title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=323 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: S100A8/9 modulates perturbation and glycolysis of macrophages in allergic asthma mice link: https://peerj.com/articles/17106 last-modified: 2024-04-18 description: BackgroundAllergic asthma is the most prevalent asthma phenotype and is associated with the disorders of immune cells and glycolysis. Macrophages are the most common type of immune cells in the lungs. Calprotectin (S100A8 and S100A9) are two pro-inflammatory molecules that target the Toll-like receptor 4 (TLR4) and are substantially increased in the serum of patients with severe asthma. This study aimed to determine the effects of S100A8/A9 on macrophage polarization and glycolysis associated with allergic asthma.MethodsTo better understand the roles of S100A8 and S100A9 in the pathogenesis of allergic asthma, we used ovalbumin (OVA)-induced MH-S cells, and OVA-sensitized and challenged mouse models (wild-type male BALB/c mice). Enzyme-linked immunosorbent assay, quantitative real-time polymerase chain reaction, flow cytometry, hematoxylin-eosin staining, and western blotting were performed. The glycolysis inhibitor 3-bromopyruvate (3-BP) was used to observe changes in glycolysis in mice.ResultsWe found knockdown of S100A8 or S100A9 in OVA-induced MH-S cells inhibited inflammatory cytokines, macrophage polarization biomarker expression, and pyroptosis cell proportion, but increased anti-inflammatory cytokine interleukin (IL)-10 mRNA; also, glycolysis was inhibited, as evidenced by decreased lactate and key enzyme expression; especially, knockdown of S100A8 or S100A9 inhibited the activity of TLR4/myeloid differentiation primary response gene 88 (MyD88)/Nuclear factor kappa-B (NF-κB) signaling pathway. Intervention with lipopolysaccharides (LPS) abolished the beneficial effects of S100A8 and S100A9 knockdown. The observation of OVA-sensitized and challenged mice showed that S100A8 or S100A9 knockdown promoted respiratory function, improved lung injury, and inhibited inflammation; knockdown of S100A8 or S100A9 also suppressed macrophage polarization, glycolysis levels, and activation of the TLR4/MyD88/NF-κB signaling pathway in the lung. Conversely, S100A9 overexpression exacerbated lung injury and inflammation, promoting macrophage polarization and glycolysis, which were antagonized by the glycolysis inhibitor 3-BP.ConclusionS100A8 and S100A9 play critical roles in allergic asthma pathogenesis by promoting macrophage perturbation and glycolysis through the TLR4/MyD88/NF-κB signaling pathway. Inhibition of S100A8 and S100A9 may be a potential therapeutic strategy for allergic asthma. creator: Xiaoyi Ji creator: Chunhua Nie creator: Yuan Yao creator: Yu Ma creator: Huafei Huang creator: Chuangli Hao uri: https://doi.org/10.7717/peerj.17106 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ji et al. title: Carbon content and other soil properties of near-surface peats before and after peatland restoration link: https://peerj.com/articles/17113 last-modified: 2024-04-18 description: Peatland restoration usually aims at restarting the peatlands’ function to store carbon within peat. The soil properties of the near-surface peat can give a first understanding of this process. Therefore, we sampled pH value, total organic carbon content (TOC), total nitrogen content (TN), C/N ratio as well as dry bulk density (BD), and describe the structure of near-surface peats in six restored fens in North-East Germany before (2002–2004) and after (2019–2021) restoration. Before restoration, the study sites showed peat degradation to various extents in their near-surface peats. pH values remained relatively stable over time. Comparing the degraded peat horizons, TOC increased significantly in four study sites, ranging from 35.7% to 47.8% in 2002–2004 and from 42.5% to 54.0% in 2019–2021. TN varied from 1.5% to 3.5% in 2002–2004 and from 1.8% to 3.2% in 2019–2021, but changes were only significant in one site, showing a slight decrease. In three sites, the increase in C/N ratio was significant, indicating lower nutrient availability. BD ranged from 0.08 to 0.48 g/cm3 in 2002–2004 and from 0.10 to 0.16 g/cm3 in 2019–2021, decreasing significantly in four sites. The structure of the degraded peat horizons changed after restoration to a more homogenous, sludge mass with larger re-aggregates. In three sites, new peat moss peat layers above the degraded soil horizon were present in 2019–2021, with a mean thickness of 6.8 to 36.1 cm. The structure