title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=658 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Social calls in humpback whale mother-calf groups off Sainte Marie breeding ground (Madagascar, Indian Ocean) link: https://peerj.com/articles/13785 last-modified: 2022-08-16 description: Humpback whales (Megaptera novaeangliae) use vocalizations during diverse social interactions or activities such as foraging or mating. Unlike songs produced only by males, social calls are produced by all types of individuals (adult males and females, juveniles and calves). Several studies have described social calls in the humpback whale’s breeding and the feeding grounds and from different geographic areas. We aimed to investigate for the first time the vocal repertoire of humpback whale mother-calf groups during the breeding season off Sainte Marie island, Madagascar, South Western Indian Ocean using data collected in 2013, 2014, 2016, and 2017. We recorded social calls using Acousonde tags deployed on the mother or the calf in mother-calf groups. A total of 21 deployments were analyzed. We visually and aurally identified 30 social call types and classified them into five categories: low, medium, high-frequency sounds, amplitude-modulated sounds, and pulsed sounds. The aural-visual classifications have been validated using random forest (RF) analyses. Low-frequency sounds constituted 46% of all social calls, mid-frequency 35%, and high frequency 10%. Amplitude-modulated sounds constituted 8% of all vocalizations, and pulsed sounds constituted 1%. While some social call types seemed specific to our study area, others presented similarities with social calls described in other geographic areas, on breeding and foraging grounds, and during migrating routes. Among the call types described in this study, nine call types were also found in humpback whale songs recorded in the same region. The 30 call types highlight the diversity of the social calls recorded in mother-calf groups and thus the importance of acoustic interactions in the relationships between the mother and her calf and between the mother-calf pair and escorts. creator: Anjara Saloma creator: Maevatiana N. Ratsimbazafindranahaka creator: Mathilde Martin creator: Aristide Andrianarimisa creator: Chloé Huetz creator: Olivier Adam creator: Isabelle Charrier uri: https://doi.org/10.7717/peerj.13785 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Saloma et al. title: Processing of Noni Liquor based on response surface methodology link: https://peerj.com/articles/13817 last-modified: 2022-08-16 description: Noni (Morinda citrifolia L.) is widely used as a health food and medicine because it is rich in polysaccharides, polyphenols, and flavonoids; it is precisely because noni is rich in these substances that people usually like to soak it in liquor to drink. This study sought to maximize the main active constituents (polysaccharides, polyphenols, and flavonoid s) dissolved in liquor and spirits soaked with noni fruit, using ethanol as the solvent to optimize the extraction conditions using response surface methodology. The highest polysaccharide yield of 16.35% was found at 60 °C for 3.5 h, a liquid-solid ratio of 52 mL/g, and an ethanol concentration of 25%. The optimal extraction conditions for polyphenols were 75 °C for 1.5 h, a liquid-solid ratio of 90 mL/g, and an ethanol concentration of 50%, resulting in a 10.37% yield. The optimum extraction conditions for flavonoids were 75 °C for 1 h, a liquid-solid ratio of 70 mL/g, and an ethanol concentration of 100%, with 1.35% yield. Many active ingredients, including polysaccharides, polyphenols, and flavonoids, were obtained via alcohol extraction of noni fruit, suggesting that liquor and spirits soaked with noni fruit are novel and promising types. This study provides a technical reference for the production of high-quality noni liquor. It is recommended to use the best conditions for the extract of polysaccharides, polyphenols, and flavonoids, and blending them to obtain the desired degree of alcohol. creator: Shusen Gong creator: Fei Yang creator: Qingfen Wang creator: Tian Wu uri: https://doi.org/10.7717/peerj.13817 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Gong et al. title: Integrated bioinformatics analysis identifies the effects of Sema3A/NRP1 signaling in oligodendrocytes after spinal cord injury in rats link: https://peerj.com/articles/13856 last-modified: 2022-08-16 description: ObjectiveTo investigate the effect of Sema3A/NRP1 signaling in oligodendrocytes (OLs) after spinal cord injury.MethodsThree analysis strategies, namely differential expression gene analysis, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were applied. The protein-protein interaction (PPI) network was constructed using the STRING website to explore the correlation between Sema3A/NRP1 and oligodendrocytes. Then, the