title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=396 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effects of 3021 meal replacement powder protect NAFLD via suppressing the ERS, oxidative stress and inflammatory responses link: https://peerj.com/articles/16154 last-modified: 2023-10-16 description: ObjectiveTo explore the specific protective mechanism of 3021 meal replacement powder (MRP) against non-alcoholic fatty liver disease (NAFLD).Materials and MethodsC57BL/6J male mice were divided into four groups: control group, 3021 MRP group, model group and test group. The lipid accumulation and endoplasmic reticulum stress (ERS)-related proteins in hepatocytes of mice were detected by hematoxylin-eosin (HE) staining, oil red O staining and Western blotting.ResultsThe expressions of GRP78, GRP94, p-PERK and p-IRE1α were significantly inhibited in test group compared with those in model group. The protein expressions of p-NF-κB, p-JNK, IL-1β, IL-18 and NOX4 in test group were also significantly lower than those in model group. In vivo and in vitro experiments revealed that the body weight and lipid droplet content, and the expressions of ERS-related proteins (including BIP and XBP-1) in liver tissues all significantly declined in model group compared with those in 3021 MRP group.ConclusionIn conclusion, 3021 MRP can greatly reduce lipid accumulation by inhibiting ERS, oxidative stress and inflammatory response in NAFLD. creator: Qi Xie creator: Shuqing Gao creator: Yuanjudi Li creator: Weifang Xi creator: Zhiyun Dong creator: Zengning Li creator: Min Lei uri: https://doi.org/10.7717/peerj.16154 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Xie et al. title: Long non‑coding RNA L13Rik promotes high glucose-induced mesangial cell hypertrophy and matrix protein expression by regulating miR-2861/CDKN1B axis link: https://peerj.com/articles/16170 last-modified: 2023-10-16 description: BackgroundDiabetic nephropathy (DN) is a frequent microvascular complication of diabetes. Glomerular mesangial cell (MC) hypertrophy occurs at the initial phase of DN and plays a critical role in the pathogenesis of DN. Given the role of long non coding RNA (lncRNA) in regulating MC hypertrophy and extracellular matrix (ECM) accumulation, our aim was to identify functional lncRNAs during MC hypertrophy.MethodsHere, an lncRNA, C920021L13Rik (L13Rik for short), was identified to be up-regulated in DN progression. The expression of L13Rik in DN patients and diabetic mice was assessed using quantitative real-time PCR (qRT-PCR), and the function of L13Rik in regulating HG-induced MC hypertrophy and ECM accumulation was assessed through flow cytometry and western blotting analysis.ResultsThe L13Rik levels were significantly increased while the miR-2861 levels were decreased in the peripheral blood of DN patients, the renal tissues of diabetic mice, and HG-treated MCs. Functionally, both L13Rik depletion and miR-2861 overexpression effectively reduced HG-induced cell hypertrophy and ECM accumulation. Mechanistically, L13Rik functioned as a competing endogenous RNA (ceRNA) to sponge miR-2861, resulting in the de-repression of cyclin-dependent kinase inhibitor 1B (CDKN1B), a gene known to regulate cell cycle and MC hypertrophy.ConclusionsCollectively, the current results demonstrate that up-regulated L13Rik is correlated with DN and may be a hopeful therapeutic target for DN. creator: Linlin Sun creator: Miao Ding creator: Fuhua Chen creator: Dingyu Zhu creator: Xinmiao Xie uri: https://doi.org/10.7717/peerj.16170 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Sun et al. title: Genome sizes and repeatome evolution in zoantharians (Cnidaria: Hexacorallia: Zoantharia) link: https://peerj.com/articles/16188 last-modified: 2023-10-16 description: Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element dynamics are not well understood. Together with phenotypic traits, they are commonly referred to as the “C-value enigma”. The order Zoantharia are benthic cnidarians found from intertidal zones to the deep sea, and some species are particularly abundant in coral reefs. Despite their high ecological relevance, zoantharians have yet to be largely studied from the genomic point of view. This study aims at investigating the role of the repeatome (total content of repeated elements) in genome size variations across the order Zoantharia. To this end, whole-genomes of 32 zoantharian species representing five families were sequenced. Genome sizes were estimated and the abundances of different repeat classes were assessed. In addition, the repeat overlap between species was assessed by a sequence clustering method. The genome sizes in the dataset varied up to 2.4 fold magnitude. Significant correlations between genome size, repeated DNA content and transposable elements, respectively (Pearson’s correlation test R2 = 0.47, p = 0.0016; R2 = 0.22, p = 0.05) were found, suggesting their involvement in the dynamics of genome expansion and reduction. In all species, long interspersed nuclear elements and DNA transposons were the most abundant identified elements. These transposable elements also appeared to have had a recent expansion event. This was in contrast to the