Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance
Antimicrobial peptides (AMPs) are the main components of the plant innate immune system. Defensins represent the most important AMP family involved in defense and non-defense functions. In this work, global RNA sequencing and de novo transcriptome assembly were performed to explore the diversity of defensin-like (DEFL) genes in the wheat Triticum kiharae and to study their role in induced resistance (IR) mediated by the elicitor metabolites of a non-pathogenic strain FS-94 of Fusarium sambucinum. Using a combination of two pipelines for DEFL mining in transcriptome data sets, as many as 143 DEFL genes were identified in T. kiharae, the vast majority of them represent novel genes. According to the number of cysteine residues and the cysteine motif, wheat DEFLs were classified into ten groups. Classical defensins with a characteristic 8-Cys motif assigned to group 1 DEFLs represent the most abundant group comprising 52 family members. DEFLs with a characteristic 4-Cys motif CX{3,5}CX{8,17}CX{4,6}C named group 4 DEFLs previously found only in legumes were discovered in wheat. Within DEFL groups, subgroups of similar sequences originated by duplication events were isolated. Variation among DEFLs within subgroups is due to amino acid substitutions and insertions/deletions of amino acid sequences. To identify IR-related DEFL genes, transcriptional changes in DEFL gene expression during elicitor-mediated IR were monitored. Transcriptional diversity of DEFL genes in wheat seedlings in response to the fungus Fusarium oxysporum, FS-94 elicitors, and the combination of both (elicitors + fungus) was demonstrated, with specific sets of up- and down-regulated DEFL genes. DEFL expression profiling allowed us to gain insight into the mode of action of the elicitors from F. sambucinum. We discovered that the elicitors up-regulated a set of 24 DEFL genes. After challenge inoculation with F. oxysporum, another set of 22 DEFLs showed enhanced expression in IR-displaying seedlings. These DEFLs, in concert with other defense molecules, are suggested to determine enhanced resistance of elicitor-pretreated wheat seedlings. In addition to providing a better understanding of the mode of action of the elicitors from FS-94 in controlling diseases, up-regulated IR-specific DEFL genes represent novel candidates for genetic transformation of plants and development of pathogen-resistant crops.
Odintsova et al. (2019) Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance. PeerJ 7:e6125 https://doi.org/10.7717/peerj.6125
Direct and indirect parental exposure to endocrine disruptors and elevated temperature influences gene expression across generations in a euryhaline model fish
Aquatic organisms inhabiting polluted waterways face numerous adverse effects, including physiological disruption by endocrine disrupting compounds (EDCs). Little is known about how the temperatures associated with global climate change may influence the response of organisms exposed to EDCs, and the effects that these combined stressors may have on molecular endpoints such as gene expression. We exposed Menidia beryllina (inland silversides) to environmentally relevant concentrations (1 ng/L) of two estrogenic EDCs (bifenthrin and 17α-ethinylestradiol; EE2) at 22 °C and 28 °C. We conducted this experiment over multiple generations to better understand the potential effects to chronically exposed populations in the wild. We exposed adult parental fish (F0) for 14 days prior to spawning of the next generation. F1 larvae were then exposed from fertilization until 21 days post hatch (dph) before being transferred to clean water tanks. F1 larvae were reared to adulthood, then spawned in clean water to test for further effects of parental exposure on offspring (F2 generation). Gene expression was quantified by performing qPCR on F0 and F1 gonads, as well as F1 and F2 larvae. We did not detect any significant differences in the expression of genes measured in the parental or F1 adult gonads. We found that the 28 °C EE2 treatment significantly decreased the expression of nearly all genes measured in the F1 larvae. This pattern was transferred to the F2 generation for expression of the follicle-stimulating hormone receptor (FSHR) gene. Expression of 17β-hydroxysteroid dehydrogenase (17β-HSD) and G protein-coupled receptor 30 (GPR30) revealed changes not measured in the previous generation. Effects of the bifenthrin treatments were not observed until the F2 generation, which were exposed to the chemicals indirectly as germ cells. Our results indicate that effects of EDCs and their interactions with abiotic factors, may not be adequately represented by singular generation testing. These findings will contribute to the determination of the risk of EDC contamination to organisms inhabiting contaminated waterways under changing temperature regimes.
