Paul Gignac

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• Gignac, P. M., Valdez, D., Morhardt, A. C., & Lynch, L. M. (2024). Buffered Lugol's Iodine Preserves DNA Fragment Lengths. Integrative organismal biology (Oxford, England), 6(1), obae017.
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  Museum collections play a pivotal role in the advancement of biological science by preserving phenotypic and genotypic history and variation. Recently, contrast-enhanced X-ray computed tomography (CT) has aided these advances by allowing improved visualization of internal soft tissues. However, vouchered specimens could be at risk if staining techniques are destructive. For instance, the pH of unbuffered Lugol's iodine (IKI) may be low enough to damage deoxyribonucleic acid (DNA). The extent of this risk is unknown due to a lack of rigorous evaluation of DNA quality between control and experimental samples. Here, we used formalin-fixed mice to document DNA concentrations and fragment lengths in nonstained, ethanol-preserved controls and 3 iodine-based staining preparations: (1) 1.25% weight-by-volume (wt/vol.) alcoholic iodine (IE); (2) 3.75% wt/vol. IKI; and (3) 3.75% wt/vol. buffered IKI. We tested a null hypothesis of no significant difference in DNA concentrations and fragment lengths between control and treatment samples. We found that DNA concentration decreases because of staining-potentially an effect of measuring intact double-stranded DNA only. Fragment lengths, however, were significantly higher for buffered IKI and control samples, which were not, themselves, significantly different. Our results implicate buffered IKI as the appropriate choice for contrast-enhanced CT imaging of museum wet collections to safely maximize their potential for understanding genetic and phenotypic diversity.
• Gignac, P., Aceves, V., Baker, S., Bell, J., Barnes, J., Boyer, D., Cunningham, D., De Carlo, F., Chase, M., Coen, K., Colbert, M., Creed, T., Daza, J., Dickinson, E., Leonardo, V., Dougan, L., Duffy, F., Dunham, C., Early, C., , Edey, D., et al. (2024). The Role of Networks to Overcome Large-scale Challenges in Tomography: The Non-Clinical Tomography Users Research Network. Tomography of Materials and Structures, 5, 100031. doi:10.1016/j.tmater.2024.100031
• Gignac, P., Balanoff, A., Ferrer, E., Saleh, L., Gold, M., Marugán-Lobón, J., Norell, M., Ouellette, D., Salerno, M., Watanabe, A., Wei, S., Bever, G., & Vaska, P. (2024). Quantitative functional imaging of the pigeon brain: implications for the evolution of avian powered flight. Proceedings of the Royal Society B: Biological Sciences, 202327172. doi:10.1098/rspb.2023.2172
• Gignac, P., Vasquez, T., Brewer, P., & Gold, M. (2024). Tumour or Hemmorrhage?: Differential Diagnosis of an Unknown Mass within the Brain of a Budgerigar using a Novel Imaging Pipeline. Veterinary Record Case Reports, e899. doi:10.1002/vrc2.899
• Gray, J. A., Gignac, P. M., & Stanley, E. L. (2024). The first full body diffusible iodine-based contrast-enhanced computed tomography dataset and teaching materials for a member of the Testudines. Anatomical record (Hoboken, N.J. : 2007), 307(3), 535-548.
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  Diffusible iodine-based contrast-enhanced Computed Tomography (diceCT) is now a widely used technique for imaging metazoan soft anatomy. Turtles present a particular challenge for anatomists; gross dissection is inherently destructive and irreversible, whereas their near complete shell of bony plates, covered with keratinous scutes, presents a barrier for iodine diffusion and significantly increases contrast-enhanced CT preparation time. Consequently, a complete dataset visualizing the internal soft anatomy of turtles at high resolution and in three dimensions has not yet been successfully achieved. Here we outline a novel method that augments traditional diceCT preparation with an iodine injection technique to acquire the first full body contrast-enhanced dataset for the Testudines. We show this approach to be an effective method of staining the soft tissues inside the shell. The resulting datasets were processed to produce anatomical 3D models that can be used in teaching and research. As diceCT becomes a widely employed method for nondestructively documenting the internal soft anatomy of alcohol preserved museum specimens, we hope that methods applicable to the more challenging of these, such as turtles, will contribute toward the growing stock of digital anatomy in online repositories.
