title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2022-09 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: An in silico study of how histone tail conformation affects the binding affinity of ING family proteins link: https://peerj.com/articles/14029 last-modified: 2022-09-30 description: BackgroundDue to its intrinsically disordered nature, the histone tail is conformationally heterogenic. Therefore, it provides specific binding sites for different binding proteins or factors through reversible post-translational modifications (PTMs). For instance, experimental studies stated that the ING family binds with the histone tail that has methylation on the lysine in position 4. However, numerous complexes featuring a methylated fourth lysine residue of the histone tail can be found in the UniProt database. So the question arose if other factors like the conformation of the histone tail affect the binding affinity.MethodsThe crystal structure of the PHD finger domain from the proteins ING1, ING2, ING4, and ING5 are docked to four histone H3 tails with two different conformations using Haddock 2.4 and ClusPro. The best four models for each combination are selected and a two-sample t-test is performed to compare the binding affinities of helical conformations vs. linear conformations using Prodigy. The protein-protein interactions are examined using LigPlot.ResultsThe linear histone conformations in predicted INGs-histone H3 complexes exhibit statistically significant higher binding affinity than their helical counterparts (confidence level of 99%). The outputs of predicted models generated by the molecular docking programs Haddock 2.4 and ClusPro are comparable, and the obtained protein-protein interaction patterns are consistent with experimentally confirmed binding patterns.ConclusionThe results show that the conformation of the histone tail is significantly affecting the binding affinity of the docking protein. Herewith, this in silico study demonstrated in detail the binding preference of the ING protein family to histone H3 tail. Further research on the effect of certain PTMs on the final tail conformation and the interaction between those factors seem to be promising for a better understanding of epigenetics. creator: Nadir Gül creator: Ahmet Yıldız uri: https://doi.org/10.7717/peerj.14029 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Gül and Yıldız title: MicroRNA-21 as a potential biomarker for detecting esophageal carcinoma in Asian populations: a meta-analysis link: https://peerj.com/articles/14048 last-modified: 2022-09-30 description: BackgroundMicroRNA-21 (miR-21) is significantly expressed in a variety of cancers and could be used as a tumor biomarker. However, the results are varied, and no studies on the diagnostic usefulness of miR-21 in Asian esophageal cancer (EC) patients have been published. This meta-analysis was aimed at exploring whether miR-21 can be used as a diagnostic marker and assessing its effectiveness.MethodsThe relevant literature was identified in six main databases: Ovid MEDLINE, PsycINFO, PubMed MEDLINE, Embase, Web of Science, and the Cochrane Library. Two researchers independently selected the literature based on the inclusion and exclusion criteria, extracted data, and evaluated the risk of bias. The meta-analysis was carried out using Review Manager 5.4, Meta-Disc 1.4 and STATA 15.1 software. In the end, 987 patients from 12 different studies were included. Quality evaluation of diagnostic accuracy studies 2 (QUADAS—2) was used to examine the risk of bias.ResultsThe pooled sensitivity (SEN) was 0.72 (95% CI [0.69–0.75]), the pooled specificity (SPE) was 0.78 (95% CI [0.75–0.81]), the pooled positive likelihood ratio (PLR) was 2.87 (95% CI [2.28–3.59]), the pooled negative likelihood ratio (NLR) was 0.36 (95% CI [0.31–0.43]), the pooled diagnostic odds ratio (DOR) was 10.00 (95% CI [7.73–12.95]), and the area under the curve 0.82 (95% CI [0.79–0.85]). A Deeks’ funnel plot shows that there was no publication bias (P = 0.99).ConclusionOur findings suggest miR-21 might be the potential biomarker for detecting EC in Asian populations, with a good diagnostic value. creator: Zheng Han creator: Lingbo Pan creator: Bangjie Lu creator: Huixia Zhu uri: https://doi.org/10.7717/peerj.14048 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Han et al. title: Irradiation with carbon ion beams affects soybean nutritional quality in early generations link: https://peerj.com/articles/14080 last-modified: 2022-09-30 description: As people’s demand for healthy diet increases, improving soybean seed nutritional quality is becoming as important as yield. Carbon ion beam radiation (CIBR) is an effective method to create soybean mutants, and thus breeding cultivars with better seed nutritional quality. In this study, the high-yield soybean line ‘Dongsheng 28’ was used, and three CIBR doses (100, 120, and 140 Gy) were used to explore the characteristics of quality separation and variation in the offspring of early mutant populations. Eleven quality traits, including protein, oil, sucrose, soluble sugar, iron (Fe), manganese (Mn), zinc (Zn), cupper (Cu), daidzin, glycitin, and genistin concentrations were analyzed in the M2 and M3 generations. The results revealed that the range of protein and oil concentration of all three CIBR doses changed by 38.5–42.9% and 18.8–23.8% in the M2 and M3 generations, respectively, while soluble sugar and sucrose concentrations changed by 48.1–123.4 and 22.7–74.7 mg/g, with significant effects by 140 Gy across the two generations. Therefore, around the optimum range, a higher CIBR dose is better for high protein, oil, and sugar varieties selection. In general, irradiation raised isoflavone concentrations, but 140 Gy had an inhibitory effect on isoflavone concentrations in the M3 generation. Although a variety could not be released in the M2 or M3 generation, the results of this study have important guiding significance for the targeted cultivation of specific nutritional quality materials. For instance, a lower irradiation dose is preferable when breeding targets are higher isoflavones and Mn concentrations. It is essential to increase the irradiation dose if the breeding targets contain high levels of protein, oil, sucrose, soluble sugars, Fe, Zn, and Cu. creator: Changkai Liu creator: Xue Wang creator: Yansheng Li creator: Heng Chen creator: Qiuying Zhang creator: Xiaobing Liu uri: https://doi.org/10.7717/peerj.14080 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: Rapid restructurization of conformationally-distinct alpha-synuclein amyloid fibrils at an elevated temperature link: https://peerj.com/articles/14137 last-modified: 2022-09-30 description: Protein aggregation in the form of amyloid fibrils is linked with the onset and progression of more than 30 amyloidoses, including multiple neurodegenerative disorders, such as Alzheimer’s or Parkinson’s disease. Despite countless studies and years of research, the process of such aggregate formation is still not fully understood. One peculiar aspect of amyloids is that they appear to be capable of undergoing structural rearrangements even after the fibrils have already formed. Such a phenomenon was reported to occur in the case of alpha-synuclein and amyloid beta aggregates after a long period of incubation. In this work, we examine whether incubation at an elevated temperature can induce the restructurization of four different conformation alpha-synuclein amyloid fibrils. We show that this structural alteration occurs in a relatively brief time period, when the aggregates are incubated at 60 °C. Additionally, it appears that during this process multiple conformationally-distinct alpha-synuclein fibrils all shift towards an identical secondary structure. creator: Mantas Ziaunys creator: Andrius Sakalauskas creator: Kamile Mikalauskaite creator: Vytautas Smirnovas uri: https://doi.org/10.7717/peerj.14137 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ziaunys et al. title: Progressive overload without progressing load? The effects of load or repetition progression on muscular adaptations link: https://peerj.com/articles/14142 last-modified: 2022-09-30 description: BackgroundProgressive overload is a principle of resistance training exercise program design that typically relies on increasing load to increase neuromuscular demand to facilitate further adaptations. However, little attention has been given to another way of increasing demand—increasing the number of repetitions.ObjectiveThis study aimed to compare the effects of two resistance training programs: (1) increasing load while keeping repetition range constant vs (2) increasing repetitions while keeping load constant. We aimed to compare the effects of these programs on lower body muscle hypertrophy, muscle strength, and muscle endurance in resistance-trained individuals over an 8-week study period.MethodsForty-three participants with at least 1 year of consistent lower body resistance training experience were randomly assigned to one of two experimental, parallel groups: A group that aimed to increase load while keeping repetitions constant (LOAD: n = 22; 13 men, nine women) or a group that aimed to increase repetitions while keeping load constant (REPS: n = 21; 14 men, seven women). Subjects performed four sets of four lower body exercises (back squat, leg extension, straight-leg calf raise, and seated calf raise) twice per week. We assessed one repetition maximum (1RM) in the Smith machine squat, muscular endurance in the leg extension, countermovement jump height, and muscle thickness along the quadriceps and calf muscles. Between-group effects were estimated using analyses of covariance, adjusted for pre-intervention scores and sex.ResultsRectus femoris growth modestly favored REPS (adjusted effect estimate (CI90%), sum of sites: 2.8 mm [−0.5, 5.8]). Alternatively, dynamic strength increases slightly favored LOAD (2.0 kg [−2.4, 7.8]), with differences of questionable practical significance. No other notable between-group differences were found across outcomes (muscle thicknesses, <1 mm; endurance, <1%; countermovement jump, 0.1 cm; body fat, <1%; leg segmental lean mass, 0.1 kg), with narrow CIs for most outcomes.ConclusionBoth progressions of repetitions and load appear to be viable strategies for enhancing muscular adaptations over an 8-week training cycle, which provides trainers and trainees with another promising approach to programming resistance training. creator: Daniel Plotkin creator: Max Coleman creator: Derrick Van Every creator: Jaime Maldonado creator: Douglas Oberlin creator: Michael Israetel creator: Jared Feather creator: Andrew Alto creator: Andrew D. Vigotsky creator: Brad J. Schoenfeld uri: https://doi.org/10.7717/peerj.14142 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Plotkin et al. title: Exercise interventions in migraine patients: a YouTube content analysis study based on grades of recommendation link: https://peerj.com/articles/14150 last-modified: 2022-09-30 description: BackgroundMigraine is the second leading cause of disability worldwide, engendering a high economic cost in developed countries. The adverse events related to pharmacological treatment use have increased interest in non-pharmacological interventions such as exercise. YouTube offers a public source of information for migraine patients regarding exercise interventions for migraine improvement. However, this information has not been validated to ensure the quality and validity of its content.ObjectiveThis qualitative content analysis study aims to review and evaluate YouTube videos regarding exercise for migraine.MethodsA systematic review of the current evidence regarding exercise for migraine was performed to establish evidence classification and grades of recommendation with the Scottish Intercollegiate Guidelines Network tool. The data sources were PubMed, PEDro, Cochrane, EBSCO, Google Scholar and Web of Science. The quality of YouTube videos on exercise in migraine was reviewed using the Global Quality Scale and DISCERN scale. Finally, the classification in grades of recommendation was used to evaluate the included videos in terms of the various exercise modalities.ResultsThe classification into recommendation grades showed a grade B for aerobic exercise, yoga and changes in lifestyle behavior regarding exercise. A total of 129 videos were included. The healthcare and exercise professional authors produced higher quality videos with a significant statistical difference, although the alternative therapists and patients’ videos had a greater impact and a higher viewership based on correlation analysis. The evaluation of the videos based on the recommendation grades could only include 90 videos. 71% of these videos showed a B grade of recommendation, which corresponded to fewer than half of the total included videos.ConclusionsYouTube needs higher quality videos on exercise for migraine, and healthcare and exercise professional authors need to improve their scoping strategies to acquire more views. The authors of YouTube videos should have better access to the best current evidence regarding exercise interventions in migraine. creator: Álvaro Reina-Varona creator: Borja Rodríguez de Rivera-Romero creator: Carlos Donato Cabrera-López creator: José Fierro-Marrero creator: Irene Sánchez-Ruiz creator: Roy La Touche uri: https://doi.org/10.7717/peerj.14150 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Reina-Varona et al. title: Optimal selection of COVID-19 vaccination sites in the Philippines at the municipal level link: https://peerj.com/articles/14151 last-modified: 2022-09-30 description: In this work, we present an approach to determine the optimal location of coronavirus disease 2019 (COVID-19) vaccination sites at the municipal level. We assume that each municipality is subdivided into smaller administrative units, which we refer to as barangays. The proposed method solves a minimization problem arising from a facility location problem, which is formulated based on the proximity of the vaccination sites to the barangays, the number of COVID-19 cases, and the population densities of the barangays. These objectives are formulated as a single optimization problem. As an alternative decision support tool, we develop a bi-objective optimization problem that considers distance and population coverage. Lastly, we propose a dynamic optimization approach that recalculates the optimal vaccination sites to account for the changes in the population of the barangays that have completed their vaccination program. A numerical scheme that solves the optimization problems is presented and the detailed description of the algorithms, which are coded in Python and MATLAB, are uploaded to a public repository. As an illustration, we apply our method to determine the optimal location of vaccination sites in San Juan, a municipality in the province of Batangas, in the Philippines. We hope that this study may guide the local government units in coming up with strategic and accessible plans for vaccine administration. creator: Kurt Izak Cabanilla creator: Erika Antonette T. Enriquez creator: Arrianne Crystal Velasco creator: Victoria May P. Mendoza creator: Renier Mendoza uri: https://doi.org/10.7717/peerj.14151 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cabanilla et al. title: Mode-specific effects of concentric and eccentric isokinetic training of the hamstring muscle at slow angular velocity on the functional hamstrings-to-quadriceps ratio-a randomized trial link: https://peerj.com/articles/13842 last-modified: 2022-09-29 description: BackgroundPrevious studies have examined the mode specificity of eccentric and concentric isokinetic training, but have reported conflicting results. Few studies have reported that eccentric and concentric isokinetic training are mode-specific, i.e., they will increase only the eccentric or concentric strength, respectively. Other studies have reported that mode specificity does not exist. Therefore, this study aimed to assess the mode-specific effects of eccentric and concentric isokinetic training of the hamstring muscle at slow angular velocity on eccentric peak torque of the hamstring (PTecc), concentric peak torque of the quadriceps (PTcon), acceleration time of the hamstring (AThams) and quadriceps (ATquad), deceleration time of the hamstring (DThams) and quadriceps (DTquad), time to peak torque of the hamstring (TPThams) and quadriceps (TPTquad), and functional Hamstring-to-Quadriceps ratio (PTecc/PTcon).SubjectsA total of 30 participants were randomly divided into eccentric and concentric groups.MethodsTwo groups pre-test-post-test experimental design was used. In the eccentric and concentric groups, eccentric and concentric isokinetic training of hamstring muscle was performed respectively, at an angular velocity of 60°/s for 6 weeks duration. PTecc, PTcon, AThams, ATquad, DThams, DTquad, TPThams, TPTquad, and PTecc/PTcon were measured before and after the completion of training.ResultsIn the eccentric group, a significant difference (p < 0.05) was observed in PTecc (increased by 21.55%), AThams (decreased by 42.33%), ATquad (decreased by 28.74%), and PTecc/PTcon (increased by 17.59%). No significant difference (p > 0.05) was observed in PTcon, TPThams, TPTquad, DThams, and DTquad. In the concentric group, a significant difference (p < 0.05) was observed in PTecc (increased by 12.95%), AThams (decreased by 27.38%) ATquad (decreased by 22.08%), DTquad (decreased by 26.86%), and PTecc/PTcon (increased by 8.35%). No significant difference (p > 0.05) was observed in PTquad, TPThams, TPTquad, and DThams. Between-group analysis revealed a significant difference (p < 0.05) only in TPTquad; otherwise, in the rest of the parameters, no significant difference (p > 0.05) was observed.ConclusionsBoth eccentric and concentric isokinetic training of the hamstring for 6 weeks increased PTecc, PTecc/PTcon, and decreased AThams and ATquad. The effects of eccentric and concentric isokinetic training of the hamstring on PTecc, PTecc/PTcon, AThams, and ATquad were not mode specific. creator: Kushla Nand Sharma creator: Nishat Quddus creator: Unaise Abdul Hameed creator: Sohrab Ahmad Khan creator: Anita Kumari creator: Ahmad H. Alghadir creator: Masood Khan uri: https://doi.org/10.7717/peerj.13842 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sharma et al. title: The preclinical pharmacological study of a novel intravenous anesthetic, ET-26 hydrochloride, in aged rats link: https://peerj.com/articles/13995 last-modified: 2022-09-29 description: BackgroundET-26 hydrochloride (ET-26HCl) is a novel analogue of etomidate approved for clinical trials. However, all results from recent studies were accomplished in young adult animals. The objective of this study was to evaluate the efficacy and safety of ET-26HCl in aged rats.MethodsAged Sprague-Dawley rats were randomly divided into three groups (three males and three females in each group) were given dose of two-fold of median effective dose (ED50) of ET-26HCl, etomidate and propofol: the measurements of loss of the righting reflex (LORR) and cardiovascular and respiratory function after injection at the two-fold dose of the median effective dose were used for evaluation of effectiveness and safety, and the modified adrenocorticotropic hormone-stimulation experiment was used to evaluate the inhibition effect of the drugs on the synthesis of adrenal cortical hormones.ResultsThere was no significant difference in the onset time among propofol, etomidate and ET-26HCl. The duration of propofol (850.5 ± 77.4 s) was significantly longer than that caused by etomidate (489.8 ± 77.0 s, p = 0.007) and ET-26HCl (347.3 ± 49.0 s, p = 0.0004). No significant difference was observed in the time to stand and normal activity among drugs. A total of 66.7% of rats in the ET-26HCl group were evaluated to have mild hematuria. Then, etomidate and ET-26HCl had a milder blood pressure inhibition effect than propofol. Apnea was observed in all rats administered propofol and the duration for this side effect was 45.0 ± 9.0 s. For etomidate and ET-26HCl, no apnea was observed. No other clinical signs of side-effect were observed, and no rats died. No significant difference was observed in corticosterone concentrations between ET-26HCl and solvent group. However, rats administered etomidate had lower corticosterone concentrations than those administered ET-26HCl at 15, 30, and 60 min.ConclusionsOur results indicate ET-26HCl in aged rats is an effective sedative-hypnotic with stable myocardial and respiratory performance and also have mild adrenocortical suppression. Thus, these findings increase the potential for the clinical use of ET-26HCl in the elderly population. creator: Pan Chang creator: YongWei Su creator: DeYing Gong creator: Yi Kang creator: Jin Liu creator: YuJun Zhang creator: Wen-sheng Zhang uri: https://doi.org/10.7717/peerj.13995 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Chang et al. title: Analysis of genetic diversity among Chinese Cyclocybe chaxingu strains using ISSR and SRAP markers link: https://peerj.com/articles/14037 last-modified: 2022-09-29 description: BackgroundCyclocybe chaxingu is an edible and medicinal fungal species commonly cultivated in China. The major problems currently facing by growers of C. chaxingu is the random labeling of strains and strains aging and degeneration. Therefore, an evaluation of genetic diversity is essential for the conservation and reproducing programs of this species.MethodsIn the present study, 24 widely cultivated strains were collected from the main producing areas of China, and the genetic diversity analysis was performed. DNA polymorphism among these Chinese C. chaxingu strains was analyzed using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers.ResultsEight ISSR primers amplified a total of 75 DNA fragments of which 61 (81.33%) were polymorphic. Fifteen SRAP primer combinations amplified 166 fragments of which 132 (79.52%) were polymorphic. Cluster analysis showed that the C. chaxnigu strains fall into five groups with a genetic distance values ranging from 0.06 to 0.60 by ISSR analysis, while the SRAP analysis divided the test strains into four groups within the range of genetic distance from 0.03 to 0.57. The results of the present study reveal a high level of genetic diversity among the widely cultivated C. chaxingu strains. creator: Jin-Hao Liu creator: Fang-Hui Ding creator: Hai-Yan Song creator: Ming-Hui Chen creator: Dian-Ming Hu uri: https://doi.org/10.7717/peerj.14037 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Macrophages play a key role in tissue repair and regeneration link: https://peerj.com/articles/14053 last-modified: 2022-09-29 description: Tissue regeneration after body injury has always been a complex problem to resolve for mammals. In adult mammals, the repair process after tissue injury is often accompanied by continuous and extensive fibrosis, which leads to scars. This process has been shown to severely hinder regeneration. Macrophages, as widely distributed innate immune cells, not only play an important role in various pathological processes, but also participate in the repair process before tissue regeneration and coordinate the regeneration process after repair. This review will discuss the various forms and indispensability of macrophages involved in repair and regeneration, and how macrophages play a role in the repair and regeneration of different tissues. creator: Yajie Yu creator: Zhongyu Yue creator: Mengli Xu creator: Meiling Zhang creator: Xue Shen creator: Zihan Ma creator: Juan Li creator: Xin Xie uri: https://doi.org/10.7717/peerj.14053 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yu et al. title: The validity and reliability of the Test of Memory Strategies among Italian healthy adults link: https://peerj.com/articles/14059 last-modified: 2022-09-29 description: BackgroundPrevious literature has shown that executive functions (EF) are related to performance in memory (M) tasks. Nevertheless, there is a shortage of psychometric tests that examine these two constructs simultaneously. The Test of Memory Strategies (TMS; previously validated in Spain and Portugal) could be a useful verbal learning task that evaluates these two constructs at once. In this study, we aimed to evaluate the psychometric properties of the TMS in an Italian adult sample.MethodOne hundred twenty-one healthy volunteers (74 F, Mean age = 45.9 years old, SD = 20.4) who underwent a neuropsychological examination participated in this study. We conducted a Confirmatory factor analysis (CFA) to evaluate the structural validity of the TMS. We conducted a latent variable analysis to examine convergent and discriminant validity of the TMS sub-scale scores reflecting executive functions and memory. We also examined the TMS reliability in terms of internal consistency through the McDonald’s omega.ResultsThe CFA confirmed the expectation that the TMS-1 and TMS-2 subtests reflect a factor and that the TMS-3, TMS-4, and TMS-5 subtests reflect a different factor. This result is in line with the prediction that TMS-1 and TMS-2 require the use of executive functions and memory simultaneously, and therefore we called this factor executive functions (EF); whereas the TMS-3, TMS-4, and TMS-5 subtests require less involvement of executive functions, thus reflecting a construct that we named memory (M). The TMS subtests for EF and M showed convergent validity with the test scores using a traditional neuropsychological battery, assessing memory and executive functions separately. Finally, the reliability of the subtests was good.ConclusionsThese preliminary findings suggest that TMS is a valid and reliable scale to simultaneously assess M and EF while among Italian healthy adults. creator: Maria Grazia Vaccaro creator: Marco Tullio Liuzza creator: Massimiliano Pastore creator: Nuria Paúl creator: Raquel Yubero creator: Andrea Quattrone creator: Gabriella Antonucci creator: Antonio Gambardella creator: Fernando Maestú uri: https://doi.org/10.7717/peerj.14059 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Vaccaro et al. title: A spectacular new species of Hyloscirtus (Anura: Hylidae) from the Cordillera de Los Llanganates in the eastern Andes of Ecuador link: https://peerj.com/articles/14066 last-modified: 2022-09-29 description: We have discovered a spectacular new species of frog in the genus Hyloscirtus, belonging to the H. larinopygion species group. The adult female is characterized by a mostly black body with large bright red spots on the dorsal and ventral surface, extremities, and toe pads. The adult male is unknown. Small juveniles are characterized by a yellow body with variable black markings on the flanks; while one larger juvenile displayed irregular orange or yellow marks on a black background color, with light orange or yellow toe pads. Additional distinctive external morphological features such as cloacal ornamentation are described, and some osteological details are imaged and analyzed. The performed phylogeny places the new species as the sister to a clade consisting of ten taxa, all of which are part of the H. larinopygion group. We use genetic distances to fit the new species into a published time-calibrated phylogeny of this group; our analysis based on the published chronology suggests that the divergence of the new species from its known congeners pre-dates the Quaternary period. The new species is currently only known only from Cerro Mayordomo, in Fundación EcoMinga´s Machay Reserve, at 2,900 m in the eastern Andes of Tungurahua province, Ecuador, near the southern edge of Los Llanganates National Park, but its real distribution may be larger. creator: Juan P. Reyes-Puig creator: Darwin Recalde creator: Fausto Recalde creator: Claudia Koch creator: Juan M. Guayasamin creator: Diego F. Cisneros-Heredia creator: Lou Jost creator: Mario H. Yánez-Muñoz uri: https://doi.org/10.7717/peerj.14066 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Reyes-Puig et al. title: Evaluation of total immunoglobulin G and subclass antibodies in an enzyme-linked immunosorbent assay for serodiagnosis of human amebic liver abscess link: https://peerj.com/articles/14085 last-modified: 2022-09-29 description: BackgroundAmebic liver abscess (ALA) caused by Entamoeba histolytica is usually diagnosed based on its clinical symptoms, medical imaging abnormalities of the liver, and serological tests, the most common being the enzyme-linked immunosorbent assay (ELISA). For more than three decades, no investigation has evaluated the diagnostic performance of immunoglobulin G (IgG) subclasses in the serodiagnosis of ALA. Herein, we assessed the efficiencies of anti-amebic IgG and IgG subclasses for diagnosing ALA.MethodsA serological ELISA-based test was performed to assess its diagnostic performance using a total of 330 serum samples from ALA patients (n = 14), healthy individuals (n = 40), and patients with other diseases (n = 276).ResultsELISA targeting the total IgG antibody to E. histolytica antigen exhibited 100% sensitivity 95% CI [76.8–100.0] and 97.8% specificity 95% CI [95.5–99.1], whereas the assay targeting IgG1 showed the same sensitivity (100% 95% CI [76.8–100.0]) and a slightly higher specificity (99.1% 95% CI [97.3–99.8]). The other IgG subclasses (IgG2, IgG3, and IgG4) displayed a lower sensitivity and specificity. The sensitivity and specificity did not significantly differ between tests measuring total IgG and IgG1 (Exact McNemar’s test; p > 0.05), with a concordance of 98.2%, represented by a Cohen’s kappa of 0.83 (p < 0.001), indicating almost perfect agreement.ConclusionELISA targeting IgG1 can provide valuable information to clinicians in differentiating ALA from other parasitic diseases, cancers, cirrhosis, and viral hepatitis. However, enzyme-conjugated anti-human total IgG is cheaper than anti-human IgG subclasses. Therefore, we suggest that total IgG-based ELISA is sufficient for the routine serodiagnosis of human ALA and possibly other clinical manifestations of invasive amebiasis. creator: Penchom Janwan creator: Lakkhana Sadaow creator: Rutchanee Rodpai creator: Hiroshi Yamasaki creator: Vor Luvira creator: Wattana Sukeepaisarnjaroen creator: Amnat Kitkhuandee creator: Krisada Paonariang creator: Oranuch Sanpool creator: Patcharaporn Boonroumkaew creator: Tongjit Thanchomnang creator: Toshihiro Mita creator: Pewpan M. Intapan creator: Wanchai Maleewong uri: https://doi.org/10.7717/peerj.14085 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Janwan et al. title: Physiological, biochemical and phytohormone responses of Elymus nutans to α-pinene-induced allelopathy link: https://peerj.com/articles/14100 last-modified: 2022-09-29 description: The α-pinene is the main allelochemical of many weeds that inhibit the growth of Elymus nutans, an important forage and ecological restoration herbage. However, the response changes of α-pinene-induced allelopathy to E. nutans is still unclear. Here, we investigated the physiological, biochemical and phytohormone changes of E. nutans exposed to different α-pinene concentrations. The α-pinene-stress had no significant effect on height and fresh weight (FW) of seedlings. The water-soluble proteins, the soluble sugars and proline (Pro) strengthened seedlings immunity at 5 and 10 µL L−1α-pinene. Superoxide dismutase (SOD) and ascorbate peroxidase (APX) increased at 5 µL L−1α-pinene to resist stress. APX reduced the membrane lipid peroxidation quickly at 10 µL L−1α-pinene. The high-activity of peroxidase (POD), APX along with the high level of GSH contributed to the cellular redox equilibrium at 15 µL L−1α-pinene. The POD, glutathione reductase (GR) activity and glutathione (GSH) level remained stable at 20 µL L−1α-pinene. The changes in antioxidant enzymes and antioxidants indicated that E. nutans was effective in counteracting the harmful effects generated by hydrogen peroxide (H2O2). The α-pinene caused severe phytotoxic effects in E. nutans seedlings at 15 and 20 µL L−1. Endogenous signal nitric oxide (NO) and cell membrane damage product Pro accumulated in leaves of E. nutans seedlings at 15 and 20 µL L−1α-pinene, while lipid peroxidation product malondialdehyde (MDA) accumulated. The chlorophylls (Chls), chlorophyll a (Chl a), chlorophyll b (Chl b) content decreased, and biomass of seedlings was severely inhibited at 20 µL L−1α-pinene. The α-pinene caused phytotoxic effects on E. nutans seedlings mainly through breaking the balance of the membrane system rather than with reactive oxygen species (ROS) productionat 15 and 20 µL L−1α-pinene. Additionally, phytohormone levels were altered by α-pinene-stress. Abscisic acid (ABA) and indole acetic acid (IAA) of E. nutans seedlings were sensitive to α-pinene. As for the degree of α-pinene stress, salicylic acid (SA) and jasmonic acid (JA) played an important role in resisting allelopathic effects at 15 µL L−1α-pinene. The ABA, Zeatin, SA, gibberellin 7 (GA7), JA and IAA levels increased at 20 µL L−1α-pinene. The α-pinene had a greatest impact on ABA and IAA levels. Collectively, our results suggest that E. nutans seedlings were effective in counteracting the harmful effects at 5 and 10 µL L−1α-pinene, and they were severely stressed at 15 and 20 µL L−1α-pinene. Our findings provided references for understanding the allelopathic mechanism about allelochemicals to plants. creator: Mengci Chen creator: Youming Qiao creator: Xiaolong Quan creator: Huilan Shi creator: Zhonghua Duan uri: https://doi.org/10.7717/peerj.14100 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: Mutualist- and antagonist-mediated selection contribute to trait diversification of flowers link: https://peerj.com/articles/14107 last-modified: 2022-09-29 description: Flowers are generally short-lived, and they all face a multidimensional challenge because they have to attract mutualists, compel them to vector pollen with minimal investment in rewards, and repel floral enemies during this short time window. Their displays are under complex selection, either consistent or conflicting, to maximize reproductive fitness under heterogeneous environments. The phenological or morphological mismatches between flowers and visitors will influence interspecific competition, resource access, mating success and, ultimately, population and community dynamics. To better understand the effects of the plant visitors on floral traits, it is necessary to determine the functional significance of specific floral traits for the visitors; how plants respond to both mutualists and antagonists through adaptive changes; and to evaluate the net fitness effects of biological mutualisms and antagonism on plants. In this review, we bring together insights from fields as diverse as floral biology, insect behavioral responses, and evolutionary biology to explain the processes and patterns of floral diversity evolution. Then, we discuss the ecological significance of plant responses to mutualists and antagonists from a community perspective, and propose a set of research questions that can guide the research field to integrate studies of plant defense and reproduction. creator: Luyao Huang creator: Yang Liu creator: Liwen Dou creator: Shaobin Pan creator: Zhuangzhuang Li creator: Jin Zhang creator: Jia Li uri: https://doi.org/10.7717/peerj.14107 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Huang et al. title: Cold water and harmful algal blooms linked to coral reef collapse in the Eastern Tropical Pacific link: https://peerj.com/articles/14081 last-modified: 2022-09-28 description: BackgroundWith conventional coral reef conservation methods proving ineffective against intensifying climate change, efforts have focussed on augmenting coral tolerance to warmer water—the primary driver of coral declines. We document coral cover and composition in relation to sea surface temperature (SST) over 25-years, of six marginal reefs in an upwelling area of Costa Rica’s Eastern Tropical Pacific.MethodsUsing reef survey data and sea surface temperature (SST) dating back over 25-years, we document coral cover and composition of six marginal reefs in an upwelling area of Costa Rica’s Eastern Tropical Pacific in relation to thermal highs and lows.Results.A ubiquitous and catastrophic coral die-off event occurred in 2009, driven by SST minima and likely by the presence of extreme harmful algal blooms. Coral cover was dramatically reduced and coral composition shifted from dominant branching Pocillopora to massive Pavona, Porites, and Gardineroseris. The lack of coral recovery in the decade since indicates a breach in ecosystem tipping-point and highlights a need for resilience-based management (RBM) and restoration. We propose a locally tailored and globally scalable approach to coral reef declines that is founded in RBM and informed by coral health dynamics. creator: Caroline Palmer creator: Carlos Jimenez creator: Giovanni Bassey creator: Eleazar Ruiz creator: Tatiana Villalobos Cubero creator: Maria Marta Chavarria Diaz creator: Xavier A. Harrison creator: Robert Puschendorf uri: https://doi.org/10.7717/peerj.14081 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Palmer et al. title: A phylogenetic analysis of Bromus (Poaceae: Pooideae: Bromeae) based on nuclear ribosomal and plastid data, with a focus on Bromus sect. Bromus link: https://peerj.com/articles/13884 last-modified: 2022-09-28 description: To investigate phylogenetic relationships among and within major lineages of Bromus, with focus on Bromus sect. Bromus, we analyzed DNA sequences from two nuclear ribosomal (ITS, ETS) and two plastid (rpl32-trnLUAG, matK) regions. We sampled 103 ingroup accessions representing 26 taxa of B. section Bromus and 15 species of other Bromus sections. Our analyses confirm the monophyly of Bromus s.l. and identify incongruence between nuclear ribosomal and plastid data partitions for relationships within and among major Bromus lineages. Results support classification of B. pumilio and B. gracillimus within B. sect. Boissiera and B. sect. Nevskiella, respectively. These species are sister groups and are closely related to B. densus (B. sect. Mexibromus) in nrDNA trees and Bromus sect. Ceratochloa in plastid trees. Bromus sect. Bromopsis is paraphyletic. In nrDNA trees, species of Bromus sects. Bromopsis, Ceratochloa, Neobromus, and Genea plus B. rechingeri of B. sect. Bromus form a clade, in which B. tomentellus is sister to a B. sect. Genea–B. rechingeri clade. In the plastid trees, by contrast, B. sect. Bromopsis species except B. tomentosus form a clade, and B. tomentosus is sister to a clade comprising B. sect. Bromus and B. sect. Genea species. Affinities of B. gedrosianus, B. pulchellus, and B. rechingeri (members of the B. pectinatus complex), as well as B. oxyodon and B. sewerzowii, are discordant between nrDNA and plastid trees. We infer these species may have obtained their plastomes via chloroplast capture from species of B. sect. Bromus and B. sect. Genea. Within B. sect. Bromus, B. alopecuros subsp. caroli-henrici, a clade comprising B. hordeaceus and B. interruptus, and B. scoparius are successive sister groups to the rest of the section in the nrDNA phylogeny. Most relationships among the remaining species of B. sect. Bromus are unresolved in the nrDNA and plastid trees. Given these results, we infer that most B. sect. Bromus species likely diversified relatively recently. None of the subdivisional taxa proposed for Bromus sect. Bromus over the last century correspond to natural groups identified in our phylogenetic analyses except for a group including B. hordeaceus and B. interruptus. creator: Akram Nasiri creator: Shahrokh Kazempour-Osaloo creator: Behnam Hamzehee creator: Roger D. Bull creator: Jeffery M. Saarela uri: https://doi.org/10.7717/peerj.13884 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Nasiri et al. title: High resolution thermal remote sensing and the limits of species’ tolerance link: https://peerj.com/articles/13911 last-modified: 2022-09-28 description: Extinction risks for many insect species, particularly across very broad spatial extents, have been linked to the growing frequency and severity of temperatures that exceed the boundaries of their realized niches. Measurement and mitigation of such impacts is hindered by the availability of high-resolution measurements