DAXX mediates high phosphate-induced endothelial cell apoptosis in vitro through activating ERK signaling
Backgroud and Purpose Hyperphosphatemia, which is a high inorganic phosphate (Pi) level in the serum, promotes endothelial cells dysfunction and is associated with cardiovascular diseases in patients with chronic kidney diseases (CKD). However, the underlying mechanism of high Pi-induced endothelia cell apoptosis remains unclear. Methods Human umbilical vein endothelial cells (HUVECs) were treated with normal Pi (1.0 mM) and high Pi (3.0 mM), and then cell apoptosis, abnormal gene expression and potential signaling pathway involvement in simulated hyperphosphatemia were examined using flow cytometry, quantitative PCR (qPCR) and western blot analysis. A two-step 5/6 nephrectomy was carried out to induce CKD and biochemical measurements were taken. Results The rat model of CKD revealed that hyperphosphatemia is correlated with an increased death-domain associated protein (DAXX) expression in endothelial cells. In vitro, high Pi increased the mRNA and protein expression level of DAXX in HUVECs, effects that were reversed by additional phosphonoformic acid treatment. Functionally, high Pi resulted in a significantly increased apoptosis in HUVECs, whereas DAXX knockdown markedly repressed high Pi-induced cell apoptosis, indicating that DAXX mediated high Pi-induced endothelial cell apoptosis. High Pi treatment and DAXX overexpression induced the activation of extracellular regulated protein kinases (ERKs), while DAXX knockdown inhibited high Pi-induced ERKs activation. Finally, we demonstrated that DAXX overexpression induced HUVECs apoptosis in the presence of normal Pi, whereas additional treatment with U0126 (a specific ERK inhibitor) reversed that effect. Conclusion Upregulated DAXX promoted high Pi-induced HUVECs apoptosis by activating ERK signaling and indicated that the DAXX/ERK signaling axis may be served as a potential target for CKD therapy.
Wang et al. (2020) DAXX mediates high phosphate-induced endothelial cell apoptosis in vitro through activating ERK signaling. PeerJ 8:e9203 https://doi.org/10.7717/peerj.9203
Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows (Aimophila and Peucaea, Passerellidae)
The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.
Cicero et al. (2020) Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows (Aimophila and Peucaea, Passerellidae). PeerJ 8:e9249 https://doi.org/10.7717/peerj.9249
Profiling tear proteomes of patients with unilateral relapsed Behcet’s disease-associated uveitis using data-independent acquisition proteomics
Purpose To explore whether unilateral relapse of Bechet’s disease-associated uveitis (BDU) causes differences in the tear proteome between the diseased and the contralateral quiescent eye and potential tear biomarkers for uveitis recurrence and disease monitoring. Method To minimize interindividual variations, bilateral tear samples were collected from the same patient (n = 15) with unilateral relapse of BDU. A data-independent acquisition (DIA) strategy was used to identify proteins that differed between active and quiescent eyes. Results A total of 1,797 confident proteins were identified in the tear samples, of which 381 (21.2%) were also highly expressed in various tissues and organs. Fifty-one (2.8%) proteins differed in terms of expression between tears in active and quiescent eyes, 9 (17.6%) of which were functionally related to immunity or inflammation. Alpha-1-acid glycoprotein 1 (fold change = 3.2, p = 0.007) was increased and Annexin A1 (fold change = −1.7, p < 0.001) was decreased in the tears of the active BDU eye compared to the contralateral quiescent eye. Conclusions A substantial amount of confident proteins were detected in the tears of BDU patients, including proteins that were deferentially expressed in the uveitis-relapsed eyes and the contralateral quiescent eyes. Some of these identified tear proteins play important roles in immune and inflammatory processes. Tear proteome might be a good source of biomarkers for uveitis.
