title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=452 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Rational synthesis of total damage during cryoprotectant equilibration: modelling and experimental validation of osmomechanical, temperature, and cytotoxic damage in sea urchin (Paracentrotus lividus) oocytes link: https://peerj.com/articles/15539 last-modified: 2023-09-01 description: Sea urchins (e.g., Paracentrotus lividus) are important for both aquaculture and as model species. Despite their importance, biobanking of urchin oocytes by cryopreservation is currently not possible. Optimized cryoprotectant loading may enable novel vitrification methods and thus successful cryopreservation of oocytes. One method for determining an optimized loading protocol uses membrane characteristics and models of damage, namely osmomechanical damage, temperature damage (e.g., chill injury) and cytotoxicity. Here we present and experimentally evaluate existing and novel models of these damage modalities as a function of time and temperature. In osmomechanical damage experiments, oocytes were exposed for 2 to 30 minutes in hypertonic NaCl or sucrose supplemented seawater or in hypotonic diluted seawater. In temperature damage experiments, oocytes were exposed to 1.7 °C, 10 °C, or 20 °C for 2 to 90 minutes. Cytotoxicity was investigated by exposing oocytes to solutions of Me2SO for 2 to 30 minutes. We identified a time-dependent osmotic damage model, a temperature-dependent damage model, and a temperature and time-dependent cytotoxicity model. We combined these models to estimate total damage during a cryoprotectant loading protocol and determined the optimal loading protocol for any given goal intracellular cryoprotectant concentration. Given our fitted models, we find sea urchin oocytes can only be loaded to 13% Me2SO v/v with about 50% survival. This synthesis of multiple damage modalities is the first of its kind and enables a novel approach to modelling cryoprotectant equilibration survival for cells in general. creator: Dominic J. Olver creator: Pablo Heres creator: Estefania Paredes creator: James D. Benson uri: https://doi.org/10.7717/peerj.15539 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Olver et al. title: High phenotypic plasticity at the dawn of the eosauropterygian radiation link: https://peerj.com/articles/15776 last-modified: 2023-09-01 description: The initial radiation of Eosauropterygia during the Triassic biotic recovery represents a key event in the dominance of reptiles secondarily adapted to marine environments. Recent studies on Mesozoic marine reptile disparity highlighted that eosauropterygians had their greatest morphological diversity during the Middle Triassic, with the co-occurrence of Pachypleurosauroidea, Nothosauroidea and Pistosauroidea, mostly along the margins of the Tethys Ocean. However, these previous studies quantitatively analysed the disparity of Eosauropterygia as a whole without focussing on Triassic taxa, thus limiting our understanding of their diversification and morphospace occupation during the Middle Triassic. Our multivariate morphometric analyses highlight a clearly distinct colonization of the ecomorphospace by the three clades, with no evidence of whole-body convergent evolution with the exception of the peculiar pistosauroid Wangosaurus brevirostris, which appears phenotypically much more similar to nothosauroids. This global pattern is mostly driven by craniodental differences and inferred feeding specializations. We also reveal noticeable regional differences among nothosauroids and pachypleurosauroids of which the latter likely experienced a remarkable diversification in the eastern Tethys during the Pelsonian. Our results demonstrate that the high phenotypic plasticity characterizing the evolution of the pelagic plesiosaurians was already present in their Triassic ancestors, casting eosauropterygians as particularly adaptable animals. creator: Antoine Laboury creator: Torsten M. Scheyer creator: Nicole Klein creator: Thomas L. Stubbs creator: Valentin Fischer uri: https://doi.org/10.7717/peerj.15776 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Laboury et al. title: An investigation into the response of the soil ecological environment to tourist disturbance in Baligou link: https://peerj.com/articles/15780 last-modified: 2023-09-01 description: The purpose of this study is to understand the response patterns of the soil ecological environment of the Macau Wetland Park to different levels of tourist interference and to provide a scientific basis for the rational development of the Bali Gou ecological