Efficient hepatocyte differentiation of primary human hepatocyte-derived organoids using three dimensional nanofibers (HYDROX) and their possible application in hepatotoxicity research.

Human liver organoids are in vitro three dimensionally (3D) cultured cells that have a bipotent stem cell phenotype. Translational research of human liver organoids for drug discovery has been limited by the challenge of their low hepatic function compared to primary human hepatocytes (PHHs). Various attempts have been made to develop functional hepatocyte-like cells from human liver organoids. However, none have achieved the same level of hepatic functions as PHHs. We here attempted to culture human liver organoids established from cryopreserved PHHs (PHH-derived organoids), using HYDROX, a chemically defined 3D nanofiber. While the proliferative capacity of PHH-derived organoids was lost by HYDROX-culture, the gene expression levels of drug-metabolizing enzymes were significantly improved. Enzymatic activities of cytochrome P450 3A4 (CYP3A4), CYP2C19, and CYP1A2 in HYDROX-cultured PHH-derived organoids (Org-HYDROX) were comparable to those in PHHs. When treated with hepatotoxic drugs such as troglitazone, amiodarone and acetaminophen, Org-HYDROX showed similar cell viability to PHHs, suggesting that Org-HYDROX could be applied to drug-induced hepatotoxicity tests. Furthermore, Org-HYDROX maintained its functions for up to 35 days and could be applied to chronic drug-induced hepatotoxicity tests using fialuridine. Our findings demonstrated that HYDROX could possibly be a novel biomaterial for differentiating human liver organoids towards hepatocytes applicable to pharmaceutical research.

Glow-type conversion and characterization of a minimal luciferase via mutational analyses.

Luciferases are widely used as reporter proteins in various fields. Recently, we developed a minimal bright luciferase, picALuc, via partial deletion of the artificial luciferase (ALuc) derived from copepods luciferases. However, the structures of copepod luciferases in the substrate-bound state remain unknown. Moreover, as suggested by structural modeling, picALuc has a larger active site cavity, unlike that in other copepod luciferases. Here, to explore the bioluminescence mechanism of picALuc and its luminescence properties, we conducted multiple mutational analyses, and identified residues and regions important for catalysis and bioluminescence. Mutations of residues likely involved in catalysis (S33, H34, and D55) markedly reduced bioluminescence, whereas that of residue (E50) (near the substrate in the structural model) enhanced luminescence intensity. Furthermore, deletion mutants (Δ70-Δ78) in the loop region (around I73) exhibited longer luminescence lifetimes (~ 30 min) and were reactivated multiple times upon re-addition of the substrate. Due to the high thermostability of picALuc, one of its representative mutant (Δ74), was able to be reused, that is, luminescence recycling, for day-scale time at room temperature. These findings provide important insights into picALuc bioluminescence mechanism and copepod luciferases and may help with sustained observations in a variety of applications.

Rational Strategy for Space-Confined Atomic Layer Deposition.

Atomic layer deposition (ALD) offers excellent controllability of spatial uniformity, film thickness at the Angstrom level, and film composition even for high-aspect-ratio nanostructured surfaces, which are rarely attainable by other conventional deposition methodologies. Although ALD has been successfully applied to various substrates under open-top circumstances, the applicability of ALD to confined spaces has been limited because of the inherent difficulty of supplying precursors into confined spaces. Here, we propose a rational methodology to apply ALD growths to confined spaces (meter-long microtubes with an aspect ratio of up to 10 000). The ALD system, which can generate differential pressures to confined spaces, was newly developed. By using this ALD system, it is possible to deposit TiOx layers onto the inner surface of capillary tubes with a length of 1000 mm and an inner diameter of 100 µm with spatial deposition uniformity. Furthermore, we show the superior thermal and chemical robustness of TiOx-coated capillary microtubes for molecular separations when compared to conventional molecule-coated capillary microtubes. Thus, the present rational strategy of space-confined ALD offers a useful approach to design the chemical and physical properties of the inner surfaces of various confined spaces.

Interfacial Molecular Compatibility for Programming Organic-Metal Oxide Superlattices.

