Different roles of urinary light chains and serum light chains as potential biomarkers for monitoring disease activity in systemic lupus erythematosus
Objective The assessment system for monitoring systemic lupus erythematosus (SLE) disease activity is complex and lacks reliable laboratory indicators. It is necessary to find rapid and noninvasive biomarkers. The aim of this study was to screen and identify the differentially expressed proteins in urine samples between active SLE and stable SLE and to further explore the expression of light chains. Methods First, we used a label-free quantitative proteomics approach to establish the urine protein expression profile of SLE, and then screened differentially expressed proteins. Subsequently, the expression of overall light chains was examined by immunofixation electrophoresis and immunoturbidimetric methods, respectively. Results Mass spectrometry data analysis found a total of 51 light chain peptides in the urinary protein expression spectrum, of which 27 light chain peptides were differentially expressed between the two groups. The largest difference was IGLV5-45 located in the variable region of the immunoglobulin Lambda light chain. The levels of urinary light chains and serum light chains were both significantly elevated in active SLE, and the levels of urinary light chains increased with the severity of disease activity. Conclusions The measurement of light chains would help to monitor SLE disease activity. Serum light chains had better discriminatory capacity than urinary light chains, while urine light chains were closely related to the severity of disease activity and could be used for dynamically monitoring the progress of disease activity.
Jiang et al. (2022) Different roles of urinary light chains and serum light chains as potential biomarkers for monitoring disease activity in systemic lupus erythematosus. PeerJ 10:e13385 https://doi.org/10.7717/peerj.13385
Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics
Classification of beaches into morphodynamic states is a common approach in sandy beach studies, due to the influence of natural variables in ecological patterns and processes. The use of remote sensing for identifying beach type and monitoring changes has been commonly applied through multiple methods, which often involve expensive equipment and software processing of images. A previous study on the South African Coast developed a method to classify beaches using conditional tree inferences, based on beach morphological features estimated from public available satellite images, without the need for remote sensing processing, which allowed for a large-scale characterization. However, since the validation of this method has not been tested in other regions, its potential uses as a trans-scalar tool or dependence from local calibrations has not been evaluated. Here, we tested the validity of this method using a 200-km stretch of the Brazilian coast, encompassing a wide gradient of morphodynamic conditions. We also compared this locally derived model with the results that would be generated using the cut-off values established in the previous study. To this end, 87 beach sites were remotely assessed using an accessible software (i.e., Google Earth) and sampled for an in-situ environmental characterization and beach type classification. These sites were used to derive the predictive model of beach morphodynamics from the remotely assessed metrics, using conditional inference trees. An additional 77 beach sites, with a previously known morphodynamic type, were also remotely evaluated to test the model accuracy. Intertidal width and exposure degree were the only variables selected in the model to classify beach type, with an accuracy higher than 90% through different metrics of model validation. The only limitation was the inability in separating beach types in the reflective end of the morphodynamic continuum. Our results corroborated the usefulness of this method, highlighting the importance of a locally developed model, which substantially increased the accuracy. Although the use of more sophisticated remote sensing approaches should be preferred to assess coastal dynamics or detailed morphodynamic features (e.g., nearshore bars), the method used here provides an accessible and accurate approach to classify beach into major states at large spatial scales. As beach type can be used as a surrogate for biodiversity, environmental sensitivity and touristic preferences, the method may aid management in the identification of priority areas for conservation.
