title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=320 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny—a case study on dwarf chameleons link: https://peerj.com/articles/17076 last-modified: 2024-04-30 description: Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work. creator: Devon C. Main creator: Jody M. Taft creator: Anthony J. Geneva creator: Bettine Jansenvan Vuuren creator: Krystal A. Tolley uri: https://doi.org/10.7717/peerj.17076 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Main et al. title: Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities link: https://peerj.com/articles/17091 last-modified: 2024-04-30 description: Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and conservation monitoring programs around the globe. creator: Alice J. Clark creator: Sophie R. Atkinson creator: Valentina Scarponi creator: Tim Cane creator: Nathan R. Geraldi creator: Ian W. Hendy creator: J. Reuben Shipway creator: Mika Peck uri: https://doi.org/10.7717/peerj.17091 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Clark et al. title: Pollen thermotolerance of a widespread plant, Lotus corniculatus, in response to climate warming: possible local adaptation of populations from different elevations link: https://peerj.com/articles/17148 last-modified: 2024-04-30 description: One of the most vulnerable phases in the plant life cycle is sexual reproduction, which depends on effective pollen transfer, but also on the thermotolerance of pollen grains. Pollen thermotolerance is temperature-dependent and may be reduced by increasing temperature associated with global warming. A growing body of research has focused on the effect of increased temperature on pollen thermotolerance in crops to understand the possible impact of temperature extremes on yield. Yet, little is known about the effects of temperature on pollen thermotolerance of wild plant species. To fill this gap, we selected Lotus corniculatus s.l. (Fabaceae), a species common to many European habitats and conducted laboratory experiments to test its pollen thermotolerance in response to artificial increase in temperature. To test for possible local adaptation of pollen thermal tolerance, we compared data from six lowland (389–451 m a.s.l.) and six highland (841–1,030 m a.s.l.) populations. We observed pollen germination in vitro at 15 °C, 25 °C, 30 °C, and 40 °C. While lowland plants maintained a stable germination percentage across a broad temperature range (15–30 °C) and exhibited reduced germination only at extremely high temperatures (40 °C), highland plants experienced reduced germination even at 30 °C–temperatures commonly exceeded in lowlands during warm summers. This suggests that lowland populations of L. corniculatus may be locally adapted to higher temperature for pollen germination. On the other hand, pollen tube length decreased with increasing temperature in a similar way in lowland and highland plants. The overall average pollen germination percentage significantly differed between lowland and highland populations, with highland populations displaying higher germination percentage. On the other hand, the average pollen tube length was slightly smaller in highland populations. In conclusion, we found that pollen thermotolerance of L. corniculatus is reduced at high temperature and that the germination of pollen from plant populations growing at higher elevations is more sensitive to increased temperature, which suggests possible local adaptation of pollen thermotolerance. creator: Karolína Jackwerth creator: Paolo Biella creator: Jan Klečka uri: https://doi.org/10.7717/peerj.17148 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jackwerth et al. title: Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease link: https://peerj.com/articles/17186 last-modified: 2024-04-30 description: Pulmonary hypertension (PH), a common complication in dogs affected by degenerative mitral valve disease (DMVD), is a progressive disorder characterized by increased pulmonary arterial pressure (PAP) and pulmonary vascular remodeling. Phosphorylation of proteins, impacting vascular function and cell proliferation, might play a role in the development and progression of PH. Unlike gene or protein studies, phosphoproteomic focuses on active proteins that function as end-target proteins within signaling cascades. Studying phosphorylated proteins can reveal active contributors to PH development. Early diagnosis of PH is crucial for effective management and improved clinical outcomes. This study aimed to identify potential serum biomarkers for diagnosing PH in dogs affected with DMVD using a phosphoproteomic approach. Serum samples were collected from