Artificially programming a sequence of organic-metal oxide multilayers (superlattices) by using atomic layer deposition (ALD) is a fascinating and challenging issue in material chemistry. However, the complex chemical reactions between ALD precursors and organic layer surfaces have limited their applications for various material combinations. Here, we demonstrate the impact of interfacial molecular compatibility on the formation of organic-metal oxide superlattices using ALD. The effects of both organic and inorganic compositions on the metal oxide layer formation processes onto self-assembled monolayers (SAM) were examined by using scanning transmission electron microscopy, in situ quartz crystal microbalance measurements, and Fourier-transformed infrared spectroscopy. These series of experiments reveal that the terminal group of organic SAM molecules must satisfy two conflicting requirements, the first of which is to promptly react with ALD precursors and the second is not to bind strongly to the bottom metal oxide layers to avoid undesired SAM conformations. OH-terminated phosphate aliphatic molecules, which we have synthesized, were identified as one of the best candidates for such a purpose. Molecular compatibility between metal oxide precursors and the -OHs must be properly considered to form superlattices. In addition, it is also important to form densely packed and all-trans-like SAMs to maximize the surface density of reactive -OHs on the SAMs. Based on these design strategies for organic-metal oxide superlattices, we have successfully fabricated various superlattices composed of metal oxides (Al-, Hf-, Mg-, Sn-, Ti-, and Zr oxides) and their multilayered structures.

Improving bioluminescence of a minimal luciferase by adding a charged oligopeptide: picALuc2.0.

Luciferases are widely used as reporter proteins in diverse fields from basic biology to medical and environmental researches. Development of luciferase applications for reporter proteins requires small size without target inhibition, appropriate genomic insertion for high expression level, and bright emission for detection sensitivity. We previously developed the minimal luciferase picALuc, but its luminescence was still dim compared to other bright luciferases in terms of expression in Escherichia coli. In this study, diverse additions of oligopeptides with charged residues (eight amino acids in total) to the C-terminus of picALuc enhanced luminescence by up to approximately 50-fold, that is, enhanced enzymatic activity. Moreover, these high luminescence activities were achieved in bacterial and mammalian expression, suggesting their further applicability in many expression systems. The finding in this study that the simple addition of oligopeptides with charged residues (or charge engineering of this kind) enhances enzymatic activity may be applied to a wide variety of enzymatic reactions and protein functions.

Breath odor-based individual authentication by an artificial olfactory sensor system and machine learning.

Breath odor sensing-based individual authentication was conducted for the first time using an artificial olfactory sensor system. Using a 16-channel chemiresistive sensor array and machine learning, a mean accuracy of >97% was successfully achieved. The impact of the number of sensors on the accuracy and reproducibility was also demonstrated.

Correction: Breath odor-based individual authentication by an artificial olfactory sensor system and machine learning.

Correction for 'Breath odor-based individual authentication by an artificial olfactory sensor system and machine learning' by Chaiyanut Jirayupat et al., Chem. Commun., 2022, DOI: https://doi.org/10.1039/D1CC06384G.

Miniaturization of Bright Light-Emitting Luciferase ALuc: picALuc.

Luciferases are widely used as sensitive reporters in various fields ranging from basic biology to medical diagnosis, public health, and food inspection. Scientists have isolated novel luciferases from bioluminescent organisms and concentrated on improving their brightness and thermostability. Recently, small bright luciferases such as artificial luciferase (ALuc) (21 kDa), NanoLuc (19 kDa), GLuc (18 kDa), and TurboLuc (16 kDa) have been reported. However, smaller, brighter, and more stable luciferases are desired for further applications. Here, we constructed the smallest and bright mutant of ALuc, named "picALuc" (13 kDa). picALuc retained the luminescence activity of the full-length ALuc; moreover, its brightness and thermostability were at the same levels as NanoLuc. Furthermore, we showed the advantage of picALuc for the bioluminescence resonance energy transfer-based assay due to its smallness. Our development has opened the door for wider and more practical applications of luciferases.

Edge-Topological Regulation for in Situ Fabrication of Bridging Nanosensors.

In situ fabrication of well-defined bridging nanostructures is an interesting and unique approach to three-dimensionally design nanosensor structures, which are hardly attainable by other methods. Here, we demonstrate the significant effect of edge-topological regulation on in situ fabrication of ZnO bridging nanosensors. When employing seed layers with a sharp edge, which is a well-defined structure in conventional lithography, the bridging angles and electrical resistances between two opposing electrodes were randomly distributed. The stochastic nature of bridging growth direction at the sharp edges inherently causes such unintentional variation of structural and electrical properties. We propose an edgeless seed layer structure using a two-layers resist method to solve the above uncontrollability of bridging nanosensors. Such bridging nanosensors not only substantially improved the uniformity of structural and electrical properties between two opposing electrodes but also significantly enhanced the sensing responses for NO2 with the smaller variance and the lower limit of detection via in situ controlled electrical contacts.

Water-Selective Nanostructured Dehumidifiers for Molecular Sensing Spaces.

