title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=602 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Does plastic type matter? Insights into non-indigenous marine larvae recruitment under controlled conditions link: https://peerj.com/articles/14549 last-modified: 2022-12-19 description: Marine plastic debris (MPD) are a global threat to marine ecosystems. Among countless ecosystem impacts, MPD can serve as a vector for marine ‘hitchhikers’ by facilitating transport and subsequent spread of unwanted pests and pathogens. The transport and spread of these non-indigenous species (NIS) can have substantial impacts on native biodiversity, ecosystem services/functions and hence, important economic consequences. Over the past decade, increasing research interest has been directed towards the characterization of biological communities colonizing plastic debris, the so called Plastisphere. Despite remarkable advances in this field, little is known regarding the recruitment patterns of NIS larvae and propagules on MPD, and the factors influencing these patterns. To address this knowledge gap, we used custom-made bioassay chambers and ran four consecutive bioassays to compare the settlement patterns of four distinct model biofouling organisms’ larvae, including the three notorious invaders Crassostrea gigas, Ciona savignyi and Mytilus galloprovincialis, along with one sessile macro-invertebrate Spirobranchus cariniferus, on three different types of polymers, namely Low-Linear Density Polyethylene (LLDPE), Polylactic Acid (PLA), Nylon-6, and a glass control. Control bioassay chambers were included to investigate the microbial community composition colonizing the different substrates using 16S rRNA metabarcoding. We observed species-specific settlement patterns, with larvae aggregating on different locations on the substrates. Furthermore, our results revealed that C. savignyi and S. cariniferus generally favoured Nylon and PLA, whereas no specific preferences were observed for C. gigas and M. galloprovincialis. We did not detect significant differences in bacterial community composition between the tested substrates. Taken together, our results highlight the complexity of interactions between NIS larvae and plastic polymers. We conclude that several factors and their potential interactions influenced the results of this investigation, including: (i) species-specific larval biological traits and ecology; (ii) physical and chemical composition of the substrates; and (iii) biological cues emitted by bacterial biofilm and the level of chemosensitivity of the different NIS larvae. To mitigate the biosecurity risks associated with drifting plastic debris, additional research effort is critical to effectively decipher the mechanisms involved in the recruitment of NIS on MPD. creator: François Audrézet creator: Anastasija Zaiko creator: Patrick Cahill creator: Olivier Champeau creator: Louis A. Tremblay creator: Dawn Smith creator: Susanna A. Wood creator: Gavin Lear creator: Xavier Pochon uri: https://doi.org/10.7717/peerj.14549 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Audrezet et al. title: Metabolomics study of flavonoids in Coreopsis tinctoria of different origins by UPLC–MS/MS link: https://peerj.com/articles/14580 last-modified: 2022-12-19 description: To analyze the flavonoids in Coreopsis tinctoria and compare the differences in flavonoids among C. tinctoria of different origins, the chemical composition of C. tinctoria capitulum was analyzed by ultra-high-performance liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS), and the flavonoid metabolites were analyzed and identified based on their retention time, mass-to-charge ratio and fragment ions in the UPLC-QTOF-MS matrix. Capitulum samples of C. tinctoria were collected from three locations in the Xinjiang region at different altitudes. A total of 204 flavonoid compounds were identified, and 31 different flavonoid metabolites were then identified from flowers of C. tinctoria of different origins. Further analysis of these 31 significantly accumulated metabolites identified seven flavonoid metabolites, namely, homoplantaginin, kaempferol, quercetin, isorhamnetin, avicularin, quercetin 3-O-(6′-galloyl)-β-D-galactopyranoside and isorhamnetin 3-O-glucoside, with high accumulation only in sample collected from Tashkurgan Tajik (TX) and low expression in sample collected from Yutian County (YT) and Shaya County (SY). Moreover, 7,4′-dihydroxyflavone and 4,4′-dimethoxychalcone showed high accumulation only in SY, and afzelin was specifically highly accumulated in YT. In addition, the identified flavonoid metabolites were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and key pathways that might regulate the biosynthesis of these flavonoid compounds were analyzed. These findings provide key information for research on flavonoids and their biosynthesis in C. tinctoria and will provide a theoretical basis for studying the herbal quality and origin of C. tinctoria. creator: Yi Wang creator: Junsen Cheng creator: Wei Jiang creator: Shu Chen uri: https://doi.org/10.7717/peerj.14580 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Genetic analysis of DNA methylation in dyslipidemia: a case-control study link: https://peerj.com/articles/14590 last-modified: 2022-12-19 description: BackgroundCoronary heart disease has become the leading cause of death in developed countries, and dyslipidemia is closely associated with the