was comparable to typical, slightly decomposed peat moss peat. Our findings suggest that within about 17 years after fen restoration, and thereby a water table rise close to surface, TOC of the near-surface peats increased to values that are typical for undisturbed peatlands. This indicates that restoration can lead to the re-establishment of peatlands as potential carbon sinks, with TOC within the near-surface peat as one key factor in this process. Further, we assume that the decrease in nutrient availability, decrease of BD, and new, undisturbed peat layers can favor the establishment of mire-specific biodiversity and support ecosystem services similar to near-natural mires. creator: Jenny Hammerich creator: Corinna Schulz creator: Robert Probst creator: Thomas Lüdicke creator: Vera Luthardt uri: https://doi.org/10.7717/peerj.17113 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hammerich et al. title: COVID-19 and malaria co-infection: a systematic review of clinical outcomes in endemic areas link: https://peerj.com/articles/17160 last-modified: 2024-04-18 description: BackgroundCOVID-19 and malaria cause significant morbidity and mortality globally. Co-infection of these diseases can worsen their impact on public health. This review aims to synthesize literature on the clinical outcomes of COVID-19 and malaria co-infection to develop effective prevention and treatment strategies.MethodsA comprehensive literature search was conducted using MeSH terms and keywords from the start of the COVID-19 pandemic to January 2023. The review included original articles on COVID-19 and malaria co-infection, evaluating their methodological quality and certainty of evidence. It was registered in PROSPERO (CRD42023393562).ResultsOut of 1,596 screened articles, 19 met the inclusion criteria. These studies involved 2,810 patients, 618 of whom had COVID-19 and malaria co-infection. Plasmodium falciparum and vivax were identified as causative organisms in six studies. Hospital admission ranged from three to 18 days. Nine studies associated co-infection with severe disease, ICU admission, assisted ventilation, and related complications. One study reported 6% ICU admission, and mortality rates of 3%, 9.4%, and 40.4% were observed in four studies. Estimated crude mortality rates were 10.71 and 5.87 per 1,000 person-days for patients with and without concurrent malaria, respectively. Common co-morbidities included Diabetes mellitus, hypertension, cardiovascular diseases, and respiratory disorders.ConclusionMost patients with COVID-19 and malaria co-infection experienced short-term hospitalization and mild to moderate disease severity. However, at presentation, co-morbidities and severe malaria were significantly associated with higher mortality or worse clinical outcomes. These findings emphasize the importance of early detection, prompt treatment, and close monitoring of patients with COVID-19 and malaria co-infection. creator: Amal H. Mohamed creator: Ebtihal Eltyeb creator: Badria Said creator: Raga Eltayeb creator: Abdullah Algaissi creator: Didier Hober creator: Abdulaziz H. Alhazmi uri: https://doi.org/10.7717/peerj.17160 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mohamed et al. title: Hand grab or noose pole? Evaluating the least stressful practice for capture of endangered Turks and Caicos Rock Iguanas Cyclura carinata link: https://peerj.com/articles/17171 last-modified: 2024-04-18 description: As the analysis of blood metabolites has become more readily accessible thanks to the use of point-of-care analyzers, it is now possible to evaluate stress level of wild animals directly in the field. Lactate is receiving much attention as a good stress level proxy in individuals subjected to capture, manual restraint, and data sampling in the wild, and appropriate protocols to maintain lactate values low should be preferred. In this study we compare how two different capture methodologies, hand grab vs. noose pole, affect the variation of blood lactate values in Cyclura carinata iguanas when captured for sampling. We used blood lactate concentration, measured immediately upon- and 15 min after-capture, as a proxy for stress level. While the primary goal of this work is to determine the least stressful capture methodology to be favored when sampling this and other wild iguanas, we also evaluated additional baseline physiological parameters relevant to the health and disease monitoring for this species. Our results show that while initial lactate values level-out in sampled individuals after 15 min in