title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=373 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Behavioral dominance interactions between two species of burying beetles (Nicrophorus orbicollis and Nicrophorus pustulatus) link: https://peerj.com/articles/16090 last-modified: 2023-11-23 description: Closely related species with ecological similarity often aggressively compete for a common, limited resource. This competition is usually asymmetric and results in one species being behaviorally dominant over the other. Trade-offs between traits for behavioral dominance and alternative strategies can result in different methods of resource acquisition between the dominant and subordinate species, with important consequences for resource partitioning and community structure. Body size is a key trait thought to commonly determine behavioral dominance. Priority effects (i.e., which species arrives at the resource first), however, can also determine the outcome of interactions, as can species-specific traits besides size that give an advantage in aggressive contests (e.g., weapons). Here, we test among these three alternative hypotheses of body size, priority effects, and species identity for what determines the outcome of competitive interactions among two species of burying beetles, Nicrophorus orbicollis and N. pustulatus. Both overlap in habitat and seasonality and exhibit aggressive competition over a shared breeding resource of small vertebrate carrion. In trials, we simulated what would happen upon the beetles’ discovery of a carcass in nature by placing a carcass and one beetle of each species in a container and observing interactions over 13 h trials (n = 17 trials). We recorded and categorized interactions between beetles and the duration each individual spent in contact with the carcass (the key resource) to determine which hypothesis predicted trial outcomes. Body size was our only significant predictor; the largest species won most aggressive interactions and spent more time in contact with the carcass. Our results offer insight into the ecology and patterns of resource partitioning of N. orbicollis and N. pustulatus, the latter of which is unique among local Nicrophorus for being a canopy specialist. N. pustulatus is also unique among all Nicrophorus in using snake eggs, in addition to other carrion, as a breeding resource. Our results highlight the importance of body size and related trade-offs in ecology and suggest parallels with other coexisting species and communities. creator: Yohanna D. Vangenne creator: Brendan Sheppard creator: Paul R. Martin uri: https://doi.org/10.7717/peerj.16090 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Vangenne et al. title: Navigating the microbial community in the trachea-oropharynx of breast cancer patients with or without neoadjuvant chemotherapy (NAC) via endotracheal tube: has NAC caused any change? link: https://peerj.com/articles/16366 last-modified: 2023-11-23 description: BackgroundWe compare the diversity and niche specificity of the microbiome in the trachea-oropharynx microbiome of malignant breast neoplasm with or without neoadjuvant chemotherapy (NAC) via NGS analysis.MethodsWe prospectively collected a total of 40 endotracheal tubes intubated from subjects, of whom 20 with NAC treated breast cancer (NAC group) and 20 with breast cancer without NAC (Non-NAC group). We generated 16S rRNA-based microbial profiles in IlluminaTM platform and alpha diversity indices were compared between groups. For the comparison of taxa abundance, linear discriminant analysis effect size method with Kruskal-Wallis test was used. The distribution of variables between the two groups was compared using the Mann-Whitney test. For beta diversity analysis, PERMANOVA was used.ResultsAmong the diversity indices, the NAC group showed significantly lower Chao1, Inverse Simpson, and Shannon indices than the Non-NAC group. The three most frequent taxa of all two groups were Streptococcus (20.4%), followed by Veillonella (11.9%), and Prevorella (10.4%). This order was the same in NAC and non-NAC groups.ConclusionHere, we provide the first comparison data of the respiratory tract microbiome of breast cancer patients with or without NAC via NGS analysis. This study ultimately seeks to contribute to future studies on the lower respiratory tract in cancer patients with cytotoxic chemotherapy by establishing reliable control data. creator: Hee Yeon Kim creator: Tae Hyun Kim creator: Jeong Hwan Shin creator: Kwangrae Cho creator: Heon-Kyun Ha creator: Anbok Lee creator: Young Jin Kim uri: https://doi.org/10.7717/peerj.16366 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kim et al. title: The impact of obesity on static and proactive balance and gait patterns in sarcopenic older adults: an analytical cross-sectional investigation link: https://peerj.com/articles/16428 last-modified: 2023-11-23 description: BackgroundObesity is increasingly recognized as a significant factor in the susceptibility of older adults to falls and related injuries. While existing literature has established a connection between obesity and reduced postural stability during stationary stances, the direct implications of obesity on walking dynamics, particularly among the older adults with sarcopenia, are not yet comprehensively understood.ObjectiveFirstly, to investigate the