Psychometric properties of the Perceived Stress Scale (PSS): measurement invariance between athletes and non-athletes and construct validity
Background Although Perceived Stress Scale (PSS, Cohen, Kamarack & Mermelstein, 1983) has been validated and widely used in many domains, there is still no validation in sports by comparing athletes and non-athletes and examining related psychometric indices. Purpose The purpose of this study was to examine the measurement invariance of PSS between athletes and non-athletes, and examine construct validity and reliability in the sports contexts. Methods Study 1 sampled 359 college student-athletes (males = 233; females = 126) and 242 non-athletes (males = 124; females = 118) and examined factorial structure, measurement invariance and internal consistency. Study 2 sampled 196 student-athletes (males = 139, females = 57, Mage = 19.88 yrs, SD = 1.35) and examined discriminant validity and convergent validity of PSS. Study 3 sampled 37 student-athletes to assess test-retest reliability of PSS. Results Results found that 2-factor PSS-10 fitted the model the best and had appropriate reliability. Also, there was a measurement invariance between athletes and non-athletes; and PSS positively correlated with athletic burnout and life stress but negatively correlated with coping efficacy provided evidence of discriminant validity and convergent validity. Further, the test-retest reliability for PSS subscales was significant (r = .66 and r = .50). Discussion It is suggested that 2-factor PSS-10 can be a useful tool in assessing perceived stress either in sports or non-sports settings. We suggest future study may use 2-factor PSS-10 in examining the effects of stress on the athletic injury, burnout, and psychiatry disorders.
Chiu et al. (2016) Psychometric properties of the Perceived Stress Scale (PSS): measurement invariance between athletes and non-athletes and construct validity. PeerJ 4:e2790 https://doi.org/10.7717/peerj.2790
Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri
Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.
Yuan et al. (2016) Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri. PeerJ 4:e2786 https://doi.org/10.7717/peerj.2786
Discovery of novel inhibitors disrupting HIF-1α/von Hippel–Lindau interaction through shape-based screening and cascade docking
Major research efforts have been devoted to the discovery and development of new chemical entities that could inhibit the protein–protein interaction between HIF-1α and the von Hippel–Lindau protein (pVHL), which serves as the substrate recognition subunit of an E3 ligase and is regarded as a crucial drug target in cancer, chronic anemia, and ischemia. Currently there is only one class of compounds available to interdict the HIF-1α/pVHL interaction, urging the need to discover chemical inhibitors with more diversified structures. We report here a strategy combining shape-based virtual screening and cascade docking to identify new chemical scaffolds for the designing of novel inhibitors. Based on this strategy, nine active hits have been identified and the most active hit, 9 (ZINC13466751), showed comparable activity to pVHL with an IC50 of 2.0 ± 0.14 µM, showing the great potential of utilizing these compounds for further optimization and serving as drug candidates for the inhibition of HIF-1α/von Hippel–Lindau interaction.
Xue et al. (2016) Discovery of novel inhibitors disrupting HIF-1α/von Hippel–Lindau interaction through shape-based screening and cascade docking. PeerJ 4:e2757 https://doi.org/10.7717/peerj.2757
In vitro gastrointestinal digestion study of a novel bio-tofu with special emphasis on the impact of microbial transglutaminase
We have developed a novel bio-tofu, made from mixed soy and cow milk (MSCM), using Lactobacillus helveticus MB2-1 and Lactobacillus plantarum B1-6 incorporated with microbial transglutaminase (MTGase) as coagulant. MTGase was added to improve the textural properties and suit for cooking. However, the effect of MTGase on the digestion of mixed-protein fermented by lactic acid bacteria was unclear. This study aimed at evaluating the effect of MTGase on protein digestion of bio-tofu under simulated gastrointestinal digestion condition. The results showed that addition of MTGase could affect the particle size distribution, degree of hydrolysis, the content of soluble proteins and free amino acids. Based on the electrophoresis data, MTGase addition enhanced protein polymerization. During gastric and intestinal digestion process, proteins from bio-tofu were degraded into low molecular mass peptides. Our results suggested that incorporation of MTGase could lead to enzymatic modification of proteins of bio-tofu which may help in controlling energy intake and decrease the chance of food allergy.
Xing et al. (2016) In vitro gastrointestinal digestion study of a novel bio-tofu with special emphasis on the impact of microbial transglutaminase. PeerJ 4:e2754 https://doi.org/10.7717/peerj.2754
In situ earthworm breeding in orchards significantly improves the growth, quality and yield of papaya (Carica papaya L.)
