Complete genome sequence of bacterium Peribacillus simplex strain IMGN11 from soil.

We report the complete genome sequence of Peribacillus simplex, a spore-forming bacterium originally classified within the Bacillus genus. Peribacillus simplex exhibits antibiotic, plant growth-promoting, and xenobiotic-degrading activities and resistance to environmental contamination. The genome sequence of Peribacillus simplex will provide insights into its capabilities and potential as a biocontrol agent.

Complete genome sequence of Pseudomonas fluorescens IMGN2 isolated from undisturbed soil.

Here, we report the complete genome sequence of Pseudomonas fluorescens IMGN2, highlighting its biocontrol and plant growth-promoting capabilities. The genome analysis reveals genetic features that contribute to its potential in agricultural biotechnology, including genes related to secondary metabolite synthesis and plant-microbe interactions.

Draft genome sequence of Priestia megaterium strain IMGN3 derived from soil.

Priestia megaterium sp. strain IMGN3 was isolated from the soil in South Korea. Here, we report its draft genome sequence, comprising 12 contigs with a total sequence length of 5.64 Mbp. This genome will provide valuable resources for future genomic studies, particularly focusing on plant growth promotion and biocontrol.

Draft genome for Pseudomonas alkylphenolica IMGN1, isolated from soil.

Biocontrol using organisms like Pseudomonas alkylphenolica offers a viable alternative to chemical pesticides, enhancing plant growth and reducing environmental impact. This study details the genome of Pseudomonas alkylphenolica IMGN1, a strain known for promoting plant growth, advancing our understanding of biocontrol mechanisms.

Complete genome sequence of Bacillus paramobilis sp. strain IMGN7 from soil.

Here, we report the complete genome sequence of Bacillus paramobilis sp. strain IMGN7, which was isolated from soil in South Korea. Its complete genome size is 5.28 Mbp. This genome will provide various insights for further studies about their function as biocontrol agents, such as bioremediation and antibiosis.

Draft genome sequence of bacterium Bacillus proteolyticus strain IMGN4 from soil.

Here, we present the draft genome of Bacillus proteolyticus IMGN4, the gram-positive, soil-dwelling bacterium discovered in mountain Maemi, Republic of Korea in May 2019. The assembly resulted in 7 contigs, comprising a total of 6,063,502 base pairs and have 6,115 coding sequences.

Ultrasonographic evaluation of nail matrix topography for preservative nail surgery of nail unit melanoma.

Recently, functional or preservative surgery has been preferred for nail unit melanoma; however, complete resection of the nail unit, particularly the matrix, is challenging because of its complex structure. This study aims to measure the distance of important nail structures through ultrasonography. Herein, 14 patients without nail deformity were included. The length from the nail cuticle to the distal interphalangeal joint (distance X), to the attachment part of the extensor muscle (distance A), to the median proximal end of the nail matrix (distance B), and to the lateral proximal end of the nail matrix (distance C) were measured. In the axial plane, the length from the highest point of the nail plate to the bottom of the distal phalanx (distance Y) and to the lateral tip of the nail plate (distance D) were measured. On the first fingernail, third fingernail, first toenail, and third toenail, the mean ratio A:X, ratio B:X, ratio C:X, and ratio D:Y were 78.6%, 44.3%, 57.2%, 40.1%, and 84.6%; 55.9%, 64.9%, 40.2%, and 66.4%; 35.6%, 50.8%, 34.3%, and 81.9%; and 57.2%, 59.6%, and 31.7%, respectively. Nail units are often invisible to the naked eye; thus, this study will help identify the approximate scope of excision.

Improving the Generalizability and Performance of an Ultrasound Deep Learning Model Using Limited Multicenter Data for Lung Sliding Artifact Identification.

