1
|
Takahashi K, Sudharsan R, Beltran WA. Mapping protein distribution in the canine photoreceptor sensory cilium and calyceal processes by ultrastructure expansion microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600953. [PMID: 38979372 PMCID: PMC11230445 DOI: 10.1101/2024.06.27.600953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Photoreceptors are highly polarized sensory neurons, possessing a unique ciliary structure known as the photoreceptor sensory cilium (PSC). Vertebrates have two subtypes of photoreceptors: rods, which are responsible for night vision, and cones, which support daylight vision and color perception. Despite identifying functional and morphological differences between these subtypes, ultrastructural analyses of the PSC molecular architecture in rods and cones are still lacking. In this study, we employed ultrastructure expansion microscopy (U-ExM) to characterize the molecular architecture of the PSC in canine retina. We demonstrated that U-ExM is applicable to both non-frozen and cryopreserved retinal tissues with standard paraformaldehyde fixation. Using this validated U-ExM protocol, we revealed the molecular localization of numerous ciliopathy-related proteins in canine photoreceptors. Furthermore, we identified significant architectural differences in the PSC, ciliary rootlet, and calyceal processes between canine rods and cones. These findings pave the way for a better understanding of alterations in the molecular architecture of the PSC in canine models of retinal ciliopathies.
Collapse
Affiliation(s)
- Kei Takahashi
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Raghavi Sudharsan
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - William A. Beltran
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|
2
|
Liu L, Chen A, Li Y, Mulder J, Heyn H, Xu X. Spatiotemporal omics for biology and medicine. Cell 2024; 187:4488-4519. [PMID: 39178830 DOI: 10.1016/j.cell.2024.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 08/26/2024]
Abstract
The completion of the Human Genome Project has provided a foundational blueprint for understanding human life. Nonetheless, understanding the intricate mechanisms through which our genetic blueprint is involved in disease or orchestrates development across temporal and spatial dimensions remains a profound scientific challenge. Recent breakthroughs in cellular omics technologies have paved new pathways for understanding the regulation of genomic elements and the relationship between gene expression, cellular functions, and cell fate determination. The advent of spatial omics technologies, encompassing both imaging and sequencing-based methodologies, has enabled a comprehensive understanding of biological processes from a cellular ecosystem perspective. This review offers an updated overview of how spatial omics has advanced our understanding of the translation of genetic information into cellular heterogeneity and tissue structural organization and their dynamic changes over time. It emphasizes the discovery of various biological phenomena, related to organ functionality, embryogenesis, species evolution, and the pathogenesis of diseases.
Collapse
Affiliation(s)
| | - Ao Chen
- BGI Research, Shenzhen 518083, China
| | | | - Jan Mulder
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Xun Xu
- BGI Research, Hangzhou 310030, China; BGI Research, Shenzhen 518083, China.
| |
Collapse
|
3
|
Lewis TR, Klementieva NV, Phan S, Castillo CM, Kim KY, Cao LY, Ellisman MH, Arshavsky VY, Alekseev O. Human rod photoreceptor outer segments are supported by accessory inner segment structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607370. [PMID: 39149258 PMCID: PMC11326293 DOI: 10.1101/2024.08.09.607370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The first steps in vision take place in photoreceptor cells, which are highly compartmentalized neurons exhibiting significant structural variation across species. The light-sensitive ciliary compartment, called the outer segment, is located atop of the cell soma, called the inner segment. In this study, we present an ultrastructural analysis of human photoreceptors, which reveals that, in contrast to this classic arrangement, the inner segment of human rods extends alongside the outer segment to form a structure hereby termed the "accessory inner segment". While reminiscent of the actin-based microvilli known as "calyceal processes" observed in other species, the accessory inner segment is a unique structure: (1) it contains an extensive microtubule-based cytoskeleton, (2) it extends far alongside the outer segment, (3) its diameter is comparable to that of the outer segment, (4) it contains numerous mitochondria, and (5) it forms electron-dense structures that likely mediate adhesion to the outer segment. Given that the spacing of extrafoveal human photoreceptors is more sparse than in non-primate species, with vast amounts of interphotoreceptor matrix present between cells, the closely apposed accessory inner segment likely provides structural support to the outer segment. This discovery expands our understanding of the human retina and directs future studies of human photoreceptor function in health and disease.
Collapse
Affiliation(s)
- Tylor R. Lewis
- Department of Ophthalmology, Duke University, Durham, NC
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | | | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA
| | | | - Keun-Young Kim
- National Center for Microscopy and Imaging Research, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA
| | - Lauren Y. Cao
- Department of Ophthalmology, Duke University, Durham, NC
| | - Mark H. Ellisman
- National Center for Microscopy and Imaging Research, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA
| | - Vadim Y. Arshavsky
- Department of Ophthalmology, Duke University, Durham, NC
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC
| | - Oleg Alekseev
- Department of Ophthalmology, Duke University, Durham, NC
| |
Collapse
|
4
|
Cvekl A, Vijg J. Aging of the eye: Lessons from cataracts and age-related macular degeneration. Ageing Res Rev 2024; 99:102407. [PMID: 38977082 DOI: 10.1016/j.arr.2024.102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
Abstract
Aging is the greatest risk factor for chronic human diseases, including many eye diseases. Geroscience aims to understand the effects of the aging process on these diseases, including the genetic, molecular, and cellular mechanisms that underlie the increased risk of disease over the lifetime. Understanding of the aging eye increases general knowledge of the cellular physiology impacted by aging processes at various biological extremes. Two major diseases, age-related cataract and age-related macular degeneration (AMD) are caused by dysfunction of the lens and retina, respectively. Lens transparency and light refraction are mediated by lens fiber cells lacking nuclei and other organelles, which provides a unique opportunity to study a single aging hallmark, i.e., loss of proteostasis, within an environment of limited metabolism. In AMD, local dysfunction of the photoreceptors/retinal pigmented epithelium/Bruch's membrane/choriocapillaris complex in the macula leads to the loss of photoreceptors and eventually loss of central vision, and is driven by nearly all the hallmarks of aging and shares features with Alzheimer's disease, Parkinson's disease, cardiovascular disease, and diabetes. The aging eye can function as a model for studying basic mechanisms of aging and, vice versa, well-defined hallmarks of aging can be used as tools to understand age-related eye disease.
Collapse
Affiliation(s)
- Ales Cvekl
- Departments of Genetics and Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Jan Vijg
- Departments of Genetics and Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| |
Collapse
|
5
|
Shi XH, Ju L, Dong L, Zhang RH, Shao L, Yan YN, Wang YX, Fu XF, Chen YZ, Ge ZY, Wei WB. Deep Learning Models for the Screening of Cognitive Impairment Using Multimodal Fundus Images. Ophthalmol Retina 2024; 8:666-677. [PMID: 38280426 DOI: 10.1016/j.oret.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/03/2024] [Accepted: 01/19/2024] [Indexed: 01/29/2024]
Abstract
OBJECTIVE We aimed to develop a deep learning system capable of identifying subjects with cognitive impairment quickly and easily based on multimodal ocular images. DESIGN Cross sectional study. SUBJECTS Participants of Beijing Eye Study 2011 and patients attending Beijing Tongren Eye Center and Beijing Tongren Hospital Physical Examination Center. METHODS We trained and validated a deep learning algorithm to assess cognitive impairment using retrospectively collected data from the Beijing Eye Study 2011. Cognitive impairment was defined as a Mini-Mental State Examination score < 24. Based on fundus photographs and OCT images, we developed 5 models based on the following sets of images: macula-centered fundus photographs, optic disc-centered fundus photographs, fundus photographs of both fields, OCT images, and fundus photographs of both fields with OCT (multimodal). The performance of the models was evaluated and compared in an external validation data set, which was collected from patients attending Beijing Tongren Eye Center and Beijing Tongren Hospital Physical Examination Center. MAIN OUTCOME MEASURES Area under the curve (AUC). RESULTS A total of 9424 retinal photographs and 4712 OCT images were used to develop the model. The external validation sets from each center included 1180 fundus photographs and 590 OCT images. Model comparison revealed that the multimodal performed best, achieving an AUC of 0.820 in the internal validation set, 0.786 in external validation set 1, and 0.784 in external validation set 2. We evaluated the performance of the multi-model in different sexes and different age groups; there were no significant differences. The heatmap analysis showed that signals around the optic disc in fundus photographs and the retina and choroid around the macular and optic disc regions in OCT images were used by the multimodal to identify participants with cognitive impairment. CONCLUSIONS Fundus photographs and OCT can provide valuable information on cognitive function. Multimodal models provide richer information compared with single-mode models. Deep learning algorithms based on multimodal retinal images may be capable of screening cognitive impairment. This technique has potential value for broader implementation in community-based screening or clinic settings. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
Collapse
Affiliation(s)
- Xu Han Shi
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Lie Ju
- Beijing Airdoc Technology Co., Ltd., Beijing, China; Augmented Intelligence and Multimodal Analytics (AIM) for Health Lab, Faculty of Information Technology, Monash University, Clayton, Australia; Faculty of Engineering, Monash University, Clayton, Australia
| | - Li Dong
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Rui Heng Zhang
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Lei Shao
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yan Ni Yan
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ya Xing Wang
- Beijing Ophthalmology and Visual Science Key Laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
| | - Xue Fei Fu
- Beijing Airdoc Technology Co., Ltd., Beijing, China
| | | | - Zong Yuan Ge
- Beijing Airdoc Technology Co., Ltd., Beijing, China; Augmented Intelligence and Multimodal Analytics (AIM) for Health Lab, Faculty of Information Technology, Monash University, Clayton, Australia; Faculty of Engineering, Monash University, Clayton, Australia
| | - Wen Bin Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China.
| |
Collapse
|
6
|
Baden T. The vertebrate retina: a window into the evolution of computation in the brain. Curr Opin Behav Sci 2024; 57:None. [PMID: 38899158 PMCID: PMC11183302 DOI: 10.1016/j.cobeha.2024.101391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 03/14/2024] [Accepted: 03/24/2024] [Indexed: 06/21/2024]
Abstract
Animal brains are probably the most complex computational machines on our planet, and like everything in biology, they are the product of evolution. Advances in developmental and palaeobiology have been expanding our general understanding of how nervous systems can change at a molecular and structural level. However, how these changes translate into altered function - that is, into 'computation' - remains comparatively sparsely explored. What, concretely, does it mean for neuronal computation when neurons change their morphology and connectivity, when new neurons appear or old ones disappear, or when transmitter systems are slowly modified over many generations? And how does evolution use these many possible knobs and dials to constantly tune computation to give rise to the amazing diversity in animal behaviours we see today? Addressing these major gaps of understanding benefits from choosing a suitable model system. Here, I present the vertebrate retina as one perhaps unusually promising candidate. The retina is ancient and displays highly conserved core organisational principles across the entire vertebrate lineage, alongside a myriad of adjustments across extant species that were shaped by the history of their visual ecology. Moreover, the computational logic of the retina is readily interrogated experimentally, and our existing understanding of retinal circuits in a handful of species can serve as an anchor when exploring the visual circuit adaptations across the entire vertebrate tree of life, from fish deep in the aphotic zone of the oceans to eagles soaring high up in the sky.