The aim of this study was to compare the effects of four fertilizer applications—control (C), chemical fertilizer (F), compost (O), and in situ earthworm breeding (E)—on the growth, quality and yield of papaya (Carica papaya L.). In this study, 5 g plant−1 urea (CH4N2O, %N = 46.3%) and 100 g plant−1 microelement fertilizer was applied to each treatment. The fertilizer applications of these four treatments are different from each other. The results showed that the E treatment had the highest growth parameters over the whole growth period. At 127 days after transplantation, the order of plant heights from greatest to smallest was E > F > O > C, and the stem diameters were E > F > O > C, with significant differences between all treatments. Soluble-solid, sugar, vitamin C, and protein content significantly increased in the E treatment. In addition, the total acid and the electrical conductivity of the fruit significantly decreased in the E treatment. Fruit firmness clearly increased in the O treatment, and decreased in the F treatment. The fresh individual fruit weights, fruit numbers, and total yields were greatly improved in the F and E treatments, and the total yield of the E treatment was higher than that in the F treatment. In conclusion, the in situ earthworm breeding treatment performed better than conventional compost and chemical fertilizer treatments. Furthermore, in situ earthworm breeding may be a potential organic fertilizer application in orchards because it not only improves the fruit quality and yield but also reduces the amount of organic wastes from agriculture as a result of the activities of earthworms.
Xiang et al. (2016) In situ earthworm breeding in orchards significantly improves the growth, quality and yield of papaya (Carica papaya L.). PeerJ 4:e2752 https://doi.org/10.7717/peerj.2752
A retrospective study: cardiac MRI of fulminant myocarditis in children—can we evaluate the short-term outcomes?
Background Fulminant myocarditis (FM) is an inflammatory disease of the myocardium that results in ventricular systolic dysfunction and causes acute-onset heart failure. Cardiac magnetic resonance (CMR) has become the primary noninvasive tool for the diagnosis and evaluation of myocarditis. The aim of our study was to assess the CMR findings at different course of FM and the short-term outcomes of fulminant myocarditis (FM) in children. Methods Eight FM children with CMR examinations were included in our study. Initial baseline CMR was performed 10 days (range, 7–20 days) after onset of FM and follow-up CMR after 55 days (range, 33–75 days). Cardiac morphology and function and myocardial tissue characterization at baseline and follow-up CMR were compared using paired T-test and Mann–Whitney U test. The clinical data and initial CMR findings were also compared to predict short-term outcomes. Results The median age of eight FM children was 8.5 years old (range, 3–14). The initial CMR findings were most common with early gadolinium enhancement (EGE, 100%), followed by signal increasing on T2WI and late gadolinium enhancement (LGE, 87.5%), increased septal thickness (75.0%) and increased left ventricle ejection fraction (LVEF, 50.0%). Only three LGE (37.5%), one signal increasing on T2WI (12.5%) and one increased LVEF (12.5%) were found at follow-up. Statistically significant differences were found between initial and follow-up CMR abnormalities in the septal thickness, left ventricular end-diastolic diameter (LVEDD), end-systolic volume (ESV), LVEF, left ventricular mass, T2 ratio and LGE area (P = 0.011, P = 0.042, P = 0.016, P = 0.001, P = 0.003, P = 0.011, P = 0.020). The children with full recovery performed higher incidence of III° atrioventricular block (AVB, five cases VS 0 case) and smaller LGE area (104.0 ± 14.5 mm2 VS 138.0 ± 25.2 mm2) at baseline CMR. Discussion The CMR findings of FM in children were characteristic and useful for early diagnosis. Full recovery of clinical manifestations, immunological features and CMR findings could be found in most FM children. The presence of III° AVB and smaller LGE area at baseline CMR might indicate better short-term outcomes.
Wang et al. (2016) A retrospective study: cardiac MRI of fulminant myocarditis in children—can we evaluate the short-term outcomes?. PeerJ 4:e2750 https://doi.org/10.7717/peerj.2750
Harvest year effects on Apulian EVOOs evaluated by 1H NMR based metabolomics
Nine hundred extra virgin olive oils (EVOO) were extracted from individual olive trees of four olive cultivars (Coratina, Cima di Mola, Ogliarola, Peranzana), originating from the provinces of Bari and Foggia (Apulia region, Southern Italy) and collected during two consecutive harvesting seasons (2013/14 and 2014/15). Following genetic identification of individual olive trees, a detailed Apulian EVOO NMR database was built using 900 oils samples obtained from 900 cultivar certified single trees. A study on the olive oil lipid profile was carried out by statistical multivariate analysis (Principal Component Analysis, PCA, Partial Least-Squares Discriminant Analysis, PLS-DA, Orthogonal Partial Least-Squares Discriminant Analysis, OPLS-DA). Influence of cultivar and weather conditions, such as the summer rainfall, on the oil metabolic profile have been evaluated. Mahalanobis distances and J2 criterion have been measured to assess the quality of resulting scores clusters for each cultivar in the two harvesting campaigns. The four studied cultivars showed non homogeneous behavior. Notwithstanding the geographical spread and the wide number of samples, Coratina showed a consistent behavior of its metabolic profile in the two considered harvests. Among the other three Peranzana showed the second more consistent behavior, while Cima di Mola and Ogliarola having the biggest change over the two years.
