Sugarcane/peanut intercropping system improves physicochemical properties by changing N and P cycling and organic matter turnover in root zone soil
Background The sugarcane/peanut intercropping system is a specific and efficient cropping pattern in South China. Intercropping systems change the bacterial diversity of soils and decrease disease rates. It can not only utilized light, heat, water and land resources efficiently, but also increased yield and economic benefits of farmers. Methods We determined soil nutrients, enzymes and microbes in sugarcane/peanut intercropping system, and analyzed relevance of the soil physicochemical properties and the genes involved in N and P cycling and organic matter turnover by metagenome sequencing. Results The results showed that sugarcane/peanut intercropping significantly boosted the content of total nitrogen, available phosphorus, total potassium, organic matter, pH value and bacteria and enhanced the activity of acid phosphatase compared to monocropping. Especially the content of available nitrogen, available phosphorus and organic matter increased significantly by 20.1%, 65.3% and 56.0% in root zone soil of IP2 treatment than monocropping treatment. The content of available potassium and microbial biomass carbon, as well as the activity of catalase, sucrase and protease, significantly decreased in intercropping root zone soil. Intercropping resulted in a significant increase by 7.8%, 16.2% and 23.0% in IS, IP1 and IP2, respectively, of the acid phosphatase content relative to MS. Metagenomic analysis showed that the pathways involved in carbohydrate and amino acid metabolism were dominant and more abundant in intercropping than in monocropping. Moreover, the relative abundances of genes related to N cycling (glnA, GLUD1_2, nirK), P cycling (phoR, phoB) and organic matter turnover (PRDX2_4) were higher in the intercropping soil than in the monocropping soil. The relative abundance of GLUD1_2 and phoR were 25.5% and 13.8% higher in the IP2 treatment respectively,and bgIX was higher in IS treatment compared to the monocropping treatment. Genes that were significantly related to phosphorus metabolism and nitrogen metabolism (TREH, katE, gudB) were more abundant in intercropping than in monocropping. Conclusion The results of this study indicate that the intercropping system changed the numbers of microbes as well as enzymes activities, and subsequently regulate genes involved in N cycling, P cycling and organic matter turnover. Finally, it leads to the increase of nutrients in root zone soil and improved the soil environment.
Tang et al. (2021) Sugarcane/peanut intercropping system improves physicochemical properties by changing N and P cycling and organic matter turnover in root zone soil. PeerJ 9:e10880 https://doi.org/10.7717/peerj.10880
Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers
Applying the knowledge that methyltransferases and demethylases can modify adjacent cytosine-phosphorothioate-guanine (CpG) sites in the same DNA strand, we found that combining multiple CpGs into a single block may improve cancer diagnosis. However, survival prediction remains a challenge. In this study, we developed a pipeline named “stacked ensemble of machine learning models for methylation-correlated blocks” (EnMCB) that combined Cox regression, support vector regression (SVR), and elastic-net models to construct signatures based on DNA methylation-correlated blocks for lung adenocarcinoma (LUAD) survival prediction. We used methylation profiles from the Cancer Genome Atlas (TCGA) as the training set, and profiles from the Gene Expression Omnibus (GEO) as validation and testing sets. First, we partitioned the genome into blocks of tightly co-methylated CpG sites, which we termed methylation-correlated blocks (MCBs). After partitioning and feature selection, we observed different diagnostic capacities for predicting patient survival across the models. We combined the multiple models into a single stacking ensemble model. The stacking ensemble model based on the top-ranked block had the area under the receiver operating characteristic curve of 0.622 in the TCGA training set, 0.773 in the validation set, and 0.698 in the testing set. When stratified by clinicopathological risk factors, the risk score predicted by the top-ranked MCB was an independent prognostic factor. Our results showed that our pipeline was a reliable tool that may facilitate MCB selection and survival prediction.
