PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Progress in the discovery of isopods (Crustacea: Peracarida)—is the description rate slowing down?
items: Chronic unpredictable mild stress promotes atherosclerosis via adipose tissue dysfunction in ApoE-/- mice
items: Assessing the impact of the 2018 tetanus guidelines on knowledge and practices of emergency physicians in trauma patients: a national survey study
items: https://peerj.com/articles/15539
items: High phenotypic plasticity at the dawn of the eosauropterygian radiation
items: An investigation into the response of the soil ecological environment to tourist disturbance in Baligou
items: Microbial signature profiles of Penaeus vannamei larvae in low-survival hatchery tanks affected by vibriosis
items: Improving the success of reinforcement programs: effects of a two-week confinement in a field enclosure on the anti-predator behaviour of captive-bred European hamsters
items: PM2.5 exposure aggravates kidney damage by facilitating the lipid metabolism disorder in diabetic mice
items: Construction and validation of a PANoptosis-related lncRNA signature for predicting prognosis and targeted drug response in thyroid cancer

Progress in the discovery of isopods (Crustacea: Peracarida)—is the description rate slowing down?
type: item
type: AcademicArticle
description: Taxonomic species are the best standardised metric of biodiversity. Therefore, there is broad scientific and public interest in how many species have already been named and how many more may exist. Crustaceans comprise about 6% of all named animal species and isopods about 15% of all crustaceans. Here, we review progress in the naming of isopods in relation to the number of people describing new species and estimate how many more species may yet be named by 2050 and 2100, respectively. In over two and a half centuries of discovery, 10,687 isopod species in 1,557 genera and 141 families have been described by 755 first authors. The number of authors has increased over time, especially since the 1950s, indicating increasing effort in the description of new species. Despite that the average number of species described per first author has declined since the 1910s, and the description rate has slowed down over the recent decades. Authors’ publication lifetimes did not change considerably over time, and there was a distinct shift towards multi-authored publications in recent decades. Estimates from a non-homogeneous renewal process model predict that an additional 660 isopod species will be described by 2100, assuming that the rate of description continues at its current pace.
format: application/pdf
format: text/html
creator: Lena Hartebrodt
creator: Simon Wilson
creator: Mark John Costello
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.15984
publisher: PeerJ Inc.
rights: © 2023 Hartebrodt et al.
abstract: Taxonomic species are the best standardised metric of biodiversity. Therefore, there is broad scientific and public interest in how many species have already been named and how many more may exist. Crustaceans comprise about 6% of all named animal species and isopods about 15% of all crustaceans. Here, we review progress in the naming of isopods in relation to the number of people describing new species and estimate how many more species may yet be named by 2050 and 2100, respectively. In over two and a half centuries of discovery, 10,687 isopod species in 1,557 genera and 141 families have been described by 755 first authors. The number of authors has increased over time, especially since the 1950s, indicating increasing effort in the description of new species. Despite that the average number of species described per first author has declined since the 1910s, and the description rate has slowed down over the recent decades. Authors’ publication lifetimes did not change considerably over time, and there was a distinct shift towards multi-authored publications in recent decades. Estimates from a non-homogeneous renewal process model predict that an additional 660 isopod species will be described by 2100, assuming that the rate of description continues at its current pace.
bibliographic citation: Hartebrodt et al. (2023) Progress in the discovery of isopods (Crustacea: Peracarida)—is the description rate slowing down?. PeerJ 11:e15984 https://doi.org/10.7717/peerj.15984
date submitted: 2023-01-16
date accepted: 2023-08-08
issued: 2023-09-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hartebrodt
  given name: Lena
author list: Agent
  family name: Wilson
  given name: Simon
author list: Agent
  family name: Costello
  given name: Mark John
doi: 10.7717/peerj.15984
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-04
copyright: ©2023 Hartebrodt et al.
attribution name: Hartebrodt et al.

Chronic unpredictable mild stress promotes atherosclerosis via adipose tissue dysfunction in ApoE-/- mice
type: item
type: AcademicArticle
description: Background Chronic unpredictable mild stress (CUMS) has been shown to exacerbate atherosclerosis, but the underlying mechanism remains unknown. Adipose tissue is an energy storage organ and the largest endocrine organ in the human body, playing a key role in the development of cardiovascular disease. In this research, it was hypothesized that CUMS may exacerbate the development of atherosclerosis by inducing the hypertrophy and dysfunction of white adipocytes. Methods The CUMS-induced atherosclerosis model was developed in Western diet-fed apolipoprotein E (ApoE)-/- mice. White adipose tissue (WAT), serum, aortic root, and the brachiocephalic trunk were collected and tested after 12 weeks of CUMS development. The mouse model of CUMS was evaluated for depression-like behavior using the open field test (OFT) and the elevated plus maze (EPM) test. Enzyme-linked immunosorbent assay (ELISA) was conducted to detect serum noradrenaline and urine adrenaline protein levels. Serological assays were used to detect serum low-density lipoprotein (LDL), high-density lipoprotein (HDL), total cholesterol (TC), and free fatty acid (FFA) concentrations. Hematoxylin and eosin (H&E) staining and oil red O were used to detect atherosclerotic plaque area, lipid deposition, and adipocyte size. The mRNA levels of genes related to aberrant adipose tissue function were determined using real-time PCR. Immunofluorescence assay and western blotting were conducted to examine the expression of proteins in the adipose tissue samples. Results CUMS aggravated vascular atherosclerotic lesions in ApoE-/- mice. It decreased body weight while increasing the percentage of WAT. The serological results indicated that the concentration of HDL decreased in CUMS mice. Notably, adipocyte hypertrophy increased, whereas the mRNA levels of Pparg and its target genes (Slc2a4 (encodes for GLUT4), Adipoq, and Plin1) decreased. Further investigation revealed that CUMS increased subcutaneous inguinal WAT (iWAT) lipid …
format: application/pdf
format: text/html
creator: Min Mao
creator: Yalan Deng
creator: Li Wang
creator: Gexin Zhao
creator: Ruomei Qi
creator: Huan Gong
creator: Tao Shen
creator: Yitian Xu
creator: Deping Liu
creator: Beidong Chen
subject: Biochemistry
subject: Obesity
subject: Mental Health
description: doi:10.7717/peerj.16029
publisher: PeerJ Inc.
