title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1432 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Changes in interleukin-27 levels in patients with acute coronary syndrome and their clinical significance link: https://peerj.com/articles/5652 last-modified: 2019-01-04 description: BackgroundThis study evaluated changes in interleukin (IL)-27 levels in patients with acute coronary syndrome (ACS) and their influence on Th1, Th2, and Th17 cells.MethodsSerum levels of IL-27, IL-4, IL-17, and interferon (IFN)-γ in healthy subjects as well as patients with ACS, including stable angina pectoris (SA), unstable angina pectoris (UA), and acute myocardial infarction (AMI), were determined using an enzyme-linked immunosorbent assay. The proportions of Th1, Th2, and Th17 cells among peripheral blood mononuclear cells (PBMCs), were measured using flow cytometry, after incubation with phorbol myristate acetate (PMA) for 4 h. The proportions of Th1 and Th17 cells among PBMCs in AMI and UA were detected after stimulation with IL-27 or PMA + IL-27 for 4, 8, and 12 h.ResultsSerum levels of IL-27 in patients with AMI and UA were significantly lower than those in SA and control groups, while serum levels of IL-17 and IFN-γ in AMI and UA groups were dramatically increased compared to those in SA and healthy control groups. However, there were no statistically significant differences in serum IL-4. The proportions of Th1 and Th17 cells among PBMCs were statistically significantly higher in the AMI and UA groups than those in the SA and control groups, while there was no statistically significant difference in the proportion of Th2 cells among different groups. For patients with AMI and UA, the effect of co-stimulation of PBMCs with PMA and IL-27 was not significantly different from that of PMA single stimulation, while PMA + IL-27 co-stimulation lowered the Th17 cell proportion significantly compared to PMA single stimulation.DiscussionCompared to SA patients and healthy controls, patients with ACS (AMI + UA) had lower serum levels of IL-27 and higher proportions of PBMC Th1 and Th17 cells, which could be attributed to the inhibitory effects of IL-27 on the proliferation of Th17 cells. These results indicated that IL-27 could be a novel therapeutic target in ACS patients. creator: Lin Zhang creator: Junfeng Zhang creator: Shaohong Su creator: Suyan Luo uri: https://doi.org/10.7717/peerj.5652 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Spiculous skeleton formation in the freshwater sponge Ephydatia fluviatilis under hypergravity conditions link: https://peerj.com/articles/6055 last-modified: 2019-01-04 description: Successful dispersal of freshwater sponges depends on the formation of dormant sponge bodies (gemmules) under adverse conditions. Gemmule formation allows the sponge to overcome critical environmental conditions, for example, desiccation or freezing, and to re-establish as a fully developed sponge when conditions are more favorable. A key process in sponge development from hatched gemmules is the construction of the silica skeleton. Silica spicules form the structural support for the three-dimensional filtration system the sponge uses to filter food particles from ambient water. We studied the effect of different hypergravity forces (1, 2.5, 5, 10, and 20 × g for 48 h)—as measure for environmental stress—on the ability of developing sponges to set-up their spiculous skeleton. Additionally, we assessed whether the addition of nutrients (i.e., dissolved 13C- and 15N-labeled amino acids) compensates for this stress. Our results show that freshwater sponges can withstand prolonged periods of hypergravity exposure and successfully set-up their skeleton, even after 48 h under 20 × g. Developing sponges were found to take up and assimilate dissolved food before forming a functional filtering system. However, fed and non-fed sponges showed no differences in skeleton formation and relative surface area growth, suggesting that the gemmules’ intrinsic energy fulfills the processes of skeleton construction. Additionally, non-fed sponges formed oscula significantly more often than fed sponges, especially under higher g-forces. This suggests that the eventual formation of a filtration system might be stimulated by food deprivation and environmentally stressful conditions. These findings indicate that the process of spiculous skeleton formation is energy-efficient and highly resilient. The uptake of dissolved food substances by freshwater sponges may contribute to the cycling of dissolved organic matter in freshwater ecosystems where sponges are abundant. creator: Martijn C. Bart creator: Sebastiaan J. de Vet creator: Didier M. de Bakker creator: Brittany E. Alexander creator: Dick van Oevelen creator: E. Emiel van Loon creator: Jack J.W.A. van Loon creator: Jasper M. de Goeij uri: https://doi.org/10.7717/peerj.6055 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bart et al. title: Temperature-mediated feeding between spring-associated and riverine-associated congeners, with implications for community segregation link: https://peerj.com/articles/6144 last-modified: 2019-01-04 description: Freshwater fish communities segregate along water temperature gradients attributed in part to temperature-mediated physiological processes