• Mass Spectrometry Letters
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• v.13 no.4
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• pp.106-114
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• 2022

A rapid and reliable approach to the identification of microorganisms is a critical requirement for large-scale culturomics analysis. MALDI-TOF MS is a suitable technique that can be a better alternative to conventional biochemical and gene sequencing methods as it is economical both in terms of cost and labor. In this review, the applications of MALDI-TOF MS for the comprehensive identification of microorganisms and bacterial strain typing for culturomics-based approaches for various environmental studies including bioremediation, plant sciences, agriculture and food microbiology have been widely explored. However, the restriction of this technique is attributed to insufficient coverage of the mass spectral database. To improve the applications of this technique for the identification of novel isolates, the spectral database should be updated with the peptide mass fingerprint (PMF) of type strains with not only microbes with clinical relevance but also from various environmental sources. Further, the development of enhanced sample processing methods and new algorithms for automation and de-replication of isolates will increase its application in microbial ecology studies.

• Mycobiology
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• v.49 no.6
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• pp.551-558
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• 2021

The Federated States of Micronesia (FSM) is an island country in the western Pacific and is a known biodiversity hotspot. However, a relatively small number of fungi (236 species) have been reported till July 2021. Since fungi play major ecological roles in ecosystems, we investigated the fungal diversity of FSM from various sources over 2016 and 2017 and constructed a local fungal inventory, which also included the previously reported species. Fruiting bodies were collected from various host trees and fungal strains were isolated from marine and terrestrial environments. A total of 99 species, of which 78 were newly reported in the FSM, were identified at the species level using a combination of molecular and morphological approaches. Many fungal species were specific to the environment, host, or source. Upon construction of the fungal inventory, 314 species were confirmed to reside in the FSM. This inventory will serve as an important basis for monitoring fungal diversity and identifying novel biological resources in FSM.

• Mycobiology
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• v.50 no.6
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• pp.429-438
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• 2022

Two fungal strains belonging to Ascomycota were discovered in Gyeonggi-do, Korea, during this investigation of soil microfungi and microbiota of insects. The strain KNUF-20-047 produced milky white on the back and a milky creamy center to white toward the margin on the front side of colonies. Conversely, the closest Xenoacremonium falcatus displayed a pale luteous to luteous center, white toward margins on the front side, and pale luteous or luteous pigment on the back side, whereas X. recifei produced white colonies. The conidiophores of KNUF-20-047 were slightly larger than those of X. falcatus, and the conidia were distinct from X. recifei. Strain KNUF-20-NI-005 produced light brown to subhyaline conidiophores up to 56.0 lm tall, whereas Rhinocladiella anceps displayed golden to dark brown conidiophores up to 350 lm. Strain KNUF-20-NI-005 also produced larger conidia than R. anceps but smaller than R. coryli and R. fasciculata. Moreover, the molecular phylogeny strongly supports the detailed description and illustration of each proposed species to be designated as Xenoacremonium minutisporum sp. nov. and Rhinocladiella terrigenum sp. nov. in Korea.

• Research in Plant Disease
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• v.29 no.1
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• pp.72-78
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• 2023

In September 2021, gray-to-brown discoloration and expanding water-soaked lesions were observed on the outer and inner layers and the core of kimchi cabbage (Brassica rapa subsp. pekinensis) in fields located in Samcheok, Gangwondo, Korea. A bacterial strain designated as KNUB-02-21 was isolated from infected cabbage samples. Phylogenetic analysis based on the sequences of the 16S rRNA region and the dnaX, leuS, and recA genes confirmed that the strain was affiliated with Pectobacterium versatile. Additionally, the biochemical and morphological profiles of the isolate were similar to those of P. versatile. Based on these results, the isolate was identified as a novel strain of P. versatile. Healthy kimchi cabbage slices developed soft rot upon inoculation with P. versatile KNUB-02-21 and exhibited symptoms similar to those observed in the diseased plants in fields. The re-isolated strains were similar to those of P. versatile. Prior to our study, P. versatile as the causative pathogen of kimchi cabbage soft rot had not been reported in Korea.

• Geomechanics and Engineering
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• v.33 no.3
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• pp.271-277
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• 2023

This article investigates the effect of viscoelastic foundations on the waves' dispersion in a beam made of ceramic-metal functionally graded material (FGM) with microstructural defects. The beam is considered to be shear deformable, and a simple three-unknown sinusoidal integral higher-order shear deformation beam theory is applied to represent the beam's displacement field. Novel to this study is the investigation of the impact of viscosity damping on imperfect FG beams, utilizing a few-unknowns theory. The stresses and strains are obtained using the two-dimensional elasticity relations of FGM, neglecting the normal strain in the beam's depth direction. The variational operation is employed to define the dispersion relations of the FGM beam. The influences of the material gradation exponent, the beam's thickness, the porosity, and visco-Pasternak foundation parameters are represented. Results showed that phase velocity was inversely proportional to the damping and porosity of the beams. Additionally, the foundation viscous damping had a stronger influence on wave velocity when porosity volume fractions were low.