rights: © 2023 Mao et al.
abstract: Background Chronic unpredictable mild stress (CUMS) has been shown to exacerbate atherosclerosis, but the underlying mechanism remains unknown. Adipose tissue is an energy storage organ and the largest endocrine organ in the human body, playing a key role in the development of cardiovascular disease. In this research, it was hypothesized that CUMS may exacerbate the development of atherosclerosis by inducing the hypertrophy and dysfunction of white adipocytes. Methods The CUMS-induced atherosclerosis model was developed in Western diet-fed apolipoprotein E (ApoE)-/- mice. White adipose tissue (WAT), serum, aortic root, and the brachiocephalic trunk were collected and tested after 12 weeks of CUMS development. The mouse model of CUMS was evaluated for depression-like behavior using the open field test (OFT) and the elevated plus maze (EPM) test. Enzyme-linked immunosorbent assay (ELISA) was conducted to detect serum noradrenaline and urine adrenaline protein levels. Serological assays were used to detect serum low-density lipoprotein (LDL), high-density lipoprotein (HDL), total cholesterol (TC), and free fatty acid (FFA) concentrations. Hematoxylin and eosin (H&E) staining and oil red O were used to detect atherosclerotic plaque area, lipid deposition, and adipocyte size. The mRNA levels of genes related to aberrant adipose tissue function were determined using real-time PCR. Immunofluorescence assay and western blotting were conducted to examine the expression of proteins in the adipose tissue samples. Results CUMS aggravated vascular atherosclerotic lesions in ApoE-/- mice. It decreased body weight while increasing the percentage of WAT. The serological results indicated that the concentration of HDL decreased in CUMS mice. Notably, adipocyte hypertrophy increased, whereas the mRNA levels of Pparg and its target genes (Slc2a4 (encodes for GLUT4), Adipoq, and Plin1) decreased. Further investigation revealed that CUMS increased subcutaneous inguinal WAT (iWAT) lipid …
bibliographic citation: Mao et al. (2023) Chronic unpredictable mild stress promotes atherosclerosis via adipose tissue dysfunction in ApoE-/- mice. PeerJ 11:e16029 https://doi.org/10.7717/peerj.16029
date submitted: 2023-02-08
date accepted: 2023-08-13
issued: 2023-09-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Min
author list: Agent
  family name: Deng
  given name: Yalan
author list: Agent
  family name: Wang
  given name: Li
author list: Agent
  family name: Zhao
  given name: Gexin
author list: Agent
  family name: Qi
  given name: Ruomei
author list: Agent
  family name: Gong
  given name: Huan
author list: Agent
  family name: Shen
  given name: Tao
author list: Agent
  family name: Xu
  given name: Yitian
author list: Agent
  family name: Liu
  given name: Deping
author list: Agent
  family name: Chen
  given name: Beidong
doi: 10.7717/peerj.16029
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-04
copyright: © 2023 Mao et al.
attribution name: Mao et al.

Assessing the impact of the 2018 tetanus guidelines on knowledge and practices of emergency physicians in trauma patients: a national survey study
type: item
type: AcademicArticle
description: Background Tetanus remains a significant public health issue in China, with the approach of anti-tetanus prophylaxis in the emergency department resulting in both overuse, particularly of human tetanus immune globulin (TIG), and underuse with the tetanus vaccine. This is largely due to the absence of updated guidelines on tetanus prophylaxis before 2018. Our study aimed to evaluate the effects of the 2018 Chinese tetanus guidelines on the knowledge and practices of emergency physicians about tetanus prevention in trauma patients. Methods From November 2019 to April 2020, we conducted a web-based survey involving 499 emergency physicians. The survey included a questionnaire covering knowledge, attitudes, and practices related to tetanus. We assessed the influence of the 2018 tetanus guidelines on the knowledge and practices of emergency physicians related to tetanus prevention for patients with trauma using multiple regression analysis. Results The survey results showed that only 45.3% of the participants had received formal training on tetanus immunization, despite 53.3% reporting the availability of tetanus vaccines at their institutions. Physicians typically prescribed tetanus antitoxin or human TIG instead of tetanus toxoid (TT) to treat injuries, regardless of the patient’s TT vaccination history. Among the respondents, those who were aware of the 2018 tetanus guidelines had higher mean scores on the general knowledge, risk knowledge, and treatment knowledge scales, with increases of 6%, 13%, and 9%, respectively, compared to those who were unaware of the guidelines. Awareness of the 2018 tetanus guidelines was associated with a high level of knowledge, as indicated by the general knowledge score, recommendation knowledge score, and total knowledge score, after adjusting for the effects of all variables on the knowledge, attitudes, and practices of the participants. A high level of education was also associated with a high level of knowledge indicated by the rec…
format: application/pdf
format: text/html
creator: Junling Gao
creator: Xiaxia Yu
creator: Guanghui Cao
creator: Xiaoming He
creator: Pingde Zhang
creator: Joseph Walline
creator: Yuanxi Wang
creator: Xingjuan Yu
creator: Jun Xu
creator: Thuan-Quoc Thach
creator: Yong Liu
subject: Emergency and Critical Care
subject: Epidemiology
subject: Hematology
subject: Infectious Diseases
description: doi:10.7717/peerj.16032
publisher: PeerJ Inc.
