title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1026 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A new nurse frog (Anura: Allobates) from Brazilian Amazonia with a remarkably fast multi-noted advertisement call link: https://peerj.com/articles/9979 last-modified: 2020-11-04 description: Nurse frogs (Aromobatidae: Allobates) are probably the most extensively studied genus by taxonomists in Brazilian Amazonia. The southwestern portion of Amazonia is the most species-rich: as many as seven species may occur in sympatry at a single locality. In this study, we describe a new species of nurse frog from this region. The description integrates data from larval and adult morphology, advertisement calls and DNA sequences. Allobates velocicantus sp. nov. is distinguished from other Allobates mainly by the absence of hourglass-shaped dark marks on the dorsum and dark transverse bars on the thigh; a throat that is white centrally and yellow marginally; basal webbing on toes II and III; finger I longer than finger II; and an advertisement call composed of 66–138 pulsed notes with a note duration of 5–13 ms, inter-note intervals of 10–18 ms and a dominant frequency of 5,512–6,158 Hz. Tadpoles of the new species have 3–4 short, rounded papillae on the anterior labium, 16–23 papillae on the posterior labium, and a labial keratodont row formula 2(2)/3(1). This is the fifth species of Allobates described from the state of Acre, southwestern Brazilian Amazonia. creator: Jesus R.D. Souza creator: Miquéias Ferrão creator: James Hanken creator: Albertina P. Lima uri: https://doi.org/10.7717/peerj.9979 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Souza et al. title: Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism link: https://peerj.com/articles/10053 last-modified: 2020-11-04 description: BackgroundSilicon (Si) is categorized as a quasi-essential element for plants thanks to the benefits on growth, development and metabolism in a hormetic manner. Si uptake is cooperatively mediated by Lsi1 and Lsi2. Nevertheless, Lsi channels have not yet been identified and characterized in pepper (Capsicum annuum), while genes involved in major physiological processes in pepper are Si-regulated. Furthermore, Si and phytohormones may act together in regulating plant growth, metabolism and tolerance against stress. Our aim was to identify potential synergies between Si and phytohormones stimulating growth and metabolism in pepper, based on in silico data.MethodsWe established a hydroponic system to test the effect of Si (0, 60, 125 and 250 mg L−1 Si) on the concentrations of this element in different pepper plant tissues. We also performed an in silico analysis of putative Lsi genes from pepper and other species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum) and Arabidopsis thaliana, to look for cis-acting elements responsive to phytohormones in their promoter regions. With the Lsi1 and Lsi2 protein sequences from various plant species, we performed a phylogenetic analysis. Taking into consideration the Lsi genes retrieved from tomato, potato and Arabidopsis, an expression profiling analysis in different plant tissues was carried out. Expression of Si-regulated genes was also analyzed in response to phytohormones and different plant tissues and developmental stages in Arabidopsis.ResultsSi concentrations in plant tissues exhibited the following gradient: roots > stems > leaves. We were able to identify 16 Lsi1 and three Lsi2 genes in silico in the pepper genome, while putative Lsi homologs were also found in other plant species. They were mainly expressed in root tissues in the genomes analyzed. Both Lsi and Si-regulated genes displayed cis-acting elements responsive to diverse phytohormones. In Arabidopsis, Si-regulated genes were transcriptionally active in most tissues analyzed, though at different expressed levels. From the set of Si-responsive genes, the NOCS2 gene was highly expressed in germinated seeds, whereas RABH1B, and RBCS-1A, were moderately expressed in developed flowers. All genes analyzed showed responsiveness to phytohormones and phytohormone precursors.ConclusionPepper root cells are capable of absorbing Si, but small amounts of this element are transported to the upper parts of the plant. We could identify putative Si influx (Lsi1) and efflux (Lsi2) channels that potentially participate in the absorption and transport of Si, since they are mainly expressed in roots. Both Lsi and Si-regulated genes exhibit cis-regulatory elements in their promoter regions, which are involved in phytohormone responses, pointing to a potential connection among Si, phytohormones, plant growth, and other vital