Bioluminescence in the ocean: origins of biological, chemical, and ecological diversity

Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation

Abyssal (3501-6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes.

Jellyfish-Inspired Visual and Sensory Bubbling Robots with Automatic 3D Morphable Films for Underwater Environmental Interactions

Coelenterates, such as Atolla jellyfish, are capable of integrating color, communication, and motion in a sophisticated manner, thereby enabling them to function as intelligent biological systems that can adapt to the challenges of the underwater environment. Extensive efforts have been dedicated to exploiting underwater visual, sensory, actuating, or combined systems. However, current biomimetic soft systems are still limited by the lack of comprehensive, integrated functional skins that can automatically deform, dynamically sense, and further send color signals when diving into underwater conditions. Here, we propose the synthetic soft skins composed of assembled entangled carbon nanotube networks and fluorescent unit-embedded elastomers which can be applied in a suspended form to allow autonomic 3D deformation, real-time perception, and dynamic fluorescence color transformation. The capabilities of the sensory and color display thresholds were controlled through the entanglement density of carbon nanotubes and the suspended area. As a demonstration, the soft thin skin was integrated into an artificial jellyfish robot, enabling the realization of a closed-loop feedback system for dynamic sensory processing, signal processing, and further 3D morphing-induced fluorescent color change, demonstrating significant potentials in underwater visual display, danger warning, and environmental exploration.

Correlation between bioluminescent blinks and swimming behavior in the splitfin flashlight fish Anomalops katoptron

BACKGROUND

The light organs of the splitfin flashlight fish Anomalops katoptron are necessary for schooling behavior, to determine nearest neighbor distance, and to feed on zooplankton under dim light conditions. Each behavior is coupled to context-dependent blink frequencies and can be regulated via mechanical occlusion of light organs. During shoaling in the laboratory individuals show moderate blink frequencies around 100 blinks per minute. In this study, we correlated bioluminescent blinks with the spatio-temporal dynamics of swimming profiles in three dimensions, using a stereoscopic, infrared camera system.

RESULTS

Groups of flashlight fish showed intermediate levels of polarization and distances to the group centroid. Individuals showed higher swimming speeds and curved swimming profiles during light organ occlusion. The largest changes in swimming direction occurred when darkening the light organs. Before A. katoptron exposed light organs again, they adapted a nearly straight movement direction.

CONCLUSIONS

We conclude that a change in movement direction coupled to light organ occlusion in A. katoptron is an important behavioral trait in shoaling of flashlight fish.

Glowing wonders: exploring the diversity and ecological significance of bioluminescent organisms in Brazil

Bioluminescence, the emission of light by living organisms, is a captivating and widespread phenomenon with diverse ecological functions. This comprehensive review explores the biodiversity, mechanisms, ecological roles, and conservation challenges of bioluminescent organisms in Brazil, a country known for its vast and diverse ecosystems. From the enchanting glow of fireflies and glow-in-the-dark mushrooms to the mesmerizing displays of marine dinoflagellates and cnidarians, Brazil showcases a remarkable array of bioluminescent species. Understanding the biochemical mechanisms and enzymes involved in bioluminescence enhances our knowledge of their evolutionary adaptations and ecological functions. However, habitat loss, climate change, and photopollution pose significant threats to these bioluminescent organisms. Conservation measures, interdisciplinary collaborations, and responsible lighting practices are crucial for their survival. Future research should focus on identifying endemic species, studying environmental factors influencing bioluminescence, and developing effective conservation strategies. Through interdisciplinary collaborations, advanced technologies, and increased funding, Brazil can unravel the mysteries of its bioluminescent biodiversity, drive scientific advancements, and ensure the long-term preservation of these captivating organisms.

Molecular mechanism for the unusual enhancement of the second-step chemiluminescence production from the carcinogenic tetrabromohydroquinone and H2O2

We have found recently that two-step intrinsic hydroxyl radical (·OH)-dependent chemiluminescence (CL) could be produced by carcinogenic tetrahaloquinone and H2O2. However, the first-step CL was too fast to clearly detect the stepwise generation of ·OH and CL, and to distinguish the exact dividing point between the first-step and second-step CL. Here we found that, extremely clear two-step intrinsic CL could be produced by the relative slow reaction of tetrabromohydroquinone (TBHQ) with H2O2, which was directly dependent on the two-step ·OH generation. Interestingly, the second-step, but not the first-step CL production of TBHQ/H2O2 (CRET donor) was markedly enhanced by fluorescein (a typical xanthene dye, CRET acceptor) through a unique chemiluminescence resonance energy transfer (CRET) process. The novel CRET system of TBHQ/H2O2/fluorescein was successfully applied for the sensitive detection of TBHQ with the detection limit as low as 2.5 µmol/L. These findings will help to develop more sensitive and highly efficient CL or CRET systems and specific CL sensor to detect the carcinogenic haloquinones, which may have broad environmental applications.

Using bioluminescence as a tool for studying diversity in marine zooplankton and dinoflagellates: an initial assessment

Bioluminescence is light chemically produced by an organism. It is widespread across all major marine phyla and has evolved multiple times, resulting in a high diversity of spectral properties and first flash kinetic parameters (FFKP). The bioluminescence of a system is often a good proxy for planktonic biomass. The species-specific parameters of bioluminescent displays can be measured to identify species in situ and describe planktonic biodiversity. Most bioluminescent organisms will flash when mechanically stimulated i.e., when subjected to supra-threshold levels of shear stress. Here we compare first flash kinetic parameters such as flash duration, peak intensity, rise time, decay time, first-flash mechanically stimulated light and e-folding time obtained with the commercially available Underwater Bioluminescence Assessment Tool (UBAT). We provide descriptions of the first flash kinetic parameters of several species of dinoflagellates Pyrocystis fusiformis, Pyrocystis noctiluca, Pyrodinium bahamense, Lingulodinium polyedra, Alexandrium monilatum and two zooplankton (the ctenophore Mnemiopsis leidyi and the larvacean Oikopleura sp.). FFKPs are then compared and discussed using non-parametric analyses of variance (ANOVAs), hierarchical clustering and a linear discriminant analysis to assess the ability to use bioluminescence signatures for identification. Once the first flash kinetic parameters of a bioluminescent species have been described, it is possible to detect its presence using emissions collected by in situ bathyphotometers. Assessing abundance and diversity of bioluminescent species may therefore be possible.

Self-Reporting Microsensors Inspired by Noctiluca Scintillans for Small-Defect Positioning and Electrical-Stress Visualization in Polymers

Small defects induce concentrated electrical stress in dielectric polymers, leading to premature failure of materials. Existing sensing methods fail to effectively visualize these defects owing to the invisible-energy state of the electric field. Thus, it is necessary to establish a nondestructive method for the real-time detection of small defects in dielectric polymers. In this study, a self-reporting microsensor (SRM) inspired by Noctiluca scintillans is designed to endow materials with the ability of self-detection for defects and electrical stress. The SRM leverages the energy of a nearby electric field to emit measurable fluorescence, enabling defect localization and diagnosis as well as electrical-stress visualization. A controllable dielectric microsphere is constructed to achieve an adjustable electroluminescence threshold for the SRM, thereby increasing its detection accuracy while decreasing the electroluminescence threshold. The potential degradation in the polymer performance owing to SRM implantation is addressed by assembling long molecular chains on the SRM surface to spontaneously generate an interpenetrating network. Results of finite element analyses and experiments demonstrate that the SRM can effectively realize nondestructive visualization and positioning of small defects and concentrated electrical stress in polymers, positioning it as a promising sensing method for monitoring the electric field and charge distribution in materials.