rights: © 2023 Gao et al.
abstract: Background Tetanus remains a significant public health issue in China, with the approach of anti-tetanus prophylaxis in the emergency department resulting in both overuse, particularly of human tetanus immune globulin (TIG), and underuse with the tetanus vaccine. This is largely due to the absence of updated guidelines on tetanus prophylaxis before 2018. Our study aimed to evaluate the effects of the 2018 Chinese tetanus guidelines on the knowledge and practices of emergency physicians about tetanus prevention in trauma patients. Methods From November 2019 to April 2020, we conducted a web-based survey involving 499 emergency physicians. The survey included a questionnaire covering knowledge, attitudes, and practices related to tetanus. We assessed the influence of the 2018 tetanus guidelines on the knowledge and practices of emergency physicians related to tetanus prevention for patients with trauma using multiple regression analysis. Results The survey results showed that only 45.3% of the participants had received formal training on tetanus immunization, despite 53.3% reporting the availability of tetanus vaccines at their institutions. Physicians typically prescribed tetanus antitoxin or human TIG instead of tetanus toxoid (TT) to treat injuries, regardless of the patient’s TT vaccination history. Among the respondents, those who were aware of the 2018 tetanus guidelines had higher mean scores on the general knowledge, risk knowledge, and treatment knowledge scales, with increases of 6%, 13%, and 9%, respectively, compared to those who were unaware of the guidelines. Awareness of the 2018 tetanus guidelines was associated with a high level of knowledge, as indicated by the general knowledge score, recommendation knowledge score, and total knowledge score, after adjusting for the effects of all variables on the knowledge, attitudes, and practices of the participants. A high level of education was also associated with a high level of knowledge indicated by the rec…
bibliographic citation: Gao et al. (2023) Assessing the impact of the 2018 tetanus guidelines on knowledge and practices of emergency physicians in trauma patients: a national survey study. PeerJ 11:e16032 https://doi.org/10.7717/peerj.16032
date submitted: 2023-01-17
date accepted: 2023-08-13
issued: 2023-09-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Junling
author list: Agent
  family name: Yu
  given name: Xiaxia
author list: Agent
  family name: Cao
  given name: Guanghui
author list: Agent
  family name: He
  given name: Xiaoming
author list: Agent
  family name: Zhang
  given name: Pingde
author list: Agent
  family name: Walline
  given name: Joseph
author list: Agent
  family name: Wang
  given name: Yuanxi
author list: Agent
  family name: Yu
  given name: Xingjuan
author list: Agent
  family name: Xu
  given name: Jun
author list: Agent
  family name: Thach
  given name: Thuan-Quoc
author list: Agent
  family name: Liu
  given name: Yong
doi: 10.7717/peerj.16032
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-04
copyright: © 2023 Gao et al.
attribution name: Gao et al.

https://peerj.com/articles/15539
type: item
type: AcademicArticle
title: Rational synthesis of total damage during cryoprotectant equilibration: modelling and experimental validation of osmomechanical, temperature, and cytotoxic damage in sea urchin (Paracentrotus lividus) oocytes
description: Sea urchins (e.g., Paracentrotus lividus) are important for both aquaculture and as model species. Despite their importance, biobanking of urchin oocytes by cryopreservation is currently not possible. Optimized cryoprotectant loading may enable novel vitrification methods and thus successful cryopreservation of oocytes. One method for determining an optimized loading protocol uses membrane characteristics and models of damage, namely osmomechanical damage, temperature damage (e.g., chill injury) and cytotoxicity. Here we present and experimentally evaluate existing and novel models of these damage modalities as a function of time and temperature. In osmomechanical damage experiments, oocytes were exposed for 2 to 30 minutes in hypertonic NaCl or sucrose supplemented seawater or in hypotonic diluted seawater. In temperature damage experiments, oocytes were exposed to 1.7 °C, 10 °C, or 20 °C for 2 to 90 minutes. Cytotoxicity was investigated by exposing oocytes to solutions of Me2SO for 2 to 30 minutes. We identified a time-dependent osmotic damage model, a temperature-dependent damage model, and a temperature and time-dependent cytotoxicity model. We combined these models to estimate total damage during a cryoprotectant loading protocol and determined the optimal loading protocol for any given goal intracellular cryoprotectant concentration. Given our fitted models, we find sea urchin oocytes can only be loaded to 13% Me2SO v/v with about 50% survival. This synthesis of multiple damage modalities is the first of its kind and enables a novel approach to modelling cryoprotectant equilibration survival for cells in general.
format: application/pdf
format: text/html
creator: Dominic J. Olver
creator: Pablo Heres
creator: Estefania Paredes
creator: James D. Benson
subject: Aquaculture, Fisheries and Fish Science
subject: Biophysics
subject: Marine Biology
subject: Mathematical Biology
subject: Zoology
description: doi:10.7717/peerj.15539
publisher: PeerJ Inc.
rights: © 2023 Olver et al.
