Modelling the ability of legumes to suppress weeds

The ability of different legume cover crops to suppress annual weeds during the early establishment phase was compared using a simulation model of inter-plant competition and field observations. Height, partitioning parameters, extinction coefficients, crop density and time of emergence were recorded for 11 species sown in monocultures. A naturally occurring population of fat hen (Chenopodium album) was present on the experiment. The competition model was run to compare the expected suppressive ability of the different species on this weed. Samples of C. album were also taken from each plot immediately prior to cutting to provide some empirical observations. Predicted suppressive ability was correlated with seed size and height with large seeded, tall species such as white sweet clover being the most competitive. However, these species may recover poorly from mowing compromising their potential to suppress perennial weeds and a mixture of contrasting species may provide the optimum weed control

Modeling growth in biological materials

The biomechanical modeling of growing tissues has recently become an area of intense interest. In particular, the interplay between growth patterns and mechanical stress is of great importance, with possible applications to arterial mechanics, embryo morphogenesis, tumor development, and bone remodeling. This review aims to give an overview of the theories that have been used to model these phenomena, categorized according to whether the tissue is considered as a continuum object or a collection of cells. Among the continuum models discussed is the deformation gradient decomposition method, which allows a residual stress field to develop from an incompatible growth field. The cell-based models are further subdivided into cellular automata, center-dynamics, and vertex-dynamics models. Of these the second two are considered in more detail, especially with regard to their treatment of cell-cell interactions and cell division. The review concludes by assessing the prospects for reconciliation between these two fundamentally different approaches to tissue growth, and by identifying possible avenues for further research. © 2012 Society for Industrial and Applied Mathematics

A transdiagnostic data-driven study of children's behaviour and the functional connectome.

Behavioural difficulties are seen as hallmarks of many neurodevelopmental conditions. Differences in functional brain organisation have been observed in these conditions, but little is known about how they are related to a child's profile of behavioural difficulties. We investigated whether behavioural difficulties are associated with how the brain is functionally organised in an intentionally heterogeneous and transdiagnostic sample of 957 children aged 5-15. We used consensus community detection to derive data-driven profiles of behavioural difficulties and constructed functional connectomes from a subset of 238 children with resting-state functional Magnetic Resonance Imaging (fMRI) data. We identified three distinct profiles of behaviour that were characterised by principal difficulties with hot executive function, cool executive function, and learning. Global organisation of the functional connectome did not differ between the groups, but multivariate patterns of connectivity at the level of Intrinsic Connectivity Networks (ICNs), nodes, and hubs significantly predicted group membership in held-out data. Fronto-parietal connector hubs were under-connected in all groups relative to a comparison sample and children with hot vs cool executive function difficulties were distinguished by connectivity in ICNs associated with cognitive control, emotion processing, and social cognition. This demonstrates both general and specific neurodevelopmental risk factors in the functional connectome

Cytoplasmic Domain of the 180-kD Bullous Pemphigoid Antigen, a Hemidesmosomal Component: Molecular and Cell Biologic Characterization

Using a serum sample of a bullous pemphigoid (BP) patient we have isolated a cDNA clone encoding a portion of a 180-kD polypeptide component of the hemidesmosome, the “BP180 autoantigen.” The identity of the clone was confirmed by the generation of a fusion protein antibody that recognizes BP180 in both a basal epithelial cell extract of bovine tongue and extract of human epidermal cells. Immunoelectron microscopy indicates that the 588-bp cDNA encodes a cytoplasmic fragment of BP180. Furthermore, the wide species reactivity of the fusion protein suggests that this portion of BP180 is highly conserved. In cultured human epidermal cells processed for confocal immunofluorescence microscopy, the fusion protein antibody generates a punctate cell substrate-associated staining pattern that is similar to that seen using BP230 antibodies. Using the original BP180 cDNA we have now isolated additional cDNA clones encoding approximately 1800bp of BP180 the 3' sequence of which overlaps with the sequence detailed in Giudice et al (J Clin Invest 87:734–738, 1991). Secondary structural analyses have been undertaken on the predicted amino acids encoded by the 1800bp. These suggest that the collagen-like sequences of BP180 described by Giudice et al (ibid.) are separated by a putative transmembrane region from the domain of BP180 recognized by our fusion protein antibody. Indeed, BP180 appears to belong to a relatively rare group of proteins in which the N-terminus is located in the cytoplasm and the C-terminus is extracellular. We detail some preliminary biochemical experiments in support of this hypothesis. We discuss possible functions of BP180 and BP230 in the hemidesmosome

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia

Co-Occurrence and Characteristics of Patients With Axial Spondyloarthritis Who Meet Criteria for Fibromyalgia : Results From a UK National Register

The British Society for Rheumatology (BSR) Biologics Register in Ankylosing Spondylitis is funded by the BSR and they have receive funds for this from Pfizer, AbbVie and UCB. These companies receive advance copies of manuscripts and can provide comments but have no input into determining the topics for analysis, publication and no input into the work involved in this analysis. This analysis is part-funded by Arthritis Research UK (Grant No: 21378)Peer reviewedPublisher PD