title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=852 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Molecular and morphological evidence for a new species of Leptopus (Phyllanthaceae) from Southeast Yunnan, China link: https://peerj.com/articles/11989 last-modified: 2021-08-24 description: Leptopus malipoensis, a new species of Phyllanthaceae from Southeast Yunnan Province, China, is described. The phylogenetic position of the new species within the genus Leptopus was analyzed based on nuclear ribosomal Internal Transcribed Spacer (nrITS) and plastid matK sequence data. The results show that L. malipoensis is highly supported to be the sister of L. fangdingianus (P. T. Li) Voronts. & Petra Hoff., a species endemic to western Guangxi Province, China. Morphologically, the new species can be distinguished from all known congeneric taxa by its long and slim branches usually pendulous or procumbent, some of its leaf laminas up to 15 cm long and 7 cm wide. It further differs from its sister species by its hirsute stems, leaves and pedicel of female flowers, longer pedicel of male flowers, 3-locular ovary and three styles. A key to all 10 accepted Leptopus species is provided. creator: Wenhua Zhang creator: Xinxin Zhu creator: Bine Xue creator: Ende Liu creator: Yuling Li creator: Gang Yao uri: https://doi.org/10.7717/peerj.11989 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: The modulatory properties of Astragalus membranaceus treatment on endometrial cancer: an integrated pharmacological method link: https://peerj.com/articles/11995 last-modified: 2021-08-24 description: Astragalus membranaceus is a traditional Chinese medicine and has been used for adjuvant clinical therapy for a variety of cancers. However, the mechanism of its action on endometrial carcinoma is unclear. Based on the Gene Expression Omnibus (GEO) database, the Cancer Genome Atlas (TCGA) database, and the Traditional Chinese Medicine System Pharmacology Database (TCMSP™), the drug and target compounds were initially screened to construct a common network module. Twenty active compounds in Astragalus membranaceus were successfully identified, which hit by 463 potential targets related to endometrial cancer. Eight of the more highly predictive compounds (such as Jaranol, Bifendate, Isorhamnetin, Calycosin, 7-O-methylisomucronulatol, Formononetin, Kaempferol, Quercetin) were involved in DNA integrity checkpoint, cyclin-dependent protein kinase holoenzyme complex, and histone kinase activity. Additionally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway confirmed that Astragalus membranaceus might play a role in the treatment of endometrial cancer through p53 signalling pathway, transcriptional misregulation in cancer, and endometrial cancer signalling pathway. Drug-target-pathway networks were constructed using Cytoscape to provide a visual perspective. In addition, we verified that formononetin inhibited the proliferation of endometrial cancer cells through cell viability tests and clone formation tests. And qPCR and western blot found that formononetin exerts anti-cancer effects by promoting the expression of estrogen receptor beta (ERβ) and p53. Based on a systematic network pharmacology approach, our works successfully predict the active ingredients and potential targets of Astragalus membranaceus for application to endometrial cancer and helps to illustrate mechanism of action on a comprehensive level. creator: Qianqian Zhang creator: Xianghua Huang uri: https://doi.org/10.7717/peerj.11995 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang and Xianghua title: Protein function prediction with gene ontology: from traditional to deep learning models link: https://peerj.com/articles/12019 last-modified: 2021-08-24 description: Protein function prediction is a crucial part of genome annotation. Prediction methods have recently witnessed rapid development, owing to the emergence of high-throughput sequencing technologies. Among the available databases for identifying protein function terms, Gene Ontology (GO) is an important resource that describes the functional properties of proteins. Researchers are employing various approaches to efficiently predict the GO terms. Meanwhile, deep learning, a fast-evolving discipline in data-driven approach, exhibits impressive potential with respect to assigning GO terms to amino acid sequences. Herein, we reviewed the currently available computational GO annotation methods for proteins, ranging from conventional to deep learning approach. Further, we selected some suitable predictors from among the reviewed tools