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Li J, Wang Y, Raina MA, Xu C, Su L, Guo Q, Ma Q, Wang J, Xu D. scBSP: A fast and accurate tool for identifying spatially variable genes from spatial transcriptomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592851. [PMID: 38765956 PMCID: PMC11100755 DOI: 10.1101/2024.05.06.592851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Spatially resolved transcriptomics have enabled the inference of gene expression patterns within two and three-dimensional space, while introducing computational challenges due to growing spatial resolutions and sparse expressions. Here, we introduce scBSP, an open-source, versatile, and user-friendly package designed for identifying spatially variable genes in large-scale spatial transcriptomics. scBSP implements sparse matrix operation to significantly increase the computational efficiency in both computational time and memory usage, processing the high-definition spatial transcriptomics data for 19,950 genes on 181,367 spots within 10 seconds. Applied to diverse sequencing data and simulations, scBSP efficiently identifies spatially variable genes, demonstrating fast computational speed and consistency across various sequencing techniques and spatial resolutions for both two and three-dimensional data with up to millions of cells. On a sample with hundreds of thousands of sports, scBSP identifies SVGs accurately in seconds to on a typical desktop computer.
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Huang L, Hardyman F, Edwards M, Galliano E. Deprivation-Induced Plasticity in the Early Central Circuits of the Rodent Visual, Auditory, and Olfactory Systems. eNeuro 2024; 11:ENEURO.0435-23.2023. [PMID: 38195533 PMCID: PMC11059429 DOI: 10.1523/eneuro.0435-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
Activity-dependent neuronal plasticity is crucial for animals to adapt to dynamic sensory environments. Traditionally, it has been investigated using deprivation approaches in animal models primarily in sensory cortices. Nevertheless, emerging evidence emphasizes its significance in sensory organs and in subcortical regions where cranial nerves relay information to the brain. Additionally, critical questions started to arise. Do different sensory modalities share common cellular mechanisms for deprivation-induced plasticity at these central entry points? Does the deprivation duration correlate with specific plasticity mechanisms? This study systematically reviews and meta-analyzes research papers that investigated visual, auditory, or olfactory deprivation in rodents of both sexes. It examines the consequences of sensory deprivation in homologous regions at the first central synapse following cranial nerve transmission (vision - lateral geniculate nucleus and superior colliculus; audition - ventral and dorsal cochlear nucleus; olfaction - olfactory bulb). The systematic search yielded 91 papers (39 vision, 22 audition, 30 olfaction), revealing substantial heterogeneity in publication trends, experimental methods, measures of plasticity, and reporting across the sensory modalities. Despite these differences, commonalities emerged when correlating plasticity mechanisms with the duration of sensory deprivation. Short-term deprivation (up to 1 d) reduced activity and increased disinhibition, medium-term deprivation (1 d to a week) involved glial changes and synaptic remodeling, and long-term deprivation (over a week) primarily led to structural alterations. These findings underscore the importance of standardizing methodologies and reporting practices. Additionally, they highlight the value of cross-modal synthesis for understanding how the nervous system, including peripheral, precortical, and cortical areas, respond to and compensate for sensory inputs loss.
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Affiliation(s)
- Li Huang
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB23EL Cambridge, United Kingdom
| | - Francesca Hardyman
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB23EL Cambridge, United Kingdom
| | - Megan Edwards
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB23EL Cambridge, United Kingdom
| | - Elisa Galliano
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB23EL Cambridge, United Kingdom
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Murakami E, Nakamori M, Nakatani K, Shibata T, Tainaka K. Intracerebral Distribution of CAG Repeat-Binding Small Molecule Visualized by Whole-Brain Imaging. Bioconjug Chem 2023; 34:2187-2193. [PMID: 37948852 DOI: 10.1021/acs.bioconjchem.3c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Understanding the pharmacokinetics of drug candidates of interest in the brain and evaluating drug delivery to the brain are important for developing drugs targeting the brain. Previously, we demonstrated that a CAG repeat-binding small molecule, naphthyridine-azaquinolone (NA), resulted in repeat contraction in mouse models of dentatorubral-pallidoluysian atrophy and Huntington's disease caused by aberrant expansion of CAG repeats. However, the intracerebral distribution and drug deliverability of NA remain unclear. Here, we report three-dimensional whole-brain imaging of an externally administered small molecule using tissue clearing and light sheet fluorescence microscopy (LSFM). We designed and synthesized an Alexa594-labeled NA derivative with a primary amine for whole-brain imaging (NA-Alexa594-NH2), revealing the intracerebral distribution of NA-Alexa594-NH2 after intraparenchymal and intracerebroventricular administrations by whole-brain imaging combined with tissue clearing and LSFM. We also clarified that intranasally administered NA-Alexa594-NH2 was delivered into the brain via multiple nose-to-brain pathways by tracking the time-dependent change in the intracerebral distribution. Whole-brain imaging of small molecules by tissue clearing and LSFM is useful for elucidating not only the intracerebral distribution but also the drug delivery pathways into the brain.
