title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=652 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Nitrate enrichment does not affect enteropathogenic Escherichia coli in aquatic microcosms but may affect other strains present in aquatic habitats link: https://peerj.com/articles/13914 last-modified: 2022-09-27 description: Eutrophication of the planet’s aquatic systems is increasing at an unprecedented rate. In freshwater systems, nitrate—one of the nutrients responsible for eutrophication—is linked to biodiversity losses and ecosystem degradation. One of the main sources of freshwater nitrate pollution in New Zealand is agriculture. New Zealand’s pastoral farming system relies heavily on the application of chemical fertilisers. These fertilisers in combination with animal urine, also high in nitrogen, result in high rates of nitrogen leaching into adjacent aquatic systems. In addition to nitrogen, livestock waste commonly carries human and animal enteropathogenic bacteria, many of which can survive in freshwater environments. Two strains of enteropathogenic bacteria found in New Zealand cattle, are K99 and Shiga-toxin producing Escherichia coli (STEC). To better understand the effects of ambient nitrate concentrations in the water column on environmental enteropathogenic bacteria survival, a microcosm experiment with three nitrate-nitrogen concentrations (0, 1, and 3 mg NO3-N /L), two enteropathogenic bacterial strains (STEC O26—human, and K99—animal), and two water types (sterile and containing natural microbiota) was run. Both STEC O26 and K99 reached 500 CFU/10 ml in both water types at all three nitrate concentrations within 24 hours and remained at those levels for the full 91 days of the experiment. Although enteropathogenic strains showed no response to water column nitrate concentrations, the survival of background Escherichia coli, imported as part of the in-stream microbiota did, surviving longer in 1 and 3 mg NO3-N/Lconcentrations (P < 0.001). While further work is needed to fully understand how nitrate enrichment and in-stream microbiota may affect the viability of human and animal pathogens in freshwater systems, it is clear that these two New Zealand strains of STEC O26 and K99 can persist in river water for extended periods alongside some natural microbiota. creator: Meredith T. Davis creator: Adam D. Canning creator: Anne C. Midwinter creator: Russell G. Death uri: https://doi.org/10.7717/peerj.13914 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Davis et al. title: Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus link: https://peerj.com/articles/13953 last-modified: 2022-09-26 description: BackgroundThe order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna.MethodsTo confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the “primer-walking” method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship.ResultsThe three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1. creator: Regina L. Cunha creator: Katy R. Nicastro creator: Gerardo I. Zardi creator: Celine Madeira creator: Christopher D. McQuaid creator: Cymon J. Cox creator: Rita Castilho uri: https://doi.org/10.7717/peerj.13953 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cunha et al. title: Presence of leptin and its receptor in the ram reproductive system and in vitro effect of leptin on sperm quality link: https://peerj.com/articles/13982 last-modified: 2022-09-26 description: Leptin is a 16 kDa hormone encoded by obese (OB) gene in adipocytes. This molecule not only regulates energy metabolism but also plays a role in the reproduction of mammals. Leptin and its receptor (OBR) have been found in male reproductive systems of human, bovine, equine and pig. The effects of leptin on sperm quality vary widely from different research findings. However, the presence of leptin and its receptor in the ram reproductive system and the in vitro effect of leptin on sperm quality have not reported yet. In the present study, we found that the OB was highly expressed in primary and secondary spermatocytes of the testes, OBR was highly expressed in secondary spermatocytes of the testes. The expressions of OB were in stereocilia of epididymis and in columnar cells of epididymal caput and cauda, the expressions of OBR were in columnar cells of epididymis and in stereocilia of epididymal corpus and cauda. The presence of both OB and OBR in testes, epididymis and sperm were confirmed through RT-PCR, immunolocalization and Western blot analyses. The RT-qPCR results indicated OB and OBR had higher expression levels in epididymal sperm than that of the ejaculated sperm in rams. When sperm were treated with 5 ng/mL leptin, the progressive motility (P < 0.01), straight-line velocity (VSL) (P < 0.05), average path velocity (VAP) (P < 0.05), membrane mitochondrial potential (MMP) (P < 0.01) and viability (P < 0.05) significantly increased, while DNA fragmentation index (DFI) and reactive oxygen species (ROS) significantly decreased compared to the control (P < 0.01), and the other semen parameters such as acrosome integrity and acrosome reaction rate had no