Collapse
|
7
|
Kong W, Ding G, Cheng G, Yang P, Xu Z. Mucosal immune responses to Ichthyophthirius multifiliis in the ocular mucosa of rainbow trout ( Oncorhynchus mykiss, Walbaum), an ancient teleost fish. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:266-279. [PMID: 38827132 PMCID: PMC11136906 DOI: 10.1007/s42995-023-00199-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/16/2023] [Indexed: 06/04/2024]
Abstract
The eye, as a specialized visual organ, is directly exposed to the external environment, and, therefore, it faces constant challenges from external pathogenic organisms and toxins. In the ocular mucosa (OM) of mammals, mucosal-associated lymphoid tissues (MALTs) constitute the primary line of defense. However, the immune defense role of the OM remains unknown in aquatic vertebrates. To gain insights into the immune processes within the OM of teleost fish, we developed an infection model of rainbow trout (Oncorhynchus mykiss) OM using a parasite, Ichthyophthirius multifiliis (Ich). Immunofluorescence, qPCR, and H&E staining revealed that Ich successfully infiltrates the OM of rainbow trout, leading to pathological structural changes, as evidenced by A&B staining. Importantly, the qPCR results indicate an up-regulation of immune-related genes following Ich infection in the OM. Moreover, transcriptome analyses were conducted to detect immune responses and impairments in eye function within the OM of rainbow trout with Ich infection. The results of the transcriptome analysis that Ich infection can cause an extensive immune response in the OM, ultimately affecting ocular function. To the best of our knowledge, our findings represent for the first time that the teleost OM could act as an invasion site for parasites and trigger a strong mucosal immune response to parasitic infection. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00199-6.
Collapse
Affiliation(s)
- Weiguang Kong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Guangyi Ding
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Gaofeng Cheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070 China
| | - Peng Yang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Zhen Xu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| |
Collapse
|
8
|
Fritzsch B, Glover JC. Gene networks and the evolution of olfactory organs, eyes, hair cells and motoneurons: a view encompassing lancelets, tunicates and vertebrates. Front Cell Dev Biol 2024; 12:1340157. [PMID: 38533086 PMCID: PMC10963430 DOI: 10.3389/fcell.2024.1340157] [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: 11/17/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Key developmental pathways and gene networks underlie the formation of sensory cell types and structures involved in chemosensation, vision and mechanosensation, and of the efferents these sensory inputs can activate. We describe similarities and differences in these pathways and gene networks in selected species of the three main chordate groups, lancelets, tunicates, and vertebrates, leading to divergent development of olfactory receptors, eyes, hair cells and motoneurons. The lack of appropriately posited expression of certain transcription factors in lancelets and tunicates prevents them from developing vertebrate-like olfactory receptors and eyes, although they generate alternative structures for chemosensation and vision. Lancelets and tunicates lack mechanosensory cells associated with the sensation of acoustic stimuli, but have gravisensitive organs and ciliated epidermal sensory cells that may (and in some cases clearly do) provide mechanosensation and thus the capacity to respond to movement relative to surrounding water. Although functionally analogous to the vertebrate vestibular apparatus and lateral line, homology is questionable due to differences in the expression of the key transcription factors Neurog and Atoh1/7, on which development of vertebrate hair cells depends. The vertebrate hair cell-bearing inner ear and lateral line thus likely represent major evolutionary advances specific to vertebrates. Motoneurons develop in vertebrates under the control of the ventral signaling molecule hedgehog/sonic hedgehog (Hh,Shh), against an opposing inhibitory effect mediated by dorsal signaling molecules. Many elements of Shh-signaling and downstream genes involved in specifying and differentiating motoneurons are also exhibited by lancelets and tunicates, but the repertoire of MNs in vertebrates is broader, indicating greater diversity in motoneuron differentiation programs.
Collapse
Affiliation(s)
- Bernd Fritzsch
- Department of Biological Sciences, University of Nebraska Medical Center, Omaha, NE, United States
| | - Joel C. Glover
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Laboratory of Neural Development and Optical Recording (NDEVOR), Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| |
Collapse
|
9
|
Varney RM, Speiser DI, Cannon JT, Aguilar MA, Eernisse DJ, Oakley TH. A morphological basis for path-dependent evolution of visual systems. Science 2024; 383:983-987. [PMID: 38422123 DOI: 10.1126/science.adg2689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/11/2024] [Indexed: 03/02/2024]
Abstract
Path dependence influences macroevolutionary predictability by constraining potential outcomes after critical evolutionary junctions. Although it has been demonstrated in laboratory experiments, path dependence is difficult to demonstrate in natural systems because of a lack of independent replicates. Here, we show that two types of distributed visual systems recently evolved twice within chitons, demonstrating rapid and path-dependent evolution of a complex trait. The type of visual system that a chiton lineage can evolve is constrained by the number of openings for sensory nerves in its shell plates. Lineages with more openings evolve visual systems with thousands of eyespots, whereas those with fewer openings evolve visual systems with hundreds of shell eyes. These macroevolutionary outcomes shaped by path dependence are both deterministic and stochastic because possibilities are restricted yet not entirely predictable.
Collapse
Affiliation(s)
| | | | | | | | | | - Todd H Oakley
- University of California, Santa Barbara, Santa Barbara, CA, USA
| |
Collapse
|
10
|
Yoshimatsu T, Baden T. New twists in the evolution of retinal direction selectivity. PLoS Biol 2024; 22:e3002538. [PMID: 38422167 PMCID: PMC10903858 DOI: 10.1371/journal.pbio.3002538] [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: 03/02/2024] Open
Abstract
In mammals, starburst amacrine cells are centrally involved in motion vision and a new study in PLOS Biology, by Yan and colleagues finds that zebrafish have them, too. They coexist with a second pair of starburst-like neurons, but neither appears to be strongly motion selective.
Collapse
Affiliation(s)
- Takeshi Yoshimatsu
- Department of the Ophthalmology and Visual Sciences, Washington University in St. Louis School of Medicine, St. Louis, Missouri, United States of America
| | - Tom Baden
- Center for Sensory Neuroscience and Computation, Sussex Neuroscience, School of Life Sciences, University of Sussex, Sussex, United Kingdom
| |
Collapse
|
11
|
Kong W, Cheng G, Cao J, Yu J, Wang X, Xu Z. Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity. MICROBIOME 2024; 12:10. [PMID: 38218870 PMCID: PMC10787490 DOI: 10.1186/s40168-023-01716-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/07/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND The visual organ plays a crucial role in sensing environmental information. However, its mucosal surfaces are constantly exposed to selective pressures from aquatic or airborne pathogens and microbial communities. Although few studies have characterized the conjunctival-associated lymphoid tissue (CALT) in the ocular mucosa (OM) of birds and mammals, little is known regarding the evolutionary origins and functions of immune defense and microbiota homeostasis of the OM in the early vertebrates. RESULTS Our study characterized the structure of the OM microbial ecosystem in rainbow trout (Oncorhynchus mykiss) and confirmed for the first time the presence of a diffuse mucosal-associated lymphoid tissue (MALT) in fish OM. Moreover, the microbial communities residing on the ocular mucosal surface contribute to shaping its immune environment. Interestingly, following IHNV infection, we observed robust immune responses, significant tissue damage, and microbial dysbiosis in the trout OM, particularly in the fornix conjunctiva (FC), which is characterized by the increase of pathobionts and a reduction of beneficial taxa in the relative abundance in OM. Critically, we identified a significant correlation between viral-induced immune responses and microbiome homeostasis in the OM, underscoring its key role in mucosal immunity and microbiota homeostasis. CONCLUSIONS Our findings suggest that immune defense and microbiota homeostasis in OM occurred concurrently in early vertebrate species, shedding light on the coevolution between microbiota and mucosal immunity. Video Abstract.
Collapse
Affiliation(s)
- Weiguang Kong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gaofeng Cheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jiafeng Cao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China
| | - Jiaqian Yu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
| | - Xinyou Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhen Xu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| |
Collapse
|
12
|
Abstract
When vertebrates first conquered the land, they encountered a visual world that was radically distinct from that of their aquatic ancestors. Fish exploit the strong wavelength-dependent interactions of light with water by differentially feeding the signals from up to 5 spectral photoreceptor types into distinct behavioural programmes. However, above the water the same spectral rules do not apply, and this called for an update to visual circuit strategies. Early tetrapods soon evolved the double cone, a still poorly understood pair of new photoreceptors that brought the "ancestral terrestrial" complement from 5 to 7. Subsequent nonmammalian lineages differentially adapted this highly parallelised retinal input strategy for their diverse visual ecologies. By contrast, mammals shed most ancestral photoreceptors and converged on an input strategy that is exceptionally general. In eutherian mammals including in humans, parallelisation emerges gradually as the visual signal traverses the layers of the retina and into the brain.