physiological processes triggered by Si in pepper. creator: Fernando Carlos Gómez-Merino creator: Libia Iris Trejo-Téllez creator: Atonaltzin García-Jiménez creator: Hugo Fernando Escobar-Sepúlveda creator: Sara Monzerrat Ramírez-Olvera uri: https://doi.org/10.7717/peerj.10053 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gómez-Merino et al. title: A model of k-mer surprisal to quantify local sequence information content surrounding splice regions link: https://peerj.com/articles/10063 last-modified: 2020-11-04 description: Molecular sequences carry information. Analysis of sequence conservation between homologous loci is a proven approach with which to explore the information content of molecular sequences. This is often done using multiple sequence alignments to support comparisons between homologous loci. These methods therefore rely on sufficient underlying sequence similarity with which to construct a representative alignment. Here we describe a method using a formal metric of information, surprisal, to analyse biological sub-sequences without alignment constraints. We applied our model to the genomes of five different species to reveal similar patterns across a panel of eukaryotes. As the surprisal of a sub-sequence is inversely proportional to its occurrence within the genome, the optimal size of the sub-sequences was selected for each species under consideration. With the model optimized, we found a strong correlation between surprisal and CG dinucleotide usage. The utility of our model was tested by examining the sequences of genes known to undergo splicing. We demonstrate that our model can identify biological features of interest such as known donor and acceptor sites. Analysis across all annotated coding exon junctions in Homo sapiens reveals the information content of coding exons to be greater than the surrounding intron regions, a consequence of increased suppression of the CG dinucleotide in intronic space. Sequences within coding regions proximal to exon junctions exhibited novel patterns within DNA and coding mRNA that are not a function of the encoded amino acid sequence. Our findings are consistent with the presence of secondary information encoding features such as DNA and RNA binding sites, multiplexed through the coding sequence and independent of the information required to define the corresponding amino-acid sequence. We conclude that surprisal provides a complementary methodology with which to locate regions of interest in the genome, particularly in situations that lack an appropriate multiple sequence alignment. creator: Sam Humphrey creator: Alastair Kerr creator: Magnus Rattray creator: Caroline Dive creator: Crispin J. Miller uri: https://doi.org/10.7717/peerj.10063 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Humphrey et al. title: Mortality of native and invasive ladybirds co-infected by ectoparasitic and entomopathogenic fungi link: https://peerj.com/articles/10110 last-modified: 2020-11-04 description: Harmonia axyridis is an invasive alien ladybird in North America and Europe. Studies show that multiple natural enemies are using Ha. axyridis as a new host. However, thus far, no research has been undertaken to study the effects of simultaneous infection by multiple natural enemies on Ha. axyridis. We hypothesized that high thallus densities of the ectoparasitic fungus Hesperomyces virescens on a ladybird weaken the host’s defenses, thereby making it more susceptible to infection by other natural enemies. We examined mortality of the North American-native Olla v-nigrum and Ha. axyridis co-infected with He. virescens and an entomopathogenic fungus—either Beauveria bassiana or Metarhizium brunneum. Laboratory assays revealed that He. virescens-infected O. v-nigrum individuals are more susceptible to entomopathogenic fungi, but Ha. axyridis does not suffer the same effects. This is in line with the enemy release hypothesis, which predicts that invasive alien species in new geographic areas experience reduced regulatory effects from natural enemies compared to native species. Considering our results, we can ask how He. virescens affects survival when confronted by other pathogens that previously had little impact on Ha. axyridis. creator: Danny Haelewaters creator: Thomas Hiller creator: Emily A. Kemp creator: Paul S. van Wielink creator: David I. Shapiro-Ilan creator: M. Catherine Aime creator: Oldřich Nedvěd creator: Donald H. Pfister creator: Ted E. Cottrell uri: https://doi.org/10.7717/peerj.10110 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Effects of food hydrocolloids on quality attributes of extruded red Jasmine rice noodle link: https://peerj.com/articles/10235 