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Abstract Hendra virus (HeV) was discovered in 1994 in Australia. Limited genomic data have hindered comprehensive understanding of HeV’s evolutionary dynamics. Here we recovered 48 HeV genomes from bats and 9 from horses from Australia between 2016 and 2020, revealing four distinct clades. Each clade was distributed over a large spatial area with multiple clades co-circulating within a single bat roost on the same day and over consecutive years. The diversity and temporal stability of co-circulating clades suggest that viral dynamics are driven by episodic shedding of existing lineages maintained at the population level, rather than immune-driven strain-replacement dynamics. HeV isolates of different clades displayed variation in phenotypic properties but minimal antigenic differences. We provide an overview of evolutionary dynamics, phenotypic properties and assessment of countermeasures for HeV, and provide insights into the processes that maintain virus diversity in bats and influence the potential for viral emergence. 

Mass spectrometry imaging (MSI) is a powerful scientific tool for understanding the spatial distribution of biochemical compounds in tissue structures. In this paper, we introduce three novel approaches in MSI data processing to perform the tasks of data augmentation, feature ranking, and image registration. We use these approaches in conjunction with non-negative matrix factorization (NMF) to resolve two of the biggest challenges in MSI data analysis, namely: 1) the large file sizes and associated computational resource requirements and 2) the complexity of interpreting the very high dimensional raw spectral data. There are many dimensionality reduction techniques that address the first challenge but do not necessarily result in readily interpretable features, leaving the second challenge unaddressed. We demonstrate that NMF is an effective dimensionality reduction algorithm that reduces the size of MSI datasets by three orders of magnitude with limited loss of information, yielding spatial and spectral components with meaningful correlation to tissue structure that may be used directly for subsequent data analysis without the need for additional clustering steps. This analysis is demonstrated on an MSI dataset from female Sprague-Dawley rats for an animal model of comorbid visceral pain hypersensitivity (CPH). We find that high-dimensional MSI data (∼ 100,000 ions per pixel) can be reduced to 20 spectral NMF components with < 20% loss in reconstruction accuracy. The resulting spatial NMF components are reproducible and correlate well with H&E-stained tissue images. These components may also be used to generate images with enhanced specificity for different tissue types. Small patches of NMF data (i.e., 20 spatial NMF components over 20 × 20 pixels) provide an accuracy of ∼ 87% in classifying CPH vs naïve control subjects. This paper presents the novel data processing methodologies that were used to produce these results, encompassing novel data processing pipelines for data augmentation to support training for classification, ranking of features according to their contribution to classification, and image registration to enhance tissue-specific imaging. 

Exposure to environmental contaminants can result in profound effects on the host immune system. One class of environmental toxicants, known as dioxins, are persistent environmental contaminants termed “forever chemicals”. The archetype toxicant from this group of chemicals is 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD), an immunotoxicant that activates the aryl-hydrocarbon receptor pathway leading to a variety of changes in immune cell responses. Immune cell functions are crucial to the development and maintenance of healthy reproduction. Immune cells facilitate tolerance between at the maternal-fetal interface between the parent and the semi-allogenic fetus and help defend the gravid reproductive tract from infectious assault. Epidemiological studies reveal that exposure to environmental contaminants (such as TCDD) are linked to adverse reproductive health outcomes including endometriosis, placental inflammation, and preterm birth. However, little is known about the molecular mechanisms that underpin h