The language of light: a review of bioluminescence in deep-sea decapod shrimps

In the dark, expansive habitat of the deep sea, the production of light through bioluminescence is commonly used among a wide range of taxa. In decapod crustaceans, bioluminescence is only known in shrimps (Dendrobranchiata and Caridea) and may occur in different modes, including luminous secretions that are used to deter predators and/or from specialised light organs called photophores that function by providing camouflage against downwelling light. Photophores exhibit an extensive amount of morphological variation across decapod families: they may be internal (of hepatic origin) or embedded in surface tissues (dermal), and may possess an external lens, suggesting independent origins and multiple functions. Within Dendrobranchiata, we report bioluminescence in Sergestidae, Aristeidae, and Solenoceridae, and speculate that it may also be found in Acetidae, Luciferidae, Sicyonellidae, Benthesicymidae, and Penaeidae. Within Caridea, we report bioluminescence in Acanthephyridae, Oplophoridae, Pandalidae, and new observations for Pasiphaeidae. This comprehensive review includes historic taxonomic literature and recent studies investigating bioluminescence in all midwater and deep benthic shrimp families. Overall, we report known or suspected bioluminescence in 157 species across 12 families of decapod shrimps, increasing previous records of bioluminescent species by 65%. Mounting evidence from personal observations and the literature allow us to speculate the presence of light organs in several families thought to lack bioluminescence, making this phenomenon much more common than previously reported. We provide a detailed discussion of light organ morphology and function within each group and indicate future directions that will contribute to a better understanding of how deep-sea decapods use the language of light.

Evolution of bioluminescence in Anthozoa with emphasis on Octocorallia

Bioluminescence is a widespread phenomenon that has evolved multiple times across the tree of life, converging among diverse fauna and habitat types. The ubiquity of bioluminescence, particularly in marine environments where it is commonly used for communication and defense, highlights the adaptive value of this trait, though the evolutionary origins and timing of emergence remain elusive for a majority of luminous organisms. Anthozoan cnidarians are a diverse group of animals with numerous bioluminescent species found throughout the world's oceans, from shallow waters to the light-limited deep sea where bioluminescence is particularly prominent. This study documents the presence of bioluminescent Anthozoa across depth and explores the diversity and evolutionary origins of bioluminescence among Octocorallia-a major anthozoan group of marine luminous organisms. Using a phylogenomic approach and ancestral state reconstruction, we provide evidence for a single origin of bioluminescence in Octocorallia and infer the age of occurrence to around the Cambrian era, approximately 540 Ma-setting a new record for the earliest timing of emergence of bioluminescence in the marine environment. Our results further suggest this trait was largely maintained in descendants of a deep-water ancestor and bioluminescent capabilities may have facilitated anthozoan diversification in the deep sea.

Systematic Distribution of Bioluminescence in Marine Animals: A Species-Level Inventory

Bioluminescence is the production of visible light by an organism. This phenomenon is particularly widespread in marine animals, especially in the deep sea. While the luminescent status of numerous marine animals has been recently clarified thanks to advancements in deep-sea exploration technologies and phylogenetics, that of others has become more obscure due to dramatic changes in systematics (themselves triggered by molecular phylogenies). Here, we combined a comprehensive literature review with unpublished data to establish a catalogue of marine luminescent animals. Inventoried animals were identified to species level in over 97% of the cases and were associated with a score reflecting the robustness of their luminescence record. While luminescence capability has been established in 695 genera of marine animals, luminescence reports from 99 additional genera need further confirmation. Altogether, these luminescent and potentially luminescent genera encompass 9405 species, of which 2781 are luminescent, 136 are potentially luminescent (e.g., suggested luminescence in those species needs further confirmation), 99 are non-luminescent, and 6389 have an unknown luminescent status. Comparative analyses reveal new insights into the occurrence of luminescence among marine animal groups and highlight promising research areas. This work will provide a solid foundation for future studies related to the field of marine bioluminescence.

A brittle star is born: Ontogeny of luminous capabilities in Amphiura filiformis

Bioluminescence is the production of visible light by living organisms thanks to a chemical reaction, implying the oxidation of a substrate called luciferin catalyzed by an enzyme, the luciferase. The luminous brittle star Amphiura filiformis depends on coelenterazine (i.e., the most widespread luciferin in marine ecosystems) and a luciferase homologous to the cnidarian Renilla luciferase to produce blue flashes in the arm's spine. Only a few studies have focused on the ontogenic apparitions of bioluminescence in marine organisms. Like most ophiuroids, A. filiformis displays planktonic ophiopluteus larvae for which the ability to produce light was not investigated. This study aims to document the apparition of the luminous capabilities of this species during its ontogenic development, from the egg to settlement. Through biochemical assays, pharmacological stimulation, and Renilla-like luciferase immunohistological detection across different developing stages, we pointed out the emergence of the luminous capabilities after the ophiopluteus larval metamorphosis into a juvenile. In conclusion, we demonstrated that the larval pelagic stage of A. filiformis is not bioluminescent compared to juveniles and adults.

Fluorescent Tools for the Imaging of Dopamine D2 -Like Receptors

The family of dopamine D2 -like receptors represents an interesting target for a variety of neurological diseases, e. g. Parkinson's disease (PD), addiction, or schizophrenia. In this study we describe the synthesis of a new set of fluorescent ligands as tools for visualization of dopamine D2 -like receptors. Pharmacological characterization in radioligand binding studies identified UR-MN212 (20) as a high-affinity ligand for D2 -like receptors (pKi (D2long R)=8.24, pKi (D3 R)=8.58, pKi (D4 R)=7.78) with decent selectivity towards D1 -like receptors. Compound 20 is a neutral antagonist in a Go1 activation assay at the D2long R, D3 R, and D4 R, which is an important feature for studies using whole cells. The neutral antagonist 20, equipped with a 5-TAMRA dye, displayed rapid association to the D2long R in binding studies using confocal microscopy demonstrating its suitability for fluorescence microscopy. Furthermore, in molecular brightness studies, the ligand's binding affinity could be determined in a single-digit nanomolar range that was in good agreement with radioligand binding data. Therefore, the fluorescent compound can be used for quantitative characterization of native D2 -like receptors in a broad variety of experimental setups.

Shedding Light on the D1 -Like Receptors: A Fluorescence-Based Toolbox for Visualization of the D1 and D5 Receptors

Dopamine D1 -like receptors are the most abundant type of dopamine receptors in the central nervous system and, even after decades of discovery, still highly interesting for the study of neurological diseases. We herein describe the synthesis of a new set of fluorescent ligands, structurally derived from D1 R antagonist SCH-23390 and labeled with two different fluorescent dyes, as tool compounds for the visualization of D1 -like receptors. Pharmacological characterization in radioligand binding studies identified UR-NR435 (25) as a high-affinity ligand for D1 -like receptors (pKi (D1 R)=8.34, pKi (D5 R)=7.62) with excellent selectivity towards D2 -like receptors. Compound 25 proved to be a neutral antagonist at the D1 R and D5 R in a Gs heterotrimer dissociation assay, an important feature to avoid receptor internalization and degradation when working with whole cells. The neutral antagonist 25 displayed rapid association and complete dissociation to the D1 R in kinetic binding studies using confocal microscopy verifying its applicability for fluorescence microscopy. Moreover, molecular brightness studies determined a single-digit nanomolar binding affinity of the ligand, which was in good agreement with radioligand binding data. For this reason, this fluorescent ligand is a useful tool for a sophisticated characterization of native D1 receptors in a variety of experimental setups.

