Cephalopod-inspired optical engineering of human cells

Multimodal factor evaluation system for organismal transparency by hyperspectral imaging

Organismal transparency constitutes a significant concern in whole-body live imaging, yet its underlying structural, genetic, and physiological foundations remain inadequately comprehended. Diverse environmental and physiological factors (multimodal factors) are recognized for their influence on organismal transparency. However, a comprehensive and integrated quantitative evaluation system for biological transparency across a broad spectrum of wavelengths is presently lacking. In this study, we have devised an evaluation system to gauge alterations in organismal transparency induced by multimodal factors, encompassing a wide range of transmittance spanning from 380 to 1000 nm, utilizing hyperspectral microscopy. Through experimentation, we have scrutinized the impact of three environmental variables (temperature, salinity, and pH) and the effect of 11 drugs treatment containing inhibitors targeting physiological processes in the ascidian Ascidiella aspersa. This particular species, known for its exceptionally transparent eggs and embryos, serves as an ideal model. We calculated bio-transparency defined as the mean transmittance ratio of visible light within the range of 400-760 nm. Our findings reveal a positive correlation between bio-transparency and temperature, while an inverse relationship is observed with salinity levels. Notably, reduced pH levels and exposure to six drugs have led to significant decreasing in bio-transparency (ranging from 4.2% to 58.6%). Principal component analysis (PCA) on the measured transmittance data classified these factors into distinct groups. This suggest diverse pathways through which opacification occurs across different spectrum regions. The outcome of our quantitative analysis of bio-transparency holds potential applicability to diverse living organisms on multiple scales. This analytical framework also contributes to a holistic comprehension of the mechanisms underlying biological transparency, which is susceptible to many environmental and physiological modalities.

Squid leucophore-inspired engineering of optically dynamic human cells

Cephalopods (e.g., squids, octopuses, and cuttlefishes) possess remarkable dynamic camouflage abilities and therefore have emerged as powerful sources of inspiration for the engineering of dynamic optical technologies. Within this context, we have focused on the development of engineered living systems that can emulate the tunable optical characteristics of some squid skin cells. Herein, we expand our ability to controllably incorporate reflectin-based structures within mammalian cells via genetic engineering methods, and demonstrate that such structures can facilitate holotomographic and standard microscopy imaging of the cells. Moreover, we show that the reflectin-based structures within our cells can be reconfigured with a straightforward chemical stimulus, and we quantify the stimulus-induced changes observed for the structures at the single cell level. The reported findings may enable a better understanding of the color- and appearance-changing capabilities of some cephalopod skin cells and could afford opportunities for reflectins as molecular probes in the fields of cell biology and biomedical optics.

Synthetic peptides for the precise transportation of proteins of interests to selectable subcellular areas

Proteins, as gifts from nature, provide structure, sequence, and function templates for designing biomaterials. As first reported here, one group of proteins called reflectins and derived peptides were found to present distinct intracellular distribution preferences. Taking their conserved motifs and flexible linkers as Lego bricks, a series of reflectin-derivates were designed and expressed in cells. The selective intracellular localization property leaned on an RMs (canonical conserved reflectin motifs)-replication-determined manner, suggesting that these linkers and motifs were constructional fragments and ready-to-use building blocks for synthetic design and construction. A precise spatiotemporal application demo was constructed in the work by integrating RLNto2 (as one representative of a synthetic peptide derived from RfA1) into the Tet-on system to effectively transport cargo peptides into nuclei at selective time points. Further, the intracellular localization of RfA1 derivatives was spatiotemporally controllable with a CRY2/CIB1 system. At last, the functional homogeneities of either motifs or linkers were verified, which made them standardized building blocks for synthetic biology. In summary, the work provides a modularized, orthotropic, and well-characterized synthetic-peptide warehouse for precisely regulating the nucleocytoplasmic localization of proteins.

Squid Skin Cell-Inspired Refractive Index Mapping of Cells, Vesicles, and Nanostructures

The fascination with the optical properties of naturally occurring systems has been driven in part by nature's ability to produce a diverse palette of vibrant colors from a relatively small number of common structural motifs. Within this context, some cephalopod species have evolved skin cells called iridophores and leucophores whose constituent ultrastructures reflect light in different ways but are composed of the same high refractive index material─a protein called reflectin. Although such natural optical systems have attracted much research interest, measuring the refractive indices of biomaterial-based structures across multiple different environments and establishing theoretical frameworks for accurately describing the obtained refractive index values has proven challenging. Herein, we employ a synergistic combination of experimental and computational methodologies to systematically map the three-dimensional refractive index distributions of model self-assembled reflectin-based structures both in vivo and in vitro. When considered together, our findings may improve understanding of squid skin cell functionality, augment existing methods for characterizing protein-based optical materials, and expand the utility of emerging holotomographic microscopy techniques.

