Reconstruction of Dynamic and Reversible Color Change Using
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Pharaoh Cuttlefish, Sepia Pharaonis, Genome Reveals Unique Reflectin
fmars-08-639670 February 9, 2021 Time: 18:18 # 1 ORIGINAL RESEARCH published: 15 February 2021 doi: 10.3389/fmars.2021.639670 Pharaoh Cuttlefish, Sepia pharaonis, Genome Reveals Unique Reflectin Camouflage Gene Set Weiwei Song1,2, Ronghua Li1,2,3, Yun Zhao1,2, Herve Migaud1,2,3, Chunlin Wang1,2* and Michaël Bekaert3* 1 Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China, 2 Collaborative Innovation Centre for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China, 3 Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom Sepia pharaonis, the pharaoh cuttlefish, is a commercially valuable cuttlefish species across the southeast coast of China and an important marine resource for the world fisheries. Research efforts to develop linkage mapping, or marker-assisted selection have been hampered by the absence of a high-quality reference genome. To address this need, we produced a hybrid reference genome of S. pharaonis using a long-read Edited by: platform (Oxford Nanopore Technologies PromethION) to assemble the genome and Andrew Stanley Mount, short-read, high quality technology (Illumina HiSeq X Ten) to correct for sequencing Clemson University, United States errors. The genome was assembled into 5,642 scaffolds with a total length of 4.79 Gb Reviewed by: and a scaffold N of 1.93 Mb. Annotation of the S. pharaonis genome assembly Simo Njabulo Maduna, 50 Norwegian Institute of Bioeconomy identified a total of 51,541 genes, including 12 copies of the reflectin gene, that enable Research (NIBIO), Norway cuttlefish to control their body coloration. -
Physics of Structural Colors
HOME | SEARCH | PACS & MSC | JOURNALS | ABOUT | CONTACT US Physics of structural colors This article has been downloaded from IOPscience. Please scroll down to see the full text article. 2008 Rep. Prog. Phys. 71 076401 (http://iopscience.iop.org/0034-4885/71/7/076401) The Table of Contents and more related content is available Download details: IP Address: 132.72.138.1 The article was downloaded on 02/07/2008 at 16:04 Please note that terms and conditions apply. IOP PUBLISHING REPORTS ON PROGRESS IN PHYSICS Rep. Prog. Phys. 71 (2008) 076401 (30pp) doi:10.1088/0034-4885/71/7/076401 Physics of structural colors S Kinoshita, S Yoshioka and J Miyazaki Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan E-mail: [email protected] Received 3 September 2007, in final form 16 January 2008 Published 6 June 2008 Online at stacks.iop.org/RoPP/71/076401 Abstract In recent years, structural colors have attracted great attention in a wide variety of research fields. This is because they are originated from complex interaction between light and sophisticated nanostructures generated in the natural world. In addition, their inherent regular structures are one of the most conspicuous examples of non-equilibrium order formation. Structural colors are deeply connected with recent rapidly growing fields of photonics and have been extensively studied to clarify their peculiar optical phenomena. Their mechanisms are, in principle, of a purely physical origin, which differs considerably from the ordinary coloration mechanisms such as in pigments, dyes and metals, where the colors are produced by virtue of the energy consumption of light. -
UNIVERSITY of CALIFORNIA, IRVINE Protonic Conduction and Photochemical Modification of Protein Reflectin THESIS Submitted In
UNIVERSITY OF CALIFORNIA, IRVINE Protonic Conduction and Photochemical Modification of Protein Reflectin THESIS submitted in partial satisfaction of the requirements for the degree of MASTER OF SCIENCE in Chemical and Biochemical Engineering by Yegor Van Dyke Thesis Committee: Professor Alon A. Gorodetsky, Chair Professor Hung D. Nguyen Professor Frank G. Shi 2016 Chapter 1 © 2016 American Chemical Society Chapter 2 © 2016 Gorodetsky Group Chapter 3 © 2016 Yegor Van Dyke TABLE OF CONTENTS LIST OF FIGURES ....................................................................................................................... iii ACKNOWLEDGMENTS ............................................................................................................. vi ABSTRACT OF THE THESIS .................................................................................................... vii CHAPTER 1: Photochemical Doping of Protonic Transistors from a Cephalopod Protein ..................................................................................................................... 1 1.1 Abstract ..................................................................................................................................... 1 1.2 Introduction ………….............................................................................................................. 4 1.3 Experimental Section ................................................................................................................ 5 1.3.1 Preparation of Wild-Type and Mutant Reflectins -
Pollia Condensata Has an Extraordinary Blue Fruit Known for Its High Intensity Reflectivity, and Glittery Appearance
