title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=772 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effects of media multitasking frequency on a novel volitional multitasking paradigm link: https://peerj.com/articles/12603 last-modified: 2022-01-27 description: The effect of media multitasking (e.g., listening to podcasts while studying) on cognitive processes has seen mixed results thus far. To date, the tasks used in the literature to study this phenomenon have been classical paradigms primarily used to examine processes such as working memory. While perfectly valid on their own, these paradigms do not approximate a real-world volitional multitasking environment. To remedy this, as well as attempt to further validate previously found effects in the literature, we designed a novel experimental framework that mimics a desktop computer environment where a “popup” associated with a secondary task would occasionally appear. Participants could choose to attend to the popup, or to ignore it. Attending to the popup would prompt a word stem completion task, while ignoring it would continue the primary math problem verification task. We predicted that individuals who are more impulsive, more frequent media multitaskers, and individuals who prefer to multitask (quantified with the Barratt Impulsiveness Scale, a modified version of the Media Use Questionnaire, and the Multitasking Preference Inventory) would be more distracted by popups, choose to switch tasks more often and more quickly, and be slower to return to the primary task compared to those who media multitask to a lesser degree. We found that as individuals media multitask to a greater extent, they are slower to return to the previous (primary) task set and are slower to complete the primary task overall whether a popup was present or not, among other task performance measures. We found a similar pattern of effects within individuals who prefer to multitask. Our findings suggest that overall, more frequent media multitaskers show a marginal decrease in task performance, as do preferential multitaskers. Attentional impulsivity was not found to influence any task performance measures, but was positively related to a preference for multitasking. While our findings may lack generalizability due to the modifications to the Media Use Questionnaire, and this initial study is statically underpowered, this paradigm is a crucial first step in establishing a more ecologically valid method to study real-world multitasking. creator: Jesus J. Lopez creator: Joseph M. Orr uri: https://doi.org/10.7717/peerj.12603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lopez and Orr title: Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities link: https://peerj.com/articles/12701 last-modified: 2022-01-27 description: Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches. creator: Julian A. Liber creator: Douglas H. Minier creator: Anna Stouffer-Hopkins creator: Judson Van Wyk creator: Reid Longley creator: Gregory Bonito uri: https://doi.org/10.7717/peerj.12701 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liber et al. title: Conservation paleobiology on Minami-Daito Island, Okinawa, Japan: anthropogenic extinction of cave-dwelling bats on a tropical oceanic island link: https://peerj.com/articles/12702 last-modified: 2022-01-27 description: BackgroundWith strong environmental and geographic filtration, vertebrates incapable of flying and swimming are often extirpated from island ecosystems. Minami-Daito Island is an oceanic island in Okinawa, Japan that harbors the Daito flying fox (Pteropus dasymallus daitoensis), a subspecies of the fruit bat and the only extant mammal endemic to the island. However, the skeleton of a cave-dwelling bat Rhinolophus sp. and fossil guano were briefly reported in a previous study.MethodsHere, we present evidence for the anthropogenic extirpation of two species of cave-dwelling bats (Miniopterus sp. & Rhinolophus sp.) from Minami-Daito Island. Our goal is to reliably constrain the ages of the extirpated bat species by a multiproxy approach. Because skeletal materials did not preserve sufficient bone collagen for direct radiocarbon dating, we alternatively examined guano-like deposits based on SEM observation and Fourier-transform infrared spectroscopy (FTIR) along with stable carbon and nitrogen isotope analyses for possible indirect dating. We also examined stable carbon isotopes in bone apatite, assuming that an isotopic signal of C4 plants on the bat bones links to sugarcane plantation on the island based on the historical knowledge that early human settlers quickly replaced the island’s native C3 forests with sugarcane (C4 perennial grass) plantation from 1900 onward.ResultsOur cave survey documents the remains of Miniopterus sp. from the island for the first time. Based on the unique taphonomic conditions (unpermineralized bones, disarticulated skeletons closely scattered without sediment cover, various degrees of calcite crystal growth around bones) and a radiocarbon age of a humic sample, we suggest that the maximum age constraint of Miniopterus sp. and Rhinolophus sp. is 