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.
Spatial and Geographic Information Science
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
First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna
The Swiss Upper Marine Molasse (OMM) documents a transgression event dated to around 21 to 17 million years in which dolphin and other vertebrate remains have been reported. We revised the whole cetacean (whales and dolphins) OMM assemblage available in main collections, focusing on the identification and interpretation of periotics (bone that contains the inner ear). Periotics are rare, but they provide the richest taxonomic information in the sample and hint to environmental associations. Micro-computerized tomography allowed the reconstruction of bony labyrinths for comparisons and environmental interpretations. Three families are represented by periotics: Kentriodontidae, Squalodelphinidae and Physeteridae. The cetacean taxonomic composition of the Swiss OMM reinforces biogeographical patterns reported for the Mediterranean and Paratethys during the Burdigalian at a regional scale and the Calvert cetacean fauna of the northwest Atlantic at oceanic scale.
Aguirre-Fernández et al. (2022) First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna. PeerJ 10:e13251 https://doi.org/10.7717/peerj.13251
Residency, movement patterns, behavior and demographics of reef manta rays in Komodo National Park
Background The reef manta ray (Mobula alfredi) is a globally threatened species and an iconic tourist attraction for visitors to Indonesia’s Komodo National Park (NP). In 2013, manta ray fishing was banned in Komodo NP and its surroundings, preceding the nationwide manta ray protection in 2014. Over a decade ago, a previous acoustic telemetry study demonstrated that reef manta rays had high fidelity to sites within the park, while more recent photo-identification data indicated that some individuals move up to 450 km elsewhere. Characterization of manta ray demographics, behavior, and a focused assessment on site use of popular tourism locations within the park is vital to assist the Komodo NP Management Authority formulate appropriate manta ray conservation and management policies. Methods This study uses a long-term library (MantaMatcher.org) of photo-identification data collected by researchers and citizen scientists to investigate manta ray demographics and habitat use within the park at four sites frequented by tour operators: Cauldron, Karang Makassar, Mawan, and Manta Alley. Residency and movements of manta rays were investigated with maximum likelihood analyses and Markov movement models. Results A total of 1,085 individual manta rays were identified from photographs dating from 2013 to 2018. In general, individual manta rays displayed a higher affinity to specific sites than others. The highest re-sighting probabilities came from the remote southern site, Manta Alley. Karang Makassar and Mawan are only ~5 km apart; however, manta rays displayed distinct site affinities. Exchange of individuals between Manta Alley and the two central sites (~35.5 km apart) occurred, particularly seasonally. More manta rays were recorded traveling from the south to the central area than vice versa. Female manta rays were more mobile than males. Similar demographic groups used Karang Makassar, Mawan, and Manta Alley for foraging, cleaning, cruising, or courtship activities. Conversely, a higher proportion of immature manta rays used the northern site, Cauldron, where foraging was commonly observed. Fishing gear-related injuries were noted on 56 individuals (~5%), and predatory injuries were present on 32 individuals (~3%). Tourism within the park increased from 2014 to 2017, with 34% more dive boats per survey at Karang Makassar and Mawan. Discussion The Komodo NP contains several distinct critical habitats for manta rays that encompass all demographics and accommodate seasonal manta ray movements. While the present study has not examined population trends, it does provide foundational data for such work. Continued research into manta ray abundance, long-range movements, and identifying and protecting other critical aggregation areas within the region is integral to securing the species’ recovery. We provide management recommendations to limit undue pressure on manta rays and their critical habitats from tourism.
Germanov et al. (2022) Residency, movement patterns, behavior and demographics of reef manta rays in Komodo National Park. PeerJ 10:e13302 https://doi.org/10.7717/peerj.13302
Drivers and hazards of consumption of unpasteurised bovine milk and milk products in high-income countries
Introduction The consumption of dairy products contributes to health, nutrition, and livelihoods globally. However, dairy products do not come without microbiological food safety risks for consumers. Despite this risk, common hygiene measures in high-income countries, particularly pasteurisation, ensures that milk is safe, and is indeed frequently mandated by law. Nevertheless, over the past two decades, there has been a global increase in the number of consumers in high-income developed countries actively seeking out unpasteurised milk in liquid and product forms for perceived nutritional and health benefits, and improved taste. The often-anecdotal claims upon which consumers make such choices are not all supported by scientific evidence; however, some recent research studies have investigated (and in some cases demonstrated) the positive impact of unpasteurised milk consumption on the prevalence of asthma, atopy, rectal cancer and respiratory illness. Methods To investigate the significance of unpasteurised milk and milk product consumption for human health in high-income countries, outbreak data between the years 2000 and 2018 were obtained for the United States of America, Canada, the European Union, the United Kingdom, Japan, New Zealand and Australia, which were then categorized into three World Health Organisation subregions: AMR A, EUR A and WPR A. Outbreak dynamic variables such as pathogens, the place of consumption, numbers of outbreaks and deaths per million capita, the average number of cases per outbreak and regulations were described and analysed using R Studio. To provide an overview of unpasteurised milk-related disease outbreaks, a rapid evidence review was also undertaken to establish an overview of what is known in the current literature about hazards and drivers of consumption. Results Foodborne outbreaks associated with unpasteurised dairy consumption have risen in high-income countries over the period 2000 to 2018, with Campylobacter spp. being the most common aetiological agent responsible, followed by Escherichia coli and Salmonella spp. The most common places of consumption are on farms or in households, indicating individuals choose to drink unpasteurised milk, rather than a widespread distribution of the product, for example, at social events and in schools. Further study is needed to better understand contributing factors, such as cultural differences in the consumption of dairy products. Conclusion There are several observable health benefits linked to consuming raw milk, but outbreaks associated with unpasteurised milk and milk products are on the rise. It cannot be definitively concluded whether the benefits outweigh the risks, and ultimately the decision lies with the individual consumer. Nevertheless, many countries have regulations in place to protect consumer health, acknowledging the definite risks to human health that unpasteurised dairy foods may pose, particularly from microbial hazards.
de Klerk et al. (2022) Drivers and hazards of consumption of unpasteurised bovine milk and milk products in high-income countries. PeerJ 10:e13426 https://doi.org/10.7717/peerj.13426