Liang et al. (2020) Profiling tear proteomes of patients with unilateral relapsed Behcet’s disease-associated uveitis using data-independent acquisition proteomics. PeerJ 8:e9250 https://doi.org/10.7717/peerj.9250
Salmo salar fish waste oil: Fatty acids composition and antibacterial activity
Background and aims Fish by-products are generally used to produce fishmeal or fertilizers, with fish oil as a by-product. Despite their importance, fish wastes are still poorly explored and characterized and more studies are needed to reveal their potentiality. The goal of the present study was to qualitatively characterize and investigate the antimicrobial effects of the fish oil extracted from Salmo salar waste samples and to evaluate the potential use of these compounds for treating pathogen infections. Methods Salmo salar waste samples were divided in two groups: heads and soft tissues. Fatty acids composition, and in particular the content in saturated (SAFAs), mono-unsaturated (MUFAs) and Polyunsaturated (PUFAs) fatty acids, was characterized through GC/MS Thermo Focus GC-DSQ II equipped with a ZB-5 fused silica capillary tubes column. The antimicrobial activity of the salmon waste oils was evaluated through the Minimum Inhibitory Concentration assay and the antibiotics contamination was determined by Liquid Chromatography with tandem Mass Spectrometry (LC-MS/MS) analysis. All experiments were done at least in triplicate. Results GC/MS analysis has shown the specific fatty acid composition of the salmon waste oils and their enrichment in MUFAs and PUFAs, with special reference to omega-3, -6, -7, -9 fatty acids. Furthermore, our study has highlighted the antimicrobial activity of the fish waste oil samples against two Gram+ and Gram- bacterial strains. Conclusions These data confirm that the fish waste is still quantitatively and qualitatively an important source of available biological properties that could be extracted and utilized representing an important strategy to counteract infective diseases in the context of the circular economy.
Inguglia et al. (2020) Salmo salar fish waste oil: Fatty acids composition and antibacterial activity. PeerJ 8:e9299 https://doi.org/10.7717/peerj.9299
Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing
Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.
Shtratnikova et al. (2020) Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing. PeerJ 8:e9309 https://doi.org/10.7717/peerj.9309
Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots
Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high–quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.
Teshome et al. (2020) Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots. PeerJ 8:e9314 https://doi.org/10.7717/peerj.9314
Beyond polyphagy and opportunism: natural prey of hunting spiders in the canopy of apple trees
Spiders (Araneae) form abundant and diverse assemblages in agroecosystems such as fruit orchards, and thus might have an important role as natural enemies of orchard pests. Although spiders are polyphagous and opportunistic predators in general, limited information exists on their natural prey at both species and community levels. Thus, the aim of this study was to assess the natural prey (realized trophic niche) of arboreal hunting spiders, their role in trophic webs and their biological control potential with direct observation of predation events in apple orchards. Hunting spiders with prey in their chelicerae were collected in the canopy of apple trees in organic apple orchards in Hungary during the growing seasons between 2013 and 2019 and both spiders and their prey were identified and measured. Among others, the composition of the actual (captured by spiders) and the potential (available in the canopy) prey was compared, trophic niche and food web metrics were calculated, and some morphological, dimensional data of the spider-prey pairs were analyzed. Species-specific differences in prey composition or pest control ability were also discussed. By analyzing a total of 878 prey items captured by spiders, we concluded that arboreal hunting spiders forage selectively and consume a large number of apple pests; however, spiders’ beneficial effects are greatly reduced by their high levels of intraguild predation and by a propensity to switch from pests to alternative prey. In this study, arboreal hunting spiders showed negative selectivity for pests, no selectivity for natural enemies and positive selectivity for neutral species. In the trophic web, the dominant hunting spider taxa/groups (Carrhotus xanthogramma, Philodromus cespitum, Clubiona spp., Ebrechtella tricuspidata, Xysticus spp. and ‘Other salticids’) exhibit different levels of predation on different prey groups and the trophic web’s structure changes depending on the time of year. Hunting spiders show a high functional redundancy in their predation, but contrary to their polyphagous nature, the examined spider taxa showed differences in their natural diet, exhibited a certain degree of prey specialization and selected prey by size and taxonomic identity. Guilds (such as stalkers, ambushers and foliage runners) did not consistently predict either prey composition or predation selectivity of arboreal hunting spider species. From the economic standpoint, Ph. cespitum and Clubiona spp. were found to be the most effective natural enemies of apple pests, especially of aphids. Finally, the trophic niche width of C. xanthogramma and Ph. cespitum increased during ontogeny, resulting in a shift in their predation. These results demonstrate how specific generalist predators can differ from each other in aspects of their predation ecology even within a relatively narrow taxonomic group.