4,640 calBP. Based on a series of analyses, we conclude that the guano-like deposits are composed not of bat guano but mainly of humic substances; however, a hydroxyapatite crust associated with bat-lying stalagmites may be derived from bat feces. Stable carbon isotope analysis of bone apatite revealed C4 signals in various degrees, confirming that small populations of cave-dwelling bats persisted on Minami-Daito Island after 1900.ConclusionsThe results of this study indicate that these populations remained rather small and did not leave many generations and that the estimated ages can be bracketed from 4,640 calBP to the post-1900 (perhaps, until the 1950s). They likely faced a continuously high mortality risk due to severe anthropogenic stresses on the island, where most of the forests were turned into sugarcane plantations within a few decades in the early 20th century. A result of hearing surveys to local residents suggests the latest remnants most likely disappeared on the island concurrently with the introduction of chemical pesticides after World War II. creator: Yuri Kimura creator: Dai Fukui creator: Mizuko Yoshiyuki creator: Kazuaki Higashi uri: https://doi.org/10.7717/peerj.12702 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kimura et al. title: Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone link: https://peerj.com/articles/12706 last-modified: 2022-01-27 description: BackgroundPseudalcantarea grandis (Schltdl.) Pinzón & Barfuss is a tank bromeliad that grows on cliffs in the southernmost portion of the Chihuahuan desert. Phytotelmata are water bodies formed by plants that function as micro-ecosystems where bacteria, algae, protists, insects, fungi, and some vertebrates can develop. We hypothesized that the bacterial diversity contained in the phytotelma formed in a bromeliad from an arid zone would differ in sites with and without surrounding vegetation. Our study aimed to characterize the bacterial composition and putative metabolic functions in P. grandis phytotelmata collected in vegetated and non-vegetated sites.MethodsWater from 10 individuals was sampled. Five individuals had abundant surrounding vegetation, and five had little or no vegetation. We extracted DNA and amplified seven hypervariable regions of the 16S gene (V2, V4, V8, V3–6, 7–9). Metabarcoding sequencing was performed on the Ion Torrent PGM platform. Taxonomic identity was assigned by the binning reads and coverage between hit and query from the reference database of at least 90%. Putative metabolic functions of the bacterial families were assigned mainly using the FAPROTAX database. The dominance patterns in each site were visualized with rank/abundance curves using the number of Operational Taxonomic Units (OTUs) per family. A percentage similarity analysis (SIMPER) was used to estimate dissimilarity between the sites. Relationships among bacterial families (identified by the dominance analysis and SIMPER), sites, and their respective putative functions were analyzed with shade plots.ResultsA total of 1.5 million useful bacterial sequences were obtained. Sequences were clustered into OTUs, and taxonomic assignment was conducted using BLAST in the Greengenes databases. Bacterial diversity was 23 phyla, 52 classes, 98 orders, 218 families, and 297 genera. Proteobacteria (37%), Actinobacteria (19%), and Firmicutes (15%) comprised the highest percentage (71%). There was a 68.3% similarity between the two sites at family level, with 149 families shared. Aerobic chemoheterotrophy and fermentation were the main metabolic functions in both sites, followed by ureolysis, nitrate reduction, aromatic compound degradation, and nitrogen fixation. The dominant bacteria shared most of the metabolic functions between sites. Some functions were recorded for one site only and were related to families with the lowest OTUs richness. Bacterial diversity in the P. grandis tanks included dominant phyla and families present at low percentage that could be considered part of a rare biosphere. A rare biosphere can form genetic reservoirs, the local abundance of which depends on external abiotic and biotic factors, while their interactions could favor micro-ecosystem resilience and resistance. creator: José Alan Herrera-García creator: Mahinda Martinez creator: Pilar Zamora-Tavares creator: Ofelia Vargas-Ponce creator: Luis Hernández-Sandoval creator: Fabián Alejandro Rodríguez-Zaragoza uri: https://doi.org/10.7717/peerj.12706 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Herrera-García et al. title: Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C4 plants link: https://peerj.com/articles/12791 last-modified: 2022-01-27 description: BackgroundThe recurrent evolution of the C4 photosynthetic pathway in angiosperms represents one of the most extraordinary examples of convergent evolution of a complex trait. Comparative genomic analyses have unveiled some of the molecular changes associated with the C4 pathway. For instance, several key enzymes involved in the transition from C3 to C4 photosynthesis have been found to share convergent amino acid replacements along C4 lineages. However, the