title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=845 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Impact of dietary level and ratio of n-6 and n-3 fatty acids on disease progression and mRNA expression of immune and inflammatory markers in Atlantic salmon (Salmo salar) challenged with Paramoeba perurans link: https://peerj.com/articles/12028 last-modified: 2021-08-31 description: The aim of the study was to investigate the influence of dietary level and ratio of n-6/n-3 fatty acids (FA) on growth, disease progression and expression of immune and inflammatory markers in Atlantic salmon (Salmo salar) following challenge with Paramoeba perurans. Fish (80 g) were fed four different diets with different ratios of n-6/n-3 FA; at 1.3, 2.4 and 6.0 and one diet with ratio of 1.3 combined with a higher level of n-3 FA and n-6 FA. The diet with the n-6/n-3 FA ratio of 6.0 was included to ensure potential n-6 FA effects were revealed, while the three other diets were more commercially relevant n-6/n-3 FA ratios and levels. After a pre-feeding period of 3 months, fish from each diet regime were challenged with a standardized laboratory challenge using a clonal culture of P. perurans at the concentration of 1,000 cells L−1. The subsequent development of the disease was monitored (by gross gill score), and sampling conducted before challenge and at weekly sampling points for 5 weeks post-challenge. Challenge with P. perurans did not have a significant impact on the growth of the fish during the challenge period, but fish given the feed with the highest n-6/n-3 FA ratio had reduced growth compared to the other groups. Total gill score for all surfaces showed a significant increase with time, reaching a maximum at 21 days post-challenge and declined thereafter, irrespective of diet groups. Challenge with P. perurans influenced the mRNA expression of examined genes involved in immune and inflammatory response (TNF-α, iNOS, IL4-13b, GATA-3, IL-1β, p53, COX2 and PGE2-EP4), but diet did not influence the gene expression. In conclusion, an increase in dietary n-6/n-3 FA ratio influenced the growth of Atlantic salmon challenged with P. perurans; however, it did not alter the mRNA expression of immune genes or progression of the disease. creator: Chandrasekar Selvam creator: Mark D. Powell creator: Nina S. Liland creator: Grethe Rosenlund creator: Nini H. Sissener uri: https://doi.org/10.7717/peerj.12028 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Selvam et al. title: COVID-19 and regional differences in the timeliness of hip-fracture surgery: an interrupted time-series analysis link: https://peerj.com/articles/12046 last-modified: 2021-08-31 description: BackgroundIt is of great importance to examine the impact of the healthcare reorganization adopted to confront the COVID-19 pandemic on the quality of care provided to non-COVID-19 patients. The aim of this study is to assess the impact of the COVID-19 national lockdown (March 9, 2020) on the quality of care provided to patients with hip fracture (HF) in Piedmont and Emilia-Romagna, two large regions of northern Italy severely hit by the pandemic.MethodsWe calculated the percentage of HF patients undergoing surgery within 2 days of hospital admission. An interrupted time-series analysis was performed on weekly data from December 11, 2019 to June 9, 2020 (≈6 months), interrupting the series in the 2nd week of March. The same data observed the year before were included as a control time series with no “intervention” (lockdown) in the middle of the observation period.ResultsBefore the lockdown, 2-day surgery was 69.9% in Piedmont and 79.2% in Emilia-Romagna; after the lockdown, these proportions were equal to 69.8% (–0.1%) and 69.3% (–9.9%), respectively. While Piedmont did not experience any drop in the amount of surgery, Emilia-Romagna exhibited a significant decline at a weekly rate of –1.29% (95% CI [−1.71 to −0.88]). Divergent trend patterns in the two study regions reflect local differences in pandemic timing as well as in healthcare services capacity, management, and emergency preparedness. creator: Davide Golinelli creator: Jacopo Lenzi creator: Emanuele Adorno creator: Maria Michela Gianino creator: Maria Pia Fantini uri: https://doi.org/10.7717/peerj.12046 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Golinelli et al. title: Germline mutation