Cinnamtannin B1 attenuates rosacea-like signs via inhibition of pro-inflammatory cytokine production and down-regulation of the MAPK pathway
Background Rosacea is a common inflammatory disease of facial skin. Dysregulation of innate immunity with enhanced inflammation and increased abundance of LL-37 at the epidermal site is a characteristic feature of rosacea. Cinnamtannin B1 (CB1) is a condensed tannin with anti-inflammatory and anti-microbial activities. The aims of the study were to evaluate the potential of CB1 as a therapy for rosacea and to characterize the potential mechanisms of action. Methods We intraperitoneally administered 20 mg/kg CB1 once daily for 2 days into the LL-37-induced mouse model of rosacea. The effects of CB1 in vivo were evaluated by the observations of lesions, histology, immunohistochemistry, and the transcription and translation of pro-inflammatory cytokines and chemokines. Human keratinocyte HaCaT and monocyte THP-1 were used to characterize the effects of CB1 on LL-37-induced inflammation in vitro. The changes in pro-inflammatory chemokine interleukin-8 (IL-8) were quantitated by enzyme-linked immunosorbent assay (ELISA), and the expressions of genes involved were determined by Western blotting. Results CB1 attenuated local redness, inflammation, and neutrophil recruitment in the mouse model of rosacea in vivo. CB1 suppressed myeloperoxidase (MPO) and macrophage inflammatory protein 2 (MIP-2) production, a functional homolog of interleukin-8 (IL-8), at the lesions. In vitro experiments confirmed that CB1 reversed the LL-37-induced IL-8 production in human keratinocytes HaCaT and monocyte THP-1 cells. CB1 inhibited IL-8 production through downregulating the phosphorylation of extracellular signal-regulated kinase (ERK) in the mitogen-activated protein kinase (MAPK) pathway. Conclusion CB1 attenuated LL-37-induced inflammation, specifically IL-8 production, through inhibiting the phosphorylation of ERK. CB1 has potential as a treatment for rosacea.
Kan et al. (2020) Cinnamtannin B1 attenuates rosacea-like signs via inhibition of pro-inflammatory cytokine production and down-regulation of the MAPK pathway. PeerJ 8:e10548 https://doi.org/10.7717/peerj.10548
Responses of branching reef corals Acropora digitifera and Montipora digitata to elevated temperature and pCO2
Anthropogenic emission of CO2 into the atmosphere has been increasing exponentially, causing ocean acidification (OA) and ocean warming (OW). The “business-as-usual” scenario predicts that the atmospheric concentration of CO2 may exceed 1,000 µatm and seawater temperature may increase by up to 3 °C by the end of the 21st century. Increases in OA and OW may negatively affect the growth and survival of reef corals. In the present study, we separately examined the effects of OW and OA on the corals Acropora digitifera and Montipora digitata, which are dominant coral species occurring along the Ryukyu Archipelago, Japan, at three temperatures (28 °C, 30 °C, and 32 °C) and following four pCO2 treatments (400, 600, 800, and 1,000 µatm) in aquarium experiments. In the OW experiment, the calcification rate (p = 0.02), endosymbiont density, and maximum photosynthetic efficiency (Fv/Fm) (both p < 0.0001) decreased significantly at the highest temperature (32 °C) compared to those at the lower temperatures (28 °C and 30 °C) in both species. In the OA experiment, the calcification rate decreased significantly as pCO2 increased (p < 0.0001), whereas endosymbiont density, chlorophyll content, and Fv/Fm were not affected. The calcification rate of A. digitifera showed greater decreases from 30 °C to 32 °C than that of M. digitata. The calcification of the two species responded differently to OW and OA. These results suggest that A. digitifera is more sensitive to OW than M. digitata, whereas M. digitata is more sensitive to OA. Thus, differences in the sensitivity of the two coral species to OW and OA might be attributed to differences in the endosymbiont species and high calcification rates, respectively.
Manullang et al. (2020) Responses of branching reef corals Acropora digitifera and Montipora digitata to elevated temperature and pCO2. PeerJ 8:e10562 https://doi.org/10.7717/peerj.10562
Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia
Background Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (n = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia. Methods Whole genome sequencing (WGS) was performed using next-generation sequencing (NGS) applied in the Illumina MiSeq instrument. Full-length virus genomes were annotated using the reference genome of hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2) and then visualized in UGENE v. 1.30. For phylogenetic analysis, a dataset of 88 available SARS-CoV-2 complete genomes from different countries, including Indonesia, was retrieved from GISAID. Results All patients were hospitalized with various severities of COVID-19. Phylogenetic analysis revealed that one and three virus samples belong to clade L and GH. These three clade GH virus samples (EPI_ISL_525492, EPI_ISL_516800 and EPI_ISL_516829) were not only located in a cluster with SARS-CoV-2 genomes from Asia but also those from Europe, whereas the clade L virus sample (EPI_ISL_516806) was located amongst SARS-CoV-2 genomes from Asia. Using full-length sequences available in the GISAID EpiCoV Database, 39 of 60 SARS-CoV-2 (65%) from Indonesia harbor the D614G mutation. Conclusion These findings indicate that SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, concurrent with the COVID-19 situation worldwide.
