Evaluation of the diagnostic and prognostic values of serum HSP90α in sepsis patients: a retrospective study
Background Sepsis is a serious syndrome that is caused by immune responses dysfunction and leads to high mortality. The abilities of heat shock protein 90α (HSP90α) in assessing the diagnosis and prognosis in patients with sepsis remain ill-defined to date. We conducted a study to reveal the possible clinical applications of HSP90α as biomarker for the diagnosis and prognosis in patients with sepsis. Methods In total, 150 patients of sepsis, 110 patients without sepsis admitted to ICU and 110 healthy subjects were involved in this study. The serum HSP90α contents, sequential organ failure assessment (SOFA) scores, procalcitonin (PCT), and short-term survival status of the participants were measured and compared. Logistic and linear regression models adjusting for potential confounders were used to examine the association of HSP90α with sepsis survival. Moreover, serum IL-1β, IL-18, MIP-3α, and ENA-78 were also determined. Finally, Spearman correlation analysis was employed to reveal a possible mechanism that HSP90α contributed to the short-term deaths. Results Serum HSP90α levels in sepsis patients were higher than those in ICU controls and healthy controls (P < 0.001), and even increased in patients who died within 28 days (P < 0.001). Logistic and linear regression models identified HSP90α was an independent risk factors for sepsis mortality. Receiver operating characteristic (ROC) analysis displayed that HSP90α had a considerable predictive performance for sepsis outcome, with an area under curve (AUC) value up to 0.79. Survival analysis demonstrated that the mortality of sepsis individuals at 28 days was positively associated with HSP90α levels, especially the levels of HSP90α were greater than 120 ng/mL (P < 0.001). Moreover, among sepsis patients, those who died had notably elevated cytokines, IL-1β, IL-18, and chemokines, MIP-3α, ENA-78, relative to survivors. Further correlation analysis demonstrated that there was a nominally positive correlation between HSP90α and IL-1β, IL-18, and MIP-3α. Conclusion HSP90α is of favorable clinical significance in sepsis diagnosis and prognosis, laying a foundation for future clinical applications.
Li et al. (2022) Evaluation of the diagnostic and prognostic values of serum HSP90α in sepsis patients: a retrospective study. PeerJ 10:e12997 https://doi.org/10.7717/peerj.12997
Effect of magnification factor by Galilean loupes on working posture of dental students in simulated clinical procedures: associations between direct and observational measurements
Objectives To determine the effect of different levels of Galilean loupe magnification on working posture as measured by compliance with ergonomic posture positions, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back region during simulated clinical conditions. Methods An experimental laboratory study was performed in which the dependent variables were compliance with ergonomic posture requirements while performing simulated restorative procedures in Restorative Dentistry, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back. The independent variable was the level of Galilean loupe magnification, which was tested at four levels (naked eye, 2.5× magnification, 3.0× magnification, and 3.5× magnification). The cavity preparations and Class I composite resin restorations were performed on artificial first molars on a mannequin in a dental chair. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) was used for the postural analysis; as was an analysis of the angular deviation from the neutral position of the neck and surface electromyography. Working posture was recorded on video over the course of the procedure. Participants were filmed from three different angles. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) assessed compliance with ergonomic posture requirements. A locally produced posture assessment software analyzed angular deviation. Surface electromyography bilaterally assessed activation of the sternocleidomastoid, descending trapezius and ascending trapezius muscles. Two-factor analysis of variance (ANOVA) and either Tukey’s post-hoc test or the Games-Howell post-hoc test were performed (α = 0.05). Results During the cavity preparations and restorations, the use of Galilean loupes at all magnifications positively influenced working posture as measured by participants’ compliance with ergonomic posture positions (p < 0.01) and neck angulation (p < 0.01); the use of these loupes did not affect muscle activation in the regions evaluated (p > 0.05). Conclusion The use of Galilean loupes had a positive effect on dental students’ working posture during the restoration procedures performed.