analyses of malignant ground glass opacity nodules in non-smoking lung adenocarcinoma patients link: https://peerj.com/articles/12048 last-modified: 2021-08-31 description: BackgroundGermline mutations play an important role in the pathogenesis of lung cancer. Nonetheless, research on malignant ground glass opacity (GGO) nodules is limited.MethodsA total of 13 participants with malignant GGO nodules were recruited in this study. Peripheral blood was used for exome sequencing, and germline mutations were analyzed using InterVar. The whole exome sequencing dataset was analyzed using a filtering strategy. KOBAS 3.0 was used to analyze KEGG pathway to further identify possible deleterious mutations.ResultsThere were seven potentially deleterious germline mutations. NM_001184790:exon8: c.C1070T in PARD3, NM_001170721:exon4:c.C392T in BCAR1 and NM_001127221:exon46: c.G6587A in CACNA1A were present in three cases each; rs756875895 frameshift in MAX, NM_005732: exon13:c.2165_2166insT in RAD50 and NM_001142316:exon2:c.G203C in LMO2, were present in two cases each; one variant was present in NOTCH3.ConclusionsOur results expand the germline mutation spectrum in malignant GGO nodules. Importantly, these findings will potentially help screen the high-risk population, guide their health management, and contribute to their clinical treatment and determination of prognosis. creator: Wenjun Mao creator: Ruo Chen creator: Rongguo Lu creator: Shengfei Wang creator: Huizhu Song creator: Dan You creator: Feng Liu creator: Yijun He creator: Mingfeng Zheng uri: https://doi.org/10.7717/peerj.12048 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Mao et al. title: Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea link: https://peerj.com/articles/12063 last-modified: 2021-08-31 description: BackgroundUnderstanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity.MethodsIn total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS.ResultsOur dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS.ConclusionsThis multispecies study provides the most comprehensive examination of the role of Dongsha Atoll in marine connectivity in the South China Sea to date. Combining new and existing population genetic data for nine coral reef species in the region with a graph theoretical analysis, this study provides evidence that Dongsha Atoll is an important hub for sustaining connectivity for the majority of coral-reef species in the region. creator: Shang Yin Vanson Liu creator: Jacob Green creator: Dana Briggs creator: Ruth Hastings creator: Ylva Jondelius creator: Skylar Kensinger creator: Hannah Leever creator: Sophia Santos creator: Trevor Throne creator: Chi Cheng creator: Hawis Madduppa creator: Robert J. Toonen creator: Michelle R. Gaither creator: Eric D. Crandall uri: https://doi.org/10.7717/peerj.12063 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Liu et al. title: Transcriptome analysis reveals gene expression differences in Liriomyza trifolii exposed to combined heat and abamectin exposure link: https://peerj.com/articles/12064 last-modified: 2021-08-31 description: Liriomyza trifolii is an invasive pest of horticultural and vegetable crops that possesses robust competitive advantages that enable it to replace closely-related species. High temperatures often occur concomitantly with insecticide usage during L. trifolii outbreaks. In this study, we compared the transcriptomes of L. trifolii exposed to high temperature (40 °C T40), insecticide (LC50 of technical grade abamectin, I50) and combined high temperature and abamectin exposure (IT5040, I50 followed by T40; and TI4050, T40 followed by I50). RNA-seq generated and revealed 44,633 unigenes with annotation data; these were compared with COG and KEGG databases for functional classification and enrichment analysis. Compared with the I50 treatment, COG classification indicated that ‘post-translational modification, protein turnover, chaperones’ was enriched in the IT5040 treatment. In the TI4050 treatment, ‘carbohydrate transport and metabolism’ was the most abundant group. The most enriched KEGG pathways in the TI4050 and IT5040 treatments were ‘longevity regulating pathway - multiple species’ and ‘protein processing in endoplasmic reticulum’, respectively. Subsequent annotation and enrichment analyses indicated that stress-related genes such as CYP450s and