title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=246 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys link: https://peerj.com/articles/17967 last-modified: 2024-10-14 description: Sampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spatial scales influence the inferred species richness and compositional turnover, we conducted a paired eDNA metabarcoding and capture (beach seining) survey of fishes on the coast of British Columbia. We found more taxa were typically detected using eDNA compared to beach seining. eDNA identified more taxa with alternative habitat preferences, and this richness difference was greater in areas of high seawater movement, suggesting eDNA has a larger spatial grain influenced by water motion. By contrast, we found that eDNA consistently missed low biomass species present in seining surveys. Spatial turnover of communities surveyed using beach seining differed from that of the eDNA and was better explained by factors that vary at small (10–1000s meters) spatial scales. Specifically, vegetation cover and shoreline exposure explained most species turnover from seining, while eDNA turnover was not explained by those factors and showed a distance decay pattern (a change from 10% to 25% similarity from 2 km to 10 km of distance), suggesting unmeasured environmental variation at larger scales drives its turnover. Our findings indicate that the eDNA sample grain is larger than that of capture surveys. Whereas seining can detect differences in fish distributions at scales of 10s–100s of meters, eDNA can best summarize fish biodiversity at larger scales possibly more relevant to regional biodiversity assessments. creator: Ben Millard-Martin creator: Kate Sheridan creator: Evan Morien creator: Matthew A. Lemay creator: Margot Hessing-Lewis creator: Rute B.G. Clemente-Carvalho creator: Jennifer M. Sunday uri: https://doi.org/10.7717/peerj.17967 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Millard-Martin et al. title: Saliva as a diagnostic tool in soccer: a scoping review link: https://peerj.com/articles/18032 last-modified: 2024-10-14 description: BackgroundA high-performance sport like soccer requires training strategies that aim to reach peak performance at the right time for the desired competitions. Thus, the investigation of biochemical markers in saliva is a tool that is beginning to be used in athletes within the physical training process. There is still no evidence on universal saliva collection and analysis protocols in soccer. This review aims to map the use of saliva as a tool for analyzing athletic performance in soccer, from the biomarkers used to the validated protocols for these analyses.MethodsA broad systematic literature search was carried out in the electronic databases Web of Science, Livivo, Scopus, PubMed, LILACS and gray literature (Google Scholar and ProQuest). Two reviewers selected the studies and extracted data on the type of salivary collection used, the salivary biomarker evaluated and monitored.ResultsNinety-three articles were included. The most frequently analyzed salivary biomarkers were cortisol (n = 53), testosterone (n = 35), secretory immunoglobulin A (SIgA) (n = 33), salivary alpha amylase (n = 7), genetic polymorphisms (n = 4) and miRNAs (n = 2). The results of the studies indicated beneficial effects in monitoring salivary biomarkers in the assessment of sports performance, although most studies did not include a control group capable of comparison. Salivary collection and analysis protocols were varied and commonly not reported.ConclusionsThis scoping review provides a comprehensive overview of the current landscape of salivary biomarker research in soccer. The findings underscore the importance of these biomarkers in assessing athletes’ physiological responses and overall well-being. Future research should focus on refining methodologies, exploring additional biomarkers, and investigating the practical implications of salivary biomarker monitoring in soccer and other sports. creator: Joyce Ferreira creator: Manuel Jimenez creator: Agatha Cerqueira creator: Joana Rodrigues da Silva creator: Bruno Souza creator: Lucas Berard creator: Andre L.L. Bachi creator: Naile Dame-Teixeira creator: Neide Coto creator: Debora Heller uri: https://doi.org/10.7717/peerj.18032 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ferreira et al. title: Evaluation of shaping ability, apical transportation and centering ratio of T-Endo Must, WaveOne Gold, and Trunatomy in resin blocks link: https://peerj.com/articles/18088 last-modified: 2024-10-14 description: PurposeThis study aimed to compare the shaping abilities of different nickel-titanium file systems.Materials and MethodsSixty-six j-shaped resin blocks were randomly divided into three groups (n = 22): Group T-Endo MUST (TE), Group WaveOne (W), Group TruNatomy (TR). After canal preparation, the amount of material removed from the canal, the centering ratio of the file systems, the direction and amount of canal transportation, and shaping errors were evaluated. Shaping time was calculated. Data of shaping time were analyzed with ANOVA and Tamhane test. Data on the shaping ability were analyzed with two- and three-way ROBUST ANOVA. The significance level was set at p = 0.05.ResultsThere was a statistically significant difference between all