Pazos et al. (2022) Effect of magnification factor by Galilean loupes on working posture of dental students in simulated clinical procedures: associations between direct and observational measurements. PeerJ 10:e13021 https://doi.org/10.7717/peerj.13021
Functional analysis of ARF1 from Cymbidium goeringii in IAA response during leaf development
Background Cymbidium is an economically important genus of flowering orchids cultivated in China because of showing graceful leaf shapes and elegant flower coloration. However, the deterioration of the ecological environment and the difficulty of conservation management have become increasing challenges for maintaining its germplasm resources. ARFs are critical transcription factors in the auxin signaling pathway and have been found to play pivotal roles in leaf growth and development in previous studies. However, their functions and mechanisms in Cymbidium goeringii remain to be clarified. Methods The sequence of the CgARF1 gene was analyzed by bioinformatics. The expression of this gene in different tissues and under IAA treatment was detected by quantitative real-time PCR analysis. The CgARF1 gene was overexpressed in wild-type Arabidopsis and Nicotiana benthamiana via the Agrobacterium infection method. Acetone-ethanol solvent extraction was applied for the determination of chlorophyll contents, and the contents of endogenous hormones were determined using the enzyme-linked immunosorbent assay technique. Results CgARF1 cloned from C. goeringii ‘Songmei’ was 2,049 bp in length and encoded 682 amino acids containing three typical domains: a B3 DNA binding domain, an Aux_resp domain and an AUX/IXX family domain. The expression pattern of CgARF1 in different tissues of C. goeringii showed that its expression was highest in the leaves and changed greatly under IAA treatment. Subcellular localization studies showed that the protein was mainly localized in the cell nucleus. CgARF1-overexpressing lines exhibited leaf senescence and a decreased chlorophyll content. Under IAA treatment, CgARF1 regulates the rooting length, rooting number and rooting rate from detached leaves. The levels of endogenous hormones in transgenic leaves were also significantly changed. Conclusion These results indicated that CgARF1 overexpression is responsive to IAA treatment during leaf development. This study provides a foundation for future research on the function of the ARF gene family in C. goeringii.
Xu et al. (2022) Functional analysis of ARF1 from Cymbidium goeringii in IAA response during leaf development. PeerJ 10:e13077 https://doi.org/10.7717/peerj.13077
Effect of precipitation change on the photosynthetic performance of Phragmites australis under elevated temperature conditions
Background As a fundamental metabolism, leaf photosynthesis not only provides necessary energy for plant survival and growth but also plays an important role in global carbon fixation. However, photosynthesis is highly susceptible to environmental stresses and can be significantly influenced by future climate change. Methods In this study, we examined the photosynthetic responses of Phragmites australis (P. australis) to three precipitation treatments (control, decreased 30%, and increased 30%) under two thermal regimes (ambient temperature and +4 °C) in environment-controlled chambers. Results Our results showed that the net CO2 assimilation rate (Pn), maximal rate of Rubisco (Vcmax), maximal rate of ribulose-bisphosphate (RuBP) regeneration (Jmax) and chlorophyll (Chl) content were enhanced under increased precipitation condition, but were declined drastically under the condition of water deficit. The increased precipitation had no significant effect on malondialdehyde (MDA) content (p > 0.05), but water deficit drastically enhanced the MDA content by 10.1%. Meanwhile, a high temperature inhibited the positive effects of increased precipitation, aggravated the adverse effects of drought. The combination of high temperature and water deficit had more detrimental effect on P. australis than a single factor. Moreover, non-stomatal limitation caused by precipitation change played a major role in determining carbon assimilation rate. Under ambient temperature, Chl content had close relationship with Pn (R2 = 0.86, p < 0.01). Under high temperature, Pn was ralated to MDA content (R2 = 0.81, p < 0.01). High temperature disrupted the balance between Vcmax and Jmax (the ratio of Jmax to Vcmax decreased from 1.88 to 1.12) which resulted in a negative effect on the photosynthesis of P. australis. Furthermore, by the analysis of Chl fluorescence, we found that the xanthophyll cycle-mediated thermal dissipation played a major role in PSII photoprotection, resulting in no significant change on actual PSII quantum yield (ΦPSII) under both changing precipitation and high temperature conditions. Conclusions Our results highlight the significant role of precipitation change in regulating the photosynthetic performance of P. australis under elevated temperature conditions, which may exacerbate the drought-induced primary productivity reduction of P. australis under future climate scenarios.