Internal Light Sources-Mediated Photodynamic Therapy Nanoplatforms: Hope for the Resolution of the Traditional Penetration Problem

Photodynamic therapy (PDT) is an alternative cancer treatment technique with a noninvasive nature, high selectivity, and minimal adverse effects. The indispensable light source used in PDT is a critical factor in determining the energy conversion of photosensitizers (PSs). Traditional light sources are primarily concentrated in the visible light region, severely limiting their penetration depth and making them prone to scattering and absorption when applied to biological tissues. For that reason, its efficacy in treating deep-seated lesions is often inadequate. Self-exciting PDT, also known as auto-PDT (APDT), is an attractive option for circumventing the limited penetration depth of traditional PDT and has acquired significant attention. APDT employs depth-independent internal light sources to excite PSs through resonance or radiative energy transfer. APDT has considerable potential for treating deep-tissue malignancies. To facilitate many researchers' comprehension of the latest research progress in this field and inspire the emergence of more novel research results. This review introduces internal light generation mechanisms and characteristics and provides an overview of current research progress based on the recently reported APDT nanoplatforms. The current challenges and possible solutions of APDT nanoplatforms are also presented and provide insights for future research in the final section of this article.

All Light, Everywhere? Photoreceptors at Nonconventional Sites

One of the biggest environmental alterations we have made to our species is the change in the exposure to light. During the day, we typically sit behind glass windows illuminated by artificial light that is >400 times dimmer and has a very different spectrum than natural daylight. On the opposite end are the nights that are now lit up by several orders of magnitude. This review aims to provide food for thought as to why this matters for humans and other animals. Evidence from behavioral neuroscience, physiology, chronobiology, and molecular biology is increasingly converging on the conclusions that the biological nonvisual functions of light and photosensory molecules are highly complex. The initial work of von Frisch on extraocular photoreceptors in fish, the identification of rhodopsins as the molecular light receptors in animal eyes and eye-like structures and cryptochromes as light sensors in nonmammalian chronobiology, still allowed for the impression that light reception would be a relatively restricted, localized sense in most animals. However, light-sensitive processes and/or sensory proteins have now been localized to many different cell types and tissues. It might be necessary to consider nonlight-responding cells as the exception, rather than the rule.

Chemical Mechanism of Fireworm Bioluminescence - A Theoretical Proposition

Odontosyllis undecimdonta is a marine worm, commonly known as a fireworm, that exhibits bluish-green bioluminescence (BL). The luciferin (L) and oxyluciferin (OL) during fireworm BL have been experimentally identified in vitro. The L and OL are the respective starting point and ending point of a series of complicated chemical reactions in the BL. However, the chemical mechanism of the fireworm BL remains largely unknown. Before the experiments provided strong evidence for the mechanism, based on our previously successful studies on several bioluminescent systems, we theoretically proposed the chemical mechanism of the fireworm BL in this article. By means of the spin-flip and time-dependent density functional calculations, we clearly described the complete process from L to OL: under the catalysis of luciferase, L undergoes deprotonation and reacts with 3O2 to form a dioxetanone anion via the single-electron transfer mechanism; the dioxetanone anion decomposes into the OL at the first singlet excited state (S1) by the gradually reversible charge-transfer-induced luminescence mechanism; and the S1-OL emits light and deexcites to OL in the ground state.

Collective synchrony of mating signals modulated by ecological cues and social signals in bioluminescent sea fireflies

Individuals often employ simple rules that can emergently synchronize behaviour. Some collective behaviours are intuitively beneficial, but others like mate signalling in leks occur across taxa despite theoretical individual costs. Whether disparate instances of synchronous signalling are similarly organized is unknown, largely due to challenges observing many individuals simultaneously. Recording field collectives and ex situ playback experiments, we describe principles of synchronous bioluminescent signals produced by marine ostracods (Crustacea; Luxorina) that seem behaviorally convergent with terrestrial fireflies, and with whom they last shared a common ancestor over 500 Mya. Like synchronous fireflies, groups of signalling males use visual cues (intensity and duration of light) to decide when to signal. Individual ostracods also modulate their signal based on the distance to nearest neighbours. During peak darkness, luminescent 'waves' of synchronous displays emerge and ripple across the sea floor approximately every 60 s, but such periodicity decays within and between nights after the full moon. Our data reveal these bioluminescent aggregations are sensitive to both ecological and social light sources. Because the function of collective signals is difficult to dissect, evolutionary convergence, like in the synchronous visual displays of diverse arthropods, provides natural replicates to understand the generalities that produce emergent group behaviour.

Enhancing luciferase activity and stability through generative modeling of natural enzyme sequences

The availability of natural protein sequences synergized with generative AI provides new paradigms to engineer enzymes. Although active enzyme variants with numerous mutations have been designed using generative models, their performance often falls short of their wild type counterparts. Additionally, in practical applications, choosing fewer mutations that can rival the efficacy of extensive sequence alterations is usually more advantageous. Pinpointing beneficial single mutations continues to be a formidable task. In this study, using the generative maximum entropy model to analyze Renilla luciferase (RLuc) homologs, and in conjunction with biochemistry experiments, we demonstrated that natural evolutionary information could be used to predictively improve enzyme activity and stability by engineering the active center and protein scaffold, respectively. The success rate to improve either luciferase activity or stability of designed single mutants is ~50%. This finding highlights nature's ingenious approach to evolving proficient enzymes, wherein diverse evolutionary pressures are preferentially applied to distinct regions of the enzyme, ultimately culminating in an overall high performance. We also reveal an evolutionary preference in RLuc toward emitting blue light that holds advantages in terms of water penetration compared to other light spectra. Taken together, our approach facilitates navigation through enzyme sequence space and offers effective strategies for computer-aided rational enzyme engineering.

Cavity-Modified Chemiluminescent Reaction of Dioxetane

Chemiluminescence is a thermally activated chemical process that emits a photon of light by forming a fraction of products in the electronic excited state. A well-known example of this spectacular phenomenon is the emission of light in the firefly beetle, where the formation of a four-membered cyclic peroxide compound and subsequent dissociation produce a light-emitting product. The smallest cyclic peroxide, dioxetane, also exhibits chemiluminescence but with a low quantum yield as compared to that of firefly dioxetane. Employing the strong light-matter coupling has recently been found to be an alternative strategy to modify the chemical reactivity. In the presence of an optical cavity, the molecular degrees of freedom greatly mix with the cavity mode to form hybrid cavity-matter states called polaritons. These newly generated hybrid light-matter states manipulate the potential energy surfaces and significantly change the reaction dynamics. Here, we theoretically investigate the effects of a strong light-matter interaction on the chemiluminescent reaction of dioxetane using the extended Jaynes-Cummings model. The cavity couplings corresponding to the electronic and vibrational degrees of freedom have been included in the interaction Hamiltonian. We explore how the cavity alters the ground- and excited-state path energy barriers and reaction rates. Our results demonstrate that the formation of excited-state products in the dioxetane decomposition process can be either accelerated or suppressed, depending on the molecular orientation with respect to the cavity polarization.

