Does the North Atlantic Oscillation show unusual persistence on intraseasonal timescales?

Previous studies have argued that the autocorrelation of the winter North Atlantic Oscillation (NAO) index provides evidence of unusually persistent intraseasonal dynamics. We demonstrate that the autocorrelation on intraseasonal time-scales of 10–30 days is sensitive to the presence of interannual variability, part of which arises from the sampling of intraseasonal variability and the remainder of which we consider to be “externally forced”. Modelling the intraseasonal variability of the NAO as a red noise process we estimate, for winter, ~70% of the interannual variability is externally forced, whereas for summer sampling accounts for almost all of the interannual variability. Correcting for the externally forced interannual variability has a major impact on the autocorrelation function for winter. When externally forced interannual variability is taken into account the intrinsic persistence of the NAO is very similar in summer and winter (~5 days). This finding has implications for understanding the dynamics of the NAO.

Reading 'The Truman Show' inside out

This essay explores how The Truman Show, Peter Weir’s film about a television show, deserves more sustained analysis than it has received since its release in 1998. I will argue that The Truman Show problematizes the binary oppositions of cinema/television, disruption/stability, reality/simulation and outside/inside that structure it. The Truman Show proposes that binary oppositions such as outside/inside exist in a mutually implicating relationship. This deconstructionist strategy not only questions the film’s critical position, but also enables a reflection on the very status of film analysis itself.

Do designers show categorical perception of typefaces?

Readers need to easily discriminate between different letters, so typefaces are designed to make these differences distinctive. But there is also a uniformity of style within a typeface. These styles are recognised by typographic designers and may be categorised to enable more efficient discrimination among typefaces. The manner in which designers perceive typefaces is explored using the paradigm of Categorical Perception (CP). A continuum of fonts is created by interpolating between two typefaces and two tasks (identification and discrimination) are used to test for CP. As the application of CP to typefaces is a new approach, various methodological issues are pursued. The experiments reveal that the conditions required to demonstrate CP are quite specific and CP was only evident in Times and Helvetica and not Garamond and Bodoni. Possible reasons for this difference are the characteristics of the two typefaces and their context of use. Speculation as to the purpose of CP in non-designers raises the under-researched question of how we identify letters in different typefaces when reading.

Crystal structures of Λ-[Ru(phen)2dppz]2+ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes

The ruthenium complex [Ru(phen)2(dppz)] (where phen is a phenanthroline and dppz a dipyridyl–phenazine ligand) is known as a ‘light switch’ complex because its luminescence in solution is significantly enhanced in the presence of DNA. This property is poised to serve in diagnostic and therapeutic applications, but its binding mode with DNA needs to be elucidated further. Here, we describe the crystal structures of the L enantiomer bound to two oligonucleotide duplexes. The dppz ligand intercalates symmetrically and perpendicularly from the minor groove of the d(CCGGTACCGG)2 duplex at the central TA/TA step, but not at the central AT/AT step of d(CCGGATCCGG)2. In both structures, however, a second ruthenium complex links the duplexes through the combination of a shallower angled intercalation into the C1C2/G9G10 step at the end of the duplex, and semi-intercalation into the G3G4 step of an adjacent duplex. The TA/TA specificity of the perpendicular intercalation arises from the packing of phenanthroline ligands against the adenosine residue.

Contrasting arbuscular mycorrhizal communities colonizing different host plants show a similar response to a soil phosphorus concentration gradient

High soil phosphorus (P) concentration is frequently shown to reduce root colonization by arbuscular mycorrhizal (AM) fungi, but the influence of P on the diversity of colonizing AM fungi is uncertain. We used terminal restriction fragment length polymorphism (T-RFLP) of 18S rDNA and cloning to assess diversity of AM fungi colonizing maize (Zea mays), soybean (Glycene max) and field violet (Viola arvensis) at three time points in one season along a P gradient of 10280mgl1 in the field. Percentage AM colonization changed between sampling time points but was not reduced by high soil P except in maize. There was no significant difference in AM diversity between sampling time points. Diversity was reduced at concentrations of P > 25mgl1, particularly in maize and soybean. Both cloning and T-RFLP indicated differences between AM communities in the different host species. Host species was more important than soil P in determining the AM community, except at the highest P concentration. Our results show that the impact of soil P on the diversity of AM fungi colonizing plants was broadly similar, despite the fact that different plants contained different communities. However, subtle differences in the response of the AM community in each host were evident.

