title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1432 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: hdac4 mediates perichondral ossification and pharyngeal skeleton development in the zebrafish link: https://peerj.com/articles/6167 last-modified: 2019-01-08 description: BackgroundHistone deacetylases (HDACs) are epigenetic factors that function to repress gene transcription by removing acetyl groups from the N-terminal of histone lysines. Histone deacetylase 4 (HDAC4), a class IIa HDAC, has previously been shown to regulate the process of endochondral ossification in mice via repression of Myocyte enhancer factor 2c (MEF2C), a transcriptional activator of Runx2, which in turn promotes chondrocyte maturation and production of bone by osteoblasts.Methods & MaterialsIn this study, we generated two zebrafish lines with mutations in hdac4 using CRISPR/Cas9 and analyzed mutants for skeletal phenotypes and expression of genes known to be affected by Hdac4 expression.ResultsLines have insertions causing a frameshift in a proximal exon of hdac4 and a premature stop codon. Mutations are predicted to result in aberrant protein sequence and a truncated protein, eliminating the Mef2c binding domain and Hdac domain. Zygotic mutants from two separate lines show a significant increase in ossification of pharyngeal ceratohyal cartilages at 7 days post fertilization (dpf) (p < 0.01, p < 0.001). At 4 dpf, mutant larvae have a significant increase of expression of runx2a and runx2b in the ceratohyal cartilage (p < 0.05 and p < 0.01, respectively). A subset of maternal-zygotic (mz) mutant and heterozygote larvae (40%) have dramatically increased ossification at 7 dpf compared to zygotic mutants, including formation of a premature anguloarticular bone and mineralization of the first and second ceratobranchial cartilages and symplectic cartilages, which normally does not occur until fish are approximately 10 or 12 dpf. Some maternal-zygotic mutants and heterozygotes show loss of pharyngeal first arch elements (25.9% and 10.2%, respectively) and neurocranium defects (30.8% and 15.2%, respectively). Analysis of RNA-seq mRNA transcript levels and in situ hybridizations from zygotic stages to 75–90% epiboly indicates that hdac4 is highly expressed in early embryos, but diminishes by late epiboly, becoming expressed again in larval stages.DiscussionLoss of function of hdac4 in zebrafish is associated with increased expression of runx2a and runx2b targets indicating that a role for hdac4 in zebrafish is to repress activation of ossification of cartilage. These findings are consistent with observations of precocious cartilage ossification in Hdac4 mutant mice, demonstrating that the function of Hdac4 in skeletal development is conserved among vertebrates. Expression of hdac4 mRNA in embryos younger than 256–512 cells indicates that there is a maternal contribution of hdac4 to the early embryo. The increase in ossification and profound loss of first pharyngeal arch elements and anterior neurocranium in a subset of maternal-zygotic mutant and heterozygote larvae suggests that maternal hdac4 functions in cartilage ossification and development of cranial neural crest-derived structures. creator: April DeLaurier creator: Cynthia Lizzet Alvarez creator: Kali J Wiggins uri: https://doi.org/10.7717/peerj.6167 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 DeLaurier et al. title: The origin of exotic pet sugar gliders (Petaurus breviceps) kept in the United States of America link: https://peerj.com/articles/6180 last-modified: 2019-01-08 description: The demand for exotic non-domesticated animals kept as pets in the United States of America (USA) is increasing the exportation rates of these species from their native ranges. Often, illegal harvesting of these species is used to boost captive-bred numbers and meet this demand. One such species, the sugar glider (Petaurus breviceps), endemic to Australia and New Guinea is a popular domestic pet due to its small size and “cute” demeanour. Despite a legal avenue for trade existing in Indonesia, concerns have been raised that sugar gliders may be entering the USA from other parts of their native range where exportation is prohibited such as Australia, Papua New Guinea and the surrounding Indonesian islands. We compared previously published DNA sequences from across the native range of sugar gliders with samples collected from domestically kept sugar gliders within the USA to determine provenance and gene flow between source and introduced populations. Here we show that as predicted, the USA sugar glider population originates from West Papua, Indonesia with no illegal harvesting from other native areas such as Papua New Guinea or Australia evident in the samples tested within this study. creator: Catriona D. Campbell creator: Jill Pecon-Slattery creator: Rebecca Pollak creator: Leo Joseph creator: Clare E. Holleley uri: https://doi.org/10.7717/peerj.6180 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Campbell et al. title: Hardly habitual: chimpanzees and gorillas show flexibility in their motor responses when presented