Humidity and moisture effects, frequently called water poisoning, in surroundings are inevitable for various molecular sensing devices, strongly affecting their sensing characteristics. Here, we demonstrate a water-selective nanostructured dehumidifier composed of ZnO/TiO2/CaCl2 core-shell heterostructured nanowires for molecular sensing spaces. The fabricated nanostructured dehumidifier is highly water-selective without detrimental adsorptions of various volatile organic compound molecules and can be repeatedly operated. The thermally controllable and reversible dehydration process of CaCl2·nH2O thin nanolayers on hydrophilic ZnO/TiO2 nanowire surfaces plays a vital role in such water-selective and repeatable dehumidifying operations. Furthermore, the limitation of detection for sensing acetone and nonanal molecules in the presence of moisture (relative humidity ∼ 90%) was improved more than 20 times using nanocomposite sensors by operating the developed nanostructured dehumidifier. Thus, the proposed water-selective nanostructured dehumidifier offers a rational strategy and platform to overcome water poisoning issues for various molecular and gas sensors.

Impact of Lateral SnO2 Nanofilm Channel Geometry on a 1024 Crossbar Chemical Sensor Array.

We propose a rational strategy to fabricate thermally robust, highly integrated molecular and gas sensors utilizing a lateral SnO2 nanofilm channel geometry on a 1024 crossbar sensor array. The proposed lateral channel geometry substantially suppresses the detrimental effects of parasitic interconnect wire resistances compared with those of a conventional vertical sandwich-type crossbar array because of its excellent resistance controllability. A conductive oxide top-contact electrode on the lateral SnO2 nanofilm channel enhances the thermal stability at temperatures of up to 500 °C in ambient air. Integrating this lateral SnO2 nanofilm geometry with analog circuits enables the operation of a 1024 crossbar sensor array without selector devices to avoid sneak currents. The developed 1024 crossbar sensor array system detects the local spatial distribution of the molecular gas concentration. The spatial data of molecular concentrations include molecule-specific data to distinguish various volatile molecules based on their vapor pressures. Thus, this integrated crossbar sensor array system using lateral nanofilm geometry offers a platform for robust, reliable, highly integrated molecular and gas sensors.

Surface Dissociation Effect on Phosphonic Acid Self-Assembled Monolayer Formation on ZnO Nanowires.

Understanding the formation process of self-assembled monolayers (SAMs) of organophosphonic acids on ZnO surfaces is essential to designing their various applications, including solar cells, heterogeneous catalysts, and molecular sensors. Here, we report the significant effect of surface dissociation on SAM formation of organophosphonic acids on single-crystalline ZnO nanowire surfaces using infrared spectroscopy. When employing the most conventional solvent-methanol (relative permittivity εr = 32.6), the production of undesired byproducts (layered zinc compounds) on the surface was identified by infrared spectral data and microscopy. On the other hand, a well-defined SAM structure with a tridentate coordination of phosphonic acids on the surface was confirmed when employing toluene (εr = 2.379) or tert-butyl alcohol (εr = 11.22-11.50). The observation of layered zinc compounds as byproducts highlights that the degree of Zn2+ dissociation from the ZnO solid surface into a solvent significantly affects the surface coordination of phosphonic acids during the SAM formation process. Although the ZnO nanowire surface (m-plane) is hydrophilic, the present results suggest that a weaker solvent polarity is preferred to form well-defined phosphonic acid SAMs on ZnO nanowire surfaces without detrimental surface byproducts.

Mechanistic Approach for Long-Term Stability of a Polyethylene Glycol-Carbon Black Nanocomposite Sensor.

Polymer-carbon nanocomposite sensor is a promising molecular sensing device for electronic nose (e-nose) due to its printability, variety of polymer materials, and low operation temperature; however, the lack of stability in an air environment has been an inevitable issue. Here, we demonstrate a design concept for realizing long-term stability in a polyethylene glycol (PEG)-carbon black (CB) nanocomposite sensor by understanding the underlying phenomena that cause sensor degradation. Comparison of the sensing properties and infrared spectroscopy on the same device revealed that the oxidation-induced consumption of PEG is a crucial factor for the sensor degradation. According to the mechanism, we introduced an antioxidizing agent (i.e., ascorbic acid) into the PEG-CB nanocomposite sensor to suppress the PEG oxidation and successfully demonstrated the long-term stability of sensing properties under an air environment for 30 days, which had been difficult in conventional polymer-carbon nanocomposite sensors.

Image Processing and Machine Learning for Automated Identification of Chemo-/Biomarkers in Chromatography-Mass Spectrometry.

