title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=555 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Palaeoecology of the Hiraiso Formation (Miyagi Prefecture, Japan) and implications for the recovery following the end-Permian mass extinction link: https://peerj.com/articles/14357 last-modified: 2022-12-19 description: The Hiraiso Formation of northeast Japan represents an important and under-explored archive of Early Triassic marine ecosystems. Here, we present a palaeoecological analysis of its benthic faunas in order to explore the temporal and spatial variations of diversity, ecological structure and taxonomic composition. In addition, we utilise redox proxies to make inferences about the redox state of the depositional environments. We then use this data to explore the pace of recovery in the Early Triassic, and the habitable zone hypothesis, where wave aerated marine environments are thought to represent an oxygenated refuge. The age of the Hiraiso Formation is equivocal due to the lack of key biostratigraphical index fossils, but new ammonoid finds in this study support an early Spathian age. The ichnofossils from the Hiraiso Formation show an onshore-offshore trend with high diversity and relatively large faunas in offshore transition settings and a low diversity of small ichnofossils in basinal settings. The body fossils do not, however, record either spatial or temporal changes, because the shell beds represent allochthonous assemblages due to wave reworking. The dominance of small burrow sizes, presence of key taxa including Thalassinoides, Rhizocorallium and Holocrinus, presence of complex trace fossils, and both erect and deep infaunal tiering organisms suggests that the benthic fauna represents an advanced stage of ecological recovery for the Early Triassic, but not full recovery. The ecological state suggests a similar level of ecological complexity to late Griesbachian and Spathian communities elsewhere, with the Spathian marking a globally important stage of recovery following the mass extinction. The onshore-offshore distribution of the benthic faunas supports the habitable zone hypothesis. This gradient is, however, also consistent with onshore-offshore ecological gradients known to be controlled by oxygen gradients in modern tropical and subtropical settings. This suggests that the habitable zone is not an oxygenated refuge that is only restricted to anoxic events. The lack of observed full recovery is likely a consequence of a persistent oxygen-limitation (dysoxic conditions), hot Early Triassic temperatures and the lack of a steep temperature/water-depth gradient within the habitable zone. creator: William J. Foster creator: Amanda Godbold creator: Arnaud Brayard creator: Anja B. Frank creator: Stephen E. Grasby creator: Richard J. Twitchett creator: Tatsuo Oji uri: https://doi.org/10.7717/peerj.14357 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Foster et al. title: You are what you eat: fungal metabolites and host plant affect the susceptibility of diamondback moth to entomopathogenic fungi link: https://peerj.com/articles/14491 last-modified: 2022-12-19 description: BackgroundBeauveria are entomopathogenic fungi of a broad range of arthropod pests. Many strains of Beauveria have been developed and marketed as biopesticides. Beauveria species are well-suited as the active ingredient within biopesticides because of their ease of mass production, ability to kill a wide range of pest species, consistency in different conditions, and safety with respect to human health. However, the efficacy of these biopesticides can be variable under field conditions. Two under-researched areas, which may limit the deployment of Beauveria-based biopesticides, are the type and amount of insecticidal compounds produced by these fungi and the influence of diet on the susceptibility of specific insect pests to these entomopathogens.MethodsTo understand and remedy this weakness, we investigated the effect of insect diet and Beauveria-derived toxins on the susceptibility of diamondback moth larvae to Beauveria infection. Two New Zealand-derived fungal isolates, B. pseudobassiana I12 Damo and B. bassiana CTL20, previously identified with high virulence towards diamondback moth larvae, were selected for this study. Larvae of diamondback moth were fed on four different plant diets, based on different types of Brassicaceae, namely broccoli, cabbage, cauliflower, and radish, before their susceptibility to the two isolates of Beauveria was assessed. A second experiment assessed secondary metabolites produced from three genetically diverse isolates of Beauveria for their virulence towards diamondback moth larvae.ResultsDiamondback moth larvae fed on broccoli were more susceptible to infection by B. pseudobassiana while larvae fed on radish were more susceptible to infection by B. bassiana. Furthermore, the supernatant from an isolate of B. pseudobassiana resulted in 55% and 65% mortality for half and full-strength culture filtrates, respectively, while the filtrates from two other Beauveria isolates, including a B. bassiana isolate, killed less than 50% of larvae. This study demonstrated different levels of susceptibility of the insects raised on different plant diets and the potential use of metabolites produced by Beauveria isolates in addition to their conidia. creator: Sereyboth Soth creator: Travis R. Glare creator: John G. Hampton creator: Stuart D. Card creator: Jenny J. Brookes creator: Josefina O. Narciso uri: https://doi.org/10.7717/peerj.14491 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Soth et al. title: Identification and validation of a ferroptosis-related lncRNA signature to robustly predict the prognosis, immune microenvironment, and immunotherapy efficiency in patients with clear cell renal cell carcinoma link: https://peerj.com/articles/14506 last-modified: 2022-12-19 description: BackgroundFerroptosis is a new type of iron- and reactive oxygen species-dependent cell death, studies on ferroptosis-related long noncoding RNAs (FerLncRNAs) in clear cell renal cell carcinoma (ccRCC) are limited. The purpose of this study was to investigate the potential prognostic value of FerLncRNAs and their relationship with the immune microenvironment and immunotherapy response of ccRCC.MethodsRNA sequencing data of 526 patients with ccRCC were downloaded from The Cancer Genome Atlas (TCGA) database. The patients with ccRCC in TCGA were randomly divided (1:1) into a training and testing cohort. ICGC and GEO databases were used for validation. Screening for FerLncRNAs was