captivity, regardless of the capture methodology, rock iguanas captured by noose pole showed significantly higher lactate concentration and increased heartbeat rate immediately after capture. While the overall health evaluation determined that all analyzed individuals were in good health, based on our results we recommend that, when possible, hand capture should be preferred over noose pole when sampling wild individuals. creator: Giuliano Colosimo creator: Gwyneth Montemuro creator: Gregory A. Lewbart creator: Gabriele Gentile creator: Glenn P. Gerber uri: https://doi.org/10.7717/peerj.17171 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Colosimo et al. title: Preliminary study on the protective effect of remazolam against sepsis-induced acute respiratory distress syndrome (ARDS) link: https://peerj.com/articles/17205 last-modified: 2024-04-18 description: BackgroundSepsis can disrupt immune regulation and lead to acute respiratory distress syndrome (ARDS) frequently. Remazolam, a fast-acting hypnotic drug with superior qualities compared to other drugs, was investigated for its potential protective effects against sepsis-induced ARDS.MethodsForty Sprague-Dawley rats were randomly divided into four groups, including the sepsis + saline group, sham operation + saline group, sham operation + remazolam group and the sepsis + remazolam group. Lung tissues of rats were extracted for HE staining to assess lung damage, and the wet weight to dry weight (W/D) ratio was calculated. The levels of proinflammatory factors, anti-inflammatory factors, CD4+ and CD8+ T cells in peripheral blood, MDA, MPO, and ATP in the lung tissue were measured by using ELISA. Western blotting was performed to determine the protein expression of HMGB1 in lung tissues.ResultsIn comparison to the sham operation + saline and sham operation + remazolam groups, the sepsis + saline group exhibited significantly higher values for W/D ratio, lung damage score, IL-1β, IL-6, TNF-α, PCT, CRP, MDP and MPO, while exhibiting lower levels of CD4+ and CD8+ T lymphocytes, PaO2, PCO2, and ATP. The rats in the sepsis + saline group displayed ruptured alveolar walls and evident interstitial lung edema. However, the rats in the sepsis + remazolam group showed improved alveolar structure. Furthermore, the HMGB1 protein expression in the sepsis + remazolam group was lower than the sepsis + saline group.ConclusionRemazolam can alleviate the inflammatory response in infected rats, thereby alleviating lung injury and improving immune function, which may be attributed to the reduction in HMGB1 protein expression. creator: Xiaoxin Gao creator: Rujun Zhang creator: Zhenzhou Wang creator: Qingan Chen creator: Zhenlin Lei creator: Yanan Yang creator: Jia Tian uri: https://doi.org/10.7717/peerj.17205 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gao et al. title: Novel monoclonal antibodies against house dust mite allergen Der p 21 and their application to analyze allergen extracts link: https://peerj.com/articles/17233 last-modified: 2024-04-18 description: BackgroundAllergen extracts and recombinant allergens are used in allergy diagnostics and immunotherapy. Since allergen extracts from different manufacturers lack proper standardization regarding their composition, monoclonal antibodies (MAbs) against specific allergen components can be used for their identification and quantification in allergen extracts. This study aimed to generate MAbs against allergen Der p 21 of Dermatophagoides pteronyssinus for the analysis of allergen extracts.MethodsRecombinant Der p 21 was expressed in E. coli and purified using affinity chromatography. MAbs against Der p 21 were generated using hybridoma technology. House dust mite (HDM) allergen extracts were analyzed using the newly developed sandwich enzyme-linked immunosorbent assay, Western blotting and microarray immunoassay.ResultsMAbs raised against recombinant Der p 21 were characterized in detail and proven to be reactive with natural Der p 21. Highly specific sandwich enzyme-linked immunosorbent assay for the quantification of Der p 21 was developed and optimized. The allergen was detected and its concentration was determined in only three of six analyzed HDM allergen extracts from different manufacturers.ConclusionHDM analysis by MAb-based immunoassays shows their differences in allergen composition. The results demonstrate the importance of allergen-specific MAbs as a tool for the characterization of allergen extracts and the need for their appropriate standardization before their use for allergy diagnostics or