PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of different proportions of stevia stalk on nutrient utilization and rumen fermentation in ruminal fluid derived from sheep
items: Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance
items: Decreased S100A9 expression alleviates Clostridium perfringens beta2 toxin-induced inflammatory injury in IPEC-J2 cells
items: Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing
items: Comparison of urine proteomes from tumor-bearing mice with those from tumor-resected mice
items: Inferring fish behaviour at the trawl mouth from escape location
items: Response of photosynthesis, the xanthophyll cycle, and wax in Japanese yew (Taxus cuspidata L.) seedlings and saplings under high light conditions
items: Construction of a ceRNA network of regulated ferroptosis in doxorubicin-induced myocardial injury
items: Scaling patterns of body plans differ among squirrel ecotypes
items: Face matching and metacognition: investigating individual differences and a training intervention

Effects of different proportions of stevia stalk on nutrient utilization and rumen fermentation in ruminal fluid derived from sheep
type: item
type: AcademicArticle
description: Background Stevia straw is a byproduct of sugar crop stevia. It is a good feed material because of richness in nutrients and active substances (steviosides and flavonoids). However, due to improper utilization such as piling, burning and so on, it became a large amount of wasted straw resources and lead to environmental pollution. Methods We added 0%, 0.2%, 0.4%, 0.6%, 0.8%, 1.0% and 1.5% of stevia stalk to study the effects of different stevia stalk concentrations on nutrient utilization and rumen fermentation in sheep (based on sheep diet). In vitro fermentation method was used, with 17 repetitions for each treatment. All fermentation substrate based on sheep diet with different stevia stalk concentrations were fermented for 2 h, 6 h, 12 h, 24 h and 48 h, then the gas production, dry matter degradability (DMD), crude protein degradability (CPD), neutral detergent fiber degradability (NDFD), acid detergent fiber degradability (ADFD), pH, ammonia nitrogen (NH3-N) and volatile fatty acids (VFAs) were determined. Results The results showed that at different fermentation time, the change trend of gas production in each teatment was basically same, but the maximum occurred in 1.0% treatment at 48 h. The DMD, CPD, NDFD and ADFD of sheep diets increased with fermentation time increasing, especially the CPD48h, NDFD48h and ADFD48h of diets in 0.8%, 1.0% and 1.5% treatments were significantly higher than those in control (P < 0.05). The pH of fermentation substrate in each treatment remained within the normal range of 6.21∼7.25. NH3-N24h–48hin 0.8%, 1.0% and 1.5% treatments were higher than that in control. At 6 h–12 h, the total acid content of 0.8% and 1.0% treatments were significantly higher than those of other treatments (P < 0.05), it reached the highest in 1.0% treatment. According to overall evaluation, effect ranking of stevia stalk on sheep nutrient utilization was as follows: 1.0% >0.8% >1.5% >0.4% >0.6% >0.2%. Overall, 1.0% stevia stalk could promote nutrient de…
format: application/pdf
format: text/html
creator: Xia Zhang
creator: Ting Jiao
creator: Shumin Ma
creator: Xin Chen
creator: Zhengwen Wang
creator: Shengguo Zhao
creator: Yue Ren
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Zoology
description: doi:10.7717/peerj.14689
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Background Stevia straw is a byproduct of sugar crop stevia. It is a good feed material because of richness in nutrients and active substances (steviosides and flavonoids). However, due to improper utilization such as piling, burning and so on, it became a large amount of wasted straw resources and lead to environmental pollution. Methods We added 0%, 0.2%, 0.4%, 0.6%, 0.8%, 1.0% and 1.5% of stevia stalk to study the effects of different stevia stalk concentrations on nutrient utilization and rumen fermentation in sheep (based on sheep diet). In vitro fermentation method was used, with 17 repetitions for each treatment. All fermentation substrate based on sheep diet with different stevia stalk concentrations were fermented for 2 h, 6 h, 12 h, 24 h and 48 h, then the gas production, dry matter degradability (DMD), crude protein degradability (CPD), neutral detergent fiber degradability (NDFD), acid detergent fiber degradability (ADFD), pH, ammonia nitrogen (NH3-N) and volatile fatty acids (VFAs) were determined. Results The results showed that at different fermentation time, the change trend of gas production in each teatment was basically same, but the maximum occurred in 1.0% treatment at 48 h. The DMD, CPD, NDFD and ADFD of sheep diets increased with fermentation time increasing, especially the CPD48h, NDFD48h and ADFD48h of diets in 0.8%, 1.0% and 1.5% treatments were significantly higher than those in control (P < 0.05). The pH of fermentation substrate in each treatment remained within the normal range of 6.21∼7.25. NH3-N24h–48hin 0.8%, 1.0% and 1.5% treatments were higher than that in control. At 6 h–12 h, the total acid content of 0.8% and 1.0% treatments were significantly higher than those of other treatments (P < 0.05), it reached the highest in 1.0% treatment. According to overall evaluation, effect ranking of stevia stalk on sheep nutrient utilization was as follows: 1.0% >0.8% >1.5% >0.4% >0.6% >0.2%. Overall, 1.0% stevia stalk could promote nutrient de…
