Asthma trajectories in early childhood: identifying modifiable factors

BackgroundThere are conflicting views as to whether childhood wheezing represents several discreet entities or a single but variable disease. Classification has centered on phenotypes often derived using subjective criteria, small samples, and/or with little data for young children. This is particularly problematic as asthmatic features appear to be entrenched by age 6/7. In this paper we aim to: identify longitudinal trajectories of wheeze and other atopic symptoms in early childhood; characterize the resulting trajectories by the socio-economic background of children; and identify potentially modifiable processes in infancy correlated with these trajectories.Data and MethodsThe Millennium Cohort Study is a large, representative birth cohort of British children born in 2000–2002. Our analytical sample includes 11,632 children with data on key variables (wheeze in the last year; ever hay-fever and/or eczema) reported by the main carers at age 3, 5 and 7 using a validated tool, the International Study of Asthma and Allergies in Childhood module. We employ longitudinal Latent Class Analysis, a clustering methodology which identifies classes underlying the observed population heterogeneity.ResultsOur model distinguished four latent trajectories: a trajectory with both low levels of wheeze and other atopic symptoms (54% of the sample); a trajectory with low levels of wheeze but high prevalence of other atopic symptoms (29%); a trajectory with high prevalence of both wheeze and other atopic symptoms (9%); and a trajectory with high levels of wheeze but low levels of other atopic symptoms (8%). These groups differed in terms of socio-economic markers and potential intervenable factors, including household damp and breastfeeding initiation.ConclusionUsing data-driven techniques, we derived four trajectories of asthmatic symptoms in early childhood in a large, population based sample. These groups differ in terms of their socio-economic profiles. We identified correlated intervenable pathways in infancy, including household damp and breastfeeding initiation.<br/

The emergence of resistance to the benzimidazole anthlemintics in parasitic nematodes of livestock is characterised by multiple independent hard and soft selective sweeps

Anthelmintic resistance is a major problem for the control of parasitic nematodes of livestock and of growing concern for human parasite control. However, there is little understanding of how resistance arises and spreads or of the “genetic signature” of selection for this group of important pathogens. We have investigated these questions in the system for which anthelmintic resistance is most advanced; benzimidazole resistance in the sheep parasites Haemonchus contortus and Teladorsagia circumcincta. Population genetic analysis with neutral microsatellite markers reveals that T. circumcincta has higher genetic diversity but lower genetic differentiation between farms than H. contortus in the UK. We propose that this is due to epidemiological differences between the two parasites resulting in greater seasonal bottlenecking of H. contortus. There is a remarkably high level of resistance haplotype diversity in both parasites compared with drug resistance studies in other eukaryotic systems. Our analysis suggests a minimum of four independent origins of resistance mutations on just seven farms for H. contortus, and even more for T. circumincta. Both hard and soft selective sweeps have occurred with striking differences between individual farms. The sweeps are generally softer for T. circumcincta than H. contortus, consistent with its higher level of genetic diversity and consequent greater availability of new mutations. We propose a model in which multiple independent resistance mutations recurrently arise and spread by migration to explain the widespread occurrence of resistance in these parasites. Finally, in spite of the complex haplotypic diversity, we show that selection can be detected at the target locus using simple measures of genetic diversity and departures from neutrality. This work has important implications for the application of genome-wide approaches to identify new anthelmintic resistance loci and the likelihood of anthelmintic resistance emerging as selection pressure is increased in human soil-transmitted nematodes by community wide treatment programs

Subsurface architecture of fluvial-deltaic deposits in high- and low-accommodation settings

