An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon
Population-specific spatial and temporal distribution data are necessary to identify mechanisms regulating abundance and to manage anthropogenic impacts. However the distributions of highly migratory species are often difficult to resolve, particularly when multiple populations’ movements overlap. Here we present an integrated model to estimate spatially-stratified, seasonal trends in abundance and population composition, using data from extensive genetic sampling of commercial and recreational Chinook salmon (Oncorhynchus tshawytscha) fisheries in southern British Columbia. We use the model to estimate seasonal changes in population-specific standardized catch per unit effort (a proxy for abundance) across six marine regions, while accounting for annual variability in sampling effort and uncertain genetic stock assignment. We also share this model as an R package stockseasonr for application to other regions and species. Even at the relatively small spatial scales considered here, we found that patterns in seasonal abundance differed among regions and stocks. While certain locations were clearly migratory corridors, regions within the Salish Sea exhibited diverse, and often weak, seasonal patterns in abundance, emphasizing that they are important, year-round foraging habitats. Furthermore, we found evidence that stocks with similar freshwater life histories and adult run timing, as well as relatively proximate spawning locations, exhibited divergent distributions. Our findings highlight subtle, but important differences in how adult Chinook salmon use marine habitats. Down-scaled model outputs could be used to inform ecosystem-based management efforts by resolving the degree to which salmon overlap with other species of concern, as well as specific fisheries. More broadly, variation in stock-specific abundance among regions indicates efforts to identify mechanisms driving changes in size-at-maturity and natural mortality should account for distinct marine distributions.
Freshwater et al. (2021) An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon. PeerJ 9:e11163 https://doi.org/10.7717/peerj.11163
Rainwater chemistry observation in a karst city: variations, influence factors, sources and potential environmental effects
The rainwater chemistry and related air contaminants are used to investigate the rainwater ions sources, variations, and influence factors from 2012 to 2014 in Guiyang city (the typical karst urban area of Southwest China). According to temporal rainwater ion concentrations, the obvious variations were presented in the study period, such as Ca2+ (125∼6,652 μeq L−1) and SO42− (11∼4,127 μeq L−1). Consequently, Ca2+, Mg2+, SO42− and Cl− are considered as the leading ions. Three critical influencing factors of rainwater ions concentrations, including sources variations, rainfall amount and long-distance migration (rainfall amount > 100 mm) are identified. Based on the typical ionic ratios, source identification suggested that anthropogenic inputs mainly contributed to F−, NO3− and SO42−, while the dusts (crustal sources) are the primary sources of Mg2+, Ca2+ and K+. Cl− Enrichment in long-distance transport is the main contributor of Cl−. According to the observation of high level of total wet acid deposition, the more detailed spatio-temporal monitoring of rainfall-related acid deposition (particularly sulfur deposition) is required to understand its potential environmental effects in the aquatic ecosystem of the earth surface.
Environmental Contamination and Remediation
Zeng et al. (2021) Rainwater chemistry observation in a karst city: variations, influence factors, sources and potential environmental effects. PeerJ 9:e11167 https://doi.org/10.7717/peerj.11167
Long non-coding RNA taurine upregulated gene 1 is downregulated in osteoporosis and influences the osteogenic differentiation of bone marrow mesenchymal stem cells
Background With aging, an imbalance in bone remodeling leading to increased bone resorption and decreased bone formation is thought to contribute to osteoporosis. Osteoblastic differentiation of bone marrow mesenchymal stem cells (BMMSCs) plays a vital role in the pathogenesis of osteoporosis. However, the detailed molecular mechanisms of osteoporosis remain incompletely understood. Given that long non-coding RNA taurine upregulated gene 1 (lnc TUG1) plays a critical role in the osteogenic differentiation, and microRNA-23b (miR-23b) as a putative sponge for lnc TUG1 has upregulated expression in osteoporosis. Therefore, this study investigated the roles of TUG1/miR-23b in osteoporotic pathology. Material and Methods TUG1 and miR-23b expression in the plasma of osteoporotic patients were evaluated by quantitative real-time PCR (qRT-PCR). The osteogenic differentiation in human BMMSCs was evaluated by qRT-PCR, western blot, Alizarin red staining after knockdown of TUG1 by small interfering RNA (siRNA) treatment. Results Decreased expression of TUG1 and increased expression of miR-23b evident in the plasma of patients with osteoporosis than in that of age- and sex-matched healthy controls. Additionally, increased miR-23b expression inhibited runt-related transcription factor 2 (RUNX2), osteocalcin, and osteopontin expression and reduced calcified nodule formation based on the results of qRT-PCR, western blot, and Alizarin Red S staining. Conclusion The study for the first time reported that silence of lncRNA TUG1 significantly suppressed the osteogenic differentiation of BMMSCs possibly by targeting the miR-23b/RUNX2 signaling pathway. This mechanism of TUG1/miR-23b/RUNX2 signaling within the osteogenic differentiation of BMMSCs might provide new insight for the development of lncRNA-directed diagnostic and therapeutic strategies for osteoporosis.
