title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=691 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Inflammation and fibrosis in the coal dust-exposed lung described by confocal Raman spectroscopy link: https://peerj.com/articles/13632 last-modified: 2022-06-23 description: BackgroundCoal workers’ pneumoconiosis (CWP) is an occupational disease that severely damages the life and health of miners. However, little is known about the molecular and cellular mechanisms changes associated with lung inflammation and fibrosis induced by coal dust. As a non-destructive technique for measuring biological tissue, confocal Raman spectroscopy provides accurate molecular fingerprints of label-free tissues and cells. Here, the progression of lung inflammation and fibrosis in a murine model of CWP was evaluated using confocal Raman spectroscopy.MethodsA mouse model of CWP was constructed and biochemical analysis in lungs exposed to coal dust after 1 month (CWP-1M) and 3 months (CWP-3M) vs control tissues (NS) were used by confocal Raman spectroscopy. H&E, immunohistochemical and collagen staining were used to evaluate the histopathology alterations in the lung tissues.ResultsThe CWP murine model was successfully constructed, and the mouse lung tissues showed progression of inflammation and fibrosis, accompanied by changes in NF-κB, p53, Bax, and Ki67. Meanwhile, significant differences in Raman bands were observed among the different groups, particularly changes at 1,248, 1,448, 1,572, and 746 cm−1. These changes were consistent with collagen, Ki67, and Bax levels in the CWP and NS groups.ConclusionConfocal Raman spectroscopy represented a novel approach to the identification of the biochemical changes in CWP lungs and provides potential biomarkers of inflammation and fibrosis. creator: Wenyang Wang creator: Min Mu creator: Yuanjie Zou creator: Bing Li creator: Hangbing Cao creator: Dong Hu creator: Xinrong Tao uri: https://doi.org/10.7717/peerj.13632 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2022 Wang et al. title: The role of the river in the functioning of marginal fen: a case study from the Biebrza Wetlands link: https://peerj.com/articles/13418 last-modified: 2022-06-22 description: Study regionThe area of interest is the Upper Biebrza Valley, located in NE Poland.Study focusWe examined water exchange at the river-fen interface in a near-natural wetland system using the combined field research-modeling approach. The authors chose the Biebrza River as the research object: it is a specific case of fen marginal valley rivers, and it flows in the peat layer without direct connection to the mineral soil layer. Our case study introduces two new aspects not yet considered in the scientific literature: (1) the riparian aquifer is fen and (2) the river has no direct contact with the mineral layer. The following research questions were investigated: What is the role of the river in feeding and draining a fen? Which drainage paths are important for water exchange in a near-natural river-fen system? How important are the morphological settings for the river-fen relations? We applied a systematic hydrological research approach based on field measurements and observations of the river and surrounding fen hydrological characteristics, as well as on the modelling results.New hydrological insights for the regionWe demonstrated that morphological settings have a significant influence on river-fen relations. We also demonstrated that due to the undeniable need to introduce increased protection and restoration of marginal fens, we may focus on river status in narrow valleys; however, in the wide valleys, the limitation of the drainage layer by decreasing the intensity of evapotranspiration is more promising. We propose to distinguish zones in the fen river valley to include them when proposing protection or conservation plans. creator: Maria Grodzka-Łukaszewska creator: Grzegorz Sinicyn creator: Mateusz Grygoruk creator: Dorota Mirosław-Świątek creator: Ignacy Kardel creator: Tomasz Okruszko uri: https://doi.org/10.7717/peerj.13418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Grodzka-Łukaszewska et al. title: Characterization of LC-MS based urine metabolomics in healthy children and adults link: https://peerj.com/articles/13545 last-modified: 2022-06-22 description: Previous studies reported that sex and age could influence urine metabolomics, which should be considered in biomarker discovery. As a consequence, for the baseline of urine metabolomics characteristics, it becomes critical to avoid confounding effects in clinical cohort studies. In this study, we provided a comprehensive lifespan characterization of urine metabolomics in a cohort of 348 healthy children and 315 adults, aged 1 to 78 years, using liquid chromatography coupled with high resolution mass spectrometry. Our results suggest that sex-dependent urine metabolites are much greater in adults than in children. The pantothenate and CoA biosynthesis and alanine metabolism pathways were enriched in early life. Androgen and estrogen metabolism showed high activity during adolescence and youth stages. Pyrimidine metabolism was enriched in the geriatric stage. Based on the above analysis, metabolomic characteristics of each age stage were provided. This work could help us understand the baseline of urine metabolism characteristics and