abstract: Sea urchins (e.g., Paracentrotus lividus) are important for both aquaculture and as model species. Despite their importance, biobanking of urchin oocytes by cryopreservation is currently not possible. Optimized cryoprotectant loading may enable novel vitrification methods and thus successful cryopreservation of oocytes. One method for determining an optimized loading protocol uses membrane characteristics and models of damage, namely osmomechanical damage, temperature damage (e.g., chill injury) and cytotoxicity. Here we present and experimentally evaluate existing and novel models of these damage modalities as a function of time and temperature. In osmomechanical damage experiments, oocytes were exposed for 2 to 30 minutes in hypertonic NaCl or sucrose supplemented seawater or in hypotonic diluted seawater. In temperature damage experiments, oocytes were exposed to 1.7 °C, 10 °C, or 20 °C for 2 to 90 minutes. Cytotoxicity was investigated by exposing oocytes to solutions of Me2SO for 2 to 30 minutes. We identified a time-dependent osmotic damage model, a temperature-dependent damage model, and a temperature and time-dependent cytotoxicity model. We combined these models to estimate total damage during a cryoprotectant loading protocol and determined the optimal loading protocol for any given goal intracellular cryoprotectant concentration. Given our fitted models, we find sea urchin oocytes can only be loaded to 13% Me2SO v/v with about 50% survival. This synthesis of multiple damage modalities is the first of its kind and enables a novel approach to modelling cryoprotectant equilibration survival for cells in general.
bibliographic citation: Olver et al. (2023) Rational synthesis of total damage during cryoprotectant equilibration: modelling and experimental validation of osmomechanical, temperature, and cytotoxic damage in sea urchin (Paracentrotus lividus) oocytes. PeerJ 11:e15539 https://doi.org/10.7717/peerj.15539
date submitted: 2023-01-24
date accepted: 2023-05-21
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olver
  given name: Dominic J.
author list: Agent
  family name: Heres
  given name: Pablo
author list: Agent
  family name: Paredes
  given name: Estefania
author list: Agent
  family name: Benson
  given name: James D.
doi: 10.7717/peerj.15539
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: ©2023 Olver et al.
attribution name: Olver et al.

High phenotypic plasticity at the dawn of the eosauropterygian radiation
type: item
type: AcademicArticle
description: The initial radiation of Eosauropterygia during the Triassic biotic recovery represents a key event in the dominance of reptiles secondarily adapted to marine environments. Recent studies on Mesozoic marine reptile disparity highlighted that eosauropterygians had their greatest morphological diversity during the Middle Triassic, with the co-occurrence of Pachypleurosauroidea, Nothosauroidea and Pistosauroidea, mostly along the margins of the Tethys Ocean. However, these previous studies quantitatively analysed the disparity of Eosauropterygia as a whole without focussing on Triassic taxa, thus limiting our understanding of their diversification and morphospace occupation during the Middle Triassic. Our multivariate morphometric analyses highlight a clearly distinct colonization of the ecomorphospace by the three clades, with no evidence of whole-body convergent evolution with the exception of the peculiar pistosauroid Wangosaurus brevirostris, which appears phenotypically much more similar to nothosauroids. This global pattern is mostly driven by craniodental differences and inferred feeding specializations. We also reveal noticeable regional differences among nothosauroids and pachypleurosauroids of which the latter likely experienced a remarkable diversification in the eastern Tethys during the Pelsonian. Our results demonstrate that the high phenotypic plasticity characterizing the evolution of the pelagic plesiosaurians was already present in their Triassic ancestors, casting eosauropterygians as particularly adaptable animals.
format: application/pdf
format: text/html
creator: Antoine Laboury
creator: Torsten M. Scheyer
creator: Nicole Klein
creator: Thomas L. Stubbs
creator: Valentin Fischer
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.15776
publisher: PeerJ Inc.
rights: © 2023 Laboury et al.
abstract: The initial radiation of Eosauropterygia during the Triassic biotic recovery represents a key event in the dominance of reptiles secondarily adapted to marine environments. Recent studies on Mesozoic marine reptile disparity highlighted that eosauropterygians had their greatest morphological diversity during the Middle Triassic, with the co-occurrence of Pachypleurosauroidea, Nothosauroidea and Pistosauroidea, mostly along the margins of the Tethys Ocean. However, these previous studies quantitatively analysed the disparity of Eosauropterygia as a whole without focussing on Triassic taxa, thus limiting our understanding of their diversification and morphospace occupation during the Middle Triassic. Our multivariate morphometric analyses highlight a clearly distinct colonization of the ecomorphospace by the three clades, with no evidence of whole-body convergent evolution with the exception of the peculiar pistosauroid Wangosaurus brevirostris, which appears phenotypically much more similar to nothosauroids. This global pattern is mostly driven by craniodental differences and inferred feeding specializations. We also reveal noticeable regional differences among nothosauroids and pachypleurosauroids of which the latter likely experienced a remarkable diversification in the eastern Tethys during the Pelsonian. Our results demonstrate that the high phenotypic plasticity characterizing the evolution of the pelagic plesiosaurians was already present in their Triassic ancestors, casting eosauropterygians as particularly adaptable animals.
bibliographic citation: Laboury et al. (2023) High phenotypic plasticity at the dawn of the eosauropterygian radiation. PeerJ 11:e15776 https://doi.org/10.7717/peerj.15776
date submitted: 2023-04-05
date accepted: 2023-06-29
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Laboury
  given name: Antoine
author list: Agent
  family name: Scheyer
  given name: Torsten M.
author list: Agent
  family name: Klein
  given name: Nicole
author list: Agent
  family name: Stubbs
  given name: Thomas L.
author list: Agent
  family name: Fischer
  given name: Valentin
doi: 10.7717/peerj.15776
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: © 2023 Laboury et al.
attribution name: Laboury et al.

