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Zhang W, Zeng W, Feng J, Li P, Wang Y, Lu H. Identification and functional assays of single-nucleotide variants of opsins genes in melanocytic tumors. Pigment Cell Melanoma Res 2022; 35:436-449. [PMID: 35527357 DOI: 10.1111/pcmr.13043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/17/2022] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
Abstract
Epidermal melanocytes sense solar light via the opsin-coupled signaling pathway which is involved in a range of biological functions, including regulating pigmentation, proliferation, apoptosis, and tumorigenesis. However, it remains unclear whether there are genetic variants within these opsins that affect opsin protein structure and function, and further melanocyte biological behaviors. Here, we examined single-nucleotide variants (SNVs) of five opsin (RGR, OPN1SW, OPN2, OPN4, and OPN5) genes in MM (malignant melanoma; n = 76) and MN (melanocytic nevi; n = 157), using next-generation sequencing. The effects of these pathogenic single-nucleotide variants (SNVs) on opsin structure and function were further investigated using molecular dynamics (MD) simulations, dynamic cross-correlation (DCC), and site-directed mutagenesis. In total, 107 SNV variants were identified. Of these variants, 14 nonsynonymous SNVs (nsSNVs) of opsin genes were detected, including three mutations in the RGR gene, three mutations in the OPN1SW gene, two mutations in the OPN2 gene, and six mutations in the OPN4 gene. The effect of these missense mutations on opsin function was then assessed using eight prediction tools to estimate the potential impact of an amino acid substitution. The impact of each nsSNV was investigated using MD simulations and DCC analysis. Furthermore, we performed in vitro fluorescence calcium imaging to assess the functional properties of nsSNV proteins using a site-directed mutagenesis method. Taken together, these results revealed that p.A103V (RGR), p.T167I (RGR), p.G141S (OPN1SW), p.R144C (OPN1SW), and p.S231F (OPN4) had more deleterious effects on protein structure and function among the 14 nsSNVs. Opsin gene alterations showed the low frequency of missense mutations in melanocytic tumors, and although rare, some mutations in these opsin genes disrupt the canonical function of opsin. Our findings provide new insight into the role of opsin variants in the loss of function.
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Affiliation(s)
- Wei Zhang
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Wen Zeng
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Jianglong Feng
- Department of Pathology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Pinhao Li
- Department of Pathology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Yu Wang
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongguang Lu
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
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Abstract
In our tendency to discuss the objective properties of the external world, we may fail to notice that our subjective perceptions of those properties differ between individuals. Variability at all levels of the color vision system creates diversity in color perception, from discrimination to color matching, appearance, and subjective experience, such that each of us lives in a unique perceptual world. In this review, I discuss what is known about individual differences in color perception and its determinants, particularly considering genetically mediated variability in cone photopigments and the paradoxical effects of visual environments in both contributing to and counteracting individual differences. I make the case that, as well as being of interest in their own right and crucial for a complete account of color vision, individual differences can be used as a methodological tool in color science for the insights that they offer about the underlying mechanisms of perception. Expected final online publication date for the Annual Review of Vision Science, Volume 8 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jenny M Bosten
- School of Psychology, University of Sussex, Brighton, United Kingdom;
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Mazur-Michałek I, Ruciński M, Sowiński M, Pietras P, Leśniczak-Staszak M, Szaflarski W, Isalan M, Mielcarek M. Identification of the Transcriptional Biomarkers Panel Linked to Pathological Remodelling of the Eye Tissues in Various HD Mouse Models. Cells 2022; 11:1675. [PMID: 35626712 PMCID: PMC9139483 DOI: 10.3390/cells11101675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Ocular abnormalities are becoming associated with a spectrum of pathological events in various neurodegenerative diseases. Huntington's disease (HD) is just such an example of a fatal neurological disorder, where mutated genes (CAG trinucleotide expansions in the Huntingtin gene) have widespread expression, leading to the production of mutant Huntingtin (mHTT) protein. It is well known that mutant HTT protein is prone to form toxic aggregates, which are a typical pathological feature, along with global transcriptome alterations. In this study, we employed well-established quantitative methods such as Affymetrix arrays and quantitative PCR (qPCR) to identify a set of transcriptional biomarkers that will track HD progression in three well-established mouse models: R6/2, R6/1, and HdhQ150. Our array analysis revealed significantly deregulated networks that are related to visual processes and muscle contractions. Furthermore, our targeted quantitative analysis identified a panel of biomarkers with some being dysregulated even at the presymptomatic stage of the disease, e.g., Opn1mw, Opn1sw, and Pfkfb2. Some of the deregulated genes identified in this study have been linked to other genetic ocular disorders such as: GNAT2, a source of achromatopsia, and REEP6, linked to Retinitis pigmentosa. It may thus be a useful platform for preclinical evaluations of therapeutic interventions.
