ELOVL2-AS1 inhibits migration of triple negative breast cancer
In this study, we identified a key enhancer RNA (eRNA) region in breast cancer (BRCA) by applying an integrated analysis method. Reported eRNA region and genes affected by them were selected as presumed target pairs. Kaplan–Meier (KM) survival and correlation analyses were performed to screen valuable eRNA region. Based on the KM value and its correlation with the paired target genes, we carefully selected ELOVL2-AS1 as a potential key eRNA region in BRCA. Subsequently, we analyzed the expression of ELOVL2-AS1 and ELOVL2 in four BRCA subtypes and in different BRCA cell lines. The expression of ELOVL2-AS1 and ELOVL2 in triple negative breast cancer (TNBC) was significantly lower than those in Luminal A. After that, we analyzed the function of genes that are positively correlated with ELOVL2-AS1. We found that the co-expression gene mainly related to cilia and cilia characteristics of TNBC is significantly weaker than that of Luminal A. Considering the stronger invasion and metastasis of TNBC (compared with Luminal A) and the close relationship between decreased cilia and metastasis, we overexpressed ELOVL2-AS1 in TNBC and observed its effect on cell migration. The results show that it can inhibit the migration of TNBC. Finally, we analyzed the assay for transposase-accessible chromatin sequencing data, chromatin interaction analysis with paired-end tag sequencing data, and chromatin immunoprecipitation sequencing data and identified the chromatin interaction between ELOVL2-AS1 and ELOVL2, suggesting a direct regulatory interaction.
Zhu et al. (2022) ELOVL2-AS1 inhibits migration of triple negative breast cancer. PeerJ 10:e13264 https://doi.org/10.7717/peerj.13264
Whole mitochondrial genome sequencing of Malaysian patients with cardiomyopathy
Cardiomyopathy (CMP) constitutes a diverse group of myocardium diseases affecting the pumping ability of the heart. Genetic predisposition is among the major factors affecting the development of CMP. Globally, there are over 100 genes in autosomal and mitochondrial DNA (mtDNA) that have been reported to be associated with the pathogenesis of CMP. However, most of the genetic studies have been conducted in Western countries, with limited data being available for the Asian population. Therefore, this study aims to investigate the mutation spectrum in the mitochondrial genome of 145 CMP patients in Malaysia. Long-range PCR was employed to amplify the entire mtDNA, and whole mitochondrial genome sequencing was conducted on the MiSeq platform. Raw data was quality checked, mapped, and aligned to the revised Cambridge Reference Sequence (rCRS). Variants were named, annotated, and filtered. The sequencing revealed 1,077 variants, including 18 novel and 17 CMP and/or mitochondrial disease-associated variants after filtering. In-silico predictions suggested that three of the novel variants (m.8573G>C, m.11916T>A and m.11918T>G) in this study are potentially pathogenic. Two confirmed pathogenic variants (m.1555A>G and m.11778G>A) were also found in the CMP patients. The findings of this study shed light on the distribution of mitochondrial mutations in Malaysian CMP patients. Further functional studies are required to elucidate the role of these variants in the development of CMP.
Kuan et al. (2022) Whole mitochondrial genome sequencing of Malaysian patients with cardiomyopathy. PeerJ 10:e13265 https://doi.org/10.7717/peerj.13265
Pre-competition mental energy and performance relationships among physically disabled table tennis players
Energy is essential to human daily functioning and performance. However, the association of mental energy with athletes’ performance has rarely been examined. We attempted to examine the pre-competition mental energy–performance relationships by two studies. Study 1 administered Athletic Mental Energy Scale (AMES, Lu et al., 2018) to nine elite physically-disabled table tennis players one day before competition in 5 international tournaments. Then, we collected their subjective performance after each competition. In Study 2, we sampled 77 National-level physically-disabled table tennis players and examined the pre-competition mental energy-performance relationship as the procedure in Study 1. Results from Study 1 provided initial findings of how pre-competition mental energy is associated with performance and portrayed in elite physically-disabled table tennis players. Results from Study 2 further confirmed the pre-competition mental energy- performance relationships. We suggested future studies to examine the mental energy–performance relationships in physically-disabled and abled athletes and different sports.
