title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=847 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation link: https://peerj.com/articles/12091 last-modified: 2021-08-27 description: Stromal cell-derived factor-1 (SDF-1) and Exendin-4 (EX-4) play beneficial roles in promoting periodontal ligament stem cells (PDLSCs) osteogenic differentiation, while the detailed mechanism has not been clarified. In this study, we aimed to evaluate the biological mechanism of SDF-1 and EX-4 alone or synergistic application in regulating PDLSCs differentiation by RNA-sequencing (RNA-seq). A total of 110, 116 and 109 differentially expressed genes (DEGs) were generated in osteogenic medium induced PDLSCs treated by SDF-1, EX-4, and SDF-1+EX-4, respectively. The DEGs in SDF-1 group were enriched in signal transduction related signaling pathways; the DEGs in EX-4 group were enriched in metabolism and biosynthesis-related pathways; and the DEGs generated in SDF-1+EX-4 group were mainly enriched in RNA polymerase II transcription, cell differentiation, chromatin organization, protein phosphorylation pathways. Based on Venn analysis, a total of 37 specific DEGs were identified in SDF-1+EX-4 group, which were mainly enriched in negative regulation of autophagy and cellular component disassembly signaling pathways. Short time-series expression miner (STEM) analysis grouped all expressed genes of PDLSCs into 49 clusters according to the dynamic expression patterns and 25 genes, including NRSN2, CHD9, TUBA1A, distributed in 10 gene clusters in SDF-1+EX-4 treated PDLSCs were significantly up-regulated compared with the SDF-1 and EX-4 alone groups. The gene set enrichment analysis indicated that SDF-1 could amplify the role of EX-4 in regulating varied signaling pathways, such as type II diabetes mellitus and insulin signaling pathways; while EX-4 could aggravate the effect of SDF-1 on PDLSCs biological roles via regulating primary immunodeficiency, tight junction signaling pathways. In summary, our study confirmed that SDF-1 and EX-4 combined application could enhance PDLSCs biological activity and promote PDLSCs osteogenic differentiation by regulating the metabolism, biosynthesis and immune-related signaling pathways. creator: Wenyan Kang creator: Lingqian Du creator: Qianyu Liang creator: Rui Zhang creator: Chunxu Lv creator: Shaohua Ge uri: https://doi.org/10.7717/peerj.12091 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kang et al. title: Computed Tomography elucidates ontogeny within the basal therapsid clade Biarmosuchia link: https://peerj.com/articles/11866 last-modified: 2021-08-26 description: Biarmosuchia is a clade of basal therapsids that includes forms possessing plesiomorphic ‘pelycosaurian’ cranial characters as well as the highly derived Burnetiamorpha which are characterised by cranial pachyostosis and a variety of cranial bosses. Potential ontogenetic variation in these structures has been suggested based on growth series of other therapsids with pachyostosed crania, which complicates burnetiamorph taxonomic distinction and thus it is essential to better understand cranial ontogeny of the Burnetiamorpha. Here, three new juvenile biarmosuchian skulls from the late Permian of South Africa are described using X-ray micro computed tomography (CT). We found that juvenile biarmosuchians are distinguished from adults by their relatively large orbits, open cranial sutures, and incomplete ossification of the braincase and bony labyrinth. Also, they manifest multiple centres of ossification within the parietal and preparietal bones. CT examination reveals that the holotype of Lemurosaurus pricei (BP/1/816), previously alleged to be a juvenile, shows no evidence of juvenility and is thus probably an adult. This suggests that the larger skull NMQR 1702, previously considered to be an adult L. pricei, may represent a new taxon. This study provides, for the first time, a list of characters by which to recognise juvenile biarmosuchians. creator: Aliénor Duhamel creator: Julien Benoit creator: Michael Day creator: Bruce Rubidge creator: Vincent Fernandez uri: https://doi.org/10.7717/peerj.11866 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Duhamel et al. title: Sponges of Western Mediterranean seamounts: new genera, new species and new records link: https://peerj.com/articles/11879 last-modified: 2021-08-26 description: BackgroundThe seamounts Ses Olives (SO), Ausias March (AM) and Emile