Article
Neurosciences
Francesco Trapani, Giulia Lia Beatrice Spampinato, Pierre Yger, Olivier Marre
Summary: Classifying neurons based on their response to stimuli provides a higher discrimination performance compared to classifying them based on their receptive field properties. This is because the response-based method can account for the nonlinear behavior of neurons.
JOURNAL OF NEUROPHYSIOLOGY
(2023)
Review
Clinical Neurology
Ungsoo Samuel Kim, Omar A. Mahroo, John D. Mollon, Patrick Yu-Wai-Man
Summary: Retinal ganglion cells (RGCs) are a diverse group with unique morphological features, functions, and pathways. Studies have revealed insights into the selective vulnerability and relative resilience of different RGC subtypes, which are crucial for developing targeted therapies for optic neuropathies. The comprehensive description of RGC diversity and potential therapeutic pathways provides hope for effective treatments for patients with these progressive blinding diseases.
FRONTIERS IN NEUROLOGY
(2021)
Article
Biology
Karthik Shekhar, Irene E. Whitney, Salwan Butrus, Yi-Rong Peng, Joshua R. Sanes
Summary: This study investigates how mouse retinal ganglion cell precursors diversify from a single type into multiple discrete types using single-cell RNA-seq. The findings suggest that the transcriptomic type identity of RGC precursors is not specified at mitotic exit but acquired gradually, and some types can only be identified a week after they are generated.
Article
Neurosciences
Xiaohuan Zhao, Mengqiao Xu, Zhenzhen Zhao, Yimin Wang, Yang Liu, Ting Zhang, Xiaoling Wan, Mei Jiang, Xueting Luo, Yao Shen, Lei Chen, Minwen Zhou, Feng Wang, Xiaodong Sun
Summary: This study found that the probiotic Bifidobacterium can promote the survival of retinal ganglion cells and optic nerve regeneration. This effect is achieved by inhibiting microglia activation and promoting Muller cell activation, leading to a reduction in the risk of optic nerve injury.
CNS NEUROSCIENCE & THERAPEUTICS
(2023)
Article
Neurosciences
Sophia Wienbar, Gregory William Schwartz
Summary: The study reveals how the intrinsic properties of retinal ganglion cells affect feature selectivity. By comparing different types of RGCs, researchers found that differences in their intrinsic properties, rather than synaptic inputs, resulted in differences in contrast response functions.
Article
Biochemistry & Molecular Biology
Gerrit Hilgen, Evgenia Kartsaki, Viktoriia Kartysh, Bruno Cessac, Evelyne Sernagor
Summary: In this study, a novel approach combining pharmacogenetics, immunohistochemistry, and large-scale retinal electrophysiology is introduced for the classification of retinal ganglion cells (RGCs). This approach allows grouping of cells based on gene expression and understanding of their responses to visual scenes. The researchers expanded the list of RGC types expressing Grik4 and provided a phenotypical description of Scnn1a-expressing RGCs for the first time. The insights and methods gained from this study can be applied to neuronal classification challenges in other brain regions as well.
Article
Pharmacology & Pharmacy
Xi Chen, Shanshan Li, Xiaoli Liu, Jingjie Zhao, Lanting Wu, Ran You, Yanling Wang
Summary: This study investigates the role of endogenous c-kit(+) cells in retinal degeneration. Stimulation of these cells by stem cell factor (SCF) provides protection against retinal degeneration. SCF administration improves visual function and prevents the loss of retinal ganglion cells. Transcriptome analysis reveals that SCF-induced changes are closely correlated with eye development-related pathways.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Cell Biology
Di Xu, Li-Ting Zhong, Hai-Yang Cheng, Zeng-Qiang Wang, Xiong-Min Chen, Ai-Ying Feng, Wei-Yi Chen, Gong Chen, Ying Xu
Summary: This study demonstrates the ability of NeuroD1 to reprogram Muller cells in the retina of adult mice into different subtypes of retinal neurons, with potential to restore vision.