bibliographic citation: Zhang et al. (2023) Effects of different proportions of stevia stalk on nutrient utilization and rumen fermentation in ruminal fluid derived from sheep. PeerJ 11:e14689 https://doi.org/10.7717/peerj.14689
date submitted: 2022-10-06
date accepted: 2022-12-13
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xia
author list: Agent
  family name: Jiao
  given name: Ting
author list: Agent
  family name: Ma
  given name: Shumin
author list: Agent
  family name: Chen
  given name: Xin
author list: Agent
  family name: Wang
  given name: Zhengwen
author list: Agent
  family name: Zhao
  given name: Shengguo
author list: Agent
  family name: Ren
  given name: Yue
doi: 10.7717/peerj.14689
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance
type: item
type: AcademicArticle
description: Acinetobacter baumannii is one of the most successful pathogens that can cause difficult-to-treat nosocomial infections. Outbreaks and infections caused by multi-drug resistant A. baumannii are prevalent worldwide, with only a few antibiotics are currently available for treatments. Plasmids represent an ideal vehicle for acquiring and transferring resistance genes in A. baumannii. Five extensively drug-resistant A. baumannii clinical isolates from three major Jordanian hospitals were fully sequenced. Whole-Genome Sequences (WGS) were used to study the antimicrobial resistance and virulence genes, sequence types, and phylogenetic relationship of the isolates. Plasmids were characterized In-silico, followed by conjugation, and plasmid curing experiments. Eight plasmids were recovered; resistance plasmids carrying either aminoglycosides or sulfonamide genes were detected. Chromosomal resistance genes included blaOXA-66, blaOXA-91, and blaOXA-23,and the detected virulence factors were involved in biofilm formation, adhesion, and many other mechanisms. Conjugation and plasmid curing experiments resulted in the transfer or loss of several resistance phenotypes. Plasmid profiling along with phylogenetic analyses revealed high similarities between two A. baumannii isolates recovered from two different intensive care units (ICU). The high similarities between the isolates of the study, especially the two ICU isolates, suggest that there is a common A. baumannii strain prevailing in different ICU wards in Jordanian hospitals. Three resistance genes were plasmid-borne, and the transfer of the resistance phenotype emphasizes the role and importance of conjugative plasmids in spreading resistance among A. baumannii clinical strains.
format: application/pdf
format: text/html
creator: Qutaiba Ababneh
creator: Sara Al Sbei
creator: Ziad Jaradat
creator: Sebawe Syaj
creator: Neda’a Aldaken
creator: Hamza Ababneh
creator: Zeina Inaya
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.14709
publisher: PeerJ Inc.
rights: © 2023 Ababneh et al.
abstract: Acinetobacter baumannii is one of the most successful pathogens that can cause difficult-to-treat nosocomial infections. Outbreaks and infections caused by multi-drug resistant A. baumannii are prevalent worldwide, with only a few antibiotics are currently available for treatments. Plasmids represent an ideal vehicle for acquiring and transferring resistance genes in A. baumannii. Five extensively drug-resistant A. baumannii clinical isolates from three major Jordanian hospitals were fully sequenced. Whole-Genome Sequences (WGS) were used to study the antimicrobial resistance and virulence genes, sequence types, and phylogenetic relationship of the isolates. Plasmids were characterized In-silico, followed by conjugation, and plasmid curing experiments. Eight plasmids were recovered; resistance plasmids carrying either aminoglycosides or sulfonamide genes were detected. Chromosomal resistance genes included blaOXA-66, blaOXA-91, and blaOXA-23,and the detected virulence factors were involved in biofilm formation, adhesion, and many other mechanisms. Conjugation and plasmid curing experiments resulted in the transfer or loss of several resistance phenotypes. Plasmid profiling along with phylogenetic analyses revealed high similarities between two A. baumannii isolates recovered from two different intensive care units (ICU). The high similarities between the isolates of the study, especially the two ICU isolates, suggest that there is a common A. baumannii strain prevailing in different ICU wards in Jordanian hospitals. Three resistance genes were plasmid-borne, and the transfer of the resistance phenotype emphasizes the role and importance of conjugative plasmids in spreading resistance among A. baumannii clinical strains.
bibliographic citation: Ababneh et al. (2023) Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance. PeerJ 11:e14709 https://doi.org/10.7717/peerj.14709
date submitted: 2022-01-28
date accepted: 2022-12-15
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ababneh
  given name: Qutaiba
author list: Agent
  family name: Al Sbei
  given name: Sara
author list: Agent
  family name: Jaradat
  given name: Ziad
author list: Agent
  family name: Syaj
  given name: Sebawe
author list: Agent
  family name: Aldaken
  given name: Neda’a
author list: Agent
  family name: Ababneh
  given name: Hamza
author list: Agent
  family name: Inaya
  given name: Zeina
doi: 10.7717/peerj.14709
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Ababneh et al.
attribution name: Ababneh et al.