Illuminating the oral microbiome and its host interactions: tools and approaches for molecular microbiology studies

Advancements in DNA sequencing technologies within the last decade have stimulated an unprecedented interest in the human microbiome, largely due the broad diversity of human diseases found to correlate with microbiome dysbiosis. As a direct consequence of these studies, a vast number of understudied and uncharacterized microbes have been identified as potential drivers of mucosal health and disease. The looming challenge in the field is to transition these observations into defined molecular mechanistic studies of symbiosis and dysbiosis. In order to meet this challenge, many of these newly identified microbes will need to be adapted for use in experimental models. Consequently, this review presents a comprehensive overview of the molecular microbiology tools and techniques that have played crucial roles in genetic studies of the bacteria found within the human oral microbiota. Here, we will use specific examples from the oral microbiome literature to illustrate the biology supporting these techniques, why they are needed in the field, and how such technologies have been implemented. It is hoped that this information can serve as a useful reference guide to help catalyze molecular microbiology studies of the many new understudied and uncharacterized species identified at different mucosal sites in the body.

Enhancing Luciferase Activity and Stability through Generative Modeling of Natural Enzyme Sequences

The availability of natural protein sequences synergized with generative artificial intelligence (AI) provides new paradigms to create enzymes. Although active enzyme variants with numerous mutations have been produced using generative models, their performance often falls short compared to their wild-type counterparts. Additionally, in practical applications, choosing fewer mutations that can rival the efficacy of extensive sequence alterations is usually more advantageous. Pinpointing beneficial single mutations continues to be a formidable task. In this study, using the generative maximum entropy model to analyze Renilla luciferase homologs, and in conjunction with biochemistry experiments, we demonstrated that natural evolutionary information could be used to predictively improve enzyme activity and stability by engineering the active center and protein scaffold, respectively. The success rate of designed single mutants is ~50% to improve either luciferase activity or stability. These finding highlights nature's ingenious approach to evolving proficient enzymes, wherein diverse evolutionary pressures are preferentially applied to distinct regions of the enzyme, ultimately culminating in an overall high performance. We also reveal an evolutionary preference in Renilla luciferase towards emitting blue light that holds advantages in terms of water penetration compared to other light spectrum. Taken together, our approach facilitates navigation through enzyme sequence space and offers effective strategies for computer-aided rational enzyme engineering.

Bioinspired simultaneous regulation in fluorescence of AIEgen-embedded hydrogels

The development of stimuli-responsive functional fluorescent hydrogels is of great significance for the realization of artificial intelligence. In the present work, we design and synthesize a stimulus-responsive hydrogel embedded with an aggregation-induced emission (AIE) monomer, in which the fluorescence brightness and intensity can be tuned. The hydrogel embedded with tetraphenylethene-grafted-poly[3-sulfopropyl methacrylate potassium salt] (TPE-PSPMA) as the functional element is prepared by the radical polymerization method. Among them, the TPE core exhibits adaptive fluorescence ability through the AIE effect, while the PSPMA chain provides tunable hydrophilic properties under an external stimulus. The effect of different cationic surfactants with different lengths of hydrophobic tails on the fluorescence properties of TPE-PSPMA in solution is systematically investigated. With cationic surfactants, such as cetyltrimethylammonium bromide (CTAB), the fluorescence intensity is gradually tuned from 1059 to 4623. And the fluorescence intensities increase with the growth of hydrophobic tails of surfactants, which results from hydrophobicity-induced electrostatic interactions among surfactants and polymer chains. Furthermore, an obvious tunable fluorescence feature of hydrogel copolymerized TPE-PSPMA is realized, resulting from the change of brightness and the dynamic increase of fluorescence intensity (from 1031 to 3138) for the hydrogel immersed in CTAB solution with different soaking times. Such a typical fluorescence-regulated behavior can be attributed to the AIE of the TPE-PSPMA chain and the electrostatic interaction between the surfactant and the anionic polymer chain. The designed TPE-PSPMA-based hydrogel is responsive to stimuli, inspiring the development of intelligent systems such as soft robots and smart wearables.

Putative photosensitivity in internal light organs (organs of Pesta) of deep-sea sergestid shrimps

Many marine species can regulate the intensity of bioluminescence from their ventral photophores in order to counterilluminate, a camouflage technique whereby animals closely match the intensity of the downwelling illumination blocked by their bodies, thereby hiding their silhouettes. Recent studies on autogenic cuticular photophores in deep-sea shrimps indicate that the photophores themselves are light sensitive. Here, our results suggest photosensitivity in a second type of autogenic photophore, the internal organs of Pesta, found in deep-sea sergestid shrimps. Experiments were conducted onboard ship on live specimens, exposing the animals to bright light, which resulted in ultrastructural changes that matched those seen in crustacean eyes during the photoreceptor membrane turnover, a process that is crucial for the proper functioning of photosensitive components. In addition, RNA-seq studies demonstrated the expression of visual opsins and phototransduction genes in photophore tissue that are known to play a role in light detection, and electrophysiological measurements indicated that the light organs are responding to light received by the eyes. The long sought after mechanism of counterillumination remains unknown, but evidence of photosensitivity in photophores may indicate a dual functionality of light detection and emission.

Development of light-emitting Episcia lilacina leaf by applying Vibrio campbellii RMT1 and extending the glowing by CaCl2 and yeast extract

Glowing Episcia lilacina was generated through foliar application of the bioluminescent bacterium Vibrio campbellii RMT1. Firstly, different nutrient formulas were tested, incorporating yeast extract and various inorganic salts, such as CaCl₂, MgCl₂, MgSO₄, KH₂PO₄, K₂HPO₄, and NaCl, in order to enhance bacterial growth and light emission. The combination of 0.15% of yeast extract and 0.3% of CaCl₂ in a nutrient broth (NB) + 1% NaCl medium extended light emission to 24 h and resulted in higher light intensity compared to other combinations of yeast extract and inorganic salts. The peak intensity reached approximately 1.26 × 10⁸ relative light units (RLU) at 7 h. The optimal presence of inorganic salt ions likely contributed to enhanced light emission, while the yeast extract acted as a nutrient source. Secondly, the effect of proline on salt-induced stress symptoms was investigated by applying 20 mM proline to the glowing plant. Additionally, a 0.5% agar nutrient was spread on the leaves prior to bacteria application to support bacterial growth and penetration. Exogenous proline application led to a significant accumulation of proline in plant cells, resulting in decreased malondialdehyde (MDA) levels. However, the proline accumulation also reduced the light intensity of the bioluminescent bacteria. This study demonstrates the potential for generating light on a living plant using bioluminescent bacteria. Further understanding of the interaction between plants and light-emitting bacteria could contribute to the development of sustainably light-emitting plants.

