Dynamic pigmentary and structural coloration within cephalopod chromatophore organs

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Abstract

Chromatophore organs in cephalopod skin are known to produce ultra-fast changes in appearance for camouflage and communication. Light-scattering pigment granules within chromatocytes have been presumed to be the sole source of coloration in these complex organs. We report the discovery of structural coloration emanating in precise register with expanded pigmented chromatocytes. Concurrently, using an annotated squid chromatophore proteome together with microscopy, we identify a likely biochemical component of this reflective coloration as reflectin proteins distributed in sheath cells that envelop each chromatocyte. Additionally, within the chromatocytes, where the pigment resides in nanostructured granules, we find the lens protein Ω- crystallin interfacing tightly with pigment molecules. These findings offer fresh perspectives on the intricate biophotonic interplay between pigmentary and structural coloration elements tightly co-located within the same dynamic flexible organ - a feature that may help inspire the development of new classes of engineered materials that change color and pattern.

Abstract

Chromatophores in cephalopod skin are known for fast changes in coloration due to light-scattering pigment granules. Here, authors demonstrate structural coloration facilitated by reflectin in sheath cells and offer insights into the interplay between structural and pigmentary coloration elements.

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Mechanisms and behavioural functions of structural coloration in cephalopods.

Roger T Hanlon, Kristin N. Marshall, E Denton … (2009)

Octopus, squid and cuttlefish are renowned for rapid adaptive coloration that is used for a wide range of communication and camouflage. Structural coloration plays a key role in augmenting the skin patterning that is produced largely by neurally controlled pigmented chromatophore organs. While most iridescence and white scattering is produced by passive reflectance or diffusion, some iridophores in squid are actively controlled via a unique cholinergic, non-synaptic neural system. We review the recent anatomical and experimental evidence regarding the mechanisms of reflection and diffusion of light by the different cell types (iridophores and leucophores) of various cephalopod species. The structures that are responsible for the optical effects of some iridophores and leucophores have recently been shown to be proteins. Optical interactions with the overlying pigmented chromatophores are complex, and the recent measurements are presented and synthesized. Polarized light reflected from iridophores can be passed through the chromatophores, thus enabling the use of a discrete communication channel, because cephalopods are especially sensitive to polarized light. We illustrate how structural coloration contributes to the overall appearance of the cephalopods during intra- and interspecific behavioural interactions including camouflage.

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On the optimal trimming of high-throughput mRNA sequence data

Matthew MacManes (2014)

The widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in functional biology and adaptation have used these technologies to sequence mRNA transcriptomes of specific tissues, which in turn are often compared to other tissues, or other individuals with different phenotypes. While these techniques are extremely powerful, careful attention to data quality is required. In particular, because high-throughput sequencing is more error-prone than traditional Sanger sequencing, quality trimming of sequence reads should be an important step in all data processing pipelines. While several software packages for quality trimming exist, no general guidelines for the specifics of trimming have been developed. Here, using empirically derived sequence data, I provide general recommendations regarding the optimal strength of trimming, specifically in mRNA-Seq studies. Although very aggressive quality trimming is common, this study suggests that a more gentle trimming, specifically of those nucleotides whose Phred score <2 or <5, is optimal for most studies across a wide variety of metrics.

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Significance analysis of spectral count data in label-free shotgun proteomics.

Hyungwon Choi, Damian Fermin, Hyungwon Choi (2008)

Spectral counting has become a commonly used approach for measuring protein abundance in label-free shotgun proteomics. At the same time, the development of data analysis methods has lagged behind. Currently most studies utilizing spectral counts rely on simple data transforms and posthoc corrections of conventional signal-to-noise ratio statistics. However, these adjustments can neither handle the bias toward high abundance proteins nor deal with the drawbacks due to the limited number of replicates. We present a novel statistical framework (QSpec) for the significance analysis of differential expression with extensions to a variety of experimental design factors and adjustments for protein properties. Using synthetic and real experimental data sets, we show that the proposed method outperforms conventional statistical methods that search for differential expression for individual proteins. We illustrate the flexibility of the model by analyzing a data set with a complicated experimental design involving cellular localization and time course.

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Author and article information

Contributors

Roger T. Hanlon:

ORCID: http://orcid.org/0000-0003-0004-5674

rhanlon@mbl.edu

Leila F. Deravi:

ORCID: http://orcid.org/0000-0003-3226-2470

l.deravi@northeastern.edu

Journal

Journal ID (nlm-ta): Nat Commun

Journal ID (iso-abbrev): Nat Commun

Title: Nature Communications

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2041-1723

Publication date (Electronic): 1 March 2019

Publication date PMC-release: 1 March 2019

Publication date Collection: 2019

Volume: 10

Electronic Location Identifier: 1004

Affiliations

[1 ]ISNI 0000 0001 2173 3359, GRID grid.261112.7, Department of Chemistry and Chemical Biology, , Northeastern University, ; Boston, MA 02115 USA

[2 ]ISNI 000000012169920X, GRID grid.144532.5, The Eugene Bell Center, , The Marine Biological Laboratory, ; Woods Hole, MA 02543 USA

[3 ]ISNI 0000 0004 1936 7531, GRID grid.429997.8, Department of Biomedical Engineering, , Tufts University, ; Medford, MA 02155 USA

[4 ]ISNI 0000 0001 2341 2786, GRID grid.116068.8, Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, , Massachusetts Institute of Technology, ; Cambridge, MA 02139 USA

[5 ]ISNI 0000 0004 0470 8006, GRID grid.418742.c, Institute of High Performance Computing, A*STAR, ; Singapore, 138632 Singapore

[6 ]ISNI 0000 0001 2192 7145, GRID grid.167436.1, Department of Molecular, Cellular, , and Biomedical Sciences, University of New Hampshire, ; Durham, NH 03824 USA

Author information

Jingjie Yeo http://orcid.org/0000-0002-6462-7422

Hieu T. Nguyen http://orcid.org/0000-0003-2153-9200

Conor M. Gomes http://orcid.org/0000-0002-2649-3689

Matthew D. MacManes http://orcid.org/0000-0002-2368-6960

Roger T. Hanlon http://orcid.org/0000-0003-0004-5674

Leila F. Deravi http://orcid.org/0000-0003-3226-2470

Article

Publisher ID: 8891

DOI: 10.1038/s41467-019-08891-x

PMC ID: 6397165

PubMed ID: 30824708

SO-VID: 34e8ee88-465d-4572-a97f-050e2ea6c4ba

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 20 July 2018

Date accepted : 23 January 2019

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Dynamic pigmentary and structural coloration within cephalopod chromatophore organs

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The Dynamic Brain

Most cited references 57

Mechanisms and behavioural functions of structural coloration in cephalopods.

On the optimal trimming of high-throughput mRNA sequence data

Significance analysis of spectral count data in label-free shotgun proteomics.

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