Decreased S100A9 expression alleviates Clostridium perfringens beta2 toxin-induced inflammatory injury in IPEC-J2 cells
type: item
type: AcademicArticle
description: Background S100 calcium-binding protein A9 (S100A9) is a commonly known pro-inflammatory factor involved in various inflammatory responses. Clostridium perfringens (C. perfringens ) type C is known to cause diarrhea in piglets. However, the role of S100A9 in C. perfringens type C-induced infectious diarrhea is unclear. Methods Here, the S100A9 gene was overexpressed and knocked down in the IPEC-J2 cells, which were treated with C. perfringens beta2 (CPB2) toxin. The role of S100A9 in CPB2 toxin-induced injury in IPEC-J2 cells was assessed by measuring the levels of inflammatory cytokines, reactive oxygen species (ROS), lactate dehydrogenase (LDH), cell proliferation, and tight junction-related proteins. Results The results showed elevated expression of S100A9 in diarrhea-affected piglet tissues, and the elevation of S100A9 expression after CPB2 toxin treatment of IPEC-J2 was time-dependent. In CPB2 toxin-induced IPEC-J2 cells, overexpression of S100A9 had the following effects: the relative expression of inflammatory factors IL-6, IL8, TNF-α, and IL-1β was increased; the ROS levels and LDH viability were significantly increased; cell viability and proliferation were inhibited; the G0/G1 phase cell ratio was significantly increased. Furthermore, overexpression of S100A9 reduced the expression of tight junction proteins in CPB2-induced IPEC-J2 cells. The knockdown of S100A9 had an inverse effect. In conclusion, our results confirmed that S100A9 exacerbated inflammatory injury in CPB2 toxin-induced IPEC-J2 cells, inhibited cell viability and cell proliferation, and disrupted the tight junctions between cells. Thus, decreased S100A9 expression alleviates CPB2 toxin-induced inflammatory injury in IPEC-J2 cells.
format: application/pdf
format: text/html
creator: Jie Li
creator: Xiaoyu Huang
creator: Kaihui Xie
creator: Juanli Zhang
creator: Jiaojiao Yang
creator: Zunqiang Yan
creator: Shuangbao Gun
subject: Biochemistry
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.14722
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background S100 calcium-binding protein A9 (S100A9) is a commonly known pro-inflammatory factor involved in various inflammatory responses. Clostridium perfringens (C. perfringens ) type C is known to cause diarrhea in piglets. However, the role of S100A9 in C. perfringens type C-induced infectious diarrhea is unclear. Methods Here, the S100A9 gene was overexpressed and knocked down in the IPEC-J2 cells, which were treated with C. perfringens beta2 (CPB2) toxin. The role of S100A9 in CPB2 toxin-induced injury in IPEC-J2 cells was assessed by measuring the levels of inflammatory cytokines, reactive oxygen species (ROS), lactate dehydrogenase (LDH), cell proliferation, and tight junction-related proteins. Results The results showed elevated expression of S100A9 in diarrhea-affected piglet tissues, and the elevation of S100A9 expression after CPB2 toxin treatment of IPEC-J2 was time-dependent. In CPB2 toxin-induced IPEC-J2 cells, overexpression of S100A9 had the following effects: the relative expression of inflammatory factors IL-6, IL8, TNF-α, and IL-1β was increased; the ROS levels and LDH viability were significantly increased; cell viability and proliferation were inhibited; the G0/G1 phase cell ratio was significantly increased. Furthermore, overexpression of S100A9 reduced the expression of tight junction proteins in CPB2-induced IPEC-J2 cells. The knockdown of S100A9 had an inverse effect. In conclusion, our results confirmed that S100A9 exacerbated inflammatory injury in CPB2 toxin-induced IPEC-J2 cells, inhibited cell viability and cell proliferation, and disrupted the tight junctions between cells. Thus, decreased S100A9 expression alleviates CPB2 toxin-induced inflammatory injury in IPEC-J2 cells.
bibliographic citation: Li et al. (2023) Decreased S100A9 expression alleviates Clostridium perfringens beta2 toxin-induced inflammatory injury in IPEC-J2 cells. PeerJ 11:e14722 https://doi.org/10.7717/peerj.14722
date submitted: 2022-09-30
date accepted: 2022-12-19
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Huang
  given name: Xiaoyu
author list: Agent
  family name: Xie
  given name: Kaihui
author list: Agent
  family name: Zhang
  given name: Juanli
author list: Agent
  family name: Yang
  given name: Jiaojiao
author list: Agent
  family name: Yan
  given name: Zunqiang
author list: Agent
  family name: Gun
  given name: Shuangbao
doi: 10.7717/peerj.14722
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: © 2023 Li et al.
attribution name: Li et al.

Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing
type: item
type: AcademicArticle
description: Background The Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated. Methods In this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function. Results After filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan.
format: application/pdf
format: text/html
creator: Shifang Wu
creator: Xiaoli Yang
creator: Haina Gao
creator: Chengrui Shi
creator: Longlin Wang
creator: Deyuan Lu
creator: Yiheng Li
creator: Jinliang Zhang
creator: Weibing Zhang
creator: Pengcheng Wen
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.14733
publisher: PeerJ Inc.
rights: © 2023 Wu et al.
abstract: Background The Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated. Methods In this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function. Results After filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan.
bibliographic citation: Wu et al. (2023) Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing. PeerJ 11:e14733 https://doi.org/10.7717/peerj.14733
date submitted: 2022-09-22
date accepted: 2022-12-21
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Shifang
author list: Agent
  family name: Yang
  given name: Xiaoli
author list: Agent
  family name: Gao
  given name: Haina
author list: Agent
  family name: Shi
  given name: Chengrui
author list: Agent
  family name: Wang
  given name: Longlin
author list: Agent
  family name: Lu
  given name: Deyuan
author list: Agent
  family name: Li
  given name: Yiheng
author list: Agent
  family name: Zhang
  given name: Jinliang
author list: Agent
  family name: Zhang
  given name: Weibing
author list: Agent
  family name: Wen
  given name: Pengcheng
doi: 10.7717/peerj.14733
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: © 2023 Wu et al.
attribution name: Wu et al.

Comparison of urine proteomes from tumor-bearing mice with those from tumor-resected mice
type: item
type: AcademicArticle
description: Objective This study aimed to address on the most important concern of surgeons—whether to completely resect tumor. Urine can indicate early changes associated with physiological or pathophysiological processes. Based on these ideas, we conducted experiments to explore changes in the urine proteome between tumor-bearing mice and tumor-resected mice. Method The tumor-bearing mouse model was established with MC38 mouse colon cancer cells, and the mice were divided into the control group, tumor-resected group, and tumor-bearing group. Urine was collected 7 and 30 days after tumor resection. Liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) was used to identify the urine proteome, which was analyzed for differentially expressed proteins and functional annotation. Results (1) Seven days after tumor resection, 20 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included circadian rhythm, Notch signaling pathway, leukocyte cell–cell adhesion, and heterophilic cell–cell adhesion via plasma membrane cell adhesion molecules. (2) Thirty days after tumor resection, 33 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included cell adhesion; complement activation, the alternative pathway; the immune system process; and angiogenesis. (3) The difference in the urine proteome between the tumor-resected group and the healthy control group was smaller 30 days after tumor resection. Conclusion Changes in the urinary proteome can reflect the complete resection of MC38 tumors.
format: application/pdf
format: text/html
creator: Ziqi Heng
creator: Chenyang Zhao
creator: Youhe Gao
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.14737
publisher: PeerJ Inc.
rights: © 2023 Heng et al.
abstract: Objective This study aimed to address on the most important concern of surgeons—whether to completely resect tumor. Urine can indicate early changes associated with physiological or pathophysiological processes. Based on these ideas, we conducted experiments to explore changes in the urine proteome between tumor-bearing mice and tumor-resected mice. Method The tumor-bearing mouse model was established with MC38 mouse colon cancer cells, and the mice were divided into the control group, tumor-resected group, and tumor-bearing group. Urine was collected 7 and 30 days after tumor resection. Liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) was used to identify the urine proteome, which was analyzed for differentially expressed proteins and functional annotation. Results (1) Seven days after tumor resection, 20 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included circadian rhythm, Notch signaling pathway, leukocyte cell–cell adhesion, and heterophilic cell–cell adhesion via plasma membrane cell adhesion molecules. (2) Thirty days after tumor resection, 33 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included cell adhesion; complement activation, the alternative pathway; the immune system process; and angiogenesis. (3) The difference in the urine proteome between the tumor-resected group and the healthy control group was smaller 30 days after tumor resection. Conclusion Changes in the urinary proteome can reflect the complete resection of MC38 tumors.
bibliographic citation: Heng et al. (2023) Comparison of urine proteomes from tumor-bearing mice with those from tumor-resected mice. PeerJ 11:e14737 https://doi.org/10.7717/peerj.14737
date submitted: 2022-06-16
date accepted: 2022-12-22
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heng
  given name: Ziqi
author list: Agent
  family name: Zhao
  given name: Chenyang
author list: Agent
  family name: Gao
  given name: Youhe
doi: 10.7717/peerj.14737
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Heng et al.
attribution name: Heng et al.