Promoter analysis and immunolocalisation show that puroindoline genes are exclusively expressed in starchy endosperm cells of wheat grain

The purolindolines are small cysteine-rich proteins which are present in the grain of wheat. They have a major impact on the utilisation of the grain as they are the major determinants of grain texture, which affects both milling and baking properties. Bread and durum wheats were transformed with constructs comprising the promoter regions of the Puroindoline a (Pina) and Puroindoline b (Pinb) genes fused to the uidA (GUS) reporter gene. Nine lines showing 3:1 segregation for the transgene and comprising all transgene/species combinations were selected for detailed analysis of transgene expression during grain development. This showed that transgene expression occurred only in the starchy endosperm cells and was not observed in any other seed or vegetative tissues. The location of the puroindoline proteins in these cells was confirmed by tissue printing of developing grain, using a highly specific monoclonal antibody for detection and an antibody to the aleurone-localised 8S globulin as a control. This provides clear evidence that puroindolines are only synthesised and accumulated in the starchy endosperm cells of the wheat grain.

Candidate genes for obesity-susceptibility show enriched association within a large genome-wide association study for BMI

Before the advent of genome-wide association studies (GWASs), hundreds of candidate genes for obesity-susceptibility had been identified through a variety of approaches. We examined whether those obesity candidate genes are enriched for associations with body mass index (BMI) compared with non-candidate genes by using data from a large-scale GWAS. A thorough literature search identified 547 candidate genes for obesity-susceptibility based on evidence from animal studies, Mendelian syndromes, linkage studies, genetic association studies and expression studies. Genomic regions were defined to include the genes ±10 kb of flanking sequence around candidate and non-candidate genes. We used summary statistics publicly available from the discovery stage of the genome-wide meta-analysis for BMI performed by the genetic investigation of anthropometric traits consortium in 123 564 individuals. Hypergeometric, rank tail-strength and gene-set enrichment analysis tests were used to test for the enrichment of association in candidate compared with non-candidate genes. The hypergeometric test of enrichment was not significant at the 5% P-value quantile (P = 0.35), but was nominally significant at the 25% quantile (P = 0.015). The rank tail-strength and gene-set enrichment tests were nominally significant for the full set of genes and borderline significant for the subset without SNPs at P < 10(-7). Taken together, the observed evidence for enrichment suggests that the candidate gene approach retains some value. However, the degree of enrichment is small despite the extensive number of candidate genes and the large sample size. Studies that focus on candidate genes have only slightly increased chances of detecting associations, and are likely to miss many true effects in non-candidate genes, at least for obesity-related traits.

Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience.

Whilst not true in all cases, the microbial communities that chronically infect the airways of patients with CF can vary little over a year despite antibiotic perturbation. The species present tended to vary more between than within subjects, suggesting that each CF airway infection is unique, with relatively stable and resilient bacterial communities. The inverse relationship between community richness and disease severity is similar to findings reported in other mucosal infections.

'You show me yours, I'll show you mine': the negotiation of shifts from textual to visual modes in computer-mediated interaction among gay men

This article explores the way users of an online gay chat room negotiate the exchange of photographs and the conduct of video conferencing sessions and how this negotiation changes the way participants manage their interactions and claim and impute social identities. Different modes of communication provide users with different resources for the control of information, affecting not just what users are able to reveal, but also what they are able to conceal. Thus, the shift from a purely textual mode for interacting to one involving visual images fundamentally changes the kinds of identities and relationships available to users. At the same time, the strategies users employ to negotiate these shifts of mode can alter the resources available in different modes. The kinds of social actions made possible through different modes, it is argued, are not just a matter of the modes themselves but also of how modes are introduced into the ongoing flow of interaction.

Transcriptomics and proteomics show that selenium affects inflammation, ctoskeleton, and cancer pathways in human rectal biopsies

Epidemiologic studies highlight the potential role of dietary selenium (Se) in colorectal cancer prevention. Our goal was to elucidate whether expression of factors crucial for colorectal homoeostasis is affected by physiologic differences in Se status. Using transcriptomics and proteomics followed by pathway analysis, we identified pathways affected by Se status in rectal biopsies from 22 healthy adults, including 11 controls with optimal status (mean plasma Se = 1.43 μM) and 11 subjects with suboptimal status (mean plasma Se = 0.86 μM). We observed that 254 genes and 26 proteins implicated in cancer (80%), immune function and inflammatory response (40%), cell growth and proliferation (70%), cellular movement, and cell death (50%) were differentially expressed between the 2 groups. Expression of 69 genes, including selenoproteins W1 and K, which are genes involved in cytoskeleton remodelling and transcription factor NFκB signaling, correlated significantly with Se status. Integrating proteomics and transcriptomics datasets revealed reduced inflammatory and immune responses and cytoskeleton remodelling in the suboptimal Se status group. This is the first study combining omics technologies to describe the impact of differences in Se status on colorectal expression patterns, revealing that suboptimal Se status could alter inflammatory signaling and cytoskeleton in human rectal mucosa and so influence cancer risk.