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Chen A, Wang Q, Zhao X, Wang G, Zhang X, Ren X, Zhang Y, Cheng X, Yu X, Mei X, Wang H, Guo M, Jiang X, Wei G, Wang X, Jiang R, Guo X, Ning Z, Qu L. Molecular genetic foundation of a sex-linked tailless trait in Hongshan chicken by whole genome data analysis. Poult Sci 2024; 103:103685. [PMID: 38603937 PMCID: PMC11017342 DOI: 10.1016/j.psj.2024.103685] [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: 01/18/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
As a Chinese local chicken breed, Hongshan chickens have 2 kinds of tail feather phenotypes, normal and taillessness. Our previous studies showed that taillessness was a sex-linked dominant trait. Abnormal development of the tail vertebrae could be explained this phenomenon in some chicken breeds. However, the number of caudal vertebrae in rumpless Hongshan chickens was normal, so rumplessness in Hongshan chicken was not related to the development of the caudal vertebrae. Afterwards, we found that rumplessness in Hongshan was due to abnormal development of tail feather rather than abnormal development of caudal vertebrae. In order to understand the genetic foundation of the rumplessness of Hongshan chickens, we compared and reanalyzed 2 sets of data in normal and rumpless Hongshan chickens from our previous studies. By joint analysis of genome-wide selection signature analysis and genome-wide association approach, we found that 1 overlapping gene (EDIL3) and 16 peak genes (ENSGALG00000051843, ENSGALG00000053498, ENSGALG00000054800, KIF27, PTPRD, ENSGALG00000047579, ENSGALG00000041052, ARHGEF28, CAMK4, SERINC5, ENSGALG00000050776, ERCC8, MCC, ADAMTS19, ENSGALG00000053322, CHRNA8) located on the Z chromosome was associated with the rumpless trait. The results of this study furtherly revealed the molecular mechanism of the rumpless trait in Hongshan chickens, and identified the candidate genes associated with this trait. Our results will help to improve the shape of chicken tail feathers and to rise individual economic value in some specific market in China.
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Affiliation(s)
- Anqi Chen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qiong Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiurong Zhao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Wang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xinye Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xufang Ren
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yalan Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xue Cheng
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaofan Yu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaohan Mei
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huie Wang
- Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China
| | - Menghan Guo
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaoyu Jiang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Guozhen Wei
- Qingliu Animal Husbandry, Veterinary and Aquatic Products Center, Sanming, China
| | - Xue Wang
- VVBK Animal Medical Diagnostic Technology (Beijing) Co., Ltd, Beijing, China
| | - Runshen Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xing Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China.
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Carlson ML, Stoddard MC. Evolution of Plumage Patterns in a Pattern Morphospace: A Phylogenetic Analysis of Melanerpine Woodpeckers. Am Nat 2024; 203:55-72. [PMID: 38207134 DOI: 10.1086/727508] [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] [Indexed: 01/13/2024]
Abstract
AbstractPlumage patterns of melanerpine (Melanerpes-Sphyrapicus) woodpeckers are strikingly diverse. Understanding the evolution and function of this diversity is challenging because of the difficulty of quantifying plumage patterns. We use a three-dimensional space to characterize the evolution of melanerpine achromatic plumage patterns. The axes of the space are three pattern features (spatial frequency, orientation, and contrast) quantified using two-dimensional fast Fourier transformation of museum specimen images. Mapping plumage in pattern space reveals differences in how species and subclades occupy the space. To quantify these differences, we derive two new measures of pattern: pattern diversity (diversity across plumage patches within a species) and pattern uniqueness (divergence of patterns from those of other species). We estimate that the melanerpine ancestor had mottled plumage and find that pattern traits across patches and subclades evolve at different rates. We also find that smaller species are more likely to display horizontal face patterning. We promote pattern spaces as powerful tools for investigating animal pattern evolution.