• Straight, P. J., Gignac, P. M., & Kuenzel, W. J. (2024). A histological and diceCT-derived 3D reconstruction of the avian visual thalamofugal pathway. Scientific reports, 14(1), 8447.
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  Amniotes feature two principal visual processing systems: the tectofugal and thalamofugal pathways. In most mammals, the thalamofugal pathway predominates, routing retinal afferents through the dorsolateral geniculate complex to the visual cortex. In most birds, the thalamofugal pathway often plays the lesser role with retinal afferents projecting to the principal optic thalami, a complex of several nuclei that resides in the dorsal thalamus. This thalamic complex sends projections to a forebrain structure called the Wulst, the terminus of the thalamofugal visual system. The thalamofugal pathway in birds serves many functions such as pattern discrimination, spatial memory, and navigation/migration. A comprehensive analysis of avian species has unveiled diverse subdivisions within the thalamic and forebrain structures, contingent on species, age, and techniques utilized. In this study, we documented the thalamofugal system in three dimensions by integrating histological and contrast-enhanced computed tomography imaging of the avian brain. Sections of two-week-old chick brains were cut in either coronal, sagittal, or horizontal planes and stained with Nissl and either Gallyas silver or Luxol Fast Blue. The thalamic principal optic complex and pallial Wulst were subdivided on the basis of cell and fiber density. Additionally, we utilized the technique of diffusible iodine-based contrast-enhanced computed tomography (diceCT) on a 5-week-old chick brain, and right eyeball. By merging diceCT data, stained histological sections, and information from the existing literature, a comprehensive three-dimensional model of the avian thalamofugal pathway was constructed. The use of a 3D model provides a clearer understanding of the structural and spatial organization of the thalamofugal system. The ability to integrate histochemical sections with diceCT 3D modeling is critical to better understanding the anatomical and physiologic organization of complex pathways such as the thalamofugal visual system.
• Straight, P. J., Gignac, P. M., & Kuenzel, W. J. (2024). Mapping the avian visual tectofugal pathway using 3D reconstruction. The Journal of comparative neurology, 532(2), e25558.
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  Image processing in amniotes is usually accomplished by the thalamofugal and/or tectofugal visual systems. In laterally eyed birds, the tectofugal system dominates with functions such as color and motion processing, spatial orientation, stimulus identification, and localization. This makes it a critical system for complex avian behavior. Here, the brains of chicks, Gallus gallus, were used to produce serial brain sections in either coronal, sagittal, or horizontal planes and stained with either Nissl and Gallyas silver myelin or Luxol fast blue stain and cresyl echt violet (CEV). The emerging techniques of diffusible iodine-based contrast-enhanced computed tomography (diceCT) coupled with serial histochemistry in three planes were used to generate a comprehensive three-dimensional (3D) model of the avian tectofugal visual system. This enabled the 3D reconstruction of tectofugal circuits, including the three primary neuronal projections. Specifically, major components of the system included four regions of the retina, layers of the optic tectum, subdivisions of the nucleus rotundus in the thalamus, the entopallium in the forebrain, and supplementary components connecting into or out of this major avian visual sensory system. The resulting 3D model enabled a better understanding of the structural components and connectivity of this complex system by providing a complete spatial organization that occupied several distinct brain regions. We demonstrate how pairing diceCT with traditional histochemistry is an effective means to improve the understanding of, and thereby should generate insights into, anatomical and functional properties of complicated neural pathways, and we recommend this approach to clarify enigmatic properties of these pathways.