influence of obesity on steady-state and proactive balance, as well as gait characteristics, among older adults with sarcopenic obesity (SO); and secondly, to unearth correlations between anthropometric characteristics and balance and gait parameters in the same demographic.MethodsA cohort of 42 participants was categorized into control (CG; n = 22; age = 81.1 ± 4.0 years; BMI = 24.9 ± 0.6 kg/m²) and sarcopenic obese (SOG; n = 20; age = 77.7 ± 2.9 years; BMI = 34.5 ± 3.2 kg/m²) groups based on body mass index (BMI, kg/m²). Participants were assessed for anthropometric data, body mass, fat and lean body mass percentages (%), and BMI. Steady-state balance was gauged using the Romberg Test (ROM). Proactive balance evaluations employed the Functional Reach (FRT) and Timed Up and Go (TUG) tests. The 10-m walking test elucidated spatiotemporal gait metrics, including cadence, speed, stride length, stride time, and specific bilateral spatiotemporal components (stance, swing, 1st and 2nd double support, and single support phases) expressed as percentages of the gait cycle.ResultsThe time taken to complete the TUG and ROM tests was significantly shorter in the CG compared to the SOG (p < 0.05). In contrast, the FRT revealed a shorter distance achieved in the SOG compared to the CG (p < 0.05). The CG exhibited a higher gait speed compared to the SOG (p < 0.05), with shorter stride and step lengths observed in the SOG compared to the CG (p < 0.05). Regarding gait cycle phases, the support phase was longer, and the swing phase was shorter in the SOG compared to the CG group (p < 0.05). LBM (%) showed the strongest positive correlation with the ROM (r = 0.77, p < 0.001), gait speed (r = 0.85, p < 0.001), TUG (r = −0.80, p < 0.001) and FRT (r = 0.74, p < 0.001).ConclusionObesity induces added complexities for older adults with sarcopenia, particularly during the regulation of steady-state and proactive balance and gait. The percentage of lean body mass has emerged as a crucial determinant, highlighting a significant impact of reduced muscle mass on the observed alterations in static postural control and gait among older adults with SO. creator: Hamza Ferhi creator: Wael Maktouf uri: https://doi.org/10.7717/peerj.16428 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ferhi and Maktouf title: Diversity of bacteria associated with lichens in Mt. Yunmeng in Beijing, China link: https://peerj.com/articles/16442 last-modified: 2023-11-23 description: Lichens host highly complex and diverse microbial communities, which may perform essential functions in these symbiotic micro-ecosystems. In this research, sequencing of 16S rRNA was used to investigate the bacterial communities associated with lichens of two growth forms (foliose and crustose). Results showed that Pseudomonadota, Actinomycetota and Acidobacteriota were dominant phyla in both types of lichens, while Acetobacterales and Hyphomicrobiales were the dominant orders. Alpha diversity index showed that the richness of bacteria hosted by foliose lichens was significantly higher than that hosted by crustose ones. Principal co-ordinates analysis showed a significant difference between beta diversity of the foliose lichen-associated bacterial communities and those of crustose lichen-associated ones. Gene function prediction showed most functions, annotated by the lichen-associated bacteria, to be related to metabolism, suggesting that related bacteria may provide nutrients to their hosts. Generally, our results propose that microbial communities play important roles in fixing nitrogen, providing nutrients, and controlling harmful microorganisms, and are therefore an integral and indispensable part of lichens. creator: Yimeng Li creator: Yinzhi Huang creator: Torsten Wronski creator: Manrong Huang uri: https://doi.org/10.7717/peerj.16442 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Glyceraldehyde-3-phosphate dehydrogenase Gh_GAPDH9 is associated with drought resistance in Gossypium hirsutum link: https://peerj.com/articles/16445 last-modified: 2023-11-23 description: BackgroundGlyceraldehyde-3-phosphate dehydrogenase (GAPDH) is the central enzyme of glycolysis and plays important regulatory roles in plant growth and development and responses to adverse stress conditions. However, studies on the characteristics and functions of cotton GAPDH family genes are still lacking.MethodsIn this study, genome-wide identification of the cotton GAPDH gene family was performed, and the phylogeny, gene structures, promoter progenitors and expression profiles of upland cotton GAPDH gene family members were explored by bioinformatics analysis to highlight potential functions. The functions of GhGAPDH9 in response to drought stress were initially validated based on RNA-seq, qRT‒PCR, VIGS techniques and overexpression laying a foundation for further studies on the functions of GAPDH genes.ResultsThis study is the first systematic analysis of the cotton GAPDH gene family, which contains a total of 84 GAPDH genes, among which upland cotton contains 27 members. Quantitative, phylogenetic and covariance analyses of the genes revealed that the GAPDH gene family has been conserved during the evolution of cotton. Promoter analysis revealed that most cis-acting elements were related to MeJA and ABA. Based on the identified promoter cis-acting elements and RNA-seq data, it was