Spatial and Geographic Information Science
Checon et al. (2022) Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics. PeerJ 10:e13413 https://doi.org/10.7717/peerj.13413
Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination
Seed germination marks the beginning of a new plant life cycle. Improving the germination rate of seeds and the consistency of seedling emergence in the field could improve crop yields. Many genes are involved in the regulation of seed germination. Our previous study found that some peanut XTHs (xyloglucan endotransglucosylases/hydrolases) were expressed at higher levels at the newly germinated stage. However, studies of the XTH gene family in peanut have not been reported. In this study, a total of 58 AhXTH genes were identified in the peanut genome. Phylogenetic analysis showed that these AhXTHs, along with 33 AtXTHs from Arabidopsis and 61 GmXTHs from soybean, were classified into three subgroups: the I/II, IIIA and IIIB subclades. All AhXTH genes were unevenly distributed on the 18 peanut chromosomes, with the exception of chr. 07 and 17, and they had relatively conserved exon-intron patterns, most with three to four introns. Through chromosomal distribution pattern and synteny analysis, it was found that the AhXTH family experienced many replication events, including 42 pairs of segmental duplications and 23 pairs of tandem duplications, during genome evolution. Conserved motif analysis indicated that their encoded proteins contained the conserved ExDxE domain and N-linked glycosylation sites and displayed the conserved secondary structural loops 1–3 in members of the same group. Expression profile analysis of freshly harvested seeds, dried seeds, and newly germinated seeds using transcriptome data revealed that 26 AhXTH genes, which account for 45% of the gene family, had relatively higher expression levels at the seed germination stage, implying the important roles of AhXTHs in regulating seed germination. The results of quantitative real-time PCR also confirmed that some AhXTHs were upregulated during seed germination. The results of GUS histochemical staining showed that AhXTH4 was mainly expressed in germinated seeds and etiolated seedlings and had higher expression levels in elongated hypocotyls. AhXTH4 was also verified to play a crucial role in the cell elongation of hypocotyls during seed germination.
Zhu et al. (2022) Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination. PeerJ 10:e13428 https://doi.org/10.7717/peerj.13428
Fluoride effect indicators in Phaseolus vulgaris seeds and seedlings
Background Fluoride (F) is one of the main environmental pollutants, and high concentrations are commonly detected in the air and in both surface and groundwater. However, the effects of this pollutant on seed germination and on the initial growth of crop seedlings are still poorly understood. In this context, the aim of this study was to assess morphoanatomical, physiological and biochemical fluoride effect indicators in Phaseolus vulgaris L. seeds and seedlings. Methods P. vulgaris seeds were exposed to a liquid potassium fluoride solution (KF, pH 6.0) at concentrations of 0 (control), 10, 20, 30 mg L−1 for 7 days. A completely randomized experimental design was applied, consisting of four treatments with four replications each. During the experimental period, physiological (7 days) anatomical and histochemical (2 days), biochemical and chemical (4 days) assessments. An analysis of variance was performed followed by Dunnett’s test. to determine significant differences between the KF-exposed groups and control seeds; and a multivariate analysis was performed. Results The germination parameters, and anatomical, morphological, physiological, biochemical and nutritional characteristics of the seedlings did not show negative effects from exposure to KF at the lowest doses evaluated. On the other hand, treatment with the highest dose of KF (30 mg L−1) resulted in a lower germination rate index and increase in abnormal seedlings, and higher electrical conductivity. A lower root length, magnesium content and photochemical efficiency were also observed. The exposure of P. vulgaris to KF, regardless the dose did not affect seeds anatomy and the accumulation of starch and proteins, in relation to the control group. Conclusions Our findings demonstrated that P. vulgaris seedlings were tolerant to KF solutions up to 20 mg L−1, and sensitive when exposed to 30 mg KF L−1.
Environmental Contamination and Remediation
© 2022 Maressa Hungria de Lima e Silva et al.
Maressa Hungria de Lima e Silva et al. (2022) Fluoride effect indicators in Phaseolus vulgaris seeds and seedlings. PeerJ 10:e13434 https://doi.org/10.7717/peerj.13434
©2022 Maressa Hungria de Lima e Silva et al.