extent of convergent replacements potentially associated with the emergence of C4 plants remains to be fully assessed. Here, we conducted an organelle-wide analysis to determine if convergent evolution occurred in multiple chloroplast proteins beside the well-known case of the large RuBisCO subunit encoded by the chloroplast gene rbcL.MethodsOur study was based on the comparative analysis of 43 C4 and 21 C3 grass species belonging to the PACMAD clade, a focal taxonomic group in many investigations of C4 evolution. We first used protein sequences of 67 orthologous chloroplast genes to build an accurate phylogeny of these species. Then, we inferred amino acid replacements along 13 C4 lineages and 9 C3 lineages using reconstructed protein sequences of their reference branches, corresponding to the branches containing the most recent common ancestors of C4-only clades and C3-only clades. Pairwise comparisons between reference branches allowed us to identify both convergent and non-convergent amino acid replacements between C4:C4, C3:C3 and C3:C4 lineages.ResultsThe reconstructed phylogenetic tree of 64 PACMAD grasses was characterized by strong supports in all nodes used for analyses of convergence. We identified 217 convergent replacements and 201 non-convergent replacements in 45/67 chloroplast proteins in both C4 and C3 reference branches. C4:C4 branches showed higher levels of convergent replacements than C3:C3 and C3:C4 branches. Furthermore, we found that more proteins shared unique convergent replacements in C4 lineages, with both RbcL and RpoC1 (the RNA polymerase beta’ subunit 1) showing a significantly higher convergent/non-convergent replacements ratio in C4 branches. Notably, more C4:C4 reference branches showed higher numbers of convergent vs. non-convergent replacements than C3:C3 and C3:C4 branches. Our results suggest that, in the PACMAD clade, C4 grasses experienced higher levels of molecular convergence than C3 species across multiple chloroplast genes. These findings have important implications for our understanding of the evolution of the C4 photosynthesis pathway. creator: Claudio Casola creator: Jingjia Li uri: https://doi.org/10.7717/peerj.12791 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Casola and Li title: Soil health and nutrient density: preliminary comparison of regenerative and conventional farming link: https://peerj.com/articles/12848 last-modified: 2022-01-27 description: Several independent comparisons indicate regenerative farming practices enhance the nutritional profiles of crops and livestock. Measurements from paired farms across the United States indicate differences in soil health and crop nutrient density between fields worked with conventional (synthetically-fertilized and herbicide-treated) or regenerative practices for 5 to 10 years. Specifically, regenerative farms that combined no-till, cover crops, and diverse rotations—a system known as Conservation Agriculture—produced crops with higher soil organic matter levels, soil health scores, and levels of certain vitamins, minerals, and phytochemicals. In addition, crops from two regenerative no-till vegetable farms, one in California and the other in Connecticut, had higher levels of phytochemicals than values reported previously from New York supermarkets. Moreover, a comparison of wheat from adjacent regenerative and conventional no-till fields in northern Oregon found a higher density of mineral micronutrients in the regenerative crop. Finally, a comparison of the unsaturated fatty acid profile of beef and pork raised on one of the regenerative farms to a regional health-promoting brand and conventional meat from local supermarkets, found higher levels of omega-3 fats and a more health-beneficial ratio of omega-6 to omega-3 fats. Despite small sample sizes, all three crop comparisons show differences in micronutrient and phytochemical concentrations that suggest soil health is an under appreciated influence on nutrient density, particularly for phytochemicals not conventionally considered nutrients but nonetheless relevant to chronic disease prevention. Likewise, regenerative grazing practices produced meat with a better fatty acid profile than conventional and regional health-promoting brands. Together these comparisons offer preliminary support for the conclusion that regenerative soil-building farming practices can enhance the nutritional profile of conventionally grown plant and animal foods. creator: David R. Montgomery creator: Anne Biklé creator: Ray Archuleta creator: Paul Brown creator: Jazmin Jordan uri: https://doi.org/10.7717/peerj.12848 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2022 Montgomery et al. title: Effects of inorganic mercury exposure in the alveolar bone of rats: an approach of qualitative and morphological aspects link: https://peerj.com/articles/12573 last-modified: 2022-01-26 description: BackgroundIn comparison to organic mercury (MeHg), the environmental inorganic mercury (IHg) can be found in some skin-lightening cosmestics were considered “harmless” for a long time. However, recent studies have shown that long-term exposure to low