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Affiliation(s)
- Iwona Mazur-Michałek
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Marcin Ruciński
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Mateusz Sowiński
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Paulina Pietras
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Marta Leśniczak-Staszak
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Witold Szaflarski
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK;
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Michal Mielcarek
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK;
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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4
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Biswas P, Villanueva AL, Soto-Hermida A, Duncan JL, Matsui H, Borooah S, Kurmanov B, Richard G, Khan SY, Branham K, Huang B, Suk J, Bakall B, Goldberg JL, Gabriel L, Khan NW, Raghavendra PB, Zhou J, Devalaraja S, Huynh A, Alapati A, Zawaydeh Q, Weleber RG, Heckenlively JR, Hejtmancik JF, Riazuddin S, Sieving PA, Riazuddin SA, Frazer KA, Ayyagari R. Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis. PLoS Genet 2021; 17:e1009848. [PMID: 34662339 PMCID: PMC8589175 DOI: 10.1371/journal.pgen.1009848] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/12/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including targeted gene(s) or mutation(s) screening, linkage analysis and exome sequencing, the gene mutations responsible for IRD in these 108 pedigrees were not determined. WGS was performed on these pedigrees using Illumina X10 at a minimum of 30X depth. The sequence reads were mapped against hg19 followed by variant calling using GATK. The genome variants were annotated using SnpEff, PolyPhen2, and CADD score; the structural variants (SVs) were called using GenomeSTRiP and LUMPY. We identified potential causative sequence alterations in 61 pedigrees (57%), including 39 novel and 54 reported variants in IRD genes. For 57 of these pedigrees the observed genotype was consistent with the initial clinical diagnosis, the remaining 4 had the clinical diagnosis reclassified based on our findings. In seven pedigrees (12%) we observed atypical causal variants, i.e. unexpected genotype(s), including 4 pedigrees with causal variants in more than one IRD gene within all affected family members, one pedigree with intrafamilial genetic heterogeneity (different affected family members carrying causal variants in different IRD genes), one pedigree carrying a dominant causative variant present in pseudo-recessive form due to consanguinity and one pedigree with a de-novo variant in the affected family member. Combined atypical and large structural variants contributed to about 20% of cases. Among the novel mutations, 75% were detected in Mexican and 50% found in European American pedigrees and have not been reported in any other population while only 20% were detected in Pakistani pedigrees and were not previously reported. The remaining novel IRD causative variants were listed in gnomAD but were found to be very rare and population specific. Mutations in known IRD associated genes contributed to pathology in 63% Mexican, 60% Pakistani and 45% European American pedigrees analyzed. Overall, contribution of known IRD gene variants to disease pathology in these three populations was similar to that observed in other populations worldwide. This study revealed a spectrum of mutations contributing to IRD in three populations, identified a large proportion of novel potentially causative variants that are specific to the corresponding population or not reported in gnomAD and shed light on the genetic architecture of IRD in these diverse global populations. The study was performed to identify the underlying cause of inherited retinal degeneration (IRD) in 409 individuals from 108 families. Primarily, these families were recruited from three different geographic regions: Mexico, Pakistan and European Americans from the United States. Blood samples were collected from all individuals for genome analysis. This analysis detected causative variants in 61 out of the 108 pedigrees. A total of 93 gene variants were found in the 61 families. Among these, 54 were previously reported as causative variants and the remaining 39 have not been reported in IRD pedigrees. Interestingly, 54% of these novel variants were not listed in gnomAD. In addition to these findings, complex causative genotypes were observed in 20% of pedigrees. Overall, causative variants were detected in 63% Mexican, 60% Pakistani and 45% European American pedigrees. This study revealed the distribution of IRD causative variants in pedigrees with diverse ethnic and geographic backgrounds.