with a causally-clear task link: https://peerj.com/articles/6195 last-modified: 2019-01-08 description: In contrast to reports of wild primates, studies of captive primates’ flexibility often reveal conservatism: individuals are unable to switch to new and more efficient strategies when task demands change. We propose that such conservatism might be a result of task design and hypothesize that conservatism might be linked to primates’ lack of causal understanding in relation to experimental apparatuses. We investigated if chimpanzees (Pan troglodytes) and western lowland gorillas (Gorilla gorilla gorilla) would show greater flexibility when presented with a causally-clear task. We presented six chimpanzees and seven gorillas with a clear tube from which they had to remove straws to release a reward. To first evaluate the apes’ causal understanding, we recorded the efficiency with which the apes solved the task (i.e., whether they only removed straws below the reward, ignoring redundant ones above it). To further explore how they solved the task, we also recorded the order in which they removed the straws, which allowed us to determine if habitual action sequences emerged. All apes spontaneously solved the task in their first trial and across repeated trials the majority of their solutions were efficient (median = 90.9%), demonstrating their understanding of the puzzle. There was individual variation in the consistency of straw removal patterns exhibited by the apes, but no ape developed an exclusive habit in the order with which they removed the straws, further indicating their causal understanding of the task. Next, we presented the apes with a new configuration of the same task that required the apes to remove fewer straws to obtain the reward. All apes switched to a more efficient straw removal sequence even though their previously-successful, but now less-efficient, solution remained available. We theorize that because the apes understood the causality of the task, they did not form habits and were not conservative. creator: Sarah L. Jacobson creator: Lydia M. Hopper uri: https://doi.org/10.7717/peerj.6195 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jacobson and Hopper title: Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes link: https://peerj.com/articles/5840 last-modified: 2019-01-07 description: Inhibition of both MEK1/2 and glycogen synthase kinase-3 (GSK3; 2i system) facilitates the maintenance of naïve stemness for embryonic stem cells in various mammalian species. However, the effect of the inhibition of the 2i system on porcine early embryogenesis is unknown. We investigated the effect of the 2i system on early embryo development, expression of pluripotency-related genes, and epigenetic modifications. Inhibition of MEK1/2 (by PD0325901) and/or GSK3 (by CHIR99021) did not alter the developmental potential of porcine parthenogenetic embryos, but improved blastocyst quality, as judged by the blastocyst cell number, diameter, and reduction in the number of apoptotic cells. The expression levels of octamer-binding transcription factor 4 and SOX2, the primary transcription factors that maintain embryonic pluripotency, were significantly increased by 2i treatments. Epigenetic modification-related gene expression was altered upon 2i treatment. The collective results indicate that the 2i system in porcine embryos improved embryo developmental potential and blastocyst quality by regulating epigenetic modifications and pluripotency-related gene expression. creator: Jeongwoo Kwon creator: Ying-Hua Li creator: Yu-Jin Jo creator: YoungJin Oh creator: Suk Namgoong creator: Nam-Hyung Kim uri: https://doi.org/10.7717/peerj.5840 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kwon et al. title: Ocean acidification alters morphology of all otolith types in Clark’s anemonefish (Amphiprion clarkii) link: https://peerj.com/articles/6152 last-modified: 2019-01-07 description: Ocean acidification, the ongoing decline of surface ocean pH and [CO${}_{3}^{2-}$32−] due to absorption of surplus atmospheric CO2, has far-reaching consequences for marine biota, especially calcifiers. Among these are teleost fishes, which internally calcify otoliths, critical elements of the inner ear and vestibular system. There is evidence in the literature that ocean acidification increases otolith size and alters shape, perhaps impacting otic mechanics and thus sensory perception. Here, larval Clark’s anemonefish, Amphiprion clarkii (Bennett, 1830), were reared in various seawater pCO2/pH treatments analogous to future ocean scenarios. At the onset of metamorphosis, all otoliths were removed from each individual fish and analyzed for treatment effects on morphometrics including area, perimeter, and circularity; scanning electron microscopy was used to screen for evidence of treatment effects on lateral development, surface roughness, and vaterite replacement. The results corroborate those of other experiments with other taxa that observed otolith growth with elevated pCO2, and provide evidence that lateral development and surface roughness increased as well. Both