of species-specific severity of extreme weather, especially temperature. While techniques enabling interpolation of broad-scale remote sensing metrics are vital for such efforts, direct remote sensing measurements of thermal conditions could improve habitat management by providing detailed insights that interpolative approaches cannot. Advances in unmanned aerial vehicle (UAV) technology have created opportunities to better evaluate the role of microclimates in local species extinctions. Here, we develop a method to create high-resolution maps of microclimates using UAV and thermal imaging technology that use species’ realized niche boundaries to assess potential effects of severity of extreme temperatures. We generated air temperature maps (5 cm resolution) and canopy height maps (1 cm resolution) for 15 sites in a rare alvar ecosystem in eastern Ontario. We validated these remote sensing observations against independent, in situ temperature observations using iButtons. Temperature observations were accurate and related to physical heterogeneity in alvar habitats. We converted temperature measures into estimates of proximity of thermal niche boundaries for three butterfly species found during field surveys. This is the first time that this method has been applied to high resolution remote sensing observations and offers potential to assess the availability and adequacy of microclimates within habitats at resolutions relevant for conservation management. creator: Gabrielle Ednie creator: Jeremy T. Kerr uri: https://doi.org/10.7717/peerj.13911 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ednie and Kerr title: Evaluation of knowledge and barriers of influenza vaccine uptake among university students in Saudi Arabia; a cross-sectional analysis link: https://peerj.com/articles/13959 last-modified: 2022-09-28 description: BackgroundInfluenza vaccine hesitancy is a significant threat to global maneuvers for reducing the burden of seasonal and pandemic influenza. This study estimated the vaccine uptake, barriers, and willingness for influenza vaccines among university students in Saudi Arabia.MethodsA cross-sectional survey was conducted among health science (HS) and non-health science (NHS) university students. A 31-item questionnaire was used to ascertain the vaccination rate, barriers, and willingness for the flu vaccine.ResultsThis study included 790 students (mean age: 21.40 ± 1.94 years), 246 (31.1%) from HS and 544 (68.9%) from NHS disciplines. About 70% did not take flu shots before the arrival of the winter. The mean knowledge score was 7.81 ± 1.96, where 20.4%, 67.6%, and 12% of respondents had good, moderate, and poor knowledge regarding flu vaccines. The relative importance index (RII) analysis showed a lack of recommendation from physicians (51.5%, RI ranked: 1) was a top-ranked barrier to vaccine uptake, followed by negative perceptions and accessibility issues. Only 36.6% of the participants were willing to get vaccinated every year, 70% were willing to receive a vaccine on their doctor’s recommendations, and 46% agreed to vaccinate if vaccines were freely available in the university. The knowledge, barriers, and willingness widely varied across students from two disciplines.ConclusionsOur analysis underscored low flu vaccine uptake among university students. In addition, the study participants’ knowledge was unsatisfactory, and they were less inclined to receive the flu vaccine in the future. Lack of recommendation from the physicians, negative perceptions towards the flu vaccine, and difficult accessibility were found as significant barriers to the vaccine uptake. A multidimensional approach at educational institutes to cover the knowledge gap and address the barriers curtailing the vaccination rate among students is recommended. creator: Tauqeer Hussain Mallhi creator: Nida Bokharee creator: Munnaza Bukhsh creator: Yusra Habib Khan creator: Abdulaziz Ibrahim Alzarea creator: Faiz Ullah Khan creator: Salah-Ud-Din Khan creator: Nasser Hadal Alotaibi creator: Abdullah Salah Alanazi creator: Muhammad Hammad Butt creator: Ahmed D. Alatawi creator: Muhammad Shahid Iqbal uri: https://doi.org/10.7717/peerj.13959 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mallhi et al. title: Associations between pro-inflammatory cytokines and fatigue in pregnant women link: https://peerj.com/articles/13965 last-modified: 2022-09-28 description: BackgroundFatigue is one of the most prevalent symptoms among pregnant women. In patients with various diseases, pro-inflammatory cytokines are associated with fatigue; however, such associations are unknown in pregnant women.ObjectivesThe objective of this study was to examine the associations between pro-inflammatory cytokines and prenatal fatigue.MethodsA cross-sectional study was conducted on 271 pregnant Chinese women in their third trimester of pregnancy. Patient-reported Outcome Measurement Information System (PROMIS) was used to evaluate women’s prenatal fatigue. Using enzyme-linked immunosorbent assay (ELISA), the serum concentrations of four pro-inflammatory cytokines, including tumor necrosis factor alpha (TNF-α), interleukin 1 beta (IL-1β), interleukin 6 (IL-6) and interleukin 8 (IL-8), were measured. The data was analyzed by correlation analysis and general linear regression analysis.ResultsIn this sample, the mean (standard deviation) of fatigue scores was 51.94 (10.79). TNF-α (r = 0.21, p < 0.001), IL-6 (r = 0.134, p = 0.027) and IL-8 (r = 0.209, p = 0.001) were positively correlated to prenatal fatigue, although IL-1β was not. TNF-α (β = 0.263, p < 0.001), along with sleep quality (β = 0.27, p < 0.001) and depression (β = 0.376, p < 0.001) independently predicted prenatal fatigue.ConclusionsTNF-α was identified as an independent biomarker for prenatal fatigue in our study. Reducing pro-inflammatory cytokines may be a unique method for lowering prenatal fatigue and, consequently, enhancing mother and child health. creator: Haiou Xia creator: Xiaoxiao Zhu creator: Chunxiang Zhu uri: https://doi.org/10.7717/peerj.13965 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xia et al. title: Effects of grazing strategy on facultative grassland bird nesting on native grassland pastures of the Mid-South USA link: https://peerj.com/articles/13968 last-modified: 2022-09-28 description: Understanding how livestock grazing strategies of native warm season grasses (NWSG) can impact facultative grassland bird nesting can provide insight for conservation efforts. We compared pre and post treatment effects of rotational grazing (ROT) and patch-burn grazing (PBG) for facultative grassland bird species nest success and nest-site selection on NWSG pastures at three Mid-South research sites. We established 14, 9.7 ha NWSG pastures and randomly assigned each to either ROT or PBG and monitored avian nest-site selection and nest success, 2014–2016. We collected nesting and vegetation data in 2014, before treatment implementation, as an experimental pre-treatment. We implemented treatments across all research sites in spring 2015. We used a step-wise model selection framework to estimate treatment effect for ROT or PBG on avian nest daily survival rate (DSR) and resource selection function (RSF) at the temporal scale and within-field variables. Daily survival rates were 0.93% (SE = 0.006) for field sparrow (Spizella pusilla), 0.96% (SE = 0.008) for red-winged blackbird (Agelaius phoeniceus), and 0.92% (SE = 0.01) for indigo bunting (Passerina cyanea). Model support for PBG treatment and vegetation height were indicated as negative and positive influences for field sparrow DSR, respectively. Red-winged blackbirds’ DSR were negatively influenced by ROT while vegetation height positively affected DSR, and DSR for indigo bunting did not differ among treatments. Combined RSF models indicated nest-site selection for all species was positively related to vegetation height and only weakly associated with other within-field variables. We provide evidence that ROT and/or PBG effects vary by species for DSR for these three facultative grassland birds, and vegetation characteristics affected their nest-site selection in the Mid-South USA. A lack of disturbance in Mid-South grasslands can lead to higher successional stages (i.e., mix shrub-grassland), but some combination of ROT, PBG, and unburned/ungrazed areas can provide adequate nesting habitat on small pasture lands (∼1.8 –7.8 ha) for various facultative grassland birds and potentially offer the opportunity to simultaneously maintain livestock production and grassland bird nesting habitat. creator: Byron R. Buckley creator: Christopher M. Lituma creator: Patrick D. Keyser creator: Elizabeth D. Holcomb creator: Ray Smith creator: John J. Morgan creator: Roger D. Applegate uri: https://doi.org/10.7717/peerj.13968 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Buckley et al. title: Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii) link: https://peerj.com/articles/13981 last-modified: 2022-09-28 description: The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. However, the characteristics of the bHLH gene family in the tung tree genome are still unclear. Hence, VfbHLHs were first searched at a genome-wide level, and their expression levels in various tissues or under low temperature were investigated systematically. In this study, we identified 104 VfbHLHs in the tung tree genome, and these genes were classified into 18 subfamilies according to bHLH domains. Ninety-eight VfbHLHs were mapped to but not evenly distributed on 11 pseudochromosomes. The domain sequences among VfbHLHs were highly conserved, and their conserved residues were also identified. To explore their expression, we performed gene expression profiling using RNA-Seq and RT-qPCR. We identified five, 18 and 28 VfbHLH genes in female flowers, male flowers and seeds, respectively. Furthermore, we found that eight genes (VfbHLH29, VfbHLH31, VfbHLH47, VfbHLH51, VfbHLH57, VfbHLH59, VfbHLH70, VfbHLH72) were significant differential expressed in roots, leaves and petioles under low temperature stress. This study lays the foundation for future studies on bHLH gene cloning, transgenes, and biological mechanisms. creator: Wenjuan Liu creator: Yaqi Yi creator: Jingyi Zhuang creator: Chang Ge creator: Yunpeng Cao creator: Lin Zhang creator: Meilan Liu uri: https://doi.org/10.7717/peerj.13981 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: When aggressiveness could be too risky: linking personality traits and predator response in superb fairy-wrens link: https://peerj.com/articles/14011 last-modified: 2022-09-28 description: Personality syndromes in animals may have adaptive benefits for survival. For example, while engaging in predator deterrence, reactive individuals tend to prioritise their own survival, while proactive individuals engage in riskier behaviours. Studies linking animal personality measured in captivity with individual fitness or behaviours in the wild are sparse, which is a gap in knowledge this study aims to address. We used playback experiments in superb fairy-wrens (Malurus cyaneus), a common Australian songbird with a cooperative breeding system, to assess whether three personality traits measured during short-term captivity correlated with behavioural responses in the wild to a perceived nest and adult predator, the grey currawong (Strepera versicolor). We used three standard measures of personality in birds: struggle responses to human handling (boldness), exploration during a novel environment test, and aggressiveness during a mirror presentation. Superb fairy-wrens showed a significantly stronger response to the predator playback than to the control (willie wagtail, Rhipidura leucophrys) playback, suggesting that they recognised the predator playback as a threat without any accompanying visual stimulus. Birds that attacked their mirror image during the mirror presentation and those that spent a moderate amount of time close to the mirror responded more strongly to predator playback (by approaching the speaker faster and closer, spending more time near the speaker, and being more likely to alarm call) compared to those with low aggressiveness or those that spent very short or long durations close to the mirror. Neither boldness nor exploration in the novel environment test predicted playback response. Our results align with a growing number of studies across species showing the importance of animal personalities as factors for fitness and survival. creator: Jack Bilby creator: Diane Colombelli-Négrel creator: Andrew C. Katsis creator: Sonia Kleindorfer uri: https://doi.org/10.7717/peerj.14011 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bilby et al. title: Description and complete mitochondrial genome of Atkinsoniella zizhongi sp. nov. (Hemiptera: Cicadellidae: Cicadellinae) from China and its phylogenetic implications link: https://peerj.com/articles/14026 last-modified: 2022-09-28 description: A new species, Atkinsoniella zizhongi sp. nov. of the subfamily Cicadellinae, was described and illustrated from China. The new species is similar to A. nigrominiatula (Jacobi, 1944), A. limba Kuoh, 1991, A. dormana Li, 1992, A. peaka Yang, Meng et Li, 2017, and A. divaricata Yang, Meng et Li, 2017. But the characteristics of aedeagus and pygofer process can be used to distinguish them easily. The complete mitochondrial genome of the paratype was sequenced and assembled. The mitogenome of A. zizhongi sp. nov. was 16,483 bp in length, with an A+T content of 75.9%, containing 37 typical genes and a control region (CR). The gene order was consistent with the inferred insect ancestral mitochondrial genome. All of the PCGs were determined to have the typical stop codon TAA or TAG, while COX2 and ND5 ended with incomplete termination codons T and TA, respectively. In addition, phylogenetic trees were reconstructed based on PCGs and rRNAs using both the maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that the intergeneric and interspecific relationships within the subfamily Cicadellinae were completely consistent in all of the phylogenetic trees, except that the different interspecific relationships within the genus Bothrogonia were detected in the ML analysis based on the amino acid sequences. This study enriches the species diversity of Cicadellinae and further promotes research on its phylogeny. creator: Yan Jiang creator: Hao-Xi Li creator: Xiao-Fei Yu creator: Mao-Fa Yang uri: https://doi.org/10.7717/peerj.14026 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jiang et al. title: Degreasing and bleaching bones using light sources as a tool to increase the safety of teaching osteology at the University of Veterinary Sciences Brno link: https://peerj.com/articles/14036 last-modified: 2022-09-28 description: The key part of creating bone material for teaching is degreasing and whitening it. However, the substances used are often dangerous and toxic. We tested and compared safer methods based on two physical variables. These are light and heat. The material for our study was 45 femurs from 23 adult domestic dogs (Canis lupus f. familiaris). The bones were divided into three groups of 15 pieces according to the method used to remove muscles and ligaments from their surface. Five femurs from each group were exposed to three different light sources for 28 days—sunlight, warm light from a classical incandescent light bulb and cold light by a LED bulb. At regular intervals, the change in the colour of the bone surface and the amount of fat loss from the medullary cavity was also monitored. The best degreasing and bleaching results were achieved in macerated bones exposed to sunlight. They achieved the required condition as early as 21 days after the start of sun exposure. The biggest problem was haemoglobin, which permeated through the Haversian canals and discoloured the bone tissue. The results showed that the use of light and heat is a suitable and safe alternative to chemical methods of degreasing and bleaching bones. The disadvantage is the length of time, especially for native material. creator: Ondřej Horák creator: Martin Pyszko creator: Václav Páral creator: Ondřej Šandor uri: https://doi.org/10.7717/peerj.14036 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Horák et al. title: The effect of high and low velocity-based training on the throwing performance of collegiate handball players link: https://peerj.com/articles/14049 last-modified: 2022-09-28 description: BackgroundThe intensity of strength training exercise is generally regarded to be the most essential element in developing muscle strength and power. The exercise intensity of strength training is known as one-repetition maximum (1RM). Velocity-based training (VBT) has been proposed as a different approach for determining training intensity. VBT relies on the use of linear position transducers and inertial measurement units, providing real-time feedback to objectively adjust the exercise intensity based on an athlete’s velocity zone.MethodsThis study investigated the effects of two different training interventions based on individualized load velocity profiles (LVP) on maximal bench press strength (i.e., 1RM), maximum throwing velocity (TV), and skeletal muscle mass (SKMM). Twenty-two university handball players were randomly assigned to Group 1 (low-movement speed training) or Group 2 (high-movement speed training). Group 1 exercised with a bar speed of 0.75–0.96 m/s, which corresponds to a resistance of approximately 60% 1RM, whereas Group 2 trained at 1.03–1.20 m/s, corresponding to a resistance of approximately 40% 1RM. Both groups exercised three times a week for five weeks, with strength and throwing tests performed at baseline and post-intervention.ResultsA two-way repeated measures ANOVA was applied, and the results showed the interaction between group and time was not statistically significant for SKMM (p = 0.537), 1RM (p = 0.883), or TV (p = 0.774). However, both groups significantly improved after the five weeks of training: SKMM (3.1% and 3.5%, p < 0.01), 1RM (15.5% and 15.0%, p < 0.01), and throwing velocity (18.7% and 18.3%, p < 0.01) in Group 1 and 2 respectively. Training at both prescribed velocities in this study elicited similar changes in strength, muscle mass, and throwing velocity. creator: Bassam Abuajwa creator: Mike Hamlin creator: Eliza Hafiz creator: Rizal Razman uri: https://doi.org/10.7717/peerj.14049 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Abuajwa et al. title: Endangered plant species under differing anthropogenic interventions: how to preserve Pterygopleurum neurophyllum in Wondong wetland? link: https://peerj.com/articles/14050 last-modified: 2022-09-28 description: Endangered wetland plants are important as the potential keystone species and mediators for plant-soil interactions. Establishing conservation strategies for endangered plants is also prioritized because of the elevating extinction risk by human-induced wetland disturbances. The present study examined the factors controlling the incidence of Pterygopleurum neurophyllum, the endangered wetland plant experiencing severe habitat loss throughout Northeast Asia. Here, P. neurophyllum populations and their surrounding environments were addressed in the last natural Korean habitat to assess the possible influential factors (vegetation coverage, species richness, exotic plant species, coarse rock content, soil bulk density, and soil electroconductivity and pH) under anthropogenic wetland interventions (with or without soil disturbance). Our results showed that P. neurophyllum occurred 6 out of 32 plots in the study area. All P. neurophyllum were found in Miscanthus-dominated area, but preferred microhabitats featuring reduced vegetation coverage, increased species richness, and undisturbed soils under vegetation removal. Multimodel inference also indicated that vegetation coverage (relative importance = 1.00) and coarse rock content (relative importance = 0.70) were the major influential factors for P. neurophyllum population size, and the surviving P. neurophyllum were strictly limited to where both of them were kept lowered. Furthermore, the wetland intervention with soil disturbance had a negative effect on P. neurophyllum by creating the rocky and compacted soil surface as a result of land reclamation treatments. Conversely, the wetland intervention without soil disturbance enhanced the P. neurophyllum incidence by decreasing vegetation coverage of the overcrowding competitive plants. Overall findings reflect that the strategies to counteract habitat loss and manage the overly dense competitive plants should be necessary for conserving P. neurophyllum, as well as other wetland plants threatened by the human-induced disturbances and excessive competition intensities. creator: Seongjun Kim creator: Hwan-Joon Park creator: Chang Woo Lee creator: Nam Young Kim creator: Jung Eun Hwang creator: Byoung-Doo Lee creator: Hyeong Bin Park creator: Jiae An creator: JuHyoung Baek uri: https://doi.org/10.7717/peerj.14050 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kim et al. title: BRCA1 overexpression attenuates breast cancer cell growth and migration by regulating the pyruvate kinase M2-mediated Warburg effect via the PI3K/AKT signaling pathway link: https://peerj.com/articles/14052 last-modified: 2022-09-28 description: This work explored the mechanism of the effect of breast-cancer susceptibility gene 1 (BRCA1) on the metabolic characteristics of breast cancer cells, including the Warburg effect and its specific signaling. We transfected MCF-7 cells with a BRCA1-encoding LXSN plasmid or PKM2 siRNA and examined cancer cell metabolism using annexin V staining, inhibitory concentration determination, Western blotting, glucose uptake and lactic acid content measurements, and Transwell assays to assess glycolytic activity, cell apoptosis, and migration, and sensitivity to anti-cancer treatment. The BRCA1-expressing MCF-7 cells demonstrated low PKM2 expression and decreased glycolytic activity (downregulated hexokinase 2 (HK2) expression, upregulated isocitrate dehydrogenase 1 (IDH1) expression, and reduced O2 and glucose consumption and lactate production) via regulation of PI3K/AKT pathway compared with the empty LXSN group. BRCA1 transfection slightly increased apoptotic activity, decreased cell migration, and increased the IC50 index for doxorubicin, paclitaxel, and cisplatin. Inhibiting PKM2 using siRNA attenuated the IC50 index for doxorubicin, paclitaxel, and cisplatin compared with the control. Inhibiting PKM2 activated PI3K/AKT signaling, increased apoptosis, and decreased MCF-7 cell migration. Our data suggest that BRCA1 overexpression reverses the Warburg effect, inhibits cancer cell growth and migration, and enhances the sensitivity to anti-cancer treatment by decreasing PKM2 expression regulated by PI3K/AKT signaling. These novel metabolic findings represent a potential mechanism by which BRCA1 exerts its inhibitory effect on breast cancer. creator: Xiuli Liu creator: Hanxu Liu creator: Lei Zeng creator: Yuetao Lv uri: https://doi.org/10.7717/peerj.14052 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: Objective monitoring of functional recovery after total knee and hip arthroplasty using sensor-derived gait measures link: https://peerj.com/articles/14054 last-modified: 2022-09-28 description: BackgroundInertial sensors hold the promise to objectively measure functional recovery after total knee (TKA) and hip arthroplasty (THA), but their value in addition to patient-reported outcome measures (PROMs) has yet to be demonstrated. This study investigated recovery of gait after TKA and THA using inertial sensors, and compared results to recovery of self-reported scores of pain and function.MethodsPROMs and gait parameters were assessed before and at two and fifteen months after TKA (n = 24) and THA (n = 24). Gait parameters were compared with healthy individuals (n = 27) of similar age. Gait data were collected using inertial sensors on the feet, lower back, and trunk. Participants walked for two minutes back and forth over a 6m walkway with 180° turns. PROMs were obtained using the Knee Injury and Osteoarthritis Outcome Scores and Hip Disability and Osteoarthritis Outcome Score.ResultsGait parameters recovered to the level of healthy controls after both TKA and THA. Early improvements were found in gait-related trunk kinematics, while spatiotemporal gait parameters mainly improved between two and fifteen months after TKA and THA. Compared to the large and early improvements found in of PROMs, these gait parameters showed a different trajectory, with a marked discordance between the outcome of both methods at two months post-operatively.ConclusionSensor-derived gait parameters were responsive to TKA and THA, showing different recovery trajectories for spatiotemporal gait parameters and gait-related trunk kinematics. Fifteen months after TKA and THA, there were no remaining gait differences with respect to healthy controls. Given the discordance in recovery trajectories between gait parameters and PROMs, sensor-derived gait parameters seem to carry relevant information for evaluation of physical function that is not captured by self-reported scores. creator: Ramon Boekesteijn creator: José Smolders creator: Vincent Busch creator: Noël Keijsers creator: Alexander Geurts creator: Katrijn Smulders uri: https://doi.org/10.7717/peerj.14054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Boekesteijn et al. title: Comparative mitogenome analysis reveals mitochondrial genome characteristics in eight strains of Beauveria link: https://peerj.com/articles/14067 last-modified: 2022-09-28 description: Despite the significant progress that has been made in the genome sequencing of Beauveria species, mitochondrial genome (mitogenome) used to examine genetic diversity within fungal populations. Complete mitogenomes of Beauveria species can be easily sequenced and assembled using various sequencing techniques. However, since mitogenome annotations are mainly derived from similar species comparison and software prediction, and are not supported by RNA-seq transcripts data, it leads to problems with the accuracy of mitochondrial annotations and the inability to understand RNA processing. In this study, we assembled and annotated the mitogenome of eight Beauveria strains using Illumina DNA and RNA sequencing data. The circular mitogenome of eight Beauveria strains ranged from 26,850 bp (B. caledonica strain ATCC 64970) to 35,999 bp (B. brongniartii strain GYU-BMZ03), with the intronic insertions accounting for most of the size variation, thus contributing to a total mitochondrial genome (mitogenome) size of 7.01% and 28.95%, respectively. Intron number variations were not directly related to the evolutionary relationship distance. Besides ribosomal protein S3 (rps3), most introns are lost too quickly and lack the stability of protein-coding genes. The short RNA-seq reads from next-generation sequencing can improve the mitochondrial annotation accuracy and help study polycistronic transcripts and RNA processing. The transcription initiation sites may be located in the control region. Most introns do not serve as taxonomic markers and also lack open reading frames (ORFs). We assumed that the poly A tail was added to the polycistronic transcript before splicing and one polycistronic transcript (trnM(1)-trnL(1)-trnA-trnF-trnK-trnL(2)-trnQ-trnH-trnM(2)-nad2-nad3-atp9-cox2-trnR(1)-nad4L-nad5-cob-trnC-cox1-trnR(2)-nad1-nad4-atp8-atp6-rns-trnY-trnD-trnS-trnN-cox3-trnG-nad6-trnV-trnI-trnS-trnW-trnP-rnl(rps3)-trnT-trnE-trnM(3)) was first processed from the mitogenome and was subsequently processed into smaller mono-, di-, or tricistronic RNAs. creator: Yu Bai creator: Xuyuan Gao creator: Hui Wang creator: Lin Ye creator: Xianqun Zhang creator: Wei Huang creator: Xiuzhen Long creator: Kang Yang creator: Guoyong Li creator: Jianlin Luo creator: Jiyue Wang creator: Yonghao Yu uri: https://doi.org/10.7717/peerj.14067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bai et al. title: Lack of a genetic cline and temporal genetic stability in an introduced barnacle along the Pacific coast of Japan link: https://peerj.com/articles/14073 last-modified: 2022-09-28 description: BackgroundLarge numbers of exotic marine species have been introduced worldwide. Monitoring of introduced species is important to reveal mechanisms underlying their establishment and expansion. Balanus glandula is a common intertidal barnacle native to the northeastern Pacific. However, this species has been introduced to Japan, South America, South Africa, and Europe. While a latitudinal genetic cline is well known in its native range, it is unclear whether such a genetic cline occurs in introduced areas. Twenty years have passed since it was first identified in Japan and its distribution now ranges from temperate to subarctic regions.MethodsIn the present study, we examined genotypes of cytochrome oxidase subunit I (COI) of mitochondrial (mt)-DNA and elongation factor 1a (EF1) across the distribution of B. glandula in Japan at high and mid intertidal zones.ResultsAt all sampling sites, native northern genotypes are abundant and I did not detect significant effects of latitude, tide levels, or their interaction on genotypic frequencies. Further, I did not detect any change of genotype composition between data collected during a study in 2004 and samples in the present study collected in 2019. Data from the present study offer an important baseline for future monitoring of this species and supply valuable insights into the mechanisms of establishment and expansion of introduced marine species generally. creator: Takefumi Yorisue uri: https://doi.org/10.7717/peerj.14073 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yorisue title: Ac2-26 attenuates hepatic ischemia-reperfusion injury in mice via regulating IL-22/IL-22R1/STAT3 signaling link: https://peerj.com/articles/14086 last-modified: 2022-09-28 description: Hepatic ischemia-reperfusion injury (HIRI) is one of the major sources of mortality and morbidity associated with hepatic surgery. Ac2-26, a short peptide of Annexin A1 protein, has been proved to have a protective effect against IRI. However, whether it exerts a protective effect on HIRI has not been reported. The HIRI mice model and the oxidative damage model of H2O2-induced AML12 cells were established to investigate whether Ac2-26 could alleviate HIRI by regulating the activation of IL-22/IL-22R1/STAT3 signaling. The protective effect of Ac2-26 was measured by various biochemical parameters related to liver function, apoptosis, inflammatory reaction, mitochondrial function and the expressions of IL-22, IL-22R1, p-STAT3Tyr705. We discovered that Ac2-26 reduced the Suzuki score and cell death rate, and increased the cell viability after HIRI. Moreover, we unraveled that Ac2-26 significantly decreased the number of apoptotic hepatocytes, and the expressions of cleaved-caspase-3 and Bax/Bcl-2 ratio. Furthermore, HIRI increased the contents of malondialdehyde (MDA), NADP+/NADPH ratio and reactive oxygen species (ROS), whereas Ac2-26 decreased them significantly. Additionally, Ac2-26 remarkably alleviated mitochondria dysfunction, which was represented by an increase in the adenosine triphosphate (ATP) content and mitochondrial membrane potential, a decrease in mitochondrial DNA (mtDNA) damage. Finally, we revealed that Ac2-26 pretreatment could significantly inhibit the activation of IL-22/IL22R1/STAT3 signaling. In conclusion, this work demonstrated that Ac2-26 ameliorated HIRI by reducing oxidative stress and inhibiting the mitochondrial apoptosis pathway, which might be closely related to the inhibition of the IL-22/IL22R1/STAT3 signaling pathway. creator: Wanzhen Li creator: Hongxin Jiang creator: Chen Bai creator: Shuna Yu creator: Yitong Pan creator: Chenchen Wang creator: Huiting Li creator: Ming Li creator: Yaxin Sheng creator: Fangfang Chu creator: Jie Wang creator: Yuting Chen creator: Jianguo Li creator: Jiying Jiang uri: https://doi.org/10.7717/peerj.14086 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: A content analysis of the reliability and quality of Youtube videos as a source of information on health-related post-COVID pain link: https://peerj.com/articles/14089 last-modified: 2022-09-28 description: BackgroundThe use of the internet as a source of information has increased during the pandemic, and YouTube has become an increasingly important source of information on Coronavirus disease 2019 (COVID-19). In the long COVID picture, which occurs when symptoms related to COVID-19 last longer than 1 month, pain involving the musculoskeletal system affects the quality of life quite negatively. The aim of this study was to investigate the informational value and quality of YouTube videos related to post-COVID pain.MethodsIn this study, 180 videos were listed using the search terms “pain after COVID,” “post-COVID pain,” and “long COVID and pain”(15 April 2022). Videos were classified according to video parameters and content analysis. Quality, reliability and accuracy of the videos were determined with the Global Quality Score (GQS), the Journal of American Medical Association (JAMA) Benchmark Criteria and the Modified DISCERN Questionnaire, respectively.ResultsOne hundred videos that met the inclusion criteria were included in the assessment. Of these videos, 74 were found to be of low quality, 14 of moderate quality, and 12 of high quality; 21% contained insufficient data, 73% contained partially sufficient data, and 6% contained completely sufficient data. Videos uploaded by academic sources (66.7%) and physicians (12.5%) made up the majority of the high-quality group. A statistically significant correlation was found between the source of upload and number of views (p = 0.014), likes (p = 0.030), comments (p = 0.007), and video duration (p = 0.004). Video duration was found to have a poor positive correlation with GQS (r = 0.500), JAMA (r = 0.528), and modified DISCERN (r = 0.470) scores (p < 0.001).ConclusionThe findings of this study revealed that the majority of YouTube videos on post-COVID pain had low quality and partially sufficient data. High-quality videos were found to have longer durations and were uploaded by academic sources and physicians. The fact that only videos with English content at a certain time can be counted among the limitations. For patients suffering from post-COVID pain whose access to healthcare services was interrupted during the COVID pandemic, YouTube can be considered as an alternative source as well as a means of telerehabilitation. It can be argued that higher quality videos created by healthcare professionals could aid in patient education in the future. creator: Erkan Ozduran creator: Sibel Büyükçoban uri: https://doi.org/10.7717/peerj.14089 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ozduran and Büyükçoban title: Do pheromone traps help to reduce new attacks of Ips typographus at the local scale after a sanitary cut? link: https://peerj.com/articles/14093 last-modified: 2022-09-28 description: The spruce bark beetle, Ips typographus, is causing severe economic losses during epidemic phases triggered by droughts and/or windstorms. Sanitation felling and salvage logging are usually the most recommended strategies to limit the damages. However, any additional control method to limit the economic impact of an outbreak would be welcome. In this respect, the efficiency of pheromone trapping is still controversial or poorly documented. In this 2-year study (2020–2021), at the peak of a severe outbreak in Belgium, we quantified the wood volume and presence/absence of new attacks at 126 sites attacked during the previous year and within 100 m from the initial attack. Each site was randomly allocated to one of three treatments: (1) three crosstraps baited with pheromones, (2) one tree-trap baited with pheromones and treated with an insecticide and (3) control sites with no trapping device. The attacked trees of the previous year were all cut and removed before the start of the experiment and newly attacked trees were removed as they were detected. The trapping devices were only active during spring to target overwintering bark beetles that might have escaped the sanitation cuts and to limit the risk of attracting dispersing beetles from outside the patch during the summer. We found a strong decrease of the attacks relative to the previous year in all treatments, including the controls (more than 50% of the control sites had no new attacks). There was no relationship between the new attacks and the attacks of the previous year. In both years, new attacks were more frequent (presence/absence) in sites with crosstraps (95% Confidence Interval [56–84%] of the sites with new attacks) than in sites with a tree-trap (26–57% - p = 0.02) and to a lesser extent than in control sites (32–63%, p = 0.08). In 2020, the attacked volumes were slightly higher in sites with crosstraps (95% Confidence Interval [3.4–14.2 m³]) than in control sites (0.2–3.5 m³, p = 0.04) and no significant difference was found with tree-trap sites (1.1–6.2 m³, p = 0.38). In 2021, there were no significant differences between the volumes attacked in the control sites (1.8–9.4 m³), crosstraps sites (0.9–6.4 m³) and tree-trap sites (0–2.5 m³). Overall, we found no evidence in favor of the efficacy of pheromone trapping during spring to reduce economic damages at the local scale when combined with sanitation felling and during a severe outbreak. The use of baited crosstraps could even be hazardous as it seemed to increase the occurrence of new attacks probably by attracting bark beetles but failing to neutralize them. creator: Alexandre Kuhn creator: Louis Hautier creator: Gilles San Martin uri: https://doi.org/10.7717/peerj.14093 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kuhn et al. title: Beyond the fish-Daphnia paradigm: testing the potential for pygmy backswimmers (Neoplea striola) to cause trophic cascades in subtropical ponds link: https://peerj.com/articles/14094 last-modified: 2022-09-28 description: Trophic cascades, or indirect effects of predators on non-adjacent lower trophic levels, are a classic phenomenon in ecology, and are thought to be strongest in aquatic ecosystems. Most research on freshwater trophic cascades focused on temperate lakes, where fish are present and where Daphnia frequently dominate the zooplankton community. These studies identified that Daphnia often play a key role in facilitating trophic cascades by linking fish to algae with strong food web interactions. However, Daphnia are rare or absent in most tropical and subtropical lowland freshwaters, and fish are absent from small and temporary water bodies, where invertebrates fill the role of top predator. While invertebrate predators are ubiquitous in freshwater systems, most have received little attention in food web research. Therefore, we aimed to test whether trophic cascades are possible in small warmwater ponds where Daphnia are absent and small invertebrates are the top predators. We collected naturally occurring plankton communities from small fishless water bodies in central Texas and propagated them in replicate pond mesocosms. We removed zooplankton from some mesocosms, left the plankton community intact in others, and added one of two densities of the predaceous insect Neoplea striola to others. Following an incubation period, we then compared biomasses of plankton groups to assess food web effects between the trophic levels, including whether Neoplea caused a trophic cascade by reducing zooplankton. The zooplankton community became dominated by copepods which prefer large phytoplankton and exhibit a fast escape response. Perhaps due to these qualities of the copepods and perhaps due to other reasons such as high turbidity impairing predation, no evidence for food web effects were found other than somewhat weak evidence for zooplankton reducing large phytoplankton. More research is needed to understand the behavior and ecology of Neoplea, but trophic cascades may generally be weak or absent in fishless low latitude lowland water bodies where Daphnia are rare. creator: Chase J. Rakowski creator: Mathew A. Leibold uri: https://doi.org/10.7717/peerj.14094 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rakowski