Hypoxia and metabolic inhibitors alter the intracellular ATP:ADP ratio and membrane potential in human coronary artery smooth muscle cells
ATP-sensitive potassium (KATP) channels couple cellular metabolism to excitability, making them ideal candidate sensors for hypoxic vasodilation. However, it is still unknown whether cellular nucleotide levels are affected sufficiently to activate vascular KATP channels during hypoxia. To address this fundamental issue, we measured changes in the intracellular ATP:ADP ratio using the biosensors Perceval/PercevalHR, and membrane potential using the fluorescent probe DiBAC4(3) in human coronary artery smooth muscle cells (HCASMCs). ATP:ADP ratio was significantly reduced by exposure to hypoxia. Application of metabolic inhibitors for oxidative phosphorylation also reduced ATP:ADP ratio. Hyperpolarization caused by inhibiting oxidative phosphorylation was blocked by either 10 µM glibenclamide or 60 mM K+. Hyperpolarization caused by hypoxia was abolished by 60 mM K+ but not by individual K+ channel inhibitors. Taken together, these results suggest hypoxia causes hyperpolarization in part by modulating K+ channels in SMCs.
Yang et al. (2020) Hypoxia and metabolic inhibitors alter the intracellular ATP:ADP ratio and membrane potential in human coronary artery smooth muscle cells. PeerJ 8:e10344 https://doi.org/10.7717/peerj.10344
Exogenous Fe2+ alleviated the toxicity of CuO nanoparticles on Pseudomonas tolaasii Y-11 under different nitrogen sources
Extensive use of CuO nanoparticles (CuO-NPs ) inevitably leads to their accumulation in wastewater and toxicity to microorganisms that effectively treat nitrogen pollution. Due to the effects of different mediums, the sources of CuO-NPs-induced toxicity to microorganisms and methods to mitigating the toxicity are still unclear. In this study, CuO-NPs were found to impact the nitrate reduction of Pseudomonas tolaasii Y-11 mainly through the action of NPs themselves while inhibiting the ammonium transformation of strain Y-11 through releasing Cu2+. As the content of CuO-NPs increased from 0 to 20 mg/L, the removal efficiency of NO3− and NH4+ decreased from 42.29% and 29.83% to 2.05% and 2.33%, respectively. Exogenous Fe2+ significantly promoted the aggregation of CuO-NPs, reduced the possibility of contact with bacteria, and slowed down the damage of CuO-NPs to strain Y-11. When 0.01 mol/L Fe2+ was added to 0, 1, 5, 10 and 20 mg/L CuO-NPs treatment, the removal efficiencies of NO3- were 69.77%, 88.93%, 80.51%, 36.17% and 2.47%, respectively; the removal efficiencies of NH4+ were 55.95%, 96.71%, 38.11%, 20.71% and 7.43%, respectively. This study provides a method for mitigating the toxicity of CuO-NPs on functional microorganisms.
Environmental Contamination and Remediation
Yang et al. (2020) Exogenous Fe2+ alleviated the toxicity of CuO nanoparticles on Pseudomonas tolaasii Y-11 under different nitrogen sources. PeerJ 8:e10351 https://doi.org/10.7717/peerj.10351
Effects of rhodioloside on the neurological functions of rats with total cerebral ischemia/reperfusion and cone neuron injury in the hippocampal CA1 region
Rhodioloside, the main effective constituent of Rhodiola rosea, demonstrates antiaging and antioxidative stress functions and inhibits calcium overloading in cells. These functions imply that rhodioloside may exert protective effects on hippocampal neurons after total cerebral ischemia/reperfusion injury. In this study, male Wistar rat models of total cerebral ischemia were constructed and randomly divided into four groups: sham-operation, ischemia/reperfusion, low-dosage, and high-dosage groups. The result showed that rhodioloside treatment reduced the apoptosis rates of hippocampal neurons and the histological grades of cone cells in the hippocampal CA1 region, but neuronal density was significantly increased. Besides, the protein expressions of Bcl-2/Bax and p53 were measured and found Bcl-2/Bax was increased and p53 protein level was reduced. Therefore, rhodioloside might have protective effects on rats with ischemia/reperfusion brain injury.
