SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells
Background RNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis. Methods We overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using the transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing. Results SERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT, PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis. Conclusions We for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression.
Zhou et al. (2022) SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells. PeerJ 10:e14084 https://doi.org/10.7717/peerj.14084
Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.)
Background DNA binding with one finger (Dof) proteins are plant-specific transcription factor (TF) that plays a significant role in various biological processes such as plant growth and development, hormone regulation, and resistance to abiotic stress. The Dof genes have been identified and reported in multiple plants, but so far, the whole genome identification and analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.) have not been reported yet. Methods Using the Vaccinium genome, we have identified 51 VcDof genes in blueberry. We have further analyzed their physicochemical properties, phylogenetic relationships, gene structure, collinear analysis, selective evolutionary pressure, cis-acting promoter elements, and tissue and abiotic stress expression patterns. Results Fifty-one VcDof genes were divided into eight subfamilies, and the genes in each subfamily contained similar gene structure and motif ordering. A total of 24 pairs of colinear genes were screened; VcDof genes expanded mainly due to whole-genome duplication, which was subjected to strong purifying selection pressure during the evolution. The promoter of VcDof genes contains three types of cis-acting elements for plant growth and development, phytohormone and stress defense responsiveness. Expression profiles of VcDof genes in different tissues and fruit developmental stages of blueberry indicated that VcDof2 and VcDof45 might play a specific role in anthesis and fruit growth and development. Expression profiles of VcDof genes in different stress indicated that VcDof1, VcDof11, and VcDof15 were highly sensitive to abiotic stress. This study provides a theoretical basis for further clarifying the biological function of Dof genes in blueberry.
Li et al. (2022) Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.). PeerJ 10:e14087 https://doi.org/10.7717/peerj.14087
Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions
Background Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification. Materials and Methods A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively. Results and discussions Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4+ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA. Conclusions PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4+, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.
Zhang et al. (2022) Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions. PeerJ 10:e14088 https://doi.org/10.7717/peerj.14088
Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis
Anthocyanin is a natural pigment that has a functional role in plants to attract pollinating insects and is important in stress response. Foxtail millet (Setaria italica) is known as a nutritional crop with high resistance to drought and barren. However, the molecular mechanism regulating anthocyanin accumulation and the relationship between anthocyanin and the stress resistance of foxtail millet remains obscure. In this study, we screened hundreds of germplasm resources and obtained several varieties with purple plants in foxtail millet. By studying the purple-leaved B100 variety and the control variety, Yugu1 with green leaves, we found that B100 could accumulate a large amount of anthocyanin in the leaf epiderma, and B100 had stronger stress tolerance. Further transcriptome analysis revealed the differences in gene expression patterns between the two varieties. We identified nine genes encoding enzymes related to anthocyanin biosynthesis using quantitative PCR validation that showed significantly higher expression levels in B100 than Yugu1. The results of this study lay the foundation for the analysis of the molecular mechanism of anthocyanin accumulation in foxtail millet, and provided genetic resources for the molecular breeding of crops with high anthocyanin content.
Zhao et al. (2022) Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis. PeerJ 10:e14099 https://doi.org/10.7717/peerj.14099
Effect of chronic unpredicted mild stress-induced depression on clopidogrel pharmacokinetics in rats
Background Clopidogrel is widely used to prevent and treat cardiovascular atherosclerosis and thrombosis. However, disturbance in the expression and activity of liver cytochrome metabolic enzymes significantly changes clopidogrel efficacy. Therefore, the effect of chronic unpredictable mild stress (CUMS)-induced depression on the expression of liver cytochrome metabolic enzymes and clopidogrel pharmacokinetics in rats were explored. Methods Nine different CUMSs were selected to establish a rat model of depression. Open field experiment and sucrose preference test were applied to explore the depressive behaviors. The concentration of serotonin in the cortex of depressed rats was determined using enzyme linked immunosorbent assay (ELISA). All rats were given 10 mg/kg clopidogrel orally after 12 weeks, and blood samples were collected at different time points. The clopidogrel concentration and CYP2C19/ CYP2C9 activity in rat liver microsomes were assayed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The rat liver drug enzymes expression was determined by Real-Time Quantitative Reverse Transcription PCR (RT-qPCR). Results Open field experiment and sucrose preference test indicated the successful construction of the CUMS-induced depression model. The concentration of serotonin in the cortex of depressed rats decreased by 42.56% (∗∗p < 0.01). The area under the curve of clopidogrel pharmacokinetics decreased by 33.13% (∗p < 0.05) in the depression rats, while distribution volume and clearance increased significantly (∗∗p < 0.01). The half-time and distribution volume did not significantly differ. The CYP2C19 and CYP2C9 activity of liver microsomes in the CUMS-induced depression group were significantly higher than that in the control group (∗∗p < 0.01). CYP2C11 and CYP1A2 mRNA expression up-regulated approximately 1.3 - fold in the depressed rat livers compared with that in the control, whereas that of CYP2C13 was down-regulated by 27.43% (∗∗p < 0.01). CYP3A1 and CYP2C12 expression were slightly up-regulated, and that of CES1 did not change. Conclusions These results indicated that CUMS-induced depression altered clopidogrel pharmacokinetics, and the change in CYP450 activity and expression in depressed rat livers might contribute to the disturbance of clopidogrel pharmacokinetics.
