Pyrrolizidine alkaloid variation in Senecio vulgaris populations from native and invasive ranges
Biological invasion is regarded as one of the greatest environmental problems facilitated by globalization. Some hypotheses about the invasive mechanisms of alien invasive plants consider the plant–herbivore interaction and the role of plant defense in this interaction. For example, the “Shift Defense Hypothesis” (SDH) argues that introduced plants evolve higher levels of qualitative defense chemicals and decreased levels of quantitative defense, as they are released of the selective pressures from specialist herbivores but still face attack from generalists. Common groundsel (Senecio vulgaris), originating from Europe, is a cosmopolitan invasive plant in temperate regions. As in other Senecio species, S. vulgaris contains pyrrolizidine alkaloids (PAs) as characteristic qualitative defense compounds. In this study, S. vulgaris plants originating from native and invasive ranges (Europe and China, respectively) were grown under identical conditions and harvested upon flowering. PA composition and concentration in shoot and root samples were determined using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). We investigated the differences between native and invasive S. vulgaris populations with regard to quantitative and qualitative variation of PAs. We identified 20 PAs, among which senecionine, senecionine N-oxide, integerrimine N-oxide and seneciphylline N-oxide were dominant in the roots. In the shoots, in addition to the 4 PAs dominant in roots, retrorsine N-oxide, spartioidine N-oxide and 2 non-identified PAs were also prevalent. The roots possessed a lower PA diversity but a higher total PA concentration than the shoots. Most individual PAs as well as the total PA concentration were strongly positively correlated between the roots and shoots. Both native and invasive S. vulgaris populations shared the pattern described above. However, there was a slight trend indicating lower PA diversity and lower total PA concentration in invasive S. vulgaris populations than native populations, which is not consistent with the prediction of SDH.
Cheng et al. (2017) Pyrrolizidine alkaloid variation in Senecio vulgaris populations from native and invasive ranges. PeerJ 5:e3686 https://doi.org/10.7717/peerj.3686
MicroRNAs tend to synergistically control expression of genes encoding extensively-expressed proteins in humans
Considering complicated microRNA (miRNA) biogenesis and action mechanisms, it was thought so high energy-consuming for a cell to afford simultaneous over-expression of many miRNAs. Thus it prompts that an alternative miRNA regulation pattern on protein-encoding genes must exist, which has characteristics of energy-saving and precise protein output. In this study, expression tendency of proteins encoded by miRNAs’ target genes was evaluated in human organ scale, followed by quantitative assessment of miRNA synergism. Expression tendency analysis suggests that universally expressed proteins (UEPs) tend to physically interact in clusters and participate in fundamental biological activities whereas disorderly expressed proteins (DEPs) are inclined to relatively independently execute organ-specific functions. Consistent with this, miRNAs that mainly target UEP-encoding mRNAs, such as miR-21, tend to collaboratively or even synergistically act with other miRNAs in fine-tuning protein output. Synergistic gene regulation may maximize miRNAs’ efficiency with less dependence on miRNAs’ abundance and overcome the deficiency that targeting plenty of genes by single miRNA makes miRNA-mediated regulation high-throughput but insufficient due to target gene dilution effect. Furthermore, our in vitro experiment verified that merely 25 nM transfection of miR-21 be sufficient to influence the overall state of various human cells. Thus miR-21 was identified as a hub in synergistic miRNA–miRNA interaction network. Our findings suggest that synergistic miRNA–miRNA interaction is an important endogenous miRNA regulation mode, which ensures adequate potency of miRNAs at low abundance, especially those implicated in fundamental biological regulation.
