Uncovering the impact of UV radiation on mitochondria in dermal cells: a STED nanoscopy study.

Mitochondria are essential organelles in cellular energy metabolism and other cellular functions. Mitochondrial dysfunction is closely linked to cellular damage and can potentially contribute to the aging process. The purpose of this study was to investigate the subcellular structure of mitochondria and their activities in various cellular environments using super-resolution stimulated emission depletion (STED) nanoscopy. We examined the morphological dispersion of mitochondria below the diffraction limit in sub-cultured human primary skin fibroblasts and mouse skin tissues. Confocal microscopy provides only the overall morphology of the mitochondrial membrane and an indiscerptible location of nucleoids within the diffraction limit. Conversely, super-resolution STED nanoscopy allowed us to resolve the nanoscale distribution of translocase clusters on the mitochondrial outer membrane and accurately quantify the number of nucleoids per cell in each sample. Comparable results were obtained by analyzing the translocase distribution in the mouse tissues. Furthermore, we precisely and quantitatively analyzed biomolecular distribution in nucleoids, such as the mitochondrial transcription factor A (TFAM), using STED nanoscopy. Our findings highlight the efficacy of super-resolution fluorescence imaging in quantifying aging-related changes on the mitochondrial sub-structure in cells and tissues.

Unlocking the Potential of Porous Bi2Te3-Based Thermoelectrics Using Precise Interface Engineering through Atomic Layer Deposition.

Porous thermoelectric materials offer exciting prospects for improving the thermoelectric performance by significantly reducing the thermal conductivity. Nevertheless, porous structures are affected by issues, including restricted enhancements in performance attributed to decreased electronic conductivity and degraded mechanical strength. This study introduces an innovative strategy for overcoming these challenges using porous Bi0.4Sb1.6Te3 (BST) by combining porous structuring and interface engineering via atomic layer deposition (ALD). Porous BST powder was produced by selectively dissolving KCl in a milled mixture of BST and KCl; the interfaces were engineered by coating ZnO films through ALD. This novel architecture remarkably reduced the thermal conductivity owing to the presence of several nanopores and ZnO/BST heterointerfaces, promoting efficient phonon scattering. Additionally, the ZnO coating mitigated the high resistivity associated with the porous structure, resulting in an improved power factor. Consequently, the ZnO-coated porous BST demonstrated a remarkable enhancement in thermoelectric efficiency, with a maximum zT of approximately 1.53 in the temperature range of 333-353 K, and a zT of 1.44 at 298 K. Furthermore, this approach plays a significant role in enhancing the mechanical strength, effectively mitigating a critical limitation of porous structures. These findings open new avenues for the development of advanced porous thermoelectric materials and highlight their potential for precise interface engineering through the ALD.

Novel Signal Peptides and Episomal Plasmid System for Enhanced Protein Secretion in Engineered Bacteroides Species.

The genus Bacteroides, a predominant group in the human gut microbiome, presents significant potential for microbiome engineering and the development of live biotherapeutics aimed at treating gut diseases. Despite its promising capabilities, tools for effectively engineering Bacteroides species have been limited. In our study, we have made a breakthrough by identifying novel signal peptides in Bacteroides thetaiotaomicron and Akkermansia muciniphila. These peptides facilitate efficient protein transport across cellular membranes in Bacteroides, a critical step for therapeutic applications. Additionally, we have developed an advanced episomal plasmid system. This system demonstrates superior protein secretion capabilities compared to traditional chromosomal integration plasmids, making it a vital tool for enhancing the delivery of therapeutic proteins in Bacteroides species. Initially, the stability of this episomal plasmid posed a challenge; however, we have overcome this by incorporating an essential gene-based selection system. This novel strategy not only ensures plasmid stability but also aligns with the growing need for antibiotic-free selection methods in clinical settings. Our work, therefore, not only provides a more robust secretion system for Bacteroides but also sets a new standard for the development of live biotherapeutics.

