title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=376 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Scrutinising an inscrutable bark-nesting ant: Exploring cryptic diversity in the Rhopalomastix javana (Hymenoptera: Formicidae) complex using DNA barcodes, genome-wide MIG-seq and geometric morphometrics link: https://peerj.com/articles/16416 last-modified: 2023-11-16 description: Overlooking cryptic species diversity has grave implications on assessments of climate change impacts on biodiversity, ecosystems and organismal populations. Discriminating between cryptic species has long been challenging even for seasoned taxonomists, as interspecies morphological differences are often indiscernible by visual observation. Multi-disciplinary methods involving genetic analyses in conjunction with quantitative morphological data, should therefore be used to investigate boundaries between cryptic species. We adopted an integrated approach combining analyses of mitochondrial COI barcodes, a genome-wide dataset obtained via multiplexed inter-simple sequence repeats (ISSRs) genotyping by sequencing (MIG-seq), and geometric morphometrics to investigate species divergences in the inscrutable Rhopalomastix javana species complex. Objective clustering of COI suggested five putative molecular species units divergent from each other by thresholds within 4.2–10.6% uncorrected pairwise distance. Phylogenetic analyses based on concatenated MIG-seq data also recovered and strongly supported the monophyly of five major lineages in agreement with COI clusters. Co-ancestry analyses based on MIG-seq data using fineRADstructure resolved variable patterns of admixture linked to geography, and potential genetic drift within some putative species. Geometric morphometric analyses of specimen images further detected statistically significant differences in at least one of three anatomical aspects (Head, Meso, Profile) between all pairs of putative species. Head shape (full-face view) was determined to be the most informative character for species diagnosis, with relatively high classification accuracy. Thin-plate spline deformation grids highlighted areas of high variation between species in each shape for deeper taxonomic scrutiny. The presence of species from multiple distinct lineages existing in near-sympatry firmly demonstrates that R. javana comprises more than one closely-related species, but exact species boundaries are difficult to ascertain. Differences in elevation and its associated abiotic effects on ant adaptations and reproductive phenology may contribute to restricting gene flow and maintaining species boundaries between sympatric populations of the R. javana complex. We further assess the advantages and limitations of geometric morphometrics as a taxonomic tool. Despite its drawbacks, our combined approach has helped draw important insights on cryptic diversity in R. javana, and also identified gaps of knowledge that await address. Results from this study will inform and prime future in-depth taxonomic investigation on the R. javana complex, including formal descriptions and establishment of the five putative species. creator: Wendy Y. Wang creator: Aiki Yamada uri: https://doi.org/10.7717/peerj.16416 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang and Yamada title: High variability of perezone content in rhizomes of Acourtia cordata wild plants, environmental factors related, and proteomic analysis link: https://peerj.com/articles/16136 last-modified: 2023-11-15 description: With the aim of exploring the source of the high variability observed in the production of perezone, in Acourtia cordata wild plants, we analyze the influence of soil parameters and phenotypic characteristics on its perezone content. Perezone is a sesquiterpene quinone responsible for several pharmacological effects and the A. cordata plants are the natural source of this metabolite. The chemistry of perezone has been widely studied, however, no studies exist related to its production under natural conditions, nor to its biosynthesis and the environmental factors that affect the yield of this compound in wild plants. We also used a proteomic approach to detect differentially expressed proteins in wild plant rhizomes and compare the profiles of high vs. low perezone-producing plants. Our results show that in perezone-producing rhizomes, the presence of high concentrations of this compound could result from a positive response to the effects of some edaphic factors, such as total phosphorus (Pt), total nitrogen (Nt), ammonium (NH4), and organic matter (O. M.), but could also be due to a negative response to the soil pH value. Additionally, we