title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=508 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Macrophyte communities as bioindicator of stormwater pollution in rivers: a quantitative analysis link: https://peerj.com/articles/15248 last-modified: 2023-06-01 description: Macrophytes are one of the important indicators used in assessing the anthropic impact on aquatic ecosystems. The structure of macrophyte communities of two rivers were compared by species composition, dominant species and projective cover using statistical methods. It is shown that the influence of storm runoff on these rivers is manifested in the form of a change in the dominant species composition. Based on the statistical analysis carried out, it can be argued that, despite the peculiarities of the flora composition of each of the rivers, the influence of storm runoffs largely neutralizes this specificity, determining the situation in local areas immediately below the runoff. In the area of the effluent discharge the dominance of individual species and an increase in the area overgrown with macrophytes was observed. In the area of stormwater discharge on the Psel River, species were usually present: Nuphar lutea, Ceratophyllum demersum, Myriophyllum spicatum and on the Bystrica River—Glyceria maxima, Sagitaria sagittiformis, Stuckenia pectinata and Potamogeton crispus. The use of the NMDS method has been found to provide good insight into the structural rearrangements in macrophyte communities affected by runoff from stormwater systems. creator: Roman Babko creator: Tetiana Diachenko creator: Jacek Zaburko creator: Yaroslav Danko creator: Tatiana Kuzmina creator: Joanna Szulżyk-Cieplak creator: Joanna Czarnota creator: Grzegorz Łagód uri: https://doi.org/10.7717/peerj.15248 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Babko et al. title: New seed coating containing Trichoderma viride with anti-pathogenic properties link: https://peerj.com/articles/15392 last-modified: 2023-06-01 description: BackgroundTo ensure food security in the face of climate change and the growing world population, multi-pronged measures should be taken. One promising approach uses plant growth-promoting fungi (PGPF), such as Trichoderma, to reduce the usage of agrochemicals and increase plant yield, stress tolerance, and nutritional value. However, large-scale applications of PGPF have been hampered by several constraints, and, consequently, usage on a large scale is still limited. Seed coating, a process that consists of covering seeds with low quantities of exogenous materials, is gaining attention as an efficient and feasible delivery system for PGPF.MethodsWe have designed a new seed coating composed of chitin, methylcellulose, and Trichoderma viride spores and assessed its effect on canola (Brassica napus L.) growth and development. For this purpose, we analyzed the antifungal activity of T. viride against common canola pathogenic fungi (Botrytis cinerea, Fusarium culmorum, and Colletotrichum sp.). Moreover, the effect of seed coating on germination ratio and seedling growth was evaluated. To verify the effect of seed coating on plant metabolism, we determined superoxide dismutase (SOD) activity and expression of the stress-related RSH (RelA/SpoT homologs).ResultsOur results showed that the T. viride strains used for seed coating significantly restricted the growth of all three pathogens, especially F. culmorum, for which the growth was inhibited by over 40%. Additionally, the new seed coating did not negatively affect the ability of the seeds to complete germination, increased seedling growth, and did not induce the plant stress response. To summarize, we have successfully developed a cost-effective and environmentally responsible seed coating, which will also be easy to exploit on an industrial scale. creator: Sena Turkan creator: Agnieszka Mierek-Adamska creator: Milena Kulasek creator: Wiktoria B. Konieczna creator: Grażyna B. Dąbrowska uri: https://doi.org/10.7717/peerj.15392 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Turkan et al. title: Phylogeography of sharks and rays: a global review based on life history traits and biogeographic partitions link: https://peerj.com/articles/15396 last-modified: 2023-06-01 description: Considerable research exists on the life history traits, evolutionary history, and environmental factors that shape the population genetic structure of marine organisms, including sharks and rays. Conservation concerns are particularly strong for this group as they are highly susceptible to anthropogenic stressors due to a combination of life history traits including late maturity and low fecundity. Here, we provide a review and synthesis of the global phylogeography of sharks and rays. We examined existing data for 40 species of sharks belonging to 17 genera and 19 species of rays belonging to 11 genera. Median joining haplotype networks were constructed for each species for the mtDNA cytochrome C oxidase subunit I (COI), and an Analysis of Molecular Variance (AMOVA) was conducted to understand patterns of genetic diversity and structure across the three major ocean basins—the Indian, Atlantic and Pacific Oceans. Haplotype