Teng et al. (2021) Long non-coding RNA taurine upregulated gene 1 is downregulated in osteoporosis and influences the osteogenic differentiation of bone marrow mesenchymal stem cells. PeerJ 9:e11251 https://doi.org/10.7717/peerj.11251
Development and validation of an oxidative stress—associated prognostic risk model for melanoma
Background Oxidative stress (OS) is key to various diseases and is implicated in cancer progression and oncogenesis. However, the potential diagnostic value of OS-related genes in skin cutaneous melanoma (SKCM) remains unclear. Methods We used data of RNA sequencing from 471 tumor tissues and one healthy tissue acquired from The Cancer Genome Atlas (TCGA)-SKCM cohort. The Genome Tissue Expression database was used to acquire transcriptome data from 812 healthy samples. OS-related genes that were differentially expressed between SKCM and healthy samples were investigated and 16 prognosis-associated OS genes were identified. The prognostic risk model was built using univariate and Cox multivariate regressions. The prognostic value of the hub genes was validated in the GSE65904 cohort, which included 214 SKCM patients. Results The overall survival rate of SKCM patients in the high-risk group was decreased compared to the low-risk group. In both TCGA and GSE65904 cohorts, the ROC curves suggested that our prognostic risk model was more accurate than other clinicopathological characteristics to diagnose SKCM. Moreover, risk score and nomograms associated with the expression of hub genes were developed. These presented reiterated our prognostic risk model. Altogether, this study provides novel insights with regards to the pathogenesis of SKCM. The 16 hub genes identified may help in SKCM prognosis and individualized clinical treatment.
Yang et al. (2021) Development and validation of an oxidative stress—associated prognostic risk model for melanoma. PeerJ 9:e11258 https://doi.org/10.7717/peerj.11258
Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis
Background Clear Cell Renal Cell Carcinoma (CCRCC) is the most aggressive subtype of Renal Cell Carcinoma (RCC) with high metastasis and recurrence rates. This study aims to find new potential key genes of CCRCC. Methods Four gene expression profiles (GSE12606, GSE53000, GSE68417, and GSE66272) were downloaded from the Gene Expression Omnibus (GEO) database. The TCGA KIRC data was downloaded from The Cancer Genome Atlas (TCGA). Using GEO2R, the differentially expressed genes (DEG) in CCRCC tissues and normal samples were analyzed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed in DAVID database. A protein-protein interaction (PPI) network was constructed and the hub gene was predicted by STRING and Cytoscape. GEPIA and Kaplan-Meier plotter databases were used for further screening of Key genes. Expression verification and survival analysis of key genes were performed using TCGA database, GEPIA database, and Kaplan-Meier plotter. Receiver operating characteristic (ROC) curve was used to analyze the diagnostic value of key genes in CCRCC, which is plotted by R software based on TCGA database. UALCAN database was used to analyze the relationship between key genes and clinical pathology in CCRCC and the methylation level of the promoter of key genes in CCRCC. Results A total of 289 up-regulated and 449 down-regulated genes were identified based on GSE12606, GSE53000, GSE68417, and GSE66272 profiles in CCRCC. The upregulated DEGs were mainly enriched with protein binding and PI3K-Akt signaling pathway, whereas down-regulated genes were enriched with the integral component of the membrane and metabolic pathways. Next, the top 35 genes were screened out from the PPI network according to Degree, and three new key genes ITGAX, LAPTM5 and SERPINE1 were further screened out through survival and prognosis analysis. Further results showed that the ITGAX, LAPTM5, and SERPINE1 levels in CCRCC tumor tissues were significantly higher than those in normal tissues and were associated with poor prognosis. ROC curve shows that ITGAX, LAPTM5, and SERPINE1 have good diagnostic value with good specificity and sensitivity. The promoter methylation levels of ITGAX, LAPTM5 and SERPINE1 in CCRCC tumor tissues were significantly lower than those in normal tissues. We also found that key genes were associated with clinical pathology in CCRCC. Conclusion ITGAX, LAPTM5, and SERPINE1 were identified as novel key candidate genes that could be used as prognostic biomarkers and potential therapeutic targets for CCRCC.
