Beagle: a near-edge X-ray absorption fine-structure spectroscopy data processing solution for beamline experiments at Pohang Accelerator Laboratory.

Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy is a powerful tool for identifying chemical bonding states at synchrotron radiation facilities. Advances in new materials require researchers in both academia and industry to measure tens to hundreds of samples during the available beam time on a synchrotron beamline, which is typically allocated to users. Automated measurement methods, along with analysis software, have been developed for beamlines. Automated measurements facilitate high-throughput experiments and accumulate vast amounts of measured spectral data. The analysis software supports various functions for analyzing the experimental data; however, these analysis methods are complicated, and learning them can be time-consuming. To process large amounts of spectral data, a new analysis software, dedicated to NEXAFS spectroscopy, that is easy to use and can provide results in a short time is desired. Herein, the development of Beagle is described, software calculating molecular orientation from NEXAFS spectroscopy data that can report results in a short time comparable with that required to measure one sample at the beamline. It was designed to progress in a single sequence from data loading to the printing of the results with a `click of a button'. The functions of the software include recognizing the dataset, correcting the background, normalizing the plot, calculating the electron yield and determining the molecular orientation. The analysis results can be saved as {\tt{.txt}} files (spectral data), {\tt{.pdf}} files (graphic images) and Origin files (spectral data and graphic images).

Eucalyptus globulus leaf-isolated isorhapontin serves as a natural insecticide via acetylcholinesterase inhibition.

Acetylcholinesterase (AChE) inhibitors cause insect death by preventing the hydrolysis of the neurotransmitter acetylcholine, which overstimulates the nervous system. In this study, isorhapontin, isolated from E. globulus leaves, was evaluated as a natural insecticide with AChE inhibition at 12.5 µM. Using kinetic analyses, we found that isorhapontin acted as a competitive inhibitor that binds to the active site of AChE. The inhibition constant (Ki) was 6.1 µM. Furthermore, isorhapontin and resveratrol, which have basic skeletons, were predicted to bind to the active site of AChE via molecular docking. A comparison of the hydrogen bonding between the two stilbenes revealed characteristic differences in their interactions with amino acids. In isorhapontin, Trp83, Gly149, Tyr162, Tyr324, and Tyr370 interacted with the sugar moiety. These results suggest that with further development, isorhapontin can be used as an insecticide alternative.

Distinct effect of exercise modes on mood-related behavior in mice.

Exercise can afford several benefits to combat mood disorders in both rodents and humans. Engagement in various physical activities upregulates levels of neurotrophic factors in several brain regions and improves mental health. However, the type of exercise that regulates mood and the underlying mechanisms in the brain remain elusive. Herein, we performed two distinct types of exercise and RNA sequencing analyses to investigate the effect of exercise on mood-related behaviors and explain the distinct patterns of gene expression. Specifically, resistance exercise exhibited reduced immobility time in the forced swim test when compared with both no exercise and treadmill exercise (in the aerobic training [AT] group). Interestingly, anxiety-like behaviors in the open field and nest-building tests were ameliorated in the AT group when compared with those in the control group; however, this was not observed in the RT group. To elucidate the mechanism underlying these different behavioral changes caused by distinct exercise types, we examined the shift in the gene expression pattern in the hippocampus, a brain region that plays a critical role in regulating mood. We discovered that 38 and 40 genes were altered in the AT and RT groups, respectively, compared with the control group. Both exercises regulated 16 common genes. Compared with the control group, mitogen-activated protein kinase (MAPK) was enriched in the AT group and phosphatidylinositol-3-kinase (PI3K)/AKT and neurotrophin signaling pathways were enriched in the RT group, as determined by bioinformatics pathway analysis. PCR results revealed that Cebpß expression was increased in AT group, and Dcx expression was upregulated in both groups. Our findings indicate that different exercise types may exert substantially distinct effects on mood-like behaviors. Accordingly, appropriate types of exercise can be undertaken based on the mood disorder to be regulated.

Inhibitory Potential of Quercetin Derivatives Isolated from the Aerial Parts of Siegesbeckia pubescens Makino against Bacterial Neuraminidase.

