ToF-SIMS mediated analysis of human lung tissue reveals increased iron deposition in COPD (GOLD IV) patients

Chronic obstructive pulmonary disease (COPD) is a debilitating lung disease that is currently the third leading cause of death worldwide. Recent reports have indicated that dysfunctional iron handling in the lungs of COPD patients may be one contributing factor. However, a number of these studies have been limited to the qualitative assessment of iron levels through histochemical staining or to the expression levels of iron-carrier proteins in cells or bronchoalveolar lavage fluid. In this study, we have used time of flight secondary ion mass spectrometry (ToF-SIMS) to visualize and relatively quantify iron accumulation in lung tissue sections of healthy donors versus severe COPD patients. An IONTOF 5 instrument was used to perform the analysis, and further multivariate analysis was used to analyze the data. An orthogonal partial least squares discriminant analysis (OPLS-DA) score plot revealed good separation between the two groups. This separation was primarily attributed to differences in iron content, as well as differences in other chemical signals possibly associated with lipid species. Further, relative quantitative analysis revealed twelve times higher iron levels in lung tissue sections of COPD patients when compared to healthy donors. In addition, iron accumulation observed within the cells was heterogeneously distributed, indicating cellular compartmentalization

Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay

BACKGROUND: The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, selection, extension, and ligation (DASL) assay is a platform for gene expression profiling from FFPE tissue and hence could allow analysis of large collections of tissue with associated clinical data from existing archives, therefore facilitating the development of novel biomarkers. METHOD: RNA isolated from matched fresh frozen (FF) and FFPE cancer specimens was profiled using both the DASL whole-genome (WG) platform, and Illumina BeadArray’s, and results were compared. Samples utilized were obtained from the breast cancer tumour bank held at the Cambridge University Hospitals NHS Foundation Trust. RESULTS: The number of reliably detected probes was comparable between the DASL and BeadArray platforms, indicating that the source of RNA did not result in a significant difference in the detection rates (Mean probes- 17114 in FFPE & 17400 in FF). There was a significant degree of correlation between replicates within the FF and FFPE sample sets (r(2) = 0.96–0.98) as well as between the two platforms (DASL vs. BeadArray r(2) = range 0.83–0.89). Hierarchical clustering using the most informative probes showed that replicate and matched samples were grouped into the same sub-cluster, regardless of whether RNA was derived from FF or FFPE tissue. CONCLUSION: Both FF and FFPE material generated reproducible gene expression profiles, although there was more noise in profiles from FFPE specimens. We have shown that the DASL WG platform is suitable for profiling formalin-fixed paraffin-embedded samples, but robust bioinformatics analysis is required

Linking space and nature syntaxes : the influence of a natural view through observed behaviour at Arcosanti, Arizona, USA

The world’s urban population is rapidly growing, now exceeding its rural population, and is expected to reach 70% of the world’s total by 2050. Research in environmental psychology increasingly supports the Biophilia Hypothesis which holds that our connection with Nature is innate. Thus, how do we maintain a human connection to Nature in an increasingly urbanising world? The research explores the boundary between built and natural environments, specifically how proximity, initially through visual connections, to Nature affects how people use social spaces. Case study work is being undertaken at Arcosanti urban laboratory in the Arizona desert. Through development of a Space/Nature Syntax methodology applied within a uniquely compact urban form, this research attempts to understand how maintaining an instinctive bond with Nature can enhance social interactions and inform future design choices within built environments. Initial results support relationships of varying strengths between spatial connectivity, visibility of Nature, and types of social interactions. This paper explores the potential of the cross-disciplinary Space/Nature Syntax methodology as a design and analysis tool, projecting where social interactions within a built space could be influenced by visibility of Nature; where informed design can allow for the essential human/Nature connection to thrive