title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=375
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Miocene sponge assemblages in the face of the Messinian Salinity Crisis—new data from the Atlanto-Mediterranean seaway
link: https://peerj.com/articles/16277
last-modified: 2023-11-16
description: The Messinian Salinity Crisis is considered as one of the most influential Cenozoic events that impacted negatively on the benthic fauna of the Mediterranean area. Changing environmental conditions, including a sharp reduction of water exchange between the Mediterranean Sea and the Atlantic Ocean, altered the geographical ranges of many organisms, including sponges (Porifera). Here, we report a unique assemblage of isolated sponge spicules from the upper Miocene of southwestern Spain. The newly recognized sponge fauna was inhabiting the Guadalquivir Basin—the corridor between the Mediterranean and the Atlantic Ocean at that time. It represents a taxonomically rich sponge community that consisted of members of “soft” and “lithistid” demosponges and hexactinellids. Demosponges are represented by at least thirty-four taxa, while hexactinellids are significantly rarer; only six taxa have been identified. From among eighteen taxa recognized to the species level, at least eight seem to be inhabiting this area to these days; six are recorded from adjacent areas, such as the Western Mediterranean, South European Atlantic Shelf, and the Azores, and three are present in the Red Sea and/or the Northern Atlantic. Intriguingly, some taxa seem to have their closest relatives in distant areas, such as the Indo-Pacific and Japanese waters which suggests that the range of some once widely-distributed populations shrunk after the isolation of the Mediterranean and the Messinian Salinity Crisis, surviving to the present day only in refugia.
creator: Magdalena Łukowiak
creator: Gerardo Meiro
creator: Beltrán Peña
creator: Perfecto Villanueva Guimerans
creator: Hugo Corbí
uri: https://doi.org/10.7717/peerj.16277
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Łukowiak et al.

title: Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors
link: https://peerj.com/articles/16342
last-modified: 2023-11-16
description: Protein kinase activity forms the backbone of cellular information transfer, acting both individually and as part of a broader network, the kinome. Their central role in signaling leads to kinome dysfunction being a common driver of disease, and in particular cancer, where numerous kinases have been identified as having a causal or modulating role in tumor development and progression. As a result, the development of therapies targeting kinases has rapidly grown, with over 70 kinase inhibitors approved for use in the clinic and over double this number currently in clinical trials. Understanding the relationship between kinase inhibitor treatment and their effects on downstream cellular phenotype is thus of clear importance for understanding treatment mechanisms and streamlining compound screening in therapy development. In this work, we combine two large-scale kinome profiling data sets and use them to link inhibitor-kinome interactions with cell line treatment responses (AUC/IC50). We then built computational models on this data set that achieve a high degree of prediction accuracy (R2 of 0.7 and RMSE of 0.9) and were able to identify a set of well-characterized and understudied kinases that significantly affect cell responses. We further validated these models experimentally by testing predicted effects in breast cancer cell lines and extended the model scope by performing additional validation in patient-derived pancreatic cancer cell lines. Overall, these results demonstrate that broad quantification of kinome inhibition state is highly predictive of downstream cellular phenotypes.
creator: Chinmaya U. Joisa
creator: Kevin A. Chen
creator: Matthew E. Berginski
creator: Brian T. Golitz
creator: Madison R. Jenner
creator: Gabriela Herrera Loeza
creator: Jen Jen Yeh
creator: Shawn M. Gomez
uri: https://doi.org/10.7717/peerj.16342
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Joisa et al.