Chen et al. (2017) MicroRNAs tend to synergistically control expression of genes encoding extensively-expressed proteins in humans. PeerJ 5:e3682 https://doi.org/10.7717/peerj.3682
Presence of the tunicate Asterocarpa humilis on ship hulls and aquaculture facilities in the coast of the Biobío Region, south central Chile
Non-native ascidians are important members of the fouling community associated with artificial substrata and man-made structures. Being efficient fouling species, they are easily spread by human-mediated transports (e.g., with aquaculture trade and maritime transports). This is exemplified by the ascidian Asterocarpa humilis which displays a wide distribution in the Southern Hemisphere and has been recently reported in the Northern Hemisphere (NW Europe). In continental Chile, its first report dates back from 2000 for the locality of Antofagasta (23°S). Although there was no evidence about the vectors of introduction and spread, nor the source, some authors suggested maritime transport by ship hulls and aquaculture devices as putative introduction pathways and vectors. In the present study, we report for the first time the presence of A. humilis on the hull of an international ship in a commercial port in Concepción bay (36°S), south central Chile. We also found one individual associated to a seashell farm, 70 km far from Concepción bay. Further individuals were subsequently identified within Concepción bay: one juvenile settled upon international harbor pilings and a dozen individuals along aquaculture seashell longlines. For the first specimens sampled, species identification was ascertained using both morphological criteria and molecular barcoding, using the mitochondrial gene cytochrome c oxidase subunit I (COI) and a nuclear gene (ribosomal RNA 18S). The nuclear 18S gene and the mitochondrial gene COI clearly assigned the specimens to A. humilis, confirming our morphological identification. Two haplotypes were obtained with COI corresponding to haplotypes previously obtained with European and Northern Chilean specimens. The present study thus reports for the first time the presence of A. humilis in the Araucanian ecoregion, documenting the apparent expansion of this non-native tunicate in Chile over 2,000 km, spanning over three ecoregions. In addition we reveal the potential implication of the international maritime transport as a vector of spread of this species along the Eastern Pacific coast, and the putative role of aquaculture facilities in promoting local establishments of non-native tunicates.
Pinochet et al. (2017) Presence of the tunicate Asterocarpa humilis on ship hulls and aquaculture facilities in the coast of the Biobío Region, south central Chile. PeerJ 5:e3672 https://doi.org/10.7717/peerj.3672
Planting of neonicotinoid-coated corn raises honey bee mortality and sets back colony development
Worldwide occurrences of honey bee colony losses have raised concerns about bee health and the sustainability of pollination-dependent crops. While multiple causal factors have been identified, seed coating with insecticides of the neonicotinoid family has been the focus of much discussion and research. Nonetheless, few studies have investigated the impacts of these insecticides under field conditions or in commercial beekeeping operations. Given that corn-seed coating constitutes the largest single use of neonicotinoid, our study compared honey bee mortality from commercial apiaries located in two different agricultural settings, i.e. corn-dominated areas and corn-free environments, during the corn planting season. Data was collected in 2012 and 2013 from 26 bee yards. Dead honey bees from five hives in each apiary were counted and collected, and samples were analyzed using a multi-residue LC-MS/MS method. Long-term effects on colony development were simulated based on a honey bee population dynamic model. Mortality survey showed that colonies located in a corn-dominated area had daily mortality counts 3.51 times those of colonies from corn crop-free sites. Chemical analyses revealed that honey bees were exposed to various agricultural pesticides during the corn planting season, but were primarily subjected to neonicotinoid compounds (54% of analysed samples contained clothianidin, and 31% contained both clothianidin and thiamethoxam). Performance development simulations performed on hive populations’ show that increased mortality during the corn planting season sets back colony development and bears contributions to collapse risk but, most of all, reduces the effectiveness and value of colonies for pollination services. Our results also have implications for the numerous large-scale and worldwide-cultivated crops that currently rely on pre-emptive use of neonicotinoid seed treatments.