Yu et al. (2021) Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers. PeerJ 9:e10884 https://doi.org/10.7717/peerj.10884
Quantile-dependent expressivity of serum C-reactive protein concentrations in family sets
Background “Quantile-dependent expressivity” occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g., C-reactive protein, CRP) is high or low relative to its distribution. We have previously shown that the heritabilities (h2) of coffee and alcohol consumption, postprandial lipemia, lipoproteins, leptin, adiponectin, adiposity, and pulmonary function are quantile-specific. Whether CRP heritability is quantile-specific is currently unknown. Methods Serum CRP concentrations from 2,036 sibships and 6,144 offspring-parent pairs were analyzed from the Framingham Heart Study. Quantile-specific heritability from full-sib (βFS, h2 ={(1 + 8rspouseβFS)0.5 − 1}/(2rspouse)) and offspring-parent regression slopes (βOP, h2 = 2βOP/(1 + rspouse)) were estimated robustly by quantile regression with nonparametric significance determined from 1,000 bootstrap samples. Results Quantile-specific h2 (±SE) increased with increasing percentiles of the offspring’s age- and sex-adjusted CRP distribution when estimated from βOP (Ptrend = 0.0004): 0.02 ± 0.01 at the 10th, 0.04 ± 0.01 at the 25th, 0.10 ± 0.02 at the 50th, 0.20 ± 0.05 at the 75th, and 0.33 ± 0.10 at the 90th percentile, and when estimated from βFS (Ptrend = 0.0008): 0.03±0.01 at the 10th, 0.06 ± 0.02 at the 25th, 0.14 ± 0.03 at the 50th, 0.24 ± 0.05 at the 75th, and 0.53 ± 0.21 at the 90th percentile. Conclusion Heritability of serum CRP concentration is quantile-specific, which may explain or contribute to the inflated CRP differences between CRP (rs1130864, rs1205, rs1800947, rs2794521, rs3091244), FGB (rs1800787), IL-6 (rs1800795, rs1800796), IL6R (rs8192284), TNF-α (rs1800629) and APOE genotypes following CABG surgery, stroke, TIA, curative esophagectomy, intensive periodontal therapy, or acute exercise; during acute coronary syndrome or Staphylococcus aureus bacteremia; or in patients with chronic rheumatoid arthritis, diabetes, peripheral arterial disease, ankylosing spondylitis, obesity or inflammatory bowel disease or who smoke.
Williams (2021) Quantile-dependent expressivity of serum C-reactive protein concentrations in family sets. PeerJ 9:e10914 https://doi.org/10.7717/peerj.10914
Immune function of miR-214 and its application prospects as molecular marker
MicroRNAs are a class of evolutionary conserved non-coding small RNAs that play key regulatory roles at the post-transcriptional level. In recent years, studies have shown that miR-214 plays an important role in regulating several biological processes such as cell proliferation and differentiation, tumorigenesis, inflammation and immunity, and it has become a hotspot in the miRNA field. In this review, the regulatory functions of miR-214 in the proliferation, differentiation and functional activities of immune-related cells, such as dendritic cells, T cells and NK cells, were briefly reviewed. Also, the mechanisms of miR-214 involved in tumor immunity, inflammatory regulation and antivirus were discussed. Finally, the value and application prospects of miR-214 as a molecular marker in inflammation and tumor related diseases were analyzed briefly. We hope it can provide reference for further study on the mechanism and application of miR-214.
Wang et al. (2021) Immune function of miR-214 and its application prospects as molecular marker. PeerJ 9:e10924 https://doi.org/10.7717/peerj.10924
A kingdom in decline: Holocene range contraction of the lion (Panthera leo) modelled with global environmental stratification
Aim We use ecological niche models and environmental stratification of palaeoclimate to reconstruct the changing range of the lion (Panthera leo) during the late Pleistocene and Holocene. Location The modern (early 21st century) range of the lion extends from southern Africa to the western Indian Subcontinent, yet through the 20th century this range has been drastically reduced in extent and become increasingly fragmented as a result of human impacts. Methods We use Global Environmental Stratification with MaxEnt ecological niche models to map environmental suitability of the lion under current and palaeoclimatic scenarios. By examining modelled lion range in terms of categorical environmental strata, we characterise suitable bioclimatic conditions for the lion in a descriptive manner. Results We find that lion habitat suitability has reduced throughout the Holocene, controlled by pluvial/interpluvial cycles. The aridification of the Sahara 6ka dramatically reduced lion range throughout North Africa. The association of Saharan aridification with the development of pastoralism and the growth of sedentary communities, who practised animal husbandry, would have placed additional and lasting anthropogenic pressures on the lion. Main Conclusions This research highlights the need to integrate the full effects of the fluctuating vegetation and desiccation of the Sahara into palaeoclimatic models, and provides a starting point for further continental-scale analyses of shifting faunal ranges through North Africa and the Near East during the Holocene. This scale of ecological niche modelling does not explain the current pattern of genetic variation in the lion, and we conclude that narrow but substantial physical barriers, such as rivers, have likely played a major role in population vicariance throughout the Late Pleistocene.
