Genome assembly of Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal.

The Genji firefly, Nipponoluciola cruciata, is an aquatic firefly endemic to Japan, inhabiting a wide area of the Japanese archipelago. The luminescence of fireflies is a scientifically interesting phenomenon, and many studies have evaluated this species in Japan. In this study, we sequenced the whole genome of male N. cruciata and constructed a high-quality genome assembly of 662 Mb with a BUSCO completeness of 99.1% in the genome mode. Using the detected set of 15,169 protein-coding genes, the genomic structures and genetic background of luminescence-related genes were also investigated. We found four new firefly luciferase-like genes in the genome. The highest bioluminescent activity was observed for LLa2, which originated from ancestral PDGY, a mitochondrial acyl-CoA synthetase. A thioesterase candidate, NcruACOT1, which is involved in d-luciferin biosynthesis, was expressed in the lantern. Two opsins were also detected and the absorption wavelength of the UV-type opsin candidate shifted from UV to blue. These findings provide an important resource for unravelling the adaptive evolution of fireflies in terms of luminescence and vision.

Diversity and evolution of serotonergic cells in taste buds of elasmobranchs and ancestral actinopterygian fish.

A subset of gustatory cells are serotonin immunoreactive (ir) in the mammalian taste bud. In the taste bud of lamprey, elongated gustatory-like cells are also serotonin-ir. In contrast, flattened serotonin-ir cells are located only in the basal region of the taste buds in the teleosts and amphibians. These serotonin-ir cells are termed as basal cells. To evaluate the evolution and diversity of serotonergic cells in the taste bud of amniote animals, we explored the distribution and morphology of serotonin-ir cells in the taste buds of ancestral actinopterygian fish (spotted gar, sturgeon, Polypterus senegalus) and elasmobranch (stingray). In all examined animals, the taste buds contained serotonin-ir cells in their basal part. The number of serotonin-ir basal cells in each taste bud was different between these fish species. They were highest in the stingray and decreased in the order of the Polypterus, sturgeon, and gar. While serotonin immunoreactivity was observed only in the basal cells in the taste buds of the ancestral actinopterygian fish, some elongated cells were also serotonin-ir in addition to the basal cells in the stingray taste buds. mRNA of tryptophan hydroxylase 1 (tph1), a rate-limiting enzyme of the serotonin synthesis, is expressed in both the elongated and basal cells of stingray taste buds, indicating that these cells synthesize the serotonin by themselves. These results suggest that the serotonin-ir basal cells arose from the ancestor of the cartilaginous fish, and serotonin-ir cells in the elasmobranch taste bud exhibit an intermediate aspect between the lamprey and actinopterygian fish.

Electrochemistry in bicontinuous microemulsions derived from two immiscible electrolyte solutions for a membrane-free redox flow battery.

HYPOTHESES: Bicontinuous microemulsions (BMEs) have attracted attention as unique heterogeneous mixture for electrochemistry. An interface between two immiscible electrolyte solutions (ITIES) is an electrochemical system that straddles the interface between a saline and an organic solvent with a lipophilic electrolyte. Although most BMEs have been reported with nonpolar oils, such as toluene and fatty acids, it should be possible to construct a sponge-like three-dimensionally expanded ITIES comprising a BME phase. EXPERIMENTS: Dichloromethane (DCM)-water microemulsions stabilized by a surfactant were investigated in terms of the concentrations of co-surfactants and hydrophilic/lipophilic salts. A Winsor III microemulsion three-layer system, consisting of an upper saline phase, a middle BME phase, and a lower DCM phase, was prepared, and electrochemistry was conducted in each phase. FINDINGS: We found the conditions for ITIES-BME phases. Regardless of where the three electrodes were placed in the macroscopically heterogeneous three-layer system, electrochemistry was possible, as in a homogeneous electrolyte solution. This indicates that the anodic and cathodic reactions can be divided into two immiscible solution phases. A redox flow battery comprising a three-layer system with a BME as the middle phase was demonstrated, paving the way for applications such as electrolysis synthesis and secondary batteries.

X-ray crystallographic and mutational analysis of the NylC precursor: catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolase.