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Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Adda L. Villanueva
- Retina and Genomics Institute, Yucatán, México
- Laboratoire de Diagnostic Moleculaire, Hôpital Maisonneuve Rosemont, Montreal, Quebec, Canada
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Jacque L. Duncan
- Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Berzhan Kurmanov
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | | | - Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kari Branham
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Bonnie Huang
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - John Suk
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Benjamin Bakall
- Ophthalmology, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, United States of America
| | - Jeffrey L. Goldberg
- Byers Eye Institute, Stanford, Palo Alto, California, United States of America
| | - Luis Gabriel
- Genetics and Ophthalmology, Genelabor, Goiânia, Brazil
| | - Naheed W. Khan
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Pongali B. Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
- School of Regenerative Medicine, Manipal University, Bengaluru, Karnataka, India
| | - Jason Zhou
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Sindhu Devalaraja
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Andrew Huynh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Akhila Alapati
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Qais Zawaydeh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Richard G. Weleber
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - John R. Heckenlively
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - Paul A. Sieving
- National Eye Institute, Bethesda, Maryland, United States of America
- Ophthalmology & Vision Science, UC Davis Medical Center, California, United States of America
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (RA); (KAF); (SAR)
| | - Kelly A. Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, Rady Children’s Hospital, Division of Genome Information Sciences, San Diego, California, United States of America
- * E-mail: (RA); (KAF); (SAR)
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (RA); (KAF); (SAR)
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Neitz M, Krekling ED, Hagen LA, Pedersen HR, Rowlan J, Barborek R, Neitz J, Crain A, Baraas RC. Tritan color vision deficiency may be associated with an OPN1SW splicing defect and haploinsufficiency. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2020; 37:A26-A34. [PMID: 32400513 PMCID: PMC7254067 DOI: 10.1364/josaa.381919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/13/2020] [Indexed: 06/11/2023]
Abstract
Here we present evidence implicating disrupted RNA splicing as a potential cause of inherited tritan color vision. Initially we tested 51 subjects for color vision deficiencies. One made significant tritan errors; the others were classified as normal trichromats. The putative tritan subject was the only one of the 51 subjects found to be heterozygous for an OPN1SW gene mutation that disrupts RNA splicing in an in vitro assay. In order to gather further support for the role of the splicing mutation in tritan color vision, the putative tritan subject's mother and sister were examined. They also made tritan errors and had the same OPN1SW gene mutation.
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Affiliation(s)
- Maureen Neitz
- University of Washington, Department of Ophthalmology, 750 Republican Street, Seattle,WA, USA 98109
| | - Elise D. Krekling
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
| | - Lene A. Hagen
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
| | - Hilde R. Pedersen
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
| | - Jessica Rowlan
- University of Washington, Department of Ophthalmology, 750 Republican Street, Seattle,WA, USA 98109
| | - Rachel Barborek
- University of Washington, Department of Ophthalmology, 750 Republican Street, Seattle,WA, USA 98109
| | - Jay Neitz
- University of Washington, Department of Ophthalmology, 750 Republican Street, Seattle,WA, USA 98109
| | - Adam Crain
- University of Washington, Department of Ophthalmology, 750 Republican Street, Seattle,WA, USA 98109
| | - Rigmor C. Baraas
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
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6
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Baraas RC, Pedersen HR, Hagen LA. Single-cone imaging in inherited and acquired colour vision deficiencies. Curr Opin Behav Sci 2019. [DOI: 10.1016/j.cobeha.2019.