title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1498 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Sorption to soil, biochar and compost: is prediction to multicomponent mixtures possible based on single sorbent measurements? link: https://peerj.com/articles/4996 last-modified: 2018-06-11 description: Amendment with biochar and/or compost has been proposed as a strategy to remediate soil contaminated with low levels of polycyclic aromatic hydrocarbons. The strong sorption potential of biochar can help sequestering contaminants while the compost may promote their degradation. An improved understanding of how sorption evolves upon soil amendment is an essential step towards the implementation of the approach. The present study reports on the sorption of pyrene to two soils, four biochars and one compost. Detailed isotherm analyzes across a wide range of concentration confirmed that soil amendments can significantly increase the sorption of pyrene. Comparisons of data obtained by a classical batch and a passive sampling method suggest that dissolved organic matter did not play a significant role on the sorption of pyrene. The addition of 10% compost to soil led to a moderate increase in sorption (<2-fold), which could be well predicted based on measurements of sorption to the individual components. Hence, our result suggest that the sorption of pyrene to soil and compost can be relatively well approximated by an additive process. The addition of 5% biochar to soil (with or without compost) led to a major increase in the sorption of pyrene (2.5–4.7-fold), which was, however, much smaller than that suggested based on the sorption measured on the three individual components. Results suggest that the strong sorption to the biochar was attenuated by up to 80% in the presence of soil and compost, much likely due to surface and pore blockage. Results were very similar in the two soils considered, and collectively suggest that combined amendments with compost and biochar may be a useful approach to remediate soils with low levels of contamination. Further studies carried out in more realistic settings and over longer periods of time are the next step to evaluate the long term viability of remediation approaches based on biochar amendments. creator: Melanie Kah creator: Gabriel Sigmund creator: Pedro Luis Manga Chavez creator: Lucie Bielská creator: Thilo Hofmann uri: https://doi.org/10.7717/peerj.4996 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kah et al. title: Trace fossils on dinosaur bones reveal ecosystem dynamics along the coast of eastern North America during the latest Cretaceous link: https://peerj.com/articles/4973 last-modified: 2018-06-11 description: Direct evidence of paleoecological processes is often rare when the fossil record is poor, as in the case of the Cretaceous of eastern North America. Here, I describe a femur and partial tibia shaft assignable to theropods from two Late Cretaceous sites in New Jersey. The former, identifiable as the femur of a large ornithomimosaur, bears several scores interpreted as shark feeding traces. The tibia shaft has punctures and flaked bone from the bites of mid-sized crocodyliforms, the first documented occurrence of crocodyliform traces on dinosaur bone from the Maastrichtian of the Atlantic Coastal Plain. The surface of the partial tibia is also littered with indentations interpreted as the traces of invertebrates, revealing a microcosm of biological interaction on the coastal seafloor of the Cretaceous Atlantic Ocean. Massive crocodyliforms, such as Deinosuchus rugosus and the slightly smaller Deltasuchus motherali, maintained the role of terrestrial vertebrate taphonomic process drivers in eastern North America during the Cretaceous. The report of crocodyliform bite marks on the ornithomimosaur tibia shaft in this manuscript reinforces the importance of the role of crocodyliforms in the modification of terrestrial vertebrate remains during the Cretaceous in North America. The preserved invertebrate traces add to the sparse record of the presence of barnacles and other marine invertebrates on dinosaur bone, and the evidence of shark feeding on the ornithomimosaur femur support the “bloat-and-float” model of terrestrial vertebrate fossil deposition in marine deposits from the Cretaceous of eastern North America. creator: Chase D. Brownstein uri: https://doi.org/10.7717/peerj.4973 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brownstein title: How well do force fields capture the strength of salt bridges in proteins? link: https://peerj.com/articles/4967 last-modified: 2018-06-11 description: Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction. creator: Mustapha Carab