Deep learning (DL) models for medical image classification frequently struggle to generalize to data from outside institutions. Additional clinical data are also rarely collected to comprehensively assess and understand model performance amongst subgroups. Following the development of a single-center model to identify the lung sliding artifact on lung ultrasound (LUS), we pursued a validation strategy using external LUS data. As annotated LUS data are relatively scarce-compared to other medical imaging data-we adopted a novel technique to optimize the use of limited external data to improve model generalizability. Externally acquired LUS data from three tertiary care centers, totaling 641 clips from 238 patients, were used to assess the baseline generalizability of our lung sliding model. We then employed our novel Threshold-Aware Accumulative Fine-Tuning (TAAFT) method to fine-tune the baseline model and determine the minimum amount of data required to achieve predefined performance goals. A subgroup analysis was also performed and Grad-CAM++ explanations were examined. The final model was fine-tuned on one-third of the external dataset to achieve 0.917 sensitivity, 0.817 specificity, and 0.920 area under the receiver operator characteristic curve (AUC) on the external validation dataset, exceeding our predefined performance goals. Subgroup analyses identified LUS characteristics that most greatly challenged the model's performance. Grad-CAM++ saliency maps highlighted clinically relevant regions on M-mode images. We report a multicenter study that exploits limited available external data to improve the generalizability and performance of our lung sliding model while identifying poorly performing subgroups to inform future iterative improvements. This approach may contribute to efficiencies for DL researchers working with smaller quantities of external validation data.

Clinical Role of Upfront F-18 FDG PET/CT in Determining Biopsy Sites for Lung Cancer Diagnosis.

PURPOSE: This study aimed to investigate the impact of FDG PET/CT timing for biopsy site selection in patients with stage IV lung cancer regarding complications and diagnostic yield. METHODS: This retrospective analysis was performed on 1297 patients (924 men and 373 women with a mean age of 71.4 ± 10.2 years) who underwent percutaneous needle biopsy (PNB) for stage IV lung cancer diagnosis in two hospitals. Data collected included the patient's characteristics, order date of the biopsy and PET/CT exams, biopsy target site (lung or non-lung), guidance modality, complications, sample adequacy, and diagnostic success. Based on the order date of the PNB and PET/CT exams, patients were categorized into upfront and delayed PET/CT groups. RESULTS: PNB for non-lung targets resulted in significantly lower rates of minor (8.1% vs. 16.2%), major (0.2% vs. 3.4%), and overall complications (8.3% vs. 19.6%) compared to PNB for lung targets (p < 0.001 for all types of complications). Compared to the delayed PET/CT group, the upfront PET/CT group exhibited a lower probability of lung target selection of PNB (53.9% vs. 67.1%, p < 0.001), including a reduced incidence of major complications (1.0% vs. 2.9%, p = 0.031). Moreover, there was no significant difference in the occurrence of minor and total complications between the two groups. Upfront PET/CT and delayed PET/CT groups showed no significant difference regarding sample adequacy and diagnostic success. CONCLUSIONS: Upfront PET/CT may have an impact on the selection of the biopsy site for patients with advanced lung cancer, which could result in a lower rate of major complications with no change in the diagnostic yield. Upfront PET/CT demonstrates potential clinical implications for enhancing the safety of lung cancer diagnosis in clinical practice.

Three consecutive cytosolic glycolysis enzymes modulate autophagic flux.

Autophagy serves as an important recycling route for the growth and survival of eukaryotic organisms in nutrient-deficient conditions. Since starvation induces massive changes in the metabolic flux that are coordinated by key metabolic enzymes, specific processing steps of autophagy may be linked with metabolic flux-monitoring enzymes. We attempted to identify carbon metabolic genes that modulate autophagy using VIGS screening of 45 glycolysis- and Calvin-Benson cycle-related genes in Arabidopsis (Arabidopsis thaliana). Here, we report that three consecutive triose-phosphate-processing enzymes involved in cytosolic glycolysis, triose-phosphate-isomerase (TPI), glyceraldehyde-3-phosphate dehydrogenase (GAPC), and phosphoglycerate kinase (PGK), designated TGP, negatively regulate autophagy. Depletion of TGP enzymes causes spontaneous autophagy induction and increases AUTOPHAGY-RELATED 1 (ATG1) kinase activity. TGP enzymes interact with ATG101, a regulatory component of the ATG1 kinase complex. Spontaneous autophagy induction and abnormal growth under insufficient sugar in TGP mutants are suppressed by crossing with the atg101 mutant. Considering that triose-phosphates are photosynthates transported to the cytosol from active chloroplasts, the TGP enzymes would be strategically positioned to monitor the flow of photosynthetic sugars and modulate autophagy accordingly. Collectively, these results suggest that TGP enzymes negatively control autophagy acting upstream of the ATG1 complex, which is critical for seedling development.

