Anatomy, morphology and evolution of the patella in squamate lizards and tuatara (Sphenodon punctatus)

The patella (kneecap) is the largest and best-known of the sesamoid bones, postulated to confer biomechanical advantages including increasing joint leverage and reinforcing the tendon against compression. It has evolved several times independently in amniotes, but despite apparently widespread occurrence in lizards, the patella remains poorly characterised in this group and is, as yet, completely undescribed in their nearest extant relative Sphenodon (Rhynchocephalia). Through radiography, osteological and fossil studies we examined patellar presence in diverse lizard and lepidosauromorph taxa, and using computed tomography, dissection and histology we investigated in greater depth the anatomy and morphology of the patella in 16 lizard species and 19 Sphenodon specimens. We have found the first unambiguous evidence of a mineralised patella in Sphenodon, which appears similar to the patella of lizards and shares several gross and microscopic anatomical features. Although there may be a common mature morphology, the squamate patella exhibits a great deal of variability in development (whether from a cartilage anlage or not, and in the number of mineralised centres) and composition (bone, mineralised cartilage or fibrotendinous tissue). Unlike in mammals and birds, the patella in certain lizards and Sphenodon appears to be a polymorphic trait. We have also explored the evolution of the patella through ancestral state reconstruction, finding that the patella is ancestral for lizards and possibly Lepidosauria as a whole. Clear evidence of the patella in rhynchocephalian or stem lepidosaurian fossil taxa would clarify the evolutionary origin(s) of the patella, but due to the small size of this bone and the opportunity for degradation or loss we could not definitively conclude presence or absence in the fossils examined. The pattern of evolution in lepidosaurs is unclear but our data suggest that the emergence of this sesamoid may be related to the evolution of secondary ossification centres and/or changes in knee joint conformation, where enhancement of extensor muscle leverage would be more beneficial.Sophie Regnault, Marc E. H. Jones, Andrew A. Pitsillides, John R. Hutchinso

Weak Interaction Studies with 6He

The 6He nucleus is an ideal candidate to study the weak interaction. To this end we have built a high-intensity source of 6He delivering ~10^10 atoms/s to experiments. Taking full advantage of that available intensity we have performed a high-precision measurement of the 6He half-life that directly probes the axial part of the nuclear Hamiltonian. Currently, we are preparing a measurement of the beta-neutrino angular correlation in 6He beta decay that will allow to search for new physics beyond the Standard Model in the form of tensor currents.Comment: 5 pages, 4 figures, proceedings for the Eleventh Conference on the Intersections of Particle and Nuclear Physics (CIPANP 2012

Development of strategies for effective communication of food risks and benefits across Europe: Design and conceptual framework of the FoodRisC project

The FoodRisC project is funded under the Seventh Framework Programme (CORDIS FP7) of the European Commission; Grant agreement no.: 245124. Copyright @ 2011 Barnett et al.BACKGROUND: European consumers are faced with a myriad of food related risk and benefit information and it is regularly left up to the consumer to interpret these, often conflicting, pieces of information as a coherent message. This conflict is especially apparent in times of food crises and can have major public health implications. Scientific results and risk assessments cannot always be easily communicated into simple guidelines and advice that non-scientists like the public or the media can easily understand especially when there is conflicting, uncertain or complex information about a particular food or aspects thereof. The need for improved strategies and tools for communication about food risks and benefits is therefore paramount. The FoodRisC project ("Food Risk Communication - Perceptions and communication of food risks/benefits across Europe: development of effective communication strategies") aims to address this issue. The FoodRisC project will examine consumer perceptions and investigate how people acquire and use information in food domains in order to develop targeted strategies for food communication across Europe.METHODS/DESIGN: This project consists of 6 research work packages which, using qualitative and quantitative methodologies, are focused on development of a framework for investigating food risk/benefit issues across Europe, exploration of the role of new and traditional media in food communication and testing of the framework in order to develop evidence based communication strategies and tools. The main outcome of the FoodRisC project will be a toolkit to enable coherent communication of food risk/benefit messages in Europe. The toolkit will integrate theoretical models and new measurement paradigms as well as building on social marketing approaches around consumer segmentation. Use of the toolkit and guides will assist policy makers, food authorities and other end users in developing common approaches to communicating coherent messages to consumers in Europe.DISCUSSION: The FoodRisC project offers a unique approach to the investigation of food risk/benefit communication. The effective spread of food risk/benefit information will assist initiatives aimed at reducing the burden of food-related illness and disease, reducing the economic impact of food crises and ensuring that confidence in safe and nutritious food is fostered and maintained in Europe.This article is available through the Brunel Open Access Publishing Fund

Microtubules in Bacteria: Ancient Tubulins Build a Five-Protofilament Homolog of the Eukaryotic Cytoskeleton