Ionic Microgel Colloidal Crystals: Responsive Chromism in Dual Physical and Chemical Colors for High-End Information Security and Encryption

Chromic materials play a decisive and escalating role in information security. However, it is challenging to develop chromic materials for encryption technologies that can hardly be imitated. Inspired by versatile metachrosis in nature, a series of coumarin-based 7-(6-bromohexyloxy)-coumarin microgel colloidal crystals (BrHC MGCC) with multiresponsive chromism are able to be assembled by ionic microgels in poly(vinyl alcohol) (PVA) solution followed by two cycles of freezing-thawing. The ionic microgels can be finely tailored by in situ quaternization with tunable size under varied temperatures and hydration energies of counterions as well as quenched luminescence under UV irradiation, which endows BrHC MGCC with intriguing chromism in the dual-channel coloration of physical structural color and chemical fluorescent color. Three types of BrHC MGCC exhibit various change ranges in structural coloration and similar quenching in fluorescence emission, which can be utilized for the development of the static-dynamic combined anticounterfeiting system with dual coloration. The information conveyed by the BrHC MGCC array presents dynamic variation versus temperature, while the static information can be only integrally read in both sunlight and a 365 nm UV lamp. The fabrication of a microgel colloidal crystal with dual coloration opens a facile and ecofriendly window for multilevel information security, camouflage, and a cumbersome authentication process.

Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods

Although the diversity, beauty, and intricacy of sexually selected courtship displays command the attention of evolutionists, the longevity of these traits in deep time is poorly understood. Population-based theory suggests sexual selection could either lower or raise extinction risk, resulting in high or low persistence of lineages with sexually selected traits. Furthermore, empirical studies that directly estimate the longevity of sexually selected traits are uncommon. Sexually selected signals-including bioluminescent courtship-originated multiple times during evolution, allowing the empirical study of their longevity after careful phylogenetic and divergence time analyses. Here, we estimate the first transcriptome-based molecular phylogeny and divergence times of Cypridinidae. We report extreme longevity of bioluminescent courtship, a trait important in mate choice and probably under sexual selection. Our relaxed-clock estimates of divergence times coupled with stochastic character mapping show luminous courtship evolved only once in Cypridinidae-in a Sub-Tribe, we name Luxorina-at least 151 millions of years ago from cypridinid ancestors that used bioluminescence only in antipredator displays, defining a Tribe we name Luminini. This time-calibrated molecular phylogeny of cypridinids will serve as a foundation for integrative and comparative studies on the biochemistry, molecular evolution, courtship, diversification, and ecology of cypridinid bioluminescence. The persistence of luminous courtship for hundreds of millions of years suggests that sexual selection did not cause a rapid loss of associated traits, and that rates of speciation within the group exceeded extinction risk, which may contribute to the persistence of a diverse clade of signaling species. [Ancestral state reconstruction; Biodiversity; co-option; divergence time estimates; macroevolution; Ostracoda; phylogenomics; sexual selection.].

Light-controlled artificial transmembrane signal transduction for 'ON/OFF'-switchable transphosphorylation of an RNA model substrate

Inspired by nature, it is of significant importance to design and construct biomimetic signaling systems to mimic natural signal transduction. Herein, we report an azobenzene/α-cyclodextrin (α-CD)-based signal transduction system with three functional modules: a light-responsive headgroup, lipid-anchored group, pro-catalyst tailgroup. The transducer can be inserted into the vesicular membrane to trigger the transmembrane translocation of molecules under the activation of light, forming a ribonuclease-like effector site and leading to the transphosphorylation of the RNA model substrate inside the vesicles. Moreover, the transphosphorylation process can be reversibly turned 'ON/OFF' over multiple cycles by the activation and deactivation of the pro-catalyst. This artificial photo-controlled signal transduction successfully constructs a signal responsive catalysis system across the membrane to utilize light to reversibly control the internal transphosphorylation process of an RNA model substrate, which might provide a new strategy for future design to utilize exogenous signals for implementing endogenous enzyme manipulation and gene regulation.

Heat-Resistant and Color-Changing Luminescent Polysulfone for Information Encryption and Fire Alarming

An intrinsic difficulty with thermally responsive photoluminescent materials is that high temperatures usually destroy luminance due to the notorious thermal quenching effect. Limited by the vulnerable chemical structure and soft skeleton, most of the existing photoluminescent responsive materials fail to indicate or work at a surging temperature over 100 °C, thus limiting application in display and alarming in harsh conditions. Herein, enlightened by chameleon's adaptive nature to external stimulus, we introduce a topologically optimized electron donor-acceptor (DA) structure and supramolecular interactions of lanthanide ions into the polymer backbone. The emission color determined by the DA structure is stable at high temperatures, and metal-ligand interaction phosphorescence is temperature-adjustable. Owing to the excellent reproducibility and heat resistance of composite films, the sensors can be bent into different three-dimensional structures and adhered to metal surfaces as flexible thermometers with superior display resolution. The polymer composite film could be directly applied as a photoluminescent quick response (QR) code, with patterns simultaneously variable to a temperature from 30 to 150 °C free of manual operation. More importantly, the polymeric composite could be in-situ-oxidized to a "sulfone" structure with an enhanced glass transition temperature of 297-304 °C. The heat- and flame-resistant characteristics of the oxidized films give rise to the application of fire alarming devices since it can locate the fire source and respond exactly depending on the distance from the fire. The unique display, encryption, and alarming functions of the polymeric composite studied in this work bring forward a new concept of developing a great information security and disaster monitoring system with the application of temperature-responsive materials.

Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla periphylla

The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. The mesopelagic jellyfish Periphylla periphylla is a well-known and widely distributed species in the mesopelagic zone; however, the diversity or the pharmaceutical potential of its cultivable microbiota has not been explored. In this study, we isolated microorganisms associated with the inner and outer umbrella of P. periphylla collected in Irminger Sea by a culture-dependent approach, and profiled their chemical composition and biological activities. Sixteen mostly gram-negative bacterial isolates were selected and subjected to an OSMAC cultivation regime approach using liquid and solid marine broth (MB) and glucose-yeast-malt (GYM) media. Their ethyl acetate (EtOAc) extracts were assessed for cytotoxicity and antimicrobial activity against fish and human pathogens. All, except one extract, displayed diverse levels of antimicrobial activities. Based on low IC₅₀ values, four most bioactive gram-negative strains; Polaribacter sp. SU124, Shewanella sp. SU126, Psychrobacter sp. SU143 and Psychrobacter sp. SU137, were prioritized for an in-depth comparative and untargeted metabolomics analysis using feature-based molecular networking. Various chemical classes such as diketopiperazines, polyhydroxybutyrates (PHBs), bile acids and other lipids were putatively annotated, highlighting the biotechnological potential in P. periphylla-associated microbiota as well as gram-negative bacteria. This is the first study providing an insight into the cultivable bacterial community associated with the mesopelagic jellyfish P. periphylla and, indeed, the first to mine the metabolome and antimicrobial activities of these microorganisms.

Exploring the Structural Space of Chemiluminescent 1,2-Dioxetanes

Chemiluminescent molecules which emit light in response to a chemical reaction are powerful tools for the detection and measurement of biological analytes and enable the understanding of complex biochemical processes in living systems. Triggerable chemiluminescent 1,2-dioxetanes have been studied and tuned over the past decades to advance quantitative measurement of biological analytes and molecular imaging in live cells and animals. A crucial determinant of success for these 1,2-dioxetane based sensors is their chemical structure, which can be manipulated to achieve desired chemical properties. In this Perspective, we survey the structural space of triggerable 1,2-dioxetane and assess how their design features affect chemiluminescence properties including quantum yield, emission wavelength, and decomposition kinetics. Based on this appraisal, we identify some structural modifications of 1,2-dioxetanes that are ripe for exploration in the context of chemiluminescent biological sensors.