Cooper et al. (2021) A kingdom in decline: Holocene range contraction of the lion (Panthera leo) modelled with global environmental stratification. PeerJ 9:e10504 https://doi.org/10.7717/peerj.10504
Magnetic resonance diffusion tensor imaging applied to rat model of contrast-induced acute kidney injury
Objectives In this preclinical investigation, the feasibility of using diffusion tensor imaging (DTI) to study contrast-induced acute kidney injury (CIAKI) is explored, comparing radiographic outcomes with histopathologic and immunohistochemical findings after repeated animal exposures to iodinated contrast agent. Materials and Methods Forty-five male wistar rats were allocated to three groups (n = 15 each), each receiving two separate injections 1 day apart: group 1 (iodixanol then saline); group 2 (iodixanol twice); and control group (saline twice). Five rats were then randomly selected from each group at three separate time points (1 h, 24 h, and 120 h) for magnetic resonance imaging (MRI). Upon MRI completion, the animals were sacrificed, examining renal tissue and serum creatinine level. DTI data served to calculate fractional anisotropy (FA) and apparent diffusion coefficient (ADC). Results FA values were significantly lower in group 2 than in the others. Compared with controls, FA assessments at 1 h, 24 h, and 120 h after injections commenced were significantly lower in group 2; and ADC was significantly more pronounced at 24 h. Serum creatinine levels at 24 h were markedly elevated in both groups 1 and 2. Pearson correlation analysis revealed significant negative correlations between FA (r = −0.730; p < 0.05) or ADC (r = −0.827; p < 0.05) and tubular injury and between FA (r = −0.563; p < 0.05) or ADC (r = −0.805; p < 0.05) and hypoxia-inducible factor-1α. Conclusions Analytic approaches to DTI with better reproducibility should aid in monitoring the early pathophysiologic derangements of CIAKI, thus facilitating timely reversal of the detrimental effects.
Wang et al. (2021) Magnetic resonance diffusion tensor imaging applied to rat model of contrast-induced acute kidney injury. PeerJ 9:e10620 https://doi.org/10.7717/peerj.10620
New data on tail lengths and variation along the caudal series in the non-avialan dinosaurs
The tails of non-avialan dinosaurs varied considerably in terms of overall length, total number of vertebrae, and gross form and function. A new dataset confirms that there is little or no consistent relationship between tail length and snout-sacrum length. Consequently, attempts to estimate one from the other are likely to be very error-prone. Patterns of changes in centra lengths across the caudal series vary among non-avian dinosaurs. However, some overarching patterns do emerge. A number of taxa show (anterior to posterior) a series of short centra, followed by a series of longer centra, with the remainder of the tail consisting of a long series of centra tapering in length. This pattern is consistent with functional constraints, and the anterior series of longer centra are coincident with the major attachments of femoral musculature. This pattern is not present in many basal taxa and may have evolved independently in different dinosaurian groups, further suggesting functional importance.
Hone et al. (2021) New data on tail lengths and variation along the caudal series in the non-avialan dinosaurs. PeerJ 9:e10721 https://doi.org/10.7717/peerj.10721
Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis
Background Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative. Nanopore sequencing technology is portable and capable of generating long sequencing reads in real-time. The aim of this study is to evaluate the potential of nanopore sequencing directly from clinical samples for the diagnosis of bacterial microbial keratitis. Methods Using full-length 16S rRNA amplicon sequences from a defined mock microbial community, we evaluated and benchmarked our bioinformatics analysis pipeline for taxonomic assignment on three different 16S rRNA databases (NCBI 16S RefSeq, RDP and SILVA) with clustering at 97%, 99% and 100% similarities. Next, we optimised the sample collection using an ex vivo porcine model of microbial keratitis to compare DNA recovery rates of 12 different collection methods: 21-gauge needle, PTFE membrane (4 mm and 6 mm), Isohelix™ SK-2S, Sugi® Eyespear, Cotton, Rayon, Dryswab™, Hydraflock®, Albumin-coated, Purflock®, Purfoam and Polyester swabs. As a proof-of-concept study, we then used the sampling technique that provided the highest DNA recovery, along with the optimised bioinformatics pipeline, to prospectively collected samples from patients with suspected microbial keratitis. The resulting nanopore sequencing results were then compared to standard microbiology culture methods. Results We found that applying alignment filtering to nanopore sequencing reads and aligning to the NCBI 16S RefSeq database at 100% similarity provided the most accurate bacterial taxa assignment. DNA concentration recovery rates differed significantly between the collection methods (p < 0.001), with the Sugi® Eyespear swab providing the highest mean rank of DNA concentration. Then, applying the optimised collection method and bioinformatics pipeline directly to samples from two patients with suspected microbial keratitis, sequencing results from Patient A were in agreement with culture results, whilst Patient B, with negative culture results and previous antibiotic use, showed agreement between nanopore and Illumina Miseq sequencing results. Conclusion We have optimised collection methods and demonstrated a novel workflow for identification of bacterial microbial keratitis using full-length 16S nanopore sequencing.
