title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=998 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: miR-21 is upregulated, promoting fibrosis and blocking G2/M in irradiated rat cardiac fibroblasts link: https://peerj.com/articles/10502 last-modified: 2020-12-10 description: BackgroundRadiation exposure of the thorax is associated with a greatly increased risk of cardiac morbidity and mortality even after several decades of advancement in the field. Although many studies have demonstrated the damaging influence of ionizing radiation on cardiac fibroblast (CF) structure and function, myocardial fibrosis, the molecular mechanism behind this damage is not well understood. miR-21, a small microRNA, promotes the activation of CFs, leading to cardiac fibrosis. miR-21 is overexpressed after irradiation; however, the relationship between increased miR-21 and myocardial fibrosis after irradiation is unclear. This study was conducted to investigate gene expression after radiation-induced CF damage and the role of miR-21 in this process in rats.MethodsWe sequenced irradiated rat CFs and performed weighted correlation network analysis (WGCNA) combined with differentially expressed gene (DEG) analysis to observe the effect on the expression profile of CF genes after radiation.ResultsDEG analysis showed that the degree of gene changes increased with the radiation dose. WGCNA revealed three module eigengenes (MEs) associated with 8.5-Gy-radiation—the Yellow, Brown, Blue modules. The three module eigengenes were related to apoptosis, G2/M phase, and cell death and S phase, respectively. By blocking with the cardiac fibrosis miRNA miR-21, we found that miR-21 was associated with G2/M blockade in the cell cycle and was mainly involved in regulating extracellular matrix-related genes, including Grem1, Clu, Gdf15, Ccl7, and Cxcl1. Stem-loop quantitative real-time PCR was performed to verify the expression of these genes. Five genes showed higher expression after 8.5 Gy-radiation in CFs. The target genes of miR-21 predicted online were Gdf15 and Rsad2, which showed much higher expression after treatment with antagomir-miR-21 in 8.5-Gy-irradiated CFs. Thus, miR-21 may play the role of fibrosis and G2/M blockade in regulating Grem1, Clu, Gdf15, Ccl7, Cxcl1, and Rsad2 post-irradiation. creator: Huan Guo creator: Xinke Zhao creator: Haixiang Su creator: Chengxu Ma creator: Kai Liu creator: Shanshan Kong creator: Kedan Liu creator: Haining Li creator: Juan Chang creator: Tao Wang creator: Hongyun Guo creator: Huiping Wei creator: Zhaoyuan Fu creator: Xinfang Lv creator: Yingdong Li uri: https://doi.org/10.7717/peerj.10502 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guo et al. title: Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease link: https://peerj.com/articles/10513 last-modified: 2020-12-10 description: We sought to identify the biomarkers related to the clinical severity of stage I to stage IV chronic obstructive pulmonary disease (COPD). Gene expression profiles from the blood samples of COPD patients at each of the four stages were acquired from the Gene Expression Omnibus Database (GEO, accession number: GSE54837). Genes showing expression changes among the different stages were sorted by soft clustering. We performed functional enrichment, protein–protein interaction (PPI), and miRNA regulatory network analyses for the differentially expressed genes. The biomarkers associated with the clinical classification of COPD were selected from logistic regression models and the relationships between TLR2 and inflammatory factors were verified in clinical blood samples by qPCR and ELISA. Gene clusters demonstrating continuously rising or falling changes in expression (clusters 1, 2, and 7 and clusters 5, 6, and 8, respectively) from stage I to IV were defined as upregulated and downregulated genes, respectively, and further analyzed. The upregulated genes were enriched in functions associated with defense, inflammatory, or immune responses. The downregulated genes were associated with lymphocyte activation and cell activation. TLR2, HMOX1, and CD79A were hub proteins in the integrated network of PPI and miRNA regulatory networks. TLR2 and CD79A were significantly correlated with clinical classifications. TLR2 was closely associated with inflammatory responses during COPD progression. Functions associated with inflammatory and immune responses as well as lymphocyte activation may play important roles in the progression of COPD from stage I to IV. TLR2 and CD79A may serve as potential biomarkers for the clinical severity of COPD. TLR2 and CD79A may also serve as independent biomarkers in the clinical classification in COPD. TLR2 may play an important