Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years
Context Yunnan Province is an important ecological security barrier in China. This study investigated the temporal and spatial changes to landscape ecology and is of great significance for guiding landscape protection and future socio-economic development. Objectives To analyze the temporal and spatial changes of the landscape patterns at the county, river basin, and provincial levels, and clarify and describe the temporal and spatial differentiation characteristics of the landscape patterns in Yunnan Province. Methods Based on landscape ecology, GIS spatial analysis, and spatio-temporal change analysis, nine landscape pattern indices, and spatial autocorrelation for different years, were calculated. Results The landscape of Yunnan Province has evolved as a whole toward isolation. The indices of separation and fragmentation changed significantly from 2010 to 2015. From 2015 to 2018 the rate of fragmentation decreased. Fragmentation in the Nu Jiang and Irrawaddy River basins was less than in other basins. The landscape patterns of the Jinsha and Pearl River basins were relatively fragmented due to human activity, socioeconomic development, and utilization. The differences between the Lancang and Red River Basins were relatively small and at an intermediate level. Conclusions Spatial autocorrelation analysis indicated that there are three areas with typical clusters, namely the Hengduan Mountains where the degree of fragmentation of the landscape was low, while landscape connectivity and aggregation were high. The subtropical region of Southern Yunnan displayed high landscape heterogeneity, a complex shape index, and high connectivity and sprawl. Central Yunnan exhibited a fragmented landscape with poor connectivity and aggregation. These three regions correspond with “the three screens and two belts” in the Main Functional Planning Area of Yunnan Province.
Spatial and Geographic Information Science
Liu et al. (2021) Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years. PeerJ 9:e10923 https://doi.org/10.7717/peerj.10923
Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes
This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p = 0.07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mixture at a lower supplemental level (20 g/day) to increase milk fat (%) and unsaturated fatty acid content in buffalo.
Hassan et al. (2021) Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes. PeerJ 9:e11241 https://doi.org/10.7717/peerj.11241
The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper
Copper (Cu) is important for plant growth, but high concentrations can lead to detrimental effects such as primary root length inhibition, vegetative tissue chlorosis, and even plant death. The interaction between plant-soil microbiota and roots can potentially affect metal mobility and availability, and, therefore, overall plant metal concentration. Cupriavidus metallidurans CH34 is a multi metal-resistant bacterial model that alters metal mobility and bioavailability through ion pumping, metal complexation, and reduction processes. The interactions between strain CH34 and plants may affect the growth, metal uptake, and translocation of Arabidopsis thaliana plants that are exposed to or not exposed to Cu. In this study, we looked also at the specific gene expression changes in C. metallidurans when co-cultured with Cu-exposed A. thaliana. We found that A. thaliana’s rosette area, primary and secondary root growth, and dry weight were affected by strain CH34, and that beneficial or detrimental effects depended on Cu concentration. An increase in some plant growth parameters was observed at copper concentrations lower than 50 µM and significant detrimental effects were found at concentrations higher than 50 µM Cu. We also observed up to a 90% increase and 60% decrease in metal accumulation and mobilization in inoculated A. thaliana. In turn, copper-stressed A. thaliana altered C. metallidurans colonization, and cop genes that encoded copper resistance in strain CH34 were induced by the combination of A. thaliana and Cu. These results reveal the complexity of the plant-bacteria-metal triad and will contribute to our understanding of their applications in plant growth promotion, protection, and phytoremediation strategies.