Ahmed creator: Elena Papaleo creator: Kresten Lindorff-Larsen uri: https://doi.org/10.7717/peerj.4967 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ahmed et al. title: Pretreating mesenchymal stem cells with electrical stimulation causes sustained long-lasting pro-osteogenic effects link: https://peerj.com/articles/4959 last-modified: 2018-06-11 description: BackgroundElectrical stimulation (ES) has a long history of successful use in the clinical treatment of refractory, non-healing bone fractures and has recently been proposed as an adjunct to bone tissue-engineering treatments to optimize their therapeutic potential. This idea emerged from ES’s demonstrated positive effects on stem cell migration, proliferation, differentiation and adherence to scaffolds, all cell behaviors recognized to be advantageous in Bone Tissue Engineering (BTE). In previous in vitro experiments we demonstrated that direct current ES, administered daily, accelerates Mesenchymal Stem Cell (MSC) osteogenic differentiation. In the present study, we sought to define the optimal ES regimen for maximizing this pro-osteogenic effect.MethodsRat bone marrow-derived MSC were exposed to 100 mV/mm, 1 hr/day for three, seven, and 14 days, then osteogenic differentiation was assessed at Day 14 of culture by measuring collagen production, calcium deposition, alkaline phosphatase activity and osteogenic marker gene expression.ResultsWe found that exposing MSC to ES for three days had minimal effect, while seven and 14 days resulted in increased osteogenic differentiation, as indicated by significant increases in collagen and calcium deposits, and expression of osteogenic marker genes Col1a1, Osteopontin, Osterix and Calmodulin. We also found that cells treated with ES for seven days, maintained this pro-osteogenic activity long (for at least seven days) after discontinuing ES exposure.DiscussionThis study showed that while three days of ES is insufficient to solicit pro-osteogenic effects, seven and 14 days significantly increases osteogenic differentiation. Importantly, we found that cells treated with ES for only seven days, maintained this pro-osteogenic activity long after discontinuing ES exposure. This sustained positive osteogenic effect is likely due to the enhanced expression of RunX2 and Calmodulin we observed. This prolonged positive osteogenic effect, long after discontinuing ES treatment, if incorporated into BTE treatment protocols, could potentially improve outcomes and in doing so help BTE achieve its full therapeutic potential. creator: Maria Eischen-Loges creator: Karla M.C. Oliveira creator: Mit B. Bhavsar creator: John H. Barker creator: Liudmila Leppik uri: https://doi.org/10.7717/peerj.4959 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Eischen-Loges et al. title: Two new species of Primulina (Gesneriaceae) from limestone karsts of China link: https://peerj.com/articles/4946 last-modified: 2018-06-11 description: The limestone karst area of South China is a major biodiversity hotspot of global terrestrial biomes. During extensive field work on the Guangxi limestone formations, two unknown species of Gesneriaceae were collected. After conducting a comprehensive study of the literature and herbarium specimens, Primulina davidioides and P. hiemalis are recognized as two species new to science, and described and illustrated here. P. davidioides is morphologically close to P. lunglinensis based on the shape of the leaf and flower, but it can be easily distinguished by the shape of the bracts, corolla and stigma, indumentum of peduncles, pedicels and pistil and number of staminodes. P. hiemalis is closely relate to P. luzhaiensis in vegetative appearance, but differs in the shape of the calyx and stigma, number of bracts and staminodes, indumentum of the leaf blade and peduncle, and position of stamens in the corolla tube. Considering that not enough is known about their populations, it is proposed that their conservation statuses should currently be classed as data deficient (DD) according to the IUCN Red List Category and Criteria. creator: Xin Hong creator: Zhong-Lin Li creator: Jia-Zhi Liu creator: Shou-Biao Zhou creator: Wei-Hua Qin creator: Fang Wen uri: https://doi.org/10.7717/peerj.4946 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hong et al. title: Cortical bone adaptation and mineral mobilization in the subterranean mammal Bathyergus suillus (Rodentia: Bathyergidae): effects of age and sex link: https://peerj.com/articles/4944 last-modified: 2018-06-11 description: The patterns of bone modeling and mineral mobilization (skeletal homeostasis) among mammals other than humans and laboratory rodents are still poorly known. In this study we assessed