Identification, classification, and expression profile analysis of heat shock transcription factor gene family in Salvia miltiorrhiza
In response to abiotic stresses, transcription factors are essential. Heat shock transcription factors (HSFs), which control gene expression, serve as essential regulators of plant growth, development, and stress response. As a model medicinal plant, Salvia miltiorrhiza is a crucial component in the treatment of cardiovascular illnesses. But throughout its growth cycle, S.miltiorrhiza is exposed to a series of abiotic challenges, including heat and drought. In this study, 35 HSF genes were identified based on genome sequencing of Salvia miltiorrhiza utilizing bioinformatics techniques. Additionally, 35 genes were classified into three groups by phylogeny and gene structural analysis, comprising 22 HSFA, 11 HSFB, and two HSFC. The distribution and sequence analysis of motif showed that SmHSFs were relatively conservative. In SmHSF genes, analysis of the promoter region revealed the presence of many cis-acting elements linked to stress, hormones, and growth and development, suggesting that these factors have regulatory roles. The majority of SmHSFs were expressed in response to heat and drought stress, according to combined transcriptome and real-time quantitative PCR (qRT-PCR) analyses. In conclusion, this study looked at the SmHSF gene family using genome-wide identification, evolutionary analysis, sequence characterization, and expression analysis. This research serves as a foundation for further investigations into the role of HSF genes and their molecular mechanisms in plant stress responses.
Liu et al. (2022) Identification, classification, and expression profile analysis of heat shock transcription factor gene family in Salvia miltiorrhiza. PeerJ 10:e14464 https://doi.org/10.7717/peerj.14464
Chemically mediated rheotaxis of endangered tri-spine horseshoe crab: potential dispersing mechanism to vegetated nursery habitats along the coast
Background An enhanced understanding of larval ecology is fundamental to improve the management of locally depleted horseshoe crab populations in Asia. Recent studies in the northern Beibu Gulf, China demonstrated that nesting sites of Asian horseshoe crabs are typically close to their nursery beaches with high-density juveniles distributed around mangrove, seagrass and other structured habitats. Methods A laboratory Y-maze chamber was used to test whether the dispersal of early-stage juvenile tri-spine horseshoe crab Tachypleus tridentatus is facilitated by chemical cues to approach suitable nursery habitats. The juvenile orientation to either side of the chamber containing controlled seawater or another with various vegetation cues, as well as their movement time, the largest distance and displacement were recorded. Results The juveniles preferred to orient toward seagrass Halophila beccarii cues when the concentration reached 0.5 g l−1, but ceased at 2 g l−1. The results can be interpreted as a shelter-seeking process to get closer to the preferred settlement habitats. However, the juveniles exhibited avoidance behaviors in the presence of mangrove Avicennia marina and invasive saltmarsh cordgrass Spartina alterniflora at 2 g l−1. The juveniles also spent less time moving in the presence of the A. marina cue, as well as reduced displacement in water containing the S. alterniflora cue at 1 and 2 g l−1. These results may explain the absence of juvenile T. tridentatus within densely vegetated areas, which have generally higher organic matter and hydrogen sulfide. Conclusion Early-stage juvenile T. tridentatus are capable of detecting and responding to habitat chemical cues, which can help guide them to high-quality settlement habitats. Preserving and restoring seagrass beds in the intertidal areas should be prioritized when formulating habitat conservation and management initiatives for the declining horseshoe crab populations.