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Mahernia S, Hassanzadeh M, Sarvari S, Amanlou M. Targeting the microRNA binding domain of argonaute 2: rational inhibitor design and study of mutation effects on protein-ligand interaction. J Biomol Struct Dyn 2019; 38:4710-4717. [PMID: 31684811 DOI: 10.1080/07391102.2019.1688688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Based on the accumulative evidences during recent decades, miRNAs have been found overexpressed in several human cancer types and also in Down syndrome patients, contributing to the neuropathology of Down syndrome. From this point of view, investigations on the structure and dynamic mechanisms related to the Argonaute 2 miRNAs binding in which silencing of the mRNA occurs, have inspired many clinical researchers to target this complex to inhibit the silencing process. In the current research, we have virtually screened the OTAVA_CNS_library to introduce new inhibitor compounds for the Ago2/miRNA complex. Ten hit compounds were obtained, with just one of them nominated as the best compound. Following the interaction analysis, by utilizing molecular dynamics (MD) simulations, effects of two mutations (Thr526 to isoleucine and Gln545 to alanine) on the dynamic properties of Ago2 in the complex with the best inhibitor compound were investigated. RMSD, RMSF and h-bond number beside other analyses, highlighted the importance of the Thr526 and Gln545 mutations for the stability and flexibility of the (Ago2)/ligand complex.[Formula: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shabnam Mahernia
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Malihe Hassanzadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Sarvari
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Massoud Amanlou
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.,Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran
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8
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Martínez-Archundia M, Hernández Mojica TG, Correa-Basurto J, Montaño S, Camacho-Molina A. Molecular dynamics simulations reveal structural differences among wild-type NPC1 protein and its mutant forms. J Biomol Struct Dyn 2019; 38:3527-3532. [DOI: 10.1080/07391102.2019.1664324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- M. Martínez-Archundia
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - T. G. Hernández Mojica
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Secretaría de Salud, Mexico City, México, Facultad de Ciencias Químico Biológicas
| | - J. Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - S. Montaño
- Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - A. Camacho-Molina
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Secretaría de Salud, Mexico City, México, Facultad de Ciencias Químico Biológicas
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Hagen LA, Arnegard S, Kuchenbecker JA, Gilson SJ, Neitz M, Neitz J, Baraas RC. The association between L:M cone ratio, cone opsin genes and myopia susceptibility. Vision Res 2019; 162:20-28. [PMID: 31254532 PMCID: PMC7122956 DOI: 10.1016/j.visres.2019.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/16/2022]
Abstract
In syndromic forms of myopia caused by long (L) to middle (M) wavelength (L/M) interchange mutations, erroneous contrast signals from ON-bipolar cells activated by cones with different levels of opsin expression are suggested to make the eye susceptible to increased growth. This susceptibility is modulated by the L:M cone ratio. Here, we examined L and M opsin genes, L:M cone ratios and their association with common refractive errors in a population with low myopia prevalence. Cycloplegic autorefraction and ocular biometry were obtained for Norwegian genetically-confirmed normal trichromats. L:M cone ratios were estimated from spectral sensitivity functions measured with full-field ERG, after adjusting for individual differences in the wavelength of peak absorption deduced from cone opsin genetics. Mean L:M cone ratios and the frequency of alanine at L opsin position 180 were higher in males than what has been reported in males in populations with high myopia prevalence. High L:M cone ratios in females were associated with lower degree of myopia, and myopia was more frequent in females who were heterozygous for L opsin exon 3 haplotypes than in those who were homozygous. The results suggest that the L:M cone ratio, combined with milder versions of L opsin gene polymorphisms, may play a role in common myopia. This may in part explain the low myopia prevalence in Norwegian adolescents and why myopia prevalence was higher in females who were heterozygous for the L opsin exon 3 haplotype, since females are twice as likely to have genetic polymorphisms carried on the X-chromosome.
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Affiliation(s)
- Lene A Hagen
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Hasbergs vei 36, 3616 Kongsberg, Norway.
| | - Solveig Arnegard
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Hasbergs vei 36, 3616 Kongsberg, Norway.
| | - James A Kuchenbecker
- Department of Ophthalmology, University of Washington Medical School, Box 358058, 750 Republican Street, Building E Room, Seattle, WA 98109, United States
| | - Stuart J Gilson
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Hasbergs vei 36, 3616 Kongsberg, Norway.
| | - Maureen Neitz
- Department of Ophthalmology, University of Washington Medical School, Box 358058, 750 Republican Street, Building E Room, Seattle, WA 98109, United States.
| | - Jay Neitz
- Department of Ophthalmology, University of Washington Medical School, Box 358058, 750 Republican Street, Building E Room, Seattle, WA 98109, United States.
| | - Rigmor C Baraas
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Hasbergs vei 36, 3616 Kongsberg, Norway.