Mezőfi et al. (2020) Beyond polyphagy and opportunism: natural prey of hunting spiders in the canopy of apple trees. PeerJ 8:e9334 https://doi.org/10.7717/peerj.9334
Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs
Early supplementary feeding of lambs before weaning is important to meet their nutritional needs, promote the development of rumen and improve performance. To study the effect of early supplementary feeding on rumen development and the microbiota of lambs, 22 Hu lambs were randomly divided into two groups: one group was fed with milk replacer (group C), and the other group was fed with milk replacer and starter (group S). At 28 days, six lambs in each group were slaughtered, and the rumen content and tissue samples were collected for detection and analysis. The starter significantly promoted the length of rumen papilla (P = 0.03), the concentration of acetate, propionate, butyrate and total volatile fatty acids (TVFA) (P < 0.01), which were higher in group S compared with group C. Group C had a higher rumen microbial diversity than group S. The dominant bacteria in the two groups were the same (Bacteroidetes, Firmicutes and Proteobacteria); however, they differed notably at the genus level. The microbial abundance of the two groups was significantly different for 22 species. In group C, the first three dominant bacteria were Bacteroides, Porphyromonas, and Campylobacter, while in group S they were Succinivibrio, unidentified_Prevotellaceae, and unidentified_Lachnospiraceae. Spearman correlation analysis showed that some ruminal bacteria were closely related to internal environmental factors, e.g., the relative abundances of unidentified_Bacteria, Euryarchaeota, Fusobacteria, and Gracilibacteria correlated negatively with acetate, propionate, butyrate, and TVFA (P < 0.05), while the relative abundances of Firmicutes correlated positively with acetate, propionate, butyrate and TVFA (P < 0.05). Bacteroidetes correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Synergistetes correlated negatively with acetate, propionate, and butyrate (P < 0.05); Deinococcus-Thermus correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Spirochaetes correlated negatively with propionate and TVFA (P < 0.05); and Elusimicrobia correlated negatively with propionate and butyrate (P < 0.05). Actinobacteria and Verrucomicrobia correlated positively correlated with NH3-N. In conclusion, supplementary feeding of lambs before weaning promoted the development of rumen tissue morphology and rumen microorganisms.
Lv et al. (2020) Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs. PeerJ 8:e9353 https://doi.org/10.7717/peerj.9353
Epifaunal invertebrate assemblages associated with branching Pocilloporids in Moorea, French Polynesia
Reef-building corals can harbour high abundances of diverse invertebrate epifauna. Coral characteristics and environmental conditions are important drivers of community structure of coral-associated invertebrates; however, our current understanding of drivers of epifaunal distributions is still unclear. This study tests the relative importance of the physical environment (current flow speed) and host quality (e.g., colony height, surface area, distance between branches, penetration depth among branches, and background partial mortality) in structuring epifaunal communities living within branching Pocillopora colonies on a back reef in Moorea, French Polynesia. A total of 470 individuals belonging to four phyla, 16 families and 39 genera were extracted from 36 Pocillopora spp. colonies. Decapods were the most abundant epifaunal organisms (accounting for 84% of individuals) found living in Pocillopora spp. While coral host characteristics and flow regime are very important, these parameters were not correlated with epifaunal assemblages at the time of the study. Epifaunal assemblages associated with Pocillopora spp. were consistent and minimally affected by differences in host characteristics and flow regime. The consistency in abundance and taxon richness among colonies (regardless of habitat characteristics) highlighted the importance of total habitat availability. With escalating effects of climate change and other localized disturbances, it is critical to preserve branching corals to support epifaunal communities.
Pisapia et al. (2020) Epifaunal invertebrate assemblages associated with branching Pocilloporids in Moorea, French Polynesia. PeerJ 8:e9364 https://doi.org/10.7717/peerj.9364
Response of arbuscular mycorrhizal fungal community in soil and roots to grazing differs in a wetland on the Qinghai-Tibet plateau
Grazing as one of the most important disturbances affects the abundance, diversity and community composition of arbuscular mycorrhizal (AM) fungi in ecosystems, but the AM fungi in response to grazing in wetland ecosystems remain poorly documented. Here, we examined AM fungi in roots and soil in grazing and non-grazing plots in Zoige wetland on the Qinghai-Tibet plateau. Grazing significantly increased AM fungal spore density and glomalin-related soil proteins, but had no significant effect on the extra radical hyphal density of AM fungi. While AM fungal richness and community composition differed between roots and soil, grazing was found to influence only the community composition in soil. This study shows that moderate grazing can increase the biomass of AM fungi and soil carbon sequestration, and maintain the AM fungal diversity in the wetland ecosystem. This finding may enhance our understanding of the AM fungi in response to grazing in the wetland on the Qinghai-Tibet plateau.
Li et al. (2020) Response of arbuscular mycorrhizal fungal community in soil and roots to grazing differs in a wetland on the Qinghai-Tibet plateau. PeerJ 8:e9375 https://doi.org/10.7717/peerj.9375