and Leibold title: A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements link: https://peerj.com/articles/14147 last-modified: 2022-09-28 description: BackgroundAlkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids.MethodsTo explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters.ResultsA total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters.ConclusionsWe conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies. creator: Shaojing Wang creator: Guoqiang Li creator: Zitong Liao creator: Tongtong Liu creator: Ting Ma uri: https://doi.org/10.7717/peerj.14147 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Nitrate enrichment does not affect enteropathogenic Escherichia coli in aquatic microcosms but may affect other strains present in aquatic habitats link: https://peerj.com/articles/13914 last-modified: 2022-09-27 description: Eutrophication of the planet’s aquatic systems is increasing at an unprecedented rate. In freshwater systems, nitrate—one of the nutrients responsible for eutrophication—is linked to biodiversity losses and ecosystem degradation. One of the main sources of freshwater nitrate pollution in New Zealand is agriculture. New Zealand’s pastoral farming system relies heavily on the application of chemical fertilisers. These fertilisers in combination with animal urine, also high in nitrogen, result in high rates of nitrogen leaching into adjacent aquatic systems. In addition to nitrogen, livestock waste commonly carries human and animal enteropathogenic bacteria, many of which can survive in freshwater environments. Two strains of enteropathogenic bacteria found in New Zealand cattle, are K99 and Shiga-toxin producing Escherichia coli (STEC). To better understand the effects of ambient nitrate concentrations in the water column on environmental enteropathogenic bacteria survival, a microcosm experiment with three nitrate-nitrogen concentrations (0, 1, and 3 mg NO3-N /L), two enteropathogenic bacterial strains (STEC O26—human, and K99—animal), and two water types (sterile and containing natural microbiota) was run. Both STEC O26 and K99 reached 500 CFU/10 ml in both water types at all three nitrate concentrations within 24 hours and remained at those levels for the full 91 days of the experiment. Although enteropathogenic strains showed no response to water column nitrate concentrations, the survival of background Escherichia coli, imported as part of the in-stream microbiota did, surviving longer in 1 and 3 mg NO3-N/Lconcentrations (P < 0.001). While further work is needed to fully understand how nitrate enrichment and in-stream microbiota may affect the viability of human and animal pathogens in freshwater systems, it is clear that these two New Zealand strains of STEC O26 and K99 can persist in river water for extended periods alongside some natural microbiota. creator: Meredith T. Davis creator: Adam D. Canning creator: Anne C. Midwinter creator: Russell G. Death uri: https://doi.org/10.7717/peerj.13914 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Davis et al. title: Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus link: https://peerj.com/articles/13953 last-modified: 2022-09-26 description: BackgroundThe order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna.MethodsTo confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the “primer-walking” method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship.ResultsThe three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1. creator: Regina L. Cunha creator: Katy R. Nicastro creator: Gerardo I. Zardi creator: Celine Madeira creator: Christopher D. McQuaid creator: Cymon J. Cox creator: Rita Castilho uri: https://doi.org/10.7717/peerj.13953 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cunha et al. title: Presence of leptin and its receptor in the ram reproductive system and in vitro effect of leptin on sperm quality link: https://peerj.com/articles/13982 last-modified: 2022-09-26 description: Leptin is a 16 kDa hormone encoded by obese (OB) gene in adipocytes. This molecule not only regulates energy metabolism but also plays a role in the reproduction of mammals. Leptin and its receptor (OBR) have been found in male reproductive systems of human, bovine, equine and pig. The effects of leptin on sperm quality vary widely from different research findings. However, the presence of leptin and its receptor in the ram reproductive system and the in vitro effect of leptin on sperm quality have not reported yet. In the present study, we found that the OB was highly expressed in primary and secondary spermatocytes of the testes, OBR was highly expressed in secondary spermatocytes of the testes. The expressions of OB were in stereocilia of epididymis and in columnar cells of epididymal caput and cauda, the expressions of OBR were in columnar cells of epididymis and in stereocilia of epididymal corpus and cauda. The presence of both OB and OBR in testes, epididymis and sperm were confirmed through RT-PCR, immunolocalization and Western blot analyses. The RT-qPCR results indicated OB and OBR had higher expression levels in epididymal sperm than that of the ejaculated sperm in rams. When sperm were treated with 5 ng/mL leptin, the progressive motility (P < 0.01), straight-line velocity (VSL) (P < 0.05), average path velocity (VAP) (P < 0.05), membrane mitochondrial potential (MMP) (P < 0.01) and viability (P < 0.05) significantly increased, while DNA fragmentation index (DFI) and reactive oxygen species (ROS) significantly decreased compared to the control (P < 0.01), and the other semen parameters such as acrosome integrity and acrosome reaction rate had no significant changes between groups (P > 0.05). In conclusion, this is probably the first report describing localization of leptin and its receptors in the reproductive system of rams and their effects on sperm quality parameters. Our findings suggest that 5 ng/mL leptin treatment enhanced sperm motility, viability and MMP, and decrease DFI and ROS without obvious influence on the acrosome reaction in ram sperm. The potential mechanisms may be related to leptin’s ability to reduce the oxidative stress and apoptosis of sperms and improve their mitochondrial function and energy supply, therefore, to maintain the physiological homeostasis of the sperm. creator: Yu Gao creator: Guodong Zhao creator: Yukun Song creator: Aerman Haire creator: Ailing Yang creator: Xi Zhao creator: Abulizi Wusiman uri: https://doi.org/10.7717/peerj.13982 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gao et al. title: Avoidance of copper by fathead minnows (Pimephales promelas) requires an intact olfactory system link: https://peerj.com/articles/13988 last-modified: 2022-09-26 description: Fish can detect and respond to a wide variety of cations in their environment, including copper. Most often fish will avoid copper during behavioural trials; however, fish may also show no response or an attraction response, depending on the concentration(s) used. While it may seem intuitive that the response to copper requires olfaction, there is little direct evidence to support this, and what evidence there is remains incomplete. In order to test if olfaction is required for avoidance of copper by fathead minnows (Pimephales promelas) copper-induced movement was compared between fish with an intact olfactory system and fish with induced anosmia. Fish in a control group or a mock-anosmic group avoided copper (approximately 10 µg/L or 62.7 nM copper sulphate) while anosmic fish did not. The evidence demonstrates that an intact olfactory system is required for copper sensing in fish. creator: Rubab Fatima creator: Robert Briggs creator: William A. Dew uri: https://doi.org/10.7717/peerj.13988 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Fatima et al. title: What’s the effectiveness of stocking actions in small creeks? The role of water discharge behind hatchery trout downstream movement link: https://peerj.com/articles/14069 last-modified: 2022-09-26 description: Fish stocking to enhance freshwater fisheries or to improve the conservation status of endangered fish species is a common practice in many countries. Little is known, however, of the effectiveness of these practices in spite of the high efforts and investments required. The movement of subadult/adult hatchery-released brown trout Salmo trutta L. was studied by passive telemetry in a small tributary of Lake Lugano (i.e., Laveggio Creek, Canton Ticino, Switzerland). Hatchery fish, together with some resident wild individuals sampled during electrofishing surveys, were tagged with Passive Integrated Transponders (PIT) tags. Hatchery fish were released upstream and downstream a submersible monitoring antenna, which was anchored to the streambed in a pass-over orientation. The number of hatchery fish detected daily by the antenna (divided between fish released upstream and downstream the antenna) was analyzed in relation to the daily water discharge, to search for similar patterns in their fluctuation over time. Only the movement of fish released upstream the antenna displayed a significant relationship with water discharge, with the highest number of fish detected during periods of high-water flow, occurring after heavy rains. High-water discharge events had a significant role in hatchery trout downstream movement in our study site, likely acting as a driver for the downstream migration to Lake Lugano. Such events contributed to the poor effectiveness of stocking actions in this small tributary, providing further evidence against stocking strategies based on subadult/adult fish. creator: Stefano Brignone creator: Vanessa De Santis creator: Tiziano Putelli creator: Christophe Molina creator: Armando Piccinini creator: Richard A. Carmichael creator: Pietro Volta uri: https://doi.org/10.7717/peerj.14069 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Brignone et al. title: Improved response inhibition induced by attentional capture is associated with physical activity link: https://peerj.com/articles/14083 last-modified: 2022-09-26 description: The ability to stop a response promptly when a stop signal is presented is named response inhibition. It is generally accepted that the process of response inhibition requires a subject to pay attention to the stop instruction and then cancel the action. A wealth of converging evidence suggests that physical activity (PA) can promote response inhibition, but the potential contributions of attentional capture to the relationship between PA and response inhibition are currently unknown. In this study, the standard stop-signal task (SST) and two novel versions of the SST were used to solve this gap. A total of 58 college students were divided into a higher PA group and a lower PA group, respectively. In Experiment 1, the classical SST determined that the participants in the higher PA group displayed a significantly faster stop-signal reaction time (SSRT) than those in the lower PA group. Experiment 2 separated the attentional capture in the SST and revealed that the participants in the higher PA group could detect the signal faster than those in the lower PA group. Experiment 3 further added a stop signal to Experiment 2 and demonstrated that the participants in the higher PA group could more effectively deploy attentional resources to complete the task. Overall, these findings indicate that PA is positively associated with response inhibition and that the positive relationship is associated with effective allocation of attentional resources for faster attentional capture. creator: Hao Zhu creator: Jiuyang Xu creator: Yue Zheng creator: Guiping Jiang creator: Xinyi Huang creator: Xiaohuan Tan creator: Xueping Wu uri: https://doi.org/10.7717/peerj.14083 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhu et al. title: Does quality of novice hand-tied square knots improve with repetition during a single training session? link: https://peerj.com/articles/14106 last-modified: 2022-09-26 description: BackgroundKnot tying is a key surgical skill for novices, and repetition over several training sessions improves knot tying. This study examined the effects of repetition within a single training session on quality of knotted loops and compared results of novice trainees and experienced surgeons.MethodsUsing 0.55 mm nylon monofilament fishing line, novices and surgeons each hand-tied 20 knotted loops, using a 2=1=1=1 configuration (surgeon’s throw and three square throws). Loops were mechanically tested with a single load to failure.ResultsAll loops tolerated five newtons (N) preload. More than 70% of novice and surgeon knots failed by slipping or untying, and 8.8% of novice knots and 2.5% of surgeon’s knots were considered dangerous. Surgeons’ loops had less extension at preload, indicating better loop security. However, during single test to failure, there was no difference in mean extension or maximum load between surgeons and novices. There was no significant difference in results of mechanical testing or modes of failure for the first and last ten knotted loops, or the first, second, third, and fourth sets of knotted loops.DiscussionWith appropriate training, novices can construct knots as strong and secure as experienced surgeons. A large percentage of knotted loops are insecure under testing conditions; extra throws may be required when using large diameter monofilament nylon. Novices may require extra training in maintenance of loop security when constructing square knots. Tying more than five or 10 knotted loops within a single training session does not provide added benefits for novices. creator: Karen Tobias creator: Pierre-Yves Mulon creator: Alec Daniels creator: Xiaocun Sun uri: https://doi.org/10.7717/peerj.14106 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tobias et al. title: Hidden interactions in the intertidal rocky shore: variation in pedal mucus microbiota among marine grazers that feed on epilithic biofilm communities link: https://peerj.com/articles/13642 last-modified: 2022-09-23 description: In marine ecosystems, most invertebrates possess diverse microbiomes on their external surfaces, such as those found in the pedal mucus of grazing gastropods and chitons that aids displacement on different surfaces. The microbes are then transported around and placed in contact with free-living microbial communities of micro and other macro-organisms, potentially exchanging species and homogenizing microbial composition and structure among grazer hosts. Here, we characterize the microbiota of the pedal mucus of five distantly related mollusk grazers, quantify differences in microbial community structure, mucus protein and carbohydrate content, and, through a simple laboratory experiment, assess their effects on integrated measures of biofilm abundance. Over 665 Amplicon Sequence Variants (ASVs) were found across grazers, with significant differences in abundance and composition among grazer species and epilithic biofilms. The pulmonate limpet Siphonaria lessonii and the periwinkle Echinolittorina peruviana shared similar microbiota. The microbiota of the chiton Chiton granosus, keyhole limpet Fissurella crassa, and scurrinid limpet Scurria araucana differed markedly from one another, and form those of the pulmonate limpet and periwinkle. Flavobacteriaceae (Bacteroidia) and Colwelliaceae (Gammaproteobacteria) were the most common among microbial taxa. Microbial strict specialists were found in only one grazer species. The pedal mucus pH was similar among grazers, but carbohydrate and protein concentrations differed significantly. Yet, differences in mucus composition were not reflected in microbial community structure. Only the pedal mucus of F. crassa and S. lessonii negatively affected the abundance of photosynthetic microorganisms in the biofilm, demonstrating the specificity of the pedal mucus effects on biofilm communities. Thus, the pedal mucus microbiota are distinct among grazer hosts and can affect and interact non-trophically with the epilithic biofilms on which grazers feed, potentially leading to microbial community coalescence mediated by grazer movement. Further studies are needed to unravel the myriad of non-trophic interactions and their reciprocal impacts between macro- and microbial communities. creator: Clara Arboleda-Baena creator: Claudia Belén Pareja creator: Isadora Pla creator: Ramiro Logares creator: Rodrigo De la Iglesia creator: Sergio Andrés Navarrete uri: https://doi.org/10.7717/peerj.13642 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Arboleda-Baena et al. title: Utilizing network pharmacology and experimental validation to investigate the underlying mechanism of phellodendrine on inflammation link: https://peerj.com/articles/13852 last-modified: 2022-09-23 description: BackgroundPhellodendrine, one of the characteristic and important active components of Cortex phellodendri, has been proven to show anti-inflammatory effects. However, the underlying mechanism of phellodendrine on inflammation remains largely unclear.Aim of the studyIn this study, network pharmacology and experimental validation were used to explore the underlying mechanism of phellodendrine on inflammation.Materials and MethodsPubChem and SwissADME database were used to evaluate the drug-likeness and other characteristics of phellodendrine. The targets of phellodendrine for the treatment of inflammation were analyzed with multiple databases. Other extensive analyses including protein–protein interaction, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment were accomplished with the STRING database, Cytoscape software, and DAVID database. Moreover, the effect of phellodendrine on anti-inflammation was proven in RAW264.7.ResultsThe network pharmacology results indicated that phellodendrine had drug potential. Phellodendrine acted directly on 12 targets, including PTGS1, PTGS2, HTR1A, and PIK3CA, and then regulated cAMP, estrogen, TNF, serotonergic synapse, and other signaling pathways to exert anti-inflammatory effects. The experimental results showed that phellodendrine reduced the levels of IL-6 compared with the LPS group in 24 h and changed the mRNA expression of PTGS1, PTGS2, HSP90ab1, AKT1, HTR1A, PI3CA, and F10.ConclusionOur research preliminarily uncovered the therapeutic mechanisms of phellodendrine on inflammation with multiple targets and pathways. Phellodendrine may be a potential treatment for inflammation-related diseases related to the cAMP and TNF signaling pathways. creator: Lili Hu creator: Jue Wang creator: Na Wu creator: Xiaoge Zhao creator: Donghui Cai uri: https://doi.org/10.7717/peerj.13852 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hu et al. title: A questionnaire development to assess the social representation of nurses in the Basque Country: a psychometric assessment link: https://peerj.com/articles/13903 last-modified: 2022-09-23 description: BackgroundOnly a few Spanish studies have explored how nurses are seen by society and no validated tools exist for this purpose in the scientific literature.ObjectivesThe aim was create and evaluate the psychometric characteristics of a questionnaire that explored the social representation of nursing in social and health care.MethodsQualitative and quantitative methods were used to develop the questionnaire and the first version was created based on existing studies. A three-round Delphi technique was used that involved nurses, doctors, journalists and a politician. The pilot questionnaire was then tested and retested with 23 journalism students, with an interval of 10–14 days between the two phases. After further modifications, the questionnaire was sent to all the third and fourth year journalism students at the University of the Basque Country. Principal component factor analysis was used to identify the key components for the questionnaire.ResultsA total of 141 third and fourth year journalism students took part in the study. The internal consistency of the 43-item perception section of the questionnaire had a Cronbach’s alpha value of 0.90. The 42.7% agreed or strongly agreed that nursing was an eminently scientific profession and 26.3% agreed or strongly agreed with the statement that nurses were presented in the media as health educators and disseminators. Just under a fifth (19.9%) agreed with the statement that society was aware of the competencies that nurses required.ConclusionsThe questionnaire provided the first validated tool that allowed researchers to assess how nursing, and all of its areas of professional development, were perceived by society. This could enable studies to assess the evolution of the profession over time and between different socio-cultural contexts. creator: Verónica Tíscar-González creator: Leire Iturregui-Mardaras creator: Eztizen Miranda-Bernabé creator: Cristina Bermúdez-Ampudia creator: Maria Ángeles Cidoncha-Moreno creator: Sendoa Ballesteros-Peña uri: https://doi.org/10.7717/peerj.13903 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tíscar-González et al. title: Interelemental osteohistological variation in Massospondylus carinatus and its implications for locomotion link: https://peerj.com/articles/13918 last-modified: 2022-09-23 description: Massospondylus carinatus Owen, 1854 is an iconic basal sauropodomorph dinosaur from the Early Jurassic of southern Africa. Over 200 specimens have been referred to this taxon, spanning the entire ontogenetic series from embryo to adult. Consequently, it provides an ideal sample for investigating dinosaur developmental biology, including growth patterns and growth rates, through osteohistological analysis. Massospondylus carinatus was the first early-branching sauropodomorph dinosaur for which a femoral growth series was sampled. Since then, growth series of other non-avian dinosaur taxa have shown that growth plasticity, interelemental variation, and ontogenetic locomotory shifts can complicate our understanding of growth curves and patterns. To investigate these questions further, it is necessary to sample multiple skeletal elements from multiple individuals across a large range of sizes, something that is often hindered by the incompleteness of the fossil record. Here, we conducted a broad, multielement osteohistological study of long bones (excluding metapodials) from 27 specimens of Massospondylus carinatus that span its ontogenetic series. Our study reveals substantial variations in growth history. A cyclical woven-parallel complex is the predominant bone tissue pattern during early and mid-ontogeny, which transitions to slower forming parallel-fibred bone during very late ontogeny. The bone tissue is interrupted by irregularly spaced cyclical growth marks (CGMs) including lines of arrested growth indicating temporary cessations in growth. These CGMs show that the previously recorded femoral growth plasticity is also visible in other long bones, with a poor correlation between body size (measured by midshaft circumference) and CGM numbers. Furthermore, we found that the growth trajectory for an individual can vary depending on which limb element is studied. This makes the establishment of an accurate growth curve and determination of the onset of reproductive maturity difficult for this taxon. Finally, we found no evidence of differential growth rates in forelimb vs hindlimb samples from the same individual, providing further evidence falsifying hypothesised ontogenetic postural shifts in Massospondylus carinatus. creator: Kimberley EJ Chapelle creator: Paul M. Barrett creator: Jonah N. Choiniere creator: Jennifer Botha uri: https://doi.org/10.7717/peerj.13918 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chapelle et al. title: Antimicrobial and cytotoxic effects of marine sponge extracts Agelas clathrodes, Desmapsamma anchorata and Verongula rigida from a Caribbean Island link: https://peerj.com/articles/13955 last-modified: 2022-09-23 description: Although marine sponges are known for their antimicrobial, antifungal and cytotoxic activity, very few studies have been carried out on endemic species of Martinique. Martinique is part of the Agoa Sanctuary, a marine protected area that includes the exclusive economic zones (EEZ) of the French Caribbean islands, making it an abundant source of marine species. To highlight the potential of this area for the discovery of marine biomolecules with antipathogenic and antitumor activities, we tested the aqueous and ethanolic extracts of sponge species Agelas clathrodes, Desmapsamma anchorata and Verongula rigida. Five bacterial strains: Bacillus cereus (CIP 78.3), Escherichia coli (CIP 54.127), Pseudomonas aeruginosa (CIP A22), Staphylococcus aureus (CIP 67.8) and Staphylococcus saprophyticus (CIP 76125) were evaluated, as well as four tumor cell lines: breast cancer (MDA-MB231), glioblastoma (RES259) and leukemia (MOLM14 and HL-60). Antimicrobial activity was evaluated using the disc diffusion technique by determining the minimum inhibitory and minimum bactericidal concentrations. Tumor cytotoxic activity was determined in vitro by defining the minimum concentration of extracts that would inhibit cell growth. Ethanolic extracts of Agelas clathrodes were bactericidal for Staphylococcus aureus and Staphylococcus saprophyticus strains, as well as strongly cytotoxic (IC50 < 20 µg/mL) on all cancer cell lines. Verongula rigida also showed strong cytotoxic activity on cell lines but no antimicrobial activity. These results are innovative for this species on these bacterial lines, highlighting the potential of sponge extracts from this area as bioactive compounds sources. creator: Julie Piron creator: Stephane Betzi creator: Jessica Pastour creator: Audrey Restouin creator: Rémy Castellano creator: Yves Collette creator: Niklas Tysklind creator: Juliette Smith-Ravin creator: Fabienne Priam uri: https://doi.org/10.7717/peerj.13955 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Piron et al. title: Influence of planting yellowhorn (Xanthoceras sorbifolium Bunge) on the bacterial and fungal diversity of fly ash link: https://peerj.com/articles/14015 last-modified: 2022-09-23 description: Phytoremediation is a low-cost solution to fly ash pollution and the rhizosphere interactions between plant roots and the fly ash microbiome were important for the phytoremediation. To analyze the dynamic changes of the rhizosphere microbiome during yellowhorn cultivation in fly ash, the bacterial 16S rRNA gene V3–V4 region and the fungal ITS region of the rhizosphere microbiome were sequenced using Illumina MiSeq technology. The changes in fly ash physicochemical properties and the heavy metal content of different yellowhorn tissues were also analyzed. The results showed that both the bacterial and fungal communities were noticeably different after yellowhorn cultivation compared with the control sample. Proteobacteria and Acidobacteria levels increased (p < 0.05) and Firmicutes and Actinobacteria decreased (p < 0.05) in the bacterial community after yellowhorn cultivation. In the fungal community, Ascomycota and Mortierellomycota decreased (p < 0.05), while Chytridiomycota increased (p < 0.05). The levels of four heavy metals (Cr, Cd, Hg, Pb and As) decreased in the fly ash after yellowhorn cultivation. These metals were absorbed by the yellowhorn plants and accumulated in the fibrous root, taproot, stem and leaf tissues of these plants. Accordingly, the abundance of bacteria that could solubilize heavy metals increased (p < 0.05). In summary, the cultivation of yellowhorn affected the composition of the rhizosphere microbial communities in fly ash, which is of great significance for the biological remediation of fly ash. creator: Zehui Liu creator: Jianguo Zhao creator: Jinxian Huo creator: Hongfang Ma creator: Zhiwen Chen uri: https://doi.org/10.7717/peerj.14015 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: Analysis of inferior nasal turbinate volume in subjects with nasal septum deviation: a retrospective cone beam tomography study link: https://peerj.com/articles/14032 last-modified: 2022-09-23 description: BackgroundThe association of the linear dimensions of the inferior turbinate hypertrophy with nasal septal deviation has been studied recently. However, the volumetric dimensions provide a more accurate status of the turbinate hypertrophy compared to linear measurements. The aim of this study was to analyze the association of inferior nasal turbinate volume with the degree of nasal septal deviation (NSD).MethodsA retrospective evaluation of the cone beam computed tomography (CBCT) scans of 412 patients was carried out to obtain 150 scans which were included in the study. The scans were categorized into three groups. Group 1 comprised of 50 scans of patients with no inferior turbinate hypertrophy (ITH) and no nasal septal deviation. Group 2 comprised of 50 scans of patients with ITH and no NSD; whereas Group 3 included 50 scans of patients with ITH and NSD. The total turbinate volume of inferior turbinates (bilateral) were determined by using Vesalius 3D software (PS-Medtech, Amsterdam, Netherlands).ResultsThe intraclass correlation coefficient (ICC) between the volumetric estimations performed by the two radiologists was 0.82. There were no significant age and gender related changes in the total turbinate volume. Patients in Group 3 had significantly higher (p = 0.001) total turbinate volume compared to Group 2 and Group 1. There was a positive and significant correlation (r = 0.52, p = 0.002) between the degree of septal deviation and total turbinate volume. When the total turbinate volume of the patients with different types of septal deviation was compared in Group 3, a statistically significant difference (p = 0.001) was observed. Regression analysis revealed that the septal deviation angle (SDA) (p = 0.001) had a relationship with total turbinate volume. From the results of the study we can conclude that the total turbinate volume is higher in patients with nasal septal deviation. It can also be concluded that the septal deviation angle has a positive correlation with total turbinate volume. The data obtained from the study can be useful in post-surgical follow up and evaluation of patients with nasal septal deviation and hypertrophied inferior nasal turbinate. creator: Shishir Shetty creator: Saad Al-Bayatti creator: Mohammad Khursheed Alam creator: Natheer H. Al-Rawi creator: Vinayak Kamath creator: Shoaib Rahman Tippu creator: Sangeetha Narasimhan creator: Sausan Al Kawas creator: Walid Elsayed creator: Kumuda Rao creator: Renita Castelino uri: https://doi.org/10.7717/peerj.14032 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Shetty et al. title: Dental caries as a risk factor for bacterial blood stream infection (BSI) in children undergoing hematopoietic cell transplantation (HCT) link: https://peerj.com/articles/14040 last-modified: 2022-09-23 description: BackgroundHematopoietic cell transplantation (HCT) is a potentially curative therapy for a wide range of pediatric malignant and nonmalignant diseases. However, complications, including blood stream infection (BSI) remain a major cause of morbidity and mortality. While certain bacteria that are abundant in the oral microbiome, such as S. mitis, can cause BSI, the role of the oral microbial community in the etiology of BSI is not well understood. The finding that the use of xylitol wipes, which specifically targets the cariogenic bacteria S. mutans is associated with reduced BSI in pediatric patients, lead us to investigate dental caries as a risk factor for BSI.MethodsA total of 41 pediatric patients admitted for allogenic or autologous HCT, age 8 months to 25 years, were enrolled. Subjects with high dental caries risk were identified as those who had dental restorations completed within 2 months of admission for transplant, or who had untreated decay. Fisher’s exact test was used to determine if there was a significant association between caries risk and BSI. Dental plaque and saliva were collected on a cotton swab from a subset of four high caries risk (HCR) and four low caries risk (LCR) children following pretransplant conditioning. 16SrRNA sequencing was used to compare the microbiome of HCR and LCR subjects and to identify microbes that were significantly different between the two groups.ResultsThere was a statistically significant association between caries risk and BSI (p < 0.035) (Fisher’s exact test). Multivariate logistic regression analysis showed children in the high dental caries risk group were 21 times more likely to have BSI, with no significant effect of age or mucositis severity. HCR subjects showed significantly reduced microbial alpha diversity as compared to LCR subjects. LEfse metagenomic analyses, showed the oral microbiome in HCR children enriched in order Lactobacillales. This order includes Streptococcus and Lactobacillus, both which contain bacteria primarily associated with dental caries.DiscussionThese findings support the possibility that the cariogenic microbiome can enhance the risk of BSI in pediatric populations. Future metagenomic analyses to measure microbial differences at, before, and after conditioning related to caries risk, may further unravel the complex relationship between the oral microbiome, and whether it affects health outcomes such as BSI. creator: Dawud Abduweli Uyghurturk creator: Ying Lu creator: Janelle Urata creator: Christopher C. Dvorak creator: Pamela Den Besten uri: https://doi.org/10.7717/peerj.14040 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 abduweli uyghurturk et al. title: 16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis link: https://peerj.com/articles/14043 last-modified: 2022-09-23 description: BackgroundThe full-length 16S rRNA sequencing can better improve the taxonomic and phylogenetic resolution compared to the partial 16S rRNA gene sequencing. The 16S-FAS-NGS (16S rRNA full-length amplicon sequencing based on a next-generation sequencing platform) technology can generate high-quality, full-length 16S rRNA gene sequences using short-read sequencers, together with assembly procedures. However there is a lack of a data analysis suite that can help process and analyze the synthetic long read data.ResultsHerein, we developed software named 16S-FASAS (16S full-length amplicon sequencing data analysis software) for 16S-FAS-NGS data analysis, which provided high-fidelity species-level microbiome data. 16S-FASAS consists of data quality control, de novo assembly, annotation, and visualization modules. We verified the performance of 16S-FASAS on both mock and fecal samples. In mock communities, we proved that taxonomy assignment by MegaBLAST had fewer misclassifications and tended to find more low abundance species than the USEARCH-UNOISE3-based classifier, resulting in species-level classification of 85.71% (6/7), 85.71% (6/7), 72.72% (8/11), and 70% (7/10) of the target bacteria. When applied to fecal samples, we found that the 16S-FAS-NGS datasets generated contigs grouped into 60 and 56 species, from which 71.62% (43/60) and 76.79% (43/56) were shared with the Pacbio datasets.Conclusions16S-FASAS is a valuable tool that helps researchers process and interpret the results of full-length 16S rRNA gene sequencing. Depending on the full-length amplicon sequencing technology, the 16S-FASAS pipeline enables a more accurate report on the bacterial complexity of microbiome samples. 