Exploring the comparative genome of rice pathogen Burkholderia plantarii: unveiling virulence, fitness traits, and a potential type III secretion system effector

This study presents a comprehensive genomic analysis of Burkholderia plantarii, a rice pathogen that causes blight and grain rot in seedlings. The entire genome of B. plantarii KACC 18964 was sequenced, followed by a comparative genomic analysis with other available genomes to gain insights into its virulence, fitness, and interactions with rice. Multiple secondary metabolite gene clusters were identified. Among these, 12 demonstrated varying similarity levels to known clusters linked to bioactive compounds, whereas eight exhibited no similarity, indicating B. plantarii as a source of potentially novel secondary metabolites. Notably, the genes responsible for tropolone and quorum sensing were conserved across the examined genomes. Additionally, B. plantarii was observed to possess three complete CRISPR systems and a range of secretion systems, exhibiting minor variations among the analyzed genomes. Genomic islands were analyzed across the four genomes, and a detailed study of the B. plantarii KACC 18964 genome revealed 59 unique islands. These islands were thoroughly investigated for their gene contents and potential roles in virulence. Particular attention has been devoted to the Type III secretion system (T3SS), a crucial virulence factor. An in silico analysis of potential T3SS effectors identified a conserved gene, aroA. Further mutational studies, in planta and in vitro analyses validated the association between aroA and virulence in rice. Overall, this study enriches our understanding of the genomic basis of B. plantarii pathogenicity and emphasizes the potential role of aroA in virulence. This understanding may guide the development of effective disease management strategies

Synthesis of Vapochromic Dyes Having Sensing Properties for Vapor Phase of Organic Solvents Used in Semiconductor Manufacturing Processes and Their Application to Textile-Based Sensors

Two vapochromic dyes (DMx and DM) were synthesized to be used for textile-based sensors detecting the vapor phase of organic solvents. They were designed to show sensitive color change properties at a low concentration of vapors at room temperature. They were applied to cotton fabrics as a substrate of the textile-based sensors to examine their sensing properties for nine organic solvents frequently used in semiconductor manufacturing processes, such as trichloroethylene, dimethylacetamide, iso-propanol, methanol, n-hexane, ethylacetate, benzene, acetone, and hexamethyldisilazane. The textile sensor exhibited strong sensing properties of polar solvents rather than non-polar solvents. In particular, the detection of dimethylacetamide was the best, showing a color difference of 15.9 for DMx and 26.2 for DM under 300 ppm exposure. Even at the low concentration of 10 ppm of dimethylacetamide, the color change values reached 7.7 and 13.6, respectively, in an hour. The maximum absorption wavelength of the textile sensor was shifted from 580 nm to 550 nm for DMx and 550 nm to 540 nm for DM, respectively, due to dimethylacetamide exposure. The sensing mechanism was considered to depend on solvatochromism, the aggregational properties of the dyes and the adsorption amounts of the solvent vapors on the textile substrates to which the dyes were applied. Finally, the reusability of the textile sensor was tested for 10 cycles

User Guide for KOTE: Korean Online Comments Emotions Dataset

Sentiment analysis that classifies data into positive or negative has been dominantly used to recognize emotional aspects of texts, despite the deficit of thorough examination of emotional meanings. Recently, corpora labeled with more than just valence are built to exceed this limit. However, most Korean emotion corpora are small in the number of instances and cover a limited range of emotions. We introduce KOTE dataset. KOTE contains 50k (250k cases) Korean online comments, each of which is manually labeled for 43 emotion labels or one special label (NO EMOTION) by crowdsourcing (Ps = 3,048). The emotion taxonomy of the 43 emotions is systematically established by cluster analysis of Korean emotion concepts expressed on word embedding space. After explaining how KOTE is developed, we also discuss the results of finetuning and analysis for social discrimination in the corpus.Comment: 16 pages, 4 figure

Poly(vinylalcohol) (PVA) Assisted Sol-Gel Fabrication of Porous Carbon Network-Na3V2(PO4)3 (NVP) Composites Cathode for Enhanced Kinetics in Sodium Ion Batteries

Na3V2(PO4)3 is regarded as one of the promising cathode materials for next-generation sodium ion batteries, but its undesirable electrochemical performances due to inherently low electrical conductivity have limited its direct use for applications. Motivated by the limit, this study employed a porous carbon network to obtain a porous carbon network–Na3V2(PO4)3 composite by using poly(vinylalcohol) assised sol-gel method. Compared with the typical carbon-coating approach, the formation of a porous carbon network ensured short ion diffusion distances, percolating electrolytes by distributing nanosized Na3V2(PO4)3 particles in the porous carbon network and suppressing the particle aggregation. As a result, the porous carbon network–Na3V2(PO4)3 composite exhibited improved electrochemical performances, i.e., a higher specific discharge capacity (~110 mAh g−1 at 0.1 C), outstanding kinetic properties (~68 mAh g−1 at 50 C), and stable cyclic stability (capacity retention of 99% over 100 cycles at 1 C)

Robust membrane protein tweezers reveal the folding speed limit of helical membrane proteins