T10 spinal cord segment of rats was injured by the Allen method to establish a spinal cord injury (SCI) model. Real-time quantitative PCR, Western blotting, Nissl staining and immunofluorescence staining were used to detect the effect of Sema3A/NRP1 signaling on oligodendrocytes in vivo.ResultsAfter the SCI model was established, significantly fewer oligodendrocytes were observed. At the same time, R software was used to analyze the expression of related genes, and NRP1 expression was increased. PCR also demonstrated similar results, and NRP1 ligand Sema3A was also upregulated. KEGG and GO functional enrichment analysis indicated that the SCI model was mainly related to cytokine interaction, cell proliferation, differentiation and maturation. Interestingly, we found that NRP1 was involved in semaphorin-plexin signaling pathway neuronal projection guidance and axon guidance, mediating cell growth and migration. Moreover, Sema3A/NRP1 signaling was closely associated with platelet-derived growth factor receptor α (PDGFRα) in the PPI network. When Sema3A/NRP1 signaling was specifically blocked at early stages, PDGFRα expression was effectively inhibited, and the expression of OLs was promoted. Furthermore, inhibition of Sema3A/NRP1 signaling increased the Basso-Beattie-Bresnahan (BBB) score of lower limb motor function in SCI rats and promoted the survival of motor neurons in the ventral horn of the injured spinal cord.ConclusionOur data suggest that Sema3A/NRP1 signaling may regulate the development of OPCs and OLs after SCI, thereby affecting functional recovery. creator: Rong Hu creator: Mengting Shi creator: Haipeng Xu creator: Xingying Wu creator: Kelin He creator: Yi Chen creator: Lei Wu creator: Ruijie Ma uri: https://doi.org/10.7717/peerj.13856 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hu et al. title: Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdom Orthornavirae link: https://peerj.com/articles/13875 last-modified: 2022-08-16 description: Research on aquatic plant viruses is lagging behind that of their terrestrial counterparts. To address this knowledge gap, here we identified viruses associated with freshwater macrophytes, a taxonomically diverse group of aquatic phototrophs that are visible with the naked eye. We surveyed pooled macrophyte samples collected at four spring sites in Florida, USA through next generation sequencing of RNA extracted from purified viral particles. Sequencing efforts resulted in the detection of 156 freshwater macrophyte associated (FMA) viral contigs, 37 of which approximate complete genomes or segments. FMA viral contigs represent putative members from all five major phyla of the RNA viral kingdom Orthornavirae. Similar to viral types found in land plants, viral sequences identified in macrophytes were dominated by positive-sense RNA viruses. Over half of the FMA viral contigs were most similar to viruses reported from diverse hosts in aquatic environments, including phototrophs, invertebrates, and fungi. The detection of FMA viruses from orders dominated by plant viruses, namely Patatavirales and Tymovirales, indicate that members of these orders may thrive in aquatic hosts. PCR assays confirmed the presence of putative FMA plant viruses in asymptomatic vascular plants, indicating that viruses with persistent lifestyles are widespread in macrophytes. The detection of potato virus Y and oat blue dwarf virus in submerged macrophytes suggests that terrestrial plant viruses infect underwater plants and highlights a potential terrestrial-freshwater plant virus continuum. Defining the virome of unexplored macrophytes will improve our understanding of virus evolution in terrestrial and aquatic primary producers and reveal the potential ecological impacts of viral infection in macrophytes. creator: Karyna Rosario creator: Noémi Van Bogaert creator: Natalia B. López-Figueroa creator: Haris Paliogiannis creator: Mason Kerr creator: Mya Breitbart uri: https://doi.org/10.7717/peerj.13875 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rosario et al. title: Chemotherapeutic resistant cholangiocarcinoma displayed distinct intratumoral microbial composition and metabolic profiles link: https://peerj.com/articles/13876 last-modified: 2022-08-16 description: BackgroundCholangiocarcinoma (CCA) is a malignancy of the cholangiocytes. One of the major issues regarding treatment for CCA patients is the development of chemotherapeutic resistance. Recently, the association of intratumoral bacteria with chemotherapeutic response has been reported in many cancer types.MethodIn the present study, we aimed to investigate the association between the intratumoral microbiome and its function on gemcitabine and cisplatin response in CCA tissues using 16S rRNA sequencing and 1H NMR spectroscopic analysis.ResultThe results of 16S rRNA sequencing demonstrated that