Chuang et al. (2022) Pre-competition mental energy and performance relationships among physically disabled table tennis players. PeerJ 10:e13294 https://doi.org/10.7717/peerj.13294
First DNA barcode library for the ichthyofauna of the Jos Plateau (Nigeria) with comments on potential undescribed fish species
Located in the central region of northern Nigeria, the Jos Plateau covers approximately 9,400 km² with an average altitude of 1,280 m and constitutes a unique terrestrial ecoregion known as the Jos Plateau forest-grassland mosaic. The biota of the Jos Plateau include endemic elements, but very limited information is available on its ichthyofauna. This is despite the fact that the ancient plateau contributes to several large rivers spanning multiple major drainage systems including the Niger and Benue Rivers, and Lake Chad. This study provides the first species list for the fishes of the Jos Plateau based mainly on 175 DNA barcoded museum voucher specimens representing 20 species, and another three species without a DNA barcode. In total, 23 species from eight families and 17 genera were collected from the Jos Plateau including five putatively new species, four in the family Cyprinidae and one in the Clariidae. With ten species, the Cyprinidae is the most diverse fish family on the Jos Plateau, followed by Clariidae and Cichlidae, each with three species. The study also provides data on species distribution and habitat parameters including information on water chemistry that strongly suggests that selected water bodies are heavily impacted by anthropogenic activities. Urgent management steps are required to preserve the unique and diverse fish communities of the Jos Plateau and their habitats.
Popoola et al. (2022) First DNA barcode library for the ichthyofauna of the Jos Plateau (Nigeria) with comments on potential undescribed fish species. PeerJ 10:e13049 https://doi.org/10.7717/peerj.13049
Determination of exercise intensity domains during upright versus supine cycling: a methodological study
Background There is a growing interest among the research community and clinical practitioners to investigate cardiopulmonary exercise test (CPET) procedures and protocols utilized in supine cycling. Materials and Methods The current study investigated the effects of posture on indicators of exercise intensity including gas exchange threshold (GET), respiratory compensation point (RCP), and the rate of peak oxygen uptake (V̇O2 peak), as well as the role of V̇O2 mean response time (MRT) in determining exercise intensity domains in nineteen healthy men (age: 22 ± 3 years). Two moderate-intensity step-transitions from 20 to 100 Watt (W) were completed, followed by a maximal CPET. After completing the ramp test, participants performed a constant-load at 90% of their attained peak power output (PPO). Results No differences were observed in the V̇O2 MRT between the two positions, although the phase II-time constant (τV̇O2p) was 7 s slower in supine position compared to upright (p = 0.001). The rate of O2 uptake in the supine position at GET and RCP were lower compared to the upright position (208 ± 200 mL·min−1 (p = 0.007) and 265 ± 235 mL·min−1 (p = 0.012) respectively). Besides, V̇O2 peak was significantly decreased (by 6%, p = 0.002) during supine position. These findings were confirmed by the wide limits of agreement between the measures of V̇O2 in different postures (V̇O2 peak: −341 to 859; constant-load test: −528 to 783; GET: −375 to 789; RCP: −520 to 1021 all in mL·min−1). Conclusion Since an accurate identification of an appropriate power output (PO) from a single-visit CPET remains a matter of debate, especially for supine cycling, we propose that moderate-intensity step-transitions preceding a ramp CPET could be a viable addition to ensure appropriate exercise-intensity domain determination, in particular upon GET-based prescription.