Sui et al. (2021) Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis. PeerJ 9:e11272 https://doi.org/10.7717/peerj.11272
The impact of functional excess of footwear on the foot shape of 7-year-old girls and boys
Background Properly fitted shoes can support the development of growing feet and prevent problems and pathologies, not only in childhood, but also in adulthood. This points to the need to conduct research on the impact of shoe fitting on the structure of the foot in order to raise awareness and importance of this problem, to enable proper decisions regarding the purchase and use of shoes. The aim of this study was to analyze indoor footwear fit and its impact on foot structure in 7-year-old schoolchildren. Methods The CQ-ST podoscope and the Clevermess device were used for measurements. The analysis was carried out using the Mann Whitney U test, Wilcoxon signed-rank test, Chi-square test, regression analysis. Results About 40% of girls and boys had shoes that were incorrectly fitted in length, while as many as 74% of girls and 66% of boys wore shoes that were incorrectly fitted in width. Regression analysis demonstrated a statistically significant influence of the footwear length on longitudinal arch of the right and left foot and the transverse arch of the right foot. In boys, the length of the shoes shows associations with the right and left hallux valgus angle. Conclusion A significant percentage of the studied 7-year-olds, regardless of gender, wears inappropriately fitted shoes. In both sexes, the length of the footwear influenced the longitudinal arch of the right and left foot and the transverse arch of the right foot. Due to the deformity of the first metatarsophalangeal joint, the boys with hallux valgus require footwear which is wider and therefore their shoes need to be bigger in size.
Puszczalowska-Lizis et al. (2021) The impact of functional excess of footwear on the foot shape of 7-year-old girls and boys. PeerJ 9:e11277 https://doi.org/10.7717/peerj.11277
Anti-atherosclerotic vaccination against Porphyromonas gingivalis as a potential comparator of statin in mice
Background Porphyromonas gingivalis (Pg) is an oral anaerobe which damages teeth and periodontal tissues. Its body infection is known to cause chronic inflammation, thereby inducing an early stage of atherosclerosis through humoral immune actions. Hence, vaccination by immunizing the proteins of P. gingivalis (Pg) post sonication with heating may prevent atherosclerosis. This study aimed to compare the effect of its vaccination with statin, which effectively prevents atherosclerosis by lowering lipids. Methods The vaccine was produced by sonicating P. gingivalis through heating, and a total of 32 male APOE-/-mice (8-week old) were subjected Western diet for 8 weeks, in order to induce atherosclerosis in a physiological manner. Then, the mice were grouped to undergo four treatment conditions (i.e., no treatment, pitavastatin, vaccine, or pitavastatin with vaccine). Vaccination was conducted through nasal immunization and confirmed by a Pg-specific humoral immune reaction. Then, half of the mice in each group were orally injected with P. gingivalis for the next 5 weeks while the other half remained uninfected, generating a total of eight groups (n = 4/group). The mice were sacrificed at 3 weeks after the last injection. After harvesting the aorta, Oil Red O staining of en face was conducted with imaging and image analysis, and plaque formation was quantitatively determined. Results Compared to no treatment, the vaccination through nasal immunization significantly reduced the atherosclerotic plaque sizes in APOE -/- mice under Western diet to the comparable level of statin group. When both vaccine and statin were used, no clear synergistic effect was observed as opposed to expectation. Conclusions This study revealed that nasal immunization of heat shock P. gingivalis has a significant impact on the prevention of arteriosclerosis and acts as a potential comparator of statin.