An investigation into the response of the soil ecological environment to tourist disturbance in Baligou
type: item
type: AcademicArticle
description: The purpose of this study is to understand the response patterns of the soil ecological environment of the Macau Wetland Park to different levels of tourist interference and to provide a scientific basis for the rational development of the Bali Gou ecological tourism plan and the protection and management of the scenic area’s ecological environment. Combine the methods of field collection and laboratory physical and chemical data analysis to analyze the impact of the strength of tourism disturbance on the soil ecological environment of Baligou. During the tourist activities in Baligou, the human factors in the process have an impact on the physical aspects of the scenic area’s soil, such as soil bulk density, color tone, porosity, compactness, capacity, and leaf litter. In addition, pH value, soil enzyme activity, organic matter, and heavy metals in the soil have caused some interference. The overall data show that the dynamic of soil indicators is background area < buffer area < disturbed area,where the sample area is affected by human trampling and infrastructure construction and other disturbances leading to regular changes in the content of Pb and Cr in the sample soil, while the content of other heavy metals is lower than the national standard.The range of the most extreme values of the SRI integrated soil ecological response evaluation index was A1 disturbance area = 4.679 and C1 background area = 1.263, respectively. The larger the value of the SRI response index, the greater the impact and negative effect of the disturbance influence of tourism activities on the soil ecological environment of the scenic area, and the higher the level of response of the soil ecological environment of the scenic area to the disturbance of tourism activities. Moderate and reasonable tourism development activities play a role in promoting soil quality in scenic areas. Therefore, it is suggested to carry out reasonable ecological environment planning and take certain macro-measur…
format: application/pdf
format: text/html
creator: Xiaolong Chen
creator: Fangyuan Cui
creator: Cora Un.In Wong
creator: Hongfeng Zhang
creator: Feiyang Wang
subject: Soil Science
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Biogeochemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.15780
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: The purpose of this study is to understand the response patterns of the soil ecological environment of the Macau Wetland Park to different levels of tourist interference and to provide a scientific basis for the rational development of the Bali Gou ecological tourism plan and the protection and management of the scenic area’s ecological environment. Combine the methods of field collection and laboratory physical and chemical data analysis to analyze the impact of the strength of tourism disturbance on the soil ecological environment of Baligou. During the tourist activities in Baligou, the human factors in the process have an impact on the physical aspects of the scenic area’s soil, such as soil bulk density, color tone, porosity, compactness, capacity, and leaf litter. In addition, pH value, soil enzyme activity, organic matter, and heavy metals in the soil have caused some interference. The overall data show that the dynamic of soil indicators is background area < buffer area < disturbed area,where the sample area is affected by human trampling and infrastructure construction and other disturbances leading to regular changes in the content of Pb and Cr in the sample soil, while the content of other heavy metals is lower than the national standard.The range of the most extreme values of the SRI integrated soil ecological response evaluation index was A1 disturbance area = 4.679 and C1 background area = 1.263, respectively. The larger the value of the SRI response index, the greater the impact and negative effect of the disturbance influence of tourism activities on the soil ecological environment of the scenic area, and the higher the level of response of the soil ecological environment of the scenic area to the disturbance of tourism activities. Moderate and reasonable tourism development activities play a role in promoting soil quality in scenic areas. Therefore, it is suggested to carry out reasonable ecological environment planning and take certain macro-measur…
bibliographic citation: Chen et al. (2023) An investigation into the response of the soil ecological environment to tourist disturbance in Baligou. PeerJ 11:e15780 https://doi.org/10.7717/peerj.15780
date submitted: 2022-12-05
date accepted: 2023-06-29
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xiaolong
author list: Agent
  family name: Cui
  given name: Fangyuan
author list: Agent
  family name: Wong
  given name: Cora Un.In
author list: Agent
  family name: Zhang
  given name: Hongfeng
author list: Agent
  family name: Wang
  given name: Feiyang
doi: 10.7717/peerj.15780
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: ©2023 Chen et al.
attribution name: Chen et al.

Microbial signature profiles of Penaeus vannamei larvae in low-survival hatchery tanks affected by vibriosis
type: item
type: AcademicArticle
description: Vibriosis is caused by some pathogenic Vibrio and produces significant mortality in Pacific white shrimp Penaeus (Litopenaeus) vannamei larvae in commercial hatcheries. Acute hepatopancreatic necrosis disease (AHPND) is an emerging vibriosis affecting shrimp-producing countries worldwide. Zoea 2 syndrome is another type of vibriosis that affects the early stages of P. vannamei larvae. Although the pathogenesis of AHPND and zoea 2 syndrome is well known, there is scarce information about microbial composition and biomarkers of P.vannamei larvae affected by AHPND, and there is no study of the microbiome of larvae affected by zoea 2 syndrome. In this work, we characterized the microbiome of P. vannamei larvae collected from 12 commercial hatchery tanks by high-throughput sequencing. Seven tanks were affected by AHPND, and five tanks were affected by zoea 2 syndrome. Subsequently, all samples were selected for sequencing of the V3–V4 region of the16S rRNA gene. Similarity analysis using the beta diversity index revealed significant differences in the larval bacterial communities between disease conditions, particularly when Vibrio was analyzed. Linear discriminant analysis with effect size determined specific microbial signatures for AHPND and zoea 2 syndrome. Sneathiella, Cyclobacterium, Haliea, Lewinella, among other genera, were abundant in AHPND-affected larvae. Meanwhile, Vibrio, Spongiimonas, Meridianimaribacter, Tenacibaculum, among other genera, were significantly abundant in larvae affected by zoea 2 syndrome. The bacterial network at the phylum level for larvae collected from tanks affected by AHPND showed greater complexity and connectivity than in samples collected from tanks affected by zoea 2 syndrome. The bacterial connections inter Vibrio genera were higher in larvae from tanks affected by zoea 2 syndrome, also presenting other connections between the genera Vibrio and Catenococcus. The identification of specific biomarkers found in this study could be u…
format: application/pdf
format: text/html
creator: Guillermo Reyes
creator: Betsy Andrade
creator: Irma Betancourt
creator: Fanny Panchana
creator: Ramiro Solórzano
creator: Cristhian Preciado
creator: Lita Sorroza
creator: Luis E. Trujillo
creator: Bonny Bayot
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.15795
publisher: PeerJ Inc.
