title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=474 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effects of company and season on blood fluke (Cardicola spp.) infection in ranched Southern Bluefin Tuna: preliminary evidence infection has a negative effect on fish growth link: https://peerj.com/articles/15763 last-modified: 2023-07-25 description: Aporocotylid blood flukes Cardicola forsteri and C. orientalis are an ongoing health concern for Southern Bluefin Tuna (SBT), Thunnus maccoyii, ranched in Australia. Therapeutic application of praziquantel (PZQ) has reduced SBT mortalities, however PZQ is not a residual treatment therefore reinfection can occur after the single treatment application. This study documents the epidemiology of Cardicola spp. infection in ranched SBT post treatment over three ranching seasons (2018, 2019 and 2021). Infection prevalence (percentage of SBT affected) and intensity (parasite load) was determined by adult fluke counts from heart, egg counts from gill filaments and the use of specific quantitative polymerase chain reaction (qPCR) for detection of C. forsteri and C. orientalis ITS-2 DNA in SBT hearts and gills. SBT Condition Index decreased as intensity of Cardicola spp. DNA in SBT gills increased, suggesting blood fluke infection had a negative effect on SBT growth (Spearman’s r = −0.2426, d.f. = 138, p = 0.0041). Prevalence and intensity of infection indicated PZQ remained highly effective at controlling Cardicola spp. infection in ranched SBT, 10 years after PZQ administration began in this industry. Company A had the highest prevalence and intensity of Cardicola spp. infection in 2018, and Company G had the highest in 2019. No consistent pattern was seen in 2021. Overall, intensity of infection did not increase as ranching duration increased post treatment. Results from this study improve our knowledge of the biology of blood flukes and helps the SBT industry to modify or design new blood fluke management strategies to reduce health risks and improve performance of SBT. creator: Cecilia Power creator: Melissa Carabott creator: Maree Widdicombe creator: Lachlan Coff creator: Kirsten Rough creator: Barbara Nowak creator: Nathan J. Bott uri: https://doi.org/10.7717/peerj.15763 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Power et al. title: Restoring South African subtropical succulent thicket using Portulacaria afra: exploring the rooting window hypothesis link: https://peerj.com/articles/15538 last-modified: 2023-07-24 description: Drought prone, arid and semi-arid ecosystems are challenging to restore once degraded due to low levels of natural recruitment and survival of reintroduced plants. This is evident in the restoration of degraded succulent thicket habitats in the Albany Subtropical Thicket Biome located in South Africa. The current restoration practice for this ecosystem focuses predominantly on reintroducing Portulacaria afra L. Jacq., which is naturally dominant in terms of cover and biomass, but largely absent in regions degraded by domestic livestock. This has been achieved by planting unrooted cuttings with limited consideration of soil water availability in a drought-prone ecosystem. This study tests the effects of the timing of water availability after planting on the root development of P. afra cuttings. Cuttings were harvested from seven individual plants and grown in a glasshouse setting. Eighty four cuttings were taken from each individual, twelve for each of the seven watering treatments per individual plant. The treatments represented a time-staggered initial watering after planting, including: on the day of planting, 4 days, 7 days, 14 days, 21 days, and 28 days after planting. After 32 days, all treatments were watered on a bi-weekly basis for two weeks; a control treatment with no watering throughout the experiment was included. The proportion of rooted cuttings per treatment and dry root mass were determined at the end of the experimental period (day 42). The early onset of watering was associated with a higher percentage of rooting (X2(5) = 11.352, p = 0.045) and had a weak, but non-significant, impact on the final dry root mass (F5,36 = 2.109, p = 0.0631). Importantly, no clear rooting window within 28 days was detected as the majority of cuttings exhibited root development (greater than 50% of cuttings rooted for each individual parent-plant); this suggests that watering at the time of planting P. afra cuttings in-field for restoration may not be necessary. An unexpected, but important, result was that parent-plant identity had a strong interaction with the accumulation of root mass (F36,460 = 5.026, p < 0.001; LR7 = 122.99, p < 0.001). The control treatment, which had no water throughout the experiment, had no root