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Liu D, Tong Y, Dong R, Ye X, Yu X. A Breeding Plumage in the Making: The Unique Process of Plumage Coloration in the Crested Ibis in Terms of Chemical Composition and Sex Hormones. Animals (Basel) 2023; 13:3820. [PMID: 38136856 PMCID: PMC10740519 DOI: 10.3390/ani13243820] [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: 10/31/2023] [Revised: 12/03/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
The Crested Ibis (Nipponia nippon) has long fascinated ornithologists with its enigmatic plumage color change. After more than a century of curiosity, the mystery was finally unraveled in the 1970s, unveiling the mechanism behind this remarkable transformation. Unlike other bird species, the Crested Ibis achieves its nuptial plumage coloration through a unique daubing behavior. After a water-bathing, it applies a sticky black substance secreted by a patch of skin in the neck and throat region. However, the chemical components of this black substance have not been studied in detail until now. To address this issue, we conducted a study to detect the components of the black substance and explore the relationship between sex hormone levels and the secretion of the black substance. We used enzyme-linked immunosorbent assay (ELISA) to measure the monthly changes in steroid hormone levels (estradiol E2, testosterone T, and progesterone PROG) levels in feces. We also analyzed the correlation between sex hormone levels and daubing behavior. The results showed that the sex hormone levels are closely related to the secretion and application of the black substance. In addition, we qualitatively analyzed the chemical components of the black substance using gas chromatography-mass spectrometry (GC-MS), uncovering the presence of 117 distinct chemical components. We assume that the black coloration results from the polymerization of selected chemical constituents among these components. These findings provide a groundwork for further exploration into the biological significance of the black substance. Overall, our study detected components in the black substance and studied how sex hormone levels relate to its secretion. Understanding the hormone effects on coloration helps in precise habitat management, like wetland preservation, crucial for Crested Ibis survival. Implementing hormone-boosting measures during breeding seasons enhances reproduction and health, vital for their conservation.
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Affiliation(s)
- Danni Liu
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China; (D.L.); (Y.T.); (X.Y.)
| | - Yiwei Tong
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China; (D.L.); (Y.T.); (X.Y.)
| | - Rong Dong
- Research Center for Qinling Giant Panda, Shaanxi Academy of Foresty, Xi’an 710082, China;
| | - Xinping Ye
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China; (D.L.); (Y.T.); (X.Y.)
- Research Center for UAV Remote Sensing, Shaanxi Normal University, Xi’an 710119, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China; (D.L.); (Y.T.); (X.Y.)
- Shaanxi Provincial Field Observation and Research Station for Golden Monkey, Giant Panda and Biodiversity, Xi’an 723400, China
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Kratochwil CF, Mallarino R. Mechanisms Underlying the Formation and Evolution of Vertebrate Color Patterns. Annu Rev Genet 2023; 57:135-156. [PMID: 37487589 PMCID: PMC10805968 DOI: 10.1146/annurev-genet-031423-120918] [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: 07/26/2023]
Abstract
Vertebrates exhibit a wide range of color patterns, which play critical roles in mediating intra- and interspecific communication. Because of their diversity and visual accessibility, color patterns offer a unique and fascinating window into the processes underlying biological organization. In this review, we focus on describing many of the general principles governing the formation and evolution of color patterns in different vertebrate groups. We characterize the types of patterns, review the molecular and developmental mechanisms by which they originate, and discuss their role in constraining or facilitating evolutionary change. Lastly, we outline outstanding questions in the field and discuss different approaches that can be used to address them. Overall, we provide a unifying conceptual framework among vertebrate systems that may guide research into naturally evolved mechanisms underlying color pattern formation and evolution.
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Affiliation(s)
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA;
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5
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Terrill RS, Shultz AJ. Feather function and the evolution of birds. Biol Rev Camb Philos Soc 2023; 98:540-566. [PMID: 36424880 DOI: 10.1111/brv.12918] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/26/2022]
Abstract
The ability of feathers to perform many functions either simultaneously or at different times throughout the year or life of a bird is integral to the evolutionary history of birds. Many studies focus on single functions of feathers, but any given feather performs many functions over its lifetime. These functions necessarily interact with each other throughout the evolution and development of birds, so our knowledge of avian evolution is incomplete without understanding the multifunctionality of feathers, and how different functions may act synergistically or antagonistically during natural selection. Here, we review how feather functions interact with avian evolution, with a focus on recent technological and discovery-based advances. By synthesising research into feather functions over hierarchical scales (pattern, arrangement, macrostructure, microstructure, nanostructure, molecules), we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into an astounding array of environments and life-history strategies. We suggest that future research into avian evolution involving feather function should consider multiple aspects of a feather, including multiple functions, seasonal wear and renewal, and ecological or mechanical interactions. With this more holistic view, processes such as the evolution of avian coloration and flight can be understood in a broader and more nuanced context.