Inferring fish behaviour at the trawl mouth from escape location
type: item
type: AcademicArticle
description: In this study, we used escape location underneath the trawl to understand groundfish herding behaviour at the trawl mouth. Three collecting bags (port, center, starboard) were mounted under the trawl and behind the footgear to collect escapees. The escape-at-length of species that escaped into the center bag were compared to the two wing bags to infer fish response behaviour, herding behaviour, and swimming capacity at the trawl mouth. For roundfish, smaller-sized individuals escaped more in the center for both Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus), <20 and 11 cm, respectively, indicating that larger-sized fish were to a greater extent seeking to escape under the trawl at the wings, vs small fish being herded to the center and likely overrun due to reduced swimming capacity. For flatfish and monkfish (Lophius piscatorius), results varied. European plaice (Pleuronectes platessa), American plaice (Hippoglossoides platessoides), and monkfish were caught most often in the wings, though not significantly for American plaice. Catches of dab (Limanda limanda) between 18 and 27 cm were significantly higher in the center, with no difference for smaller and larger individuals. The differences between fish escape location likely result from a combination of varying herding behaviour, size, and swimming capacity. Here, we were able to show how these size-dependent behaviours relate to fish response behaviour, escape behaviour, size, and likely swimming capacity.
format: application/pdf
format: text/html
creator: Vang Y. Nguyen
creator: Shannon M. Bayse
creator: Haraldur Arnar Einarsson
creator: Ólafur Arnar Ingólfsson
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.14746
publisher: PeerJ Inc.
rights: © 2023 Nguyen et al.
abstract: In this study, we used escape location underneath the trawl to understand groundfish herding behaviour at the trawl mouth. Three collecting bags (port, center, starboard) were mounted under the trawl and behind the footgear to collect escapees. The escape-at-length of species that escaped into the center bag were compared to the two wing bags to infer fish response behaviour, herding behaviour, and swimming capacity at the trawl mouth. For roundfish, smaller-sized individuals escaped more in the center for both Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus), <20 and 11 cm, respectively, indicating that larger-sized fish were to a greater extent seeking to escape under the trawl at the wings, vs small fish being herded to the center and likely overrun due to reduced swimming capacity. For flatfish and monkfish (Lophius piscatorius), results varied. European plaice (Pleuronectes platessa), American plaice (Hippoglossoides platessoides), and monkfish were caught most often in the wings, though not significantly for American plaice. Catches of dab (Limanda limanda) between 18 and 27 cm were significantly higher in the center, with no difference for smaller and larger individuals. The differences between fish escape location likely result from a combination of varying herding behaviour, size, and swimming capacity. Here, we were able to show how these size-dependent behaviours relate to fish response behaviour, escape behaviour, size, and likely swimming capacity.
bibliographic citation: Nguyen et al. (2023) Inferring fish behaviour at the trawl mouth from escape location. PeerJ 11:e14746 https://doi.org/10.7717/peerj.14746
date submitted: 2022-10-25
date accepted: 2022-12-27
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nguyen
  given name: Vang Y.
author list: Agent
  family name: Bayse
  given name: Shannon M.
author list: Agent
  family name: Einarsson
  given name: Haraldur Arnar
author list: Agent
  family name: Ingólfsson
  given name: Ólafur Arnar
doi: 10.7717/peerj.14746
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: © 2023 Nguyen et al.
attribution name: Nguyen et al.

Response of photosynthesis, the xanthophyll cycle, and wax in Japanese yew (Taxus cuspidata L.) seedlings and saplings under high light conditions
type: item
type: AcademicArticle
description: In order to understand the adaptative changes of the Japanese yew (Taxus cuspidate L.) to high light conditions, this study investigated gas-exchange, chlorophyll fluorescence, chlorophyll, and the impact of epicuticular wax on the gas-exchange and photoinhibition of Japanese yew seedlings and saplings. The chlorophyll content per unit area and photosynthetic rate in seedling leaves were significantly lower than in sapling leaves. When leaves from seedlings and saplings were exposed to 1,200 μmol·m−2·s−1 photon flux density (PFD) for 2 h, seedling leaves exhibited a greater down-regulation of maximum quantum yield (Fv/Fm) and actual photosystem II efficiency ( $\Phi$Φ PSII). Non-photochemical quenching (NPQ) and high energy quenching (qE) in sapling leaves were much higher than in seedling leaves when both were exposed to 1,200 μmol·m−2·s−1 PFD for 2 h. At a low level of O2, the photorespiration rate (Pr) and the ratio of photorespiration/gross photosynthetic rate (Pr/Pg) in seedling leaves were lower than in sapling leaves when both were exposed to 1,200 μmol·m−2·s−1 PFD, but this difference did not reach statistical significance (P < 0.05). Compared with sapling leaves, seedling leaves exhibited lower levels of xanthophyll pool. Epicuticular wax content on seedling leaves was significantly lower than on sapling leaves. The results of this study showed that wax coverage on the leaf surface decreased the photosynthetic rate in sapling leaves as a consequence of decreased stomatal conductance. Epicuticular wax is related to tree age and photoinhibition prevention in the Japanese yew. It is possible that lower photosynthetic rate, lower NPQ depending on the xanthophyll cycle, and lower deposition of epicuticular wax results in seedling plants that are not adapted to high light conditions.