risk of cardiovascular disease. Dyslipidemia is caused by the abnormal regulation of several genes and signaling pathways, and dyslipidemia is influenced mainly by genetic variation. AMFR, FBXW7, INSIG1, INSIG2, and MBTPS1 genes are associated with lipid metabolism. In a recent GWAS study, the GRINA gene has been reported to be associated with dyslipidemia, but its molecular mechanism has not been thoroughly investigated. The correlation between the DNA methylation of these genes and lipid metabolism has not been studied. This study aimed to examine the relationship between the DNA methylation of these genes and the risk of dyslipidemia by comparing the methylation levels of dyslipidemia and control samples.MethodsA case-control research method was used in this study. The patient’s blood samples were collected at the Heart Center of the First Affiliated Hospital of Xinjiang Medical University. In the Xinjiang Han population, 100 cases of hyperlipidemia and 80 cases of the control group were selected. The two groups were age and gender-matched. Quantitative methylation analysis of CpG sites in the gene promoter regions of six genes was performed by Solexa high-throughput sequencing.ResultsThe DNA methylation levels of 23 CpG sites in six genes were shown to be associated with hyperlipidemia, and a total of 20 DNA methylation haplotypes showed statistically significant differences between the two groups. When compared with the control group, the dyslipidemia group had significantly higher levels of methylation in the GRINA gene (2.68 vs 2.36, P = 0.04). Additionally, we also discovered a significant methylation haplotype of GRINA (P = 0.017).ConclusionThe findings of this study reveal that the DNA methylation of GRINA increases the risk for dyslipidemia in humans. creator: Shuai Liu creator: Yang Li creator: Xian Wei creator: Dilare Adi creator: Yong-Tao Wang creator: Min Han creator: Fen Liu creator: Bang-Dang Chen creator: Xiao-Mei Li creator: Yi-Ning Yang creator: Zhen-Yan Fu creator: Yi-Tong Ma uri: https://doi.org/10.7717/peerj.14590 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: On the improvement of heart rate prediction using the combination of singular spectrum analysis and copula-based analysis approach link: https://peerj.com/articles/14601 last-modified: 2022-12-19 description: In recent years, many people have been working from home due to the exceptional circumstances concerning the coronavirus disease 2019 (COVID-19) pandemic. It has also negatively influenced general health and quality of life. Therefore, physical activity has been gaining much attention in preventing the spread of Severe Acute Respiratory Syndrome Coronavirus. For planning an effective physical activity for different clients, physical activity intensity and load degree needs to be appropriately adjusted depending on the individual’s physical/health conditions. Heart rate (HR) is one of the most critical health indicators for monitoring exercise intensity and load degree because it is closely related to the heart rate. Heart rate prediction estimates the heart rate at the next moment based on now and other influencing factors. Therefore, an accurate short-term HR prediction technique can deliver efficient early warning for human health and decrease the happening of harmful events. The work described in this article aims to introduce a novel hybrid approach to model and predict the heart rate dynamics for different exercises. The results indicate that the combination of singular spectrum analysis (SSA) and the Clayton Copula model can accurately predict HR for the short term. creator: Asieh Namazi uri: https://doi.org/10.7717/peerj.14601 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Namazi title: Transcriptome-wide identification of NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors potentially involved in salt stress response in garlic link: https://peerj.com/articles/14602 last-modified: 2022-12-19 description: Soil salinity has been an increasing problem worldwide endangering crop production and human food security. It is an ideal strategy to excavate stress resistant genes and develop salt tolerant crops. NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors have been demonstrated to be involved in salt stress response. However, relevant studies have not been observed in garlic, an important vegetable consumed in the world. In this study, a total of 46 AsNAC genes encoding NAC proteins were identified in garlic plant by transcriptome data. Phylogenetic analysis showed that the examined AsNAC proteins were clustered into 14 subgroups. Motif discovery revealed that the conserved domain region was mainly composed of five conserved subdomains. Most of the genes selected could be induced by salt stress in different tissues, indicating a potential role in salt stress response. Further studies may focus on the molecular mechanisms of the AsNAC genes in salt stress response. The results of the current work provided valuable resources for researchers aimed at developing salt tolerant crops. creator: Guang-Long Wang creator: Ya-Hong An creator: Cheng-Ling Zhou creator: Zhen-Zhu Hu creator: Xu-Qin Ren creator: Ai-Sheng Xiong uri: https://doi.org/10.7717/peerj.14602 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Using Peromyscus leucopus as a biomonitor to determine the impact of heavy metal exposure on the kidney and bone mineral density: results from the Tar Creek Superfund Site link: https://peerj.com/articles/14605 last-modified: 2022-12-19 description: BackgroundHuman population growth and industrialization contribute to increased pollution of wildlife habitats. Heavy metal exposure from industrial and environmental sources is still a threat to public health, increasing disease susceptibility. In this study, I investigated the effects of heavy metals (cadmium (Cd), lead (Pb), and zinc (Zn)) on kidney and bone density.ObjectiveThis study aims to determine the concentrations of Cd, Pb, and Zn in soil and compare them to the levels of the same metals in Peromyscus leucopus kidney tissue. Furthermore, the study seeks to investigate the impact of heavy metals on bone density and fragility using the fourth lumbar vertebra (L4) of P. leucopus.MethodsCd, Pb, and Zn concentrations in soil specimens collected from Tar Creek Superfund Site (TCSFS), Beaver Creek (BC), and two reference sites (Oologah Wildlife Management Area (OWMA) and Sequoyah National Wildlife Refuge (SNWR)). Heavy metal concentrations were analyzed using inductively coupled plasma-mass spectroscopy (ICP-MS). Micro-computed tomography (µCT) was used to assess the influence of heavy metals on bone fragility and density.ResultsOn the one hand, soil samples revealed that Pb is the most common pollutant in the sediment at all of the investigated sites (the highest contaminated site with Pb was TCSFS). Pb levels in the soil of TCSFS, BC, OWMA, and SNWR were found to be 1,132 ± 278, 6.4 ± 1.1, and 2.3 ± 0.3 mg/kg in the soil of TCSFS, BC and OWMA and SNWR, respectively. This is consistent with the fact that Pb is one of the less mobile heavy metals, causing its compounds to persist in soils and sediments and being barely influenced by microbial decomposition. On the other hand, the kidney samples revealed greater Cd levels, even higher than those found in the soil samples from the OWMA and SNWR sites. Cd concentrations in the kidney specimens were found to be 4.62 ± 0.71, 0.53 ± 0.08, and 0.53 ± 0.06 µg/kg, respectively. In addition, micro-CT analysis of L4 from TCSFS showed significant Pearson’s correlation coefficients between Cd concentrations and trabecular bone number (−0.67, P ≤ 0.05) and trabecular separation (0.72, P ≤ 0.05). The results showed no correlation between bone parameters and metal concentrations at reference sites. This study is one of the few that aims to employ bone architecture as an endpoint in the field of biomonitoring. Furthermore, this study confirmed some earlier research by demonstrating substantial levels of heavy metal contamination in soil samples, kidney samples, and P. leucopus L4 trabecular bone separations from TCSFS. Moreover, this is the first study to record information regarding bone microarchitecture parameters in P. leucopus in North America. creator: Maha Abdulftah Elturki uri: https://doi.org/10.7717/peerj.14605 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Elturki title: Forty new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds link: https://peerj.com/articles/13919 last-modified: 2022-12-16 description: Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur–bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most complete morphological assessment of the postcranial skeleton of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis, the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal phalanges are preserved, revealing a remarkably enlarged pes presumably related to foot-propelled swimming. Although diagnosable as Ichthyornis, the new specimens exhibit a substantial degree of morphological variation, some of which may relate to ontogenetic changes. Phylogenetic analyses incorporating our new data and employing alternative morphological datasets recover Ichthyornis stemward of Hesperornithes and Iaceornis, in line with some recent hypotheses regarding the topology of the crownward-most portion of the avian stem group, and we establish phylogenetically-defined clade names for relevant avialan subclades to help facilitate consistent discourse in future work. The new information provided by these specimens improves our understanding of morphological evolution among the crownward-most non-neornithine avialans immediately preceding the origin of crown group birds. creator: Juan Benito creator: Albert Chen creator: Laura E. Wilson creator: Bhart-Anjan S. Bhullar creator: David Burnham creator: Daniel J. Field uri: https://doi.org/10.7717/peerj.13919 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Benito et al. title: Guttigomphus avilionis gen. et sp. nov., a trirachodontid cynodont from the upper Cynognathus Assemblage Zone, Burgersdorp Formation of South Africa link: https://peerj.com/articles/14355 last-modified: 2022-12-16 description: The Burgersdorp Formation of South Africa is a richly fossiliferous rock sequence at the top of the Permian–Triassic Beaufort Group and is known for its abundance of Early–Middle Triassic vertebrate remains, particularly cynodonts. Fossils from the Burgersdorp Formation are referred biostratigraphically to the Cynognathus Assemblage Zone (CAZ), which is further divided into three subzones: Langbergia-Garjainia, Trirachodon-Kannemeyeria, and Cricodon-Ufudocyclops. Each subzone is characterised by the presence of a distinct species of trirachodontid, a group of gomphodont cynodonts found relatively abundantly throughout the CAZ, with the lower two subzones characterised by the medium-sized trirachodontids Langbergia