networks showed very shallow coalescence in most species, a finding previously reported for marine teleosts. Star topologies were predominant among sharks while complex mutational topologies predominated among rays, a finding we attribute to extremely limited dispersal in the early life history of rays. Population structuring varied amongst species groups, apparently due to differences in life history traits including reproductive philopatry, site fidelity, pelagic habitat, migratory habits, and dispersal ability. In comparison to reef-associated and demersal species, pelagic and semi pelagic species showed lower levels of structure between and within ocean basins. As expected, there is variation between taxa and groups, but there are also some broad patterns that can guide management and conservation strategies. creator: Sudha Kottillil creator: Chetan Rao creator: Brian W. Bowen creator: Kartik Shanker uri: https://doi.org/10.7717/peerj.15396 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kottillil et al. title: Baseline dynamics of Symbiodiniaceae genera and photochemical efficiency in corals from reefs with different thermal histories link: https://peerj.com/articles/15421 last-modified: 2023-06-01 description: Ocean warming and marine heatwaves induced by climate change are impacting coral reefs globally, leading to coral bleaching and mortality. Yet, coral resistance and resilience to warming are not uniform across reef sites and corals can show inter- and intraspecific variability. To understand changes in coral health and to elucidate mechanisms of coral thermal tolerance, baseline data on the dynamics of coral holobiont performance under non-stressed conditions are needed. We monitored the seasonal dynamics of algal symbionts (family Symbiodiniaceae) hosted by corals from a chronically warmed and thermally variable reef compared to a thermally stable reef in southern Taiwan over 15 months. We assessed the genera and photochemical efficiency of Symbiodiniaceae in three coral species: Acropora nana, Pocillopora acuta, and Porites lutea. Both Durusdinium and Cladocopium were present in all coral species at both reef sites across all seasons, but general trends in their detection (based on qPCR cycle) varied between sites and among species. Photochemical efficiency (i.e., maximum quantum yield; Fv/Fm) was relatively similar between reef sites but differed consistently among species; no clear evidence of seasonal trends in Fv/Fm was found. Quantifying natural Symbiodiniaceae dynamics can help facilitate a more comprehensive interpretation of thermal tolerance response as well as plasticity potential of the coral holobiont. creator: Crystal J. McRae creator: Shashank Keshavmurthy creator: Hung-Kai Chen creator: Zong-Min Ye creator: Pei-Jie Meng creator: Sabrina L. Rosset creator: Wen-Bin Huang creator: Chaolun Allen Chen creator: Tung-Yung Fan creator: Isabelle M. Côté uri: https://doi.org/10.7717/peerj.15421 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 McRae et al. title: The role of exercise in improving hyperlipidemia-renal injuries induced by a high-fat diet: a literature review link: https://peerj.com/articles/15435 last-modified: 2023-06-01 description: A diet that is high in sugar and fat is a precursor to various chronic diseases, especially hyperlipidemia. Patients with hyperlipidemia have increased levels of plasma free fatty acids and an ectopic accumulation of lipids. The kidney is one of the main organs affected by this disease and, recently, there have been more studies conducted on renal injury caused by hyperlipidemia. The main pathological mechanism is closely related to renal lipotoxicity. However, in different kidney cells, the reaction mechanism varies due to the different affinities of the lipid receptors. At present, it is believed that in addition to lipotoxicity, hyperlipidemia induced-renal injury is also closely related to oxidative stress, endoplasmic reticulum stress, and inflammatory reactions, which are the result of multiple factors. Exercise plays an important role in the prevention of various chronic diseases and recently emerging researches indicated its positive effects to renal injury caused by hyperlipidemia. However, there are few studies summarizing the effects of exercise on this disease and the specific mechanisms need to be further explored. This article summarizes the mechanisms of hyperlipidemia induced-renal injury at the cellular level and discusses the ways in which exercise may regulate it. The results provide theoretical support and novel approaches for identifying the intervention target to treat hyperlipidemia induced-renal injury. creator: Jun Shunzi Chen creator: Peng Fei Xie creator: Hong Feng uri: https://doi.org/10.7717/peerj.15435 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Clinical diagnostic value of amino acids in laryngeal squamous cell carcinomas link: https://peerj.com/articles/15469 last-modified: 2023-06-01 description: BackgroundEarly diagnosis and treatment can improve the survival rates of patients with laryngeal squamous cell carcinoma (LSCC). Therefore, it is necessary to discover new biomarkers for laryngeal cancer screening and early