hypothesized that Gh_GAPDH9, Gh_GAPDH11, Gh_GAPDH19 and Gh_GAPDH21 are involved in the response of cotton to abiotic stress. The expression levels of the Gh_GAPDH9 gene in two drought-resistant and two drought-sensitive materials were analyzed by qRT‒PCR and found to be high early in the treatment period in the drought-resistant material. The silencing of Gh_GAPDH9 based on virus-induced gene silencing (VIGS) technology resulted in significant leaf wilting or whole-plant dieback in silenced plants after drought stress compared to the control. The content of—malondialdehyde (MDA) in cotton leaves was significantly increased, and the content of proline (Pro) and chlorophyll (Chl) was reduced. In addition, the leaf wilting and dryness of transgenic lines under drought stress were lower than those of wild-type Arabidopsis, indicating that Gh_GAPDH9 is a positive regulator of drought resistance. In conclusion, our results demonstrate that GAPDH genes play an important role in the response of cotton to abiotic stresses and provide preliminary validation of the function of the Gh_GAPDH9 gene under drought stress. These findings provide an important theoretical basis for further studies on the function of the Gh_GAPDH9 gene and the molecular mechanism of the drought response in cotton. creator: Shiwei Geng creator: Shengmei Li creator: Jieyin Zhao creator: Wenju Gao creator: Qin Chen creator: Kai Zheng creator: Yuxiang Wang creator: Yang Jiao creator: Yilei Long creator: Pengfei Liu creator: Yanying Qu creator: Quanjia Chen uri: https://doi.org/10.7717/peerj.16445 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Geng et al. title: Individual and combined ecotoxic effects of water-soluble polymers link: https://peerj.com/articles/16475 last-modified: 2023-11-23 description: Water-soluble polymers (WSPs) are a class of high-molecular-weight compounds which are widely used in several applications, including water treatment, food processing, and pharmaceuticals. Therefore, they pose a potential threat for water resources and aquatic ecosystems. We assessed the ecotoxicity of four WSPs—non-ionic polyacrylamide (PAM) and polyethylene glycol (PEG-200), anionic homopolymer of acrylic acid (P-AA), and cationic polyquaternium-6 (PQ-6)—as single compounds and in mixture. For this purpose in vitro and in vivo assays were used to record baseline toxicity, mutagenic potential, endocrine effects, and growth inhibition in the freshwater alga Raphidocelis subcapitata. Furthermore, the mixture toxicity of the two polymers P-AA and PQ-6 which showed effects in the algae tests was evaluated with the concentration addition (CA), independent action (IA), and generalized concentration addition (GCA) model and compared with experimental data. No toxic effects were observed among the polymers and their mixtures in the in vitro assays. On the contrary, in the growth inhibition test with R. subcapitata the cationic PQ-6 caused high inhibition while the anionic P-AA and its mixture with the cationic polymer caused low inhibition. The non-ionic polymers PEG-200 and PAM showed no effect in R. subcapitata in the tested concentration range up to 100 mg/L. The IA model represented the mixture effect of the combination experiment better than the CA and GCA models. The results indicate (1) that the toxic effects of anionic and cationic polymers are most likely due to interactions of the polymers with the surfaces of organisms or with nutrients in the water and (2) that the polymers elicit their effects through different mechanisms of action that do not interact with each other. creator: Olcay Hisar creator: Jörg Oehlmann uri: https://doi.org/10.7717/peerj.16475 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hisar and Oehlmann title: Genomic analyses indicate resilience of a commercially and culturally important marine gastropod snail to climate change link: https://peerj.com/articles/16498 last-modified: 2023-11-23 description: Genomic vulnerability analyses are being increasingly used to assess the adaptability of species to climate change and provide an opportunity for proactive management of harvested marine species in changing oceans. Southeastern Australia is a climate change hotspot where many marine species are shifting poleward. The turban snail, Turbo militaris is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades presenting an ongoing challenge for sustainable fisheries management. We investigate the impact of future climate change on T. militaris using genotype-by-sequencing to project patterns of gene flow and local adaptation across its range under climate change scenarios. A single admixed, and potentially panmictic, demographic unit was revealed with no evidence of genetic subdivision across the species range. Significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation. creator: Matt J. Nimbs creator: Curtis Champion creator: Simon E. Lobos creator: Hamish A. Malcolm creator: Adam D. Miller creator: Kate Seinor creator: Stephen D.A. Smith creator: Nathan Knott creator: David Wheeler creator: Melinda A. Coleman uri: https://doi.org/10.7717/peerj.16498 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Nimbs et al. title: Predicting carrying capacity of a large carnivore from prey densities: a new approach link: https://peerj.com/articles/15914 last-modified: 2023-11-22 description: BackgroundLarge