LIVING LIGHT 2018 3 CONTENTS Introduction ....................................................... 3 Scientific commitee ............................................. 4 Local organising commitee ................................... 4 Graphics ............................................................ 4 History .............................................................. 5 Timetable .......................................................... 6 Find us .............................................................11 Abstracts, invited lectures ...................................13 Abstracts, lectures .............................................21 Abstracts, posters ..............................................67 List of participants .............................................92 Contacts...........................................................96 Sponsors ..........................................................97 Notes ...............................................................98 4 5 INTRODUCTION Dear Living Light 2018 Participant, It is an honour for us to host such an exciting meeting in Cambridge and we thank you for joining us! We designed the meeting with the intention of maximising interaction between the participants and with the hope that you will go back home with a new set of collaborators and friends which are as passionate as you are about working at the interface between biology, chemistry, physics, and engineering! We truly hope that you will enjoy the conference and we ask for your collaboration to keep the meeting -
The Optical Janus Effect: Asymmetric Structural Color Reflection Materials
The Optical Janus Effect: Asymmetric Structural Color Reflection Materials The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation England, Grant T., Calvin Russell, Elijah Shirman, Theresa Kay, Nicolas Vogel, and Joanna Aizenberg. 2017. “The Optical Janus Effect: Asymmetric Structural Color Reflection Materials.” Advanced Materials 29 (29) (June 6): 1606876. doi:10.1002/adma.201606876. Published Version doi:10.1002/adma.201606876 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:37235483 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP DOI: 10.1002/ ((please add manuscript number)) Article type: Full Paper The Optical Janus Effect: Asymmetric Structural Color Reflection Materials Grant T. Englanda, Calvin Russella, Elijah Shirmanab, Theresa Kayb, Nicolas Vogelc, and Joanna Aizenberg*abd aJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, USA bWyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, USA cInstitute of Particle Technology, Friedrich-Alexander University Erlangen-Nürnberg, Cauerstrasse 4, 91058 Erlangen, Germany dDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, USA Keywords: structural color, absorption, multilayer, photonic crystals, thin film. Abstract: Structurally colored materials are often used for their resistance to photobleaching and their complex viewing direction-dependent optical properties. Frequently, absorption has been added to these types of materials in order to improve the color saturation by mitigating the effects of nonspecific scattering that is present in most samples due to imperfect manufacturing procedures. -
Condition and Brightness of Structural Blue-Green: Motmot Tail-Racket Brightness Is Related to Speed of Feather Growth in Males, but Not in Females
Trinity University Digital Commons @ Trinity Biology Faculty Research Biology Department 7-2012 Condition and Brightness of Structural Blue- Green: Motmot Tail-Racket Brightness is Related to Speed of Feather Growth in Males, But Not in Females Troy G. Murphy Trinity University, [email protected] Tiffany T. Pham Trinity University Follow this and additional works at: https://digitalcommons.trinity.edu/bio_faculty Part of the Biology Commons Repository Citation Murphy, T. G. and Pham, T. T. (2012), Condition and brightness of structural blue-green: Motmot tail-racket brightness is related to speed of feather growth in males, but not in females. Biological Journal of the Linnean Society, 106(3), 673–681. doi: 10.1111/ j.1095-8312.2012.01891.x This Article is brought to you for free and open access by the Biology Department at Digital Commons @ Trinity. It has been accepted for inclusion in Biology Faculty Research by an authorized administrator of Digital Commons @ Trinity. For more information, please contact [email protected]. bs_bs_banner Biological Journal of the Linnean Society, 2012, 106, 673–681. With 3 figures Condition and brightness of structural blue-green: motmot tail-racket brightness is related to speed of feather growth in males, but not in females TROY G. MURPHY* and TIFFANY T. PHAM Trinity University, Department of Biology, One Trinity Place, San Antonio, TX 78212, USA Received 21 November 2011; revised 18 January 2012; accepted for publication 19 January 2012bij_1891 673..681 Coloration plays an important role in sexual and social communication, and in many avian species both males and females maintain elaborate colours. Recent research has provided strong support for the hypothesis that elaborate female traits can be maintained by sexual or social selection; however, most research on female ornamentation has focused on pigment-based colours, and less is known about how structural colours are maintained. -