Environmental Contamination and Remediation
Clavero-León et al. (2021) The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper. PeerJ 9:e11373 https://doi.org/10.7717/peerj.11373
DZNep, an inhibitor of the histone methyltransferase EZH2, suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 pathway
Background Hepatic fibrosis is a common response to chronic liver injury. Recently, the role of DZNep (a histone methyltransferase EZH2 inhibitor) in repressing pulmonary and renal fibrosis was verified. However, the potential effect of DZNep on hepatic fibrosis has not been elucidated. Methods The hepatic fibrosis model was established in rats treated with CCl4 and in hepatic stellate cells (HSCs) treated with TGF-β1. The liver tissues were stained with H&E and Masson’s trichrome. The expression of EZH2, SOCS7, collagen I, αSMA mRNA and miR-199-5p was assessed using qPCR, immunohistochemical or western blot analysis. A dual-luciferase reporter assay was carried out to validate the regulatory relationship of miR-199a-5p with SOCS7. Results The EZH2 level was increased in CCl4-treated rats and in TGF-β1-treated HSCs, whereas DZNep treatment significantly inhibited EZH2 expression. DZNep repressed hepatic fibrosis in vivo and in vitro, as evidenced by the decrease of hepatic fibrosis markers (α-SMA and Collagen I). Moreover, miR-199a-5p expression was repressed by DZNep in TGF-β1-activated HSCs. Notably, downregulation of miR-199a-5p decreased TGF-β1-induced expression of fibrosis markers. SOCS7 was identified as a direct target of miR-199a-5p. The expression of SOCS7 was decreased in TGF-β1-activated HSCs, but DZNep treatment restore d SOCS7 expression. More importantly, SOCS7 knockdown decreased the effect of DZNep on collagen I and α SMA expression in TGF-β1-activated HSCs. Conclusions DZNep suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 axis, suggesting that DZNep may represent a novel treatment for fibrosis.
Ding et al. (2021) DZNep, an inhibitor of the histone methyltransferase EZH2, suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 pathway. PeerJ 9:e11374 https://doi.org/10.7717/peerj.11374
Oxidative stress induces cell death partially by decreasing both mRNA and protein levels of nicotinamide phosphoribosyltransferase in differentiated PC12 cells
Background. Multiple studies have indicated crucial roles of NAD+ deficiency in several neurological diseases and aging. It is critical to discover the mechanisms underlying the NAD+ deficiency. A decreased level of Nicotinamide phosphoribosyltransferase (Nampt)—an important enzyme in the salvage pathway of NAD+ synthesis—has been found under certain pathological conditions, while the mechanisms underlying the Nampt decrease are unclear. The purpose of this study is to test the hypothesis that oxidative stress can produce decreased Nampt, and to investigate the biological effects of Nampt on NAD+ synthesis and cell survival under both basal and oxidative stress conditions. Methods. We used differentiated PC12 cells as a cellular model to investigate the effects of oxidative stress on the levels of Nampt. Multiple assays, including flow cytometry-based cell death assays and NAD+ assays were conducted. Results. First, oxidative stress can decrease the levels of Nampt mRNA and Nampt protein; second, Nampt plays significant roles in NAD+ synthesis under both basal conditions and oxidative stress conditions; third, Nampt plays critical roles in cell survival under both basal conditions and oxidative stress conditions; and fourth, oxidative stress produced decreased NAD+ levels and cell survival partially by decreasing Nampt. Collectively, our study has indicated that oxidative stress is a pathological factor leading to decreased Nampt, which plays important roles in oxidative stress-produced decreases in NAD+ levels and cell survival. Our findings have indicated major roles of Nampt in maintaining NAD+ levels and cell survival under both basal and oxidative stress conditions.
Zhou et al. (2021) Oxidative stress induces cell death partially by decreasing both mRNA and protein levels of nicotinamide phosphoribosyltransferase in differentiated PC12 cells. PeerJ 9:e11401 https://doi.org/10.7717/peerj.11401
The relationship between PLOD1 expression level and glioma prognosis investigated using public databases
Background Glioma is the most common type of intracranial tumor with high malignancy and poor prognosis despite the use of various aggressive treatments. Targeted therapy and immunotherapy are not effective and new biomarkers need to be explored. Some Procollagen-lysine 2-oxyglutarate 5-dioxygenase (PLOD) family members have been found to be involved in the metastasis and progression of tumors. Both PLOD2 and PLOD3 had been reported to be highly expressed in gliomas, while the prognostic value of PLOD1 remains to be further illustrated, so we want to investigate the PLOD1 expression in glioma and its clinical implication. Methods We collected gene expression and corresponding clinical data of glioma from the Chinese Glioma Genome Atlas (CGGA) database, The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. First, we analyzed the expression and mutation of PLOD1 in gliomas and its relationship with clinicopathologic characteristics. Then, we conducted survival analysis, prognostic analysis and nomogram construction of the PLOD1 gene. Finally, we conducted gene ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) to explore possible mechanisms and gene co-expression analysis was also be performed. Results The results showed that the expression level of PLOD1 was higher in gliomas than normal tissues, and high expression of PLOD1 was related to poor survival which can serve as an oncogenic factor and an independent prognostic indicator for glioma patients. Both the GO and GSEA analysis showed high expression of PLOD1 were enriched in Extracellular matrix (ECM) related pathways, the co-expression analysis revealed that PLOD1 was positively related to HSPG2, COL6A2, COL4A2, FN1, COL1A1, COL4A1, CD44, COL3A1, COL1A2 and SPP1, and high expression of these genes were also correlated to poor prognosis of glioma. Conclusions The results showed that high expression of PLOD1 leads to poor prognosis, and PLOD1 is an independent prognostic factor and a novel biomarker for the treatment of glioma. Furthermore, targeting PLOD1 is most likely a potential therapeutic strategy for glioma patients.