format: application/pdf
format: text/html
creator: Wei Li
creator: Jiacheng Li
creator: Jia Wei
creator: Chunda Niu
creator: Deguang Yang
creator: Baiwen Jiang
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.14757
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: In order to understand the adaptative changes of the Japanese yew (Taxus cuspidate L.) to high light conditions, this study investigated gas-exchange, chlorophyll fluorescence, chlorophyll, and the impact of epicuticular wax on the gas-exchange and photoinhibition of Japanese yew seedlings and saplings. The chlorophyll content per unit area and photosynthetic rate in seedling leaves were significantly lower than in sapling leaves. When leaves from seedlings and saplings were exposed to 1,200 μmol·m−2·s−1 photon flux density (PFD) for 2 h, seedling leaves exhibited a greater down-regulation of maximum quantum yield (Fv/Fm) and actual photosystem II efficiency ( $\Phi$Φ PSII). Non-photochemical quenching (NPQ) and high energy quenching (qE) in sapling leaves were much higher than in seedling leaves when both were exposed to 1,200 μmol·m−2·s−1 PFD for 2 h. At a low level of O2, the photorespiration rate (Pr) and the ratio of photorespiration/gross photosynthetic rate (Pr/Pg) in seedling leaves were lower than in sapling leaves when both were exposed to 1,200 μmol·m−2·s−1 PFD, but this difference did not reach statistical significance (P < 0.05). Compared with sapling leaves, seedling leaves exhibited lower levels of xanthophyll pool. Epicuticular wax content on seedling leaves was significantly lower than on sapling leaves. The results of this study showed that wax coverage on the leaf surface decreased the photosynthetic rate in sapling leaves as a consequence of decreased stomatal conductance. Epicuticular wax is related to tree age and photoinhibition prevention in the Japanese yew. It is possible that lower photosynthetic rate, lower NPQ depending on the xanthophyll cycle, and lower deposition of epicuticular wax results in seedling plants that are not adapted to high light conditions.
bibliographic citation: Li et al. (2023) Response of photosynthesis, the xanthophyll cycle, and wax in Japanese yew (Taxus cuspidata L.) seedlings and saplings under high light conditions. PeerJ 11:e14757 https://doi.org/10.7717/peerj.14757
date submitted: 2022-08-22
date accepted: 2022-12-27
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Li
  given name: Jiacheng
author list: Agent
  family name: Wei
  given name: Jia
author list: Agent
  family name: Niu
  given name: Chunda
author list: Agent
  family name: Yang
  given name: Deguang
author list: Agent
  family name: Jiang
  given name: Baiwen
doi: 10.7717/peerj.14757
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: © 2023 Li et al.
attribution name: Li et al.

Construction of a ceRNA network of regulated ferroptosis in doxorubicin-induced myocardial injury
type: item
type: AcademicArticle
description: Background Ferroptosis and long-noncoding RNAs (lncRNAs) play crucial roles in doxorubicin (DOX)-induced myocardial injury (DIMI). Nevertheless, there is no research to construct competing endogenous RNAs (ceRNAs) network between lncRNAs and ferroptosis-related key gene. So our research was designed to screen ferroptosis-related genes from differentially expressed mRNAs in DIMI and construct lncRNAs regulated ferroptosis-related key gene ceRNAs network. Methods The male mice were injected with DOX intraperitoneally to induce myocardial injury, myocardial injury was evaluated by hematoxylin and eosin (HE) staining, and ferroptosis-related protein-glutathione peroxidase 4 (GPx4) protein expression was detected. The differentially expressed lncRNAs and mRNAs were detected by microarray, and the ferroptosis-related genes were screened to construct a protein-protein associations (PPA) network, the highest maximal clique centrality (MCC) score gene were identified by Cytoscape software, miRNAs bound to key genes and lncRNAs bound to miRNAs were predicted; then, the obtained lncRNAs were intersected with differentially expressed lncRNAs detected by microarray. Finally, the lncRNA/miRNA/mRNA ceRNA network of the highest MCC score gene regulating ferroptosis in DIMI was constructed. The expressions of the key components in ceRNA network were detected by qRT-PCR. Results Compared with the control group, in the DOX group, myocardial enzymes and HE staining showed that myocardium structure was changed, and GPx4 protein expression was decreased. The differentially expressed 10,265 lncRNAs and 6,610 mRNAs in the DOX group were detected via microarray. Among them, 114 ferroptosis-related genes were obtained to construct PPA networks, and Becn1 was identified as the key gene. Finally, the ceRNA network including Becn1, three miRNAs and four lncRNAs was constructed by predicting data of the Starbase database. The relative expressions of these components in ceRNA net were up-regulate…
format: application/pdf
format: text/html
creator: Hongwei Ye
creator: Yuping Li
creator: Lu Li
creator: Yuhui Huang
creator: Jiahui Wang
creator: Qin Gao
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
description: doi:10.7717/peerj.14767
publisher: PeerJ Inc.
