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Hispidulin is a natural bioactive flavonoid that has been studied for its potential therapeutic properties, including its anti-inflammatory, antioxidant, and neuroprotective effects. The aim of this study was to explore whether hispidulin could inhibit the endothelial inflammation triggered by Porphyromonas gingivalis ( P. gingivalis ) lipopolysaccharide (LPS). The adhesion of monocytes to the vascular endothelium was evaluated through in vitro and ex vivo monocyte adhesion assays. We analyzed the migration of monocytes across the endothelial layer using a transmigration assay. The results showed that treatment with hispidulin decreased the P. gingivalis LPS-induced adhesion of monocytes to endothelial cells and their migration by suppressing the P. gingivalis LPS-triggered expression of intercellular adhesion molecule-1 (ICAM-1) through downregulating nuclear factor-қB (NF-қB). In addition, hispidulin inhibited P. gingivalis LPS-induced mitogen-activated protein kinases (MAPKs) and AKT in endothelial cells. Altogether, the results indicate that hispidulin suppresses the vascular inflammation induced by P. gingivalis LPS. Mechanistically, it prevents the adhesion of monocytes to the vascular endothelium and migration and inhibits NF-қB, MAPKs, and AKT signaling in endothelial cells.

Airlines provide one of the most popular and important transportation services for passengers. While the importance of the airline industry is rising, flight cancellations are also increasing due to abnormal weather factors, such as rainfall and wind speed. Although previous studies on cancellations due to weather factors considered both aircraft and weather factors concurrently, the complex network studies only treated the aircraft factor with a single-layer network. Therefore, the aim of this study was to apply a multilayer complex network (MCN) method that incorporated three different factors, namely, aircraft, rainfall, and wind speed, to investigate aircraft cancellations at 14 airports in the Republic of Korea. The results showed that rainfall had a greater impact on aircraft cancellations compared with wind speed. To find out the most important node in the cancellation, we applied centrality analysis based on information entropy. According to the centrality analysis, Jeju Airport was identified as the most influential node since it has a high demand for aircraft. Also, we showed that characteristics and factors of aircraft cancellation should be appropriately defined by links in the MCN. Furthermore, we verified the applicability of the MCN method in the fields of aviation and meteorology. It is expected that the suggested methodology in this study can help to understand aircraft cancellation due to weather factors.

Background: Macaque species share >93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g., HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort., Results: To close this gap and enhance functional genomics approaches, we used a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells derived from the same animal. Reconstruction of the evolutionary tree using whole-genome annotation and orthologous comparisons among 3 macaque species, human, and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques., Conclusions: These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways., (© The Author(s) 2020. Published by Oxford University Press.)

Background: Genomic data have become major resources to understand complex mechanisms at fine-scale temporal and spatial resolution in functional and evolutionary genetic studies, including human diseases, such as cancers. Recently, a large number of whole genomes of evolving populations of yeast (Saccharomyces cerevisiae W303 strain) were sequenced in a time-dependent manner to identify temporal evolutionary patterns. For this type of study, a chromosome-level sequence assembly of the strain or population at time zero is required to compare with the genomes derived later. However, there is no fully automated computational approach in experimental evolution studies to establish the chromosome-level genome assembly using unique features of sequencing data., Methods and Results: In this study, we developed a new software pipeline, the integrative meta-assembly pipeline (IMAP), to build chromosome-level genome sequence assemblies by generating and combining multiple initial assemblies using three de novo assemblers from short-read sequencing data. We significantly improved the continuity and accuracy of the genome assembly using a large collection of sequencing data and hybrid assembly approaches. We validated our pipeline by generating chromosome-level assemblies of yeast strains W303 and SK1, and compared our results with assemblies built using long-read sequencing and various assembly evaluation metrics. We also constructed chromosome-level sequence assemblies of S. cerevisiae strain Sigma1278b, and three commonly used fungal strains: Aspergillus nidulans A713, Neurospora crassa 73, and Thielavia terrestris CBS 492.74, for which long-read sequencing data are not yet available. Finally, we examined the effect of IMAP parameters, such as reference and resolution, on the quality of the final assembly of the yeast strains W303 and SK1., Conclusions: We developed a cost-effective pipeline to generate chromosome-level sequence assemblies using only short-read sequencing data. Our pipeline combines the strengths of reference-guided and meta-assembly approaches. Our pipeline is available online at http://github.com/jkimlab/IMAP including a Docker image, as well as a Perl script, to help users install the IMAP package, including several prerequisite programs. Users can use IMAP to easily build the chromosome-level assembly for the genome of their interest., Competing Interests: The authors have declared that no competing interests exist.