and conducted a mini comparison of their performance using a worldwide challenge dataset. Finally, we discussed the remaining major challenges in the field, and emphasized the future directions for protein function prediction with GO. creator: Thi Thuy Duong Vu creator: Jaehee Jung uri: https://doi.org/10.7717/peerj.12019 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vu and Jung title: Genetic diversity and population structure of Euscaphis japonica, a monotypic species link: https://peerj.com/articles/12024 last-modified: 2021-08-24 description: BackgroundUnderstanding plant genetic diversity is important for effective conservation and utilization of genetic resources. Euscaphis japonica (Thunb.) Dippel, is a monotypic species with high phenotypic diversity, narrow distribution, and small population size. In this study, we estimated the genetic diversity and population structure of E. japonica using nine natural populations and inter-simple sequence repeat (ISSR) markers. Our results could provide a theoretical reference for future conservation and utilization of E. japonica.ResultsWe obtained a total of 122 DNA bands, of which 121 (99.18%) were polymorphic. The average number of effective alleles (Ne = 1.4975), Nei’s gene diversity index (H = 0.3016), and Shannon’s information index (I = 0.4630) revealed that E. japonica possessed a high level of genetic diversity. We observed that E. japonica consisted of both deciduous and evergreen populations. UPGMA tree showed that the evergreen and deciduous E. japonica form a sister group. There is little genetic differentiation among geographic populations based on STRUCTURE analysis. The Dice’s similarity coefficient between the deciduous and evergreen populations was low, and the Fst value was high, indicating that these two types of groups have high degree of differentiation.ConclusionRich genetic diversity has been found in E. japonica, deciduous E. japonica and evergreen E. japonica populations, and genetic variation mainly exists within the population. The low-frequency gene exchange between deciduous and evergreen populations may be the result of the differentiation of deciduous and evergreen populations. We suggest that in-situ protection, seed collection, and vegetative propagation could be the methods for maintenance and conservation of E. japonica populations. creator: Wei-Hong Sun creator: De-Qiang Chen creator: Rebeca Carballar-Lejarazu creator: Yi Yang creator: Shuang Xiang creator: Meng-Yuan Qiu creator: Shuang-Quan Zou uri: https://doi.org/10.7717/peerj.12024 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Sun et al. title: Discriminating three motor imagery states of the same joint for brain-computer interface link: https://peerj.com/articles/12027 last-modified: 2021-08-24 description: The classification of electroencephalography (EEG) induced by the same joint is one of the major challenges for brain-computer interface (BCI) systems. In this paper, we propose a new framework, which includes two parts, feature extraction and classification. Based on local mean decomposition (LMD), cloud model, and common spatial pattern (CSP), a feature extraction method called LMD-CSP is proposed to extract distinguishable features. In order to improve the classification results multi-objective grey wolf optimization twin support vector machine (MOGWO-TWSVM) is applied to discriminate the extracted features. We evaluated the performance of the proposed framework on our laboratory data sets with three motor imagery (MI) tasks of the same joint (shoulder abduction, extension, and flexion), and the average classification accuracy was 91.27%. Further comparison with several widely used methods showed that the proposed method had better performance in feature extraction and pattern classification. Overall, this study can be used for developing high-performance BCI systems, enabling individuals to control external devices intuitively and naturally. creator: Shan Guan creator: Jixian Li creator: Fuwang Wang creator: Zhen Yuan creator: Xiaogang Kang creator: Bin Lu uri: https://doi.org/10.7717/peerj.12027 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Guan et al. title: A new threat to local marine biodiversity: filamentous mats proliferating at mesophotic depths off Rapa Nui link: https://peerj.com/articles/12052 last-modified: 2021-08-24 description: Mesophotic and deeper habitats (∼40 to 350 m in depth) around Rapa Nui (Easter Island) were investigated using a remotely operated vehicle. We observed extensive fields of filamentous cyanobacteria-like mats covering sandy substrates and