A new perleidid neopterygian fish from the Early Triassic (Dienerian, Induan) of South China, with a reassessment of the relationships of Perleidiformes
Neopterygii is the largest clade of ray-finned fishes, including Teleostei, Holostei, and their closely related fossil taxa. This clade was first documented in the Early Carboniferous and underwent rapid evolutionary radiation during the Early to Middle Triassic. This article describes a new perleidid neopterygian species, Teffichthys elegans sp. nov., based on 13 well-preserved specimens from the lower Daye Formation (Dienerian, Induan) in Guizhou, China. The new species documents one of the oldest perleidids, providing insights into the early diversification of this family. The results of a phylogenetic analysis recover Teffichthys elegans sp. nov. as the sister taxon to Teffichthys madagascariensis within the Perleididae. T. elegans sp. nov. shares three derived features of Perleididae: the length of the anteroventral margin of the dermohyal nearly half the length of the anterodorsal margin of the preopercle; the anteroventral margin of the preopercle nearly equal to the anterior margin of the subopercle in length; and the anteroventral margin of the preopercle one to two times as long as the anterodorsal margin of the preopercle. It possesses diagnostic features of Teffichthys but differs from T. madagascariensis by the following features: presence of three supraorbitals; six pairs of branchiostegal rays; relatively deep anterodorsal process of subopercle; absence of spine on the posterior margin of the jugal; and pterygial formula of D26/P14, A22, C36/T39-41. The Perleidiformes are restricted to include only the Perleididae, and other previously alleged ‘perleidiform’ families (e.g., Hydropessidae and Gabanellidae) are excluded to maintain the monophyly of the order. Similar to many other perleidids, T. elegans sp. nov. was likely a durophagous predator with dentition combining grasping and crushing morphologies. The new finding also may indicate a relatively complex trophic structure of the Early Triassic marine ecosystem in South China.
Yuan et al. (2022) A new perleidid neopterygian fish from the Early Triassic (Dienerian, Induan) of South China, with a reassessment of the relationships of Perleidiformes. PeerJ 10:e13448 https://doi.org/10.7717/peerj.13448
LncRNA OIP5-AS1 modulates the proliferation and apoptosis of Jurkat cells by sponging miR-181c-5p to regulate IL-7 expression in myasthenia gravis
Background Myasthenia gravis (MG) is an antibody-mediated autoimmune disease. In recent years, accumulating evidence has indicated that long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs), contributing to the progression of various autoimmune diseases. Nevertheless, the regulatory roles of ceRNAs in MG pathogenesis remain unclear. In this study, we aimed to elucidate the role of lncRNA OIP5-AS1 as a ceRNA associated with MG progression. Methods Real-time PCR was used to detect OIP5-AS1 levels in peripheral blood mononuclear cells (PBMCs) from patients with MG. Luciferase reporter assays were performed to validate the relationship between OIP5-AS1 and miR-181c-5p. CCK-8 and flow cytometry were performed to test the proliferation and apoptotic abilities of OIP5-AS1 in Jurkat cells. Furthermore, real-time PCR and Western blot assays were performed to explore the interactions between OIP5-AS1, miR-181c-5p, and IL-7. Results The expression of OIP5-AS1 was up-regulated in patients with MG. Luciferase reporter assay indicated that OIP5-AS1 targeted the miR-181c-5p. Functional assays showed that OIP5-AS1 suppressed Jurkat cell apoptosis and promoted cell proliferation by sponging miR-181c-5p. Mechanistically, knockdown of OIP5-AS1 inhibited IL-7 expression at both the mRNA and protein levels in Jurkat cells, whereas the miR-181c-5p inhibitor blocked the reduction of IL-7 expression induced by OIP5-AS1 suppression. Conclusions We confirmed that OIP5-AS1 serves as an endogenous sponge for miR-181c-5p to regulate the expression of IL-7. Our findings provide novel insights into MG processes and suggests potential therapeutic targets for patients with MG.
