title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=851 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Reef manta rays forage on tidally driven, high density zooplankton patches in Hanifaru Bay, Maldives link: https://peerj.com/articles/11992 last-modified: 2021-08-23 description: Manta rays forage for zooplankton in tropical and subtropical marine environments, which are generally nutrient-poor. Feeding often occurs at predictable locations where these large, mobile cartilaginous fishes congregate to exploit ephemeral productivity hotspots. Investigating the zooplankton dynamics that lead to such feeding aggregations remains a key question for understanding their movement ecology. The aim of this study is to investigate the feeding environment at the largest known aggregation for reef manta rays Mobula alfredi in the world. We sampled zooplankton throughout the tidal cycle, and recorded M. alfredi activity and behaviour, alongside environmental variables at Hanifaru Bay, Maldives. We constructed generalised linear models to investigate possible relationships between zooplankton dynamics, environmental parameters, and how they influenced M. alfredi abundance, behaviour, and foraging strategies. Zooplankton biomass changed rapidly throughout the tidal cycle, and M. alfredi feeding events were significantly related to high zooplankton biomass. Mobula alfredi switched from non-feeding to feeding behaviour at a prey density threshold of 53.7 mg dry mass m−3; more than double the calculated density estimates needed to theoretically meet their metabolic requirements. The highest numbers of M. alfredi observed in Hanifaru Bay corresponded to when they were engaged in feeding behaviour. The community composition of zooplankton was different when M. alfredi was feeding (dominated by copepods and crustaceans) compared to when present but not feeding (more gelatinous species present than in feeding samples). The dominant zooplankton species recorded was Undinula vulgaris. This is a large-bodied calanoid copepod species that blooms in oceanic waters, suggesting offshore influences at the site. Here, we have characterised aspects of the feeding environment for M. alfredi in Hanifaru Bay and identified some of the conditions that may result in large aggregations of this threatened planktivore, and this information can help inform management of this economically important marine protected area. creator: Asia O. Armstrong creator: Guy M.W. Stevens creator: Kathy A. Townsend creator: Annie Murray creator: Michael B. Bennett creator: Amelia J. Armstrong creator: Julian Uribe-Palomino creator: Phil Hosegood creator: Christine L. Dudgeon creator: Anthony J. Richardson uri: https://doi.org/10.7717/peerj.11992 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Armstrong et al. title: Diclofenac toxicity in susceptible bird species results from a combination of reduced glomerular filtration and plasma flow with subsequent renal tubular necrosis link: https://peerj.com/articles/12002 last-modified: 2021-08-23 description: Diclofenac caused the death of millions of vultures on the Asian subcontinent. Other non-steroidal anti-inflammatory drugs (NSAIDs) have since also been shown to be toxic to vultures with the exception of meloxicam. For this study, we evaluated the effect of diclofenac on renal uric acid transport and glomerulus filtration in an acute toxicity model. In a two-phase study with the same birds, healthy chickens (a validated model species) were treated intravenously with para-amino hippuric acid (PAH) and iohexol (IOH) in combination in phase 1. In phase 2, the same PAH and IOH combination was then combined with diclofenac (10 mg/kg). In both phases, blood and faeces were sequentially collected. In phase 1, the birds showed no signs of ill health. Moreover, PAH, IOH and uric acid clearance was rapid. In phase 2, two chickens showed early signs of hyperuricemia 8 hours after exposure and died approximately 24h later. Necropsy showed classic signs of renal damage and gout. Diclofenac had a rapid plasma half-life of elimination of less than 2 hours indicating that toxicity was likely due to an irreversible destruction of a physiological process. All the birds in phase 2 had decreased uric acid, PAH and IOH clearance in comparison to phase 1. The decrease in PAH clearance was variable between the birds (average of 71%) but was near 98% reduced in the two birds that died. It is concluded that diclofenac alters both renal perfusion and renal plasma flow, with death associated with tubular secretion being reduced to negligible functionality for a prolonged period. This would support previous in vitro findings of early cell death from ROS accumulation. However, further evaluation is needed to elucidate this final step. creator: Bono Nethathe creator: John Chipangura creator: Ibrahim Zubairu Hassan creator: Neil Duncan creator: Emmanuel Oluwasegun Adawaren creator: Lauren Havenga creator: Vinny Naidoo uri: https://doi.org/10.7717/peerj.12002 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Nethathe et al. title: Effects of drip tape modes on soil hydrothermal conditions and cotton yield (Gossypium hirsutum L.) under machine-harvest patterns link: https://peerj.com/articles/12004 last-modified: 2021-08-23 description: BackgroundThe layout of drip tapes under mulch has changed in Xinjiang, China, with the development of machine-harvest cotton (Gossypium hirsutum L.) planting technology. This study aims to demonstrate the effects of drip tape modes on soil hydrothermal conditions, cotton yield, and water use efficiency (WUE) of machine-harvest cotton under mulch in Xinjiang.MethodsA field experiment was conducted to set up two machine-harvest cotton planting patterns (T1: the cotton planting model with one film, two drip tapes and six rows; T2: the cotton planting model with one film, three drip tapes and six rows), and a conventional planting mode (T3: the cotton planting