diagnosis.MethodsWe collected fasting plasma from LSCC patients and healthy volunteers, as well as cancer and para-carcinoma tissues from LSCC patients, and performed quantitative detection of amino acid levels using liquid chromatography-mass spectrometry. We used overall analysis and multivariate statistical analysis to screen out the statistically significant differential amino acids in the plasma and tissue samples, conducted receiver operating characteristic (ROC) analysis of the differential amino acids to evaluate the sensitivity and specificity of the differential amino acids, and finally determined the diagnostic value of amino acids for laryngeal cancer. Additionally, we identified amino acids in the plasma and tissue samples that are valuable for the early diagnosis of laryngeal cancer classified according to the tumor-node-metastasis (TNM) classification.ResultsAsparagine (Asp) and homocysteine (Hcy) were two amino acids of common significance in plasma and tissue samples, and their specificity and sensitivity analysis showed that they may be new biomarkers for the diagnosis and treatment of LSCC. According to the TNM staging system, phenylalanine (Phe) and isoleucine (Ile) were screened out in the plasma of LSCC patients at early (I and II) and advanced (III and IV) stages; ornithine hydrochloride (Orn), glutamic acid (Glu), and Glycine (Gly) were selected in the tissue. These dysregulated amino acids found in LSCC patients may be useful as clinical biomarkers for the early diagnosis and screening of LSCC. creator: Shousen Hu creator: Chang Zhao creator: Zi’an Wang creator: Zeyun Li creator: Xiangzhen Kong uri: https://doi.org/10.7717/peerj.15469 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hu et al. title: Integrating robotics into wildlife conservation: testing improvements to predator deterrents through movement link: https://peerj.com/articles/15491 last-modified: 2023-06-01 description: BackgroundAgricultural and pastoral landscapes can provide important habitat for wildlife conservation, but sharing these landscapes with wildlife can create conflict that is costly and requires managing. Livestock predation is a good example of the challenges involving coexistence with wildlife across shared landscapes. Integrating new technology into agricultural practices could help minimize human-wildlife conflict. In this study, we used concepts from the fields of robotics (i.e., automated movement and adaptiveness) and agricultural practices (i.e., managing livestock risk to predation) to explore how integration of these concepts could aid the development of more effective predator deterrents.MethodsWe used a colony of captive coyotes as a model system, and simulated predation events with meat baits inside and outside of protected zones. Inside the protected zones we used a remote-controlled vehicle with a state-of-the art, commercially available predator deterrent (i.e., Foxlight) mounted on the top and used this to test three treatments: (1) light only (i.e., without movement or adaptiveness), (2) predetermined movement (i.e., with movement and without adaptiveness), and (3) adaptive movement (i.e., with both movement and adaptiveness). We measured the time it took for coyotes to eat the baits and analyzed the data with a time-to-event survival strategy.ResultsSurvival of baits was consistently higher inside the protected zone, and the three movement treatments incrementally increased survival time over baseline except for the light only treatment in the nonprotected zone. Incorporating predetermined movement essentially doubled the efficacy of the light only treatment both inside and outside the protected zone. Incorporating adaptive movement exponentially increased survival time both inside and outside the protected zone. Our findings provide compelling evidence that incorporating existing robotics capabilities (predetermined and adaptive movement) could greatly enhance protection of agricultural resources and aid in the development of nonlethal tools for managing wildlife. Our findings also demonstrate the importance of marrying agricultural practices (e.g., spatial management of livestock at night) with new technology to improve the efficacy of wildlife deterrents. creator: Stewart W. Breck creator: Jeffrey T. Schultz creator: David Prause creator: Cameron Krebs creator: Anthony J. Giordano creator: Byron Boots uri: https://doi.org/10.7717/peerj.15491 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: © 2023 Breck et al. title: Tolerogenic dendritic cell reporting: Has a minimum information model made a difference? link: https://peerj.com/articles/15352 last-modified: 2023-05-31 description: Minimum information models are reporting frameworks that describe the essential information that needs to be provided in a publication, so that the work can be repeated or compared to other work. In 2016, Minimum Information about Tolerogenic Antigen-Presenting cells (MITAP) was created to standardize the reporting on tolerogenic antigen-presenting cells, including tolerogenic dendritic cells (tolDCs). tolDCs is a generic term for dendritic cells that have the ability to (re-)establish immune tolerance; they have been