16S-FASAS is freely available for use at https://github.com/capitalbio-bioinfo/FASAS. creator: Ke Zhang creator: Rongnan Lin creator: Yujun Chang creator: Qing Zhou creator: Zhi Zhang uri: https://doi.org/10.7717/peerj.14043 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Clinical tool to measure fluorescein patterns in orthokeratology link: https://peerj.com/articles/14068 last-modified: 2022-09-23 description: BackgroundOrthokeratology (ortho-k) is an overnight clinical contact lens wear technique to correct myopia and to reduce myopia progression wearing reverse-geometry rigid gas-permeable lenses. The lens fitting procedure in clinical practice usually requires subjective assessment of fluorescein pattern (fluorescein “bull’s eye” pattern). The aim of this study was to develop a novel tool for fluorescein pattern measurements to reduce subjective practitioner dependency, especially in inexperienced practitioners, in ortho-k practice.MethodsA new MATLAB customized algorithm to measure the horizontal width of the four main zones of ortho-k fluorescein patterns (central bearing, tear reservoir, mid-peripheral bearing and edge lift) was designed. The algorithm was tested on a small image database consisting of 26 ortho-k fluorescein pattern images of 13 volunteers fitted with reverse geometry lenses (Seefree, Conoptica-Hecht Contactlinsen). The agreement between two independent observers and the ImageJ measurements was determined.ResultsThe new clinical tool provided similar measurements to ImageJ software for the central bearing (4.20 ± 0.74 and 4.27 ± 0.69 mm; P = 0.21), tear reservoir (1.69 ± 0.41 and 1.69 ± 0.45 mm; P = 0.69), mid-peripheral bearing (1.17 ± 0.11 and 1.13 ± 0.10 mm; P < 0.01) and edge lift (0.48 ± 0.06 and 0.48 ± 0.06 mm; P = 0.81) zones. Good agreement between the software (limits of agreement lower than ±0.55 mm) and inter-observer measurements (limits of agreement lower than ±0.66 mm) was found.ConclusionsThe proposed clinical tool for semiautomatic fluorescein pattern measurements in ortho-k could help to reduce practitioner dependency in fluorescein pattern assessment with future potential to introduce prediction algorithms or artificial intelligence methods in myopia control management. creator: Marina López García Rosuero creator: Alejandro Arranz Bombin creator: Roberto Romero creator: Roberto Hornero creator: Raul Martin uri: https://doi.org/10.7717/peerj.14068 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 López García Rosuero et al. title: BMSC-derived exosomal miR-27a-3p and miR-196b-5p regulate bone remodeling in ovariectomized rats link: https://peerj.com/articles/13744 last-modified: 2022-09-22 description: BackgroundIn the bone marrow microenvironment of postmenopausal osteoporosis (PMOP), bone marrow mesenchymal stem cell (BMSC)-derived exosomal miRNAs play an important role in bone formation and bone resorption, although the pathogenesis has yet to be clarified.MethodsBMSC-derived exosomes from ovariectomized rats (OVX-Exo) and sham-operated rats (Sham-Exo) were co-cultured with bone marrow-derived macrophages to study their effects on osteoclast differentiation. Next-generation sequencing was utilized to identify the differentially expressed miRNAs (DE-miRNAs) between OVX-Exo and Sham-Exo, while target genes were analyzed using bioinformatics. The regulatory effects of miR-27a-3p and miR-196b-5p on osteogenic differentiation of BMSCs and osteoclast differentiation were verified by gain-of-function and loss-of-function analyses.ResultsOsteoclast differentiation was significantly enhanced in the OVX-Exo treatment group compared to the Sham-Exo group. Twenty DE-miRNAs were identified between OVX-Exo and Sham-Exo, among which miR-27a-3p and miR-196b-5p promoted the expressions of osteogenic differentiation markers in BMSCs. In contrast, knockdown of miR-27a-3p and miR-196b-5p increased the expressions of osteoclastic markers in osteoclast. These 20 DE-miRNAs were found to target 11435 mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these target genes were involved in several biological processes and osteoporosis-related signaling pathways.ConclusionBMSC-derived exosomal miR-27a-3p and miR-196b-5p may play a positive regulatory role in bone remodeling. creator: Guohua Lai creator: Renli Zhao creator: Weida Zhuang creator: Zuoxu Hou creator: Zefeng Yang creator: Peipei He creator: Jiachang Wu creator: Hongxun Sang uri: https://doi.org/10.7717/peerj.13744 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lai et al. title: Comparative analysis of combined phosphorus and drought stress-responses in two winter wheat link: https://peerj.com/articles/13887 last-modified: 2022-09-22 description: Phosphorus stress and drought stress are common abiotic stresses for wheat. In this study, two winter wheat varieties “Xindong20” and “Xindong23” were cultured in a hydroponic system using Hoagland nutrient solution and treated with drought stress under conventional (CP: 1.0 mmol/L) and low (LP: 0.05 mmol/L) phosphorus levels. Under drought stress, the root growth was better under LP than under CP. Under LP, root phosphorus content was increased by 94.2% in Xindong20 and decreased by 48.9% in Xindong23 at 3 d after re-watering, compared with those at 0 d under drought stress. However, the potassium (K) content was the highest among the four elements studied and the phosphorus (P) and calcium (Ca) content were reduced in the root of the two varieties. Under CP, the zinc (Zn) content was higher than that under LP in Xindong23. The GeneChip analysis showed that a total of 4,577 and 202 differentially expressed genes (DEGs) were detected from the roots of Xindong20 and Xindong23, respectively. Among them, 89.9% of DEGs were involved in organelles and vesicles in Xindong20, and 69.8% were involved in root anatomical structure, respiratory chain, electron transport chain, ion transport, and enzyme activity in Xindong23. Overall, LP was superior to CP in mitigating drought stress on wheat, and the regulatory genes were also different in the two varieties. Xindong20 had higher drought tolerance for more up-regulated genes involved in the responses compared to Xindong23. creator: Xiangchi Zhang creator: Chao Li creator: Weidan Lu creator: Xiaoli Wang creator: Bin Ma creator: Kaiyong Fu creator: Chunyan Li creator: Cheng Li uri: https://doi.org/10.7717/peerj.13887 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Population dynamics and resource availability drive seasonal shifts in the consumptive and competitive impacts of introduced house mice (Mus musculus) on an island ecosystem link: https://peerj.com/articles/13904 last-modified: 2022-09-22 description: BackgroundHouse mice (Mus musculus) are widespread and invasive on many islands where they can have both direct and indirect impacts on native ecological communities. Given their opportunistic, omnivorous nature the consumptive and competitive impacts of house mice on islands have the potential to vary over time in concert with resource availability and mouse population dynamics.MethodsWe examined the ecological niche of invasive house mice on Southeast Farallon Island, California, USA using a combination of mouse trapping, food resource surveys, and stable isotope analysis to better understand their trophic interactions with native flora and fauna. Specifically, we coupled the analysis of seasonal variation in resource availability over a 17-year period (2001–2017), carbon (δ13C) and nitrogen (δ15N) stable isotope values of mouse tissue and prey resources in a single year (2013), and isotopic niche and mixing models to quantify seasonal variation in mouse diets and the potential for resource overlap with native species.ResultsWe found that plants were the most important resource for house mice during the spring months when vegetation is abundant and mouse populations are low following heavy precipitation and declines in mouse abundance during the winter. While still consumed, plants declined in dietary importance throughout the summer and fall as mouse populations increased, and seabird and arthropod resources became relatively more available and consumed by house mice. Mouse abundance peaks and other resource availability are low on the island in the fall months when the isotopic niches of house mice and salamanders overlap significantly indicating the potential for competition, most likely for arthropod prey.DiscussionOur results indicate how seasonal shifts in both mouse abundance and resource availability are key factors that mediate the consumptive and competitive impacts of introduced house mice on this island ecosystem. As mice consume and/or compete with a wide range of native taxa, eradication has the potential to provide wide-reaching restoration benefits on Southeast Farallon Island. Post-eradication monitoring focused on plant, terrestrial invertebrate, salamander, and seabird populations will be crucial to confirm these predictions. creator: Michael J. Polito creator: Bret Robinson creator: Pete Warzybok creator: Russell W. Bradley uri: https://doi.org/10.7717/peerj.13904 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Polito et al. title: Cultivation has selected for a wider niche and large range shifts in maize link: https://peerj.com/articles/14019 last-modified: 2022-09-22 description: BackgroundMaize (Zea mays L.) is a staple crop cultivated on a global scale. However, its ability to feed the rapidly growing human population may be impaired by climate change, especially if it has low climatic niche and range lability. One important question requiring clarification is therefore whether maize shows high niche and range lability.MethodsWe used the COUE scheme (a unified terminology representing niche centroid shift, overlap, unfilling and expansion) and species distribution models to study the niche and range changes between maize and its wild progenitors using occurrence records of maize, lowland teosinte (Zea mays ssp. parviglumis) and highland teosinte (Zea mays ssp. mexicana), respectively, as well as explore the mechanisms underlying the niche and range changes.ResultsIn contrast to maize in Mexico, maize did not conserve its niche inherited from lowland and highland teosinte at the global scale. The niche breadth of maize at the global scale was wider than that of its wild progenitors (ca. 5.21 and 3.53 times wider compared with lowland and highland teosinte, respectively). Compared with its wild progenitors, maize at global scale can survive in regions with colder, wetter climatic conditions, as well as with wider ranges of climatic variables (ca. 4.51 and 2.40 times wider compared with lowland and highland teosinte, respectively). The niche changes of maize were largely driven by human introduction and cultivation, which have exposed maize to climatic conditions different from those experienced by its wild progenitors. Small changes in niche breadth had large effects on the magnitude of range shifts; changes in niche breadth thus merit increased attention.DiscussionOur results demonstrate that maize shows wide climatic niche and range lability, and this substantially expanded its realized niche and potential range. Our findings also suggest that niche and range shifts probably triggered by natural and artificial selection in cultivation may enable maize to become a global staple crop to feed the growing population and adapting to changing climatic conditions. Future analyses are needed to determine the limits of the novel conditions that maize can tolerate, especially relative to projected climate change. creator: Rujing Yang creator: Runyao Cao creator: Xiang Gong creator: Jianmeng Feng uri: https://doi.org/10.7717/peerj.14019 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yang et al. title: Genome-wide identification, characterization and expression analysis of HAK genes and decoding their role in responding to potassium deficiency and abiotic stress in Medicago truncatula link: https://peerj.com/articles/14034 last-modified: 2022-09-22 description: BackgroundThe HAK family is the largest potassium (K+) transporter family, vital in K+ uptake, plant growth, and both plant biotic and abiotic stress responses. Although HAK family members have been characterized and functionally investigated in many species, these genes are still not studied in detail in Medicago truncatula, a good model system for studying legume genetics.MethodsIn this study, we screened the M. truncatula HAK family members (MtHAKs). Furthermore, we also conducted the identification, phylogenetic analysis, and prediction of conserved motifs of MtHAKs. Moreover, we studied the expression levels of MtHAKs under K+ deficiency, drought, and salt stresses using quantitative real-time PCR (qRT-PCR).ResultsWe identified 20 MtHAK family members and classified them into three clusters based on phylogenetic relationships. Conserved motif analyses showed that all MtHAK proteins besides MtHAK10 contained the highly conserved K+ transport domain (GVVYGDLGTSPLY). qRT-PCR analysis showed that several MtHAK genes in roots were induced by abiotic stress. In particular, MtHAK15, MtHAK17, and MtHAK18 were strongly up-regulated in the M. truncatula roots under K+ deficiency, drought, and salt stress conditions, thereby implying that these genes are good candidates for high-affinity K+ uptake and therefore have essential roles in drought and salt tolerance.DiscussionsOur results not only provided the first genetic description and evolutionary relationships of the K+ transporter family in M. truncatula, but also the potential information responding to K+ deficiency and abiotic stresses, thereby laying the foundation for molecular breeding of stress-resistant legume crops in the future. creator: Yanxue Zhao creator: Lei Wang creator: Pengcheng Zhao creator: Zhongjie Liu creator: Siyi Guo creator: Yang Li creator: Hao Liu uri: https://doi.org/10.7717/peerj.14034 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhao et al. title: Dynamics of soil properties and bacterial community structure by mulched fertigation system in semi-arid area of Northeast China link: https://peerj.com/articles/14044 last-modified: 2022-09-22 description: The agricultural irrigation and fertigation systems have a non-negligible impact on the soil microenvironment in arid and semi-arid areas. Therefore, studying the processes and changes of soil microenvironment under different plastic mulch drip irrigation systems can reveal the “soil-microbe” mechanism and provide a theoretical support for the optimal irrigation and nutrition management of maize in the semi-arid area of Northeast China. Three treatments were used for this study in the semi-arid area of northeast China, namely; mulched fertigation system (MF), drip irrigation system (DI), and farmers’ practices system (FP). We used high-throughput sequencing to study the soil bacterial community structure targeting the 16S rRNA gene. The agricultural irrigation and fertigation systems significantly affected soil properties. MF significantly increased bacterial abundance and bacterial diversity and richness. Moreover, MF and DI markedly increased some relative abundance of beneficial bacterial. The bacterial network in MF was more conducive to the health and stability of the agroecosystem and the relationships among species in MF bacterial network were more complex. The agricultural irrigation and fertigation systems had indirect effects on community composition and bacterial diversity through soil organic carbon (SOC), ammonium nitrogen (${\mathrm{NH}}_{4}^{+}$NH4+-N), nitrate nitrogen (${\mathrm{NO}}_{3}^{-}$NO3−-N), pH, moisture, ${\mathrm{NH}}_{4}^{+}$NH4+-N and ${\mathrm{NO}}_{3}^{-}$NO3−-N had indirect effects on yield through bacterial community composition, bacterial diversity and bacterial abundance. These findings suggested that MF was the most effective treatment to improve soil bacterial abundance and diversity, and stabilize the functional quality of soil biological processes. creator: Ling Wang creator: Meng Wang creator: Qian Li creator: Jinjing Zhang creator: Cuilan Li creator: Yuhan Yuan creator: Pan Tan creator: Hang Liu uri: https://doi.org/10.7717/peerj.14044 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Six-minute rowing test: a valid and reliable method for assessing power output in amateur male rowers link: https://peerj.com/articles/14060 last-modified: 2022-09-22 description: BackgroundStandardized tests are currently available to assess power output in elite rowers. However, there are no valid and reliable tests to assess power output in amateur rowers.ObjectiveThis study aimed to determine the validity and reliability of a 6-min rowing ergometer test (6-minRT) as a predictor of power output (PO) in amateur male rowers.MethodsTwelve male amateur rowers were part of the study. All participants were instructed to perform an incremental test (IT), a 6-minRT test, and a retest. The validity of the 6-minRT was determined by comparing maximum oxygen uptake (VO2max) and power output (PO) between the IT and 6-minRT. Reliability included the coefficient of variation (CV), intra-class correlation coefficient (ICC), and mean standard error between the 6-minRT test and retest. The significance level was p < 0.05.ResultsThere was no significant difference in VO2max in both IT and 6-minRT (p = 0.18), while the mean power output (Pmean) generated in the 6-minRT equaled 91.96% of the maximal aerobic power (MAP) generated in the IT (p = 0.004). Reliability analysis for the 6-minRT showed a CV = 0.50% and ICC = 0.97 for distance, a CV = 1.85% and ICC = 0.96 for Pmean.ConclusionFrom a ventilatory and mechanical point of view, the 6-minRT is a maximally valid test for establishing MAP in amateur rowers. Also, the 6-minRT evidences a high degree of agreement between days. Therefore, the 6-minRT is a valid and reliable test for assessing PO in amateur male rowers. creator: Álvaro Huerta Ojeda creator: Miguel Riquelme Guerra creator: Walter Coronado Román creator: María-Mercedes Yeomans-Cabrera creator: Rodrigo Fuentes-Kloss uri: https://doi.org/10.7717/peerj.14060 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Huerta Ojeda et al. title: Ovarian development, spawning season, size at maturity and fecundity of Acentrogobius viridipunctatus (Valenciennes, 1837) in the Vietnamese Mekong Delta link: https://peerj.com/articles/14077 last-modified: 2022-09-22 description: This present study provides an overview of the reproductive traits, including ovarian development, spawning season, size at maturity (Lm), and fecundity of Acentrogobius viridipunctatus – a high economic value fish in the Vietnamese Mekong Delta (VMD). A total of 432 females were collected using trawl nets from January to December 2020 at four sites, including Long Huu-Tra Vinh (LHTV), Trung Binh-Soc Trang (TBST), Dien Hai-Bac Lieu (DHBL), and Tan Thuan-Ca Mau (TTCM). The ovarian diameter was seen to increase from 2.09 (stage I) to 6.57 mm (stage V). Histological analysis showed that the goby was a multi-spawner due to the different oocyte stages found in stages IV and V of ovaries. It can release eggs all year-round due to the monthly appearance of ovarian stages IV and V during the study period, with the main peak in the 2–4 months of the wet season noted with the highest value of gonadosomatic index at that time. The Lm increased from 6.6 cm at TBST to 9.4 cm at TTCM. This species displayed relatively high fecundity, ranging from 5,481 to 130,683 eggs/female. The average fecundity of this fish was 27,698 ± 7,983 eggs/female at LHTV, 46,592 ± 7,264 eggs/female at TBST, 23,271 ± 4,985 eggs/female at DHBL, and 31,408 ± 2,515 eggs/female at TTCM. Egg diameter ranged from 0.45 ± 0.01 at DHBL to 0.50 ± 0.01 at TBST. For sustainable exploitation, local governments should ask the fishers to avoid catching fish during the main spawning period, and the fish length at first capture should be >Lm. creator: Quang Minh Dinh creator: Ton Huu Duc Nguyen creator: Ngon Trong Truong creator: Diep Xuan Doan creator: Tien Thi Kieu Nguyen uri: https://doi.org/10.7717/peerj.14077 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Dinh et al. title: In situ observation of holopelagic Sargassum distribution and aggregation state across the entire North Atlantic from 2011 to 2020 link: https://peerj.com/articles/14079 last-modified: 2022-09-22 description: Between 2011 and 2020, 6,790 visual observations of holopelagic Sargassum were recorded across the North Atlantic Ocean to describe regional distribution, presence, and aggregation state at hourly and 10 km scales. Influences of oceanographic region and wind/sea conditions as well as temporal trends were considered; marine megafauna associates documented the ecological value of aggregations. Holopelagic Sargassum was present in 64% of observations from the western North Atlantic. Dispersed holopelagic Sargassum fragments and clumps were found in 97% of positive observations whereas aggregated windrows (37%) and mats (1%) were less common. Most field observations noted holopelagic Sargassum in quantities below the AFAI algorithm detection limit for the MODIS sensor. Aggregation state patterns were similar across regions; windrow proportion increased with higher wind speeds. In 8 of 10 years in the Sargasso Sea holopelagic Sargassum was found in over 65% of observations. In contrast, the Tropical Atlantic and Caribbean Sea exhibited greater inter-annual variability (1–88% and 11–78% presence, respectively) that did not align with extremes in central Atlantic holopelagic Sargassum areal coverage determined from satellite observations. Megafauna association patterns varied by taxonomic group. While some study regions were impacted by holopelagic Sargassum dynamics in the equatorial Atlantic, the Sargasso Sea had consistently high presence and operated independently. Field observations capture important dynamics occurring at fine spatiotemporal scales, including transient aggregation processes and ecological value for megafauna associates, and therefore remain essential to future studies of holopelagic Sargassum. creator: Deborah S. Goodwin creator: Amy N.S. Siuda creator: Jeffrey M. Schell uri: https://doi.org/10.7717/peerj.14079 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Goodwin et al. title: Effect of nitrogen fertilizer on seed yield and quality of Kengyilia melanthera (Triticeae, Poaceae) link: https://peerj.com/articles/14101 last-modified: 2022-09-22 description: Widely distributed in the alpine sandy grassland in east Qinghai-Tibet Plateau (QTP), Kengyilia melanthera is considered as an ideal pioneer grass for the restoration of degraded and desertification grassland in the region. Under the special ecological and climatic conditions in the northwest Sichuan plateau located in east QTP, it is of great significance to optimize the amount of nitrogen fertilizer for the seed production of this species. The impact of nitrogen (N) fertilizer application on seed yield and quality of K. melanthera ‘Aba’, the only domesticated variety in the Kengyilia genus of Poaceae, was investigated based on two-year field experiments in the northwestern Sichuan plateau. The results showed that with the increase of N fertilizer application, the number of tillers, number of fertile tillers, 1,000-seed weight and seed yield of this species increased likewise. The optimum N fertilizer rate deduced in the present study was 180 kg·hm−2, where the number of fertile tillers 1,000-seed weight and seed yield reached the peak values. Interestingly, the standard germination rate, germination energy, accelerated aging germination rate, dehydrogenase and acid phosphatase activity of seeds were not affected by the increasing the input of N fertilizer. The comprehensive evaluation of membership function showed that the optimal N fertilizer treatment was 180 kg·hm−2 both for 2016 and 2017. This study provided a certain practical suggestion for the improvement of seed production of K. melanthera in the northwest Sichuan plateau. creator: Shuai Yuan creator: Yao Ling creator: Yi Xiong creator: Chenglin Zhang creator: Lina Sha creator: Minghong You creator: Xiong Lei creator: Shiqie Bai creator: Xiao Ma uri: https://doi.org/10.7717/peerj.14101 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yuan et al. title: Applying SARIMA, ETS, and hybrid models for prediction of tuberculosis incidence rate in Taiwan link: https://peerj.com/articles/13117 last-modified: 2022-09-21 description: BackgroundTuberculosis (TB) remained one of the world’s most deadly chronic communicable diseases. Future TB incidence prediction is a benefit for intervention options and resource-allocation planning. We aimed to develop rapid univariate prediction models for epidemics forecasting employment.MethodsThe surveillance data regarding Taiwan monthly TB incidence rates which from January 2005 to June 2017 were utilized for simulation modelling and from July 2017 to December 2020 for model validation. The modeling approaches including the Seasonal Autoregressive Integrated Moving Average (SARIMA), the Exponential Smoothing (ETS), and SARIMA-ETS hybrid algorithms were constructed and compared. The modeling performance of in-sample simulating training sets and pseudo-out-of-sample validating sets were evaluated by metrics of the root mean square error (RMSE), mean absolute percentage error (MAPE), mean absolute error (MAE), and mean absolute scaled error (MASE).ResultsA total of 191,526 TB cases with a highest incidence rate in 2005 (72.5 per 100,000 person-year) and lowest in 2020 (33.2 per 100,000 person-year), from January-2005 to December-2020 showed a seasonality and steadily declining trend in Taiwan. The monthly incidence rates data were utilized to formulate these forecasting models. Through stepwise screening and assessing of the accuracy metrics, the optimized SARIMA(3,0,0)(2,1,0)12, ETS(A,A,A) and SARIMA-ETS-hybrid models were respectively selected as the candidate models. Regarding the outcome assessment of model performance, the SARIMA-ETS-hybrid model outperformed the ARIMA and ETS in the short term prediction with metrics of RMSE, MAE MAPE, and MASE of 0.084%, 0.067%, 0.646%, and 0.870%, during the pseudo-out-of-sample forecasting period. After projecting ahead to the long term forecasting TB incidence rates, ETS model showed the best performance resulting as a 41.69% (range: 22.1–56.38%) reduction of TB epidemics in 2025 and a 54.48% (range: 33.7–68.7%) reduction in 2030 compared with the 2015 levels.ConclusionThis time series modeling might offer us a rapid surveillance tool for facilitating WHO’s future TB elimination milestone. Our proposed SARIMA-ETS or ETS model outperformed the SARIMA in predicting less or 12–30 months ahead of epidemics, and all models showed better in short or medium-term forecasting than long-term forecasting. creator: Mei-Mei Kuan uri: https://doi.org/10.7717/peerj.13117 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2022 Kuan title: Antimicrobial resistance among Streptococcus equi subspecies zooepidemicus and Rhodococcus equi isolated from equine specimens submitted to a diagnostic laboratory in Kentucky, USA link: https://peerj.com/articles/13682 last-modified: 2022-09-21 description: BackgroundSurveillance of antimicrobial resistance (AMR) among veterinary pathogens is necessary to identify clinically relevant patterns of AMR and to inform antimicrobial use practices. Streptococcus equi subsp. zooepidemicus and Rhodococcus equi are bacterial pathogens of major clinical importance in horses and are frequently implicated in respiratory tract infections. The objectives of this study were to describe antimicrobial resistance patterns and identify predictors of AMR and multidrug resistance (MDR) (resistance to three or more antimicrobial classes) among equine S. zooepidemicus and R. equi isolates.MethodsAntimicrobial susceptibility data from equine specimens submitted to the University of Kentucky Veterinary Diagnostic Laboratory between 2012 and 2017 were used in the study. Temporal trends in AMR and MDR were assessed using the Cochran-Armitage test. Logistic regression was used to identify associations between patient characteristics and the following outcomes: (a) MDR among S. zooepidemicus isolates, and (b) resistance to macrolides and ansamycins (rifampin) among R. equi isolates. Logistic regression was also used to investigate whether resistance of S. zooepidemicus and R. equi isolates to an antimicrobial class could be predicted by resistance to other drug classes.ResultsThe vast majority of S. zooepidemicus (99.6%) and R. equi isolates (83%) were resistant to at least one antimicrobial agent, but no significant temporal trends in AMR were observed. Approximately half (53.3%) of the S. zooepidemicus isolates were multidrug-resistant, and there was a significant (p < 0.001) increasing temporal trend of MDR among S. zooepidemicus isolates. Resistance to penicillin, which is typically recommended for treatment of suspected S. zooepidemicus infections, also increased during the study period, from 3.3% to 9.5%. Among R. equi isolates, 19.2% were resistant to one or more macrolide antibiotics, 24% were resistant to rifampin, and 15.6% were resistant to both macrolide(s) and rifampin. For both organisms, resistance to an antimicrobial class could be predicted based on resistance profiles to other drug classes. For instance, significant (p < 0.01) predictors of β-lactam resistance among S. zooepidemicus isolates included resistance to macrolides (Odds Ratio (OR) = 14.7) and ansamycins (OR = 9.3). Resistance to phenicols (OR = 3.7) and ansamycins (OR = 19.9) were associated with higher odds of macrolide resistance among R. equi isolates.ConclusionsThe increase in MDR among S. zooepidemicus isolates is concerning. The observed levels of resistance to macrolides and rifampin among R. equi are also worrisome given the limited number of antimicrobials available for treatment of this organism. The findings of this study highlight the importance of ongoing surveillance of AMR to guide treatment decisions and directions for future research. creator: Jennifer Lord creator: Craig Carter creator: Jacqueline Smith creator: Stephan Locke creator: Erica Phillips creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.13682 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lord et al. title: Association between EPHA5 methylation status in peripheral blood leukocytes and the risk and prognosis of gastric cancer link: https://peerj.com/articles/13774 last-modified: 2022-09-21 description: PurposeAltered DNA methylation, genetic alterations, and environmental factors are involved in tumorigenesis. As a tumor suppressor gene, abnormal EPHA5 methylation was found in gastric cancer (GC) tissues and was linked to the initiation, progression and prognosis of GC. In this study, the EPHA5 methylation level in peripheral blood leukocytes (PBLs) was detected to explore its relationship with GC risk and prognosis.MethodsA total of 366 GC cases and 374 controls were selected as the subjects of this study to collect their environmental factors, and the EPHA5 methylation status was detected through the methylation-sensitive high-resolution melting method. Logistic regression analysis was utilized to evaluate the associations among EPHA5 methylation, environmental factors and GC risk. Meanwhile, the propensity score (PS) was used to adjust the imbalance of some independent variables.ResultsAfter PS adjustment, EPHA5 Pm (positive methylation) was more likely to increase the GC risk than EPHA5 Nm (negative methylation) (ORb = 1.827, 95% CI [1.202–2.777], P = 0.005). EPHA5 Pm had a more significant association with GC risk in the elderly (ORa = 2.785, 95% CI [1.563–4.961], P = 0.001) and H. pylori-negative groups (ORa = 2.758, 95% CI [1.369–5.555], P = 0.005). Moreover, the combined effects of EPHA5 Pm and H. pylori infection (ORca = 3.543, 95% CI [2.233–5.621], P < 0.001), consumption of alcohol (ORca = 2.893, 95% CI [1.844–4.539], P < 0.001), and salty food intake (ORca = 4.018, 95% CI [2.538–6.362], P < 0.001) on increasing the GC risk were observed. In addition, no convincing association was found between EPHA5 Pm and the GC prognosis.ConclusionsEPHA5 methylation in PBLs and its combined effects with environmental risk factors are related to the GC risk. creator: Xu Han creator: Tianyu Liu creator: Jiabao Zhai creator: Chang Liu creator: Wanyu Wang creator: Chuang Nie creator: Qi Wang creator: Xiaojie Zhu creator: Haibo Zhou creator: Wenjing Tian uri: https://doi.org/10.7717/peerj.13774 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Han et al. title: DNA metabarcoding reveals that coyotes in New York City consume wide variety of native prey species and human food link: https://peerj.com/articles/13788 last-modified: 2022-09-21 description: Carnivores are currently colonizing cities where they were previously absent. These urban environments are novel ecosystems characterized by habitat degradation and fragmentation, availability of human food, and different prey assemblages than surrounding areas. Coyotes (Canis latrans) established a breeding population in New York City (NYC) over the last few decades, but their ecology within NYC is poorly understood. In this study, we used non-invasive scat sampling and DNA metabarcoding to profile vertebrate, invertebrate, and plant dietary items with the goal to compare the diets of urban coyotes to those inhabiting non-urban areas. We found that both urban and non-urban coyotes consumed a variety of plants and animals as well as human food. Raccoons (Procyon lotor) were an important food item for coyotes within and outside NYC. In contrast, white-tailed deer (Odocoileus virginianus) were mainly eaten by coyotes inhabiting non-urban areas. Domestic chicken (Gallus gallus) was the human food item found in most scats from both urban and non-urban coyotes. Domestic cats (Felis catus) were consumed by urban coyotes but were detected in only a small proportion of the scats (<5%), which differs markedly from high rates of cat depredation in some other cities. In addition, we compared our genetic metabarcoding analysis to a morphological analysis of the same scat samples. We found that the detection similarity between the two methods was low and it varied depending on the type of diet item. creator: Carol S. Henger creator: Emily Hargous creator: Christopher M. Nagy creator: Mark Weckel creator: Claudia Wultsch creator: Konstantinos Krampis creator: Neil Duncan creator: Linda Gormezano creator: Jason Munshi-South uri: https://doi.org/10.7717/peerj.13788 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Henger et al. title: DDX17 modulates the expression and alternative splicing of genes involved in apoptosis and proliferation in lung adenocarcinoma cells link: https://peerj.com/articles/13895 last-modified: 2022-09-21 description: BackgroundThe DEAD-box RNA-binding protein (RBP) DDX17 has been found to be involved in the tumorigenesis of many types of cancers. However, the role of DDX17 in lung adenocarcinoma (LUAD) remains unclear.MethodsWe silenced DDX17 expression in A549 LUAD cells by small interfering RNA (siRNA). Cell proliferation and apoptosis assays were performed to explore the functions of DDX17. Knockdown of DDX17 by siRNA significantly inhibited proliferation and induced apoptosis in A549 cells. We used high-throughput RNA sequencing (RNA-seq) to identify differentially expressed genes (DEGs) and alternative splicing (AS) events in DDX17 knockdown LUAD cells.ResultsDDX17 knockdown increased the expression levels of proapoptotic genes and decreased those of proproliferative genes. Moreover, the DDX17-regulated AS events in A549 cells revealed by computational analysis using ABLas software were strongly validated by quantitative reverse transcription–polymerase chain reaction (RT–qPCR) and were also validated by analysis of The Cancer Genome Atlas (TCGA)-LUAD dataset. These findings suggest that DDX17 may function as an oncogene by regulating both the expression and AS of proliferation- and apoptosis-associated genes in LUAD cells. Our findings may offer new insights into understanding the molecular mechanisms of LUAD and provide a new therapeutic direction for LUAD. creator: Cheng He creator: Gan Zhang creator: Yanhong Lu creator: Jingyue Zhou creator: Zixue Ren uri: https://doi.org/10.7717/peerj.13895 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 He et al. title: Exploring the trends of adaptation and evolution of sclerites with regards to habitat depth in sea pens link: https://peerj.com/articles/13929 last-modified: 2022-09-21 description: Octocorals possess sclerites, small elements comprised of calcium carbonate (CaCO3) that are important diagnostic characters in octocoral taxonomy. Among octocorals, sea pens comprise a unique order (Pennatulacea) that live in a wide range of depths. Habitat depth is considered to be important in the diversification of octocoral species, but a lack of information on sea pens has limited studies on their adaptation and evolution across depth. Here, we aimed to reveal trends of adaptation and evolution of sclerite shapes in sea pens with regards to habitat depth via phylogenetic analyses and ancestral reconstruction analyses. Colony form of sea pens is suggested to have undergone convergent evolution and the loss of axis has occurred independently across the evolution of sea pens. Divergences of sea pen taxa and of sclerite forms are suggested to depend on habitat depths. In addition, their sclerite forms may be related to evolutionary history of the sclerite and the surrounding chemical environment as well as water temperature. Three-flanged sclerites may possess the tolerance towards the environment of the deep sea, while plate sclerites are suggested to be adapted towards shallower waters, and have evolved independently multiple times. The common ancestor form of sea pens was predicted to be deep-sea and similar to family Pseudumbellulidae in form, possessing sclerites intermediate in form to those of alcyonaceans and modern sea pens such as spindles, rods with spines, and three-flanged sclerites with serrated edges sclerites, as well as having an axis and bilateral traits. creator: Yuka Kushida creator: Yukimitsu Imahara creator: Hin Boo Wee creator: Iria Fernandez-Silva creator: Jane Fromont creator: Oliver Gomez creator: Nerida Wilson creator: Taeko Kimura creator: Shinji Tsuchida creator: Yoshihiro Fujiwara creator: Takuo Higashiji creator: Hiroaki Nakano creator: Hisanori Kohtsuka creator: Akira Iguchi creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.13929 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kushida et al. title: Trans-Arctic vicariance in Strongylocentrotus sea urchins link: https://peerj.com/articles/13930 last-modified: 2022-09-21 description: The sea urchins Strongylocentotus pallidus and S. droebachiensis first invaded the Atlantic Ocean from the Pacific following the opening of the Bering seaway in the late Miocene. While trans-Arctic dispersal during the Pleistocene is thought to have maintained species’ integrity, a recent genomic analysis identified a reproductively isolated cryptic species within S. droebachiensis. Based on previous studies, the distribution of one of these lineages (S. droebachiensis W) includes the shallow water habitats of the northwest Atlantic and Pacific, while the other (S. droebachiensis E) is found throughout the shallow habitat in the northeast but is mostly restricted to deep habitats (>65 m) in the northwest Atlantic. However, since genetic variation within S. droebachiensis has been largely unstudied in the north Pacific and Arctic oceans, the biogeography of the cryptic species is not well known, and it is difficult to identify the mechanisms driving population subdivision and speciation. Here we use population genetic analyses to characterize the distribution of each species, and to test hypotheses about the role of vicariance in the evolution of systematic and genomic divergence within the genus. We collected individuals of all three Strongylocentrotus species (n = 365) from 10 previously unsampled locations in the northeast Pacific and north Atlantic (Labrador Sea and Norway), and generated mtDNA sequence data for a 418 bp fragment of cytochrome c oxidase subunit I (COI). To assess the biogeography of all three species, we combined our alignment with five previously published data sets (total n = 789) and used statistical parsimony and maximum likelihood to identify species and characterize their distribution within and among oceans. Patterns of haplotype sharing, pairwise FST, and hierarchical analyses of molecular variance (AMOVA) identified trans-Arctic dispersal in S. pallidus and S. droebachiensis W, but other than 5 previously reported singletons we failed to detect additional mtDNA haplotypes of S. droebachiensis E in the north Pacific. Within the Atlantic, patterns of habitat segregation suggests that temperature may play a role in limiting the distribution of S. droebachiensis E, particularly throughout the warmer coastal waters along the coast of Nova Scotia. Our results are consistent with the cycles of trans-Arctic dispersal and vicariance in S. pallidus and S. droebachiensis W, but we suggest that the evolution of Atlantic populations of S. droebachiensis E has been driven by persistent trans-Arctic vicariance that may date to the initial invasion in the late Pliocene. creator: Jason A. Addison creator: Jinhong Kim uri: https://doi.org/10.7717/peerj.13930 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Addison and Kim title: RNA sequencing-based identification of microRNAs in the antler cartilage of Gansu red deer (Cervus elaphus kansuensis) link: https://peerj.com/articles/13947 last-modified: 2022-09-21 description: BackgroundThe velvet antler is a complex mammalian bone organ with unique biological characteristics, such as regeneration. The rapid growth stage (RGS) is a special period in the regeneration process of velvet antler.MethodsTo elucidate the functions of microRNAs (miRNAs) at the RGS of antler development in Gansu red deer (Cervus elaphus kansuensis), we used RNA sequencing (RNA-seq) to analyze miRNA expression profiles in cartilage tissues of deer antler tips at three different growth stages.ResultsThe RNA-seq results revealed 1,073 known and 204 novel miRNAs, including 1,207, 1,242, and 1,204 from 30-, 60-, and 90-d antler cartilage tissues, respectively. To identify key miRNAs controlling rapid antler growth, we predicted target genes of screened 25 differentially expressed miRNAs (DEMs) and specifically expressed miRNAs (SEMs) in 60 d and annotated their functions. The KEGG results revealed that target genes of 25 DEMs and 30 SEMs were highly classified in the “Metabolic pathways”, “Pathways in cancer”, “Proteoglycans in cancer” and “PI3K-Akt signaling pathway”. In addition, a novel miRNA (CM008039.1_315920), highly enriched in “NF-kappa B signaling pathway”, may need further study.ConclusionsThe miRNAs identified in our study are potentially important in rapid antler growth. Our findings provide new insights to help elucidate the miRNA-mediated regulatory mechanisms involved during velvet antler development in C. elaphus kansuensis. creator: Yanxia Chen creator: Zhenxiang Zhang creator: Jingjing Zhang creator: Xiaxia Chen creator: Yuqin Guo creator: Changzhong Li uri: https://doi.org/10.7717/peerj.13947 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: IRF7-deficient MDCK cell based on CRISPR/Cas9 technology for enhancing influenza virus replication and improving vaccine production link: https://peerj.com/articles/13989 last-modified: 2022-09-21 description: The influenza virus is a cause of seasonal epidemic disease and enormous economic injury. The best way to control influenza outbreaks is through vaccination. The Madin-Darby canine kidney cell line (MDCK) is currently approved to manufacture influenza vaccines. However, the viral load from cell-based production is limited by host interferons (IFN). Interferon regulating factor 7 (IRF7) is a transcription factor for type-I IFN that plays an important role in regulating the anti-viral mechanism and eliminating viruses. We developed IRF7 knock-out MDCK cells (IRF7−/ − MDCK) using CRISPR/Cas9 technology. The RNA expression levels of IRF7 in the IRF7−/ − MDCK cells were reduced by 94.76% and 95.22% under the uninfected and infected conditions, respectively. Furthermore, the IRF7 protein level was also significantly lower in IRF7−/ − MDCK cells for both uninfected (54.85% reduction) and viral infected conditions (32.27% reduction) compared to WT MDCK. The differential expression analysis of IFN-related genes demonstrated that the IRF7−/ − MDCK cell had a lower interferon response than wildtype MDCK under the influenza-infected condition. Gene ontology revealed down-regulation of the defense response against virus and IFN-gamma production in IRF7−/ − MDCK. The evaluation of influenza viral titers by RT-qPCR and hemagglutination assay (HA) revealed IRF7−/ − MDCK cells had higher viral titers in cell supernatant, including A/pH1N1 (4 to 5-fold) and B/Yamagata (2-fold). Therefore, the IRF7−/ − MDCK cells could be applied to cell-based influenza vaccine production with higher capacity and efficiency. creator: Oraphan Mayuramart creator: Witthaya Poomipak creator: Somruthai