Structure, Self-Assembly, and Properties of a Truncated Reflectin Variant
Structure, self-assembly, and properties of a truncated reflectin variant Mehran J. Umerania,1, Preeta Pratakshyab,1, Atrouli Chatterjeec, Juana A. Cerna Sanchezd, Ho Shin Kime, Gregor Ilcf, Matic Kovaciˇ cˇf, Christophe Magnang, Benedetta Marmirolih, Barbara Sartorih, Albert L. Kwansae, Helen Orinsc, Andrew W. Bartlettc, Erica M. Leungc, Zhijing Fenga, Kyle L. Naughtoni, Brenna Norton-Bakerb, Long Phana, James Longc, Alex Allevatoa, Jessica E. Leal-Cruza, Qiyin Linj, Pierre Baldig, Sigrid Bernstorffk, Janez Plavecf, Yaroslava G. Yinglinge, and Alon A. Gorodetskya,b,c,2 aDepartment of Materials Science and Engineering, University of California, Irvine, CA 92697; bDepartment of Chemistry, University of California, Irvine, CA 92697; cDepartment of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697; dDepartment of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697; eDepartment of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695; fSlovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia; gDepartment of Computer Science, University of California, Irvine, CA 92697; hInstitute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria; iDepartment of Physics and Astronomy, University of California, Irvine, CA 92697; jIrvine Materials Research Institute, University of California, Irvine, CA 92697; and kElettra–Sincrotrone Trieste, 34149 Trieste, Italy Edited by Jacqueline K. Barton, California Institute of Technology, -
Changes in Reflectin Protein Phosphorylation Are Associated with Dynamic Irides
Classification: Biochemistry Changes in reflectin protein phosphorylation are associated with dynamic irides- cence in squid Michi Izumi*, Alison M. Sweeney*, Daniel DeMartini*, James C. Weaver*, Meghan L. Pow- ers*, Andrea Tao*, Tania V. Silvas*, Ryan M. Kramer†, Wendy J. Crookes-Goodson†, Lydia M. ‡ † ‡ Mäthger , Rajesh R. Naik , Roger T. Hanlon and Daniel E. Morse* *Institute for Collaborative Biotechnologies, Materials Research Laboratory, California Nano- Systems Institute and the Department of Molecular, Cellular and Developmental Biology, Uni- versity of California, Santa Barbara, Santa Barbara, CA 93106; †Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH 45433; ‡Marine Biolog- ical Laboratory, Woods Hole, MA 02543 §To whom correspondence should be addressed. E-mail: [email protected], [email protected] Corresponding author: Daniel E. Morse University of California, Santa Barbara, Santa Barbara, CA 93106 Tel: 805-893-7442 Fax: 805-893-2998 Manuscript information: Number of text pages; 21 Number of figures; 6 Abbreviations: ACh, acetylcholine; mAChRs, muscarinic acetylcholine receptors; DTT, dithiothreitol; HPLC, high performance liquid chromatography; IEF, isoelectric focusing; PVDF, polyvinylidene fluoride; HRP, horseradish peroxidase; MALDI-TOF MS, matrix-assisted laser desorption time-of-flight mass spectroscopy; RM, reflectin mo- tif; PKC, protein kinase C Abstract Many cephalopods exhibit remarkable dermal iridescence, a component of their complex, dynamic camouflage -
Light-Matter Interaction and the Structural Coloration of Birds
Light-Matter Interaction and the Structural Coloration of Birds Carmem Maia Gilardoni Research Paper Top Master in Nanoscience, Zernike Institute for Advanced Materials Supervised by: Prof. Dr. Doekele Stavenga [February-March 2016] Contents 1 Introduction 1 2 Bird Feather Structure 2 3 Physical Models 5 3.1 Maxwell's Equations . .5 3.2 Finite Difference Time Domain (FDTD) Formalism . .6 3.3 Band Structure Formalism . .7 3.3.1 The Eigenvalue Problem in Frequency Domain . .7 3.3.2 The Periodic Dielectric . .8 3.4 Effective Medium Description . 10 3.4.1 Thin Film Theory . 10 3.4.2 The Transfer Matrix . 12 3.4.3 Homogenization of the Refractive Index . 13 4 Application of the Models 16 5 Conclusion 19 Abstract Birds feathers have evolved showing an impressive pallet of colors and optical effects generated by the diverse arrangement of keratin, melanin and air in their barbules. Small changes to only a few parameters in the structure of the barbules are responsible for varied optical features. In order to understand the role of each parameter involved in the description of the photonic structures responsible for the structural coloration of birds, valid physical models for these arrangements must be obtained. We develop a description of the physical models generally applied to the description of the structure of the barbules, specifically the complete solution of Maxwell's equations in the time domain (FDTD) or in the frequency domain (photonic band structure), and the thin-film description of the structure through the effective-medium theory for the refractive index. In the context of the papers analyzed in this report, potential applications of an effective- medium theory for complex photonic structures are identified. -
Elucidating the Role of Nanostructured Pigment Granules in the Dynamic Coloration of Cephalopods: a Pathway Towards New Bioinspired Materials