A Mini-Review on Reflectins, from Biochemical Properties to Bio-Inspired Applications

Some cephalopods (squids, octopuses, and cuttlefishes) produce dynamic structural colors, for camouflage or communication. The key to this remarkable capability is one group of specialized cells called iridocytes, which contain aligned membrane-enclosed platelets of high-reflective reflectins and work as intracellular Bragg reflectors. These reflectins have unusual amino acid compositions and sequential properties, which endows them with functional characteristics: an extremely high reflective index among natural proteins and the ability to answer various environmental stimuli. Based on their unique material composition and responsive self-organization properties, the material community has developed an impressive array of reflectin- or iridocyte-inspired optical systems with distinct tunable reflectance according to a series of internal and external factors. More recently, scientists have made creative attempts to engineer mammalian cells to explore the function potentials of reflectin proteins as well as their working mechanism in the cellular environment. Progress in wide scientific areas (biophysics, genomics, gene editing, etc.) brings in new opportunities to better understand reflectins and new approaches to fully utilize them. The work introduced the composition features, biochemical properties, the latest developments, future considerations of reflectins, and their inspiration applications to give newcomers a comprehensive understanding and mutually exchanged knowledge from different communities (e.g., biology and material).

Genomes of Two Flying Squid Species Provide Novel Sights into Adaptations of Cephalopods to Pelagic Life

Pelagic cephalopods have evolved a series of fascinating traits, such as excellent visual acuity, high-speed agility, and photophores for adaptation to open pelagic oceans. However, the genetic mechanisms underpinning these traits are not well understood. Thus, in this study, we obtained high-quality genomes of two purpleback flying squid species (Sthenoteuthis oualaniensis and Sthenoteuthis sp.), with sizes of 5450 Mb and 5651 Mb, respectively. Comparative genomic analyses revealed that the S-crystallin subfamily SL20-1 associated with visual acuity in the purpleback flying squid lineage was significantly expanded, and the evolution of high-speed agility for the species was accompanied by significant positive selection pressure on genes related to energy metabolism. These molecular signals might have contributed to the evolution of their adaptative predatory and anti-predatory traits. In addition, the transcriptomic analysis provided clear indications of the evolution of the photophores of purpleback flying squids, especially the recruitment of new genes and energy metabolism-related genes which may have played key functional roles in the process.

Color-Tunable Fluorescent Hierarchical Nanoassemblies with Concentration-Encoded Emission

Cephalopods possess a dynamic coloration behavior to change their iridescence due to the concentration-induced optical properties of chromatophores and hierarchical assembly of reflectin. However, cephalopods rarely have iridescence in the darkfield. It would be interesting to develop color-tunable fluorescent hierarchical nanoassemblies with concentration-encoded emission. Herein, to construct the bioavailable fluorophore with dynamic coloration properties, a histidine-rich peptide is designed, which can self-assemble into hierarchical nanoassemblies stabilized by hydrogen bonds and π-π stacking interactions. The peptidyl nanoassemblies emit fluorescent iridescence, encompassing the blue to orange region due to the assembly-induced emission. The fluorescence of histidine-rich peptides is color-tunable and reversible, which can be dynamically controlled in a concentration-encoded mode. Due to the coloration ability of histidine-rich peptides, fluorescent polychromatic human cells are developed, highlighting its potential role as a fluorescent candidate for future applications such as bioimaging, implantable light-emitting diodes, and photochromic camouflage.

Tunable Cellular Localization and Extensive Cytoskeleton-Interplay of Reflectins

Reflectin proteins are natural copolymers consisting of repeated canonical domains. They are located in a biophotonic system called Bragg lamellae and manipulate the dynamic structural coloration of iridocytes. Their biological functions are intriguing, but the underlying mechanism is not fully understood. Reflectin A1, A2, B1, and C were found to present distinguished cyto-/nucleoplasmic localization preferences in the work. Comparable intracellular localization was reproduced by truncated reflectin variants, suggesting a conceivable evolutionary order among reflectin proteins. The size-dependent access of reflectin variants into the nucleus demonstrated a potential model of how reflectins get into Bragg lamellae. Moreover, RfA1 was found to extensively interact with the cytoskeleton, including its binding to actin and enrichment at the microtubule organizing center. This implied that the cytoskeleton system plays a fundamental role during the organization and transportation of reflectin proteins. The findings presented here provide evidence to get an in-depth insight into the evolutionary processes and working mechanisms of reflectins, as well as novel molecular tools to achieve tunable intracellular transportation.

At the Intersection of Natural Structural Coloration and Bioengineering

Most of us get inspired by and interact with the world around us based on visual cues such as the colors and patterns that we see. In nature, coloration takes three primary forms: pigmentary coloration, structural coloration, and bioluminescence. Typically, pigmentary and structural coloration are used by animals and plants for their survival; however, few organisms are able to capture the nearly instantaneous and visually astounding display that cephalopods (e.g., octopi, squid, and cuttlefish) exhibit. Notably, the structural coloration of these cephalopods critically relies on a unique family of proteins known as reflectins. As a result, there is growing interest in characterizing the structure and function of such optically-active proteins (e.g., reflectins) and to leverage these materials across a broad range of disciplines, including bioengineering. In this review, I begin by briefly introducing pigmentary and structural coloration in animals and plants as well as highlighting the extraordinary appearance-changing capabilities of cephalopods. Next, I outline recent advances in the characterization and utilization of reflectins for photonic technologies and and discuss general strategies and limitations for the structural and optical characterization of proteins. Finally, I explore future directions of study for optically-active proteins and their potential applications. Altogether, this review aims to bring together an interdisciplinary group of researchers who can resolve the fundamental questions regarding the structure, function, and self-assembly of optically-active protein-based materials.