model with one film, two drip tapes and four rows) as a control.ResultsOur results showed that the heat preservation and warming effects of the cotton planting model with one film, two drip tapes and six rows and the cotton planting model with one film, three drip tapes and six rows were better than that of the conventional planting mode. Soil temperature under the mulching film quickly increased and slowly decreased, which was beneficial to the early growth and development of cotton. The mean soil moisture content of the 0–60 cm soil layer in the cotton planting model with one film, three drip tapes and six rows was significantly higher than the other two treatments at the middle and late stage of cotton growth (90 days after sowing (DAS) and 135 DAS). Moreover, the water holding capacity of the middle and upper part of the tillage layer in the cotton planting model with one film, three drip tapes and six rows was the best. At the medium cotton growth stage, the main root layer in the cotton planting model with one film, three drip tapes and six rows formed a desalination zone. At the late cotton growth stage, the soil salinity content of the 0–60 cm soil layer showed that the cotton planting model with one film, three drip tapes and six rows was the lowest, the cotton planting model with one film, two drip tapes and six rows was the highest, and the conventional planting pattern was in the middle. Among these three modes, the cotton planting model with one film, three drip tapes and six rows was more efficient in controlling soil salt accumulation. The agronomic traits and cotton quality in the cotton planting model with one film, three drip tapes and six rows were better than that for the other two treatments. Compared with the other treatments, the cotton yield in the cotton planting model with one film, three drip tapes and six rows increased by 6.15% and 11.0% and 8.1% and 12.3%, in 2017 and 2018, respectively, and WUE increased by 17.4% and 22.7% and 20.9% and 22.8%, in 2017 and 2018 respectively. In conclusion, the cotton planting model with one film, three drip tapes and six rows can be recommended for machine-harvest cotton planting for arid areas in Xinjiang, considering water conservation and improving cotton yield. creator: Dongwang Wang creator: Zhenhua Wang creator: Tingbo Lv creator: Rui Zong creator: Yan Zhu creator: Jinzhu Zhang creator: Tianyu Wang uri: https://doi.org/10.7717/peerj.12004 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: First report of leopard fossils from a limestone cave in Kenting area, southern Taiwan link: https://peerj.com/articles/12020 last-modified: 2021-08-23 description: Longshia-dong Cave, a limestone cave located in the Kenting area within the Kenting National Park of southern Taiwan, yields numerous terrestrial mammalian fossils. Many of them were not reported in historical literature and are neither present in Taiwan. For instance, no historical literature mentioned leopards inhabited in Taiwan, and thus their existence remained unknown. This study describes three fossil leopard (Panthera pardus) teeth uncovered from Longshia-dong Cave. Two isolated lower premolars and one lower molar, respectively p3, p4 and m1, were discovered in a very small area (11 × 6 cm) and show a series of progressive increase in size. Thus, the three teeth should have been belonging to the same individual from the subfamily of Pantherinae. Traditional linear measurements and two-dimensional geometric morphometric analysis for the occlusal surface outlines were conducted on the fossil teeth and extant pantherines inhabited in Asia such as clouded leopards (Neofelis nebulosa), leopards (Panthera pardus), and tigers (Panthera tigiris). Results show that the fossil teeth are similar both in size and morphology to the teeth of extant leopards, suggesting the assignment of the fossil teeth to leopards. This study, for the first time, reported the presence of leopards in the Late Pleistocene of Taiwan. In addition, the smaller size of the fossil teeth in comparison with Chinese fossil leopards is putatively attributed to insular dwarfism or individual size variability, yet more studies are required. creator: Tzu-Chin Chi creator: Yi Gan creator: Tzu-Ruei Yang creator: Chun-Hsiang Chang uri: https://doi.org/10.7717/peerj.12020 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chi et al. title: covid19.Explorer: a web application and R package to explore United States COVID-19 data link: https://peerj.com/articles/11489 last-modified: 2021-08-20 description: Appearing at the end of 2019, a novel virus (later identified as SARS-CoV-2) was characterized in the city of Wuhan in Hubei Province, China. As of the time of writing, the disease caused by this virus (known as COVID-19) has already resulted in over three million deaths worldwide. SARS-CoV-2 infections and deaths, however, have been highly unevenly distributed among age groups, sexes, countries, and jurisdictions over the course of the pandemic. Herein, I present a tool (the covid19.Explorer R package and web application) that has been designed to explore and analyze publicly available United States COVID-19 infection and death data from the 2020/21 U.S. SARS-CoV-2 pandemic. The analyses and visualizations that this R package and web application facilitate can help users better comprehend the geographic progress of the pandemic, the effectiveness of non-pharmaceutical interventions (such as lockdowns and other measures, which have varied widely among U.S. states), and the relative risks posed by COVID-19 to different age groups within the U.S. population. The end result is an interactive tool that will help its users develop an improved understanding of the temporal and geographic dynamics of the SARS-CoV-2 pandemic, accessible to lay people and scientists alike. creator: Liam J. Revell uri: https://doi.org/10.7717/peerj.11489 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Revell