rights: © 2023 Reyes et al.
abstract: Vibriosis is caused by some pathogenic Vibrio and produces significant mortality in Pacific white shrimp Penaeus (Litopenaeus) vannamei larvae in commercial hatcheries. Acute hepatopancreatic necrosis disease (AHPND) is an emerging vibriosis affecting shrimp-producing countries worldwide. Zoea 2 syndrome is another type of vibriosis that affects the early stages of P. vannamei larvae. Although the pathogenesis of AHPND and zoea 2 syndrome is well known, there is scarce information about microbial composition and biomarkers of P.vannamei larvae affected by AHPND, and there is no study of the microbiome of larvae affected by zoea 2 syndrome. In this work, we characterized the microbiome of P. vannamei larvae collected from 12 commercial hatchery tanks by high-throughput sequencing. Seven tanks were affected by AHPND, and five tanks were affected by zoea 2 syndrome. Subsequently, all samples were selected for sequencing of the V3–V4 region of the16S rRNA gene. Similarity analysis using the beta diversity index revealed significant differences in the larval bacterial communities between disease conditions, particularly when Vibrio was analyzed. Linear discriminant analysis with effect size determined specific microbial signatures for AHPND and zoea 2 syndrome. Sneathiella, Cyclobacterium, Haliea, Lewinella, among other genera, were abundant in AHPND-affected larvae. Meanwhile, Vibrio, Spongiimonas, Meridianimaribacter, Tenacibaculum, among other genera, were significantly abundant in larvae affected by zoea 2 syndrome. The bacterial network at the phylum level for larvae collected from tanks affected by AHPND showed greater complexity and connectivity than in samples collected from tanks affected by zoea 2 syndrome. The bacterial connections inter Vibrio genera were higher in larvae from tanks affected by zoea 2 syndrome, also presenting other connections between the genera Vibrio and Catenococcus. The identification of specific biomarkers found in this study could be u…
bibliographic citation: Reyes et al. (2023) Microbial signature profiles of Penaeus vannamei larvae in low-survival hatchery tanks affected by vibriosis. PeerJ 11:e15795 https://doi.org/10.7717/peerj.15795
date submitted: 2023-01-30
date accepted: 2023-07-05
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reyes
  given name: Guillermo
author list: Agent
  family name: Andrade
  given name: Betsy
author list: Agent
  family name: Betancourt
  given name: Irma
author list: Agent
  family name: Panchana
  given name: Fanny
author list: Agent
  family name: Solórzano
  given name: Ramiro
author list: Agent
  family name: Preciado
  given name: Cristhian
author list: Agent
  family name: Sorroza
  given name: Lita
author list: Agent
  family name: Trujillo
  given name: Luis E.
author list: Agent
  family name: Bayot
  given name: Bonny
doi: 10.7717/peerj.15795
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: ©2023 Reyes et al.
attribution name: Reyes et al.

Improving the success of reinforcement programs: effects of a two-week confinement in a field enclosure on the anti-predator behaviour of captive-bred European hamsters
type: item
type: AcademicArticle
description: Captive breeding programs are an important pillar in biodiversity conservation, aiming to prevent the extinction of threatened species. However, the establishment of self-sustaining populations in the wild through the release of captive-bred animals is often hampered by a high mortality upon release. In this study, we investigated how a 2-week confinement period within a large field enclosure affected the anti-predator behaviour of ‘naive’ captive-bred hamsters and how potential modifications persisted over time. During three consecutive tests, hamsters were confronted with a moving predator model (a red fox mount, Vulpes vulpes) and their behaviour was filmed. After the initial round of confrontation with the predator model, one group of hamsters (field group) was released into a field enclosure protected from predators, while the other group (control) remained in their individual laboratory cages. After 2 weeks, hamsters from the field group were recaptured and individuals of both groups underwent a second confrontation test. A total of 1 month after their return from the field enclosure, field hamsters were subjected to a last confrontation test. Video analysis, investigating four behavioural variables, revealed that field hamsters significantly modified their behavioural response following the 2 weeks confinement in the enclosure, while this was not the case for control hamsters. In addition, most behavioural modifications in field hamsters persisted over 1 month, while others started to revert. We suggest that an appropriate pre-release period inside a field enclosure will enable naive (captive-bred) hamsters to develop an adequate anti-predator behaviour that will increase their immediate survival probability upon release into the wild. We believe that such measure will be of great importance for hamster conservation programs.
format: application/pdf
format: text/html
creator: Julie Fleitz
creator: Manfred R. Enstipp
creator: Emilie Parent
creator: Jonathan Jumeau
creator: Yves Handrich
creator: Mathilde L. Tissier
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.15812
publisher: PeerJ Inc.
rights: © 2023 Fleitz et al.
