Construction and validation of a PANoptosis-related lncRNA signature for predicting prognosis and targeted drug response in thyroid cancer
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.
Li et al. (2023) Construction and validation of a PANoptosis-related lncRNA signature for predicting prognosis and targeted drug response in thyroid cancer. PeerJ 11:e15884 https://doi.org/10.7717/peerj.15884
Effects of home-based telerehabilitation on dynamic alterations in regional intrinsic neural activity and degree centrality in stroke patients
Objective To 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. Methods The 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. Results The 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. Conclusions This 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.
Chen et al. (2023) Effects of home-based telerehabilitation on dynamic alterations in regional intrinsic neural activity and degree centrality in stroke patients. PeerJ 11:e15903 https://doi.org/10.7717/peerj.15903
Wheat gibberellin oxidase genes and their functions in regulating tillering
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.
Wang et al. (2023) Wheat gibberellin oxidase genes and their functions in regulating tillering. PeerJ 11:e15924 https://doi.org/10.7717/peerj.15924
Assessment of selection criteria using multi-year study for effective breeding program of Zingiber officinale L
Background Ginger 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. Methods In 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. Results Analysis 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.
Begum et al. (2023) Assessment of selection criteria using multi-year study for effective breeding program of Zingiber officinale L. PeerJ 11:e15966 https://doi.org/10.7717/peerj.15966
Metabolome and transcriptome analyses identify the characteristics and expression of related saponins of the three genealogical plants of bead ginseng
Objective The classification and clinical usage of the different species of bead ginseng are often confused. Therefore, we conducted an integrated metabolomics and transcriptome analysis of three main species of Panax, including Panax japonicas, Panax pseudoginseng, and Panax pseudo-ginseng var. elegantior. Methods A broad metabolome and transcriptome analysis for three origins of bead ginseng plants was performed using UPLC-ESI-MS/MS, RNA sequencing and annotation, and bioinformatic analysis of transcriptome data. Results The levels of 830 metabolites were determined. A total of 291 differentially accumulated metabolites (DAMs) between Panax pseudo-ginseng var. elegantior and Panax japonicas (Group A), with 73 upregulated and 218 downregulated. A total of 331 DAMs (110 upregulated and 221 downregulated) were found between Panax pseudoginseng and Panax japonicas (group B). There were 160 DAMs (102 up-regulated and 58 down-regulated) between Panax pseudoginseng and Panax pseudo-ginseng var. elegantior (group C). In addition, RNA sequencing was performed in the above three ways. A total of 16,074 differential expression genes (DEGs) were detected between Group A, in which 7,723 genes were upregulated and 8,351 genes were downregulated by RNA sequencing. Similarly, 15,705 genes were differentially expressed between group B, in which 7,436 genes were upregulated and 8,269 genes were downregulated. However, only 1,294 genes were differentially expressed between group C, in which 531 genes were upregulated and 763 genes were downregulated. We performed differential gene analysis on three groups of samples according to the Venn diagram and found that 181 differential genes were present. A total of 3,698 and 2,834 unique genes were in groups A and B, while 130 unique genes were in group C. Conclusions This study provides metabolome and transcriptome information for three bead ginseng plants. The analysis of the metabolite content showed differences in the attributes of the three bead ginseng, contained mainly flavonoids, phenolic acids as well as terpenes.
Ye et al. (2023) Metabolome and transcriptome analyses identify the characteristics and expression of related saponins of the three genealogical plants of bead ginseng. PeerJ 11:e16034 https://doi.org/10.7717/peerj.16034
Over 20% of marine fishes shifting in the North and Barents Seas, but not in the Norwegian Sea
Climate warming generally induces poleward range expansions and equatorward range contractions of species’ environmental niches on a global scale. Here, we examined the direction and magnitude of species biomass centroid geographic shifts in relation to temperature and depth for 83 fish species in 9,522 standardised research trawls from the North Sea (1998–2020) to the Norwegian (2000–2020) and Barents Sea (2004–2020). We detected an overall significant northward shift of the marine fish community biomass in the North Sea, and individual species northward shifts in the Barents and North Seas, in 20% and 25% of the species’ biomass centroids in each respective region. We did not detect overall community shifts in the Norwegian Sea, where two species (8%) shifted in each direction (northwards and southwards). Among 9 biological traits, species biogeographic assignation, preferred temperature, age at maturity and maximum depth were significant explanatory variables for species latitudinal shifts in some of the study areas, and Arctic species shifted significantly faster than boreal species in the Barents Sea. Overall, our results suggest a strong influence of other factors, such as biological interactions, in determining several species’ recent geographic shifts.