doses of IHg may affect biological systems. Therefore, this study investigated the effects of IHg long-term exposure to the alveolar bone of adult rats.MethodsAdult Wistar rats were distributed in control and HgCl2 exposed (0.375 mg/kg/day). After 45 days, the rats were euthanized and both blood and hemimandibles were collected. Total blood Hg levels were measured and both inorganic and organic components of the alveolar bone were determined through XRD and ATR-FTIR. The microstructure of the alveolar bone was assessed by using micro-CT and the morphometric analysis was performed by using stereomicroscopy.ResultsAlterations in the physicochemical components of the alveolar bone of exposed animals were observed. The bone changes represented a tissue reaction at the microstructural level, such as bone volume increase. However, no significant dimensional changes (bone height) were observed.ConclusionExposure to IHg at this dose can promote microstructural changes and alteration in the organic and inorganic components in the alveolar bone. creator: Paula Beatriz de Oliveira Nunes creator: Maria Karolina Martins Ferreira creator: Deborah Ribeiro Frazão creator: Leonardo Oliveira Bittencourt creator: Victória dos Santos Chemelo creator: Márcia Cristina Freitas Silva creator: Armando Lopes Pereira-Neto creator: Alan Rodrigo Leal Albuquerque creator: Simone Patricia Aranha Paz creator: Rômulo Simões Angélica creator: Sofia Pessanha creator: Rafael Rodrigues Lima uri: https://doi.org/10.7717/peerj.12573 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Nunes et al. title: miR-148a-3p inhibits the proliferation and migration of bladder cancer via regulating the expression of ROCK-1 link: https://peerj.com/articles/12724 last-modified: 2022-01-26 description: PurposeTo investigate the mechanism of miR-148a-3p regulating the proliferation and migration of bladder tumor cells.Materials and MethodsWe conducted a preliminary study to detect the relative expression of miR-148a-3p in bladder cancer and para-cancerous tissue samples. Three bladder tumor cell lines, T24, 5,637 and UM-UC-3, were selected. The expression levels of miR-148a-3p were artificially regulated with miR-148a-3p mimics and the miR-148a-3p inhibitor. The relative expression levels of miR-148a-3p in the samples of each cell line were determined. Cell Counting Kit-8 (CCK-8) was used to detect cell proliferation, while the effect of the miR-148a-3p mimics and inhibitor on tumor cell migration was detected by wound healing assay. Flow cytometry assay was carried out to explore the effect of miR-148a-3p on cell apoptosis. Dual-luciferase reporter assay was performed in order to verify miR-148a-3p’s target gene. The expressions of ROCK-1 and Bcl-2 were analyzed by western blot.ResultsThe relative expression of miR-148a-3p in tumor and adjacent tissues was assessed with qRT-PCR (P < 0.05) and found to be significantly lower in the tumor tissues than the adjacent tissues. The data obtained from the CCK-8 and wound healing assay showed that intracellular transfection of miR-148a-3p mimics could inhibit cell proliferation and migration, while the miR-148a-3p inhibitor promoted them. Overexpression of miR-148a-3p promoted cell apoptosis in the T24 and 5,637 cell lines. The dual-luciferase reporter assay verified that ROCK-1 is a direct target of miR-148a-3p. Western blot showed that miR-148a-3p overexpression downregulated the expression of ROCK-1 and Bcl-2, while miR-148a-3p knockdown upregulated the expression of ROCK-1 and Bcl-2.ConclusionsWe confirmed that miR-148a-3p was significantly decreased in bladder cancer cells. miR-148a-3p overexpression inhibited bladder cancer cell proliferation and migration, whereas miR-148a-3p knockdown promoted bladder cancer cell proliferation and migration. Moreover, we found that ROCK-1 was a downstream target of miR-148a-3p. We also found that miR-148a-3p induced cell apoptosis by regulating the expression of Bcl-2. However, the deeper mechanism of this regulatory relationship needs further study. creator: Chao Xu creator: Guanwen Zhou creator: Zhuang Sun creator: Zhaocun Zhang creator: Haifeng Zhao creator: Xianzhou Jiang uri: https://doi.org/10.7717/peerj.12724 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2022 Xu et al. title: The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women link: https://peerj.com/articles/12745 last-modified: 2022-01-26 description: BackgroundBody composition indices can be related to musculoskeletal injuries (MI), particularly in physically active groups. However, little is known about the accuracy of these diagnoses as potential predictors of musculoskeletal injuries. Therefore, this study aims to indicate the cut-off points of relative body mass (BMI), fat mass index (FMI), skeletal muscle mass (SMI), and muscle to fat ratio (MFR) and establish its reliability in injury prediction for physically active men and women.MethodsThe sample included 119 physically active individuals aged 23.72 ± 1.12 (66 men body height 1.79 ± 0.07 (m); body weight 80.51 ± 9.85 (kg) and 53 women body height 1.67 ± 0.08 (m); body weight 62 ± 10.72 (kg)), students at