development. These findings suggest that water availability is required for the onset of rooting in P. afra cutting. However, the duration of the experiment was insufficient to detect the point at which P. afra cuttings could no longer initiate rooting once exposed to soil moisture, and thus no rooting window could be defined. Despite harvesting material from the same source population, parent-plant identity strongly impacted root development. Further work is required to characterise the rooting window, and to explore the effect of parent-plant condition on in-field and experimental restoration results; we urge that experiments using P. afra closely track the parent-source at the individual level as this may be a factor that may have a major impact on results. creator: Nicholas C. Galuszynski creator: Ryan E. Forbes creator: Gavin M. Rishworth creator: Alastair J. Potts uri: https://doi.org/10.7717/peerj.15538 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Galuszynski et al. title: Phosphorylation of the N-terminus of Syntaxin-16 controls interaction with mVps45 and GLUT4 trafficking in adipocytes link: https://peerj.com/articles/15630 last-modified: 2023-07-24 description: The ability of insulin to stimulate glucose transport in muscle and fat cells is mediated by the regulated delivery of intracellular vesicles containing glucose transporter-4 (GLUT4) to the plasma membrane, a process known to be defective in disease such as Type 2 diabetes. In the absence of insulin, GLUT4 is sequestered in tubules and vesicles within the cytosol, collectively known as the GLUT4 storage compartment. A subset of these vesicles, known as the ‘insulin responsive vesicles’ are selectively delivered to the cell surface in response to insulin. We have previously identified Syntaxin16 (Sx16) and its cognate Sec1/Munc18 protein family member mVps45 as key regulatory proteins involved in the delivery of GLUT4 into insulin responsive vesicles. Here we show that mutation of a key residue within the Sx16 N-terminus involved in mVps45 binding, and the mutation of the Sx16 binding site in mVps45 both perturb GLUT4 sorting, consistent with an important role of the interaction of these two proteins in GLUT4 trafficking. We identify Threonine-7 (T7) as a site of phosphorylation of Sx16 in vitro. Mutation of T7 to D impairs Sx16 binding to mVps45 in vitro and overexpression of T7D significantly impaired insulin-stimulated glucose transport in adipocytes. We show that both AMP-activated protein kinase (AMPK) and its relative SIK2 phosphorylate this site. Our data suggest that Sx16 T7 is a potentially important regulatory site for GLUT4 trafficking in adipocytes. creator: Shaun K. Bremner creator: Rebecca Berends creator: Alexandra Kaupisch creator: Jennifer Roccisana creator: Calum Sutherland creator: Nia J. Bryant creator: Gwyn W. Gould uri: https://doi.org/10.7717/peerj.15630 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Bremner et al. title: The prognostic significance of KLRB1 and its further association with immune cells in breast cancer link: https://peerj.com/articles/15654 last-modified: 2023-07-24 description: BackgroundKiller cell lectin-like receptor B1 (KLRB1) is an important member of the natural killer cell gene family. This study explored the potential value of KLRB1 as a breast cancer (BC) biomarker and its close association with the tumor immune microenvironment during the development of BC.MethodsWe examined the differential expression of KLRB1 in pan-cancer. Clinical and RNA-Seq data from BC samples were evaluated in The Cancer Genome Atlas (TCGA) and validated in Gene Expression Omnibus (GEO) datasets and by immunohistochemistry (IHC) staining. The relationship between KLRB1 and clinical parameters was explored through Chi-square tests. The diagnostic value of KLRB1 was evaluated using a receiver operating characteristic (ROC) curve. Survival analysis was tested by Kaplan-Meier curves to demonstrate the relationship between KLRB1 and survival. Univariable and multivariate cox regression analyses were carried out as well. The analysis of immune infiltration level and gene set enrichment analysis (GSEA) were conducted to examine KLRB1’s mechanism during the progression of BC. We used the Tumor Immune Estimation Resource (TIMER), the Cancer Single-cell Expression Map (CancerSCEM) database, the Tumor Immune Single-cell Hub (TISCH) database, and the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) method to explore KLRB1’s association with immune infiltration level and different quantitative distribution of immune cells. The relevant signaling pathways in BC associated with KLRB1 were identified using GSEA.ResultsThe expression of KLRB1 was downregulated across the majority of cancers including BC. The lower