Kwan et al. (2022) Chemically mediated rheotaxis of endangered tri-spine horseshoe crab: potential dispersing mechanism to vegetated nursery habitats along the coast. PeerJ 10:e14465 https://doi.org/10.7717/peerj.14465
Effects of cleaning sports mouthguards with ethylene-vinyl acetate on oral bacteria
Background Sports mouthguards, worn in the oral cavity to prevent sports injuries, are constantly exposed to various microorganisms that cause oral infections. Hence, the optimal cleaning methods for sports mouthguards have been thoroughly examined. In this study, we evaluated the efficiency of cleaning effects with a mouthguard cleaner (MC) on microbial biofilm formation in sports mouthguards in vitro and in vivo. Methods We evaluated the cleaning effects of the discs produced by ethylene-vinyl acetate (EVA) on bacterial biofilms formed by the commensal bacterium Streptococcus oralis, the cariogenic bacterium Streptococcus mutans, and the opportunistic pathogen Staphylococcus aureus in vitro. EVA discs with biofilm were subjected to sterile distilled water (CTRL) and ultrasonic washing (UW), followed by treatment with MC and sodium hypochlorite (NaClO) as positive controls. Thereafter, the viable bacterial cell counts were determined. The bacteria adhering to the sheets before and after the treatment were observed under an electron microscope. The degree of cleanliness and measurement of viable microbial cell counts for total bacteria, Streptococci and Candida, opportunistic fungi, were evaluated on the used experimental sports mouthguards with and without UW and MC treatment in vivo. Results The number of bacterial cells significantly decreased against all the tested biofilm bacteria upon treatment with MC, compared with CTRL and UW. Electron microscopy analysis revealed the biofilm formation by all bacteria on the EVA discs before cleaning. We observed fewer bacteria on the EVA discs treated with MC than those treated with CTRL and UW. Furthermore, the degree of cleanliness of the used experimental sports mouthguards cleaned using MC was significantly higher than that of the CTRL-treated mouthguards. Moreover, the viable microbial cell counts on the used experimental sports mouthguard were considerably lower than those on the CTRL ones. Conclusion The cleaning effect of MC against oral bacteria was more effective than that of UW. MC treatment might have a potential future application as a cleaning method for sports mouthguards to protect athletes from oral infection.
Hayashi et al. (2022) Effects of cleaning sports mouthguards with ethylene-vinyl acetate on oral bacteria. PeerJ 10:e14480 https://doi.org/10.7717/peerj.14480
Efficacy and indications of tonsillectomy in patients with IgA nephropathy: a retrospective study
Background The efficacy and indications of tonsillectomy in IgA nephropathy (IgAN) remain uncertain. Methods We performed a retrospective cohort study of 452 patients with primary IgAN, including 226 patients who received tonsillectomy and 226 controls selected by propensity score matching who had never undergone tonsillectomy. Study outcomes were clinical remission defined as negative hematuria and proteinuria on three consecutive visits over a 6-month period, the endpoint defined as end-stage renal disease or an irreversible 100% increase in serum creatinine from the baseline value. In addition, we further analyzed the critical level of proteinuria in the efficacy of tonsillectomy and the correlation between MEST-C score and tonsillectomy. Results Up to December 2019, the follow-up period lasted 46 ± 23 months (12–106 months). Kaplan–Meier and multivariate Cox regression analysis revealed that tonsillectomy was beneficial for clinical remission and renal survival. Whether proteinuria was ≤ 1 g/24h or >1 g/24h, the clinical remission and renal survival rates were greater in patients treated with tonsillectomy than without. When the pathological damage was mild or relatively severe, tonsillectomy may be beneficial to clinical remission or renal survival. Conclusions Tonsillectomy had a favorable effect on clinical remission and delayed renal deterioration in IgAN. In addition to patients with early stage IgAN, it may also be beneficial to IgAN patients with higher levels of proteinuria and relatively severe pathological damage.
Li et al. (2022) Efficacy and indications of tonsillectomy in patients with IgA nephropathy: a retrospective study. PeerJ 10:e14481 https://doi.org/10.7717/peerj.14481
Modeling the drying process of Masson pine needle fuel beds under different packing ratios based on two-phase models in the laboratory
Background When the moisture content of a fuel bed is higher than the fiber saturation moisture content (0.35 g g−1), the drying process is controlled by evaporation (>0.35 g g−1) and diffusion (>0.35 g g−1). Packing ratio has a significant effect on the drying process. Ignoring the impacts of packing ratio or the separate phases of the drying process is one main reason for inaccurate moisture content predictions. Method This study simulated the drying process in five Masson pine (Pinus massoniana Lamb.) needle beds with different packing ratios. Using the fiber saturation moisture content as the cut-off point, we divided the drying process into two phases. The drying mechanism of each phase was different and had its own drying equation. Using a model that does not distinguish the two phases of the drying process as a comparison, the prediction effect of the two-phase model was analyzed. The influence of the fuel bed packing ratio on the drying process was also analyzed. Results We found that, regardless of any changes in packing ratio, the two-phase model could better simulate the drying process, with a mean absolute error (MAE) and mean relative error (MRE) of the two-phase model 18.4% and 25.6% less than the one-phase model, respectively. The time-lag prediction model was established with the packing ratio, and the errors were all within the allowable range, but the prediction effect of the time-lag prediction model based on the two-phase model was larger. Conclusion It was further demonstrated that considering the packing ratio of the fuel bed and distinguishing the two separate phases of the drying process could both effectively improve the prediction accuracy of the moisture content of fuel beds based on the semi-physical method.