title: Thinking about it: the impact of COVID-19-related stimuli on prospective memory
link: https://peerj.com/articles/16389
last-modified: 2023-11-16
description: BackgroundSince 2020, information regarding COVID-19 has been a constant presence in the news, in our conversations and thoughts. Continuous exposure to this type of stimuli could have an impact on cognitive processes essential for our everyday activities, such as prospective memory (PM). PM is the ability to remember to perform an intention at a specific point in the future, like remembering to take prescribed medicines at a specific time or to turn off the stove after cooking. Do COVID-related stimuli affect our ability to perform a PM task?MethodsTo answer this question, we proposed a novel version of the classical paradigm used to investigate PM. Namely, this paradigm includes a baseline condition, in which an ongoing task is presented alone, and a PM condition in which the same task is proposed again together with a second (prospective) task. In this study, a short video clip was presented between the baseline and the PM condition. The video clip displayed either neutral, negative, or COVID-related content. Additionally, participants were asked to respond to two questionnaires and a series of questions regarding their well-being and experience with the pandemic. Namely, the DASS-21 scale (evaluating depression, anxiety, and stress), and the COVID-19-PTSD questionnaire (a questionnaire evaluating post-traumatic stress disorder symptoms related to the pandemic experience) were administered. Participants’ performance and responses were analyzed using a linear mixed effect (LME) model approach, and correlation analyses were run to highlight possible correlations between participants’ scores in the DASS-21, the COVID-19-PTSD, and the additional questions on their personal experience with the pandemic.ResultsThe LME models revealed significant effects of the displayed video on performance: in line with previous studies, the clip displaying standard negative contents led to impaired accuracy in the ongoing task in the PM condition, compared to the Baseline. In contrast, participants who saw the COVID-related clip showed improved accuracy in the ongoing task compared to the other participants, selectively in the block performed after the video clip was displayed (PM condition). Furthermore, the explanatory power of the LME model calculated on accuracy to the ongoing trials was enhanced by the inclusion of the scores in the anxiety subscale of the DASS-21, suggesting a detrimental role of anxiety. Altogether, these results indicate a different effect of the exposure to classical negative contents (associated with a cost in terms of accuracy in the ongoing task between the baseline and the PM condition) and the pandemic-related one, which was instead characterized by a higher accuracy to ongoing trials compared to the other video clips. This counterintuitive finding seems to suggest that COVID-related stimuli are processed as “acute stressors” rather than negative stimuli, thus inducing a state of increased alertness and responsivity.
creator: Stefano Vicentin
creator: Giovanni Cantarella
creator: Giorgia Cona
creator: Patrizia Bisiacchi
uri: https://doi.org/10.7717/peerj.16389
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Vicentin et al.

title: Sensitivity analysis of selection bias: a graphical display by bias-correction index
link: https://peerj.com/articles/16411
last-modified: 2023-11-16
description: BackgroundIn observational studies, how the magnitude of potential selection bias in a sensitivity analysis can be quantified is rarely discussed. The purpose of this study was to develop a sensitivity analysis strategy by using the bias-correction index (BCI) approach for quantifying the influence and direction of selection bias.MethodsWe used a BCI, a function of selection probabilities conditional on outcome and covariates, with different selection bias scenarios in a logistic regression setting. A bias-correction sensitivity plot was illustrated to analyze the associations between proctoscopy examination and sociodemographic variables obtained using the data from the Taiwan National Health Interview Survey (NHIS) and of a subset of individuals who consented to having their health insurance data further linked.ResultsWe included 15,247 people aged ≥20 years, and 87.74% of whom signed the informed consent. When the entire sample was considered, smokers were less likely to undergo proctoscopic examination (odds ratio (OR): 0.69, 95% CI [0.57–0.84]), than nonsmokers were. When the data of only the people who provided consent were considered, the OR was 0.76 (95% CI [0.62–0.94]). The bias-correction sensitivity plot indicated varying ORs under different degrees of selection bias.ConclusionsWhen data are only available in a subsample of a population, a bias-correction sensitivity plot can be used to easily visualize varying ORs under different selection bias scenarios. The similar strategy can be applied to models other than logistic regression if an appropriate BCI is derived.
creator: Ping-Chen Chung
creator: I-Feng Lin
uri: https://doi.org/10.7717/peerj.16411
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Chung and Lin

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