Engineered Methylococcus capsulatus Bath for efficient methane conversion to isoprene.

Isoprene has numerous industrial applications, including rubber polymer and potential biofuel. Microbial methane-based isoprene production could be a cost-effective and environmentally benign process, owing to a reduced carbon footprint and economical utilization of methane. In this study, Methylococcus capsulatus Bath was engineered to produce isoprene from methane by introducing the exogenous mevalonate (MVA) pathway. Overexpression of MVA pathway enzymes and isoprene synthase from Populus trichocarpa under the control of a phenol-inducible promoter substantially improved isoprene production. M. capsulatus Bath was further engineered using a CRISPR-base editor to disrupt the expression of soluble methane monooxygenase (sMMO), which oxidizes isoprene to cause toxicity. Additionally, optimization of the metabolic flux in the MVA pathway and culture conditions increased isoprene production to 228.1 mg/L, the highest known titer for methanotroph-based isoprene production. The developed methanotroph could facilitate the efficient conversion of methane to isoprene, resulting in the sustainable production of value-added chemicals.

Alcoholic Solvent-Mediated Excited-State Proton Transfer Dynamics of a Novel Dihydroxynaphthalene Dye.

The excited-state proton transfer (ESPT) reaction is an important primary photochemical process because it is closely related to photophysical properties. Although ESPT research in aqueous solutions is predominant, alcoholic solvent-mediated ESPT studies are also significant in terms of photoacid-based reactions. Especially, the research for dihydroxynaphthalenes (DHNs) has been largely neglected due to the challenging data interpretation of two hydroxyl groups. A novel fluorescent dye, resveratrone, synthesized by light irradiation of resveratrol, which is famous for its antioxidant properties, can be regarded as a type of DHN, and it has distinctive optical properties, including high quantum yield, a large two-photon absorption coefficient, a large Stokes shift, and very high biocompatibility. In this study, we investigate the overall kinetics of the optical properties of resveratrone and find evidence for alcoholic solvent-mediated ESPT involvement in the radiative properties of resveratrone with a large Stokes shift. Our investigation provides an opportunity to revisit the overlooked photophysical properties of intriguing photoacid behavior and the large Stokes shift of the dihydroxynaphthalene dye.

Nucleation and Layer Closure Behavior of Iridium Films Grown Using Atomic Layer Deposition.

Understanding the initial growth process during atomic layer deposition (ALD) is essential for various applications employing ultrathin films. This study investigated the initial growth of ALD Ir films using tricarbonyl-(1,2,3-η)-1,2,3-tri(tert-butyl)-cyclopropenyl-iridium and O2. Isolated Ir nanoparticles were formed on the oxide surfaces during the initial growth stage, and their density and size were significantly influenced by the growth temperature and substrate surface, which strongly affected the precursor adsorption and surface diffusion of the adatoms. Higher-density and smaller nanoparticles were formed at high temperatures and on the Al2O3 surface, forming a continuous Ir film with a smaller thickness, resulting in a very smooth surface. These findings suggest that the initial growth behavior of the Ir films affects their surface roughness and continuity and that a comprehensive understanding of this behavior is necessary for the formation of continuous ultrathin metal films.

Breathable MOFs Layer on Atomically Grown 2D SnS2 for Stable and Selective Surface Activation.

2D transition metal dichalcogenides (TMDs) have significant research interests in various novel applications due to their intriguing physicochemical properties. Notably, one of the 2D TMDs, SnS2 , has superior chemiresistive sensing properties, including a planar crystal structure, a large surface-to-volume ratio, and a low electronic noise. However, the long-term stability of SnS2 in humid conditions remains a critical shortcoming towards a significant degradation of sensitivity. Herein, it is demonstrated that the subsequent self-assembly of zeolite imidazolate framework (ZIF-8) can be achieved in situ growing on SnS2 nanoflakes as the homogeneous porous materials. ZIF-8 layer on SnS2 allows the selective diffusion of target gas species, while effectively preventing the SnS2 from severe oxidative degradation. Molecular modeling such as molecular dynamic simulation and DFT calculation, further supports the mechanism of sensing stability and selectivity. From the results, the in situ grown ZIF-8 porous membrane on 2D materials corroborates the generalizable strategy for durable and reliable high-performance electronic applications of 2D materials.

