Soil bacterial and fungal communities of six bahiagrass cultivars
Background Cultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance. Objectives This study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities. Methods Six bahiagrass cultivars (‘Argentine’, ‘Pensacola’, ‘Sand Mountain’, ‘Tifton 9’, ‘TifQuik’, and ‘UF-Riata’) were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano. Results The soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few differences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. The relative abundance of sequences assigned to nitrite-oxidizing Nitrospira was greater under ‘Sand Mountain’ than ‘UF-Riata’. Indicator species analysis revealed that several bacterial and fungal indicators associated with either a single cultivar or a combination of cultivars are likely to be plant pathogens or antagonists. Conclusions Our results suggest a low impact of plant cultivar choice on the soil bacterial community composition, whereas the soil fungal community was unaffected. Shifts in the relative abundance of Nitrospira members in response to cultivar choice may have implications for soil N dynamics. The cultivars associated with presumptive plant pathogens or antagonists indicates that the ability of bahiagrass to control plant pathogens may be cultivar-dependent, however, physiological studies on plant-microbe interactions are required to confirm this presumption. We therefore suggest that future studies should explore the potential of different bahiagrass cultivars on plant pathogen control, particularly in sod-based crop rotation.
Beule et al. (2019) Soil bacterial and fungal communities of six bahiagrass cultivars. PeerJ 7:e7014 https://doi.org/10.7717/peerj.7014
Unilateral hamstring foam rolling does not impair strength but the rate of force development of the contralateral muscle
Background Self-administered foam rolling (SAFR) is an effective massage technique often used in sport and rehabilitation settings to improve range of motion (ROM) without impairing the strength performance. However, the effects of unilateral SAFR on contralateral non-intervened muscle’s rate of force development (RFD) are unknown. Therefore, the purpose of this investigation was to examine the acute effects of unilateral hamstrings SAFR on the contralateral limb flexibility, the isometric strength, and the RFD parameters. Methods Thirty-four subjects (21 women) completed two separate randomly sequenced experimental visits, during which the control (rested for 10 min) or ten, 30-second SAFR were performed with the dominant hamstring muscle group. Before (Pre) and after (Post) the interventions, the contralateral hip flexion passive ROM, the maximal explosive isometric strength of the contralateral knee flexors with the corresponding prime mover muscles’ surface electromyographic (EMG) amplitude were measured. Separate two-way (time ×intervention) repeated measures analyses of variance (ANOVAs) were used to examine the potential changes of the dependent variables. Results The SAFR significantly improved the contralateral limb ROM (Pre vs. Post: 68.3 ± 21.0 vs. 73.2 ± 23.2 degrees, p < 0.001; d = 0.22). No change was found for the contralateral isometric strength or the maximal EMG amplitude. For the RFD parameters, the percent changes of the RFDs for the first 50, 100, and 200 ms of the maximal explosive isometric contraction were −31.2%, −16.8%, and −10.1%, respectively, following the unilateral SAFR, relative to the control condition. In addition, the decrement of the first 50-ms RFD reached statistical significance (p = 0.007; Cohen’s d = 0.44). Conclusion Ten sets of 30-second unilateral hamstring SAFR improved the ROM of the non-intervened contralateral limb, but decreased its ability to generate force, especially during the early phase (e.g., 50 ms) of the maximal explosive contraction.