This study aimed to isolate bacterial neuraminidase (BNA) inhibitory O-methylated quercetin derivatives from the aerial parts of S. pubescens. All the isolated compounds were identified as O-methylated quercetin (1-4), which were exhibited to be noncompetitive inhibitors against BNA, with IC50 ranging from 14.0 to 84.1 µM. The responsible compounds (1-4) showed a significant correlation between BNA inhibitory effects and the number of O-methyl groups on quercetin; mono (1, IC50 = 14.0 µM) > di (2 and 3, IC50 = 24.3 and 25.8 µM) > tri (4, IC50 = 84.1 µM). In addition, the binding affinities between BNA and inhibitors (1-4) were also examined by fluorescence quenching effect with the related constants (KSV, KA, and n). The most active inhibitor 1 possessed a KSV with 0.0252 × 105 L mol-1. Furthermore, the relative distribution of BNA inhibitory O-methylated quercetins (1-4) in S. pubescens extract was evaluated using LC-Q-TOF/MS analysis.

A chimeric MERS-CoV virus-like particle vaccine protects mice against MERS-CoV challenge.

BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe respiratory disease in humans, with a case fatality rate of approximately 35%, thus posing a considerable threat to public health. The lack of approved vaccines or antivirals currently constitutes a barrier in controlling disease outbreaks and spread. METHODS: In this study, using a mammalian expression system, which is advantageous for maintaining correct protein glycosylation patterns, we constructed chimeric MERS-CoV virus-like particles (VLPs) and determined their immunogenicity and protective efficacy in mice. RESULTS: Western blot and cryo-electron microscopy analyses demonstrated that MERS-CoV VLPs were efficiently produced in cells co-transfected with MERS-CoV spike (S), envelope, membrane and murine hepatitis virus nucleocapsid genes. We examined their ability as a vaccine in a human dipeptidyl peptidase 4 knock-in C57BL/6 congenic mouse model. Mice immunized with MERS VLPs produced S-specific antibodies with virus neutralization activity. Furthermore, MERS-CoV VLP immunization provided complete protection against a lethal challenge with mouse-adapted MERS-CoV and improved virus clearance in the lung. CONCLUSIONS: Overall, these data demonstrate that MERS-CoV VLPs have excellent immunogenicity and represent a promising vaccine candidate.

Heat shock protein 70 could enhance porcine epidemic diarrhoea virus replication by interacting with membrane proteins.

In this study, we investigated the role of heat shock protein 70 (HSP70) in porcine epidemic diarrhoea virus (PEDV) replication. We found that PEDV infection induced strong HSP70 overexpression in the very early stage of infection. We also confirmed that HSP70 overexpression increased the speed of PEDV replication, resulting in the generation of more virions. In contrast, knockout of HSP70 in cells significantly downregulated PEDV protein expression, resulting in a significant reduction in PEDV replication. Most importantly, we confirmed that among the structural proteins of PEDV, membrane (M) proteins have this important role. We found that membrane proteins control cellular HSP70 expression in PEDV-infected cells. We confirmed HSP70/M complex formation by both immunoprecipitation and immunofluorescence assays. Additionally, PEDV M overexpression induced strong HSP70 expression. All our results clearly confirmed that in PEDV-infected cells, the M protein plays a very important role in PEDV replication in collaboration with HSP70.

Zernike phase-contrast full-field transmission X-ray nanotomography for 400 micrometre-sized samples.

Full-field X-ray nanotomography based on a Fresnel zone plate offers a promising and intuitive approach to acquire high-quality phase-contrast images with a spatial resolution of tens of nanometres, and is applicable to both synchrotron radiation and laboratory sources. However, its small field of view (FOV) of tens of micrometres provides limited volume information, which primarily limits its application fields. This work proposes a method for expanding the FOV as the diameter of the objective zone plate, which provides a 400 µm FOV at below 500 nm resolution with Zernike phase contrast. General applications of large-volume nanotomography are demonstrated in integrated circuit microchips and Artemia cysts. This method can be useful for imaging/analyzing industrial and biological samples where bulk properties are important or the sample is difficult to section.

Development of XANES nanoscopy on BL7C at PLS-II.

X-ray absorption near-edge structure (XANES) imaging is a powerful tool to visualize the chemical state distribution of transition-metal-based materials at synchrotron radiation facilities. In recent years, the electrochemical working rechargeable battery has been the most studied material in XANES imaging owing to the large increase of portable electronics and electric vehicles. This work acknowledges the importance of battery analysis and has developed the XANES imaging system on BL7C at Pohang Light Source-II (PLS-II). BL7C employs an undulator taper configuration to obtain an energy band >130 eV near the K-absorption edge of the target element with a minimum energy interval >0.2 eV. While measuring energy-dependent images, the zone plate translation maintains the best focus, and then various data processes such as background correction, image registration and clustering allow single XANES spectrum extraction and chemical distribution mapping. Here, the XANES imaging process is described, the XANES spectrum quality is identified and the chemical states of the partially charged cathode material used in lithium-ion batteries as an application example are examined.

