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Background: Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn. For example, a range of traditional statistical and computational pathway analysis approaches have been used to identify over-represented processes in microarray data derived from various disease states. However, most of these approaches tend not to exploit the full spectrum of gene expression data, or the various relationships and dependencies. Previously, we described a pathway enrichment analysis tool created in MATLAB that yields a Pathway Regulation Score (PRS) by considering signalling pathway topology, and the overrepresentation and magnitude of differentially-expressed genes (J Comput Biol 19:563-573, 2012). Herein, we extended this approach to include metabolic pathways, and described the use of a graphical user interface (GUI)., Results: Using input from a variety of microarray platforms and species, users are able to calculate PRS scores, along with a corresponding z-score for comparison. Further pathway significance assessment may be performed to increase confidence in the pathways obtained, and users can view Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway diagrams marked-up to highlight impacted genes., Conclusions: The PRS tool provides a filter in the isolation of biologically-relevant insights from complex transcriptomic data.

Background: Acne is a common disorder of the human pilosebaceous unit, yet the mechanisms underlying hyperkeratinisation and subsequent inflammation (comedogenesis) remain to be determined, although cutaneous pathogens are implicated. Previously, it was reported that the release of the cytokine interleukin-1α (IL-1α) by keratinocytes of the sebaceous duct was pivotal in the life cycle of the comedone, mediating both its development and its spontaneous resolution. Toll-like receptors are a family of molecules that recognise pathogen associated molecular patterns (PAMPs) presented by microorganisms, initiating a signalling cascade terminating in the release of antimicrobial compounds and cytokines., Methods: We used ex vivo sebaceous gland and primary monolayer keratinocyte culture, alongside ELISAs, immunohistochemistry, Western blotting and RT-PCR to investigate the contribution of TLR activation to acne pathogenesis., Results: We found TLR2 to be expressed in basal and infundibular keratinocytes, and sebaceous glands, and its activation provoked the release of IL-1α from primary human keratinocytes in vitro. The exposure of microdissected human sebaceous glands to PAMPs specific for TLR2 in vitro resulted in a pattern of IL-1α like cornification after seven days of exposure., Conclusions: TLR activation and secretion of IL-1α from keratinocytes may be initiating steps in comedogenesis and, therefore, critical to the pathophysiology of acne.

Background: Texture within biological specimens may reveal critical insights, while being very difficult to quantify. This is a particular problem in histological analysis. For example, cross-polar images of picrosirius stained skin reveal exquisite structure, allowing changes in the basketweave conformation of healthy collagen to be assessed. Existing techniques measure gross pathological changes, such as fibrosis, but are not sufficiently sensitive to detect more subtle and progressive pathological changes in the dermis, such as those seen in ageing. Moreover, screening methods for cutaneous therapeutics require accurate, unsupervised and high-throughput image analysis techniques., Results: By analyzing spectra of images post Gabor filtering and Fast Fourier Transform, we were able to measure subtle changes in collagen fibre orientation intractable to existing techniques. We detected the progressive loss of collagen basketweave structure in a series of chronologically aged skin samples, as well as in skin derived from a model of type 2 diabetes mellitus., Conclusions: We describe a novel bioimaging approach with implications for the evaluation of pathology in a broader range of biological situations.