Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages
Background MicroRNA172 (miR172) has been proven to be critical for fruit growth, since elevated miR172 activity blocks the growth of apple (Malus x domestica Borkh.) fruit. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes. Methods To answer this question, the present study, analyzed global transcriptional changes in miR172-overexpressing (miR172OX) and nongenetically modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. In addition, two cultivars, ‘Hanfu’ and ‘M9’, which have naturally fruit size variation, were included to identify miR172-dependent DEGs. qRT–PCRwas used to verify the reliability of our RNA-seq data. Results Overexpression of miR172 altered the expression levels of many cell proliferation- and cell expansion-related genes. Twenty-four libraries were generated, and 10,338 differentially expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. ‘Hanfu’ and ‘M9’ are two common cultivars that bear fruit of different sizes (250 g and 75 g, respectively). Six libraries were generated, and 3,627 DEGs were detected between ‘Hanfu’ and ‘M9’. After merging the two datasets, 6,888 candidate miR172-specific DEGs were identified. The potential networks associated with fruit size triggered traits were defined among genes belonging to the families of hormone synthesis, signaling pathways, and transcription factors. Our comparative transcriptome analysis provides insights into transcriptome responses to miR172 overexpression in apple fruit and a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple.
Zhou et al. (2021) Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages. PeerJ 9:e12675 https://doi.org/10.7717/peerj.12675
A review of starch biosynthesis in cereal crops and its potential breeding applications in rice (Oryza Sativa L.)
Starch provides primary storage of carbohydrates, accounting for approximately 85% of the dry weight of cereal endosperm. Cereal seeds contribute to maximum annual starch production and provide the primary food for humans and livestock worldwide. However, the growing demand for starch in food and industry and the increasing loss of arable land with urbanization emphasizes the urgency to understand starch biosynthesis and its regulation. Here, we first summarized the regulatory signaling pathways about leaf starch biosynthesis. Subsequently, we paid more attention to how transcriptional factors (TFs) systematically respond to various stimulants via the regulation of the enzymes during starch biosynthesis. Finally, some strategies to improve cereal yield and quality were put forward based on the previous reports. This review would collectively help to design future studies on starch biosynthesis in cereal crops.
Li et al. (2021) A review of starch biosynthesis in cereal crops and its potential breeding applications in rice (Oryza Sativa L.). PeerJ 9:e12678 https://doi.org/10.7717/peerj.12678
An estimate of the area of occupancy and population size of Brachycephalus tridactylus (Anura: Brachycephalidae) to reassess its conservation status, with a proposal for conservation measures
Background We are experiencing a global crisis in conservation, which has led to the prioritization of targets, such as nations, regions, and animal groups, which are necessary while resources are disputed. Brazil is a priority not only because of its megadiversity, high rates of endemism, and frequent descriptions of new species but also because of its high levels of deforestation. Among the species groups prioritized for conservation is the anurans (Amphibia: Anura), the population of which is severely declining. One group of anurans is the genus Brachycephalus, which includes 37 endemic species in the Brazilian Atlantic Rainforest. Some of these species have highly restricted distributions (<100 ha). Thirty new species have been described since 2000, and 55.3% of all species are threatened with extinction. Brachycephalus tridactylus was only recently described and remains restricted to its type locality. Because of its reduced geographical distribution (0.41 km2), it has been proposed to be considered as Vulnerable. The objective of this study is to reevaluate the conservation status of Brachycephalus tridactylus and propose conservation measures. Methods We searched for new populations during 2016–2020, evaluated in loco impacts and potential impacts on the species’ population, and performed an analysis of the density of this population and estimated its size. International Union for Conservation of Nature (IUCN) criteria were used to assess the conservation status of the species. Results We recorded the species in seven new localities (from 715–1,140 m above sea level) in the state of São Paulo up to 33 km from the type locality of the species (in state of Paraná). We estimated the area of occupancy as 148.44 km2, densities as one calling male per 4.05 m2 and 130.00 m2, and a total population size of 4,429,722 adult individuals. Based on our finding, we proposed three lines of management: (1) formation of fire brigades, (2) management of residents’ mules in the conservation unit and surrounding areas, and (3) management of degraded areas. We recommend changing the species’ conservation status from Vulnerable to Endangered because of its fragmented distribution and decline in the area of occupancy and in the quality of its habitat. Our results have expanded the species previous geographic distribution and delimited areas without previous records. Our estimates of population density and size are in accordance with those verified for congeners. The conservation of this species benefits the environments and other species that inhabit them, being, therefore, strategic for receiving conservation actions that will spread throughout the ecosystem.