comparative clustering analysis which revealed species-specific patterns of satellite elements’ amplification. In summary, the genome sizes of zoantharians likely result from the complex dynamics of repeated elements. Finally, the majority of repeated elements (up to 70%) could not be annotated to a known repeat class, highlighting the need to further investigate non-model cnidarian genomes. More research is needed to understand how repeated DNA dynamics relate to zoantharian evolution and their biology. creator: Chloé Julie Loïs Fourreau creator: Hiroki Kise creator: Mylena Daiana Santander creator: Stacy Pirro creator: Maximiliano M. Maronna creator: Angelo Poliseno creator: Maria E.A. Santos creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.16188 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Fourreau et al. title: Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae) link: https://peerj.com/articles/16217 last-modified: 2023-10-16 description: BackgroundThoracotremata belong to the large group of “true” crabs (infraorder Brachyura), and they exhibit a wide range of physiological and morphological adaptations to living in terrestrial, freshwater and marine habitats. Moreover, the clade comprises various symbiotic taxa (Aphanodactylidae, Cryptochiridae, Pinnotheridae, some Varunidae) that are specialised in living with invertebrate hosts, but the evolutionary history of these symbiotic crabs is still partially unresolved.MethodsHere we assembled and characterised the complete mitochondrial genomes (hereafter mitogenomes) of three gall crab species (Cryptochiridae): Kroppcarcinus siderastreicola, Opecarcinus hypostegus and Troglocarcinus corallicola. A phylogenetic tree of the Thoracotremata was reconstructed using 13 protein-coding genes and two ribosomal RNA genes retrieved from three new gall crab mitogenomes and a further 72 available thoracotreme mitogenomes. Furthermore, we applied a comparative analysis to characterise mitochondrial gene order arrangement, and performed a selection analysis to test for selective pressure of the protein-coding genes in symbiotic Cryptochiridae, Pinnotheridae, and Varunidae (Asthenognathus inaequipes and Tritodynamia horvathi).ResultsThe results of the phylogenetic reconstruction confirm the monophyly of Cryptochiridae, which clustered separately from the Pinnotheridae. The latter clustered at the base of the tree with robust branch values. The symbiotic varunids A. inaequipes and T. horvathi clustered together in a clade with free-living Varunidae species, highlighting that symbiosis in the Thoracotremata evolved independently on multiple occasions. Different gene orders were detected in symbionts and free-living species when compared with the ancestral brachyuran gene order. Lastly, the selective pressure analysis detected two positively selected sites in the nad6 gene of Cryptochiridae, but the evidence for positive selection in Pinnotheridae and A. inaequipes and T. horvathi was weak. Adaptive evolution of mitochondrial protein-coding genes is perhaps related to the presumably higher energetic demands of a symbiotic lifestyle. creator: Tao Xu creator: Henrique Bravo creator: Sancia E.T. van der Meij uri: https://doi.org/10.7717/peerj.16217 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al. title: Identification and validation of key genes associated with pathogenesis and prognosis of gastric cancer link: https://peerj.com/articles/16243 last-modified: 2023-10-16 description: BackgroundGastric cancer (GC) is the fourth leading cause of cancer-related death worldwide. However, the precise mechanisms and specific biomarkers of GC have not been fully elucidated. We therefore sought to identify and validate the genes associated with GC.MethodsRNA sequencing was performed on gastric tissue specimens from 10 cases each of non-atrophic gastritis (NAG), intestinal metaplasia (IM), and GC. Validation of gene expression was conducted through immunohistochemistry (IHC) staining. The Kaplan–Meier Plotter database was utilized to screen genes associated with prognosis, while protein–protein interaction analysis was conducted to identify hub genes.ResultsIn GC-IM, the differentially expressed genes (DEGs) were predominantly enriched in pathways related to ECM-receptor interaction, focal adhesion, PI3K-Akt pathway, and pathways in cancer. Conversely, in IM-NAG, the DEGs were primarily enriched in pathways associated with fat digestion and absorption, pancreatic secretion, and retinol metabolism. IHC staining revealed elevated expression levels of KLK7 and KLK10 in GC. Specifically, KLK7 expression was found to be correlated with differentiation (P = 0.025) and depth of invasion (P = 0.007) in GC, while both KLK7 and KLK10 were associated with the overall survival (P < 0.05). Furthermore, a total of ten hub genes from DEGs in GC-NAG (COL6A2, COL1A1, COL4A1, COL1A2, SPARC, COL4A2, FN1, PCOLCE, SERPINH1, LAMB1) and five hub genes in IM-NAG (SI, DPP4, CLCA1, MEP1A, OLFM4) were demonstrated to have a significant correlation with the prognosis of GC.ConclusionsThe present study successfully identified and validated crucial genes associated with GC, providing valuable insights into the underlying mechanisms