Differential role of lipoteichoic acids isolated from Staphylococcus aureus and Lactobacillus plantarum on the aggravation and alleviation of atopic dermatitis.

Lipoteichoic acid (LTA), a cell wall component of gram-positive bacteria, up-regulates inflammatory cytokine production through the toll-like receptor 2 (TLR2) signaling pathway, and also contributes to anti-inflammatory responses against immune cells stimulated by lipopolysaccharides. In the current study, we examined the effects of LTAs isolated from Staphylococcus aureus (aLTA) and Lactobacillus plantarum (pLTA) on the aggravation and alleviation of atopic dermatitis (AD). aLTA strongly induced CCL2 production in THP-1 cells. CCL2 was regulated by the TLR2 pathway including the activation of IRAK2, NF-κB and JNK. CCL2 induced Th2 polarization of CD4+T cells through induction of interleukin (IL)-2, -4, and -5 and inhibition of interferon-gamma (IFN-γ). CCL2 levels and immunoglobulin E (IgE) production were increased in aLTA-injected mice. On the other hand, pLTA moderately affected CCL2 production and it inhibited aLTA-mediated CCL2 production. The serum levels of CCL2 and IgE were inhibited by pLTA pre-injection followed by aLTA reinjection, which resulted in the alleviation of irritant contact dermatitis (ICD) symptoms. Our results suggest that S. aureus infection causes an increase in CCL2 production, and may exacerbate atopic dermatitis (AD)-like symptoms through the excessive IgE production. Alternatively, pLTA alleviated AD-like symptoms by inhibiting aLTA-induced CCL2 and IgE production.

X-ray beam-position feedback system with easy-to-use beam-position monitor.

X-ray beam-position stability is indispensable in cutting-edge experiments using synchrotron radiation. Here, for the first time, a beam-position feedback system is presented that utilizes an easy-to-use X-ray beam-position monitor incorporating a diamond-fluorescence screen. The acceptable range of the monitor is above 500 µm and the feedback system maintains the beam position within 3 µm. In addition to being inexpensive, the system has two key advantages: it works without a scale factor for position calibration, and it has no dependence on X-ray energy, X-ray intensity, beam size or beam shape.

Zinc Oxide-Based Nanomaterials for Microbiostatic Activities: A Review.

The world is fighting infectious diseases. Therefore, effective antimicrobials are required to prevent the spread of microbes and protect human health. Zinc oxide (ZnO) nano-materials are known for their antimicrobial activities. Because of their distinctive physical and chemical characteristics, they can be used in medical and environmental applications. ZnO-based composites are among the leading sources of antimicrobial research. They are effective at killing (microbicidal) and inhibiting the growth (microbiostatic) of numerous microorganisms, such as bacteria, viruses, and fungi. Although most studies have focused on the microbicidal features, there is a lack of reviews on their microbiostatic effects. This review provides a detailed overview of available reports on the microbiostatic activities of ZnO-based nano-materials against different microorganisms. Additionally, the factors that affect the efficacy of these materials, their time course, and a comparison of the available antimicrobials are highlighted in this review. The basic properties of ZnO, challenges of working with microorganisms, and working mechanisms of microbiostatic activities are also examined. This review underscores the importance of further research to better understand ZnO-based nano-materials for controlling microbial growth.

Effect of exercise-induced Neutrophil maturation on skeletal muscle repair in vitro.

Neutrophils as first line defender initiate a cascade of healing process immediately after muscle injury. At muscle injury site, neutrophils remove damaged muscle fibers and recruit other immune cells and these functions show in mature neutrophils. In the previous study, physical exercise can mediate neutrophils' functional changes such as phagocytosis and chemotaxis, though there is no research on how exercise-induced neutrophils contribute the muscle regeneration. In this present study, we investigated the maturation of neutrophils after 4 weeks of mouse treadmill exercise and assessed wound healing assay to evaluate whether treatment with exercise-activated neutrophils is effective for skeletal muscle repair in vitro. In the exercise group, significantly higher mRNA levels of maturation markers compared to the sedentary group and exercise-activated neutrophils improved wound healing of mouse muscle cells. To confirm at the human cell level, based on the well-known fact that exercise increases circulating cortisol levels, neutrophil-like cells were treated with dexamethasone (dHL60 + dex) as exercise mimetics. dHL60 + dex had significantly higher mRNA levels of neutrophil maturation marker and improved wound healing of human skeletal muscle cells compared to the control. These findings suggest that exercise affects neutrophil maturation and that exercise-induced neutrophils contribute to skeletal muscle repair in vitro.