Baudot (EB) at the Mallorca Channel (Balearic Islands, western Mediterranean), are poorly explored areas containing rich and singular sponge communities. Previous works have shown a large heterogeneity of habitats, including rhodolith beds, rocky, gravel and sandy bottoms and steeped slopes. This diversity of habitats provides a great opportunity for improving the knowledge of the sponges from Mediterranean seamounts.MethodsSponges were collected during several surveys carried out by the Balearic Center of the Spanish Institute of Oceanography at the Mallorca Channel seamounts. Samples were obtained using a beam-trawl, rock dredge and remote operated vehicle. Additional samples were obtained from fishing grounds of the Balearic Islands continental shelf, using the sampling device GOC-73. Sponges were identified through the analysis of morphological and molecular characters.ResultsA total of 60 specimens were analyzed, from which we identified a total of 19 species. Three species and one genus are new to science: Foraminospongia balearicagen. nov. sp. nov., Foraminospongia minutagen. nov. sp. nov. and Paratimea massutiisp. nov.Heteroxya cf. beauforti represents the first record of the genus Heteroxya in the Mediterranean Sea. Additionally, this is the second report of Axinella spatula and Haliclona (Soestella) fimbriata since their description. Moreover, the species Petrosia (Petrosia) raphida, Calyx cf. tufa and Lanuginella pupa are reported for the first time in the Mediterranean Sea. Petrosia (Strongylophora) vansoesti is reported here for the first time in the western Mediterranean Sea. Haliclona (S.) fimbriata is reported here for the first time in the north-western Mediterranean Sea. Hemiasterella elongata is reported here for the second time in the Mediterranean Sea. The species Melonanchora emphysema, Rhabdobaris implicata, Polymastia polytylota, Dragmatella aberrans, Phakellia ventilabrum and Pseudotrachya hystrix are reported for first time off Balearic Islands. Following the Sponge Barcoding project goals, we have sequenced the Cytochrome Oxidase subunit I (COI) and the 28S ribosomal fragment (C1–D2 domains) for Foraminospongia balearicasp. nov., Foraminospongia minutasp. nov., H. cf. beauforti and C. cf. tufa, and the COI for Paratimea massuti sp. nov. We also provide a phylogenetic analysis to discern the systematic location of Foraminospongiagen. nov., which, in accordance to skeletal complement, is placed in the Hymerhabdiidae family. A brief biogeographical discussion is provided for all these species, with emphasis on the sponge singularity of SO, AM and the EB seamounts and the implications for their future protection. creator: Julio A. Díaz creator: Sergio Ramírez-Amaro creator: Francesc Ordines uri: https://doi.org/10.7717/peerj.11879 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Díaz et al. title: Issues of under-representation in quantitative DNA metabarcoding weaken the inference about diet of the tundra vole Microtus oeconomus link: https://peerj.com/articles/11936 last-modified: 2021-08-26 description: During the last decade, methods based on high-throughput sequencing such as DNA metabarcoding have opened up for a range of new questions in animal dietary studies. One of the major advantages of dietary metabarcoding resides in the potential to infer a quantitative relationship between sequence read proportions and biomass of ingested food. However, this relationship’s robustness is highly dependent on the system under study, calling for case-specific assessments. Herbivorous small rodents often play important roles in the ecosystem, and the use of DNA metabarcoding for analyses of rodent diets is increasing. However, there has been no direct validation of the quantitative reliability of DNA metabarcoding for small rodents. Therefore, we used an experimental approach to assess the relationship between input plant biomass and sequence reads proportions from DNA metabarcoding in the tundra vole Microtus oeconomus. We found a weakly positive relationship between the number of high-throughput DNA sequences and the expected biomass proportions of food plants. The weak relationship was possibly caused by a systematic under-amplification of one of the three plant taxa fed. Generally, our results add to the growing evidence that case-specific validation studies are required to reliably make use of sequence read abundance as a proxy of relative food proportions in the diet. creator: Magne Neby creator: Stefaniya Kamenova creator: Olivier Devineau creator: Rolf A. Ims creator: Eeva M. Soininen uri: https://doi.org/10.7717/peerj.11936 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Neby et al. title: Transcriptome analysis of two Pogostemon cablin chemotypes reveals genes related to patchouli alcohol biosynthesis link: https://peerj.com/articles/12025 last-modified: 2021-08-26 description: Pogostemon cablin, a medicinally and economically important perennial herb, is cultivated around the world due to its medicinal and aromatic properties. Different P. cablin cultivars exhibit different morphological traits and patchouli oil components and contents (especially patchouli alcohol (PA) and pogostone (PO)). According to the signature constituent of the leaf, P. cablin was classified into two different chemotypes, including PA-type and PO-type. To better understand the molecular mechanisms of PA biosynthesis, the transcriptomes of Chinese-cultivated P. cablin cv. PA-type “Nanxiang” (NX) and PO-type “Paixiang” (PX) were analyzed and compared with ribonucleic acid sequencing (RNA-Seq) technology. We obtained a total of 36.83 G clean bases from the two chemotypes, compared them with seven databases and revealed 45,394 annotated unigenes. Thirty-six candidate unigenes participating in the biosynthesis of PA were found in the P. cablin transcriptomes. Overall, 8,390 differentially expressed unigenes were identified between the chemotypes, including 2,467 upregulated and 5,923 downregulated unigenes. Furthermore, six and nine differentially expressed genes (DEGs) were mapped to the terpenoid backbone biosynthetic and sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. One key sesquiterpene synthase gene involved in the sesquiterpenoid and triterpenoid biosynthetic pathways, encoding patchoulol synthase variant 1, was significantly upregulated in NX. Additionally, GC-MS analysis of the two chemotypes in this study showed that the content of PA in NX was significantly higher than that of PX, while the content of PO showed the opposite phenotype. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the DEG expression tendency was consistent with the transcriptome sequencing results. Overall, 23 AP2/ERF, 13 bHLH, 11 MYB, 11 NAC, three Trihelix, 10 WRKY and three bZIP genes that were differentially expressed may act as regulators of terpenoid biosynthesis. Altogether, 8,314 SSRs were recognized within 6,825 unigenes, with a distribution frequency of 18.32%, among which 1,202 unigenes contained more than one SSR. The transcriptomic characteristics of the two P. cablin chemotypes are comprehensively reported in this study, and these results will contribute to a better understanding of the molecular mechanism of PA biosynthesis. Our transcriptome data also provide a valuable genetic resource for further studies on P. cablin. creator: Wuping Yan creator: Zhouchen Ye creator: Shijia Cao creator: Guanglong Yao creator: Jing Yu creator: Dongmei Yang creator: Ping Chen creator: Junfeng Zhang creator: Yougen Wu uri: https://doi.org/10.7717/peerj.12025 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yan et al. title: Measuring walking impairment in patients with intermittent claudication: psychometric properties of the Walking Estimated-Limitation Calculated by History (WELCH) questionnaire link: https://peerj.com/articles/12039 last-modified: 2021-08-26 description: ObjectivesPatient-reported outcome measures can facilitate the assessment of walking impairment in peripheral artery disease patients with intermittent claudication in clinical trials and practice. The aim of this study was to test the psychometric properties of the German version of the ‘Walking Estimated-Limitation Calculated by History’ (WELCH) questionnaire.MethodsThe assessed properties included feasibility, test-retest reliability, construct validity (i.e., convergent, divergent and known-groups validity) and responsiveness using classic psychometric methods. Psychometric properties were tested as part of a randomized controlled home-based exercise trial for patients with symptomatic peripheral artery disease at Fontaine stage IIA/B.ResultsAnalyses were conducted in subgroups of 1,696 patients at baseline and 1,233 patients at 12-month follow-up (i.e., post-intervention) who completed the WELCH along with a battery of other self-report measures. The WELCH did not exhibit relevant floor or ceiling effects (< 15% achieved