the pattern of bone formation and bone resorption in the femur of a wild population of Cape dune molerats, Bathyergus suillus (n = 41) (Bathyergidae), a solitary subterranean mammal with a marked extended longevity among rodents, and which also lives in a naturally deficient state of vitamin D. In order to determine ontogenetic and sex effects on histomorphometric parameters of transversal undecalcified bone sections, two-way ANOVA, linear mixed-effects model and regression statistical analyses were performed. During ontogeny, B. suillus increased their cross sectional area, cortical area and cortical thickness, and most importantly, they showed scarce endosteal bone resorption which resulted in a retained medullary cavity size during ontogeny. This resulted in a positively imbalanced bone modeling, where bone formation considerably surpasses bone loss by almost 100-fold in adulthood. This differs markedly from other terrestrial mammals with relatively thin cortical walls. Regarding bone loss and remodeling, three main processes involving intracortical resorption were observed: modeling-related bone loss in early postnatal growth; secondary osteon formation occurring in both sexes; and subendosteal secondary reconstruction observed only in females. The latter is accompanied by females having six-fold more relative bone loss than males, which is evidenced by the development of enlarged resorption cavities (RCs) distributed circumferentially around the medullary cavity. Males have smaller, more circular and randomly distributed RCs. In general, our data indicate no age-related decline in mineral content in B. suillus, and provides strong support for a pattern of sexual dimorphism in skeletal homeostasis, similar to that occurring in humans and other mammals, with females losing more bone throughout aging as compared to males due to reproductive factors. Interestingly as well, despite the high mechanical loads experienced during burrow construction, bone remodeling in B. suillus is kept at very low levels throughout their lifespan, and dense Haversian tissue never forms. This study represents the first comprehensive assessment of skeletal homeostasis in a subterranean mammal, and it enables a better understanding of the complex processes governing the acquisition and maintenance of bone properties in this species with extraordinary fossorial adaptations. creator: Germán Montoya-Sanhueza creator: Anusuya Chinsamy uri: https://doi.org/10.7717/peerj.4944 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Montoya-Sanhueza and Chinsamy title: Sex-based differences in anti-predator response of crickets to chemical cues of a mammalian predator link: https://peerj.com/articles/4923 last-modified: 2018-06-11 description: Anti-predator behaviors like vigilance or hiding come at the expense of other fitness increasing behaviors such as foraging. To compensate for this trade-off, prey assess predation risk and modify the frequency of anti-predator behaviors according to the likelihood of the threat. In this study, we tested the ability of house crickets (Acheta domesticus) to indirectly assess predation risk via odors from a mammalian predator, Elliot’s short-tailed shrew (Blarina hylophaga). As natural differences in encounter rates and predation risk differs between sexes, we tested if male and female crickets perceive similar rates of predation risk from the presence of shrew odor measured via anti-predator behavioral response. Crickets were placed in enclosed, cardboard-lined chambers either treated with shrew odor or control, along with a food source. Time until foraging was measured for each individual and compared across treatment and sex. We found that in the presence of shrew odor, female crickets delayed foraging while males showed no response. These results suggest adult crickets can use chemical cues to detect mammalian predators. Furthermore, we demonstrate that female crickets associate greater predation risk from shrew predators than do male crickets, which are more stationary yet acoustically conspicuous. As predation risk potentially differs drastically for each sex, changes to the operational sex ratios of wild cricket populations could be influenced by the identity of the predator community. creator: Brian P. Tanis creator: Bradley Bott creator: Brian J. Gaston uri: https://doi.org/10.7717/peerj.4923 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tanis et al. title: Diversity and abundance of conspicuous macrocrustaceans on coral reefs differing in level of degradation link: https://peerj.com/articles/4922 last-modified: 2018-06-11 description: Coral reefs sustain abundant and diverse macrocrustaceans that perform multiple ecological