identified 616 differentially expressed proteins between high and low perezone producers. According to the functional annotation of this comparison, the upregulated proteins were grouped in valine biosynthesis, breakdown of leucine and isoleucine, and secondary metabolism such as terpenoid biosynthesis. Downregulated proteins were grouped in basal metabolism processes, such as pyruvate and purine metabolism and glycolysis/gluconeogenesis. Our results suggest that soil parameters can impact the content of perezone in wild plants. Furthermore, we used proteomic resources to obtain data on the pathways expressed when A. cordata plants produce high and low concentrations of perezone. These data may be useful to further explore the possible relationship between perezone production and abiotic or biotic factors and the molecular mechanisms related to high and low perezone production. creator: Ma del Carmen García Méndez creator: Sergio Encarnación-Guevara creator: Ángel Gabriel Martínez Batallar creator: Leopoldo Gómez-Caudillo creator: Roque Bru-Martínez creator: Ascensión Martínez Márquez creator: Susana Selles Marchart creator: Efraín Tovar-Sánchez creator: Laura Álvarez-Berber creator: Silvia Marquina Bahena creator: Irene Perea-Arango creator: José de Jesús Arellano-García uri: https://doi.org/10.7717/peerj.16136 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Garcia Mendez et al. title: Determining Minnesota bee species’ distributions and phenologies with the help of participatory science link: https://peerj.com/articles/16146 last-modified: 2023-11-15 description: The Minnesota Bee Atlas project contributed new information about bee distributions, phenologies, and community structure by mobilizing participatory science volunteers to document bees statewide. Volunteers submitted iNaturalist (©2016 California Academy of Sciences) photograph observations, monitored nest-traps for tunnel-nesting bees, and conducted roadside observational bumble bee surveys. By pairing research scientists and participatory science volunteers, we overcame geographic and temporal challenges to document the presence, phenologies, and abundances of species. Minnesota Bee Atlas project observations included new state records for Megachile inimica, Megachile frugalis, Megachile sculpturalis, Osmia georgica, Stelis permaculata, and Bombus nevadensis, nesting phenology for 17 species, a new documentation of bivoltinism for Megachile relativa in Minnesota, and over 500 observations of the endangered species Bombus affinis. We also expanded known ranges for 16 bee species compared with specimens available from the University of Minnesota (UMN) Insect Collection. Surveys with standardized effort across the state found ecological province associations for six tunnel-nesting species and lower bumble bee abundance in the Prairie Parkland ecological province than the Laurentian Mixed Forest or Eastern Broadleaf Forest ecological provinces, indicating potential benefit of a focus on bumble bee habitat management in the Prairie Parkland. Landcover analysis found associations for four tunnel-nesting species, as well as a possible association of B. affinis with developed areas. These data can inform management decisions affecting pollinator conservation and recovery of endangered species. By engaging over 2,500 project volunteers and other iNaturalist users, we also promoted conservation action for pollinators through our educational programs and interactions. creator: Colleen D. Satyshur creator: Elaine C. Evans creator: Britt M. Forsberg creator: Thea A. Evans creator: Robert Blair uri: https://doi.org/10.7717/peerj.16146 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Satyshur et al. title: Pharmacokinetic and pharmacodynamic herb-drug interactions—part I. Herbal medicines of the central nervous system link: https://peerj.com/articles/16149 last-modified: 2023-11-15 description: Unlike conventional drug substances, herbal medicines are composed of a complex of biologically active compounds. Therefore, the potential occurrence of herb-drug interactions is even more probable than for drug-drug interactions. Interactions can occur on both the pharmacokinetic and pharmacodynamic level. Herbal medicines may affect the resulting efficacy of the concomitantly used (synthetic) drugs, mainly on the pharmacokinetic level, by changing their absorption, distribution, metabolism, and excretion. Studies on the pharmacodynamic interactions of herbal medicines and conventional drugs are still very limited. This interaction level is related to the mechanism of action of different plant constituents. Herb-drug interactions can cause changes in drug levels and activities