Insights into the Pathogenesis and Development of Recombinant Japanese Encephalitis Virus Genotype 3 as a Vaccine.

Japanese encephalitis virus (JEV), a flavivirus transmitted by mosquitoes, has caused epidemics and severe neurological diseases in Asian countries. In this study, we developed a cDNA infectious clone, pBAC JYJEV3, of the JEV genotype 3 strain (EF571853.1) using a bacterial artificial chromosome (BAC) vector. The constructed infectious clone was transfected into Vero cells, where it exhibited infectivity and induced cytopathic effects akin to those of the parent virus. Confocal microscopy confirmed the expression of the JEV envelope protein. Comparative analysis of growth kinetics revealed similar replication dynamics between the parental and recombinant viruses, with peak titers observed 72 h post-infection (hpi). Furthermore, plaque assays demonstrated comparable plaque sizes and morphologies between the viruses. Cryo-electron microscopy confirmed the production of recombinant virus particles with a morphology identical to that of the parent virus. Immunization studies in mice using inactivated parental and recombinant viruses revealed robust IgG responses, with neutralizing antibody production increasing over time. These results showcase the successful generation and characterization of a recombinant JEV3 virus and provide a platform for further investigations into JEV pathogenesis and vaccine development.

A one-step immunoassay based on switching peptides for diagnosis of porcine epidemic diarrhea virus (PEDV) using screened Fv-antibodies.

In this study, a one-step immunoassay for porcine epidemic diarrhea virus (PEDV) based on Fv-antibodies and switching peptides was developed, and the assay results of PEDV were obtained by just mixing samples without any further reaction or washing steps. The Fv-antibodies with binding affinity to the spike protein of PEDV were screened from the Fv-antibody library using the receptor-binding domain (RBD) of the spike protein as a screening probe. Screened Fv-antibodies with binding affinities to the RBD antigen were expressed, and the binding constants (KD) were calculated to be 83-142 nM. The one-step immunoassay for the detection of PEDV was configured as a displacement immunoassay using a fluorescence-labeled switching peptide. The one-step immunoassay based on switching peptides was performed using PEDV, and the limit of detection (LOD) values for PEDV detection were estimated to be Ct = 39.7-36.4. Compared with the LOD value for a conventional lateral flow immunoassay (Ct = 33.0), the one-step immunoassay showed a remarkably improved LOD for the detection of PEDV. Finally, the interaction between the screened Fv-antibodies and the PEDV RBD was investigated using docking simulations and compared with the amino acid sequences of the receptors on host cells, such as aminopeptidase N (APN) and angiotensin-converting enzyme-2 (ACE-2).

The newly described heterotrophic dinoflagellate Gyrodinium moestrupii, an effective protistan grazer of toxic dinoflagellates.

Few protistan grazers feed on toxic dinoflagellates, and low grazing pressure on toxic dinoflagellates allows these dinoflagellates to form red-tide patches. We explored the feeding ecology of the newly described heterotrophic dinoflagellate Gyrodinium moestrupii when it fed on toxic strains of Alexandrium minutum, Alexandrium tamarense, and Karenia brevis and on nontoxic strains of A. tamarense, Prorocentrum minimum, and Scrippsiella trochoidea. Specific growth rates of G. moestrupii feeding on each of these dinoflagellates either increased continuously or became saturated with increasing mean prey concentration. The maximum specific growth rate of G. moestrupii feeding on toxic A. minutum (1.60/d) was higher than that when feeding on nontoxic S. trochoidea (1.50/d) or P. minimum (1.07/d). In addition, the maximum growth rate of G. moestrupii feeding on the toxic strain of A. tamarense (0.68/d) was similar to that when feeding on the nontoxic strain of A. tamarense (0.71/d). Furthermore, the maximum ingestion rate of G. moestrupii on A. minutum (2.6 ng C/grazer/d) was comparable to that of S. trochoidea (3.0 ng C/grazer/d). Additionally, the maximum ingestion rate of G. moestrupii on the toxic strain of A. tamarense (2.1 ng C/grazer/d) was higher than that when feeding on the nontoxic strain of A. tamarense (1.3 ng C/grazer/d). Thus, feeding by G. moestrupii is not suppressed by toxic dinoflagellate prey, suggesting that it is an effective protistan grazer of toxic dinoflagellates.