contribute to further studies of clinical disease biomarker discovery. creator: Xiaoyan Liu creator: Xiaoyi Tian creator: Shi Qinghong creator: Haidan Sun creator: Li Jing creator: Xiaoyue Tang creator: Zhengguang Guo creator: Ying Liu creator: Yan Wang creator: Jie Ma creator: Ren Na creator: Chengyan He creator: Wenqi Song creator: Wei Sun uri: https://doi.org/10.7717/peerj.13545 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Integrated metabolomics and transcriptome analysis on flavonoid biosynthesis in flowers of safflower (Carthamus tinctorius L.) during colour-transition link: https://peerj.com/articles/13591 last-modified: 2022-06-22 description: BackgroundSafflower (Carthamus tinctorius L.), well known for its flower, is widely used as a dye and traditional Chinese medicine. Flavonoids, especially flavonoid glycosides, are the main pigments and active components. However, their biosynthesis is largely unknown. Interestingly, the colour of flowers in safflower changed from yellow to red during flower development, while much of the gene and chemical bases during colour transition are unclear.MethodsIn this research, widely targeted metabolomics and transcriptomics were used to elucidate the changes in flavonoid biosynthesis from the gene and chemical points of view in flowers of safflower during colour transition. The screening of differential metabolites depended on fold change and variable importance in project (VIP) value. Differential expressed genes (DEGs) were screened by DESeq2 method. RT-PCR was used to analyse relative expressions of DEGs.ResultsA total of 212 flavonoid metabolites, including hydroxysafflor yellow A, carthamin and anthocyanins, were detected and showed a large difference. The candidate genes of glycosyltransferases and flavonoid hydroxylase that might participate in flavonoid glycoside biosynthesis were screened. Ten candidate genes were screened. Through integrated metabolomics and transcriptome analysis, a uridine diphosphate glucose glycosyltransferase gene, CtUGT9 showed a significant correlation with flavonoid glycosides in safflower. In addition, expression analysis showed that CtUGT9 was mainly expressed in the middle development of flowers and was significantly upregulated under MeJA treatment. Our results indicated that CtUGT9 might play an important role in flavonoid glycoside biosynthesis during colour-transition in safflower. creator: Chaoxiang Ren creator: Chao Chen creator: Shuai Dong creator: Rui Wang creator: Bin Xian creator: Tianlei Liu creator: Ziqing Xi creator: Jin Pei creator: Jiang Chen uri: https://doi.org/10.7717/peerj.13591 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ren et al. title: Adapting mark-recapture methods to estimating accepted species-level diversity: a case study with terrestrial Gastropoda link: https://peerj.com/articles/13139 last-modified: 2022-06-21 description: We introduce a new method of estimating accepted species diversity by adapting mark-recapture methods to comparisons of taxonomic databases. A taxonomic database should become more complete over time, so the error bar on an estimate of its completeness and the known diversity of the taxon it treats will decrease. Independent databases can be correlated, so we use the time course of estimates comparing them to understand the effect of correlation. If a later estimate is significantly larger than an earlier one, the databases are positively correlated, if it is significantly smaller, they are negatively correlated, and if the estimate remains roughly constant, then the correlations have averaged out. We tested this method by estimating how complete MolluscaBase is for accepted names of terrestrial gastropods. Using random samples of names from an independent database, we determined whether each name led to a name accepted in MolluscaBase. A sample tested in August 2020 found that 16.7% of tested names were missing; one in July 2021 found 5.3% missing. MolluscaBase grew by almost 3,000 accepted species during this period, reaching 27,050 species. The estimates ranged from 28,409 ± 365 in 2021 to 29,063 ± 771 in 2020. All estimates had overlapping 95% confidence intervals, indicating that correlations between the databases did not cause significant problems. Uncertainty beyond sampling error added 475 ± 430 species, so our estimate for accepted terrestrial gastropods species at the end of 2021 is 28,895 ± 630 species. This estimate is more than 4,000 species higher than previous ones. The estimate does not account for ongoing flux of species into and out of synonymy, new discoveries, or changing taxonomic methods and concepts. The species naming curve for terrestrial gastropods is still far from reaching an asymptote, and combined with the additional uncertainties, this means that predicting how many more species might ultimately be recognized is presently not feasible. Our methods can be applied to estimate the total number of names of Recent mollusks (as opposed to names currently accepted), the known diversity of fossil mollusks, and known diversity in other phyla. creator: Gary Rosenberg creator: Kurt Auffenberg creator: Ruud Bank creator: Rüdiger Bieler creator: Philippe Bouchet creator: David Herbert creator: Frank Köhler creator: Thomas A. Neubauer creator: Eike Neubert creator: Barna Páll-Gergely creator: Ira Richling creator: Simon Schneider uri: https://doi.org/10.7717/peerj.13139 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rosenberg et al. title: Effects of soft rock on soil properties and bacterial community in Mu Us Sandy Land, China link: https://peerj.com/articles/13561 last-modified: 2022-06-21 description: Soft rock is a new material that could be used for the improvement of Mu Us Sandy Land, China. It can be utilized for wind prevention and sand fixation, both of which are of great importance to ecological restoration aims and cultivated land replenishment in desert areas. Four treatments with different compound ratios of soft rock and sand—0:1 (CK), 1:5 (P1), 1:2 (P2), and 1:1 (P3)—were studied. Fluorescence quantitative PCR (qPCR) and high-throughput sequencing were used to analyze the structure and diversity of the bacterial community in the compound soil and its relationship with physical and chemical parameters in the soil. The results showed that in comparison to CK treatment, soil organic carbon (SOC), total nitrogen (TN), and NH4+-N increased significantly in the P1 treatment; available phosphorus (AP), available potassium (AK), and NO3−-N increased significantly in the P3 treatment. The bacterial gene copy number with P3 treatment was highest, showing a significant increase of 182.05% compared with the CK treatment. The three bacterial groups with the highest relative abundance at the phylum level were Actinobacteria, Proteobacteria, and Chloroflexi, accounting for more than 70% of the total population. The bacterial α diversity showed the same trend, the diversity and abundance indices of the P1 and P3 treatments were the highest, and the β diversity showed that the community structure of the two groups in these treatments were similar. norank_f__Roseiflexaceae and Gaiella (belonging to Actinobacteria) significantly differed with differing compound ratios in each treatment. NO3−-N, NH4+-N and SOC were the main factors affecting bacterial community structure, and had a significant positive correlation with Gaiella abundance. These species are known to play an important role in stabilizing the soil structure of sandy land. Overall, 1:5 and 1:1 compound soil mixtures were beneficial towards the microbial community of sandy land, which plays an important role in biological sand fixation. This study provides an important theoretical basis for the supplementation of arable land area and the improvement of sandy land productivity, and has a good promotion prospect. creator: Zhen Guo creator: Wei Hui creator: Juan Li creator: Chenxi Yang creator: Haiou Zhang creator: Huanyuan Wang uri: https://doi.org/10.7717/peerj.13561 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Guo et al. title: Targeted metabolomics suggests a probable role of the FTO gene in the kynurenine pathway in prediabetes link: https://peerj.com/articles/13612 last-modified: 2022-06-21 description: BackgroundGenome-wide association studies have identified the alpha-ketoglutarate dependent dioxygenase gene (FTO) as the first susceptibility gene of obesity. In the present study, we utilized targeted metabolomics in an attempt to further elucidate mechanisms underlying the action of the FTO gene.MethodsThis study was part of a health survey of employees of the Electricity Generating Authority of Thailand (n = 79, 10 female and 69 male). Targeted metabolomics was performed by liquid chromatography–mass spectrometry using Biocrates AbsoluteIDQ-p180 kit. Genotyping of FTO rs9939609 was performed by real-time PCR (TaqMan™ MGB probes).ResultsUsing OPLS-DA variable importance in projection (VIP), tryptophan was found to be among the metabolites with the 10 highest VIP scores. Pearson’s correlation analysis showed that kynurenine and tryptophan were positively correlated only in subjects with the rs9939609 A allele (n = 32, r = 0.56, p < 0.001) and the correlation coefficients were significantly higher in subjects having the A allele than in those without the A allele (p < 0.05). Moreover, the kynurenine/tryptophan ratio was significantly associated with the presence of the A allele, independently of body mass index and sex.ConclusionsThe FTO gene is likely to influences the conversion of tryptophan to kynurenine. creator: La-or Chailurkit creator: Suwannee Chanprasertyothin creator: Nisakron Thongmung creator: Piyamitr Sritara creator: Boonsong Ongphiphadhanakul uri: https://doi.org/10.7717/peerj.13612 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chailurkit et al. title: The influence of a manipulation of threat on experimentally-induced secondary hyperalgesia link: https://peerj.com/articles/13512 last-modified: 2022-06-20 description: Pain is thought to be influenced by the threat value of the particular context in which it occurs. However, the mechanisms by which a threat achieves this influence on pain are unclear. Here, we explore how threat influences experimentally-induced secondary hyperalgesia, which is thought to be a manifestation of central sensitization. We developed an experimental study to investigate the effect of a manipulation of threat on experimentally-induced secondary hyperalgesia in 26 healthy human adults (16 identifying as female; 10 as male). We induced secondary hyperalgesia at both forearms using high-frequency electrical stimulation. Prior to the induction, we used a previously successful method to manipulate threat of