Zubac et al. (2022) Determination of exercise intensity domains during upright versus supine cycling: a methodological study. PeerJ 10:e13199 https://doi.org/10.7717/peerj.13199
Effects of nitrogen and phosphorus addition on growth and leaf nitrogen metabolism of alfalfa in alkaline soil in Yinchuan Plain of Hetao Basin
Alkaline soil is widely distributed in China. Its rational utilization is an effective measure to solve land shortage and improve the environment. Alfalfa is characterized by strong salt and alkali tolerance and high yield and protein content. Nitrogen (N) and phosphorus (P) are the main nutrients for plant growth, and N metabolism is one of the primary forms of plant metabolism, which plays a vital role in quality and yield formation. The exploration of the effect of N and P on N metabolism and alfalfa growth will provide a theoretical basis for scientific fertilization for alfalfa in the alkaline soil of the Yinchuan Plain of the Hetao Basin. Therefore, a 2-year experiment of N and P addition was conducted. Six treatments were set up with a randomized block design, including without N (WN), medium N (MN), high N (HN), without P (WP), medium P (MP), and high P (HP). It was found that the MN and MP treatments increased plant height, stem diameter, stem/leaf, dry/fresh, and dry matter of alfalfa. The HN and HP treatments inhibited alfalfa biomass formation. The MN and MP treatments increased key products and enzymes of leaf N metabolism of alfalfa and promoted activities of leaf nitrate reductase (NR), glutamine synthase (GS), glutamate synthase (GOGAT), glutamic-oxalacetic transaminase (GOT), and glutamic-pyruvate transaminase (GPT), and inhibited activities of leaf protease of alfalfa. The MN and MP treatments increased contents of leaf N, P, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3−-N), total chlorophyll, and protein and reduced leaf chlorophyll a/b and amino acid, results after HN and HP treatments were opposite. The correlation among leaf P, N, NO3−-N, amino acid, and protein reached significant levels (P < 0.01). It is suggested that MN and MP treatments can improve the yield and quality of alfalfa by increasing key products and enzymes of N metabolism and can be adopted to promote alfalfa production in the alkaline soil of the Yinchuan Plain of the Hetao Basin.
Xudong et al. (2022) Effects of nitrogen and phosphorus addition on growth and leaf nitrogen metabolism of alfalfa in alkaline soil in Yinchuan Plain of Hetao Basin. PeerJ 10:e13261 https://doi.org/10.7717/peerj.13261
Identifying and characterizing Stagonosporopsis cucurbitacearum causing spot blight on Pinellia ternata in China
Background Pinellia ternata (Thunb.), a perennial herbal plant in the Araceae family, has great medicinal value and market demand. In August 2020, an outbreak of severe leaf spot blight disease resulted in a huge yield loss of P. ternata. It is necessary to isolate and identify the pathogens that cause spot blight on P. ternata. Methods In this study, we isolated and identified the pathogens by fulfilling Koch’s postulates. Disease samples with typical spot blight symptoms were collected and pathogens were isolated from the diseased tissues. The pathogen was identified based on its biological characteristics and molecular analysis of internal transcribed (rDNA-ITS) and large subunit (LSU) sequences. Phylogenetic tree were constructed using MEGA7 software and pathogenicity tests were performed using in vivo inoculation. Finally, the pathogen was recovered and identified from the inoculated plants. Results Based on Koch’s postulates, we identified the pathogen causing spot blight on P. ternata as Stagonosporopsis cucurbitacearum. To our knowledge, this is the first study to explore spot blight on P. ternata caused by S. cucurbitacearum in China.
Zhou et al. (2022) Identifying and characterizing Stagonosporopsis cucurbitacearum causing spot blight on Pinellia ternata in China. PeerJ 10:e13278 https://doi.org/10.7717/peerj.13278
PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification
Motivation Since the identification of the novel coronavirus (SARS-CoV-2), the scientific community has made a huge effort to understand the virus biology and to develop vaccines. Next-generation sequencing strategies have been successful in understanding the evolution of infectious diseases as well as facilitating the development of molecular diagnostics and treatments. Thousands of genomes are being generated weekly to understand the genetic characteristics of this virus. Efficient pipelines are needed to analyze the vast amount of data generated. Here we present a new pipeline designed for genomic analysis and variant identification of the SARS-CoV-2 virus. Results PipeCoV shows better performance when compared to well-established SARS-CoV-2 pipelines, with a lower content of Ns and higher genome coverage when compared to the Wuhan reference. It also provides a variant report not offered by other tested pipelines. Availability https://github.com/alvesrco/pipecov.