abstract: Captive breeding programs are an important pillar in biodiversity conservation, aiming to prevent the extinction of threatened species. However, the establishment of self-sustaining populations in the wild through the release of captive-bred animals is often hampered by a high mortality upon release. In this study, we investigated how a 2-week confinement period within a large field enclosure affected the anti-predator behaviour of ‘naive’ captive-bred hamsters and how potential modifications persisted over time. During three consecutive tests, hamsters were confronted with a moving predator model (a red fox mount, Vulpes vulpes) and their behaviour was filmed. After the initial round of confrontation with the predator model, one group of hamsters (field group) was released into a field enclosure protected from predators, while the other group (control) remained in their individual laboratory cages. After 2 weeks, hamsters from the field group were recaptured and individuals of both groups underwent a second confrontation test. A total of 1 month after their return from the field enclosure, field hamsters were subjected to a last confrontation test. Video analysis, investigating four behavioural variables, revealed that field hamsters significantly modified their behavioural response following the 2 weeks confinement in the enclosure, while this was not the case for control hamsters. In addition, most behavioural modifications in field hamsters persisted over 1 month, while others started to revert. We suggest that an appropriate pre-release period inside a field enclosure will enable naive (captive-bred) hamsters to develop an adequate anti-predator behaviour that will increase their immediate survival probability upon release into the wild. We believe that such measure will be of great importance for hamster conservation programs.
bibliographic citation: Fleitz et al. (2023) Improving the success of reinforcement programs: effects of a two-week confinement in a field enclosure on the anti-predator behaviour of captive-bred European hamsters. PeerJ 11:e15812 https://doi.org/10.7717/peerj.15812
date submitted: 2023-04-10
date accepted: 2023-07-07
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fleitz
  given name: Julie
author list: Agent
  family name: Enstipp
  given name: Manfred R.
author list: Agent
  family name: Parent
  given name: Emilie
author list: Agent
  family name: Jumeau
  given name: Jonathan
author list: Agent
  family name: Handrich
  given name: Yves
author list: Agent
  family name: Tissier
  given name: Mathilde L.
doi: 10.7717/peerj.15812
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: © 2023 Fleitz et al.
attribution name: Fleitz et al.

PM2.5 exposure aggravates kidney damage by facilitating the lipid metabolism disorder in diabetic mice
type: item
type: AcademicArticle
description: Background Ambient fine particulate matter ≤ 2.5 µm (PM2.5) air pollution exposure has been identified as a global health threat, the epidemiological evidence suggests that PM2.5 increased the risk of chronic kidney disease (CKD) among the diabetes mellitus (DM) patients. Despite the growing body of research on PM2.5 exposure, there has been limited investigation into its impact on the kidneys and the underlying mechanisms. Past studies have demonstrated that PM2.5 exposure can lead to lipid metabolism disorder, which has been linked to the development and progression of diabetic kidney disease (DKD). Methods In this study, db/db mice were exposed to different dosage PM2.5 for 8 weeks. The effect of PM2.5 exposure was analysis by assessment of renal function, pathological staining, immunohistochemical (IHC), quantitative real-time PCR (qPCR) and liquid chromatography with tandem mass spectrometry (LC–MS/MS) based metabolomic analyses. Results The increasing of Oil Red staining area and adipose differentiation related protein (ADRP) expression detected by IHC staining indicated more ectopic lipid accumulation in kidney after PM2.5 exposure, and the increasing of SREBP-1 and the declining of ATGL detected by IHC staining and qPCR indicated the disorder of lipid synthesisandlipolysis in DKD mice kidney after PM2.5 exposure. The expressions of high mobility group nucleosome binding protein 1 (HMGN1) and kidney injury molecule 1 (KIM-1) that are associated with kidney damage increased in kidney after PM2.5 exposure. Correlation analysis indicated that there was a relationship between HMGN1-KIM-1 and lipid metabolic markers. In addition, kidneys of mice were analyzed using LC–MS/MS based metabolomic analyses. PM2.5 exposure altered metabolic profiles in the mice kidney, including 50 metabolites. In conclusion the results of this study show that PM2.5 exposure lead to abnormal renal function and further promotes renal injury by disturbance of renal lipid metabolism and alt…
format: application/pdf
format: text/html
creator: Yuecheng Jiang
creator: Yanzhe Peng
creator: Xia Yang
creator: Jiali Yu
creator: Fuxun Yu
creator: Jing Yuan
creator: Yan Zha
subject: Nephrology
subject: Environmental Health
description: doi:10.7717/peerj.15856
publisher: PeerJ Inc.
rights: © 2023 Jiang et al.
abstract: Background Ambient fine particulate matter ≤ 2.5 µm (PM2.5) air pollution exposure has been identified as a global health threat, the epidemiological evidence suggests that PM2.5 increased the risk of chronic kidney disease (CKD) among the diabetes mellitus (DM) patients. Despite the growing body of research on PM2.5 exposure, there has been limited investigation into its impact on the kidneys and the underlying mechanisms. Past studies have demonstrated that PM2.5 exposure can lead to lipid metabolism disorder, which has been linked to the development and progression of diabetic kidney disease (DKD). Methods In this study, db/db mice were exposed to different dosage PM2.5 for 8 weeks. The effect of PM2.5 exposure was analysis by assessment of renal function, pathological staining, immunohistochemical (IHC), quantitative real-time PCR (qPCR) and liquid chromatography with tandem mass spectrometry (LC–MS/MS) based metabolomic analyses. Results The increasing of Oil Red staining area and adipose differentiation related protein (ADRP) expression detected by IHC staining indicated more ectopic lipid accumulation in kidney after PM2.5 exposure, and the increasing of SREBP-1 and the declining of ATGL detected by IHC staining and qPCR indicated the disorder of lipid synthesisandlipolysis in DKD mice kidney after PM2.5 exposure. The expressions of high mobility group nucleosome binding protein 1 (HMGN1) and kidney injury molecule 1 (KIM-1) that are associated with kidney damage increased in kidney after PM2.5 exposure. Correlation analysis indicated that there was a relationship between HMGN1-KIM-1 and lipid metabolic markers. In addition, kidneys of mice were analyzed using LC–MS/MS based metabolomic analyses. PM2.5 exposure altered metabolic profiles in the mice kidney, including 50 metabolites. In conclusion the results of this study show that PM2.5 exposure lead to abnormal renal function and further promotes renal injury by disturbance of renal lipid metabolism and alt…
bibliographic citation: Jiang et al. (2023) PM2.5 exposure aggravates kidney damage by facilitating the lipid metabolism disorder in diabetic mice. PeerJ 11:e15856 https://doi.org/10.7717/peerj.15856
date submitted: 2023-02-27
date accepted: 2023-07-16
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Yuecheng
author list: Agent
  family name: Peng
  given name: Yanzhe
author list: Agent
  family name: Yang
  given name: Xia
author list: Agent
  family name: Yu
  given name: Jiali
author list: Agent
  family name: Yu
  given name: Fuxun
author list: Agent
  family name: Yuan
  given name: Jing
author list: Agent
  family name: Zha
  given name: Yan
doi: 10.7717/peerj.15856
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: ©2023 Jiang et al.