Gunadi et al. (2020) Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. PeerJ 8:e10575 https://doi.org/10.7717/peerj.10575
Dnajb8, a target gene of SOX30, is dispensable for male fertility in mice
Background The DNAJ family of molecular chaperones maintains protein homeostasis in mitotic and postmeiotic cells, especially germ cells. Recently, we found that the transcription factor SOX30 initiates transcription of Dnajb8 during late meiosis and spermiogenesis in mouse testes. Methods We used the CRISPR/Cas9 system to generate Dnajb8 mutant mice and analyze the phenotype of the Dnajb8 mutants. Results AlthoughDnajb8 is an evolutionarily conserved gene, it is not essential for spermatogenesis and male fertility. We provide this phenotypic information, which could prevent duplicative work by other groups.
Wang et al. (2020) Dnajb8, a target gene of SOX30, is dispensable for male fertility in mice. PeerJ 8:e10582 https://doi.org/10.7717/peerj.10582
Estimating salt content of vegetated soil at different depths with Sentinel-2 data
The accurate and timely monitoring of the soil salt content (SSC) at different depths is the prerequisite for the solution to salinization in the arid and semiarid areas. Sentinel-2 has demonstrated significant superiority in SSC inversion for its higher temporal, spatial and spectral resolution, but previous research on SSC inversion with Sentinel-2 mainly focused on the unvegetated surface soil. Based on Sentinel-2 data, this study aimed to build four machine learning models at five depths (0∼20 cm, 20∼40 cm, 40∼60 cm, 0∼40 cm, and 0∼60 cm) in the vegetated area, and evaluate the sensitivity of Sentinel-2 to SSC at different depths and the inversion capability of the models. Firstly, 117 soil samples were collected from Jiefangzha Irrigation Area (JIA) in Hetao Irrigation District (HID), Inner Mongolia, China during August, 2019. Then a set of independent variables (IVs, including 12 bands and 32 spectral indices) were obtained based on the Sentinel-2 data (released by the European Space Agency), and the full subset selection was used to select the optimal combination of IVs at five depths. Finally, four machine learning algorithms, back propagation neural network (BPNN), support vector machine (SVM), extreme learning machine (ELM) and random forest (RF), were used to build inversion models at each depth. The model performance was assessed using adjusted coefficient of determination (R2adj), root mean square error (RMSE) and mean absolute error (MAE). The results indicated that 20∼40 cm was the optimal depth for SSC inversion. All the models at this depth demonstrated a good fitting (R2adj≈ 0.6) and a good control of the inversion errors (RMSE < 0.16%, MAE < 0.12%). At the depths of 40∼60 cm and 0∼20 cm the inversion performance showed a slight and a great decrease respectively. The sensitivity of Sentinel-2 to SSC at different depths was as follows: 20∼40 cm > 40∼60 cm > 0∼40 cm > 0∼60 cm > 0∼20 cm. All four machine learning models demonstrated good inversion performance (R2adj > 0.46). RF was the best model with high fitting and inversion accuracy. Its R2adj at five depths were between 0.5 to 0.68. The SSC inversion capabilities of all the four models were as follows: RF model > ELM model > SVM model > BPNN model. This study can provide a reference for soil salinization monitoring in large vegetated area.
Spatial and Geographic Information Science
Chen et al. (2020) Estimating salt content of vegetated soil at different depths with Sentinel-2 data. PeerJ 8:e10585 https://doi.org/10.7717/peerj.10585
Sevoflurane preconditioning attenuates hypoxia/reoxygenation injury of H9c2 cardiomyocytes by activation of the HIF-1/PDK-1 pathway
Background Sevoflurane preconditioning (SPC) can provide myocardial protective effects similar to ischemic preconditioning (IPC). However, the underlying molecular mechanism of SPC remains unclear. Studies confirm that hypoxia-inducible factor-1 (HIF-1) can transform cells from aerobic oxidation to anaerobic glycolysis by activating the switch protein pyruvate dehydrogenase kinase-1 (PDK-1), thus providing energy for the normal life activities of cells under hypoxic conditions. The purpose of this study was to investigate whether the cardioprotective effects of SPC are associated with activation of the HIF-1a/PDK-1 signal pathway. Methods The H9c2 cardiomyocytes hypoxia/reoxygenation model was established and treated with 2.4% sevoflurane at the end of equilibration. Lactate dehydrogenase (LDH) level, cell viability, cell apoptosis, mitochondrial membrane potential, key enzymes of glycolysis, ATP concentration of glycolysis were assessed after the intervention. Apoptosis related protein(Bcl-2, Bax), HIF-1a protein, and PDK-1 protein were assessed by western blot. Results Compared with the H/R group, SPC significantly increased the expression of HIF-1a, PDK-1, and Bcl-2 and reduced the protein expression of Bax, which markedly decreased the apoptosis ratio and Lactate dehydrogenase (LDH) level, increasing the cell viability, content of key enzymes of glycolysis, ATP concentration of glycolysis and stabilizing the mitochondrial membrane potential. However, the cardioprotective effects of SPC were disappeared by treatment with a HIF-1a selective inhibitor. Conclusion This study demonstrates that the cardioprotective effects of SPC are associated with the activation of the HIF-1a/PDK-1 signaling pathway. The mechanism may be related to increasing the content of key enzymes and ATP of glycolysis in the early stage of hypoxia.