Oliveira et al. (2022) PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification. PeerJ 10:e13300 https://doi.org/10.7717/peerj.13300
Sleep health of Australian community tennis players during the COVID-19 lockdown
Background Poorer sleep health outcomes have been documented in the general population during the COVID-19 outbreak. However, the impact of the COVID-19 outbreak on sleep health outcomes in specific population groups, including the sporting community, has not been extensively investigated. This study evaluated sleep health outcomes and their relationship with lifestyle behaviours during the initial COVID-19 lockdown period in Australian community tennis players. Methods This cross-sectional study evaluated sleep health outcomes and lifestyle behaviours using an online survey. The survey was disseminated online between the 24th of April and the 6th of June 2020 and comprised the Sleep Health Index, Sleep Satisfaction Tool and questions regarding weekly hours of tennis play, general physical activity, training location and alcohol consumption. Two-hundred and eighty-five individuals completed the survey. Results Compared to normative data, respondents displayed positive sleep health values during the initial COVID-19 lockdown period, with median values (IQR) of 85.3 (73.4, 91.7) and 64.8 (54.4, 73.4) for the Sleep Health Index and Sleep Satisfaction Tool, respectively. Sleep health outcomes were not significantly correlated (p > 0.05) with tennis play (Tb = 0.054–0.077), physical activity (Tb = −0.008 to 0.036), training location (Tb = −0.012 to −0.005) or alcohol consumption (Tb = −0.079 to −0.018). Conclusion Positive sleep health values were observed in Australian community-level tennis players during the initial COVID-19 pandemic. Sleep health values were not associated with lifestyle behaviours. Other unexplored factors may have influenced sleep health outcomes, including personal finances and socialisation, however these factors need to be investigated in future studies.
Beranek et al. (2022) Sleep health of Australian community tennis players during the COVID-19 lockdown. PeerJ 10:e13045 https://doi.org/10.7717/peerj.13045
Maternal self-efficacy and emotional well-being in Chilean adolescent mothers: the relationship with their children’s social-emotional development
Background Low maternal self-efficacy and high levels of anxiety, depression, and stress can be triggered in adolescent mothers due to an incomplete development process that makes them physically or psychologically unprepared for the responsibilities of motherhood and parenting. These factors may be linked to difficulties with their children’s social-emotional development. The present study aims to: (a) analyze the relationship between maternal self-efficacy and stress, depression, and anxiety levels in low-income adolescent mothers; (b) examine the relationship between maternal self-efficacy and well-being with children’s social-emotional development; and (c) describe the effects of maternal self-efficacy on children’s social-emotional development, mediated by maternal well-being. Methods A sample of 79 dyads comprising low-income Chilean adolescent mothers aged from 15 to 21 years old (M = 19.1, SD = 1.66) and their children aged 10 to 24 months (M = 15.5, SD = 4.2) participated in this research. A set of psychometric scales was used to measure maternal self-efficacy (Parental Evaluation Scale, EEP), the mothers’ anxiety and depression (Hospital Anxiety and Depression Scale, HADS), maternal stress (Parental Stress Scale, PSS), and the children’s social-emotional development (Ages and Stages Questionnaire Socio-emotional, ASQ-SE). Bivariate analyses and mediation models were employed to estimate and test the relevant relationships. Results A bivariate analysis showed that maternal self-efficacy was negatively related to the mother’s anxiety, depression, and stress. Moreover, there was a significant relationship between maternal self-efficacy and maternal stress, and children’s self-regulation and social-emotional development. Maternal self-efficacy, mediated by maternal anxiety, depression, and stress scores, had a significant effect on the development of children’s self-regulation. Conclusions The results confirm the importance of adolescent mothers’ emotional well-being and maternal self- efficacy with respect to their children’s social-emotional development. This makes it necessary to have detailed information about how emotional and self-perception status influences a mother’s role in the development of her children.
Léniz-Maturana et al. (2022) Maternal self-efficacy and emotional well-being in Chilean adolescent mothers: the relationship with their children’s social-emotional development. PeerJ 10:e13162 https://doi.org/10.7717/peerj.13162