developed as a cell therapy for autoimmune diseases or for the prevention of transplant rejection. Because protocols to generate these therapeutic cells vary widely, MITAP was deemed to be a pivotal reporting tool by and for the tolDC community. In this paper, we explored the impact that MITAP has had on the tolDC field. We did this by examining a subset of the available literature on tolDCs. Our analysis shows that MITAP is used in only the minority of relevant papers (14%), but where it is used the amount of metadata available is slightly increased over where it is not. From this, we conclude that MITAP has been a partial success, but that much more needs to be done if standardized reporting is to become common within the discipline. creator: Ayesha Sahar creator: Ioana Nicorescu creator: Gabrielle Barran creator: Megan Paterson creator: Catharien M.U. Hilkens creator: Phillip Lord uri: https://doi.org/10.7717/peerj.15352 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sahar et al. title: Quiz-style online training tool helps to learn birdsong identification and support citizen science link: https://peerj.com/articles/15387 last-modified: 2023-05-31 description: Citizen science is an important approach to monitoring for biodiversity conservation because it allows for data acquisition or analysis on a scale that is not possible for researchers alone. In citizen science projects, the use of online training is increasing to improve such skills. However, the effectiveness of quiz-style online training, assumed to be efficient to enhance participants’ skills, has not been evaluated adequately on species identification for citizen science biodiversity monitoring projects. Memory mechanisms in adaptive learning were hypothesized to guide the development of quiz-based online training tools for learning birdsong identification and for improving interest in birds and natural environments. To examine the hypothesis, we developed a quiz-style online training tool called TORI-TORE. We experimentally applied TORI-TORE in Fukushima, Japan, and examined its effectiveness for bird identification training using test scores and questionnaires to determine participants’ attitudes in a randomized control trial. We obtained the following key results: (1) TORI-TORE had positive effects on test scores and trainees’ attitudes toward birds. (2) Adaptive training, in which questions focused preferentially on unmastered bird species based on the answer history of individual trainees inspired by adaptive learning, unexpectedly led to lower scores and satisfaction in TORI-TORE. (3) Focusing on species that are relatively easy to remember, short lag times between training and testing, and long question intervals positively affected scores. While there is room for improvement, we expect TORI-TORE to contribute to online capacity building and to increase interest in natural environments. creator: Yui Ogawa creator: Keita Fukasawa creator: Akira Yoshioka creator: Nao Kumada creator: Akio Takenaka creator: Taiichi Ito uri: https://doi.org/10.7717/peerj.15387 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ogawa et al. title: Ontogenetic progression of individual head size in the larvae of the beetle Trypoxylus dichotomus (Coleoptera: Scarabaeidae): catch-up growth within stages and per-stage growth rate changes across stages link: https://peerj.com/articles/15451 last-modified: 2023-05-31 description: The ontogenetic progression of insect larval head size has received much attention due to its fundamental and practical importance. However, although previous studies have analyzed the population mean head size, such an approach may not be appropriate for developmental studies of larval head sizes when the trajectory of individual head size growth is correlated with pre-molt head size and developmental stage. Additionally, there is covariation between the head and body sizes; however, few studies have compared the ontogenetic progression of individual head sizes with that of individual body sizes. In this investigation, the per-stage growth rates (PSGRs) for head width (HW) and cubic-rooted body mass at the beginning of each instar (body size, BS) were assessed in Trypoxylus dichotomus. Linear models were used to test the size- and instar-dependence of the ontogenetic progression of individual HW and BS. The individual PSGRs of the HW (iPSGRH) and BS (iPSGRB) were then compared. In addition, the allometric relationship between HW and BS was examined. The iPSGRH was negatively correlated with the pre-molt HW at every instar (i.e., head catch-up growth). Furthermore, the mean iPSGRH at L2 was relatively higher than that at L1 when the pre-molt HW was used as covariate in the analysis (i.e., instar-effect), whereas the mean iPSGRH decreased ontogenetically. The iPSGRB showed catch-up growth and instar-effects similar to those of iPSGRH; however, iPSGRH was found to be lower than iPSGRB. Due to the differences between the PSGRs for the larval head and body, the larval head size showed negative ontogenetic allometry against body size. creator: Sugihiko Hoshizaki uri: https://doi.org/10.7717/peerj.15451 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hoshizaki