role in the inflammatory responses of COPD. creator: Jie Zhang creator: Changli Zhu creator: Hong Gao creator: Xun Liang creator: Xiaoqian Fan creator: Yulong Zheng creator: Song Chen creator: Yufeng Wan uri: https://doi.org/10.7717/peerj.10513 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Deep-sea water displacement from a turbidity current induced by the Super Typhoon Hagibis link: https://peerj.com/articles/10429 last-modified: 2020-12-09 description: Turbidity currents are the main drivers behind the transportation of terrestrial sediments to the deep sea, and turbidite deposits from such currents have been widely used in geological studies. Nevertheless, the contribution of turbidity currents to vertical displacement of seawater has rarely been discussed. This is partly because until recently, deep-sea turbidity currents have rarely been observed due to their unpredictable nature, being usually triggered by meteorological or geological events such as typhoons and earthquakes. Here, we report a direct observation of a deep-sea turbidity current using the recently developed Edokko Mark 1 monitoring system deployed in 2019 at a depth of 1,370 m in Suruga Bay, central Japan. A turbidity current occurred two days after its probable cause, the Super Typhoon Hagibis (2019), passed through Suruga Bay causing devastating damage. Over aperiod of 40 hours, we observed increased turbidity with turbulent conditions confirmed by a video camera. The turbidity exhibited two sharp peaks around 3:00 and 11:00 on October 14 (Japan Standard Time). The temperature and salinity characteristics during these high turbidity events agreed with independent measurements for shallow water layers in Suruga Bay at the same time, strongly suggesting that the turbidity current caused vertical displacement in the bay’s water column by transporting warmer and shallower waters downslope of the canyon. Our results add to the previous few examples that show meteorological and geological events may have significant contributions in the transportation of shallower seawater to the deep sea. Recent technological developments pertaining to the Edokko Mark 1 and similar devices enable straightforward, long-term monitoring of the deep-seafloor and will contribute to the understanding of similar spontaneous events in the deep ocean. creator: Shinsuke Kawagucci creator: Tetsuya Miwa creator: Dhugal J. Lindsay creator: Eri Ogura creator: Hiroyuki Yamamoto creator: Kenichiro Nishibayashi creator: Hiroyuki Yokooka creator: Shotaro Nishi creator: Ayu Takahashi creator: Sangkyun Lee uri: https://doi.org/10.7717/peerj.10429 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kawagucci et al. title: Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream (Sparus aurata) link: https://peerj.com/articles/10430 last-modified: 2020-12-09 description: BackgroundIn the last two decades, research has focused on testing cheaper and sustainable alternatives to fish oil (FO), such as vegetable oils (VO), in aquafeeds. However, FO cannot be entirely replaced by VOs due to their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), particularly eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3) acids. The oilseed plant, Camelina sativa, may have a higher potential to replace FO since it can contains up to 40% of the omega-3 precursors α-linolenic acid (ALA; 18:3n-3) and linoleic acid (LA; 18:2n-6).MethodsA 90-day feeding trial was conducted with 600 gilthead sea bream (Sparus aurata) of 32.92 ±  0.31 g mean initial weight fed three diets that replaced 20%, 40% and 60% of FO with CO and a control diet of FO. Fish were distributed into triplicate tanks per diet and with 50 fish each in a flow-through open marine system. Growth performance and fatty acid profiles of the fillet were analysed. The Illumina MiSeq platform for sequencing of 16S rRNA gene and Mothur pipeline were used to identify bacteria in the faeces, gut mucosa and diets in addition to metagenomic analysis by PICRUSt.Results and ConclusionsThe feed conversion rate and specific growth rate were not affected by diet, although final weight was significantly lower for fish fed the 60% CO diet. Reduced final weight was attributed to lower levels of EPA and DHA in the CO ingredient. The lipid profile of fillets were similar between the dietary groups in regards to total saturated, monounsaturated, PUFA (n-3 and n-6), and the ratio of n-3/n-6. Levels of EPA and DHA in the fillet reflected the progressive replacement of FO by CO in the diet and the EPA was significantly lower in fish fed the 60% CO diet, while ALA was increased. Alpha and beta-diversities of gut bacteria in both the faeces and mucosa were not affected by any dietary