The application and trend of ultra-weak photon emission in biology and medicine

Ultra-weak bioluminescence, also known as ultra-weak photon emission (UPE), is one of the functional characteristics of biological organisms, characterized by specialized, low-energy level luminescence. Researchers have extensively studied UPE for decades, and the mechanisms by which UPE is generated and its properties have been extensively investigated. However, there has been a gradual shift in research focus on UPE in recent years toward exploring its application value. To better understand the application and trend of UPE in biology and medicine, we have conducted a review of relevant articles in recent years. Among the several topics covered in this review is UPE research in biology and medicine (including traditional Chinese medicine), primarily focused on UPE as a promising non-invasive tool for diagnosis and oxidative metabolism monitoring as well as a potential tool for traditional Chinese medicine research.

Biophysical analysis of Gaussia Luciferase bioluminescence mechanisms using a non-oxidizable coelenterazine

Gaussia luciferase (GLuc 18.2kDa; 168 residues) is a marine copepod luciferase that emits a bright blue light when oxidizing coelenterazine (CTZ). It is a helical protein where two homologous sequential repeats form two anti-parallel bundles, each made of four helices. We previously identified a hydrophobic cavity as a prime candidate for the catalytic site, but GLuc's fast bioluminescence reaction hampered a detailed analysis. Here, we used azacoelenterazine (Aza-CTZ), a non-oxidizable coelenterazine (CTZ) analog, as a probe to investigate its binding mode to GLuc. While analysing GLuc's activity, we unexpectedly found that salt and monovalent anions are absolutely required for Gluc's bioluminescence, which retrospectively appears reasonable for a sea-dwelling organism. The NMR-based investigation, using chemical shift perturbations monitored by ¹⁵N-¹H HSQC, suggested that Aza-CTZ (and thus unoxidized CTZ) binds to residues in or near the hydrophobic cavity. These NMR data are in line with a recent structural prediction of GLuc, hypothesizing that large structural changes occur in regions remote from the hydrophobic cavity upon the addition of CTZ. Interestingly, these results point toward a unique mode of catalysis to achieve CTZ oxidative decarboxylation.

New insight into the application of fluorescence platforms in tumor diagnosis: From chemical basis to clinical application

Early and rapid diagnosis of tumors is essential for clinical treatment or management. In contrast to conventional means, bioimaging has the potential to accurately locate and diagnose tumors at an early stage. Fluorescent probe has been developed as an ideal tool to visualize tumor sites and to detect biological molecules which provides a requirement for noninvasive, real-time, precise, and specific visualization of structures and complex biochemical processes in vivo. Rencently, the development of synthetic organic chemistry and new materials have facilitated the development of near-infrared small molecular sensing platforms and nanoimaging platforms. This provides a competitive tool for various fields of bioimaging such as biological structure and function imaging, disease diagnosis, in situ at the in vivo level, and real-time dynamic imaging. This review systematically focused on the recent progress of small molecular near-infrared fluorescent probes and nano-fluorescent probes as new biomedical imaging tools in the past 3-5 years, and it covers the application of tumor biomarker sensing, tumor microenvironment imaging, and tumor vascular imaging, intraoperative guidance and as an integrated platform for diagnosis, aiming to provide guidance for researchers to design and develop future biomedical diagnostic tools.

Delicate and Independent Manipulation of Dynamic Fluorescence Behavior of Polymer Nanoparticles Based on a Core-Shell Strategy

Fluorescent polymer nanomaterials with dynamic fluorescence properties hold great potential in many advanced applications, including but not limited to information encryption, adaptive camouflage, and biosensors. The key to improving the application value of materials is to establish an accurate control strategy for dynamic fluorescence behavior. Herein, we develop a core-shell engineering strategy to precisely and independently manipulate the dynamic fluorescence behavior through the shell polymeric matrix. The core-shell fluorescent polymer nanoparticles (CS-FPNPs) are constructed through a sequential process of miniemulsion polymerization and seeded emulsion polymerization. Taking advantage of the core-shell structure, the rigid core matrix ensures the strong initial emission of AIE units, while the photoisomerization behavior of spiropyrane (SP) units is delicately and independently regulated by the rigidness of the shell matrix. Thereby, CS-FPNPs exhibit bright time-dependent reversible dynamic fluorescence behavior under alternating UV/vis irradiation. Benefited from the excellent processability and film formation ability, we have successfully applied CS-FPNPs to dynamic decorative painting, warning labels, and dynamic QR code security. Impressively, the fluorescence manipulation strategy based on core-shell engineering allows the independent regulation of specific luminescent units in complicated emission systems to accurately embody designed emission behavior.

Mimicking Color-Changing Organisms to Enable the Multicolors and Multifunctions of Smart Fluorescent Polymeric Hydrogels

Fluorescent polymer hydrogels (FPHs) are of significant interest for diverse emerging applications such as visualized sensing, smart display, camouflaging skins, soft actuators/robots, because they can synergize the features of classic fluorescent polymers and hydrogels. With great efforts in the past decades, the major challenge in this field has been believed to be not whether a given FPH of interest can be prepared but how to fabricate robust FPHs with multicolor tunability and multifunctional synergy. Such materials will conceptually minimize the contribution of passive materials to the mass and size of the final system, holding great potential to facilitate multiple applications. To this end, one promising way is to learn from the Nature that has superb capability to forge delicate or sometimes beyond-imagination materials. Chameleons and cephalopods serve as typical examples, which are famous for not only diverse skin color adaptability under changing environmental demands, but also synergistic skin color and body gesture changes to communicate, warn, camouflage, etc. Biological studies revealed their structural color-changing capacity derives from different types of skin chromatophores and their rational multilayer arrangement in under-skin tissues. Besides, their superb ability to heterogeneously integrate soft tissues with disparate functions into topology-optimized architectures has led to various multifunctional performances. Such natural strategies, if replicated and implemented in artificial systems, would significantly benefit and advance the development of robust FPHs for various applications.In this Account, we summarizes the key advances of smart FPHs mainly achieved by our groups. We start by introducing the unique hierarchical multilayer structures of skin chromatophores in structural color-changing reptiles, followed by an in-depth discussion on how a rational integration of bioinspiration and man-made design makes it possible to largely expand the fluorescence color-changing range of smart FPHs to almost cover the whole visible spectrum. Then, to closely mimic the multifunctional behaviors of chameleons and cephalopods, we further develop efficient strategies to introduce supramolecular interactions or heterogeneously integrating smart FPHs with other soft materials with disparate functions, producing a number of multifunctional fluorescent polymeric hydrogel systems. These robust FPHs can find many frontier applications, including bioinspired synergistic color/shape switchable hydrogel actuators/robots, smart systems with on-demand fluorescent patterning capacities for displaying or information encryption, as well as robust chemosensors for important food or environmental analytes. We expect that the discussion presented in this Account would promote better understanding of the discoloration systems in nature, and advance the development of bioinspired color-changing materials.