groups for shaping time (p < 0.001). There was a statistically significant difference between groups for the total amount of material removed (p < 0.001). The directions of canal transportation were the inner surface of the curvature for W and TR and the outer for TE. There was no statistically significant difference between the groups for the amount of transportation (p > 0.05). The centering ratio of TE and W was statistically higher than TruNatomy (p < 0.001).ConclusionsTruNatomy removed the least material that supported the minimally invasive endodontic approach. All file systems caused similar transportation and did not change the original canal shape. creator: Aybüke Karaca Sakallı creator: Mügem Aslı Ekici uri: https://doi.org/10.7717/peerj.18088 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Karaca Sakallı and Ekici title: Wind energy and insects: reviewing the state of knowledge and identifying potential interactions link: https://peerj.com/articles/18153 last-modified: 2024-10-14 description: In 2023 the wind industry hit a milestone of one terawatt of installed capacity globally. That amount is expected to double within the next decade as billions of dollars are invested in new wind projects annually. Wildlife mortality is a primary concern regarding the proliferation of wind power, and many studies have investigated bird and bat interactions. Little is known about the interactions between wind turbines and insects, despite these animals composing far more biomass than vertebrates. Turbine placement, coloration, shape, heat output, and lighting may attract insects to turbines. Insects attract insectivorous animals, which may be killed by the turbines. Compiling current knowledge about these interactions and identifying gaps in knowledge is critical as wind power grows rapidly. We reviewed the state of the literature investigating insects and wind energy facilities, and evaluated hypotheses regarding insect attraction to turbines. We found evidence of insect attraction due to turbine location, paint color, shape, and temperature output. We provide empirical data on insect abundance and richness near turbines and introduce a risk assessment tool for comparing wind development with suitable climate for insects of concern. This understudied topic merits further investigation as insects decline globally. Compiling information will provide a resource for mitigation and management strategies, and will inform conservation agencies on what insects may be most vulnerable to the expansion of wind technologies. creator: Michelle Weschler creator: Lusha Tronstad uri: https://doi.org/10.7717/peerj.18153 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Weschler and Tronstad title: The effects of resistance training to near volitional failure on motor unit recruitment during neuromuscular fatigue link: https://peerj.com/articles/18163 last-modified: 2024-10-14 description: BackgroundIt is unclear whether chronically training close to volitional failure influences motor unit recruitment strategies during fatigue.PurposeWe compared resistance training to near volitional failure vs. non-failure on individual motor unit action potential amplitude (MUAP) and surface electromyographic excitation (sEMG) during fatiguing contractions.MethodsNineteen resistance-trained adults (11 males, 8 females) underwent 5 weeks (3×/week) of either low repetitions-in-reserve (RIR; 0–1 RIR) or high RIR training (4–6 RIR). Before and after the intervention, participants performed isometric contractions of the knee extensors at 30% of maximal peak torque until exhaustion while vastus lateralis sEMG signals were recorded and later decomposed. MUAP and sEMG excitation for the vastus lateralis were quantified at the beginning, middle, and end of the fatigue assessment.ResultsBoth training groups improved time-to-task failure (mean change = 43.3 s, 24.0%), with no significant differences between low and high RIR training groups (low RIR = 28.7%, high RIR = 19.4%). Our fatigue assessment revealed reduced isometric torque steadiness and increased MUAP amplitude and sEMG excitation during the fatiguing task, but these changes were consistent between groups.ConclusionBoth low and high RIR training improved time-to-task failure, but resulted in comparable motor unit recruitment during fatiguing contractions. Our findings indicate that both low and high RIR training can be used to enhance fatiguability among previously resistance-trained adults. creator: Jonathan P. Beausejour creator: Kevan S. Knowles creator: Jason I. Pagan creator: Juan P. Rodriguez creator: Daniel Sheldon creator: Bradley A. Ruple creator: Daniel L. Plotkin creator: Morgan A. Smith creator: Joshua S. Godwin creator: Casey L. Sexton creator: Mason C. McIntosh creator: Nicholas J. Kontos creator: Cleiton A. Libardi creator: Kaelin Young creator: Michael D. Roberts creator: Matt S. Stock uri: https://doi.org/10.7717/peerj.18163 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Beausejour et al. title: Characterization of the complete mitochondrial genome of the Sunda stink-badger (Mydaus javanensis) from the island of Borneo link: https://peerj.com/articles/18190 last-modified: 2024-10-14 description: BackgroundThe Mephitidae is a family of skunks and stink-badgers that includes 12 extant species in four genera, namely, Mydaus, Conepatus, Mephitis