Using Data-Dependent and -Independent Hybrid Acquisitions for Fast Liquid Chromatography-Based Untargeted Lipidomics.

Untargeted lipidomics using liquid chromatography (LC) coupled with tandem mass spectrometry (MS) is essential for large cohort studies. Using a fast LC gradient of less than 10 min for the rapid screening of lipids decreases the annotation rate, because of the lower coverage of the MS/MS spectra caused by the narrow peak width. A systematic procedure is proposed in this study to achieve a high annotation rate in fast LC-based untargeted lipidomics by integrating data-dependent acquisition (DDA) and sequential window acquisition of all-theoretical mass spectrometry data-independent acquisition (SWATH-DIA) techniques using the updated MS-DIAL program. This strategy uses variable SWATH-DIA methods for quality control (QC) samples, which are a mixture of biological samples that were analyzed multiple times to correct the MS signal drift. In contrast, biological samples are analyzed using DDA to facilitate the structural elucidation of lipids using the pure spectrum to the maximum extent. The workflow is demonstrated using an 8.6 min LC gradient, where the QC samples are analyzed using five different SWATH-DIA methods. The use of both DDA and SWATH-DIA achieves a 1.7-fold annotation coverage from publicly available benchmark data obtained using a fast LC-DDA-MS technique and offers 95.3% lipid coverage, as compared to the benchmark data set from a 25 min LC gradient. This study demonstrates that harmonized improvements in analytical conditions and informatics tools provide a comprehensive lipidome in fast LC-based untargeted lipidomics, not only for large-scale studies but also for small-scale experiments, contributing to both clinical applications and basic biology.

Observation of Coherent Perfect Absorption in Oil Film on Water Surface and Sensitive Detection of Refractive Index Anisotropy in the Film.

Sharp reflection dips of 50% were observed when white light was incident from the side of a cell on a 1 µm thick film of silicone oil (polydimethylsiloxane, PDMS, nearly transparent in visible light, with the extinction coefficient κ ≈ 0.0001) above a water surface in the cell so that the total reflection condition was satisfied at the oil-air interface. This is the first observation of a coherent perfect absorption (CPA) phenomenon in liquid. The experimental results can be reproduced by the Fresnel reflectance of the monolayer film, but the wavelength positions at which the dip appears for s-polarized and p-polarized light are reversed if the refractive index of the oil film is assumed to be isotropic. The experimental results were correctly reproduced by assuming that the extraordinary-ray refractive index (light polarized perpendicular to the interface) is 1% larger than the ordinary-ray refractive index (light polarized parallel to the interface). This indicates that the polarization dependence of the CPA phenomenon is extremely sensitive to the difference between the in-plane and out-of-plane refractive indices of the thin film.

Polyunsaturated fatty acids-rich dietary lipid prevents high fat diet-induced obesity in mice.

Diet is the primary factor affecting host nutrition and metabolism, with excess food intake, especially high-calorie diets, such as high-fat and high-sugar diets, causing an increased risk of obesity and related disorders. Obesity alters the gut microbial composition and reduces microbial diversity and causes changes in specific bacterial taxa. Dietary lipids can alter the gut microbial composition in obese mice. However, the regulation of gut microbiota and host energy homeostasis by different polyunsaturated fatty acids (PUFAs) in dietary lipids remains unknown. Here, we demonstrated that different PUFAs in dietary lipids improved host metabolism in high-fat diet (HFD)-induced obesity in mice. The intake of the different PUFA-enriched dietary lipids improved metabolism in HFD-induced obesity by regulating glucose tolerance and inhibiting colonic inflammation. Moreover, the gut microbial compositions were different among HFD and modified PUFA-enriched HFD-fed mice. Thus, we have identified a new mechanism underlying the function of different PUFAs in dietary lipids in regulating host energy homeostasis in obese conditions. Our findings shed light on the prevention and treatment of metabolic disorders by targeting the gut microbiota.

Inflammatory Bowel Diseases and Gut Microbiota.

Inflammatory bowel disease (IBD) is an inflammatory disease of the gastrointestinal tract, the incidence of which has rapidly increased worldwide, especially in developing and Western countries. Recent research has suggested that genetic factors, the environment, microbiota, and immune responses are involved in the pathogenesis; however, the underlying causes of IBD are unclear. Recently, gut microbiota dysbiosis, especially a decrease in the abundance and diversity of specific genera, has been suggested as a trigger for IBD-initiating events. Improving the gut microbiota and identifying the specific bacterial species in IBD are essential for understanding the pathogenesis and treatment of IBD and autoimmune diseases. Here, we review the different aspects of the role played by gut microbiota in the pathogenesis of IBD and provide a theoretical basis for modulating gut microbiota through probiotics, fecal microbiota transplantation, and microbial metabolites.

Sodium p-Toluenesulfinate Enhances the Bonding Durability of Universal Adhesives on Deproteinized Eroded Dentin.