Nylon hydrolase (NylC), a member of the N-terminal nucleophile (Ntn) hydrolase superfamily, is responsible for the degradation of various aliphatic nylons, including nylon-6 and nylon-66. NylC is initially expressed as an inactive precursor (36 kDa), but the precursor is autocatalytically cleaved at Asn266/Thr267 to generate an active enzyme composed of 27 and 9 kDa subunits. We isolated various mutants with amino acid changes at the catalytic centre. X-ray crystallographic analysis revealed that the NylC precursor forms a doughnut-shaped quaternary structure composed of four monomers (molecules A-D) with D2 symmetry. Catalytic residues in the precursor are covered by loop regions at the A/B interface (equivalent to the C/D interface). However, the catalytic residues are exposed to the solvent environment through autocleavage followed by movements of the loop regions. T267A, D306A and D308A mutations resulted in a complete loss of autocleavage. By contrast, in the T267S mutant, autocleavage proceeded slowly at a constant reaction rate (k = 2.8 × 10-5  s-1 ) until complete conversion, but the reaction was inhibited by K189A and N219A mutations. Based on the crystallographic and molecular dynamic simulation analyses, we concluded that the Asp308-Asp306-Thr267 triad, resembling the Glu-Ser-Ser triad conserved in Ntn-hydrolase family enzymes, is responsible for autocleavage and that hydrogen-bonding networks connecting Thr267 with Lys189 and Asn219 are required for increasing the nucleophilicity of Thr267-OH in both the water accessible and water inaccessible systems. Furthermore, we determined that NylC employs the Asp308-Asp306-Thr267 triad as catalytic residues for substrate hydrolysis, but the reaction requires Lys189 and Tyr146 as additional catalytic/substrate-binding residues specific for nylon hydrolysis.

Biosynthesis-Inspired Deracemizative Production of D-Luciferin In Vitro by Combining Luciferase and Thioesterase.

Due to the strict enantioselectivity of firefly luciferase (FLuc), only D-luciferin can be used as a substrate for the bioluminescence (BL) reaction. Unfortunately, luciferin racemizes easily and accumulation of nonluminous L-luciferin has negative influences on the light-emitting reaction. By a detailed analysis of luciferin chirality, however, it becomes clarified that L-luciferin is the biosynthetic precursor of D-luciferin in fireflies and undergoes the enzymatic chiral inversion. By the chiral inversion reaction, the enantiopurity of luciferin can be maintained in the reaction mixture for applications using FLuc. Thus, chirality is crucial for the BL reaction and essential for investigating and applying the biosynthesis of D-luciferin. Here, we describe the methods for the analysis of chiral inversion reaction using high-performance liquid chromatography (HPLC) with a chiral column. We also introduce an example of an in vitro deracemizative BL reaction system using a combination of FLuc and fatty acyl-CoA thioesterase, which is inspired by the chiral inversion mechanism in the biosynthetic pathway of D-luciferin.

Vertically Oriented Metallic Heterodimer Array Semiembedded in Flat Conductive Carbon Film for Electrochemical Application.

General synthesis of a highly oriented metallic heterodimer array based on a selective electrodeposition technique onto a metal nanoparticle-embedded carbon film is proposed, which enables the preparation of heterodimers with a wide variety of metal combinations. This method requires no surfactant, capping agent, organic solvent, or heat treatment. As a representative metal combination, a nickel (Ni)/palladium (Pd) heterodimer array was prepared by selective electrodeposition of Ni nanoparticles (Ni NPs) on top of partially exposed Pd NPs embedded in carbon film electrodes fabricated by a cosputtering technique. Such a selective electrodeposition becomes possible by utilizing the difference in electrodeposition overpotentials between carbon and Pd NP surfaces. X-ray photoelectron spectroscopy revealed a charge transfer from Ni NPs to Pd NPs, implying that the catalytic and optical properties can be expected to be controllable. The formed heterodimer array structure was mechanically stable against ultrasonication in ethanol for over 1 h because most parts of the Pd NPs were tightly embedded in the carbon film. After conversion from Ni to nickel hydroxide (Ni(OH)2), the electrode showed high electrocatalytic activity toward glucose oxidation, with a higher turnover rate and lower overpotential compared to Ni(OH)2 electrodeposited on pure carbon film electrodes.