and Spilogale. Mydaus is the only genus within Mephitidae found outside the American continent, with its distribution limited to the islands of Borneo, Indonesia and Philippines. There are two extant species of Mydaus i.e., javanensis and marchei. Currently, complete mitogenomes are unavailable for either species. Here, we present the characterization of the first complete mitogenome for the Sunda stink-badger (Mydaus javanensis) from the island of Borneo.MethodsMuscle tissue was obtained and the DNA was sequenced using a combination of Illumina Barcode Tagged Sequence (BTSeq) and Sanger sequencing techniques. The genome was annotated with MITOS and manually checked for accuracy. A circular map of the mitogenome was constructed with Proksee. Relative synonymous codon usage (RSCU) and codon frequency were calculated using MEGA-X. The protein coding genes (PCGs) were aligned with reference sequences from GenBank and used for the construction of phylogenetic trees (maximum liklihood (ML) and Bayesian inference (BI)). Additionally, due to the lack of available complete genomes in public databases, we constructed another tree with the cyt b gene.ResultsThe complete circular mitogenome was 16,391 base pairs in length. It comprises the typical 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes, one control region (CR) and an L-strand replication origin (OL). The G+C content was 38.1% with a clear bias towards A and T nucleotides. Of the 13 PGCs, only ND6 was positioned in the reverse direction, along with five other tRNAs. Five PCGs had incomplete stop codons and rely on post-transcriptional polyadenylation (TAA) for termination. Based on the codon count, Leucine was the most common amino acid (589), followed by Threonine (332) and Isoleucine (325). The ML and BI phylogenetic trees, based on concatenated PCGs and the cyt b gene, respectively, correctly clustered the species with other members of the Mephitidae family but were unique enough to set it apart from Conepatus, Mephitis and Spilogale. The results confirm Mydaus as a member of the mephitids and the mitogenome will be useful for evolutionary analysis and conservation of the species. creator: Vijay Kumar Subbiah creator: Chrishen Robert Gomez creator: Dexter Miller Robben creator: Ranjita Subramaniam creator: Andrew James Hearn uri: https://doi.org/10.7717/peerj.18190 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Subbiah et al. title: UV-B irradiation promotes anthocyanin biosynthesis in the leaves of Lycium ruthenicum Murray link: https://peerj.com/articles/18199 last-modified: 2024-10-14 description: Anthocyanins are the most valuable pigments in Lycium ruthenicum Murray (L. ruthenicum). Although ultraviolet-B (UV-B) irradiation is a key environmental factor influencing anthocyanin biosynthesis in L. ruthenicum, the deep molecular mechanism remains unclear. Herein, we examined the changes in the total anthocyanin content and transcriptomic characteristics of L. ruthenicum leaves following UV-B irradiation treatment. The results showed a twofold increase in anthocyanin content in the leaves of L. ruthenicum after the treatment. The transcriptome analysis showed that the expression of 24 structural genes identified in the anthocyanin synthesis pathway was up-regulated. In particular, F3’H (Unigene0009145) and C4H (Unigene0046607) exhibit notable up-regulation, suggesting their potential roles in anthocyanin synthesis. Protein interaction network results revealed that MYB1 (Unigene0047706) had the highest connectivity, followed by bHLH (Unigene0014085). Additionally, UVR8 (Unigene0067978) and COP1 (Unigene0008780) were found to be highly involved in UV-B signal transduction. These findings provide new insights into the genetic and biochemical mechanisms that regulate anthocyanin production, and could guide agricultural practices to reduce environmental impacts and improve crop yield and quality. creator: Shengrong Chen creator: Yunzhang Xu creator: Weimin Zhao creator: Guomin Shi creator: Shuai Wang creator: Tao He uri: https://doi.org/10.7717/peerj.18199 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Exploring the density and morphology of coconut structures at two locations: a time-based analysis using computer tomography link: https://peerj.com/articles/18206 last-modified: 2024-10-14 description: BackgroundThe study aimed to observe the internal structure of coconuts from two locations (coastal and non-coastal) using computed tomography (CT).MethodsSeventy-six mature coconuts were collected from Wenchang and Ding’an cities in Hainan Province. These coconuts were scanned four times using CT, with a two-week interval between each scan. CT data were post-processed to reconstruct two-dimensional slices and three-dimensional models. The density and morphological parameters of coconut structures were measured, and the differences in these characteristics between the two groups and the changes over time were analyzed.ResultsTime and location had interactive effects on CT values of embryos, solid endosperms and mesocarps, morphological information such as major axis of coconut, thickness of mesocarp, volume of coconut water and height of bud (p < 0.05).ConclusionsPlanting location and observation time can affect the density and morphology of some coconut structures. creator: Shenghuang Lin creator: Chengxu Sun creator: Li’an Luo creator: Mengxing Huang creator: JeromeJeyakumar John Martin creator: Hongxing Cao creator: Jinyue Hu creator: Zhiming Bai creator: Zhanping He creator: Yu Zhang creator: Jing Chen uri: https://doi.org/10.7717/peerj.18206 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lin et al. title: Effects of different ratios of nitrogen base fertilizer to topdressing on soil nitrogen form and enzyme activity in sugar beet under shallow drip irrigation link: https://peerj.com/articles/18219 last-modified: 2024-10-14 description: Sugar beets account for 30% of global sugar production each year, and their byproducts are an important source of bioethanol and animal feed. Sugar beet is an important cash crop in Inner Mongolia, China. To achieve high yields and sugar content, it is essential to supply nitrogen fertilizer in accordance with the growth characteristics of sugar beet, thereby enhancing the efficiency of nitrogen fertilizer utilization. A two-year experiment was carried out in the experimental field of the Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences. The impact of varying ratios of nitrogen-based fertilizer to topdressing on nitrate nitrogen and ammonium nitrogen levels in the 20–60 cm soil layer, as well as the activities of protease, urease, catalase, and sucrose in the 20–40 cm soil layer were investigated during the rapid leaf growth period and root and sugar growth period. Results indicated that different ratios of nitrogen-based fertilizer to topdressing significantly influenced the levels of nitrate nitrogen and ammonium nitrogen, and the activities of protease and urease in the 0–20 cm soil layer, with these effects diminishing as soil depth increased. The activities of catalase and sucrose were minimally impacted. Nitrogen was applied at 150 kg/ha during the growth period of sugar beet, according to the growth characteristics of sugar beet to maximize nitrogen utilization efficiency. Topdressing was completed with irrigation at the rapid growth stage. The nitrogen-based fertilizer to topdressing ratio of 6:4 resulted in optimal crop yield and sugar yield of sugar beet under shallow drip irrigation. Additionally, the activities of protease and urease in different soil treatments were significantly different, and the activities of protease and urease in the 0–40 cm soil layer were identified as useful soil physiological indicators for nitrogen utilization in sugar beet. creator: Zhi Li creator: Caiyuan Jian creator: Xiaoxia Guo creator: Lu Tian creator: Kang Han creator: Yinghao Li creator: Peng Zhang creator: Dejuan Kong creator: Huimin Ren creator: Alehesi Jiaerdemulati creator: Zhenzhen Wang creator: Huiyu Liu creator: Chunyan Huang creator: Wenbin Su uri: https://doi.org/10.7717/peerj.18219 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens link: https://peerj.com/articles/18229 last-modified: 2024-10-14 description: Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity. creator: Mihaela C. Ion creator: Caitlin C. Bloomer creator: Tudor I. Bărăscu creator: Francisco J. Oficialdegui creator: Nathaniel F. Shoobs creator: Bronwyn W. Williams creator: Kevin Scheers creator: Miguel Clavero creator: Frédéric Grandjean creator: Marc Collas creator: Thomas Baudry creator: Zachary Loughman creator: Jeremy J. Wright creator: Timo J. Ruokonen creator: Christoph Chucholl creator: Simone Guareschi creator: Bram Koese creator: Zsombor M. Banyai creator: James Hodson creator: Margo Hurt creator: Katrin Kaldre creator: Boris Lipták creator: James W. Fetzner creator: Tommaso Cancellario creator: András Weiperth creator: Jạnis Birzaks creator: Teodora Trichkova creator: Milcho Todorov creator: Maksims Balalaikins creator: Bogna Griffin creator: Olga N. Petko creator: Ada Acevedo-Alonso creator: Guillermo D’Elía creator: Karolina Śliwińska creator: Anatoly Alekhnovich creator: Henry Choong creator: Josie South creator: Nick Whiterod creator: Katarina Zorić creator: Peter Haase creator: Ismael Soto creator: Daniel J. Brady creator: Phillip J. Haubrock creator: Pedro J. Torres creator: Denis Şadrin creator: Pavel Vlach creator: Cüneyt Kaya creator: Sang Woo Jung creator: Jin-Young Kim creator: Xavier H.C. Vermeersch creator: Maciej Bonk creator: Radu Guiaşu creator: Muzaffer M. Harlioğlu creator: Jane Devlin creator: Irmak Kurtul creator: Dagmara Błońska creator: Pieter Boets creator: Hossein Masigol creator: Paul R. Cabe creator: Japo Jussila creator: Trude Vrålstad creator: David V. Beresford creator: Scott M. Reid creator: Jiří Patoka creator: David A. Strand creator: Ali S. Tarkan creator: Frédérique Steen creator: Thomas Abeel creator: Matthew Harwood creator: Samuel Auer creator: Sandor Kelly creator: Ioannis A. Giantsis creator: Rafał Maciaszek creator: Maria V. Alvanou creator: Önder Aksu creator: David M. Hayes creator: Tadashi Kawai creator: Elena Tricarico creator: Adroit Chakandinakira creator: Zanethia C. Barnett creator: Ştefan G. Kudor creator: Andreea E. Beda creator: Lucian Vîlcea creator: Alexandru E. Mizeranschi creator: Marian Neagul creator: Anton Licz creator: Andra D. Cotoarbă creator: Adam Petrusek creator: Antonín Kouba creator: Christopher A. Taylor creator: Lucian Pârvulescu uri: https://doi.org/10.7717/peerj.18229 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ion et al.