tourism plan and the protection and management of the scenic area’s ecological environment. Combine the methods of field collection and laboratory physical and chemical data analysis to analyze the impact of the strength of tourism disturbance on the soil ecological environment of Baligou. During the tourist activities in Baligou, the human factors in the process have an impact on the physical aspects of the scenic area’s soil, such as soil bulk density, color tone, porosity, compactness, capacity, and leaf litter. In addition, pH value, soil enzyme activity, organic matter, and heavy metals in the soil have caused some interference. The overall data show that the dynamic of soil indicators is background area < buffer area < disturbed area,where the sample area is affected by human trampling and infrastructure construction and other disturbances leading to regular changes in the content of Pb and Cr in the sample soil, while the content of other heavy metals is lower than the national standard.The range of the most extreme values of the SRI integrated soil ecological response evaluation index was A1 disturbance area = 4.679 and C1 background area = 1.263, respectively. The larger the value of the SRI response index, the greater the impact and negative effect of the disturbance influence of tourism activities on the soil ecological environment of the scenic area, and the higher the level of response of the soil ecological environment of the scenic area to the disturbance of tourism activities. Moderate and reasonable tourism development activities play a role in promoting soil quality in scenic areas. Therefore, it is suggested to carry out reasonable ecological environment planning and take certain macro-measures to prevent the deterioration of the soil ecological environment, so as to achieve a win-win situation of ecological environmental protection while developing the tourism economy in scenic areas. creator: Xiaolong Chen creator: Fangyuan Cui creator: Cora Un.In Wong creator: Hongfeng Zhang creator: Feiyang Wang uri: https://doi.org/10.7717/peerj.15780 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Microbial signature profiles of Penaeus vannamei larvae in low-survival hatchery tanks affected by vibriosis link: https://peerj.com/articles/15795 last-modified: 2023-09-01 description: Vibriosis is caused by some pathogenic Vibrio and produces significant mortality in Pacific white shrimp Penaeus (Litopenaeus) vannamei larvae in commercial hatcheries. Acute hepatopancreatic necrosis disease (AHPND) is an emerging vibriosis affecting shrimp-producing countries worldwide. Zoea 2 syndrome is another type of vibriosis that affects the early stages of P. vannamei larvae. Although the pathogenesis of AHPND and zoea 2 syndrome is well known, there is scarce information about microbial composition and biomarkers of P.vannamei larvae affected by AHPND, and there is no study of the microbiome of larvae affected by zoea 2 syndrome. In this work, we characterized the microbiome of P. vannamei larvae collected from 12 commercial hatchery tanks by high-throughput sequencing. Seven tanks were affected by AHPND, and five tanks were affected by zoea 2 syndrome. Subsequently, all samples were selected for sequencing of the V3–V4 region of the16S rRNA gene. Similarity analysis using the beta diversity index revealed significant differences in the larval bacterial communities between disease conditions, particularly when Vibrio was analyzed. Linear discriminant analysis with effect size determined specific microbial signatures for AHPND and zoea 2 syndrome. Sneathiella, Cyclobacterium, Haliea, Lewinella, among other genera, were abundant in AHPND-affected larvae. Meanwhile, Vibrio, Spongiimonas, Meridianimaribacter, Tenacibaculum, among other genera, were significantly abundant in larvae affected by zoea 2 syndrome. The bacterial network at the phylum level for larvae collected from tanks affected by AHPND showed greater complexity and connectivity than in samples collected from tanks affected by zoea 2 syndrome. The bacterial connections inter Vibrio genera were higher in larvae from tanks affected by zoea 2 syndrome, also presenting other connections between the genera Vibrio and Catenococcus. The identification of specific biomarkers found in this study could be useful for understanding the microbial dynamics during different types of vibriosis. creator: Guillermo Reyes creator: Betsy Andrade creator: Irma Betancourt creator: Fanny Panchana creator: Ramiro Solórzano creator: Cristhian Preciado creator: Lita Sorroza creator: Luis E. Trujillo creator: Bonny Bayot uri: https://doi.org/10.7717/peerj.15795 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Reyes et al. title: Improving the success of reinforcement programs: effects of a two-week confinement in a field enclosure on the anti-predator behaviour of captive-bred European hamsters link: https://peerj.com/articles/15812 last-modified: 2023-09-01 description: Captive breeding programs are an important pillar in biodiversity conservation, aiming to prevent the extinction of threatened species. However, the establishment of self-sustaining populations in the wild through the release of captive-bred animals is often hampered by a high mortality upon release. In this study, we investigated how a 2-week confinement period within a large field enclosure affected the anti-predator behaviour of ‘naive’ captive-bred hamsters and how potential modifications persisted over time. During three consecutive tests, hamsters were confronted with a moving predator model (a red fox mount, Vulpes vulpes) and their behaviour was filmed. After the initial round of confrontation with the predator model, one group of hamsters (field group) was released into a field enclosure protected from predators, while the other group (control) remained in their individual laboratory cages. After 2 weeks, hamsters from the field group were recaptured and individuals of both groups underwent a second confrontation test. A total of 1 month after their return from the field enclosure, field hamsters were subjected to a last confrontation test. Video analysis, investigating four behavioural variables, revealed that field hamsters significantly modified their behavioural response following the 2 weeks confinement in the enclosure, while this was not the case for control hamsters. In addition, most behavioural modifications in field hamsters persisted over 1 month, while others started to revert. We suggest that an appropriate pre-release period inside a field enclosure will enable naive (captive-bred) hamsters to develop an adequate anti-predator behaviour that will increase their immediate survival probability upon release into the wild. We believe that such measure will be of great importance for hamster conservation programs. creator: Julie Fleitz creator: Manfred R. Enstipp creator: Emilie Parent creator: Jonathan Jumeau creator: Yves Handrich creator: Mathilde L. Tissier uri: https://doi.org/10.7717/peerj.15812 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Fleitz et al. title: PM2.5 exposure aggravates kidney damage by facilitating the lipid metabolism disorder in diabetic mice link: https://peerj.com/articles/15856 last-modified: 2023-09-01 description: BackgroundAmbient fine particulate matter ≤ 2.5 µm (PM2.5) air pollution exposure has been identified as a global health threat, the epidemiological evidence suggests that PM2.5 increased the risk of chronic kidney disease (CKD) among the diabetes mellitus (DM) patients. Despite the growing body of research on PM2.5 exposure, there has been limited investigation into its impact on the kidneys and the underlying mechanisms. Past studies have demonstrated that PM2.5 exposure can lead to lipid metabolism disorder, which has been linked to the development and progression of diabetic kidney disease (DKD).MethodsIn this study, db/db mice were exposed to different dosage PM2.5 for 8 weeks. The effect of PM2.5 exposure was analysis by assessment of renal function, pathological staining, immunohistochemical (IHC), quantitative real-time PCR (qPCR) and liquid chromatography with tandem mass spectrometry (LC–MS/MS) based metabolomic analyses.ResultsThe increasing of Oil Red staining area and adipose differentiation related protein (ADRP) expression detected by IHC staining indicated more ectopic lipid accumulation in kidney after PM2.5 exposure, and the increasing of SREBP-1 and the declining of ATGL detected by IHC staining and qPCR indicated the disorder of lipid synthesisandlipolysis in DKD mice kidney after PM2.5 exposure. The expressions of high mobility group nucleosome binding protein 1 (HMGN1) and kidney injury molecule 1 (KIM-1) that are associated with kidney damage increased in kidney after PM2.5 exposure. Correlation analysis indicated that there was a relationship between HMGN1-KIM-1 and lipid metabolic markers. In addition, kidneys of mice were analyzed using LC–MS/MS based metabolomic analyses. PM2.5 exposure altered metabolic profiles in the mice kidney, including 50 metabolites. In conclusion the results of this study show that PM2.5 exposure lead to abnormal renal function and further promotes renal injury by disturbance of renal lipid metabolism and alter