title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=215 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Clocks at a snail pace: biological rhythms in terrestrial gastropods link: https://peerj.com/articles/18318 last-modified: 2024-10-29 description: Biological rhythms are ubiquitous across the tree of life. Organisms must allocate their activities into moments of the day and of the season that will increase their probability of surviving and reproducing, which is done in the form of daily and annual rhythms. So far, the vast majority of studies on biological rhythms have focused on classical laboratory model species. Still, the use of non-model species is gaining traction, as part of an effort to achieve a more holistic understanding of clock/calendar mechanisms in the “real world” but this requires species that can be studied in both the lab and in nature. Terrestrial gastropods, i.e., land snails and slugs, have the potential to be exciting models for the study of biological rhythms in nature. Therefore, we provide a review of the research on biological rhythms in terrestrial gastropods, with a focus on ecology and evolution. We present the state of the art in the field while giving a historical perspective of the studies, exploring each of the main lineages of terrestrial gastropods. We also point out some interesting directions that future studies could take to fill some of the more urgent gaps in current knowledge. We hope that our contribution will renew interest in this area and spark novel projects. creator: Rodrigo Brincalepe Salvador creator: Barbara Mizumo Tomotani uri: https://doi.org/10.7717/peerj.18318 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Salvador and Tomotani title: Cordyceps cateniannulata, a new potential strain for controlling Allantus luctifer from China link: https://peerj.com/articles/18345 last-modified: 2024-10-29 description: Allantus luctifer is one of the most serious pests of buckwheat, with its larvae mainly damaging leaves during the seedling and flowering stages. Entomogenous fungi play a crucial role as biological regulators of arthropod populations in nature. In this paper, a newly isolated strain 19GZAl-1, was identified as Cordyceps. cateniannulata through the observetions of macroscopic and microscopic morphological features, and the results of rDNA- ITS sequence alignment and phylogenetic analysis. By comparing the efficacy of ten entomopathogenic fungal strains, including six strains of C. cateniannulata and four other Cordyceps species, against A. luctifer larvae, the new strain 19GZAl-1 exhibited the highest mortality rate. Mortality rates of A. luctifer larvae treated by spraying with the strain 19GZAl-1 increased as larval stage decreased, with first instar larvae showing the highest mortality rate of 85%. The appressorium from conidia invaded the larval body through areas with thin cuticle, such as larva pod base and internode folds, after which the hyphae grew rapidly, filling the haemocoel, and finally protruding from the integument upon melanization and decomposition of the intestinal wall cells. The results suggest that the strain 19GZAL-1 of C. cateniannulata has potential against A. luctifer larvae, which is significant for further study on the infection mechanism of C. cateniannulata on insects. creator: Xiaona Zhang creator: Yu Wu creator: Xue Peng creator: Can Liu creator: Guimin Yang creator: Qingfu Chen creator: Daochao Jin uri: https://doi.org/10.7717/peerj.18345 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zhang et al. title: In-depth study of pyroptosis-related genes and immune infiltration in colon cancer link: https://peerj.com/articles/18374 last-modified: 2024-10-29 description: BackgroundPyroptosis is a form of regulated necrosis that occurs in many cell and tissue types and plays a critical role in tumor progression. The diagnostic value of pyroptosis-related genes (PRGs) in colon cancer has been widely investigated. In the present study, we explored the relationship between PRG expression and colon cancer.MethodsWe retrieved genomic and clinical data pertaining to The Cancer Genome Atlas-Colon Adenocarcinoma from the UCSC Xena database, along with the corresponding genome annotation information from the GENCODE data portal. Utilising these data and a list of 33 pyrogenic genes, we performed principal component analysis and unsupervised clustering analysis to assess the pyroptosis subtypes. We analysed the differential expression between these subtypes to obtain PRGs, ultimately selecting 10 PRGs. We conducted Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set variation analysis, protein–protein interaction, and immune infiltration analyses of these PRGs. We validated the expression of TNNC1 via immunohistochemistry (IHC) and real-time quantitative PCR.ResultsAfter rigorous screening, excluding patients with incomplete survival data and unmatched transcriptomes, we refined our study cohort to 431 patients. We performed differential mRNA analysis and identified 445 PRGs, 10 of which were selected as hub genes. These genes were associated with various immune cell types. Specifically, TNNC1 expression was positively associated with immature dendritic cells and NK CD56+ cells. IHC staining indicated higher TNNC1 expression levels in tumor samples. Notably, TNNC1 expression levels were high in all the colon cancer cell lines, particularly in SW480 cells.ConclusionIn this