Ha et al. (2021) Anti-atherosclerotic vaccination against Porphyromonas gingivalis as a potential comparator of statin in mice. PeerJ 9:e11293 https://doi.org/10.7717/peerj.11293
Characteristics of craniofacial morphology and factors affecting them in patients with isolated cleft palate
Background Myriad maxillo-mandibular occlusal relationships are observed in patients with isolated cleft palate (ICP), unlike in patients with other cleft types, such as cleft lip and palate. Objectives This study aimed to categorise the characteristics of craniofacial morphology in patients with ICP, and investigate the clinical factors affecting these categorised morphological characteristics. Methods Thirty-six girls with ICP (age (mean ± SD): 5.36 ± 0.36 years) underwent cephalometric measurement. Their craniofacial morphology was categorised using cluster analysis. Profilograms were created and superimposed onto the standard Japanese profilograms to visualise the morphological characteristics of each group (cluster). The mean values and variations in the linear and angular measurements of each group were compared with the Japanese standards and statistically analysed using Dunnett’s test after the analysis of variance. Fisher’s exact test was used to analyse the differences between the cleft types (cleft in the hard and/or soft palate) and skills of the operating surgeons in the groups. Results Cluster analysis of craniofacial morphologies in patients with ICP resulted in the formation of three categories: the first cluster exhibited a relatively harmonious anteroposterior relationship between the maxilla and the mandible (22.2%); the second cluster exhibited crossbite owing to a significantly smaller maxilla (33.3%); and the third cluster exhibited a smaller mandible with posterior rotation showing skeletal class II malocclusion (44.4%). Differences in cleft types and surgeons were not associated with the distribution of patients in each cluster. Conclusions Patients with ICP exhibited characteristic morphological patterns, such as bimaxillary retrusion or severe mandibular retrusion, besides the anterior crossbite frequently found in patients with cleft lip and palate . Understanding the typical morphological characteristics could enable better diagnostic categorisation of patients with ICP, which may eventually improve orthodontic treatment planning.
Tsuji et al. (2021) Characteristics of craniofacial morphology and factors affecting them in patients with isolated cleft palate. PeerJ 9:e11297 https://doi.org/10.7717/peerj.11297
Identification and comparison of circular RNAs in preeclampsia
Background Preeclampsia (PE) is a pregnancy-specific syndrome, belongs to the gestational hypertension diseases category and is considered among the causes of maternal and perinatal mortality and morbidity. However, the pathogenesis of PE is still vague. Methods In the present study, the circular RNA (circRNA) expression patterns of normal pregnant women and PE patients were investigated using whole RNA sequencing. Results A total of 151 differential expressed circRNAs were identified including 121 upregulated and 30 downregulated ones. Functional and pathway enrichment analysis was conducted on the differentially expressed circRNAs using Gene Ontology and KEGG databases. The results of this analysis indicated that several crucial biological processes and pathways were enriched in PE patients. circRNA–microRNA (miRNA) interaction analysis indicated that the reported differentially expresse circRNAs may be associated with some regulatory functions through miRNAs in PE patients. Two ceRNAs networks were constructed according to the targeting relationship between circRNAs/miRNAs and miRNAs/mRNAs. One sub-network contained one upregulated circRNA, four downregulated miRNAs and five upregulated mRNAs, and another sub-network contained 10 downregulated circRNAs, 21 upregulated miRNAs and 15 downregulated mRNAs. Conclusion CircRNA expression patterns have been investigated and this analysis revealed their potential regulatory mechanisms in PE patients. We constructed the ceRNAs (competing endogenous RNA) to reveal the potential molecular roles of dysregulated circRNAs in the PE patients using RNA sequencing data. circRNA_13301 was the only one upregulated circRNA in ceRNA being targeted by four miRNAs.
Ping et al. (2021) Identification and comparison of circular RNAs in preeclampsia. PeerJ 9:e11299 https://doi.org/10.7717/peerj.11299
Sexual dimorphism and skull size and shape in the highly specialized snake species, Aipysurus eydouxii (Elapidae: Hydrophiinae)
Background Snakes exhibit sexual dimorphism in both head size and shape. Such differences are often attributed to different reproductive roles and feeding habits. We aim to investigate how sexual dimorphism is displayed in the highly specialised fish-egg-eating snake, Aipysurus eydouxii, by analysing two complementary features: body size and skull morphology. Methods We used data on body length, weight, and skull shape from 27 measurements of 116 males and females of A. eydouxii. We investigated both sexual dimorphism and allometric (multivariate and bi-variate) properties of skull growth in the analysed data set. Results We found that although there was female-biased sexual size dimorphism in body length, females were not heavier than males, contrary to what is commonly observed pattern among snakes. Moreover, females tend to possess relatively smaller heads than males. However, we only found very subtle differences in skull shape reflected in nasal width, mandibular fossa, quadrate crest and quadrate length. Discussion We suggest that the feeding specialisation in A. eydouxii does not allow for an increase in body thickness and the size of the head above a certain threshold. Our results may be interpreted as support for prey-size divergence as a factor driving skull dimorphism since such species in which the sexes do not differ in prey size also shows very subtle or no differences in skull morphology.
Borczyk et al. (2021) Sexual dimorphism and skull size and shape in the highly specialized snake species, Aipysurus eydouxii (Elapidae: Hydrophiinae). PeerJ 9:e11311 https://doi.org/10.7717/peerj.11311