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Affiliation(s)
- Ryan S Terrill
- Moore Laboratory of Zoology, Occidental College, 1600 Campus rd., Los Angeles, CA, 90042, USA
- Department of Biological Sciences, California State University, Stanislaus, Turlock, CA, 95382, USA
| | - Allison J Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA, 90007, USA
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Heo S, Cho S, Dinh PTN, Park J, Jin DH, Cha J, Kim YK, Koh YJ, Lee SH, Lee JH. A genome-wide association study for eumelanin pigmentation in chicken plumage using a computer vision approach. Anim Genet 2023; 54:355-362. [PMID: 36855963 DOI: 10.1111/age.13303] [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: 07/25/2022] [Revised: 11/28/2022] [Accepted: 01/26/2023] [Indexed: 03/02/2023]
Abstract
Chicken plumage colouration is an important trait related to productivity in poultry industry. Therefore, the genetic basis for pigmentation in chicken plumage is an area of great interest. However, the colour trait is generally regarded as a qualitative trait and representing colour variations is difficult. In this study, we developed a method to quantify and classify colour using an F2 population crossed from two pure lines: White Leghorn and the Korean indigenous breed Yeonsan Ogye. Using red, green, and blue values in the cropped body region, we identified significant genomic regions on chromosomes 33:3 160 480-7 447 197 and Z:78 748 287-79 173 793. Furthermore, we identified two potential candidate genes (PMEL and MTAP) that might have significant effects on melanin-based plumage pigmentation. Our study presents a new phenotyping method using a computer vision approach and provides new insights into the genetic basis of melanin-based feather colouration in chickens.
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Affiliation(s)
- Seonyeong Heo
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea
| | - Sunghyun Cho
- Research and Development Center, Insilicogen Inc., Yongin, South Korea
| | | | - Jongho Park
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea
| | - Dae-Hyeok Jin
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang, South Korea
| | - Jihye Cha
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju, South Korea
| | - Young-Kuk Kim
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea.,Department of Computer Science & Engineering, Chungnam National University, Daejeon, South Korea
| | - Yeong Jun Koh
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea.,Department of Computer Science & Engineering, Chungnam National University, Daejeon, South Korea
| | - Seung Hwan Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea.,Division of Animal and Dairy Science, Chungnam National University, Daejeon, South Korea
| | - Jun Heon Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea.,Division of Animal and Dairy Science, Chungnam National University, Daejeon, South Korea
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7
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Shen Q, Zhou J, Li J, Zhao X, Zheng L, Bao H, Wu C. Genome-Wide Association Study Identifies Candidate Genes for Stripe Pattern Feather Color of Rhode Island Red Chicks. Genes (Basel) 2022; 13:genes13091511. [PMID: 36140679 PMCID: PMC9498448 DOI: 10.3390/genes13091511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022] Open
Abstract
Feather colors of chickens are not only characteristics of breeds but also as phenotypic markers in chicken breeding. Pure-bred Rhode Island Red (RIR) chicks have a stripe pattern and a non-stripe pattern on the back. The stripe pattern of RIR is generally shown as four longitudinal black stripes on the back and is more likely to appear in females. In this study, we performed a genome-wide association study (GWAS) to identify candidate genes controlling the stripe pattern of RIR chicks, and then, based on physical location and biological functions, quantitative RT-PCR analysis was used to validate the differential expression of candidate genes between stripe pattern and non-stripe pattern back skin tissue. The GWAS showed that a major signal contains 768 significant single nucleotide polymorphisms (SNPs) and 87 significant small insertions-deletions (INDELs) spanning 41.78 to 43.05 Mb (~1.27 Mb) on GGA1, corresponding to 16 genes associated with stripe pattern phenotype. Among these 16 genes, KITLG and TMTC3 could be considered candidate genes as they showed different expressions between back skin tissues of stripe pattern and non-stripe pattern chicks in value (p = 0.062) and the significant level (p < 0.05), respectively. This study provided novel insight into the mechanisms underlying feather pigmentation and stripe formation in RIR chicks.