sagittae exhibited increasing area, perimeter, lateral development, and roughness; left lapilli exhibited increasing area and perimeter while right lapilli exhibited increasing lateral development and roughness; and left asterisci exhibited increasing perimeter, roughness, and ellipticity with increasing pCO2. Right lapilli and left asterisci were only impacted by the most extreme pCO2 treatment, suggesting they are resilient to any conditions short of aragonite undersaturation, while all other impacted otoliths responded to lower concentrations. Finally, fish settlement competency at 10 dph was dramatically reduced, and fish standard length marginally reduced with increasing pCO2. Increasing abnormality and asymmetry of otoliths may impact inner ear function by altering otolith-maculae interactions. creator: Robert J. Holmberg creator: Eric Wilcox-Freeburg creator: Andrew L. Rhyne creator: Michael F. Tlusty creator: Alan Stebbins creator: Steven W. Nye Jr. creator: Aaron Honig creator: Amy E. Johnston creator: Christine M. San Antonio creator: Bradford Bourque creator: Robyn E. Hannigan uri: https://doi.org/10.7717/peerj.6152 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Holmberg et al. title: Relationship between physical and cognitive performance in community dwelling, ethnically diverse older adults: a cross-sectional study link: https://peerj.com/articles/6159 last-modified: 2019-01-07 description: BackgroundRegular exercise training stimulates physiological adaptations to improve physical performance, reduce chronic disease risk, and slow age-related cognitive decline. Since the physiological mechanisms responsible for aging-associated cognitive decline are not yet fully understood, and training-induced physiological adaptations responsible for performance measure improvements are specific to the type (aerobic vs. strength) and intensity of training, studies are needed to assess the relationships between physical performance measures and cognitive performance in older adults. These results could be used to guide exercise prescriptions with the goal of improving age-related cognitive performance. The purpose of this study was to investigate the relationship between physical performance measures and cognitive performance in a population of community dwelling, ethnically diverse older adults.MethodsThe cognitive performance of ninety independent, community dwelling participants (69 female, 21 male), aged 75 ± 9.5 years (mean ± SD) was measured with the Modified Mini-Mental State Test (3MS), Trailmaking Tests A and B (TMT A & B), and the Animal Naming test. Sociodemographic (age, sex, ethnicity, medication use, years of education) and anthropometric data were collected, physical activity was assessed with the Physical Activity Scale for the Elderly (PASE), peak hand-grip strength, distance walked in the 6MWT, and heart rate pre-, during, and up to 5 min. post- 6MWT were measured. Forward stepwise multiple regression analyses were performed with each cognitive measure as a dependent variable.Results and DiscussionControlling for sociodemographic covariates, peak heart rate during the 6MWT (6MWT HRPEAK) was positively correlated with performance in the 3MS (p < 0.017), and TMT A (p < 0.001) and B (p < 0.029). Controlling for sociodemographic covariates, PASE was positively (p = 0.001), and β-blocker use negatively (p = 0.035), correlated with performance on the Animal Naming test. Also, controlling for sociodemographic covariates, PASE was positively correlated with performance on the TMT A (p = 0.017). Here we show that higher peak heart rate during the 6MWT is positively correlated with cognitive performance in a population of community dwelling, ethnically diverse older adults (ages 60–95 years).ConclusionHigher peak heart rate during the 6MWT was found to be independently and positively correlated with cognitive function in community-dwelling older adults. Although additional work is needed, these results are promising and suggest that physicians, exercise professionals, and/or fitness/fall prevention programs may use peak heart rate during the 6MWT to easily monitor exercise intensity to support cognitive health. creator: Jennifer J. Sherwood creator: Cathy Inouye creator: Shannon L. Webb creator: Ange Zhou creator: Erik A. Anderson creator: Nicole S. Spink uri: https://doi.org/10.7717/peerj.6159 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sherwood et al. title: Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range link: https://peerj.com/articles/6162 last-modified: 2019-01-07 description: Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant–bacteria interactions in the invasion of this species in China. creator: Dandan Cheng creator: Zhongsai Tian creator: Liang Feng creator: Lin Xu creator: Hongmei Wang uri: https://doi.org/10.7717/peerj.6162 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cheng et al. title: Intestinal parasitic infection alters bacterial gut microbiota in children link: https://peerj.com/articles/6200 last-modified: 2019-01-07 description: The study of the burden that parasites can exert upon the