performed using Pearson’s correlation analysis with the reported ferroptosis-related genes. A FerLncRNA signature was constructed using univariate, LASSO, and multivariate Cox regression analyses in the training cohort. Internal and external datasets were performed to verify the FRlncRNA signature. Four major FRlncRNAs were verified through in vitro experiment.ResultsWe identified seven FerLncRNAs (LINC00894, DUXAP8, LINC01426, PVT1, PELATON, LINC02609, and MYG1-AS1), and established a risk signature and nomogram for predicting the prognosis of ccRCC. Four major FRlncRNAs were verified with the prognosis of ccRCC in the GEPIA and K-M Plotter databases, and their expressions were validated by realtime PCR. The risk signature can also effectively reflect the immune environment, immunotherapy response and drug sensitivity of ccRCC. These FRlncRNAs have great significance to the implementation of individualized treatment and disease monitoring of ccRCC patients. creator: Lincheng Ju creator: Yaxing Shi creator: Gang Liu uri: https://doi.org/10.7717/peerj.14506 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ju et al. title: Are children and dogs best friends? A scoping review to explore the positive and negative effects of child-dog interactions link: https://peerj.com/articles/14532 last-modified: 2022-12-19 description: Personal wellbeing is greatly influenced by our childhood and adolescence, and the relationships formed during those phases of our development. The human-dog bond represents a significant relationship that started thousands of years ago. There is a higher prevalence of dog ownership around the world, especially in households including children. This has resulted in a growing number of researchers studying our interactions with dogs and an expanding evidence base from the exploration of child-dog interactions. We review the potential effects of child-dog interactions on the physical, mental, and social wellbeing of both species. A search of the SCOPUS database identified documents published between January 1980 and April 2022. Filtering for key inclusion criteria, duplicate removals, and inspecting the references of these documents for additional sources, we reviewed a total of 393 documents, 88% of which were scientific articles. We were able to define the numerous ways in which children and dogs interact, be it neutral (e.g., sharing a common area), positive (e.g., petting), or negative (e.g., biting). Then, we found evidence for an association between childhood interaction with dogs and an array of benefits such as increased physical activities, a reduction of stress, and the development of empathy. Nonetheless, several detrimental outcomes have also been identified for both humans and dogs. Children are the most at-risk population regarding dog bites and dog-borne zoonoses, which may lead to injuries/illness, a subsequent fear of dogs, or even death. Moreover, pet bereavement is generally inevitable when living with a canine companion and should not be trivialized. With a canine focus, children sometimes take part in caretaking behaviors toward them, such as feeding or going for walks. These represent opportunities for dogs to relieve themselves outside, but also to exercise and socialize. By contrast, a lack of physical activity can lead to the onset of obesity in both dogs and children. Dogs may present greater levels of stress when in the presence of children. Finally, the welfare of assistance, therapy, and free-roaming dogs who may interact with children remains underexplored. Overall, it appears that the benefits of child-dog interactions outweigh the risks for children but not for dogs; determination of the effects on both species, positive as well as negative, still requires further development. We call for longitudinal studies and cross-cultural research in the future to better understand the impact of child-dog interactions. Our review is important for people in and outside of the scientific community, to pediatricians, veterinarians, and current or future dog owners seeking to extend their knowledge, and to inform future research of scientists studying dogs and human-animal interactions. creator: Claire S. E. Giraudet creator: Kai Liu creator: Alan G. McElligott creator: Mia Cobb uri: https://doi.org/10.7717/peerj.14532 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Giraudet et al. title: Belief in just deserts regarding individuals infected with COVID-19 in Japan and its associations with demographic factors and infection-related and socio-psychological characteristics: a cross-sectional study link: https://peerj.com/articles/14545 last-modified: 2022-12-19 description: Prejudice related to the coronavirus disease 2019 (COVID-19) is a social issue worldwide. A possible psychological factor that promotes prejudice is the belief in just deserts (BJD) regarding individuals infected with COVID-19 (i.e., the belief that the infected individual deserves to be infected). The BJD is based on the belief in immanent justice. It is reportedly higher in Japan than in other countries. Therefore, we conducted a cross-sectional study to investigate the BJD among Japanese individuals and clarify its associations with demographic factors or infection-related and socio-psychological characteristics. To this end, we conducted an online questionnaire survey in Japan from August 7–8, 2020, with 1,207 respondents aged 20–69 years. We performed screening to exclude inappropriate responses. We investigated the association between the BJD and demographic factors such as gender and age. We also investigated the association between the BJD and infection-related and socio-psychological characteristics, including risk perception of COVID-19 infection and human rights restrictions (i.e., the degree of agreement with government restrictions on individuals’ behavior during emergencies). Among the surveyed items, human rights restrictions showed a strong association with BJD, followed by risk perception of COVID-19 infection. Men had a slightly higher BJD than women. Our study is significant in that it is the first to investigate the items associated with the BJD, thereby providing foundational information for revising individual perceptions of justice related to COVID-19 and solving prejudice-related issues. creator: Michio Murakami creator: Kai Hiraishi creator: Mei Yamagata creator: Daisuke Nakanishi creator: Asako Miura uri: https://doi.org/10.7717/peerj.14545 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Murakami et al. 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.