PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification, classification, and expression profile analysis of heat shock transcription factor gene family in Salvia miltiorrhiza
items: Chemically mediated rheotaxis of endangered tri-spine horseshoe crab: potential dispersing mechanism to vegetated nursery habitats along the coast
items: Effects of cleaning sports mouthguards with ethylene-vinyl acetate on oral bacteria
items: Efficacy and indications of tonsillectomy in patients with IgA nephropathy: a retrospective study
items: Modeling the drying process of Masson pine needle fuel beds under different packing ratios based on two-phase models in the laboratory
items: Knowledge, attitudes, and practices towards mosquito control and used vehicle tire dumping by median household income, in metropolitan New Orleans, Louisiana
items: M1 macrophage-derived extracellular vesicle containing tsRNA-5006c promotes osteogenic differentiation of aortic valve interstitial cells through regulating mitophagy
items: Effects of PAHs on meiofauna from three estuaries with different levels of urbanization in the South Atlantic
items: Transcriptome-wide identification of WRKY transcription factors and their expression profiles under different stress in Cynanchum thesioides
items: Multi-omics analyses reveal that the gut microbiome and its metabolites promote milk fat synthesis in Zhongdian yak cows

Identification, classification, and expression profile analysis of heat shock transcription factor gene family in Salvia miltiorrhiza
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Rui Liu
creator: Peijin Zou
creator: Zhu-Yun Yan
creator: Xin Chen
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14464
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-08-16
date accepted: 2022-11-03
issued: 2022-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Rui
author list: Agent
  family name: Zou
  given name: Peijin
author list: Agent
  family name: Yan
  given name: Zhu-Yun
author list: Agent
  family name: Chen
  given name: Xin
doi: 10.7717/peerj.14464
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-05
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Chemically mediated rheotaxis of endangered tri-spine horseshoe crab: potential dispersing mechanism to vegetated nursery habitats along the coast
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Kit Yue Kwan
creator: Xin Yang
creator: Chun-Chieh Wang
creator: Yang Kuang
creator: Yulong Wen
creator: Kian Ann Tan
creator: Peng Xu
creator: Wenquan Zhen
creator: Xueping Wang
creator: Junhua Zhu
creator: Xing Huang
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.14465
publisher: PeerJ Inc.
rights: © 2022 Kwan et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-03-22
date accepted: 2022-11-04
issued: 2022-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kwan
  given name: Kit Yue
author list: Agent
  family name: Yang
  given name: Xin
author list: Agent
  family name: Wang
  given name: Chun-Chieh
author list: Agent
  family name: Kuang
  given name: Yang
author list: Agent
  family name: Wen
  given name: Yulong
author list: Agent
  family name: Tan
  given name: Kian Ann
author list: Agent
  family name: Xu
  given name: Peng
author list: Agent
  family name: Zhen
  given name: Wenquan
author list: Agent
  family name: Wang
  given name: Xueping
author list: Agent
  family name: Zhu
  given name: Junhua
author list: Agent
  family name: Huang
  given name: Xing
doi: 10.7717/peerj.14465
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-05
copyright: ©2022 Kwan et al.
attribution name: Kwan et al.

Effects of cleaning sports mouthguards with ethylene-vinyl acetate on oral bacteria
type: item
type: AcademicArticle
description: 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 ef…
format: application/pdf
format: text/html
creator: Hiroki Hayashi
creator: Yoshikazu Naiki
creator: Masahiro Murakami
creator: Akihiro Oishi
creator: Rihoko Takeuchi
creator: Masayoshi Nakagawa
creator: Suguru Kimoto
creator: Yoshiaki Hasegawa
creator: Akizumi Araki
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.14480
publisher: PeerJ Inc.
rights: © 2022 Hayashi et al.
abstract: 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 ef…
bibliographic citation: 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
date submitted: 2022-09-01
date accepted: 2022-11-07
issued: 2022-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hayashi
  given name: Hiroki
author list: Agent
  family name: Naiki
  given name: Yoshikazu
author list: Agent
  family name: Murakami
  given name: Masahiro
author list: Agent
  family name: Oishi
  given name: Akihiro
author list: Agent
  family name: Takeuchi
  given name: Rihoko
author list: Agent
  family name: Nakagawa
  given name: Masayoshi
author list: Agent
  family name: Kimoto
  given name: Suguru
author list: Agent
  family name: Hasegawa
  given name: Yoshiaki
author list: Agent
  family name: Araki
  given name: Akizumi
doi: 10.7717/peerj.14480
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-05
copyright: ©2022 Hayashi et al.
attribution name: Hayashi et al.