and lead to therapeutic failure and/or side effects (sometimes toxicities, even fatal). This review aims to provide a summary of recent information on the potential drug interactions involving commonly used herbal medicines that affect the central nervous system (Camellia, Valeriana, Ginkgo, Hypericum, Humulus, Cannabis) and conventional drugs. The survey databases were used to identify primary scientific publications, case reports, and secondary databases on interactions were used later on as well. Search keywords were based on plant names (botanical genera), officinal herbal drugs, herbal drug preparations, herbal drug extracts. creator: Szilvia Czigle creator: Milan Nagy creator: Přemysl Mladěnka creator: Jaroslav Tóth uri: https://doi.org/10.7717/peerj.16149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Czigle et al. title: Comparison of feeding preferences of herbivorous fishes and the sea urchin Diadema antillarum in Little Cayman link: https://peerj.com/articles/16264 last-modified: 2023-11-15 description: On Caribbean coral reefs, losses of two key groups of grazers, herbivorous fishes and Diadema antillarum, coincided with dramatic increases in macroalgae, which have contributed to decreases in the resilience of these coral reefs and continued low coral cover. In some locations, herbivorous reef fishes and D. antillarum populations have begun to recover, and reductions in macroalgal cover and abundance have followed. Harder to determine, and perhaps more important, are the combined grazing effects of herbivorous fishes and D. antillarum on the structure of macroalgal communities. Surprisingly few studies have examined the feeding preferences of D. antillarum for different macroalgal species, and there have been even fewer comparative studies between these different herbivore types. Accordingly, a series of in-situ and ex-situ feeding assays involving herbivorous fishes and D. antillarum were used to examine feeding preferences. Ten macrophytes representing palatable and chemically and/or structurally defended species were used in these assays, including nine macroalgae, and one seagrass. All species were eaten by at least one of the herbivores tested, although consumption varied greatly. All herbivores consumed significant portions of two red algae species while avoiding Halimeda tuna, which has both chemical and structural defenses. Herbivorous fishes mostly avoided chemically defended species while D. antillarum consumed less of the structurally defended algae. These results suggest complementarity and redundancy in feeding by these different types of herbivores indicating the most effective macroalgal control and subsequent restoration of degraded coral reefs may depend on the recovery of both herbivorous fishes and D. antillarum. creator: Lindsay Spiers creator: Thomas K. Frazer uri: https://doi.org/10.7717/peerj.16264 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Spiers and Frazer title: In-silico study of antisense oligonucleotide antibiotics link: https://peerj.com/articles/16343 last-modified: 2023-11-15 description: BackgroundThe rapid emergence of antibiotic-resistant bacteria directly contributes to a wave of untreatable infections. The lack of new drug development is an important driver of this crisis. Most antibiotics today are small molecules that block vital processes in bacteria. To optimize such effects, the three-dimensional structure of targeted bacterial proteins is imperative, although such a task is time-consuming and tedious, impeding the development of antibiotics. The development of RNA-based therapeutics has catalyzed a new platform of antibiotics—antisense oligonucleotides (ASOs). These molecules hybridize with their target mRNAs with high specificity, knocking down or interfering with protein translation. This study aims to develop a bioinformatics pipeline to identify potent ASO targets in essential bacterial genes.MethodsThree bacterial species (P. gingivalis, H. influenzae, and S. aureus) were used to demonstrate the utility of the pipeline. Open reading frames of bacterial essential genes were downloaded from the Database of Essential Genes (DEG). After filtering for specificity and accessibility, ASO candidates were ranked based on their self-hybridization score, predicted melting temperature, and the position on the gene in an operon. Enrichment analysis was conducted on genes associated with putative potent ASOs.ResultsA total of 45,628 ASOs were generated from 348 unique essential genes in P. gingivalis. A total of 1,117 of them were considered putative. A total of 27,273 ASOs were generated from 191 unique essential genes in H. influenzae. A total of 847 of them