Teng et al. (2022) Effect of precipitation change on the photosynthetic performance of Phragmites australis under elevated temperature conditions. PeerJ 10:e13087 https://doi.org/10.7717/peerj.13087
Feature screening for survival trait with application to TCGA high-dimensional genomic data
Background In high-dimensional survival genomic data, identifying cancer-related genes is a challenging and important subject in the field of bioinformatics. In recent years, many feature screening approaches for survival outcomes with high-dimensional survival genomic data have been developed; however, few studies have systematically compared these methods. The primary purpose of this article is to conduct a series of simulation studies for systematic comparison; the second purpose of this article is to use these feature screening methods to further establish a more accurate prediction model for patient survival based on the survival genomic datasets of The Cancer Genome Atlas (TCGA). Results Simulation studies prove that network-adjusted feature screening measurement performs well and outperforms existing popular univariate independent feature screening methods. In the application of real data, we show that the proposed network-adjusted feature screening approach leads to more accurate survival prediction than alternative methods that do not account for gene-gene dependency information. We also use TCGA clinical survival genetic data to identify biomarkers associated with clinical survival outcomes in patients with various cancers including esophageal, pancreatic, head and neck squamous cell, lung, and breast invasive carcinomas. Conclusions These applications reveal advantages of the new proposed network-adjusted feature selection method over alternative methods that do not consider gene-gene dependency information. We also identify cancer-related genes that are almost detected in the literature. As a result, the network-based screening method is reliable and credible.
Wang et al. (2022) Feature screening for survival trait with application to TCGA high-dimensional genomic data. PeerJ 10:e13098 https://doi.org/10.7717/peerj.13098
The association between non-suicidal self-injury and negative life events in children and adolescents in underdeveloped regions of south-western China
Background The association between negative life events and Non-suicidal self-injury (NSSI) in children and adolescents has been extensively discussed. Nevertheless, little is known about the relationship between negative life events and repetition and severity of NSSI. This survey aims to understand the association between NSSI prevalence, severity, repetition and the negative life events in children and adolescents in underdeveloped regions in south-western China. Methods In this population-based cross-sectional study, 3,146 children and adolescents were included from underdeveloped regions of south-western China, and each of them requested to complete a self-assessment questionnaire. The Modified Version of Adolescents Self-Harm Scale (MASHS) and the Adolescent Self-rating negative Life Events Check-list were used to evaluate NSSI behaviors and negative life events, respectively. The statistical implementation of this study was carried out in the R statistical software, and the logistic regression analysis method was used to analyze the relationship between negative life events and adolescents’ non-suicidal self-injury behaviors. Results The average age of all included participants was 13.31 years old. The lifetime prevalence of NSSI was 47.0% (95% CI [36.3–58.0%]). Gender, grade level and ASLEC was positively associated with NSSI. Further analysis revealed that, for all five dimensions of ASLEC, only interpersonal relationship factor (IRF) (OR 1.77 (95% CI [1.06–2.97])), health adaptation factor (HAF) (OR 2.08 (95% CI [1.31–3.31])) showed prominent association with NSSI. Multivariate Logistic regression models revealed that, repetitive NSSI (OR 4.54 (95% CI [3.66–5.63])) and NSSI severity (OR 9.01 (95% CI [6.11–13.29])) were positively associated with ASLEC. Conclusion NSSI is very common among children and adolescents in underdeveloped regions of south-western China. Negative life event are positively associated with NSSI, repeated NSSI, and severe NSSI. Negative life events centered intervention measures might be effective in reducing NSSI among school children and adolescents in underdeveloped regions of south-western China.
Yang et al. (2022) The association between non-suicidal self-injury and negative life events in children and adolescents in underdeveloped regions of south-western China. PeerJ 10:e12665 https://doi.org/10.7717/peerj.12665
Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic
Three new species of Microlaimus are described from the continental shelf of the Campos Basin, southwest Atlantic, Brazil. Microlaimus campiensis sp. n. differs from all other species in the presence of two anterior testes, slender spicules with enlarged proximal ends, 7–11 pre-cloacal papilliform supplements, and females with a pair of constriction structures, one on each branch of the ovary. Microlaimus alexandri sp. n. shows sexual dimorphism in the size of the amphidial fovea, which occupies 100% of the diameter of the corresponding area in the male; the buccal cavity provided with five teeth and a slightly cuticularized cuticular ring. Microlaimus vitorius sp. n. has four longitudinal-lateral rows of glands associated with small pores, one seta and three pores small pre-cloacal, and the gubernaculum has a triangular base. An amendment to the diagnosis of the genus is proposed, where the number of teeth was modified.
Lima et al. (2022) Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic. PeerJ 10:e12734 https://doi.org/10.7717/peerj.12734
Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii
Background Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. Methods We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. Results The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Conclusion Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.