last-modified: 2020-11-04 description: The aim of this study was to examine the quality characteristics of extruded red Jasmine rice flour (RJF) noodle that had been prepared with hydrocolloids, namely guar gum (GG), carboxymethyl cellulose (CMC), and xanthan gum (XG) at the concentrations of 0.0 (control sample), 0.2, and 0.4% (w/w), respectively. The use of hydrocolloids had no effect on total phenolic contents, antioxidant properties (DPPH, ABTS, and FRAP), color, and X-ray diffraction patterns (p > 0.05). In contrast, the hydrocolloids tended to increase the expansion ration of the noodle. GG and CMC improved cooking, textural, and sensory properties. Ultimately, 0.2%-GG showed the lowest cooking loss (5.07%) when compared with others. Moreover, it also provided the noodle with better textural properties such as tensile strength, extensibility, hardness, cohesiveness, and chewiness (p < 0.05). For these reasons, the highest acceptability (6.75) for the noodle was achieved with GG02. XG resulted in lower overall acceptability (5.05), particularly the 0.4%-XG recipe (p < 0.05). Thus, usage of 0.2%-GG was the best option for improving the qualities of extruded RJF noodle. XG was deemed ineffective for improving the noodle. creator: Supaluck Kraithong creator: Saroat Rawdkuen uri: https://doi.org/10.7717/peerj.10235 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kraithong and Rawdkuen title: Prognostic model of invasive ductal carcinoma of the breast based on differentially expressed glycolysis-related genes link: https://peerj.com/articles/10249 last-modified: 2020-11-04 description: BackgroundInvasive ductal carcinoma (IDC) is a common pathological type of breast cancer that is characterized by high malignancy and rapid progression. Upregulation of glycolysis is a hallmark of tumor growth, and correlates with the progression of breast cancer. We aimed to establish a model to predict the prognosis of patients with breast IDC based on differentially expressed glycolysis-related genes (DEGRGs).MethodsTranscriptome data and clinical data of patients with breast IDC were from The Cancer Genome Atlas (TCGA). Glycolysis-related gene sets and pathways were from the Molecular Signatures Database (MSigDB). DEGRGs were identified by comparison of tumor tissues and adjacent normal tissues. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression were used to screen for DEGRGs with prognostic value. A risk-scoring model based on DEGRGs related to prognosis was constructed. Receiver operating characteristic (ROC) analysis and calculation of the area under the curve (AUC) were used to evaluate the performance of the model. The model was verified in different clinical subgroups using an external dataset (GSE131769). A nomogram that included clinical indicators and risk scores was established. Gene function enrichment analysis was performed, and a protein-protein interaction network was developed.ResultsWe analyzed data from 772 tumors and 88 adjacent normal tissues from the TCGA database and identified 286 glycolysis-related genes from the MSigDB. There were 185 DEGRGs. Univariate Cox regression and LASSO regression indicated that 13 of these genes were related to prognosis. A risk-scoring model based on these 13 DEGRGs allowed classification of patients as high-risk or low-risk according to median score. The duration of overall survival (OS) was longer in the low-risk group (P < 0.001), and the AUC was 0.755 for 3-year OS and 0.726 for 5-year OS. The results were similar when using the GEO data set for external validation (AUC for 3-year OS: 0.731, AUC for 5-year OS: 0.728). Subgroup analysis showed there were significant differences in OS among high-risk and low-risk patients in different subgroups (T1-2, T3-4, N0, N1-3, M0, TNBC, non-TNBC; all P < 0.01). The C-index was 0.824, and the AUC was 0.842 for 3-year OS and 0.808 for 5-year OS from the nomogram. Functional enrichment analysis demonstrated the DEGRGs were mainly involved in regulating biological functions.ConclusionsOur prognostic model, based on 13 DEGRGs, had excellent performance in predicting the survival of patients with IDC of the breast. These DEGRGs appear to have important biological functions in the progression of this cancer. creator: Xiaoping Li creator: Qihe Yu creator: Jishang Chen creator: Hui Huang creator: Zhuangsheng Liu creator: Chengxing Wang creator: Yaoming He creator: Xin Zhang creator: Weiwen Li creator: Chao Li creator: Jinglin Zhao creator: Wansheng Long uri: https://doi.org/10.7717/peerj.10249 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Identifying myocardial injuries in “normal-appearing” myocardium in