Samson-Robert et al. (2017) Planting of neonicotinoid-coated corn raises honey bee mortality and sets back colony development. PeerJ 5:e3670 https://doi.org/10.7717/peerj.3670
Exercise training with dietary restriction enhances circulating irisin level associated with increasing endothelial progenitor cell number in obese adults: an intervention study
Objective Circulating endothelial progenitor cells (EPCs) correlate negatively with obesity. Previous studies have shown that exercise significantly restores circulating EPC levels in obese people; however, the underlying mechanisms have not been elucidated. Recently, irisin has been reported to have a critical role in the regulation of EPCs. This exercise-induced myokine has been demonstrated to play a therapeutic role in obesity. In this study, we hypothesized that the increase in circulating irisin may form a link with increasing EPC levels in obese people after exercise. Methods Seventeen obese adults completed an 8-week program of combined exercise and dietary intervention. Clinical characteristics, blood biochemistry, and circulating irisin levels of subjects were measured before and after eight weeks of training. EPC levels were evaluated via flow cytometry, and EPC migratory and adhesive functions were also determined. Results Circulating irisin levels significantly increased following the 8-week training program (P < 0.05). We furthermore observed an improvement in EPC numbers (P < 0.05), and EPC migratory and adhesive functions (P < 0.001 and P < 0.05, respectively) after the intervention. Additionally, we detected a positive correlation between changes in irisin and changes in EPC number (r = 0.52, P < 0.05). Discussion For the first time, a positive correlation between increasing irisin levels and increasing EPC levels has been reported after an 8-week program, consisting of exercise and dietary intervention. This result suggests a novel effect of irisin on the regulation of EPC mobilization, which might contribute to improvement of endothelial function in obese people.
Huang et al. (2017) Exercise training with dietary restriction enhances circulating irisin level associated with increasing endothelial progenitor cell number in obese adults: an intervention study. PeerJ 5:e3669 https://doi.org/10.7717/peerj.3669
The effects of captive versus wild rearing environments on long bone articular surfaces in common chimpanzees (Pan troglodytes)
The physical environments of captive and wild animals frequently differ in substrate types and compliance. As a result, there is an assumption that differences in rearing environments between captive and wild individuals produce differences in skeletal morphology. Here, this hypothesis is tested using a sample of 42 captive and wild common chimpanzees (Pan troglodytes). Articular surface areas of the humerus, radius, ulna, femur, and tibia were calculated from linear breadth measurements, adjusted for size differences using Mosimann shape variables, and compared across sex and environmental groups using two-way ANOVA. Results indicate that the articular surfaces of the wrist and knee differ between captive and wild chimpanzees; captive individuals have significantly larger distal ulna and tibial plateau articular surfaces. In both captive and wild chimpanzees, males have significantly larger femoral condyles and distal radius surfaces than females. Finally, there is an interaction effect between sex and rearing in the articular surfaces of the femoral condyles and distal radius in which captive males have significantly larger surface areas than all other sex-rearing groups. These data suggest that long bone articular surfaces may be sensitive to differences experienced by captive and wild individuals, such as differences in diet, body mass, positional behaviors, and presumed loading environments. Importantly, these results only find differences due to rearing environment in some long bone articular surfaces. Thus, future work on skeletal morphology could cautiously incorporate data from captive individuals, but should first investigate potential intraspecific differences between captive and wild individuals.