metabolic profiles. creator: Yuecheng Jiang creator: Yanzhe Peng creator: Xia Yang creator: Jiali Yu creator: Fuxun Yu creator: Jing Yuan creator: Yan Zha uri: https://doi.org/10.7717/peerj.15856 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jiang et al. title: Construction and validation of a PANoptosis-related lncRNA signature for predicting prognosis and targeted drug response in thyroid cancer link: https://peerj.com/articles/15884 last-modified: 2023-09-01 description: Thyroid cancer (TC) is the most prevalent malignancy of the endocrine system. PANoptosis, a newly discovered cell death pathway, is of interest in tumor research. However, the relationship between PANoptosis-related lncRNAs (PRlncRNAs) and TC remains unclear. The study aimed to develop a prognostic model based on PRlncRNAs in TC. Gene expression data of PANoptosis-associated genes and clinical information on TC from The Cancer Genome Atlas (TCGA) database were analyzed by Pearson correlation analysis, univariate/multivariate Cox analysis, and Lasso Cox regression analysis. A PRlncRNA signature was constructed and used to develop a nomogram to predict overall survival (OS). We further explored the correlation between the risk score and tumor immune microenvironment, immune checkpoints, and drug sensitivity. Moreover, we verified the expression and biological function of lncRNAs in TC cell lines. Finally, seven PRlncRNAs were used to construct a prognostic model for predicting the OS of TC patients. We found that the risk score was associated with the tumor microenvironment (TME) and the expression of critical immune checkpoints. In addition, we screened for drugs that high- or low-risk TC groups might be sensitive to. Quantitative real-time polymerase chain reaction (qRT-PCR) results showed differential expression of four PRlncRNAs (GAPLINC, IDI2-AS1, LINC02154, and RBPMS-AS1) between tumor and normal tissues. Besides, a GEO database (GSE33630) was used to verify the expression differences of PRLncRNAs in THCA tissues and normal tissues. Finally, RBPMS-AS1 was found to inhibit the proliferation and migration of TC cells. In conclusion, we developed a PANoptosis-related lncRNA prognostic risk model that offers a comprehensive understanding of TME status in patients with TC and establishes a foundation for the choice of sensitive medications and immunotherapy. creator: Ruowen Li creator: Mingjian Zhao creator: Min Sun creator: Chengxu Miao creator: Jinghui Lu uri: https://doi.org/10.7717/peerj.15884 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Effects of home-based telerehabilitation on dynamic alterations in regional intrinsic neural activity and degree centrality in stroke patients link: https://peerj.com/articles/15903 last-modified: 2023-09-01 description: ObjectiveTo explore the effects of home-based telerehabilitation (TR) on dynamic alterations in regional intrinsic neural activity and degree centrality in stroke patients by resting-state functional MRI (fMRI) methods.MethodsThe neuroimaging data of 52 stroke patients were analyzed. Dynamic regional spontaneous neural activity (dynamic amplitude of low-frequency fluctuations, dALFF; and dynamic regional homogeneity, dReHo) and dynamic degree centrality (dDC) were compared between the TR and conventional rehabilitation (CR) groups. A flexible factorial model was employed to investigate the expected effects.ResultsThe patients in the TR group showed increased dALFF in the right precuneus and bilateral precentral gyrus (PreCG) and reduced dALFF in the right inferior parietal lobule by the analysis of main effects. Significant differences between groups were detected in the right precuneus, right fusiform gyrus and left middle frontal gyrus for dReHo and in the left cingulate gyrus, right middle temporal gyrus and left precuneus for dDC. A significant correlation was found in the TR group between the changed dALFF in the left PreCG and the changed Fugl-Meyer assessment (FMA) scores from baseline to postrehabilitation.ConclusionsThis study implied that home-based TR training can alter the patterns of dynamic spontaneous brain activity and functional connectivity in certain brain regions. The identification of key brain regions by neuroimaging indicators such as dynamic regional brain activity and degree centrality in the recovery process would provide a theoretical basis for noninvasive brain stimulation technology and strategies for formulating targeted rehabilitation programs for stroke patients with motor dysfunction. creator: Jing Chen creator: Jing Li creator: Fenglei Qiao creator: Zhang Shi creator: Weiwei Lu uri: https://doi.org/10.7717/peerj.15903 