Collapse
Affiliation(s)
- Tom Baden
- University of Sussex, Sussex Neuroscience, Sussex Center for Sensory Neuroscience and Computation, Brighton, United Kingdom
| |
Collapse
|
13
|
Zheng J, Song W, Zhou Y, Li X, Wang M, Zhang C. Cross-species single-cell landscape of vertebrate pineal gland. J Pineal Res 2024; 76:e12927. [PMID: 38018267 DOI: 10.1111/jpi.12927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023]
Abstract
The pineal gland has evolved from a photoreceptive organ in fish to a neuroendocrine organ in mammals. This study integrated multiple daytime single-cell RNA-seq datasets from the pineal glands of zebrafish, rats, and monkeys, providing a detailed examination of the evolutionary transition at single-cell resolution. We identified key factors responsible for the anatomical and functional transformation of the pineal gland. We retrieved and integrated daytime single-cell transcriptomic datasets from the pineal glands of zebrafish, rats, and monkeys, resulting in a total of 22 431 cells after rigorous quality filtering. Comparative analysis was then conducted to elucidate the evolution of pineal cells, their photosensitivity, their role in melatonin production, and the signaling processes within the glands of these species. Our analysis identified distinct cellular compositions of the pineal gland in zebrafish, rats, and monkeys. Zebrafish photoreceptors exhibited comprehensive phototransduction gene expression, while specific genes, including transducin (Gngt1, Gnb3, and Gngt2) and phosducin (Pdc), were consistently present in mammalian pinealocytes. We found transcriptional similarities between the pineal gland and retina, underscoring shared evolutionary and functional pathways. Zebrafish displayed unique light-responsive circadian gene activity compared to rats and monkeys. Key ligand-receptor interactions were identified, especially involving MDK and PTN, influencing melatonin synthesis across species. Furthermore, we observed species-specific GPCR (G protein-coupled receptors) expressions related to melatonin synthesis and their alignment with retinal expressions. Our findings also highlighted specific transcription factors (TFs) and regulatory networks associated with pineal gland evolution and function. Our study provides a detailed analysis of the pineal gland's evolution from fish to mammals. We identified key transcriptional changes and controls that highlight the gland's functional diversity. Notably, we found significant ligand-receptor interactions influencing melatonin synthesis and demonstrated parallels between pineal and retinal expressions. These insights enhance our understanding of the pineal gland's role in phototransduction, melatonin production, and circadian rhythms in vertebrates.
Collapse
Affiliation(s)
- Jihong Zheng
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenqi Song
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yihang Zhou
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xuan Li
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Meng Wang
- Songjiang Research Institute, Songjiang District Central Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Zhang
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| |
Collapse
|
14
|
Rasys AM, Wegerski A, Trainor PA, Hufnagel RB, Menke DB, Lauderdale JD. Dynamic changes in ocular shape during human development and its implications for retina fovea formation. Bioessays 2024; 46:e2300054. [PMID: 38037292 DOI: 10.1002/bies.202300054] [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: 03/27/2023] [Revised: 10/10/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
The human fovea is known for its distinctive pit-like appearance, which results from the displacement of retinal layers superficial to the photoreceptors cells. The photoreceptors are found at high density within the foveal region but not the surrounding retina. Efforts to elucidate the mechanisms responsible for these unique features have ruled out cell death as an explanation for pit formation and changes in cell proliferation as the cause of increased photoreceptor density. These findings have led to speculation that mechanical forces acting within and on the retina during development underly the formation of foveal architecture. Here we review eye morphogenesis and retinal remodeling in human embryonic development. Our meta-analysis of the literature suggests that fovea formation is a protracted process involving dynamic changes in ocular shape that start early and continue throughout most of human embryonic development. From these observations, we propose a new model for fovea development.
Collapse
Affiliation(s)
- Ashley M Rasys
- Department of Cellular Biology, The University of Georgia, Athens, Georgia, USA
| | - Andrew Wegerski
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
- Department of Anatomy & Cell Biology, The University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Douglas B Menke
- Department of Genetics, The University of Georgia, Athens, Georgia, USA
| | - James D Lauderdale
- Department of Cellular Biology, The University of Georgia, Athens, Georgia, USA
- Neuroscience Division of the Biomedical and Health Sciences Institute, The University of Georgia, Athens, Georgia, USA
| |
Collapse
|
15
|
Li G, Chen L, Jiang Z, Yau KW. Coexistence within one cell of microvillous and ciliary phototransductions across M1- through M6-IpRGCs. Proc Natl Acad Sci U S A 2023; 120:e2315282120. [PMID: 38109525 PMCID: PMC10756192 DOI: 10.1073/pnas.2315282120] [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: 09/02/2023] [Accepted: 11/16/2023] [Indexed: 12/20/2023] Open
Abstract
Intrinsically photosensitive retinal ganglion cells (ipRGCs) serve as primary photoceptors by expressing the photopigment, melanopsin, and also as retinal relay neurons for rod and cone signals en route to the brain, in both cases for the purpose of non-image vision as well as aspects of image vision. So far, six subtypes of ipRGCs (M1 through M6) have been characterized. Regarding their phototransduction mechanisms, we have previously found that, unconventionally, rhabdomeric (microvillous) and ciliary signaling motifs co-exist within a given M1-, M2-, and M4-ipRGC, with the first mechanism involving PLCβ4 and TRPC6,7 channels and the second involving cAMP and HCN channels. We have now examined M3-, M5-, and M6-cells and found that each cell likewise uses both signaling pathways for phototransduction, despite differences in the percentage representation by each pathway in a given ipRGC subtype for bright-flash responses (and saturated except for M6-cells). Generally, M3- and M5-cells show responses quite similar in kinetics to M2-responses, and M6-cell responses resemble broadly those of M1-cells although much lower in absolute sensitivity and amplitude. Therefore, similar to rod and cone subtypes in image vision, ipRGC subtypes possess the same phototransduction mechanism(s) even though they do not show microvilli or cilia morphologically.
Collapse
Affiliation(s)
- Guang Li
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Lujing Chen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Neuroscience Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Zheng Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - King-Wai Yau
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
| |
Collapse
|
16
|
Gupta M, Pazour GJ. Intraflagellar transport: A critical player in photoreceptor development and the pathogenesis of retinal degenerative diseases. Cytoskeleton (Hoboken) 2023:10.1002/cm.21823. [PMID: 38140908 PMCID: PMC11193844 DOI: 10.1002/cm.21823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
In vertebrate vision, photons are detected by highly specialized sensory cilia called outer segments. Photoreceptor outer segments form by remodeling the membrane of a primary cilium into a stack of flattened disks. Intraflagellar transport (IFT) is critical to the formation of most types of eukaryotic cilia including the outer segments. This review covers the state of knowledge of the role of IFT in the formation and maintenance of outer segments and the human diseases that result from mutations in genes encoding the IFT complex and associated motors.
Collapse
Affiliation(s)
- Mohona Gupta
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Suite 213 Biotech II, 373 Plantation Street, Worcester MA USA 01605
- Morningside Graduate School of Biological Sciences, University of Massachusetts Chan Medical School, 55 Lake Avenue North, Worcester MA USA 01655
| | - Gregory J. Pazour
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Suite 213 Biotech II, 373 Plantation Street, Worcester MA USA 01605
| |
Collapse
|
17
|
Wang X, Ding G, Yang P, Cheng G, Kong W, Xu Z. Teleost Eye Is the Portal of IHNV Entry and Contributes to a Robust Mucosal Immune Response. Int J Mol Sci 2023; 25:160. [PMID: 38203332 PMCID: PMC10778588 DOI: 10.3390/ijms25010160] [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: 11/13/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
The ocular mucosa (OM) is an important and unique part of the vertebrate mucosal immune system. The OM plays an important role in maintaining visual function and defending against foreign antigens or microorganisms, while maintaining a balance between the two through complex regulatory mechanisms. However, the function of ocular mucosal defense against foreign pathogens and mucosal immune response in bony fish are still less studied. To acquire deeper understanding into the mucosal immunity of the OM in teleost fish, we established a study of the immune response of rainbow trout (Oncorhynchus mykiss) infected with the infectious hematopoietic necrosis virus (IHNV). Our findings revealed that IHNV could successfully infiltrate the trout's OM, indicating that the OM could be an important portal for the IHNV. Furthermore, qPCR and RNA-Seq analysis results showed that a large number of immune-related genes were significantly upregulated in the OM of trout with IHNV infection. Critically, the results of our RNA-Seq analysis demonstrated that viral infection triggered a robust immune response, as evidenced by the substantial induction of antiviral, innate, and adaptive immune-related genes in the OM of infected fish, which underscored the essential role of the OM in viral infection. Overall, our findings revealed a previously unknown function of teleost OM in antiviral defense, and provided a theoretical basis for the study of the mucosal immunity of fish.
Collapse
Affiliation(s)
- Xinyou Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China;
| | - Guangyi Ding
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (G.D.); (G.C.); (W.K.)
| | - Peng Yang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (G.D.); (G.C.); (W.K.)
| | - Gaofeng Cheng
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (G.D.); (G.C.); (W.K.)
| | - Weiguang Kong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (G.D.); (G.C.); (W.K.)
| | - Zhen Xu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (G.D.); (G.C.); (W.K.)
| |
Collapse
|
18
|
Pan D, Wang Z, Chen Y, Cao J. Melanopsin-mediated optical entrainment regulates circadian rhythms in vertebrates. Commun Biol 2023; 6:1054. [PMID: 37853054 PMCID: PMC10584931 DOI: 10.1038/s42003-023-05432-7] [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: 07/08/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023] Open
Abstract
Melanopsin (OPN4) is a light-sensitive protein that plays a vital role in the regulation of circadian rhythms and other nonvisual functions. Current research on OPN4 has focused on mammals; more evidence is needed from non-mammalian vertebrates to fully assess the significance of the non-visual photosensitization of OPN4 for circadian rhythm regulation. There are species differences in the regulatory mechanisms of OPN4 for vertebrate circadian rhythms, which may be due to the differences in the cutting variants, tissue localization, and photosensitive activation pathway of OPN4. We here summarize the distribution of OPN4 in mammals, birds, and teleost fish, and the classical excitation mode for the non-visual photosensitive function of OPN4 in mammals is discussed. In addition, the role of OPN4-expressing cells in regulating circadian rhythm in different vertebrates is highlighted, and the potential rhythmic regulatory effects of various neuropeptides or neurotransmitters expressed in mammalian OPN4-expressing ganglion cells are summarized among them.