that affect species fitness. In spring complexes of southwest USA, spring complexes with narrow range of water temperatures are dominated by a community of fishes (i.e., spring-associated fishes), whereas riverine habitats with wide-range of water temperatures are dominated by a different community of fishes (i.e., riverine-associated fishes). The purpose of this study was to test a prediction of the concept that temperature-mediated species performance is a mechanism in maintaining community segregation. We predicted that a spring-associated fish (Largespring Gambusia Gambusia geiseri) would feed first and more often in a pairing with a riverine-associated fish (Western Mosquitofish G. affinis) at an average spring temperature (23 °C) and that the riverine-associated fish would feed first and more often in a pairing with the spring-associated fish at a warm riverine temperature (30 °C). Among four trails consisting of 30 pairings, at the spring complex temperature (23 °C), Largespring Gambusia had a greater number of first feeds (mean ± 1 SD, 5.0 ± 0.82) than Western Mosquitofish (2.5 ± 1.73) and had greater mean number of total feeds (1.9 ± 0.31) than Western Mosquitofish (0.81 ± 0.70). At the riverine environment temperature (30 °C), Western Mosquitofish had a greater number of first feeds (5.25 ± 1.71) than Largespring Gambusia (2.5 ± 1.73) and had greater mean number of total feeds (2.78 ± 1.05) than Largespring Gambusia (0.94 ± 0.68). Our findings suggest that temperature-mediated species performance could be maintaining segregation between the two fish communities. This study benefits our understanding of distributional patterns and improves threat assessments of stenothermal aquatic organisms. creator: Cody A. Craig creator: Jeremy D. Maikoetter creator: Timothy H. Bonner uri: https://doi.org/10.7717/peerj.6144 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Craig et al. title: Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens link: https://peerj.com/articles/6150 last-modified: 2019-01-04 description: Climate change, changing farming practices, social and demographic changes and rising levels of antibiotic resistance are likely to lead to future increases in opportunistic bacterial infections that are more difficult to treat. Uncovering the prevalence and identity of pathogenic bacteria in the environment is key to assessing transmission risks. We describe the first use of the Wax moth larva Galleria mellonella, a well-established model for the mammalian innate immune system, to selectively enrich and characterize pathogens from coastal environments in the South West of the UK. Whole-genome sequencing of highly virulent isolates revealed amongst others a Proteus mirabilis strain carrying the Salmonella SGI1 genomic island not reported from the UK before and the recently described species Vibrio injenensis hitherto only reported from human patients in Korea. Our novel method has the power to detect bacterial pathogens in the environment that potentially pose a serious risk to public health. creator: Rafael J. Hernandez creator: Elze Hesse creator: Andrea J. Dowling creator: Nicola M. Coyle creator: Edward J. Feil creator: Will H. Gaze creator: Michiel Vos uri: https://doi.org/10.7717/peerj.6150 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hernandez et al. title: Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis link: https://peerj.com/articles/6151 last-modified: 2019-01-04 description: In marine invertebrates, the modes of development at early stages are related to the type and capacity of larval feeding to achieve growth. Therefore, studying the factors that determine larval feeding strategies can help to understand the diversity of life histories and evolution of marine invertebrates. The polychaete Boccardia wellingtonensis is a poecilogonous species that encapsulates and incubates its offspring. This species produces two types of larvae: (1) larvae that do not feed within the capsule and hatch as planktotrophic larvae (indirect development), and (2) adelphophagic larvae that feed on nurse eggs and other larvae inside the capsule to hatch as advanced larvae or juveniles (direct development). Otherwise, the larval types are indistinguishable at the same stage of development. The non-apparent morphological differences between both types of larvae suggest that other factors are influencing their feeding behavior. This work studied the potential role of the activity of 19 digestive enzymes on the different feeding capacities of planktotrophic and adelphophagic larvae of B. wellingtonensis. Also, differences in larval feeding structures and the larval capacity to feed from intracapsular fluid were evaluated by electron and fluorescence microscopy. Results showed that both types of larvae present similar feeding structures and had the capacity to ingest intracapsular fluid protein. Adelphophagic larvae showed overall the highest activities of digestive enzymes. Significant differences between larval types were observed in nine enzymes related to the use of internal and external nutritional sources. Given that larval feeding is closely related to larval development in species with encapsulation, this work supports that the study of the digestive enzymatic machinery of larvae may contribute to