Interview: Chris Anderton, CDRS Web Developer

Chris Anderton, Web Developer at the Center for Digital Research and Scholarship, discusses his experiences adapting to an Agile project methodology and designing the user interfaces for Dangerous Citizens

Relationships between polymer additive molecular structure and intumescent flame retardant behaviour.

This thesis describes studies of the relationship between the molecular structure of a range of organophosphorus-based polymer additives and their ability to confer intumescent flame retardant properties on the resulting polymers. The development of intumescent fire retardants is discussed along with the principles of flame retardancy in general. Much of the work centred around the chemistry of a key starting material, pentaerythritol phosphate (PEPA). This compound was found to be less reactive than expected, due to a combination of its neopentyl type structure and the electron withdrawing effect of the phosphoric ester functionality.Various derivatives of PEPA were synthesised, most containing reactive functional groups which facilitated future development of the compound. The derivatives containing no reactive groups were investigated for their intumescent behaviour in their own right. Derivatives of PEPA containing an acidic functionality were utilised in the production of intumescent salt systems using cations with a high nitrogen content in the form of s-triazines. The most promising was the trimethylolmelamine salt of a bis-PEPA derivative of phosphoric acid, which, on testing, proved to be more effective than the current "state of the art" intumescent additive. Metal salts of acidic PEPA-derivatives were also investigated. Derivatives of PEPA containing a carbon-carbon double bond were investigated for their potential to polymerise and thus form more stable additives. Only one such polymer was successfully synthesised, that being poly (PEPA methacrylate). Despite being non-intumescent, due to its high thermal stability this polymer has potential as a flame retardant additive. The monomer was found to copolymerise with methyl methacrylate to form a polymer of high thermal stability. When investigating the relationship between the molecular structure of the compounds developed and their intumescent behaviour, it was observed that only compounds containing an ionisable hydrogen atom exhibited intumescent decomposition on pyrolysis

Neurofilament heavy chain side arm phosphorylation regulates axonal transport of neurofilaments

Neurofilaments possess side arms that comprise the carboxy-terminal domains of neurofilament middle and heavy chains (NFM and NFH); that of NFH is heavily phosphorylated in axons. Here, we demonstrate that phosphorylation of NFH side arms is a mechanism for regulating transport of neurofilaments through axons. Mutants in which known NFH phosphorylation sites were mutated to preclude phosphorylation or mimic permanent phosphorylation display altered rates of transport in a bulk transport assay. Similarly, application of roscovitine, an inhibitor of the NFH side arm kinase Cdk5/p35, accelerates neurofilament transport. Analyses of neurofilament movement in transfected living neurons demonstrated that a mutant mimicking permanent phosphorylation spent a higher proportion of time pausing than one that could not be phosphorylated. Thus, phosphorylation of NFH slows neurofilament transport, and this is due to increased pausing in neurofilament movement

Expanding Molecular Coverage in Mass Spectrometry Imaging of Microbial Systems Using Metal-Assisted Laser Desorption/Ionization

Mass spectrometry imaging (MSI) is becoming an increasingly popular analytical technique to investigate microbial systems. However, differences in the ionization efficiencies of distinct MSI methods lead to biases in terms of what types and classes of molecules can be detected. Here, we sought to increase the molecular coverage of microbial colonies by employing metal-assisted laser desorption/ionization (MetA-LDI) MSI, and we compared our results to more commonly utilized matrix-assisted laser desorption/ionization MALDI MSI. We found substantial ( approximately 67%) overlap in the molecules detected in our analysis of Bacillus subtilis colony biofilms using both methods, but each ionization technique did lead to the identification of a unique subset of molecular species. MetA-LDI MSI tended to identify more small molecules and neutral lipids, whereas MALDI MSI more readily detected other lipids and surfactin species. Putative annotations were made using METASPACE, Metlin, and the BsubCyc database. These annotations were then confirmed from analyses of replicate bacterial colonies using liquid extraction surface analysis tandem mass spectrometry. Additionally, we analyzed B. subtilis biofilms in a polymer-based emulated soil micromodel using MetA-LDI MSI to better understand bacterial processes and metabolism in a native, soil-like environment. We were able to detect different molecular signatures within the micropore regions of the micromodel. We also show that MetA-LDI MSI can be used to analyze microbial biofilms from electrically insulating material. Overall, this study expands the molecular universe of microbial metabolism that can be visualized by MSI. IMPORTANCE Matrix-assisted laser desorption/ionization mass spectrometry imaging is becoming an important technique to investigate molecular processes within microbial colonies and microbiomes under different environmental conditions. However, this method is limited in terms of the types and classes of molecules that can be detected. In this study, we utilized metal-assisted laser desorption/ionization mass spectrometry imaging, which expanded the range of molecules that could be imaged from microbial samples. One advantage of this technique is that the addition of a metal helps facilitate ionization from electrically nonconductive substrates, which allows for the investigation of biofilms grown in polymer-based devices, like soil-emulating micromodels

Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams

High resolution imaging mass spectrometry could become a valuable tool for cell and developmental biology, but both, high spatial and mass spectral resolution are needed to enable this. In this report, we employed Bi3 bombardment time-of-flight (Bi3 ToF-SIMS) and C60 bombardment Fourier transform ion cyclotron resonance secondary ion mass spectrometry (C60 FTICR-SIMS) to image Dictyostelium discoideum aggregation streams. Nearly 300 lipid species were identified from the aggregation streams. High resolution mass spectrometry imaging (FTICR-SIMS) enabled the generation of multiple molecular ion maps at the nominal mass level and provided good coverage for fatty acyls, prenol lipids, and sterol lipids. The comparison of Bi3 ToF-SIMS and C60 FTICR-SIMS suggested that while the first provides fast, high spatial resolution molecular ion images, the chemical complexity of biological samples warrants the use of high resolution analyzers for accurate ion identification

An exploratory study looking at the relationship marketing techniques used in the music festival industry

There are current issues and trends in the music festival market, which may affect the success of an event, and market saturation is at the forefront of these issues. Previous literature, maintaining the need for a marketing approach to festivals, identifi es the need for maintaining strong stakeholder relationships in order to succeed in a business environment; attention has been focused to the theory of relationship marketing (RM) because of the recognition that this practice is complementary to the marketing of festivals. The very nature of the music festival as an annual, usually, 4-day event means that effective marketing is needed to keep connections with the consumer throughout the year. This article focuses on the RM techniques utilised within the music festival industry from the viewpoint of the festival organiser in an attempt to establish how festival organisations value and monitor organisational relationships. This article explores the extent to which these relationships are valued and managed; furthermore, the variations between these intricate relationships are considered by focusing on those held with the organisation ’ s consumers and sponsors, the results of which have provided the ability to establish the importance and relevance of RM to the industry and further identify the marketing communication methods employed to establish and maintain such relationships. In-depth, convergent interviews have been conducted with a segment of music festival organisers from a range of events. The results have been integrated with the study of current literature to best exemplify these issues. It has been established that RM has a strong role in today ’ s commercial and independent music festival industry; technological advances are enabling the organiser to support online relationships further and increase consumer loyalty. There is a need to expand the research further because of the complexity of organisational relationships and the varying categories of festivals

Metabolic Noise and Distinct Subpopulations Observed by Single Cell LAESI Mass Spectrometry of Plant Cells in situ

Phenotypic variations and stochastic expression of transcripts, proteins, and metabolites in biological tissues lead to cellular heterogeneity. As a result, distinct cellular subpopulations emerge. They are characterized by different metabolite expression levels and by associated metabolic noise distributions. To capture these biological variations unperturbed, highly sensitive in situ analytical techniques are needed that can sample tissue embedded single cells with minimum sample preparation. Optical fiber-based laser ablation electrospray ionization mass spectrometry (f-LAESI-MS) is a promising tool for metabolic profiling of single cells under ambient conditions. Integration of this MS-based platform with fluorescence and brightfield microscopy provides the ability to target single cells of specific type and allows for the selection of rare cells, e.g., excretory idioblasts. Analysis of individual Egeria densa leaf blade cells (n = 103) by f-LAESI-MS revealed significant differences between the prespecified subpopulations of epidermal cells (n = 97) and excretory idioblasts (n = 6) that otherwise would have been masked by the population average. Primary metabolites, e.g., malate, aspartate, and ascorbate, as well as several glucosides were detected in higher abundance in the epidermal cells. The idioblasts contained lipids, e.g., PG(16:0/18:2), and triterpene saponins, e.g., medicoside I and azukisaponin I, and their isomers. Metabolic noise for the epidermal cells were compared to results for soybean (Glycine max) root nodule cells (n = 60) infected by rhizobia (Bradyrhizobium japonicum). Whereas some primary metabolites showed lower noise in the latter, both cell types exhibited higher noise for secondary metabolites. Post hoc grouping of epidermal and root nodule cells, based on the abundance distributions for certain metabolites (e.g., malate), enabled the discovery of cellular subpopulations characterized by different mean abundance values, and the magnitudes of the corresponding metabolic noise. Comparison of prespecified populations from epidermal cells of the closely related E. densa (n = 20) and Elodea canadensis (n = 20) revealed significant differences, e.g., higher sugar content in the former and higher levels of ascorbate in the latter, and the presence of species-specific metabolites. These results demonstrate that the f-LAESI-MS single cell analysis platform has the potential to explore cellular heterogeneity and metabolic noise for hundreds of tissue-embedded cells

First Plant Cell Atlas symposium report

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber-infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA’s success: identifying homologous cell-type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user-friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community-supported data evaluation metrics, accelerating plant research necessary for human and environmental health

The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T_eff<5000 K and in metallicity estimates for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SDSS-III Sloan Extension for Galactic Understanding and Exploration-2 (SEGUE-2). The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) along with another year of data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at http://www.sdss3.org/dr