Gammaproteobacteria were significantly higher in both gemcitabine- and cisplatin-resistance groups compared to sensitive groups. In addition, intratumoral microbial diversity and abundance were significantly different compared between gemcitabine-resistant and sensitive groups. Furthermore, the metabolic phenotype of the low dose gemcitabine-resistant group significantly differed from that of low dose gemcitabine-sensitive group. Increased levels of acetylcholine, adenine, carnitine and inosine were observed in the low dose gemcitabine-resistant group, while the levels of acetylcholine, alpha-D-glucose and carnitine increased in the low dose cisplatin-resistant group. We further performed the intergrative microbiome-metabolome analysis and revealed a correlation between the intratumoral bacterial and metabolic profiles which reflect the chemotherapeutics resistance pattern in CCA patients.ConclusionOur results demonstrated insights into the disruption of the microbiome and metabolome in the progression of chemotherapeutic resistance. The altered microbiome-metabolome fingerprints could be used as predictive markers for drug responses potentially resulting in the development of an appropriate chemotherapeutic drug treatment plan for individual CCA patients. creator: Sirinya Sitthirak creator: Manida Suksawat creator: Jutarop Phetcharaburanin creator: Arporn Wangwiwatsin creator: Poramate Klanrit creator: Nisana Namwat creator: Narong Khuntikeo creator: Attapol Titapun creator: Apiwat Jarearnrat creator: Sakkarn Sangkhamanon creator: Watcharin Loilome uri: https://doi.org/10.7717/peerj.13876 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sitthirak et al. title: The effects of brodifacoum cereal bait pellets on early life stages of the rice coral Montipora capitata link: https://peerj.com/articles/13877 last-modified: 2022-08-16 description: Midway Atoll in the Northwestern Hawaiian Islands is home to ground nesting birds that are threatened by invasive mice. Planned rodent eradication efforts for the island involve aerial application of cereal bait pellets containing the chemical rodenticide brodifacoum. Given the nature of the application method, drift of cereal bait pellets into the coastal waters surrounding Midway Atoll is unavoidable. To understand whether cereal bait pellets impact marine invertebrates, gametes and larvae of the reef-building coral Montipora capitata were exposed to brodifacoum, cereal bait pellets containing brodifacoum, and inert cereal bait pellets without the rodenticide. Fertilization success and larval survival were assessed at nominal brodifacoum concentrations of 1, 10, and 100 ppb. Fertilization success decreased by 15% after exposure to 100 ppb brodifacoum solutions. Larval survival was not reduced by exposure to brodifacoum solutions. Cereal bait pellets containing brodifacoum reduced fertilization success at 10 ppb brodifacoum in 0.4 g per L pellet solutions by 34.84%, and inhibited fertilization at 100 ppb brodifacoum in 4 g of pellet per L solution. Inert cereal bait pellets had similar effects, reducing fertilization success at 0.4 g of pellet per L by 40.50%, and inhibiting fertilization at 4 g per L pellet solutions. Larval survival was reduced by >43% after prolonged exposure to 4 g per L pellet solutions. The highest concentration used in this study was meant to represent an extreme and unlikely condition resulting from an accidental spill. Our findings indicate large amounts of cereal bait pellets entering the coastal environment of Midway Atoll, if occurring during a coral spawning event, would reduce coral reproduction by decreasing fertilization success. It is difficult to know the ecologically relevant concentrations of cereal bait pellets in coastal environments due to unavoidable bait drift after land applications, but results indicate small amounts of pellet drifting into coastal environments would not severely reduce coral reproductive capacity. Best management practices should consider known coral reproductive periods when scheduling applications of pellets on tropical islands to reduce the risk of negative impacts of large-scale accidents on corals. creator: Alexandria L. Barkman creator: Robert H. Richmond uri: https://doi.org/10.7717/peerj.13877 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Barkman and Richmond title: Catch composition and risk assessment of two fishing gears used in small-scale fisheries of Bandon Bay, the Gulf of Thailand link: https://peerj.com/articles/13878 last-modified: 2022-08-16 description: We examined catch compositions and vulnerability of target and bycatch species in two fishing gears, namely the bottom-set gillnet and collapsible crab trap, used in small-scale fisheries of Bandon Bay, Suratthani Province, Thailand. Both gears mainly target the blue swimming crab (BSC) Portunus pelagicus, and together contribute about