High Cell-Density Cultivation of Methylococcus capsulatus Bath for Efficient Methane-Derived Mevalonate Production.

The engineered Methylococcus capsulatus Bath presents a promising approach for converting methane, a potent greenhouse gas, into valuable chemicals. High cell-density culture (HCDC) is necessary for high-titer growth-associated bioproducts, but it often requires time-consuming and labor-intensive optimization processes. In this study, we aimed to achieve efficient HCDC of M. capsulatus Bath by measuring the residual nutrient levels during bioreactor operations and analyzing the specific uptake of each medium component. By controlling the concentrations of nutrients, particularly calcium and phosphorus via intermittent feeding, we achieved a high cell density of 28.2 g DCW/L and a significantly elevated production of mevalonate at a concentration of 1.8 g/L from methane. Our findings demonstrate that the methanotroph HCDC approach presented herein offers a promising strategy for promoting sustainable development, with an exceptional g-scale production titer for value-added synthetic biochemicals.

A Genetically Encoded Biosensor for the Detection of Levulinic Acid.

Levulinic acid (LA) is a valuable chemical used in fuel additives, fragrances, and polymers. In this study, we proposed possible biosynthetic pathways for LA production from lignin and poly(ethylene terephthalate). We also created a genetically encoded biosensor responsive to LA, which can be used for screening and evolving the LA biosynthesis pathway genes, by employing an LvaR transcriptional regulator of Pseudomonas putida KT2440 to express a fluorescent reporter gene. The LvaR regulator senses LA as a cognate ligand. The LA biosensor was first examined in an Escherichia coli strain and was found to be non-functional. When the host of the LA biosensor was switched from E. coli to P. putida KT2440, the LA biosensor showed a linear correlation between fluorescence intensity and LA concentration in the range of 0.156-10 mM LA. In addition, we determined that 0.156 mM LA was the limit of LA detection in P. putida KT2440 harboring an LA-responsive biosensor. The maximal fluorescence increase was 12.3-fold in the presence of 10 mM LA compared to that in the absence of LA. The individual cell responses to LA concentrations reflected the population-averaged responses, which enabled high-throughput screening of enzymes and metabolic pathways involved in LA biosynthesis and sustainable production of LA in engineered microbes.

Characterization of a Potential Probiotic Lactiplantibacillus plantarum LRCC5310 by Comparative Genomic Analysis and its Vitamin B6 Production Ability.

Safety assessment and functional analysis of probiotic candidates are important for their industrial applications. Lactiplantibacillus plantarum is one of the most widely recognized probiotic strains. In this study we aimed to determine the functional genes of L. plantarum LRCC5310, isolated from kimchi, using next-generation, whole-genome sequencing analysis. Genes were annotated using the Rapid Annotations using Subsystems Technology (RAST) server and the National Center for Biotechnology Information (NCBI) pipelines to establish the strain's probiotic potential. Phylogenetic analysis of L. plantarum LRCC5310 and related strains showed that LRCC5310 belonged to L. plantarum. However, comparative analysis revealed genetic differences between L. plantarum strains. Carbon metabolic pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database showed that L. plantarum LRCC5310 is a homofermentative bacterium. Furthermore, gene annotation results indicated that the L. plantarum LRCC5310 genome encodes an almost complete vitamin B6 biosynthetic pathway. Among five L. plantarum strains, including L. plantarum ATCC 14917T, L. plantarum LRCC5310 detected the highest concentration of pyridoxal 5'-phosphate with 88.08 ± 0.67 nM in MRS broth. These results indicated that L. plantarum LRCC5310 could be used as a functional probiotic for vitamin B6 supplementation.

