A perfusion protocol for lizards, including a method for brain removal

The goal of fixation is to rapidly and uniformly preserve tissue in a life-like state. Perfusion achieves optimal fixation by pumping fixative directly through an animal's circulatory system. Standard perfusion techniques were developed primarily for application in mammals, which are traditional neuroscience research models. Increasingly, other vertebrate groups are also being used in neuroscience. Following mammalian perfusion protocols for non-mammalian vertebrates often results in failed perfusions. Here, I present a modified perfusion protocol suitable for lizards. Though geared towards standard brain perfusion, this protocol is easily modified for the perfusion of other tissues and for various specialized histological techniques. The two aortas of the lizard heart, emerging from a single ventricle, mean that care must be taken to place the perfusion needle in the correct aorta, unlike in mammals.Only the head and neck perfuse - the visceral organs will not decolour, and the body may not twitch.I also include a method for removing a lizard brain, which differs from mammals due to the incomplete and thicker skull of the lizard.Funding was provided by grants from the Australian National University (APA-31/2011) and the Canadian National Science and Engineering Research Council (PGSD3-415253-2012)

Automatic Layout and Label Management for UML Sequence Diagrams

Sequence diagrams belong to the most commonly used types of UML diagrams. There is research on desirable aesthetics, but to our knowledge no published layout algorithms, although several have been developed. This might be due to the rigid specifcation of sequence diagrams that seems to make laying them out quite easy. However, as we argue here, naive algorithms do not always produce desirable solutions. We present a layout algorithm that can compute the order of lifelines according to different optimization criteria. We also look at the problem of diagram size by introducing vertical compaction to sequence diagrams and by applying label management to compact them horizontally. We evaluate our methods with 50 real-world sequence diagrams

State-resolved translation energy distributions for NCO photodissociation

Alexandra A. Hoops, Ryan T. Bise, Jason R. Gascooke, and Daniel M. Neumar

Retinal topography and microhabitat diversity in a group of dragon lizards

The well‐studied phylogeny and ecology of dragon lizards and their range of visually mediated behaviors provide an opportunity to examine the factors that shape retinal organization. Dragon lizards consist of three evolutionarily stable groups based on their shelter type, including burrows, shrubs, and rocks. This allows us to test whether microhabitat changes are reflected in their retinal organization. We examined the retinae of three burrowing species (Ctenophorus pictus, C. gibba, and C. nuchalis), and three species that shelter in rock crevices (C. ornatus, C. decresii, and C. vadnappa). We used design‐based stereology to sample both the photoreceptor array and neurons within the retinal ganglion cell layer to estimate areas specialized for acute vision. All species had two retinal specializations mediating enhanced spatial acuity: a fovea in the retinal center and a visual streak across the retinal equator. Furthermore, all species featured a dorsoventrally asymmetric photoreceptor distribution with higher photoreceptor densities in the ventral retina. This dorsoventral asymmetry may provide greater spatial summation of visual information in the dorsal visual field. Burrow‐dwelling species had significantly larger eyes, higher total numbers of retinal cells, higher photoreceptor densities in the ventral retina, and higher spatial resolving power than rock‐dwelling species. C. pictus, a secondary burrow‐dwelling species, was the only species that changed burrow usage over evolutionary time, and its retinal organization revealed features more similar to rock‐dwelling species than other burrow‐dwelling species. This suggests that phylogeny may play a substantial role in shaping retinal organization in Ctenophorus species compared to microhabitat occupation

