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Savage JT, Ramirez J, Risher WC, Wang Y, Irala D, Eroglu C. SynBot: An open-source image analysis software for automated quantification of synapses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.26.546578. [PMID: 37425715 PMCID: PMC10327002 DOI: 10.1101/2023.06.26.546578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The formation of precise numbers of neuronal connections, known as synapses, is crucial for brain function. Therefore, synaptogenesis mechanisms have been one of the main focuses of neuroscience. Immunohistochemistry is a common tool for visualizing synapses. Thus, quantifying the numbers of synapses from light microscopy images enables screening the impacts of experimental manipulations on synapse development. Despite its utility, this approach is paired with low throughput analysis methods that are challenging to learn and results are variable between experimenters, especially when analyzing noisy images of brain tissue. We developed an open-source ImageJ-based software, SynBot, to address these technical bottlenecks by automating the analysis. SynBot incorporates the advanced algorithms ilastik and SynQuant for accurate thresholding for synaptic puncta identification, and the code can easily be modified by users. The use of this software will allow for rapid and reproducible screening of synaptic phenotypes in healthy and diseased nervous systems.
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Affiliation(s)
- Justin T. Savage
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Juan Ramirez
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - W. Christopher Risher
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University,Huntington, WV 25755, USA
| | - Yizhi Wang
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Dolores Irala
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cagla Eroglu
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Lead contact
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Neumann AM, Britsch S. Molecular Genetics of Acquired Temporal Lobe Epilepsy. Biomolecules 2024; 14:669. [PMID: 38927072 PMCID: PMC11202058 DOI: 10.3390/biom14060669] [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: 05/07/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
An epilepsy diagnosis reduces a patient's quality of life tremendously, and it is a fate shared by over 50 million people worldwide. Temporal lobe epilepsy (TLE) is largely considered a nongenetic or acquired form of epilepsy that develops in consequence of neuronal trauma by injury, malformations, inflammation, or a prolonged (febrile) seizure. Although extensive research has been conducted to understand the process of epileptogenesis, a therapeutic approach to stop its manifestation or to reliably cure the disease has yet to be developed. In this review, we briefly summarize the current literature predominately based on data from excitotoxic rodent models on the cellular events proposed to drive epileptogenesis and thoroughly discuss the major molecular pathways involved, with a focus on neurogenesis-related processes and transcription factors. Furthermore, recent investigations emphasized the role of the genetic background for the acquisition of epilepsy, including variants of neurodevelopmental genes. Mutations in associated transcription factors may have the potential to innately increase the vulnerability of the hippocampus to develop epilepsy following an injury-an emerging perspective on the epileptogenic process in acquired forms of epilepsy.
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Affiliation(s)
| | - Stefan Britsch
- Institute of Molecular and Cellular Anatomy, Ulm University, 89081 Ulm, Germany;
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Hassinan CW, Sterrett SC, Summy B, Khera A, Wang A, Bai J. Dimensionality of locomotor behaviors in developing C. elegans. PLoS Comput Biol 2024; 20:e1011906. [PMID: 38437243 PMCID: PMC10939432 DOI: 10.1371/journal.pcbi.1011906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/14/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Adult animals display robust locomotion, yet the timeline and mechanisms of how juvenile animals acquire coordinated movements and how these movements evolve during development are not well understood. Recent advances in quantitative behavioral analyses have paved the way for investigating complex natural behaviors like locomotion. In this study, we tracked the swimming and crawling behaviors of the nematode Caenorhabditis elegans from postembryonic development through to adulthood. Our principal component analyses revealed that adult C. elegans swimming is low dimensional, suggesting that a small number of distinct postures, or eigenworms, account for most of the variance in the body shapes that constitute swimming behavior. Additionally, we found that crawling behavior in adult C. elegans is similarly low dimensional, corroborating previous studies. Further, our analysis revealed that swimming and crawling are distinguishable within the eigenworm space. Remarkably, young L1 larvae are capable of producing the postural shapes for swimming and crawling seen in adults, despite frequent instances of uncoordinated body movements. In contrast, late L1 larvae exhibit robust coordination of locomotion, while many neurons crucial for adult locomotion are still under development. In conclusion, this study establishes a comprehensive quantitative behavioral framework for understanding the neural basis of locomotor development, including distinct gaits such as swimming and crawling in C. elegans.