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10
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Pedersen HR, Hagen LA, Landsend ECS, Gilson SJ, Utheim ØA, Utheim TP, Neitz M, Baraas RC. Color Vision in Aniridia. Invest Ophthalmol Vis Sci 2019; 59:2142-2152. [PMID: 29801149 PMCID: PMC6110168 DOI: 10.1167/iovs.17-23047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Purpose To assess color vision and its association with retinal structure in persons with congenital aniridia. Methods We included 36 persons with congenital aniridia (10–66 years), and 52 healthy, normal trichromatic controls (10–74 years) in the study. Color vision was assessed with Hardy-Rand-Rittler (HRR) pseudo-isochromatic plates (4th ed., 2002); Cambridge Color Test and a low-vision version of the Color Assessment and Diagnosis test (CAD-LV). Cone-opsin genes were analyzed to confirm normal versus congenital color vision deficiencies. Visual acuity and ocular media opacities were assessed. The central 30° of both eyes were imaged with the Heidelberg Spectralis OCT2 to grade the severity of foveal hypoplasia (FH, normal to complete: 0–4). Results Five participants with aniridia had cone opsin genes conferring deutan color vision deficiency and were excluded from further analysis. Of the 31 with aniridia and normal opsin genes, 11 made two or more red-green (RG) errors on HRR, four of whom also made yellow-blue (YB) errors; one made YB errors only. A total of 19 participants had higher CAD-LV RG thresholds, of which eight also had higher CAD-LV YB thresholds, than normal controls. In aniridia, the thresholds were higher along the RG than the YB axis, and those with a complete FH had significantly higher RG thresholds than those with mild FH (P = 0.038). Additional increase in YB threshold was associated with secondary ocular pathology. Conclusions Arrested foveal formation and associated alterations in retinal processing are likely to be the primary reason for impaired red-green color vision in aniridia.
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Affiliation(s)
- Hilde R Pedersen
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University College of Southeast Norway, Kongsberg, Norway
| | - Lene A Hagen
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University College of Southeast Norway, Kongsberg, Norway
| | | | - Stuart J Gilson
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University College of Southeast Norway, Kongsberg, Norway
| | - Øygunn A Utheim
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway.,Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Tor P Utheim
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University College of Southeast Norway, Kongsberg, Norway.,Department of Ophthalmology, Oslo University Hospital, Oslo, Norway.,Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Ophthalmology, Drammen Hospital, Drammen, Norway
| | - Maureen Neitz
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
| | - Rigmor C Baraas
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University College of Southeast Norway, Kongsberg, Norway
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11
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Ooe E, Kuse Y, Yako T, Sogon T, Nakamura S, Hara H, Shimazawa M. Bilberry extract and anthocyanins suppress unfolded protein response induced by exposure to blue LED light of cells in photoreceptor cell line. Mol Vis 2018; 24:621-632. [PMID: 30294201 PMCID: PMC6161804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 09/21/2018] [Indexed: 11/16/2022] Open
Abstract
Purpose The purpose of this study was to investigate the effects of bilberry extract with its anthocyanins on retinal photoreceptor cell damage and on the endoplasmic reticulum (ER) stress induced by exposure to blue light-emitting diode (LED) light. Methods Cultured murine photoreceptor cells (661W) were exposed to blue LED light with or without bilberry extract or its anthocyanins in the culture media. Aggregated short-wavelength opsin (S-opsin) in murine photoreceptor cells was observed with immunostaining. The expression of factors involved in the unfolded protein response was examined with immunoblot analysis and quantitative real-time reverse transcription (RT)-PCR. Furthermore, cell death was observed with double staining with Hoechst 33342 and propidium iodide after dithiothreitol (DTT) treatment. Results Bilberry extract and anthocyanins suppressed the aggregation of S-opsin, activation of ATF4, and expression of the mRNA of the factors associated with the unfolded protein response (UPR). In addition, bilberry extract and the anthocyanins inhibited the death of photoreceptor cells induced by DTT, an ER stress inducer. Conclusions These findings suggest that bilberry extract containing anthocyanins can alter the effects of blue LED light and DTT-induced retinal photoreceptor cell damage. These effects were achieved by modulating the activation of ATF4 and through the suppression of the abnormal aggregation of S-opsin.