Combined seismic and well interpretation methods can be used to elucidate detail of the subsurface architecture of fluvial and fluvio-deltaic deposits. Observations made from wireline and core logs, including facies and analysing the relative proportions of architectural elements and facies associations indicative of depositional sub-environments, can be used to interpret patterns of cyclicity, changes in local accommodation conditions, and periods of increased seasonal, tidal and marine influence. Horizon slices, taken from 3D seismic volumes aid in the visualisation of laterally discontinuous, often thinly-bedded, fluvial deposits. Seismic facies, when combined with core and wireline log facies, can be interpreted as a series of ‘seismic elements’. The relative proportions of seismic elements mapped out on horizon slices allows the interpretation of depositional environments and accommodation setting; allowing the distinction between fluvial and deltaic settings. A number of data conditioning and seismic interpretation techniques can be used to enhance the visualisation of channelized and non-channelized fluvio-deltaic deposits in the subsurface. Frequency decomposition (and the making of colour-blended volumes) allows the visualisation of the detail of channel belt deposits such as channel belt migration and lateral accretion deposits. Allogenic processes, particularly base-level (buttress) rise and fall have been shown to exert a control on the overall stacking pattern of the studied fluvio-deltaic deposits, whereas autogenic processes are interpreted as the major control on the local arrangement and architecture of channel belt and overbank deposits. The first study in this thesis uses the Upper Permian Rangal Coal Measures, a large-scale fluvial system, which accumulated in a foreland basin setting in the Bowen Basin, Queensland, Australia. The study investigates the architecture and connectivity of splay and distributary channels. The second study uses the Late Triassic Mungaroo Formation, a Mississippi-scale fluvio-deltaic system with a fluvially-dominated, tidally-influenced delta, which accumulated in the Northern Carnarvon Basin, Northwest Shelf, Australia. The study investigates different seismic interpretation techniques and investigates the relative control on fluvio-deltaic deposition of allogenic and autogenic processes

Crystal structure of the human p58 killer cell inhibitory receptor (KIR2DL3) specific for HLA-Cw3-related MHC class I

AbstractBackground: T cells and natural killer (NK) cells perform complementary roles in the cellular immune system. T cells identify infected cells directly through recognition of antigenic peptides that are displayed at the target cell surface by the classical major histocompatibility complex (MHC) class I molecules. NK cells monitor the target cell surface for malfunction of this display system, lysing potentially infected cells that might otherwise evade recognition by the T cells. Human killer cell inhibitory receptors (KIRs) control this process by either inhibiting or activating the cytotoxic activity of NK cells via specific binding to MHC class I molecules on the target cell.Results: We report the crystal structure of the extracellular region of the human p58 KIR (KIR2DL3), which is specific for the human MHC class I molecule HLA-Cw3 and related alleles. The structure shows the predicted topology of two tandem immunoglobulin-like domains, but comparison with the previously reported structure of the related receptor KIR2DL1 reveals an unexpected change of 23° in the relative orientation of these domains.Conclusions: The altered orientation of the immunoglobulin-like domains maintains an unusually acute interdomain elbow angle, which therefore appears to be a distinctive feature of the KIRs. The putative MHC class I binding site is located on the outer surface of the elbow, spanning both domains. The unexpected observation that this binding site can be modulated by differences in the relative domain orientations has implications for the general mechanism of KIR–MHC class I complex formation

Where dignity ends and uBuntu begins : an amplification of, as well as an identification of a tension in, Drucilla Cornell’s thoughts

In the decade or so in which Professor Cornell has engaged South Africa's jurisprudence, her name has become synonymous with academic discourse on the values of dignity and uBuntu. As colleagues and collaborators, it is often hard to know where Drucilla Cornell's thoughts on these subjects end and one's own ruminations begin. What follows then is an amplification of, or a riff upon, Professor Cornell's lead essay: 'Is there a difference that makes a difference?' Contestation is not on the cards