Bornschein et al. (2021) An estimate of the area of occupancy and population size of Brachycephalus tridactylus (Anura: Brachycephalidae) to reassess its conservation status, with a proposal for conservation measures. PeerJ 9:e12687 https://doi.org/10.7717/peerj.12687
Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum
The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition.
Li et al. (2021) Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum. PeerJ 9:e12689 https://doi.org/10.7717/peerj.12689
Transcriptomic identification of HBx-associated hub genes in hepatocellular carcinoma
Background Hepatocellular carcinoma (HCC) is one of the most common malignancies around the world. Among the risk factors involved in liver carcinogenesis, hepatitis B virus (HBV) X protein (HBx) is considered to be a key regulator in hepatocarcinogenesis. Whether HBx promotes or protects against HCC remains controversial, therefore exploring new HBx-associated genes is still important. Methods HBx was overexpressed in HepG2, HepG2.2.15 and SMMC-7721 cell lines, primary mouse hepatocytes and livers of C57BL/6N mice. High-throughput RNA sequencing profiling of HepG2 cells with HBx overexpression and related differentially-expressed genes (DEGs), pathway enrichment analysis, protein-protein interaction networks (PPIs), overlapping analysis were conducted. In addition, Gene Expression Omnibus (GEO) and proteomic datasets of HBV-positive HCC datasets were used to verify the expression and prognosis of selected DEGs. Finally, we also evaluated the known oncogenic role of HBx by oncogenic array analysis. Results A total of 523 DEGs were obtained from HBx-overexpressing HepG2 cells. Twelve DEGs were identified and validated in cells transiently transfected with HBx and three datasets of HBV-positive HCC transcription profiles. In addition, using the Kaplan-Meier plotter database, the expression levels of the twelve different genes were further analyzed to predict patient outcomes. Conclusion Among the 12 identified HBx-associated hub genes, HBV-positive HCC patients expressing ARG1 and TAT showed a good overall survival (OS) and relapse-free survival (RFS). Thus, ARG1 and TAT expression could be potential prognostic markers.
Ni et al. (2021) Transcriptomic identification of HBx-associated hub genes in hepatocellular carcinoma. PeerJ 9:e12697 https://doi.org/10.7717/peerj.12697
Early detection of cyanide, organophosphate and rodenticide pollution based on locomotor activity of zebrafish larvae
Cyanide, organophosphate and rodenticides are highly toxic substances widely used in agriculture and industry. These toxicants are neuro- and organotoxic to mammals at low concentrations, thus early detection of these chemicals in the aqueous environment is of utmost importance. Here, we employed the behavioral toxicity test with wildtype zebrafish larvae to determine sublethal concentrations of the above mentioned common environmental pollutants. After optimizing the test with cyanide, nine rodenticides and an organophosphate were successfully tested. The compounds dose-dependently initially (0–60-min exposure) stimulated locomotor activity of larvae but induced toxicity and reduced swimming during 60–120-min exposure. IC50 values calculated based on swimming distance after 2-h exposure, were between 0.1 and 10 mg/L for both first-generation and second-generation anticoagulant rodenticides. Three behavioral characteristics, including total distance travelled, sinuosity and burst count, were quantitatively analyzed and compared by hierarchical clustering of the effects measured by each three parameters. The toxicity results for all three behavioral endpoints were consistent, suggesting that the directly measured parameter of cumulative swimming distance could be used as a promising biomarker for the aquatic contamination. The optimized method herein showed the potential for utilization as part of a monitoring system and an ideal tool for the risk assessment of drinking water in the military and public safety.
