Transcriptome-wide identification and expression analysis of the KT/HAK/KUP family in Salicornia europaea L. under varied NaCl and KCl treatments
Background The KT/HAK/KUP (KUP) transporters play important roles in potassium (K+) uptake and translocation, regulation of osmotic potential, salt tolerance, root morphogenesis and plant development. However, the KUP family has not been systematically studied in the typical halophyte Salicornia europaea L., and the specific expression patterns of SeKUPs under NaCl condition and K+ deficiency are unknown. Methods In this study, SeKUPs were screened from PacBio transcriptome data of Salicornia europaea L. using bioinformatics. The identification, phylogenetic analysis and prediction of conserved motifs of SeKUPs were extensively explored. Moreover, the expression levels of 24 selected SeKUPs were assayed by real-time quantitative polymerase chain reaction (RT-qPCR). Results In this study, a total of 24 putative SeKUPs were identified in S. europaea. Nineteen SeKUPs with the fixed domain EA[ML]FADL were used to construct the phylogenetic tree, and they were divided into four clusters (clusters I–IV). MEME analysis identified 10 motifs in S. europaea, and the motif analysis suggested that 19 of the identified SeKUPs had at least four K+ transporter motifs existed in all SeKUPs (with the exception of SeKUP-2). The RT-qPCR analysis showed that the expression levels of most SeKUPs were significantly up-regulated in S. europaea when they were exposed to K+ deficiency and high salinity, implying that these SeKUPs may play a key role in the absorption and transport of K+ and Na+ in S. europaea. Discussions Our results laid the foundation for revealing the salt tolerance mechanism of SeKUPs, and provided key candidate genes for further studies on the function of KUP family in S. europaea.
Wei et al. (2022) Transcriptome-wide identification and expression analysis of the KT/HAK/KUP family in Salicornia europaea L. under varied NaCl and KCl treatments. PeerJ 10:e12989 https://doi.org/10.7717/peerj.12989
East palearctic treefrog past and present habitat suitability using ecological niche models
Ecological niche modeling is a tool used to determine current potential species’ distribution or habitat suitability models which can then be used to project suitable areas in time. Projections of suitability into past climates can identify locations of climate refugia, or areas with high climatic stability likely to contain the highest levels of genetic diversity and stable populations when climatic conditions are less suitable in other parts of the range. Modeling habitat suitability for closely related species in recent past can also reveal potential periods and regions of contact and possible admixture. In the east palearctic, there are five Dryophytes (Hylid treefrog) clades belonging to two groups: Dryophytes japonicus group: Clades A and B; and Dryophytes immaculatus group: Dryophytes immaculatus, Dryophytes flaviventris, and Dryophytes suweonensis. We used maximum entropy modeling to determine the suitable ranges of these five clades during the present and projected to the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. We also calculated climatic stability for each clade to identify possible areas of climate refugia. Our models indicated suitable range expansion during the LGM for four clades with the exclusion of D. immaculatus. High climatic stability in our models corresponded to areas with the highest numbers of recorded occurrences in the present. The models produced here can additionally serve as baselines for models of suitability under climate change scenarios and indicate species ecological requirements.
Spatial and Geographic Information Science
Andersen et al. (2022) East palearctic treefrog past and present habitat suitability using ecological niche models. PeerJ 10:e12999 https://doi.org/10.7717/peerj.12999
Although the Multiple Object Tracking (MOT) task is a widely used experimental method for studying divided attention, tracking objects in the real world usually looks different. For example, in the real world, objects are usually clearly distinguishable from each other and also possess different movement patterns. One such case is tracking groups of creatures, such as tracking fish in an aquarium. We used movies of fish in an aquarium and measured general tracking performance in this task (Experiment 1). In Experiment 2, we compared tracking accuracy within-subjects in fish tracking, tracking typical MOT stimuli, and in a third condition using standard MOT uniform objects which possessed movement patterns similar to the real fish. This third condition was added to further examine the impact of different motion characteristics on tracking performance. Results within a Bayesian framework showed that tracking real fish shares similarities with tracking simple objects in a typical laboratory MOT task. Furthermore, we observed a close relationship between performance in both laboratory MOT tasks (typical and fish-like) and real fish tracking, suggesting that the commonly used laboratory MOT task possesses a good level of ecological validity.
