Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida
Background Teosinte branched1/Cycloidea/proliferating cell factors (TCPs) are plant-specific transcription factors widely involved in leaf development, flowering, shoot branching, the circadian rhythm, hormone signaling, and stress responses. However, the TCP function in Brassica juncea var. tumida, the tumorous stem mustard, has not yet been reported. This study identified and characterized the entire TCP family members in B. juncea var. tumida. Methods We identified 62 BjTCP genes from the B. juncea var. tumida genome and analyzed their phylogenetic relationship, gene structure, protein motifs, chromosome location, and expression profile in different tissues. Results Of the 62 BjTCP genes we identified in B. juncea var. tumida, containing 34 class I and 28 class II subfamily members, 61 were distributed on 18 chromosomes. Gene structure and conserved motif analysis showed that the same clade genes displayed a similar exon/intron gene structure and conserved motifs. Cis-acting element results showed that the same clade genes also had a similar cis-acting element; however, subtle differences implied a different regulatory pathway. The BjTCP18s members were low-expressed in Dayejie strains and the unswelling stage of Yonganxiaoye strains. Treatment with gibberellin (GA) and salicylic acid (SA) showed that GA and SA affect the expression levels of multiple TCP genes. Conclusion We performed the first genome-wide analysis of the TCP gene family of B. juncea var. tumida. Our results have provided valuable information for understanding the classification and functions of TCP genes in B. juncea var. tumida.
He et al. (2020) Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida. PeerJ 8:e9130 https://doi.org/10.7717/peerj.9130
Drivers of beta diversity in modern and ancient reef-associated soft-bottom environments
Beta diversity, the compositional variation among communities, is often associated with environmental gradients. Other drivers of beta diversity include stochastic processes, priority effects, predation, or competitive exclusion. Temporal turnover may also explain differences in faunal composition between fossil assemblages. To assess the drivers of beta diversity in reef-associated soft-bottom environments, we investigate community patterns in a Middle to Late Triassic reef basin assemblage from the Cassian Formation in the Dolomites, Northern Italy, and compare results with a Recent reef basin assemblage from the Northern Bay of Safaga, Red Sea, Egypt. We evaluate beta diversity with regard to age, water depth, and spatial distance, and compare the results with a null model to evaluate the stochasticity of these differences. Using pairwise proportional dissimilarity, we find very high beta diversity for the Cassian Formation (0.91 ± 0.02) and slightly lower beta diversity for the Bay of Safaga (0.89 ± 0.04). Null models show that stochasticity only plays a minor role in determining faunal differences. Spatial distance is also irrelevant. Contrary to expectations, there is no tendency of beta diversity to decrease with water depth. Although water depth has frequently been found to be a key factor in determining beta diversity, we find that it is not the major driver in these reef-associated soft-bottom environments. We postulate that priority effects and the biotic structuring of the sediment may be key determinants of beta diversity.
Roden et al. (2020) Drivers of beta diversity in modern and ancient reef-associated soft-bottom environments. PeerJ 8:e9139 https://doi.org/10.7717/peerj.9139
A low caffeine dose improves maximal strength, but not relative muscular endurance in either heavier-or lighter-loads, or perceptions of effort or discomfort at task failure in females
Background The body of literature considering caffeine as an ergogenic aid has primarily considered typically aerobic based exercise, male participants and moderate-to large-caffeine doses. With this in mind the aim of this project was to explore the effects of a low-caffeine dose upon maximal voluntary contraction (MVC) and muscular endurance (time to task failure, TTF) at heavier-and lighter-loads. Methods Nineteen physically active, habitual caffeine consuming females randomly performed four testing conditions; two with a low-dose of caffeine (100 mg equating to mean = 1.5 ± 0.18 mg·kg−1) and two placebo conditions, where they performed a maximal strength test (MVC) knee extension at 45° followed by a task of relative muscular endurance (sustained isometric contraction for TTF) using either heavier-(70% MVC) and lighter-(30% MVC) loads. Each participant performed each load condition following both caffeine and placebo consumption. Immediately following cessation of the muscular endurance test participants were asked to report their rating of perceived effort (RPE) and rating of perceived discomfort (RPD). Results Analyses revealed a significant effect for caffeine upon MVC compared to placebo (p = 0.007). We also found a significantly greater TTF for the lighter-compared to the heavier-load condition (p < 0.0001); however, there was no significant effect comparing caffeine to placebo (p = 0.2368), but insufficient precision of estimates to infer equivalence in either lighter-(p = 0.750) or heavier-load (p = 0.262) conditions. There were no statistically significant effects for caffeine compared with placebo, or lighter-compared with heavier-loads, for RPE and RPD (all p > 0.05). RPE was statistically equivalent between caffeine and placebo for both lighter-(p = 0.007) and heavier-load (p = 0.002) conditions and RPD for heavier-(p = 0.006) but not lighter-load (p = 0.136). Discussion This is the first study to demonstrate a positive effect on strength from a low caffeine dose in female participants. However, it is unclear whether caffeine positively impacts upon relative muscular endurance in either heavier-or lighter-loads. Further, both RPE and RPD appear to be relatively similar during isometric tasks performed to task failure independently of caffeine supplementation or load. These findings may have implications for persons wishing to avoid side-effects or withdrawal symptoms associated with larger caffeine doses whilst still attaining the positive strength responses.