healthy control dogs (n = 28), dogs with DMVD (n = 24), and dogs with DMVD and PH (n = 29). Phosphoproteins were enriched from the serum samples and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Data analysis was performed to identify uniquely expressed phosphoproteins in each group and differentially expressed phosphoproteins among groups. Phosphoproteomic analysis revealed nine uniquely expressed phosphoproteins in the serum of dogs in the DMVD+PH group and 15 differentially upregulated phosphoproteins in the DMVD+PH group compared to the DMVD group. The phosphoproteins previously implicated in PH and associated with pulmonary arterial remodeling, including small nuclear ribonucleoprotein G (SNRPG), alpha-2-macroglobulin (A2M), zinc finger and BTB domain containing 42 (ZBTB42), hemopexin (HPX), serotransferrin (TRF) and complement C3 (C3), were focused on. Their unique expression and differential upregulation in the serum of DMVD dogs with PH suggest their potential as biomarkers for PH diagnosis. In conclusion, this phosphoproteomic study identified uniquely expressed and differentially upregulated phosphoproteins in the serum of DMVD dogs with PH. Further studies are warranted to validate the diagnostic utility of these phosphoproteins. creator: Siriwan Sakarin creator: Anudep Rungsipipat creator: Sittiruk Roytrakul creator: Janthima Jaresitthikunchai creator: Narumon Phaonakrop creator: Sawanya Charoenlappanit creator: Siriwan Thaisakun creator: Sirilak Surachetpong uri: https://doi.org/10.7717/peerj.17186 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sakarin et al. title: Interactions between chaperone and energy storage networks during the evolution of Legionella pneumophila under heat shock link: https://peerj.com/articles/17197 last-modified: 2024-04-30 description: Waterborne transmission of the bacterium Legionella pneumophila has emerged as a major cause of severe nosocomial infections of major public health impact. The major route of transmission involves the uptake of aerosolized bacteria, often from the contaminated hot water systems of large buildings. Public health regulations aimed at controlling the mesophilic pathogen are generally concerned with acute pasteurization and maintaining high temperatures at the heating systems and throughout the plumbing of hot water systems, but L. pneumophila is often able to survive these treatments due to both bacterium-intrinsic and environmental factors. Previous work has established an experimental evolution system to model the observations of increased heat resistance in repeatedly but unsuccessfully pasteurized L. pneumophila populations. Here, we show rapid fixation of novel alleles in lineages selected for resistance to heat shock and shifts in mutational profile related to increases in the temperature of selection. Gene-level and nucleotide-level parallelisms between independently-evolving lineages show the centrality of the DnaJ/DnaK chaperone system in the heat resistance of L. pneumophila. Inference of epistatic interactions through reverse genetics shows an unexpected interaction between DnaJ/DnaK and the polyhydroxybutyrate-accumulation energy storage mechanism used by the species to survive long-term starvation in low-nutrient environments. creator: Jeffrey Liang creator: Sebastien P. Faucher uri: https://doi.org/10.7717/peerj.17197 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liang and Faucher title: The low survival rate of European hare leverets in arable farmland: evidence from the predation experiment link: https://peerj.com/articles/17235 last-modified: 2024-04-30 description: The low survival rate of leverets may significantly contribute to steep population declines and slow recovery of European hares (Lepus europaeus). However, the leveret survival rate in farmlands with different landscape structures is poorly understood, and the existing evidence comes mainly from Western Europe. In this study, we explored the survival of leveret hare dummies along linear semi-natural habitats in homogeneous Central European arable farmland during the main part of the European hare reproduction period (March–April) in 2019 and 2020. The survival rate of hare leverets during the 14-day period was only 22.2%, and all predation events were recorded during the first six days of the experiment. Mammalian predators were responsible for 53.1% of predation events, avian predators for 40.8%, and agricultural operations for 6.1%. The red fox (Vulpes vulpes) was the dominant predator in our study area and was the primary cause of leveret dummy mortality (32.7%), but it also had the highest use-intensity and visit frequency of all of the study plots. Predation