• Integrated analytics of microarray big data reveals robust gene signature

      Liu, Wanting; Peng, Yonghong; Tobin, Desmond J. (2015)
      The advance of high throughput biotechnology enables the generation of large amount of biomedical data. The microarray is increasingly a popular approach for the detection of genome-wide gene expression. Microarray data have thus increased significantly in public accessible database repositories, which provide valuable big data for scientific research. To deal with the challenge of microarray big data collected in different research labs using different experimental set-ups and on different bio-samples, this paper presents a primary study to evaluate the impact of two important factors (the origin of bio-samples and the quality of microarray data) on the integrated analytics of multiple microarray data. The aim is to enable the extraction of reliable and robust gene biomarkers from microarray big data. Our work showed that in order to enhance biomarker discovery from microarray big data (i) it is necessary to treat the microarray data differently in terms of their quality, (ii) it is recommended to stratifying (i.e., sub-group) the data according to the origin of bio-samples in the analytics.
    • Nano-Scale Observations of Tattoo Pigments in Skin by Atomic Force Microscopy

      Grant, Colin A.; Twigg, Peter C.; Tobin, Desmond J. (2015-03-26)
      In this study, we have shown how particles in carbon black tattoo ink accumulate in the human skin dermis using fine-resolution atomic force microscopy, with which a single ink particle in the collagenous network can be imaged. This information further demonstrates that tattoo inks are nano-particles. Further, we have deposited a commercially available tattoo ink on a glass slide and calculated a range of volumes for single ink particles.
    • Static and dynamic nanomechanical properties of human skin tissue using atomic force microscopy: Effect of scarring in the upper dermis.

      Grant, Colin A.; Twigg, Peter C.; Tobin, Desmond J. (06/07/2012)
      Following traumatic injury, skin has the capacity to repair itself through a complex cascade of biochemical change. The dermis, which contains a load-bearing collagenous network structure, is remodelled over a long period of time, affecting its mechanical behaviour. This study examines the nanomechanical and viscoelastic properties of the upper dermis from human skin that includes both healthy intact and scarred tissue. Extensive nanoindentation analysis shows that the dermal scar tissue exhibits stiffer behaviour than the healthy intact skin. The scar skin also shows weaker viscoelastic creep and capability to dissipate energy at physiologically relevant frequencies than the adjacent intact skin. These results are discussed in conjunction with a visual change in the orientation of collagenous fibrils in the scarred dermis compared with normal dermis, as shown by atomic force microscopy imaging.
    • Systematic associations between germ-line mutations and human cancers

      Al-Shammari, Mohamad H.; Tobin, Desmond J.; Peng, Yonghong (2016)
      The revolution in Big Data has opened the gate for new research challenges in biomedical science. The aim of this study was to investigate whether germ-line gene mutations are a significant factor in 29 major primary human cancers. Using data obtained from multiple biological databases, we identified 424 genes from 8879 cancer mutation records. By integrating these gene mutation records a human cancer map was constructed from which several key results were obtained. These include the observations that missense/nonsense and regulatory mutations might play central role in connecting cancers/genes, and tend to be distributed in all chromosomes. This suggests that, of all mutation classes missense/nonsense and regulatory mutation classes are over-expressed in human genome and so are likely to have a significant impact on human cancer aetiology and pathomechanism. This offers new insights into how the distribution and interconnections of gene mutations influence the development of cancers.
    • Tattoo ink nanoparticles in skin tissue and fibroblasts

      Grant, Colin A.; Twigg, Peter C.; Baker, Richard; Tobin, Desmond J. (2015-05-20)
      Tattooing has long been practised in various societies all around the world and is becoming increasingly common and widespread in the West. Tattoo ink suspensions unquestionably contain pigments composed of nanoparticles, i.e., particles of sub-100 nm dimensions. It is widely acknowledged that nanoparticles have higher levels of chemical activity than their larger particle equivalents. However, assessment of the toxicity of tattoo inks has been the subject of little research and ink manufacturers are not obliged to disclose the exact composition of their products. This study examines tattoo ink particles in two fundamental skin components at the nanometre level. We use atomic force microscopy and light microscopy to examine cryosections of tattooed skin, exploring the collagen fibril networks in the dermis that contain ink nanoparticles. Further, we culture fibroblasts in diluted tattoo ink to explore both the immediate impact of ink pigment on cell viability and also to observe the interaction between particles and the cells.