Girelli et al. (2016) Harvest year effects on Apulian EVOOs evaluated by 1H NMR based metabolomics. PeerJ 4:e2740 https://doi.org/10.7717/peerj.2740
RNA interference as a gene silencing tool to control Tuta absoluta in tomato (Solanum lycopersicum)
RNA interference (RNAi), a gene-silencing mechanism that involves providing double-stranded RNA molecules that match a specific target gene sequence, is now widely used in functional genetic studies. The potential application of RNAi-mediated control of agricultural insect pests has rapidly become evident. The production of transgenic plants expressing dsRNA molecules that target essential insect genes could provide a means of specific gene silencing in larvae that feed on these plants, resulting in larval phenotypes that range from loss of appetite to death. In this report, we show that the tomato leafminer (Tuta absoluta), a major threat to commercial tomato production, can be targeted by RNAi. We selected two target genes (Vacuolar ATPase-A and Arginine kinase) based on the RNAi response reported for these genes in other pest species. In view of the lack of an artificial diet for T. absoluta, we used two approaches to deliver dsRNA into tomato leaflets. The first approach was based on the uptake of dsRNA by leaflets and the second was based on “in planta-induced transient gene silencing” (PITGS), a well-established method for silencing plant genes, used here for the first time to deliver in planta-transcribed dsRNA to target insect genes. Tuta absoluta larvae that fed on leaves containing dsRNA of the target genes showed an ∼60% reduction in target gene transcript accumulation, an increase in larval mortality and less leaf damage. We then generated transgenic ‘Micro-Tom’ tomato plants that expressed hairpin sequences for both genes and observed a reduction in foliar damage by T. absoluta in these plants. Our results demonstrate the feasibility of RNAi as an alternative method for controlling this critical tomato pest.
Camargo et al. (2016) RNA interference as a gene silencing tool to control Tuta absoluta in tomato (Solanum lycopersicum). PeerJ 4:e2673 https://doi.org/10.7717/peerj.2673
Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
Premise of the Study The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. Methodology A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Principal Findings Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Conclusion The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.
Mishra et al. (2016) Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae). PeerJ 4:e2638 https://doi.org/10.7717/peerj.2638
Examination of Mycobacterium avium subspecies paratuberculosis mixed genotype infections in dairy animals using a whole genome sequencing approach
Many pathogenic mycobacteria are known to cause severe disease in humans and animals. M. avium subspecies paratuberculosis (Map) is the causative agent of Johne’s disease—a chronic wasting disease affecting ruminants such as cattle and sheep, responsible for significant economic losses in the dairy and beef industries. Due to the lack of treatment options or effective vaccines, mitigating losses can be difficult. In addition, the early stages of Map infection may occur in asymptomatic hosts that continue to shed viable bacteria in their faeces, leading to the infection of other healthy animals. Using multi-locus short sequence repeat (ML-SSR) analysis we previously reported that individual Johne’s positive dairy cattle from farms across the island of Newfoundland were infected by Map with multiple SSR-types simultaneously. The occurrence of multiple mixed genotype infections has the potential to change pathogen and disease dynamics as well as reduce the efficacy of treatments and vaccines. Therefore, we conducted whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis on a subset of these isolates for a more in-depth examination. We also implemented a PCR assay using two discriminatory SNPs and demonstrated the incidence of a mixed infection by three genotypically diverse Map isolates in a single animal. In addition, results show that WGS and SNP analysis can provide a better understanding of the relationship between Map isolates from individual and different animals. In the future such studies on the occurrence of mixed genotype infections could potentially lead to the identification of variable pathogenicity of different genotypes and allow for better tracking of Map isolates for epidemiological studies.
Davidson et al. (2016) Examination of Mycobacterium avium subspecies paratuberculosis mixed genotype infections in dairy animals using a whole genome sequencing approach. PeerJ 4:e2793 https://doi.org/10.7717/peerj.2793