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Affiliation(s)
- Emi Ooe
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Yoshiki Kuse
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Tomohiro Yako
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Tetsuya Sogon
- Wakasa Seikatsu Co. Ltd, 22 Naginataboko-cho, Shijo-Karasuma, Shimogyo-ku, Kyoto, Japan
| | - Shinsuke Nakamura
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Hideaki Hara
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Masamitsu Shimazawa
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
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Greenwald SH, Kuchenbecker JA, Rowlan JS, Neitz J, Neitz M. Role of a Dual Splicing and Amino Acid Code in Myopia, Cone Dysfunction and Cone Dystrophy Associated with L/ M Opsin Interchange Mutations. Transl Vis Sci Technol 2017; 6:2. [PMID: 28516000 PMCID: PMC5433808 DOI: 10.1167/tvst.6.3.2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/02/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Human long (L) and middle (M) wavelength cone opsin genes are highly variable due to intermixing. Two L/M cone opsin interchange mutants, designated LIAVA and LVAVA, are associated with clinical diagnoses, including red-green color vision deficiency, blue cone monochromacy, cone degeneration, myopia, and Bornholm Eye Disease. Because the protein and splicing codes are carried by the same nucleotides, intermixing L and M genes can cause disease by affecting protein structure and splicing. METHODS Genetically engineered mice were created to allow investigation of the consequences of altered protein structure alone, and the effects on cone morphology were examined using immunohistochemistry. In humans and mice, cone function was evaluated using the electroretinogram (ERG) under L/M- or short (S) wavelength cone isolating conditions. Effects of LIAVA and LVAVA genes on splicing were evaluated using a minigene assay. RESULTS ERGs and histology in mice revealed protein toxicity for the LVAVA but not for the LIAVA opsin. Minigene assays showed that the dominant messenger RNA (mRNA) was aberrantly spliced for both variants; however, the LVAVA gene produced a small but significant amount of full-length mRNA and LVAVA subjects had correspondingly reduced ERG amplitudes. In contrast, the LIAVA subject had no L/M cone ERG. CONCLUSIONS Dramatic differences in phenotype can result from seemingly minor differences in genotype through divergent effects on the dual amino acid and splicing codes. TRANSLATIONAL RELEVANCE The mechanism by which individual mutations contribute to clinical phenotypes provides valuable information for diagnosis and prognosis of vision disorders associated with L/M interchange mutations, and it informs strategies for developing therapies.
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Affiliation(s)
| | | | - Jessica S. Rowlan
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Jay Neitz
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Maureen Neitz
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
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13
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Samanfar B, Molnar SJ, Charette M, Schoenrock A, Dehne F, Golshani A, Belzile F, Cober ER. Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:377-390. [PMID: 27832313 DOI: 10.1007/s00122-016-2819-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/27/2016] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE E10 is a new maturity locus in soybean and FT4 is the predicted/potential functional gene underlying the locus. Flowering and maturity time traits play crucial roles in economic soybean production. Early maturity is critical for north and west expansion of soybean in Canada. To date, 11 genes/loci have been identified which control time to flowering and maturity; however, the molecular bases of almost half of them are not yet clear. We have identified a new maturity locus called "E10" located at the end of chromosome Gm08. The gene symbol E10e10 has been approved by the Soybean Genetics Committee. The e10e10 genotype results in 5-10 days earlier maturity than E10E10. A set of presumed E10E10 and e10e10 genotypes was used to identify contrasting SSR and SNP haplotypes. These haplotypes, and their association with maturity, were maintained through five backcross generations. A functional genomics approach using a predicted protein-protein interaction (PPI) approach (Protein-protein Interaction Prediction Engine, PIPE) was used to investigate approximately 75 genes located in the genomic region that SSR and SNP analyses identified as the location of the E10 locus. The PPI analysis identified FT4 as the most likely candidate gene underlying the E10 locus. Sequence analysis of the two FT4 alleles identified three SNPs, in the 5'UTR, 3'UTR and fourth exon in the coding region, which result in differential mRNA structures. Allele-specific markers were developed for this locus and are available for soybean breeders to efficiently develop earlier maturing cultivars using molecular marker assisted breeding.