• Earthquakes and Structures
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• v.25 no.2
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• pp.113-123
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• 2023

A novel type of buckling restrained brace with built-up angle steel was developed. The core segment was formed by welding angle steel, and the middle section was reduced by cutting technology to solve the problem that the end of BRB was easy to buckle. The experimental program has been undertaken to study the performance of BRBs with different unbonded materials (silica gel, kraft paper) and different filler materials (ordinary concrete, full light-weight concrete). Four specimens were designed and fabricated for low cycle reciprocating load tests to simulate horizontal seismic action. The failure mode, hysteretic curves, tension-compression unbalance coefficient and other mechanical parameters were compared and analyzed. The finite element software ABAQUS was used to conduct numerical simulation, and the simulation results were compared with the experimental phenomena. The test results indicated that the hysteretic curve of each specimen was plump. Sustaining cumulative strains of each specimen was greater than the minimum value of 200 required by the code, which indicated the ductility of BRB was relatively good. The energy dissipation coefficient of the specimen with silica gel as unbonded material was about 13% higher than that with kraft paper. The experimental results were in good agreement with the simulation results.

• Journal of Microbiology and Biotechnology
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• v.33 no.8
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• pp.1050-1056
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• 2023

Weizmannia coagulans (formerly Bacillus coagulans) is Gram-positive, and spore-forming bacteria causing food spoilage, especially in acidic canned food products. To control W. coagulans, we isolated a bacteriophage Youna2 from a sewage sludge sample. Morphological analysis revealed that phage Youna2 belongs to the Siphoviridae family with a non-contractile and flexible tail. Youna2 has 52,903 bp double-stranded DNA containing 61 open reading frames. There are no lysogeny-related genes, suggesting that Youna2 is a virulent phage. plyYouna2, a putative endolysin gene was identified in the genome of Youna2 and predicted to be composed of a N-acetylmuramoyl-L-alanine amidase domain (PF01520) at the N-terminus and unknown function DUF5776 domain (PF19087) at the C-terminus. While phage Youna2 has a narrow host range, infecting only certain strains of W. coagulans, PlyYouna2 exhibited a broad antimicrobial spectrum beyond the Bacillus genus. Interestingly, PlyYouna2 can lyse Gram-negative bacteria such as Escherichia coli, Yersinia enterocolitica, Pseudomonas putida and Cronobacter sakazakii without other additives to destabilize bacterial outer membrane. To the best of our knowledge, Youna2 is the first W. coagulans-infecting phage and we speculate its endolysin PlyYouna2 can provide the basis for the development of a novel biocontrol agent against various foodborne pathogens.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.3-13
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• 2020

Pseudomonas aeruginosa is a ubiquitous gram-negative bacterium causing serious infections. The P. aeruginosa T3SS is a syringe-like apparatus on the bacterial surface, with 4 effector toxins: ExoS, ExoT, ExoY, and ExoU. Here, we investigated the effect of ExoS and ExoT of the T3SS of P. aeruginosa K strain (PAK). The type three secretion system (T3SS) is a major virulence system of Pseudomonas aeruginosa (P. aeruginosa). The effector protein Exotoxin S (ExoS) produced by P. aeruginosa is secreted into the host cells via the T3SS. For the purpose of screening the inhibitors with regard to ExoS secretion, we developed the sandwich-type enzyme-linked immunosorbent assay (ELISA) system. PAK clinical strains induce proinflammatory cytokine production through the T3SS, and this involves NF-κB activation in pneumonia mouse models. We tried to confirm the role of the NF-κB transcription factor in ExoS- and ExoT-induced pneumonia mouse models. pro-inflammatory cytokines induction in response to ExoS and ExoT infection relied on NF-κB activation. Our findings highlight the roles of natural poduct in inhibiting proinflammatory cytokine expression during ExoS and ExoT exposure in PAK infections, paving the way for a novel therapeutic approach for the treatment of pulmonary infections.

• Geomechanics and Engineering
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• v.37 no.2
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• pp.109-122
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• 2024

Standard triaxial cells are commonly used to measure the mechanical behavior of saturated soils. However, this type of standard system is difficult to use for unsaturated soil specimens since it cannot measure the changes in the pore-air volume and pressure. This paper proposes to extend the measurement possibilities of the standard triaxial testing device in a simple way and to adapt it to partially saturated soils. The system is supplied by two hygrometers installed at each end of the cylindrical unsaturated specimen to measure local relative humidity, which allows the derivation of suction. The volumetric strain of the specimen is calculated by analyzing digital photos captured from the outside of the transparent cell wall. Specimens made of kaolin clay, having different hydraulic properties, were tested to verify the reliability of the measurements, and thus, the relevance of the proposed techniques to study the mechanical behavior of unsaturated soils.

• Molecules and Cells
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• v.46 no.11
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• pp.710-724
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• 2023

The plant defense responses to microbial infection are tightly regulated and integrated with the developmental program for optimal resources allocation. Notably, the defense-associated hormone salicylic acid (SA) acts as a promoter of flowering while several plant pathogens actively target the flowering signaling pathway to promote their virulence or dissemination. Ralstonia pseudosolanacearum inject tens of effectors in the host cells that collectively promote bacterial proliferation in plant tissues. Here, we characterized the function of the broadly conserved R. pseudosolanacearum effector RipL, through heterologous expression in Arabidopsis thaliana. RipL-expressing transgenic lines presented a delayed flowering, which correlated with a low expression of flowering regulator genes. Delayed flowering was also observed in Nicotiana benthamiana plants transiently expressing RipL. In parallel, RipL promoted plant susceptibility to virulent strains of Pseudomonas syringae in the effector-expressing lines or when delivered by the type III secretion system. Unexpectedly, SA accumulation and SA-dependent immune signaling were not significantly affected by RipL expression. Rather, the RNA-seq analysis of infected RipL-expressing lines revealed that the overall amplitude of the transcriptional response was dampened, suggesting that RipL could promote plant susceptibility in an SA-independent manner. Further elucidation of the molecular mechanisms underpinning RipL effect on flowering and immunity may reveal novel effector functions in host cells.