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

<p>Abstract</p> <p>Background</p> <p>RNA-Seq exploits the rapid generation of gigabases of sequence data by Massively Parallel Nucleotide Sequencing, allowing for the mapping and digital quantification of whole transcriptomes. Whilst previous comparisons between RNA-Seq and microarrays have been performed at the level of gene expression, in this study we adopt a more fine-grained approach. Using RNA samples from a normal human breast epithelial cell line (MCF-10a) and a breast cancer cell line (MCF-7), we present a comprehensive comparison between RNA-Seq data generated on the Applied Biosystems SOLiD platform and data from Affymetrix Exon 1.0ST arrays. The use of Exon arrays makes it possible to assess the performance of RNA-Seq in two key areas: detection of expression at the granularity of individual exons, and discovery of transcription outside annotated loci.</p> <p>Results</p> <p>We found a high degree of correspondence between the two platforms in terms of exon-level fold changes and detection. For example, over 80% of exons detected as expressed in RNA-Seq were also detected on the Exon array, and 91% of exons flagged as changing from Absent to Present on at least one platform had fold-changes in the same direction. The greatest detection correspondence was seen when the read count threshold at which to flag exons Absent in the SOLiD data was set to <it>t</it><1 suggesting that the background error rate is extremely low in RNA-Seq. We also found RNA-Seq more sensitive to detecting differentially expressed exons than the Exon array, reflecting the wider dynamic range achievable on the SOLiD platform. In addition, we find significant evidence of novel protein coding regions outside known exons, 93% of which map to Exon array probesets, and are able to infer the presence of thousands of novel transcripts through the detection of previously unreported exon-exon junctions.</p> <p>Conclusions</p> <p>By focusing on exon-level expression, we present the most fine-grained comparison between RNA-Seq and microarrays to date. Overall, our study demonstrates that data from a SOLiD RNA-Seq experiment are sufficient to generate results comparable to those produced from Affymetrix Exon arrays, even using only a single replicate from each platform, and when presented with a large genome.</p

Functional and Genetic Analysis of Coronavirus Replicase-Transcriptase Proteins

The coronavirus replicase-transcriptase complex is an assembly of viral and cellular proteins that mediate the synthesis of genome and subgenome-sized mRNAs in the virus-infected cell. Here, we report a genetic and functional analysis of 19 temperature-sensitive (ts) mutants of Murine hepatitis virus MHV-A59 that are unable to synthesize viral RNA when the infection is initiated and maintained at the non-permissive temperature. Both classical and biochemical complementation analysis leads us to predict that the majority of MHV-A59 ORF1a replicase gene products (non-structural proteins nsp1–nsp11) form a single complementation group (cistron1) while the replicase gene products encoded in ORF1b (non-structural proteins nsp12–nsp16) are able to function in trans and comprise at least three, and possibly five, further complementation groups (cistrons II–VI). Also, we have identified mutations in the non-structural proteins nsp 4, nsp5, nsp10, nsp12, nsp14, and nsp16 that are responsible for the ts phenotype of eight MHV-A59 mutants, which allows us to conclude that these proteins are essential for the assembly of a functional replicase-transcriptase complex. Finally, our analysis of viral RNA synthesis in ts mutant virus-infected cells allows us to discriminate three phenotypes with regard to the inability of specific mutants to synthesize viral RNA at the non-permissive temperature. Mutant LA ts6 appeared to be defective in continuing negative-strand synthesis, mutant Alb ts16 appeared to form negative strands but these were not utilized for positive-strand RNA synthesis, and mutant Alb ts22 was defective in the elongation of both positive- and negative-strand RNA. On the basis of these results, we propose a model that describes a pathway for viral RNA synthesis in MHV-A59-infected cells. Further biochemical analysis of these mutants should allow us to identify intermediates in this pathway and elucidate the precise function(s) of the viral replicase proteins involved

Decision-making in communication aid recommendations in the UK : cultural and contextual influencers

High-tech communication aids are one form of augmentative and alternative communication (AAC) intervention offered to children following an assessment process to identify the most appropriate system based on their needs. Professional recommendations are likely to include consideration of child characteristics and communication aid attributes. Recommendations may be influenced by contextual factors related to the cultural work practices and service context of professionals involved, as well as by contextual factors from the child’s life including their family environment and wider settings. The aim of this study was to explore the influence of cultural and contextual factors on the real-time decision-making processes of specialized AAC professionals in the UK. A total of six teams were recruited to the study. Each team carried out an assessment appointment related to a communication aid recommendation for a child and family. Following the appointment, each team participated in a focus group examining their decision-making processes during the preceding assessment. Inductive coding was used to analyse the transcribed data, and three organizing themes emerged relating to the global theme of Cultural and Contextual Influencers on communication aid decision-making. An explanatory model was developed to illustrate the funnelling effect that contextual factors may have on decision-making, which can substantially alter the nature and timing of a communication aid recommendation. Implications for clinical practice and future research are discussed