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Wheat gibberellin oxidase genes and their functions in regulating tillering link: https://peerj.com/articles/15924 last-modified: 2023-09-01 description: Multiple genetic factors control tillering, a key agronomy trait for wheat (Triticum aestivum L.) yield. Previously, we reported a dwarf-monoculm mutant (dmc) derived from wheat cultivar Guomai 301, and found that the contents of gibberellic acid 3 (GA3) in the tiller primordia of dmc were significantly higher. Transcriptome analysis indicated that some wheat gibberellin oxidase (TaGAox) genes TaGA20ox-A2, TaGA20ox-B2, TaGA3ox-A2, TaGA20ox-A4, TaGA2ox-A10 and TaGA2ox-B10 were differentially expressed in dmc. Therefore, this study systematically analyzed the roles of gibberellin oxidase genes during wheat tillering. A total of 63 TaGAox genes were identified by whole genome analysis. The TaGAoxs were clustered to four subfamilies, GA20oxs, GA2oxs, GA3oxs and GA7oxs, including seven subgroups based on their protein structures. The promoter regions of TaGAox genes contain a large number of cis-acting elements closely related to hormone, plant growth and development, light, and abiotic stress responses. Segmental duplication events played a major role in TaGAoxs expansion. Compared to Arabidopsis, the gene collinearity degrees of the GAoxs were significantly higher among wheat, rice and maize. TaGAox genes showed tissue-specific expression patterns. The expressions of TaGAox genes (TaGA20ox-B2, TaGA7ox-A1, TaGA2ox10 and TaGA3ox-A2) were significantly affected by exogenous GA3 applications, which also significantly promoted tillering of Guomai 301, but didn’t promote dmc. TaGA7ox-A1 overexpression transgenic wheat lines were obtained by Agrobacterium mediated transformation. Genomic PCR and first-generation sequencing demonstrated that the gene was integrated into the wheat genome. Association analysis of TaGA7ox-A1 expression level and tiller number per plant demonstrated that the tillering capacities of some TaGA7ox-A1 transgenic lines were increased. These data demonstrated that some TaGAoxs as well as GA signaling were involved in regulating wheat tillering, but the GA signaling pathway was disturbed in dmc. This study provided valuable clues for functional characterization of GAox genes in wheat. creator: Ting Wang creator: Junchang Li creator: Yumei Jiang creator: Jing Zhang creator: Yongjing Ni creator: Peipei Zhang creator: Ziping Yao creator: Zhixin Jiao creator: Huijuan Li creator: Lei Li creator: Yufan Niu creator: Qiaoyun Li creator: Guihong Yin creator: Jishan Niu uri: https://doi.org/10.7717/peerj.15924 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: Assessment of selection criteria using multi-year study for effective breeding program of Zingiber officinale L link: https://peerj.com/articles/15966 last-modified: 2023-09-01 description: BackgroundGinger has been an important cash crop with numerous applications since ancient times. As the demand for ginger is ever-growing and being a seasonal crop, a high-yielding variety of ginger would be economically profitable.MethodsIn this study, 150 germplasm were collected from different regions of NE India and evaluated for three years in CRBD design with three replications. The present study thus focused on the variability, association, and diversity studies for the first time on 150 ginger germplasm from across North East India. The genotypic and phenotypic coefficient of variation, heritability, correlation, and path analysis were evaluated for the germplasm.ResultsAnalysis of variance (ANOVA) revealed considerable differences among the studied germplasm for studied characters, revealing sufficient variability in the materials. The Mahalanobis D2 and Tocher methods grouped the 150 ginger germplasm into ten clusters. Based on the results of the path coefficient analysis determined for essential oil yield and rhizome yield per plant, it can be concluded that the characters’ initial rhizome weight, the weight of mother rhizome, and weight of secondary rhizome were the most important and appeared promising in improving the overall yield potential of ginger rhizome and essential oil yield. Thus, selection based on the identified traits would lead to an effective ginger breeding program for higher rhizome and essential oil yield. creator: Twahira Begum creator: Roktim Gogoi creator: Ankita Gogoi creator: Tanmita Gupta creator: Sanjoy Kumar Chanda creator: Himangshu Lekhak creator: Mohan Lal uri: https://doi.org/10.7717/peerj.15966 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Begum et al.