Lewton (2017) The effects of captive versus wild rearing environments on long bone articular surfaces in common chimpanzees (Pan troglodytes). PeerJ 5:e3668 https://doi.org/10.7717/peerj.3668
The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes
Background Hypoxia-inducible factor (HIF)-1 is involved in the regulation of hypoxic preconditioning in cardiomyocytes. Under hypoxic conditions, HIF-1α accumulates and is translocated to the nucleus, where it forms an active complex with HIF-1β and activates transcription of approximately 60 kinds of hypoxia-adaptive genes. Microtubules are hollow tubular structures in the cell that maintain cellular morphology and that transport substances. This study attempted to clarify the role of microtubule structure in the endonuclear aggregation of HIF-1α following hypoxic preconditioning of cardiomyocytes. Methods Primary rat cardiomyocytes were isolated and cultured. The cardiomyocyte culture system was used to establish a hypoxia model and a hypoxic preconditioning model. Interventions were performed on primary cardiomyocytes using a microtubule-depolymerizing agent and different concentrations of a microtubule stabilizer. The microtubule structure and the degree of HIF-1α nuclear aggregation were observed by confocal laser scanning microscopy. The expression of HIF-1α in the cytoplasm and nucleus was detected using Western blotting. Cardiomyocyte energy content, reflected by adenosine triphosphate/adenosine diphosphate (ATP/ADP), and key glycolytic enzymes were monitored by colorimetry and high-performance liquid chromatography (HPLC). Reactive oxygen species (ROS) production was also used to comprehensively assess whether microtubule stabilization can enhance the myocardial protective effect of hypoxic preconditioning. Results During prolonged hypoxia, it was found that the destruction of the microtubule network structure of cardiomyocytes was gradually aggravated. After this preconditioning, an abundance of HIF-1α was clustered in the nucleus. When the microtubules were depolymerized and hypoxia pretreatment was performed, HIF-1α clustering occurred around the nucleus, and HIF-1α nuclear expression was low. The levels of key glycolytic enzymes were significantly higher in the microtubule stabilizer group than in the hypoxia group. Additionally, the levels of lactate dehydrogenase and ROS were significantly lower in the microtubule stabilizer group than in the hypoxia group. Conclusion The microtubules of cardiomyocytes may be involved in the process of HIF-1α endonuclear aggregation, helping to enhance the anti-hypoxic ability of cardiomyocytes.
Guo et al. (2017) The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes. PeerJ 5:e3662 https://doi.org/10.7717/peerj.3662
Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton
Calcineurin B-like (CBL) proteins, as calcium sensors, play pivotal roles in plant responses to diverse abiotic stresses and in growth and development through interaction with CBL-interacting protein kinases (CIPKs). However, knowledge about functions and evolution of CBLs in Gossypium plants is scarce. Here, we conducted a genome-wide survey and identified 13, 13 and 22 CBL genes in the progenitor diploid Gossypium arboreum and Gossypium raimondii, and the cultivated allotetraploid Gossypium hirsutum, respectively. Analysis of physical properties, chromosomal locations, conserved domains and phylogeny indicated rather conserved nature of CBLs among the three Gossypium species. Moreover, these CBLs have closer genetic evolutionary relationship with the CBLs from cocoa than with those from other plants. Most CBL genes underwent evolution under purifying selection in the three Gossypium plants. Additionally, nearly all G. hirsutum CBL (GhCBL) genes were expressed in the root, stem, leaf, flower and fiber. Many GhCBLs were preferentially expressed in the flower while several GhCBLs were mainly expressed in roots. Expression patterns of GhCBL genes in response to potassium deficiency were also studied. The expression of most GhCBLs were moderately induced in roots after treatments with low-potassium stress. Yeast two-hybrid experiments indicated that GhCBL1-2, GhCBL1-3, GhCBL4-4, GhCBL8, GhCBL9 and GhCBL10-3 interacted with GhCIPK23, respectively. Our results provided a comprehensive view of the CBLs and valuable information for researchers to further investigate the roles and functional mechanisms of the CBLs in Gossypium.