were considered putative. A total of 175,606 ASOs were generated from 346 essential genes in S. aureus. A total of 7,061 of them were considered putative. Critical biological processes associated with these genes include translation, regulation of cell shape, cell division, and peptidoglycan biosynthetic process. Putative ASO targets generated for each bacterial species are publicly available here: https://github.com/EricSHo/AOA. The results demonstrate that our bioinformatics pipeline is useful in identifying unique and accessible ASO targets in bacterial species that post major public health issues. creator: Erica S. Chen creator: Eric S. Ho uri: https://doi.org/10.7717/peerj.16343 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chen and Ho title: Seq2science: an end-to-end workflow for functional genomics analysis link: https://peerj.com/articles/16380 last-modified: 2023-11-15 description: Sequencing databases contain enormous amounts of functional genomics data, making them an extensive resource for genome-scale analysis. Reanalyzing publicly available data, and integrating it with new, project-specific data sets, can be invaluable. With current technologies, genomic experiments have become feasible for virtually any species of interest. However, using and integrating this data comes with its challenges, such as standardized and reproducible analysis. Seq2science is a multi-purpose workflow that covers preprocessing, quality control, visualization, and analysis of functional genomics sequencing data. It facilitates the downloading of sequencing data from all major databases, including NCBI SRA, EBI ENA, DDBJ, GSA, and ENCODE. Furthermore, it automates the retrieval of any genome assembly available from Ensembl, NCBI, and UCSC. It has been tested on a variety of species, and includes diverse workflows such as ATAC-, RNA-, and ChIP-seq. It consists of both generic as well as advanced steps, such as differential gene expression or peak accessibility analysis and differential motif analysis. Seq2science is built on the Snakemake workflow language and thus can be run on a range of computing infrastructures. It is available at https://github.com/vanheeringen-lab/seq2science. creator: Maarten van der Sande creator: Siebren Frölich creator: Tilman Schäfers creator: Jos G.A. Smits creator: Rebecca R. Snabel creator: Sybren Rinzema creator: Simon J. van Heeringen uri: https://doi.org/10.7717/peerj.16380 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 van der Sande et al. title: Impact of nitrogen application and crop stage on epiphytic microbial communities on silage maize leaf surfaces link: https://peerj.com/articles/16386 last-modified: 2023-11-15 description: This study aimed to examine the impact of nitrogen (N) fertilization on phyllosphere microorganisms in silage maize (Zea mays) to enhance the production of high-quality silage. The effects of different N application rates (160, 240, and 320 kg ha−1) and maturity stages (flowering and dough stages) on microbial diversity, abundance and physiochemical properties of the leaf surfaces were evaluated in a field experiment. The results showed that N application rates did not significantly impact the abundance of lactic acid bacteria (LAB), aerobic bacteria (AB), yeasts, or molds on the leaf surfaces. However, these microbes were more abundant during the flowering stage compared to the dough stage. Furthermore, the N application rate had no significant impact on inorganic phosphorus, soluble sugar, free amino acids, total phenolic content, and soluble protein concentrations, or pH levels on the leaf surfaces. Notably, these chemical indices were lower during the dough stage. The abundance of Pantoea decreased with higher N application rates, while that of other microorganisms did not changes significantly. The abundance of AB, LAB, yeasts, and molds were positively correlated with soluble sugar, soluble protein, inorganic phosphorus, free amino acids, and total phenolic concentrations on leaf surfaces. Moreover, water loss was negatively correlated with the abundance of AB, LAB, yeasts, and molds, whereas water retention capacity and stomatal density were positively correlated with microbial abundance. We recommend applying an optimal N rate of 160 kg ha−1 to silage maize and harvesting at the flowering stage is recommended. creator: Dan Wu creator: Xueling Ma creator: Yuanyan Meng creator: Rongjin Cai creator: Xiaolong Zhang creator: Li Liu creator: Lianping Deng creator: Changjing Chen creator: Fang Wang creator: Qingbiao Xu creator: Bin He creator: Mingzhu He creator: Rensheng Hu creator: Jinjing Zhen creator: Yan Han creator: Shaoshen He creator: Liuxing Xu