Global analysis of A-to-I RNA editing reveals association with common disease variants
RNA editing modifies transcripts and may alter their regulation or function. In humans, the most common modification is adenosine to inosine (A-to-I). We examined the global characteristics of RNA editing in 4,301 human tissue samples. More than 1.6 million A-to-I edits were identified in 62% of all protein-coding transcripts. mRNA recoding was extremely rare; only 11 novel recoding sites were uncovered. Thirty single nucleotide polymorphisms from genome-wide association studies were associated with RNA editing; one that influences type 2 diabetes (rs2028299) was associated with editing in ARPIN. Twenty-five genes, including LRP11 and PLIN5, had editing sites that were associated with plasma lipid levels. Our findings provide new insights into the genetic regulation of RNA editing and establish a rich catalogue for further exploration of this process.
Franzén et al. (2018) Global analysis of A-to-I RNA editing reveals association with common disease variants. PeerJ 6:e4466 https://doi.org/10.7717/peerj.4466
Immobilized TiO2 on glass spheres applied to heterogeneous photocatalysis: photoactivity, leaching and regeneration process
Heterogeneous photocatalysis using titanium dioxide as catalyst is an attractive advanced oxidation process due to its high chemical stability, good performance and low cost. When immobilized in a supporting material, additional benefits are achieved in the treatment. The purpose of this study was to develop a simple protocol for impregnation of TiO2-P25 on borosilicate glass spheres and evaluate its efficiency in the photocatalytic degradation using an oxidizable substrate (methylene blue), in a Compound Parabolic Concentrator (CPC) reactor. The assays were conducted at lab-scale using radiation, which simulated the solar spectrum. TiO2 leaching from the glass and the catalyst regeneration were both demonstrated. A very low leaching ratio (0.03%) was observed after 24 h of treatment, suggesting that deposition of TiO2 resulted in good adhesion and stability of the photocatalyst on the surface of borosilicate. This deposition was successfully achieved after calcination of the photocatalyst at 400 °C (TiO2-400 °C). The TiO2 film was immobilized on glass spheres and the powder was characterized by scanning electron microscopy (SEM), X-ray diffraction and BET. This characterization suggested that thermal treatment did not introduce substantial changes in the measured microstructural characteristics of the photocatalyst. The immobilized photocatalyst degraded more than 96% of the MB in up to 90 min of reaction. The photocatalytic activity decreased after four photocatalytic cycles, but it was recovered by the removal of contaminants adsorbed on the active sites after washing in water under UV-Vis irradiation. Based on these results, the TiO2-400 °C coated on glass spheres is potentially a very attractive option for removal of persistent contaminants present in the environment.
Environmental Contamination and Remediation
Cunha et al. (2018) Immobilized TiO2 on glass spheres applied to heterogeneous photocatalysis: photoactivity, leaching and regeneration process. PeerJ 6:e4464 https://doi.org/10.7717/peerj.4464
The enhancement by arbuscular mycorrhizal fungi of the Cd remediation ability and bioenergy quality-related factors of five switchgrass cultivars in Cd-contaminated soil
A greenhouse experiment was carried out to investigate the effects of arbuscular mycorrhizal fungi (AMF) on the growth, P and Cd concentrations and bioenergy quality-related factors of five cultivars of switchgrass, including three lowland cultivars (Alamo (Ala), Kanlow (Kan), Performer (Per)) and two highland cultivars (Blackwell (Bw), Summer (Sum)), with 0, 1 and 10 mg/kg Cd addition levels. The results showed that AMF inoculation notably increased the biomass and P concentrations of all the cultivars. The Cd concentrations in the roots were higher than those in the shoots of all cultivars irrespective of inoculation, but the AMF had different effects on Cd accumulation in highland and lowland cultivars. AMF inoculation decreased the shoot and root concentrations in Ala and Kan, increased the shoot and root concentrations of Cd in Bw and Sum, and increased shoot Cd concentrations and decreased root Cd concentrations in Per. The highest Cd concentrations were detected in the roots of Bw and in the shoots of Sum with AMF symbiosis. Bw contained the highest total extracted Cd which was primarily in the roots. Ala had the second highest extracted Cd in the shoots, reaching 32% with 1 mg/kg of added Cd, whereas Sum had the lowest extracted Cd. AMF symbiosis had varied effects on bioenergy quality-related factors: for example, AMF decreased the ash lignin content in Ala and the C/N in Sum, increased the nitrogen, gross calorie values, and maintained the hemicellulose and cellulose contents in all cultivars with all tested concentrations of Cd. A principal component analysis (PCA) showed that AMF inoculation could enhance, weaken or transform (positive-negative, PC1-PC2) the correlations of these factors with the principle components under Cd stress. Therefore, AMF symbiosis enhanced the growth of different cultivars of switchgrass, increased/decreased Cd accumulation, promoted Cd extraction, and regulated the bioenergy quality-related factors in Cd-polluted areas. Bw is a suitable cultivar for phytostabilization due to high root Cd stabilization, whereas Ala is an appropriate cultivar for phytoremediation of less polluted areas because of its high Cd extraction and excellent bioenergy quality.