Synthesis of Isolated DNA Aptamer and Its Application of AC-Electrothermal Flow-Based Rapid Biosensor for the Detection of Dengue Virus in a Spiked Sample.

Dengue fever is an infectious disease caused by the dengue virus (DENV) and is transmitted by mosquitoes in tropical and subtropical regions. The early detection method at a low cost is essential. To address this, we synthesized the isolated DENV aptamer for fabricating a rapid electrochemical biosensor on a Au interdigitated microgap electrode (AuIMGE). The DENV aptamers were generated using the SELEX (systemic evolution of ligands by exponential enrichment) method for binding to DENV surface envelope proteins. To reduce the manufacturing cost, unnecessary nucleotide sequences were excluded from the isolation process of the DENV aptamer. To reduce the detection time, the alternating current electrothermal flow (ACEF) technique was applied to the fabricated biosensor, which can shorten the detection time to 10 min. The performance of the biosensor was evaluated using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). In the diluted DENV protein solution, the linear range of the concentrations was from 1 pM to 1 µM and the LOD was 76.7 fM. Moreover, the proposed biosensor detected DENV in a diluted spiked sample at a linear range of 10-6 to 106 TCID50/mL, while the detection performance was proven with an LOD of 1.74 × 10-7 TCID50/mL along with high selectivity.

Construction of a rapid electrochemical biosensor consisting of a nanozyme/aptamer conjugate for waterborne microcystin detection.

Microcystin-LR (MC-LR) is a hepatotoxin generated by the excessive proliferation of cyanobacteria, which is a threat to humans and wildlife. Therefore, rapid detection of MC-LR is an important challenge. This study describes a rapid electrochemical biosensor comprising nanozymes and aptamers. Alternating current electrothermal flow (ACEF) significantly reduced the MC-LR detection period to 10 min. We also used MnO2/MC-LR aptamer conjugates to improve the sensitivity to MC-LR detection. Here, MnO2 amplified the electrochemical signal and the aptamer showed high selectivity for MC-LR. Under the optimal conditions, the limit of detection (LOD) and selectivity in freshwater were detected using cyclic voltammetry and differential pulse voltammetry. As a result, an LOD of 3.36 pg mL-1 was observed in the linear concentration range of 10 pg mL-1 to 1 µg mL-1. This study quickly and sensitively detected MC-LR in a situation where it causes serious damage worldwide. In addition, the ACEF technology introduction is the first example of MC-LR detection, suggesting a wide range of possibilities for MC-LR biosensors.

Correction: Optical humidity sensors based on lead-free Cu-based perovskite nanomaterials.

[This corrects the article DOI: 10.1039/D2NA00168C.].

Optical humidity sensors based on lead-free Cu-based perovskite nanomaterials.

Organometallic halide perovskite materials possess unique and tunable optical properties with a wide range of optoelectronic applications. However, these materials suffer from humidity-driven degradation in ambient atmospheres. In this paper we investigate stable copper-based perovskite nanocrystals for potential use in humidity sensors, specifically examining their unique humidity-dependent optical properties and reversibility. We controlled stoichiometric ratios of Cu-based perovskites and demonstrated that (methylammonium)2CuBr4 nanocrystals showed excellent reversible physisorption of water molecules. These perovskite nanocrystals exhibited reversible hydro-optical properties, including transparency changes in response to variations in relative humidity under ambient conditions. The perovskite nanomaterial humidity sensor was highly reliable and stable, with a linear correlation in a relative humidity range of 7% to 98%. Accordingly, the lead-free Cu-based perovskite materials developed herein have the potential to be employed as real-time, self-consistent humidity sensors.