rights: © 2023 Ye et al.
abstract: Background Ferroptosis and long-noncoding RNAs (lncRNAs) play crucial roles in doxorubicin (DOX)-induced myocardial injury (DIMI). Nevertheless, there is no research to construct competing endogenous RNAs (ceRNAs) network between lncRNAs and ferroptosis-related key gene. So our research was designed to screen ferroptosis-related genes from differentially expressed mRNAs in DIMI and construct lncRNAs regulated ferroptosis-related key gene ceRNAs network. Methods The male mice were injected with DOX intraperitoneally to induce myocardial injury, myocardial injury was evaluated by hematoxylin and eosin (HE) staining, and ferroptosis-related protein-glutathione peroxidase 4 (GPx4) protein expression was detected. The differentially expressed lncRNAs and mRNAs were detected by microarray, and the ferroptosis-related genes were screened to construct a protein-protein associations (PPA) network, the highest maximal clique centrality (MCC) score gene were identified by Cytoscape software, miRNAs bound to key genes and lncRNAs bound to miRNAs were predicted; then, the obtained lncRNAs were intersected with differentially expressed lncRNAs detected by microarray. Finally, the lncRNA/miRNA/mRNA ceRNA network of the highest MCC score gene regulating ferroptosis in DIMI was constructed. The expressions of the key components in ceRNA network were detected by qRT-PCR. Results Compared with the control group, in the DOX group, myocardial enzymes and HE staining showed that myocardium structure was changed, and GPx4 protein expression was decreased. The differentially expressed 10,265 lncRNAs and 6,610 mRNAs in the DOX group were detected via microarray. Among them, 114 ferroptosis-related genes were obtained to construct PPA networks, and Becn1 was identified as the key gene. Finally, the ceRNA network including Becn1, three miRNAs and four lncRNAs was constructed by predicting data of the Starbase database. The relative expressions of these components in ceRNA net were up-regulate…
bibliographic citation: Ye et al. (2023) Construction of a ceRNA network of regulated ferroptosis in doxorubicin-induced myocardial injury. PeerJ 11:e14767 https://doi.org/10.7717/peerj.14767
date submitted: 2022-07-12
date accepted: 2022-12-28
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Hongwei
author list: Agent
  family name: Li
  given name: Yuping
author list: Agent
  family name: Li
  given name: Lu
author list: Agent
  family name: Huang
  given name: Yuhui
author list: Agent
  family name: Wang
  given name: Jiahui
author list: Agent
  family name: Gao
  given name: Qin
doi: 10.7717/peerj.14767
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: © 2023 Ye et al.
attribution name: Ye et al.

Scaling patterns of body plans differ among squirrel ecotypes
type: item
type: AcademicArticle
description: Body size is often hypothesized to facilitate or constrain morphological diversity in the cranial, appendicular, and axial skeletons. However, how overall body shape scales with body size (i.e., body shape allometry) and whether these scaling patterns differ between ecological groups remains poorly investigated. Here, we test whether and how the relationships between body shape, body size, and limb lengths differ among species with different locomotor specializations, and describe the underlying morphological components that contribute to body shape evolution among squirrel (Sciuridae) ecotypes. We quantified the body size and shape of 87 squirrel species from osteological specimens held at museum collections. Using phylogenetic comparative methods, we first found that body shape and its underlying morphological components scale allometrically with body size, but these allometric patterns differ among squirrel ecotypes: chipmunks and gliding squirrels exhibited more elongate bodies with increasing body sizes whereas ground squirrels exhibited more robust bodies with increasing body size. Second, we found that only ground squirrels exhibit a relationship between forelimb length and body shape, where more elongate species exhibit relatively shorter forelimbs. Third, we found that the relative length of the ribs and elongation or shortening of the thoracic region contributes the most to body shape evolution across squirrels. Overall, our work contributes to the growing understanding of mammalian body shape evolution and how it is influenced by body size and locomotor ecology, in this case from robust subterranean to gracile gliding squirrels.
format: application/pdf
format: text/html
creator: Tate J. Linden
creator: Abigail E. Burtner
creator: Johannah Rickman
creator: Annika McFeely
creator: Sharlene E. Santana
creator: Chris J. Law
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.14800
publisher: PeerJ Inc.
rights: © 2023 Linden et al.
