in Arctic Marine Bivalve Molluscs Exposed to Experimentally Spilled Oil

Following two experimental spills of chemically dispersed and undispersed crude oil in shallow bays on the northwest coast of Baffin Island, Canadian Arctic, the bivalve molluscs Mya truncata and Macoma calcarea accumulated significant amounts of petroleum hydrocarbons in bays receiving dispersed oil and in those receiving crude oil alone (Boehm et all., 1987). Following the spills, Mya released accumulated hydrocarbons more rapidly than Macoma. ... The results of the biochemical analyses indicate that Mya from the four bays were not severely stressed by either dispersed oil or oil alone. Immediately after the spill, clams from the dispersal oil bays were nearly normal, while those from the bay receiving oil alone appeared stressed. These results seem to corroborate results from analytical chemistry and histopathology: that the acute effects of dispersed oil are greater than those of undispersed oil, but effects of undispersed oil on infaunal molluscs develop more slowly and persist longer than those from dispersed oil.Key words: oil spill, dispersant, Mya truncata, Macoma calcarea, histopathology, biochemistry, neoplasia, free amino acids, glycogen, parasitesMots clés: marée noire, agent de dispersion, Mya truncata, Macoma calcarea, histopathologie, biochimie, néoplasme, acides aminés libres, glycogène, parasite

Spatial Analysis of Arabidopsis thaliana Gene Expression in Response to Turnip mosaic virus Infection

Virus-infected leaf tissues comprise a heterogeneous mixture of cells at different stages of infection. The spatial and temporal relationships between sites of virus accumulation and the accompanying host responses, such as altered host gene expression, are not well defined. To address this issue, we utilized Turnip mosaic virus (TuMV) tagged with the green fluorescent protein to guide the dissection of infection foci into four distinct zones. The abundance of Arabidopsis thaliana mRNA transcripts in each of the four zones then was assayed using the Arabidopsis ATH1 GeneChip oligonucleotide microarray (Affymetrix). mRNA transcripts with significantly altered expression profiles were determined across gradients of virus accumulation spanning groups of cells in and around foci at different stages of infection. The extent to which TuMV-responsive genes were up- or downregulated primarily correlated with the amount of virus accumulation regardless of gene function. The spatial analysis also allowed new suites of coordinately regulated genes to be identified that are associated with chloroplast functions (decreased), sulfate assimilation (decreased), cell wall extensibility (decreased), and protein synthesis and turnover (induced). The functions of these downregulated genes are consistent with viral symptoms, such as chlorosis and stunted growth, providing new insight into mechanisms of pathogenesis

Geology of drill hole UE25p#1; a test hole into pre-Tertiary rocks near Yucca Mountain, southern Nevada

Yucca Mountain in southern Nye County, Nevada, has been proposed as a potential site for the underground disposal of high-level nuclear waste. An exploratory drill hole designated UE25p#1 was drilled 3 km east of the proposed repository site to investigate the geology and hydrology of the rocks that underlie the Tertiary volcanic and sedimentary rock sequence forming Yucca Mountain. Silurian dolomite assigned to the Roberts Mountain and Lone Mountain Formations was intersected below the Tertiary section between a depth of approximately 1244 m (4080 ft) and the bottom of the drill hole at 1807 m (5923 ft). These formations are part of an important regional carbonate aquifer in the deep ground-water system. Tertiary units deeper than 1139 m (3733 ft) in drill hole UE25p#1 are stratigraphically older than any units previously penetrated by drill holes at Yucca Mountain. These units are, in ascending order, the tuff of Yucca Flat(?), an unnamed calcified ash-flow tuff, and a sequence of clastic deposits. The upper part of the Tertiary sequence in drill hole UE25p#1 is similar to that found in other drill holes at Yucca Mountain. The Tertiary sequence is in fault contact with the Silurian rocks. This fault between Tertiary and Paleozoic rocks may correlate with the Fran Ridge fault, a steeply westward-dipping fault exposed approximately 0.5 km east of the drill hole. Another fault intersects UE25p#1 at 873 m (2863 ft), but its surface trace is concealed beneath the valley west of the Fran Ridge fault. The Paintbrush Canyon fault, the trace of which passes less than 100 m (330 ft) east of the drilling site, intersects drill hole UE25p#1 at a depth of approximately 78 m (255 ft). The drill hole apparently intersected the west flank of a structural high of pre-Tertiary rocks, near the eastern edge of the Crater Flat structural depression

Pulmonary function deficits in newborn screened infants with cystic fibrosis managed with standard UK care are mild and transient