We present a method named NPFimg, which automatically identifies multivariate chemo-/biomarker features of analytes in chromatography-mass spectrometry (MS) data by combining image processing and machine learning. NPFimg processes a two-dimensional MS map (m/z vs retention time) to discriminate analytes and identify and visualize the marker features. Our approach allows us to comprehensively characterize the signals in MS data without the conventional peak picking process, which suffers from false peak detections. The feasibility of marker identification is successfully demonstrated in case studies of aroma odor and human breath on gas chromatography-mass spectrometry (GC-MS) even at the parts per billion level. Comparison with the widely used XCMS shows the excellent reliability of NPFimg, in that it has lower error rates of signal acquisition and marker identification. In addition, we show the potential applicability of NPFimg to the untargeted metabolomics of human breath. While this study shows the limited applications, NPFimg is potentially applicable to data processing in diverse metabolomics/chemometrics using GC-MS and liquid chromatography-MS. NPFimg is available as open source on GitHub (http://github.com/poomcj/NPFimg) under the MIT license.

The impact of surface Cu2+ of ZnO/(Cu1-x Zn x )O heterostructured nanowires on the adsorption and chemical transformation of carbonyl compounds.

The surface cation composition of nanoscale metal oxides critically determines the properties of various functional chemical processes including inhomogeneous catalysts and molecular sensors. Here we employ a gradual modulation of cation composition on a ZnO/(Cu1-x Zn x )O heterostructured nanowire surface to study the effect of surface cation composition (Cu/Zn) on the adsorption and chemical transformation behaviors of volatile carbonyl compounds (nonanal: biomarker). Controlling cation diffusion at the ZnO(core)/CuO(shell) nanowire interface allows us to continuously manipulate the surface Cu/Zn ratio of ZnO/(Cu1-x Zn x )O heterostructured nanowires, while keeping the nanowire morphology. We found that surface exposed copper significantly suppresses the adsorption of nonanal, which is not consistent with our initial expectation since the Lewis acidity of Cu2+ is strong enough and comparable to that of Zn2+. In addition, an increase of the Cu/Zn ratio on the nanowire surface suppresses the aldol condensation reaction of nonanal. Surface spectroscopic analysis and theoretical simulations reveal that the nonanal molecules adsorbed at surface Cu2+ sites are not activated, and a coordination-saturated in-plane square geometry of surface Cu2+ is responsible for the observed weak molecular adsorption behaviors. This inactive surface Cu2+ well explains the mechanism of suppressed surface aldol condensation reactions by preventing the neighboring of activated nonanal molecules. We apply this tailored cation composition surface for electrical molecular sensing of nonanal and successfully demonstrate the improvements of durability and recovery time as a consequence of controlled surface molecular behaviors.

Maximizing Conversion of Surface Click Reactions for Versatile Molecular Modification on Metal Oxide Nanowires.

Click reactions (e.g., Huisgen cycloaddition) on metal oxide nanostructures offer a versatile and robust surface molecular modification for various applications because they form strong covalent bonds in a wide range of molecular substrates. This study reports a rational strategy to maximize the conversion rate of surface click reactions on single-crystalline ZnO nanowires by monitoring the reaction progress. p-Polarized multiple-angle incidence resolution spectrometry (pMAIRS) and Fourier-transformed infrared (FT-IR) spectroscopy were employed to monitor the reaction progress of an azide-terminated self-assembled monolayer (SAM) on single-crystalline ZnO nanowires. Although various reaction parameters including the concentration of Cu(I) catalysts, triazolyl ligands, solvents, and target alkynes were systematically examined for the surface click reactions, 10-30% of terminal azide on the nanowire surface remained unreacted. Temperature-dependent FT-IR measurements revealed that such unreacted residual azides deteriorate the thermal stability of the nanowire molecular layer. To overcome this observed conversion limitation of click reactions on nanostructure surfaces, we considered the steric hindrance around the closely packed SAM reaction points, then experimented with dispersing the azide moiety into a methyl-terminated SAM. The mixed-SAM method significantly improved the azide conversion rate to almost 100%. This reaction method enables the construction of spatially patterned molecular surface modifications on metal oxide nanowire arrays without detrimental unreacted azide groups.

Rational Strategy for Space-Confined Seeded Growth of ZnO Nanowires in Meter-Long Microtubes.