HSPs were differentially expressed in the I50 vs. TI4050 or I50 vs. IT5040 treatment groups. Three commercial insecticide formulations were also used to further verify the expression of selected differentially-expressed genes. This study will be conductive to consider the temperature effect on insecticide tolerance in L. trifolii, and provides a framework for improving the application efficiency of insecticides in hot weather, which will ultimately reduce the overuse of pesticides. creator: Yu-Cheng Wang creator: Ya-Wen Chang creator: Yu-Zhou Du uri: https://doi.org/10.7717/peerj.12064 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Wang et al. title: Investigation of inhibition effect of daidzein on osteosarcoma cells based on experimental validation and systematic pharmacology analysis link: https://peerj.com/articles/12072 last-modified: 2021-08-31 description: ObjectiveThis study aims to explore the effect of daidzein, which is a natural isoflavone compound mainly extracted from soybeans, on osteosarcoma and the potential molecular mechanism.Material and Methods143B and U2OS osteosarcoma cells were treated with gradient concentrations of daidzein, and MTT assay was used to determine the cell proliferation capacity and IC50. Hoechst 33342 staining and Annexin V-FITC/PI detection were used to determine apoptosis. Cell cycle was analyzed by flow cytometry, and migration ability were detected by transwell assays and scratch wound assay. An osteosarcoma xenograft mice model was applied to investigate the effect of daidzein on osteosarcoma in vivo. Systematic pharmacology and molecular modeling analysis were applied to predict the target of daidzein to osteosarcoma, and the target Src was verified by western blotting. We also observed the effect of daidzein on cell proliferation and apoptosis of Src-overexpressing osteosarcoma cells.ResultsIn vitro, daidzein significantly inhibited 143B and U2OS osteosarcoma cell proliferation and migration, and induced cell cycle arrest. In vivo, daidzein exerts antitumor effects in osteosarcoma xenograft mice. After systematic screening and analysis, Src-MAPK signaling pathway was predicted as the highest-ranked pathway. Western blot demonstrated that daidzein inhibited phosphorylation of the Src-ERK pathway in osteosarcoma cells. Also, overexpression of Src could partially reverse the inhibitory effects of daidzein on osteosarcoma cell proliferation.ConclusionDaidzein exerts an antitumor effect on osteosarcoma, and the mechanism may be through the Src-ERK pathway. creator: Yufan Zhu creator: Zhiqiang Yang creator: Yuanlong Xie creator: Min Yang creator: Yufeng Zhang creator: Zhouming Deng creator: Lin Cai uri: https://doi.org/10.7717/peerj.12072 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhu et al. title: Hallmarks of glycogene expression and glycosylation pathways in squamous and adenocarcinoma cervical cancer link: https://peerj.com/articles/12081 last-modified: 2021-08-31 description: BackgroundDysregulation of glycogene expression in cancer can lead to aberrant glycan expression, which can promote tumorigenesis. Cervical cancer (CC) displays an increased expression of glycogenes involved in sialylation and sialylated glycans. Here, we show a comprehensive analysis of glycogene expression in CC to identify glycogene expression signatures and the possible glycosylation pathways altered.MethodsFirst, we performed a microarray expression assay to compare glycogene expression changes between normal and cervical cancer tissues. Second, we used 401 glycogenes to analyze glycogene expression in adenocarcinoma and squamous carcinoma from RNA-seq data at the cBioPortal for Cancer Genomics.ResultsThe analysis of the microarray expression assay indicated that CC displayed an increase in glycogenes related to GPI-anchored biosynthesis and a decrease in genes associated with chondroitin and dermatan sulfate with respect to normal tissue. Also, the glycogene analysis of CC samples by the RNA-seq showed that the glycogenes involved in the chondroitin and dermatan sulfate pathway were downregulated. Interestingly the adenocarcinoma tumors displayed a unique glycogene expression signature compared to squamous cancer that shows heterogeneous glycogene expression divided into six types. Squamous carcinoma type 5 (SCC-5) showed increased expression of genes implicated in keratan