Lu et al. (2017) Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton. PeerJ 5:e3653 https://doi.org/10.7717/peerj.3653
Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model
Objective The trabecular meshwork (TM) is the primary substrate of outflow resistance in glaucomatous eyes. Repopulating diseased TM with fresh, functional TM cells might be a viable therapeutic approach. Decellularized TM scaffolds have previously been produced by ablating cells with suicide gene therapy or saponin, which risks incomplete cell removal or dissolution of the extracellular matrix, respectively. We hypothesized that improved trabecular meshwork cell ablation would result from freeze-thaw cycles compared to chemical treatment. Materials and Methods We obtained 24 porcine eyes from a local abattoir, dissected and mounted them in an anterior segment perfusion within two hours of sacrifice. Intraocular pressure (IOP) was recorded continuously by a pressure transducer system. After 72 h of IOP stabilization, eight eyes were assigned to freeze-thaw (F) ablation (−80 °C × 2), to 0.02% saponin (S) treatment, or the control group (C), respectively. The TM was transduced with an eGFP expressing feline immunodeficiency viral (FIV) vector and tracked via fluorescent microscopy to confirm ablation. Following treatment, the eyes were perfused with standard tissue culture media for 180 h. TM histology was assessed by hematoxylin and eosin staining. TM viability was evaluated by a calcein AM/propidium iodide (PI) assay. The TM extracellular matrix was stained with Picro Sirius Red. We measured IOP and modeled it with a linear mixed effects model using a B-spline function of time with five degrees of freedom. Results F and S experienced a similar IOP reduction of 30% from baseline (P = 0.64). IOP reduction of about 30% occurred in F within 24 h and in S within 48 h. Live visualization of eGFP demonstrated that F conferred a complete ablation of all TM cells and only a partial ablation in S. Histological analysis and Picro Sirius staining confirmed that no TM cells survived in F while the extracellular matrix remained. The viability assay showed very low PI and no calcein staining in F in contrast to many PI-labeled, dead TM cells and calcein-labeled viable TM cells in S. Conclusion We developed a rapid TM ablation method that uses cyclic freezing that is free of biological or chemical agents and able to produce a decellularized TM scaffold with preserved TM extracellular matrix in an organotypic perfusion culture.
Dang et al. (2017) Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model. PeerJ 5:e3629 https://doi.org/10.7717/peerj.3629
Microbial communities in the reef water at Kham Island, lower Gulf of Thailand
Coral reefs are among the most biodiverse habitats on Earth, but knowledge of their associated marinemicrobiome remains limited. To increase the understanding of the coral reef ecosystem in the lower Gulf of Thailand, this study utilized 16S and 18S rRNA gene-based pyrosequencing to identify the prokaryotic and eukaryotic microbiota present in the reef water at Kham Island, Trat province, Thailand (N6.97 E100.86). The obtained result was then compared with the published microbiota from different coral reef water and marine sites. The coral reefs at Kham Island are of the fringe type. The reefs remain preserved and abundant. The community similarity indices (i.e., Lennon similarity index, Yue & Clayton similarity index) indicated that the prokaryotic composition of Kham was closely related to that of Kra, another fringing reef site in the lower Gulf of Thailand, followed by coral reef water microbiota at GS048b (Cooks Bay, Fr. Polynesia), Palmyra (Northern Line Islands, United States) and GS108b (Coccos Keeling, Australia), respectively. Additionally, the microbial eukaryotic populations at Kham was analyzed and compared with the available database at Kra. Both eukaryotic microbiota, in summer and winter seasons, were correlated. An abundance of Dinophysis acuminata was noted in the summer season, in accordance with its reported cause of diarrhoeatic shellfish outbreak in the summer season elsewhere. The slightly lower biodiversity in Kham than at Kra might reflect the partly habitat difference due to coastal anthropogenic activities and minor water circulation, as Kham locates close to the mainland and is surrounded by islands (e.g., Chang and Kut islands). The global marine microbiota comparison suggested relatively similar microbial structures among coral sites irrespective of geographical location, supporting the importance of coral-associated marine microbiomes, and Spearman’s correlation analysis between community membership and factors of shore distance and seawater temperature indicated potential correlation of these factors (p-values < 0.05) with Kham, Kra, and some other coral and coastal sites. Together, this study provided the second marine microbial database for the coral reef of the lower Gulf of Thailand, and a comparison of the coral-associated marine microbial diversity among global ocean sites.
Somboonna et al. (2017) Microbial communities in the reef water at Kham Island, lower Gulf of Thailand. PeerJ 5:e3625 https://doi.org/10.7717/peerj.3625