Gordó-Vilaseca et al. (2023) Over 20% of marine fishes shifting in the North and Barents Seas, but not in the Norwegian Sea. PeerJ 11:e15801 https://doi.org/10.7717/peerj.15801
Urine based near-infrared spectroscopy analysis reveals a noninvasive and convenient diagnosis method for cancers: a pilot study
Background The challenges in cancer diagnosis underline the need for continued research and development of new diagnostic tools and methods. This study aims to explore an effective, noninvasive, and convenient diagnostic tool using urine based near-infrared spectroscopy (NIRS) analysis combined with machine learning algorithm. Methods Urine samples were collected from a total of 327 participants, including 181 cancer cases and 146 healthy controls. These participants were randomly spit into train set (n = 218) and test set (n = 109). NIRS analysis (4,000 ∼10,000 cm−1) was performed for each sample in both train and test sets. Five pretreatment methods, including Savitzky-Golay (SG) smoothing, multiplicative scatter correction (MSC), baseline removal (BSL) with fitting polynomials to be used as baselines, the first derivative (DERIV1), and the second derivative (DERIV2), and combination with “scaling” and “center”, were investigated. Then partial least-squares (PLS) and linear support-vector machine (SVM) classification models were established, and prediction performance was evaluated in test set. Results NIRS had greatly overlapping in peaks, and PCA analysis failed in separation between cancers and healthy controls. In modeling with urine based NIRS data, PLS model showed its highest prediction accuracy of 0.780, with DERIV2, “scaling” and “center” pretreatment, while linear SVM displayed its best prediction accuracy of 0.844, with raw NIRS. With optimization in SVM, the prediction accuracy could improve to 0.862, when the top 262 features were involved as variables. Discussion This pilot study combining urine based NIRS analysis and machine learning is effective and convenient that might facilitate in cancer diagnosis, encouraging further evaluation with a large-size multi-center study.
Zhu et al. (2023) Urine based near-infrared spectroscopy analysis reveals a noninvasive and convenient diagnosis method for cancers: a pilot study. PeerJ 11:e15895 https://doi.org/10.7717/peerj.15895
A decade of study on the condition of western Cuban coral reefs, with low human impact
Background The long-time study of coral reefs with low human impacts can provide information on the effects of regional pressures like climate change, and is an opportunity to document how these pressures are reflected in coral communities. An example of minimal local anthropogenic impacts are the Guanahacabibes coral reefs, located in the westernmost region of Cuba. The objectives of this study were: to evaluate the temporal variability of six benthic biological indicators of coral reefs, and to explore the possible relationship between predictive abiotic variables and biological response variables. Methods Four coral reef sites were sampled between 2008 and 2017, to analyze biological indicators (living coral cover, fleshy algae index, coral species richness, coral species abundance, coral trait groups species abundance, Functional Reef Index). Seven abiotic variables (wave exposure, sea surface temperature, degree heating week, chlorophyll-a concentration, particulate organic carbon, photosynthetically available radiation, and the diffuse attenuation coefficient) were compiled between 2007 and 2016, from remote sensing datasets, to analyze their relationship with the biological indicators. Permanova statistical analysis was used to evaluate trends in biological variables between sites and years, and Routine Analysis Based on Linear Distances (DISTLM) was used to explore some dependencies between biotic and abiotic variables. Results We found significant variability in the temporal analysis, with a decrease in living coral cover, a decline in the predominance of the branching and massive framework reef-building species, a decline in Orbicella species abundance, and an increase in the fleshy algae index. Some abiotic variables (average of degree heating weeks, standard deviation of the diffuse attenuation coefficient, average of the sea surface temperature, among others) significantly explained the variability of biological indicators; however, determination coefficients were low. Conclusions Certain decrease in the functionality of the coral reef was appreciated, taking into account the predominance of secondary and nom-massive framework reef-building species in the last years. A weak association between abiotic and biological variables was found in the temporal analysis. The current scenario of the condition of the coral reefs seems to be regulated by the global effects of climate change, weakly associated effects, and in longer terms.
