Everything in Its Place

In this issue of Immunity, Griffith et al. (2009) define the thymic midcortex as a functionally inert zone between subcapsular and cortico-medullary regions, and Ehrlich et al. (2009) infer that structural features of the cortex and medulla regulate migration of thymocytes

Common ground breakdown during collaborative virtual environment navigation with wall-sized and desktop displays

During collaborative data analysis participants are reliant on a shared common ground to be able to understand others' locations and actions, breakdowns in which require remedial action before other activities can continue. This thesis investigates the frequency and severity of common ground breakdowns that occur during collaborative navigation, when a wall-sized display user (master) directs a desktop user (slave) within a Collaborative Virtual Environment (CVE). A series of experiments were conducted to investigate this form of collaborative navigation and evaluate the developed solutions. These experiments required participants using a desktop display to view a wall-sized display user's navigation to targets within a 3D landscape, before attempting to re-visit these targets themselves. Experiments 1 and 2 were conducted to establish the typical frequency and severity of common ground breakdowns when the desktop user is attempting to find singular and multiple targets. Participants exhibited non-trivial levels of common ground breakdown over different types of movement and input device used by the wall-sized display master. Although they frequently had sufficient common ground to reach the approximate area of a target, this was insufficient for them to be able to complete the task. The remainder of the research investigated two distinct classes of solution to these breakdown: additional views and path visualisations. For additional views, a large field of view (FOV) context view and local overview map were provided. Experiment 3 evaluated their effect and demonstrated that neither of which reduced the level of common ground breakdown exhibited by desktop users. Behavioural changes of participants using the context view still led to similar task failures. For path visualisation, two representations of paths between targets, string and heatmap were provided. Experiment 4 provides evidence that both representations significantly increased participant's success rate. Behavioural data showed that participants visited areas unrelated to their search less frequently and remained closer to the desired path. In conclusion, this research has four major contributions. First, a classification of the types, severity and frequency of common ground breakdowns that occur between desktop and wall-sized display users conducting master-slave navigation within a CVE. Second, evidence is provided that additional views are not beneficial in reducing the level of breakdown for the desktop users. Third, path visualisations are shown to be effective in reducing the level of breakdown experienced by the desktop users, and allowing more effective navigational behaviour. Finally, the successful application of heatmaps in aiding navigation when previous applications have been limited to analytical use

Hippurate: the natural history of a mammalian-microbial co-metabolite

Hippurate, the glycine conjugate of benzoic acid, is a normal constituent of the endogenous urinary metabolite profile and has long been associated with the microbial degradation of certain dietary components, hepatic function and toluene exposure, and is also commonly used as a measure of renal clearance. Here we discuss the potential relevance of hippurate excretion with regards to normal endogenous metabolism and trends in excretion relating to gender, age, and the intestinal microbiota. Additionally, the significance of hippurate excretion with regards to disease states including obesity, diabetes, gastrointestinal diseases, impaired renal function, psychological disorders and autism, as well as toxicity and parasitic infection, are considered

NKG2D function protects the host from tumor initiation

The activation NKG2D receptor has been shown to play an important role in the control of experimental tumor growth and metastases expressing ligands for NKG2D; however, a function for this recognition pathway in host protection from de novo tumorigenesis has never been demonstrated. We show that neutralization of NKG2D enhances the sensitivity of wild-type (WT) C57BL/6 and BALB/c mice to methylcholanthrene (MCA)-induced fibrosarcoma. The importance of the NKG2D pathway was additionally illustrated in mice deficient for either IFN-γ or tumor necrosis factor–related apoptosis-inducing ligand, whereas mice depleted of natural killer cells, T cells, or deficient for perforin did not display any detectable NKG2D phenotype. Furthermore, IL-12 therapy preventing MCA-induced sarcoma formation was also largely dependent on the NKG2D pathway. Although NKG2D ligand expression was variable or absent on sarcomas emerging in WT mice, sarcomas derived from perforin-deficient mice were Rae-1+ and immunogenic when transferred into WT syngeneic mice. These findings suggest an important early role for the NKG2D in controlling and shaping tumor formation