Rattanaburi creator: Kritsada Khongnomnan creator: Songtham Anuntakarun creator: Suthat Saengchoowong creator: Tanit Chavalit creator: Naphat Chantaravisoot creator: Sunchai Payungporn uri: https://doi.org/10.7717/peerj.13989 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mayuramart et al. title: Identification and expression profile analysis of the SnRK2 gene family in cucumber link: https://peerj.com/articles/13994 last-modified: 2022-09-21 description: The sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a plant-specific type of serine/threonine protein kinase that plays an important role in the physiological regulation of stress. The objective of this study was to identify and analyze the members of the SnRK2 gene family in cucumber and lay a foundation for further exploration of the mechanism of CsSnRK2 resistance to stress. Here, 12 SnRK2 genes were isolated from cucumber and distributed on five chromosomes, phylogenetic clustering divided these into three well-supported clades. In addition, collinearity analysis showed that the CsSnRK2 gene family underwent purifying selection pressure during evolution. CsSnRK2 genes of the same group have similar exons and conserved motifs, and intron length may be a specific imprint for the evolutionary amplification of the CsSnRK2 gene family. By predicting cis elements in the promoter, we found that the promoter region of CsSnRK2 gene members had various cis-regulatory elements in response to hormones and stress. Relative expression analysis showed that CsSnRK2.11 (group II) and CsSnRK2.12 (group III) were strongly induced by ABA, NaCl and PEG stress; whereas CsSnRK2.2 (group III) was not activated by any treatment. The response of group I CsSnRK2 to ABA, NaCl and PEG was weak. Furthermore, protein interaction prediction showed that multiple CsSnRK2 proteins interacted with four proteins including protein phosphatase 2C (PP2C), and it is speculated that the CsSnRK2 genes may also an independent role as a third messenger in the ABA signaling pathway. This study provides a reference for analyzing the potential function of CsSnRK2 genes in the future research. creator: Zilong Wan creator: Shilei Luo creator: Zeyu Zhang creator: Zeci Liu creator: Yali Qiao creator: Xueqin Gao creator: Jihua Yu creator: Guobin Zhang uri: https://doi.org/10.7717/peerj.13994 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wan et al. title: Effect of ZnO and CuO nanoparticles on the growth, nutrient absorption, and potential health risk of the seasonal vegetable Medicago polymorpha L. link: https://peerj.com/articles/14038 last-modified: 2022-09-21 description: BackgroundMedicago polymorpha L., a seasonal vegetable, is commonly grown in China. The increasing use of nanoparticles (NPs) such as ZnO and CuO NPs in agriculture has raised concerns about their potential risks for plant growth and for human consumption. There is a lack of research on the effects of ZnO and CuO NPs on agronomic performance of Medicago polymorpha L. and their potential risks for human health.MethodsIn this study, different treatment concentrations of ZnO NPs (25, 50, 100, and 200 mg kg−1) and CuO NPs (10, 25, 50, and 100 mg kg−1) were used to determine their effects on the growth and nutrient absorption of Medicago polymorpha L., as well as their potential risk for human health.ResultsThe results showed that ZnO and CuO NPs increased the fresh weight of Medicago polymorpha L. by 5.8–11.8 and 3.7–8.1%, respectively. The best performance for ZnO NPs occurred between 25–50 mg kg−1 and the best performance for CuO NPs occurred between 10–25 mg kg−1. Compared with the control, ZnO and CuO NPs improved the macronutrients phosphorus (P), potassium (K), magnesium (Mg), and calcium (Ca). The following micronutrients were also improved: iron (Fe), nickel (Ni), copper (Cu), zinc (Zn), and manganese (Mn), with the exception of nitrogen (N) accumulation. Low treatment concentrations exhibited more efficient nutrient uptake than high treatment concentrations. A comprehensive analysis showed that the optimum concentrations were 25 mg kg−1 for ZnO NPs and 10 mg kg−1 for CuO NPs. The potential non-carcinogenic health risk of Medicago polymorpha L. treated with ZnO and CuO NPs was analyzed according to the estimated daily intake (EDI), the hazard quotient (HQ), and the cumulative hazard quotient (CHQ). Compared with the oral reference dose, the EDI under different ZnO and CuO NPs treatments was lower. The HQ and CHQ under different ZnO and CuO NPs treatments were far below 1. This indicated that Medicago polymorpha L. treated with ZnO and CuO NPs did not pose any non-carcinogenic health risk to the human body. Therefore, ZnO and CuO NPs were considered as a safe nano fertilizer for Medicago polymorpha L. production according to growth analysis and a human health risk assessment. creator: Hongting Ji creator: Zhi Guo creator: Guodong Wang creator: Xin Wang creator: Hongjiang Liu uri: https://doi.org/10.7717/peerj.14038 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ji et al. title: Physiological and biochemical responses of hybrid maize (Zea mays L.) varieties grown under heat stress conditions link: https://peerj.com/articles/14141 last-modified: 2022-09-21 description: Maize (Zea mays L.) is the second most commonly produced and consumed crop after wheat globally and is adversely affected by high heat, which is a significant abiotic stress factor. This study was carried out to determine the physiological and biochemical responses of hybrid corn varieties under heat stress (‘HS’) compared to control (‘C’) conditions during the 2020 and 2021 growing seasons. The experiment was conducted under natural conditions in the Southeastern region of Turkey, where the most intense temperatures are experienced. This experiment used split plots in randomized blocks with three replications, with ‘HS’ and ‘C’ growing conditions applied to the main plots and the different hybrid corn varieties (FAO 650) planted on the sub plots. Mean values of days to 50% tasseling (DT, day), grain yield (GY, kg ha−1), leaf water potential (LWP, %), chlorophyll-a (Chl-a, mg g−1), cell membrane damage (CMD, %), and total phenol content (TPC, μg g−1) were significantly different between years, growing conditions, and hybrid corn varieties. Changes in the climate played a significant role in the differences between the years and growing conditions (GC), while the genetic characteristics of the different corn varieties explained the differences in outcomes between them. The values of DT, GY, LWP, Chl-a, CMD, and TPC ranged from 49.06–53.15 days, 9,173.0–10,807.2 kg ha−1, 78.62–83.57%, 6.47–8.62 mg g−1, 9.61–13.54%, and 232.36–247.01 μg g−1, respectively. Significant correlations were recorded between all the parameters. Positive correlations were observed between all the variables except for CMD. The increased damage to cell membranes under ‘HS’ caused a decrease in the other measured variables, especially GY. In contrast, the GY increased with decreased CMD. CMD was important in determining the stress and tolerance level of corn varieties under ‘HS’ conditions. The GY and other physiological parameters of ADA 17.4 and SYM-307 candidate corn varieties surpassed the control hybrid corn cultivars. The results revealed that the ADA 17.4 and SYM-307 cultivars might have ‘HS’-tolerate genes. creator: Timucin Tas uri: https://doi.org/10.7717/peerj.14141 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tas title: High metabolic load distance in professional soccer according to competitive level and playing positions link: https://peerj.com/articles/13318 last-modified: 2022-09-20 description: BackgroundHigh metabolic load distance provides global information about the soccer players’ total high-intensity activities. Thus, this study aimed to examine the Spanish professional soccer players’ high metabolic load distance profile, comparing competitive level and playing positions.MethodsA total of 18,131 individual match observations were collected from outfield players competing during the 2018/2019 and 2019/20 seasons in the First and Second Spanish Professional Soccer Leagues (LaLiga™). High Metabolic Load Distance (HMLD; distance covered with a power consumption above 25.5 W·kg−1 and accelerations or decelerations (e.g., accelerating from 2 to 4 m·s−2 for 1 s) were included), and HMLD per minute (HMLDmin) were analyzed by the ChryonHego® video-tracking system. Players were classified according to their playing position as follows: Central Backs (CB), Full Backs (FB), Center Midfields (CM), Wide Midfields (WM), and Forwards (FW).ResultsNo differences between competitive levels were found in any variable when all players were analyzed conjointly except for HMLDmin overall and during the second half. However, when playing positions were considered, differences between competitive levels were observed in all positions, mainly in HMLD and HMLD during the first-half variables. In addition, several differences between playing positions were observed, with CB presenting the lowest values in all variables compared to their counterparts in both competitive levels, whereas CM in First Division and WM in Second Division showed the highest values in the HMLD variables.DiscussionThe findings are of interest to analyze the HMLD in professional soccer players, enabling the adaptation and individualization of training in this population according to the competitive level and specific playing position of each player. creator: Tomás García-Calvo creator: José Carlos Ponce-Bordón creator: Eduard Pons creator: Roberto López del Campo creator: Ricardo Resta creator: Javier Raya-González uri: https://doi.org/10.7717/peerj.13318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 García-Calvo et al. title: Context dependent prediction in DNA sequence using neural networks link: https://peerj.com/articles/13666 last-modified: 2022-09-20 description: One way to better understand the structure in DNA is by learning to predict the sequence. Here, we trained a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model was a neural network that obtained an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, the neural network performed significantly better than any of the alternative models by a large margin. We report on where the accuracy was obtained, first observing that the performance appeared to be uniform over the chromosomes. The models performed best in repetitive sequences, as expected, although their performance far from random in the more difficult coding sections, the proportions being ~70:40%. We further explored the sources of the accuracy, Fourier transforming the predictions revealed weak but clear periodic signals. In the human genome the characteristic periods hinted at connections to nucleosome positioning. We found similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before. On other large genomes similarly high accuracy was found, while lower predictive accuracy was observed on smaller genomes. Only in the mouse genome did we see periodic signals in the same range as in the human genome, though weaker and of a different type. This indicates that the sources of these signals are other or more than nucleosome arrangement. Interestingly, applying a model trained on the mouse genome to the human genome resulted in a performance far below that of the human model, except in the difficult coding regions. Despite the clear outcomes of the likelihood-ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures. creator: Christian Grønbæk creator: Yuhu Liang creator: Desmond Elliott creator: Anders Krogh uri: https://doi.org/10.7717/peerj.13666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Grønbæk et al. title: Bioinformatics prediction and experimental verification of key biomarkers for diabetic kidney disease based on transcriptome sequencing in mice link: https://peerj.com/articles/13932 last-modified: 2022-09-20 description: BackgroundDiabetic kidney disease (DKD) is the leading cause of death in people with type 2 diabetes mellitus (T2DM). The main objective of this study is to find the potential biomarkers for DKD.Materials and MethodsTwo datasets (GSE86300 and GSE184836) retrieved from Gene Expression Omnibus (GEO) database were used, combined with our RNA sequencing (RNA-seq) results of DKD mice (C57 BLKS-32w db/db) and non-diabetic (db/m) mice for further analysis. After processing the expression matrix of the three sets of data using R software “Limma”, differential expression analysis was performed. The significantly differentially expressed genes (DEGs) (—logFC— > 1, p-value < 0.05) were visualized by heatmaps and volcano plots respectively. Next, the co-expression genes expressed in the three groups of DEGs were obtained by constructing a Venn diagram. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were further analyzed the related functions and enrichment pathways of these co-expression genes. Then, qRT-PCR was used to verify the expression levels of co-expression genes in the kidney of DKD and control mice. Finally, protein-protein interaction network (PPI), GO, KEGG analysis and Pearson correlation test were performed on the experimentally validated genes, in order to clarify the possible mechanism of them in DKD.ResultsOur RNA-seq results identified a total of 125 DEGs, including 59 up-regulated and 66 down-regulated DEGs. At the same time, 183 up-regulated and 153 down-regulated DEGs were obtained in GEO database GSE86300, and 76 up-regulated and 117 down-regulated DEGs were obtained in GSE184836. Venn diagram showed that 13 co-expression DEGs among the three groups of DEGs. GO analysis showed that biological processes (BP) were mainly enriched inresponse to stilbenoid, response to fatty acid, response to nutrient, positive regulation of macrophage derived foam cell differentiation, triglyceride metabolic process. KEGG pathway analysis showed that the three major enriched pathways were cholesterol metabolism, drug metabolism–cytochrome P450, PPAR signaling pathway. After qRT-PCR validation, we obtained 11 genes that were significant differentially expressed in the kidney tissues of DKD mice compared with control mice. (The mRNA expression levels of Aacs, Cpe, Cd36, Slc22a7, Slc1a4, Lpl, Cyp7b1, Akr1c14 and Apoh were declined, whereas Abcc4 and Gsta2 were elevated).ConclusionOur study, based on RNA-seq results, GEO databases and qRT-PCR, identified 11 significant dysregulated DEGs, which play an important role in lipid metabolism and the PPAR signaling pathway, which provide novel targets for diagnosis and treatment of DKD. creator: Jing Zhao creator: Kaiying He creator: Hongxuan Du creator: Guohua Wei creator: Yuejia Wen creator: Jiaqi Wang creator: Xiaochun Zhou creator: Jianqin Wang uri: https://doi.org/10.7717/peerj.13932 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhao et al. title: Sexual dimorphism in the walrus mandible: comparative description and geometric morphometrics link: https://peerj.com/articles/13940 last-modified: 2022-09-20 description: The modern walrus Odobenus rosmarus is characterized by marked sexual dimorphism, related to its polygynous behavior and the aggressive competition between males during the breeding season. Previous studies treated skeletal sexual dimorphism in walruses either qualitatively or with basic quantitative measurements. The present study combines a detailed qualitative comparison of male and female walrus mandibles with quantitative two-dimensional geometric morphometrics analysis (principal component analysis, Procrustes ANOVA and a linear discriminant analysis). In addition to identifying previously recognized sexually dimorphic features (e.g., convexity of the anterior margin of the mandible in adult males), our study finds new morphological differences between males and females, such as a relative dorsal expansion of the anterior part of the mandible and an accentuated concavity between the dorsal margin and the coronoid process in adult males. Both our qualitative comparisons and quantitative analyses demonstrate that sexual dimorphism as expressed in the mandible of extant walruses is statistically significant and that (variation in) mandibular morphology can be used as tool to attribute sex with a good degree of accuracy to isolated mandibles or skeletons lacking the cranium. Sexual dimorphism in walruses is directly related to their sexual behavior, characterized as aggressive in males and linked to a polygynous reproduction system. Indeed, the difference in size of the tusks between males and females but also the use of these during intraspecific fights, can reasonably account for this great mandibular morphological disparity between adult males and females, but also among different ontogenetic stages. Finally, the results obtained in the present study may serve as a starting point for assessing sexual dimorphism more in-depth and studying inter- and intraspecific variation in the mandibles of fossil walruses by identifying quantified size and shape mandibular features. creator: Mathieu Boisville creator: Narimane Chatar creator: Olivier Lambert creator: Leonard Dewaele uri: https://doi.org/10.7717/peerj.13940 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Boisville et al. title: Thermography in ergonomic assessment: a study of wood processing industry workers link: https://peerj.com/articles/13973 last-modified: 2022-09-20 description: BackgroundWorkers in the wood processing industry perform activities that demand great physical and ergonomic demands, which favors the emergence of inflammatory processes and in turn the occurrence of heat regions in the body, thus making it possible to assess the inflammatory level by means of temperature gradients. This study aimed to evaluate the use of thermography as an ergonomic analysis tool to identify regions with musculoskeletal overload in workers in a wood processing industry.MethodsThe study was conducted with nine workers in the central-west region of Brazil. The evaluations to obtain the thermographic images were carried out before the beginning of the workday, on Monday (day I) and on Friday (day II), in order to verify the overload regions in the accumulation of days worked. The thermal images were collected in an acclimatized room with controlled conditions where the participants remained with the upper part of their bodies bare for acclimatization, and then the lumbar and scapular regions were evaluated. The images were obtained using the FLUKE TI 400 Thermal Imager, with analysis using the SmartView software program to demarcate the body regions of interest.ResultsThe mean temperature values obtained on day I did not significantly differ from the mean values obtained on day II. Qualitative analysis showed thermal patterns with high temperature at the same points on both evaluated days. Although the thermographic analysis performed in this study cannot provide definitive results, they generally helped to provide evidence for a more accurate diagnosis in the evaluated workers. creator: Denise Ransolin Soranso creator: Luciano José Minette creator: Marcio Marçal creator: João Carlos Bouzas Marins creator: Stanley Schettino creator: Roldão Carlos A. Lima creator: Michel Oliveira uri: https://doi.org/10.7717/peerj.13973 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Soranso et al. title: Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of Plukenetia volubilis link: https://peerj.com/articles/13998 last-modified: 2022-09-20 description: BackgroundPlukenetia volubilis is cultivated as a valuable oilseed crop, and its mature seeds are rich in polyunsaturated fatty acids (FAs), which are widely used in food and pharmaceutical industries. Recently, next-generation sequencing (NGS) transcriptome studies in P. volubilis indicated that some candidate genes were involved in oil biosynthesis. The NGS were inaccuracies in assembly of some candidate genes, leading to unknown errors in date analyses. However, single molecular real-time (SMRT) sequencing can overcome these assembled errors. Unfortunately, this technique has not been reported in P. volubilis.MethodsThe total oil content of P. volubilis seed (PVS) was determined using Soxhlet extraction system. The FA composition were analyzed by gas chromatography. Combining PacBio SMRT and Illumina technologies, the transcriptome analysis of developing PVS was performed. Functional annotation and differential expression were performed by BLAST software (version 2.2.26) and RSEM software (version 1.2.31), respectively. The lncRNA-targeted transcripts were predicted in developing PVS using LncTar tool.ResultsBy Soxhlet extraction system, the oil content of superior plant-type (SPT) was 13.47% higher than that of inferior plant-type (IPT) at mature PVS. The most abundant FAs were C18:2 and C18:3, among which C18:3 content of SPT was 1.11-fold higher than that of IPT. Combined with PacBio and Illumina platform, 68,971 non-redundant genes were obtained, among which 7,823 long non-coding RNAs (lncRNAs) and 7,798 lncRNA-targeted genes were predicted. In developing seed, the expressions of 57 TFs showed a significantly positive correlation with oil contents, including WRI1-like1, LEC1-like1, and MYB44-like. Comparative analysis of expression profiles between SPT and IPT implied that orthologs of FAD3, PDCT, PDAT, and DAGT2 were possibly important for the accumulation of polyunsaturated FAs. Together, these results provide a reference for oil biosynthesis of P. volubilis and genetic improvement of oil plants. creator: Yijun Fu creator: Kaisen Huo creator: Xingjie Pei creator: Chongjun Liang creator: Xinya Meng creator: Xiqiang Song creator: Jia Wang creator: Jun Niu uri: https://doi.org/10.7717/peerj.13998 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Fu et al. title: Estuarine microbial networks and relationships vary between environmentally distinct communities link: https://peerj.com/articles/14005 last-modified: 2022-09-20 description: Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO3, and SiO4; only NH4 was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. Coastal networks may also be driven by shifts in the abundance of certain taxonomic or functional groups. Sustained monitoring of microbial communities over environmental gradients, both spatial and temporal, is critical to predict microbial dynamics and biogeochemistry in future marine ecosystems. creator: Sean R. Anderson creator: Elizabeth L. Harvey uri: https://doi.org/10.7717/peerj.14005 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Anderson and Harvey title: Hepatic metabolite responses to 4-day complete fasting and subsequent refeeding in rats link: https://peerj.com/articles/14009 last-modified: 2022-09-20 description: BackgroundFasting has been widely used to improve various metabolic diseases in humans. Adaptive fasting is necessary for metabolic adaptation during prolonged fasting, which could overcome the great advantages of short-term fasting. The liver is the main organ responsible for energy metabolism and metabolic homeostasis. To date, we lack literature that describes the physiologically relevant adaptations of the liver during prolonged fasting and refeeding. For that reason, this study aims to evaluate the response of the liver of Sprague-Dawley (SD) rats to prolonged fasting and refeeding.MethodsSixty-six male SD rats were divided into the fasting groups, which were fasted for 0, 4, 8, 12, 24, 48, 72, or 96 h, and the refeeding groups, which were refed for 1, 3, or 6 days after 96 h of fasting. Serum glucose, TG, FFA, β-hydroxybutyrate, insulin, glucagon, leptin, adiponectin and FGF21 levels were assessed. The glucose content, PEPCK activity, TG concentration and FFA content were measured in liver tissue, and the expression of genes involved in gluconeogenesis (PEPCK and G6Pase), ketogenesis (PPARα, CPT-1a and HMGCS2) and the protein expression of nutrient-sensing signaling molecules (AMPK, mTOR and SIRT1) were determined by RT-qPCR and western blotting, respectively.ResultsFasting significantly decreased the body weight, which was totally recovered to baseline after 3 days of refeeding. A 4-day fast triggered an energy metabolic substrate shift from glucose to ketones and caused serum hormone changes and changes in the protein expression levels of nutrient-sensing signaling molecules. Glycogenolysis served as the primary fuel source during the first 24 h of fasting, while gluconeogenesis supplied the most glucose thereafter. Serum FFA concentrations increased significantly with 48 h of fasting. Serum FFAs partly caused high serum β-hydroxybutyrate levels, which became an important energy source with the prolongation of the fasting duration. One day of refeeding quickly reversed the energy substrate switch. Nutrient-sensing signaling molecules (AMPK and SIRT1 but not mTOR signaling) were highly expressed at the beginning of fasting (in the first 4 h). Serum insulin and leptin decreased with fasting initiation, and serum glucagon increased, but adiponectin and FGF21 showed no significant changes. Herein, we depicted in detail the timing of the metabolic response and adaptation of the liver to a 4-day water-only fast and subsequent refeeding in rats, which provides helpful support for the design of safe prolonged and intermittent fasting regimens. creator: Xiukun Sui creator: Hailong Wang creator: Feng Wu creator: Chao Yang creator: Hongyu Zhang creator: Zihan Xu creator: Yaxiu Guo creator: ZhiFeng Guo creator: Bingmu Xin creator: Ting Ma creator: Yinghui Li creator: Zhongquan Dai uri: https://doi.org/10.7717/peerj.14009 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sui et al. title: Melanoleuca subgriseoflava and M. substridula—two new Melanoleuca species (Agaricales, Basidiomycota) described from China link: https://peerj.com/articles/13807 last-modified: 2022-09-19 description: Two new Melanoleuca species, Melanoleuca subgriseoflava and M. substridula, are originally reported and described in China based on both morphological and molecular methods. Melanoleuca subgriseoflava, collected in Liaoning province, is mainly characterized by its greyish-brown to yellowish-grey pileus, creamy to light orange lamellae, greyish-yellow context, round and warted basidiospores and fusiform hymenial cystidia. Melanoleuca substridula, discovered in Sichuan province, is mainly characterized by its light brown to dark brown pileus, whitish lamellae, light brown to greyish-brown stipe, round and warted basidiospores and lack of any forms of cystidia. The phylogenetic relationships as well as divergence-time estimation were analyzed using the combined data set (ITS-nrLSU-RPB2), and the results showed that the two Melanoleuca species formed two distinct lineages. Based on the combination of morphological and molecular data, M. subgriseoflava and M. substridula are confirmed as two new species to science. A theoretical basis is provided for the species diversity of Melanoleuca. creator: Yue Qi creator: Cai-Hong Li creator: Yu-Meng Song creator: Ming Zhang creator: Hong-Bo Guo creator: Xiao-Dan Yu uri: https://doi.org/10.7717/peerj.13807 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Qi et al. title: The antioxidant system response to drought-stressed Diospyros lotus treated with exogenous melatonin link: https://peerj.com/articles/13936 last-modified: 2022-09-19 description: Drought is one of the major abiotic stresses adversely impacting the growth of persimmon, which is a widely cultivated traditional fruit tree in North China. Melatonin is a bio-stimulator involved in mediating plant responses to drought. The role of exogenous melatonin application in the drought tolerance of Diospyros lotus was examined under drought stress with different doses of melatonin (0, 10, 50, and 100 µM). Exogenous melatonin application significantly mitigated the adverse effects of drought stress on chlorophyll fluorescence, lipid peroxidation, reactive oxygen species (ROS) accumulation and nitric oxide (NO) content. The 100-µM melatonin application produced the most beneficial impacts against drought stress. The melatonin-enhanced tolerance could be attributed to improved antioxidant enzymes, reduced drought-induced ROS accumulation, and lipid peroxidation. Melatonin application activated major antioxidant enzymes such as superoxide dismutase, catalase, peroxidase, glutathione reductase, and ascorbate peroxidase. Interestingly, NO concentration was significantly higher in 10 and 50 µM melatonin treatments and lower in 100 µM melatonin treatment compared to the control. Moreover, exogenous melatonin application affected the mRNA transcript levels of several genes involved in ROS metabolism, including DlRBOHA, DlSOD, DlCAT, and DlPOD. Hence, the responses of Diospyros lotus to drought varied with different doses of melatonin. Our results provide a concrete insight into the effects of melatonin with varying doses in alleviating drought as well as a platform for its potential application in the related fields. creator: Peng Zhang creator: Yi Hu creator: Ruijin Zhou creator: Xiaona Zhang creator: Huiling Hu creator: Dongmei Lang uri: https://doi.org/10.7717/peerj.13936 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: The effect of enhanced variability after performance stabilization through constant practice link: https://peerj.com/articles/13733 last-modified: 2022-09-16 description: There is a controversy about the benefits of variable practice on motor learning. This study aimed to analyze the effect of variable practice after the learner stabilized their performance. Thirty-two healthy adults performed a computer-simulated discrete accuracy task in which they had to release a virtual ball to try to hit a target. After a pre-test, the participants were distributed into three training groups: constant practice, variable practice and a group that started practicing in constant conditions, and when their performance stabilized, changed to variable practice. The participants performed 44 sets of 10 repetitions of the task. A post-test and two retention tests were carried out. Variable practice did not show a significant improvement compared to constant practice. Variable practice did not show higher benefits even when performance was stabilized through constant practice, but its effects seem to be modulated by the initial variability of the learners. creator: Carmen Ruano creator: Carla Caballero creator: Francisco J. Moreno uri: https://doi.org/10.7717/peerj.13733 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ruano et al. title: Molecular and behavioral studies reveal differences in olfaction between winter and summer morphs of Drosophila suzukii link: https://peerj.com/articles/13825 last-modified: 2022-09-16 description: Spotted-wing drosophila, Drosophila suzukii (Matsumura), is a major economic pest of several fruit crops in Europe, North and South America, and other parts of the world because it oviposits in ripening thin-skinned fruits. This vinegar fly exhibits two distinct morphotypes: a summer and a winter morph. Although adaptations associated with the winter morph enhance this invasive pest’s capacity to survive in cold climates, winter is still a natural population bottleneck. Since monitoring early spring populations is important for accurate population forecasts, understanding the winter morph’s response to olfactory cues may improve current D. suzukii management programs. In this study, a comparative transcriptome analysis was conducted to assess gene expression differences between the female heads of the two D. suzukii morphs, which showed significant differences in 738 genes (p ≤ 0.0001). Out of twelve genes related to olfaction determined to be differentially expressed in the transcriptome, i.e., those related to location of food sources, chemosensory abilities, and mating behavior, nine genes were upregulated in the winter morph while three were downregulated. Three candidate olfactory-related genes that were most upregulated or downregulated in the winter morph were further validated using RT-qPCR. In addition, behavioral assays were performed at a range of temperatures to confirm a differing behavioral response of the two morphs to food odors. Our behavioral assays showed that, although winter morphs were more active at lower temperatures, the summer morphs were generally more attracted to food odors. This study provides new insights into the molecular and behavioral differences in response to olfactory cues between the two D. suzukii morphs that will assist in formulating more effective monitoring and physiological-based control tools. creator: Timothy W. Schwanitz creator: James J. Polashock creator: Dara G. Stockton creator: Cesar Rodriguez-Saona creator: Diego Sotomayor creator: Greg Loeb creator: Chloe Hawkings uri: https://doi.org/10.7717/peerj.13825 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Schwanitz et al. title: Ontogenetic, dietary, and environmental shifts in Mesosauridae link: https://peerj.com/articles/13866 last-modified: 2022-09-16 description: Mesosaurs are the first secondarily aquatic amniotes and one of the most enigmatic clades of reptiles from the early Permian. They have long puzzled paleontologists with their unique morphologies: possessing an elongated skull with thin needle-like teeth, a long neck, large webbed hindlimbs, banana-shaped pachyosteosclerotic ribs, and a long tail. Here, we look at a large dataset of morphometric measurements from 270 mesosaur specimens in collections around the world. These measurements characterize skull, tooth, and limb proportions and their variation with size. This data presents evidence of surprising ontogenetic changes in these animals as well as new insights into their taxonomy. Our results support the recent hypothesis that Mesosaurus tenuidens is the only valid species within Mesosauridae and suggest that “Stereosternum tumidum” and “Brazilosaurus sanpauloensis” represent immature stages or incomplete specimens of Mesosaurus by showing that all three species occupy an incomplete portion of the overall size range of mesosaurs. Under the single-species hypothesis, we highlight a number of ontogenetic trends: (1) a reduction in skull length accompanied by an elongation of the snout within the skull, (2) an elongation of teeth, (3) a reduction in hind limb length, and (4) a reduction in manus length. Concurrent with these changes, we hypothesize that mesosaurs went through a progressive ecological shift during their growth, with juveniles being more common in shallow water deposits, whereas large adults are more frequent in pelagic sediments. These parallel changes suggest that mesosaurs underwent a diet and lifestyle transition during ontogeny, from an active predatory lifestyle as juveniles to a more filter-feeding diet as adults. We propose that this change in lifestyle and environments may have been driven by the pursuit of different food sources, but a better understanding of the Irati Sea fauna will be necessary to obtain a more definitive answer to the question of young mesosaur diet. creator: Antoine Verrière creator: Jörg Fröbisch uri: https://doi.org/10.7717/peerj.13866 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Verrière and Fröbisch title: Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes link: https://peerj.com/articles/13958 last-modified: 2022-09-16 description: Microbes participate in ecological communities, much like multicellular organisms. However, microbial communities lack the centuries of observation and theory describing and predicting ecological processes available for multicellular organisms. Here, we examine early bacterial community assembly in the water-filled internodes of Amazonian bamboos from the genus Guadua. Bamboo stands form distinct habitat patches within the lowland Amazonian rainforest and provide habitat for a suite of vertebrate and invertebrate species. Guadua bamboos develop sealed, water-filled internodes as they grow. Internodes are presumed sterile or near sterile while closed, but most are eventually opened to the environment by animals, after which they are colonized by microbes. We find that microbial community diversity increases sharply over the first few days of environmental exposure, and taxonomic identity of the microbes changes through this time period as is predicted for early community assembly in macroscopic communities. Microbial community taxonomic turnover is consistent at the bacteria phylum level, but at the level of Operational Taxonomic Units (OTUs), internode communities become increasingly differentiated through time. We argue that these tropical bamboos form an ideal study system for microbial community ecology due to their near-sterile condition prior to opening, relatively consistent environment after opening, and functionally limitless possibilities for replicates. Given the possible importance of opened internode habitats as locations of transmission for both pathogenic and beneficial microbes among animals, understanding the microbial dynamics of the internode habitat is a key conservation concern for the insect and amphibian species that use this microhabitat. creator: Sonia Ahluwalia creator: Iris Holmes creator: Rudolf von May creator: Daniel L. Rabosky creator: Alison R. Davis Rabosky uri: https://doi.org/10.7717/peerj.13958 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ahluwalia et al. title: Effects of L-carnitine supplementation for women with polycystic ovary syndrome: a systematic review and meta-analysis link: https://peerj.com/articles/13992 last-modified: 2022-09-16 description: BackgroundPolycystic ovary syndrome (PCOS) is a disorder in reproductive age women and is characterized by hyperandrogenic anovulation and oligo-amenorrhea, which leads to infertility. Anovulation in PCOS is associated with low follicle-stimulating hormone levels and the arrest of antral follicle development in the final stages of maturation. L-carnitine (LC) plays a role in fatty acid metabolism, which is found to be lacking in PCOS patients. This systematic review and meta-analysis aimed to determine the effectiveness of LC supplementation for patients with PCOS.MethodsWe searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Psychological Information Database (PsycINFO), and the World Health Organization International Clinical Trials Registry Platform for all randomized control trials, comparing LC alone or in combination with other standard treatments for the treatment of PCOS from inception till June 2021. We independently screened titles and abstracts to identify available trials, and complete texts of the trials were checked for eligibility. Data on the methods, interventions, outcomes, and risk of bias from the included trials were independently extracted by the authors. The estimation of risk ratios and mean differences with a 95 percent confidence interval (CI) was performed using a random-effects model.ResultsNine studies with 995 participants were included in this review. Five comparison groups were involved. In one comparison group, LC reduced the fasting plasma glucose (FPG) (mean differences (MD) −5.10, 95% CI [−6.25 to −3.95]; P = 0.00001), serum low-density lipoprotein (LDL) (MD −25.00, 95% CI [−27.93 to −22.07]; P = 0.00001), serum total cholesterol (MD −21.00, 95% CI [−24.14 to −17.86]; P = 0.00001), and serum triglyceride (TG) (MD −9.00, 95% CI [−11.46 to −6.54]; P = 0.00001) with moderate certainty of evidence. Another comparison group demonstrated that LC lowers the LDL (MD −12.00, 95% CI [−15.80 to −8.20]; P = 0.00001), serum total cholesterol (MD −24.00, 95% CI [−27.61 to −20.39]; P = 0.00001), and serum TG (MD −19.00, 95% CI [−22.79 to −15.21]; P = 0.00001) with moderate certainty of evidence.ConclusionThere was low to moderate certainty of evidence that LC improves Body Mass Index (BMI) and serum LDL, TG, and total cholesterol levels in women with PCOS. creator: Mohd Falihin Mohd Shukri creator: Mohd Noor Norhayati creator: Salziyan Badrin creator: Azidah Abdul Kadir uri: https://doi.org/10.7717/peerj.13992 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mohd Shukri et al. title: Understanding the distribution and fine-scale habitat selection of mesocarnivores along a habitat quality gradient in western Himalaya link: https://peerj.com/articles/13993 last-modified: 2022-09-16 description: Background: Human activities have resulted in a