Seeded crystal growths of nanostructures within confined spaces offer an interesting approach to design chemical reaction spaces with tailored inner surface properties. However, such crystal growth within confined spaces tends to be inherently difficult as the length increases as a result of confinement effects. Here, we demonstrate a space-confined seeded growth of ZnO nanowires within meter-long microtubes of 100 µm inner diameter with the aspect ratio of up to 10 000, which had been unattainable to previous methods of seeded crystal growths. ZnO nanowires could be grown via seeded hydrothermal crystal growth for relatively short microtubes below the length of 40 mm, while any ZnO nanostructures were not observable at all for longer microtubes above 60 mm with the aspect ratio of 600. Microstructural and mass spectrometric analysis revealed that a conventional seed layer formation using zinc acetate is unfeasible within the confined space of long microtubes as a result of the formation of detrimental residual Zn complex compounds. To overcome this space-confined issue, a flow-assisted seed layer formation is proposed. This flow-assisted method enables growth of spatially uniform ZnO nanowires via removing residual compounds even for 1 m long microtubes with the aspect ratio of up to 10 000. Finally, the applicably of ZnO-nanowire-decorated long microtubes for liquid-phase separations was demonstrated.

Development of a 3D Cell Culture System Using Amphiphilic Polydepsipeptides and Its Application to Hepatic Differentiation.

Various three-dimensional (3D) culture systems are available to provide more accurate in vivo mimicry than two-dimensional (2D) cultures. Synthetic and/or xeno-free biomaterials are desired, as they would provide lower batch-to-batch variability and high repeatability. Here, we introduce a 3D culture system using nanofibers composed of an amphiphilic polydepsipeptide-based polymer named HYDROX, which turns into 3D nanofibers after hydration. Our system produces a large amount of cell aggregates and requires only the seeding of a cell mixture. In addition, cells cultured with HYDROX can be collected with only a centrifugation procedure, and analytical assays can then be performed. Here, we applied HYDROX to hepatic differentiation from induced pluripotent stem cells. The cells cultured with HYDROX formed aggregates and HYDROX strongly promoted hepatic differentiation and maturation in terms of functions such as the positive ratio of alpha-1 antitrypsin, the production of albumin, the cytochrome P450 (CYP) 3A4 activity, and the low-density-lipoprotein uptake ability. In addition, primary human hepatocytes cultured with HYDROX showed significantly improved CYP3A4 gene expression and activity. The viscoelasticity and stiffness of HYDROX can be modulated by varying the concentration of the synthetic polymer, thereby providing a suitable microenvironment for the differentiation of cells with various characteristics toward a target cell type. Our findings demonstrated that HYDROX is a promising biomaterial for 3D cultures in research fields ranging from basic cell research to drug discovery.

Oxygen-Induced Reversible Sn-Dopant Deactivation between Indium Tin Oxide and Single-Crystalline Oxide Nanowire Leading to Interfacial Switching.

An impurity doping in semiconductors is an important irreversible process of manipulating the electrical properties of advanced electron devices. Here, we report an unusual reversible dopant activation/deactivation phenomenon, which emerges at an interface between indium tin oxide (ITO) and single-crystalline oxide channel. We found that the interface electrical resistance between ITO electrodes and single-crystalline oxide nanowire channel can be repeatedly switched between a metallic state and a near-insulative state by applying thermal treatments in air or vacuum. Interestingly, this electrical switching phenomenon disappears when the oxide nanowire changes from the single-crystalline structure to the lithography-defined polycrystalline structure. Atmosphere-controlled annealing experiments reveal that atmospheric oxygen induces repeatable change in the interfacial electrical resistance. Systematic investigations on metal cation species and channel crystallinity demonstrate that the observed electrical switching is related to an interface-specific reversible Sn-dopant activation/deactivation of ITO electrode in contact with a single-crystalline oxide channel.

Phosphonic Acid Modified ZnO Nanowire Sensors: Directing Reaction Pathway of Volatile Carbonyl Compounds.

Surface molecular transformations on nanoscale metal oxides are inherently complex, and directing those reaction pathways is still challenging but important for designing their various applications, including molecular sensing, catalysts, and others. Here, a rational strategy to direct a reaction pathway of volatile carbonyl compounds (nonanal: biomarker) on single-crystalline ZnO nanowire surfaces via molecular modification is demonstrated. The introduction of a methylphosphonic acid modification on the ZnO nanowire surface significantly alters the surface reaction pathway of nonanal via suppressing the detrimental aldol condensation reaction. This is directed by intentionally decreasing the probability of two neighboring molecular activations on the nanowire surface. Spectrometric measurements reveal the correlation between the suppression of the aldol condensation surface reaction and the improvement in the sensor performance. This tailored surface reaction pathway effectively reduces the operating temperature from 200 to 100 °C while maintaining the sensitivity. This is because the aldol condensation product ((E)-2-heptyl-2-undecenal) requires a higher temperature to desorb from the surface. Thus, the proposed facile strategy offers an interesting approach not only for the rational design of metal oxide sensors for numerous volatile carbonyl compounds but also for tailoring various surface reaction pathways on complex nanoscale metal oxides.