treatment, although a few indicator bacteria, such as Corynebacterium and Rhodospirillales, were associated with the 60% CO diet. However, lower abundance of lactic acid bacteria, specifically Lactobacillus, in the gut of fish fed the 60% CO diet may indicate a potential negative effect on gut microbiota. PICRUSt analysis revealed similar predictive functions of bacteria in the faeces and mucosa, although a higher abundance of Corynebacterium in the mucosa of fish fed 60% CO diet increased the KEGG pathway of fatty acid synthesis and may act to compensate for the lack of fatty acids in the diet. In summary, this study demonstrated that up to 40% of FO can be replaced with CO without negative effects on growth performance, fillet composition and gut microbiota of gilthead sea bream. creator: David Huyben creator: Simona Rimoldi creator: Chiara Ceccotti creator: Daniel Montero creator: Monica Betancor creator: Federica Iannini creator: Genciana Terova uri: https://doi.org/10.7717/peerj.10430 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huyben et al. title: Measuring stress in podiatric students in Spain: psychometric validation and adaptation of the KEZKAK questionnaire link: https://peerj.com/articles/10439 last-modified: 2020-12-09 description: ObjectiveThe study aim was to develop a linguistic-cultural adaptation of the KEZKAK questionnaire to be completed during the practicum of podiatric medical students in Spain, to validate the questionnaire and to evaluate its psychometric properties.MethodsThe cross-sectional study was carried out in two stages: 1. Cross-cultural adaptation; 2. Clinimetric validation based on assessments of interobserver reliability, test-retest reliability and internal consistency. The participants were podiatric medical students at the universities of Malaga and Miguel Hernandez, Alicante (Spain) and were recruited during the period February–October 2019. The following inclusion criteria were applied: aged at least 18 years, studying the third or fourth year of a university degree in Podiatry. All gave signed informed consent and completed the State-Trait Anxiety Inventory and the Podiatry version of the KEZKAK questionnaire. No sampling was performed and thus the entire eligible population was included in the study.ResultsThe analysis was based on 205 participants (33.5% male, 66.5% female), with a mean age of 23.05 (SD 5.37) years. Internal consistency was excellent, with a Cronbach’s alpha of 0.95. This version of the questionnaire had five factorial structures (61.18%). No floor/ceiling effect was observed in any item. The KEZKAK presented high test-retest reliability after 21 days, with an overall ICC of 0.95 (95% CI [0.93–0.98]).ConclusionFor university students of podiatry in Spain, the KEZKAK Podiatry version questionnaire is a valid, reliable instrument for measuring stressors during the practicum. creator: Ana Belen Ortega-Avila creator: Pablo Cervera-Garvi creator: Ana Maria Jimenez-Cebrian creator: Esther Chicharro-Luna creator: Irene Garcia-Paya creator: Gabriel Gijon-Nogueron uri: https://doi.org/10.7717/peerj.10439 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ortega-Avila et al. title: Experimental lung injury induces cerebral cytokine mRNA production in pigs link: https://peerj.com/articles/10471 last-modified: 2020-12-09 description: BackgroundAcute respiratory distress syndrome (ARDS) is an important disease with a high incidence among patients admitted to intensive care units. Over the last decades, the survival of critically ill patients has improved; however, cognitive deficits are among the long-term sequelae. We hypothesize that acute lung injury leads to upregulation of cerebral cytokine synthesis.MethodsAfter approval of the institutional and animal care committee, 20 male pigs were randomized to one of three groups: (1) Lung injury by oleic acid injection (OAI), (2) ventilation only (CTR) or (3) untreated. We compared neuronal numbers, proportion of neurons with markers for apoptosis, activation state of Iba-1 stained microglia cells and cerebral mRNA levels of different cytokines between the groups 18 hours after onset of lung injury.ResultsWe found an increase in hippocampal TNFalpha (p < 0.05) and IL-6 (p < 0.05) messenger RNA (mRNA) in the OAI compared to untreated group as well as higher hippocampal IL-6 mRNA compared to control (p < 0.05). IL-8 and IL-1beta mRNA showed no differences between the groups. We found histologic markers for beginning apoptosis in OAI compared to untreated (p < 0.05) and more active microglia cells in OAI and CTR compared to untreated (p < 0.001 each).ConclusionHippocampal cytokine transcription increases within 18 hours after the induction of acute lung injury with