Zhang (2022) Modeling the drying process of Masson pine needle fuel beds under different packing ratios based on two-phase models in the laboratory. PeerJ 10:e14484 https://doi.org/10.7717/peerj.14484
Knowledge, attitudes, and practices towards mosquito control and used vehicle tire dumping by median household income, in metropolitan New Orleans, Louisiana
Background Discarded vehicle tires are an important artificial habitat for the larvae of many container-breeding mosquito species worldwide, including in the United States. Unmanaged discarded vehicle tires create health, environmental and social costs, and with budget and staffing constraints, effective management of discarded used vehicle tires a mosquito larval habitat depends in part on the knowledge, attitude, and practices (KAP) of community residents. Objectives This study aims to examine the knowledge, attitude and practices of New Orleans, Louisiana residents toward illegally discarded vehicle tires, and larval mosquito control. Methods A descriptive cross-sectional design study was used where 422 households were selected using a two-stage cluster random sampling procedure in New Orleans, Louisiana. Heads of households or a person aged 18 years or older self-administered the survey. The questionnaire comprised five parts: screening, tire sightings, preferred communication method, knowledge, attitude and precautionary measures against mosquito control, disease risk and illegal discarding. We then statistically compared above and below median income household responses to identify likely causes of detected differences. The data were analyzed using ordinal regression models via IBM SPSS statistics V.26.0. Statistical significance was set at p < 0.05. Results Out of 290 responding households, 95.5% strongly agree or agree that mosquitoes can spread serious diseases like West Nile, Zika or Dengue. Only 2.3% of the sample had high knowledge of illegally discarded tires dumping and mosquito larval control. Those employed were 1.0 times more likely to possess good knowledge than the unemployed (p < 0.001). Despite low knowledge levels regarding mosquito breeding and polluted water in discarded tires, 29.9% of respondents had positive attitude and 20.5% reported sufficient practices. Among the socio-demographic variables, only home ownership and being employed were predictors of knowledge and attitude towards mosquito breeding in illegally discarded tires (p < 0.05). Conclusions Despite the observed increasing number of illegally discarded vehicle tires in New Orleans, the knowledge of people about illegal tire dumping and their associated risk factors as suitable larval habitants was low. Therefore, there is a need for developing community-based and place-based tailored sensitization campaigns to prevent illegal used tire dumping, and larval control.