Ye et al. (2019) Unilateral hamstring foam rolling does not impair strength but the rate of force development of the contralateral muscle. PeerJ 7:e7028 https://doi.org/10.7717/peerj.7028
The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species
Background The rat snake genus Elaphe once comprised several dozens of species distributed in temperate through tropical zones of the New and Old World. Based on molecular-genetic analyses in early 2000s, the genus was split into several separate genera, leaving only 15 Palearctic and Oriental species as its members. One of the three species also occurring in Europe is Elaphe sauromates, a robust snake from the Balkans, Anatolia, Caucasus, Ponto-Caspian steppes, and Levant that has been suspected to be composed of two or more genetically diverse populations. Here, we studied the genetic structure and morphological variation of E. sauromates, aiming to better understand its inter-population relationships and biogeography, and subsequently revise its taxonomy. Methods We reconstructed the phylogeography and analyzed the genetic structure of E. sauromates populations originating from most of its geographic range using both mitochondrial (COI, ND4) and nuclear (C-MOS, MC1R, PRLR, RAG1) DNA gene fragments. We employed Maximum likelihood and Bayesian inference methods for the phylogenetic tree reconstructions, supplemented with species delimitation methods, analysis of haplotype networks, and calculation of uncorrected p-distances. Morphological variation in 15 metric and 18 meristic characters was studied using parametric univariate tests as well as multivariate general linearized models. In total, we analyzed sequences originating from 63 specimens and morphological data from 95 specimens of E. sauromates sensu lato. Results The molecular phylogeny identified two clearly divergent sister lineages within E. sauromates, with both forming a lineage sister to E. quatuorlineata. The genetic distance between them (5.80–8.24% in mtDNA) is similar to the distances among several other species of the genus Elaphe. Both lineages are also moderately morphologically differentiated and, while none of the characters are exclusively diagnostic, their combination can be used for confident lineage identification. Here, following the criteria of genetic and evolutionary species concepts, we describe the lineage from eastern Anatolia and parts of the Lesser and Great Caucasus as a new species E. urartica sp. nov. Discussion Elaphe urartica sp. nov. represents a cryptic species whose ancestors presumably diverged from their common ancestor with E. sauromates around the Miocene-Pliocene boundary. The intraspecific genetic structure indicates that the recent diversity of both species has been predominantly shaped by Pleistocene climatic oscillations, with glacial refugia mainly located in the Balkans, Crimea, and/or Anatolia in E. sauromates and Anatolia and/or the Caucasus in E. urartica sp. nov.
Jablonski et al. (2019) The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species. PeerJ 7:e6944 https://doi.org/10.7717/peerj.6944
Genetic assessment of three Fagaceae species in forest restoration trials
Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our results indicated a high degree of genetic diversity (He) in C. tribuloides (0.736) and C. calathiformis (0.481); however, a low level of genetic diversity was observed in L. polystachyus (0.281) within the restored forest. The fixation index for the second generation of L. polystachyus and C. calathiformis in the restored forest showed evidence of inbreeding. These results imply the efficiency of the seed sample collection method and verify that it does not reduce the level of genetic diversity in C. tribuloides and C. calathiformis. However, it may result in incidences of an inbreeding phenomena, suggesting the need to increase the number of adult trees used at the seed collection stage.
Thongkumkoon et al. (2019) Genetic assessment of three Fagaceae species in forest restoration trials. PeerJ 7:e6958 https://doi.org/10.7717/peerj.6958
Secondary Succession under invasive species (Pteridium aquilinum) conditions in a seasonal dry tropical forest in southeastern Mexico
The role of invasive species in ecosystem functioning represents one of the main challenges in ecology. Pteridium aquilinum is a successful cosmopolitan invasive species with negative effects on the ecological mechanisms that allow secondary succession. In this study, we evaluated the influence of P. aquilinumon secondary succession under different disturbances in a seasonal dry forest of the Yucatán Peninsula. We determined species richness, composition and the relative importance value in four sampling units. Fabaceae followed by Asteraceae, Meliaceae, Rubiaceae, Sapindaceae and Verbenaceae were the most species rich families. A dissimilarity analysis determined significant differences in beta diversity between sampling units. With a generalized linear model we found that species richness was best explained by site conditions, followed by calcium and soil organic matter. Also, the generalized linear model showed that abundance resulted in a strong correlation with site conditions and soil characteristics. Specific soil conditions related to phosphoro and calcium were also detected as beneficiary to the successional processes. Our results suggest that applying fire restriction and periodic cutting of the bracken fern, this can increase a higher diversity of species.