significant changes between groups (P > 0.05). In conclusion, this is probably the first report describing localization of leptin and its receptors in the reproductive system of rams and their effects on sperm quality parameters. Our findings suggest that 5 ng/mL leptin treatment enhanced sperm motility, viability and MMP, and decrease DFI and ROS without obvious influence on the acrosome reaction in ram sperm. The potential mechanisms may be related to leptin’s ability to reduce the oxidative stress and apoptosis of sperms and improve their mitochondrial function and energy supply, therefore, to maintain the physiological homeostasis of the sperm. creator: Yu Gao creator: Guodong Zhao creator: Yukun Song creator: Aerman Haire creator: Ailing Yang creator: Xi Zhao creator: Abulizi Wusiman uri: https://doi.org/10.7717/peerj.13982 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gao et al. title: Avoidance of copper by fathead minnows (Pimephales promelas) requires an intact olfactory system link: https://peerj.com/articles/13988 last-modified: 2022-09-26 description: Fish can detect and respond to a wide variety of cations in their environment, including copper. Most often fish will avoid copper during behavioural trials; however, fish may also show no response or an attraction response, depending on the concentration(s) used. While it may seem intuitive that the response to copper requires olfaction, there is little direct evidence to support this, and what evidence there is remains incomplete. In order to test if olfaction is required for avoidance of copper by fathead minnows (Pimephales promelas) copper-induced movement was compared between fish with an intact olfactory system and fish with induced anosmia. Fish in a control group or a mock-anosmic group avoided copper (approximately 10 µg/L or 62.7 nM copper sulphate) while anosmic fish did not. The evidence demonstrates that an intact olfactory system is required for copper sensing in fish. creator: Rubab Fatima creator: Robert Briggs creator: William A. Dew uri: https://doi.org/10.7717/peerj.13988 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Fatima et al. title: What’s the effectiveness of stocking actions in small creeks? The role of water discharge behind hatchery trout downstream movement link: https://peerj.com/articles/14069 last-modified: 2022-09-26 description: Fish stocking to enhance freshwater fisheries or to improve the conservation status of endangered fish species is a common practice in many countries. Little is known, however, of the effectiveness of these practices in spite of the high efforts and investments required. The movement of subadult/adult hatchery-released brown trout Salmo trutta L. was studied by passive telemetry in a small tributary of Lake Lugano (i.e., Laveggio Creek, Canton Ticino, Switzerland). Hatchery fish, together with some resident wild individuals sampled during electrofishing surveys, were tagged with Passive Integrated Transponders (PIT) tags. Hatchery fish were released upstream and downstream a submersible monitoring antenna, which was anchored to the streambed in a pass-over orientation. The number of hatchery fish detected daily by the antenna (divided between fish released upstream and downstream the antenna) was analyzed in relation to the daily water discharge, to search for similar patterns in their fluctuation over time. Only the movement of fish released upstream the antenna displayed a significant relationship with water discharge, with the highest number of fish detected during periods of high-water flow, occurring after heavy rains. High-water discharge events had a significant role in hatchery trout downstream movement in our study site, likely acting as a driver for the downstream migration to Lake Lugano. Such events contributed to the poor effectiveness of stocking actions in this small tributary, providing further evidence against stocking strategies based on subadult/adult fish. creator: Stefano Brignone creator: Vanessa De Santis creator: Tiziano Putelli creator: Christophe Molina creator: Armando Piccinini creator: Richard A. Carmichael creator: Pietro Volta uri: https://doi.org/10.7717/peerj.14069 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Brignone et al. title: Improved response inhibition induced by attentional capture is associated with physical activity link: https://peerj.com/articles/14083 last-modified: 2022-09-26 description: The ability to stop a response promptly when a stop signal is presented is named response inhibition. It is generally accepted that the process of response inhibition requires a subject to pay attention to the stop instruction and then cancel the action. A wealth of converging evidence suggests that physical activity (PA) can promote response inhibition, but the potential contributions of attentional capture to the relationship between PA and response inhibition are currently unknown. In this study, the standard stop-signal task (SST) and two novel versions of the SST were used to solve this gap. A total of 58 college students were divided into a higher PA group and a lower PA