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Affiliation(s)
- Qingmiao Shen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jieke Zhou
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaoyu Zhao
- Dawu Breeding Company, Baoding 072550, China
| | - Lijie Zheng
- Dawu Breeding Company, Baoding 072550, China
| | - Haigang Bao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Correspondence:
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Salgado Pardo JI, Navas González FJ, González Ariza A, Arando Arbulu A, León Jurado JM, Delgado Bermejo JV, Camacho Vallejo ME. Traditional sexing methods and external egg characteristics combination allow highly accurate early sex determination in an endangered native turkey breed. Front Vet Sci 2022; 9:948502. [PMID: 36046507 PMCID: PMC9420986 DOI: 10.3389/fvets.2022.948502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Early sex determination methods are not only crucial in the worldwide massive poultry industry, but also for small-holder producers. The profitability of sexing techniques must be accounted for when aiming to boost management, nutrition, and conservation practices in endangered poultry breeds. This becomes pivotal when the local breed dealt with belongs to an understudied species, such as the turkey. So, the main objective of this study is to identify which method combination may report a higher likelihood of successful sex determination in poults across the three-pattern varieties of the Andalusian turkey breed. A total of 84 one to two days old Andalusian turkey poults (42 black, 28 black-roan, and 14 bronze-roan) were evaluated in this study. Sex determination was performed using 15 methods, which included testing external egg metrics and eggshell color, poult morphological appraisal and phaneroptics, and behavioral traits. Possible differences across plumage varieties and the interaction between sex and plumage were observed when external egg quality was measured. Sex determination through behavioral methods in black base feathered (black and black-roan) male sex individuals showed seven times higher sensitivity when compared to the rest of the studied individuals (χ2 = 7.14, df = 1, P < 0.01). In contrast, for the black-roan plumage females, the method based on the color of down feathers was approximately four times more sensitive (χ2 = 3.95, df = 1, P ≤ 0.05). For the bronze-roan pattern, none of the sexing techniques was reported to efficiently predict sex itself. However, the most proper method combination to determine sex, independent of plumage color, was physical external egg characteristics, the color of down feathers, and behavioral approaches (“English method” and “slap technique”). The specificity values were found to be 49.12, 93.33, and 100%, while the sensitivity values were observed to be 74.64, 91.03, and 100%, which translated into accuracy of 63.10, 92.26, and 100% in black, black-roan, and bronze-roan poults, respectively. Our results suggest that the method combination tested in this study could be considered a highly accurate, simple, and affordable alternative for sex determination in turkeys. This could mean a pivotal advance for small producers of turkeys, as early sex detection can help to plan timely conservational management strategies, which is of prominent importance in the context of endangered poultry breeds.