Comparative studies for amyloid beta degradation: "Neprilysin vs insulysin", "monomeric vs aggregate", and "whole Aß40 vs its peptide fragments".

Amyloid beta (Aß) proteins are produced from amyloid precursor protein cleaved by ß- and γ-secretases, and are the main components of senile plaques pathologically found in Alzheimer's disease (AD) patient brains. Therefore, the relationship between AD and Aßs has been well studied for both therapeutic and diagnostic purposes. Several enzymes have been reported to degrade Aßs in vivo, with neprilysin (NEP) and insulysin (insulin-degrading enzyme, IDE) being the most prominent. In this article, we describe the mass spectrometric characterization of peptide fragments generated using NEP and IDE, and clarify the differences in digestion specificities between these two enzymes for non-aggregated Aß40, aggregated Aß40, and Aß40 peptide fragments, including Aß16. Our results allowed identification of all the peptide fragments from non-aggregated Aß40: NEP, 23 peptide fragments consisting of 2-11 amino-acid residues, 17 cleavage sites; IDE, 23 peptide fragments consisting of 6-33 amino-acid residues, 15 cleavage sites. Also, we confirmed that IDE can digest only whole Aß40, whereas NEP can digest both Aß40 and partial structures such as Aß16 and peptide fragments generated by the digestion of Aß40 by IDE. Furthermore, we confirmed that IDE and NEP are unable to digest aggregated Aß40.

Lipophilic probe behavior in microemulsions evaluated by fluorescence correlation spectroscopy.

We evaluated the dispersion and diffusion of fluorescent-labeled lipophilic vitamin E (VE) in microemulsions (MEs) including water-in-oil (W/O) type ME, oil-in-water (O/W) type ME, and bicontinuous ME (BME), using fluorescence correlation spectroscopy (FCS). We prepared a fluorescent ATTO 488 or BODIPY group labeled VE (VE-ATTO or VE-BODIPY). VE-ATTO possesses lipophilic and hydrophilic parts, while VE-BODIPY consists solely of the lipophilic part. The VE-ATTO dissolved in heptane solution as an oil phase appeared hot pink in color due to the solvatochromism effect under room light and almost no fluorescent signal, which was unlike the VE-ATTO dissolved in ME solutions and all the VE-BODIPY solutions (typical fluorescent green color). The FCS measurement proved that VE-BODIPY diffuses faster than VE-ATTO. This is presumably because the "surfactant-like" VE-ATTO is localized and trapped at the micro-water/micro-oil interface of the MEs, while the VE-BODIPY exists in the ME phase and macro-oil phase with good dispersion. These results demonstrate that FCS is a powerful tool for the rapid evaluation of the lipophilic probe behavior in heterogeneous ME solutions.

Immobilization of Baeyer-Villiger monooxygenase from acetone grown Fusarium sp.

OBJECTIVE: A novel biocatalyst for Baeyer-Villiger oxidations is necessary for pharmaceutical and chemical industries, so this study aims to find a Baeyer-Villiger monooxygenase (BVMO) and to improve its stability by immobilization. RESULTS: Acetone, the simplest ketone, was selected as the only carbon source for the screening of microorganisms with a BVMO. A eukaryote, Fusarium sp. NBRC 109816, with a BVMO (FBVMO), was isolated from a soil sample. FBVMO was overexpressed in E. coli and successfully immobilized by the organic-inorganic nanocrystal formation method. The immobilization improved the thermostability of FBVMO. Substrate specificity investigation revealed that both free and immobilized FBVMO were found to show catalytic activities not only for Baeyer-Villiger oxidation of ketones to esters but also for oxidation of sulfides to sulfoxides. Furthermore, a preparative scale reaction using immobilized FBVMO was successfully conducted. CONCLUSIONS: FBVMO was discovered from an environmental sample, overexpressed in E. coli, and immobilized by the organic-inorganic nanocrystal formation method. The immobilization successfully improved its thermostability.

Morphological analysis of the cerebellum and its efferent system in a basal actinopterygian fish, Polypterus senegalus.