A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry : application to the characterisation of metabolites in rat urine

A comprehensive Collision Cross Section (CCS) library was obtained via Travelling Wave Ion Guide mobility measurements through direct infusion (DI). The library consists of CCS and Mass Spectral (MS) data in negative and positive ElectroSpray Ionisation (ESI) mode for 463 and 479 endogenous metabolites, respectively. For both ionisation modes combined, TWCCSN2 data were obtained for 542 non-redundant metabolites. These data were acquired on two different ion mobility enabled orthogonal acceleration QToF MS systems in two different laboratories, with the majority of the resulting TWCCSN2 values (from detected compounds) found to be within 1% of one another. Validation of these results against two independent, external TWCCSN2 data sources and predicted TWCCSN2 values indicated to be within 1-2% of these other values. The same metabolites were then analysed using a rapid reversed-phase ultra (high) performance liquid chromatographic (U(H)PLC) separation combined with IM and MS (IM-MS) thus providing retention time (tr), m/z and TWCCSN2 values (with the latter compared with the DI-IM-MS data). Analytes for which TWCCSN2 values were obtained by U(H)PLC-IM-MS showed good agreement with the results obtained from DI-IM-MS. The repeatability of the TWCCSN2 values obtained for these metabolites on the different ion mobility QToF systems, using either DI or LC, encouraged the further evaluation of the U(H)PLC-IM-MS approach via the analysis of samples of rat urine, from control and methotrexate-treated animals, in order to assess the potential of the approach for metabolite identification and profiling in metabolic phenotyping studies. Based on the database derived from the standards 63 metabolites were identified in rat urine, using positive ESI, based on the combination of tr, TWCCSN2 and MS data.</p

A nonclassical non-Vα14Jα18 CD1d-restricted (type II) NKT cell is sufficient for down-regulation of tumor immunosurveillance

The importance of immunoregulatory T cells has become increasingly apparent. Both CD4+CD25+ T cells and CD1d-restricted NKT cells have been reported to down-regulate tumor immunity in mouse tumor models. However, the relative roles of both T cell populations have rarely been clearly distinguished in the same tumor models. In addition, CD1d-restricted NKT cells have been reported to play a critical role not only in the down-regulation of tumor immunity but also in the promotion of the immunity. However, the explanation for these apparently opposite roles in different tumor models remains unclear. We show that in four mouse tumor models in which CD1d-restricted NKT cells play a role in suppression of tumor immunity, depletion of CD4+CD25+ T cells did not induce enhancement of immunosurveillance. Surprisingly, among the two subpopulations of CD1d-restricted NKT cells, Vα14Jα18+ (type I) and Vα14Jα18− (type II) NKT cells, type I NKT cells were not necessary for the immune suppression. These unexpected results may now resolve the paradox in the role of CD1d-restricted NKT cells in the regulation of tumor immunity, in that type II NKT cells may be sufficient for negative regulation, whereas protection has been found to be mediated by α-galactosylceramide–responsive type I NKT cells

An integrated model for developing research skills in an undergraduate medical curriculum:appraisal of an approach using student selected components

Student selected components (SSCs), at that time termed special study modules, were arguably the most innovative element in Tomorrow’s Doctors (1993), the document from the General Medical Council that initiated the modernization of medical curricula in the UK. SSCs were proposed to make up one-third of the medical curriculum and provide students with choice, whilst allowing individual schools autonomy in how SSCs were utilized. In response, at the University of Edinburgh the undergraduate medical curriculum provides an integrated and sequential development and assessment of research skill learning outcomes, for all students in the SSC programme. The curriculum contains SSCs which provide choice to students in all 5 years. There are four substantial timetabled SSCs where students develop research skills in a topic and speciality of their choice. These SSCs are fully integrated and mapped with core learning outcomes and assessment, particularly with the ‘Evidence-Based Medicine and Research’ programme theme. These research skills are developed incrementally and applied fully in a research project in the fourth year. One-third of students also perform an optional intercalated one-year honours programme between years 2 and 3, usually across a wide range of honours schools at the biomedical science interface. Student feedback is insightful and demonstrates perceived attainment of research competencies. The establishment of these competencies is discussed in the context of enabling junior graduate doctors to be effective and confident at utilizing their research skills to effectively practice evidence-based medicine. This includes examining their own practice through clinical audit, developing an insight into the complexity of the evidence base and uncertainty, and also gaining a view into a career as a clinical academic

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high- quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open- source software pipeline, ‘ResPipe’

Microbes central to human reproduction

As studies uncover the breadth of microbes associated with human life, opportunities will emerge to manipulate and augment their functions in ways that improve health and longevity. From involvement in the complexities of reproduction and fetal/infant development, to delaying the onset of disease, and indeed countering many maladies, microbes offer hope for human well-being. Evidence is emerging to suggest that microbes may play a beneficial role in body sites traditionally viewed as being sterile. Although further evidence is required, we propose that much of medical dogma is about to change significantly through recognition and understanding of these hitherto unrecognized microbe–host interactions. A meeting of the International Scientific Association for Probiotics and Prebiotics held in Aberdeen, Scotland (June 2014), presented new views and challenged established concepts on the role of microbes in reproduction and health of the mother and infant. This article summarizes some of the main aspects of these discussions

Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: an exploratory study across Cambodia, Kenya, and the UK

Background: Antimicrobial resistance (AMR) in Enterobacterales is a global health threat. Capacity for individual-level surveillance remains limited in many countries, whilst population-level surveillance approaches could inform empiric antibiotic treatment guidelines. Methods: In this exploratory study, a novel approach to population-level prediction of AMR in Enterobacterales clinical isolates using metagenomic (Illumina) profiling of pooled DNA extracts from human faecal samples was developed and tested. Taxonomic and AMR gene profiles were used to derive taxonomy-adjusted population-level AMR metrics. Bayesian modelling, and model comparison based on cross-validation, were used to evaluate the capacity of each metric to predict the number of resistant Enterobacterales invasive infections at a population-level, using available bloodstream/cerebrospinal fluid infection data. Findings: Population metagenomes comprised samples from 177, 157, and 156 individuals in Kenya, the UK, and Cambodia, respectively, collected between September 2014 and April 2016. Clinical data from independent populations included 910, 3356 and 197 bacterial isolates from blood/cerebrospinal fluid infections in Kenya, the UK and Cambodia, respectively (samples collected between January 2010 and May 2017). Enterobacterales were common colonisers and pathogens, and faecal taxonomic/AMR gene distributions and proportions of antimicrobial-resistant Enterobacterales infections differed by setting. A model including terms reflecting the metagenomic abundance of the commonest clinical Enterobacterales species, and of AMR genes known to either increase the minimum inhibitory concentration (MIC) or confer clinically-relevant resistance, had a higher predictive performance in determining population-level resistance in clinical Enterobacterales isolates compared to models considering only AMR gene information, only taxonomic information, or an intercept-only baseline model (difference in expected log predictive density compared to best model, estimated using leave-one-out cross-validation: intercept-only model = -223 [95% credible interval (CI): -330,-116]; model considering only AMR gene information = -186 [95% CI: -281,-91]; model considering only taxonomic information = -151 [95% CI: -232,-69]). Interpretation: Whilst our findings are exploratory and require validation, intermittent metagenomics of pooled samples could represent an effective approach for AMR surveillance and to predict population-level AMR in clinical isolates, complementary to ongoing development of laboratory infrastructures processing individual samples