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
Evaluation of the correlation of dorsal root ganglia and spinal nerves with clinical symptoms in patients with postherpetic neuralgia using magnetic resonance neurography
Purpose To assess changes of dorsal root ganglia (DRG) and spinal nerves in patients with postherpetic neuralgia (PHN), and investigate the correlation between DRG morphology and clinical symptoms in PHN patients using magnetic resonance neurography (MRN). Methods In this case-control study, forty-nine lesioned DRG in 30 patients and 49 normal DRG in 30 well-matched (age, sex, height, weight) healthy controls were assessed. Clinical symptoms of patients (pain, allodynia, itching, and numbness) were assessed. MRN features (DRG volume (VDRG), the largest diameter (Dmax) of spinal nerves, signal intensity of DRG and spinal nerves (M-value)) were measured in all participants. Multilinear regression analysis was used to evaluate the relationship between the DRG morphology and clinical symptoms in patients. Results The volume and relative M-value of lesioned DRG in patients were significantly higher than those on the same side of healthy controls (p = 0.013, p < 0.001, respectively). The mean Dmax and relative M-value of spinal nerves on the lesioned side were significantly higher than those on the contralateral and same side of healthy controls (p < 0.0001, p = 0.0001, p = 0.0011, p = 0.0053, respectively). No difference was found between the mean VDRG of the lesioned and contralateral sides. Multiple linear regression analysis revealed that disease duration was independent risk factor for the maximum rate of VDRG differences (p = 0.013). Conclusions DRG and spinal nerves on the lesioned side are swollen during PHN. Disease duration is an independent risk factor for morphological differences in the lesioned DRG of PHN patients. This study provides important guidance for individualized treatments of PHN.
Cao et al. (2023) Evaluation of the correlation of dorsal root ganglia and spinal nerves with clinical symptoms in patients with postherpetic neuralgia using magnetic resonance neurography. PeerJ 11:e15998 https://doi.org/10.7717/peerj.15998
A multi-sensor array for detecting and analyzing nocturnal avian migration
Avian migration has fascinated humans for centuries. Insights into the lives of migrant birds are often elusive; however, recent, standalone technological innovations have revolutionized our understanding of this complex biological phenomenon. A future challenge for following these highly mobile animals is the necessity of bringing multiple technologies together to capture a more complete understanding of their movements. Here, we designed a proof-of-concept multi-sensor array consisting of two weather surveillance radars (WSRs), one local and one regional, an autonomous moon-watching sensor capable of detecting birds flying in front of the moon, and an autonomous recording unit (ARU) capable of recording avian nocturnal flight calls. We deployed this array at a field site in central Oklahoma on select nights in March, April, and May of 2021 and integrated data from this array with wind data corresponding to this site to examine the influence of wind on the movements of spring migrants aloft across these spring nights. We found that regional avian migration intensity is statistically significantly negatively correlated with wind velocity, in line with previous research. Furthermore, we found evidence suggesting that when faced with strong, southerly winds, migrants take advantage of these conditions by adjusting their flight direction by drifting. Importantly, we found that most of the migration intensities detected by the sensors were intercorrelated, except when this correlation could not be ascertained because we lacked the sample size to do so. This study demonstrates the potential for multi-sensor arrays to reveal the detailed ways in which avian migrants move in response to changing atmospheric conditions while in flight.
Strand et al. (2023) A multi-sensor array for detecting and analyzing nocturnal avian migration. PeerJ 11:e15622 https://doi.org/10.7717/peerj.15622
Adrenal SGLT1 or SGLT2 as predictors of atherosclerosis under chronic stress based on a computer algorithm
Background Chronic stress promotes the development of atherosclerosis, causing disruptions in the body’s hormone levels and changes in the structural function of organs. Objective The purpose of this study was to investigate the pathological changes in the adrenal gland in a model of atherosclerosis under chronic stress and to verify the expression levels of Sodium-glucose cotransporter (SGLT) 1 and SGLT2 in the adrenal gland and their significance in the changes of adrenal gland. Methods The model mice were constructed by chronic unpredictable stress, high-fat diet, and Apoe-/- knockout, and they were tested behaviorally at 0, 4, 8 and 12 weeks. The state of the abdominal artery was examined by ultrasound, and the pathological changes of the aorta and adrenal glands were observed by histological methods, and the expression levels and distribution of SGLT1 and SGLT2 in the adrenal gland were observed and analyzed by immunofluorescence and immunohistochemistry. The predictive value of SGLT1 and SGLT2 expression levels on intima-media thickness, internal diameter and adrenal abnormalities were verified by receiver operating characteristic (ROC) curves, support vector machine (SVM) and back-propagation (BP) neural network. Results The results showed that chronic stress mice had elevated expression levels of SGLT1 and SGLT2. The model mice developed thickening intima-media and smaller internal diameter in the aorta, and edema, reticular fiber rupture, increased adrenal glycogen content in the adrenal glands. More importantly, analysis of ROC, SVM and BP showed that SGLT1 and SGLT2 expression levels in the adrenal glands could predict the above changes in the aorta and were also sensitive and specific predictors of adrenal abnormalities. Conclusion SGLT1 and SGLT2 could be potential biomarkers of adrenal injury in atherosclerosis under chronic stress.
Li et al. (2023) Adrenal SGLT1 or SGLT2 as predictors of atherosclerosis under chronic stress based on a computer algorithm. PeerJ 11:e15647 https://doi.org/10.7717/peerj.15647
RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA
Background N6-methyladenosine (m6A) methylation epigenetically regulates normal hematopoiesis and plays a role in the pathogenesis of acute myeloid leukemia (AML). However, its potential value for prognosis remains elusive. Methods Analysis of the datasets downloaded from The Cancer Genome Atlas and Genotype Tissue Expression databases revealed that the expression level of 20 regulators related to m6A RNA methylation differ between patients with AML and normal individuals. A prognostic risk model with three genes (YTHDF3, IGF2BP3, and HNRNPA2B1) was developed using univariate Cox regression and the least absolute shrinkage and selection operator Cox regression methods. Results This established signature demonstrated good predictive efficacy with an area under the curve of 0.892 and 0.731 in the training cohort and the validation cohort, respectively. Patients with AML and an increased level of Insulin growth factor 2 mRNA binding protein 3 (IGF2BP3) expression exhibited a poor prognosis. IGF2BP3 knockdown significantly induced G0/G1 phase arrest and inhibited cell proliferation, apoptosis, and/or differentiation. Further, the JAK/STAT pathway may be involved in the regulation of EPOR expression by IGF2BP3-mediated m6A RNA methylation. Conclusion These findings indicate that IGF2BP3 plays a carcinogenic role in AML, implying that it can predict patient survival and could be an effective strategy for AML therapy.
Fan et al. (2023) RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA. PeerJ 11:e15706 https://doi.org/10.7717/peerj.15706