We have developed a reflection-mode switchable subwavelength Bessel-beam (BB) and Gaussian-beam (GB) photoacoustic microscopy (PAM) system. To achieve both reflection-mode and high resolution, we tightly attached a very small ultrasound transducer to an optical objective lens with numerical aperture of 1.0 and working distance of 2.5 mm. We used axicon and an achromatic doublet in our system to obtain the extended depth of field (DOF) of the BB. To compare the DOF performance achieved with our BB-PAM system against GB-PAM system, we designed our system so that the GB can be easily generated by simply removing the lenses. Using a 532 nm pulse laser, we achieved the lateral resolutions of 300 and 270 nm for BB-PAM and GB-PAM, respectively. The measured DOF of BB-PAM was approximately 229 μm, which was about 7× better than that of GB-PAM. We imaged the vasculature of a mouse ear using BB-PAM and GB-PAM and confirmed that the DOF of BB-PAM is much better than the DOF of GB-PAM. Thus, we believe that the high resolution achieved at the extended DOF by our system is very practical for wide range of biomedical research including red blood cell (RBC) migration in blood vessels at various depths and observation of cell migration or cell culture., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

While searching for lactic acid bacteria that can restore aging-impaired immune responses, we isolated the Toll-like receptor (TLR) 2/NF-kappaB-activating strain Lactobacillus plantarum HY7712 from kimchi and investigated its immunomodulating effect in whole-body γ-irradiated mice. Exposure to HY7712 strongly activated NF-kappaB signaling in RAW264.7 cells, but inhibited lipopolysaccharide-stimulated NF-kappaB activation. Moreover, HY7712 protected against the downregulation of interferon (IFN)-γ and upregulation of interleukin (IL)-13 caused by γ-irradiation in mice. In mice, γ-irradiation impaired NK-cell activity against YAC-1 tumor cells, but following HY7712 exposure, the activity of NK cells was restored to 91.5% of the level measured in control mice (p < 0.05). These findings suggest that HY7712 activates the TLR2/NF-kappaB signaling pathway and protects against the impairment of NK-cell activity caused by γ-irradiation or aging.

The histidine-rich Ca(2+)-binding protein (HRC) is located in the lumen of the sarcoplasmic reticulum (SR) and exhibits high-capacity Ca(2+)-binding properties. Overexpression of HRC in the heart resulted in impaired SR Ca(2+) uptake and depressed relaxation through its interaction with SERCA2a. However, the functional significance of HRC in overall regulation of calcium cycling and contractility is not currently well defined. To further elucidate the role of HRC in vivo under physiological and pathophysiological conditions, we generated and characterized HRC-knockout (KO) mice. The KO mice were morphologically and histologically normal compared to wild-type (WT) mice. At the cellular level, ablation of HRC resulted in significantly enhanced contractility, Ca(2+) transients, and maximal SR Ca(2+) uptake rates in the heart. However, after-contractions were developed in 50 % of HRC-KO cardiomyocytes, compared to 11 % in WT mice under stress conditions of high-frequency stimulation (5 Hz) and isoproterenol application. A parallel examination of the electrical activity revealed significant increases in the occurrence of Ca(2+) spontaneous SR Ca(2+) release and delayed afterdepolarizations with ISO in HRC-KO, compared to WT cells. The frequency of Ca(2+) sparks was also significantly higher in HRC-KO cells with ISO, consistent with the elevated SR Ca(2+) load in the KO cells. Furthermore, HRC-KO cardiomyocytes showed significantly deteriorated cell contractility and Ca(2+)-cycling caused possibly by depressed SERCA2a expression after transverse-aortic constriction (TAC). Also HRC-null mice exhibited severe cardiac hypertrophy, fibrosis, pulmonary edema and decreased survival after TAC. Our results indicate that ablation of HRC is associated with poorly regulated SR Ca(2+)-cycling, and severe pathology under pressure-overload stress, suggesting an essential role of HRC in maintaining the integrity of cardiac function.