Sun et al. (2018) The enhancement by arbuscular mycorrhizal fungi of the Cd remediation ability and bioenergy quality-related factors of five switchgrass cultivars in Cd-contaminated soil. PeerJ 6:e4425 https://doi.org/10.7717/peerj.4425
The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages
The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120–253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000–400,000 yr) than the Western Atlantic population (95% HPD = 300,000–760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000–1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.
Dudoit et al. (2018) The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages. PeerJ 6:e4409 https://doi.org/10.7717/peerj.4409
Genetic analysis of ‘Candidatus Phytoplasma aurantifolia’ associated with witches’ broom on acid lime trees
“Candidatus Phytoplasma aurantifolia” is associated with witches’ broom disease of lime in Oman and the UAE. A previous study showed that an infection by phytoplasma may not necessarily result in the physical appearance of witches’ broom symptoms in some locations in Oman and the UAE. This study investigated whether phytoplasma strains belonging to “Ca. P. aurantifolia” (based on the 16S rRNA gene analysis) in locations where disease symptoms are expressed are different from phytoplasma in locations where disease symptoms are not expressed. About 21 phytoplasma strains (15 from areas and trees with disease symptoms and six from areas and trees without disease symptoms) were included in the analysis. The study utilized sequences of the imp and SAP11 genes to characterize the 21 strains. Phylogenetic analysis of both genes showed that the 21 strains are similar to each other and to reference strains in GenBank. The study shows that there is a low level of diversity among all phytoplasma strains. In addition, it shows that phytoplasma in places where witches’ broom symptoms are not expressed are similar to phytoplasma in places where disease symptoms are expressed. This may suggest that disease expression is not linked to the presence of different phytoplasma strains, but may be due to other factors such as weather conditions.
Al-Ghaithi et al. (2018) Genetic analysis of ‘Candidatus Phytoplasma aurantifolia’ associated with witches’ broom on acid lime trees. PeerJ 6:e4480 https://doi.org/10.7717/peerj.4480
The adipokine C1q TNF related protein 3 (CTRP3) is elevated in the breast milk of obese mothers
Background C1q TNF related protein 3 (CTRP3) is a relatively novel hormonal factor primarily derived from adipose tissue and has anti-diabetic properties. To determine if CTRP3 could play a role in early childhood development, the purpose of this study was to establish the presence of CTRP3 in breast milk (BM) and to determine whether CTRP3 levels were correlated with pregravid obesity status of the mother. Methods Breast milk was collected from breast-feeding mothers who had a pregravid body mass index (BMI) classification of normal weight (BMI 18–25 kg/m2, n = 23) or obese (BMI > 30 kg/m2, n = 14). Immunoprecipitation followed by immunoblot analysis confirmed the presence of CTRP3 in BM. The concentration of CTRP3 in BM samples was determined by ELISA. Additional bioactive components were also measured by commercially available assays: ghrelin, insulin, leptin, adiponectin, interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and glucose. Bioactive components in normal weight and obese mothers were compared using unpaired t-test (parametric) and Mann–Whitney U-test (non-parametric), as appropriate. Results The primary findings of this study are that the adipokine CTRP3 is present in BM and CTRP3 levels are increased with pregravid obesity. Additionally, this study independently confirmed previous work that BM from obese mothers has a higher concentration of insulin and leptin. Further, no differences were observed in BM between obese and normal weight mothers in ghrelin, adiponectin, IL-6, TNF-α, or glucose levels. Conclusion This study identified a novel factor in BM, CTRP3, and showed that BM CTRP3 levels higher in obese mothers. Because of the purported insulin sensitizing effect of CTRP3, it is possible that the elevated levels of CTRP3 in the BM of obese mothers may offset negative effects of elevated leptin and insulin levels in the BM of obese mothers. Future studies will need to be conducted to determine the relevance of CTRP3 in BM and to examine the presence of other adipose tissue-derived hormonal factors.