Wang et al. (2021) Early detection of cyanide, organophosphate and rodenticide pollution based on locomotor activity of zebrafish larvae. PeerJ 9:e12703 https://doi.org/10.7717/peerj.12703
Differential expression profiles of microRNAs in musk gland of unmated and mated forest musk deer (Moschus berezovskii)
Background The formation of musk is a complex biophysical and biochemical process that change with the rut of male forest musk deer. We have reported that the mating status of male forest musk deer might result to the variations of chemical composition and microbiota of musk and its yields. Critical roles for microRNAs (miRNAs) of multi-tissues were profiled in our previous study; however, the role for miRNAs of the musk gland remains unclear in this species. Methods In this study, we used Illumina deep sequencing technology to sequence the small RNA transcriptome of unmated male (UM) and mated male (UM) of Chinese forest musk deer. Results We identified 1,652 known miRNAs and 45 novel miRNAs, of which there were 174 differentially expressed miRNAs between UM and MM. chi-miR-21-5p, ipu-miR-99b and bta-miR-26a were up-regulated in UM among the 10 most differentially expressed miRNAs. Functional enrichment of the target genes showed that monosaccharide biosynthetic process, protein targeting, cellular protein catabolic process enriched higher in MM. Meanwhile, structural molecule activity, secretion by cell, regulated exocytosis and circulatory system process enriched more in UM, hinting that the formation of musk in UM was mediated by target genes related to exocytosis. The miRNA-mRNA pairs such as miR-21: CHD7, miR143: HSD17B7, miR-141/200a: Noc2 might involve in musk gland development and musk secretion, which need to be verified in future study.
Jie et al. (2021) Differential expression profiles of microRNAs in musk gland of unmated and mated forest musk deer (Moschus berezovskii). PeerJ 9:e12710 https://doi.org/10.7717/peerj.12710
Electroencephalogram-derived pain index for evaluating pain during labor
Background The discriminative ability of a point-of-care electroencephalogram (EEG)-derived pain index (Pi) for objectively assessing pain has been validated in chronic pain patients. The current study aimed to determine its feasibility in assessing labor pain in an obstetric setting. Methods Parturients were enrolled from the delivery room at the department of obstetrics in a tertiary hospital between February and June of 2018. Pi values and relevant numerical rating scale (NRS) scores were collected at different stages of labor in the presence or absence of epidural analgesia. The correlation between Pi values and NRS scores was analyzed using the Pearson correlation analysis. The receiver operating characteristic (ROC) curve was plotted to estimate the discriminative capability of Pi to detect labor pain in parturients. Results Eighty paturients were eligible for inclusion. The Pearson correlation analysis exhibited a positive correlation between Pi values and NRS scores in parturients (r = 0.768, P < 0.001). The ROC analysis revealed a cut-off Pi value of 18.37 to discriminate between mild and moderate-to-severe labor pain in parturients. Further analysis indicated that Pi values had the best diagnostic accuracy reflected by the highest area under the curve (AUC) of 0.857, with a sensitivity and specificity of 0.767 and 0.833, respectively, and a Youden index of 0.6. Subgroup analyses further substantiated the correlations between Pi values and NRS scores, especially in parturients with higher pain intensity. Conclusion This study indicates that Pi values derived from EEGs significantly correlate with the NRS scores, and can serve as a way to quantitatively and objectively evaluate labor pain in parturients.