Preparation of the luciferase-labeled antibody for improving the detection sensitivity of viral antigen

Background

Viral antigen detection test is the most common method used to detect viruses in the field rapidly. However, due to the low sensitivity, it can only be used as an auxiliary diagnosis method for virus infection. Improving sensitivity is crucial for developing more accurate viral antigen tests. Nano luciferase (Nluc) is a sensitive reporter that has not been used in virus detection.

Results

In this study, we produced an intracellularly Nluc labeled detection antibody (Nluc-ch2C5) and evaluated its ability to improve the detection sensitivity of respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens. Compared with the traditional horse-radish peroxidase (HRP) labeled antibody (HRP-ch2C5), Nluc-ch2C5 was 41 times more sensitive for inactivated SARS-CoV-2 virus by sandwich chemiluminescence ELISA. Then we applied Nluc-ch2C5 to establish an automatic magnet chemiluminescence immune assay (AMCA) for the SARS-CoV-2 viral spike protein, the limit of detection was 68 pfu/reaction. The clinical sensitivity and specificity reached 75% (24/32) and 100% (48/48) using 32 PCR-positive and 48 PCR-negative swab samples for clinical evaluation, which is more sensitive than the commercial ELSA kit and colloid gold strip kit.

Conclusions

Here, monoclonal antibody ch2C5 served as a model antibody and the SARS-CoV-2 served as a model pathogen. The Nluc labeled detecting antibody (Nluc-ch2C5) significantly improved the detection sensitivity of SARS-CoV-2 antigen. This labeling principle applies to other viral infections, so this labeling and test format could be expected to play an important role in detecting other virus antigens.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01855-6.

Beetle bioluminescence outshines extant aerial predators

We understand very little about the timing and origins of bioluminescence, particularly as a predator avoidance strategy. Understanding the timing of its origins, however, can help elucidate the evolution of this ecologically important signal. Using fireflies, a prevalent bioluminescent group where bioluminescence primarily functions as aposematic and sexual signals, we explore the origins of this signal in the context of their potential predators. Divergence time estimations were performed using genomic-scale datasets providing a robust estimate for the origin of firefly bioluminescence as both a terrestrial and as an aerial signal. Our results recover the origin of terrestrial beetle bioluminescence at 141.17 (122.63-161.17) Ma and firefly aerial bioluminescence at 133.18 (117.86-152.47) Ma using a large dataset focused on Lampyridae; and terrestrial bioluminescence at 148.03 (130.12-166.80) Ma, with the age of aerial bioluminescence at 104.97 (99.00-120.90) Ma using a complementary Elateroidea dataset. These ages pre-date the origins of all known extant aerial predators (i.e. bats and birds) and support much older terrestrial predators (assassin bugs, frogs, ground beetles, lizards, snakes, hunting spiders and harvestmen) as the drivers of terrestrial bioluminescence in beetles. These ages also support the hypothesis that sexual signalling was probably the original function of this signal in aerial fireflies.

Highly robust and soft biohybrid mechanoluminescence for optical signaling and illumination

Biohybrid is a newly emerging and promising approach to construct soft robotics and soft machines with novel functions, high energy efficiency, great adaptivity and intelligence. Despite many unique advantages of biohybrid systems, it is well known that most biohybrid systems have a relatively short lifetime, require complex fabrication process, and only remain functional with careful maintenance. Herein, we introduce a simple method to create a highly robust and power-free soft biohybrid mechanoluminescence, by encapsulating dinoflagellates, bioluminescent unicellular marine algae, into soft elastomeric chambers. The dinoflagellates retain their intrinsic bioluminescence, which is a near-instantaneous light response to mechanical forces. We demonstrate the robustness of various geometries of biohybrid mechanoluminescent devices, as well as potential applications such as visualizing external mechanical perturbations, deformation-induced illumination, and optical signaling in a dark environment. Our biohybrid mechanoluminescent devices are ultra-sensitive with fast response time and can maintain their light emission capability for weeks without special maintenance.

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.

Whiskers as hydrodynamic prey sensors in foraging seals

Unlike humans, most mammals have mobile facial whiskers, yet their natural movement and function are unknown due to observational difficulties, even in well-studied terrestrial whisker specialists (rodents). We report a remarkable case of whiskers contributing to mammal foraging in an extreme underwater environment: the deep, dark ocean. Our animal-borne video cameras revealed that elephant seals captured moving prey by sensing water movement. Their whiskers extended forward ahead of the mouth. Seals performed rhythmic whisker movement to search for hydrodynamic cues, a whisker movement homologous to terrestrial mammals exploring their environment. Based on direct observations, we show how deep-diving seals locate their prey without the biosonar used by whales, revealing another mammalian adaptation to complete darkness.

The darkness of the deep ocean limits the vision of diving predators, except when prey emit bioluminescence. It is hypothesized that deep-diving seals rely on highly developed whiskers to locate their prey. However, if and how seals use their whiskers while foraging in natural conditions remains unknown. We used animal-borne tags to show that free-ranging elephant seals use their whiskers for hydrodynamic prey sensing. Small, cheek-mounted video loggers documented seals actively protracting their whiskers in front of their mouths with rhythmic whisker movement, like terrestrial mammals exploring their environment. Seals focused their sensing effort at deep foraging depths, performing prolonged whisker protraction to detect, pursue, and capture prey. Feeding-event recorders with light sensors demonstrated that bioluminescence contributed to only about 20% of overall foraging success, confirming that whiskers play the primary role in sensing prey. Accordingly, visual prey detection complemented and enhanced prey capture. The whiskers’ role highlights an evolutionary alternative to echolocation for adapting to the extreme dark of the deep ocean environment, revealing how sensory abilities shape foraging niche segregation in deep-diving mammals. Mammals typically have mobile facial whiskers, and our study reveals the significant function of whiskers in the natural foraging behavior of a marine predator. We demonstrate the importance of field-based sensory studies incorporating multimodality to better understand how multiple sensory systems are complementary in shaping the foraging success of predators.

Bioluminescence of the tropical Indian Ocean: a multiple-scale variation

Large-scale surveys represented by 5800 bathymetric casts in the western Indian Ocean (0-22^o N, 54-58^o E), elucidated the 10-fold variation of the bioluminescent potential (BP) in the upper mixed layer, during the winter (north-east) monsoon season. The mesoscale survey in February 2017 consisted of 26 drift stations (4^o N-3^o S, 65-68^o E) on which 5-10 bathymetric casts were deployed down to 60 m. The maximal BP was associated with the periphery of a cyclonic eddy. The two-fold to three-fold variation of BP characterized the spatial heterogeneity modulated by a detected eddy. High-frequency casts on drift stations resembled the fine-scale heterogeneity in which the three-fold variation was observed within the BP maximum at a 37 ± 13 m depth. The latter one was located above the deep chlorophyll maximum at a 80 m depth. A general decline of the BP variance from the large scale through mesoscale to fine scale, fits that of the zooplankton biomass.