NEURAL REGENERATION RESEARCH
(2023)
Article
Ophthalmology
You-Ren Wu, Tomoyo Hashiguchi, Junki Sho, Shih-Hwa Chiou, Masayo Takahashi, Michiko Mandai
Summary: The study shows the potential for therapeutic use of pluripotent cell-derived RGCs by grafting the cells in healthy conditions and with an appropriate technical approach. Transplanted mESC-derived RGCs survived and extended neurites into the host retina, forming presumptive synapses with host bipolar cells. The ratio of integrated THY1-EGFP(+) neurites in the host IPL was higher in RGC-injured mice compared to healthy controls.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Neurosciences
Aiwen Xu, Michael Beyeler
Summary: This study used a biophysical model to simulate the retina and investigated the impact of neuroanatomical changes on cellular responses during retinal degeneration. The findings revealed that retinal cell activity increased and electrical stimulation thresholds also increased during retinal degeneration, and testable predictions about the underlying neuroanatomical mechanisms were proposed.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Neurosciences
Yvonne Koelsch, Joshua Hahn, Anna Sappington, Manuel Stemmer, Antonio M. Fernandes, Thomas O. Helmbrecht, Shriya Lele, Salwan Butrus, Eva Laurell, Irene Arnold-Ammer, Karthik Shekhar, Joshua R. Sanes, Herwig Baier
Summary: This study systematically classified RGCs in adult and larval zebra fish using single-cell transcriptomics, identifying marker genes for various mature types and developmental intermediates. The research also engineered transgenic driver lines based on this dataset, enabling specific experimental access to a subset of RGC types. Furthermore, molecularly defined RGCs were shown to exhibit specific functional tuning through in vivo calcium imaging.
Article
Pharmacology & Pharmacy
Shisi Hu, Yaoyao Li, Yuanjie Zhang, Ruyi Shi, Ping Tang, Di Zhang, Xiuli Kuang, Jiangfan Chen, Jia Qu, Ying Gao
Summary: The study found that adenosine A(2A) receptors have different regulatory effects on the morphogenesis of different types of retinal ganglion cells during postnatal development and neonatal inflammation. In normal development, A(2A)Rs can regulate the morphology of RGC dendrites, while in neonatal inflammation, they mainly suppress the volume of RGC soma and dendrites.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Mathematical & Computational Biology
Yang Liu, Feng Li, Junliang Shang, Jinxing Liu, Juan Wang, Daohui Ge
Summary: Recently developed single-cell RNA-seq (scRNA-seq) technology enables researchers to study disease development at the single-cell level. Clustering is a key strategy for analyzing scRNA-seq data, and choosing high-quality feature sets can greatly improve the results of single-cell clustering and classification. However, computationally burdensome and highly expressed genes cannot provide a stable and predictive feature set due to technical reasons. In this study, we propose scFED, a feature-engineered gene selection framework that identifies prospective feature sets, eliminates noise fluctuations, and incorporates existing knowledge from a tissue-specific cellular taxonomy reference database (CellMatch) to minimize the influence of subjective factors. We also introduce a reconstruction approach for noise reduction and amplification of crucial information. Applying scFED to four genuine single-cell datasets and comparing it with other techniques, we demonstrate that scFED improves clustering, reduces the dimensionality of scRNA-seq data, enhances cell type identification when combined with clustering algorithms, and outperforms other methods. Therefore, scFED offers distinct benefits in gene selection for scRNA-seq data.
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
(2023)
Article
Neurosciences
Subha Nasir-Ahmad, Sammy C. S. Lee, Paul R. Martin, Ulrike Grunert
Summary: The study investigates the expression of Satb2 in ganglion cells in three primate species, revealing a low proportion of Satb2 cells in the ganglion cell population with species-specific differences. The findings suggest rapid species-specific adaptations in Satb2 expression during primate evolution, as the expression is not conserved across Old World and New World suborders.