Environmental Contamination and Remediation
Moise et al. (2022) Knowledge, attitudes, and practices towards mosquito control and used vehicle tire dumping by median household income, in metropolitan New Orleans, Louisiana. PeerJ 10:e14188 https://doi.org/10.7717/peerj.14188
M1 macrophage-derived extracellular vesicle containing tsRNA-5006c promotes osteogenic differentiation of aortic valve interstitial cells through regulating mitophagy
Background Osteogenic differentiation of aortic valve interstitial cells (AVICs) plays a key role in the calcific aortic valve disease progression. Extracellular vesicles (EVs)-derived from M1-polarized macrophages (M1-EVs) orchestrated intercellular communication by delivering non-coding RNAs such as tRNA-derived small RNAs (tsRNAs) is crucial for cardiovascular disease. However, the role and mechanism of M1-EVs tsRNAs in osteogenic differentiation of AVICs remains largely unclear. Methods M1-EVs and PBS treated-RAW 264.7 cell-derived EVs (NC-EVs) were incubated with AVICs and subjected to small RNA sequencing. Candidate tsRNA in M1-EVs was silenced to explore their effects on AVIC osteogenic differentiation and mitophagy. Results DiI-labeled M1-EVs were internalized by AVICs, resulting in significantly increased calcium nodule formation and expression of osteogenesis-related genes in AVICs, including RUNX2, BMP2, osteopontin, and SPP1, compared with NC-EVs. Small RNA sequencing revealed that 17 tsRNAs were significantly up-regulated such as tsRNA-5006c, while 28 tsRNAs were significantly down-regulated in M1-EVs compared with NC-EVs. Intriguingly, tsRNA-5006c-deleted M1-EVs treatment significantly reduced calcium nodule formation and expression of osteogenesis-related genes in AVICs relative to control group. Moreover, target genes of tsRNA-5006c were mainly involved in autophagy-related signaling pathways, such as MAPK, Ras, Wnt, and Hippo signaling pathway. Hallmarks of mitophagy activation in AVICs including mitophagosome formation, TMRM fluorescence, expression of LC3-II, BINP3, and PGC1α, were significantly elevated in the M1-EVs group compared with NC-EVs group, whereas M1-EVs tsRNA-5006c inhibitor led to a significant reduction in these indicators. Conclusion M1-EVs carried tsRNA-5006c regulates AVIC osteogenic differentiation from the perspective of mitophagy, and we provide a new target for the prevention and treatment of aortic valve calcification.
Xia et al. (2022) M1 macrophage-derived extracellular vesicle containing tsRNA-5006c promotes osteogenic differentiation of aortic valve interstitial cells through regulating mitophagy. PeerJ 10:e14307 https://doi.org/10.7717/peerj.14307
Effects of PAHs on meiofauna from three estuaries with different levels of urbanization in the South Atlantic
Estuarine environments are suggested to be the final receivers of human pollution and are impacted by surrounding urbanization and compounds carried by the river waters that flow from the continent. Polycyclic aromatic hydrocarbons (PAHs) are among the contaminants that can reach estuaries and can directly affect marine conservation, being considered highly deleterious to organisms living in these environments. This research investigated the meiofauna of three estuaries exposed to different levels of urbanization and consequently different levels of PAH concentrations, in order to assess how these compounds and environmental factors affect the distribution, structure and diversity of these interstitial invertebrates. A total of 15 major meiofauna groups were identified, with Nematoda being the dominant taxon (74.64%), followed by Copepoda (9.55%) and Polychaeta (8.56%). It was possible to observe significant differences in all diversity indices studied in the estuaries. With the exception of average density, the diversity indices (richness, Shannon index and evenness) were higher in the reference estuary, Goiana estuarine system (GES). On the other hand, the Timbó estuarine system (TES) had the lowest Shannon index value and richness, while the Capibaribe estuarine system (CES) had the lowest evenness value. The latter two estuaries (TES and CES) presented intermediate and high levels of urbanization, respectively. The ecological quality assessment (EcoQ) in the studied estuaries was classified from Poor to Moderate and the estuary with the lowest demographic density in its surroundings, GES, showed a better ecological quality (Moderate EcoQ). A significant distance-based multivariate linear modelling regression (DistLM) was observed between the environmental variables and the density of the meiobenthic community, where PAHs and pH were the main contributors to organism variation. The sediments were characterized by predominance of very fine sand and silt-clay in the most polluted environments, while the control site environment (GES) was dominated by medium grains. The highest concentrations of PAHs were found in the most urbanized estuaries, and directly affected the structure of the interstitial benthic community. The metrics used in the present study proved to be adequate for assessing the environmental quality of the investigated estuaries.