Theoretical Study of the Thermolysis Reaction and Chemiexcitation of Coelenterazine Dioxetanes

Coelenterazine and other imidazopyrazinones are important bioluminescent substrates widespread in marine species and can be found in eight phyla of luminescent organisms. Light emission from these systems is caused by the formation and subsequent thermolysis of a dioxetanone intermediate, whose decomposition allows for efficient chemiexcitation to singlet excited states. Interestingly, some studies have also reported the involvement of unexpected dioxetane intermediates in the chemi- and bioluminescent reactions of Coelenterazine, albeit with little information on the underlying mechanisms of these new species. Herein, we have employed a theoretical approach based on density functional theory to study for the first time the thermolysis reaction and chemiexcitation profile of two Coelenterazine dioxetanes. We have found that the thermolysis reactions of these species are feasible but with relevant energetic differences. More importantly, we found that the singlet chemiexcitation profiles of these dioxetanes are significantly less efficient than the corresponding dioxetanones. Furthermore, we identified triplet chemiexcitation pathways for the Coelenterazine dioxetanes. Given this, the chemiexcitation of these dioxetanes should lead only to minimal luminescence. Thus, our theoretical investigation of these systems indicates that the thermolysis of these dioxetanes should only provide "dark" pathways for the formation of nonluminescent degradation products of the chemi- and bioluminescent reactions of Coelenterazine and other imidazopyrazinones.

Discovery of alkene-conjugated luciferins for redshifted and improved bioluminescence imaging in vitro and in vivo

The firefly luciferase system is the most extensively utilized bioluminescence system in the field of life science at the moment. In this work, we designed and synthesized a series of alkene-conjugated luciferins to develop new firefly bioluminescence substrates, and further evaluated their activities in vitro and in vivo. It is worth noting that the maximum biological emission wavelength of novel luciferin analogue AL3 ((S,E)-2-(6-hydroxy-5-(3-methoxy-3-oxoprop-1-en-1-yl)benzo[d]thiazol-2-yl)-4,5-dihydrothiazole-4-carboxylic acid) is 100 nm red-shifted compared with D-luciferin, while that of analogue AL4 ((S,E)-2-(5-(2-cyanovinyl)-6-hydroxybenzo[d]thiazol-2-yl)-4,5-dihydrothiazole-4-carboxylic acid) is 75 nm red-shifted. The new substrate AL2 ((S,E)-2-(6-hydroxy-7-(3-methoxy-3-oxoprop-1-en-1-yl)benzo[d]thiazol-2-yl)-4,5-dihydrothiazole-4-carboxylic acid) showed better bioluminescence performance in vivo.

Cryo-EM structure of the fatty acid reductase LuxC-LuxE complex provides insights into bacterial bioluminescence

The discovery of reduced flavin mononucleotide and fatty aldehydes as essential factors of light emission facilitated study of bacterial luminescence. Although the molecular mechanisms underlying bacterial luminescence have been studied for more than 60 years, the structure of the bacterial fatty acid reductase complex remains unclear. Here, we report the cryo-EM structure of the Photobacterium phosphoreum fatty acid reductase complex LuxC–LuxE to a resolution of 2.79 Å. We show that the active site Lys238/Arg355 pair of LuxE is >30 Å from the active site Cys296 of LuxC, implying that catalysis relies on a large conformational change. Furthermore, mutagenesis and biochemical experiments support that the L-shaped cleft inside LuxC plays an important role in substrate binding and reaction. We obtained a series of mutants with significantly improved activity as measured by in vitro bioluminescence assays and demonstrated that the double mutant W111A/F483K displayed the highest activity (370% of the WT). Our results indicated that the activity of LuxC significantly affects the bacterial bioluminescence reaction. Finally, we expressed this mutated lux operon in Escherichia coli but observed that the in vivo concentrations of ATP and NADPH limited the enzyme activity; thus, we conclude that the luminous intensity mainly depends on the level of metabolic energy.

Thermosensitive Microgels Containing AIEgens: Enhanced Luminescence and Distinctive Photochromism for Dynamic Anticounterfeiting

The proposal of the aggregation-induced emission (AIE) effect shines a light on the practical application of luminescent materials. The AIE-active luminescence microgels (TPEC MGs) with photo-induced color-changing behavior were developed by integrating positively charged AIE luminogens (AIEgens) into the anionic network of microgels, where AIEgens of TPEC were obtained from the quaternization reaction between tetra-(4-pyridylphenyl)ethylene (TPE-4Py) and 7-(6-bromohexyloxy)-coumarin. The aqueous suspensions of TPEC MGs exhibit a significant AIE effect following the enhancement of quantum yield. In addition, further increase in fluorescence intensity and blueshift occur at elevated temperatures due to the collapse of microgels. The distinctive photochromic behavior of TPEC MGs was observed, which presents as the transition from orange-yellow to blue-green color under UV irradiation, which is different from TPEC in good organic solvents. The phenomenon of color changing can be ascribed to the competition between photodimerization of the coumarin part and photocyclization of TPE-4Py in TPEC. The photochromic TPEC MG aqueous suspensions can be conducted as aqueous microgel inks for information display, encryption, and dynamic anticounterfeiting.

Endogenous Fluorescent Proteins in the Mucus of an Intertidal Polychaeta: Clues for Biotechnology

The vast ocean holds many unexplored organisms with unique adaptive features that enable them to thrive in their environment. The secretion of fluorescent proteins is one of them, with reports on the presence of such compounds in marine annelids being scarce. The intertidal Eulalia sp. is an example. The worm secretes copious amounts of mucus, that when purified and concentrated extracts, yield strong fluorescence under UV light. Emission has two main maxima, at 400 nm and at 500 nm, with the latter responsible for the blue–greenish fluorescence. Combining proteomics and transcriptomics techniques, we identified ubiquitin, peroxiredoxin, and 14-3-3 protein as key elements in the mucus. Fluorescence was found to be mainly modulated by redox status and pH, being consistently upheld in extracts prepared in Tris-HCl buffer with reducing agent at pH 7 and excited at 330 nm. One of the proteins associated with the fluorescent signal was localized in secretory cells in the pharynx. The results indicate that the secretion of fluorescent proteinaceous complexes can be an important defense against UV for this dweller. Additionally, the internalization of fluorescent complexes by ovarian cancer cells and modulation of fluorescence of redox status bears important considerations for biotechnological application of mucus components as markers.

Multi-level encryption of information in morphing hydrogels with patterned fluorescence

Fluorescent hydrogels have attracted tremendous attention recently in the field of information security due to the booming development of information technology. Along this line, it is highly desired to improve the security level of concealed information by the advancements of materials and encryption technologies. Here we report multi-level encryption of information in a bilayer hydrogel with shape-morphing ability and patterned fluorescence. This hydrogel is composed of a fluorescence layer containing chromophore units in the poly(acrylic acid) network and an active layer with UV-absorption agents in the poly(N-isopropylacrylamide-co-acrylic acid) network. The former layer exhibits tunable fluorescence tailored by UV light irradiation to induce unimer-to-dimer transformation of the chromophores, facilitating the write-in of information through photolithography. The latter layer is responsive to temperature, enabling morphing of the bilayer hydrogel. Therefore, the bilayer hydrogel encoded with patterned fluorescent patterns can deform into three-dimensional configurations at room temperature to conceal the information, which is readable only after successive procedures of shape recovery at an appropriate temperature and under UV light irradiation from the right direction. The combination of morphing materials and patterned fluorescence as a new avenue to improve the encryption level of information should merit the design of other smart materials with integrated functions for specific applications.