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Affiliation(s)
- Eitaro Murakami
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka 567-0047, Japan
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka 567-0047, Japan
| | - Tomonori Shibata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka 567-0047, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Center for Bioresources, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
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Torres MV, Ortiz-Leal I, Ferreiro A, Rois JL, Sanchez-Quinteiro P. Immunohistological study of the unexplored vomeronasal organ of an endangered mammal, the dama gazelle (Nanger dama). Microsc Res Tech 2023; 86:1206-1233. [PMID: 37494657 DOI: 10.1002/jemt.24392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023]
Abstract
Dama gazelle is a threatened and rarely studied species found primarily in northern Africa. Human pressure has depleted the dama gazelle population from tens of thousands to a few hundred individuals. Since 1970, a founder population consisting of the last 17 surviving individuals in Western Sahara has been maintained in captivity, reproducing naturally. In preparation for the future implementation of assisted reproductive technology, certain aspects of dama gazelle reproductive biology have been established. However, the role played by semiochemical-mediated communications in the sexual behavior of dama gazelle remains unknown due partially to a lack of a neuroanatomical or morphofunctional characterization of the dama gazelle vomeronasal organ (VNO), which is the sensory organ responsible for pheromone processing. The present study characterized the dama gazelle VNO, which appears fully equipped to perform neurosensory functions, contributing to current understanding of interspecies VNO variability among ruminants. By employing histological, lectin-histochemical, and immunohistochemical techniques, we conducted a detailed morphofunctional evaluation of the dama gazelle VNO along its entire longitudinal axis. Our findings of significant structural and neurochemical transformation along the entire VNO suggest that future studies of the VNO should take a similar approach. The present study contributes to current understanding of dama gazelle VNO, providing a basis for future studies of semiochemical-mediated communications and reproductive management in this species. RESEARCH HIGHLIGHTS: This exhaustive immunohistological study of the vomeronasal organ (VNO) of the dama gazelle provides the first evidence of notable differences in the expression of neuronal markers along the rostrocaudal axis of the VNO. This provides a morphological basis for the implementation of pheromones in captive populations of dama gazelle.
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Affiliation(s)
- Mateo V Torres
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Irene Ortiz-Leal
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | | | | | - Pablo Sanchez-Quinteiro
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
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Téllez de Meneses PG, Pérez-Revuelta L, Canal-Alonso Á, Hernández-Pérez C, Cocho T, Valero J, Weruaga E, Díaz D, Alonso JR. Immunohistochemical distribution of secretagogin in the mouse brain. Front Neuroanat 2023; 17:1224342. [PMID: 37711587 PMCID: PMC10498459 DOI: 10.3389/fnana.2023.1224342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Calcium is essential for the correct functioning of the central nervous system, and calcium-binding proteins help to finely regulate its concentration. Whereas some calcium-binding proteins such as calmodulin are ubiquitous and are present in many cell types, others such as calbindin, calretinin, and parvalbumin are expressed in specific neuronal populations. Secretagogin belongs to this latter group and its distribution throughout the brain is only partially known. In the present work, the distribution of secretagogin-immunopositive cells was studied in the entire brain of healthy adult mice. Methods Adult male C57BL/DBA mice aged between 5 and 7 months were used. Their whole brain was sectioned and used for immunohistochemistry. Specific neural populations were observed in different zones and nuclei identified according to Paxinos mouse brain atlas. Results Labelled cells were found with a Golgi-like staining, allowing an excellent characterization of their dendritic and axonal arborizations. Many secretagogin-positive cells were observed along different encephalic regions, especially in the olfactory bulb, basal ganglia, and hypothalamus. Immunostained populations were very heterogenous in both size and distribution, as some nuclei presented labelling in their entire extension, but in others, only scattered cells were present. Discussion Secretagogin can provide a more complete vision of calcium-buffering mechanisms in the brain, and can be a useful neuronal marker in different brain areas for specific populations.
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Affiliation(s)
- Pablo G. Téllez de Meneses
- Institute for Neuroscience of Castile and Leon (INCyL), Universidad de Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Laura Pérez-Revuelta
- Institute for Neuroscience of Castile and Leon (INCyL), Universidad de Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Ángel Canal-Alonso
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Bioinformatics, Intelligent Systems and Educational Technology (BISITE) Research Group, Universidad de Salamanca, Salamanca, Spain
| | - Carlos Hernández-Pérez
- Institute for Neuroscience of Castile and Leon (INCyL), Universidad de Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Teresa Cocho
- Institute for Neuroscience of Castile and Leon (INCyL), Universidad de Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Jorge Valero
- Institute for Neuroscience of Castile and Leon (INCyL), Universidad de Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Eduardo Weruaga
- Institute for Neuroscience of Castile and Leon (INCyL), Universidad de Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - David Díaz
- Institute for Neuroscience of Castile and Leon (INCyL), Universidad de Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - José R. Alonso
- Institute for Neuroscience of Castile and Leon (INCyL), Universidad de Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
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Ortiz-Leal I, Torres MV, Vargas-Barroso V, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. The olfactory limbus of the red fox ( Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Front Neuroanat 2023; 16:1097467. [PMID: 36704406 PMCID: PMC9871471 DOI: 10.3389/fnana.2022.1097467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents. Methods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques. Results: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity. Discussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.