Jean Baptiste et al. (2019) Secondary Succession under invasive species (Pteridium aquilinum) conditions in a seasonal dry tropical forest in southeastern Mexico. PeerJ 7:e6974 https://doi.org/10.7717/peerj.6974
Performance evaluation of deep neural ensembles toward malaria parasite detection in thin-blood smear images
Background Malaria is a life-threatening disease caused by Plasmodium parasites that infect the red blood cells (RBCs). Manual identification and counting of parasitized cells in microscopic thick/thin-film blood examination remains the common, but burdensome method for disease diagnosis. Its diagnostic accuracy is adversely impacted by inter/intra-observer variability, particularly in large-scale screening under resource-constrained settings. Introduction State-of-the-art computer-aided diagnostic tools based on data-driven deep learning algorithms like convolutional neural network (CNN) has become the architecture of choice for image recognition tasks. However, CNNs suffer from high variance and may overfit due to their sensitivity to training data fluctuations. Objective The primary aim of this study is to reduce model variance, improve robustness and generalization through constructing model ensembles toward detecting parasitized cells in thin-blood smear images. Methods We evaluate the performance of custom and pretrained CNNs and construct an optimal model ensemble toward the challenge of classifying parasitized and normal cells in thin-blood smear images. Cross-validation studies are performed at the patient level to ensure preventing data leakage into the validation and reduce generalization errors. The models are evaluated in terms of the following performance metrics: (a) Accuracy; (b) Area under the receiver operating characteristic (ROC) curve (AUC); (c) Mean squared error (MSE); (d) Precision; (e) F-score; and (f) Matthews Correlation Coefficient (MCC). Results It is observed that the ensemble model constructed with VGG-19 and SqueezeNet outperformed the state-of-the-art in several performance metrics toward classifying the parasitized and uninfected cells to aid in improved disease screening. Conclusions Ensemble learning reduces the model variance by optimally combining the predictions of multiple models and decreases the sensitivity to the specifics of training data and selection of training algorithms. The performance of the model ensemble simulates real-world conditions with reduced variance, overfitting and leads to improved generalization.
Rajaraman et al. (2019) Performance evaluation of deep neural ensembles toward malaria parasite detection in thin-blood smear images. PeerJ 7:e6977 https://doi.org/10.7717/peerj.6977
Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma
Backround Tongue squamous cell carcinoma (TSCC) is the most common malignant tumor in the oral cavity. An increasing number of studies have suggested that long noncoding RNA (lncRNA) plays an important role in the biological process of disease and is closely related to the occurrence and development of disease, including TSCC. Although many lncRNAs have been discovered, there remains a lack of research on the function and mechanism of lncRNAs. To better understand the clinical role and biological function of lncRNAs in TSCC, we conducted this study. Methods In this study, 162 tongue samples, including 147 TSCC samples and 15 normal control samples, were investigated and downloaded from The Cancer Genome Atlas (TCGA). We constructed a competitive endogenous RNA (ceRNA) regulatory network. Then, we investigated two lncRNAs as key lncRNAs using Kaplan–Meier curve analysis and constructed a key lncRNA-miRNA-mRNA subnetwork. Furthermore, gene set enrichment analysis (GSEA) was carried out on mRNAs in the subnetwork after multivariate survival analysis of the Cox proportional hazards regression model. Results The ceRNA regulatory network consists of six differentially expressed miRNAs (DEmiRNAs), 29 differentially expressed lncRNAs (DElncRNAs) and six differentially expressed mRNAs (DEmRNAs). Kaplan-Meier curve analysis of lncRNAs in the TSCC ceRNA regulatory network showed that only two lncRNAs, including LINC00261 and PART1, are correlated with the total survival time of TSCC patients. After we constructed the key lncRNA-miRNA -RNA sub network, the GSEA results showed that key lncRNA are mainly related to cytokines and the immune system. High expression levels of LINC00261 indicate a poor prognosis, while a high expression level of PART1 indicates a better prognosis.