Although all vertebrate cerebella contain granule cells, Purkinje cells, and efferent neurons, the cellular arrangement and neural circuitry are highly diverse. In amniotes, cerebellar efferent neurons form clusters, deep cerebellar nuclei, lie deep in the cerebellum, and receive synaptic inputs from Purkinje cells but not granule cells. However, in the cerebellum of teleosts, the efferent neurons, called eurydendroid cells, lie near the cell bodies of Purkinje cells and receive inputs both from axons of Purkinje cells and granule cell parallel fibers. It is largely unknown how the cerebellar structure evolved in ray-finned fish (actinopterygians). To address this issue, we analyzed the cerebellum of a bichir Polypterus senegalus, one of the most basal actinopterygians. We found that the cell bodies of Purkinje cells are not aligned in a layer; incoming climbing fibers terminate mainly on the basal portion of Purkinje cells, revealing that the Polypterus cerebellum has unique features among vertebrate cerebella. Retrograde labeling and marker analyses of the efferent neurons revealed that their cell bodies lie in restricted granular areas but not as deep cerebellar nuclei in the cerebellar white matter. The efferent neurons have long dendrites like eurydendroid cells, although they do not reach the molecular layer. Our findings suggest that the efferent system of the bichir cerebellum has intermediate features between teleosts and amniote vertebrates, and provides a model to understand the basis generating diversity in actinopterygian cerebella.

Lipophilic Vitamin E Diffusion through Bicontinuous Microemulsions.

We studied the diffusion properties of lipophilic vitamin E (VE) through bicontinuous microemulsions (BME) using both electrochemical and fluorescence correlation spectroscopy (FCS) measurements. We investigated the effect of different composition ratios of micro-water and micro-oil phases in BMEs (W/OBME). When we employed the BME with a lower W/OBME value of 40/60 (oil-rich BME) as an electrolyte solution, we obtained a larger current response from VE at a fluorinated nanocarbon film electrode. Further voltammetric studies revealed that a higher VE diffusion coefficient was observed in the oil-rich BME. The FCS results also exhibited faster diffusion through the oil-rich BME, which played a significant role in accelerating the VE diffusion probably due to the widening of the micro-oil phase pathway in the BME. Moreover, the effect of increasing the VE diffusion was pronounced at the interface between the electrode surface and the BME solution. These results indicate that controlling the conditions of the BME as the measurement electrolyte is very effective for achieving superior electrochemical measurements in a BME.

Structural and functional characterization of nylon hydrolases.

Biodegradation of synthetic polymers is recognized as a useful way to reduce their environmental load and pollution, loss of natural resources, extensive energy consumption, and generation of greenhouse gases. The potential use of enzymes responsible for the degradation of the targeted polymers is an effective approach which enables the conversion of the used polymers to original monomers and/or other useful compounds. In addition, the enzymes are expected to be applicable in industrial processes such as improving the surface structures of the polymers. Especially, conversion of the solid polymers to soluble oligomers/monomers is a key step for the biodegradation of the polymers. Regarding the hydrolysis of polyamides, three enzymes, 6-aminohexanoate-cyclic-dimer hydrolase (NylA), 6-aminohexanoate-dimer hydrolase (NylB), and 6-aminohexanoate-oligomer endo-hydrolase (nylon hydrolase, NylC), are found in several bacterial strains. In this chapter, we describe our approach for the screening of microorganisms which degrade nylons and related compounds; preparation of substrates; assay of hydrolytic activity for soluble and insoluble substrates; and X-ray crystallographic and computational approaches for analysis of structure and catalytic mechanisms of the nylon-degrading enzymes.

Hybrid Carbon Film Electrodes for Electroanalysis.

Carbon materials have been widely used for electrochemical analysis and include carbon nanotubes, graphene, and boron-doped diamond electrodes in addition to conventional carbon electrodes, such as those made of glassy carbon and graphite. Of the carbon-based electrodes, carbon film has advantages because it can be fabricated reproducibly and micro- or nanofabricated into electrodes with a wide range of shapes and sizes. Here, we report two categories of hybrid-type carbon film electrodes for mainly electroanalytical applications. The first category consists of carbon films doped or surface terminated with other atoms such as nitrogen, oxygen and fluorine, which can control surface hydrophilicity and lipophilicity or electrocatalytic performance, and are used to detect various electroactive biochemicals. The second category comprises metal nanoparticles embedded in carbon film electrodes fabricated by co-sputtering, which exhibits high electrocatalytic activity for environmental and biological samples including toxic heavy metal ions and clinical sugar markers, which are difficult to detect at pure carbon-based electrodes.