Low et al. (2021) Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis. PeerJ 9:e10778 https://doi.org/10.7717/peerj.10778
Prevalence of Xanthomonas euvesicatoria (formally X. perforans) associated with bacterial spot severity in Capsicum annuum crops in South Central Chihuahua, Mexico
Background Xanthomonas spp. causes bacterial spot disease, which reduces quality and yield of pepper crops in Mexico. Identification of phytopathogen species is necessary to implement more effective control strategies. Objective The aim of this study was to isolate and identify infecting Xanthomonas species in South Central Chihuahua pepper-producing areas. Methods Diseased plants were collected from 30 cultivation lots and bacteria were isolated from damaged tissues. Potential causative agents were isolated, identified, and characterized by biochemical and molecular analysis. Pathogenicity tests from each isolate were then performed on 30-d-old pepper seedlings, exposing five leaves to 10 µL of 1 × 108 CFU/mL bacterial suspensions of each isolate, using sterile distilled water as a control. Disease severity was determined after 10 d by calculating leaf damage percentage. Furthermore, we evaluated the susceptibility of the highest bacterial spot severity-causing isolates (13 isolates) to copper sulphate (CuS), copper gluconate (CuG), copper oxychloride + oxytetracycline hydrochloride (Cu + Ox), gentamicin + oxytetracycline hydrochloride (Gen + Ox), and gentamicin sulphate (GenS). Copper-resistance genes (copLAB) were detected by PCR analysis among isolates. Results Thirty-seven foliage isolates were identified as Xanthomonas euvesicatoria (14%), which were associated with bacterial spot disease in jalapeño pepper. Tested Xanthomonas isolates were resistant to Cu-based compounds, but susceptible to Cu + Ox. All isolates were susceptible to Gen + Ox and GenS. CopLAB genes were detected in all but one strain. Conclusions X. euvesicatoria (formally X. perforans) may be considered as an emerging pathogen of bacterial spot pepper in Mexico. Among disease management strategies, alternatives to copper should be taken into consideration.
Hernández-Huerta et al. (2021) Prevalence of Xanthomonas euvesicatoria (formally X. perforans) associated with bacterial spot severity in Capsicum annuum crops in South Central Chihuahua, Mexico. PeerJ 9:e10913 https://doi.org/10.7717/peerj.10913
Effect of incubation temperature and substrate moisture on embryonic development, hatchling phenotypes and post-hatching growth in the Reeves’ Turtle, Mauremys reevesii
Background Reeves’ Turtles (Mauremys reevesii) are economically important in aquaculture in China. Understanding the effects of incubation temperature and substrate moisture on embryos and hatchlings is of great significance for improving the artificial culture of M. reevesii. However, available studies have not yet determined the thermal and hydric optima for M. reevesii eggs, and the potential interaction between the two factors. Methods In this study, eggs of M. reevesii were incubated at five temperature levels (23, 26, 29, 32 and 35 °C, fluctuation range ± 0.5 °C). In each temperature level, there were three substrate moisture levels (1:0.5, 1:0.9 and 1:1.2, weight ratio of vermiculite to water). Thus, a total of 15 combinations of temperature and moisture were used to examine the effects of incubation temperature and substrate moisture on incubation duration, hatching success, hatchling phenotypes, post-hatching growth and hatchling survival. Results Substrate moisture did not significantly affect most development parameters (except incubation duration and carapace width of hatchlings). Eggs incubated at low moisture level (1:0.5) had a longer incubation duration and produced hatchlings with smaller carapace widths than those incubated at medium (1:0.9) or high (1:1.2) moisture levels. Incubation temperature had a significant effect on incubation duration, hatching success, hatchling phenotypes and hatchling survival. Incubation duration decreased as incubation temperature increased. Eggs incubated at 23, 26 and 29 °C showed higher hatching success than those incubated at 32 and 35 °C. Hatchlings incubated at 32 °C were smaller in body size and mass than those incubated at 23, 26 and 29 °C. At 12 months of age, incubation temperature had no long-lasting effect on body mass, but hatchlings incubated at 23 and 35 °C had lower survival rates than those incubated at 26, 29 and 32 °C. For the development of embryos and hatchlings, the interaction between incubation temperature and substrate moisture was not significant. Conclusions Our results indicate that incubation temperature has a significant influence on the development of embryos and hatchlings of M. reevesii, while substrate moisture only significantly affects the incubation duration and carapace width of hatchlings. The combination of an incubation temperature of 29 ± 0.5 °C and a substrate moisture level of 1:1.2 represented optimal incubation conditions in this experiment. Such incubation conditions are helpful in obtaining higher hatching success, shorter incubation duration and higher survival rates for this aquaculture species.
Wei et al. (2021) Effect of incubation temperature and substrate moisture on embryonic development, hatchling phenotypes and post-hatching growth in the Reeves’ Turtle, Mauremys reevesii. PeerJ 9:e10553 https://doi.org/10.7717/peerj.10553