Elucidating the Role of Nanostructured Pigment Granules in the Dynamic Coloration of Cephalopods: A Pathway Towards New Bioinspired Materials by Thomas L. Williams B.A. in Chemistry, Colby College A dissertation submitted to The Faculty of the College of Science of Northeastern University in partial fulfillment of the requirements for the degree of Doctor of Philosophy February 14th, 2019 Dissertation directed by Leila Deravi Professor of Chemistry and Chemical Biology 1 Acknowledgements First, I would like to sincerely extend my gratitude to my advisor, Prof. Leila Deravi, for an incredible amount of direction, advice, and patience. I would also like to thank my dissertation committee members: Profs. Steven Lopez, Eugene Smotkin, and Rudi Seitz. Each of you have contributed significantly to this work and to my growth as a chemist through your comments and guidance. Thanks to my family, who have always been supportive of my academic endeavors. I also need to extend my thanks to all the current and previous members of the Biomaterials Design Group, especially Christopher Dibona, Dr. Sean Dinneen, Dr. Amrita Kumar, and Camille Martin, aka Team Pigment, for their assistance, advice and support. I would also like to thank Conor Gomes, Cassandra Martin, and Dr. Jeff Paten for their insight and friendship. I would also like to thank Northeastern University and the Department of Chemistry and Chemical Biology for the opportunity to work and study here. I would like to specifically thank Prof. Jared Auclair and Dr. John de la Parra for their assistance with mass spectrometry, as well as Prof. Jason Guo, for his assistance with NMR. -
Advanced Methods for Studying Pigments and Coloration Using Avian Specimens*,†
CHAPTER THREE Advanced Methods for Studying Pigments and Coloration Using Avian Specimens*,† Kevin J. Burns, Kevin J. McGraw, Allison J. Shultz, Mary C. Stoddard, and Daniel B. Thomas Abstract. Advanced analyses of feathers, eggs, and usage, limitations, and other considerations for other colorful tissues in ornithology collections analyzing museum specimens. Structural colors are revealing fresh insights into the life histories in feathers and the surface coloration of eggs are of birds. Here, we describe the methods used in particularly emphasized. these studies, including high-performance liq- uid chromatography, digital photography, Raman Key Words: digital photography, egg pigmentation, spectroscopy, and spectrophotometry. We use high-performance liquid chromatography, hyper- case studies from across the diversity of birds and spectral imaging, Raman spectroscopy, spectro- from deep in the fossil record to illustrate method photometry, structural coloration. olors are essential for the life history strate- mechanisms of color generation, and the do-or- gies of many animals, including birds (Hill die importance of their colorful displays, birds are Cand McGraw 2006a,b). Bright and vivid col- particular marvels of coloration. Birds have col- ors often function as visual signals, communicat- orful eggs, eyes, plumage, skin, and scales, and ing the quality of an individual to potential mates, can show substantial variation in coloration across rivals, or predators (Hill 1991, Pryke and Griffith species, populations, and individuals. 2006, Maan and Cummings 2012). Muted and The significance and evolution of color varia- dark colors also can be important social signals tion among birds is often revealed through (Møller 1987, Hoi and Griggio 2008, Karubian comparative analyses, and ornithology collec- et al. -
How to Define and Study Structural Proteins As Biopolymer Materials
Polymer Journal (2020) 52:1043–1056 https://doi.org/10.1038/s41428-020-0362-5 FOCUS REVIEW How to define and study structural proteins as biopolymer materials Keiji Numata 1,2 Received: 1 April 2020 / Revised: 25 April 2020 / Accepted: 27 April 2020 / Published online: 22 May 2020 © The Author(s) 2020. This article is published with open access Abstract Structural proteins, including silk fibroins, play an important role in shaping the skeletons and structures of cells, tissues, and organisms. The amino acid sequences of structural proteins often show characteristic features, such as a repeating tandem motif, that are notably different from those of functional proteins such as enzymes and antibodies. In recent years, materials composed of or containing structural proteins have been studied and developed as biomedical, apparel, and structural materials. This review outlines the definition of structural proteins, methods for characterizing structural proteins as polymeric materials, and potential applications. Definition considered [3], defining a structural protein is even more 1234567890();,: 1234567890();,: difficult and complicated. Therefore, in this focus review, I Proteins are polymers in which the 20 natural amino acids would like to define a structural protein as “a protein that are linked by amide bonds. In addition to the 20 natural possesses a characteristic amino acid sequence or motif amino acids, there are amino acids that are not directly that repeats and forms a skeleton or contributes to the synthesized from ribosomes, such as L-3,4-dihydrox- mechanical properties of a living organism, cell, or mate- yphenylalanine (DOPA), hydroxyproline (Hyp), dityrosine, rial” (Fig. 1). Structural proteins can be globular or fibrillar and selenomethionine, and these compounds are synthe- proteins.