Suppression of Surface Oxygen on Nanocarbon Film Electrodes for Maintaining Electrode Activity.

We investigated sputtered nanocarbon films with respect to the effect of suppressing surface oxygen on their electrochemical properties. The nanocarbon film consisted of nanocrystallites with mixed sp2 and sp3 bonds formed by unbalanced magnetron sputtering. Ultraviolet/ozone (UV/O3) irradiation and electrochemical pretreatment (ECP) were conducted to change the surface oxygen concentration of nanocarbon film. X-ray photoelectron spectroscopy (XPS) measurements revealed that nanocarbon films with different amounts of surface oxygen could be prepared. In addition, we observed no significant increase of the surface roughness (Ra) at the angstrom level after treatments, owing to a stable structure containing 40% of sp3 bonds. The electrode characteristics, including the potential window and electrochemical properties for some redox species, such as Ru(NH3)63+/2+, were investigated. Some electrochemical measurements of zinc ions (Zn2+) and hydrogen peroxide (H2O2) showed that the electrochemical reaction was improved by suppressing the surface oxygen. These results clearly indicated that the low surface oxygen concentration plays an important role in these electrochemical reactions.

Supporting effects of a N-doped carbon film electrode on an electrodeposited Ni@Ni(OH)2 core-shell nanocatalyst in accelerating electrocatalytic oxidation of oligosaccharides.

The supporting effect of a N-doped carbon film induced superior crystallinity in electrodeposited Ni@Ni(OH)2 core-shell nanoparticles. This improvement resulted in a much higher regeneration rate of catalytic sites (NiOOH), leading to higher oxidation currents of sugars. Also, the overpotential of the maltopentaose (G5) oxidation reaction decreased significantly, probably due to the effect of the electrostatic interaction between NPs and G5.

Stand-Alone Semi-Solid-State Electrochemical Systems Based on Bicontinuous Microemulsion Gel Films.

Bicontinuous microemulsion (BME)-based hydrogel films were integrated with screen-printed electrodes (SPEs) comprising working, counter, and reference electrodes to form stand-alone, semi-solid-state electrochemical systems that do not require an outer electrolyte solution. The gel network of the BME hydrogel only exists in the microaqueous phase and retains the structure of the entire BME gel. Following gelation, a microaqueous phase with sufficient ionic strength ensured effective ionic conductivity, even in thin gel films. This enabled the electrochemical reaction to proceed using a thin gel film as an electrolyte solution. However, an intact micro-oil phase with no gel network enabled efficient extraction from an external oil solution and exhibited rapid electrochemistry that was comparable to that of a BME solution. Cyclic voltammograms of lipophilic redox species in oil using the gel-integrated SPE system demonstrated successfully in the oil itself and in the air with dropped oil onto the system.

Evaluation of the population structure and phylogeography of the Japanese Genji firefly, Luciola cruciata, at the nuclear DNA level using RAD-Seq analysis.

The Genji firefly, Luciola cruciata, is widely distributed throughout the major Japanese islands (Honshu, Shikoku, and Kyushu) and distinguished into two ecological types on the basis of the flash interval of the mate-seeking males (4-sec slow-flash or 2-sec fast-flash intervals). The boundary of the ecological types corresponds to the Fossa Magna, a great rupture zone that separates eastern and western Japan. Although the degree of genetic differentiation of the two types has been evaluated using allozyme and mitochondrial DNA sequence data, it has not been evaluated using genome-wide data. Based on the genome-wide data obtained using single-end restriction-site-associated DNA (RAD-Seq), principal component, gene-level phylogenetic tree, admixture, and Wright's fixation index analyses, we identified three phylogenetic groups in L. cruciata: East-Honshu, West-Honshu, and Kyushu. This grouping corresponds to the ecological types: East-Honshu to the slow-flash type and West-Honshu and Kyushu to the fast-flash type. Although introgression was exceptionally observed around adjacent or artificially transplanted areas, gene flow among the groups was almost absent in the natural populations. The phylogenetic tree under the coalescent model also evaluated differentiation among the East-Honshu, West-Honshu and Kyushu groups. Furthermore, because the distribution patterns of the three groups are consistent with the geological history of Japanese islands, a vicariant speciation scenario of L. cruciata is concluded. In addition, we identified genetic markers that can be used to distinguish the three genetic groups for genetic management of firefly transplantation in nature conservation and regeneration.