Jiang et al. (2022) Effect of chronic unpredicted mild stress-induced depression on clopidogrel pharmacokinetics in rats. PeerJ 10:e14111 https://doi.org/10.7717/peerj.14111
The fungal pathogen Batrachochytrium salamandrivorans is not detected in wild and captive amphibians from Mexico
The recent emergence of the pathogen Batrachochytrium salamandrivorans (Bsal) is associated with rapid population declines of salamanders in Europe and its arrival to new areas could cause dramatic negative effects on other amphibian populations and species. Amphibian species, present in areas with high amphibian diversity such as Mexico, could be highly threatened due to the arrival of Bsal, particularly salamander species which are more vulnerable to chytridiomycosis caused by this pathogen. Thus, immediate surveillance is needed as a strategy to efficiently contend with this emerging infectious disease. In this study, we analyzed 490 wild and captive amphibians from 48 species across 76 sites in the North, Central, and South of Mexico to evaluate the presence of Bsal. Amphibians were sampled in sites with variable degrees of amphibian richness and suitability for Bsal according to previous studies. From the 76 sampling sites, 10 of them were located in areas with high amphibian richness and potential moderate to high Bsal habitat suitability. We did not detect Bsal in any of the samples, and no signs of the disease were observed in any individual at the time of sampling. Our results suggest that Bsal has not yet arrived at the sampled sites or could be at low prevalence within populations with low occurrence probability. This is the first study that evaluates the presence of Bsal in different regions and amphibian species in Mexico, which is the second most diverse country in salamander species in the world. We highlight the risk and the importance of continuing surveillance of Bsal in Mexico and discuss control strategies to avoid the introduction and spread of Bsal in the country.
Basanta et al. (2022) The fungal pathogen Batrachochytrium salamandrivorans is not detected in wild and captive amphibians from Mexico. PeerJ 10:e14117 https://doi.org/10.7717/peerj.14117
Effects of quarantine on Physical Activity prevalence in Italian Adults: a pilot study
Background COVID-19 is a respiratory disease that caused a global pandemic status in March 2020. Due to its fast diffusion, many governments adopted forced solutions including social restrictions, which could negatively affect citizens’ habits as physical activity. Our study aimed to investigate how and why the physical activity prevalence varied from the period before the quarantine up to the period after it, and understand what citizens thought of physical inactivity COVID-19 related to and whether they were satisfied with physical activity promotion during the lockdown. Methods A new questionnaire was created and administered online. A sample of 749 interviews (female = 552 (73.7%), male = 197 (26.3%)) was collected and analysed. Results The prevalence of people who were older than 50 years reduced both during and after the lockdown (P < 0.05) and the most common reason for which they have quitted physical activity practice was related to psychological problems (lockdown = 64.57%; post-lockdown = 62.17%). In addition, youngers seemed to be more sensitive than elders to unhealthy consequences generated by forced isolation (P < 0.05), and they believed that children/adolescents and older adults practised an insufficient amount of physical activity and/or sport, which could negatively impact public health. Conclusions Although many strategies were implemented during the lockdown to promote regular physical activity practice, several results suggested that quarantine negatively affected citizens’ habits. The future government should focus on adequate measures to improve health behaviours.