Děchtěrenko et al. (2022) Tracking multiple fish. PeerJ 10:e13031 https://doi.org/10.7717/peerj.13031
Overexpression of the Tectona grandis TgNAC01 regulates growth, leaf senescence and confer salt stress tolerance in transgenic tobacco plants
NAC transcription factors play critical roles in xylem secondary development and in regulation of stress response in plants. NAC proteins related to secondary cell wall development were recently identified and characterized in Tectona grandis (teak), one of the hardwood trees of highest economic importance in the world. In this work, we characterized the novel TgNAC01 gene, which is involved in signaling pathways that mediate teak response to stress. Abscisic acid (ABA) increases TgNAC01 expression in teak plants. Therefore, this gene may have a role in signaling events that mediate ABA-dependent osmotic stress responsive in this plant species. Stable expression in tobacco plants showed that the TgNAC01 protein is localized in the cell nucleus. Overexpression of TgNAC01 in two out three independent transgenic tobacco lines resulted in increased growth, leaf senescence and salt tolerance compared to wild type (WT) plants. Moreover, the stress tolerance of transgenic plants was affected by levels of TgNAC01 gene expression. Water potential, gas exchange and chlorophyll fluorescence were used to determine salt stress tolerance. The 35S:TgNAC01-6 line under 300 mM NaCl stress responded with a significant increase in photosynthesis rate, stomatal conductance, transpiration and carboxylation efficiency, but lower water potential compared to WT plants. The data indicate that the TgNAC01 transcription factor acts as a transcriptional activator of the ABA-mediated regulation and induces leaf senescence.
Matias et al. (2022) Overexpression of the Tectona grandis TgNAC01 regulates growth, leaf senescence and confer salt stress tolerance in transgenic tobacco plants. PeerJ 10:e13039 https://doi.org/10.7717/peerj.13039
Lacunes and type 2 diabetes mellitus have a joint effect on cognitive impairment: a retrospective study
Objective To evaluate the joint effects of cerebral small vessel disease (CSVD)-related imaging biomarkers in patients of type 2 diabetes mellitus (T2DM) with cognitive impairment. Methods This study is a retrospective cohort study. A total of 227 participants (115 patients with T2DM and 112 healthy control subjects) were enrolled in this study. Cognitive function assessments were evaluated using the Mini-Mental State Examination and the Montreal Cognitive Assessment. The burden of CSVD markers, including the lacunes, white matter hyperintensities (WMH), cerebral microbleeds (CMBs), and enlarged perivascular spaces (PVS), was identified by magnetic resonance imaging and evaluated using small vessel disease (SVD) scores (0–4). The subjects were divided into two groups based on the results of the cognitive function assessments. The synergy index was used to estimate the biological interactions between T2DM and lacunes. Results There was a significant correlation between T2DM and cognitive impairment (p < 0.001, χ2 test). In patients with diabetes, cognitive impairment was significantly associated with both the presence of lacunes (p < 0.01, χ2 test) and increased total SVD burden scores (p < 0.01, χ2 test). Regarding CMBs, only the existence of lobar CMBs was correlated with cognitive impairment (p < 0.05, χ2 test). The joint effect tended to be larger than the independent effects of T2DM and lacunes on cognitive impairment (adjusted odds ratio [OR]: 7.084, 95% CI [2.836–17.698]; synergy index: 10.018, 95% CI [0.344–291.414]). Conclusions T2DM and the presence of lacunes are significantly correlated with cognitive impairment. There was a joint effect of T2DM and lacunes on cognitive impairment.
Zhou et al. (2022) Lacunes and type 2 diabetes mellitus have a joint effect on cognitive impairment: a retrospective study. PeerJ 10:e13069 https://doi.org/10.7717/peerj.13069
Soybean (Glycine max L. Merrill) responds to phosphorus application and rhizobium inoculation on Acrisols of the semi-deciduous forest agro-ecological zone of Ghana
Soybean cultivation in Ghana is limited mainly to the Guinea savanna and the forest/savanna transitional agro-ecological zones. Although soybean can be cultivated in the semi-deciduous forest zone, low soil pH and limited nodulation limit its productivity in this zone. In this study, a randomized complete block design, with four replications, was used to test if rhizobia inoculation and/or p-fertilizer could improve yield of soybean in the semi-deciduous forest zone. The residual effects of the treatments were tested on maize and soybean sequentially during the 2018 and 2019 cropping seasons. The inoculation study was repeated in 2020. Phosphorus and inoculation significantly (p = 0.0009) increased soybean grain yield in the 2018 cropping season by 88% and 108%, respectively over the control. Co-application of P and inoculant increased grain yield 3-fold over the control. Maize grain yield ranged from 4.3 t ha−1 in the control plots to 5.2 t ha−1 in treated plots but did not differ significantly among treatments. In 2020, the combined application of P and inoculant produced a significantly (0.002) higher yield than any of the other treatments. This demonstrates that soybean can be grown economically in the semi-deciduous forest agro-ecological zone of Ghana. Co-application of P and inoculant appeared cost-effective, in terms of return on investment.