Kwon et al. (2018) The adipokine C1q TNF related protein 3 (CTRP3) is elevated in the breast milk of obese mothers. PeerJ 6:e4472 https://doi.org/10.7717/peerj.4472
Identification and characterization of the cytosine-5 DNA methyltransferase gene family in Salvia miltiorrhiza
Cytosine DNA methylation is highly conserved epigenetic modification involved in a wide range of biological processes in eukaryotes. It was established and maintained by cytosine-5 DNA methyltransferases (C5-MTases) in plants. Through genome-wide identification, eight putative SmC5-MTase genes were identified from the genome of Salvia miltiorrhiza, a well-known traditional Chinese medicine material and an emerging model medicinal plant. Based on conserved domains and phylogenetic analysis, eight SmC5-MTase genes were divided into four subfamilies, including MET, CMT, DRM and DNMT2. Genome-wide comparative analysis of the C5-MTase gene family in S. miltiorrhiza and Arabidopsis thaliana, including gene structure, sequence features, sequence alignment and conserved motifs, was carried out. The results showed conservation and divergence of the members of each subfamily in plants. The length of SmC5-MTase open reading frames ranges widely from 1,152 (SmDNMT2) to 5,034 bp (SmMET1). The intron number of SmC5-MTases varies between 7 (SmDRM1) and 20 (SmCMT1 and SmCMT2b). These features were similar to their counterparts from Arabidopsis. Sequence alignment and conserved motif analysis showed the existence of highly conserved and subfamily-specific motifs in the C5-MTases analyzed. Differential transcript abundance was detected for SmC5-MTases, implying genome-wide variance of DNA methylation in different organs and tissues. Transcriptome-wide analysis showed that the transcript levels of all SmC5-MTase genes was slightly changed under yeast extract and methyl jasmonate treatments. Six SmC5-MTases, including SmMET1, SmCMT1, SmCMT2a, SmCMT2b, SmCMT3 and SmDRM1, were salicylic acid-responsive, suggesting the involvement of SmC5-MTases in salicylic acid-dependent immunity. These results provide useful information for demonstrating the role of DNA methylation in bioactive compound biosynthesis and Dao-di herb formation in medicinal plants.
Li et al. (2018) Identification and characterization of the cytosine-5 DNA methyltransferase gene family in Salvia miltiorrhiza. PeerJ 6:e4461 https://doi.org/10.7717/peerj.4461
Use of seaweed Ulva lactuca for water bioremediation and as feed additive for white shrimp Litopenaeus vannamei
Two experimental feeding trials were conducted during four weeks to evaluate the use of Ulva lactuca in shrimp culture: (1) for wastewater bioremediation, and (2) using different inclusion levels of U. lactuca meal in shrimp feed. In feeding trial 1, shrimp reared under seaweed U. lactuca water exchange in a re-circulation system (SWE) resulted in similar growth and feed utilization as shrimp reared with clean water exchange (CWE). Shrimp under no water exchange (NWE) resulted in significant lower growth and higher feed conversion rate (FCR) compared to the other treatments (p < 0.05). Nitrogen compounds and phosphate in water from SWE and CWE treatments did not present significant differences during the experimental trial (p > 0.05). In feeding trial 2, U. lactuca biomass produced by wastewater bioremediation in SWE treatment were dried and ground to formulate diets containing 0, 1, 2, and 3% U. lactuca meal (0UL, 1UL, 2UL, and 3UL). Shrimp fed the 3 UL diet resulted in a significant (p < 0.05) improvement of growth and FCR, and enhanced whole shrimp lipid and carotenoid content by 30 and 60%, respectively, compared to control diet. Seaweed U. lactuca is suggested as a desirable species for wastewater bioremediation in integrated aquaculture systems, and its meal as a good feed additive for farmed shrimp.