histological evidence of neuronal damage. It remains to be elucidated if increased cytokine mRNA synthesis plays a role in the cognitive decline observed in survivors of ARDS. creator: Jens Kamuf creator: Andreas Garcia Bardon creator: Alexander Ziebart creator: Katrin Frauenknecht creator: Konstantin Folkert creator: Johannes Schwab creator: Robert Ruemmler creator: Miriam Renz creator: Denis Cana creator: Serge C. Thal creator: Erik K. Hartmann uri: https://doi.org/10.7717/peerj.10471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kamuf et al. title: Assessment of the effects of ischaemia/ hypoxia on angiogenesis in rat myofascial trigger points using colour Doppler flow imaging link: https://peerj.com/articles/10481 last-modified: 2020-12-09 description: Background & AimsMyofascial pain syndrome (MPS) is a common non-articular disorder of the musculoskeletal system that is characterized by the presence of myofascial trigger points (MTrPs). Despite the high prevalence of MPS, its pathogenesis, which induces the onset and maintenance of MTrPs, is still not completely understood. To date, no studies have investigated the changes in the biochemical milieu caused by ischaemia/hypoxia in the MTrP regions of muscle that are proposed in the integrated hypothesis. Therefore, this study investigated whether ischaemic/hypoxic conditions participate in the formation of active MTrPs and affect angiogenesis using colour Doppler flow imaging (CDFI).MethodsTwenty-five Sprague-Dawley rats were randomly divided into a model group and a normal control group. A model of active MTrPs was established by a blunt strike combined with eccentric exercise. Enzyme-linked immunosorbent assays (ELISAs) were employed to detect the levels of HIF-1α and VEGF. Microvessel density (MVD) was evaluated using immunohistochemistry. CDFI was applied to observe the blood flow signals in the MTrPs, which were classified into four grades based on their strengths.ResultsCompared with the control group, the active MTrP group exhibited significantly higher HIF-1α and VEGF levels and MVD values. These differences were accompanied by increased blood flow signals. In the active MTrP group, the blood flow signal grade was positively correlated with the MVD (P < 0.05) and independently correlated with the VEGF level (P < 0.05) but was not correlated with the expression of HIF-1α (P > 0.05).ConclusionIschaemic/hypoxic conditions may be involved in the formation of MTrPs. CDFI is useful for detection of the features of angiogenesis in or surrounding MTrPs via assessment of blood flow signals. creator: Fangyan Jiang creator: Shuangcheng Yu creator: Haiqing Su creator: Shangyong Zhu uri: https://doi.org/10.7717/peerj.10481 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jiang et al. title: Oncolytic effects of the recombinant Newcastle disease virus, rAF-IL12, against colon cancer cells in vitro and in tumor-challenged NCr-Foxn1nu nude mice link: https://peerj.com/articles/9761 last-modified: 2020-12-08 description: Colon cancer remains one of the main cancers causing death in men and women worldwide as certain colon cancer subtypes are resistant to conventional treatments and the development of new cancer therapies remains elusive. Alternative modalities such as the use of viral-based therapeutic cancer vaccine is still limited, with only the herpes simplex virus (HSV) expressing granulocyte-macrophage colony- stimulating factor (GM-CSF) or talimogene laherparepvec (T-Vec) being approved in the USA and Europe so far. Therefore, it is imperative to continue the search for a new treatment modality. This current study evaluates a combinatorial therapy between the oncolytic Newcastle disease virus (NDV) and interleukin-12 (IL-12) cytokine as a potential therapeutic vaccine to the current anti-cancer drugs. Several in vitro analyses such as MTT assay, Annexin V/FITC flow cytometry, and cell cycle assay were performed to evaluate the cytotoxicity effect of recombinant NDV, rAF-IL12. Meanwhile, serum cytokine, serum biochemical, histopathology of organs and TUNEL assay were carried out to assess the anti-tumoral effects of rAF-IL12 in HT29 tumor-challenged nude mice. The apoptosis mechanism underlying the effect of rAF-IL12 treatment was also investigated using NanoString Gene expression analysis. The recombinant NDV, rAF-IL12 replicated in HT29 colon cancer cells as did its parental virus, AF2240-i. The rAF-IL12 treatment had slightly better cytotoxicity effects towards HT29 cancer cells when compared to the AF2240-i as revealed by the MTT, Annexin V FITC and cell cycle assay. Meanwhile, the 28-day treatment with rAF-IL12 had significantly (p < 0.05) perturbed the growth and progression of HT29 tumor