study, we explored the characteristics of PRGs in colon cancer and identified novel biological targets for early individualised treatment and accurate diagnosis of colon cancer, thus contributing to the advancement of clinical oncology. creator: Bingbing Shang creator: Haiyan Qiao creator: Liang Wang creator: Jingyu Wang uri: https://doi.org/10.7717/peerj.18374 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Shang et al. title: Genomic evaluation of the probiotic and pathogenic features of Enterococcus faecalis from human breast milk and comparison with the isolates from animal milk and clinical specimens link: https://peerj.com/articles/18392 last-modified: 2024-10-29 description: Enterococcus faecalis is considered a probiotic, commensal lactic acid bacterium in human breast milk (HBM), but there are circulating antibiotic resistant and virulence determinants that could pose a risk in some strains. The study aimed to conduct genomic analysis of E. faecalis isolates recovered from HBM and animal milk and to evaluate their probiotic and pathogenic features through comparative genomics with isolates from clinical specimens (e.g., urine, wound, and blood). Genomic analysis of 61 isolates was performed, including E. faecalis isolates recovered from HBM in Saudi Arabia. Genome sequencing was conducted using the MiSeq system. The fewest antibiotic resistance genes (lsaA, tetM, ermB) were identified in isolates from HBM and animal milk compared to clinical isolates. Several known and unknown mutations in the gyrA and parC genes were observed in clinical isolates. However, 11 virulence genes were commonly found in more than 95% of isolates, and 13 virulence genes were consistently present in the HBM isolates. Phylogenetically, the HBM isolates from China clustered with the probiotic reference strain Symbioflor 1, but all isolates from HBM and animal milk clustered separately from the clinical reference strain V583. Subsystem functions 188 of 263 were common in all analyzed genome assemblies. Regardless of the source of isolation, genes associated with carbohydrate metabolism, fatty acid, and vitamin biosynthesis were commonly found in E. faecalis isolates. In conclusion, comparative genomic analysis can help distinguish the probiotic or pathogenic potential of E. faecalis based on genomic features. creator: Lobna Badr creator: Muhammad Yasir creator: Areej A. Alkhaldy creator: Samah A. Soliman creator: Magdah Ganash creator: Safaa A. Turkistani creator: Asif A. Jiman-Fatani creator: Ibrahim A. Al-Zahrani creator: Esam I. Azhar uri: https://doi.org/10.7717/peerj.18392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Badr et al. title: Forkhead box D subfamily genes in colorectal cancer: potential biomarkers and therapeutic targets link: https://peerj.com/articles/18406 last-modified: 2024-10-29 description: BackgroundThe forkhead box (FOX) family members regulate gene transcription and expression. FOX family members regulate various biological processes, such as cell proliferation and tumorigenesis. FOXD, a FOX protein subfamily, is associated with poor prognosis for various cancers. However, the potential clinical value of FOXD subfamily members in colorectal cancer (CRC) has not yet been elucidated. Therefore, in this study, we aimed to determine the role of the FOXD subfamily members in CRC development.MethodsUsing HTSeq-count data, clinical data, and single-nucleotide polymorphisms (obtained from The Cancer Genome Atlas Project), and bioinformatics analyses (using DESEQ2 software), we identified differentially expressed genes (DEGs) in CRC. Next, each DEG expression was validated in vitro using reverse transcription-quantitative polymerase chain reaction, western blotting, and immunohistochemistry (IHC).ResultsAmong the FOXD subfamily members, the area under the receiver operating characteristic curve of FOXD3 was 0.949, indicating that FOXD3 has a high overall diagnostic accuracy for CRC. Gene Set Enrichment Analysis revealed that FOXD-DEGs were mainly related to pathways such as cytokine, cytokine, and extracellular matrix receptor interactions. Kaplan–Meier curves and nomograms showed that FOXD1, FOXD3, and FOXD4 were prognostically significant. In conclusion, FOXD subfamily members (especially FOXD3) could serve as diagnostic and prognostic biomarkers for CRC and an immunotherapy target in patients with CRC. creator: Ying Chen creator: Haiyan Qiao creator: Ruiqi Zhong creator: Lei Sun creator: Bingbing Shang uri: https://doi.org/10.7717/peerj.18406 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Using a natural capital risk register to support the funding of seagrass habitat enhancement in Plymouth Sound link: https://peerj.com/articles/17969 last-modified: 2024-10-28 description: Seagrass is an important marine habitat that provides benefits to society in the form of ecosystem services. Services include the provision of food via fisheries, the regulation of water quality and the ability to sequester and store carbon. In the UK, seagrass beds are in decline, increasing the risk of ecosystem service loss. Current efforts to protect, restore and create seagrass habitat, beyond spatial management measures, rely on grant funding and donations. Emerging carbon, biodiversity and wider ecosystem service markets offering potential revenue sources could facilitate the enhancement of seagrass habitat at scale. Participation in ecosystem service markets, requires that projects