Collapse
Affiliation(s)
- Deng Pan
- Laboratory of Anatomy of Domestic Animals, National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Haidian, 100193, Beijing, China
| | - Zixu Wang
- Laboratory of Anatomy of Domestic Animals, National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Haidian, 100193, Beijing, China
| | - Yaoxing Chen
- Laboratory of Anatomy of Domestic Animals, National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Haidian, 100193, Beijing, China
| | - Jing Cao
- Laboratory of Anatomy of Domestic Animals, National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Haidian, 100193, Beijing, China.
| |
Collapse
|
19
|
Ostrovsky MA, Smitienko OA, Bochenkova AV, Feldman TB. Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1528-1543. [PMID: 38105022 DOI: 10.1134/s0006297923100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/20/2023] [Accepted: 08/12/2023] [Indexed: 12/19/2023]
Abstract
The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.
Collapse
Affiliation(s)
- Mikhail A Ostrovsky
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
| | - Olga A Smitienko
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
| | | | - Tatiana B Feldman
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
| |
Collapse
|
20
|
Ricci V, Ronco F, Boileau N, Salzburger W. Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika. SCIENCE ADVANCES 2023; 9:eadg6568. [PMID: 37672578 PMCID: PMC10482347 DOI: 10.1126/sciadv.adg6568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Tuning the visual sensory system to the ambient light is essential for survival in many animal species. This is often achieved through duplication, functional diversification, and/or differential expression of visual opsin genes. Here, we examined 753 new retinal transcriptomes from 112 species of cichlid fishes from Lake Tanganyika to unravel adaptive changes in gene expression at the macro-evolutionary and ecosystem level of one of the largest vertebrate adaptive radiations. We found that, across the radiation, all seven cone opsins-but not the rhodopsin-rank among the most differentially expressed genes in the retina, together with other vision-, circadian rhythm-, and hemoglobin-related genes. We propose two visual palettes characteristic of very shallow- and deep-water living species, respectively, and show that visual system adaptations along two major ecological axes, macro-habitat and diet, occur primarily via gene expression variation in a subset of cone opsin genes.
Collapse
Affiliation(s)
- Virginie Ricci
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Fabrizia Ronco
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Nicolas Boileau
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| |
Collapse
|
21
|
Kalluraya CA, Weitzel AJ, Tsu BV, Daugherty MD. Reply to Redmond and McLysaght: Uncertainty in the origin of amphioxus IRBP homologs. Proc Natl Acad Sci U S A 2023; 120:e2310867120. [PMID: 37579166 PMCID: PMC10450401 DOI: 10.1073/pnas.2310867120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Affiliation(s)
- Chinmay A. Kalluraya
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
| | - Alexander J. Weitzel
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
| | - Brian V. Tsu
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
| | - Matthew D. Daugherty
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
| |
Collapse
|
22
|
Nerli E, Kretzschmar J, Bianucci T, Rocha‐Martins M, Zechner C, Norden C. Deterministic and probabilistic fate decisions co-exist in a single retinal lineage. EMBO J 2023; 42:e112657. [PMID: 37184124 PMCID: PMC10350840 DOI: 10.15252/embj.2022112657] [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: 09/29/2022] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023] Open
Abstract
Correct nervous system development depends on the timely differentiation of progenitor cells into neurons. While the output of progenitor differentiation is well investigated at the population and clonal level, how stereotypic or variable fate decisions are during development is still more elusive. To fill this gap, we here follow the fate outcome of single neurogenic progenitors in the zebrafish retina over time using live imaging. We find that neurogenic progenitor divisions produce two daughter cells, one of deterministic and one of probabilistic fate. Interference with the deterministic branch of the lineage affects lineage progression. In contrast, interference with fate probabilities of the probabilistic branch results in a broader range of fate possibilities than in wild-type and involves the production of any neuronal cell type even at non-canonical developmental stages. Combining the interference data with stochastic modelling of fate probabilities revealed that a simple gene regulatory network is able to predict the observed fate decision probabilities during wild-type development. These findings unveil unexpected lineage flexibility that could ensure robust development of the retina and other tissues.
Collapse
Affiliation(s)
- Elisa Nerli
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | | | - Tommaso Bianucci
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Physics of Life, Cluster of ExcellenceTU DresdenDresdenGermany
| | - Mauricio Rocha‐Martins
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Christoph Zechner
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Physics of Life, Cluster of ExcellenceTU DresdenDresdenGermany
| | - Caren Norden
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| |
Collapse
|
23
|
Townes-Anderson E, Halász É, Sugino I, Davidow AL, Frishman LJ, Fritzky L, Yousufzai FAK, Zarbin M. Injury to Cone Synapses by Retinal Detachment: Differences from Rod Synapses and Protection by ROCK Inhibition. Cells 2023; 12:1485. [PMID: 37296606 PMCID: PMC10253016 DOI: 10.3390/cells12111485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Attachment of a detached retina does not always restore vision to pre-injury levels, even if the attachment is anatomically successful. The problem is due in part to long-term damage to photoreceptor synapses. Previously, we reported on damage to rod synapses and synaptic protection using a Rho kinase (ROCK) inhibitor (AR13503) after retinal detachment (RD). This report documents the effects of detachment, reattachment, and protection by ROCK inhibition on cone synapses. Conventional confocal and stimulated emission depletion (STED) microscopy were used for morphological assessment and electroretinograms for functional analysis of an adult pig model of RD. RDs were examined 2 and 4 h after injury or two days later when spontaneous reattachment had occurred. Cone pedicles respond differently than rod spherules. They lose their synaptic ribbons, reduce invaginations, and change their shape. ROCK inhibition protects against these structural abnormalities whether the inhibitor is applied immediately or 2 h after the RD. Functional restoration of the photopic b-wave, indicating cone-bipolar neurotransmission, is also improved with ROCK inhibition. Successful protection of both rod and cone synapses with AR13503 suggests this drug will (1) be a useful adjunct to subretinal administration of gene or stem cell therapies and (2) improve recovery of the injured retina when treatment is delayed.
Collapse
Affiliation(s)
- Ellen Townes-Anderson
- Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA;
| | - Éva Halász
- Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA;
| | - Ilene Sugino
- Institute of Ophthalmology and Visual Science, Rutgers New Jersey Medical School, 90 Bergen Street, Newark, NJ 07103, USA; (I.S.); (M.Z.)
| | - Amy L. Davidow
- Department of Biostatistics, New York University School of Global Public Health, 708 Broadway, New York, NY 10003, USA;
| | - Laura J. Frishman
- Department of Vision Sciences, College of Optometry, University of Houston, Martin Luther King Blvd, Houston, TX 77204, USA;
| | - Luke Fritzky
- Cellular Imaging and Histology Core, Rutgers New Jersey Medical School, 205 South Orange Avenue, Newark, NJ 07103, USA; (L.F.); (F.A.K.Y.)
| | - Fawad A. K. Yousufzai
- Cellular Imaging and Histology Core, Rutgers New Jersey Medical School, 205 South Orange Avenue, Newark, NJ 07103, USA; (L.F.); (F.A.K.Y.)
| | - Marco Zarbin
- Institute of Ophthalmology and Visual Science, Rutgers New Jersey Medical School, 90 Bergen Street, Newark, NJ 07103, USA; (I.S.); (M.Z.)
| |
Collapse
|
24
|
Kalluraya CA, Weitzel AJ, Tsu BV, Daugherty MD. Bacterial origin of a key innovation in the evolution of the vertebrate eye. Proc Natl Acad Sci U S A 2023; 120:e2214815120. [PMID: 37036996 PMCID: PMC10120077 DOI: 10.1073/pnas.2214815120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/28/2023] [Indexed: 04/12/2023] Open
Abstract
The vertebrate eye was described by Charles Darwin as one of the greatest potential challenges to a theory of natural selection by stepwise evolutionary processes. While numerous evolutionary transitions that led to the vertebrate eye have been explained, some aspects appear to be vertebrate specific with no obvious metazoan precursor. One critical difference between vertebrate and invertebrate vision hinges on interphotoreceptor retinoid-binding protein (IRBP, also known as retinol-binding protein, RBP3), which enables the physical separation and specialization of cells in the vertebrate visual cycle by promoting retinoid shuttling between cell types. While IRBP has been functionally described, its evolutionary origin has remained elusive. Here, we show that IRBP arose via acquisition of novel genetic material from bacteria by interdomain horizontal gene transfer (iHGT). We demonstrate that a gene encoding a bacterial peptidase was acquired prior to the radiation of extant vertebrates >500 Mya and underwent subsequent domain duplication and neofunctionalization to give rise to vertebrate IRBP. Our phylogenomic analyses on >900 high-quality genomes across the tree of life provided the resolution to distinguish contamination in genome assemblies from true instances of horizontal acquisition of IRBP and led us to discover additional independent transfers of the same bacterial peptidase gene family into distinct eukaryotic lineages. Importantly, this work illustrates the evolutionary basis of a key transition that led to the vertebrate visual cycle and highlights the striking impact that acquisition of bacterial genes has had on vertebrate evolution.