of this disease. The findings of this study have the potential to inform clinical practice. creator: Ai Li creator: Yan Li creator: Yueyue Li creator: Mingming Zhang creator: Hong Zhang creator: Feixue Chen uri: https://doi.org/10.7717/peerj.16243 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Developing a semi-pelagic trawl to capture redfish in the Gulf of St. Lawrence, Canada link: https://peerj.com/articles/16244 last-modified: 2023-10-16 description: In this study, we developed a semi-pelagic trawl to target redfish (Sebastes spp.) and potentially reduce the capture of bycatch species and seabed impacts in the Gulf of St. Lawrence, Canada. The new trawl used an innovative technique connecting the upper bridles of the trawl to the warps, anterior of the trawl doors, leading to the trawl system being fished off the seabed. Such a technique can be used to match the heights of redfish as they move above the seabed during their diurnal cycle while allowing bycatch species related to the seabed to escape under the trawl. A 1:10 scale model of the trawl was constructed and evaluated in a flume tank to optimize the rigging and then a full-scale trawl was constructed for sea trials. Two field experiments subsequently evaluated the trawl at sea. The first field experiment concentrated on the experimental trawl’s operation and video observations of redfish behaviour in the trawl mouth and its effect on trawl entry. The second field experiment concentrated on a small-scale preliminary test on the catch of redfish and bycatch species when the trawl was on or off the seabed. Capture results, though preliminary, indicate that redfish can be targeted commercially with a semi-pelagic trawl, though some redfish will escape under the trawl. Additionally, results suggest that the catches of bycatch species may be reduced. In conclusion, this study suggests that a semi-pelagic trawl could be considered an effective technique to harvest redfish sustainably. creator: Vang Y. Nguyen creator: Shannon M. Bayse creator: Paul D. Winger creator: Harold DeLouche creator: George Legge uri: https://doi.org/10.7717/peerj.16244 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nguyen et al. title: The transcriptome of the entomopathogenic fungus Culicinomyces clavisporus contains an ortholog of the insecticidal ribotoxin Hirsutellin link: https://peerj.com/articles/16259 last-modified: 2023-10-16 description: The entomopathogenic fungus Culicinomyces clavisporus is known to infect and kill mosquito larvae and therefore has been seen as a potential biological control agent against disease vector mosquitoes. Whereas most fungal entomopathogens infect hosts by penetrating the external cuticle, C. clavisporus initiates infection through ingestion (per os). This unique infection strategy suggests that the C. clavisporus genome may be mined for novel pathogenicity factors with potential for vector control. To this end, an Isoseq-based transcriptome analysis was initiated, and resulted in a total of 3,512,145 sequences, with an average length of 1,732 bp. Transcripts assembly and annotation suggested that the C. clavisporus transcriptome lacked the cuticle-degrading proteins that have been associated with other entomopathogenic fungi, supporting the per os pathogenicity process. Furthermore, mining of the sequence data unexpectedly revealed C. clavisporus transcripts homologous to the Hirsutellin toxin. Comparative sequence analyses indicated that the C. clavisporus Hirsutellin predicted protein has retained the canonical molecular features that have been associated with the ribotoxic and insecticidal properties of the original toxin isolated from Hirsutella thompsonii. The identification of an Hirsutellin ortholog in C. clavisporus was supported by phylogenetic analyses demonstrating that Culicinomyces and Hirsutella were closely related genera in the Ophiocordycipitaceae family. Validation of the mosquitocidal activity of this novel C. clavisporus protein has yet to be performed but may help position Hirsutellin orthologs as prime candidates for the development of alternative biocontrol approaches complementing the current toolbox of vector mosquito management strategies. creator: Dana Foresman creator: Aurélien Tartar uri: https://doi.org/10.7717/peerj.16259 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Foresman and Tartar title: Effect of 8-week frequency-specific electrical muscle stimulation combined with resistance exercise training on muscle mass, strength, and body composition in men and women: a feasibility and safety study link: https://peerj.com/articles/16303 last-modified: 2023-10-16 description: In recent years, electrical muscle stimulation (EMS) devices have been developed as a complementary training technique that is novel, attractive, and time-saving for physical fitness and rehabilitation. While it is known that EMS training can improve muscle mass and strength, most studies have focused on the elderly or specific patient populations. The aim of this study was to investigate the effects of frequency-specific EMS combined with resistance exercise training for 8 weeks on muscle mass, strength, power, body composition, and parameters related to exercise