Hou et al. (2020) Sevoflurane preconditioning attenuates hypoxia/reoxygenation injury of H9c2 cardiomyocytes by activation of the HIF-1/PDK-1 pathway. PeerJ 8:e10603 https://doi.org/10.7717/peerj.10603
Improved plaque assay for human coronaviruses 229E and OC43
In light of the COVID-19 pandemic, studies that work to understand SARS-CoV-2 are urgently needed. In turn, the less severe human coronaviruses such as HCoV-229E and OC43 are drawing newfound attention. These less severe coronaviruses can be used as a model to facilitate our understanding of the host immune response to coronavirus infection. SARS-CoV-2 must be handled under biosafety level 3 (BSL-3) conditions. Therefore, HCoV-229E and OC43, which can be handled at BSL-2 provide an alternative to SARS-CoV-2 for preclinical screening and designing of antivirals. However, to date, there is no published effective and efficient method to titrate HCoVs other than expensive indirect immunostaining. Here we present an improved approach using an agarose-based conventional plaque assay to titrate HCoV 229E and OC43 with mink lung epithelial cells, Mv1Lu. Our results indicate that titration of HCoV 229E and OC43 with Mv1Lu is consistent and reproducible. The titers produced are also comparable to those produced using human rhabdomyosarcoma (RD) cells. More importantly, Mv1Lu cells display a higher tolerance for cell-cell contact stress, decreased temperature sensitivity, and a faster growth rate. We believe that our improved low-cost plaque assay can serve as an easy tool for researchers conducting HCoV research.
Bracci et al. (2020) Improved plaque assay for human coronaviruses 229E and OC43. PeerJ 8:e10639 https://doi.org/10.7717/peerj.10639
Uncovering the hidden diversity of Mississippian crinoids (Crinoidea, Echinodermata) from Poland
Partial crinoid crowns and aboral cups are reported from the Mississippian of Poland for the first time. Most specimens are partially disarticulated or isolated plates, which prevent identification to genus and species, but regardless these remains indicate a rich diversity of Mississippian crinoids in Poland during the Mississippian, especially during the late Viséan. Lanecrinus? sp. is described from the late Tournaisian of the Dębnik Anticline region. A high crinoid biodiversity occurred during late Viséan of the Holy Cross Mountains, including the camerate crinoids Gilbertsocrinus? sp., Platycrinitidae Indeterminate; one flexible crinoid; and numerous eucladid crinoids, including Cyathocrinites mammillaris (Phillips), three taxa represented by partial cups left in open nomenclature, and numerous additional taxa known only from isolated radial plates, brachial plates, and columnals. To date, the youngest occurrence of Gilbertsocrinus was the early Viséan of the United States, thus the present finding in upper Viséan extends this genus range. Furthermore, the occurrence of Lanecrinus? sp. expands the Western European range of this genus into the Tournaisian. A single partially disarticulated crown, Crinoidea Indeterminate B, is described from the Serpukhovian of the Upper Silesian Coal Basin. In addition, several echinoid test plates and spines are also reported.
Salamon et al. (2020) Uncovering the hidden diversity of Mississippian crinoids (Crinoidea, Echinodermata) from Poland. PeerJ 8:e10641 https://doi.org/10.7717/peerj.10641
Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes
Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.
Song et al. (2020) Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes. PeerJ 8:e9859 https://doi.org/10.7717/peerj.9859
Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species
Research on the gut microbiome of host organisms has rapidly advanced with next generation sequencing (NGS) and high-performance computing capabilities. Nonetheless, gut microbiome research has focused on mammalian organisms in laboratory settings, and investigations pertaining to wild fish gut microbiota remain in their infancy. We applied a procedure (available at https://github.com/bngallo1994) for sampling of the fish gut for use in NGS to describe microbial community structure. Our approach allowed for high bacterial OTU diversity coverage (>99.7%, Good’s Coverage) that led to detection of differences in gut microbiota of an invasive (Round Goby) and native (Yellow Bullhead) fish species and collected from the upper St. Lawrence River, an environment where the gut microbiota of fish had not previously been tested. Additionally, results revealed habitat level differences in gut microbiota using two distance metrics (Unifrac, Bray–Curtis) between nearshore littoral and offshore profundal collections of Round Goby. Species and habitat level differences in intestinal microbiota may be of importance in understanding individual and species variation and its importance in regulating fish health and physiology.
Gallo et al. (2020) Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species. PeerJ 8:e10237 https://doi.org/10.7717/peerj.10237