Adjei-Nsiah et al. (2022) Soybean (Glycine max L. Merrill) responds to phosphorus application and rhizobium inoculation on Acrisols of the semi-deciduous forest agro-ecological zone of Ghana. PeerJ 10:e12671 https://doi.org/10.7717/peerj.12671
The Female Athlete Triad—the impact of running and type of diet on the regularity of the menstrual cycle assessed for recreational runners
Background The Female Athlete Triad (FAT) included three interrelated conditions including disordered eating, amenorrhea, and osteoporosis. The American College of Sports Medicine updated the definition of FAT to reflect the interdependence of low energy availability with or without eating disorders. The main aim of the study was to assess the impact of recreational running on potential disturbances in the regularity of women’s menstrual cycles. Additionally, this work compared differences in the menstrual cycle between women runners and women who did not regularly practice sports. The respondents were also asked about the type of diet they consumed. Methods A total of 360 women took part in the research. This group included 217 runners and 143 control. The authors’ questionnaire was used in the research. Results When compared to the control group, the runners had an increased frequency of menstrual cycles of <24 days (10.14% vs. 3.50%), fewer typical cycles of 25–31 days (75.58% vs. 86.71%), had fewer regular cycles per year (9.62 vs. 11.22), shorter duration of bleeding (4.79 vs. 5.27 days), and an increased frequency of painless menstruation (23.96% vs. 7.69%). A positive predictor of menstrual cycle disorders was the use of a ‘special diet’ (R:1.67; 95% C:0.47–2.87). Conclusions The runners had shorter and less regular monthly cycles and shorter and more often painless menstrual bleeding when compared to the control group. The frequency of menstrual disorders in runners was increased by following a ‘special diet’. The frequency of menstrual cycle disorders in runners, however, did not differ significantly from the control group.
Witkoś et al. (2022) The Female Athlete Triad—the impact of running and type of diet on the regularity of the menstrual cycle assessed for recreational runners. PeerJ 10:e12903 https://doi.org/10.7717/peerj.12903
Development and validation of a multi-parameter nomogram for predicting prostate cancer: a retrospective analysis from Handan Central Hospital in China
Background To explore the possible predicting factors related to prostate cancer and develop a validated nomogram for predicting the probability of patients with prostate cancer. Method Clinical data of 697 patients who underwent prostate biopsy in Handan Central Hospital from January 2014 to January 2020 were retrospectively collected. Cases were randomized into two groups: 80% (548 cases) as the development group, and 20% (149 cases) as the validation group. Univariate and multivariate logistic regression analyses were performed to determine the independent risk factors for prostate cancer. The nomogram prediction model was generated using the finalized independent risk factors. Decision curve analysis (DCA) and the area under receiver operating characteristics curve (ROC) of both development group and validation group were calculated and compared to validate the accuracy and efficiency of the nomogram prediction model. Clinical utility curve (CUC) helped to decide the desired cut-off value for the prediction model. The established nomogram with Prostate Cancer Prevention Trial Derived Cancer Risk Calculator (PCPT-CRC) and other domestic prediction models using the entire study population were compared. Results The independent risk factors determined through univariate and multivariate logistic regression analyses were: age, tPSA, fPSA, PV, DRE, TRUS and BMI. Nomogram prediction model was developed with the cut-off value of 0.31. The AUC of development group and validation group were 0.856 and 0.797 respectively. DCA exhibits consistent observations with the findings. Through validating our prediction model as well as other three domestic prediction models based on the entire study population of 697 cases, our prediction model demonstrated significantly higher predictive value than all the other models. Conclusion The nomogram for predicting prostate cancer can facilitate more accurate evaluation of the probability of having prostate cancer, and provide better ground for prostate biopsy.