Metabolic profiling of the fecal extracts of male mice was carried out to assess the effects of probiotics on colonic inflammation using (1)H NMR spectroscopy coupled with multivariate data analysis. The control group (n = 5) was administered phosphate buffered saline for 14 days. Acute colitis was induced with dextran sulfate sodium (DSS) for 7 days following administration of phosphate buffered saline for 7 days (DSS-treated group, n = 5). LAB + DSS-treated group (n = 5) was administered lactic acid bacteria (LAB) daily for 7 days followed by treatment with DSS for 7 days to investigate protective effect of LAB against DSS-inducible colitis. Histological damage, myeloperoxidase activity, and malondialdehyde content of colon tissue were reduced, whereas colon length increased in LAB + DSS-treated mice compared to those in DSS-treated mice. DSS treatment was associated with fecal excretion of amino acids, short chain fatty acids, and nucleotides, revealing significant decreases of threonine, alanine, glutamate, glutamine, aspartate, lysine, glycine, butyrate, uracil, and hypoxanthine together with increases of monosaccharides, glucose, and trimethylamine in the feces of mice with DSS-induced colitis. Increased levels of acetate, butyrate, and glutamine and decreased levels of trimethylamine were found in the feces of LAB + DSS-treated mice compared to DSS-treated mice alone. The increased short chain fatty acids levels in the feces of mice fed with LAB indicate that the probiotics have protective effects against DSS-induced colitis via modulation of the gut microbiota. This work highlights the possibility for alternative approach of metabonomics in feces for assessing the probiotic effect in an animal model of inflammatory bowel disease.

Objective: To investigate the mechanisms of the preventive activity of lactic acid bacteria in colitis, the inhibitory effect of Bifidobacterium longum HY8004, which potently inhibited lipid peroxidation in vitro, was examined in 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitic mice., Methods: We measured the ability of lactic acid bacteria (LAB) to inhibit lipid peroxidation in vitro and to inhibit colitis outcomes, colon shortening, and myeloperoxidase activity in TNBS-induced colitis in C3H/HeN and C3H/HeJ mice. We also measured levels of the inflammatory markers interleukin (IL)-1 beta and tumor necrosis factor (TNF)-alpha and their transcription factor, NF-kappaB, in the colon by enzyme-linked immunosorbent assay and immunoblot analysis., Results: Among the LAB tested, B. logum HY8004 most potently inhibited lipid peroxidation in vitro but did not inhibit TLR-4-linked NF-kappaB activation in HEK cells. Oral administration of HY8004 inhibited TNBS-induced colon shortening and myeloperoxidase activity in the colon of C3H/HeN and C3H/HeJ mice as well as IL-1 beta and TNF-alpha expression. B. longum HY8004 also inhibited TNBS-induced lipid peroxidation, TLR-4 expression, and NF-kappaB activation in the colon of C3H/HeN and C3H/HeJ mice., Conclusion: B. longum HY8004 can improve colitis via the inhibition of lipid peroxidation as well as NF-kappaB activation.

To evaluate the anti-colitic effect of lactic acid bacteria by cDNA microarray analysis, a lactic acid bacteria mixture (LM) consisting of Lactobacillus brevis HY7401, L. suntoryeus HY7801 and Bifidobacterium longum HY8004 was orally administered to dextran sulfate (DSS)-induced colitic mice and the expression profile of numerous genes was assessed. DSS treatment caused colitic outcomes such as inflammation and colon shortening. DSS also up-regulated the expression of inflammation-related genes: pro-inflammatory and chemotactic cytokines, including IL-1beta, TNF-alpha, IL-6, CCL2, CCL4, CCL7, CCL24, CXCL1, CXCL2, CXCL5, CXCL9 and CXCL10, and their receptors CCR3 and CCR7, and other colitis-related genes such as COX-2, PAP, MMP family, S100a8, S100a9 and DEFA1. LM treatment inhibited the mRNA expression of inflammation-related and tissue remodeling genes induced by DSS as well as the colitic symptoms. LM inhibition for the DSS-induced expression of the representative inflammatory markers, IL-1beta, TNF-alpha and COX-2, was supported by quantitative real-time polymerase chain reaction analysis. These findings suggest that LM ameliorates DSS-induced colitis by regulating inflammatory-related cytokines as well as tissue remodeling genes.