Elizondo-González et al. (2018) Use of seaweed Ulva lactuca for water bioremediation and as feed additive for white shrimp Litopenaeus vannamei. PeerJ 6:e4459 https://doi.org/10.7717/peerj.4459
Changes in nutrients and decay rate of Ginkgo biloba leaf litter exposed to elevated O3 concentration in urban area
Ground-level ozone (O3) pollution has been widely concerned in the world, particularly in the cities of Asia, including China. Elevated O3 concentrations have potentially influenced growth and nutrient cycling of trees in urban forest. The decomposition characteristics of urban tree litters under O3 exposure are still poorly known. Ginkgo biloba is commonly planted in the cities of northern China and is one of the main tree species in the urban forest of Shenyang, where concentrations of ground-level O3 are very high in summer. Here, we hypothesized that O3 exposure at high concentrations would alter the decomposition rate of urban tree litter. In open-top chambers (OTCs), 5-year-old G. biloba saplings were planted to investigate the impact of elevated O3 concentration (120 ppb) on changes in nutrient contents and decomposition rate of leaf litters. The results showed that elevated O3 concentration significantly increased K content (6.31 ± 0.29 vs 17.93 ± 0.40, P < 0.01) in leaves of G. biloba, significantly decreased the contents of total phenols (2.82 ± 0.93 vs 1.60 ± 0.44, P < 0.05) and soluble sugars (86.51 ± 19.57 vs 53.76 ± 2.40, P < 0.05), but did not significantly alter the contents of C, N, P, lignin and condensed tannins, compared with that in ambient air. Furthermore, percent mass remaining in litterbags after 150 days under ambient air and elevated O3 concentration was 56.0% and 52.8%, respectively. No significant difference between treatments was observed in mass remaining at any sampling date during decomposition. The losses of the nutrients in leaf litters of G. biloba showed significant seasonal differences regardless of O3 treatment. However, we found that elevated O3 concentration slowed down the leaf litter decomposition only at the early decomposition stage, but slightly accelerated the litter decomposition at the late stage (after 120 days). This study provides our understanding of the ecological processes regulating biogeochemical cycles from deciduous tree species in high-O3 urban area.
Fu et al. (2018) Changes in nutrients and decay rate of Ginkgo biloba leaf litter exposed to elevated O3 concentration in urban area. PeerJ 6:e4453 https://doi.org/10.7717/peerj.4453
Effects of xylo-oligosaccharide and flavomycin on the immune function of broiler chickens
This study investigated the effects of xylo-oligosaccharide (XOS) and flavomycin (FLA) on the performance and immune function of broiler chickens. A total of 150 ArborAcres broilers were randomly divided into three groups and fed for six weeks from one day of age in cascade cages. The diets of each test group were (1) a basal diet, (2) the basal diet supplemented with 2 mg/kg FLA, and (3) the basal diet supplemented with 2 mg/kg XOS. At 21 and 42 days, the growth performance index values and short-chain fatty acid (SCFA) concentrations in the cecum were quantified. Furthermore, immunoglobulin G (IgG) and plasma interleukin 2 (IL-2) as well as mRNA expression of LPS-Induced TNF-alpha Factor (LITAF), Toll-like receptor-5 (TLR5) and interferon gamma (IFNγ) in the jejunum were quantified. The results showed that administration of XOS or FLA to chickens significantly improved the average daily gain. Supplementation with XOS increased acetate and butyrate in the cecum, while FLA supplementation increased propionate in the cecum. An increase in plasma IgG was observed in XOS-fed 21-day-old broilers, but FLA supplementation decreased IgG in the plasma of 42-day-old broilers and increased plasma IL-2. Furthermore, FLA or XOS supplementation downregulated mRNA expression of IFNγ, LITAF and TLR5. The above data suggest that addition of XOS and FLA to the diet could improve the growth performance of broilers and reduce the expression of cytokine genes by stimulating SCFA.
Yuan et al. (2018) Effects of xylo-oligosaccharide and flavomycin on the immune function of broiler chickens. PeerJ 6:e4435 https://doi.org/10.7717/peerj.4435