Tian et al. (2021) The relationship between PLOD1 expression level and glioma prognosis investigated using public databases. PeerJ 9:e11422 https://doi.org/10.7717/peerj.11422
DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi
Background Snow scorpionflies (genus Boreus) belong to a family of Mecoptera, Boreidae, that has been vastly neglected by entomological researchers due to their shift in seasonality to the winter months. Their activity during this time is regarded as a strategy for predator avoidance and regular sightings on snow fields suggest that this also facilitates dispersal. However, many aspects about snow scorpionflies, especially systematics, taxonomy, distribution of species, phylogenetics and phylogeography have remained fairly unexplored until today. In this study, we fill some of these gaps by generating a reference DNA barcode database for Austrian snow scorpionflies in the frame of the Austrian Barcode of Life initiative and by characterising morphological diversity in the study region. Methods Initial species assignment of all 67 specimens was based on male morphological characters previously reported to differ between Boreus species and, for females, the shape of the ovipositor. DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was carried out for all 67 samples and served as a basis for BIN assignment, genetic distance calculations, as well as alternative species delimitation analyses (ABGD, GMYC, bGMYC, bPTP) and a statistical parsimony network to infer phylogenetic relationships among individual samples/sampling sites. Results Morphological investigations suggested the presence of both Boreus hyemalis and Boreus westwoodi in Austria. DNA barcoding also separated the two species, but resulted in several divergent clades, the paraphyly of B. westwoodi in Austria, and high levels of phylogeographic structure on a small geographic scale. Even though the different molecular species delimitation methods disagreed on the exact number of species, they unequivocally suggested the presence of more than the traditionally recognized two Boreus species in Austria, thus indicating potential cryptic species within the genus Boreus in general and especially in B. westwoodi.
Zangl et al. (2021) DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi. PeerJ 9:e11424 https://doi.org/10.7717/peerj.11424
Identification of diagnostic genes and vital microRNAs involved in rheumatoid arthritis: based on data mining and experimental verification
Background The pathogenesis of rheumatoid arthritis (RA) is complex. This study aimed to identify diagnostic biomarkers and transcriptional regulators that underlie RA based on bioinformatics analysis and experimental verification. Material and Methods We applied weighted gene co-expression network analysis (WGCNA) to analyze dataset GSE55457 and obtained the key module most relevant to the RA phenotype. We then conducted gene function annotation, gene set enrichment analysis (GSEA) and immunocytes quantitative analysis (CIBERSORT). Moreover, the intersection of differentially expressed genes (DEGs) and genes within the key module were entered into the STRING database to construct an interaction network and to mine hub genes. We predicted microRNA (miRNA) using a web-based tool (miRDB). Finally, hub genes and vital miRNAs were validated with independent GEO datasets, RT-qPCR and Western blot. Results A total of 367 DEGs were characterized by differential expression analysis. The WGCNA method divided genes into 14 modules, and we focused on the turquoise module containing 845 genes. Gene function annotation and GSEA suggested that immune response and inflammatory signaling pathways are the molecular mechanisms behind RA. Nine hub genes were screened from the network and seven vital regulators were obtained using miRNA prediction. CIBERSORT analysis identified five cell types enriched in RA samples, which were closely related to the expression of hub genes. Through ROC curve and RT-qPCR validation, we confirmed five genes that were specific for RA, including CCL25, CXCL9, CXCL10, CXCL11, and CXCL13. Moreover, we selected a representative gene (CXCL10) for Western blot validation. Vital miRNAs verification showed that only the differences in has-miR-573 and has-miR-34a were statistically significant. Conclusion Our study reveals diagnostic genes and vital microRNAs highly related to RA, which could help improve our understanding of the molecular mechanisms underlying the disorder and provide theoretical support for the future exploration of innovative therapeutic approaches.
