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
Thecodont tooth attachment and replacement in bolosaurid parareptiles
Permian bolosaurid parareptiles are well-known for having complex tooth crowns and complete tooth rows in the jaws, in contrast to the comparatively simple teeth and frequent replacement gaps in all other Paleozoic amniotes. Analysis of the specialized dentition of the bolosaurid parareptiles Bolosaurus from North America and Belebey from Russia, utilizing a combination of histological and tomographic data, reveals unusual patterns of tooth development and replacement. The data confirm that bolosaurid teeth have thecodont implantation with deep roots, the oldest known such example among amniotes, and independently evolved among much younger archosauromorphs (including dinosaurs and crocodilians) and among synapsids (including mammals). High-resolution CT scans were able to detect the density boundary between the alveolar bone and the jawbone, as confirmed by histology, and revealed the location and size of developing replacement teeth in the pulp cavity of functional teeth. Evidence provided by the paratype dentary of Belebey chengi indicates that replacement teeth are present along the whole tooth row at slightly different stages of development, with the ontogenetically more developed teeth anteriorly, suggesting that tooth replacement was highly synchronized. CT data also show tooth replacement is directly related to the presence of lingual pits in the jaw, and that migration of tooth buds occurs initially close to these resorption pits to a position immediately below the functional tooth within its pulp cavity. The size and complex shape of the replacement teeth in the holotype of Bolosaurus grandis indicate that the replacement teeth can develop within the pulp cavity to an advanced stage while the previous generation remains functional for an extended time, reminiscent of the condition seen in other amniotes with occluding dentitions, including mammals.
Snyder et al. (2020) Thecodont tooth attachment and replacement in bolosaurid parareptiles. PeerJ 8:e9168 https://doi.org/10.7717/peerj.9168
Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development
Background The gut microbiota is closely linked to host development, diet and health and is influenced by both the host and the environment. Although many studies have focused on the dynamics of the gut microbiota during development in captive animals, few studies have focused on the dynamics of the gut microbiota during development in wild animals, especially for the order Chiroptera. Methods In this study, we characterized the gut microbiota of the wild Asian particolored bat (Vespertilio sinensis) from 1 day to 6 weeks after birth. We explored the changes in their gut microbial community compositions, examined possible influencing factors, and predicted the feeding transition period. Results The gut microbiota changed during the development of V. sinensis. The alpha diversity of the bats’ gut microbiota gradually increased but did not change significantly from the 1st day to the 4th week after birth; however, the alpha diversity decreased significantly in week 5, then stabilized. The beta diversity differed slightly in weeks 4–6. In week 4, the fecal samples showed the highest diversity in bacterial community composition. Thus, we predicted that the potential feeding transition period for V. sinensis may occur during week 4. Redundancy analysis showed that age and body mass index significantly affected the compositional changes of the gut microbiota in Asian particolored bats. Conclusion The gut microbiota changed during the development of V. sinensis. We suggest that changes in the alpha and beta diversity during week 4 after birth indicate a potential feeding transition, highlighting the importance of diet in the gut microbiota during the development of V. sinensis.
Yin et al. (2020) Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development. PeerJ 8:e9003 https://doi.org/10.7717/peerj.9003
Extent, patterns and demographic correlates for physical fighting among school-attending adolescents in Namibia: examination of the 2013 Global School-based Health Survey
Background Physical fighting is particularly detrimental for young people, often affecting other areas of their developing lives, such as relationships with friends and family and participating in risky behaviors. We aim to quantify the amount of problematic physical fighting in Namibian adolescents and identify modifiable risk factors for intervention. Methods We used the Namibia 2013 Global School-based Student Health Survey (GSHS). This survey collects health-related information on school-attending adolescents in grades 7 to 12. We defined physical fighting as having participated in at least two physical fights in the 12 months prior to responding to the survey. Factors that may be associated with physical fighting were identified a prior based on the literature and included age, sex, anxiety, suicide planning, truancy, physical activity, bullying victimization, presence of supportive parental figures, presence of helpful peers, extent of social network, and food insecurity. Multivariable logistic regression models were created to identify factors associated with physical fighting. Results A total of 4,510 adolescents were included in the study. A total of 52.7% female. 16.9% of adolescents reported engaging in at least two physical fights in the previous year. Factors associated with an increased odds of physical fighting included having a suicide plan, anxiety, truancy, food deprivation and being bullied. Increased age and loneliness were associated with a decreased odds of physical fighting. Conclusion This study identifies problematic physical fighting among adolescents in Namibia. We recommend public health and school-based programming that simultaneously targets risk behaviours and conflict resolution to reduce rates of physical fighting.
Davis et al. (2020) Extent, patterns and demographic correlates for physical fighting among school-attending adolescents in Namibia: examination of the 2013 Global School-based Health Survey. PeerJ 8:e9075 https://doi.org/10.7717/peerj.9075
EEG based assessment of stress in horses: a pilot study
As has been hypothesized more than 20 years ago, data derived from Electroencephalography (EEG) measurements can be used to distinguish between behavioral states associated with animal welfare. In our current study we found a high degree of correlation between the modulation index of phase related amplitude changes in the EEG of horses (n = 6 measurements with three different horses, mare and gelding) and their facial expression, measured by the use of the horse grimace scale. Furthermore, the pattern of phase amplitude coupling (PAC) was significantly different between a rest condition and a stress condition in horses. This pilot study paves the way for a possible use of EEG derived PAC as an objective tool for the assessment of animal welfare. Beyond that, the method might be useful to assess welfare aspects in the clinical setting for human patients, as for example in the neonatal intensive care unit.
de Camp et al. (2020) EEG based assessment of stress in horses: a pilot study. PeerJ 8:e8629 https://doi.org/10.7717/peerj.8629
Phylogenetic study of extirpated Korean leopard using mitochondrial DNA from an old skin specimen in South Korea
The leopard, Panthera pardus, is a threatened species in its range throughout the world. Although, historically, the Korean Peninsula had a high population density of leopards, they were extirpated from South Korea by 1970, leaving almost no genetic specimens. Traditionally, Korean leopards are classified as Panthera pardus orientalis; however, their classification is based only on locality and morphology. Therefore, there is a need for genetic studies to identify the phylogenetic status of Korean leopards at the subspecies level. Presently, no extant wild specimen is available from South Korea; therefore, we extracted genetic material from the old skin of a leopard captured in Jirisan, South Korea in the 1930s and conducted the first phylogenetic study of the South Korean leopard. A total of 726 bp of mitochondrial DNA, including segments of the NADH5 and control region, were amplified by PCR. A phylogenetic analysis of the fragment, along with sequences of nine leopard subspecies from GenBank revealed that the extinct South Korean leopard belonged to the Asian leopard group and in the same clade as the Amur leopard (Panthera pardus orientalis). Thus, the leopard that inhabited South Korea in the past was of the same subspecies as the Amur leopard population currently inhabiting the transboundary region of Russia, China, and North Korea. These results emphasize the importance of conserving the endangered wild Amur leopard population (estimated to be about 60–80 individuals) in Russia and China, for future restoration of leopards in the Korean Peninsula.
Hyun et al. (2020) Phylogenetic study of extirpated Korean leopard using mitochondrial DNA from an old skin specimen in South Korea. PeerJ 8:e8900 https://doi.org/10.7717/peerj.8900