Selective Dissolution-Derived Nanoporous Design of Impurity-Free Bi2 Te3 Alloys with High Thermoelectric Performance.

Thermoelectric technology, which has been receiving attention as a sustainable energy source, has limited applications because of its relatively low conversion efficiency. To broaden their application scope, thermoelectric materials require a high dimensionless figure of merit (ZT). Porous structuring of a thermoelectric material is a promising approach to enhance ZT by reducing its thermal conductivity. However, nanopores do not form in thermoelectric materials in a straightforward manner; impurities are also likely to be present in thermoelectric materials. Here, a simple but effective way to synthesize impurity-free nanoporous Bi0.4 Sb1.6 Te3 via the use of nanoporous raw powder, which is scalably formed by the selective dissolution of KCl after collision between Bi0.4 Sb1.6 Te3 and KCl powders, is proposed. This approach creates abundant nanopores, which effectively scatter phonons, thereby reducing the lattice thermal conductivity by 33% from 0.55 to 0.37 W m-1 K-1 . Benefitting from the optimized porous structure, porous Bi0.4 Sb1.6 Te3 achieves a high ZT of 1.41 in the temperature range of 333-373 K, and an excellent average ZT of 1.34 over a wide temperature range of 298-473 K. This study provides a facile and scalable method for developing high thermoelectric performance Bi2 Te3 -based alloys that can be further applied to other thermoelectric materials.

CRISPRi-based programmable logic inverter cascade for antibiotic-free selection and maintenance of multiple plasmids.

Antibiotics have been widely used for plasmid-mediated cell engineering. However, continued use of antibiotics increases the metabolic burden, horizontal gene transfer risks, and biomanufacturing costs. There are limited approaches to maintaining multiple plasmids without antibiotics. Herein, we developed an inverter cascade using CRISPRi by building a plasmid containing a single guide RNA (sgRNA) landing pad (pSLiP); this inhibited host cell growth by repressing an essential cellular gene. Anti-sgRNAs on separate plasmids restored cell growth by blocking the expression of growth-inhibitory sgRNAs in pSLiP. We maintained three plasmids in Escherichia coli with a single antibiotic selective marker. To completely avoid antibiotic use and maintain the CRISPRi-based logic inverter cascade, we created a novel d-glutamate auxotrophic E. coli. This enabled the stable maintenance of the plasmid without antibiotics, enhanced the production of the terpenoid, (-)-α-bisabolol, and generation of an antibiotic-resistance gene-free plasmid. CRISPRi is therefore widely applicable in genetic circuits and may allow for antibiotic-free biomanufacturing.

Cytosine methylation regulates DNA bendability depending on the curvature.

Cytosine methylation plays an essential role in many biological processes, such as nucleosome inactivation and regulation of gene expression. The modulation of DNA mechanics may be one of the regulatory mechanisms influenced by cytosine methylation. However, it remains unclear how methylation influences DNA mechanics. Here, we show that methylation has contrasting effects on the bending property of dsDNA depending on DNA curvature. We directly applied bending force on 30 base pairs of dsDNA using a D-shaped DNA nanostructure and measured the degree of bending using single-molecule fluorescence resonance energy transfer without surface immobilization. When dsDNA is weakly bent, methylation increases the stiffness of dsDNA. The stiffness of dsDNA increased by approximately 8% with a single methylation site for 30 bp dsDNA. When dsDNA is highly bent by a strong force, it forms a kink, i.e., a sharp bending of dsDNA. Under strong bending, methylation destabilizes the non-kink form compared with the kink form, which makes dsDNA near the kink region apparently more bendable. However, if the kink region is methylated, the kink form is destabilized, and dsDNA becomes stiffer. As a result, methylation increases the stiffness of weakly bent dsDNA and concurrently can promote kink formation, which may stabilize the nucleosome structure. Our results provide new insight into the effect of methylation, showing that cytosine methylation has opposite effects on DNA mechanics depending on its curvature and methylation location.