half of Thailand’s annual BSC catch of around 2.5 thousand tonnes. Field sampling was conducted from January to November of 2018. Specimens from bottom-set gillnets and collapsible crab traps comprised 111 and 118 taxa, respectively. Of these, 26 and 27 crab species and 41 and 46 fish species were collected by gillnets and traps, respectively. The index of relative importance of BSC was higher in gillnets (48.8 ± 16.6%) than in traps (25.0 ± 15.5%), where another swimming crab (Charybdis affinis) was more common. Cluster analysis revealed that catch compositions were seasonal and differed between the two monsoonal seasons, i.e., northeast monsoon (October to February) and southwest monsoon (May to September), and the transition period (March and April). Potential impact from both fishing gears on various stocks was assessed by standard productivity and susceptibility analysis (PSA). Vulnerability scores of the BSC stock as the main target species suggested it was at moderate risk, as assessed by PSA. The impacts of both gears to stocks of the other species in Bandon Bay showed either low or moderate risk. Ten fish stocks, including two stingrays, six species of sole and two other bony fishes, were near the threshold of high risk from gillnet fishing. creator: Tuantong Jutagate creator: Amonsak Sawusdee uri: https://doi.org/10.7717/peerj.13878 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jutagate and Sawusdee title: Rainforest conversion to rubber and oil palm reduces abundance, biomass and diversity of canopy spiders link: https://peerj.com/articles/13898 last-modified: 2022-08-16 description: Rainforest canopies, home to one of the most complex and diverse terrestrial arthropod communities, are threatened by conversion of rainforest into agricultural production systems. However, little is known about how predatory arthropod communities respond to such conversion. To address this, we compared canopy spider (Araneae) communities from lowland rainforest with those from three agricultural systems in Jambi Province, Sumatra, Indonesia, i.e., jungle rubber (rubber agroforest) and monoculture plantations of rubber and oil palm. Using canopy fogging, we collected 10,676 spider specimens belonging to 36 families and 445 morphospecies. The four most abundant families (Salticidae N = 2,043, Oonopidae N = 1,878, Theridiidae N = 1,533 and Clubionidae N = 1,188) together comprised 62.2% of total individuals, while the four most speciose families, Salticidae (S = 87), Theridiidae (S = 83), Araneidae (S = 48) and Thomisidae (S = 39), contained 57.8% of all morphospecies identified. In lowland rainforest, average abundance, biomass and species richness of canopy spiders was at least twice as high as in rubber or oil palm plantations, with jungle rubber showing similar abundances as rainforest, and intermediate biomass and richness. Community composition of spiders was similar in rainforest and jungle rubber, but differed from rubber and oil palm, which also differed from each other. Canonical Correspondence Analysis showed that canopy openness, aboveground tree biomass and tree density together explained 18.2% of the variation in spider communities at family level. On a morphospecies level, vascular plant species richness and tree density significantly affected the community composition but explained only 6.8% of the variance. While abundance, biomass and diversity of spiders declined strongly with the conversion of rainforest into monoculture plantations of rubber and oil palm, we also found that a large proportion of the rainforest spider community can thrive in extensive agroforestry systems such as jungle rubber. Despite being very different from rainforest, the canopy spider communities in rubber and oil palm plantations may still play a vital role in the biological control of canopy herbivore species, thus contributing important ecosystem services. The components of tree and palm canopy structure identified as major determinants of canopy spider communities may aid in decision-making processes toward establishing cash-crop plantation management systems which foster herbivore control by spiders. creator: Daniel Ramos creator: Tamara R. Hartke creator: Damayanti Buchori creator: Nadine Dupérré creator: Purnama Hidayat creator: Mayanda Lia creator: Danilo Harms creator: Stefan Scheu creator: Jochen Drescher uri: https://doi.org/10.7717/peerj.13898 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ramos et al. title: Building a synthesis of economic costs of biological invasions in New Zealand link: https://peerj.com/articles/13580 last-modified: 2022-08-15 description: Biological invasions are a major component of anthropogenic environmental change, incurring substantial economic costs across all sectors of society and ecosystems. There have been recent syntheses of costs for a number of countries using the newly