uri: https://doi.org/10.7717/peerj.16386 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wu et al. title: Genetic divergences and hybridization within the Sebastes inermis complex link: https://peerj.com/articles/16391 last-modified: 2023-11-15 description: The Sebastes inermis complex includes three sympatric species (Sebastes cheni, viz Sebastes inermis, and Sebastes ventricosus) with clear ecomorphological differences, albeit incomplete reproductive isolation. The presence of putative morphological hybrids (PMH) with plausibly higher fitness than the parent species indicates the need to confirm whether hybridization occurs within the complex. In this sense, we assessed the dynamics of genetic divergence and hybridization within the species complex using a panel of 10 microsatellite loci, and sequences of the mitochondrial control region (D-loop) and the intron-free rhodopsin (RH1) gene. The analyses revealed the presence of three distinct genetic clusters, large genetic distances using D-loop sequences, and distinctive mutations within the RH1 gene. These results are consistent with the descriptions of the three species. Two microsatellite loci had signatures of divergent selection, indicating that they are linked to genomic regions that are crucial for speciation. Furthermore, nonsynonymous mutations within the RH1 gene detected in S. cheni and “Kumano” (a PMH) suggest dissimilar adaptations related to visual perception in dim-light environments. The presence of individuals with admixed ancestry between two species confirmed hybridization. The presence of nonsynonymous mutations within the RH1 gene and the admixed ancestry of the “Kumano” morphotype highlight the potential role of hybridization in generating novelties within the species complex. We discuss possible outcomes of hybridization within the species complex, considering hybrid fitness and assortative mating. Overall, our findings indicate that the genetic divergence of each species is maintained in the presence of hybridization, as expected in a scenario of speciation-with-gene-flow. creator: Diego Deville creator: Kentaro Kawai creator: Hiroki Fujita creator: Tetsuya Umino uri: https://doi.org/10.7717/peerj.16391 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Deville et al. title: Profile of the bile acid FXR-FGF15 pathway in the glucolipid metabolism disorder of diabetic mice suffering from chronic stress link: https://peerj.com/articles/16407 last-modified: 2023-11-15 description: BackgroundImbalances in bile acid (BA) synthesis and metabolism are involved in the onset of diabetes and depression in humans and rodents. However, the role of BAs and the farnesoid X receptor (FXR)/fibroblast growth factor (FGF) 15 signaling pathway in the development of diabetes and depression is still largely unknown. Therefore, we investigated the potential molecular mechanisms of BAs that may be associated with glucolipid metabolism disorders in diabetic mice subjected to chronic stress.MethodsThe type 2 diabetes mellitus (T2DM) mouse model was induced by feeding mice a high-fat diet and administering an intraperitoneal injection of streptozotocin (STZ). The chronic unpredictable mild stress (CUMS) procedure was performed by introducing a series of mild stressors. Forty mice were randomly divided into the regular chow feeding group and the high-fat diet feeding group. After two weeks of feeding, the mice were randomly divided into four groups: the Control group, CUMS group, T2DM group, and T2DM+CUMS group. The T2DM group and T2DM+CUMS group received an intraperitoneal injection of STZ to induce the T2DM model. The CUMS and T2DM+CUMS groups were exposed to CUMS to induce depressive-like phenotypes. Blood and tissue samples were obtained for pertinent analysis and detection.ResultsCompared with the T2DM mice, T2DM+CUMS mice had higher blood glucose and lipid levels, insulin resistance, inflammation of the liver and pancreas, impaired liver function, and increased total bile acids. These changes were accompanied by attenuated FXR signaling. Chronic stress was found to attenuate FXR expression and its downstream target, FGF15, in the ileum when compared with the T2DM group.ConclusionFXR may play a role in the diabetic disorder of glucolipid metabolism when aggravated by chronic stress. FXR and its downstream target, FGF15, may be therapeutic targets for treating comorbid T2DM and depression. creator: Weijia Cai creator: Canye Li creator: Zuanjun Su creator: Jinming Cao creator: Zhicong Chen creator: Yitian Chen creator: Zhijun Guo creator: Jian Cai creator: Feng Xu uri: https://doi.org/10.7717/peerj.16407 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cai et al.