deliver on the ecosystem service benefits defined. As the benefits will have been paid for, there are risks associated with not delivering on ecosystem service benefits. It is important that the risk is clearly defined. In this study we further the marine natural capital and risk register approach and apply the method to a case study area to support the development of sustainable funding options for seagrass habitat enhancement in Plymouth Sound, UK. Habitat Suitability modelling is also used to map potential areas for seagrass habitat enhancement. We find that, in the Plymouth Sound area, the risk of loss of ecosystem services for subtidal seagrass habitats is, at present, high. This is primarily linked to the declining extent and condition of subtidal seagrass assets. Under current governance, all of Plymouth Sound’s subtidal seagrass are within a Marine Protected Area, though this conservation designation does not guarantee that the seagrass bed is protected from damaging activity. Under current environmental conditions there is opportunity for widespread seagrass restoration and creation. Risk to seagrass beds and any future private funding could be reduced by governance actions that enable effective direct protection of the seagrass assets and mitigate harmful pressures (e.g., reduction of water pollution). Emerging financial ‘products’ from seagrass ecosystem services that can support restoration and creation, require a high degree of integrity. The natural capital asset and risk register framework can provide information to underpin product development. With the development of revenue streams from ecosystem services there is a need for more intentional governance and site-based monitoring of these habitats as natural capital assets. Further research is needed to define any social or economic outcomes.Synthesis and ApplicationBy assessing the risk to the status of seagrass assets through this approach, it is possible to determine the complementary governance actions needed to underpin investment in seagrass habitat enhancement. The methods are transferable to other locations where data exists to define the asset status. These specific findings are relevant nationally where similar vectors of risk (pressures) are identified. creator: Guy Hooper creator: Matthew Ashley creator: Tom Mullier creator: Martin Attrill creator: Amelia Sturgeon creator: Zoe Sydenham creator: Mark Parry creator: Katey Valentine creator: Sian Rees uri: https://doi.org/10.7717/peerj.17969 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hooper et al. title: An interpretable deep learning model for detecting BRCA pathogenic variants of breast cancer from hematoxylin and eosin-stained pathological images link: https://peerj.com/articles/18098 last-modified: 2024-10-28 description: BackgroundDetermining the status of breast cancer susceptibility genes (BRCA) is crucial for guiding breast cancer treatment. Nevertheless, the need for BRCA genetic testing among breast cancer patients remains unmet due to high costs and limited resources. This study aimed to develop a Bi-directional Self-Attention Multiple Instance Learning (BiAMIL) algorithm to detect BRCA status from hematoxylin and eosin (H&E) pathological images.MethodsA total of 319 histopathological slides from 254 breast cancer patients were included, comprising two dependent cohorts. Following image pre-processing, 633,484 tumor tiles from the training dataset were employed to train the self-developed deep-learning model. The performance of the network was evaluated in the internal and external test sets.ResultsBiAMIL achieved AUC values of 0.819 (95% CI [0.673–0.965]) in the internal test set, and 0.817 (95% CI [0.712–0.923]) in the external test set. To explore the relationship between BRCA status and interpretable morphological features in pathological images, we utilized Class Activation Mapping (CAM) technique and cluster analysis to investigate the connections between BRCA gene mutation status and tissue and cell features. Significantly, we observed that tumor-infiltrating lymphocytes and the morphological characteristics of tumor cells appeared to be potential features associated with BRCA status.ConclusionsAn interpretable deep neural network model based on the attention mechanism was developed to predict the BRCA status in breast cancer. Keywords: Breast cancer, BRCA, deep learning, self-attention, interpretability. creator: Yi Li creator: Xiaomin Xiong creator: Xiaohua Liu creator: Yihan Wu creator: Xiaoju Li creator: Bo Liu creator: Bo Lin creator: Yu Li creator: Bo Xu uri: https://doi.org/10.7717/peerj.18098 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: The impact of the filling technique with two sealers in bulk or associated with gutta-percha on the fatigue behavior and failure patterns of endodontically treated teeth link: https://peerj.com/articles/18221 last-modified: 2024-10-28 description: BackgroundThe present in vitro study aimed to evaluate the fatigue behavior of teeth filled with a calcium silicate-based sealer (Bio-C Sealer, BC) or an epoxy resin-based sealer (AH Plus, AH), in bulk or associated with gutta-percha as main core material.MethodsSeventy-two sound human maxillary anterior teeth were initially selected. Sixty of them, were randomly chosen, and had their root canals prepared using nickel-titanium reciprocating instruments, being again randomly assigned to five experimental groups (n = 12): C+ (control + prepared but not filled); BC-B (BC in bulk); BC-GP (BC+ gutta-percha); AP-B (AH in bulk); AP-GP (AH+ gutta-percha). An additional negative control group (C−) was considered (n = 12), consisting only on sound teeth, without preparation and filling. The specimens were submitted to a survival analysis after the cyclic fatigue test.ResultsSound teeth (C−) presented the best fatigue performance (P < 0.05), being similar only to the AP-GP group (P > 0.05). Despite that, all experimental groups showed similar fatigue behavior (P > 0.05) to C+ (BC-B = BC-GP = AP-B = AP-GP = C+). Based on that, it can be seen that the use of gutta-percha, as a main core material, associated with the AH Plus sealer, reestablished the mechanical fatigue performance of endodontically treated teeth comparable to sound teeth, still consisting on the most promising approach to rehabilitate such scenario. Teeth filled in bulk, had discreetly higher risk of premature failures and inferior fatigue performance. creator: Isabella Marian Lena creator: Luiza Colpo Chiaratti creator: Rafaela Oliveira Pilecco creator: Renan Vaz Machry creator: João Paulo Mendes Tribst creator: Cornelis Johannes Kleverlaan creator: Gabriel Kalil Rocha Pereira creator: Renata Dornelles Morgental uri: https://doi.org/10.7717/peerj.18221 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lena et al. title: Seed priming enhances seed germination and plant growth in four neglected cultivars of Capsicum annuum L. link: https://peerj.com/articles/18293 last-modified: 2024-10-28 description: Priming is basically a water-based technique inducing controlled seed rehydration to trigger the metabolic processes normally activated during the early phase of germination. It is regarded as an ecofriendly approach alternative to fertilizers in traditional agriculture, but also a method to synchronize off-field crops and resume stored seeds, improving vigor, and allowing for a rapid, uniform seedling emergence. In this work we tested several methods of seed priming (i.e., hydro-priming, halopriming by KNO3, and acid priming with HCl) in four ancient and neglected cultivars of Capsicum annuum L., a crop species belonging to Solanaceae family cultivated worldwide. We followed germination performance, seedling growth and selected morphological traits, antioxidant production in the leaves, and protein content of the seeds. Apart from acid priming, which inhibited root emergence, both hydropriming and halopriming decreased the mean germination time in all cultivars. The best treatments were KNO3 6% for 96 h > KNO3 4% for 48 h > hydropriming for 24 h. In particular, KNO3 6% for 96 h in all four cultivars significantly increased plant growth, simple vigor index, development germination index, leaf antioxidant concentration and protein content in the seeds, in comparison to control and other priming treatments, indicating the prompt activation of pre-germinative processes. creator: Angelo Granata creator: Fiore Capozzi creator: Anna Gaglione creator: Riccardo Riccardi creator: Patrizia Spigno creator: Simonetta Giordano creator: Maria Cristina Sorrentino creator: Valeria Spagnuolo uri: https://doi.org/10.7717/peerj.18293 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Granata et al. title: Genome-wide identification and expression analysis of the OSC gene family in Platycodon grandiflorus link: https://peerj.com/articles/18322 last-modified: 2024-10-28 description: Platycodon grandiflorus stands as one of the most extensively utilized traditional Chinese medicinal herbs, with triterpenoids and their derivatives serving as its primary medicinal components. Oxido squalene cyclase (OSC), serving as a crucial enzyme in the triterpenoid synthesis pathway, has the capability to enzymatically generate significant quantities of sterols and triterpenoid intermediates. While the OSC gene family has been identified in numerous species, bioinformatics research on this family remains scant. Presently, the specific members of this gene family in Platycodon grandiflorus have yet to be definitively determined. In this study, we successfully identified a total of 15 PgOSC genes within the genome of Platycodon grandiflorus by conducting homology comparisons. These genes were discovered to be unevenly distributed across the five chromosomes of the species, organized in the form of gene clusters. Subsequently, we conducted a thorough analysis of the OSC gene family’s evolutionary relationship by constructing a phylogenetic tree. Other characteristics of PgOSC family members, including gene structure, conserved motifs, protein three-dimensional structure, subcellular localization, and cis-acting elements were thoroughly characterized. Furthermore, We analyzed the expression of PgOSC gene in different tissues of Platycodon grandiflorus by qRT-PCR, and found that the expression of PgOSC genes in root was higher than that in stem and leaf. Upon comparing the effects of salt, heat, and drought treatments, we observed a significant induction of PgOSC gene expression in Platycodon grandiflorus specifically under salt stress conditions. In summary, this study comprehensively identified and analyzed the OSC gene family, aiming to provide basic biological information for exploring the members of PgOSC gene family. creator: Xiaoqin Wang creator: Dong Yan creator: Ling Chen uri: https://doi.org/10.7717/peerj.18322 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al.