Ren et al. (2021) Identification of diagnostic genes and vital microRNAs involved in rheumatoid arthritis: based on data mining and experimental verification. PeerJ 9:e11427 https://doi.org/10.7717/peerj.11427
EGFR mutation status yield from bronchoalveolar lavage in patients with primary pulmonary adenocarcinoma compared to a venous blood sample and tissue biopsy
Background In recent years, there has been a revolution in the genomic profiling and molecular typing of lung cancer. A key oncogene is the epidermal growth factor receptor (EGFR). The gold standard for determining EGFR mutation status is tissue biopsy, where a histological specimen is taken by a bronchoscopic or surgical method (transbronchial biopsy, forceps biopsy, etc.). However, in clinical practice the tissue sample is often insufficient for morphological and molecular analysis. Bronchoalveolar lavage is a validated diagnostic method for pathogenic infections in the lower respiratory tract, yet its diagnostic value for oncogenic mutation testing in lung cancer has not been extensively investigated. This study aims to compare the prevalence of EGFR mutation status in bronchoalveolar lavage and peripheral blood referring to the gold standard - tissue biopsy in patients with primary lung adenocarcinoma. Methods Twenty-six patients with adenocarcinoma were examined for EGFR mutation from tissue biopsy, peripheral blood sample and bronchoalveolar lavage. Results Thirteen patients had wild type EGFR and the other 13 had EGFR mutation. EGFR mutation from a peripheral blood sample was identified in 38.5% (5/13) of patients, whereas EGFR mutation obtained from bronchoalveolar lavage (BAL) was identified in 92.3% (12/13). This study demonstrates that a liquid biopsy sample for EGFR status from BAL has a higher sensitivity compared to a venous blood sample.
Yanev et al. (2021) EGFR mutation status yield from bronchoalveolar lavage in patients with primary pulmonary adenocarcinoma compared to a venous blood sample and tissue biopsy. PeerJ 9:e11448 https://doi.org/10.7717/peerj.11448
Seasonal variation of 25-Hydroxyvitamin D and indices of carbohydrate and lipid metabolism in postmenopausal women
Background Some studies indicate vitamin D’s significant contribution to metabolic processess. Therefore, the purpose of this study was to evaluate the level of carbohydrate and lipid metabolism indices in relation to seasonal changes in 25-hydroxyvitamin D (25(OH)D) concentration in postmenopausal women. Methods Sixteen postmenopausal women meeting health criteria and not using vitamin D supplementation were included in the study. Seasonal variation of somatic features and the serum concentration of 25(OH)D, glucose, insulin, parathormon, sclerostin and lipid profile were determined on two terms (autumn-winter). Results Comparative analysis of the variables between the study terms revealed a marked decrease in the concentration of 25(OH)D (p ≤ 0.0001), insulin (p < 0.05), insulin resistance index (HOMA-IR), (p < 0.05). The significant positive correlations of changes (Δ) between autumn and winter in 25(OH)D with body mass (p < 0.05), and fat mass (p ≤ 0.01), measured in the first study term, in the group of women with normal body mass index (BMI), and negative correlation with fat mass (p < 0.05) in women with a BMI value above the reference values, were found. The relationship analysis showed that in women with normal BMI, the decrease in 25(OH)D concentrations was greater when the body fat percentage was higher, whereas in women with a BMI value above the reference values, the higher the fat percentage, the smaller was the decrease in 25(OH)D concentration. Conclusions Seasonal changes in 25(OH)D concentration did not significantly affect the concentration of carbohydrate and lipid metabolism indices. The magnitude of decline in 25(OH)D levels depends on the fat mass. We suppose that environmental or lifestyle-related factors, e.g., nutritional behaviours, may have had more influence on metabolic indices than changes in 25(OH)D.
Huta-Osiecka et al. (2021) Seasonal variation of 25-Hydroxyvitamin D and indices of carbohydrate and lipid metabolism in postmenopausal women. PeerJ 9:e11341 https://doi.org/10.7717/peerj.11341