Waller et al. (2020) A low caffeine dose improves maximal strength, but not relative muscular endurance in either heavier-or lighter-loads, or perceptions of effort or discomfort at task failure in females. PeerJ 8:e9144 https://doi.org/10.7717/peerj.9144
Effects of rumen bypass melatonin feeding (RBMF) on milk quality and mastitis of Holstein cows
Cow mastitis is a major problem frequently encountered by dairy farmers and it is manifested by the high number of somatic cells and the low quality of the milk. The conventional treatment for mastitis is use of antibiotics. In the current study, a new approach is applied to target this disorder: rumen bypass melatonin feeding (RBMF). The RBMF significantly reduced milk somatic cell count and improved milk nutritional values with the elevated protein, fat and dry matter levels. This approach also suppresses the stress and proinflammatory responses of the cows indicated by the reduced serum cortisol, TNF-α and IL-6 and increased IL-10 levels. Importantly, the beneficial effects of RBMF have lasted for several days after termination of the treatment. The effects of melatonin on the mastitis are probably attributed to the antioxidant and anti-inflammatory activities of melatonin. Considering the none or low toxicity of melatonin to organisms and the no invasive nature of this approach, we recommend that RBMF could be used in large scale in the dairy farming to target the cow mastitis.
Yao et al. (2020) Effects of rumen bypass melatonin feeding (RBMF) on milk quality and mastitis of Holstein cows. PeerJ 8:e9147 https://doi.org/10.7717/peerj.9147
Inventory statistics meet big data: complications for estimating numbers of species
We point out complications inherent in biodiversity inventory metrics when applied to large-scale datasets. The number of units of inventory effort (e.g., days of inventory effort) in which a species is detected saturates, such that crucial numbers of detections of rare species approach zero. Any rare errors can then come to dominate species richness estimates, creating upward biases in estimates of species numbers. We document the problem via simulations of sampling from virtual biotas, illustrate its potential using a large empirical dataset (bird records from Cape May, NJ, USA), and outline the circumstances under which these problems may be expected to emerge.
Khalighifar et al. (2020) Inventory statistics meet big data: complications for estimating numbers of species. PeerJ 8:e8872 https://doi.org/10.7717/peerj.8872
The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda)
The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.
Kim et al. (2020) The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda). PeerJ 8:e9108 https://doi.org/10.7717/peerj.9108
Nonalcoholic fatty liver disease, a potential risk factor of non-specific ST-T segment changes: data from a cross-sectional study
Background Non-specific ST-T segment changes are prevalent and are proven risk factors for early onset of cardiovascular diseases. They can increase all-cause mortality by 100∼200% and are candidate for early signs of cardiovascular changes. Nonalcoholic fatty liver disease (NAFLD) is prevalent worldwide and is one facet of a multisystem disease that confers substantial increases morbidity and mortality of nonalcoholic fatty liver-related cardiovascular diseases. It is unclear whether NAFLD is associated with non-specific ST-T changes warning early signs of cardiovascular changes. Therefore, we investigated this association. Methods A cross-sectional study was designed that included a sample consisting of 32,922 participants who underwent health examinations. Participants with missing information, excessive alcohol intake, viral hepatitis, chronic liver disease or established cardiovascular diseases were excluded. Electrocardiograms were used for analysis of non-specific ST-T segment changes. NAFLD was diagnosed by ultrasonographic detection of hepatic steatosis without other liver diseases. A multivariable logistic regression model was served to calculate the OR and 95% CI for non-specific ST-T segment changes. Results The prevalence of non-specific ST-T segment changes was 6.5% in participants with NAFLD, however, the prevalence of NAFLD was 42.9% in participants with non-specific ST-T segment changes. NAFLD was independently associated with non-specific ST-T segment changes (OR: 1.925, 95% CI: 1.727-2.143, P < 0.001). After adjusting for age, sex, heart rate, hypertension, body mass index, fasting glucose, total cholesterol, triglycerides, HDL-C, NAFLD remained an independent risk factor of non-specific ST-T segment changes (OR: 1.289, 95% CI: 1.122-1.480). Conclusion Non-specific ST-T segment changes were independently associated with the presence of NAFLD after adjusting for potential confounders.