Sun et al. (2021) Electroencephalogram-derived pain index for evaluating pain during labor. PeerJ 9:e12714 https://doi.org/10.7717/peerj.12714
Phenotypic differentiation of the slow worm lizards (Squamata: Anguis) across their contact zone in Central Europe
Background The application of molecular-phylogenetic approaches to taxonomy has had a dramatic effect on our understanding of the diversity of reptiles. These approaches have allowed researchers to reveal previously hidden lineages as well as taxonomic overestimation in morphologically plastic taxa. Slow worms, legless lizards of the genus Anguis (Squamata: Anguidae), were previously considered to comprise either one or two species, and morphology-based intraspecific taxonomy of Anguis fragilis remained controversial throughout the 20th century. After the discovery of deep genetic divergences within the genus, its taxonomy was reconsidered, and as a result, five extant species have been recognized. In order to better understand the patterns of their interspecific differentiation, here we studied phenotypic differences between the two most widespread of them—A. fragilis and A. colchica, and their putative hybrids across the contact zone of both species in Central Europe. Methods We used multivariate and univariate statistics and analyzed ten metric, eleven meristic, and six categorical phenotypic variables in material comprising a total of 326 individuals. We also genotyped individuals from the contact zone for one mitochondrial and two nuclear DNA fragments in order to delineate the distribution of individuals of hybrid and non-hybrid origin. The clines in morphological traits were studied using HZAR. Results We show that the two species are morphologically differentiated. Anguis fragilis has a less robust head, fewer scales covering the body, lower frequency of the external ear opening presence, lower frequency of separated prefrontal scales, higher frequency of prefrontal scales in contact with each other, and body coloration more similar to the juvenile coloration than A. colchica. Slow worms from the contact/hybrid zone are characterized by an intermediate morphology, with more similarities to A. fragilis than to A. colchica. Discussion None of the analyzed characters alone proved to be fully diagnostic, although more than 90% of all individuals could be successfully assigned to one or another species based on numbers of scales around the body. Our results indicate concordant, coincident, and steep clines in character states change. We present several hypotheses on the origin and evolutionary maintenance of the morphological divergence between both species and suggest that different evolutionary histories of the taxa rather than recently acting selection explain the observed morphological variation.
Benkovský et al. (2021) Phenotypic differentiation of the slow worm lizards (Squamata: Anguis) across their contact zone in Central Europe. PeerJ 9:e12482 https://doi.org/10.7717/peerj.12482
Interoceptive awareness and beliefs about health and the body as predictors of the intensity of emotions experienced at the beginning of the pandemic
Background The COVID-19 pandemic is a type of stressful event which might have an impact on psychological state. A prolonged threat of getting a serious, contagious illness is expected to be associated with an increase of negative emotions and, conversely, with a decrease of positive emotions. As the stressor is strongly linked to health and the body, we decided to investigate what types of factors related to body perception and appraisal are associated with different types of reported emotions. The purpose of the study was to verify the associations between three types of variables: interoceptive awareness as described by Mehling and colleagues (2012a, 2018), negative beliefs about health and body, and different types of emotions. Methodology A Multidimensional Assessment of Interoceptive Awareness questionnaire was applied to evaluate interoceptive awareness. The declared emotional state was diagnosed with a list of 20 emotions–divided by valence and origin. Additionally, a list of 10 negative beliefs about health and body was used. The study was held in a correlational schema with 299 subjects recruited via the social media platform Facebook who took part in an online survey. Results The study revealed that the scales of Self-Regulation and Trusting are primarily associated with negative automatic and reflective emotions and positive automatic emotions. Furthermore, the Self-Regulation, Trusting dimensions of interoceptive awareness predict an intensity of emotions categorised on the basis of valence and origin. In addition, negative beliefs about health and the body provided an adequate explanation of the variance of most of the types of emotions experienced during the pandemic. Conclusions Factors related to body perception, such as interoceptive awareness and negative beliefs about health and body provide a significant contribution to explaining emotional state at the beginning of the pandemic.
Modzelewska et al. (2021) Interoceptive awareness and beliefs about health and the body as predictors of the intensity of emotions experienced at the beginning of the pandemic. PeerJ 9:e12542 https://doi.org/10.7717/peerj.12542