Nan et al. (2022) Development and validation of a multi-parameter nomogram for predicting prostate cancer: a retrospective analysis from Handan Central Hospital in China. PeerJ 10:e12912 https://doi.org/10.7717/peerj.12912
Physiological stress and higher reproductive success in bumblebees are both associated with intensive agriculture
Free-living organisms face multiple stressors in their habitats, and habitat quality often affects development and life history traits. Increasing pressures of agricultural intensification have been shown to influence diversity and abundance of insect pollinators, and it may affect their elemental composition as well. We compared reproductive success, body concentration of carbon (C) and nitrogen (N), and C/N ratio, each considered as indicators of stress, in the buff-tailed bumblebee (Bombus terrestris). Bumblebee hives were placed in oilseed rape fields and semi-natural old apple orchards. Flowering season in oilseed rape fields was longer than that in apple orchards. Reproductive output was significantly higher in oilseed rape fields than in apple orchards, while the C/N ratio of queens and workers, an indicator of physiological stress, was lower in apple orchards, where bumblebees had significantly higher body N concentration. We concluded that a more productive habitat, oilseed rape fields, offers bumblebees more opportunities to increase their fitness than a more natural habitat, old apple orchards, which was achieved at the expense of physiological stress, evidenced as a significantly higher C/N ratio observed in bumblebees inhabiting oilseed rape fields.
Krama et al. (2022) Physiological stress and higher reproductive success in bumblebees are both associated with intensive agriculture. PeerJ 10:e12953 https://doi.org/10.7717/peerj.12953
Influence of Lymphangio vascular (V) and perineural (N) invasion on survival of patients with resected esophageal squamous cell carcinoma (ESCC): a single-center retrospective study
Background Lymphangio vascular invasion (LVI) and perineural invasion (PNI) are associated with survival following resection for gastrointestinal cancer. But the relationship between LVI/PNI and survival of esophageal squamous cell carcinoma (ESCC) is still unclear. We aim to demonstrate the prognostic significance of LVI/PNI in ESCC. Methods A total of 195 ESCC patients underwent curative surgery from 2012 to 2018 was collected in the 2nd Affiliated Hospital of Fujian Medical University. All the patients were divided into four groups based on the status of the neurovascular invasion: (1) neither LVI nor PNI (V0N0); (2) LVI alone (V1N0); (3) PNI alone (V0N1); (4) combined LVI and PNI (V1N1). First, the analysis included the Kaplan-Meier survival estimates with the Log rank test were performed to determine median overall survival (OS) in different groups divided according to the clinical factor, respectively. And the association between OS with multi clinical factors was examined using Cox regression analysis. Next, the risk factors for recurrence in patients with V1N1 were analyzed with univariate and multivariate logistic regression analyses, respectively. Results The cases in V0N0, V1N0, V0N1, and V1N1 groups were 91 (46.7%), 62 (31.8%), 9 (4.6%) and 33 (16.9%), respectively. The OS in the four groups was different (P < 0.001). The 1-, 3- and 5-year OS in V0N0 group was higher than that in V1N1 group, respectively (1-year OS: 93.4% vs 75.8%, 3-year OS: 53.8 % vs 24.2%, 5-year OS: 48.1% vs 10.5%). The OS in stage I-II for patients with V1N1 was significantly lower than that in the other groups (V0N0, V1N0, V0N1) (P < 0.001). The postoperative adjuvant chemotherapy was a significant impact factor of OS for ESCC patients with V1N1 (P = 0.004). Lymphatic invasion and LVI were significantly prognosis factors associated (P = 0.036, P = 0.030, respectively). The ulcerative type is a risk factor for V1N1 occurance (P = 0.040). Conclusions The LVI and PNI are important prognosis factors for ESCC patients. ESCC patients with simultaneous lymphangio vascular and perineural invasion (V1N1) showed worse OS than patients with either lymphangio vascular or perineural invasion alone (V1N0 or V0N1) or none (V0N0). In addition, adjuvant chemotherapy may prolong the OS for ESCC patients with V1N1.
Xie et al. (2022) Influence of Lymphangio vascular (V) and perineural (N) invasion on survival of patients with resected esophageal squamous cell carcinoma (ESCC): a single-center retrospective study. PeerJ 10:e12974 https://doi.org/10.7717/peerj.12974