Silencing of the Target of Rapamycin Complex Genes Stimulates Tomato Fruit Ripening.

The target of rapamycin complex (TORC) plays a key role in plant cell growth and survival by regulating the gene expression and metabolism according to environmental information. TORC activates transcription, mRNA translation, and anabolic processes under favorable conditions, thereby promoting plant growth and development. Tomato fruit ripening is a complex developmental process promoted by ethylene and specific transcription factors. TORC is known to modulate leaf senescence in tomato. In this study, we investigated the function of TORC in tomato fruit ripening using virus-induced gene silencing (VIGS) of the TORC genes, TOR, lethal with SEC13 protein 8 (LST8), and regulatory-associated protein of TOR (RAPTOR). Quantitative reverse transcription-polymerase chain reaction showed that the expression levels of tomato TORC genes were the highest in the orange stage during fruit development in Micro-Tom tomato. VIGS of these TORC genes using stage 2 tomato accelerated fruit ripening with premature orange/red coloring and decreased fruit growth, when control tobacco rattle virus 2 (TRV2)-myc fruits reached the mature green stage. TORC-deficient fruits showed early accumulation of carotenoid lycopene and reduced cellulose deposition in pericarp cell walls. The early ripening fruits had higher levels of transcripts related to fruit ripening transcription factors, ethylene biosynthesis, carotenoid synthesis, and cell wall modification. Finally, the early ripening phenotype in Micro-Tom tomato was reproduced in the commercial cultivar Moneymaker tomato by VIGS of the TORC genes. Collectively, these results demonstrate that TORC plays an important role in tomato fruit ripening by modulating the transcription of various ripening-related genes.

Rapid electrochemical dual-target biosensor composed of an Aptamer/MXene hybrid on Au microgap electrodes for cytokines detection.

Rapid detection methods for cytokine storm markers, such as tumor necrosis factor α (TNF-α) and interferon gamma (IFN-γ), are required. Herein, we describe the fabrication of a rapid electrochemical dual-target biosensor composed of aptamer/MXene (Ti3C2) nanosheet on an Au microgap electrode. Alternating current electrothermal flow (ACEF) significantly reduced the detection time (<10 min) to achieve the rapid biosensor construction. Additionally, MXene nanosheet was synthesized to improve the detection sensitivity. A dual-type Au microgap electrode was designed to measure TNF-α and IFN-γ levels using a single biosensor. Moreover, it performs 12 measurements using a small sample volume. To reduce detection time with stable aptamer-target complex formation, various ACEF conditions were evaluated and optimized to 10 min. Using the optimal conditions, the limit of detection (LOD) and selectivity were determined by electrochemical impedance spectroscopy (EIS). A linear region was observed in the concentration range of 1 pg/mL to 10 ng/mL of TNF-α and IFN-γ. The LOD of TNF-α and IFN-γ were 0.15 pg/mL and 0.12 pg/mL within 10 min, respectively. Furthermore, the proposed biosensor detected TNF-α and IFN-γ diluted in 10% human serum in the concentration range of 1 pg/mL to 10 ng/mL with LODs of 0.25 pg/mL and 0.26 pg/mL, respectively.

RGI-GOLVEN signaling promotes cell surface immune receptor abundance to regulate plant immunity.