group, respectively. In Experiment 1, the classical SST determined that the participants in the higher PA group displayed a significantly faster stop-signal reaction time (SSRT) than those in the lower PA group. Experiment 2 separated the attentional capture in the SST and revealed that the participants in the higher PA group could detect the signal faster than those in the lower PA group. Experiment 3 further added a stop signal to Experiment 2 and demonstrated that the participants in the higher PA group could more effectively deploy attentional resources to complete the task. Overall, these findings indicate that PA is positively associated with response inhibition and that the positive relationship is associated with effective allocation of attentional resources for faster attentional capture. creator: Hao Zhu creator: Jiuyang Xu creator: Yue Zheng creator: Guiping Jiang creator: Xinyi Huang creator: Xiaohuan Tan creator: Xueping Wu uri: https://doi.org/10.7717/peerj.14083 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhu et al. title: Does quality of novice hand-tied square knots improve with repetition during a single training session? link: https://peerj.com/articles/14106 last-modified: 2022-09-26 description: BackgroundKnot tying is a key surgical skill for novices, and repetition over several training sessions improves knot tying. This study examined the effects of repetition within a single training session on quality of knotted loops and compared results of novice trainees and experienced surgeons.MethodsUsing 0.55 mm nylon monofilament fishing line, novices and surgeons each hand-tied 20 knotted loops, using a 2=1=1=1 configuration (surgeon’s throw and three square throws). Loops were mechanically tested with a single load to failure.ResultsAll loops tolerated five newtons (N) preload. More than 70% of novice and surgeon knots failed by slipping or untying, and 8.8% of novice knots and 2.5% of surgeon’s knots were considered dangerous. Surgeons’ loops had less extension at preload, indicating better loop security. However, during single test to failure, there was no difference in mean extension or maximum load between surgeons and novices. There was no significant difference in results of mechanical testing or modes of failure for the first and last ten knotted loops, or the first, second, third, and fourth sets of knotted loops.DiscussionWith appropriate training, novices can construct knots as strong and secure as experienced surgeons. A large percentage of knotted loops are insecure under testing conditions; extra throws may be required when using large diameter monofilament nylon. Novices may require extra training in maintenance of loop security when constructing square knots. Tying more than five or 10 knotted loops within a single training session does not provide added benefits for novices. creator: Karen Tobias creator: Pierre-Yves Mulon creator: Alec Daniels creator: Xiaocun Sun uri: https://doi.org/10.7717/peerj.14106 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tobias et al. title: Hidden interactions in the intertidal rocky shore: variation in pedal mucus microbiota among marine grazers that feed on epilithic biofilm communities link: https://peerj.com/articles/13642 last-modified: 2022-09-23 description: In marine ecosystems, most invertebrates possess diverse microbiomes on their external surfaces, such as those found in the pedal mucus of grazing gastropods and chitons that aids displacement on different surfaces. The microbes are then transported around and placed in contact with free-living microbial communities of micro and other macro-organisms, potentially exchanging species and homogenizing microbial composition and structure among grazer hosts. Here, we characterize the microbiota of the pedal mucus of five distantly related mollusk grazers, quantify differences in microbial community structure, mucus protein and carbohydrate content, and, through a simple laboratory experiment, assess their effects on integrated measures of biofilm abundance. Over 665 Amplicon Sequence Variants (ASVs) were found across grazers, with significant differences in abundance and composition among grazer species and epilithic biofilms. The pulmonate limpet Siphonaria lessonii and the periwinkle Echinolittorina peruviana shared similar microbiota. The microbiota of the chiton Chiton granosus, keyhole limpet Fissurella crassa, and scurrinid limpet Scurria araucana differed markedly from one another, and form those of the pulmonate limpet and periwinkle. Flavobacteriaceae (Bacteroidia) and Colwelliaceae (Gammaproteobacteria) were the most common among microbial taxa. Microbial strict specialists were found in only one grazer species. The pedal mucus pH was similar among grazers, but carbohydrate and protein concentrations differed significantly. Yet, differences in mucus composition were not reflected in microbial community structure. Only the pedal mucus of F. crassa and S. lessonii negatively affected the abundance of photosynthetic microorganisms in the biofilm, demonstrating the specificity of the pedal mucus effects on biofilm communities. Thus, the