Collapse
Affiliation(s)
- Chinmay A. Kalluraya
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
| | - Alexander J. Weitzel
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
| | - Brian V. Tsu
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
| | - Matthew D. Daugherty
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
| |
Collapse
|
25
|
Karthikeyan R, Davies WI, Gunhaga L. Non-image-forming functional roles of OPN3, OPN4 and OPN5 photopigments. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2023. [DOI: 10.1016/j.jpap.2023.100177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
|
26
|
Wang X, Roberts PA, Yoshimatsu T, Lagnado L, Baden T. Amacrine cells differentially balance zebrafish color circuits in the central and peripheral retina. Cell Rep 2023; 42:112055. [PMID: 36757846 DOI: 10.1016/j.celrep.2023.112055] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/01/2022] [Accepted: 01/18/2023] [Indexed: 02/10/2023] Open
Abstract
The vertebrate inner retina is driven by photoreceptors whose outputs are already pre-processed; in zebrafish, outer retinal circuits split "color" from "grayscale" information across four cone-photoreceptor types. It remains unclear how the inner retina processes incoming spectral information while also combining cone signals to shape grayscale functions. We address this question by imaging the light-driven responses of amacrine cells (ACs) and bipolar cells (BCs) in larval zebrafish in the presence and pharmacological absence of inner retinal inhibition. We find that ACs enhance opponency in some bipolar cells while at the same time suppressing pre-existing opponency in others, so that, depending on the retinal region, the net change in the number of color-opponent units is essentially zero. To achieve this "dynamic balance," ACs counteract intrinsic color opponency of BCs via the On channel. Consistent with these observations, Off-stratifying ACs are exclusively achromatic, while all color-opponent ACs stratify in the On sublamina.
Collapse
Affiliation(s)
- Xinwei Wang
- School of Life Sciences, University of Sussex, Biology Road, Brighton BN1 9QG, UK.
| | - Paul A Roberts
- School of Life Sciences, University of Sussex, Biology Road, Brighton BN1 9QG, UK
| | - Takeshi Yoshimatsu
- School of Life Sciences, University of Sussex, Biology Road, Brighton BN1 9QG, UK
| | - Leon Lagnado
- School of Life Sciences, University of Sussex, Biology Road, Brighton BN1 9QG, UK.
| | - Tom Baden
- School of Life Sciences, University of Sussex, Biology Road, Brighton BN1 9QG, UK; Institute of Ophthalmic Research, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany.
| |
Collapse
|
27
|
Confalonieri F, Josifovska N, Boix-Lemonche G, Stene-Johansen I, Bragadottir R, Lumi X, Petrovski G. Vitreous Substitutes from Bench to the Operating Room in a Translational Approach: Review and Future Endeavors in Vitreoretinal Surgery. Int J Mol Sci 2023; 24:3342. [PMID: 36834754 PMCID: PMC9961686 DOI: 10.3390/ijms24043342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Vitreous substitutes are indispensable tools in vitreoretinal surgery. The two crucial functions of these substitutes are their ability to displace intravitreal fluid from the retinal surface and to allow the retina to adhere to the retinal pigment epithelium. Today, vitreoretinal surgeons can choose among a plethora of vitreous tamponades, and the tamponade of choice might be difficult to determine in the ever-expanding range of possibilities for a favorable outcome. The currently available vitreous substitutes have disadvantages that need to be addressed to improve the surgical outcome achievable today. Herein, the fundamental physical and chemical proprieties of all vitreous substitutes are reported, and their use and clinical applications are described alongside some surgical techniques of intra-operative manipulation. The major upcoming developments in vitreous substitutes are extensively discussed, keeping a translational perspective throughout. Conclusions on future perspectives are derived through an in-depth analysis of what is lacking today in terms of desired outcomes and biomaterials technology.
Collapse
Affiliation(s)
- Filippo Confalonieri
- Department of Ophthalmology, Oslo University Hospital, Kirkeveien 166, 0450 Oslo, Norway
- Center for Eye Research and Innovative Diagnostics, Department of Ophthalmology, Institute for Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy
| | - Natasha Josifovska
- Center for Eye Research and Innovative Diagnostics, Department of Ophthalmology, Institute for Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
| | - Gerard Boix-Lemonche
- Center for Eye Research and Innovative Diagnostics, Department of Ophthalmology, Institute for Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
| | - Ingar Stene-Johansen
- Department of Ophthalmology, Oslo University Hospital, Kirkeveien 166, 0450 Oslo, Norway
| | - Ragnheidur Bragadottir
- Department of Ophthalmology, Oslo University Hospital, Kirkeveien 166, 0450 Oslo, Norway
- Center for Eye Research and Innovative Diagnostics, Department of Ophthalmology, Institute for Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
| | - Xhevat Lumi
- Center for Eye Research and Innovative Diagnostics, Department of Ophthalmology, Institute for Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
- Eye Hospital, University Medical Centre Ljubljana, Zaloška cesta 7, 1000 Ljubljana, Slovenia
| | - Goran Petrovski
- Department of Ophthalmology, Oslo University Hospital, Kirkeveien 166, 0450 Oslo, Norway
- Center for Eye Research and Innovative Diagnostics, Department of Ophthalmology, Institute for Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
- Department of Ophthalmology, University of Split School of Medicine and University Hospital Centre, 21000 Split, Croatia
| |
Collapse
|
28
|
Collin HB, Ratcliffe J, Collin SP. The functional anatomy of the cornea of the Shorthead lamprey, Mordacia mordax (Mordaciidae, Agnatha): A comparison between downstream and upstream migrants. J Morphol 2023; 284:e21552. [PMID: 36601696 DOI: 10.1002/jmor.21552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023]
Abstract
The Shorthead lamprey Mordacia mordax (Mordaciidae, Agnatha) represents one of the earliest stages of vertebrate evolution. This study investigates the ultrastructural anatomy of the cornea, iris and anterior chamber in the eyes of this species in both the downstream and upstream migrant phases of its protracted lifecycle to assess the morphological and quantitative changes associated with growth, corneal function and vision. Using light and both scanning and transmission electron microscopy, the cornea is found to be divided into dermal and scleral components separated by a mucoid layer. A range of distinguishing corneal features are compared in the two adult phases of the lifecycle, including epithelial microprojections, mucus-secreting epithelial cells, the number, thickness, formation and level of branching and anastomosing of collagen lamellae, the type and distribution of vertical sutures, the structure of the mucoid layer and annular ligament and the number and distribution of a large number of basement membranes throughout the cornea. Significant differences are found between the two phases, which are thought to reflect adaptations to the variable environmental conditions encountered throughout this species' lifecycle. The study provides insights into the evolutionary pressures on extant representatives of the earliest stages in the evolution of the vertebrate eye.
Collapse
Affiliation(s)
- Hermann Barry Collin
- Department of Optometry and Vision Science, University of New South Wales, Kensington, New South Wales, Australia
| | - Julian Ratcliffe
- Bioimaging Platform, La Trobe University, Bundoora, Victoria, Australia
| | - Shaun P Collin
- School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia.,Oceans Graduate School and Oceans Institute, The University of Western Australia, Crawley, Western Australia, Australia
| |
Collapse
|
29
|
Cardozo MJ, Sánchez-Bustamante E, Bovolenta P. Optic cup morphogenesis across species and related inborn human eye defects. Development 2023; 150:dev200399. [PMID: 36714981 PMCID: PMC10110496 DOI: 10.1242/dev.200399] [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] [Indexed: 01/31/2023]
Abstract
The vertebrate eye is shaped as a cup, a conformation that optimizes vision and is acquired early in development through a process known as optic cup morphogenesis. Imaging living, transparent teleost embryos and mammalian stem cell-derived organoids has provided insights into the rearrangements that eye progenitors undergo to adopt such a shape. Molecular and pharmacological interference with these rearrangements has further identified the underlying molecular machineries and the physical forces involved in this morphogenetic process. In this Review, we summarize the resulting scenarios and proposed models that include common and species-specific events. We further discuss how these studies and those in environmentally adapted blind species may shed light on human inborn eye malformations that result from failures in optic cup morphogenesis, including microphthalmia, anophthalmia and coloboma.
Collapse
Affiliation(s)
- Marcos J. Cardozo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
| | - Elena Sánchez-Bustamante
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
| |
Collapse
|
30
|
Unusual phototransduction via cross-motif signaling from G q to adenylyl cyclase in intrinsically photosensitive retinalganglion cells. Proc Natl Acad Sci U S A 2023; 120:e2216599120. [PMID: 36584299 PMCID: PMC9910442 DOI: 10.1073/pnas.2216599120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nonimage-forming vision in mammals is mediated primarily by melanopsin (OPN4)-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs). In mouse M1-ipRGCs, melanopsin predominantly activates, via Gαq,11,14, phospholipase C-β4 to open transient receptor 6 (TRPC6) and TRPC7 channels. In M2- and M4-ipRGCs, however, a prominent phototransduction mechanism involves the opening of hyperpolarization- and cyclic nucleotide-gated channels via cyclic nucleotide, although the upstream steps remain uncertain. We report here experiments, primarily on M4-ipRGCs, with photo-uncaging of cyclic nucleotides and virally expressed CNGA2 channels to conclude that the second messenger is cyclic adenosine monophosphate (cAMP) - very surprising considering that cyclic guanosine monophosphate (cGMP) is used in almost all cyclic nucleotide-mediated phototransduction mechanisms across the animal kingdom. We further found that the upstream G protein is likewise Gq, which via its Gβγ subunits directly activates adenylyl cyclase (AC). Our findings are a demonstration in a native cell of a cross-motif GPCR signaling pathway from Gq directly to AC with a specific function.
Collapse
|
31
|
Hagen JFD, Roberts NS, Johnston RJ. The evolutionary history and spectral tuning of vertebrate visual opsins. Dev Biol 2023; 493:40-66. [PMID: 36370769 PMCID: PMC9729497 DOI: 10.1016/j.ydbio.2022.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
Many animals depend on the sense of vision for survival. In eumetazoans, vision requires specialized, light-sensitive cells called photoreceptors. Light reaches the photoreceptors and triggers the excitation of light-detecting proteins called opsins. Here, we describe the story of visual opsin evolution from the ancestral bilaterian to the extant vertebrate lineages. We explain the mechanisms determining color vision of extant vertebrates, focusing on opsin gene losses, duplications, and the expression regulation of vertebrate opsins. We describe the sequence variation both within and between species that has tweaked the sensitivities of opsin proteins towards different wavelengths of light. We provide an extensive resource of wavelength sensitivities and mutations that have diverged light sensitivity in many vertebrate species and predict how these mutations were accumulated in each lineage based on parsimony. We suggest possible natural and sexual selection mechanisms underlying these spectral differences. Understanding how molecular changes allow for functional adaptation of animals to different environments is a major goal in the field, and therefore identifying mutations affecting vision and their relationship to photic selection pressures is imperative. The goal of this review is to provide a comprehensive overview of our current understanding of opsin evolution in vertebrates.