Efficacy and indications of tonsillectomy in patients with IgA nephropathy: a retrospective study
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Yan Li
creator: Qi Wan
creator: Zhixin Lan
creator: Ming Xia
creator: Haiyang Liu
creator: Guochun Chen
creator: Liyu He
creator: Chang Wang
creator: Hong Liu
subject: Internal Medicine
subject: Nephrology
subject: Otorhinolaryngology
subject: Public Health
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.14481
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2021-03-10
date accepted: 2022-11-08
issued: 2022-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Wan
  given name: Qi
author list: Agent
  family name: Lan
  given name: Zhixin
author list: Agent
  family name: Xia
  given name: Ming
author list: Agent
  family name: Liu
  given name: Haiyang
author list: Agent
  family name: Chen
  given name: Guochun
author list: Agent
  family name: He
  given name: Liyu
author list: Agent
  family name: Wang
  given name: Chang
author list: Agent
  family name: Liu
  given name: Hong
doi: 10.7717/peerj.14481
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-05
copyright: ©2022 Li et al.
attribution name: Li et al.

Modeling the drying process of Masson pine needle fuel beds under different packing ratios based on two-phase models in the laboratory
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Yunlin Zhang
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.14484
publisher: PeerJ Inc.
rights: © 2022 Zhang
abstract: 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.
bibliographic citation: 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
date submitted: 2022-08-09
date accepted: 2022-11-08
issued: 2022-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yunlin
doi: 10.7717/peerj.14484
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-05
copyright: ©2022 Zhang
attribution name: Zhang

Knowledge, attitudes, and practices towards mosquito control and used vehicle tire dumping by median household income, in metropolitan New Orleans, Louisiana
type: item
type: AcademicArticle
description: 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 …
format: application/pdf
format: text/html
creator: Imelda K. Moise
creator: Ashley Archer
creator: Claudia Riegel
subject: Public Health
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
subject: Environmental Health
description: doi:10.7717/peerj.14188
publisher: PeerJ Inc.
rights: © 2022 Moise et al.
abstract: 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 …
bibliographic citation: 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
date submitted: 2022-02-22
date accepted: 2022-09-14
issued: 2022-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moise
  given name: Imelda K.
author list: Agent
  family name: Archer
  given name: Ashley
author list: Agent
  family name: Riegel
  given name: Claudia
doi: 10.7717/peerj.14188
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-02
copyright: ©2022 Moise et al.
attribution name: Moise et al.

M1 macrophage-derived extracellular vesicle containing tsRNA-5006c promotes osteogenic differentiation of aortic valve interstitial cells through regulating mitophagy
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Hao Xia
creator: Mingjian Gao
creator: Jun Chen
creator: Guanshen Huang
creator: Xiuting Xiang
creator: Yuyan Wang
creator: Zhaohui Huang
creator: Yongchun Li
creator: Shuang Su
creator: Zewei Zhao
creator: Qingchun Zeng
creator: Yunjun Ruan
subject: Molecular Biology
subject: Cardiology
description: doi:10.7717/peerj.14307
publisher: PeerJ Inc.
rights: © 2022 Xia et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-08-18
date accepted: 2022-10-05
issued: 2022-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Hao
author list: Agent
  family name: Gao
  given name: Mingjian
author list: Agent
  family name: Chen
  given name: Jun
author list: Agent
  family name: Huang
  given name: Guanshen
author list: Agent
  family name: Xiang
  given name: Xiuting
author list: Agent
  family name: Wang
  given name: Yuyan
author list: Agent
  family name: Huang
  given name: Zhaohui
author list: Agent
  family name: Li
  given name: Yongchun
author list: Agent
  family name: Su
  given name: Shuang
author list: Agent
  family name: Zhao
  given name: Zewei
author list: Agent
  family name: Zeng
  given name: Qingchun
author list: Agent
  family name: Ruan
  given name: Yunjun
doi: 10.7717/peerj.14307
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-02
copyright: ©2022 Xia et al.
attribution name: Xia et al.