Novel High-Throughput DNA Part Characterization Technique for Synthetic Biology.

This study presents a novel DNA part characterization technique that increases throughput by combinatorial DNA part assembly, solid plate-based quantitative fluorescence assay for phenotyping, and barcode tagging-based long-read sequencing for genotyping. We confirmed that the fluorescence intensities of colonies on plates were comparable to fluorescence at the single-cell level from a high-end, flow-cytometry device and developed a high-throughput image analysis pipeline. The barcode tagging-based long-read sequencing technique enabled rapid identification of all DNA parts and their combinations with a single sequencing experiment. Using our techniques, forty-four DNA parts (21 promoters and 23 RBSs) were successfully characterized in 72 h without any automated equipment. We anticipate that this high-throughput and easy-to-use part characterization technique will contribute to increasing part diversity and be useful for building genetic circuits and metabolic pathways in synthetic biology.

Single-molecule study of the effects of temperature, pH, and RNA base on the stepwise enzyme kinetics of 10-23 deoxyribozyme.

We investigated how the stepwise enzyme kinetics of 10-23 deoxyribozyme was affected by temperature, pH, and RNA residue of the substrate at the single-molecule level. A deoxyribozyme-substrate system was employed to temporally categorize a single-turnover reaction into four distinct steps: binding, cleavage, dissociation of one of the cleaved fragments, and dissociation of the other fragment. The dwell time of each step was measured as the temperature was varied from 26 to 34 °C, to which the transition state theory was applied to obtain the enthalpy and entropy of activation for individual steps. In addition, we found that only the cleavage step was significantly affected by pH, indicating that it involves deprotonation of a single proton. We also found that different RNA residues specifically affect the cleavage step and cause the dwell time to change by as much as 5 times.

Dynamic interaction of BRCA2 with telomeric G-quadruplexes underlies telomere replication homeostasis.

BRCA2-deficient cells precipitate telomere shortening upon collapse of stalled replication forks. Here, we report that the dynamic interaction between BRCA2 and telomeric G-quadruplex (G4), the non-canonical four-stranded secondary structure, underlies telomere replication homeostasis. We find that the OB-folds of BRCA2 binds to telomeric G4, which can be an obstacle during replication. We further demonstrate that BRCA2 associates with G-triplex (G3)-derived intermediates, which are likely to form during direct interconversion between parallel and non-parallel G4. Intriguingly, BRCA2 binding to G3 intermediates promoted RAD51 recruitment to the telomere G4. Furthermore, MRE11 resected G4-telomere, which was inhibited by BRCA2. Pathogenic mutations at the OB-folds abrogated the binding with telomere G4, indicating that the way BRCA2 associates with telomere is innate to its tumor suppressor activity. Collectively, we propose that BRCA2 binding to telomeric G4 remodels it and allows RAD51-mediated restart of the G4-driven replication fork stalling, simultaneously preventing MRE11-mediated breakdown of telomere.

The Evasion Mechanisms of Cancer Immunity and Drug Intervention in the Tumor Microenvironment.

Recently, in the field of cancer treatment, the paradigm has changed to immunotherapy that activates the immune system to induce cancer attacks. Among them, immune checkpoint inhibitors (ICI) are attracting attention as excellent and continuous clinical results. However, it shows not only limitations such as efficacy only in some patients or some indications, but also side-effects and resistance occur. Therefore, it is necessary to understand the factors of the tumor microenvironment (TME) that affect the efficacy of immunotherapy, that is, the mechanism by which cancer grows while evading or suppressing attacks from the immune system within the TME. Tumors can evade attacks from the immune system through various mechanisms such as restricting antigen recognition, inhibiting the immune system, and inducing T cell exhaustion. In addition, tumors inhibit or evade the immune system by accumulating specific metabolites and signal factors within the TME or limiting the nutrients available to immune cells. In order to overcome the limitations of immunotherapy and develop effective cancer treatments and therapeutic strategies, an approach is needed to understand the functions of cancer and immune cells in an integrated manner based on the TME. In this review, we will examine the effects of the TME on cancer cells and immune cells, especially how cancer cells evade the immune system, and examine anti-cancer strategies based on TME.