Collapse
Affiliation(s)
- Joanna F D Hagen
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Natalie S Roberts
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA.
| |
Collapse
|
32
|
Kon T, Fukuta K, Chen Z, Kon-Nanjo K, Suzuki K, Ishikawa M, Tanaka H, Burgess SM, Noguchi H, Toyoda A, Omori Y. Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization. Commun Biol 2022; 5:1404. [PMID: 36572749 PMCID: PMC9792465 DOI: 10.1038/s42003-022-04351-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022] Open
Abstract
The recent whole-genome duplication (WGD) in goldfish (Carassius auratus) approximately 14 million years ago makes it a valuable model for studying gene evolution during the early stages after WGD. We analyzed the transcriptome of the goldfish retina at the level of single-cell (scRNA-seq) and open chromatin regions (scATAC-seq). We identified a group of genes that have undergone dosage selection, accounting for 5% of the total 11,444 ohnolog pairs. We also identified 306 putative sub/neo-functionalized ohnolog pairs that are likely to be under cell-type-specific genetic variation at single-cell resolution. Diversification in the expression patterns of several ohnolog pairs was observed in the retinal cell subpopulations. The single-cell level transcriptome analysis in this study uncovered the early stages of evolution in retinal cell of goldfish after WGD. Our results provide clues for understanding the relationship between the early stages of gene evolution after WGD and the evolution of diverse vertebrate retinal functions.
Collapse
Affiliation(s)
- Tetsuo Kon
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Japan
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Kentaro Fukuta
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan
| | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Koto Kon-Nanjo
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Kota Suzuki
- Yatomi Station, Aichi Fisheries Research Institute, Yatomi, Japan
| | | | | | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Yoshihiro Omori
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Japan.
| |
Collapse
|
33
|
Vöcking O, Macias-Muñoz A, Jaeger SJ, Oakley TH. Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals. Cells 2022; 11:cells11243966. [PMID: 36552730 PMCID: PMC9776813 DOI: 10.3390/cells11243966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/19/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a "deep diversity" of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.
Collapse
Affiliation(s)
- Oliver Vöcking
- Department of Biology, University of Kentucky, Lexington, KY 40508, USA
| | - Aide Macias-Muñoz
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Stuart J. Jaeger
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
- Correspondence:
| |
Collapse
|
34
|
Szabó L, Erdei G, Maák PA. Optical analysis of Müller glia cells as light transporters through the retina. BIOMEDICAL OPTICS EXPRESS 2022; 13:6335-6356. [PMID: 36589561 PMCID: PMC9774881 DOI: 10.1364/boe.462568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 06/17/2023]
Abstract
One and half decades ago, Müller glia cells of the retina became subjects of extended research as optical waveguides. It was demonstrated that outside the fovea, these cells are capable of providing light transmission through the thicker parts of the retina from the vitreous surface to the photoreceptor cells. We combined optical modeling of the eye's optical system with numerical methods that describe light guiding within Müller cells to analyze efficiency of light capture and guidance at different peripheral positions. We show that higher order guided modes play an important role, especially in the case of higher incidence angles and extended geometry of the electromagnetic field distributions predicted by the eye's optical model. We analyze the mode structure excited at different retinal peripheral positions and show that actual construction of these cells optimizes light guiding. Our results refine previously published modeling results regarding Müller cells as waveguides and provide extension to the whole area of the retina.
Collapse
Affiliation(s)
- Levente Szabó
- Department of Sociology and Communication, Budapest Univ. of Technology and Economics, Hungary
| | - Gábor Erdei
- Department of Atomic Physics, Inst. of Physics, Budapest Univ. of Technology and Economics, Hungary
| | - Pál Andor Maák
- Department of Atomic Physics, Inst. of Physics, Budapest Univ. of Technology and Economics, Hungary
| |
Collapse
|
35
|
Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
Collapse
Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| |
Collapse
|
36
|
Gölz L, Baumann L, Pannetier P, Braunbeck T, Knapen D, Vergauwen L. AOP Report: Thyroperoxidase Inhibition Leading to Altered Visual Function in Fish Via Altered Retinal Layer Structure. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:2632-2648. [PMID: 35942927 DOI: 10.1002/etc.5452] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Thyroid hormones (THs) are involved in the regulation of many important physiological and developmental processes, including vertebrate eye development. Thyroid hormone system-disrupting chemicals (THSDCs) may have severe consequences, because proper functioning of the visual system is a key factor for survival in wildlife. However, the sequence of events leading from TH system disruption (THSD) to altered eye development in fish has not yet been fully described. The development of this adverse outcome pathway (AOP) was based on an intensive literature review of studies that focused on THSD and impacts on eye development, mainly in fish. In total, approximately 120 studies (up to the end of 2021) were used in the development of this AOP linking inhibition of the key enzyme for TH synthesis, thyroperoxidase (TPO), to effects on retinal layer structure and visual function in fish (AOP-Wiki, AOP 363). In a weight-of-evidence evaluation, the confidence levels were overall moderate, with ample studies showing the link between reduced TH levels and altered retinal layer structure. However, some uncertainties about the underlying mechanism(s) remain. Although the current weight-of-evidence evaluation is based on fish, the AOP is plausibly applicable to other vertebrate classes. Through the re-use of several building blocks, this AOP is connected to the AOPs leading from TPO and deiodinase inhibition to impaired swim bladder inflation in fish (AOPs 155-159), together forming an AOP network describing THSD in fish. This AOP network addresses the lack of thyroid-related endpoints in existing fish test guidelines for the evaluation of THSDCs. Environ Toxicol Chem 2022;41:2632-2648. © 2022 SETAC.
Collapse
Affiliation(s)
- Lisa Gölz
- Aquatic Ecology and Toxicology Research Group, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Lisa Baumann
- Aquatic Ecology and Toxicology Research Group, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Pauline Pannetier
- Aquatic Ecology and Toxicology Research Group, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Thomas Braunbeck
- Aquatic Ecology and Toxicology Research Group, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Dries Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Lucia Vergauwen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| |
Collapse
|
37
|
Pillai AS, Hochberg GK, Thornton JW. Simple mechanisms for the evolution of protein complexity. Protein Sci 2022; 31:e4449. [PMID: 36107026 PMCID: PMC9601886 DOI: 10.1002/pro.4449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/26/2023]
Abstract
Proteins are tiny models of biological complexity: specific interactions among their many amino acids cause proteins to fold into elaborate structures, assemble with other proteins into higher-order complexes, and change their functions and structures upon binding other molecules. These complex features are classically thought to evolve via long and gradual trajectories driven by persistent natural selection. But a growing body of evidence from biochemistry, protein engineering, and molecular evolution shows that naturally occurring proteins often exist at or near the genetic edge of multimerization, allostery, and even new folds, so just one or a few mutations can trigger acquisition of these properties. These sudden transitions can occur because many of the physical properties that underlie these features are present in simpler proteins as fortuitous by-products of their architecture. Moreover, complex features of proteins can be encoded by huge arrays of sequences, so they are accessible from many different starting points via many possible paths. Because the bridges to these features are both short and numerous, random chance can join selection as a key factor in explaining the evolution of molecular complexity.
Collapse
Affiliation(s)
- Arvind S. Pillai
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Institute for Protein DesignUniversity of WashingtonSeattleWAUSA
| | - Georg K.A. Hochberg
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Department of Chemistry, Center for Synthetic MicrobiologyPhilipps University MarburgMarburgGermany
| | - Joseph W. Thornton
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Departments of Human Genetics and Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
| |
Collapse
|
38
|
Roberts RJV, Pop S, Prieto-Godino LL. Evolution of central neural circuits: state of the art and perspectives. Nat Rev Neurosci 2022; 23:725-743. [DOI: 10.1038/s41583-022-00644-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/09/2022]
|
39
|
Faiq MA, Sengupta T, Nath M, Velpandian T, Saluja D, Dada R, Dada T, Chan KC. Ocular manifestations of central insulin resistance. Neural Regen Res 2022; 18:1139-1146. [PMID: 36255004 PMCID: PMC9827783 DOI: 10.4103/1673-5374.355765] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Central insulin resistance, the diminished cellular sensitivity to insulin in the brain, has been implicated in diabetes mellitus, Alzheimer's disease and other neurological disorders. However, whether and how central insulin resistance plays a role in the eye remains unclear. Here, we performed intracerebroventricular injection of S961, a potent and specific blocker of insulin receptor in adult Wistar rats to test if central insulin resistance leads to pathological changes in ocular structures. 80 mg of S961 was stereotaxically injected into the lateral ventricle of the experimental group twice at 7 days apart, whereas buffer solution was injected to the sham control group. Blood samples, intraocular pressure, trabecular meshwork morphology, ciliary body markers, retinal and optic nerve integrity, and whole genome expression patterns were then evaluated. While neither blood glucose nor serum insulin level was significantly altered in the experimental or control group, we found that injection of S961 but not buffer solution significantly increased intraocular pressure at 14 and 24 days after first injection, along with reduced porosity and aquaporin 4 expression in the trabecular meshwork, and increased tumor necrosis factor α and aquaporin 4 expression in the ciliary body. In the retina, cell density and insulin receptor expression decreased in the retinal ganglion cell layer upon S961 injection. Fundus photography revealed peripapillary atrophy with vascular dysregulation in the experimental group. These retinal changes were accompanied by upregulation of pro-inflammatory and pro-apoptotic genes, downregulation of anti-inflammatory, anti-apoptotic, and neurotrophic genes, as well as dysregulation of genes involved in insulin signaling. Optic nerve histology indicated microglial activation and changes in the expression of glial fibrillary acidic protein, tumor necrosis factor α, and aquaporin 4. Molecular pathway architecture of the retina revealed the three most significant pathways involved being inflammation/cell stress, insulin signaling, and extracellular matrix regulation relevant to neurodegeneration. There was also a multimodal crosstalk between insulin signaling derangement and inflammation-related genes. Taken together, our results indicate that blocking insulin receptor signaling in the central nervous system can lead to trabecular meshwork and ciliary body dysfunction, intraocular pressure elevation, as well as inflammation, glial activation, and apoptosis in the retina and optic nerve. Given that central insulin resistance may lead to neurodegenerative phenotype in the visual system, targeting insulin signaling may hold promise for vision disorders involving the retina and optic nerve.