pediatric patients with clinically suspected myocarditis using mapping techniques link: https://peerj.com/articles/10252 last-modified: 2020-11-04 description: BackgroundMapping techniques using cardiac magnetic resonance imaging have significantly improved the diagnostic accuracy for myocarditis with focal myocardial injuries. The aim of our study was to determine whether T1 and T2 mapping techniques could identify diffuse myocardial injuries in “normal-appearing” myocardium in pediatric patients with clinically suspected myocarditis and to evaluate the associations between diffuse myocardial injuries and cardiac function parameters.MethodsForty-six subjects were included in this study: 20 acute myocarditis patients, 11 subacute/chronic myocarditis patients and 15 control children. T2 values, native T1 values and the extracellular volume (ECV) of “normal-appearing” myocardium were compared among the three groups of patients. Associations between diffuse myocardial injuries and cardiac function parameters were also evaluated.ResultsThe ECV of “normal-appearing” myocardium was significantly higher in the subacute/chronic myocarditis group than in the control group (30.1 ± 0.9 vs 27.0 ± 0.6, P =0.004). No significant differences in T1 and T2 values between the acute myocarditis and control groups were found. In the subacute/chronic myocarditis group, a significant association between ECV and left ventricle ejection fraction was found (P=0.03).ConclusionsDiffuse myocardial injuries are likely to occur in subacute/chronic myocarditis patients with prolonged inflammatory responses. Mapping techniques have great value for the diagnosis and monitoring of myocarditis. creator: Haipeng Wang creator: Bin Zhao creator: Huan Yang creator: Tianyi Qian creator: Bo Han creator: Haipeng Jia creator: Jing An creator: Junyu Zhao creator: Ximing Wang creator: Cuiyan Wang uri: https://doi.org/10.7717/peerj.10252 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Tnni1b-ECR183-d2, an 87 bp cardiac enhancer of zebrafish link: https://peerj.com/articles/10289 last-modified: 2020-11-04 description: BackgroundSeveral heart malformations are associated with mutations in the regulatory regions of cardiac genes. Troponin I type 1b (tnni1b) is important for the formation of the atrioventricular canal in zebrafish hearts; however, the regulation of tnni1b is poorly understand. We aimed to identify a small but functional enhancer that is distal to tnni1b.MethodsEvolutionary Conserved Region (ECR) Browser was used to analyze the 219 kb zebrafish and human genomes covering the tnni1b gene as well as the 100 kb regions upstream and downstream of tnni1b. Putative transcription factor binding sites (TFBSs) were analyzed using JASPAR and PROMO, and the enhancer activity was identified using zebrafish embryos and the luciferase reporter assay. A correlation analysis between the enhancer and transcription factors (TFs) was performed via TF overexpression and TFBS mutation experiments and the electrophoretic mobility shift assay (EMSA). To analyze the conservation between zebrafish and human enhancers, human DNA fragments were functionally verified. Images were captured and analyzed by fluorescence microscopy or confocal microscopy.ResultsCombined with comparative analysis and functional validation, we identified a 183 bp ECR (termed tnni1b-ECR183) that was located approximately 84 kb upstream of tnni1b that had the heart-specific enhancer activity in zebrafish. TFBS analysis and the enhancer activity detection assay data showed that the 87 bp core region (termed tnni1b-ECR183-d2) was capable of driving specific GFP expression near the atrioventricular junction and increased luciferase expression in HEK293 and HL1 cell lines. The GFP pattern in zebrafish embryos was similar to the expression profiles of tnni1b. A correlation analysis showed that the enhancer activity of tnni1b-ECR183-d2 was increased when NKX2.5 (p = 0.0006) or JUN (p < 0.0001) was overexpressed and was decreased when the TFBSs of NKX2.5 (p < 0.0001) or JUN (p = 0.0018) were mutated. In addition, DNA-protein interactions were not observed between these TFs and tnni1b-ECR183-d2 in the EMSA experiment. The conservation analysis showed that tnni1b-ECR183-h179 (aligned from tnni1b-ECR183) drove GFP expression in the heart and skeletal muscles and increased the luciferase expression after NKX2.5 (p < 0.0001), JUN (p < 0.0001) or ETS1 (p < 0.0001) was overexpressed. Interestingly, the truncated fragment tnni1b-ECR183-h84 mainly drove GFP expression in the skeletal muscles of zebrafish and the enhancer activity decreased when NKX2.5 (p = 0.0028), ETS1 (p = 0.0001) or GATA4 (p < 0.0001) was