Controlling Surface Oxygen Concentration of a Nanocarbon Film Electrode for Improvement of Target Analytes.

A nanocarbon film consisting of nanocrystallites with mixed sp2 and sp3 bonds formed by unbalanced magnetron sputtering, was studied with respect to changes in the characteristics caused by the surface oxygen concentration. An electrochemical pretreatment (ECP) was conducted to change the surface oxygen concentration of the nanocarbon film. X-ray photoelectron spectroscopy (XPS) measurements revealed that nanocarbon films with different amounts of surface oxygen could be prepared. In addition, we observed no significant increase of surface roughness (Ra) at the angstrom level after ECP, owing to a stable structure containing 40% of sp3 bonds. The electrode characteristics, including the potential window, and electrochemical properties for some redox species, such as Ru(NH3)63+/2+, Fe(CN)63-/4- and some biomolecules, were investigated. The anodic potential limit became wider and ΔEp of Fe(CN)63-/4- became smaller at the treated nanocarbon film electrode than those of the as-deposited nanocarbon film electrode. Based on these results, we realized to measure uridylic acid (UMP) and inosine triphosphate (ITP) with a high oxidation potential by direct oxidation, which was difficult to measure at the as-deposited nanocarbon film electrode.

Efficient Screening and Design of Variable Domain of Heavy Chain Antibody Ligands Through High Throughput Sequencing for Affinity Chromatography to Purify Fab Fragments.

To design an affinity ligand for purification of antigen-binding fragment (Fab) antibody, variable domain of heavy chain antibody (VHH) phage libraries were constructed from Fab-immunized Alpaca and subjected to biopanning against Fabs. To find the specific binders, we directly applied high-throughput sequencing (HTS) analysis of the VHH sequences in the panned phages on next-generation sequencer. The efficiently enriched sequences were aligned for construction of the phylogenetic tree to be categorized into five groups. VHHs from three major groups were first selected to analyze their properties as an affinity ligand. However, those VHHs were not suitable as an affinity ligand because of lack of resistance against alkaline pH and/or difficulty in acidic elution from the affinity column. So, we further searched the candidates from minor group sequences. Among five, one VHH showed the binding ability but with low affinity against Fabs. Therefore, we improved its affinity-by-affinity maturation through error-prone PCR library techniques. The final designed VHH showed highly alkaline pH resistance and easy acidic elution together with high affinity to Fabs. These results indicate that HTS techniques combined with biopanning and followed by error-prone PCR library techniques is powerful in designing specific binders with desired properties.

Electrochemical performance at sputter-deposited nanocarbon film with different surface nitrogen-containing groups.

Carbon materials containing nitrogen have been extensively studied as electrode materials for use in non-platinum cathodes of fuel cells due to their high electrocatalytic activity for oxygen reduction. The activity is strongly dependent on the structure of surface nitrogen-containing functional groups. Carbon film containing nitrogen is also suitable for analytical applications because of its low background noise and its electrocatalytic activity, which is superior to that of pure carbon film. Here, we fabricated sputter-deposited nanocarbon film with a nitrogen-containing group and estimated the efficacy of a surface nitrogen-containing group for detecting biomolecules. Two types of carbon films, one rich in graphite-like nitrogen-containing bonds and the other rich in pyridine-like bonds, were successfully fabricated without changing their nitrogen concentration, sp2/sp3 ratio or surface flatness. The carbon film rich in pyridine-like bonds shows a positive oxygen reduction peak of about 250 mV compared with pure carbon film and is also 200 mV more positive compared with film with graphite-like nitrogen-containing bonds. This indicates that pyridine-like bonds contribute more effectively to electrocatalytic activity than graphite-like nitrogen-containing bonds. For detecting biomolecules, carbon film rich in pyridine-like bonds also exhibits more negative peak potentials for the oxidation of NADH and l-ascorbic acid, suggesting that carbon film rich in pyridine-like bonds will show improved performance for detecting electroactive biomolecules.