Wang et al. (2022) LncRNA OIP5-AS1 modulates the proliferation and apoptosis of Jurkat cells by sponging miR-181c-5p to regulate IL-7 expression in myasthenia gravis. PeerJ 10:e13454 https://doi.org/10.7717/peerj.13454
Forecasting effects of transport infrastructure on endangered tigers: a tool for conservation planning
The rapid development of transport infrastructure is a major threat to endangered species worldwide. Roads and railways can increase animal mortality, fragment habitats, and exacerbate other threats to biodiversity. Predictive models that forecast the future impacts to endangered species can guide land-use planning in ways that proactively reduce the negative effects of transport infrastructure. Agent-based models are well suited for predictive scenario testing, yet their application to endangered species conservation is rare. Here, we developed a spatially explicit, agent-based model to forecast the effects of transport infrastructure on an isolated tiger (Panthera tigris) population in Nepal’s Chitwan National Park—a global biodiversity hotspot. Specifically, our model evaluated the independent and interactive effects of two mechanisms by which transport infrastructure may affect tigers: (a) increasing tiger mortality, e.g., via collisions with vehicles, and (b) depleting prey near infrastructure. We projected potential impacts on tiger population dynamics based on the: (i) existing transportation network in and near the park, and (ii) the inclusion of a proposed railway intersecting through the park’s buffer zone. Our model predicted that existing roads would kill 46 tigers over 20 years via increased mortality, and reduced the adult tiger population by 39% (133 to 81). Adding the proposed railway directly killed 10 more tigers over those 20 years; deaths that reduced the overall tiger population by 30 more individuals (81 to 51). Road-induced mortality also decreased the proportion of time a tiger occupied a given site by 5 years in the 20-year simulation. Interestingly, we found that transportation-induced depletion of prey decreased tiger occupancy by nearly 20% in sites close to roads and the railway, thereby reducing tiger exposure to transportation-induced mortality. The results of our model constitute a strong argument for taking into account prey distributions into the planning of roads and railways. Our model can promote tiger-friendly transportation development, for example, by improving Environmental Impact Assessments, identifying “no go” zones where transport infrastructure should be prohibited, and recommending alternative placement of roads and railways.
Carter et al. (2022) Forecasting effects of transport infrastructure on endangered tigers: a tool for conservation planning. PeerJ 10:e13472 https://doi.org/10.7717/peerj.13472
The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma
Background The genome map of hepatocellular carcinoma (HCC) is complex. In order to explore whether circulating tumor cell DNA (ctDNA) can be used as the basis for sequencing and use ctDNA to find tumor related biomarkers, we analyzed the mutant genes of ctDNA in patients with liver cancer by sequencing. Methods We used next-generation targeted sequencing technology to identify mutations in patients with liver cancer. The ctDNA from 10 patients with hepatocellular carcinoma (including eight cases of primary hepatocellular carcinoma and two cases of secondary hepatocellular carcinoma) was sequenced. We used SAMtools to detect and screen single nucleotide polymorphisms (SNPs) and insertion deletion mutations (INDELs) and ANNOVAR to annotate the structure and function of the detected mutations. Screening of pathogenic and possible pathogenic genes was performed using American College of Medical Genetics and Genomics (ACMG) guidelines. GO analysis and KEGG analysis of pathogenic and possible pathogenic genes were performed using the DAVID database, and protein–protein interaction network analysis of pathogenic and possible pathogenic genes was performed using the STRING database. Then, the Kaplan–Meier plotter database, GEPIA database and HPA database were used to analyse the relationship between pathogenic and possible pathogenic genes and patients with liver cancer. Results Targeted capture and deep sequencing of 560 cancer-related genes in 10 liver cancer ctDNA samples revealed 8,950 single nucleotide variation (SNV) mutations and 70 INDELS. The most commonly mutated gene was PDE4DIP, followed by SYNE1, KMT2C, PKHD1 and FN1. We compared these results to the COSMIC database and determined that ctDNA could be used for sequencing. According to the ACMG guidelines, we identified 54 pathogenic and possible pathogenic mutations in 39 genes in exons and splice regions of 10 HCC patients and performed GO analysis, KEGG analysis, and PPI network analysis. Through further analysis, four genes significantly related to the prognosis of liver cancer were identified. Conclusion In this study, our findings indicate that ctDNA can be used for sequencing. Our results provide some molecular data for the mapping of genetic variation in Chinese patients with liver cancer, which enriches the understanding of HCC pathogenesis and provides new ideas for the diagnosis and prognosis of HCC patients.