DeCourten et al. (2019) Direct and indirect parental exposure to endocrine disruptors and elevated temperature influences gene expression across generations in a euryhaline model fish. PeerJ 7:e6156 https://doi.org/10.7717/peerj.6156
High tempo music prolongs high intensity exercise
Music has been shown to reduce rating of perceived exertion, increase exercise enjoyment and enhance exercise performance, mainly in low-moderate intensity exercises. However, the effects of music are less conclusive with high-intensity activities. The purpose of this with-participant design study was to compare the effects of high tempo music (130 bpm) to a no-music condition during repeated high intensity cycling bouts (80% of peak power output (PPO)) on the following measures: time to exercise end-point, rating of perceived exertion (RPE), heart rate (HR), breathing frequency, ventilatory kinetics and blood lactate (BL). Under the music condition, participants exercised 10.7% longer (p = 0.035; Effect size (ES) = 0.28) (increase of 1 min) and had higher HR (4%; p = 0.043; ES = 0.25), breathing frequency (11.6%; p < 0.001; ES = 0.57), and RER (7% at TTF; p = 0.021; ES = 1.1) during exercise, as measured at the exercise end-point. Trivial differences were observed between conditions in RPE and other ventilatory kinetics during exercise. Interestingly, 5 min post-exercise termination, HR recovery was 13.0% faster following the music condition (p < 0.05) despite that music was not played during this period. These results strengthen the notion that music can alter the association between central motor drive, central cardiovascular command and perceived exertion, and contribute to prolonged exercise durations at higher intensities along with a quicken HR recovery.
Maddigan et al. (2019) High tempo music prolongs high intensity exercise. PeerJ 6:e6164 https://doi.org/10.7717/peerj.6164
hdac4 mediates perichondral ossification and pharyngeal skeleton development in the zebrafish
Background Histone 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 & Materials In 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. Results Lines 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. Discussion Loss 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.
DeLaurier et al. (2019) hdac4 mediates perichondral ossification and pharyngeal skeleton development in the zebrafish. PeerJ 7:e6167 https://doi.org/10.7717/peerj.6167
The origin of exotic pet sugar gliders (Petaurus breviceps) kept in the United States of America
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.
Campbell et al. (2019) The origin of exotic pet sugar gliders (Petaurus breviceps) kept in the United States of America. PeerJ 7:e6180 https://doi.org/10.7717/peerj.6180
Hardly habitual: chimpanzees and gorillas show flexibility in their motor responses when presented with a causally-clear task
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.
Jacobson et al. (2019) Hardly habitual: chimpanzees and gorillas show flexibility in their motor responses when presented with a causally-clear task. PeerJ 7:e6195 https://doi.org/10.7717/peerj.6195
Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes
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.
Kwon et al. (2019) Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes. PeerJ 6:e5840 https://doi.org/10.7717/peerj.5840
Ocean acidification alters morphology of all otolith types in Clark’s anemonefish (Amphiprion clarkii)
Ocean acidification, the ongoing decline of surface ocean pH and [CO ${}_{3}^{2-}$ 3 2 − ] 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.
Holmberg et al. (2019) Ocean acidification alters morphology of all otolith types in Clark’s anemonefish (Amphiprion clarkii). PeerJ 7:e6152 https://doi.org/10.7717/peerj.6152
Relationship between physical and cognitive performance in community dwelling, ethnically diverse older adults: a cross-sectional study
Background Regular 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. Methods The 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 Discussion Controlling 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). Conclusion Higher 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.
Sherwood et al. (2019) Relationship between physical and cognitive performance in community dwelling, ethnically diverse older adults: a cross-sectional study. PeerJ 7:e6159 https://doi.org/10.7717/peerj.6159
Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range
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.
Cheng et al. (2019) Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range. PeerJ 6:e6162 https://doi.org/10.7717/peerj.6162