Plant immune responses must be tightly controlled for proper allocation of resources for growth and development. In plants, endogenous signaling peptides regulate developmental and growth-related processes. Recent research indicates that some of these peptides also have regulatory functions in the control of plant immune responses. This classifies these peptides as phytocytokines as they show analogies with metazoan cytokines. However, the mechanistic basis for phytocytokine-mediated regulation of plant immunity remains largely elusive. Here, we identify GOLVEN2 (GLV2) peptides as phytocytokines in Arabidopsis thaliana. GLV2 signaling enhances sensitivity of plants to elicitation with immunogenic bacterial elicitors and contributes to resistance against virulent bacterial pathogens. GLV2 is perceived by ROOT MERISTEM GROWTH FACTOR 1 INSENSITIVE (RGI) receptors. RGI mutants show reduced elicitor sensitivity and enhanced susceptibility to bacterial infection. RGI3 forms ligand-induced complexes with the pattern recognition receptor (PRR) FLAGELLIN SENSITIVE 2 (FLS2), suggesting that RGIs are part of PRR signaling platforms. GLV2-RGI signaling promotes PRR abundance independent of transcriptional regulation and controls plant immunity via a previously undescribed mechanism of phytocytokine activity.

Oral administration of East Asian herbal medicine for peripheral neuropathy: A protocol for systematic review and meta-analysis with using association rule analysis to identify core herb pattern.

BACKGROUND: Peripheral neuropathy (PN) is one of the most common medical problems encountered. Since the pathophysiology and symptom manifestation characteristics of PN are very diverse, it is difficult to provide an appropriate treatment. East Asian herbal medicine (EAHM) has long contributed to the treatment of neurological and pain disorders. The goal of this systematic review is to measure the efficacy and safety of EAHM for PN and to identify core herb patterns. In order to derive a more conservative result, a random effect model will be applied regardless of the significance of heterogeneity. METHODS: We will search 10 databases to identify suitable studies. There will be no restrictions regarding language or publication date. Primary outcomes will be nerve conduction velocity and response rate. Secondary outcomes will be any objective tool that can measure the efficacy of EAHM, and adverse events will be included. We will perform a meta-analysis of trials with the same intervention and outcome with comparator in a similar population. Meanwhile, in order to explore significant potential correlation in herb preparation, association rule analysis based on the Apriori algorithm will be performed on the collected composition data of herbal medicines. RESULTS: This study will provide scientific evidence for the treatment of EAHM for PN. CONCLUSIONS: Based on the results of this review, it is expected that the efficacy and safety of EAHM for PN can be confirmed. In addition, through additional analysis using data mining techniques, it will be possible to present a core herb pattern related to this research topic.

Chaperone-like protein DAY plays critical roles in photomorphogenesis.

Photomorphogenesis, light-mediated development, is an essential feature of all terrestrial plants. While chloroplast development and brassinosteroid (BR) signaling are known players in photomorphogenesis, proteins that regulate both pathways have yet to be identified. Here we report that DE-ETIOLATION IN THE DARK AND YELLOWING IN THE LIGHT (DAY), a membrane protein containing DnaJ-like domain, plays a dual-role in photomorphogenesis by stabilizing the BR receptor, BRI1, as well as a key enzyme in chlorophyll biosynthesis, POR. DAY localizes to both the endomembrane and chloroplasts via its first transmembrane domain and chloroplast transit peptide, respectively, and interacts with BRI1 and POR in their respective subcellular compartments. Using genetic analysis, we show that DAY acts independently on BR signaling and chlorophyll biogenesis. Collectively, this work uncovers DAY as a factor that simultaneously regulates BR signaling and chloroplast development, revealing a key regulator of photomorphogenesis that acts across cell compartments.

Coding of plant immune signals by surface receptors.

The detection of molecular signals derived from other organisms is central to the evolutionary success of plants in the colonization of Earth. The sensory coding of these signals is critical for marshaling local and systemic immune responses that keep most invading organisms at bay. Plants detect immune signals inside and outside their cells using receptors. Here, we focus on receptors that function at the cell surface. We present recent work that expands our understanding of the repertoire of immune signals sensed by this family of receptors.