Ding et al. (2022) The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma. PeerJ 10:e13473 https://doi.org/10.7717/peerj.13473
TFR1 expression in induced sputum is associated with asthma severity
Background Asthma is characterized as a chronic inflammatory airway disease. Iron accumulation is related to asthma pathogenesis. Transferrin receptor 1(TFR1) expression is associated with intracellular iron overload in macrophages. In our study, we explored the association among TFR1 expression, the inflammatory macrophage phenotype, and asthma severity. Methods Induced sputum was collected from 50 asthma patients. Real-time PCR was used to evaluate mRNA expression. The status of inflammatory macrophage phenotype was assessed using flow cytometry. Results TFR1 levels were inversely correlated with forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) and FEV1/vital capacity (VC). Among inflammatory cytokines, TFR1 expression was positively correlated with IL-1β, TNF-α, IL-6, IFN-γ, and IL-17A mRNA expression in induced sputum. Moreover, TFR1 expression was positively correlated with the number of proinflammatory M1 macrophages and iNOS expression in induced sputum. Neutrophil counts in induced sputum were significantly and positively related to TFR1 expression. Furthermore, TFR1 expression showed an increasing trend in asthma patients with no family history. Our findings indicated that TFR1 expression was consistent with the asthma severity index, especially the proinflammatory M1 macrophage phenotype. TFR1 expression may be a good marker to indicate asthma severity.
Wang et al. (2022) TFR1 expression in induced sputum is associated with asthma severity. PeerJ 10:e13474 https://doi.org/10.7717/peerj.13474
The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation
Located in northwestern South China Sea (SCS), the Beibu Gulf constitutes an environmentally sensitive region shaped by land-ocean-atmosphere interactions in Asia between the western Pacific and eastern Indian Oceans. This study aims to provide a comprehensive view of the sub-fossil diatom biogeography, distribution pattern and oceanographic environmental controls with support of multivariate methods based on Beibu Gulf core-top samples. Cluster analysis of diatom assemblages divides the distribution pattern into four subclusters. Sea surface salinity (SSS), temperature (SST), trophic state (chlorophyll a concentration in this study) and water depth constrain the diatom distribution pattern through canonical redundancy analysis although only partly support an interpretation of the relationship between these various variables. Chlorophyll a has a strong correlation to diatom distribution, and responds to Paralia sulcata occurrence, while SSS and SST also have significant influence and indicate warm water invasion from the open SCS. Water depth is a subordinate factor in terms of Beibu Gulf diatom distribution. The ca. 25 m water-depth marks the upper extent of Paralia sulcata dominance in the northern Beibu Gulf. A strong mixing area with a complex diatom distribution exists below this water depth in the middle of Beibu Gulf. Coastal currents from north of SCS invade Beibu Gulf through Qiongzhou Strait and south of Hainan Island, as recorded by higher percentages of Paralia sulcata and Cyclotella striata at these sites. Our results provide a selection of evaluation method for a marine ecological red-line definition for sustainable development. This study highlights the perspective relationships between the spatial distribution of sub-fossil diatom assemblages in surface sediments and oceanographic variables, which could serve as a model for paleoenvironmental and paleoclimatic reconstruction in future marginal sea geoscience research for the Beibu Gulf, northwestern SCS.
Zhang et al. (2022) The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation. PeerJ 10:e13115 https://doi.org/10.7717/peerj.13115