Podcasts Episode 02: Greg Stilson

At the time of this podcast, Mr. Greg Stilson was a Product Director at Humanware and since has become a Product Director at Aira. In this podcast, Mr. Stilson, who happens to be blind, reflects on the advances in orientation aids and the ways that these technologies complement older technologies, such as canes and tactile maps. Image credit: LinkedIn Greg Stilson profilehttps://pdxscholar.library.pdx.edu/sped_podcast/1001/thumbnail.jp

Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers

Background: Gene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny of their DNA sequence. Whilst comparative genomics approaches have identified thousands of putative regulatory elements, our knowledge of their mechanism of action is poor and very little progress has been made in systematically de-coding them. Results: Here, we identify ancient functional signatures within vertebrate conserved non-coding elements (CNEs) through a combination of phylogenetic footprinting and functional assay, using genomic sequence from the sea lamprey as a reference. We uncover a striking enrichment within vertebrate CNEs for conserved binding-site motifs of the Pbx-Hox hetero-dimer. We further show that these predict reporter gene expression in a segment specific manner in the hindbrain and pharyngeal arches during zebrafish development. Conclusions: These findings evoke an evolutionary scenario in which many CNEs evolved early in the vertebrate lineage to co-ordinate Hox-dependent gene-regulatory interactions that pattern the vertebrate head. In a broader context, our evolutionary analyses reveal that CNEs are composed of tightly linked transcription-factor binding-sites (TFBSs), which can be systematically identified through phylogenetic footprinting approaches. By placing a large number of ancient vertebrate CNEs into a developmental context, our findings promise to have a significant impact on efforts toward de-coding gene-regulatory elements that underlie vertebrate development, and will facilitate building general models of regulatory element evolution

Partnership Handbook for Primary Education (2012-13)

A handbook for partners working in collaboration with Edge Hill University in the Primary Phase of Education. The handbook contains all aspects relating to partnership, including policies and procedures relevant to training teachers

Host behaviour and exposure risk in an insect-pathogen interaction

1. Studies of variability in host resistance to disease generally emphasize variability in susceptibility given exposure, neglecting the possibility that hosts may vary in behaviours that affect the risk of exposure. 2. In many insects, horizontal transmission of baculoviruses occurs when larvae consume foliage contaminated by the cadavers of virus-infected conspecific larvae; so, host behaviour may have a strong effect on the risk of infection. 3. We studied variability in the behaviour of gypsy moth (Lymantria dispar) larvae, which are able to detect and avoid virus-contaminated foliage. 4. Our results show that detection ability can be affected by the family line that larvae originate from, even at some distance froma virus-infected cadaver, and suggest that cadaver-detection ability may be heritable. 5. There is thus the potential for natural selection to act on cadaver-detection ability, and thereby to affect the dynamics of pathogen-driven cycles in gypsy moth populations. 6. We argue that host behaviour is a neglected component in studies of variability in disease resistance. © 2010 The Authors. Journal compilation © 2010 British Ecological Society

Nature-based solutions forming urban intervention approaches to anthropogenic climate change:a quantitative literature review

Discussion around anthropogenic climate change has occurred for over 100 years. However, in recent decades, these discussions have intensified due to increased confidence in scientific research highlighting adverse effects, increased knowledge breadth in climate science, and heightened public and political awareness and engagement on the topic. Climate change is now acknowledged as one of the biggest challenges and threats to modern lifestyles. Nature-based solutions (NBS), as a mediator and mitigator to adverse climate change effects, is an emerging area of expanding research collateral and practitioner literacy. To highlight current NBS knowledge, existing knowledge gaps, and research trends, a Quantitative Systematic Literature Review (QSLR) was undertaken (n = 54). This QSLR reveals the short temporal span of articles relating to NBS as a response to climate change, with most articles being of a research style format. NBS research focus areas were found to be dominated by ecological and infrastructure approaches to climate change mitigation, and ecological and technical positions were found to be most topical across the current climate change literature. Multiple knowledge gaps were identified by the review, namely the lack of broader conceptual approaches and knowledge acquisition regarding climate change responses via NBS, as well as the psychological relationship humans share with NBS and climate change, adverse or otherwise. These knowledge gaps highlight where future research inquiry may be directed to increase the value and completion of this research area. It is hoped that this QSLR will assist in increasing the profile of NBS in the multidisciplinary and complex response to anthropogenic climate change, as well as contribute to the growth in investment and implementation of NBS assets for a rigid and resilient global future

Robust processing of diffusion weighted image data

The work presented in this thesis comprises a proposed robust diffusion weighted magnetic resonance imaging (DW-MRI) pipeline, each chapter detailing a step designed to ultimately transform raw DW-MRI data into segmented bundles of coherent fibre ready for more complex analysis or manipulation. In addition to this pipeline we will also demonstrate, where appropriate, ways in which each step could be optimized for the maxillofacial region, setting the groundwork for a wider maxillofacial modelling project intended to aid surgical planning. Our contribution begins with RESDORE, an algorithm designed to automatically identify corrupt DW-MRI signal elements. While slower than the closest alternative, RESDORE is also far more robust to localised changes in SNR and pervasive image corruptions. The second step in the pipeline concerns the retrieval of accurate fibre orientation distribution functions (fODFs) from the DW-MRI signal. Chapter 4 comprises a simulation study exploring the application of spherical deconvolution methods to `generic' fibre; finding that the commonly used constrained spherical harmonic deconvolution (CSHD) is extremely sensitive to calibration but, if handled correctly, might be able to resolve muscle fODFs in vivo. Building upon this information, Chapter 5 conducts further simulations and in vivo image experimentation demonstrating that this is indeed the case, allowing us to demonstrate, for the first time, anatomically plausible reconstructions of several maxillofacial muscles. To complete the proposed pipeline, Chapter 6 then introduces a method for segmenting whole volume streamline tractographies into anatomically valid bundles. In addition to providing an accurate segmentation, this shape-based method does not require computationally expensive inter-streamline comparisons employed by other approaches, allowing the algorithm to scale linearly with respect to the number of streamlines within the dataset. This is not often true for comparison based methods which in the best case scale in higher linear time but more often by O(N2) complexity

Student aspirations for higher education in Central Queensland : a survey of school students’ navigational capacities

In recent times, student aspiration for higher education has become the subject of Australian Government policy and school/university partnerships. A perceived shortfall in aspiration for higher education – particularly by under-represented groups – is seen to be frustrating the achievement of the Government’s targets for universities

A Reporter Assay in Lamprey Embryos Reveals Both Functional Conservation and Elaboration of Vertebrate Enhancers

The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species