lowest or highest possible scores), showed evidence for good test-retest reliability (ICC = .81, 95% CI [.71–.88]) and was found to be well suited for self-completion by patients (< 5% missing data per item). WELCH scores showed moderate to strong correlations with related measures of walking impairment at both time points (Walking Impairment Questionnaire: r = .56 − .74; VascuQoL-25 activity subscale: r = .61 − .66) and distinguished well among patients with poor and high quality of life when adjusting for confounders (t = 13.67, p < .001, d = .96). Adequate divergent validity was indicated by a weaker correlation between the WELCH and general anxiety at both time points (GAD-7: r =  − .14 to  − .22). The WELCH improved by 6.61 points (SD = 17.04, 95% CI [5.13–8.10], d = 0.39) in response to exercise treatment and was able to identify large clinically important improvements observed on the walking distance (AUC = .78, 95% CI [.71–.84]) and speed subscales (AUC = .77, 95% CI [.68–.86]) of the Walking Impairment Questionnaire.ConclusionsThe WELCH is considered a feasible, reliable and valid patient-reported outcome measure for the measurement of walking impairment in patients with peripheral artery disease. The WELCH showed evidence for responsiveness to changes in walking impairment, yet further studies are warranted to conclusively determine the WELCH’s ability to detect intervention effects. creator: Farhad Rezvani creator: Martin Härter creator: Jörg Dirmaier uri: https://doi.org/10.7717/peerj.12039 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rezvani et al. title: Camostat mesilate inhibits pro-inflammatory cytokine secretion and improves cell viability by regulating MFGE8 and HMGN1 in lipopolysaccharide-stimulated DF-1 chicken embryo fibroblasts link: https://peerj.com/articles/12053 last-modified: 2021-08-26 description: Camostat mesilate (CM) possesses potential anti-viral and anti-inflammatory activities. However, it remains unknown whether CM is involved in lipopolysaccharide (LPS)-mediated inflammatory responses and cell injury. In this project, differentially expressed proteins (DEPs, fold change ≥ 1.2 or ≤ 0.83 and Q value ≤ 0.05) in response to LPS stimulation alone or in combination with CM were identified through tandem mass tags (TMT)/mass spectrometry (MS)-based proteomics analysis in DF-1 chicken embryo fibroblasts. The mRNA expression levels of filtered genes were determined by RT-qPCR assay. The results showed that CM alleviated the detrimental effect of LPS on cell viability and inhibited LPS-induced TNF-α and IL-6 secretions in DF-1 chicken embryo fibroblasts. A total of 141 DEPs that might be involved in mediating functions of both LPS and CM were identified by proteomics analysis in DF-1 chicken embryo fibroblasts. LPS inhibited milk fat globule EGF and factor V/VIII domain containing (MFGE8) expression and induced high mobility group nucleosome binding domain 1 (HMGN1) expression, while these effects were abrogated by CM in DF-1 chicken embryo fibroblasts. MFGE8 knockdown facilitated TNF-α and IL-6 secretions , reduced cell viability, stimulated cell apoptosis in DF-1 chicken embryo fibroblasts co-treated with LPS and CM. HMGN1 loss did not influence TNF-α and IL-6 secretions, cell viability, and cell apoptosis in DF-1 chicken embryo fibroblasts co-treated with LPS and CM. In conclusion, CM exerted anti-inflammatory and pro-survival activities by regulating MFGE8 in LPS-stimulated DF-1 chicken embryo fibroblasts, deepening our understanding of the roles and molecular basis of CM in protecting against Gram-negative bacteria. creator: Lin Yuan creator: Mengjie Li creator: Zhishuai Zhang creator: Wanli Li creator: Wei Jin creator: Mingfa Wang uri: https://doi.org/10.7717/peerj.12053 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yuan et al. title: Factors influencing intention to intervene in elder abuse among nursing students link: https://peerj.com/articles/12079 last-modified: 2021-08-26 description: PurposeThis study aimed to identify the factors influencing the intention to intervene in elder abuse among nursing students.MethodsA descriptive survey design was used, and questionnaires were completed by 182 nursing students. Statistical analysis was performed on the data collected, using SPSS 25.0, χ2-test, t-test, correlation, and regression analysis to confirm predictors of intention to intervene in elder abuse.ResultsAwareness of abuse, legal and