and Trirachodon. The uppermost part of the formation, the Cricodon-Ufudocyclops subzone, yields trirachodontids of larger size. The majority of these trirachodontid specimens have previously been referred to Cricodon metabolus, a taxon also known from the Manda Beds of Tanzania and the Ntawere Formation of Zambia. Here we identify one of the specimens (BP/1/5538) previously referred to Cricodon as a new taxon, Guttigomphus avilionis. Guttigomphus can be distinguished from other gomphodont cynodonts by features of the upper postcanine teeth, such as an asymmetric crown in occlusal view (crown narrower along the lingual margin than the labial). Our phylogenetic analysis recovers Guttigomphus as a basal member of Trirachodontidae, outside of the clade including Cricodon, Langbergia and Trirachodon. creator: Romy R. Rayner creator: Richard J. Butler creator: Christian F. Kammerer creator: Jonah N. Choiniere uri: https://doi.org/10.7717/peerj.14355 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rayner et al. title: Physical fitness changes in adolescents due to social distancing during the coronavirus disease pandemic in Korea link: https://peerj.com/articles/14494 last-modified: 2022-12-16 description: BackgroundAt least 60 min of moderate-intensity physical activity per day is recommended for physical and mental health of adolescents. Schools are one of the most suitable places for promoting students’ health as it is a place where vigorous physical activity occurs. However, the physical activity of students is threatened because schools are closed worldwide owing to the coronavirus disease (COVID-19) outbreak in 2019. Therefore, this study aimed to analyze the physical fitness changes in 27,782 Korean adolescents during the pandemic and present alternative education and health policies to the school.MethodsWe included 29,882 middle school students (age: 13–15 years; males: 14,941, females: 12,841) in Korea from 2019 to 2021 . Participants’ physical fitness at school was measured using the physical activity promotion system (PAPS) manual developed to measure students’ physical fitness. Physical fitness variables included body mass index (BMI), 20 m shuttle run, handgrip strength, sit-and-reach, and 50 m run.ResultsThe COVID-19 pandemic has had a negative impact on the BMI and cardiorespiratory endurance of Korean middle school students. Specifically, male students’ BMI increased, while body composition, cardiorespiratory endurance, and grip strength decreased significantly. Female students showed significant decreases in BMI and sit-and-reach test scores. It is clear that the physical fitness level of adolescents decreased by a greater degree after the COVID-19 pandemic than before, and the decrease in the physical fitness level of male students was noticeable. Therefore, a lesson strategy should be prepared that considers the contents and methods of physical education classes to improve the physical fitness level of male and female adolescents.ConclusionsFitness-based classes suitable for online methods should be urgently added as alternative physical education classes to prepare for the second COVID-19 outbreak. In addition, it is necessary to create an environment in which physical activity is a possibility in physical education classes, in any situation using artificial intelligence and virtual reality. creator: Kwang-Jin Lee creator: Se-Young Seon creator: Byungjoo Noh creator: Keun-Ok An uri: https://doi.org/10.7717/peerj.14494 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lee et al. title: Genetic diversity of Venturia inaequalis isolates from the scabs in apple trees in Gansu Province, China, using AFLP markers link: https://peerj.com/articles/14512 last-modified: 2022-12-16 description: Apple scab is a serious disease that restricts the growth of cultivated apples. The objective of this study is to investigate the genetic variations and genetic structure of Venturia inaequalis in Gansu Province, China. 108 isolates of the pathogen V. inaequalis from the Jingning, Lingtai, Jingchuan, Xifeng, Ning and Maiji regions were collected, and their genetic diversity was analyzed using AFLP molecular marker technique. The results showed that genetic diversity was present among the isolates but was not statistically significant. Genetic distance values ranged from 0.0095 to 0.0762. Cluster analysis results showed that the 108 isolates could be divided into two clusters using a similarity coefficient of 0.69. A total of 104 isolates were contained in cluster I while four isolates were contained in Cluster II. From the AMOVA analysis, 98% of variations were observed within the same region, while 2% were observed across different regions. The analysis of population structure showed that 108 isolates had two common ancestors, with the Jingning isolates mainly being derived from the red ancestor. PCoA analysis showed that the Jingning isolates were independent to a certain extent. The different geographical location caused the genetic difference of the isolates. The genetic diversity of apple scab in Gansu Province is greatly aided by this work, which also offers a theoretical foundation for the use of molecular markers in assisted breeding to create novel resistant types. creator: Zhaolong Lü creator: Nana Hui creator: Li Wang creator: Guo Zheng creator: Senshan Wang creator: Jiping Li uri: https://doi.org/10.7717/peerj.14512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lü et al.