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-

Segmentation of the C57BL/6J mouse cerebellum in magnetic resonance images

The C57BL mouse is the centerpiece of efforts to use gene-targeting technology to understand cerebellar pathology, thus creating a need for a detailed magnetic resonance imaging (MRI) atlas of the cerebellum of this strain. In this study we present a methodology for systematic delineation of the vermal and hemispheric lobules of the C57BL/6J mouse cerebellum in magnetic resonance images. We have successfully delineated 38 cerebellar and cerebellar-related structures. The higher signal-to-noise ratio achieved by group averaging facilitated the identification of anatomical structures. In addition, we have calculated average region volumes and created probabilistic maps for each structure. The segmentation method and the probabilistic maps we have created will provide a foundation for future studies of cerebellar disorders using transgenic mouse models

Visualization of mouse barrel cortex using ex-vivo track density imaging

We describe the visualization of the barrel cortex of the primary somatosensory area (S1) of ex vivo adult mouse brain with short-tracks track density imaging (stTDI). stTDI produced much higher definition of barrel structures than conventional fractional anisotropy (FA), directionally-encoded color FA maps, spin-echo and T2-weighted imaging and gradient echo Ti/T2*-weighted imaging. 3D high angular resolution diffusion imaging (HARDI) data were acquired at 48 micron isotropic resolution for a (3 mm)3 block of cortex containing the barrel field and reconstructed using stTDI at 10 micron isotropic resolution. HARDI data were also acquired at 100 micron isotropic resolution to image the whole brain and reconstructed using stTDI at 20 micron isotropic resolution. The 10 micron resolution stTDI maps showed exceptionally clear delineation of barrel structures. Individual barrels could also be distinguished in the 20 micron stTDI maps but the septa separating the individual barrels appeared thicker compared to the 10 micron maps, indicating that the ability of stTDI to produce high quality structural delineation is dependent upon acquisition resolution. Close homology was observed between the barrel structure delineated using stTDI and reconstructed histological data from the same samples. stTDI also detects barrel deletions in the posterior medial barrel sub-field in mice with infraorbital nerve cuts. The results demonstrate that stTDI is a novel imaging technique that enables three-dimensional characterization of complex structures such as the barrels in S1 and provides an important complementary non-invasive imaging tool for studying synaptic connectivity, development and plasticity of the sensory system. (C) 2013 Elsevier Inc. All rights reserved

Three-dimensional imaging of the teleost brain

Magnetic resonance imaging (MRI) is a vital technique for neuroscience. The ability to non-invasively image the central nervous system (CNS) has drastically improved our understanding of the structure and function of the brain. While in vivo and functional magnetic resonance imaging (fMRI) scans are desirable, as they are true representations of the living brain, they require larger radiofrequency coils, larger acquisition matrixes and shorter scan times. Consequently, in situ or ex vivo scans are often preferable as longer scan times can be used, resulting in increased contrast and signal to noise ratios. MRI was initially developed as a clinical technique; however, over the past thirty years the brains of a wide range of other taxa have also been examined. In particular, mice have been well studied and today MRI is an important tool for anatomical analyses of phenotype. Surprisingly, teleosts, the largest group of vertebrates and an important model for a range of neuroscience fields, have scarcely been studied with MRI. Consequently, the aim of the thesis was to perform the first thorough examination of the teleost central nervous system using MRI. Since the logistics for in vivo imaging of teleosts are challenging, in this original study we sought to image the teleost CNS in situ and ex vivo. Fixation and ‘staining’ of samples is routinely performed for in situ and ex vivo imaging, however, their effects on a whole brain sample were unknown. Therefore, as part of our objective of creating a protocol to obtain high-quality images of the brains of teleosts, we examined the relaxation rates of seven fixatives and two commercially available contrast agents. We determined that immersing a brain in a solution of 4% paraformaldehyde (in a 0.1M phosphate buffered saline) and 0.5% Magnevist® for a period of 12 hours resulted in the best images. Subsequently, we scanned two teleost species, zebrafish (Danio rerio) a common laboratory model and barramundi (Lates calcarifer) a representative perciform, and acquired high-resolution and high-contrast T2*-weighted images of their brains. The resolutions obtained were some of the highest achieved in a vertebrate brain and allowed us to delineate a large number of neuronal structures. In the zebrafish brain, we segmented 53 neuronal structures and created the first three-dimensional anatomical and quantitative zebrafish brain atlas, while in the barramundi nearly 100 brain regions were identified including, cellular layers, fiber tracts and numerous ventricles. The ability to identify neuronal regions and obtain quantitative information also makes MRI an ideal method for comparative brain studies. As few studies have utilized MRI for comparative studies, we sequentially compared brain volumes of three different brain regions (olfactory bulbs, telencephalon and optic tectum) obtained via MRI, the ellipsoid method and histology. We found that histology and the ellipsoid method are poor measures of brain volumes as histological processing results in significant heterogeneous shrinkage in all brain areas and the ellipsoid method significantly overestimates brain volumes. Therefore, when possible, we suggest future studies should utilize MRI. Additional contrast was investigated by performing diffusion weighted imaging (DWI). Images were acquired with a 24 µm isotropic resolution that provided unique information about fiber orientation in the zebrafish brain. Lamination not seen in T2*-weighted images could be distinguished and 27 fiber bundles were tracked. However, in contrast to T2*-weighted imaging, resolution not contrast was the limiting factor. Magnetic resonance imaging (MRI) is a vital technique to acquire detailed neuroanatomical information of an intact brain. Although a greater number of structures can be delineated with conventional histology, MRI presents exciting opportunities for imaging the anatomy and physiology of the CNS. This study is vital to that future research as it establishes teleosts as a model for MRI contrast and resolution studies and provides the crucial framework for a range of future research areas