Collapse
Affiliation(s)
- Muneeb A. Faiq
- Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India,Neuroimaging and Visual Science Laboratory, Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, NY, USA,Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Trina Sengupta
- Dr. Baldev Singh Sleep Laboratory, Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Madhu Nath
- Department of Ocular Pharmacology, Dr. Rajendra Prasad Center for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Thirumurthy Velpandian
- Department of Ocular Pharmacology, Dr. Rajendra Prasad Center for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Rima Dada
- Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Tanuj Dada
- Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India,Correspondence to: Tanuj Dada, ; Kevin C. Chan, .
| | - Kevin C. Chan
- Neuroimaging and Visual Science Laboratory, Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, NY, USA,Correspondence to: Tanuj Dada, ; Kevin C. Chan, .
| |
Collapse
|
40
|
Vij R, Arora S. A systematic survey of advances in retinal imaging modalities for Alzheimer's disease diagnosis. Metab Brain Dis 2022; 37:2213-2243. [PMID: 35290546 DOI: 10.1007/s11011-022-00927-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/04/2022] [Indexed: 01/06/2023]
Abstract
Recent advances in retinal imaging pathophysiology have shown a new function for biomarkers in Alzheimer's disease diagnosis and prognosis. The significant improvements in Optical coherence tomography (OCT) retinal imaging have led to significant clinical translation, particularly in Alzheimer's disease detection. This systematic review will provide a comprehensive overview of retinal imaging in clinical applications, with a special focus on biomarker analysis for use in Alzheimer's disease detection. Articles on OCT retinal imaging in Alzheimer's disease diagnosis were identified in PubMed, Google Scholar, IEEE Xplore, and Research Gate databases until March 2021. Those studies using simultaneous retinal imaging acquisition were chosen, while those using sequential techniques were rejected. "Alzheimer's disease" and "Dementia" were searched alone and in combination with "OCT" and "retinal imaging". Approximately 1000 publications were searched, and after deleting duplicate articles, 145 relevant studies focused on the diagnosis of Alzheimer's disease utilizing retinal imaging were chosen for study. OCT has recently been demonstrated to be a valuable technique in clinical practice as according to this survey, 57% of the researchers employed optical coherence tomography, 19% used ocular fundus imaging, 13% used scanning laser ophthalmoscopy, and 11% have used multimodal imaging to diagnose Alzheimer disease. Retinal imaging has become an important diagnostic technique for Alzheimer's disease. Given the scarcity of available literature, it is clear that future prospective trials involving larger and more homogeneous groups are necessary, and the work can be expanded by evaluating its significance utilizing a machine-learning platform rather than simply using statistical methodologies.
Collapse
Affiliation(s)
- Richa Vij
- School of Computer Science & Engineering, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Sakshi Arora
- School of Computer Science & Engineering, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India.
| |
Collapse
|
41
|
Panda NR, Sahoo AK. A Detailed Systematic Review on Retinal Image Segmentation Methods. J Digit Imaging 2022; 35:1250-1270. [PMID: 35508746 PMCID: PMC9582172 DOI: 10.1007/s10278-022-00640-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/27/2022] Open
Abstract
The separation of blood vessels in the retina is a major aspect in detecting ailment and is carried out by segregating the retinal blood vessels from the fundus images. Moreover, it helps to provide earlier therapy for deadly diseases and prevent further impacts due to diabetes and hypertension. Many reviews already exist for this problem, but those reviews have presented the analysis of a single framework. Hence, this article on retinal segmentation review has revealed distinct methodologies with diverse frameworks that are utilized for blood vessel separation. The novelty of this review research lies in finding the best neural network model by comparing its efficiency. For that, machine learning (ML) and deep learning (DL) were compared and have been reported as the best model. Moreover, different datasets were used to segment the retinal blood vessels. The execution of each approach is compared based on the performance metrics such as sensitivity, specificity, and accuracy using publically accessible datasets like STARE, DRIVE, ROSE, REFUGE, and CHASE. This article discloses the implementation capacity of distinct techniques implemented for each segmentation method. Finally, the finest accuracy of 98% and sensitivity of 96% were achieved for the technique of Convolution Neural Network with Ranking Support Vector Machine (CNN-rSVM). Moreover, this technique has utilized public datasets to verify efficiency. Hence, the overall review of this article has revealed a method for earlier diagnosis of diseases to deliver earlier therapy.
Collapse
Affiliation(s)
- Nihar Ranjan Panda
- Department of Electronics and Communication Engineering, Silicon Institute of Technology, Bhubaneswar, Orissa, 751024, India.
| | - Ajit Kumar Sahoo
- Department of Electronics and Communication Engineering, National Institute of Technology, Rourkela, Odisha, 769008, India
| |
Collapse
|
42
|
Krueger LA, Morris AC. Eyes on CHARGE syndrome: Roles of CHD7 in ocular development. Front Cell Dev Biol 2022; 10:994412. [PMID: 36172288 PMCID: PMC9512043 DOI: 10.3389/fcell.2022.994412] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
The development of the vertebrate visual system involves complex morphogenetic interactions of cells derived from multiple embryonic lineages. Disruptions in this process are associated with structural birth defects such as microphthalmia, anophthalmia, and coloboma (collectively referred to as MAC), and inherited retinal degenerative diseases such as retinitis pigmentosa and allied dystrophies. MAC and retinal degeneration are also observed in systemic congenital malformation syndromes. One important example is CHARGE syndrome, a genetic disorder characterized by coloboma, heart defects, choanal atresia, growth retardation, genital abnormalities, and ear abnormalities. Mutations in the gene encoding Chromodomain helicase DNA binding protein 7 (CHD7) cause the majority of CHARGE syndrome cases. However, the pathogenetic mechanisms that connect loss of CHD7 to the ocular complications observed in CHARGE syndrome have not been identified. In this review, we provide a general overview of ocular development and congenital disorders affecting the eye. This is followed by a comprehensive description of CHARGE syndrome, including discussion of the spectrum of ocular defects that have been described in this disorder. In addition, we discuss the current knowledge of CHD7 function and focus on its contributions to the development of ocular structures. Finally, we discuss outstanding gaps in our knowledge of the role of CHD7 in eye formation, and propose avenues of investigation to further our understanding of how CHD7 activity regulates ocular and retinal development.
Collapse
Affiliation(s)
| | - Ann C. Morris
- Department of Biology, University of Kentucky, Lexington, KY, United States
| |
Collapse
|
43
|
Lapajne L, Rudzitis CN, Cullimore B, Ryskamp D, Lakk M, Redmon SN, Yarishkin O, Krizaj D. TRPV4: Cell type-specific activation, regulation and function in the vertebrate eye. CURRENT TOPICS IN MEMBRANES 2022; 89:189-219. [PMID: 36210149 PMCID: PMC9879314 DOI: 10.1016/bs.ctm.2022.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The architecture of the vertebrate eye is optimized for efficient delivery and transduction of photons and processing of signaling cascades downstream from phototransduction. The cornea, lens, retina, vasculature, ciliary body, ciliary muscle, iris and sclera have specialized functions in ocular protection, transparency, accommodation, fluid regulation, metabolism and inflammatory signaling, which are required to enable function of the retina-light sensitive tissue in the posterior eye that transmits visual signals to relay centers in the midbrain. This process can be profoundly impacted by non-visual stimuli such as mechanical (tension, compression, shear), thermal, nociceptive, immune and chemical stimuli, which target these eye regions to induce pain and precipitate vision loss in glaucoma, diabetic retinopathy, retinal dystrophies, retinal detachment, cataract, corneal dysfunction, ocular trauma and dry eye disease. TRPV4, a polymodal nonselective cation channel, integrate non-visual inputs with homeostatic and signaling functions of the eye. The TRPV4 gene is expressed in most if not all ocular tissues, which vary widely with respect to the mechanisms of TRPV4 channel activation, modulation, oligomerization, and participation in protein- and lipid interactions. Under- and overactivation of TRPV4 may affect intraocular pressure, maintenance of blood-retina barriers, lens accommodation, neuronal function and neuroinflammation. Because TRPV4 dysregulation precipitates many pathologies across the anterior and posterior eye, the channel could be targeted to mitigate vision loss.
Collapse
Affiliation(s)
- Luka Lapajne
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States; Department of Ophthalmology, University Medical Centre, University of Ljubljana, Ljubljana, Slovenia
| | - Christopher N Rudzitis
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Brenan Cullimore
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Daniel Ryskamp
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Monika Lakk
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Sarah N Redmon
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Oleg Yarishkin
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - David Krizaj
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States; Department of Neurobiology, University of Utah, Salt Lake City, UT, United States; Department of Bioengineering, University of Utah, Salt Lake City, UT, United States.
| |
Collapse
|
44
|
Vee S, Barclay G, Lents NH. The glow of the night: The tapetum lucidum as a co-adaptation for the inverted retina. Bioessays 2022; 44:e2200003. [PMID: 36028472 DOI: 10.1002/bies.202200003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 11/07/2022]
Abstract
The vertebrate retina is said to be inverted because the photoreceptors are oriented in the posterior direction and are thus unable to maximize photodetection under conditions of low illumination. The tapetum lucidum is a photoreflective structure located posterior to the photoreceptors in the eyes of some fish and terrestrial animals. The tapetum reflects light forward, giving incident photons a "second chance" to collide with a photoreceptor, substantially enhancing retinal photosensitivity in dim light. Across vertebrates (and arthropods), there are a wide variety of tapeta that vary in structure, chemical composition, and even tissue architecture, indicating repeated convergent evolution. To date, the tapetum has not been observed in any cephalopod, however, which also possess a camera-like eye, but with the retinal photoreceptors oriented in the anterior direction. We therefore hypothesize that the tapetum lucidum is a compensatory adaptation for the suboptimal design of the inverted retina of vertebrates.