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Affiliation(s)
- Cera W Hassinan
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Scott C Sterrett
- Graduate Program in Neuroscience, University of Washington, Seattle, Washington, United States of America
| | - Brennan Summy
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Arnav Khera
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Angie Wang
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Pomona College, Claremont, California, United States of America
| | - Jihong Bai
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Graduate Program in Neuroscience, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
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Wang Z, Lipshutz A, Liu ZL, Trzeciak AJ, Miranda IC, Martínez de la Torre C, Schild T, Lazarov T, Rojas WS, Saavedra PHV, Romero-Pichardo JE, Baako A, Geissmann F, Faraco G, Gan L, Etchegaray JI, Lucas CD, Parkhurst CN, Zeng MY, Keshari KR, Perry JSA. Early life high fructose exposure disrupts microglia function and impedes neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553242. [PMID: 37645894 PMCID: PMC10462086 DOI: 10.1101/2023.08.14.553242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Despite the success of fructose as a low-cost food additive, recent epidemiological evidence suggests that high fructose consumption by pregnant mothers or during adolescence is associated with disrupted neurodevelopment 1-7 . An essential step in appropriate mammalian neurodevelopment is the synaptic pruning and elimination of newly-formed neurons by microglia, the central nervous system's (CNS) resident professional phagocyte 8-10 . Whether early life high fructose consumption affects microglia function and if this directly impacts neurodevelopment remains unknown. Here, we show that both offspring born to dams fed a high fructose diet and neonates exposed to high fructose exhibit decreased microglial density, increased uncleared apoptotic cells, and decreased synaptic pruning in vivo . Importantly, deletion of the high affinity fructose transporter SLC2A5 (GLUT5) in neonates completely reversed microglia dysfunction, suggesting that high fructose directly affects neonatal development. Mechanistically, we found that high fructose treatment of both mouse and human microglia suppresses synaptic pruning and phagocytosis capacity which is fully reversed in GLUT5-deficient microglia. Using a combination of in vivo and in vitro nuclear magnetic resonance- and mass spectrometry-based fructose tracing, we found that high fructose drives significant GLUT5-dependent fructose uptake and catabolism, rewiring microglia metabolism towards a hypo-phagocytic state. Importantly, mice exposed to high fructose as neonates exhibited cognitive defects and developed anxiety-like behavior which were rescued in GLUT5-deficient animals. Our findings provide a mechanistic explanation for the epidemiological observation that early life high fructose exposure is associated with increased prevalence of adolescent anxiety disorders.
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Hassinan CW, Sterrett SC, Summy B, Khera A, Wang A, Bai J. A Quantitative Analysis of Locomotor Patterns in Developing C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.03.543584. [PMID: 37333370 PMCID: PMC10274735 DOI: 10.1101/2023.06.03.543584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Adult animals display robust locomotion, yet the timeline and mechanisms of how juvenile animals acquire coordinated movements and how these movements evolve during development are not well understood. Recent advances in quantitative behavioral analyses have paved the way for investigating complex natural behaviors like locomotion. In this study, we tracked the swimming and crawling behaviors of the nematode Caenorhabditis elegans from postembryonic development through to adulthood. Our principal component analyses revealed that adult C. elegans swimming is low dimensional, suggesting that a small number of distinct postures, or eigenworms, account for most of the variance in the body shapes that constitute swimming behavior. Additionally, we found that crawling behavior in adult C. elegans is similarly low dimensional, corroborating previous studies. However, our analysis revealed that swimming and crawling are distinct gaits in adult animals, clearly distinguishable within the eigenworm space. Remarkably, young L1 larvae are capable of producing the postural shapes for swimming and crawling seen in adults, despite frequent instances of uncoordinated body movements. In contrast, late L1 larvae exhibit robust coordination of locomotion, while many neurons crucial for adult locomotion are still under development. In conclusion, this study establishes a comprehensive quantitative behavioral framework for understanding the neural basis of locomotor development, including distinct gaits such as swimming and crawling in C. elegans.
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Affiliation(s)
- Cera W. Hassinan
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98019, USA
| | - Scott C. Sterrett
- Graduate Program in Neuroscience, University of Washington, Seattle, WA 98109, USA
| | - Brennan Summy
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
| | - Arnav Khera
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
| | - Angie Wang
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
- Pomona College, 333 N College Way, Claremont, CA 91711, USA
| | - Jihong Bai
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98019, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA 98109, USA
- Department of Biochemistry, University of Washington, WA 98195, USA
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Li X, Syed MH. Time, space, and diversity. Semin Cell Dev Biol 2023; 142:1-3. [PMID: 36100475 DOI: 10.1016/j.semcdb.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Xin Li
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Segura I, Egea J. Editorial: Molecular and Cellular Crosstalk on Neuronal Functionality and Regulation, From Development to Pathology. Front Mol Neurosci 2022; 15:966423. [PMID: 35845614 PMCID: PMC9280617 DOI: 10.3389/fnmol.2022.966423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Inmaculada Segura
- Max Planck Institute for Biological Intelligence (in Foundation), Planegg, Germany
- Department of Cellular Physiology, Biomedical Center Munich, Ludwig Maximilian University, Planegg, Germany
- *Correspondence: Inmaculada Segura
| | - Joaquim Egea
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
- Biomedical Research Institute of Lleida (IRBLLEIDA), Lleida, Spain
- Serra Húnter Programme, Generalitat de Catalunya, Barcelona, Spain
- Joaquim Egea
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