Cell-based biocomposite engineering directed by polymers

Biological cells such as bacterial, fungal, and mammalian cells always exploit sophisticated chemistries and exquisite micro- and nano-structures to execute life activities, providing numerous templates for engineering bioactive and biomorphic materials, devices, and systems. To transform biological cells into functional biocomposites, polymer-directed cell surface engineering and intracellular functionalization have been developed over the past two decades. Polymeric materials can be easily adopted by various cells through polymer grafting or in situ hydrogelation and can successfully bridge cells with other functional materials as interfacial layers, thus achieving the manufacture of advanced biocomposites through bioaugmentation of living cells and transformation of cells into templated materials. This review article summarizes the recent progress in the design and construction of cell-based biocomposites by polymer-directed strategies. Furthermore, the applications of cell-based biocomposites in broad fields such as cell research, biomedicine, and bioenergy are discussed. Last, we provide personal perspectives on challenges and future trends in this interdisciplinary area.

Roadmap on Digital Holography-Based Quantitative Phase Imaging

Quantitative Phase Imaging (QPI) provides unique means for the imaging of biological or technical microstructures, merging beneficial features identified with microscopy, interferometry, holography, and numerical computations. This roadmap article reviews several digital holography-based QPI approaches developed by prominent research groups. It also briefly discusses the present and future perspectives of 2D and 3D QPI research based on digital holographic microscopy, holographic tomography, and their applications.

Long-Range Proton Transport in Films from a Reflectin-Derived Polypeptide

Protein- and peptide-based proton conductors have been extensively studied because of their important roles in biological processes and established potential for bioelectronic device applications. However, despite much progress, the demonstration of long-range proton transport for such materials has remained relatively rare. Herein, we fabricate, electrically interrogate, and physically characterize films from a reflectin-derived polypeptide. The electrical measurements indicate that device-integrated films exhibit proton conductivities with values of ∼0.4 mS/cm and sustain proton transport over distances of ∼1 mm. The accompanying physical characterization indicates that the polypeptide possesses characteristics analogous to those of the parent protein class and furnishes insight into the relationship between the polypeptide's electrical functionality and structure in the solid state. When considered together, our findings hold significance for the continued development and engineering of not only reflectin-based materials but also other bioinspired proton conductors.

Toward whole tissue imaging of axolotl regeneration

The axolotl is a highly regenerative organism and has been studied in laboratories for over 150 years. Despite a long‐standing fascination with regeneration in general and axolotl specifically, we are still scratching the surface trying to visualize and understand the complex cellular behavior that underlies axolotl regeneration. In this review, we will discuss the progress that has been made in visualizing these processes focusing on four major aspects: cell labeling approaches, the removal of pigmentation, reductionist approaches to perform live cell imaging, and finally recent developments applying tissue clearing strategies to visualize the processes that underly regeneration. We also provide several suggestions that the community could consider exploring, notably the generation of novel alleles that further reduce pigmentation as well as improvements in tissue clearing strategies.

Historical perspective on axolotl imaging and lineage tracing

Description of tissue clearing approaches

Refractive index matching strategies

Strategies to further reduce pigmentation in axolotl

Structure, self-assembly, and properties of a truncated reflectin variant

Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant's hierarchical assembly, and establish a direct correlation between the protein's structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells' color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.

Phylogenetic comparison of egg transparency in ascidians by hyperspectral imaging

The transparency of animals is an important biological feature. Ascidian eggs have various degrees of transparency, but this characteristic has not yet been measured quantitatively and comprehensively. In this study, we established a method for evaluating the transparency of eggs to first characterize the transparency of ascidian eggs across different species and to infer a phylogenetic relationship among multiple taxa in the class Ascidiacea. We measured the transmittance of 199 eggs from 21 individuals using a hyperspectral camera. The spectrum of the visual range of wavelengths (400–760 nm) varied among individuals and we calculated each average transmittance of the visual range as bio-transparency. When combined with phylogenetic analysis based on the nuclear 18S rRNA and the mitochondrial cytochrome c oxidase subunit I gene sequences, the bio-transparencies of 13 species were derived from four different families: Ascidiidae, Cionidae, Pyuridae, and Styelidae. The bio-transparency varied 10–90% and likely evolved independently in each family. Ascidiella aspersa showed extremely high (88.0 ± 1.6%) bio-transparency in eggs that was maintained in the “invisible” larva. In addition, it was indicated that species of the Ascidiidae family may have a phylogenetic constraint of egg transparency.