KLRB1 expression group exhibited shorter relapse free survival (RFS) and overall survival (OS). IHC staining showed that KLRB1 staining was weaker in breast tumor tissues than in paratumors. Additionally, GSEA identified several pathway items distinctly enriched in BC. KLRB1 expression level was also positively related to the infiltrating number of immune cells in BC. Moreover, the CancerSCEM and TISCH databases as well as the CIBERSORT method demonstrated the close relationship between KLRB1 and immune cells, particularly macrophages.ConclusionLow KLRB1 expression was considered an independent prognostic biomarker and played an important role in the tumor immune microenvironment of BC patients. creator: Ning Xu creator: Xiangyu Meng creator: Hongyu Chu creator: Zhaoying Yang creator: Yan Jiao creator: Youjun Li uri: https://doi.org/10.7717/peerj.15654 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al. title: Comparison of the elastic recovery and strain-in-compression of commercial and novel vinyl polysiloxane impression materials incorporating a novel crosslinking agent and a surfactant link: https://peerj.com/articles/15677 last-modified: 2023-07-24 description: This study aims to formulate experimental vinylpolysiloxane (VPS) impression materials and compare their elastic recovery and strain-in-compressions with three commercial VPS materials (Aquasil, Elite, and Extrude). Five experimental materials (Exp), two hydrophobic (Exp-I and II) and three hydrophilic (Exp-III, IV and V) were developed. Exp 1 contained vinyl-terminated poly-dimethyl siloxane and a conventional cross-linking agent (poly methylhydrosiloxane), while Exp- II contained a novel cross-linking agent that is tetra-functional dimethyl-silyl-ortho-silicate (TFDMSOS). Exp III–V (hydrophilic materials) were formulated by incorporating different concentrations of non-ionic surfactant (Rhodasurf CET-2) into Exp II formulation. Measurement of elastic recovery and strain-in-compression for commercial and experimental materials were performed according to ISO4823 standard using the calibrated mechanical testing machine (Tinius Olsen). One-way analysis of variance (one-way ANOVA) and Tukey’s post-hoc (HSD) test were used for statistical analysis and a p-value of ≤ 0.05 was considered significant. Exp-I has statistically similar values to commercial VPS. The Exp-II showed the highest elastic recovery, while % elastic recovery was reduced with the addition of the non-ionic surfactant (Rhodasurf CET-2). The % reduction was directly related to the concentration of Rhodasurf CET-2. In addition, Exp II had significantly higher strain-in-compression values compared to Exp-I and commercial materials. These values were further increased with the addition of a non-ionic surfactant (Rhodasurf CET-2) was added (Exp-III, IV and V). creator: Shahab Ud Din creator: Osama Khattak creator: Farooq Ahmad Chaudhary creator: Asfia Saeed creator: Azhar Iqbal creator: Jamaluddin Syed creator: Alaa Ahmed Kensara creator: Thani Alsharari creator: Mohammed Mustafa creator: Sherif Elsayed Sultan creator: Mangala Patel uri: https://doi.org/10.7717/peerj.15677 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ud Din et al. title: Identifying the critical state of cancers by single-sample Markov flow entropy link: https://peerj.com/articles/15695 last-modified: 2023-07-24 description: BackgroundThe progression of complex diseases sometimes undergoes a drastic critical transition, at which the biological system abruptly shifts from a relatively healthy state (before-transition stage) to a disease state (after-transition stage). Searching for such a critical transition or critical state is crucial to provide timely and effective scientific treatment to patients. However, in most conditions where only a small sample size of clinical data is available, resulting in failure when detecting the critical states of complex diseases, particularly only single-sample data.MethodsIn this study, different from traditional methods that require multiple samples at each time, a model-free computational method, single-sample Markov flow entropy (sMFE), provides a solution to the identification problem of critical states/pre-disease states of complex diseases, solely based on a single-sample. Our proposed method was employed to characterize the dynamic changes of complex diseases from the perspective of network entropy.ResultsThe proposed approach was verified by unmistakably identifying the critical state just before the occurrence of disease deterioration for four tumor datasets from The Cancer Genome Atlas (TCGA) database. In addition, two new prognostic biomarkers, optimistic sMFE (O-sMFE) and pessimistic sMFE (P-sMFE) biomarkers, were identified by our method and enable the prognosis