da Silva et al. (2022) Effects of PAHs on meiofauna from three estuaries with different levels of urbanization in the South Atlantic. PeerJ 10:e14407 https://doi.org/10.7717/peerj.14407
Transcriptome-wide identification of WRKY transcription factors and their expression profiles under different stress in Cynanchum thesioides
Cynanchum thesioides (Freyn) K. Schum. is an important economic and medicinal plant widely distributed in northern China. WRKY transcription factors (TFs) play important roles in plant growth, development and regulating responses. However, there is no report on the WRKY genes in Cynanchum thesioides. A total of 19 WRKY transcriptome sequences with complete ORFs were identified as WRKY transcriptome sequences by searching for WRKYs in RNA sequencing data. Then, the WRKY genes were classified by phylogenetic and conserved motif analysis of the WRKY family in Cynanchum thesioides and Arabidopsis thaliana. qRT–PCR was used to determine the expression patterns of 19 CtWRKY genes in different tissues and seedlings of Cynanchum thesioides under plant hormone (ABA and ETH) and abiotic stresses (cold and salt). The results showed that 19 CtWRKY genes could be divided into groups I-III according to their structure and phylogenetic characteristics, and group II could be divided into five subgroups. The prediction of CtWRKY gene protein interactions indicates that CtWRKY is involved in many biological processes. In addition, the CtWRKY gene was differentially expressed in different tissues and positively responded to abiotic stress and phytohormone treatment, among which CtWRKY9, CtWRKY18, and CtWRKY19 were significantly induced under various stresses. This study is the first to identify the WRKY gene family in Cynanchum thesioides, and the systematic analysis lays a foundation for further identification of the function of WRKY genes in Cynanchum thesioides.
Chang et al. (2022) Transcriptome-wide identification of WRKY transcription factors and their expression profiles under different stress in Cynanchum thesioides. PeerJ 10:e14436 https://doi.org/10.7717/peerj.14436
Multi-omics analyses reveal that the gut microbiome and its metabolites promote milk fat synthesis in Zhongdian yak cows
Background Yak cows produce higher quality milk with higher concentrations of milk fat than dairy cows. Recently, studies have found the yak milk yield and milk fat percentage have decreased significantly over the past decade, highlighting the urgency for yak milk improvement. Therefore, we aimed to analyze how the gut microbiome impacts milk fat synthesis in Zhongdian yak cows. Methods We collected milk samples from Zhongdian yak cows and analyzed the milk fat percentage, selecting five Zhongdian yak cows with a very high milk fat percentage (>7%, 8.70 ± 1.89%, H group) and five Zhongdian yak cows with a very low milk fat percentage (<5%, 4.12 ± 0.43%, L group), and then obtained gut samples of these ten Zhongdian yak cows through rectal palpation. Gut metagenomics, metabolomics, and conjoint metagenomics and metabolomics analyses were performed on these samples, identifying taxonomic changes, functional changes, and changes in gut microbes-metabolite interactions within the milk fat synthesis-associated Zhongdian yak cows gut microbiome, to identify potential regulatory mechanisms of milk fat at the gut microbiome level in Zhongdian yak cows. Results The metagenomics analysis revealed Firmicutes and Proteobacteria were significantly more abundant in the gut of the high-milk fat Zhongdian yak cows. These bacteria are involved in the biosynthesis of unsaturated fatty acids and amino acids, leading to greater efficiency in converting energy to milk fat. The metabolomics analysis showed that the elevated gut metabolites in high milk fat percentage Zhongdian yak cows were mainly enriched in lipid and amino acid metabolism. Using a combined metagenomic and metabolomics analysis, positive correlations between Firmicutes (Desulfocucumis, Anaerotignum, Dolosiccus) and myristic acid, and Proteobacteria (Catenovulum, Comamonas, Rubrivivax, Marivita, Succinimouas) and choline were found in the gut of Zhongdian yak cows. These interactions may be the main contributors to methanogen inhibition, producing less methane leading to higher-efficient milk fat production. Conclusions A study of the gut microbe, gut metabolites, and milk fat percentage of Zhongdian yak cows revealed that the variations in milk fat percentage between yak cows may be caused by the gut microbes and their metabolites, especially Firmicutes-myristic acid and Proteobacteria-choline interactions, which are important to milk fat synthesis. Our study provides new insights into the functional roles of the gut microbiome in producing small molecule metabolites and contributing to milk performance traits in yak cows.
Liu et al. (2022) Multi-omics analyses reveal that the gut microbiome and its metabolites promote milk fat synthesis in Zhongdian yak cows. PeerJ 10:e14444 https://doi.org/10.7717/peerj.14444