Changes in chromatin structure during processing of wax-embedded tissue sections

The use of immunofluorescence (IF) and fluorescence in situ hybridisation (FISH) underpins much of our understanding of how chromatin is organised in the nucleus. However, there has only recently been an appreciation that these types of study need to move away from cells grown in culture and towards an investigation of nuclear organisation in cells in situ in their normal tissue architecture. Such analyses, however, especially of archival clinical samples, often requires use of formalin-fixed paraffin wax-embedded tissue sections which need addition steps of processing prior to IF or FISH. Here we quantify the changes in nuclear and chromatin structure that may be caused by these additional processing steps. Treatments, especially the microwaving to reverse fixation, do significantly alter nuclear architecture and chromatin texture, and these must be considered when inferring the original organisation of the nucleus from data collected from wax-embedded tissue sections

The reengineering of a software system for glaucoma analysis

Glaucoma is a destructive eye disease that causes blindness in individuals displaying little or no symptoms. There is no cure as yet though there are treatments that can arrest its effects or slow its development. The earlier the disease is detected, the more likely the treatment will be successful; however early detection of the disease can be difficult. This highlights the importance of ophthalmologists having access to tools that can assist in accurately diagnosing glaucoma and other retinal diseases as early as possible. The stereo optic disc analyser (SODA) software package is a tool intended to be used by ophthalmologists, to aid in the accurate detection of retinal diseases. SODA will use stereoscopy and three-dimensional image analysis to assist in accurately detecting changes in the retina, caused by diseases such as glaucoma. This paper will focus on the reengineering and redesign of the SODA software package to overcome the shortcomings inherent in its prototype implementation and develop a package that can be commercialised. Software Engineering principles and the software development lifecycle, along with principles of object-orientation and usability, have been used to establish a framework for SODA, improve its accuracy, enhance its usability and to redevelop the product into an implementation that can later be commercialised

The longitudinal assessment of vascular parameters of the retine and their correlations with systemic characteristics in type 2 diabetes: a pilot study

The aim of the study was to assess various retinal vessel parameters of diabetes mellitus (DM) patients and their correlations with systemic factors in type 2 DM. A retrospective exploratory study in which 21 pairs of baseline and follow-up images of patients affected by DM were randomly chosen from the Sankara Nethralaya–Diabetic Retinopathy Study (SN DREAMS) I and II datasets. Patients’ fundus was photographed, and the diagnosis was made based on Klein classification. Vessel thickness parameters were generated using a web-based retinal vascular analysis platform called VASP. The thickness changes between the baseline and follow-up images were computed and normalized with the actual thicknesses of baseline images. The majority of parameters showed 10~20% changes over time. Vessel width in zone C for the second vein was significantly reduced from baseline to follow-up, which showed positive correlations with systolic blood pressure and serum high-density lipoproteins. Fractal dimension for all vessels in zones B and C and fractal dimension for vein in zones A, B and C showed a minimal increase from baseline to follow-up, which had a linear relationship with diastolic pressure, mean arterial pressure, serum triglycerides (p \u3c 0.05). Lacunarity for all vessels and veins in zones A, B and C showed a minimal decrease from baseline to follow-up which had a negative correlation with pulse pressure and positive correlation with serum triglycerides (p \u3c 0.05). The vessel widths for the first and second arteries significantly increased from baseline to follow-up and had an association with high-density lipoproteins, glycated haemoglobin A1C, serum low-density lipoproteins and total serum cholesterol. The central reflex intensity ratio for the second artery was significantly decreased from baseline to follow-up, and positive correlations were noted with serum triglyceride, serum low-density lipoproteins and total serum cholesterol. The coefficients for branches in zones B and C artery and the junctional exponent deviation for the artery in zone A decreased from baseline to follow-up showed positive correlations with serum triglycerides, serum low-density lipoproteins and total serum cholesterol. Identifying early microvascular changes in diabetic patients will allow for earlier intervention, improve visual outcomes and prevent vision loss