Effects of PAHs on meiofauna from three estuaries with different levels of urbanization in the South Atlantic
type: item
type: AcademicArticle
description: 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 th…
format: application/pdf
format: text/html
creator: Renan B. da Silva
creator: Giovanni A. P. Dos Santos
creator: Ana Luiza L. de Farias
creator: Débora A. A. França
creator: Raianne Amorim Cavalcante
creator: Eliete Zanardi-Lamardo
creator: Jose Roberto Botelho de Souza
creator: Andre M. Esteves
subject: Conservation Biology
description: doi:10.7717/peerj.14407
publisher: PeerJ Inc.
rights: © 2022 da Silva et al.
abstract: 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 th…
bibliographic citation: 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
date submitted: 2022-07-13
date accepted: 2022-10-26
issued: 2022-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: da Silva
  given name: Renan B.
author list: Agent
  family name: Dos Santos
  given name: Giovanni A. P.
author list: Agent
  family name: de Farias
  given name: Ana Luiza L.
author list: Agent
  family name: França
  given name: Débora A. A.
author list: Agent
  family name: Cavalcante
  given name: Raianne Amorim
author list: Agent
  family name: Zanardi-Lamardo
  given name: Eliete
author list: Agent
  family name: de Souza
  given name: Jose Roberto Botelho
author list: Agent
  family name: Esteves
  given name: Andre M.
doi: 10.7717/peerj.14407
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-02
copyright: © 2022 da Silva et al.
attribution name: da Silva et al.

Transcriptome-wide identification of WRKY transcription factors and their expression profiles under different stress in Cynanchum thesioides
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Xiaoyao Chang
creator: Zhongren Yang
creator: Xiaoyan Zhang
creator: Fenglan Zhang
creator: Xiumei Huang
creator: Xu Han
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.14436
publisher: PeerJ Inc.
rights: © 2022 Chang et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-08-29
date accepted: 2022-10-31
issued: 2022-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Xiaoyao
author list: Agent
  family name: Yang
  given name: Zhongren
author list: Agent
  family name: Zhang
  given name: Xiaoyan
author list: Agent
  family name: Zhang
  given name: Fenglan
author list: Agent
  family name: Huang
  given name: Xiumei
author list: Agent
  family name: Han
  given name: Xu
doi: 10.7717/peerj.14436
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-02
copyright: ©2022 Chang et al.
attribution name: Chang et al.

Multi-omics analyses reveal that the gut microbiome and its metabolites promote milk fat synthesis in Zhongdian yak cows
type: item
type: AcademicArticle
description: 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 metha…
format: application/pdf
format: text/html
creator: Lily Liu
creator: Peifu Wu
creator: Fenfen Chen
creator: Jielong Zhou
creator: Aiwei Guo
creator: Kerong Shi
creator: Qin Zhang
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Zoology
subject: Nutrition
description: doi:10.7717/peerj.14444
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: 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 metha…
bibliographic citation: 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
date submitted: 2022-04-02
date accepted: 2022-11-01
issued: 2022-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Lily
author list: Agent
  family name: Wu
  given name: Peifu
author list: Agent
  family name: Chen
  given name: Fenfen
author list: Agent
  family name: Zhou
  given name: Jielong
author list: Agent
  family name: Guo
  given name: Aiwei
author list: Agent
  family name: Shi
  given name: Kerong
author list: Agent
  family name: Zhang
  given name: Qin
doi: 10.7717/peerj.14444
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-02
copyright: ©2022 Liu et al.
attribution name: Liu et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359