abstract: Body size is often hypothesized to facilitate or constrain morphological diversity in the cranial, appendicular, and axial skeletons. However, how overall body shape scales with body size (i.e., body shape allometry) and whether these scaling patterns differ between ecological groups remains poorly investigated. Here, we test whether and how the relationships between body shape, body size, and limb lengths differ among species with different locomotor specializations, and describe the underlying morphological components that contribute to body shape evolution among squirrel (Sciuridae) ecotypes. We quantified the body size and shape of 87 squirrel species from osteological specimens held at museum collections. Using phylogenetic comparative methods, we first found that body shape and its underlying morphological components scale allometrically with body size, but these allometric patterns differ among squirrel ecotypes: chipmunks and gliding squirrels exhibited more elongate bodies with increasing body sizes whereas ground squirrels exhibited more robust bodies with increasing body size. Second, we found that only ground squirrels exhibit a relationship between forelimb length and body shape, where more elongate species exhibit relatively shorter forelimbs. Third, we found that the relative length of the ribs and elongation or shortening of the thoracic region contributes the most to body shape evolution across squirrels. Overall, our work contributes to the growing understanding of mammalian body shape evolution and how it is influenced by body size and locomotor ecology, in this case from robust subterranean to gracile gliding squirrels.
bibliographic citation: Linden et al. (2023) Scaling patterns of body plans differ among squirrel ecotypes. PeerJ 11:e14800 https://doi.org/10.7717/peerj.14800
date submitted: 2022-10-14
date accepted: 2023-01-04
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Linden
  given name: Tate J.
author list: Agent
  family name: Burtner
  given name: Abigail E.
author list: Agent
  family name: Rickman
  given name: Johannah
author list: Agent
  family name: McFeely
  given name: Annika
author list: Agent
  family name: Santana
  given name: Sharlene E.
author list: Agent
  family name: Law
  given name: Chris J.
doi: 10.7717/peerj.14800
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Linden et al.
attribution name: Linden et al.

Face matching and metacognition: investigating individual differences and a training intervention
type: item
type: AcademicArticle
description: Background Although researchers have begun to consider metacognitive insight during face matching, little is known about the underlying mechanism. Here, I investigated whether objective ability, as well as self-assessed ability, were able to predict metacognitive performance, that is, the ability to differentiate correct and incorrect responses in terms of confidence. In addition, I considered whether a training intervention resulted in improvements to both face matching performance and metacognitive insight. Methods In this experiment (N = 220), participants completed a face matching task, with either a diagnostic feature training course or a control course presented at the halfway point. In addition, a second face matching task, as well as a self-report questionnaire regarding ability, were completed to provide measures of objective and self-assessed ability respectively. Results Higher self-assessed ability with faces, as well as higher objective ability with face matching, predicted better metacognitive performance, i.e., greater confidence in correct, in comparison with incorrect, responses. This pattern of results was evident both when objective ability was measured through performance on the same task used to measure metacognitive insight and when a different task was used. Finally, the training intervention failed to produce improvements in face matching performance and showed no evidence of altering metacognitive ability. Discussion The current work begins to address the mechanism underlying individual differences in metacognitive insight during face matching. Although support was provided for a competence-based account, where better face matchers showed greater performance on the task and were more successful in monitoring their performance, further work might focus on decoupling task performance and competence in order to more conclusively explain why some people are more insightful than others.
format: application/pdf
format: text/html
creator: Robin S. S. Kramer
subject: Psychiatry and Psychology
subject: Human-Computer Interaction
description: doi:10.7717/peerj.14821
publisher: PeerJ Inc.
rights: © 2023 Kramer
abstract: Background Although researchers have begun to consider metacognitive insight during face matching, little is known about the underlying mechanism. Here, I investigated whether objective ability, as well as self-assessed ability, were able to predict metacognitive performance, that is, the ability to differentiate correct and incorrect responses in terms of confidence. In addition, I considered whether a training intervention resulted in improvements to both face matching performance and metacognitive insight. Methods In this experiment (N = 220), participants completed a face matching task, with either a diagnostic feature training course or a control course presented at the halfway point. In addition, a second face matching task, as well as a self-report questionnaire regarding ability, were completed to provide measures of objective and self-assessed ability respectively. Results Higher self-assessed ability with faces, as well as higher objective ability with face matching, predicted better metacognitive performance, i.e., greater confidence in correct, in comparison with incorrect, responses. This pattern of results was evident both when objective ability was measured through performance on the same task used to measure metacognitive insight and when a different task was used. Finally, the training intervention failed to produce improvements in face matching performance and showed no evidence of altering metacognitive ability. Discussion The current work begins to address the mechanism underlying individual differences in metacognitive insight during face matching. Although support was provided for a competence-based account, where better face matchers showed greater performance on the task and were more successful in monitoring their performance, further work might focus on decoupling task performance and competence in order to more conclusively explain why some people are more insightful than others.
bibliographic citation: Kramer (2023) Face matching and metacognition: investigating individual differences and a training intervention. PeerJ 11:e14821 https://doi.org/10.7717/peerj.14821
date submitted: 2022-09-09
date accepted: 2023-01-06
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kramer
  given name: Robin S. S.
doi: 10.7717/peerj.14821
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: © 2023 Kramer
attribution name: Kramer

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