evaluation of tumors.ConclusionsThe proposed method has shown its capability to accurately detect pre-disease states of four cancers and provide two novel prognostic biomarkers, O-sMFE and P-sMFE biomarkers, to facilitate the personalized prognosis of patients. This is a remarkable achievement that could have a major impact on the diagnosis and treatment of complex diseases. creator: Juntan Liu creator: Yuan Tao creator: Ruoqi Lan creator: Jiayuan Zhong creator: Rui Liu creator: Pei Chen uri: https://doi.org/10.7717/peerj.15695 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liu et al. title: Oleanolic acid and moderate drinking increase the pancreatic GLP-1R expression of the β-cell mass deficiency induced hyperglycemia link: https://peerj.com/articles/15705 last-modified: 2023-07-24 description: BackgroundOleanolic acid (OA) and moderate drinking have been reported to attenuate diabetes. However, the underlying mechanism of OA and moderate drinking alone or in combination on the islet β-cell deficiency induced diabetes is not fully elucidated.MethodsMale Sprague Dawley (SD) rats were intraperitoneally injected with 55 mg/kg streptozotocin (STZ) to induce β-cell deficiency. OA, 5% ethanol (EtOH), or a mixture of OA in 5% ethanol (OA+EtOH) were applied to three treatment groups of hyperglycemia rats for 6 weeks.ResultsSTZ caused the increase of fast blood glucose (FBG) level.OA and EtOH treatment alone or in combination decreased the STZ increased FBG level during the 6 weeks of treatment. In addition, OA treatment also significantly increased the β-cell to total islet cell ratio. Both EtOH and OA+EtOH treatments promoted the increase of total islet cell number and α-cell to β-cell ratio when compared to OA group. STZ induced hyperglycemia dramatically reduced the glucagon-like peptide-1 receptor (GLP-1R) positive cells in islets, all the three treatments significantly increased the pancreatic GLP-1R positive cell number. In the meantime, STZ induced hyperglycemia suppressed the insulin mRNA expression and boosted the glucagon mRNA expression. EtOH and OA+EtOH treatments increased the insulin mRNA expression, but none of the 3 treatments altered the elevated glucagon level.ConclusionGLP-1R positive cell ratio in islets is crucial for the blood glucose level of diabetes. OA and 5% ethanol alone or in combination suppresses the blood glucose level of β-cell deficiency induced diabetes by increasing islet GLP-1R expression. creator: Li Xu creator: Ruibin Hu creator: Shreyas Venkataraman Jois creator: Lei Zhang uri: https://doi.org/10.7717/peerj.15705 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al. title: Comparison of dental anesthetic efficacy between the periodontal intraligamentary anesthesia and other infiltration anesthesia: a systematic review and meta-analysis link: https://peerj.com/articles/15734 last-modified: 2023-07-24 description: BackgroundUncertainty exists regarding the pain scores and the success rate of intraligamentary anesthesia compared to other infiltration anesthesia. Based on the conditions of clinical anesthesia techniques, we conducted a systematic review and meta-analysis to compare the efficacy of intraligamentary anesthesia with other infiltration anesthesia.MethodsThe search was carried out in PubMed Central, Cochrane Central Register of Controlled Trials, MEDLINE (via OVID), Embase (via OVID), and Scopus from the inception to March 26, 2023.ResultsSeven eligible randomized controlled trials were included in the meta-analysis. The results indicated no significant difference in the success rate (RR = 0.96; 95% CI [0.81–1.14]; p = 0.65; I2= 73%) and visual analog scale (VAS) during dental procedures (MD = 3.81; 95% CI [−0.54–8.16]; p = 0.09; I2= 97%) between intraligamentary anesthesia and other infiltration anesthesia. However, intraligamentary anesthesia exhibited a higher VAS score during injection than other infiltration anesthesia (MD = 8.83; 95% CI [4.86–12.79]; p < 0.0001; I2= 90%). A subgroup analysis according to infiltration techniques showed that supraperiosteal anesthesia had a lower VAS score during dental procedures than intraligamentary anesthesia.ConclusionsIntraligamentary anesthesia and other infiltration anesthesias have the same success rate and pain during dental procedures. However, the pain during injection of intraligamentary anesthesia is heavier than that of other infiltration anesthesia. creator: Jialei Pan creator: Yan Wang creator: Yuran Qian creator: Jing Zou creator: Qiong Zhang uri: https://doi.org/10.7717/peerj.15734 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Pan et al. title: Impact of climate change on the geographical distribution and niche dynamics of Gastrodia elata link: https://peerj.com/articles/15741 last-modified: 2023-07-24 