carnivores play a crucial role in maintaining the balance of the ecosystem. Successful conservation initiatives have often led to a huge increase in predators which has often led to negative interactions with humans. Without the knowledge of the carrying capacity of the top predator, such decisions become challenging. Here, we have derived a new equation to estimate the carrying capacity of tigers based on the individual prey species density.MethodsWe used tiger densities and respective prey densities of different protected areas. Relative prey abundance was used instead of absolute prey density as this could be a better surrogate of the prey preference. We used a regression approach to derive the species-wise equation. We have also scaled these coefficients accordingly to control the variation in the standard error (heteroscedasticity) of the tiger density. Furthermore, we have extended this regression equation for different species to different weight classes for more generalized application of the method.ResultsThe new equations performed considerably better compared to the earlier existing carrying capacity equations. Incorporating the species-wise approach in the equation also reflected the preference of the prey species for the tiger. This is the first carrying capacity equation where the individual prey densities are used to estimate the carnivore population density. The coefficient estimates of the model with the comparison with prey-predator power laws also reflect the differential effect of tigers on different prey species. The carrying capacity estimates will aid in a better understanding of the predator-prey interaction and will advance better management of the top predator. creator: Nilanjan Chatterjee creator: Indranil Mukhopadhyay creator: Parag Nigam creator: Bilal Habib uri: https://doi.org/10.7717/peerj.15914 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chatterjee et al. title: Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains link: https://peerj.com/articles/16276 last-modified: 2023-11-22 description: PacBio HiFi sequencing was employed in combination with metagenomic binning to produce a high-quality reference genome of Cosmopolites sordidus. We compared k-mer and alignment reference based pre-binning and post-binning approaches to remove contamination. We were also interested to know if the post-binning approach had interspersed bacterial contamination within intragenic regions of Arthropoda binned contigs. Our analyses identified 3,433 genes that were composed with reads identified as of putative bacterial origins. The pre-binning approach yielded a C. sordidus genome of 1.07 Gb genome composed of 3,089 contigs with 98.6% and 97.1% complete and single copy genome and protein BUSCO scores respectively. In this article we demonstrate that in this case the pre-binning approach does not sacrifice assembly quality for more stringent metagenomic filtering. We also determine post-binning allows for increased intragenic contamination increased with increasing coverage, but the frequency of gene contamination increased with lower coverage. Future work should focus on developing reference free pre-binning approaches for HiFi reads produced from eukaryotic based metagenomic samples. creator: Alfredo Rodriguez Ruiz creator: Alex R. Van Dam uri: https://doi.org/10.7717/peerj.16276 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rodriguez Ruiz and Van Dam title: Basic psychological need satisfaction and aggressive behavior: the role of negative affect and its gender difference link: https://peerj.com/articles/16372 last-modified: 2023-11-22 description: BackgroundBasic psychological need satisfaction (BPNS) is a significant factor in a person’s development, especially for adolescents, and the failure to satisfy these basic needs may contribute to individuals’ aggressive behavior. However, it is still unclear about the underlying mechanism by which BPNS is negatively associated with aggressive behavior. This study aimed to explore the relationship between BPNS and aggressive behavior in Chinese adolescents, with a focus on the mediating role of negative affect and its gender differences.MethodA sample of 1,064 junior high school students from three schools in China were selected randomly for the cross-sectional survey. The revised Need Satisfaction Scale, the Positive and Negative Affect Schedule, and Youth’s Self-Report were used to measure BPNS, affect, and aggressive behavior. The proposed model was examined by the structural equation modeling test and multi-group comparison analysis.ResultsThe results showed that BPNS was negatively linked with adolescents’ aggressive behavior, and this effect was mediated by negative affect. Moreover, multigroup analysis demonstrated that there existed a stronger negative association between BPNS and negative affect in female group. Also, the mediating effect of negative affect in the model was greater for girls.ConclusionsOur findings highlighted the importance of BPNS in adolescents’ social behavior (i.e., aggressive behavior), and reveal disparate patterns in how BPNS affects aggressive behavior in girls as compared to boys. creator: Fen Dou creator: Qinglin Wang creator: Minghui Wang creator: Entao Zhang creator: Guoxiang Zhao uri: https://doi.org/10.7717/peerj.16372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dou et al.