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Affiliation(s)
- Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Stephen J Molnar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Martin Charette
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Andrew Schoenrock
- School of Computer Science, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - François Belzile
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Elroy R Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada.
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14
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Davidoff C, Neitz M, Neitz J. Genetic Testing as a New Standard for Clinical Diagnosis of Color Vision Deficiencies. Transl Vis Sci Technol 2016; 5:2. [PMID: 27622081 PMCID: PMC5017313 DOI: 10.1167/tvst.5.5.2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 06/20/2016] [Indexed: 11/24/2022] Open
Abstract
Purpose The genetics underlying inherited color vision deficiencies is well understood: causative mutations change the copy number or sequence of the long (L), middle (M), or short (S) wavelength sensitive cone opsin genes. This study evaluated the potential of opsin gene analyses for use in clinical diagnosis of color vision defects. Methods We tested 1872 human subjects using direct sequencing of opsin genes and a novel genetic assay that characterizes single nucleotide polymorphisms (SNPs) using the MassArray system. Of the subjects, 1074 also were given standard psychophysical color vision tests for a direct comparison with current clinical methods. Results Protan and deutan deficiencies were classified correctly in all subjects identified by MassArray as having red–green defects. Estimates of defect severity based on SNPs that control photopigment spectral tuning correlated with estimates derived from Nagel anomaloscopy. Conclusions The MassArray assay provides genetic information that can be useful in the diagnosis of inherited color vision deficiency including presence versus absence, type, and severity, and it provides information to patients about the underlying pathobiology of their disease. Translational Relevance The MassArray assay provides a method that directly analyzes the molecular substrates of color vision that could be used in combination with, or as an alternative to current clinical diagnosis of color defects.
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Affiliation(s)
- Candice Davidoff
- Department of Ophthalmology University of Washington Seattle, WA, USA
| | - Maureen Neitz
- Department of Ophthalmology University of Washington Seattle, WA, USA
| | - Jay Neitz
- Department of Ophthalmology University of Washington Seattle, WA, USA
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Shinomori K, Panorgias A, Werner JS. Discrimination thresholds of normal and anomalous trichromats: Model of senescent changes in ocular media density on the Cambridge Colour Test. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2016; 33:A65-76. [PMID: 26974943 PMCID: PMC5316232 DOI: 10.1364/josaa.33.000a65] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Age-related changes in chromatic discrimination along dichromatic confusion lines were measured with the Cambridge Colour Test (CCT). One hundred and sixty-two individuals (16 to 88 years old) with normal Rayleigh matches were the major focus of this paper. An additional 32 anomalous trichromats classified by their Rayleigh matches were also tested. All subjects were screened to rule out abnormalities of the anterior and posterior segments. Thresholds on all three chromatic vectors measured with the CCT showed age-related increases. Protan and deutan vector thresholds increased linearly with age while the tritan vector threshold was described with a bilinear model. Analysis and modeling demonstrated that the nominal vectors of the CCT are shifted by senescent changes in ocular media density, and a method for correcting the CCT vectors is demonstrated. A correction for these shifts indicates that classification among individuals of different ages is unaffected. New vector thresholds for elderly observers and for all age groups are suggested based on calculated tolerance limits.