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Affiliation(s)
- J. I. Salgado Pardo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
- Department of Agriculture and Ecological Husbandry, Area of Agriculture and Environment, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Córdoba, Spain
- *Correspondence: Francisco Javier Navas González
| | - Antonio González Ariza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
- Antonio González Ariza
| | - A. Arando Arbulu
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
| | - J. M. León Jurado
- Agropecuary Provincial Centre, Córdoba Provincial Government, Córdoba, Spain
| | - J. V. Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
| | - M. E. Camacho Vallejo
- Department of Agriculture and Ecological Husbandry, Area of Agriculture and Environment, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Córdoba, Spain
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Akat E, Yenmiş M, Pombal MA, Molist P, Megías M, Arman S, Veselỳ M, Anderson R, Ayaz D. Comparison of Vertebrate Skin Structure at Class Level: A Review. Anat Rec (Hoboken) 2022; 305:3543-3608. [DOI: 10.1002/ar.24908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Esra Akat
- Ege University, Faculty of Science, Biology Department Bornova, İzmir Turkey
| | - Melodi Yenmiş
- Ege University, Faculty of Science, Biology Department Bornova, İzmir Turkey
| | - Manuel A. Pombal
- Universidade de Vigo, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía‐IBIV Vigo, España
| | - Pilar Molist
- Universidade de Vigo, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía‐IBIV Vigo, España
| | - Manuel Megías
- Universidade de Vigo, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía‐IBIV Vigo, España
| | - Sezgi Arman
- Sakarya University, Faculty of Science and Letters, Biology Department Sakarya Turkey
| | - Milan Veselỳ
- Palacky University, Faculty of Science, Department of Zoology Olomouc Czechia
| | - Rodolfo Anderson
- Departamento de Zoologia, Instituto de Biociências Universidade Estadual Paulista São Paulo Brazil
| | - Dinçer Ayaz
- Ege University, Faculty of Science, Biology Department Bornova, İzmir Turkey
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Kondo S, Watanabe M, Miyazawa S. Studies of Turing pattern formation in zebrafish skin. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200274. [PMID: 34743596 PMCID: PMC8580470 DOI: 10.1098/rsta.2020.0274] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 05/08/2023]
Abstract
Skin patterns are the first example of the existence of Turing patterns in living organisms. Extensive research on zebrafish, a model organism with stripes on its skin, has revealed the principles of pattern formation at the molecular and cellular levels. Surprisingly, although the networks of cell-cell interactions have been observed to satisfy the 'short-range activation and long-range inhibition' prerequisites for Turing pattern formation, numerous individual reactions were not envisioned based on the classical reaction-diffusion model. For example, in real skin, it is not an alteration in concentrations of chemicals, but autonomous migration and proliferation of pigment cells that establish patterns, and cell-cell interactions are mediated via direct contact through cell protrusions. Therefore, the classical reaction-diffusion mechanism cannot be used as it is for modelling skin pattern formation. Various studies are underway to adapt mathematical models to the experimental findings on research into skin patterns, and the purpose of this review is to organize and present them. These novel theoretical methods could be applied to autonomous pattern formation phenomena other than skin patterns. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
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Affiliation(s)
- Shigeru Kondo
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masakatsu Watanabe
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Seita Miyazawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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11
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Maclary ET, Phillips B, Wauer R, Boer EF, Bruders R, Gilvarry T, Holt C, Yandell M, Shapiro MD. Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia). Mol Biol Evol 2021; 38:5376-5390. [PMID: 34459920 PMCID: PMC8662629 DOI: 10.1093/molbev/msab260] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our study identifies two candidate genes for eye colors variation, and establishes a genetic link between iris and plumage color, two traits that vary widely in the evolution of birds and other vertebrates.
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Affiliation(s)
- Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Elena F Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Rebecca Bruders
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Tyler Gilvarry
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Carson Holt
- Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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Schwochow D, Bornelöv S, Jiang T, Li J, Gourichon D, Bed’Hom B, Dorshorst BJ, Chuong CM, Tixier-Boichard M, Andersson L. The feather pattern autosomal barring in chicken is strongly associated with segregation at the MC1R locus. Pigment Cell Melanoma Res 2021; 34:1015-1028. [PMID: 33793042 PMCID: PMC8484376 DOI: 10.1111/pcmr.12975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/26/2021] [Indexed: 01/14/2023]
Abstract
Color patterns within individual feathers are common in birds but little is known about the genetic mechanisms causing such patterns. Here, we investigate the genetic basis for autosomal barring in chicken, a horizontal striping pattern on individual feathers. Using an informative backcross, we demonstrate that the MC1R locus is strongly associated with this phenotype. A deletion at SOX10, underlying the dark brown phenotype on its own, affects the manifestation of the barring pattern. The coding variant L133Q in MC1R is the most likely causal mutation for autosomal barring in this pedigree. Furthermore, a genetic screen across six different breeds showing different patterning phenotypes revealed that the most striking shared characteristics among these breeds were that they all carried the MC1R alleles Birchen or brown. Our data suggest that the presence of activating MC1R mutations enhancing pigment synthesis is an important mechanism underlying pigmentation patterns on individual feathers in chicken. We propose that MC1R and its antagonist ASIP play a critical role for determining within-feather pigmentation patterns in birds by acting as activator and inhibitor possibly in a Turing reaction-diffusion model.