JOURNAL OF COMPARATIVE NEUROLOGY
(2021)
Review
Biology
Yue Hu, Lynn Michelle Grodzki, Susanne Bartsch, Udo Bartsch
Summary: This review summarizes preclinical studies assessing the efficacy of cell-based neuroprotective treatment strategies to rescue retinal ganglion cells from cell death. Intraocular transplantations of diverse cell types or cells engineered to overexpress neurotrophic factors have shown significant attenuation of ganglion cell loss. Combinatorial cell-based neuroprotective approaches may further increase the survival rates of retinal ganglion cells, but long-term impact and potential adverse effects are still limited, making it challenging to assess their therapeutic potential.
Article
Computer Science, Interdisciplinary Applications
Uygar Suembuel, Juan M. Santos, John M. Pauly
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2009)
Article
Computer Science, Interdisciplinary Applications
Uygar Suembuel, Juan M. Santos, John M. Pauly
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2009)
Review
Neurosciences
H. Sebastian Seung, Uygar Suembuel
Correction
Multidisciplinary Sciences
Uygar Sumbul, Sen Song, Kyle McCulloch, Michael Becker, Bin Lin, Joshua R. Sanes, Richard H. Masland, H. Sebastian Seung
NATURE COMMUNICATIONS
(2014)
Article
Multidisciplinary Sciences
Nobuhiko Miyasaka, Ignacio Arganda-Carreras, Noriko Wakisaka, Miwa Masuda, Uygar Suembuel, H. Sebastian Seung, Yoshihiro Yoshihara
NATURE COMMUNICATIONS
(2014)
Article
Multidisciplinary Sciences
Uygar Suembuel, Sen Song, Kyle McCulloch, Michael Becker, Bin Lin, Joshua R. Sanes, Richard H. Masland, H. Sebastian Seung
NATURE COMMUNICATIONS
(2014)
Article
Biology
Stephen J. Smith, Uygar Sumbul, Lucas T. Graybuck, Forrest Collman, Sharmishtaa Seshamani, Rohan Gala, Olga Gliko, Leila Elabbady, Jeremy A. Miller, Trygve E. Bakken, Jean Rossier, Zizhen Yao, Ed Lein, Hongkui Zeng, Bosiljka Tasic, Michael Hawrylycz
Article
Neurosciences
Daniel Maxim Lascone, Yujie Li, Uygar Sumbul, Michael Doron, Hanbo Chen, Valentine Andreu, Finola Goudy, Heike Blockus, Larry F. Abbott, Idan Segev, Hanchuan Peng, Franck Polleux
Review
Neurosciences
Stephen J. Smith, Michael Hawrylycz, Jean Rossier, Uygar Sumbul
CURRENT OPINION IN NEUROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Ian Covert, Rohan Gala, Tim Wang, Karel Svoboda, Uygar Sumbul, Su-In Lee
Summary: In this study, the authors propose a flexible deep learning framework called PERSIST, which uses existing scRNA-seq data to identify gene targets for spatial transcriptomics. They demonstrate that PERSIST can capture more information with fewer genes and reliably predict the genome-wide expression profile in different brain regions, species, and scRNA-seq technologies.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Yuhan Helena Liu, Stephen Smith, Stefan Mihalas, Eric Shea-Brown, Uygar Sumbul
Summary: The study presents a normative theory for synaptic learning, suggesting that neurons communicate their contribution to the learning outcome to nearby neurons via cell-type-specific local neuromodulation, which may be a critical part of solving the synaptic credit-assignment problem. Computational tests also propose algorithms for improved artificial neural network learning efficiency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Proceedings Paper
Computer Science, Artificial Intelligence
Rohan Gala, Nathan Gouwens, Zizhen Yao, Agata Budzillo, Osnat Penn, Bosiljka Tasic, Gabe Murphy, Hongkui Zeng, Uygar Sumbul
ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 32 (NIPS 2019)
(2019)
Proceedings Paper
Engineering, Biomedical
James Gornet, Kalman Umadevi Venkataraju, Arun Narasimhan, Nicholas Turner, Kisuk Lee, H. Sebastian Seung, Pavel Osten, Uygar Sumbul
2019 IEEE 16TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI 2019)
(2019)
Article
Engineering, Electrical & Electronic
Haldun M. Ozaktas, Uygar Sumbul
IEEE TRANSACTIONS ON SIGNAL PROCESSING
(2006)