pedal mucus microbiota are distinct among grazer hosts and can affect and interact non-trophically with the epilithic biofilms on which grazers feed, potentially leading to microbial community coalescence mediated by grazer movement. Further studies are needed to unravel the myriad of non-trophic interactions and their reciprocal impacts between macro- and microbial communities. creator: Clara Arboleda-Baena creator: Claudia Belén Pareja creator: Isadora Pla creator: Ramiro Logares creator: Rodrigo De la Iglesia creator: Sergio Andrés Navarrete uri: https://doi.org/10.7717/peerj.13642 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Arboleda-Baena et al. title: Utilizing network pharmacology and experimental validation to investigate the underlying mechanism of phellodendrine on inflammation link: https://peerj.com/articles/13852 last-modified: 2022-09-23 description: BackgroundPhellodendrine, one of the characteristic and important active components of Cortex phellodendri, has been proven to show anti-inflammatory effects. However, the underlying mechanism of phellodendrine on inflammation remains largely unclear.Aim of the studyIn this study, network pharmacology and experimental validation were used to explore the underlying mechanism of phellodendrine on inflammation.Materials and MethodsPubChem and SwissADME database were used to evaluate the drug-likeness and other characteristics of phellodendrine. The targets of phellodendrine for the treatment of inflammation were analyzed with multiple databases. Other extensive analyses including protein–protein interaction, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment were accomplished with the STRING database, Cytoscape software, and DAVID database. Moreover, the effect of phellodendrine on anti-inflammation was proven in RAW264.7.ResultsThe network pharmacology results indicated that phellodendrine had drug potential. Phellodendrine acted directly on 12 targets, including PTGS1, PTGS2, HTR1A, and PIK3CA, and then regulated cAMP, estrogen, TNF, serotonergic synapse, and other signaling pathways to exert anti-inflammatory effects. The experimental results showed that phellodendrine reduced the levels of IL-6 compared with the LPS group in 24 h and changed the mRNA expression of PTGS1, PTGS2, HSP90ab1, AKT1, HTR1A, PI3CA, and F10.ConclusionOur research preliminarily uncovered the therapeutic mechanisms of phellodendrine on inflammation with multiple targets and pathways. Phellodendrine may be a potential treatment for inflammation-related diseases related to the cAMP and TNF signaling pathways. creator: Lili Hu creator: Jue Wang creator: Na Wu creator: Xiaoge Zhao creator: Donghui Cai uri: https://doi.org/10.7717/peerj.13852 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hu et al. title: A questionnaire development to assess the social representation of nurses in the Basque Country: a psychometric assessment link: https://peerj.com/articles/13903 last-modified: 2022-09-23 description: BackgroundOnly a few Spanish studies have explored how nurses are seen by society and no validated tools exist for this purpose in the scientific literature.ObjectivesThe aim was create and evaluate the psychometric characteristics of a questionnaire that explored the social representation of nursing in social and health care.MethodsQualitative and quantitative methods were used to develop the questionnaire and the first version was created based on existing studies. A three-round Delphi technique was used that involved nurses, doctors, journalists and a politician. The pilot questionnaire was then tested and retested with 23 journalism students, with an interval of 10–14 days between the two phases. After further modifications, the questionnaire was sent to all the third and fourth year journalism students at the University of the Basque Country. Principal component factor analysis was used to identify the key components for the questionnaire.ResultsA total of 141 third and fourth year journalism students took part in the study. The internal consistency of the 43-item perception section of the questionnaire had a Cronbach’s alpha value of 0.90. The 42.7% agreed or strongly agreed that nursing was an eminently scientific profession and 26.3% agreed or strongly agreed with the statement that nurses were presented in the media as health educators and disseminators. Just under a fifth (19.9%) agreed with the statement that society was aware of the competencies that nurses required.ConclusionsThe questionnaire provided the first validated tool that allowed researchers to assess how nursing, and all of its areas of professional development, were perceived by society. This could enable studies to assess the evolution of the profession over time and between different socio-cultural contexts. creator: Verónica Tíscar-González creator: Leire Iturregui-Mardaras creator: Eztizen Miranda-Bernabé creator: Cristina Bermúdez-Ampudia creator: Maria Ángeles Cidoncha-Moreno creator: Sendoa Ballesteros-Peña uri: https://doi.org/10.7717/peerj.13903 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tíscar-González et al.