Caballero-Aragón et al. (2023) A decade of study on the condition of western Cuban coral reefs, with low human impact. PeerJ 11:e15953 https://doi.org/10.7717/peerj.15953
Effectiveness of virtual reality on activities of daily living in children with cerebral palsy: a systematic review and meta-analysis
Background No meta-analysis has been conducted on the effect of specific virtual reality (VR) treatment modes on activities of daily living (ADL) in children with cerebral palsy (CP). Therefore, this study aimed to confirm whether VR therapy is effective in improving ADL in children with CP according to subgroups. Methodology Literature published in the Cumulated Index to Nursing and Allied Health Literature (CINAHL), Embase, the Physiotherapy Evidence Database (PEDro), and PubMed was reviewed, and Risk of Bias 2.0 (RoB 2) was used to evaluate the quality of the literature. A funnel plot was visually observed to confirm publication bias, supplemented with Egger’s regression test. Data analysis was performed using R version 4.2.1. Subgroup analysis was performed according to the Gross Motor Function Classification System (GMFCS), the Manual Ability Classification System (MACS), treatment minutes per week, treatment period, age, and RoB. Results Eleven of 2,978 studies were included, and the overall effect size was 0.37 (95% confidence interval = 0.17–0.57). Regarding GMFCS, effect sizes of 0.41 and 0.33 was observed for the low- and high-function groups, respectively. For MACS, 0.27 and 0.43 were observed for the low and high-function groups. Regarding treatment minutes per week, the values were 0.22, 0.44, and 0.27 in the 1–100, 101–200, and 201–300 min groups, respectively. In the classification according to age, 0.29 was observed for school-age children and 0.98 for preschool children. Lastly, in the classification according to the RoB, 0.52, −0.01, and 0.23 indicated studies with low risk, some concern, and high risk, respectively. Conclusions The highest effect was observed when VR was applied within 6 weeks of 101-200 per week. Therefore, it is suggested that if the results of this review are applied to children with cerebral palsy in the community, it will be an effective intervention method. Systematic review registration PROPEROS (registration number CRD42023409801).
Han et al. (2023) Effectiveness of virtual reality on activities of daily living in children with cerebral palsy: a systematic review and meta-analysis. PeerJ 11:e15964 https://doi.org/10.7717/peerj.15964
Accumulation and transfer of polystyrene microplastics in Solanum nigrum seedlings
Microplastic (MP) pollution is lately receiving increasing attention owing to its harmful impact on terrestrial ecosystems. In this microcosm study, we assessed the uptake and transfer of MPs in Solanum nigrum seedlings exposed to 50 mg L–1 of 0.2-µm polystyrene (PS) beads for 30 d. Confocal laser scanning micrographs helped detect highly intense red fluorescence signals from PS-MP beads in S. nigrum root compared with the controls. Confocal images revealed that the PS beads were primarily distributed in the epidermis and xylem of roots and vascular systems of stems and leaves. Scanning electron microscopy showed that PS beads were scattered on the cell walls of the root xylem and leaf vascular system. Few PS beads were transferred from roots to stems and leaves via the vascular system following the transpiration stream. In conclusion, our findings showed that PS beads accumulated in S. nigrum roots and were transferred from the roots to the aerial parts.
Environmental Contamination and Remediation
Zhang et al. (2023) Accumulation and transfer of polystyrene microplastics in Solanum nigrum seedlings. PeerJ 11:e15967 https://doi.org/10.7717/peerj.15967