Zhang et al. (2020) Effects of rhodioloside on the neurological functions of rats with total cerebral ischemia/reperfusion and cone neuron injury in the hippocampal CA1 region. PeerJ 8:e10056 https://doi.org/10.7717/peerj.10056
The land flatworm Amaga expatria (Geoplanidae) in Guadeloupe and Martinique: new reports and molecular characterization including complete mitogenome
Background The land flatworm Amaga expatria Jones & Sterrer, 2005 (Geoplanidae) was described from two specimens collected in Bermuda in 1963 and 1988 and not recorded since. Methods On the basis of a citizen science project, we received observations in the field, photographs and specimens from non-professionals and local scientists in Martinique and Guadeloupe. We barcoded (COI) specimens from both islands and studied the histology of the reproductive organs of one specimen. Based on Next Generation Sequencing, we obtained the complete mitogenome of A. expatria and some information on its prey from contaminating DNA. Results We add records from 2006 to 2019 in two French islands of the Caribbean arc, Guadeloupe (six records) and Martinique (14 records), based on photographs obtained from citizen science and specimens examined. A specimen from Martinique was studied for histology of the copulatory organs and barcoded for the COI gene; its anatomy was similar to the holotype, therefore confirming species identification. The COI gene was identical for several specimens from Martinique and Guadeloupe and differed from the closest species by more than 10%; molecular characterisation of the species is thus possible by standard molecular barcoding techniques. The mitogenome is 14,962 bp in length and contains 12 protein coding genes, two rRNA genes and 22 tRNA genes; for two protein genes it was not possible to determine the start codon. The mitogenome was compared with the few available mitogenomes from geoplanids and the most similar was Obama nungara, a species from South America. An analysis of contaminating DNA in the digestive system suggests that A. expatria preys on terrestrial molluscs, and citizen science observations in the field suggest that prey include molluscs and earthworms; the species thus could be a threat to biodiversity of soil animals in the Caribbean.
Justine et al. (2020) The land flatworm Amaga expatria (Geoplanidae) in Guadeloupe and Martinique: new reports and molecular characterization including complete mitogenome. PeerJ 8:e10098 https://doi.org/10.7717/peerj.10098
Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats
Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.
Fu et al. (2020) Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats. PeerJ 8:e10217 https://doi.org/10.7717/peerj.10217
Loading history changes the morphology and compressive force-induced expression of receptor activator of nuclear factor kappa B ligand/osteoprotegerin in MLO-Y4 osteocytes
Background In this study, we investigated the effect of the mechanical loading history on the expression of receptor activator of nuclear factor kappa B ligand (RANKL) and osteoprotegerin (OPG) in MLO-Y4 osteocyte-like cells. Methods Three hours after MLO-Y4 osteocytes were seeded, a continuous compressive force (CCF) of 31 dynes/cm2 with or without additional CCF (32 dynes/cm2) was loaded onto the osteocytes. After 36 h, the additional CCF (loading history) was removed for a recovery period of 10 h. The expression of RANKL, OPG, RANKL/OPG ratio, cell numbers, viability and morphology were time-dependently examined at 0, 3, 6 and 10 h. Then, the same additional CCF was applied again for 1 h to all osteocytes with or without the gap junction inhibitor to examine the expression of RANKL, OPG, the RANKL/OPG ratio and other genes that essential to characterize the phenotype of MLO-Y4 cells. Fluorescence recovery after photobleaching technique was also applied to test the differences of gap-junctional intercellular communications (GJIC) among MLO-Y4 cells. Results The expression of RANKL and OPG by MLO-Y4 osteocytes without a loading history was dramatically decreased and increased, respectively, in response to the 1-h loading of additional weight. However, the expression of RANKL, OPG and the RANKL/OPG ratio were maintained at the same level as in the control group in the MLO-Y4 osteocytes with a loading history but without gap junction inhibitor treatment. Treatment of loading history significantly changed the capacity of GJIC and protein expression of connexin 43 (Cx43) but not the mRNA expression of Cx43. No significant difference was observed in the cell number or viability between the MLO-Y4 osteocyte-like cells with and without a loading history or among different time checkpoints during the recovery period. The cell morphology showed significant changes and was correlated with the expression of OPG, Gja1 and Dmp1 during the recovery period. Conclusion Our findings indicated that the compressive force-induced changes in the RANKL/OPG expression could be habituated within at least 11 h by 36-h CCF exposure. GJIC and cell morphology may play roles in response to loading history in MLO-Y4 osteocyte-like cells.