Ultrasensitive Near-Infrared Circularly Polarized Light Detection Using 3D Perovskite Embedded with Chiral Plasmonic Nanoparticles.

Chiral organic ligand-incorporated low-dimensional metal-halide perovskites have received increasing attention for next-generation photodetectors because of the direct detection capability of circularly polarized light (CPL), which overcomes the requirement for subsidiary optical components in conventional CPL photodetectors. However, most chiral perovskites have been based on low-dimensional structures that confine chiroptical responses to the ultraviolet (UV) or short-wavelength visible region and limit photocurrent due to their wide bandgap and poor charge transport. Here, chiroptical properties of 3D Cs0.05 FA0.5 MA0.45 Pb0.5 Sn0.5 I3 polycrystalline films are achieved by incorporating chiral plasmonic gold nanoparticles (AuNPs) into the mixed PbSn perovskite, without sacrificing its original optoelectronic properties. CPL detectors fabricated using chiral AuNP-embedded perovskite films can operate without external power input; they exhibit remarkable chirality in the near-infrared (NIR) region with a high anisotropy factor of responsivity (gres ) of 0.55, via giant plasmon resonance shift of chiral plasmonic AuNPs. In addition, a CPL detector array fabricated on a plastic substrate demonstrates highly sensitive self-powered NIR detection with superior flexibility and durability.

Quantitative assessment of engineered Cas9 variants for target specificity enhancement by single-molecule reaction pathway analysis.

There have been many engineered Cas9 variants that were developed to minimize unintended cleavage of off-target DNAs, but detailed mechanism for the way they regulate the target specificity through DNA:RNA heteroduplexation remains poorly understood. We used single-molecule FRET assay to follow the dynamics of DNA:RNA heteroduplexation for various engineered Cas9 variants with respect to on-target and off-target DNAs. Just like wild-type Cas9, these engineered Cas9 variants exhibit a strong correlation between their conformational structure and nuclease activity. Compared with wild-type Cas9, the fraction of the cleavage-competent state dropped more rapidly with increasing base-pair mismatch, which gives rise to their enhanced target specificity. We proposed a reaction model to quantitatively analyze the degree of off-target discrimination during the successive process of R-loop expansion. We found that the critical specificity enhancement step is activated during DNA:RNA heteroduplexation for evoCas9 and HypaCas9, while it occurs in the post-heteroduplexation stage for Cas9-HF1, eCas9, and Sniper-Cas9. This study sheds new light on the conformational dynamics behind the target specificity of Cas9, which will help strengthen its rational designing principles in the future.

Strain-Induced Modulation of Localized Surface Plasmon Resonance in Ultrathin Hexagonal Gold Nanoplates.

Anisotropic gold nanoplates (NPLs) have raised the interesting possibility that their reduced geometrical symmetry allows fine tuning of their optical properties associated with the excitation of localized surface plasmon resonances (LSPRs). Recent developments have greatly improved LSPR tunability by utilizing the spatial distribution of LSPR modes. However, the nanoscale interplay between defect-induced mechanical strain and the spatial variation of LSPR modes remains poorly understood. In this work, the combination of high spatial- and spectral-resolution mapping of LSPR modes and nanoscale strain mapping using aberration-corrected transmission electron microscopy are applied to investigate the nanoscale distribution of LSPR modes in an ultrathin single hexagonal gold NPL and the effect of defect-induced strains on its LSPR properties. The electron energy-loss spectral maps reveal four distinct LSPR components and intensity distributions of all LSPR modes in a hexagonal gold NPL. Furthermore, the strain maps provide experimental evidence that the tensile strain field induced by a Z-shaped faulted dipole is responsible for the asymmetric distribution of LSPR intensity in a hexagonal gold NPL.