fatigue. Additionally, we aimed to evaluate the feasibility and safety of EMS as an exercise aid to improve body composition. We recruited 14 male and 14 female subjects who were randomly assigned to two groups with gender parity (seven male and seven female/group): (1) no EMS group (age: 21.6 ± 1.7; height: 168.8 ± 11.8 cm; weight: 64.2 ± 14.4 kg) and (2) daily EMS group (age: 21.8 ± 2.0; height: 167.8 ± 9.9 cm; weight: 68.5 ± 15.5 kg). The two groups of subjects were very similar with no significant difference. Blood biochemical routine analysis was performed every 4 weeks from pre-intervention to post-intervention, and body composition, muscle strength, and explosive power were evaluated 8 weeks before and after the intervention. We also performed an exercise challenge analysis of fatigue biochemical indicators after 8 weeks of intervention. Our results showed that resistance exercise training combined with daily EMS significantly improved muscle mass (p = 0.002) and strength (left, p = 0.007; right, p = 0.002) and significantly reduced body fat (p < 0.001) than the no EMS group. However, there was no significant advantage for biochemical parameters of fatigue and lower body power. In summary, our study demonstrates that 8 weeks of continuous resistance training combined with daily upper body, lower body, and abdominal EMS training can significantly improve muscle mass and upper body muscle strength performance, as well as significantly reduce body fat percentage in healthy subjects. creator: Mon-Chien Lee creator: Chin-Shan Ho creator: Yi-Ju Hsu creator: Ming-Fang Wu creator: Chi-Chang Huang uri: https://doi.org/10.7717/peerj.16303 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lee et al. title: Macrophage polarization in tissue fibrosis link: https://peerj.com/articles/16092 last-modified: 2023-10-13 description: Fibrosis can occur in all major organs with relentless progress, ultimately leading to organ failure and potentially death. Unfortunately, current clinical treatments cannot prevent or reverse tissue fibrosis. Thus, new and effective antifibrotic therapeutics are urgently needed. In recent years, a growing body of research shows that macrophages are involved in fibrosis. Macrophages are highly heterogeneous, polarizing into different phenotypes. Some studies have found that regulating macrophage polarization can inhibit the development of inflammation and cancer. However, the exact mechanism of macrophage polarization in different tissue fibrosis has not been fully elucidated. This review will discuss the major signaling pathways relevant to macrophage-driven fibrosis and profibrotic macrophage polarization, the role of macrophage polarization in fibrosis of lung, kidney, liver, skin, and heart, potential therapeutics targets, and investigational drugs currently in development, and hopefully, provide a useful review for the future treatment of fibrosis. creator: Huidan Yang creator: Hao Cheng creator: Rongrong Dai creator: Lili Shang creator: Xiaoying Zhang creator: Hongyan Wen uri: https://doi.org/10.7717/peerj.16092 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al. title: Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis link: https://peerj.com/articles/16193 last-modified: 2023-10-13 description: As important regulators of alternative splicing (AS) events, serine/arginine (SR)-rich proteins play indispensable roles in the growth and development of organisms. Until now, the study of SR genes has been lacking in plants. In the current study, we performed genome-wide analysis on the SR gene family in rice. A total of 24 OsSR genes were phylogenetically classified into seven groups, corresponding to seven subfamilies. The OsSR genes’ structures, distribution of conserved domains, and protein tertiary structure of OsSR were conserved within each subfamily. The synteny analysis revealed that segmental duplication events were critical for the expansion of OsSR gene family. Moreover, interspecific synteny revealed the distribution of orthologous SR gene pairs between rice and Arabidopsis, sorghum, wheat, and maize. Among all OsSR genes, 14 genes exhibited NAGNAG acceptors, and only four OsSR genes had AS events on the NAGNAG acceptors. Furthermore, the distinct tissue-specific expression patterns of OsSR genes showed that these genes may function in different developmental stages in rice. The AS patterns on the same OsSR gene were variable among the root, stem, leaf, and grains at different filling stages, and some isoforms could only be detected in one or a few of tested tissues. Meanwhile, our results showed that the expression of some OsSR genes changed dramatically under ABA, GA, salt, drought, cold or heat treatment, which were related to the wide distribution of corresponding cis-elements in their promoter regions, suggesting their specific roles in stress and hormone response. This research facilitates our understanding of SR gene family in rice and provides clues for further exploration of the function of OsSR genes. creator: Rui Gao creator: Yingying Lu creator: Nan Wu creator: Hui Liu creator: Xiaoli Jin uri: https://doi.org/10.7717/peerj.16193 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gao et al.