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Affiliation(s)
- Keizo Shinomori
- School of Information, Kochi University of Technology, Tosayamada-Miyanokuchi, Kami, Kochi 782-8502, Japan
- Vision and Affective Science Integrated Research Laboratory, Research Institute, Kochi University of Technology, Kochi, Japan
- Corresponding author:
| | - Athanasios Panorgias
- Department of Ophthalmology & Vision Science, University of California Davis, Sacramento, California 95813, USA
- Department of Vision Science, New England College of Optometry, Boston, Massachusetts 02115, USA
| | - John S. Werner
- Department of Ophthalmology & Vision Science, University of California Davis, Sacramento, California 95813, USA
- Department of Experimental Psychology, University of Cambridge, Cambridge, UK
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Hofmann L, Palczewski K. Advances in understanding the molecular basis of the first steps in color vision. Prog Retin Eye Res 2015; 49:46-66. [PMID: 26187035 DOI: 10.1016/j.preteyeres.2015.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/05/2023]
Abstract
Serving as one of our primary environmental inputs, vision is the most sophisticated sensory system in humans. Here, we present recent findings derived from energetics, genetics and physiology that provide a more advanced understanding of color perception in mammals. Energetics of cis-trans isomerization of 11-cis-retinal accounts for color perception in the narrow region of the electromagnetic spectrum and how human eyes can absorb light in the near infrared (IR) range. Structural homology models of visual pigments reveal complex interactions of the protein moieties with the light sensitive chromophore 11-cis-retinal and that certain color blinding mutations impair secondary structural elements of these G protein-coupled receptors (GPCRs). Finally, we identify unsolved critical aspects of color tuning that require future investigation.
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Affiliation(s)
- Lukas Hofmann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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Abstract
AbstractS cones expressing the short wavelength-sensitive type 1 (SWS1) class of visual pigment generally form only a minority type of cone photoreceptor within the vertebrate duplex retina. Hence, their primary role is in color vision, not in high acuity vision. In mammals, S cones may be present as a constant fraction of the cones across the retina, may be restricted to certain regions of the retina or may form a gradient across the retina, and in some species, there is coexpression of SWS1 and the long wavelength-sensitive (LWS) class of pigment in many cones. During retinal development, SWS1 opsin expression generally precedes that of LWS opsin, and evidence from genetic studies indicates that the S cone pathway may be the default pathway for cone development. With the notable exception of the cartilaginous fishes, where S cones appear to be absent, they are present in representative species from all other vertebrate classes. S cone loss is not, however, uncommon; they are absent from most aquatic mammals and from some but not all nocturnal terrestrial species. The peak spectral sensitivity of S cones depends on the spectral characteristics of the pigment present. Evidence from the study of agnathans and teleost fishes indicates that the ancestral vertebrate SWS1 pigment was ultraviolet (UV) sensitive with a peak around 360 nm, but this has shifted into the violet region of the spectrum (>380 nm) on many separate occasions during vertebrate evolution. In all cases, the shift was generated by just one or a few replacements in tuning-relevant residues. Only in the avian lineage has tuning moved in the opposite direction, with the reinvention of UV-sensitive pigments.
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Losses of functional opsin genes, short-wavelength cone photopigments, and color vision--a significant trend in the evolution of mammalian vision. Vis Neurosci 2013; 30:39-53. [PMID: 23286388 DOI: 10.1017/s0952523812000429] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
All mammalian cone photopigments are derived from the operation of representatives from two opsin gene families (SWS1 and LWS in marsupial and eutherian mammals; SWS2 and LWS in monotremes), a process that produces cone pigments with respective peak sensitivities in the short and middle-to-long wavelengths. With the exception of a number of primate taxa, the modal pattern for mammals is to have two types of cone photopigment, one drawn from each of the gene families. In recent years, it has been discovered that the SWS1 opsin genes of a widely divergent collection of eutherian mammals have accumulated mutational changes that render them nonfunctional. This alteration reduces the retinal complements of these species to a single cone type, thus rendering ordinary color vision impossible. At present, several dozen species from five mammalian orders have been identified as falling into this category, but the total number of mammalian species that have lost short-wavelength cones in this way is certain to be much larger, perhaps reaching as high as 10% of all species. A number of circumstances that might be used to explain this widespread cone loss can be identified. Among these, the single consistent fact is that the species so affected are nocturnal or, if they are not technically nocturnal, they at least feature retinal organizations that are typically associated with that lifestyle. At the same time, however, there are many nocturnal mammals that retain functional short-wavelength cones. Nocturnality thus appears to set the stage for loss of functional SWS1 opsin genes in mammals, but it cannot be the sole circumstance.
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