by avian predators was associated with patches of lower vegetation height and cover (such as plowed fields) and during daylight hours, whereas the opposite was true for mammalian predators. We propose that improving the habitat quality of arable landscapes by increasing the proportion and quality of extensively used non-farmed habitats (e.g., set-asides, wildflower areas, extensive meadows, fallow land, and semi-natural habitats on arable land) providing cover and shelter for leverets could be an effective management measure for reducing predation risk on leverets. creator: Jan Cukor creator: Jan Riegert creator: Aleksandra Krivopalova creator: Zdeněk Vacek creator: Martin Šálek uri: https://doi.org/10.7717/peerj.17235 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cukor et al. title: Cystatin C: immunoregulation role in macrophages infected with Porphyromonas gingivalis link: https://peerj.com/articles/17252 last-modified: 2024-04-30 description: BackgroundPeriodontitis is a chronic infectious disease, characterized by an exacerbated inflammatory response and a progressive loss of the supporting tissues of the teeth. Porphyromonas gingivalis is a key etiologic agent in periodontitis. Cystatin C is an antimicrobial salivary peptide that inhibits the growth of P. gingivalis. This study aimed to evaluate the antimicrobial activity of this peptide and its effect on cytokine production, nitric oxide (NO) release, reactive oxygen species (ROS) production, and programmed cell death in human macrophages infected with P. gingivalis.MethodsMonocyte-derived macrophages generated from peripheral blood were infected with P. gingivalis (MOI 1:10) and stimulated with cystatin C (2.75 µg/ml) for 24 h. The intracellular localization of P. gingivalis and cystatin C was determined by immunofluorescence and transmission electron microscopy (TEM). The intracellular antimicrobial activity of cystatin C in macrophages was assessed by counting Colony Forming Units (CFU). ELISA assay was performed to assess inflammatory (TNFα, IL-1β) and anti-inflammatory (IL-10) cytokines. The production of nitrites and ROS was analyzed by Griess reaction and incubation with 2′,7′-dichlorodihydrofluorescein diacetate (H2DCFDA), respectively. Programmed cell death was assessed with the TUNEL assay, Annexin-V, and caspase activity was also determined.ResultsOur results showed that cystatin C inhibits the extracellular growth of P. gingivalis. In addition, this peptide is internalized in the infected macrophage, decreases the intracellular bacterial load, and reduces the production of inflammatory cytokines and NO. Interestingly, peptide treatment increased ROS production and substantially decreased bacterial-induced macrophage apoptosis.ConclusionsCystatin C has antimicrobial and immuno-regulatory activity in macrophages infected with P. gingivalis. These findings highlight the importance of understanding the properties of cystatin C for its possible therapeutic use against oral infections such as periodontitis. creator: Blanca Esther Blancas-Luciano creator: Ingeborg Becker-Fauser creator: Jaime Zamora-Chimal creator: Luis Jiménez-García creator: Reyna Lara-Martínez creator: Armando Pérez-Torres creator: Margarita González del Pliego creator: Elsa Liliana Aguirre-Benítez creator: Ana María Fernández-Presas uri: https://doi.org/10.7717/peerj.17252 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Blancas-Luciano et al. title: Analysis of drought and heat stress response genes in rice using co-expression network and differentially expressed gene analyses link: https://peerj.com/articles/17255 last-modified: 2024-04-30 description: Studies on Oryza sativa (rice) are crucial for improving agricultural productivity and ensuring global sustenance security, especially considering the increasing drought and heat stress caused by extreme climate change. Currently, the genes and mechanisms underlying drought and heat resistance in rice are not fully understood, and the scope for enhancing the development of new strains remains considerable. To accurately identify the key genes related to drought and heat stress responses in rice, multiple datasets from the Gene Expression Omnibus (GEO) database were integrated in this study. A co-expression network was constructed using a Weighted Correlation Network Analysis (WGCNA) algorithm. We further distinguished the core network and intersected it with differentially expressed genes and multiple expression datasets for screening. Differences in gene expression levels were verified using quantitative real-time polymerase chain reaction (PCR). OsDjC53, MBF1C, BAG6, HSP23.2, and HSP21.9 were found to be associated with the heat