The effects of deproteinization using sodium hypochlorite (NaOCl) and the subsequent application of an antioxidant (sodium p-toluenesulfinate, STS) onto the bonding durability of universal adhesives on eroded dentin were investigated. Untreated sound dentin served as the control, whereas eroded dentin, which had been prepared by pH-cycling in 1% citric acid and a remineralization solution, was either untreated, deproteinized with a 10% NaOCl gel or deproteinized with the 10% NaOCl gel and subsequently treated with an STS-containing agent. The dentin surfaces were bonded using a universal adhesive (Clearfil Universal Bond Quick, Scotchbond Universal or G-Premio Bond), and the micro-tensile bond strength (µTBS) test was performed after 24 h or 10,000 thermal cycles. The µTBS data were statistically analyzed using a three-way ANOVA and Tukey's HSD post hoc tests. The lowest µTBS was measured on untreated eroded dentin (p < 0.001). Deproteinization of eroded dentin resulted in µTBS similar to untreated sound dentin (p > 0.05), but the highest µTBS was obtained if deproteinization was followed by the application of STS. Thermocycling significantly decreased µTBS in all groups (p < 0.001), except for STS-treated deproteinized eroded dentin (p > 0.05). This indicated that deproteinization, followed by the application of STS, could enhance the bonding durability of universal adhesives on eroded dentin.

SARS-CoV-2 seroprevalence in healthcare workers at a frontline hospital in Tokyo.

Healthcare workers (HCWs) are highly exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The actual coronavirus disease (COVID-19) situation, especially in regions that are less affected, has not yet been determined. This study aimed to assess the seroprevalence of SARS-CoV-2 in HCWs working in a frontline hospital in Tokyo, Japan. In this cross-sectional observational study, screening was performed on consented HCWs, including medical, nursing, and other workers, as part of a mandatory health checkup. The screening test results and clinical characteristics of the participants were recorded. The antibody seroprevalence rate among the 4147 participants screened between July 6 and August 21, 2020, was 0.34% (14/4147). There was no significant difference in the seroprevalence rate between frontline HCWs with a high exposure risk and HCWs working in other settings with a low exposure risk. Of those seropositive for SARS-CoV-2, 64% (9/14) were not aware of any symptoms and had not previously been diagnosed with COVID-19. In conclusion, this study provides insights into the extent of infection and immune status in HCWs in Japan, which has a relatively low prevalence of COVID-19. Our findings aid in formulating public health policies to control virus spread in regions with low-intensity COVID-19.

Degree of conversion and dentin bond strength of light-cured multi-mode adhesives pretreated or mixed with sulfinate agents.

The influence of sulfinate agents applied as a dentin pretreatment or a mixture with multi-mode one-step self-etch adhesives (1-SEAs) on the degree of conversion (DC) and micro-tensile bond strength (µTBS) of light-cured 1-SEAs was investigated. 1-SEAs Clearfil Universal Bond Quick (UBQ) or Scotchbond Universal Adhesive (SBU) were applied to dentin in etch&rinse or self-etch mode using various application strategies: 1) no pretreatment, 2) pretreatment with 90 wt% ethanol, 3) pretreatment with a sulfinate agent Clearfil DC Activator (UDC) or Scotchbond Universal DCA (SDC), or 4) a mixture of UBQ+UDC or SBU+SDC. µTBS was measured after 24 h. Additionally, DC was measured using attenuated total reflectance Fourier-transform infrared spectroscopy. Pretreatment with sulfinate agents resulted in the highest µTBS and DC, significantly improving them especially in etch&rinse mode. The mixture of sulfinate agents with 1-SEAs was less effective. Pretreatment with ethanol significantly improved µTBS in etch&rinse mode but compromised µTBS in self-etch mode.

Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome.

UV-DDB, an initiation factor for the nucleotide excision repair pathway, recognizes 6-4PP lesions through a base flipping mechanism. As genomic DNA is almost entirely accommodated within nucleosomes, the flipping of the 6-4PP bases is supposed to be extremely difficult if the lesion occurs in a nucleosome, especially on the strand directly contacting the histone surface. Here we report that UV-DDB binds efficiently to nucleosomal 6-4PPs that are rotationally positioned on the solvent accessible or occluded surface. We determined the crystal structures of nucleosomes containing 6-4PPs in these rotational positions, and found that the 6-4PP DNA regions were flexibly disordered, especially in the strand exposed to the solvent. This characteristic of 6-4PP may facilitate UV-DDB binding to the damaged nucleosome. We present the first atomic-resolution pictures of the detrimental DNA cross-links of neighboring pyrimidine bases within the nucleosome, and provide the mechanistic framework for lesion recognition by UV-DDB in chromatin.

A non-isotopic assay uses bromouridine and RNA synthesis to detect DNA damage responses.

Individuals with inherited xeroderma pigmentosum (XP) disorder and Cockayne syndrome (CS) are deficient in nucleotide excision repair and experience hypersensitivity to sunlight. Although there are several diagnostic assays for these disorders, the recovery of RNA synthesis (RRS) assay that can discriminate between XP cells and CS cells is very laborious. Here, we report on a novel non-radioisotope RRS assay that uses bromouridine (a uridine analog) as an alternative to (3)H-uridine. This assay can easily detect RNA polymerase I transcription in nucleoli and RNA polymerase II transcription in nuclei. The non-RI RSS assay also can rapidly detect normal RRS activity in HeLa cells. Thus, this assay is useful as a novel and easy technique for CS diagnosis. Because RRS is thought to be related to transcription-coupled DNA repair, which is triggered by the blockage of transcriptional machinery by DNA lesions, this assay may be of use for analysis of DNA repair, transcription, and/or genetic toxicity.