description: BackgroundGastrodia elata is widely used in China as a valuable herbal medicine. Owing to its high medicinal and nutrient value, wild resources of G. elata have been overexploited and its native areas have been severely damaged. Understanding the impacts of climate change on the distribution of this endangered species is important for the conservation and sustainable use of G. elata.MethodsWe used the optimized maximum entropy model to simulate the potential distribution of G. elata under contemporary and future time periods (1970–2000, 2050s, 2070s, and 2090s) and different climate change scenarios (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5). Under these conditions, we investigated the key environmental factors influencing the distribution of G. elata as well as the spatial and temporal characteristics of its niche dynamics.ResultsWith high Maxent model accuracy (AUCmean = 0.947 ± 0.012, and the Kappa value is 0.817), our analysis revealed that annual precipitation, altitude, and mean temperature of driest quarter are the most important environmental factors influencing the distribution of G. elata. Under current bioclimatic conditions, the potentially suitable area for G. elata in China is 71.98 × 104 km2, while the highly suitable region for G. elata growth is 7.28 × 104 km2. Our models for three future periods under four climate change scenarios indicate that G. elata can maintain stable distributions in southern Shaanxi, southwestern Hubei, and around the Sichuan basin, as these areas are highly suitable for its growth. However, the center of the highly suitable areas of G. elata shift depending on different climatic scenarios. The values of niche overlap for G. elata show a decreasing trend over the forecasted periods, of which the niche overlap under the SSP3-7.0 scenario shows the greatest decrease.DiscussionsUnder the condition of global climate change in the future, our study provides basic reference data for the conservation and sustainable utilization of the valuable and endangered medicinal plant G. elata. It is important to carefully choose the protection area of G. elata wild resources according the suitable area conditions modeled. Moreover, these findings will be valuable for providing insights into the breeding and artificial cultivation of this plant, including the selection of suitable areas for planting. creator: Juan Hu creator: Ying Feng creator: Haotian Zhong creator: Wei Liu creator: Xufang Tian creator: Yehong Wang creator: Tao Tan creator: Zhigang Hu creator: Yifei Liu uri: https://doi.org/10.7717/peerj.15741 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hu et al. title: Effects of hydraulic retention time and influent nitrate concentration on solid-phase denitrification system using wheat husk as carbon source link: https://peerj.com/articles/15756 last-modified: 2023-07-24 description: Solid-phase denitrification shows promise for removing nitrate (NO3−-N) from water. Biological denitrification uses external carbon sources to remove nitrogen from wastewater, among which agriculture waste is considered the most promising source due to its economic and efficiency advantages. Hydraulic retention time (HRT) and influent nitrate concentration (INC) are the main factors influencing biological denitrification. This study explored the effects of HRT and INC on solid-phase denitrification using wheat husk (WH) as a carbon source. A solid-phase denitrification system with WH carbon source was constructed to explore denitrification performance with differing HRT and INC. The optimal HRT and INC of the wheat husk-denitrification reactor (WH-DR) were 32 h and 50 mg/L, respectively. Under these conditions, NO3−-N and total nitrogen removal rates were 97.37 ± 2.68% and 94.08 ± 4.01%, respectively. High-throughput sequencing revealed that the dominant phyla in the WH-DR operation were Proteobacteria, Bacteroidetes, and Campilobacterota. Among the dominant genera, Diaphorobacter (0.85%), Ideonella (0.38%), Thiobacillus (4.22%), and Sulfurifustis (0.60%) have denitrification functions; Spirochaeta (0.47%) is mainly involved in the degradation of WH; and Acidovorax (0.37%) and Azospira (0.86%) can both denitrify and degrade WH. This study determined the optimal HRT and INC for WH-DR and provides a reference for the development and application of WH as a novel, slow-release carbon source in treating aquaculture wastewater. creator: Shuhui Niu creator: Shuwei Gao creator: Kai Zhang creator: Zhifei Li creator: Guangjun Wang creator: Hongyan Li creator: Yun Xia creator: Jingjing Tian creator: Ermeng Yu creator: Jun Xie creator: Minting Zhang creator: Wangbao Gong uri: https://doi.org/10.7717/peerj.15756 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Niu et al.