institutional knowledge, and attitude were positively correlated with the intention to intervene in elder abuse. Factors influencing the intention to intervene by nursing students were education courses about elder abuse, awareness of elder abuse, legal and institutional knowledge, and attitude.ConclusionThe findings suggest that it is necessary to provide educational protocols for nursing students to improve their awareness and knowledge of elder abuse. Based on the findings of this study, there is a need for specific education programs and guidelines to increase the assessment of, and intervention in, elder abuse. creator: Hee-Jeong Kim creator: Min-Sook Seo creator: Dahye Park uri: https://doi.org/10.7717/peerj.12079 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kim et al. title: Influence of rigid taping on the acromiohumeral distance in healthy recreational weightlifters link: https://peerj.com/articles/12093 last-modified: 2021-08-26 description: BackgroundSubacromial pain syndrome is one of the most frequent injuries in overhead athletes, and it takes place when the acromiohumeral distance (AHD) is narrowed. Conservative treatment is the first approach to this syndrome, being shoulder taping one of the most used techniques. Although there are quite a few studies that analyse the effect of taping on the AHD, most of them do not include sham tapings. This study aimed to examine if the Relocation of the humeral head (RHH) taping produced an increase in the AHD in healthy recreationally weightlifter males, quantifying the change that may be due to a placebo effect.MethodsThe design of this study was a two-group pretest-posttest, in which eighteen healthy recreationally weightlifter males were measured. in a laboratory of the University of Valencia. RHH using rigid or sham taping was randomly applied to the participants. The AHD was measured and registered before and after the application of the taping for both groups by a blinded examiner using ultrasound.ResultsThere were no significant differences between pre and post measures in the sham group (p = 0.51). The experimental group showed a significant AHD increase of 9.2% (10.75 ± 1.89 vs 11.74 ± 1.82, respectively, with p < 0.001). Significant differences in the effects of each taping on the AHD were found between groups (p < 0.001). The results of this study indicate that the RHH rigid taping increases the AHD in the shoulders of recreationally weightlifters, dismissing the possibility of a placebo effect of the taping. creator: Rodrigo Martín-San Agustín creator: Alba Cuerda-Del Pino creator: Noemi Moreno-Segura creator: Adrian Escriche-Escuder creator: Mariana Sánchez-Barbadora uri: https://doi.org/10.7717/peerj.12093 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Martín-San Agustín et al. title: Recommended nitrogen rates and the verification of effects based on leaf SPAD readings of rice link: https://peerj.com/articles/12107 last-modified: 2021-08-26 description: Modern rice production systems need a reliable, easy-to-use, efficient, and environmentally-friendly method to determine plant nitrogen (N) status , predict grain yield, and optimize N management. We conducted field experiments to determine the influence of different N rates on Soil Plant Analysis Development (SPAD) readings of rice leaves. We also performed field validations to evaluate the grain yield and N use efficiency under recommended N rates. Our results showed that leaf SPAD readings increased as N rates increased. We applied the recommended N based on the relationships between the N rates and leaf SPAD readings at the tillering and booting stages. The recommended N decreased N rates and improved N use efficiency without sacrificing grain yield. When compared to farmer practices (FP), the recommended N rates of optimization (OPT) decreased by 5.8% and 10.0%, respectively. In comparison with FP, the N agronomic efficiency of OPT increased by 5.8 and 10.0% while the partial factor productivity of N increased by 6.0 and 14.2%, respectively. The SPAD meter may be a reliable tool to analyze the N in rice, estimate real-time N fertilization, and improve N use efficiency. creator: Wenfeng Hou creator: Juan Shen creator: Weitao Xu creator: Muhammad Rizwan Khan creator: Yin Wang creator: Xue Zhou creator: Qiang Gao creator: Behzad Murtaza creator: Zhongqing Zhang uri: https://doi.org/10.7717/peerj.12107 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hou et al.