mostly dead mesophotic Leptoseris spp. reefs. These mats covered up to 100% of the seafloor off Hanga Roa, the main village on the island, located on its western side. The highest mortality of corals was observed at depths between 70 and 95 m in this area. Healthy Leptoseris reefs were documented off the northern and southeastern sides of the island, which are also the least populated. A preliminary morphologic analysis of samples of the mats indicated that the assemblage is composed of at least four filamentous taxa, including two cyanobacteria (cf. Lyngbya sp. and Pseudoanabaena sp.), a brown alga (Ectocarpus sp.), and a green alga (Cladophora sp.). An ongoing eutrophication process is suggested as a potential driver of the proliferation of these filamentous mats off Hanga Roa village. creator: Javier Sellanes creator: Matthias Gorny creator: Germán Zapata-Hernández creator: Gonzalo Alvarez creator: Praxedes Muñoz creator: Fadia Tala uri: https://doi.org/10.7717/peerj.12052 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sellanes et al. title: Full-length transcriptome analysis of Spodoptera frugiperda larval brain reveals detoxification genes link: https://peerj.com/articles/12069 last-modified: 2021-08-24 description: BackgroundSpodoptera frugiperda (J. E. Smith), commonly known as fall armyworm (FAW), is one of the most destructive agricultural pests in the world and has posed a great threat to crops. The improper use of insecticides has led to rapid development of resistance. However, the genetic data available for uncovering the insecticide resistance mechanisms are scarce.MethodsIn this study, we used PacBio single-molecule real-time (SMRT) sequencing aimed at revealing the full-length transcriptome profiling of the FAW larval brain to obtain detoxification genes.ResultsA total of 18,642 high-quality transcripts were obtained with an average length of 2,371 bp, and 11,230 of which were successfully annotated in six public databases. Among these, 5,692 alternative splicing events were identified. creator: Lei Yang creator: Binglin Xing creator: Fen Li creator: Li Kui Wang creator: Linlin Yuan creator: Amosi Leonard Mbuji creator: Zhengqiang Peng creator: Farag Malhat creator: Shaoying Wu uri: https://doi.org/10.7717/peerj.12069 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang et al. title: Prediction of the mechanism of miRNAs in laryngeal squamous cell carcinoma based on the miRNA-mRNA regulatory network link: https://peerj.com/articles/12075 last-modified: 2021-08-24 description: In this study, a bioinformatics analysis is conducted to screen differentially expressed miRNAs and mRNAs in laryngeal squamous cell carcinoma (LSCC). Based on this information, we explored the possible roles of miRNAs in the pathogenesis of LSCC. The RNA-Seq data from 79 laryngeal cancer samples in the Gene Expression Omnibus (GEO) database were sorted. Differentially expressed miRNAs and mRNAs in LSCC are screened using the PERL programming language, and it was analysed by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The miRNA-mRNA regulatory network of LSCC is constructed using Cytoscape software. Then, quantitative real-time PCR (QRT- PCR), Cell Counting Kit-8 (CCK8) and flow cytometry analysis we are used to further validate key miRNAs. We identified 99 differentially expressed miRNAs and 2,758 differentially expressed mRNAs in LSCC tissues from the GEO database. Four more important miRNAs displaying a high degree of connectivity are selected, these results suggest that they play an important role in the pathogenesis of LSCC. As shown in the present study, we identified specific miRNA-mRNA networks associated with the occurrence and development of LSCC through bioinformatics analysis. We found a miRNA molecule closely related to LSCC based on miRNA-mRNA network: miR-140-3p was down-regulated in LSCC. In addition, the potential antitumor effect of miR-140-3p in LSCC was verified in the experiment, and it was proved that overexpression of miR-140-3p could inhibit the proliferation of LSCC cells and promote cell apoptosis, suggesting that miR-140-3p may be a potential tumor marker in LSCC. creator: Jinhua Ma creator: Xiaodong Hu creator: Baoqiang Dai creator: Qiang Wang creator: Hongqin Wang uri: https://doi.org/10.7717/peerj.12075 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ma et al. title: StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs link: https://peerj.com/articles/11884 last-modified: 2021-08-23 description: Current studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs. Meanwhile, in metagenomic samples, resolving