MRI atlas of a lizard brain

Magnetic resonance imaging (MRI) is an established technique for neuroanatomical analysis, being particularly useful in the medical sciences. However, the application of MRI to evolutionary neuroscience is still in its infancy. Few magnetic resonance brain atlases exist outside the standard model organisms in neuroscience and no magnetic resonance atlas has been produced for any reptile brain. A detailed understanding of reptilian brain anatomy is necessary to elucidate the evolutionary origin of enigmatic brain structures such as the cerebral cortex. Here, we present a magnetic resonance atlas for the brain of a representative squamate reptile, the Australian tawny dragon (Agamidae: Ctenophorus decresii), which has been the subject of numerous ecological and behavioral studies. We used a high-field 11.74T magnet, a paramagnetic contrasting-enhancing agent and minimum-deformation modeling of the brains of thirteen adult male individuals. From this, we created a high-resolution three-dimensional model of a lizard brain. The 3D-MRI model can be freely downloaded and allows a better comprehension of brain areas, nuclei, and fiber tracts, facilitating comparison with other species and setting the basis for future comparative evolution imaging studies. The MRI model and atlas of a tawny dragon brain (Ctenophorus decresii) can be viewed online and downloaded using the Wiley Biolucida Server at wiley.biolucida.net.Government of Australia, Grant/Award Numbers: APA#31/2011, IPRS#1182/2010; National Science and Engineering Research Council of Canada, Grant/Award Number: PGSD3-415253-2012; Quebec Nature and Technology Research Fund, Grant/AwardNumber: 208332; National Imaging Facility of Australia; Spanish Ministerio de Economía y Competitividad and Fondo Europeo de Desarrollo Regional, Grant/Award Number:BFU2015-68537-

Photodissociation dynamics of the HCNN radical

The photodissociation dynamics of the diazomethyl (HCNN) radical have been studied using fast radical beam photofragment translational spectroscopy. A photofragment yield spectrum was obtained for the range of 25 510-40 820 cm-1, and photodissociation was shown to occur for energies above 25 600 cm-1. The only product channel observed was the formation of CH and N2. Fragment translational energy and angular distributions were obtained at several energies in the range covered by the photofragment yield spectrum. The fragment translational energy distributions showed at least two distinct features at energies up to 4.59 eV, and were not well fit by phase space theory at any of the excitation energies studied. A revised C-N bond dissociation energy and heat of formation for HCNN, D0 (HC-NN) =1.139±0.019 eV and Δf H0 (HCNN) =5.010±0.023 eV, were determined. © 2006 American Institute of Physics.Ann Elise Faulhaber, Jason R. Gascooke, Alexandra A. Hoops, and Daniel M. Neumar

Photodissociation spectroscopy and dynamics of the CH(2)CFO radical

Alexandra A. Hoops, Jason R. Gascooke, Kathryn E. Kautzman, Ann Elise Faulhaber, and Daniel M. Neumar

Microscopic Investigation of Reversible Nanoscale Surface Size Dependent Protein Conjugation

Aβ1–40 coated 20 nm gold colloidal nanoparticles exhibit a reversible color change as pH is externally altered between pH 4 and 10. This reversible process may contain important information on the initial reversible step reported for the fibrillogenesis of Aβ (a hallmark of Alzheimer’s disease). We examined this reversible color change by microscopic investigations. AFM images on graphite surfaces revealed the morphology of Aβ aggregates with gold colloids. TEM images clearly demonstrate the correspondence between spectroscopic features and conformational changes of the gold colloid

A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data

The phosphatidylinositol (PI) cycle is central to eukaryotic cell signaling. Its complexity, due to the number of reactions and lipid and inositol phosphate intermediates involved makes it difficult to analyze experimentally. Computational modelling approaches are seen as a way forward to elucidate complex biological regulatory mechanisms when this cannot be achieved solely through experimental approaches. Whilst mathematical modelling is well established in informing biological systems, many models are often informed by data sourced from multiple unrelated cell types (mosaic data) or from purified enzyme data. In this work, we develop a model of the PI cycle informed by experimental and omics data taken from a single cell type, namely platelets. We were able to make a number of predictions regarding the regulation of PI cycle enzymes, the importance of the number of receptors required for successful GPCR signaling and the importance of lipid- and protein-binding proteins in regulating second messenger outputs. We then consider how pathway behavior differs, when fully informed by data for HeLa cells and show that model predictions remain consistent. However, when informed by mosaic experimental data model predictions greatly vary illustrating the risks of using mosaic datasets from unrelated cell types