bacterial gut microbiota was restricted by the available technologies and their costs. Currently, next-generation sequencing coupled with traditional methodologies allows the study of eukaryotic parasites (protozoa and helminths) and its effects on the human bacterial gut microbiota diversity. This diversity can be altered by a variety of factors such as age, diet, genetics and parasitic infections among others. The disturbances of the gut microbiota have been associated with a variety of illnesses. Children population in developing countries, are especially susceptible to parasitic infections because of the lack of proper sanitation and undernutrition, allowing both, the thriving of intestinal parasites and profound alteration of the gut microbiota. In this work, we have sampled the stool of 23 children from four different children’s care-centers in Medellin, Colombia, and we have identified the eukaryotic parasites by traditional and molecular methodologies coupled with microbial profiling using 16S rDNA sequencing. This mixed methodology approach has allowed us to establish an interesting relationship between Giardia intestinalis and helminth infection, having both effects upon the bacterial gut microbiota enterotypes, causing a switch from a type I to a type II enterotype upon infection. creator: Miguel A. Toro-Londono creator: Katherine Bedoya-Urrego creator: Gisela M. Garcia-Montoya creator: Ana L. Galvan-Diaz creator: Juan F. Alzate uri: https://doi.org/10.7717/peerj.6200 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Toro-Londono et al. title: Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix link: https://peerj.com/articles/5565 last-modified: 2019-01-04 description: The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH)—though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved—we document and justify all changes to the matrix—but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the “polyphyly hypothesis” (PH—R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid “nectrideans” and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Casineria, in which we tentatively identify a postbranchial lamina, emerges rather far from amniote origins in a gephyrostegid-chroniosuchian grade. Bayesian inference (Analysis EB, settings as in R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes (e.g. preaxial/postaxial polarity in limb development), and prospects for further improvement of this matrix. Even in its revised state, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates. Sufficient improvement will be laborious—but not difficult. creator: David Marjanović creator: Michel Laurin uri: https://doi.org/10.7717/peerj.5565 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Marjanović and Laurin title: Changes in interleukin-27 levels in patients with acute coronary syndrome and their clinical significance link: https://peerj.com/articles/5652 last-modified: 2019-01-04 description: BackgroundThis study evaluated changes in interleukin (IL)-27 levels in patients with acute coronary syndrome (ACS) and their influence on Th1, Th2, and Th17 cells.MethodsSerum levels of IL-27, IL-4, IL-17, and interferon (IFN)-γ in healthy subjects as well as patients with ACS, including stable angina pectoris (SA), unstable angina pectoris (UA), and acute myocardial infarction (AMI), were determined using an enzyme-linked immunosorbent assay. The proportions of Th1, Th2, and Th17 cells among peripheral blood mononuclear cells (PBMCs), were measured using flow cytometry, after incubation with phorbol myristate acetate (PMA) for 4 h. The proportions of Th1 and Th17 cells among PBMCs in AMI and UA were detected after stimulation with IL-27 or PMA + IL-27 for 4, 8, and 12 h.ResultsSerum levels of IL-27 in patients with AMI and UA were significantly lower than those in SA and control groups, while serum levels of IL-17 and IFN-γ in AMI and UA groups were dramatically increased compared to those in SA and healthy control groups. However, there were no statistically significant differences in serum IL-4. The proportions of Th1 and Th17 cells among PBMCs were statistically significantly higher in the AMI and UA groups than those in the SA and control groups, while there was no statistically significant difference in the proportion of Th2 cells among different groups. For patients with AMI and UA, the effect of co-stimulation of PBMCs with PMA and IL-27 was not significantly different from that of PMA single stimulation, while PMA + IL-27 co-stimulation lowered the Th17 cell proportion significantly compared to PMA single stimulation.DiscussionCompared to SA patients and healthy controls, patients with ACS (AMI + UA) had lower serum levels of IL-27 and higher proportions of PBMC Th1 and Th17 cells, which could be attributed to the inhibitory effects of IL-27 on the proliferation of Th17 cells. These results indicated that IL-27 could be a novel therapeutic target in ACS patients. creator: Lin Zhang creator: Junfeng Zhang creator: Shaohong Su creator: Suyan Luo uri: https://doi.org/10.7717/peerj.5652 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al.