overexpressed.ConclusionsAn 87 bp cardiac-specific enhancer located 84 kb upstream of tnni1b in zebrafish was positively correlated with NKX2.5 or JUN. The zebrafish and human enhancers in this study target different tissues. The GFP expression mediated by tnni1b-ECR183-d2 is a valuable tool for marking the domain around the atrioventricular junction. creator: Yawen Zhang creator: Feng Wang creator: Fang Wu creator: Youhua Wang creator: Xu Wang creator: Yonghao Gui creator: Qiang Li uri: https://doi.org/10.7717/peerj.10289 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Identification of the miRNA-mRNA regulatory pathways and a miR-21-5p based nomogram model in clear cell renal cell carcinoma link: https://peerj.com/articles/10292 last-modified: 2020-11-04 description: BackgroundThe purpose of this study was to determine the key microRNAs (miRNAs) and their regulatory networks in clear cell renal cell carcinoma (ccRCC).MethodsFive mRNA and three microRNA microarray datasets were downloaded from the Gene Expression Omnibus database and used to screen the differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs). Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed with Metascape. A miRNA-mRNA network was mapped with the Cytoscape tool. The results were validated with data from The Cancer Genome Atlas (TCGA) and qRT-PCR. A nomogram model based on independent prognostic key DEMs, stage and grade was constructed for further investigation.ResultsA total of 26 key DEMs and 307 DEGs were identified. Dysregulation of four key DEMs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) was identified to correlate with overall survival. The results were validated with TCGA data and qRT-PCR. The nomogram model showed high accuracy in predicting the prognosis of patients with ccRCC.ConclusionWe identified 26 DEMs that may play vital roles in the regulatory networks of ccRCC. Four miRNAs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) were considered as potential biomarkers in the prognosis of ccRCC, among which only miR-21-5p was found to be an independent prognostic factor. A nomogram model was then created on the basis of independent factors for better prediction of prognosis for patients with ccRCC. Our results suggest a need for further experimental validation studies. creator: Yiqiao Zhao creator: Zijia Tao creator: Xiaonan Chen uri: https://doi.org/10.7717/peerj.10292 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al. title: Biomechanics of lower limb in badminton lunge: a systematic scoping review link: https://peerj.com/articles/10300 last-modified: 2020-11-04 description: BackgroundBadminton is a popular sport activity in both recreational and elite levels. A lot of biomechanical studies have investigated badminton lunge, since good lunge performance may increase the chances to win the game. This review summarized the current trends, research methods, and parameters-of-interest concerning lower-extremity biomechanics in badminton lunges.MethodologyDatabases including Web of Science, Cochrane Library, Scopus, and PubMed were searched from the oldest available date to September 2020. Two independent authors screened all the articles and 20 articles were eligible for further review. The reviewed articles compared the differences among playing levels, footwear designs, and lunge directions/variations, using parameters including ground reaction forces, plantar pressure distribution, kinematics, and kinetics.ResultsElite badminton players demonstrated higher impact attenuation capability, more aggressive knee and ankle strategy (higher mechanical moment), and higher medial plantar load than amateur players. Footwear modifications can influence comfort perception and movement mechanics, but it remains inconclusive regarding how these may link with lunging performance. Contradicting findings in kinematics is possibly due to the variations in lunge and instructions.ConclusionsPlaying levels and shoe designs have significant effects on biomechanics in badminton lunges. Future studies can consider to use an unanticipated testing protocol and realistic movement intensity. They can study the inter-limb coordination as well as the contributions and interactions of intrinsic and extrinsic factors to injury risk. Furthermore, current findings can stimulate further research studying whether some specific footwear materials with structural design could potentially compromise impact attenuation, proprioception, and performance. creator: Wing-Kai Lam creator: Duo Wai-Chi Wong creator: Winson Chiu-Chun Lee uri: https://doi.org/10.7717/peerj.10300 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lam et al.