compiled InvaCost database, but New Zealand—a country renowned for its approach to invasive species management—has so far not been examined. Here we analyse reported economic damage and management costs incurred by biological invasions in New Zealand from 1968 to 2020. In total, US$69 billion (NZ$97 billion) is currently reported over this ∼50-year period, with approximately US$9 billion of this considered highly reliable, observed (c.f. projected) costs. Most (82%) of these observed economic costs are associated with damage, with comparatively little invested in management (18%). Reported costs are increasing over time, with damage averaging US$120 million per year and exceeding management expenditure in all decades. Where specified, most reported costs are from terrestrial plants and animals, with damages principally borne by primary industries such as agriculture and forestry. Management costs are more often associated with interventions by authorities and stakeholders. Relative to other countries present in the InvaCost database, New Zealand was found to spend considerably more than expected from its Gross Domestic Product on pre- and post-invasion management costs. However, some known ecologically (c.f. economically) impactful invasive species are notably absent from estimated damage costs, and management costs are not reported for a number of game animals and agricultural pathogens. Given these gaps for known and potentially damaging invaders, we urge improved cost reporting at the national scale, including improving public accessibility through increased access and digitisation of records, particularly in overlooked socioeconomic sectors and habitats. This also further highlights the importance of investment in management to curtail future damages across all sectors. creator: Thomas W. Bodey creator: Zachary T. Carter creator: Phillip J. Haubrock creator: Ross N. Cuthbert creator: Melissa J. Welsh creator: Christophe Diagne creator: Franck Courchamp uri: https://doi.org/10.7717/peerj.13580 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bodey et al. title: Neighborhood-based inference and restricted Boltzmann machine for microbe and drug associations prediction link: https://peerj.com/articles/13848 last-modified: 2022-08-15 description: BackgroundEfficient identification of microbe-drug associations is critical for drug development and solving problem of antimicrobial resistance. Traditional wet-lab method requires a lot of money and labor in identifying potential microbe-drug associations. With development of machine learning and publication of large amounts of biological data, computational methods become feasible.MethodsIn this article, we proposed a computational model of neighborhood-based inference (NI) and restricted Boltzmann machine (RBM) to predict potential microbe-drug association (NIRBMMDA) by using integrated microbe similarity, integrated drug similarity and known microbe-drug associations. First, NI was used to obtain a score matrix of potential microbe-drug associations by using different thresholds to find similar neighbors for drug or microbe. Second, RBM was employed to obtain another score matrix of potential microbe-drug associations based on contrastive divergence algorithm and sigmoid function. Because generalization ability of individual method is poor, we used an ensemble learning to integrate two score matrices for predicting potential microbe-drug associations more accurately. In particular, NI can fully utilize similar (neighbor) information of drug or microbe and RBM can learn potential probability distribution hid in known microbe-drug associations. Moreover, ensemble learning was used to integrate individual predictor for obtaining a stronger predictor.ResultsIn global leave-one-out cross validation (LOOCV), NIRBMMDA gained the area under the receiver operating characteristics curve (AUC) of 0.8666, 0.9413 and 0.9557 for datasets of DrugVirus, MDAD and aBiofilm, respectively. In local LOOCV, AUCs of 0.8512, 0.9204 and 0.9414 were obtained for NIRBMMDA based on datasets of DrugVirus, MDAD and aBiofilm, respectively. For five-fold cross validation, NIRBMMDA acquired AUC and standard deviation of 0.8569 ± −0.0027, 0.9248 ± −0.0014 and 0.9369 ± −0.0020 on the basis of datasets of DrugVirus, MDAD and aBiofilm, respectively. Moreover, case study for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showed that 13 out of the top 20 predicted drugs were verified by searching literature. The other two case studies indicated that 17 and 17 out of the top 20 predicted microbes for the drug of ciprofloxacin and minocycline were confirmed by identifying published literature, respectively. creator: Xiaolong Cheng creator: Jia Qu creator: Shuangbao Song creator: Zekang Bian uri: https://doi.org/10.7717/peerj.13848 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cheng et al.