Song et al. (2019) Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma. PeerJ 7:e6991 https://doi.org/10.7717/peerj.6991
Fisher linear discriminant analysis for classification and prediction of genomic susceptibility to stomach and colorectal cancers based on six STR loci in a northern Chinese Han population
Objective Gastrointestinal cancer is the leading cause of cancer-related death worldwide. The aim of this study was to verify whether the genotype of six short tandem repeat (STR) loci including AR, Bat-25, D5S346, ER1, ER2, and FGA is associated with the risk of gastric cancer (GC) and colorectal cancer (CRC) and to develop a model that allows early diagnosis and prediction of inherited genomic susceptibility to GC and CRC. Methods Alleles of six STR loci were determined using the peripheral blood of six colon cancer patients, five rectal cancer patients, eight GC patients, and 30 healthy controls. Fisher linear discriminant analysis (FDA) was used to establish the discriminant formula to distinguish GC and CRC patients from healthy controls. Leave-one-out cross validation and receiver operating characteristic (ROC) curves were used to validate the accuracy of the formula. The relationship between the STR status and immunohistochemical (IHC) and tumor markers was analyzed using multiple correspondence analysis. Results D5S346 was confirmed as a GC- and CRC-related STR locus. For the first time, we established a discriminant formula on the basis of the six STR loci, which was used to estimate the risk coefficient of suffering from GC and CRC. The model was statistically significant (Wilks’ lambda = 0.471, χ2 = 30.488, df = 13, and p = 0.004). The results of leave-one-out cross validation showed that the sensitivity of the formula was 73.7% and the specificity was 76.7%. The area under the ROC curve (AUC) was 0.926, with a sensitivity of 73.7% and a specificity of 93.3%. The STR status was shown to have a certain relationship with the expression of some IHC markers and the level of some tumor markers. Conclusions The results of this study complement clinical diagnostic criteria and present markers for early prediction of GC and CRC. This approach will aid in improving risk awareness of susceptible individuals and contribute to reducing the incidence of GC and CRC by prevention and early detection.
Hao et al. (2019) Fisher linear discriminant analysis for classification and prediction of genomic susceptibility to stomach and colorectal cancers based on six STR loci in a northern Chinese Han population. PeerJ 7:e7004 https://doi.org/10.7717/peerj.7004
Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis
Background Osteoarthritis (OA) is one of the most important age-related degenerative diseases, and the leading cause of disability and chronic pain in the aging population. Recent studies have identified several lncRNA-associated functions involved in the development of OA. Because age is a key risk factor for OA, we investigated the differential expression of age-related lncRNAs in each stage of OA. Methods Two gene expression profiles were downloaded from the GEO database and differentially expressed genes (DEGs) were identified across each of the different developmental stages of OA. Next, gene ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate the function of the DEGs. Finally, a lncRNA-targeted DEG network was used to identify hub-lncRNAs. Results A total of 174 age-related DEGs were identified. GO analyses confirmed that age-related degradation was strongly associated with cell adhesion, endodermal cell differentiation and collagen fibril organization. Significantly enriched KEGG pathways associated with these DEGs included the PI3K–Akt signaling pathway, focal adhesion, and ECM–receptor interaction. Further analyses via a protein–protein interaction (PPI) network identified two hub lncRNAs, CRNDE and LINC00152, involved in the process of age-related degeneration of articular cartilage. Our findings suggest that lncRNAs may play active roles in the development of OA. Investigation of the gene expression profiles in different development stages may supply a new target for OA treatment.
Hu et al. (2019) Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis. PeerJ 7:e7024 https://doi.org/10.7717/peerj.7024
Returning a lost process by reintroducing a locally extinct digging marsupial
The eastern bettong (Bettongia gaimardi), a medium-sized digging marsupial, was reintroduced to a predator-free reserve after 100 years of absence from the Australian mainland. The bettong may have the potential to restore temperate woodlands degraded by a history of livestock grazing, by creating numerous small disturbances by digging. We investigated the digging capacity of the bettong and compared this to extant fauna, to answer the first key question of whether this species could be considered an ecosystem engineer, and ultimately if it has the capacity to restore lost ecological processes. We found that eastern bettongs were frequent diggers and, at a density of 0.3–0.4 animals ha−1, accounted for over half the total foraging pits observed (55%), with echidnas (Tachyglossus aculeatus), birds and feral rabbits (Oryctolagus cuniculus) accounting for the rest. We estimated that the population of bettongs present dug 985 kg of soil per ha per year in our study area. Bettongs dug more where available phosphorus was higher, where there was greater basal area of Acacia spp. and where kangaroo grazing was less. There was no effect on digging of eucalypt stem density or volume of logs on the ground. While bettong digging activity was more frequent under trees, digging also occurred in open grassland, and bettongs were the only species observed to dig in scalds (areas where topsoil has eroded to the B Horizon). These results highlight the potential for bettongs to enhance soil processes in a way not demonstrated by the existing fauna (native birds and echidna), and introduced rabbit.
Munro et al. (2019) Returning a lost process by reintroducing a locally extinct digging marsupial. PeerJ 7:e6622 https://doi.org/10.7717/peerj.6622