Collapse
Affiliation(s)
- Samantha Vee
- Department of Ecology and Evolution, Stony Book University, The State University of New York, Stony Brook, New York, USA
| | - Gerald Barclay
- Department of Life Sciences, Highline College, Des Moines, Washington, USA
| | - Nathan H Lents
- Department of Sciences, John Jay College, The City University of New York, New York, New York, USA
| |
Collapse
|
45
|
Sakai K, Ikeuchi H, Fujiyabu C, Imamoto Y, Yamashita T. Convergent evolutionary counterion displacement of bilaterian opsins in ciliary cells. Cell Mol Life Sci 2022; 79:493. [PMID: 36001156 PMCID: PMC11071972 DOI: 10.1007/s00018-022-04525-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/26/2022]
Abstract
Opsins are universal photoreceptive proteins in animals. Vertebrate rhodopsin in ciliary photoreceptor cells photo-converts to a metastable active state to regulate cyclic nucleotide signaling. This active state cannot photo-convert back to the dark state, and thus vertebrate rhodopsin is categorized as a mono-stable opsin. By contrast, mollusk and arthropod rhodopsins in rhabdomeric photoreceptor cells photo-convert to a stable active state to stimulate IP3/calcium signaling. This active state can photo-convert back to the dark state, and thus these rhodopsins are categorized as bistable opsins. Moreover, the negatively charged counterion position crucial for the visible light sensitivity is different between vertebrate rhodopsin (Glu113) and mollusk and arthropod rhodopsins (Glu181). This can be explained by an evolutionary scenario where vertebrate rhodopsin newly acquired Glu113 as a counterion, which is thought to have led to higher signaling efficiency of vertebrate rhodopsin. However, the detailed evolutionary steps which led to the higher efficiency in vertebrate rhodopsin still remain unknown. Here, we analyzed the xenopsin group, which is phylogenetically distinct from vertebrate rhodopsin and functions in protostome ciliary cells. Xenopsins are blue-sensitive bistable opsins that regulate cAMP signaling. We found that a bistable xenopsin of Leptochiton asellus had Glu113 as a counterion but did not exhibit elevated signaling efficiency. Therefore, our results show that vertebrate rhodopsin and L. asellus xenopsin regulate cyclic nucleotide signaling in ciliary cells and displaced the counterion position from Glu181 to Glu113 via convergent evolution, whereas subsequently only vertebrate rhodopsin elevated its signaling efficiency by acquiring the mono-stable property.
Collapse
Affiliation(s)
- Kazumi Sakai
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Hiroki Ikeuchi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Chihiro Fujiyabu
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Yasushi Imamoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
| |
Collapse
|
46
|
Liu K, Wu P, Chen B, Cai Y, Yuan R, Zou J. Implicating Causal Brain Magnetic Resonance Imaging in Glaucoma Using Mendelian Randomization. Front Med (Lausanne) 2022; 9:956339. [PMID: 35847794 PMCID: PMC9283577 DOI: 10.3389/fmed.2022.956339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 12/31/2022] Open
Abstract
Background Glaucoma is hypothesized to originate in the brain but manifests as an eye disease as it possesses the common features of neurodegeneration diseases. But there is no evidence to demonstrate the primary brain changes in glaucoma patients. In the present study, we have used Mendelian randomization (MR) to understand the causal effect of brain alterations on glaucoma. Methods Our MR study was carried out using summary statistics from genome-wide associations for 110 diffusion tensor imaging (DTI) measurements of white matter (WM) tracts (17,706 individuals), 101 brain region-of-interest (ROI) volumes (19,629 individuals), and glaucoma (8,591 cases, 210,201 control subjects). The causal relationship was evaluated by multiplicative random effects inverse variance weighted (IVW) method and verified by two other MR methods, including MR Egger, weighted median, and extensive sensitivity analyses. Results Genetic liability to fornix fractional anisotropy (FX.FA) (OR = 0.71, 95%CI = 0.56–0.88, P = 2.44 × 10–3), and uncinate fasciculus UNC.FA (OR = 0.65, 95%CI = 0.48–0.88, P = 5.57 × 10–3) was associated with a low risk of glaucoma. Besides, the right ventral diencephalon (OR = 1.72, 95%CI = 1.17–2.52, P = 5.64 × 10–3) and brain stem (OR = 1.35, 95%CI = 1.08–1.69, P = 8.94 × 10–3) were associated with the increased risk of glaucoma. No heterogeneity and pleiotropy were detected. Conclusion Our study suggests that the fornix and uncinate fasciculus degenerations and injures of the right ventral diencephalon and brain stem potentially increase the occurrence of glaucoma and reveal the existence of the brain-eye axis.
Collapse
Affiliation(s)
- Kangcheng Liu
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Jiangxi Research Institute of Ophthalmology and Visual Science, Affiliated Eye Hospital of Nanchang University, Nanchang, China
| | - Pengfei Wu
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Bolin Chen
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yingjun Cai
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ruolan Yuan
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Zou
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Jing Zou,
| |
Collapse
|
47
|
Peña JS, Vazquez M. Harnessing the Neuroprotective Behaviors of Müller Glia for Retinal Repair. FRONT BIOSCI-LANDMRK 2022; 27:169. [PMID: 35748245 PMCID: PMC9639582 DOI: 10.31083/j.fbl2706169] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/18/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022]
Abstract
Progressive and irreversible vision loss in mature and aging adults creates a health and economic burden, worldwide. Despite the advancements of many contemporary therapies to restore vision, few approaches have considered the innate benefits of gliosis, the endogenous processes of retinal repair that precede vision loss. Retinal gliosis is fundamentally driven by Müller glia (MG) and is characterized by three primary cellular mechanisms: hypertrophy, proliferation, and migration. In early stages of gliosis, these processes have neuroprotective potential to halt the progression of disease and encourage synaptic activity among neurons. Later stages, however, can lead to glial scarring, which is a hallmark of disease progression and blindness. As a result, the neuroprotective abilities of MG have remained incompletely explored and poorly integrated into current treatment regimens. Bioengineering studies of the intrinsic behaviors of MG hold promise to exploit glial reparative ability, while repressing neuro-disruptive MG responses. In particular, recent in vitro systems have become primary models to analyze individual gliotic processes and provide a stepping stone for in vivo strategies. This review highlights recent studies of MG gliosis seeking to harness MG neuroprotective ability for regeneration using contemporary biotechnologies. We emphasize the importance of studying gliosis as a reparative mechanism, rather than disregarding it as an unfortunate clinical prognosis in diseased retina.
Collapse
Affiliation(s)
- Juan S. Peña
- Department of Biomedical Engineering, Rutgers, The State
University of New Jersey, Piscataway (08854), New Jersey, USA
| | - Maribel Vazquez
- Department of Biomedical Engineering, Rutgers, The State
University of New Jersey, Piscataway (08854), New Jersey, USA
| |
Collapse
|
48
|
Baden T, Nilsson DE. Is our retina really upside down? Curr Biol 2022; 32:R300-R303. [PMID: 35413251 DOI: 10.1016/j.cub.2022.02.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In the vertebrate eye, photoreceptors are covered beneath a thick sheet of neural retina and face away from the light. This seemingly awkward arrangement has led to the popular notion that our retinas are upside down, implying a deep design flaw. Baden and Nilsson argue that, from an evolutionary perspective, an inverted design actually offers many notable benefits that might have never been exploited if things had started off the other way round.
Collapse
Affiliation(s)
- Tom Baden
- School of Life Sciences, University of Sussex, Brighton, UK; Institute of Ophthalmic Research, University of Tübingen, Tübingen, Germany.
| | | |
Collapse
|
49
|
Fritzsch B, Martin PR. Vision and retina evolution: how to develop a retina. IBRO Neurosci Rep 2022; 12:240-248. [PMID: 35449767 PMCID: PMC9018162 DOI: 10.1016/j.ibneur.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/30/2022] [Indexed: 12/29/2022] Open
Abstract
Early in vertebrate evolution, a single homeobox (Hox) cluster in basal chordates was quadrupled to generate the Hox gene clusters present in extant vertebrates. Here we ask how this expanded gene pool may have influenced the evolution of the visual system. We suggest that a single neurosensory cell type split into ciliated sensory cells (photoreceptors, which transduce light) and retinal ganglion cells (RGC, which project to the brain). In vertebrates, development of photoreceptors is regulated by the basic helix-loop-helix (bHLH) transcription factor Neurod1 whereas RGC development depends on Atoh7 and related bHLH genes. Lancelet (a basal chordate) does not express Neurod or Atoh7 and possesses a few neurosensory cells with cilia that reach out of the opening of the neural tube. Sea-squirts (Ascidians) do not express Neurod and express a different bHLH gene, Atoh8, that is likely expressed in the anterior vesicle. Recent data indicate the neurosensory cells in lancelets may correspond to three distinct eye fields in ascidians, which in turn may be the basis of the vertebrate retina, pineal and parapineal. In this review we contrast the genetic control of visual structure development in these chordates with that of basal vertebrates such as lampreys and hagfish, and jawed vertebrates. We propose an evolutionary sequence linking whole-genome duplications, initially to a split between photoreceptor and projection neurons (RGC) and subsequently between pineal and lateral eye structures.
Collapse
|
50
|
Mylona I, Floros GD. Blue Light Blocking Treatment for the Treatment of Bipolar Disorder: Directions for Research and Practice. J Clin Med 2022; 11:jcm11051380. [PMID: 35268469 PMCID: PMC8911317 DOI: 10.3390/jcm11051380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
Recent results from a small number of clinical studies have resulted in the suggestion that the process of blocking the transmission of shorter-wavelength light (‘blue light’ with a wave length of 450 nm to 470 nm) may have a beneficial role in the treatment of bipolar disorder. This critical review will appraise the quality of evidence so far as to these claims, assess the neurobiology that could be implicated in the underlying processes while introducing a common set of research criteria for the field.
Collapse
Affiliation(s)
- Ioanna Mylona
- 2nd Department of Ophthalmology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | - Georgios D. Floros
- 2nd Department of Psychiatry, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
- Correspondence: ; Tel.: +30-69-4432-4565
| |
Collapse
|