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)

Structure and Evolution of Dragon Brains

This thesis is about the evolution of brain structure in lizards, with a particular focus on the agamid lizards of the genus Ctenophorus. Achieving this required advancing the methods with which to study lizard brains. Therefore, this thesis is split about equally between developing the tools to study lizard brain structure and the evolution of brain structure in Ctenophorus. Below I present short summaries of each chapter. Full abstracts are presented with each chapter. Section 1: Development of the framework and tools necessary for the study of the dragon brain Chapter 1 Among vertebrates, reptiles have lagged far behind birds, mammals, fishes and amphibians in neurobiological research. Nonetheless, in the past twenty years there have been significant advances in our understanding of the neurobiology of reptiles, particularly among squamates (lizards and snakes). The first chapter of this thesis presents a broad literature review of lizard brain research. All peer-reviewed publications since the last major review in 1998 are summarized to give a complete overview of the state of the published literature on squamate neurobiology. I use this overview to highlight what is unique about squamate brains and identify gaps that remain in our understanding of these systems. Finally, I provide a framework for future studies that includes exciting new and unanswered questions about squamate brain evolution, structure and function. Chapter 2 Perfusion is the most common technique for preserving brains for neuroscience research. Standard perfusion techniques were developed primarily for application in mammals, which are traditional neuroscience research models. A perfusion method has never been published for lizards and following mammalian perfusion protocols for lizards results in failed perfusions. In this chapter, I present a modified perfusion protocol suitable for lizards. Chapter 3 In this chapter we present a magnetic resonance-based atlas for the brain of an agamid lizard, the tawny dragon (Ctenophorus decresii). We use literature sources as well as histological sections to identify and delineate, in three dimensions, the cell regions and fiber tracts visible in this model. This atlas has acted as a guide for measuring and analyzing brains in the subsequent chapters, and as a template with which to automate brain measurements across many individuals from multiple species. Section 2: Evolutionary patterns in dragon brain structure Chapter 4 Two models have been proposed to explain the patterns observed in evolutionary changes in brain morphology: the concerted model and the mosaic model of brain evolution. It is now well understood that both models are relevant in explaining brain evolution but the relative influence of each mode on brain structure varies between vertebrate groups. It remains unclear what factors favour concerted or mosaic brain evolution. In this chapter, we found evidence for both mosaic and concerted brain evolution in dragon lizards. Brains showed a pattern of concerted brain evolution with respect to the morphological characters. In contrast, they showed a pattern of mosaic brain evolution with respect to ecological and life history characters. Chapter 5 The role of sexual selection in altering brain organisation and structure over evolutionary time is poorly understood. In this chapter we compare the brains of species under strong and weak sexual selection. Males belonging to species that experience strong sexual selection had a larger medial preoptic nucleus and a smaller ventromedial hypothalamic nucleus. Conversely, females did not show any obvious variation in these brain regions. The medial preoptic nucleus controls male reproductive behaviour while the ventromedial hypothalamic nucleus controls female reproductive behaviour and is also involved in male aggression. Therefore, the primary brain nuclei underlying reproductive behavior evolve in a mosaic fashion in dragons, differently between males and females, likely in response to the strength of sexual selection. Collectively, these findings describe in detail the structure of an agamid brain and some of the ways in which that structure has changed through evolution. In doing so, these results have highlighted both how labile the brain can be in response to evolution, and how conserved brain structure is in general. Lizards, and reptiles in general, are the most understudied vertebrate group in neuroscience, but there is huge potential for discovery in this field.

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

Minimum Information About a Simulation Experiment (MIASE)

The original publication is available at www.ploscompbiol.orgReproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of simulations difficult. It is therefore essential to define the core information necessary to perform simulations of those models. The Minimum Information About a Simulation Experiment describes the minimal set of information that must be provided to make the description of a simulation experiment available to others. It includes the list of models to use and their modifications, all the simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any simulation experiment. The provision of this information, along with a set of required models, guarantees that the simulation experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and simulation of biological processes.The discussions that led to the definition of MIASE benefited from the support of a Japan Partnering Award by the UK Biotechnology and Biological Sciences Research Council. DW was supported by the Marie Curie program and by the German Research Association (DFG Research Training School ‘‘dIEM oSiRiS’’ 1387/1). This publication is based on work (EJC) supported in part by Award No KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). FTB acknowledges support by the NIH (grant 1R01GM081070- 01). JC is supported by the European Commission, DG Information Society, through the Seventh Framework Programme of Information and Communication Technologies, under the VPH NoE project (grant number 223920). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Publishers versio