Konstantinov et al. (2022) Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii. PeerJ 10:e12737 https://doi.org/10.7717/peerj.12737
Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology
Background Septic cardiomyopathy (SC) is a common complication of sepsis that leads to an increase in mortality. The pathogenesis of septic cardiomyopathy is unclear, and there is currently no effective treatment. EGCG (epigallocatechin gallate) is a polyphenol that has anti-inflammatory, antiapoptotic, and antioxidative stress effects. However, the role of EGCG in septic cardiomyopathy is unknown. Methods Network pharmacology was used to predict the potential targets and molecular mechanisms of EGCG in the treatment of septic cardiomyopathy, including the construction and analysis of protein-protein interaction (PPI) network, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and molecular docking. The mouse model of septic cardiomyopathy was established after intraperitoneal injection of LPS (lipopolysaccharide). The myocardial protective effect of EGCG on septic mice is observed by cardiac ultrasound and HE staining. RT-PCR is used to verify the expression level of the EGCG target in the septic cardiomyopathy mouse model. Results A total of 128 anti-SC potential targets of EGCGareselected for analysis. The GO enrichment analysis and KEGG pathway analysis results indicated that the anti-SC targets of EGCG mainly participate in inflammatory and apoptosis processes. Molecular docking results suggest that EGCG has a high affinity for the crystal structure of six targets (IL-6 (interleukin-6), TNF (tumor necrosis factor), Caspase3, MAPK3 (Mitogen-activated protein kinase 3), AKT1, and VEGFA (vascular endothelial growth factor)), and the experimental verification result showed levated expression of these 6 hub targets in the LPS group, but there is an obvious decrease in expression in the LPS + EGCG group. The functional and morphological changes found by echocardiography and HE staining show that EGCG can effectively improve the cardiac function that is reduced by LPS. Conclusion Our results reveal that EGCG may be a potentially effective drug to improve septic cardiomyopathy. The potential mechanism by which EGCG improves myocardial injury in septic cardiomyopathy is through anti-inflammatory and anti-apoptotic effects. The anti-inflammatory and anti-apoptotic effects of EGCG occur not only through direct binding to six target proteins (IL-6,TNF-α, Caspase3, MAPK3, AKT1, and VEGFA) but also by reducing their expression.
Wu et al. (2022) Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology. PeerJ 10:e12994 https://doi.org/10.7717/peerj.12994
Optimizing seawater temperature conditions to increase the productivity of ex situ coral nurseries
Large scale ex situ propagation of coral colonies for reef restoration is a relatively new and developing field. One of the many advantages of utilizing ex situ coral nurseries is the ability to optimize water quality conditions for coral health and survival. Slight alterations in environmental parameters (light, pH, temperature etc.) can affect the health and grow-out time of cultured coral, ultimately influencing production rates. However, corals are also subjected to pests associated with culture facilities such as ciliates, cyanobacterial blooms, and infectious diseases. Therefore, adjusting environmental parameters to optimize coral growth for a shorter ex situ residency time will lead to greater survival and faster restoration. Studies indicate that some coral species demonstrate parabolic tissue growth in response to increasing sea-surface temperatures until the maximum temperature tolerance is reached, whereafter they bleach. To maximize coral growth in Mote Marine Laboratory’s ex situ system, we tested the effect of two water temperature treatments (high temperature: 29.5 ± 0.03 °C; control: 25.2 ± 0.08 °C) on two coral species commonly used in reef restoration. To quantify this, we used four replicates of three genotypes each of Montastraea cavernosa (n = 12) and Acropora palmata (n = 12). Two-dimensional tissue area was recorded monthly using ImageJ and survival rates within each treatment were documented for 7 months. Results found that M. cavernosa had greater growth rates and equal survivorship in the high temperature treatment compared to the control treatment. A. palmata grew faster and had equal survivorship in the control treatment compared with the high temperature treatment. These results suggest that temperature preferences exist among coral species within ex situ systems and restoration practitioners should consider species-specific temperature regimes to maximize ex situ coral growth rates. This information is critical for optimizing production when corals are in the grow-out stage and should also be considered when designing ex situ systems to ensure temperature regulation can be controlled on a species-specific basis.
Merck et al. (2022) Optimizing seawater temperature conditions to increase the productivity of ex situ coral nurseries. PeerJ 10:e13017 https://doi.org/10.7717/peerj.13017