Ostreol A: a new cytotoxic compound isolated from the epiphytic dinoflagellate Ostreopsis cf. ovata from the coastal waters of Jeju Island, Korea.

Ostreol A was isolated from cultures of the epiphytic dinoflagellate Ostreopsis cf. ovata from the coastal waters of Jeju Island, Korea. The compound, a non-palytoxin derivative, has a polyhydroxy chain ending with the primary amino group and contains an amide bond, along with two tetrahydropyran rings in the chain. Its chemical structure was elucidated by nuclear magnetic resonance (NMR) spectroscopy methods and confirmed by mass analysis. The compound exhibited significant cytotoxicity in the brine shrimp lethality test at a concentration of 0.9µg/mL.

Peroxisome disruption alters lipid metabolism and potentiates antitumor response with MAPK-targeted therapy in melanoma.

Melanomas reprogram their metabolism to rapidly adapt to therapy-induced stress conditions, allowing them to persist and ultimately develop resistance. We report that a subpopulation of melanoma cells tolerate MAPK pathway inhibitors (MAPKis) through a concerted metabolic reprogramming mediated by peroxisomes and UDP-glucose ceramide glycosyltransferase (UGCG). Compromising peroxisome biogenesis, by repressing PEX3 expression, potentiated the proapoptotic effects of MAPKis via an induction of ceramides, an effect limited by UGCG-mediated ceramide metabolism. Cotargeting PEX3 and UGCG selectively eliminated a subset of metabolically active, drug-tolerant CD36+ melanoma persister cells, thereby sensitizing melanoma to MAPKis and delaying resistance. Increased levels of peroxisomal genes and UGCG were found in patient-derived MAPKi-relapsed melanomas, and simultaneously inhibiting PEX3 and UGCG restored MAPKi sensitivity in multiple models of therapy resistance. Finally, combination therapy consisting of a newly identified inhibitor of the PEX3-PEX19 interaction, a UGCG inhibitor, and MAPKis demonstrated potent antitumor activity in preclinical melanoma models, thus representing a promising approach for melanoma treatment.

The future of butyric acid in industry.

In this paper, the different applications of butyric acid and its current and future production status are highlighted, with a particular emphasis on the biofuels industry. As such, this paper discusses different issues regarding butyric acid fermentations and provides suggestions for future improvements and their approaches.

Porcine Epidemic Diarrhea Virus Infection Induces Autophagosome Formation but Inhibits Autolysosome Formation during Replication.

In this study, we investigated the correlation between the mechanism involved in porcine epidemic diarrhea virus (PEDV) replication and autophagic flux. In this study, we found that as PEDV replicated, production of LC3-II was significantly induced up to 24 h post-infection (hpi). Interestingly, although there was significant production of LC3-II, greater p62 accumulation was simultaneously found. Pretreatment with rapamycin significantly induced PEDV replication, but autolysosome formation was reduced. These results were confirmed by the evaluation of ATG5/ATG12 and LAMP1/LAMP2. Taken together, we conclude that PEDV infection induces autophagosome formation but inhibits autolysosome formation during replication.

Switching to Hidden Metallic Crystal Phase in Phase-Change Materials by Photoenhanced Metavalent Bonding.

Metavalent bonding is crucial for the determination of phase transition and improvement of device performance in phase-change materials, which are attracting interest for use in memory devices. Although monitoring dielectric and phononic parameters provides a direct measure of the metavalent bonding, the control of phase-change phenomena and metavalent bonding in the dynamical regime has yet to be demonstrated. This study reports the photoenhanced metavalent bonding and resulting hidden metallic crystalline state of Ti-doped Sb2Te3, a representative phase-change material with ultralong sustainability. Using ultrafast terahertz spectroscopy, Ti0.4Sb2Te3 was discovered to possess ultralong pump-probe dynamics, which is retained over hundreds of picoseconds, unlike the short-lived state of undoped Sb2Te3. Moreover, for Ti0.4Sb2Te3 during the long-lived transmission change, the infrared-active phonon is highly softened, even more than the amount of a thermal phonon shift, indicating the photoenhancement of lattice anharmonicity. Such a long-lived relaxation implies photoinduced transition into a crystalline state of ultrastrong metavalent bonding in Ti0.4Sb2Te3, on the basis of comparisons of the dynamical dielectric constant and temporal phonon shift. Our results show the realization of photoengineering of phase-change materials by tuning electron sharing or transferring.