roles, but coral reefs are undergoing massive degradation that may be driving changes in the species composition and abundance of reef-associated macrocrustaceans. To provide insight into this issue, we used non-destructive visual census techniques to compare the diversity and abundance of conspicuous macrocrustaceans (i.e., those >1 cm and visible without disturbance) between two shallow Caribbean coral reefs similar in size (∼1.5 km in length) and close to each other, but one (“Limones”) characterized by extensive stands of the branching coral Acropora palmata, and the other (“Bonanza”) dominated by macroalgae and relic coral skeletons and rubble (i.e., degraded). We also assessed the structural complexity of each reef and the percent cover of various benthic community components. Given the type of growth of A. palmata, we expected to find a greater structural complexity, a higher cover of live coral, and a lower cover of macroalgae on Limones, and hence a more diverse and abundant macrocrustacean community on this reef compared with Bonanza. Overall, we identified 63 macrocrustacean species (61 Decapoda and two Stomatopoda). Contrary to our expectations, structural complexity did not differ significantly between the back-reef zones of these reefs but varied more broadly on Limones, and the diversity and abundance of macrocrustaceans were higher on Bonanza than on Limones despite live coral cover being higher on Limones and macroalgal cover higher on Bonanza. However, the use of various types of microhabitats by macrocrustaceans differed substantially between reefs. On both reefs, the dominant species were the clinging crab Mithraculus coryphe and the hermit crab Calcinus tibicen, but the former was more abundant on Bonanza and the latter on Limones. M. coryphe occupied a diverse array of microhabitats but mostly coral rubble and relic skeletons, whereas C. tibicen was often, but not always, found associated with colonies of Millepora spp. A small commensal crab of A. palmata, Domecia acanthophora, was far more abundant on Limones, emerging as the main discriminant species between reefs. Our results suggest that local diversity and abundance of reef-associated macrocrustaceans are partially modulated by habitat degradation, the diversity of microhabitat types, and the establishment of different commensal associations rather than by structural complexity alone. creator: Roberto González-Gómez creator: Patricia Briones-Fourzán creator: Lorenzo Álvarez-Filip creator: Enrique Lozano-Álvarez uri: https://doi.org/10.7717/peerj.4922 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 González-Gómez et al. title: BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees link: https://peerj.com/articles/4987 last-modified: 2018-06-08 description: Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other methods try to find minimum cuts in some graph. Recently, we introduced Bad Clade Deletion (BCD) supertrees which combines the graph-based computation of minimum cuts with optimizing a global objective function on the matrix representation of the input trees. The BCD supertree method has guaranteed polynomial running time and is very swift in practice. The quality of reconstructed supertrees was superior to matrix representation with parsimony (MRP) and usually on par with SuperFine for simulated data; but particularly for biological data, quality of BCD supertrees could not keep up with SuperFine supertrees. Here, we present a beam search extension for the BCD algorithm that keeps alive a constant number of partial solutions in each top-down iteration phase. The guaranteed worst-case running time of the new algorithm is still polynomial in the size of the input. We present an exact and a randomized subroutine to generate suboptimal partial solutions. Both beam search approaches consistently improve supertree quality on all evaluated datasets when keeping 25 suboptimal solutions alive. Supertree quality of the BCD Beam Search algorithm is on par with MRP and SuperFine even for biological data. This is the best performance of a polynomial-time supertree algorithm reported so far. creator: Markus Fleischauer creator: Sebastian Böcker uri: https://doi.org/10.7717/peerj.4987 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Fleischauer and Böcker title: Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam link: https://peerj.com/articles/4970 last-modified: 2018-06-08 description: Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region. creator: Ton That Huu Dat creator: Georg Steinert creator: Nguyen Thi Kim Cuc creator: Hauke Smidt creator: Detmer Sipkema uri: https://doi.org/10.7717/peerj.4970 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Dat et al.