Single-molecule tweezers, such as magnetic tweezers, are powerful tools for probing nm-scale structural changes in single membrane proteins under force. However, the weak molecular tethers used for the membrane protein studies have limited the observation of long-time, repetitive molecular transitions due to force-induced bond breakage. The prolonged observation of numerous transitions is critical in reliable characterizations of structural states, kinetics, and energy barrier properties. Here, we present a robust single-molecule tweezer method that uses dibenzocyclooctyne cycloaddition and traptavidin binding, enabling the estimation of the folding ???speed limit??? of helical membrane proteins. This method is >100 times more stable than a conventional linkage system regarding the lifetime, allowing for the survival for ~12 hr at 50 pN and ~1000 pulling cycle experiments. By using this method, we were able to observe numerous structural transitions of a designer single-chained transmembrane homodimer for 9 hr at 12 pN and reveal its folding pathway including the hidden dynamics of helix-coil transitions. We characterized the energy barrier heights and folding times for the transitions using a model-independent deconvolution method and the hidden Markov modeling analysis, respectively. The Kramers rate framework yields a considerably low-speed limit of 21 ms for a helical hairpin formation in lipid bilayers, compared to ??s scale for soluble protein folding. This large discrepancy is likely due to the highly viscous nature of lipid membranes, retarding the helix-helix interactions. Our results offer a more valid guideline for relating the kinetics and free energies of membrane protein folding

Tribological Behaviors of Ni-P Coatings on PEO-Treated AA1050 Alloy

Tribological behaviors of the plasma electrolytic oxidation (PEO)-treated Al1050 alloy surface without and with Ni-P deposits was examined by analyzing of the width of abrasion groove, weight loss, friction coefficient and composition at the wear track after a 100 m ball-on-disc test. The surface color, surface and cross-sectional morphologies and surface roughness (Ra) were also investigated to explain different wear behaviors of PEO films without and with Ni-P deposit. After the 100 m ball-on-disc test, a circular abrasion groove with relatively large width and shallow depth was formed when Ni-P particles cover the top surface of PEO films, but a relatively narrow and deep circular abrasion groove was formed on the Ni-P layer-covered PEO film surface. Iron was only detected at the wear track of 5 and 10 μm PEO films without Ni-P deposit, suggesting that the steel ball is worn out by the PEO films but not by the Ni-P deposit. An extremely large amount of weight loss was obtained from the Ni-P layer-covered PEO film surface, which could be related to the high density and low hardness of the Ni-P layer

Understanding <i>Burkholderia glumae</i> BGR1 Virulence through the Application of Toxoflavin-Degrading Enzyme, TxeA

Rice (Oryzae sativa cv. dongjin) is a cornerstone of global food security; however, Burkholderia glumae BGR1, which is responsible for bacterial panicle blight (BPB), threatens its productive output, with dire consequences for rice and other crops. BPB is primarily caused by toxoflavin, a potent phytotoxin that disrupts plant growth at various developmental stages. Therefore, understanding the mechanisms through which toxoflavin and BPB affect rice plants is critical. Toxoflavin biosynthesis in B. glumae BGR1 relies on the toxABCDE operon, with ToxA playing a central role. In response to this threat, our study explores a metagenome-derived toxoflavin-degrading enzyme, TxeA, as a potential defense mechanism against toxoflavin’s destructive impact. TxeA-induced degradation of toxoflavin represents a potential strategy to mitigate crop damage. We introduce a groundbreaking approach: engineering transgenic rice plants to produce toxoflavin-degrading enzymes. These genetically modified plants, armed with TxeA, hold significant potential for combating toxoflavin-related crop losses. However, removal of toxoflavin, a major virulence factor in B. glumae BGR1, does not completely inhibit virulence. This innovative perspective offers a new shift from pathogen eradication to leveraging transgenic plants’ power, offering a beacon of hope for crop protection and disease management. Our study offers insights into the intricate interplay between toxoflavin, BPB, and TxeA, providing a promising avenue to safeguard rice crops, ensure food security, and potentially enhance the resilience of various agricultural crops to B. glumae BGR1-induced diseases

alpha-Gallium Oxide Films on Microcavity-Embedded Sapphire Substrates Grown by Mist Chemical Vapor Deposition for High-Breakdown Voltage Schottky Diodes

alpha-Gallium oxide, with its large band gap energy, is a promising material for utilization in power devices. Sapphire, which has the same crystal structure as alpha-Ga2O3, has been used as a substrate for alpha-Ga2O3 epitaxial growth. However, lattice and thermal expansion coefficient mismatches generate a high density of threading dislocations (TDs) and cracks in films. Here, we demonstrated the growth of alpha-Ga2O3 films with reduced TD density and residual stress on microcavity-embedded sapphire substrates (MESS). We fabricated the two types of substrates with microcavities: diameters of 1.5 and 2.2 mu m, respectively. We confirmed that round conical-shaped cavities with smaller diameters are beneficial for the lateral overgrowth of alpha-Ga2O3 crystals with lower TD densities by mist chemical vapor deposition. We could obtain crack-free high-crystallinity alpha-Ga2O3 films on MESS, while the direct growth on a bare sapphire substrate resulted in an alpha-Ga2O3 film with a number of cracks. TD densities of alpha-Ga2O3 films on MESS with 1.5 and 2.2 mu m cavities were measured to be 1.77 and 6.47 x 10(8) cm(-2), respectively. Furthermore, cavities in MESS were certified to mitigate the residual stress via the redshifted Raman peaks of alpha-Ga2O3 films. Finally, we fabricated Schottky diodes based on alpha-Ga2O3 films grown on MESS with 1.5 and 2.2 mu m cavities, which exhibited high breakdown voltages of 679 and 532 V, respectively. This research paves the way to fabricating Schottky diodes with high breakdown voltages based on high-quality alpha-Ga2O3 films.N

Origin of extra diffraction spots for high crystalline alpha-Ga2O3

This work has investigated the microstructure characteristics of high-quality alpha-Ga2O3 thin film grown on the Al2O3 single crystal substrate membrane. Hetero-epitaxial alpha Ga2O3 crystals reveal the formation of a three-fold symmetry at the initial stage of the growth by the oxygen template provided by the Al2O3. Inversion domains are found, and they have a 180 &amp; DEG; inverted configuration from the surroundings. These IDs lead to extra diffraction spots when observed along [110] and [010].(c) 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Y