tissue damage at one forearm (threat site). The effect of the threat manipulation was determined by comparing participant-rated anxiety, perceived threat, and pain during the experimental induction of secondary hyperalgesia, between the threat and control sites. We hypothesized that the threat site would show greater secondary hyperalgesia (primary outcome) and greater surface area (secondary outcome) of induced secondary hyperalgesia than the control site. Despite a thorough piloting procedure to test the threat manipulation, our data showed no main effect of site on pain, anxiety, or threat ratings during high-frequency electrical stimulation. In the light of no difference in threat between sites, the primary and secondary hypotheses cannot be tested. We discuss reasons why we were unable to replicate the efficacy of this established threat manipulation in our sample, including: (1) competition between threats, (2) generalization of learned threat value, (3) safety cues, (4) trust, and requirements for participant safety, (5) sampling bias, (6) sample-specific habituation to threat, and (7) implausibility of (sham) skin examination and report. Better strategies to manipulate threat are required for further research on the mechanisms by which threat influences pain. creator: Gillian J. Bedwell creator: Caron Louw creator: Romy Parker creator: Emanuel van den Broeke creator: Johan W. Vlaeyen creator: G. Lorimer Moseley creator: Victoria J. Madden uri: https://doi.org/10.7717/peerj.13512 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bedwell et al. title: Remote sensing techniques for automated marine mammals detection: a review of methods and current challenges link: https://peerj.com/articles/13540 last-modified: 2022-06-20 description: Marine mammals are under pressure from multiple threats, such as global climate change, bycatch, and vessel collisions. In this context, more frequent and spatially extensive surveys for abundance and distribution studies are necessary to inform conservation efforts. Marine mammal surveys have been performed visually from land, ships, and aircraft. These methods can be costly, logistically challenging in remote locations, dangerous to researchers, and disturbing to the animals. The growing use of imagery from satellite and unoccupied aerial systems (UAS) can help address some of these challenges, complementing crewed surveys and allowing for more frequent and evenly distributed surveys, especially for remote locations. However, manual counts in satellite and UAS imagery remain time and labor intensive, but the automation of image analyses offers promising solutions. Here, we reviewed the literature for automated methods applied to detect marine mammals in satellite and UAS imagery. The performance of studies is quantitatively compared with metrics that evaluate false positives and false negatives from automated detection against manual counts of animals, which allows for a better assessment of the impact of miscounts in conservation contexts. In general, methods that relied solely on statistical differences in the spectral responses of animals and their surroundings performed worse than studies that used convolutional neural networks (CNN). Despite mixed results, CNN showed promise, and its use and evaluation should continue. Overall, while automation can reduce time and labor, more research is needed to improve the accuracy of automated counts. With the current state of knowledge, it is best to use semi-automated approaches that involve user revision of the output. These approaches currently enable the best tradeoff between time effort and detection accuracy. Based on our analysis, we identified thermal infrared UAS imagery as a future research avenue for marine mammal detection and also recommend the further exploration of object-based image analysis (OBIA). Our analysis also showed that past studies have focused on the automated detection of baleen whales and pinnipeds and that there is a gap in studies looking at toothed whales, polar bears, sirenians, and mustelids. creator: Esteban N. Rodofili creator: Vincent Lecours creator: Michelle LaRue uri: https://doi.org/10.7717/peerj.13540 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rodofili et al. title: Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect link: https://peerj.com/articles/13579 last-modified: 2022-06-20 description: We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Ciénegas Basin (CCB) in the Chihuahuan Desert of Coahuila, México. We collected ten samples on a small scale transect (1.5-m) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faith’s Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties. creator: Laura Espinosa-Asuar creator: Camila Monroy-Guzmán creator: David Madrigal-Trejo creator: Marisol Navarro-Miranda creator: Jazmin Sánchez-Pérez creator: Jhoselinne Buenrostro Muñoz creator: Juan Villar creator: Julián Felipe Cifuentes Camargo creator: Maria Kalambokidis creator: Diego A. Esquivel-Hernandez creator: Mariette Viladomat Jasso creator: Ana E. Escalante creator: Patricia Velez creator: Mario Figueroa creator: Anahi Martinez-Cardenas creator: Santiago Ramirez-Barahona creator: Jaime Gasca-Pineda creator: Luis E. Eguiarte creator: Valeria Souza uri: https://doi.org/10.7717/peerj.13579 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Espinosa-Asuar et al.