Neuroimaging phenotypes in zebrafish

The zebrafish has become an established model in neuroscience due to the ease with which gene discovery, chemical screening, behaviour, and disease modelling can be performed. More recently, neuroimaging, a crucial pre-clinical technique for probing tissue structure, examining volumetric changes, and studying in vivo brain activity has also been applied to zebrafish. The zebrafish brain is particularly attractive for neuroimaging due to its small size, numerous translucent strains, and distinct forebrain organization. In this chapter we discuss the range of imaging techniques which have been utilized to examine the zebrafish brain. While many of these methods have only begun to be utilized in zebrafish, correlating neuroimaging phenotypes with behaviour in zebrafish has a bright future

A method for detecting molecular transport within the cerebral ventricles of live zebrafish (Danio rerio) larvae

The production and flow of cerebrospinal fluid performs an important role in the development and homeostasis of the central nervous system. However, these processes are difficult to study in the mammalian brain because the ventricles are situated deep within the parenchyma. In this communication we introduce the zebrafish larva as an in vivo model for studying cerebral ventricle and blood-brain barrier function. Using confocal microscopy we show that zebrafish ventricles are topologically similar to those of the mammalian brain. We describe a new method for measuring the dynamics of molecular transport within the ventricles of live zebrafish by means of the uncaging of a fluorescein derivative. Furthermore, we determine that in 5-6 days post-fertilization zebrafish, the dispersal of molecules in the ventricles is driven by a combination of ciliary motion and diffusion. The zebrafish presents a tractable system with the advantage of genetics, size and transparency for exploring ventricular physiology and for mounting large-scale high throughput experiments

Improving treatment of neurodevelopmental disorders: recommendations based on preclinical studies

Introduction: Neurodevelopmental disorders (NDDs) are common and severely debilitating. Their chronic nature and reliance on both genetic and environmental factors makes studying NDDs and their treatment a challenging task.Areas covered: Herein, the authors discuss the neurobiological mechanisms of NDDs, and present recommendations on their translational research and therapy, outlined by the International Stress and Behavior Society. Various drugs currently prescribed to treat NDDs also represent a highly diverse group. Acting on various neurotransmitter and physiological systems, these drugs often lack specificity of action, and are commonly used to treat multiple other psychiatric conditions. There has also been relatively little progress in the development of novel medications to treat NDDs. Based on clinical, preclinical and translational models of NDDs, our recommendations cover a wide range of methodological approaches and conceptual strategies.Expert opinion: To improve pharmacotherapy and drug discovery for NDDs, we need a stronger emphasis on targeting multiple endophenotypes, a better dissection of genetic/epigenetic factors or "hidden heritability," and a careful consideration of potential developmental/trophic roles of brain neurotransmitters. The validity of animal NDD models can be improved through discovery of novel (behavioral, physiological and neuroimaging) biomarkers, applying proper environmental enrichment, widening the spectrum of model organisms, targeting developmental trajectories of NDD-related behaviors and comorbid conditions beyond traditional NDDs. While these recommendations cannot be addressed all in once, our increased understanding of NDD pathobiology may trigger innovative cross-disciplinary research expanding beyond traditional methods and concepts

Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator

© 2020 Elsevier Inc. One-photon fluorescent imaging of calcium signals can capture the activity of hundreds of neurons across large fields of view but suffers from crosstalk from neuropil. Shemesh et al. engineer cell-body-targeted variants of fluorescent calcium indicators and show in mice and zebrafish that artifactual spikes and correlations are greatly reduced