Wang et al. (2020) Loading history changes the morphology and compressive force-induced expression of receptor activator of nuclear factor kappa B ligand/osteoprotegerin in MLO-Y4 osteocytes. PeerJ 8:e10244 https://doi.org/10.7717/peerj.10244
MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpressed transcripts, it is possible to efficiently narrow candidate genes encoding pathway enzymes and more easily predict both functions and functional associations. Mutual Rank (MR)-based coexpression analyses in plants accurately demonstrate functional associations for many specialized metabolic pathways; however, despite the clear predictive value of MR analyses, the application is uncommonly used to drive new pathway discoveries. Moreover, many coexpression databases aid in the prediction of both functional associations and gene functions, but lack customizability for refined hypothesis testing. To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses. MutRank provides an intuitive graphical user interface with multiple customizable features that integrates user-provided data and supporting information suitable for personal computers. Tabular and graphical outputs facilitate the rapid analyses of both unbiased and user-defined coexpression results that accelerate gene function predictions. We highlight the recent utility of MR analyses for functional predictions and discoveries in defining two maize terpenoid antibiotic pathways. Beyond applications in biosynthetic pathway discovery, MutRank provides a simple, customizable and user-friendly interface to enable coexpression analyses relating to a breadth of plant biology inquiries. Data and code are available at GitHub: https://github.com/eporetsky/MutRank.
Poretsky et al. (2020) MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. PeerJ 8:e10264 https://doi.org/10.7717/peerj.10264
Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans
Effects of substrate and water depth on the physiological status of a submerged macrophyte, Vallisneria natans (Lour.) H. Hara, were determined by measuring biomarkers in leaves and roots, to understand factors limiting the re-establishment of V. natans in urban eutrophic ponds. Ramets of V. natans were grown in the laboratory using aquaria containing water and bottom mud from a eutrophic pond and maintained under sufficient light in an incubator. The growth and chlorophyll-a (Chl-a) content of leaves were greater in aquaria with mud than in those with sand, which was used as the reference substrate. The contents of a peroxidation product (malondialdehyde (MDA)) and three antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD)) in leaves and roots, used as stress biomarkers, changed during the experiment, although differences in these contents between mud and sand were not consistent across the experimental days. To control water depth in the field, ramets of V. natans were grown in cages with different substrates (mud and sand) installed at different depths (0.5, 1.2, and 2.0 m) in the pond. The mean light quantum during the experiment decreased with increasing depth, from 79.3 μmol/m2 s at 0.5 m to 7.9 μmol/m2 s at 2.0 m. The Chl-a content in leaves decreased, whereas the MDA content in both leaves and roots increased with increasing water depth. All enzyme activities increased at the beginning and then decreased to the end of the experiment at 2.0 m depth, suggesting deterioration of enzyme activities due to depth-related stress. The MDA content and CAT activity were higher for sand than for mud, whereas the difference in the growth and the leaf Chl-a content between substrates remained unclear in the pond. On comparing the laboratory and field experiments, the leaf Chl-a content was found to be lower and the MDA content and enzyme activities exhibited sharp increase for ramets grown in the pond, even at 0.5 m depth, when compared with those grown in the aquaria. Our results suggest that the bottom mud of the pond is not the major limiting factor in the re-establishment of V. natans. Because water depth and light attenuation exerted strong stress on V. natans, shallow areas or measures to improve water transparency are required to promote the introduction of V. natans in eutrophic ponds for successful restoration in urban areas.
Hao et al. (2020) Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans. PeerJ 8:e10273 https://doi.org/10.7717/peerj.10273
The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species
Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.
Santos et al. (2020) The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species. PeerJ 8:e10274 https://doi.org/10.7717/peerj.10274
Foraging efficiency, social status and body condition in group-living horses and ponies
Individual animals experience different costs and benefits associated with group living, which may impact on their foraging efficiency in ways not yet well specified. This study investigated associations between social dominance, body condition and interruptions to foraging behaviour in a cross-sectional study of 116 domestic horses and ponies, kept in 20 discrete herds. Social dominance was measured for each individual alongside observations of winter foraging behaviour. During bouts of foraging, the duration, frequency and category (vigilance, movement, social displacements given and received, scratching and startle responses) of interruptions were recorded, with total interruption time taken as a proxy measure of foraging efficiency. Total foraging time was not influenced by body condition or social dominance. Body condition was associated with social dominance, but more strongly associated with foraging efficiency. Specifically, lower body condition was associated with greater vigilance. This demonstrates that factors other than social dominance can result in stable differences in winter body condition.
Giles et al. (2020) Foraging efficiency, social status and body condition in group-living horses and ponies. PeerJ 8:e10305 https://doi.org/10.7717/peerj.10305