strain-level abundances is a major step in microbiome studies, as associations between strain variants and phenotype are of great interest for diagnostic and therapeutic purposes. We developed StrainFLAIR with the aim of showing the feasibility of using variation graphs for indexing highly similar genomic sequences up to the strain level, and for characterizing a set of unknown sequenced genomes by querying this graph. On simulated data composed of mixtures of strains from the same bacterial species Escherichia coli, results show that StrainFLAIR was able to distinguish and estimate the abundances of close strains, as well as to highlight the presence of a new strain close to a referenced one and to estimate its abundance. On a real dataset composed of a mix of several bacterial species and several strains for the same species, results show that in a more complex configuration StrainFLAIR correctly estimates the abundance of each strain. Hence, results demonstrated how graph representation of multiple close genomes can be used as a reference to characterize a sample at the strain level. creator: Kévin Da Silva creator: Nicolas Pons creator: Magali Berland creator: Florian Plaza Oñate creator: Mathieu Almeida creator: Pierre Peterlongo uri: https://doi.org/10.7717/peerj.11884 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Da Silva et al. title: Evaluation of a strawberry fermented beverage with potential health benefits link: https://peerj.com/articles/11974 last-modified: 2021-08-23 description: BackgroundFunctional fermented beverages are popular worldwide due to their potential to promote health. Starter culture is the main determinant of the final quality and flavor of fermented beverages. The co-cultivation of lactic acid bacteria (LAB) and yeast makes a significant contribution to the safe flavor of fermented beverages. However, the research on the potential of antioxidant, antimicrobial, and anti-biofilm formation of strawberry fermented beverage obtained by combining the LAB and yeast as starter cultures has not been well explored.MethodsIn this study, LAB and yeast were combined as starter culture to obtain strawberry fermented beverage. Fourier transform infrared (FTIR ) spectroscopy was used for the qualitative analysis of the fresh strawberry juice and fermented beverage. From the changes in antioxidant content, free radical scavenging ability, total superoxide dismutase (T-SOD) activity and total antioxidant capacity (T-AOC) to evaluate the antioxidant capacity of fermented beverage in vitro. The antibacterial ability was tested by the Oxford cup method. The biofilms of Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 6538 under fermented beverages treatment was observed by Fluorescence microscope. In addition, sensory analysis was conducted in this study.ResultsIn this study, the absorption peaks of Fourier transform infrared between 1,542 cm−1 and 976 cm−1, suggest the existence of organic acids, sugars and ethanol. The total phenols and total flavonoids content decreased by 91.1% and 97.5%, respectively. T-SOD activity increased by 33.33%.The scavenging ability of fermented beverage on superoxide anion free radicals was enhanced, and the scavenging ability on DPPH free radicals, hydroxyl free radicals, and ABTS free radicals was weakened. However, the T-AOC increased from 4.15 ± 0.81 to 8.43 ± 0.27 U/mL. Fermented beverage shows antibacterial activity against four pathogens. The minimum inhibitory concentration (MIC) values of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 6538 were 0.05 mL/mL and 0.025 mL/mL, respectively, and the minimum bactericidal concentration (MBC) were both 0.2 mL/mL. It was observed by fluorescence microscope that the green fluorescence area of the two biofilms is greatly reduced after being treated with fermented beverage. Sensory analysis results show that the average scores of fermented beverage in color, appearance and taste were increased. The overall impression and flavor were decreased.ConclusionThese results demonstrated that strawberry fermented beverage has potential benefits such as an antioxidant, antibacterial, and anti-biofilm formation, providing the potential for the fermented beverage to become promising candidates for natural antioxidants, antibacterial agents and anti-biofilm agents. creator: Zhiqiao Zhao creator: Xulong Wu creator: Hong Chen creator: Yuntao Liu creator: Yirong Xiao creator: Hui Chen creator: Zizhong Tang creator: Qingfeng Li creator: Huipeng Yao uri: https://doi.org/10.7717/peerj.11974 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhao et al.