Microtubules play crucial roles in cytokinesis, transport, and motility, and are therefore superb targets for anti-cancer drugs. All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ, but while eukaryotic tubulins evolved into highly conserved microtubule-forming heterodimers, bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today. Microtubules have not previously been found in bacteria, and we lack insight into their evolution from the tubulin/FtsZ ancestor. Using electron cryomicroscopy, here we show that the tubulin homologs BtubA and BtubB form microtubules in bacteria and suggest these be referred to as “bacterial microtubules” (bMTs). bMTs share important features with their eukaryotic counterparts, such as straight protofilaments and similar protofilament interactions. bMTs are composed of only five protofilaments, however, instead of the 13 typical in eukaryotes. These and other results suggest that rather than being derived from modern eukaryotic tubulin, BtubA and BtubB arose from early tubulin intermediates that formed small microtubules. Since we show that bacterial microtubules can be produced in abundance in vitro without chaperones, they should be useful tools for tubulin research and drug screening

Composing first species counterpoint with a variable neighbourhood search algorithm

In this article, a variable neighbourhood search (VNS) algorithm is developed that can generate musical fragments consisting of a melody for the cantus firmus and the first species counterpoint. The objective function of the algorithm is based on a quantification of existing rules for counterpoint. The VNS algorithm developed in this article is a local search algorithm that starts from a randomly generated melody and improves it by changing one or two notes at a time. A thorough parametric analysis of the VNS reveals the significance of the algorithm's parameters on the quality of the composed fragment, as well as their optimal settings. A comparison of the VNS algorithm with a developed genetic algorithm shows that the VNS is more efficient. The VNS algorithm has been implemented in a user-friendly software environment for composition, called Optimuse. Optimuse allows a user to specify a number of characteristics such as length, key and mode. Based on this information, Optimuse 'composes' both cantus firmus and first species counterpoint. Alternatively, the user may specify a cantus firmus, and let Optimuse compose the accompanying first species counterpoint. © 2012 Taylor & Francis

A new rhynchocephalian from the late jurassic of Germany with a dentition that is unique amongst tetrapods.

Rhynchocephalians, the sister group of squamates (lizards and snakes), are only represented by the single genus Sphenodon today. This taxon is often considered to represent a very conservative lineage. However, rhynchocephalians were common during the late Triassic to latest Jurassic periods, but rapidly declined afterwards, which is generally attributed to their supposedly adaptive inferiority to squamates and/or Mesozoic mammals, which radiated at that time. New finds of Mesozoic rhynchocephalians can thus provide important new information on the evolutionary history of the group. A new fossil relative of Sphenodon from the latest Jurassic of southern Germany, Oenosaurus muehlheimensis gen. et sp. nov., presents a dentition that is unique amongst tetrapods. The dentition of this taxon consists of massive, continuously growing tooth plates, probably indicating a crushing dentition, thus representing a previously unknown trophic adaptation in rhynchocephalians. The evolution of the extraordinary dentition of Oenosaurus from the already highly specialized Zahnanlage generally present in derived rhynchocephalians demonstrates an unexpected evolutionary plasticity of these animals. Together with other lines of evidence, this seriously casts doubts on the assumption that rhynchocephalians are a conservative and adaptively inferior lineage. Furthermore, the new taxon underlines the high morphological and ecological diversity of rhynchocephalians in the latest Jurassic of Europe, just before the decline of this lineage on this continent. Thus, selection pressure by radiating squamates or Mesozoic mammals alone might not be sufficient to explain the demise of the clade in the Late Mesozoic, and climate change in the course of the fragmentation of the supercontinent of Pangaea might have played a major role

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

A gene signature for post-infectious chronic fatigue syndrome

Background: At present, there are no clinically reliable disease markers for chronic fatigue syndrome. DNA chip microarray technology provides a method for examining the differential expression of mRNA from a large number of genes. Our hypothesis was that a gene expression signature, generated by microarray assays, could help identify genes which are dysregulated in patients with post-infectious CFS and so help identify biomarkers for the condition. Methods: Human genome-wide Affymetrix GeneChip arrays (39,000 transcripts derived from 33,000 gene sequences) were used to compare the levels of gene expression in the peripheral blood mononuclear cells of male patients with post-infectious chronic fatigue (n = 8) and male healthy control subjects (n = 7). Results: Patients and healthy subjects differed significantly in the level of expression of 366 genes. Analysis of the differentially expressed genes indicated functional implications in immune modulation, oxidative stress and apoptosis. Prototype biomarkers were identified on the basis of differential levels of gene expression and possible biological significance Conclusion: Differential expression of key genes identified in this study offer an insight into the possible mechanism of chronic fatigue following infection. The representative biomarkers identified in this research appear promising as potential biomarkers for diagnosis and treatment