understanding the evolution of developmental modes. creator: Daniel Doherty-Weason creator: Fernanda X. Oyarzun creator: Luciano Vera creator: Miguel Bascur creator: Fabián Guzmán creator: Francisco Silva creator: Ángel Urzúa creator: Antonio Brante uri: https://doi.org/10.7717/peerj.6151 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Doherty-Weason et al. title: Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles link: https://peerj.com/articles/6153 last-modified: 2019-01-04 description: Secreted Frizzled-related Protein 4 (sFRP4) belongs to Wnt inhibitors. Previously, we reported that sFRP4 inhibited the differentiation of melanocyte. Here, by using of immunostaining, we showed that sFRP4 is expressed in both human and mouse hair follicles, especially in the outer root sheath and inner root sheath. To reveal the role of sFRP4 in hair follicle growth and hair cycle, we induced synchronized hair cycle in the dorsal skin of mice by depilation, and injected sFRP4 intradermally into the skin. By hematoxylin and eosin staining, we found that the regeneration of hair follicles was inhibited by sFRP4. However, the structure of hair follicles remained complete. Compared with phosphate buffer saline-treated hair follicles, the sFRP4-treated hair follicles still had the same expression pattern of keratins. Our findings reveal that sFRP4 inhibits but not blocks the regeneration of hair follicles, and supply a potential therapeutic application to treat hair follicle regeneration disorders. creator: Haiying Guo creator: Yizhan Xing creator: Fang Deng creator: Ke Yang creator: Yuhong Li uri: https://doi.org/10.7717/peerj.6153 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guo et al. title: Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China link: https://peerj.com/articles/6157 last-modified: 2019-01-04 description: A new Primulina species from Guangdong, China with an unusual inflorescence is described here. Primulina anisocymosa is vegetatively most similar to P. bobaiensis. It can be distinguished from all species within Primulina morphologically by its unique zigzag monochasial cyme and infructescence. To confirm the phylogenetic relationships and generic placement of this species, not only morphological anatomical features but also chromosome and DNA sequence data were examined and analysed here. Two samples from different populations identified as Primulina anisocymosa are monophyletic and were nested in a monophyletic clade within Primulina with high branch support. The somatic chromosome number of the new species is also reported (2n = 36), supporting its placement in the genus. creator: Xin Hong creator: Jeremy Keene creator: Zhi-Jing Qiu creator: Fang Wen uri: https://doi.org/10.7717/peerj.6157 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hong et al. title: Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies link: https://peerj.com/articles/6160 last-modified: 2019-01-04 description: Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions. creator: Paul P. Gardner creator: Renee J. Watson creator: Xochitl C. Morgan creator: Jenny L. Draper creator: Robert D. Finn creator: Sergio E. Morales creator: Matthew B. Stott uri: https://doi.org/10.7717/peerj.6160 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gardner et al. title: Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system link: https://peerj.com/articles/6171 last-modified: 2019-01-04 description: BackgroundSoil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice–wheat rotation systems.MethodsThe effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice–wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed.ResultsCompared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0–20 and 20–40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0–20 cm soil and Neurospora in macroaggregates in 20–40 cm soil); decreased pathogenic fungi (Monographella in macroaggregates and Gibberella in microaggregates in 0–20 cm soil) and CO2-emission-related fungi (Pyrenochaetopsis in microaggregates and silt clay in 0–40 cm soil) (p < 0.05). Straw and biochar with inorganic fertilizer counteracted some of the adverse effects of the inorganic fertilizer with biochar showing better effects than straw. creator: Naling Bai creator: Hanlin Zhang creator: Shuangxi Li creator: Xianqing Zheng creator: Juanqin Zhang creator: Haiyun Zhang creator: Sheng Zhou creator: Huifeng Sun creator: Weiguang Lv uri: https://doi.org/10.7717/peerj.6171 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bai et al. title: Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern link: https://peerj.com/articles/6175 last-modified: 2019-01-04 description: BackgroundDyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population.MethodsA total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software.ResultsAll SNPs conformed to Hardy–Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups.ConclusionSNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exploration. creator: Wei Bai creator: Changgui Kou creator: Lili Zhang creator: Yueyue You creator: Weiying Yu creator: Wanqing Hua creator: Yuanyuan Li creator: Yaqin Yu creator: Tiancheng Zhao creator: Yanhua Wu uri: https://doi.org/10.7717/peerj.6175 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bai et al.