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Affiliation(s)
- Doreen Schwochow
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Susanne Bornelöv
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tingxing Jiang
- Department of Pathology, University of Southern California, Los Angeles, CS, USA
| | - Jingyi Li
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, USA
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | | | - Bertrand Bed’Hom
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Ben J. Dorshorst
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CS, USA
| | | | - Leif Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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13
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Li J, Lee MO, Chen J, Davis BW, Dorshorst BJ, Siegel PB, Inaba M, Jiang TX, Chuong CM, Andersson L. Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens. Proc Natl Acad Sci U S A 2021; 118:e2109363118. [PMID: 34607956 PMCID: PMC8521658 DOI: 10.1073/pnas.2109363118] [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] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
Melanotic (Ml) is a mutation in chickens that extends black (eumelanin) pigmentation in normally brown or red (pheomelanin) areas, thus affecting multiple within-feather patterns [J. W. Moore, J. R. Smyth Jr, J. Hered. 62, 215-219 (1971)]. In the present study, linkage mapping using a back-cross between Dark Cornish (Ml/Ml) and Partridge Plymouth Rock (ml+/ml+ ) chickens assigned Ml to an 820-kb region on chromosome 1. Identity-by-descent mapping, via whole-genome sequencing and diagnostic tests using a diverse set of chickens, refined the localization to the genomic region harboring GJA5 encoding gap-junction protein 5 (alias connexin 40) previously associated with pigmentation patterns in zebrafish. An insertion/deletion polymorphism located in the vicinity of the GJA5 promoter region was identified as the candidate causal mutation. Four different GJA5 transcripts were found to be expressed in feather follicles and at least two showed differential expression between genotypes. The results showed that Melanotic constitutes a cis-acting regulatory mutation affecting GJA5 expression. A recent study established the melanocortin-1 receptor (MC1R) locus and the interaction between the MC1R receptor and its antagonist agouti-signaling protein as the primary mechanism underlying variation in within-feather pigmentation patterns in chickens. The present study advances understanding the mechanisms underlying variation in plumage color in birds because it demonstrates that the activity of connexin 40/GJA5 can modulate the periodic pigmentation patterns within individual feathers.
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Affiliation(s)
- Jingyi Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Mi-Ok Lee
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Junfeng Chen
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Benjamin J Dorshorst
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Paul B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Masafumi Inaba
- Department of Pathology, University of Southern California, Los Angeles, CA 90033
| | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, CA 90033
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843;
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
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14
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Shen H, Wu W, Liu S, Zhang J, Lam JWY, Tang BZ. Photodegradation‐Induced Turn‐On
Luminescence of
Tetraphenylethylene‐Based
Trithiocarbonate Polymers
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hanchen Shen
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute of Advanced Study The Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong China
| | - Wenjie Wu
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute of Advanced Study The Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong China
| | - Shunjie Liu
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute of Advanced Study The Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong China
| | - Jing Zhang
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute of Advanced Study The Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong China
- Department of Laboratory Medicine, Nanfang Hospital Southern Medical University Guangzhou Guangdong 510515 China
| | - Jacky W. Y. Lam
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute of Advanced Study The Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong China
- HKUST Shenzhen Research Institute No. 9 Yuexing 1 st RD, South Area Hi‐tech Park, Nanshan Shenzhen Guangdong 518057 China
| | - Ben Zhong Tang
- Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute of Advanced Study The Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong China
- HKUST Shenzhen Research Institute No. 9 Yuexing 1 st RD, South Area Hi‐tech Park, Nanshan Shenzhen Guangdong 518057 China
- Center for Aggregation‐induced Emission, SCUT‐HKUST Joint Research Institute, State Key Laboratory of Luminescent Materials and Devices South China University of Technology Guangzhou Guangdong 510640 China