university of physical education in Poland. The participants’ physical activity was measured with the International Physical Activity Questionnaire (IPAQ). The relevance of body mass index (BMI), fat mass index (FMI), skeletal muscle mass index (SMI), and muscle to fat ratio (MFR) in detecting injury risk was examined. Musculoskeletal injuries during 1 year before examination were registered using a self-reporting questionnaire. The areas under the curve (AUC) and Youden Index in the receiver operating characteristic curve (ROC) were calculated.ResultsThe cut-off points used to classify the indices among men were BMI = 24.38; FMI = 3.74; SMI = 16.40; MFR = 3.70; and for women BMI = 20.90; FMI = 4.17; SMI = 8.96; MFR = 1.67. Results suggested the greatest reliability in the prediction of musculoskeletal injuries among men had BMI (AUC = 0.623; Youden = 0.30) and SMI (AUC = 0.608; Youden = 0.23) whereas among women, MFR (AUC = 0.628; Youden = 0.29) and FMI (AUC = 0.614; Youden = 0.32).ConclusionBMI and SMI are the most appropriate indices to predict the risk of musculoskeletal injury in physically active men, whereas in women, MFR and FMI are more reliable. These results indicate that the indices with more muscle mass meaning are better in predicting injury among men. In contrast, indices with a higher contribution of fat are better for women. It indicates sex differentiation of injury risk conditions. Men should focus on developing muscle mass, whereas women should reduce body fat to decrease injury risk. However, widespread use seemed to be limited to the specific examined group. Therefore, cut-off points should be used with caution, and calculated values should be verified and confirmed in subsequent studies. creator: Jarosław Domaradzki creator: Dawid Koźlenia uri: https://doi.org/10.7717/peerj.12745 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Domaradzki and Koźlenia title: Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals link: https://peerj.com/articles/12840 last-modified: 2022-01-26 description: In massive bleaching events (losing symbiotic algae from corals), more sensitive corals are bleached earlier than other corals. To perform a comparison of bleaching susceptibility within and across coral species, a simple quantitative method is required. Accordingly, we present a laboratory-based method for comparing the bleaching susceptibility of various coral species by using a standardized image analysis protocol. Coral fragments were sampled from the colonies of five species selected from Kenting, southern Taiwan, and maintained in the same aquarium tank with circulating seawater; 2 seawater temperature regimes were used (i.e., fast-heating program (FHP), with a heating rate of 1 °C per day; and slow-heating program (SHP), with a heating rate of 1 °C per 3 days). Each coral fragment was photographed periodically, and the colored images were subsequently converted to grayscale images and then digitally analyzed to determine the standardized grayscale values (G0) by comparing with that of standard color strip. The G0 of a sample at each time of photographing during bleaching was divided by the difference of G0 between the acclimating and the same but completely bleached fragment to derive the relative grayscale (RG%) at a particular stage of bleaching; this is done for each coral fragment of a colony. The smaller the RG% of a coral fragment the closer it is approaching completely bleached condition. The level of decrease in RG% within a time series of images in each heating regime was used to establish a bleaching time index (BTI). The lower the BTI, the sooner to reach a defined bleaching level (e.g., 30%), this indicates the coral is more sensitive to thermal bleaching. In the experiment, we compared the bleaching susceptibility of the five species. Based on the proposed BTI, the five species were ranked in terms of bleaching susceptibility, and the rankings were identical between the two temperature regimes; three species in Pocilloporidae had lower BTI, whereas the hydrocoral Millepora species had the highest BTI. Within each heating regime, the BTI of different species were ranked and used to indicate susceptibility. In the FHP, the three Pocilloporidae species could be divided into two groups in terms of bleaching susceptibility. FHP not only displayed a higher differentiating capability on coal bleaching susceptibility than SHP, but also had a faster completion time, thus reducing the likelihood of unforeseen complications during the tank experiments. Our color-based method is easier and less effort-intensive than methods involving the assessment of zooxanthellae densities. Moreover, it requires much fewer replicates and all samples in one large tank (e.g., 300 L) for the studies considering multiple species comparisons. This method opens opportunities for studying the effects of species types, acclimatization (e.g., seasons), and environmental factors other than temperature on coral bleaching. creator: Jih-Terng Wang creator: Chi-Wei Chu creator: Keryea Soong uri: https://doi.org/10.7717/peerj.12840 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al.