stress response, and it is also possible that UGT83A1 and OsCPn60a1, although not directly related, are affected by drought stress. This study offers significant insights into the molecular mechanisms underlying stress responses in rice, which could promote the development of stress-tolerant rice breeds. creator: Gaohui Cao creator: Hao Huang creator: Yuejiao Yang creator: Bin Xie creator: Lulu Tang uri: https://doi.org/10.7717/peerj.17255 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cao et al. title: Structural equation models of health behaviour, psychological well-being, symptom severity and quality of life in abdominal bloating link: https://peerj.com/articles/17265 last-modified: 2024-04-30 description: BackgroundThe objective of this study was to investigate the inter-relationship between psychosocial variables and their impact on symptom severity and quality of life (QoL) concerning abdominal bloating.MethodsThe study adopted a cross-sectional design with purposive sampling. Participants who consented and met the criteria for bloating based on the Rome IV classification completed designated questionnaires. Independent variables comprised health beliefs, intentions, health-promoting behaviors, social support, depression, and anxiety, while dependent variables included bloating severity (general and within 24 h) and QoL. Structural Equation Modeling (SEM) was conducted utilizing Mplus 8.0 to analyze the relationships between these factors.ResultsA total of 323 participants, with a mean age of 27.69 years (SD = 11.50), predominantly females (64.7%), volunteered to participate in the study. The final SEM model exhibited good fit based on various indices (CFI = 0.922, SRMR = 0.064, RMSEA (95% CI) = 0.048 (0.041–0.054), p-value = 0.714), with 15 significant path relationships identified. The model explained 12.0% of the variance in severity within 24 h, 6% in general severity, and 53.8% in QoL.ConclusionThe findings underscore the significant influence of health beliefs, intentions, behaviors, social support, depression, and anxiety on symptom severity and QoL in individuals experiencing abdominal bloating. creator: Nurzulaikha Abdullah creator: Yee Cheng Kueh creator: Garry Kuan creator: Mung Seong Wong creator: Vincent Tee creator: Tengku Ahmad Iskandar Tengku Alang creator: Nurhazwani Hamid creator: Yeong Yeh Lee uri: https://doi.org/10.7717/peerj.17265 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Abdullah et al. title: Photoactivated disinfection procedure for denture stomatitis in diabetic rats link: https://peerj.com/articles/17268 last-modified: 2024-04-30 description: ObjectiveTo study the efficacy of PADTM Plus-based photoactivated disinfection (PAD) for treating denture stomatitis (DS) in diabetic rats by establishing a diabetic rat DS model.MethodsThe diabetic rat DS model was developed by randomly selecting 2-month-old male Sprague-Dawley rats and dividing them into four groups. The palate and denture surfaces of rats in the PAD groups were incubated with 1 mg/mL toluidine blue O for 1 min each, followed by a 1-min exposure to 750-mW light-emitting diode light. The PAD-1 group received one radiation treatment, and the PAD-2 group received three radiation treatments over 5 days with a 1-day interval. The nystatin (NYS) group received treatment for 5 days with a suspension of NYS of 100,000 IU. The infection group did not receive any treatment. In each group, assessments included an inflammation score of the palate, tests for fungal load, histological evaluation, and immunohistochemical detection of interleukin-17 (IL-17) and tumor necrosis factor (TNF-α) conducted 1 and 7 days following the conclusion of treatment.ResultsOne day after treatment, the fungal load on the palate and dentures, as well as the mean optical density values of IL-17 and TNF-α, were found to be greater in the infection group than in the other three treatment groups (P < 0.05). On the 7th day after treatment, these values were significantly higher in the infection group than in the PAD-2 and NYS groups (P < 0.05). Importantly, there were no differences between the infection and PAD-1 groups nor between the PAD-2 and NYS groups (P > 0.05).ConclusionsPAD effectively reduced the fungal load and the expressions of IL-17 and TNF-α in the palate and denture of diabetic DS rats. The efficacy of multiple-light treatments was superior to that of single-light treatments and similar to that of NYS. creator: Xiao Zhang creator: Zirui Zhao creator: Ruiqi Zhang creator: Juan Liu creator: Zhijiao Guo creator: Qiaoyu Hu creator: Na Liu creator: Qing Liu uri: https://doi.org/10.7717/peerj.17268 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al.