immunotherapy. creator: Vytautas Rudokas creator: Laimis Silimavicius creator: Indre Kucinskaite-Kodze creator: Aiste Sliziene creator: Milda Pleckaityte creator: Aurelija Zvirbliene uri: https://doi.org/10.7717/peerj.17233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rudokas et al. title: Transcriptome analysis during 4-vinylcyclohexene diepoxide exposure-induced premature ovarian insufficiency in mice link: https://peerj.com/articles/17251 last-modified: 2024-04-18 description: The occupational chemical 4-Vinylcyclohexene diepoxide (VCD) is a reproductively toxic environmental pollutant that causes follicular failure, leading to premature ovarian insufficiency (POI), which significantly impacts a woman’s physical health and fertility. Investigating VCD’s pathogenic mechanisms can offer insights for the prevention of ovarian impairment and the treatment of POI. This study established a mouse model of POI through intraperitoneal injection of VCD into female C57BL/6 mice for 15 days. The results were then compared with those of the control group, including a comparison of phenotypic characteristics and transcriptome differences, at two time points: day 15 and day 30. Through a comprehensive analysis of differentially expressed genes (DEGs), key genes were identified and validated some using RT-PCR. The results revealed significant impacts on sex hormone levels, follicle number, and the estrous cycle in VCD-induced POI mice on both day 15 and day 30. The DEGs and enrichment results obtained on day 15 were not as significant as those obtained on day 30. The results of this study provide a preliminary indication that steroid hormone synthesis, DNA damage repair, and impaired oocyte mitosis are pivotal in VCD-mediated ovarian dysfunction. This dysfunction may have been caused by VCD damage to the primordial follicular pool, impairing follicular development and aggravating ovarian damage over time, making it gradually difficult for the ovaries to perform their normal functions. creator: Yi Li creator: Ruifen He creator: Xue Qin creator: Qinying Zhu creator: Liangjian Ma creator: Xiaolei Liang uri: https://doi.org/10.7717/peerj.17251 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Cytokine profiles of mild-to-moderate SARS-CoV-2 infected and recovered pre-vaccinated individuals residing in Indonesia link: https://peerj.com/articles/17257 last-modified: 2024-04-18 description: BackgroundAccumulating evidence suggests the involvement of cytokine-mediated inflammation, in clinical severity and death related to SARS-CoV-2 infection, especially among pre-vaccinated individuals. An increased risk of death was also described among SARS-CoV-2 recovered individuals, which might be correlated with prolonged inflammatory responses. Despite being among the countries with the highest cumulative deaths due to COVID-19, evidence regarding cytokine profiles among SARS-CoV-2 infected and recovered pre-vaccinated individuals in Indonesia is scarce. Thus, this study aimed to describe the cytokines profiles of pre-vaccinated individuals residing in Indonesia, with mild-to-moderate SARS-CoV-2 infection and those who recovered.MethodsSixty-one sera from 24 hospitalized patients with mild-to-moderate SARS-CoV-2 infection, 24 individuals recovered from asymptomatic-to-moderate SARS-CoV-2 infection, and 13 healthy controls unexposed to SARS-CoV-2 were used in this study. Quantification of serum cytokine levels, including IL-6, IL-8, IP-10, TNF-α, CCL-2, CCL-3, CCL-4, and CXCL-13, was performed using a Luminex multi-analyte-profiling (xMAP)-based assay.ResultsThe levels of IL-8 along with CCL-2 and CCL-4, were significantly higher (p ≤ 0.01) in hospitalized patients with mild-to-moderate SARS-CoV-2 infection and recovered individuals compared to healthy controls. However, no significant difference was observed in these cytokine levels between infected and recovered individuals. On the other hand, there were no significant differences in several other cytokine levels, including IL-6, IL-10, TNF-α, CCL-3, and CXCL-13, among all groups.ConclusionIL-8, CCL-2, and CCL-4 were significantly elevated in pre-vaccinated Indonesian individuals with mild-to-moderate SARS-CoV-2 infection and those who recovered. The cytokine profiles described in this study might indicate inflammatory responses not only among SARS-CoV-2 infected, but also recovered individuals. creator: Ni Luh Ayu Megasari creator: Siti Qamariyah Khairunisa creator: Radita Yuniar Arizandy creator: I. Komang Evan Wijaksana creator: Citrawati Dyah Kencono Wungu uri: https://doi.org/10.7717/peerj.17257 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Megasari et al. title: Citizen science initiatives document biodiversity baselines at an urban lake link: https://peerj.com/articles/17209 last-modified: 2024-04-17 description: Changes to biodiversity from urbanization are occurring worldwide, and baseline data is vital to document the magnitude and direction of these alterations. We set out to document the biodiversity of an urban lake in Eastern Iowa that was devoid of baseline data prior to a renovation project that will convert the site into a major area for human recreation. Throughout the course of one year, we studied the biodiversity at Cedar Lake utilizing the citizen-science application iNaturalist coupled with semi-structured BioBlitz events, which we compared to previous opportunistic observations at the site. From a semi-structured approach to document biodiversity with citizen science, our analyses revealed more diverse community metrics over a shorter period compared to more than a decade of prior observations. creator: Alyssah Ahern creator: Daniel F. Hughes uri: https://doi.org/10.7717/peerj.17209 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ahern and Hughes title: Gene expression profiles of Japanese precious coral Corallium japonicum during gametogenesis link: https://peerj.com/articles/17182 last-modified: 2024-04-16 description: BackgroundCorallium japonicum, a prized resource in Japan, plays a vital role in traditional arts and fishing industries. Because of diminished stock due to overexploitation, ongoing efforts are focused on restoration through transplantation. This study aimed to enhance our understanding of the reproductive biology of these valuable corals and find more efficient methods for sex determination, which may significantly contribute to conservation initiatives.MethodsWe used 12 three-month aquarium reared C. japonicum colony fragments, conducted histological analysis for maturity and sex verification, and performed transcriptome analysis via de novo assembly and mapping using the C. rubrum transcriptome to explore gene expression differences between female and male C. japonicum.ResultsOur histological observations enabled sex identification in 33% of incompletely mature samples. However, the sex of the remaining 67% of samples, classified as immature, could not be identified. RNA-seq yielded approximately 21–31 million short reads from 12 samples. De novo assembly yielded 404,439 highly expressed transcripts. Among them, 855 showed significant differential expression, with 786 differentially expressed transcripts between females and males. Heatmap analysis highlighted 283 female-specific and 525 male-specific upregulated transcripts. Transcriptome assembly mapped to C. rubrum yielded 28,092 contigs, leading to the identification of 190 highly differentially expressed genes, with 113 upregulated exclusively in females and 70 upregulated exclusively in males. Blastp analysis provided putative protein annotations for 83 female and 72 male transcripts. Annotation analysis revealed that female biological processes were related to oocyte proliferation and reproduction, whereas those in males were associated with cell adhesion.DiscussionTranscriptome analysis revealed sex-specific gene upregulation in incompletely mature C. japonicum and shared transcripts with C. rubrum, providing insight into its gene expression patterns. This study highlights the importance of using both de novo and reference-based assembly methods. Functional enrichment analysis showed that females exhibited enrichment in cell proliferation and reproduction pathways, while males exhibited enrichment in cell adhesion pathways. To the best of our knowledge, this is the first report on the gene expressions of each sex during the spawning season. Our findings offer valuable insights into the physiological ecology of incompletely mature red Japanese precious corals and suggest a method for identifying sex using various genes expressed in female and male individuals. In the future, techniques such as transplantation, artificial fertilization, and larval rearing may involve sex determination methods based on differences in gene expression to help conserve precious coral resources and ecosystems. creator: Ma. Marivic Capitle Pepino creator: Sam Edward Manalili creator: Satoko Sekida creator: Takuma Mezaki creator: Tomoyo Okumura creator: Satoshi Kubota uri: https://doi.org/10.7717/peerj.17182 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pepino et al.