attribution name: Jiang et al.

Construction and validation of a PANoptosis-related lncRNA signature for predicting prognosis and targeted drug response in thyroid cancer
type: item
type: AcademicArticle
description: Thyroid cancer (TC) is the most prevalent malignancy of the endocrine system. PANoptosis, a newly discovered cell death pathway, is of interest in tumor research. However, the relationship between PANoptosis-related lncRNAs (PRlncRNAs) and TC remains unclear. The study aimed to develop a prognostic model based on PRlncRNAs in TC. Gene expression data of PANoptosis-associated genes and clinical information on TC from The Cancer Genome Atlas (TCGA) database were analyzed by Pearson correlation analysis, univariate/multivariate Cox analysis, and Lasso Cox regression analysis. A PRlncRNA signature was constructed and used to develop a nomogram to predict overall survival (OS). We further explored the correlation between the risk score and tumor immune microenvironment, immune checkpoints, and drug sensitivity. Moreover, we verified the expression and biological function of lncRNAs in TC cell lines. Finally, seven PRlncRNAs were used to construct a prognostic model for predicting the OS of TC patients. We found that the risk score was associated with the tumor microenvironment (TME) and the expression of critical immune checkpoints. In addition, we screened for drugs that high- or low-risk TC groups might be sensitive to. Quantitative real-time polymerase chain reaction (qRT-PCR) results showed differential expression of four PRlncRNAs (GAPLINC, IDI2-AS1, LINC02154, and RBPMS-AS1) between tumor and normal tissues. Besides, a GEO database (GSE33630) was used to verify the expression differences of PRLncRNAs in THCA tissues and normal tissues. Finally, RBPMS-AS1 was found to inhibit the proliferation and migration of TC cells. In conclusion, we developed a PANoptosis-related lncRNA prognostic risk model that offers a comprehensive understanding of TME status in patients with TC and establishes a foundation for the choice of sensitive medications and immunotherapy.
format: application/pdf
format: text/html
creator: Ruowen Li
creator: Mingjian Zhao
creator: Min Sun
creator: Chengxu Miao
creator: Jinghui Lu
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.15884
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Thyroid cancer (TC) is the most prevalent malignancy of the endocrine system. PANoptosis, a newly discovered cell death pathway, is of interest in tumor research. However, the relationship between PANoptosis-related lncRNAs (PRlncRNAs) and TC remains unclear. The study aimed to develop a prognostic model based on PRlncRNAs in TC. Gene expression data of PANoptosis-associated genes and clinical information on TC from The Cancer Genome Atlas (TCGA) database were analyzed by Pearson correlation analysis, univariate/multivariate Cox analysis, and Lasso Cox regression analysis. A PRlncRNA signature was constructed and used to develop a nomogram to predict overall survival (OS). We further explored the correlation between the risk score and tumor immune microenvironment, immune checkpoints, and drug sensitivity. Moreover, we verified the expression and biological function of lncRNAs in TC cell lines. Finally, seven PRlncRNAs were used to construct a prognostic model for predicting the OS of TC patients. We found that the risk score was associated with the tumor microenvironment (TME) and the expression of critical immune checkpoints. In addition, we screened for drugs that high- or low-risk TC groups might be sensitive to. Quantitative real-time polymerase chain reaction (qRT-PCR) results showed differential expression of four PRlncRNAs (GAPLINC, IDI2-AS1, LINC02154, and RBPMS-AS1) between tumor and normal tissues. Besides, a GEO database (GSE33630) was used to verify the expression differences of PRLncRNAs in THCA tissues and normal tissues. Finally, RBPMS-AS1 was found to inhibit the proliferation and migration of TC cells. In conclusion, we developed a PANoptosis-related lncRNA prognostic risk model that offers a comprehensive understanding of TME status in patients with TC and establishes a foundation for the choice of sensitive medications and immunotherapy.
bibliographic citation: Li et al. (2023) Construction and validation of a PANoptosis-related lncRNA signature for predicting prognosis and targeted drug response in thyroid cancer. PeerJ 11:e15884 https://doi.org/10.7717/peerj.15884
date submitted: 2023-04-12
date accepted: 2023-07-20
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ruowen
author list: Agent
  family name: Zhao
  given name: Mingjian
author list: Agent
  family name: Sun
  given name: Min
author list: Agent
  family name: Miao
  given name: Chengxu
author list: Agent
  family name: Lu
  given name: Jinghui
doi: 10.7717/peerj.15884
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: © 2023 Li et al.
attribution name: Li et al.

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