rapid increase of modified habitats in proximity to wildlife habitats in the Himalaya. However, it is crucial to understand the extent to which human habitat modification affects wildlife. Mesocarnivores generally possess broader niches than large carnivores and adapt quickly to human activities. Here, we use a case study in the western Himalaya to test the hypothesis that human disturbance influenced mesocarnivore habitat use.Methods: We used camera trapping and mitochondrial DNA-based species identification from faecal samples to obtain mesocarnivore detections. We then compared the responses of mesocarnivores between an anthropogenic site and a less disturbed park along a contiguous gradient in habitat quality. The non-linear pattern in species-specific habitat selection and factors responsible for space usage around villages was captured using hierarchical generalized additive modelling (HGAM) and non-metric multidimensional scaling (NMDS) ordination.Results: Wildlife occurrences along the gradient varied by species. Leopard cat and red fox were the only terrestrial mesocarnivores that occurred in both anthropogenic site and park. We found a shift in habitat selection from less disturbed habitat in the park to disturbed habitat in anthropogenic site for the species detected in both the habitat types. For instance, red fox showed habitat selection towards high terrain ruggedness (0.5 to 0.7 TRI) and low NDVI (−0.05 to 0.2) in the park but no such specific selection in anthropogenic site. Further, leopard cat showed habitat selection towards moderate slope (20°) and medium NDVI (0.5) in park but no prominent habitat selections in anthropogenic site. The results revealed their constrained behaviour which was further supported by the intensive site usage close to houses, agricultural fields and human trails in villages.Conclusions: Our results indicate shifts in habitat selection and intensive site usage by mesocarnivores in the human-modified habitat. In future, this suggests the possibility of conflict and disease spread affecting both the people and wildlife. Therefore, this study highlights the requisite to test the wildlife responses to rapidly growing human expansions in modified habitats to understand the extent of impact. The management strategies need to have an integrated focus for further expansions of modified habitat and garbage disposal strategies, especially in the human-wildlife interface area. creator: Meghna Bandyopadhyay creator: A. Cole Burton creator: Sandeep Kumar Gupta creator: Ramesh Krishnamurthy uri: https://doi.org/10.7717/peerj.13993 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bandyopadhyay et al. title: Shifts in water column microbial composition associated to lakes with different trophic conditions: “Lagunas de Montebello” National Park, Chiapas, México link: https://peerj.com/articles/13999 last-modified: 2022-09-16 description: Eutrophication is a global problem causing the reduction of water quality and the loss of ecosystem goods and services. The lakes of the “Lagunas de Montebello” National Park (LMNP), Chiapas, Mexico, not only represent unique and beautiful natural scenic sites in southern Mexico but are also a national protected area and RAMSAR site. Unfortunately, some of these lakes started showing eutrophication signs since 2003. Anthropogenic activities (e.g., land-use change from forested to agricultural and urban development) are leading to water quality and trophic state alterations of the lakes of the LMNP. This study shows the results of a coupled limnological characterization and high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene to analyze the microbial composition of the water column in a set of oligotrophic and eutrophic lakes. Chlorophyll a (Chl-a) was the main environmental parameter correlated with the trophic conditions of the lakes. Although the microbial diversity was similar, the microbial composition changed significantly from oligo to eutrophic lakes. Proteobacteria, Firmicutes, and Cyanobacteria were the main components of oligotrophic lakes, and Cyanobacteria, Proteobacteria, and Bacteroidetes of eutrophic lakes. While Acinetobacter (Proteobacteria) and Cyanobium (a unicellular cyanobacterium) dominated in oligotrophic lakes, the filamentous, bloom-forming, and toxin-producing cyanobacteria Planktothrix was the dominant genus in eutrophic lakes. High-throughput sequencing allowed the detection of changes in the composition of the microbial component in oligotrophic lakes, suggesting a shift towards eutrophication, highlighting the relevance of sensitive monitoring protocols of these ecosystems to implement remediation programs for eutrophicated lakes and conservation strategies for those yet pristine. creator: Alfredo Yanez-Montalvo creator: Bernardo Aguila creator: Elizabeth Selene Gómez-Acata creator: Miriam Guerrero-Jacinto creator: Luis A. Oseguera creator: Luisa I. Falcón creator: Javier Alcocer uri: https://doi.org/10.7717/peerj.13999 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yanez-Montalvo et al. title: Sex differences in peripheral monoamine transmitter and related hormone levels in chronic stress mice with a depression-like phenotype link: https://peerj.com/articles/14014 last-modified: 2022-09-16 description: BackgroundsChronic stress could induce depression-like phenotype in animal models. Previous data showed that sex differences exist after chronic stress model establishment, however, the detailed information about the difference of blood biochemical indexes is not clear. In this study, we aim to supply comparison of monoamine transmitters and related hormone markers in serum between male and female depressed mice, and in order to better understand the sex difference in transmitters and hormone levels in depression occurrence and development.MethodsSixty C57BL/6 mice (both male and female) were divided into two groups by gender. Same gender mice were then divided randomly into the non-treated control group and chronic stress group which was exposed to 8 weeks of chronic unpredictable mild stress (CUMS). Depression-like behavior was assessed with open-field test and sucrose preference test. Blood sample was collected and monoamine transmitter and related hormone in serum were measured by ELISA.ResultsThe depression-like phenotype mice model was established successfully after 8 weeks of chronic stress. The locomotion activity scores in male stressed mice declined more than that in female stressed mice, while the exploratory behavior scores in female stressed mice declined more than that in male stressed mice. Compared to non-treated control group mice, mice in the chronic stress group in response to stress showed greater declines in monoamine transmitters (5-HT, dopamine, norepinephrine) and sex hormones (androgen, estrogen, oxytocin and prolactin), while stress hormones (adrenaline, corticosterone and ACTH) were significantly increased. The decrease of norepinephrine, androgen and estrogen in female stressed mice was greater than in male stressed mice, whereas the 5-HT and oxytocin in male stressed mice decreased more than in female stressed mice, and the corticosterone in male stressed mice increased more than in female stressed mice.ConclusionSex differences of monoamine transmitter and related hormone levels in serum occurred in chronic stress induced depression-like phenotype mice model. It may provide a useful reference to guide precise antidepressant treatment in different gender population in clinical care. creator: Yitian Chen creator: Weijia Cai creator: Canye Li creator: Zuanjun Su creator: Zhijun Guo creator: Zhuman Li creator: Chen Wang creator: Feng Xu uri: https://doi.org/10.7717/peerj.14014 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: Bayesian estimation of rainfall dispersion in Thailand using gamma distribution with excess zeros link: https://peerj.com/articles/14023 last-modified: 2022-09-16 description: The gamma distribution is commonly used to model environmental data. However, rainfall data often contain zero observations, which violates the assumption that all observations must be positive in a gamma distribution, and so a gamma model with excess zeros treated as a binary random variable is required. Rainfall dispersion is important and interesting, the confidence intervals for the variance of a gamma distribution with excess zeros help to examine rainfall intensity, which may be high or low risk. Herein, we propose confidence intervals for the variance of a gamma distribution with excess zeros by using fiducial quantities and parametric bootstrapping, as well as Bayesian credible intervals and highest posterior density intervals based on the Jeffreys’, uniform, or normal-gamma-beta prior. The performances of the proposed confidence interval were evaluated by establishing their coverage probabilities and average lengths via Monte Carlo simulations. The fiducial quantity confidence interval performed the best for a small probability of the sample containing zero observations (δ) whereas the Bayesian credible interval based on the normal-gamma-beta prior performed the best for large δ. Rainfall data from the Kiew Lom Dam in Lampang province, Thailand, are used to illustrate the efficacies of the proposed methods in practice. creator: Wansiri Khooriphan creator: Sa-Aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.14023 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Khooriphan et al. title: Simulating physiological flexibility in the acute glucocorticoid response to stressors reveals limitations of current empirical approaches link: https://peerj.com/articles/14039 last-modified: 2022-09-16 description: Wild animals often experience unpredictable challenges that demand rapid and flexible responses. The glucocorticoid mediated stress response is one of the major systems that allows vertebrates to rapidly adjust their physiology and behavior. Given its role in responding to challenges, evolutionary physiologists have focused on the consequences of between-individual and, more recently, within-individual variation in the acute glucocorticoid response. However, empirical studies of physiological flexibility are severely limited by the logistical challenges of measuring the same animal multiple times. Data simulation is a powerful approach when empirical data are limited, but has not been adopted to date in studies of physiological flexibility. In this article, I develop a simulation that can generate realistic acute glucocorticoid response data with user specified characteristics. Simulated animals can be sampled continuously through an acute response and across as many separate responses as desired, while varying key parameters. Using the simulation, I develop several scenarios that address key questions in physiological flexibility. These scenarios demonstrate the conditions under which a single glucocorticoid trait can be accurately assessed with typical experimental designs, the consequences of covariation between different components of the acute stress response, and the way that context specific differences in variability of acute responses can influence the power to detect relationships between the strength of the acute stress response and fitness. I also describe how to use the simulation tools to aid in the design and evaluation of empirical studies of physiological flexibility. creator: Conor Taff uri: https://doi.org/10.7717/peerj.14039 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Taff title: Sophocarpine inhibits tumor progression by antagonizing the PI3K/AKT/mTOR signaling pathway in castration-resistant prostate cancer link: https://peerj.com/articles/14042 last-modified: 2022-09-16 description: ObjectiveThe objective of this study was to investigate the inhibitory effect of sophocarpine on the progression of castration-resistant prostate cancer (CRPC) and the underlying molecular mechanism.MethodsDU145 and PC3 cells (two CRPC cell lines), incubated with different concentrations of sophocarpine, were used. Cell Counting Kit-8 assay, real-time cellular analysis, and colony formation assay were conducted to evaluate the proliferation of CRPC cells. Cytometry flow analysis was performed to evaluate the apoptosis rate of CRPC cells. Wound healing and Transwell invasion assays were performed and the levels of the epithelial-mesenchymal transition (EMT)-related proteins were determined to analyze cell migration and invasion abilities. A xenografted tumor model of nude mice was used to examine the anti-cancer effect of sophocarpine on CRPC. Western blotting was performed to evaluate the activities of the PI3K/AKT/mTOR signaling pathway both in cells and tumor tissues.ResultsIn vitro tests showed that sophocarpine suppressed the proliferation of CRPC cells, reduced the migration and invasion abilities, and increased the apoptosis rate. In vivo, sophocarpine decreased the weight and volume of tumor tissues. Mechanically, sophocarpine exerted its anti-cancer effects by inactivating PI3K/AKT/mTOR signaling.ConclusionSophocarpine inhibited the progression of CRPC by downregulating the PI3K/AKT/mTOR signaling pathway and showed a potential to be an anti-cancer agent against CRPC. creator: Min Weng creator: Chenghao Shi creator: Hui Han creator: Hengyue Zhu creator: Yanyi Xiao creator: Hangcheng Guo creator: Zhixian Yu creator: Cunzao Wu uri: https://doi.org/10.7717/peerj.14042 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Weng et al. title: Bombardier beetles repel invasive bullfrogs link: https://peerj.com/articles/13805 last-modified: 2022-09-15 description: Invasive non-native predators negatively affect native species; however, some native species can survive the predation pressures of invasive species by using pre-existing antipredator strategies or evolving defenses against invasive predators. The American bullfrog Lithobates catesbeianus (Anura: Ranidae) has been intentionally introduced to many countries and regions, and has impacted native animals through direct predation. Bombardier beetles (Coleoptera: Carabidae: Brachininae: Brachinini) discharge chemicals at a temperature of approximately 100 °C from the tip of the abdomen when they are attacked by predators. This “bombing” can successfully repel predators. However, adults of a native bombardier beetle Pheropsophus (Stenaptinus) occipitalis jessoensis have been reportedly found in the gut contents of the introduced bullfrog L. catesbeianus in Japan. These records suggest that the invasive bullfrog L. catesbeianus attacks the native bombardier beetle P. occipitalis jessoensis under field conditions in Japan; however, the effectiveness of the bombing defense against invasive bullfrogs is unclear. To test the effectiveness of the bombing defense against bullfrogs, we investigated the behavioral responses of L. catesbeianus juveniles to P. occipitalis jessoensis adults under laboratory conditions. Contrary to previous gut content results, almost all the bullfrogs (96.3%) rejected bombardier beetles before swallowing them; 88.9% rejected the beetles after being bombed, and 7.4% stopped attacking the beetles before being bombed. Only 3.7% successfully swallowed and digested the beetle. All of the beetles collected from non-bullfrog-invaded sites could deter bullfrogs, suggesting that the pre-existing defenses of bombardier beetles played an essential role in repelling bullfrogs. When treated beetles that were unable to discharge hot chemicals were provided, 77.8% of bullfrogs successfully swallowed and digested the treated beetles. These results indicate that bombing is important for the successful defense of P. occipitalis jessoensis against invasive bullfrogs. Although invasive bullfrogs have reportedly impacted native insect species, P. occipitalis jessoensis has an existing defense mechanism strong enough to repel the invasive predators. creator: Shinji Sugiura creator: Tomoki Date uri: https://doi.org/10.7717/peerj.13805 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sugiura and Date title: The backbone symptoms of depression: a network analysis after the initial wave of the COVID-19 pandemic in Macao link: https://peerj.com/articles/13840 last-modified: 2022-09-15 description: BackgroundThe coronavirus disease 2019 (COVID-19) pandemic disrupted the working lives of Macau residents, possibly leading to mental health issues such as depression. The pandemic served as the context for this investigation of the network structure of depressive symptoms in a community sample. This study aimed to identify the backbone symptoms of depression and to propose an intervention target.MethodsThis study recruited a convenience sample of 975 Macao residents between 20th August and 9th November 2020. In an electronic survey, depressive symptoms were assessed with the Patient Health Questionnaire-9 (PHQ-9). Symptom relationships and centrality indices were identified using directed and undirected network estimation methods. The undirected network was constructed using the extended Bayesian information criterion (EBIC) model, and the directed network was constructed using the Triangulated Maximally Filtered Graph (TMFG) method. The stability of the centrality indices was evaluated by a case-dropping bootstrap procedure. Wilcoxon signed rank tests of the centrality indices were used to assess whether the network structure was invariant between age and gender groups.ResultsLoss of energy, psychomotor problems, and guilt feelings were the symptoms with the highest centrality indices, indicating that these three symptoms were backbone symptoms of depression. The directed graph showed that loss of energy had the highest number of outward projections to other symptoms. The network structure remained stable after randomly dropping 50% of the study sample, and the network structure was invariant by age and gender groups.ConclusionLoss of energy, psychomotor problems and guilt feelings constituted the three backbone symptoms during the pandemic. Based on centrality and relative influence, loss of energy could be targeted by increasing opportunities for physical activity. creator: Yan-Jie Zhao creator: Wei Bai creator: Hong Cai creator: Sha Sha creator: Qinge Zhang creator: Si Man Lei creator: Ka-In Lok creator: Ines Hang Iao Chow creator: Teris Cheung creator: Zhaohui Su creator: Lloyd Balbuena creator: Yu-Tao Xiang uri: https://doi.org/10.7717/peerj.13840 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhao et al. title: On the move: spatial ecology and habitat use of red fox in the Trans-Himalayan cold desert link: https://peerj.com/articles/13967 last-modified: 2022-09-15 description: Red fox (Vulpes vulpes) is the most widespread wild carnivore globally, occupying diverse habitats. The species is known for its adaptability to survive in dynamic anthropogenic landscapes. Despite being one of the most extensively studied carnivores, there is a dearth of information on red fox from the Trans-Himalayan region. We studied the home range sizes of red fox using the different estimation methods: minimum convex polygon (MCP), kernel density estimator (KDE), local convex hull (LoCoH) and Brownian-bridge movement model (BBMM). We analysed the daily movement and assessed the habitat selection with respect to topographic factors (ruggedness, elevation and slope), environmental factor (distance to water) and anthropogenic factors (distance to road and human settlements). We captured and GPS-collared six red fox individuals (three males and three females) from Chiktan and one female from Hemis National Park, Ladakh, India. The collars were programmed to record GPS fixes every 15-min. The average BBMM home range estimate (95% contour) was 22.40 ± 12.12 SD km2 (range 3.81–32.93 km2) and the average core area (50% contour) was 1.87 ± 0.86 SD km2 (range 0.55–2.69 km2). The estimated average daily movement of red fox was 17.76 ± 8.45 SD km/d (range 10.91–34.22 km/d). Red fox significantly selected lower elevations with less rugged terrain and were positively associated with water. This is the first study in the Trans-Himalayan landscape which aims to understand the daily movement of red fox at a fine temporal scale. Studying the movement and home range sizes helps understand the daily energetics and nutritional requirements of red fox. Movement information of a species is important for the prioritisation of areas for conservation and can aid in understanding ecosystem functioning and landscape management. creator: Hussain S. Reshamwala creator: Pankaj Raina creator: Zehidul Hussain creator: Shaheer Khan creator: Rodolfo Dirzo creator: Bilal Habib uri: https://doi.org/10.7717/peerj.13967 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Reshamwala et al. title: Transcriptomic analysis and physiological characteristics of exogenous naphthylacetic acid application to regulate the healing process of oriental melon grafted onto squash link: https://peerj.com/articles/13980 last-modified: 2022-09-15 description: The plant graft healing process is an intricate development influenced by numerous endogenous and environmental factors. This process involves the histological changes, physiological and biochemical reactions, signal transduction, and hormone exchanges in the grafting junction. Studies have shown that applying exogenous plant growth regulators can effectively promote the graft healing process and improve the quality of grafted plantlets. However, the physiological and molecular mechanism of graft healing formation remains unclear. In our present study, transcriptome changes in the melon and cucurbita genomes were analyzed between control and NAA treatment, and we provided the first view of complex networks to regulate graft healing under exogenous NAA application. The results showed that the exogenous NAA application could accelerate the graft healing process of oriental melon scion grafted onto squash rootstock through histological observation, increase the SOD, POD, PAL, and PPO activities during graft union development and enhance the contents of IAA, GA3, and ZR except for the IL stage. The DEGs were identified in the plant hormone signal-transduction, phenylpropanoid biosynthesis, and phenylalanine metabolism through transcriptome analysis of CK vs. NAA at the IL, CA, and VB stage by KEGG pathway enrichment analysis. Moreover, the exogenous NAA application significantly promoted the expression of genes involved in the hormone signal-transduction pathway, ROS scavenging system, and vascular bundle formation. creator: Chuanqiang Xu creator: Fang Wu creator: Jieying Guo creator: Shuan Hou creator: Xiaofang Wu creator: Ying Xin uri: https://doi.org/10.7717/peerj.13980 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al. title: Interactions of semiconductor Cd-based quantum dots and Cd2+ with gut bacteria isolated from wild Salmo trutta fry link: https://peerj.com/articles/14025 last-modified: 2022-09-15 description: BackgroundWith the rapid development of nanotechnology, more and more nanoproducts are being released into the environment where they may both pose ecological risks and be toxic to living organisms. The ecotoxicological impact of quantum dots (QDs), a class of nanoparticles (NPs), on aquatic organisms is becoming an emerging issue, this due to their nano-specific properties, to the physico-chemical transformation in the environment and to the possible release of toxic metals from their structure such as Cd.MethodsIn this work, (i) spectroscopic measurements of commercially available Cd-based QDs (CdSe/ZnS-COOH) were made at various pH values (5.0 and 7.0) to study their interactions (at a concentration of 4 nm) with various strains of Gram-positive and Gram-negative gut bacteria after short-term exposure and (ii) the antibacterial efficacy of QDs and Cd2+ (at a concentration 0.09–3.56 mM) against gut bacteria isolated from wild freshwater Salmo trutta fry was studied at different temperatures (15 °C and 25 °C) and pH values (5.0 and 7.0) by applying a well-established disc diffusion assay.ResultsTwenty-six gut bacterial isolates from wild Salmo trutta fry were identified as Aeromonas spp., A. popoffii, A. salmonicida, A. sobria, Carnobacterium maltaromaticum, Buttiauxella sp., Listeria sp., Microbacterium sp., Shewanella putrefaciens and Serratia sp. Cd-based (CdSe/ZnS-COOH) QDs at a concentration of 4 nm were found to be stable in aqueous media (with pH 7.0) or starting to form aggregates (at pH 5.0), thus, apparently, did not release heavy metals (HMs) into the media over 48 h in conditions of light or dark and did not show antibacterial efficacy on the gut bacteria isolated from wild Salmo trutta fry after short-term (9 h and 48 h) incubations. Cd2+ was found to produce significant dose-dependent toxic effects on bacterial growth, and the size of the inhibition zones on some of the tested strains significantly correlated with temperature. The most sensitive and the most resistant to Cd2+ were the Gram-positive bacteria, for which the minimum inhibitory concentration (MIC) values of Cd2+ were 0.09–0.27 mM and 3.11–3.29 mM respectively and varied significantly between the tested temperatures (15 °C and 25 °C). The MIC values of Cd2+ for the Gram-negative bacteria (18 out of 22 strains) ranged from 0.44 to 0.71 mM and did not differ significantly between the tested temperatures. Among the selected Gram-positive and Gram-negative strains, those with the higher sensitivity towards Cd2+ also revealed relatively stronger signals of QDs photoluminescence (PL) when transferred after incubation into fresh medium without QDs. In addition, the formation of endogenous metalloporphyrins observed spectroscopically in some bacterial strains indicates certain differences in metabolic activity that may play a protective role against potential oxidative damage. creator: Renata Butrimienė creator: Agnė Kalnaitytė creator: Emilija Januškaitė creator: Saulius Bagdonas creator: Živilė Jurgelėnė creator: Dalius Butkauskas creator: Tomas Virbickas creator: Danguolė Montvydienė creator: Nijolė Kazlauskienė creator: Vesta Skrodenytė-Arbačiauskienė uri: https://doi.org/10.7717/peerj.14025 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Butrimienė et al. title: CAV1 alleviated CaOx stones formation via suppressing autophagy-dependent ferroptosis link: https://peerj.com/articles/14033 last-modified: 2022-09-15 description: BackgroundCalcium oxalate (CaOx) is the most common type of kidney stone, but the mechanism of CaOx stones formation remains unclear. The injury of renal cells such as ferroptosis and autophagy has been considered a basis for stones formation.MethodsWe conducted transmission electron microscope (TEM), reactive oxygen species (ROS), malondialdehyde (MDA), glutathione (GSH), and C11-BODIPY analysis to explore whether CaOx could induce autophagy-dependent ferroptosis in vivo and in vitro. To explore the possible mechanism, we conducted bioinformatic analysis of patients with or without CaOx stones, Western blot and qPCR were used to identify the different genes we found in bioinformatic analysis.ResultsIn our study, we found that CaOx could induce autophagy-dependent ferroptosis no matter in vivo or in vitro, which might finally lead to urolithiasis. Bioinformatic analysis of the GSE73680 dataset indicated that the expression of caveolin-1 (CAV1) was higher in control patients than CaOx stone patients, the STRING database indicated that CAV1 might interact with low density lipoprotein receptro-related protein 6 (LRP6), Gene Set Enrichment Analysis (GSEA) showed that the WNT pathway positively associated with the control group while negatively related to the stone group, and LRP6 was the core gene of the WNT pathway. Western blot found that CAV1, LRP6, and Wnt/β-Catenin were decreased in Human Kidney2 (HK2) cells stimulated with CaOx. Furthermore, the WNT pathway was considered to be involved in autophagy and ferroptosis.ConclusionsWe presumed that CAV1 could ameliorate autophagy-dependent ferroptosis through the LRP6/Wnt/β-Catenin axis, and finally alleviate CaOx stone formation. creator: Yuanyuan Yang creator: Senyuan Hong creator: Yuchao Lu creator: Qing Wang creator: Shaogang Wang creator: Yang Xun uri: https://doi.org/10.7717/peerj.14033 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yang et al. title: Analysis of road traffic injuries and casualties in China: a ten-year nationwide longitudinal study link: https://peerj.com/articles/14046 last-modified: 2022-09-15 description: BackgroundRoad traffic injuries (RTIs) are a serious global problem, and a huge challenge for both economic development and public health.MethodsThis longitudinal study was based on the national data from Chinese authorities. Descriptive analysis was utilized to analyze the prevalence and trend of RTIs among different types, groups and regions. In addition, ridge regression or/and curve regression were also used to explore the relationship between those possible influencing factors and RTIs.ResultsFrom 2010 to 2019, the death toll from motor vehicle accidents (MVAs) decreased firstly and then increased, while the death toll from non-MVAs continued to rise since 2012, and the death toll from pedestrian and occupant accidents fluctuated only a little. The mortality rate of MVA was relatively stable from 2010 to 2012, and declined from 2013. The mortality rate of motor vehicle accidents was higher in rural than urban, the same to male compared with female. The results of ridge regression showed that gross domestic product (GDP)-per-capita, total population, number of health personnel and car ownership were positively correlated with the death toll of non-MVAs (P < 0.05). Additionally, the results of curve regression suggested that the quadratic or cubic relationship between each factor and the number of MVAs was well fitted, while only partially fitted in fatalities.ConclusionsIn recent years, RTIs in China show different trends, and the problem of non-motor vehicle traffic injuries has been neglected which should be paid more attention. Moreover, according to the new trends and traffic conditions in RTIs revealed in this study, it is necessary to formulate targeted intervention measures establish a multi-faceted comprehensive safety system to reduce the disease burden of RTIs as well as the total injuries. creator: Miao Qi creator: Xiuli Hu creator: Xiahong Li creator: Xue Wang creator: Xiuquan Shi uri: https://doi.org/10.7717/peerj.14046 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Qi et al. title: Correlation and agreement of regional cerebral oxygen saturation measured from sensor sites at frontal and temporal areas in adult patients undergoing cardiovascular anesthesia link: https://peerj.com/articles/14058 last-modified: 2022-09-15 description: BackgroundThe function and viability of the brain depend on adequate oxygen supply. A decrease in cerebral blood supply causing cerebral desaturation may lead to many neurological complications. Direct measurement of regional cerebral oxygen saturation (rScO2) assists in early detection and management. Near-infrared spectroscopy (NIRS) has been introduced for measuring rScO2. A pair of sensors are attached to the right and left forehead. However, there are some situations where the forehead of the patient is not accessible for sensor attachment (e.g., neurosurgery involving the frontal area; a bispectral index (BIS) sensor already attached, or a wound to the forehead); therefore, alternate sites for sensor attachment are required. The temporal area was proposed as an alternate site. The objective of this study was to assess the correlation and agreement of rScO2 measured at the forehead vs. the temporal area.MethodsAdult patients undergoing cardiothoracic or vascular surgery were monitored for rScO2 using two pairs of ForeSight sensors. The first pair (A1 and A2) were attached to the right and left forehead, while the second pair (B1 and B2) were attached to the right and left temporal area. The rScO2 values measured from A1 vs. B1 and A2 vs. B2 were assessed for correlation and agreement using the Bland-Altman analysis.ResultsData from 19 patients with 14,364 sets of data were analyzed. The data from A1 vs. B1 and A2 vs. B2 showed moderate positive correlation (r = 0.627; P < 0.0001 and r = 0.548; P < 0.0001). The biases of A1 vs. B1 and A2 vs. B2 were −2.3% (95% CI [−2.5 to −2.2]; P < 0.0001) and 0.7% (95% CI [0.6–0.8]; P < 0.0001). The lower and upper limits of agreement of A1 vs. B1 were −17.5% (95% CI [−17.7 to −17.3]) and 12.8% (95% CI [12.6–13.0]). The lower and upper limits of agreement of A2 vs. B2 were −14.6% (95% CI [−14.8 to −14.4]) and 16.0% (95% [CI 15.8–16.3]).ConclusionsThe rScO2 values measured from sensors at the frontal and temporal areas show a moderate correlation with sufficiently good agreement. The temporal area may be an alternative to the frontal area for cerebral oximetry monitoring. creator: Sirirat Tribuddharat creator: Kriangsak Ngamsaengsirisup creator: Phatcharakamon Mahothorn creator: Thepakorn Sathitkarnmanee uri: https://doi.org/10.7717/peerj.14058 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tribuddharat et al. title: Cancer, platelet distribution width, and total protein levels as predictors of rebleeding in upper gastrointestinal bleeding link: https://peerj.com/articles/14061 last-modified: 2022-09-15 description: BackgroundRebleeding is associated with poor outcomes in upper gastrointestinal bleeding (UGIB). Identifying predictors of rebleeding can assist in risk assessment. The aim of the study is to investigate the factors affecting rebleeding in patients with UGIB admitted to the emergency department.MethodsThis retrospective, observational, cross-sectional study was conducted on patients with UGIB presented to the emergency department. Patients who did not arrest in the first 24 h, who were not diagnosed with GI malignancy, and who were clinically diagnosed with UGIB were included in the study. Patient demographic characteristics, hemodynamic parameters, patient parameters, and bleeding that may affect rebleeding were evaluated. The primary endpoint was rebleeding within 7 days.ResultsThe study included 371 patients. A total of 55 patients (14.8%) had rebleeding within 7 days, and 62 patients (16.7%) presented without bleeding manifestations. Rebleeding rates were higher in those who presented with bloody or coffee-ground vomitus, had a diagnosis of cancer, had blood in their nasogastric tube, and had peptic ulcers due to endoscopy. Mean cell hemoglobin concentration, lymphocyte, albumin, and total protein values of patients with rebleeding were low; red blood cell distribution width, neutrophil count, platelet distribution width (PDW), and neutrophil lymphocyte ratio were high. In-hospital mortality and 30-day mortality values of patients with rebleeding were significantly increased. In the multivariate analysis, cancer, PDW, and total protein levels were statistically significant.ConclusionThe presence of cancer, low total protein level, and high PDW are effective parameters in predicting 7-day rebleeding in patients with UGIB admitted to the emergency department. creator: Ali Cankut Tatlıparmak creator: Özlem Dikme creator: Özgür Dikme creator: Hakan Topaçoğlu uri: https://doi.org/10.7717/peerj.14061 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tatlıparmak et al. title: miR-378 associated with proliferation, migration and apoptosis properties in A549 cells and targeted NPNT in COPD link: https://peerj.com/articles/14062 last-modified: 2022-09-15 description: BackgroundmicroRNAs contribute to the development and progression of chronic obstructive pulmonary disease (COPD). However, the underlying molecular mechanisms are largely unclear. The goal of this study was to investigate the roles of miR-378 in alveolar epithelial type II cells and identify molecular mechanisms which contribute to the pathogenesis of COPD.Materials and methodsHuman alveolar epithelial (A549) cells were cultured in Dulbecco’s Modified Eagle Medium. Cell proliferation was studied by using a cell counting kit-8 (CCK-8) and colony formation assays. Cell apoptosis and cell cycle were analyzed by flow cytometry and wound healing and Transwell were used to analyze the cell migration and. We performed bioinformatics analysis including target gene prediction, gene ontology (GO), Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment and construction of protein-protein interaction (PPI) network. The expression of miR-378 and NPNT from publically available expression microarray of COPD lung tissues was analyzed.ResultsOverexpression of miR-378 significantly increases cell proliferation, migration, and suppress apoptosis. GO analysis demonstrated that the miR-378 involved in transcription, vascular endothelial growth factor receptor signaling pathway, phosphatidylinositol 3-kinase signaling, cell migration, blood coagulation, cell shape, protein stabilization and phosphorylation. Pathway enrichment showed that the 1,629 target genes of miR-378 were associated with mTOR, ErbB, TGF-β, MAPK, and FoxO signaling pathways. Notably, miR-378 directly targets Nephronectin in A549 cells, and miR-378 was upregulated while NPNT was downregulated in COPD lung tissue samples.ConclusionsThese findings suggest that miR-378 can regulate the proliferation, migration, and apoptosis of A549 cells and target NPNT. miR-378 increased in COPD lung tissues while NPNT decreased, and might prove a potential target for novel drug therapy. creator: Guoqing Qian creator: Qi Liao creator: Guoxiang Li creator: Fengying Yin uri: https://doi.org/10.7717/peerj.14062 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Qian et al. title: Effects of CRISPR/Cas9-mediated stearoyl-Coenzyme A desaturase 1 knockout on mouse embryo development and lipid synthesis link: https://peerj.com/articles/13945 last-modified: 2022-09-14 description: BackgroundLipid synthesis is an indispensable process during embryo and growth development. Abnormal lipid synthesis metabolism can cause multiple metabolic diseases including obesity and hyperlipidemia. Stearoyl-Coenzyme A desaturase 1 (SCD1) is responsible for catalyzing the synthesis of monounsaturated fatty acids (MUFA) and plays an essential role in lipid metabolism. The aim of our study was to evaluate the effects of SCD1 on embryo development and lipid synthesis in a knockout mice model.MethodsWe used the CRISPR/Cas9 system together with microinjection for the knockout mouse model generation. Ten-week-old female C57BL/6 mice were used for zygote collection. RNase-free water was injected into mouse zygotes at different cell phases in order to select the optimal time for microinjection. Five sgRNAs were designed and in vitro transcription was performed to obtain sgRNAs and Cas9 mRNA. RNase-free water, NC sgRNA/Cas9 mRNA, and Scd1 sgRNA/Cas9 mRNA were injected into zygotes to observe the morula and blastocyst formation rates. Embryos that were injected with Scd1 sgRNA/Cas9 mRNA and developed to the two-cell stage were used for embryo transfer. Body weight, triacylglycerol (TAG), and cholesterol in Scd1 knockout mice serum were analyzed to determine the effects of SCD1 on lipid metabolism.ResultsMicroinjection performed during the S phase presented with the highest zygote survival rate (P < 0.05). Of the five sgRNAs targeted to Scd1, two sgRNAs with relatively higher gene editing efficiency were used for Scd1 knockout embryos and mice generation. Genome sequence modification was observed at Scd1 exons in embryos, and Scd1 knockout reduced blastocyst formation rates (P < 0.05). Three Scd1 monoallelic knockout mice were obtained. In mice, the protein level of SCD1 decreased (P < 0.05), and the body weight and serum TAG and cholesterol contents were all reduced (P < 0.01). creator: Huibin Tian creator: Huimin Niu creator: Jun Luo creator: Weiwei Yao creator: Wenchang Gao creator: Yang Wen creator: Min Cheng creator: Anmin Lei creator: Jinlian Hua uri: https://doi.org/10.7717/peerj.13945 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tian et al. title: Phenotypic spectrum of FGF10-related disorders: a systematic review link: https://peerj.com/articles/14003 last-modified: 2022-09-14 description: FGF10, as an FGFR2b-specific ligand, plays a crucial role during cell proliferation, multi-organ development, and tissue injury repair. The developmental importance of FGF10 has been emphasized by