and heparan sulfate synthesis, glycosaminoglycan degradation, ganglio, and globo glycosphingolipid synthesis was related to poorly differentiated tumors and poor survival. Squamous carcinoma type 6 (SCC-6) displayed an increased expression of genes involved in chondroitin/dermatan sulfate synthesis and lacto and neolacto glycosphingolipid synthesis and was associated with nonkeratinizing squamous cancer and good survival. In summary, our study showed that CC tumors are not a uniform entity, and their glycome signatures could be related to different clinicopathological characteristics. creator: Patricia Martinez-Morales creator: Irene Morán Cruz creator: Lorena Roa-de la Cruz creator: Paola Maycotte creator: Juan Salvador Reyes Salinas creator: Victor Javier Vazquez Zamora creator: Claudia Teresita Gutierrez Quiroz creator: Alvaro Jose Montiel-Jarquin creator: Verónica Vallejo-Ruiz uri: https://doi.org/10.7717/peerj.12081 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Martinez-Morales et al. title: Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins link: https://peerj.com/articles/12084 last-modified: 2021-08-31 description: Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species’ guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent. creator: Ruber Rodríguez-Barreras creator: Eduardo L. Tosado-Rodríguez creator: Filipa Godoy-Vitorino uri: https://doi.org/10.7717/peerj.12084 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rodríguez-Barreras et al. title: Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives link: https://peerj.com/articles/12106 last-modified: 2021-08-31 description: The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes. creator: Mikhail I. Schelkunov creator: Maxim S. Nuraliev creator: Maria D. Logacheva uri: https://doi.org/10.7717/peerj.12106 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Schelkunov et al. title: Ciprofloxacin reduces tenocyte viability and proteoglycan synthesis in short-term explant cultures of equine tendon link: https://peerj.com/articles/12003 last-modified: 2021-08-30 description: Fluoroquinolones are an effective, broad-spectrum antibiotic used to treat an array of bacterial infections. However, they are associated with an increased risk of tendinopathy and tendon rupture even after discontinuation of treatment. This condition is known as fluoroquinolone-associated tendinopathy, the underlying mechanisms of which are poorly understood. While many factors may be involved in the pathophysiology of tendinopathies in general, changes in tenocyte metabolism and viability, as well as alteration of proteoglycan metabolism are prominent findings in the scientific literature. This study investigated the effects of ciprofloxacin, a common fluoroquinolone, on cell viability, proteoglycan synthesis, and proteoglycan mRNA expression in equine superficial digital flexor tendon explants after 96 h treatment with between 1–300 µg/mL ciprofloxacin, and again after 8 days discontinuation of treatment. Ciprofloxacin caused significant reductions in cell viability by between 25–33% at all dosages except 10 µg/mL, and viability decreased further after 8 days discontinuation of treatment. Proteoglycan synthesis significantly decreased by approximately 50% in explants treated with 100 µg/mL and 300 µg/mL, however this effect reversed after 8 days in the absence of treatment. No significant mRNA expression changes were observed after the treatment period with the exception of versican which was down-regulated at the highest concentration of ciprofloxacin. After the recovery period, aggrecan, biglycan and versican genes were all significantly downregulated in explants initially treated with 1–100 µg/mL. Results from this study corroborate previously reported findings of reduced cell viability and proteoglycan synthesis in a whole tissue explant model and provide further insight into the mechanisms underlying fluoroquinolone-associated tendinopathy and rupture. This study further demonstrates that certain ciprofloxacin induced cellular changes are not rapidly reversed upon cessation of treatment which is a novel finding in the literature. creator: Stuart James creator: Johannes Schuijers creator: John Daffy creator: Jill Cook creator: Tom Samiric uri: https://doi.org/10.7717/peerj.12003 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 James et al.