With the advent of novel designer molecules for cystic fibrosis (CF) treatment, there is huge need for early-life clinical trial outcomes, such as infant lung function (ILF). We investigated the degree and tracking of ILF abnormality during the first 2 years of life in CF newborn screened infants. Forced expiratory volume in 0.5 s (FEV₀.₅), lung clearance index (LCI) and plethysmographic functional residual capacity were measured at ∼3 months, 1 year and 2 years in 62 infants with CF and 34 controls. By 2 years there was no significant difference in FEV₀.₅ z-score between CF and controls, whereas mean LCI z-score was 0.81 (95% CI 0.45–1.17) higher in CF. However, there was no significant association between LCI z-score at 2 years with either 3-month or 1-year results. Despite minimal average group changes in any ILF outcome during the second year of life, marked within-subject changes occurred. No child had abnormal LCI or FEV₀.₅ on all test occasions, precluding the ability to identify “high-risk” infants in early life. In conclusion, changes in lung function are mild and transient during the first 2 years of life in newborn screened infants with CF when managed according to a standardised UK treatment protocol. Their potential role in tracking disease to later childhood will be ascertained by ongoing follow-up

Conceptualising social justice and sociocultural issues within physical education teacher education: international perspectives

Background: Physical education (PE) and physical education teacher education (PETE) have a substantial literature base that advocates for students to develop a critical consciousness, appreciate multiple perspectives, and engage in actions to enhance social justice (Tinning 2016). Analysing sociocultural issues, critically reflecting on beliefs, knowledge, biography and values, and developing a sense of agency to enact change, have been recognised as an integral part of the PETE knowledge base for some time (Fernández-Balboa 1997). However, there remain differences in how social justice itself is conceptualised and enacted. Social justice is aligned heavily with critical and ‘post’ theories where taking action for justice, democracy and power are central; but social justice is also found in humanist beliefs in student-centredness and equality and has been co-opted by neoliberal forces that promote individual responsibility. While a lack of consensus is not in itself a problem (Bialystok 2014), diverse definitions might contribute to confusion (Randall and Robinson 2016) and lead to uncertainty over what and how to teach for social justice. Purpose: In order to work towards greater certainty around concepts of social justice in the PETE community, this project sought to map variations in definition and conceptualisation of social justice and sociocultural issues among physical education teacher educators (PETEs) and physical education and sport pedagogy (PESP) educators, as part of a wider project on social justice and sociocultural perspectives and practices in PETE. Methods: PETE and PESP faculty (n=72) in North America, Europe, and Australasia engaged in an in-depth interview, during which they were asked how they define social justice and sociocultural issues. Additional information about participants’ social identity was collected. A constant comparative method of analysing participants’ definitions mapped a range of concepts building on the theoretical framework of neoliberal, humanist, critical and ‘post’ approaches to social justice. Findings: The data demonstrate that there are a range of understandings about sociocultural issues and social justice. Most commonly, some participants articulated a humanist approach to social justice by encouraging their pre-service teachers (PSTs) to have awareness of equality of opportunity in relation to gender, sexuality and/or racism. Less prevalent, but strongly stated by those who conceptualised social justice in these terms, was the importance to take action for democracy, empowerment or critical reflection. The terms diversity and equality, framed in neoliberal and humanist discourses, were most commonly used within the United States (US), while critical pedagogy and alignment with critical and ‘post’ theories were more prevalent in Australia and New Zealand. Conclusion: Differences exist in the ways social justice is conceptualised in PETE. While this can be attributed to the influence of local issues, it is also reflective of what intellectual tools, such as humanism or critical theory, are available for problematising social issues. The range of non-critical concepts found raises concern that PSTs are not getting the tools to enact social justice or tackle sociocultural issues.

Quasi-continuous Interpolation Scheme for Pathways between Distant Configurations

A quasi-continuous interpolation (QCI) scheme is introduced for characterizing physically realistic initial pathways from which to initiate transition state searches and construct kinetic transition networks. Applications are presented for peptides, proteins, and a morphological transformation in an atomic cluster. The first step in each case involves end point alignment, and we describe the use of a shortest augmenting path algorithm for optimizing permutational isomers. The QCI procedure then employs an interpolating potential, which preserves the covalent bonding framework for the biomolecules and includes repulsive terms between unconstrained atoms. This potential is used to identify an interpolating path by minimizing contributions from a connected set of images, including terms corresponding to minima in the interatomic distances between them. This procedure detects unphysical geometries in the line segments between images. The most difficult cases, where linear interpolation would involve chain crossings, are treated by growing the structure an atom at a time using the interpolating potential. To test the QCI procedure, we carry through a series of benchmark calculations where the initial interpolation is coupled to explicit transition state searches to produce complete pathways between specified local minima.This work was supported by the Engineering and Physical Sciences Research Council [grant number EP/H042660/1]This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in the Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review. To access the final edited and published work see http://dx.doi.org/10.1021/ct300483

Mutation screening of retinal dystrophy patients by targeted capture from tagged pooled DNAs and next generation sequencing.

Purpose: Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies. Methods: Patient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing. Results: Molecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D). Conclusions: Tagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics