Make Art Real

The Make Art Real project aims to introduce new audiences to the arts. It supports Theme II of VCU’s Quest for Distinction by promoting and fostering creative expression through innovative collaborations. The project involves displaying existing connections between art and non-art disciplines, as well as making new connections. These unusual pairings are then placed on exhibition through a lunch-time lecture series named “Unexpected_Connections,” which allow faculty, staff, and students to lead and participate in discussions about the reality of art. The lecture series is the first sustainable and reoccurring program to be held in the Depot building, a multidisciplinary facility which is intended to foster interdisciplinary collaborations. The targeted audience includes faculty, staff, students, and members of the greater VCU community

rRNA sequencing in molecular microbiological diagnosis of bacterial infections in the autopsy setting

Diagnosing the aetiology of infectious diseases at autopsy, such as pneumonia, meningitis, sepsis or SUDI, is complicated due to issues including post mortem contamination, difficulty culturing fastidious organisms and subjective interpretation of polymicrobial cultures. Death of organisms may also occur post mortem, especially if antibiotics were given to the patient, but residual DNA from non-viable organisms, amenable to molecular detection, may remain. The 16S rRNA gene is present in all bacteria with conserved and hyper-variable regions along its length, allowing amplification and sequencing of all bacterial 16S sequences present in a sample. 16S sequencing offers potential advantages over culture-based diagnostics and is increasingly used in clinical practice. It has been used to identify bacteria in formalin fixed paraffin embedded (FFPE) surgical pathology specimens but its use has not been reported in autopsy diagnosis. This talk will summarise a study aimed to assess the utility of 16S sequencing as an adjunctive microbiological test in the autopsy. Our preliminary work has used post mortem lung tissue samples from children dying with pneumonia as part of the Pneumonia Etiology Research for Child Health (PERCH) project. The technique has identified known pathogens in some cases and provided additional diagnostic information in others. The presentation will discuss the technical aspects of 16S sequencing from FFPE and autopsy material, and the issues surrounding its application to diagnosis in comparison with standard culture based diagnostics on surgical/autopsy material

Ray Parenchymal Cells Contribute to Lignification of Tracheids in Developing Xylem of Norway Spruce

A comparative transcriptomic study and a single-cell metabolome analysis were combined to determine whether parenchymal ray cells contribute to the biosynthesis of monolignols in the lignifying xylem of Norway spruce (Picea abies). Ray parenchymal cells may function in the lignification of upright tracheids by supplying monolignols. To test this hypothesis, parenchymal ray cells and upright tracheids were dissected with laser-capture microdissection from tangential cryosections of developing xylem of spruce trees. The transcriptome analysis revealed that among the genes involved in processes typical for vascular tissues, genes encoding cell wall biogenesis-related enzymes were highly expressed in both developing tracheids and ray cells. Interestingly, most of the shikimate and monolignol biosynthesis pathway-related genes were equally expressed in both cell types. Nonetheless, 1,073 differentially expressed genes were detected between developing ray cells and tracheids, among which a set of genes expressed only in ray cells was identified. In situ single cell metabolomics of semi-intact plants by picoliter pressure probe-electrospray ionization-mass spectrometry detected monolignols and their glycoconjugates in both cell types, indicating that the biosynthetic route for monolignols is active in both upright tracheids and parenchymal ray cells. The data strongly support the hypothesis that in developing xylem, ray cells produce monolignols that contribute to lignification of tracheid cell walls. Transcriptomics combined with single-cell metabolomics give new information on the role of rays in lignification of developing xylem in Norway spruce.Peer reviewe

El Nin˜o Impact on Mollusk Biomineralization: Implications for Trace Element Proxy Reconstructions and the Paleo-Archeological Record

Marine macroinvertebrates are ideal sentinel organisms to monitor rapid environmental changes associated with climatic phenomena. These organisms build up protective exoskeletons incrementally by biologically-controlled mineralization, which is deeply rooted in long-term evolutionary processes. Recent studies relating potential rapid environmental fluctuations to climate change, such as ocean acidification, suggest modifications on carbonate biominerals of marine invertebrates. However, the influence of known, and recurrent, climatic events on these biological processes during active mineralization is still insufficiently understood. Analysis of Peruvian cockles from the 1982–83 large magnitude El Nin˜o event shows significant alterations of the chemico-structure of carbonate biominerals. Here, we show that bivalves modify the main biomineralization mechanism during the event to continue shell secretion. As a result, magnesium content increases to stabilize amorphous calcium carbonate (ACC), inducing a rise in Mg/Ca unrelated to the associated increase in sea-surface temperature. Analysis of variations in Sr/Ca also suggests that this proxy should not be used in these bivalves to detect the temperature anomaly, while Ba/Ca peaks are recorded in shells in response to an increase in productivity, or dissolved barium in seawater, after the event. Presented data contribute to a better understanding of the effects of abrupt climate change on shell biomineralization, while also offering an alternative view of bivalve elemental proxy reconstructions.Furthermore, biomineralization changes in mollusk shells can be used as a novel potential proxy to provide a more nuanced historical record of El Nin˜o and similar rapid environmental change events

A key role for apoplastic H2O2 in Norway spruce phenolic metabolism

Apoplastic events such as monolignol oxidation and lignin polymerization are difficult to study in intact trees. To investigate the role of apoplastic hydrogen peroxide (H2O2) in gymnosperm phenolic metabolism, an extracellular lignin-forming cell culture of Norway spruce (Picea abies) was used as a research model. Scavenging of apoplastic H2O2 by potassium iodide repressed lignin formation, in line with peroxidases activating monolignols for lignin polymerization. Time-course analyses coupled to candidate substrate-product pair network propagation revealed differential accumulation of low-molecular-weight phenolics, including (glycosylated) oligolignols, (glycosylated) flavonoids, and proanthocyanidins, in lignin-forming and H2O2-scavenging cultures and supported that monolignols are oxidatively coupled not only in the cell wall but also in the cytoplasm, where they are coupled to other monolignols and proanthocyanidins. Dilignol glycoconjugates with reduced structures were found in the culture medium, suggesting that cells are able to transport glycosylated dilignols to the apoplast. Transcriptomic analyses revealed that scavenging of apoplastic H2O2 resulted in remodulation of the transcriptome, with reduced carbon flux into the shikimate pathway propagating down to monolignol biosynthesis. Aggregated coexpression network analysis identified candidate enzymes and transcription factors for monolignol oxidation and apoplastic H2O2 production in addition to potential H2O2 receptors. The results presented indicate that the redox state of the apoplast has a profound influence on cellular metabolism

Teachers as writers: a systematic review

This paper is a critical literature review of empirical work from 1990-2015 on teachers as writers. It interrogates the evidence on teachers’ attitudes to writing, their sense of themselves as writers and the potential impact of teacher writing on pedagogy or student outcomes in writing. The methodology was carried out in four stages. Firstly, educational databases keyword searches located 438 papers. Secondly, initial screening identified 159 for further scrutiny, 43 of which were found to specifically address teachers’ writing identities and practices. Thirdly, these sources were screened further using inclusion/exclusion criteria. Fourthly, the 22 papers judged to satisfy the criteria were subject to in-depth analysis and synthesis. The findings reveal that the evidence base in relation to teachers as writers is not strong, particularly with regard to the impact of teachers’ writing on student outcomes. The review indicates that teachers have narrow conceptions of what counts as writing and being a writer and that multiple tensions exist, relating to low self-confidence, negative writing histories, and the challenge of composing and enacting teacher and writer positions in school. However, initial training and professional development programmes do appear to afford opportunities for reformulation of attitudes and sense of self as writer

Evaluation of sequence hybridisation for respiratory viruses using the Twist Biosciences Respiratory panel and the OneCodex Respiratory Virus sequence analysis workflow

Respiratory viral infections are a major global clinical problem, and rapid, cheap, scalable and agnostic diagnostic tests that capture genome-level information on viral variation are urgently needed. Metagenomic approaches would be ideal, but remain currently limited in that much of the genetic content in respiratory samples is human, and amplifying and sequencing the viral/pathogen component in an unbiased manner is challenging. PCR-based tests, including those which detect multiple pathogens, are already widely used, but do not capture information on strain-level variation; tests with larger viral repertoires are also expensive on a per-test basis. One intermediate approach is the use of large panels of viral probes or ‘baits’, which target or ‘capture’ sequences representing complete genomes amongst several different common viral pathogens; these are then amplified, sequenced and analysed with a sequence analysis workflow. Here we evaluate one such commercial bait capture method (the Twist Bioscience Respiratory Virus Research Panel) and sequence analysis workflow (OneCodex), using control (simulated) and patient samples head-to-head with a validated multiplex PCR clinical diagnostic test (BioFire FilmArray). We highlight the limited sensitivity and specificity of the joint Twist Bioscience/OneCodex approach, which are further reduced by shortening workflow times and increasing sample throughput to reduce per-sample costs. These issues with performance may be driven by aspects of both the laboratory (e.g. capacity to enrich for viruses present in low numbers), bioinformatics methods used (e.g. a limited viral reference database) and thresholds adopted for calling a virus as present or absent. As a result, this workflow would require further optimization prior to any implementation for respiratory virus characterization in a routine diagnostic healthcare setting

Species‐level, metagenomic and proteomic analysis of microbe‐immune interactions in severe asthma

Background: The airway microbiome in severe asthma has not been characterised at species‐level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in ‘type‐2 low’, neutrophilic asthma been defined. We performed an integrated species‐level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses. Methods: Sputum and nasal lavage samples were analysed using long‐read metagenomic sequencing with Nanopore and qPCR in two cross‐sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species‐level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O‐link. Results: The sputum microbiome in health and mild asthma displayed comparable microbial diversity. By contrast, 23% (19/81) of severe asthma microbiomes were dominated by a single respiratory pathogen, namely H. influenzae (n = 10), M. catarrhalis (n = 4), S. pneumoniae (n = 4) and P. aeruginosa (n = 1). Neutrophilic asthma was associated with H. influenzae, M. catarrhalis, S. pneumoniae and T. whipplei with elevated type‐1 cytokines and proteases; eosinophilic asthma with higher M. catarrhalis, but lower H. influenzae, and S. pneumoniae abundance. H. influenzae load correlated with Eosinophil Cationic Protein, elastase and IL‐10. R. mucilaginosa associated positively with IL‐6 and negatively with FGF. Bayesian network analysis also revealed close and distinct relationships of H. influenzae and M. catarrhalis with type‐1 airway inflammation. The microbiomes and cytokine milieu were distinct between upper and lower airways. Conclusions: This species‐level integrated analysis reveals central, but distinct associations between potentially pathogenic bacteria and airways inflammation in severe asthma