in NCr-Foxn1nu nude mice when compared to the untreated and parental wild-type NDV strain AF2240-i. The rAF-IL12 also modulated the immune system in nude mice by significantly (p < 0.05) increased the level of IL-2, IL-12, and IFN-γ cytokines. Treatment with rAF-IL12 had also significantly (p < 0.05) increased the expression level of apoptosis-related genes such as Fas, caspase-8, BID, BAX, Smad3 and granzyme B in vitro and in vivo. Besides, rAF-IL12 intra-tumoral delivery was considered safe and was not hazardous to the host as evidenced in pathophysiology of the normal tissues and organs of the mice as well as from the serum biochemistry profile of liver and kidney. Therefore, this study proves that rAF-IL12 had better cytotoxicity effects than its parental AF2240-i and could potentially be an ideal treatment for colon cancer in the near future. creator: Syed Umar Faruq Syed Najmuddin creator: Zahiah Mohamed Amin creator: Sheau Wei Tan creator: Swee Keong Yeap creator: Jeevanathan Kalyanasundram creator: Abhimanyu Veerakumarasivam creator: Soon Choy Chan creator: Suet Lin Chia creator: Khatijah Yusoff creator: Noorjahan Banu Alitheen uri: https://doi.org/10.7717/peerj.9761 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Syed Najmuddin et al. title: Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico link: https://peerj.com/articles/10339 last-modified: 2020-12-08 description: BackgroundCoastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites.MethodsThe potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation.ResultsWe found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution. creator: Pablo Suárez-Moo creator: Araceli Lamelas creator: Itza Garcia-Bautista creator: Luis Felipe Barahona-Pérez creator: Gloria Sandoval-Flores creator: David Valdes-Lozano creator: Tanit Toledano-Thompson creator: Erik Polanco-Lugo creator: Ruby Valdez-Ojeda uri: https://doi.org/10.7717/peerj.10339 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Suárez-Moo et al. title: Insights into dog owner perspectives on risks, benefits, and nutritional value of raw diets compared to commercial cooked diets link: https://peerj.com/articles/10383 last-modified: 2020-12-08 description: BackgroundThe practice of feeding a raw meat-based diet (RMBD) to dogs is a topic of increasing interest to owners and veterinary professionals alike. Despite the research around the practice, particularly about the risk of nutritional imbalances and microbial contamination, an increasing number of dog owners are adopting a raw diet for their dogs. This study expands the research into owner motivations for feeding RMBDs and cooked diets and asks them their opinions about risk and nutritional value.MethodsAn anonymized, online, internationally accessible questionnaire was developed to ascertain owner perspectives on the risks, benefits, and nutritional value of commercially prepared and homemade RMBDs as compared with commercially prepared cooked diets (CCDs).ResultsThe questionnaire was completed by 419 dog owners of diverse backgrounds across the world. Of the participants, 25.3% fed RMBDs. Just over 70.0% of all participants had spoken to their veterinarian about their dog’s nutrition. Owners who fed RMBDs ranked their veterinarian’s knowledge lower and their own knowledge of canine nutrition higher than owners who fed CCDs. They rated commercial and homemade RMBDs as highly nutritious 83.5% and 73.6% of the time, respectively, while only 12.5% rated CCDs as highly nutritious. Owners who fed CCDs ranked RMBDs as highly nutritious less often, but also only ranked CCDs as highly nutritious 52.7% of the time. All participants agreed that CCDs were low risk to human health. Owners who fed RMBDs ranked raw diets as highly risky to human or dog health under 20.0% of the time but deemed CCDs risky to animal health over 65.0% of the time. When asked about benefits of raw diets, the most repeated words offered by owners were “health”, “better”, “coat” and “teeth”. The most repeated risks presented were “bacteria”, “nutrition”, “risk” and “Salmonella”. Owners who fed RMBDs tended to use vague terminology like “health” and “better” when asked why they fed a raw diet. Owners who did not feed RMBDs used more specific terminology like “expensive”, “time” and “risk” when asked why they did not feed a raw diet. Overall, the two groups differed in their perceptions around RMBD and CCD feeding, which highlights the need for a better line of communication and education between veterinarians and owners. creator: Alysia Empert-Gallegos creator: Sally Hill creator: Philippa S. Yam uri: https://doi.org/10.7717/peerj.10383 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Empert-Gallegos et al.