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Affiliation(s)
- Irene Ortiz-Leal
- Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Mateo V. Torres
- Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Víctor Vargas-Barroso
- Cellular Neuroscience, IST Austria (Institute of Science and Technology Austria), Klosterneuburg, Austria
| | | | | | - Jorge A. Larriva-Sahd
- Institute of Neurobiology, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Pablo Sánchez-Quinteiro
- Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain,*Correspondence: Pablo Sanchez-Quinteiro
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DeOliveira-Mello L, Vicente I, Gonzalez-Nunez V, Santos-Ledo A, Velasco A, Arévalo R, Lara JM, Mack AF. Doublecortin in the Fish Visual System, a Specific Protein of Maturing Neurons. BIOLOGY 2022; 11:biology11020248. [PMID: 35205114 PMCID: PMC8869232 DOI: 10.3390/biology11020248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 11/30/2022]
Abstract
Simple Summary Doublecortin (DCX) is an essential protein in the development of the central nervous system and in lamination of the mammalian cortex. It is known that the expression of DCX is restricted to newborn neurons. The visual system of teleost fish has been postulated as an ideal model since it continuously grows throughout the animal’s life. Here, we report a comparative expression analysis of DCX between two teleost fish species as well as a bioinformatic analysis with other animal groups. Our results demonstrate that DCX is very useful for identifying new neurons in the visual systems of Astatotilapia burtoni, but is absent in Danio rerio. Abstract Doublecortin (DCX) is a microtubule associated protein, essential for correct central nervous system development and lamination in the mammalian cortex. It has been demonstrated to be expressed in developing—but not in mature—neurons. The teleost visual system is an ideal model to study mechanisms of adult neurogenesis due to its continuous life-long growth. Here, we report immunohistochemical, in silico, and western blot analysis to detect the DCX protein in the visual system of teleost fish. We clearly determined the expression of DCX in newly generated cells in the retina of the cichlid fish Astatotilapia burtoni, but not in the cyprinid fish Danio rerio. Here, we show that DCX is not associated with migrating cells but could be related to axonal growth. This work brings to light the high conservation of DCX sequences between different evolutionary groups, which make it an ideal marker for maturing neurons in various species. The results from different techniques corroborate the absence of DCX expression in zebrafish. In A. burtoni, DCX is very useful for identifying new neurons in the transition zone of the retina. In addition, this marker can be applied to follow axons from maturing neurons through the neural fiber layer, optic nerve head, and optic nerve.
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Affiliation(s)
- Laura DeOliveira-Mello
- Institute of Neurosciences of Castilla and León, University of Salamanca, 37007 Salamanca, Spain; (V.G.-N.); (A.S.-L.); (A.V.); (R.A.); (J.M.L.)
- Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
- Correspondence:
| | - Isabel Vicente
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy;
| | - Veronica Gonzalez-Nunez
- Institute of Neurosciences of Castilla and León, University of Salamanca, 37007 Salamanca, Spain; (V.G.-N.); (A.S.-L.); (A.V.); (R.A.); (J.M.L.)
- Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
| | - Adrian Santos-Ledo
- Institute of Neurosciences of Castilla and León, University of Salamanca, 37007 Salamanca, Spain; (V.G.-N.); (A.S.-L.); (A.V.); (R.A.); (J.M.L.)
- Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
| | - Almudena Velasco
- Institute of Neurosciences of Castilla and León, University of Salamanca, 37007 Salamanca, Spain; (V.G.-N.); (A.S.-L.); (A.V.); (R.A.); (J.M.L.)
- Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
| | - Rosario Arévalo
- Institute of Neurosciences of Castilla and León, University of Salamanca, 37007 Salamanca, Spain; (V.G.-N.); (A.S.-L.); (A.V.); (R.A.); (J.M.L.)
- Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
| | - Juan M. Lara
- Institute of Neurosciences of Castilla and León, University of Salamanca, 37007 Salamanca, Spain; (V.G.-N.); (A.S.-L.); (A.V.); (R.A.); (J.M.L.)
- Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca, 37007 Salamanca, Spain
| | - Andreas F. Mack
- Institute of Clinical Anatomy and Cell Analysis, Eberhard-Karls Universität Tübingen, 72074 Tübingen, Germany;
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