Objective: Lactic acid bacteria (LAB) can improve disturbances of indigenous microflora as well as inflammatory bowel diseases (IBD) such as ulcerative colitis and Crohn's disease. We examined the anticolitic effect of Lactobacillus suntoryeus HY7801, which inhibited toll-like receptor (TLR)-4-linked NF-kappaB activation in human embryonic kidney (HEK) cells, in 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced colitic mice., Materials and Methods: We measured the ability of commercial and intestinal LAB to inhibit lipopolysaccharide (LPS)-stimulated, TLR-4-linked NF-kappaB activation in HEK cells, as well as to inhibit colitis outcomes in TNBS-induced colitic mice. We also measured levels of the inflammatory markers, interleukin (IL)-1beta, tumor necrosis factor (TNF)-alpha, and IL-6, and their transcription factor, NF-kappaB, in intestinal mucosa by enzyme-linked immunosorbent assay and immunoblotting., Results and Discussion: LAB inhibited TLR-4-linked NF-kappaB activation, and L. suntoryeus HY7801 was the most potent inhibitor. Intrarectal treatment of TNBS in mice caused colon shortening and also increased colonic expression of IL-1beta, IL-6, and TNF-alpha expression. However, oral administration of Lactobacillus HY7801 (100 mg/kg) inhibited colon shortening (p < 0.001) and myeloperoxidase activity in TNBS-induced colitic mice (p < 0.0002) and also decreased colonic expression of IL - 1beta (p < 0.003), IL-6 (p < 0.0001), and TNF-alpha (p < 0.0001). Lactobacillus HY7801 inhibited the NF-kappaB activation and TLR-4 expression induced by TNBS, as well as the expression of cyclooxygenase 2. Lactobacillus HY7801 also reduced the activity of intestinal bacterial glycosaminoglycan degradation and beta-glucuronidase induced by TNBS., Conclusion: L. suntoryeus HY7801 can improve colitis via the inhibition of TLR-4-linked NF-kappaB activation.

Comprehensive understanding of the molecular and physiological events occurring in cardiac muscle requires identification of unknown genes expressed in this tissue. We analyzed the mouse cardiac muscle UniGene library containing 827 gene-oriented transcript clusters, predicting that 19% of these genes are unknown. We systematically identified 15 authentic novel genes abundantly expressed in cardiac muscle. Northern blot analysis revealed transcriptional characteristics of the genes, such as transcript size and presence of isoforms. Transfection assays performed using various cell lines including mouse cardiac muscle cells provided information on the cellular characteristics of the novel proteins. Using correlation analysis, we identified co-regulated genes from previously reported microarray data sets. Our in silico and in vitro data suggest that a number of the novel genes are implicated in calcium metabolism, mitochondrial functions and gene transcription. In particular, we obtained new and direct evidence that one of the novel proteins is a calcium-binding protein. Taken together, we identified and characterized a number of novel cardiac genes by integrative approach. Our inclusive data establish a firm basis for future investigation into the cardiac gene network and functions of these genes.

Background: Maturation of spermatozoa, including development of motility and the ability to fertilize the oocyte, occurs during transit through the microenvironment of the epididymis. Comprehensive understanding of sperm maturation requires identification and characterization of unique genes expressed in the epididymis., Results: We systematically identified 32 novel genes with epididymis-specific or -predominant expression in the mouse epididymis UniGene library, containing 1505 gene-oriented transcript clusters, by in silico and in vitro analyses. The Northern blot analysis revealed various characteristics of the genes at the transcript level, such as expression level, size and the presence of isoform. We found that expression of the half of the genes is regulated by androgens. Further expression analyses demonstrated that the novel genes are region-specific and developmentally regulated. Computational analysis showed that 15 of the genes lack human orthologues, suggesting their implication in male reproduction unique to the mouse. A number of the novel genes are putative epididymal protease inhibitors or beta-defensins. We also found that six of the genes have secretory activity, indicating that they may interact with sperm and have functional roles in sperm maturation., Conclusion: We identified and characterized 32 novel epididymis-specific or -predominant genes by an integrative approach. Our study is unique in the aspect of systematic identification of novel epididymal genes and should be a firm basis for future investigation into molecular mechanisms underlying sperm maturation in the epididymis.