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Donald, A.

Publications and source records attributed to Donald, A..

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The impact of fibronection stripe patterns on the cellular and nuclear morphology of fibroblasts

The effect of biochemical environmental signals on cell mechanisms has been the subject of numerous studies for a long time. However, the in-vitro studies of biophysical cues on cells and tissues have recently become a popular focus of research. The development of micro-fabrication techniques has allowed the study of certain aspects of cell-substrate interactions in a more detailed form. Micro-topographical patterns on the cell substrates have been used to study many cell functions such as cell migration, adhesion, gene expression, cell division and differentiation. An understanding of cell-substrate interactions and the potential ability to control the interactions have very important applications in the field of tissue engineering and regenerative medicine. We have fabricated ridge-groove micro patterns on polydimethylsiloxane (PDMS) substrates with different ridge widths (8m, 10m, 12 m, 25m and 50m) using standard photolithography technique. We used these patterns to print fibronectin stripes on PDMS substrates. NIH/3T3 fibroblast cells were cultured on these stripes and the dynamics of morphological changes were monitored in steady spreading phase (S-phase). Our data revealed that the thickness of the cell, measured by confocal microscopy, is considerably larger (approximately 40%) among the cells spreading on narrower stripes (8m, 10m and 12m) compared to the cells expanding on wider (including control) patterns. The number of perinuclear actin stress fibers is significantly lower among narrower stripes which probably explains the cell thickness results. Confocal microscopy revealed that the cellular volume increases during cell adhesion processes and volume increase is positively correlated with the width of stripes. Nuclear volume also increases considerably during cell adhesion; however, confining cells on fibronectin stripes reduces nuclear volume enlargement independent from the of stripe size.

biophysics

Detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

PurposeMutations in GBA cause Gaucher disease when biallelic, and are strong risk factors for Parkinsons disease when heterozygous. GBA analysis is complicated by the nearby pseudogene. We aimed to design and validate a method for sequencing GBA on the Oxford Nanopore MinION.\n\nMethodsWe sequenced an 8.9 kb amplicon from DNA samples of 17 individuals, including patients with Parkinsons and Gaucher disease, on older and current (R9.4) flow cells. These included samples with known mutations, assessed in a blinded fashion on the R9.4 data. We used NanoOK for quality metrics, two different aligners (Graphmap and NGMLR), Nanopolish and Sniffles to call variants, and Whatshap for phasing.\n\nResultsWe detected all known mutations, including the common p.N409S (N370S) and p.L483P (L444P), and three rarer ones, at the correct zygosity, as well as intronic SNPs. In a sample with the complex RecNciI allele, we detected an additional coding mutation, and a 55-base pair deletion. We confirmed compound heterozygosity where relevant. False positives were easily identified.\n\nConclusionThe Oxford Nanopore MinION can detect missense mutations and an exonic deletion in this difficult gene, with the added advantage of phasing and intronic analysis. It can be used as an efficient diagnostic tool.

genetics