- HKUST AIE Institute Guangzhou Development District, Huangpu Guangzhou Guangdong 510530 China
- Guangdong‐Hong Kong‐Macao Joint laboratory of Optoelectronic and Magnetic Functional Materials The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong, China
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15
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Xi Y, Xu Q, Huang Q, Ma S, Wang Y, Han C, Zhang R, Wang J, Liu H, Li L. Genome-wide association analysis reveals that EDNRB2 causes a dose-dependent loss of pigmentation in ducks. BMC Genomics 2021; 22:381. [PMID: 34034661 PMCID: PMC8146663 DOI: 10.1186/s12864-021-07719-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
Background Birds have various plumage color patterns, and spot is a common phenotype. Herein, we conducted genome-wide association studies (GWAS) in a population of 225 ducks with different sized black spots to reveal the genetic basis of this phenomenon. Results First, we quantified the black spot phenotype within the duck population. The results showed that the uncolored area of the body surface first appeared on the ventral side. With increasing duck age, the area of the black spots was highly conserved across the whole body surface. The GWAS results identified a 198 kb (Chr4: 10,149,651 bp to 10,348,068 bp) genetic region that was significantly associated with the black spot phenotype. The conditional GWAS and linkage disequilibrium (LD) analysis further narrowed the ultimate candidate region to 167 kb (Chr4: 10,180,939 bp to 10,348,068 bp). A key gene regulating melanoblast migration and differentiation, EDNRB2 (Endothelin B receptor-like), was found in the candidate region and having significant mRNA expression level changes in embryonic duck skin tissue with different spot sizes. The significant SNPs (single nucleotide polymorphisms) associated with the EDNRB2 gene were annotated, and two mutations (Chr4: 10,180,939 T > C and Chr4: 10,190,671 A > T) were found to result in the loss of binding sites for two trans-factors, XBP1 and cMYB. The phenotypic effect of these two mutations suggested that they can regulate the size of black spots in a dose-dependent manner, and Chr4: 10,180,939 T > C was the major allele locus. Conclusions Our results revealed that EDNRB2 was the gene responsible for the variation in duck body surface spot size. Chr4: 10,180,939 T > C was the major allele that explained 49.5 % (dorsal side) and 32.9 % (ventral side) of the variation in duck body surface spot size, while 32.1 % (dorsal side) and 19.1 % (ventral side) of the variation could be explained by Chr4: 10,190,671 A > T. The trans-factor prediction also suggested that XBP1 and cMYB have the potential to interact with EDNRB2, providing new insights into the mechanism of action of these genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07719-7.
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Affiliation(s)
- Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Qian Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Qin Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Yushi Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Rongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China.
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China.
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16
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Chen CK, Juan WT, Liang YC, Wu P, Chuong CM. Making region-specific integumentary organs in birds: evolution and modifications. Curr Opin Genet Dev 2021; 69:103-111. [PMID: 33780743 DOI: 10.1016/j.gde.2021.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022]
Abstract
Birds are the most diversified terrestrial vertebrates due to highly diverse integumentary organs that enable robust adaptability to various eco-spaces. Here we show that this complexity is built upon multi-level regional specifications. Across-the-body (macro-) specification includes the evolution of beaks and feathers as new integumentary organs that are formed with regional specificity. Within-an-organ (micro-) specification involves further modifications of organ shapes. We review recent progress in elucidating the molecular mechanisms underlying feather diversification as an example. (1) β-Keratin gene clusters are regulated by typical enhancers or high order chromatin looping to achieve macro- and micro-level regional specification, respectively. (2) Multi-level symmetry-breaking of feather branches confers new functional forms. (3) Complex color patterns are produced by combinations of macro-patterning and micro-patterning processes. The integration of these findings provides new insights toward the principle of making a robustly adaptive bio-interface.
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Affiliation(s)
- Chih-Kuan Chen
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| | - Wen-Tau Juan
- Integrative Stem Cell Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Ya-Chen Liang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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