Mauro et al. (2022) Effects of quarantine on Physical Activity prevalence in Italian Adults: a pilot study. PeerJ 10:e14123 https://doi.org/10.7717/peerj.14123
Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands
In recent years, a rare edible mushroom Stropharia rugosoannulata has become popular. S. rugosoannulata has the characteristics of easy cultivation, low cost, high output value, and low labor requirement, making its economic benefits significantly superior to those of other planting industries. Accumulating research demonstrates that cultivating edible fungus is advantageous for farming soil. The present experiment used idle croplands in winter for S. rugosoannulata cultivation. We explored the effects of S. rugosoannulata cultivation on soil properties and soil microbial community structure in paddy and dry fields, respectively. We cultivated S. rugosoannulata in the fields after planting chili and rice, respectively. The results showed that Chili-S. rugosoannulata and Rice-S. rugosoannulata planting patterns increased the yield, quality and amino acid content of S. rugosoannulata. By analyzing the soil properties, we found that the Chili-S. rugosoannulata and Rice-S. rugosoannulata cropping patterns increased the total nitrogen, available phosphorus, soil organic carbon, and available potassium content of the soil. We used 16s amplicons for bacteria and internal transcribed spacer (ITS) region for fungi to analyze the microbial communities in rhizosphere soils. Notably, S. rugosoannulata cultivation significantly increased the abundance of beneficial microorganisms such as Chloroflexi, Cladosporium and Mortierella and reduce the abundance of Botryotrichumin and Archaeorhizomyces. We consider S. rugosoannulata cultivation in cropland can improve soil properties, regulate the community structure of soil microorganisms, increase the expression abundance of beneficial organisms and ultimately improve the S. rugosoannulata yield and lay a good foundation for a new round of crops after this edible mushroom cultivation.
Tang et al. (2022) Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands. PeerJ 10:e14130 https://doi.org/10.7717/peerj.14130
Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach
MicroRNAs represent major regulatory components of the disease epigenome and they constitute powerful biomarkers for the accurate diagnosis and prognosis of various diseases, including cancers. The advent of high-throughput technologies facilitated the generation of a vast amount of miRNA-cancer association data. Computational approaches have been utilized widely to effectively analyze and interpret these data towards the identification of miRNA signatures for diverse types of cancers. Herein, a novel computational workflow was applied to discover core sets of miRNA interactions for the major groups of neoplastic diseases by employing network-based methods. To this end, miRNA-cancer association data from four comprehensive publicly available resources were utilized for constructing miRNA-centered networks for each major group of neoplasms. The corresponding miRNA-miRNA interactions were inferred based on shared functionally related target genes. The topological attributes of the generated networks were investigated in order to detect clusters of highly interconnected miRNAs that form core modules in each network. Those modules that exhibited the highest degree of mutual exclusivity were selected from each graph. In this way, neoplasm-specific miRNA modules were identified that could represent potential signatures for the corresponding diseases.
Arshinchi Bonab et al. (2022) Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach. PeerJ 10:e14149 https://doi.org/10.7717/peerj.14149
Association between clinical oral health status and perceived oral health in different age groups
Objective The perceived oral health refers to the very own perception of a person’s oral health (OH). This study aims to explore the association of perceived oral health status (PSR-OHS) with clinically determined OHS in three age groups: young adults, adults and older adults. This study also aims to identify demographic, socio-economic and/or clinical factors that influence PSR-OHS. Methods A cross-sectional study was conducted in ten different dental hospitals of Pakistan. The one-way ANOVA test was used to analyze patient’s demographic distribution with PSR-OHS and oral functions. The complex sample general linear model was used to determine association between clinical OH and PSR-OHS. Analyses of each age group were conducted separately. Results A total of 1,804 outdoor patients participated in the study, out of which 660 were young adults, 685 adults and 459 were older adults. Overall self-perception of all age groups about their oral health was ‘good’ (mean = 3.71). Female gender and education status were a significant factor in young adults and adults. Family income affected PSR-OHS of only the adult age group. Frequent visit to dental clinic and preventive reason of dental attendance were associated with good PSR-OHS. DMFT score, prosthesis score and periodontal score also affected the PSR-OHS of individuals. Association between PSR-OHS and clinical examination was confirmed by complex general linear model. Conclusion There are differences in the perceived oral health status of young adults, adults and older adults. The variables, age, education, family income, DMFT score, prosthesis score and periodontal score directly influence the self-perception of individuals.
Fahim et al. (2022) Association between clinical oral health status and perceived oral health in different age groups. PeerJ 10:e14152 https://doi.org/10.7717/peerj.14152