Xiao et al. (2020) Nonalcoholic fatty liver disease, a potential risk factor of non-specific ST-T segment changes: data from a cross-sectional study. PeerJ 8:e9090 https://doi.org/10.7717/peerj.9090
Application of 16S rRNA gene sequencing in Helicobacter pylori detection
Helicobacter pylori is one of the major stomach microbiome components, promoting development of inflammation and gastric cancer in humans. H. pylori has a unique ability to transform into a coccoidal form which is difficult to detect by many diagnostic methods, such as urease activity detection, and even histopathological examination. Here we present a comparison of three methods for H. pylori identification: histological assessment (with eosin, hematoxylin, and Giemsa staining), polymerase chain reaction (PCR) detection of urease (ureA specific primers), and detection by 16S rRNA gene sequencing. The study employed biopsies from the antral part of the stomach (N = 40). All samples were assessed histologically which revealed H. pylori in eight patients. Bacterial DNA isolated from the bioptates was used as a template for PCR reaction and 16S rRNA gene sequencing that revealed H. pylori in 13 and in 20 patients, respectively. Thus, 16S rRNA gene sequencing was the most sensitive method for detection of H. pylori in stomach biopsy samples.
Szymczak et al. (2020) Application of 16S rRNA gene sequencing in Helicobacter pylori detection. PeerJ 8:e9099 https://doi.org/10.7717/peerj.9099
The biomarkers of key miRNAs and target genes associated with acute myocardial infarction
Background Acute myocardial infarction (AMI) is considered one of the most prominent causes of death from cardiovascular disease worldwide. Knowledge of the molecular mechanisms underlying AMI remains limited. Accurate biomarkers are needed to predict the risk of AMI and would be beneficial for managing the incidence rate. The gold standard for the diagnosis of AMI, the cardiac troponin T (cTnT) assay, requires serial testing, and the timing of measurement with respect to symptoms affects the results. As attractive candidate diagnostic biomarkers in AMI, circulating microRNAs (miRNAs) are easily detectable, generally stable and tissue specific. Methods The Gene Expression Omnibus (GEO) database was used to compare miRNA expression between AMI and control samples, and the interactions between miRNAs and mRNAs were analysed for expression and function. Furthermore, a protein-protein interaction (PPI) network was constructed. The miRNAs identified in the bioinformatic analysis were verified by RT-qPCR in an H9C2 cell line. The miRNAs in plasma samples from patients with AMI (n = 11) and healthy controls (n = 11) were used to construct receiver operating characteristic (ROC) curves to evaluate the clinical prognostic value of the identified miRNAs. Results We identified eight novel miRNAs as potential candidate diagnostic biomarkers for patients with AMI. In addition, the predicted target genes provide insight into the molecular mechanisms underlying AMI.
Wang et al. (2020) The biomarkers of key miRNAs and target genes associated with acute myocardial infarction. PeerJ 8:e9129 https://doi.org/10.7717/peerj.9129
Dental fear association between mothers and adolescents—a longitudinal study
Aim To assess the longitudinal association between adolescents’ and their mothers’ dental fear. Study Design A longitudinal questionnaire survey study. Methods A randomized sample of 12-year-old adolescents were selected from local Hong Kong schools. Adolescents and their mothers self-completed the Modified Dental Anxiety Scale (MDAS). The sociodemographic background of the mothers and the oral health habits of the adolescents were also collected and these measurements were repeated at 15- and 18-years-old. Non-parametric tests (Mann–Whitney U test/Kruskall Wallis test) were used to test associations between MDAS dental fear items and independent variables. Logistic regression (adjusted for family’s sociodemographic background and adolescent’s oral health habits) was performed to evaluate the longitudinal association between adolescents’ and mothers’ dental fear. Results A total of 212 mother-child pairs were recruited at baseline (12-year-old adolescents). In the first and second follow-ups (15- and 18-years-old), 195 and 182 mother-child pairs completed the survey. Significant associations between mother’s and child’s scores in “feeling about having their teeth scraped and polished”, “having teeth drilled”, and ‘having an injection in the gum’ were found when adolescents were 12- years-old (P < 0.01) and 18-years-old (P < 0.05), but not at 15-years-old. Conclusion Adolescents’ and mothers’ dental fear is associated at 12-years-old and 18-years-old, but not at 15-years-old, which is likely specific to the Hong Kong context but may be extrapolated to other industrialized countries with caution.
Wong et al. (2020) Dental fear association between mothers and adolescents—a longitudinal study. PeerJ 8:e9154 https://doi.org/10.7717/peerj.9154