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
Exploring environmental coverages of species: a new variable contribution estimation methodology for rulesets from the genetic algorithm for rule-set prediction
Variable contribution estimation for, and determination of variable importance within, ecological niche models (ENMs) remain an important area of research with continuing challenges. Most ENM algorithms provide normally exhaustive searches through variable space; however, selecting variables to include in models is a first challenge. The estimation of the explanatory power of variables and the selection of the most appropriate variable set within models can be a second challenge. Although some ENMs incorporate the variable selection rubric inside the algorithms, there is no integrated rubric to evaluate the variable importance in the Genetic Algorithm for Ruleset Production (GARP). Here, we designed a novel variable selection methodology based on the rulesets generated from a GARP experiment. The importance of the variables in a GARP experiment can be estimated based on the consideration of the prevalence of each environmental variable in the dominant presence rules of the best subset of models and its coverage. We tested the performance of this variable selection method based on simulated species with both weak and strong responses to simulated environmental covariates. The variable selection method generally performed well during the simulations with over 2/3 of the trials correctly identifying most covariates. We then predict the distribution of Toxostoma rufum (a bird with a cosmopolitan distribution) in the continental United States (US) and apply our variable selection procedure as a real-world example. We found that the distribution of T. rufum could be accurately modeled with 13 or 10 of 21 variables, using an UI cutoff of 0.5 or 0.25, respectively, arriving at parsimonious environmental coverages with good model accuracy. We also provide tools to simulate species distributions for testing ENM approaches using R.
Spatial and Geographic Information Science
Yang et al. (2020) Exploring environmental coverages of species: a new variable contribution estimation methodology for rulesets from the genetic algorithm for rule-set prediction. PeerJ 8:e8968 https://doi.org/10.7717/peerj.8968
EZH2/H3K27Me3 and phosphorylated EZH2 predict chemotherapy response and prognosis in ovarian cancer
Background EZH2 acts as an oncogene through canonical pathway EZH2/H3K27Me3 and uncanonical pathway pAkt1/pS21EZH2 in many solid tumors including ovarian cancer. However, the clinical value of EZH2/H3K27Me3 and pAkt1/pS21EZH2 remain unclear. In the current study, we aim to investigate the correlation between these two pathways to clinical-pathological parameters and prognosis. Methods EZH2, H3K27Me3, pAkt1 and pS21EZH2 expression were evaluated by tissue micro-array and immunohistochemistry in a cohort of ovarian cancer patients. The results were analyzed based on clinical characteristics and survival outcomes. Results EZH2, H3K27Me3, pAkt1 and pS21EZH2 were universally expressed in ovarian cancer specimens with a positive expression rate of 81.54% (53/65), 88.89% (48/54), 63.07% (41/65) and 75.38% (49/65). EZH2-pS21EZH2 (Spearman r = 0.580, P < 0.0001) and pS21EZH2-pAkt1 (Spearman r = 0.546, P < 0.0001) were closely correlated while EZH2- H3K27Me3 were less closely correlated (Spearman r = 0.307, P = 0.002). Low pS21EZH2 associated with better chemotherapy response (OR = 0.184; 95% CI [0.052–0.647], P = 0.008) according to logistic regression with an area under the curve of 0.789 (specificity 89.36%, sensitivity 68.42%) by ROC analysis and predicted improved progression-free survival (HR = 0.453; 95% CI [0.229–0.895], P = 0.023) as indicated by multivariate cox regression. A combination of EZH2low/H3K27Me3low status predicted better chemotherapy response (OR = 0.110; 95% CI [0.013–0.906], P = 0.040) and better progression-free survival (HR = 0.388; 95% CI [0.164–0.917], P = 0.031). The results suggested that EZH2/H3K27Me3 and pEZH2 predicted chemotherapy response and progression-free survival in ovarian cancer.
Sun et al. (2020) EZH2/H3K27Me3 and phosphorylated EZH2 predict chemotherapy response and prognosis in ovarian cancer. PeerJ 8:e9052 https://doi.org/10.7717/peerj.9052