the identification of FGF10 abnormalities in human congenital disorders affecting different organs and systems. Single-nucleotide variants in FGF10 or FGF10-involving copy-number variant deletions have been reported in families with lacrimo-auriculo-dento-digital syndrome, aplasia of the lacrimal and salivary glands, or lethal lung developmental disorders. Abnormalities involving FGF10 have also been implicated in cleft lip and palate, myopia, or congenital heart disease. However, the exact developmental role of FGF10 and large phenotypic heterogeneity associated with FGF10 disruption remain incompletely understood. Here, we review human and animal studies and summarize the data on FGF10 mechanism of action, expression, multi-organ function, as well as its variants and their usefulness for clinicians and researchers. creator: Katarzyna Bzdega creator: Justyna A. Karolak uri: https://doi.org/10.7717/peerj.14003 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bzdega and Karolak title: 5-Methylindole kills various bacterial pathogens and potentiates aminoglycoside against methicillin-resistant Staphylococcus aureus link: https://peerj.com/articles/14010 last-modified: 2022-09-14 description: Antibiotic resistance of bacterial pathogens has become a severe threat to human health. To counteract antibiotic resistance, it is of significance to discover new antibiotics and also improve the efficacy of existing antibiotics. Here we show that 5-methylindole, a derivative of the interspecies signaling molecule indole, is able to directly kill various Gram-positive pathogens (e.g., Staphylococcus aureus and Enterococcus faecalis) and also Gram-negative ones (e.g., Escherichia coli and Pseudomonas aeruginosa), with 2-methylindole being less potent. Particularly, 5-methylindole can kill methicillin-resistant S. aureus, multidrug-resistant Klebsiella pneumoniae, Mycobacterium tuberculosis, and antibiotic-tolerant S. aureus persisters. Furthermore, 5-methylindole significantly potentiates aminoglycoside antibiotics, but not fluoroquinolones, killing of S. aureus. In addition, 5-iodoindole also potentiates aminoglycosides. Our findings open a new avenue to develop indole derivatives like 5-methylindole as antibacterial agents or adjuvants of aminoglycoside. creator: Zhongyan Li creator: Fengqi Sun creator: Xinmiao Fu creator: Yajuan Chen uri: https://doi.org/10.7717/peerj.14010 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: The emergence of spiraling tracheary element bundles in incompatible grafts link: https://peerj.com/articles/14020 last-modified: 2022-09-14 description: In distantly-related plant grafting, incompatibility often occurs between scion and rootstock, resulting in growth stagnation, and eventually graft failure. In this study, we found that an emergent structure, or the spiraling tracheary element (TE) bundles consisting of TE masses occurring at the graft interface, was extensively present in the highly incompatible interfamilial graft of Brassica napus/Portulaca oleracea (Bn/Po) and Nicotiana benthamiana/Portulaca oleracea (Nb/Po). This special structure mostly appeared in the local area near the grafting union, and the frequency and quantity of the spiraling tracheary element bundles were much higher in the scion than in the rootstock. Nevertheless, only a small portion of Arabidopsis thaliana/Portulaca oleracea (At/Po) interfamilial grafts showed a less spiraled TEs at the grafting union (usually a circular TE), which is consistent with its growth performance. This study consolidated that spiraling TE bundles were an important indicator for graft incompatibility. The possible reason for the formation of spiraling TE bundles in interfamilial grafts was discussed. creator: Huiyan Wu creator: Zhuying Deng creator: Xue Wang creator: Dacheng Liang uri: https://doi.org/10.7717/peerj.14020 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wu et al. title: The below-ground carbon and nitrogen cycling patterns of different mycorrhizal forests on the eastern Qinghai-Tibetan Plateau link: https://peerj.com/articles/14028 last-modified: 2022-09-14 description: Mycorrhizal fungi can form symbiotic associations with tree species, which not only play an important role in plant survival and growth, but also in soil carbon (C) and nitrogen (N) cycling. However, the understanding of differences in soil C and N cycling patterns among forests with different mycorrhizal types is still incomplete. In order to determine the similarities and differences of soil C and N cycling patterns in different mycorrhizal forest types, three primary forests dominated by ectomycorrhizal (EcM), arbuscular mycorrhizal (AM) and ericoid mycorrhizal (ErM) trees respectively were studied on the eastern Qinghai-Tibetan Plateau. Indicators associated with soil C and N cycling, including leaf litter quality, soil C and N contents, soil C and N fluxes, and soil microbial biomass C and N contents were measured in each mycorrhizal type forest. The results showed that leaf litter quality was significantly lower with high C:N ratio and lignin: N ratio in ErM forest than that in AM and EcM forests. Soil CO2 flux (508.25 ± 65.51 mg m−2 h−1) in AM forest was significantly higher than that in EcM forest (387.18 ± 56.19 mg m−2 h−1) and ErM forest (177.87 ± 58.40 mg m−2 h−1). Furthermore, soil inorganic N content was higher in the AM forest than that in EcM and ErM forests. Soil net N mineralization rate (−0.02 ± 0.03 mg kg−1 d−1) was lower in ErM forest than that in EcM and AM forests. We speculated that AM and EcM forests were relatively characterized by rapid soil C cycling comparing to ErM forest. The soil N cycling in EcM and ErM forests were lower, implying they were ‘organic’ N nutrition patterns, and the pattern in ErM forest was more obvious. creator: Miaomiao Zhang creator: Shun Liu creator: Miao Chen creator: Jian Chen creator: Xiangwen Cao creator: Gexi Xu creator: Hongshuang Xing creator: Feifan Li creator: Zuomin Shi uri: https://doi.org/10.7717/peerj.14028 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: A novel virtual reality application for autonomous assessment of cervical range of motion: development and reliability study link: https://peerj.com/articles/14031 last-modified: 2022-09-14 description: BackgroundNeck pain, one of the most common musculoskeletal diseases, affects 222 million people worldwide. The cervical range of motion (CROM) is a tool used to assess the neck’s state across three movement axes: flexo-extension, rotation, and lateral flexion. People with neck pain often have a reduced CROM, and they feel pain at the end-range and/or accompany neck movements with compensatory trunk movements. Virtual reality (VR) setups can track the movement of the head and other body parts in order to create the sensation of immersion in the virtual environment. Using this tracking position information, a CROM assessment can be performed using a VR setup that may be carried out autonomously from the user’s home. The objectives of this study were to develop a VR experience that could be used to perform a CROM assessment, and to evaluate the intra-rater and inter-rater reliability of the CROM measures guided by this VR experience. To the best of our knowledge, a study of this type has not been carried out before.Materials & MethodsA total of 30 asymptomatic adults were assessed using a VR device (HTC Vive Pro Eye™). Two raters provided support with the VR setup, and the participants were guided by the VR experience as they performed the movements. Each rater tested each subject twice, in random order. In addition to a head-mounted display (HMD), a tracker located on the subject’s back was used to measure trunk compensatory movements. The CROM was estimated using only the HMD position and this measurement was corrected using the tracker data. The mean and standard deviation were calculated to characterize the CROM. To evaluate the reliability, the interclass correlation coefficients (ICC) were calculated for intra-rater and inter-rater analysis. The standard error of measurement and minimum detectable change were also calculated. The usability of the VR system was measured using the Spanish version of the System Usability Scale.ResultsThe mean CROM values in each axis of movement were compatible with those described in the literature. ICC values ranged between 0.86 and 0.96 in the intra-rater analysis and between 0.83 and 0.97 in the inter-rater analysis; these values were between good and excellent. When applying the correction of the trunk movements, both the intra-rater and inter-rater ICC values slightly worsened except in the case of the lateral flexion movement, where they slightly improved. The usability score of the CROM assessment/VR system was 86 points, which is an excellent usability score.ConclusionThe reliability of the measurements and the usability of the system indicate that a VR setup can be used to assess CROM. The reliability of the VR setup can be affected by slippage of the HMD or tracker. Both slippage errors are additive, i.e., only when the sum of these two errors is less than the compensatory movement do the measurements improve when considering the tracker data. creator: Jose Angel Santos-Paz creator: Álvaro Sánchez-Picot creator: Ana Rojo creator: Aitor Martín-Pintado-Zugasti creator: Abraham Otero creator: Rodrigo Garcia-Carmona uri: https://doi.org/10.7717/peerj.14031 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Santos-Paz et al. title: The effects of rumen-protected tryptophan (RPT) on production performance and relevant hormones of dairy cows link: https://peerj.com/articles/13831 last-modified: 2022-09-13 description: Tryptophan is an essential amino acid that cannot be synthesized in mammals. Therefore, the dietary supply of tryptophan is critical for the health and production performance (e.g., milk) of mammals. In the present study, 36 lactating Holstein cows were used, of which 24 cows were in the rumen-protected tryptophan (RPT) feeding groups with different doses at 14 g/d and 28 g/d, respectively and 12 cows were in the control group. This approach could avoid dietary tryptophan being degraded by the rumen microorganisms and improve its bioavailability for cows. The results showed that RPT increased milk protein percentage, milk protein yield, milk solid non-fat (SNF), and milk yield. In response to RPT treatment, the levels of melatonin (MT), prolactin (PRL), and insulin-like growth factor-1 (IGF-1) were significantly increased in the serum of cows compared to the controls. RPT feeding improved nutrient utilization efficiency and lactation performance of dairy cows, which enhanced the quality of milk. creator: Hui Ma creator: Songyang Yao creator: Libing Bai creator: Sarvvl Bai creator: Guoshi Liu uri: https://doi.org/10.7717/peerj.13831 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ma et al. title: High temperature mortality of Wolbachia impacts the sex ratio of the parasitoid Ooencyrtus mirus (Hymenoptera: Encyrtidae) link: https://peerj.com/articles/13912 last-modified: 2022-09-13 description: BackgroundWolbachia bacteria are estimated to occur in more than half of all insect species. In Hymenoptera, Wolbachia often manipulates its host’s reproduction to its own advantage. Wolbachia is likely the reason that males are rare in the uniparental Ooencyrtus mirus Triapitsyn & Power (Hymenoptera: Encyrtidae). The likelihood of producing male offspring can be increased by giving mothers a continuous supply of Bagrada hilaris (Burmeister) (Heteroptera: Pentatomidae) host eggs to parasitize for 2–3 weeks, by feeding the parents antibiotics, or by rearing parent wasps at high temperatures; all variables that have been shown to correlate with depleting Wolbachia titers in other organisms. The purpose of the current study was to determine whether thelytoky in O. mirus is due to Wolbachia, and if so, at what time in development the sex change occurs. We also wished to determine if Wolbachia removal results in the production of intersexes, as in some other hymenopterans. Finally, mating behavior was observed to see if and where it breaks down as a result of the species becoming thelytokous.MethodsFemales were collected from parental lines of O. mirus reared at 26, 30, 31, 32, 33, 34, and 36 °C. The offspring of these females were reared at 26 °C, and their sex-ratio was determined. In a subsequent experiment, the parental generation was switched between 26 °C and 36 °C during development to narrow down the critical period at which changes occurred that subsequently affected the sex-ratio of their offspring.ResultsThe sex ratio was male biased in the offspring of O. mirus parents reared at 34 °C and 36 °C (high temperatures), even if the offspring themselves were reared at 26 °C. The constant temperature at which the percentage of males started to increase after two generations was 31 °C (10% males), rising to 39% males at 33 °C, and 100% males at 34 °C and 36 °C. Lasting more than 2 days, the critical period for the change toward a male biased sex ratio was during the second half of the parent’s development. Molecular diagnostic assays confirmed that O. mirus females contain Wolbachia and males do not. Examination of preserved males and male-female pairs under a dissecting microscope showed no signs of intersex characters. Observation of the mating behavior of live O. mirus showed that males initiate courtship by drumming their antennae on a female’s antennae, but after a few seconds, the females typically turn and walk away. However, a few instances of possible copulation were noted.ConclusionsAs hypothesized, the results indicated that thelytoky in O. mirus is likely mediated by Wolbachia bacteria. To maximize the population growth rate without generating males, the best temperature for mass rearing this species is 30 °C. creator: Nancy R. Power creator: Paul F. Rugman-Jones creator: Richard Stouthamer creator: Fatemeh Ganjisaffar creator: Thomas M. Perring uri: https://doi.org/10.7717/peerj.13912 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Power et al. title: PTC2 region genotypes counteract Biomphalaria glabrata population differences between M-line and BS90 in resistance to infection by Schistosoma mansoni link: https://peerj.com/articles/13971 last-modified: 2022-09-13 description: BackgroundBiomphalaria glabrata is a snail intermediate host for Schistosoma mansoni, a trematode responsible for human schistosomiasis. BS90 is one of the most well studied strains of B. glabrata owing to its high resistance to infection by most strains of S. mansoni. An F2 mapping study from 1999 identified two RAPD markers that associated with what appeared to be single-locus, dominant resistance by the BS90 population relative to the susceptible M-line population. One marker cannot be mapped, but the other, OPM-04, maps to within 5 Mb of PTC2, a region we recently showed has a very large effect on resistance within another snail population challenged by the same strain of parasite (PR1). Here we tested the hypothesis that the PTC2 region contains the causal gene/s that explain the iconic resistance of BS90 snails.MethodsWe used marker-assisted backcrossing to drive the BS90 version of the PTC2 region (+/−~1 Mb on either side) into an M-line (susceptible strain) genetic background, and the M-line version into a BS90 genetic background. We challenged the offspring with PR1-strain schistosomes and tested for effects of allelic variation in the PTC2 region in a common genetic background.ResultsRelative to M-line haplotypes, the BS90 haplotype actually confers enhanced susceptibility. So we reject our original hypothesis. One possible explanation for our result was that the causal gene linked to OPM-04 is near, but not in the PTC2 block that we introgressed into each line. So we used an F2 cross to independently test the effects of the PTC2 and OPM-04 regions in a randomized genetic background. We confirmed that the BS90 haplotype confers increased susceptibility, and we see a similar, although non-significant effect at OPM-04. We discuss possible reasons why our results differed so dramatically from those of the 1999 study. We also present Pacbio assemblies of the PTC2 and flanking region in BS90 and M-line, compare with previously published PTC2 haplotypes, and discuss candidate genes that might be behind the enhanced susceptibility of the BS90 haplotype. creator: Michael S. Blouin creator: Stephanie R. Bollmann creator: Jacob A. Tennessen uri: https://doi.org/10.7717/peerj.13971 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Blouin et al. title: Screening of potential key ferroptosis-related genes in sepsis link: https://peerj.com/articles/13983 last-modified: 2022-09-13 description: BackgroundSepsis leads to multiple organ dysfunction caused by a dysregulated host response to infection with a high incidence and mortality. The effect of ferroptosis on the development of sepsis remains unclear. In this study, we aimed to identify the key ferroptosis-related genes involved in sepsis and further explore the potential biological functions of these ferroptosis-related genes in sepsis using bioinformatics analysis.MethodsThe GSE13904 (from children) and GSE28750 (from adults) datasets were downloaded from the Gene Expression Omnibus (GEO). The ferroptosis-related genes were obtained from the FerrDb database. The ferroptosis-related differentially expressed genes (DEGs) were screened by the limma R package. The DAVID online database or clusterProfiler R package was used for the functional enrichment analysis. Then, the STRING database was used to predict the interactions of proteins, and the CytoHubba plugin of Cytoscape was used to confirm key clustering modules. Then, the miRNAs and lncRNAs associated with the key clustering modules were predicted by miRWalk 2.0 and LncBase v.2 respectively. Finally, we generated a cecal ligation and puncture (CLP) polymicrobial sepsis model in C57 male mice and examined the expression of the mRNAs and noncoding RNAs of interest in peripheral blood leukocytes by PCR during the acute inflammation phase.ResultsIn total, 34 ferroptosis-related DEGs were identified in both adult and pediatric septic patients. These ferroptosis-related DEGs were mainly enriched in inflammatory pathways. Then, a significant clustering module containing eight genes was identified. Among them, the following five genes were closely associated with the MAPK signaling pathway: MAPK14, MAPK8, DUSP1, MAP3K5 and MAPK1. Then, crucial miRNAs and lncRNAs associated with biomarker MAPK-related genes were also identified. In particular, let-7b-5p and NEAT1 were selected as noncoding RNAs of interest because of their correlation with ferroptosis in previous studies. Finally, we examined the mRNAs, miRNAs and lncRNAs of interest using CLP-induced sepsis in peripheral blood leukocytes of mice. The results showed that MAPK14, MAPK8, MAP3K5, MAPK1 and NEAT1 were upregulated, while DUSP1 and let-7b-5p were downregulated in the CLP group compared with the sham group.ConclusionsThe MAPK signaling pathway may play a key role in regulating ferroptosis during sepsis. This study provides a valuable resource for future studies investigating the mechanism of MAPK-related ferroptosis in sepsis. creator: Shunan Cui creator: Kun Niu creator: Yining Xie creator: Shuo Li creator: Wenzhi Zhu creator: Ling Yu creator: Hongyu Tan uri: https://doi.org/10.7717/peerj.13983 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cui et al. title: Moonlighting proteins in medically relevant fungi link: https://peerj.com/articles/14001 last-modified: 2022-09-13 description: Moonlighting proteins represent an intriguing area of cell biology, due to their ability to perform two or more unrelated functions in one or many cellular compartments. These proteins have been described in all kingdoms of life and are usually constitutively expressed and conserved proteins with housekeeping functions. Although widely studied in pathogenic bacteria, the information about these proteins in pathogenic fungi is scarce, but there are some reports of their functions in the etiological agents of the main human mycoses, such as Candida spp., Paracoccidioides brasiliensis, Histoplasma capsulatum, Aspergillus fumigatus, Cryptococcus neoformans, and Sporothrix schenckii. In these fungi, most of the described moonlighting proteins are metabolic enzymes, such as enolase and glyceraldehyde-3-phosphate dehydrogenase; chaperones, transcription factors, and redox response proteins, such as peroxiredoxin and catalase, which moonlight at the cell surface and perform virulence-related processes, contributing to immune evasion, adhesions, invasion, and dissemination to host cells and tissues. All moonlighting proteins and their functions described in this review highlight the limited information about this biological aspect in pathogenic fungi, representing this a relevant opportunity area that will contribute to expanding our current knowledge of these organisms’ pathogenesis. creator: Verania J. Arvizu-Rubio creator: Laura C. García-Carnero creator: Héctor Manuel Mora-Montes uri: https://doi.org/10.7717/peerj.14001 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Arvizu-Rubio et al. title: Effects of establishing cultivated grassland on soil organic carbon fractions in a degraded alpine meadow on the Tibetan Plateau link: https://peerj.com/articles/14012 last-modified: 2022-09-13 description: BackgroundThe degradation of alpine meadows has induced substantial losses of soil organic carbon (SOC) on the Tibetan Plateau. A commonly-used method for rehabilitating degraded alpine meadows in this region is establishing cultivated grasslands through sowing seed mixtures, but its impact on the biochemical stability of SOC has remained inadequately explored.MethodsIn this study, a total of 20 composited 0-20 cm soil samples were collected from a heavily degraded alpine meadow (DM) and three adjacent cultivated grasslands established for 3 years (CG3), 12 years (CG12), and 17 years (CG17) on the eastern Tibetan Plateau, and the SOC pool was separated into labile C pool I (LOC I), labile C pool II (LOC II), and recalcitrant C pool (ROC) in order to investigate changes in contents of SOC fractions that have different biochemical stabilities after the establishment of cultivated grassland.ResultsAlthough the establishment of cultivated grasslands led to increases in soil total organic C content, the increase was only significant in samples with 17 years of cultivation. We found that the contents of the three SOC fractions were higher at CG3 and CG12 compared with those in the DM, and the differences were only significant for soil LOC II. By comparison, 17 years of cultivation led to significant increases in all of the SOC fraction contents. The results implied that different cultivation years had distinct impacts on SOC fractions in cultivated grasslands, and longer cultivation years contributed to accumulated soil ROC. The recalcitrance index of SOC in the DM was higher than that at CG3 and CG12, but lower than that at CG17. This was possibly due to the generally low litter quality of cultivated grasslands, which led to a slow release of complex compounds to soils. Moreover, it was observed that soil C:N ratio was a potential indicator of SOC biochemical stability because of their close correlation.ConclusionsOur findings suggest that the long-term establishment of cultivated grasslands on DM is a promising solution to recovering both the quantity and stability of SOC on the Tibetan Plateau. creator: Xiang Liu creator: Xiaotao Huang creator: Wenping Qin creator: Xiaoan Li creator: Zhiwen Ma creator: Hongxiao Shi creator: Lanhai Li creator: Changzhong Li uri: https://doi.org/10.7717/peerj.14012 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon (Oncorhynchus keta) as determined by comparative transcriptome analysis link: https://peerj.com/articles/13585 last-modified: 2022-09-12 description: Chum salmon (Oncorhynchus keta) migrate from freshwater to saltwater, and incur developmental, physiological and molecular adaptations as the salinity changes. The molecular regulation for salinity adaptation in chum salmon is currently not well defined. In this study, 1-g salmon were cultured under 0 (control group, D0), 8‰ (D8), 16‰ (D16), and 24‰ (D24) salinity conditions for 42 days. Na+/K+-ATPase and Ca2+/Mg2+-ATPase activities in the gill first increased and then decreased in response to higher salinity environments where D8 exhibited the highest Na+/K+ATPase and Ca2+/Mg2+-ATPase activity and D24 exhibited the lowest. Alkaline phosphatase (AKP) activity was elevated in all salinity treatment groups relative to controls, while no significant difference in acid phosphatase (ACP) activity was observed across treatment groups. De novo transcriptome sequencing in the D0 and D24 groups using RNA-Seq analysis identified 187,836 unigenes, of which 2,143 were differentially expressed in response to environmental salinity (71 up-regulated and 2,072 down-regulated). A total of 56,020 putative single nucleotide polymorphisms (SNPs) were also identified. The growth, development, osmoregulation and maturation factors of N-methyl-D-aspartate receptors (nmdas) expressed in memory formation, as well as insulin-like growth factor 1 (igf-1) and igf-binding proteins (igfbps) were further investigated using targeted qRT-PCR. The lowest expression of all these genes occurred in the low salinity environments (D8 or D16), while their highest expression occurred in the high salinity environments (D24). These results provide preliminary insight into salinity adaptation in chum salmon and a foundation for the development of marker-assisted breeding for this species. creator: Peilun Li creator: Wei Liu creator: Wanqiao Lu creator: Jilong Wang uri: https://doi.org/10.7717/peerj.13585 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Environment and density-dependency explain the fine-scale aggregation of tree recruits before and after thinning in a mixed forest of Southern Europe link: https://peerj.com/articles/13892 last-modified: 2022-09-12 description: Thinning in forest management primarily reduces the density of trees and alters the patchiness and spatial complexity of environmental factors and individual interactions between plant recruits. At fine spatial scales, little is known about the relative weight of ecological processes affecting tree regeneration before and after thinning events. Here we studied the density and aggregation of tree recruits in fully-mapped plots located in mixed forests in Northern Iberian Peninsula (Southern Europe) for over four years, which comprises one year before and three years after a thinning event. We applied spatial point-pattern analyses to examine (a) the aggregation of recruits, and their association with trees and (b) the relative effect of both environmental (i.e., the patchiness of the local environment) and density-dependent factors (i.e., the aggregation of trees and/or recruits) to predict the density, aggregation, and survival of recruits. We found, in thinning plots, that recruits were less dense, their aggregation pattern was more heterogeneous, were distributed randomly in respect of trees and their survival was almost unaffected by the tree proximity. By contrast, recruits in control plots were denser, were only aggregated at distances lower than 1.0 m, were closer to trees, and such closer distance to trees affected negatively in their survival. Independently of the treatment, the aggregation of recruits was chiefly determined by the density-dependent factors at less than 1.0 m and environmental factors at distances beyond that proximity. Overall, our results suggest that thinning affected the aggregation of recruits at two spatial scales: (a) by favoring the tree-recruit and recruit-recruit facilitation at less than 1.0 m and (b) by modifying spatial heterogeneity of the environment at distances beyond that proximity. creator: Javier Rodríguez-Pérez creator: Bosco Imbert creator: Javier Peralta uri: https://doi.org/10.7717/peerj.13892 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rodríguez-Pérez et al. title: Study on the cultivation of seedlings using buds of potato (Solanum tuberosum L.) link: https://peerj.com/articles/13804 last-modified: 2022-09-09 description: BackgroundPotato, a vegetable crop grown worldwide, has many uses, a short growth period, a large market demand and high economic benefits. The loss of potato seediness due to traditional potato growing methods is becoming increasingly evident, and research on new ways of growing potatoes is particularly important. Bud planting technology has the advantages of more reproduction, faster growth, and simplified maintenance of crop plants under cultivation.MethodsIn this study, a bud planting method was adopted for the cultivation of potato seedlings. Specifically, we assessed different types of treatments for the production of high-quality buds and seedlings of potato. A total of four disease-free potato varieties (Fujin, Youjin, Zhongshu 4, and Feiwuruita) were selected, potato buds with three different lengths (3 cm, 5 cm, and 7 cm) were considered the T1, T2, and T3 treatments, and terminal buds, middle buds, and tail buds were used as the T4, T5, and T6 treatments. A nutrient pot experiment was performed following a randomized complete block design (RCBD) with three replicates and a natural control (CK) treatment. Cultivation was performed with the common horticultural practices of weeding and hoeing applied as needed. The photosynthetic indices, physiological indices, growth indices and quality of potato seedlings and quality of potato buds were measured at two-week intervals, and yield indices were measured when the final crop was harvested 14 weeks after planting.Results and ConclusionsCultivation of seedlings from potato buds of different lengths increased the reproduction coefficient and reduced the number of seed potatoes needed for cultivation. All morphological, physiological, and yield indices showed positive trends. A potato bud length of 7 cm was optimal for raising seedlings. Moreover, buds located at the terminal of the potato yielded seedlings with the best quality. In conclusion, we recommend that our proven bud planting technique be adopted at the commercial level, which could support good crop production with maximum yield. creator: Chaonan Wang creator: Chong Du creator: Zhongmin Yang creator: Huilin Wang creator: Leijuan Shang creator: Lili Liu creator: Zhiyi Yang creator: Shuyao Song creator: Sikandar Amanullah uri: https://doi.org/10.7717/peerj.13804 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Genome-wide identification of the trehalose-6-phosphate synthase gene family in sweet orange (Citrus sinensis) and expression analysis in response to phytohormones and abiotic stresses link: https://peerj.com/articles/13934 last-modified: 2022-09-09 description: BackgroundTrehalose-6-phosphate synthase (TPS) is an essential enzyme for synthesizing trehalose and is a significant regulator of plant development and stress response. Sweet orange (Citrus sinensis) is an economically important fruit tree crop and a common transgenic material. At present, little information is available about the TPS gene family in sweet orange.MethodsThe TPS gene family were identified from sweet orange genome by bioinformatics analysis. Additionally, the expression of CisTPS genes was analyzed under phytohormones and abiotic stresses by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).ResultsHere, eight TPS genes were identified and were found to be randomly distributed in five sweet orange chromosomes. TPS and trehalose-6-phosphate phosphatase (TPP) domains were observed in all CisTPS proteins. The phylogenetic tree showed that CisTPS genes were divided into two subfamilies, and genes in each subfamily had conserved intron structures and motif compositions. The cis-acting elements of CisTPS genes suggested their roles in phytohormone and stress responses. All CisTPS genes were ubiquitously expressed in roots, leaves, and stems, and six members were highly expressed in roots. Expression profiles showed that CisTPS genes exhibited tissue specificity and were differentially expressed in response to phytohormones and abiotic stresses. This study lays a foundation for revealing the functions of the TPS gene family in trehalose regulation in sweet orange, and provides a valuable reference for this gene family in other plants. creator: Kehong Liu creator: Yan Zhou uri: https://doi.org/10.7717/peerj.13934 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu and Zhou title: A retrospective study of real-world effectiveness and safety of rivaroxaban in patients with non-valvular atrial fibrillation and venous thromboembolism in Saudi Arabia link: https://peerj.com/articles/13974 last-modified: 2022-09-09 description: BackgroundReal-world evidence on factor Xa inhibitor (rivaroxaban) prescribing patterns, safety, and efficacy in patients with non-valvular atrial fibrillation (NVAF) and venous thromboembolism (VTE) is rare. Herein, we sought to examine the above outcomes in the largest academic center in the Kingdom of Saudi Arabia (KSA).MethodsThis is a retrospective observational study designed to examine the prescribing pattern, safety and real-world effectiveness of the factor Xa inhibitor rivaroxaban in patients with NVAF and VTE. Data on rivaroxaban prescriptions were collected and analyzed. Bleeding outcomes were defined as per the International Society on Thrombosis and Hemostasis (ISTH) definition.ResultsA total of 2,316 patients taking rivaroxaban recruited through several departments of King Saud University Medical City (KSUMC). The mean age was 61 years (±17.8) with 55% above the age of 60 and 58% were females. Deep vein thrombosis and pulmonary embolism (VTE) was the most prevalent reason for prescribing rivaroxaban, followed by NVAF. A total daily dosage of 15 mg was given to 23% of the patients. The incidence rate of recurrent thrombosis and recurrent stroke was 0.2%. Furthermore, rivaroxaban had a 0.04 percent incidence rate of myocardial infarction. Half of the patients with recurrent thrombosis and stroke were taking 15 mg per day. The incidence rate of major bleeding was 1.1%. More over half of the patients who experienced significant bleeding were taking rivaroxaban at a dosage of 20 mg per day. According to the HAS-BLED Score (>2 score), 48 percent of patients who experienced significant bleeding had a high risk of bleeding. Non-major bleeding occurred in 0.6% of cases. Similarly, 40% of patients with non-major bleeding were taking rivaroxaban at a dosage of 20 mg per day. According to the HAS-BLED Score, just 6.6% of these individuals had a high risk of bleeding. 93.4% of the patients, on the other hand, were at intermediate risk.ConclusionThe prescription of rivaroxaban in this real-life cohort study differs from the prescribing label and the outcomes of a phase 3 randomised clinical trial. However, for individuals with VTE and NVAF, the 20 mg dose looked to be more efficacious than the pivotal trial outcomes. Furthermore, among patients with VTE and NVAF, rivaroxaban was linked to a decreased incidence of safety events such as recurrent thrombosis, recurrent stroke, MI, major bleeding, and non-major haemorrhage in a real-world environment. creator: Hind M. Alosaimi creator: Saeed Alqahtani creator: Bander Balkhi creator: Mishari Alqahtani creator: Faisal Alzamil creator: Abdulaziz Alhossan creator: Fatmah S. Alqahtany creator: Abdullah A. Alharbi creator: Nawaf Abdullah Alqahtani creator: Hanan Albackr creator: Ghada Elgohary creator: Farjah H. Algahtani uri: https://doi.org/10.7717/peerj.13974 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Alosaimi et al. title: Semi-field evaluation of human landing catches versus human double net trap for estimating human biting rate of Anopheles minimus and Anopheles harrisoni in Thailand link: https://peerj.com/articles/13865 last-modified: 2022-09-08 description: BackgroundWhilst the human landing catch (HLC) technique is considered the ‘gold standard’ for estimating human-biting rates, it is labor-intensive and fraught with potential risk of exposure to infectious mosquito bites. This study evaluated the feasibility and performance of an alternative method, the human double net trap (HDNT) relative to HLC for monitoring host-seeking malaria vectors of the Anopheles minimus complex in a semi-field system (SFS).MethodsHDNT and HLC were positioned in two rooms, 30 m apart at both ends of the SFS. Two human volunteers were rotated between both traps and collected released mosquitoes (n = 100) from 6:00 pm till 6:00 am. Differences in Anopheles mosquito densities among the trapping methods were compared using a generalized linear model based on a negative binomial distribution.ResultsThere were 82.80% (2,136/2,580) of recaptures of wild-caught and 94.50% (2,835/3,000) of laboratory-reared mosquitoes that were molecularly identified as An. harrisoni and An. minimus, respectively. Mean density of An. harrisoni was significantly lower in HNDT (15.50 per night, 95% CI [12.48–18.52]) relative to HLC (25.32 per night (95% CI [22.28–28.36]), p < 0.001). Similarly, the mean density of a laboratory strain of An. minimus recaptured in HDNT was significantly lower (37.87 per night, 95% CI [34.62–41.11]) relative to HLC (56.40 per night, 95% CI [55.37–57.43]), p < 0.001. Relative sampling efficiency analysis showed that HLC was the more efficient trap in collecting the An. minimus complex in the SFS.ConclusionHDNT caught proportionately fewer An. minimus complex than HLC. HDNT was not sensitive nor significantly correlated with HLC, suggesting that it is not an alternative method to HLC. creator: Chanly Yan creator: Jeffrey Hii creator: Ratchadawan Ngoen-Klan creator: Manop Saeung creator: Theeraphap Chareonviriyaphap uri: https://doi.org/10.7717/peerj.13865 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yan et al. title: Floral ontogeny of Tachigali (Caesalpinioideae, Fabaceae) species link: https://peerj.com/articles/13975 last-modified: 2022-09-08 description: BackgroundThe present ontogenetic study reveals variations throughout floral development in three morphologically representative species from the genus Tachigali, allowing a better understanding of floral organs diversity, flower symmetry and their homologies, especially in Fabaceae, a diverse family that exhibits a wide variation in floral architecture. Tachigali (Caesalpinioideae) corresponds to an important Neotropical legumes tree genus with 58 species in Brazil. Species of the genus Sclerolobium Vogel were incorporated in its circumscription, increasing the diversity of its floral morphology.MethodsThis work aims to perform an ontogenetic study of T. denudata, T. paratyensis and T. spathulipetala, morphologically representative species of Tachigali, in order to describe the floral development and to better comprehend the floral morphology varieties among the species, using scanning electron microscopy.ResultsWe found the studied species to have floral buds with acropetal and helical development along the inflorescence axis; sepals and petals with helical development, varying the position of the primordia in the bud, according to the different species; stamens with unilateral development and carpel with adaxial curvature. These data correspond to original records of Tachigali ontogeny and contribute to an improved understanding of floral morphology and symmetry with data related to the zygomorphic and early development of the sepals and petals. creator: Jamile Marques Casanova creator: Domingos Cardoso creator: Claudia Franca Barros creator: Haroldo Cavalcante de Lima creator: Karen L.G. De Toni uri: https://doi.org/10.7717/peerj.13975 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Marques Casanova et al. title: The cold-stress responsive gene DREB1A involved in low-temperature tolerance in Xinjiang wild walnut link: https://peerj.com/articles/14021 last-modified: 2022-09-08 description: BackgroundLow-temperatures have the potential to be a serious problem for plants and can negatively affect the normal growth and development of walnuts. DREB1/CBF (Dehydration Responsive Element Binding Protein 1/C-repeat Binding Factor), one of the most direct transcription factors in response to low-temperature stress, may improve the resistance of plants to low-temperatures by regulating their functional genes. However, few studies have been conducted in walnut. The Xinjiang wild walnut is a rare wild plant found in China, with a large number of excellent trait genes, and is hardier than cultivated walnuts in Xinjiang.MethodsIn this work, we identified all of the DREB1 members from the walnut genome and analyzed their expression levels in different tissues and during low-temperature stress on the Xinjiang wild walnut. The JfDREB1A gene of the Xinjiang wild walnut was cloned and transformed into Arabidopsis thaliana for functional verification.ResultsThere were five DREB1 transcription factors in the walnut genome. Among them, the relative expression level of the DREB1A gene was significantly higher than other members in the different tissues (root, stem, leaf) and was immediately un-regulated under low-temperature stress. The overexpression of the JfDREB1A gene increased the survival rates of transgenic Arabidopsis lines, mainly through maintaining the stability of cell membrane, decreasing the electrical conductivity and increasing the activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). Additionally, the expression levels of cold-inducible genes like AtKIN1, AtERD10, AtRD29A, AtCOR15A and AtCOR47, were significantly increased. These results showed that the JfDREB1A gene may play an important role in the response to cold stress of the Xinjiang wild walnut. This study contributes to our understanding of the molecular mechanism of the Xinjiang wild walnut’s response to low-temperature stress and will be beneficial for developing walnut cultivars with improved cold resistance. creator: Liqun Han creator: Kai Ma creator: Yu Zhao creator: Chuang Mei creator: Aisajan Mamat creator: Jixun Wang creator: Ling Qin creator: Tianming He uri: https://doi.org/10.7717/peerj.14021 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Han et al. title: First photographic evidence of oceanic manta rays (Mobula birostris) at two locations in the Fiji islands link: https://peerj.com/articles/13883 last-modified: 2022-09-07 description: Until the revision of the genus Manta in 2009, when a second manta species (Manta alfredi) was resurrected based on morphological and meristic data, all available records in Fijian literature were recorded as Manta birostris. Subsequently, documented sightings were recorded as M. alfredi. Another reclassification of the genus Manta was undertaken in 2018 when both manta ray species (Manta alfredi, Manta birostris) were moved to Mobula based on phylogenetic analysis. Here, we present the first unequivocal evidence of oceanic manta ray (Mobula birostris) occurrence in Fijian waters. In November 2018, two individuals were sighted foraging in Laucala Bay, a large lagoon adjacent to Suva, the capital city of Fiji. Subsequently, three more individuals were sighted in December 2018, two individuals in July 2020, at least six individuals were observed in November 2021, and eight individuals in May/June 2022, all foraging in the same geographical area. Unique ventral identification patterns could be obtained for nine individuals, and all nine individuals have been re-sighted since first identification, with one individual being documented in 2018, 2020, 2021 and 2022. Two additional individuals were recorded in the Yasawa Island Group in the west of Fiji while passing through and foraging in a channel between Drawaqa and Naviti Island in April and September 2020. We provide photographic identification of ten M. birostris individuals from two sites and discuss our findings in the context of local environmental parameters and other recorded sightings in the South Pacific region. In light of the global extinction risk of M. birostris and the recent reclassification from Vulnerable to Endangered on the Red List of Threatened Species, the expansion of their known distribution range to Fijian waters and the recurrence of individuals over consecutive years in the same location adds valuable information for the development of effective and data-driven conservation strategies. creator: Luke Gordon creator: Tom Vierus uri: https://doi.org/10.7717/peerj.13883 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Gordon and Vierus title: Investigation and research on elderly people’s willingness to combine medical and health care and related factors in coastal cities in eastern China link: https://peerj.com/articles/14004 last-modified: 2022-09-07 description: BackgroundThe problem of global aging was becoming increasingly prominent. At present, the empty nest and miniaturization of family structure reduce the function of home-based elderly care.MethodsA questionnaire survey was conducted on 347 elderly people in multiple communities and nursing homes in eastern coastal cities of China, and 13 institutional staff members of eight nursing institutions that carried out the medical-nursing integration model were interviewed as the research objects. The survey mainly focuses on the basic characteristics of the elderly, the family support system, and the acceptance of medical care and health care. The influencing factors were screened by t test, univariate analysis and multivariate logistic regression analysis. SPSS software was used to test the reliability and validity of the questionnaire, and the Crobach’s was 0.792, which can be considered that the questionnaire had good internal reliability. The classification of the questionnaire was reasonable, the reliability of the questionnaire was high, and the internal consistency of the scale was high. According to KMO and Bartlett test, KMO = 0.826, χ2 = 853.731, the degree of freedom was 36, and the P value was 0.000.ResultsThe proportion of male and female respondents was 48.1% and 51.9% respectively. Multivariate logistic regression analysis results showed that gender had no statistical significances on the degree of support for combine medical and health care in the elderly (P > 0.05). The results showed that gender, age, marital status, medical insurance type and old-age insurance type had little effect on the support of the combination of medical care and health care for the elderly (P > 0.05). Compared with the control group with education below primary school, the elderly with bachelor’s degree or above are more willing to support the combination of medical care and health (P < 0.05). The registered residence type is more obvious than that of the urban residents (P < 0.05). Compared with the enterprise employees in the control group, the elderly who were employed as migrant workers before retirement were more willing to support the combination of medical care and health (P < 0.05). From the perspective of family monthly income, the elderly with family income ≥10,000 RMB have more obvious support for the combination of medical care and health than the elderly with family monthly income <3,000 RMB in the control group (P < 0.05). In terms of the degree of understanding, the degree of understanding and support in different degrees are significantly higher than that in the control group (P < 0.05).ConclusionThrough multivariate logistic regression analysis, education level, registered residence, pre-retirement occupation and family income are more obvious for the elderly to support medical care and health. It is necessary to increase investment in elderly activity centers, actively carry out activities. creator: Yehong Wei creator: Yanxiang Sun creator: Yuting Li creator: Xufeng Chen creator: Yingyu Wu creator: Xindi Fang creator: Ruichen Zhu uri: https://doi.org/10.7717/peerj.14004 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wei et al. title: An optimistic future of C4 crop broomcorn millet (Panicum miliaceum L.) for food security under increasing atmospheric CO2 concentrations link: https://peerj.com/articles/14024 last-modified: 2022-09-07 description: Broomcorn millet, a C4 cereal, has better tolerance to environmental stresses. Although elevated atmospheric CO2 concentration has led to grain nutrition reduction in most staple crops, studies evaluating its effects on broomcorn millet are still scarce. The yield, nutritional quality and metabolites of broomcorn millet were investigated under ambient CO2 (aCO2, 400 µmol mol–1) and elevated CO2 (eCO2, aCO2+ 200 µmol mol–1) for three years using open-top chambers (OTC). The results showed that the yield of broomcorn millet was markedly increased under eCO2 compared with aCO2. On average, eCO2 significantly increased the concentration of Mg (27.3%), Mn (14.6%), and B (21.2%) over three years, whereas it did not affect the concentration of P, K, Fe, Ca, Cu or Zn. Protein content was significantly decreased, whereas starch and oil concentrations were not changed by eCO2. With the greater increase in grain yield, eCO2 induced increase in the grain accumulations of P (23.87%), K (29.5%), Mn (40.08%), Ca (22.58%), Mg (51.31%), Zn (40.95%), B (48.54%), starch (16.96%) and oil (28.37%) on average for three years. Flavonoids such as kaempferol, apigenin, eriodictyol, luteolin, and chrysoeriol were accumulated under eCO2. The reduction in L-glutamine and L-lysine metabolites, which were the most representative amino acid in grain proteins, led to a reduction of protein concentration under eCO2. Broomcorn millet has more desirable nutritional traits for combating hidden hunger. This may potentially be useful for breeding more nutritious plants in the era of climate change. creator: Xinrui Shi creator: Jie Shen creator: Bingjie Niu creator: Shu Kee Lam creator: Yuzheng Zong creator: Dongsheng Zhang creator: Xingyu Hao creator: Ping Li uri: https://doi.org/10.7717/peerj.14024 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Shi et al. title: Effects of continuous and rotational cropping practices on soil fungal communities in pineapple cultivation link: https://peerj.com/articles/13937 last-modified: 2022-09-06 description: BackgroundRotational cropping practices can change the fungal structure and diversity of cropping soil, and these changes can promote crop development. However, only a few studies have explored the effects of rotational cropping of pineapple on soil fungal diversity.MethodsIn this study, we investigated fungal diversity in continuous and rotational cropping soil of pineapple in Xuwen and Leizhou of China in summer and winter through high throughput sequencing of the fungal internal transcribed spacer region.ResultsThe diversity and richness of the fungal community were observed to be significantly increased after rotational cropping in Xuwen and Leizhou in summer, whereas no changes were observed in winter. Furthermore, Ascomycota, Basidiomycota, Zygomcota, and Chytridiomycota were the dominant phyla, and Chaetomium, Penicillium, Fusarium, Trichoderma, and Cryptococcus were the dominant genera in the continuous and rotational cropping soil of pineapple, respectively, in both summer and winter. Chytridiomycota at phylum level and Gibberella at genus level were observed in rotational cropping soil; however, Ascomycota at the phylum level and Chaetomium at the genus level were the most abundant fungi, and their abundance dramatically decreased in continuous cropping soil. Redundancy analysis revealed that rotational cropping reduced the correlation between environmental parameters and the fungal community in winter. In addition, several fungal biomarkers were found in Xuwen in both continuous and rotational cropping soil samples, including Sporobolomyces, Aspergillus, Corynascus sp JHG 2007, and Corynascus at the genus level, Penicillium and fungal sp p1s11 at the species level in rotational cropping soil, and ales family Incertae sedis and Sordariomycetes at the class level in continuous cropping soil. These results revealed the changes in the structure and diversity of fungal community in continuous and rotational cropping practices for pineapple cultivation, which may be associated with crop yield and quality. creator: Jing Chen creator: Hui Zeng uri: https://doi.org/10.7717/peerj.13937 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen and Zeng title: Predictors of tuberculosis disease in smokers: a case-control study in northeastern Malaysia link: https://peerj.com/articles/13984 last-modified: 2022-09-06 description: ObjectiveTuberculosis (TB) is a leading infectious disease. However, many TB cases remain undetected and only present symptoms at a late stage of the infection. Therefore, targeted TB screening in high-risk populations, including smokers, is crucial. This study aimed to determine the predictors of TB disease among the smoker population in northeast Malaysia from 2019 to 2020.MethodsA case-control study was conducted involving smokers aged 18 years and older from health clinics in Bachok Kelantan, Malaysia. Data were collected via face-to-face interviews or telephone calls from 159 participants, randomly selected from outpatient TB records. Simple and multiple logistic regression, using R software, were used to identify the determinants of TB.ResultsMost participants were male (59.1%) and had a secondary education (56.0%). Active smokers constituted 35.2% of the group, and the mean (SD) duration of exposure to smoking was 23.9 (16.47) and 18.4 (12.84) years for the case and control groups, respectively. Being an ex-smoker (adjusted odds ratio (AOR) 6.17; 95% CI [1.55–28.32]; p = 0.013), weight loss (AOR 13.45; 95% CI [4.58–44.46]; p < 0.005), night sweats (AOR 63.84; 95% CI [8.99–1392.75]; p < 0.005) and duration of symptoms (AOR 1.02; 95% CI [1.01–1.04]; p = 0.022) were shown to be significant predictors for TB disease.ConclusionFour predictors of TB disease in the population of smokers were recognised in this study and should be prioritised for early TB screening and diagnosis. This may help increase TB detection, initiate prompt treatment and reduce complications among the group at risk for TB. creator: Tengku Noor Farhana Tengku Khalid creator: Wan Mohd Zahiruddin Wan Mohammad creator: Razan Ab Samat creator: Nik Rosmawati Nik Husain uri: https://doi.org/10.7717/peerj.13984 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tengku Khalid et al. title: Antibiotic resistance and genomic features of Clostridioides difficile in southwest China link: https://peerj.com/articles/14016 last-modified: 2022-09-05 description: BackgroundClostridioides difficile infection (CDI) caused by toxigenic strains leads to antibiotic-related diarrhea, colitis, or even fatal pseudomembranous enteritis. Previously, we conducted a cross-sectional study on prevalence of CDI in southwest China. However, the antibiotics resistance and characteristics of genomes of these isolates are still unknown.MethodsAntibiotic susceptibility testing with E-test strips and whole genome sequence analysis were used to characterize the features of these C. difficile isolates.ResultsForty-nine strains of C. difficile were used in this study. Five isolates were non-toxigenic and the rest carried toxigenic genes. We have previously reported that ST35/RT046, ST3/RT001 and ST3/RT009 were the mostly distributed genotypes of strains in the children group. In this study, all the C. difficile isolates were sensitive to metronidazole, meropenem, amoxicillin/clavulanic acid and vancomycin. Most of the strains were resistant to erythromycin, gentamicin and clindamycin. The annotated resistant genes, such as macB, vanRA, vanRG, vanRM, arlR, and efrB were mostly identified related to macrolide, glycopeptide, and fluoroquinolone resistance. Interestingly, 77.55% of the strains were considered as multi-drug resistant (MDR). Phylogenetic analysis based on core genome of bacteria revealed all the strains were divided into clade 1 and clade 4. The characteristics of genome diversity for clade 1 could be found. None of the isolates showed 18-bp deletion of tcdC as RT027 strain as described before, and polymorphism of tcdB showed a high degree of conservation than tcdA gene.ConclusionsMost of the C. difficile isolates in this study were resistant to macrolide and aminoglycoside antibiotics. Moreover, the MDR strains were commonly found. All the isolates belonged to clade 1 and clade 4 according to phylogenetic analysis of bacterial genome, and highly genomic diversity of clade 1 was identified for these strains. creator: Wenpeng Gu creator: Wenge Li creator: Senquan Jia creator: Yongming Zhou creator: Jianwen Yin creator: Yuan Wu creator: Xiaoqing Fu uri: https://doi.org/10.7717/peerj.14016 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gu et al. title: Benchmark datasets for SARS-CoV-2 surveillance bioinformatics link: https://peerj.com/articles/13821 last-modified: 2022-09-05 description: BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset.MethodsWe identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study.ResultsThe benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2.DiscussionThe datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines. creator: Lingzi Xiaoli creator: Jill V. Hagey creator: Daniel J. Park creator: Christopher A. Gulvik creator: Erin L. Young creator: Nabil-Fareed Alikhan creator: Adrian Lawsin creator: Norman Hassell creator: Kristen Knipe creator: Kelly F. Oakeson creator: Adam C. Retchless creator: Migun Shakya creator: Chien-Chi Lo creator: Patrick Chain creator: Andrew J. Page creator: Benjamin J. Metcalf creator: Michelle Su creator: Jessica Rowell creator: Eshaw Vidyaprakash creator: Clinton R. Paden creator: Andrew D. Huang creator: Dawn Roellig creator: Ketan Patel creator: Kathryn Winglee creator: Michael R. Weigand creator: Lee S. Katz uri: https://doi.org/10.7717/peerj.13821 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xiaoli et al. title: Practical guidance for firefighter applicants preparing for cardiorespiratory fitness testing: a secondary analysis of self-reported physical activity levels link: https://peerj.com/articles/13832 last-modified: 2022-09-05 description: Adequate cardiorespiratory fitness is critical for firefighters since an insufficient level of fitness threatens the integrity of their operations and could be dangerous for their lives. In fact, the leading cause of mortality for on-duty firefighters is not injury but sudden cardiac death. Therefore, to mitigate these risks, potential firefighter recruits are often required to perform a graded exercise test to determine their cardiorespiratory fitness as part of the recruitment process. However, there are currently limited data available to prospective firefighters on the amounts and types of exercises needed to be successful in the graded exercise test, commonly known as a V̇O2max test. Physiological parameters for the current secondary analysis were collected on firefighter applicants who performed the graded exercise test where 72% were successful and 28% were unsuccessful to meet the minimum standard set at 42.5 ml kg−1 min−1. Prior to their test, applicants were asked to describe their exercise training routine by indicating the number of minutes per week spent exercising. Activities were then divided into one of two categories: endurance exercise or strength and power exercise training. The total exercise training describes the sum of all activities performed each week. The sum of endurance exercise activities and the sum of strength and power exercise activities were compared between the successful and the unsuccessful groups and results showed that successful applicants had a higher training volume and performed more endurance exercise training as compared to unsuccessful applicants. Therefore, practical recommendations related to exercise training regime are presented for firefighter applicants to embrace as guidance to prepare for their graded exercise test as part of their recruitment process. creator: Sylvie Fortier creator: Liam P. Kelly creator: Fabien A. Basset uri: https://doi.org/10.7717/peerj.13832 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Fortier et al. title: Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers link: https://peerj.com/articles/13952 last-modified: 2022-09-05 description: Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 µm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities. creator: Jan-Niklas Macher creator: Dimitra Maria Bloska creator: Maria Holzmann creator: Elsa B. Girard creator: Jan Pawlowski creator: Willem Renema uri: https://doi.org/10.7717/peerj.13952 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Macher et al. title: Bone mesenchymal stem cell-derived exosomes prevent hyperoxia-induced apoptosis of primary type II alveolar epithelial cells in vitro link: https://peerj.com/articles/13692 last-modified: 2022-09-02 description: BackgroundThe presence of alveolar epithelial type II cells (AECIIs) is one of the most important causes of bronchopulmonary dysplasia (BPD). Exosomes from bone mesenchymal stem cells (BMSCs) can reduce hyperoxia-induced damage and provide better results in terms of alveolar and pulmonary vascularization parameters than BMSCs. Currently, intervention studies using BMSC-derived exosomes on the signaling pathways regulating proliferation and apoptosis of alveolar epithelial cells under the condition of BPD have not been reported. This study investigated the effects of rat BMSC-derived exosomes on the proliferation and apoptosis of hyperoxia-induced primary AECIIs in vitro.MethodsThe isolated AECIIs were grouped as follows: normal control (21% oxygen), hyperoxia (85% oxygen), hyperoxia+exosome (20 µg/mL), hyperoxia+exosome+LY294002 (PI3K/Akt inhibitor, 20 µM), and hyperoxia+exosome+rapamycin (mTOR inhibitor, 5 nM). We used the PI3K/Akt inhibitor LY294002 and the mTOR inhibitor rapamycin to determine the roles of the PI3K/Akt and mTOR signaling pathways. The effects of BMSC-derived exosomes on AECII proliferation and apoptosis were assessed, respectively.ResultsDecreased levels of the antiapoptotic protein Bcl-2, the cell proliferation protein Ki67, p-PI3K, p-Akt, and p-mTOR, as well as increased levels of AECII apoptosis and the proapoptotic protein Bax in the hyperoxia group were observed. Notably, Sprague Dawley rat BMSC-derived exosomes could reverse the effect of hyperoxia on AECII proliferation. However, the application of LY294002 and rapamycin inhibited the protective effects of BMSC-derived exosomes.ConclusionOur findings revealed that BMSC-derived exosomes could regulate the expression of apoptosis-related proteins likely via the PI3K/Akt/mTOR signaling pathway, thereby preventing hyperoxia-induced AECII apoptosis. creator: Wei Yang creator: Chao Huang creator: Wenjian Wang creator: Baozhu Zhang creator: Yunbin Chen creator: Xinlin Xie uri: https://doi.org/10.7717/peerj.13692 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Examining the ability to track multiple moving targets as a function of postural stability: a comparison between team sports players and sedentary individuals link: https://peerj.com/articles/13964 last-modified: 2022-09-02 description: BackgroundThe ability to track multiple objects plays a key role in team ball sports actions. However, there is a lack of research focused on identifying multiple object tracking (MOT) performance under rapid, dynamic and ecologically valid conditions. Therefore, we aimed to assess the effects of manipulating postural stability on MOT performance.MethodsNineteen team sports players (soccer, basketball, handball) and sixteen sedentary individuals performed the MOT task under three levels of postural stability (high, medium, and low). For the MOT task, participants had to track three out of eight balls for 10 s, and the object speed was adjusted following a staircase procedure. For postural stability manipulation, participants performed three identical protocols (randomized order) of the MOT task while standing on an unstable platform, using the training module of the Biodex Balance System SD at levels 12 (high-stability), eight (medium-stability), and four (low-stability).ResultsWe found that the ability to track moving targets is dependent on the balance stability conditions (F2,66 = 8.7, p < 0.001, η² = 0.09), with the disturbance of postural stability having a negative effect on MOT performance. Moreover, when compared to sedentary individuals, team sports players showed better MOT scores for the high-stability and the medium-stability conditions (corrected p-value = 0.008, Cohen’s d = 0.96 and corrected p-value = 0.009, Cohen’s d = 0.94; respectively) whereas no differences were observed for the more unstable conditions (low-stability) between-groups.ConclusionsThe ability to track moving targets is sensitive to the level of postural stability, with the disturbance of balance having a negative effect on MOT performance. Our results suggest that expertise in team sports training is transferred to non-specific sport domains, as shown by the better performance exhibited by team sports players in comparison to sedentary individuals. This study provides novel insights into the link between individual’s ability to track multiple moving objects and postural control in team sports players and sedentary individuals. creator: Teresa Zwierko creator: Piotr Lesiakowski creator: Beatriz Redondo creator: Jesús Vera uri: https://doi.org/10.7717/peerj.13964 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zwierko et al. title: Satellite remote sensing of environmental variables can predict acoustic activity of an orthopteran assemblage link: https://peerj.com/articles/13969 last-modified: 2022-09-02 description: Passive acoustic monitoring (PAM) is a promising method for biodiversity assessment, which allows for longer and less intrusive sampling when compared to traditional methods (e.g., collecting specimens), by using sound recordings as the primary data source. Insects have great potential as models for the study and monitoring of acoustic assemblages due to their sensitivity to environmental changes. Nevertheless, ecoacoustic studies focused on insects are still scarce when compared to more charismatic groups. Insects’ acoustic activity patterns respond to environmental factors, like temperature, moonlight, and precipitation, but community acoustic perspectives have been barely explored. Here, we provide an example of the usefulness of PAM to track temporal patterns of acoustic activity for a nocturnal assemblage of insects (Orthoptera). We integrate satellite remote sensing and astronomically measured environmental factors at a local scale in an Andean Forest of Colombia and evaluate the acoustic response of orthopterans through automated model detections of their songs for nine weeks (March and April of 2020). We describe the acoustic frequency range and diel period for the calling song of each representative species. Three species overlapped in frequency and diel acoustics but inhabit different strata: canopy, understory, and ground surface level. Based on the acoustic frequency and activity, we identified three trends: (i) both sampled cricket species call at lower frequency for shorter periods of time (dusk); (ii) all sampled katydid species call at higher frequency for longer time periods, including later hours at night; and (iii) the diel acoustic activity span window seems to increase proportionally with dominant acoustic frequency, but further research is required. We also identified a dusk chorus in which all the species sing at the same time. To quantify the acoustic response to environmental factors, we calculated a beta regression with the singing activity as a response variable and moon phase, surface temperature and daily precipitation as explanatory variables. The response to the moon phase was significant for the katydids but not for the crickets, possibly due to differences in diel activity periods. Crickets are active during dusk, thus the effects of moonlight on acoustic activity are negligible. The response to precipitation was significant for the two crickets and not for the katydids, possibly because of higher likelihood of rain interrupting crickets’ shorter diel activity period. Our study shows how the local survey of orthopteran acoustic assemblages, with a species taxonomic resolution coupled with remote-sensing environmental measurements can reveal responses to environmental factors. In addition, we demonstrate how satellite data might prove to be a useful alternative source of environmental data for community studies with geographical, financial, or other constraints. creator: Diego A. Gomez-Morales creator: Orlando Acevedo-Charry uri: https://doi.org/10.7717/peerj.13969 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gomez-Morales and Acevedo-Charry title: Variation in genetics, morphology, and recruitment of the invasive barnacle Amphibalanus eburneus (Gould, 1841) in the southern Korean peninsula link: https://peerj.com/articles/14002 last-modified: 2022-09-02 description: The ivory barnacle Amphibalanus eburneus is a marine crustacean, which presents near-cosmopolitan distribution due to extensive introduction and exhibits a wide spectrum of phenotypic variation. To elucidate geographical differentiation among populations through invasion, we investigated variation in genetic structure, shell morphology, and recruitment pattern for A. eburneus, from the southern Korean Peninsula where it has been established since the late 1980s. We selected samples from four populations in corresponding ecologically-relevant regions representing all surrounding South Korean waters. From these we amplified the mitochondrial genetic marker cytochrome oxidase subunit I (COI) from 57 individuals and performed a populational genetic analyses with 11 additional GenBank sequences to evaluate population structure. To examine morphological variation, we applied two-dimensional landmark-based geometric morphometrics to the scutum and tergum for 148 and 151 individuals, respectively. Furthermore, we estimated the density of year-old individuals in the field to compare recruitment responses among localities. We detected 33 haplotypes among the four locations belonging to three distinct clades based on moderate intraspecific pairwise genetic distance (≥3.5%). The haplotypes in these clades were not locality-specific in their distribution. In contrast, we did detect interpopulation variation in opercular shape and morphospace structure, and one population could be separated from the rest based on its distinct tergum morphotype alone. This morphologically distinct population was also differentiated by displaying the lowest mean recruitment density. Our results indicate that although there is no relationship between molecular variation in the COI gene and geographic regions in South Korea, association with locality for operculum morphology, and recruitment response suggest ecological adaptation by this barnacle in a new habitat. creator: Jeongho Kim creator: Michael Ubagan creator: Soyeon Kwon creator: Il-Hoi Kim creator: Sook Shin uri: https://doi.org/10.7717/peerj.14002 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kim et al. title: Effects of plastic film mulching on the spatiotemporal distribution of soil water, temperature, and photosynthetic active radiation in a cotton field link: https://peerj.com/articles/13894 last-modified: 2022-09-01 description: Plastic film mulching (PFM) affects the spatiotemporal distribution of soil moisture and temperature, which in turn affects cotton growth and the spatiotemporal distribution of canopy photosynthetically active radiation (PAR). Due to the spatial heterogeneity of soil moisture, temperature and limited monitoring methods, the issues such as relatively few sampling points and long sampling intervals in most existing studies prevent the accurate quantification of spatiotemporal changes in moisture and temperature along soil profile. To investigate the effects of PFM on spatiotemporal changes in soil moisture, temperature, and canopy PAR in cotton fields, two field trials of plastic film-mulched (M) and nonmulched (NM) cultivations were performed in 2018 and 2019. The grid method was used for the soil information continuous monitoring and multiple-time fixed-site canopy PAR monitoring during the duration of cotton growth. Two-year field trial data showed that, M cultivation increased soil moisture by approximately 13.6%–25% and increased temperature by 2–4 °C in the 0–50 cm soil layer before the first irrigation (June 20) and by 1–2 °C in the 70–110 cm soil layer, compared with NM cultivation. In addition, the temperature difference between the two treatments gradually decreased with the increase in irrigation and air temperature. The M treatment reached the peak PAR interception rate 10 days earlier than the NM treatment. In 2018 and 2019, the PAR peak value under the M treatment was 4.62% and 1.8% higher than that under the NM treatment, respectively, but the PAR interception rate was decreased rapidly in the late growth stage. Overall, PFM had an effect on soil moisture retention during the whole growth period and greatly increased the soil temperature before budding stage, thus promoted the early growth of cotton. Considering this, we suggest that the irrigation quota and frequency could be appropriately decreased in the case of plastic film mulching cultivation. For nonmulching cultivation, the irrigation quota and frequency should be increased, and it is necessary to take measures to improve the soil temperature before middle July. creator: Beifang Yang creator: Lu Feng creator: Xiaofei Li creator: Guozheng Yang creator: Yunzhen Ma creator: Yabing Li uri: https://doi.org/10.7717/peerj.13894 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: CPUE standardization for southern bluefin tuna (Thunnus maccoyii) in the Korean tuna longline fishery, accounting for spatiotemporal variation in targeting through data exploration and clustering link: https://peerj.com/articles/13951 last-modified: 2022-09-01 description: Accounting for spatial and temporal variation in targeting is a concern in many catch per unit effort (CPUE) standardization exercises. In this study we standardized southern bluefin tuna (Thunnus maccoyii, SBT) CPUE from the Korean tuna longline fishery (1996–2018) using generalized linear models (GLMs) with operational set by set data. Data were first explored to investigate the operational characteristics of Korean tuna longline vessels fishing for SBT, such as the spatial and temporal distributions of effort, and changes in the nominal catch rates among major species and species composition. Then we estimated SBT CPUE by area used for the stock assessment in the CCSBT (Commission for the Conservation of Southern Bluefin Tuna) and identified two separate areas in which Korean tuna longline vessels have targeted SBT and albacore tuna (T. alalunga), with targeting patterns varying spatially, seasonally and longer term. We applied two approaches, data selection and cluster analysis of species composition, and compared their ability to address concerns about the changing patterns of targeting through time. Explanatory variables for the GLM analyses were year, month, vessel identifier, fishing location (5° cell), number of hooks, moon phase, and cluster. GLM results for each area suggested that location, year, targeting, and month effects were the principal factors affecting the nominal CPUE. The standardized CPUEs for both areas decreased until the mid-2000s and have shown an increasing trend since that time. creator: Simon D. Hoyle creator: Sung Il Lee creator: Doo Nam Kim uri: https://doi.org/10.7717/peerj.13951 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Hoyle et al. title: Plant traits and environment: floating leaf blade production and turnover of Nymphoides peltata (S.G. Gmel.) O. Kuntze (Menyanthaceae) link: https://peerj.com/articles/13976 last-modified: 2022-09-01 description: BackgroundNymphaeid macrophytes, rooting in the sediment of water bodies and characterized by floating leaves, play an important role in wetland ecosystems. The present research deals with the effects of limited space, limited nutrient availability, water temperature and an unexpected inundation on the production, turnover and plasticity of floating leaves of the globally widespread species Nymphoides peltata (Fringed waterlily).MethodsThe effects of these environmental conditions were studied in two plots in outdoor concrete tanks (CT1, CT2, mesocosms simulating occurrence in small ponds) and in two plots in the floodplain oxbow lake Bemmelse Strang (BS1, BS2). Plot CT1 was situated in a stand coexisting with helophytes, plot CT2 in a monospecific stand, plot BS1 in the center and plot BS2 at the open water border of a monospecific stand. All floating leaf blades within the plots were marked at appearance at the water surface and subsequently length, width and damage of each leaf and maximum and minimum water temperatures were measured bi-weekly. Area and biomass of leaf blades were calculated based on leaf length and width and were used to calculate turnover rates and production.ResultsThe growth period started in May and ended mid-October with continuous production of floating leaves during nearly the whole vegetation period. In the tanks the water level was very stable, but the lake underwent an inundation by river water, causing a sudden loss of existing leaves. Considering environmental conditions and based on the assumed ranking from low to high nutrient availability, the ranking of the plots was CT1, CT2, BS1, BS2. This order was found for maximum leaf life span and maximum leaf length, and the reverse order was found for number of leaves, new leaves per day and duration of the vegetation period. Turnover rates appeared to be relatively similar for plots CT1, CT2 and BS1, but for the deeper border plot BS2 lower ratios were found. These results indicate that increased enclosure with expected nutrient limitation causes (1) the production of high numbers of small leaves with larger totals for leaf area and biomass, (2) a shift towards increased sexual reproduction by the production of more flowering stem leaves. creator: Peter F. Klok creator: Gerard van der Velde uri: https://doi.org/10.7717/peerj.13976 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Klok and van der Velde title: Association of military-specific reaction time performance with physical fitness and visual skills link: https://peerj.com/articles/14007 last-modified: 2022-09-01 description: BackgroundThe aim of the present study was to explore whether military-specific reaction time (RT) test performance is affected by individuals’ physical and visual skills.MethodIn a single testing session, the military-specific Simple and Go, No-Go RT, aerobic power (20-m Multistage Shuttle Run test), maximal upper- and lower-body mechanical capacities (bench press and squat against different loads), and visual skills (multiple object tracking and dynamic visual acuity) of 30 young men (15 active-duty military personnel and 15 sport science students) were evaluated.ResultsThe main findings revealed that the Simple RT and Go, No-Go RT presented (1) with aerobic power non-significant small correlations in military personnel (r = −0.39 and −0.35, respectively) and non-significant negligible correlations in sport science students (r = −0.10 and 0.06, respectively), (2) inconsistent and generally non-significant correlations with the maximal mechanical capacities of the upper- and lower-body muscles (r range = −0.10, 0.67 and −0.27, 0.48, respectively), (3) non-significant correlations with visual skills (r magnitude ≥ 0.58) with the only exception of the Go, No-Go RT that was significantly correlated to all visual variables in the group of students (i.e., students who achieved better results during visual tests had shorter RT; r magnitude ≥ 0.58), and (4) none of the physical and visual variables significantly predicted the Simple RT or Go, No-Go RT.ConclusionAltogether, these results indicate that military-specific RT performance is generally independent of physical and visual skills in both military personnel and active university students. creator: Danica Janicijevic creator: Sergio Miras-Moreno creator: Alejandro Pérez Castilla creator: Jesus Vera creator: Beatriz Redondo creator: Raimundo Jiménez creator: Amador García-Ramos uri: https://doi.org/10.7717/peerj.14007 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Janicijevic et al.