PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland
items: Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation
items: Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.
items: What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors
items: A complete season with attendance restrictions confirms the relevant contribution of spectators to home advantage and referee bias in association football
items: Effect of icaritin on autophagy-related protein expression in TDP-43-transfected SH-SY5Y cells
items: Newly described nesting sites of the green sea turtle (Chelonia mydas) and the hawksbill sea turtle (Eretmochelys imbricata) in the central Red Sea
items: Can high-intensity interval training and small-sided games be effective for improving physical fitness after detraining? A parallel study design in youth male soccer players
items: Dopamine receptor activation elicits a possible stress-related coping behavior in a wild-caught songbird
items: Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae)

Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland
type: item
type: AcademicArticle
description: Excrement-shaped ferruginous masses have been recovered from the Miocene of Turów mine in south-western Poland. These siderite masses have been the subject of much controversy, having been interpreted either as being coprolites, cololithes or pseudofossils created by mechanical deformation of plastic sediment. Here we present the results of mineralogical, geochemical, petrographic and microtomographical analyses. Our data indicate that these masses consist of siderite and iron oxide rather than phosphate, and rarely contain recognizable food residues, which may suggest abiotic origins of these structures. On the other hand, evidence in support of a fecal origin include: (i) the presence of two distinct morphotypes differing in size and shape, (ii) the presence of rare hair-like structures or coalified inclusions and (iii) the presence of rare fine striations on the surface. Importantly, comparative actualistic study of recent vertebrate feces shows overall resemblance of the first morphotype (sausage-shaped with rare coalified debris) to excrements of testudinoid turtles (Testudinoidea), whose shell fragment was found in the investigated locality. The second morphotype (rounded to oval-shaped with hair-like structures), in turn, is similar to the feces of some snakes (Serpentes), the remains of which were noted in the Miocene of the neighborhood areas. Other potential producers (such as lizards and crocodiles) and even abiotic origins cannot be fully excluded but are less likely.
format: application/pdf
format: text/html
creator: Tomasz Brachaniec
creator: Dorota Środek
creator: Dawid Surmik
creator: Robert Niedźwiedzki
creator: Georgios L. Georgalis
creator: Bartosz J. Płachno
creator: Piotr Duda
creator: Alexander Lukeneder
creator: Przemysław Gorzelak
creator: Mariusz A. Salamon
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.13652
publisher: PeerJ Inc.
rights: © 2022 Brachaniec et al.
abstract: Excrement-shaped ferruginous masses have been recovered from the Miocene of Turów mine in south-western Poland. These siderite masses have been the subject of much controversy, having been interpreted either as being coprolites, cololithes or pseudofossils created by mechanical deformation of plastic sediment. Here we present the results of mineralogical, geochemical, petrographic and microtomographical analyses. Our data indicate that these masses consist of siderite and iron oxide rather than phosphate, and rarely contain recognizable food residues, which may suggest abiotic origins of these structures. On the other hand, evidence in support of a fecal origin include: (i) the presence of two distinct morphotypes differing in size and shape, (ii) the presence of rare hair-like structures or coalified inclusions and (iii) the presence of rare fine striations on the surface. Importantly, comparative actualistic study of recent vertebrate feces shows overall resemblance of the first morphotype (sausage-shaped with rare coalified debris) to excrements of testudinoid turtles (Testudinoidea), whose shell fragment was found in the investigated locality. The second morphotype (rounded to oval-shaped with hair-like structures), in turn, is similar to the feces of some snakes (Serpentes), the remains of which were noted in the Miocene of the neighborhood areas. Other potential producers (such as lizards and crocodiles) and even abiotic origins cannot be fully excluded but are less likely.
bibliographic citation: Brachaniec et al. (2022) Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland. PeerJ 10:e13652 https://doi.org/10.7717/peerj.13652
date submitted: 2022-02-04
date accepted: 2022-06-08
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brachaniec
  given name: Tomasz
author list: Agent
  family name: Środek
  given name: Dorota
author list: Agent
  family name: Surmik
  given name: Dawid
author list: Agent
  family name: Niedźwiedzki
  given name: Robert
author list: Agent
  family name: Georgalis
  given name: Georgios L.
author list: Agent
  family name: Płachno
  given name: Bartosz J.
author list: Agent
  family name: Duda
  given name: Piotr
author list: Agent
  family name: Lukeneder
  given name: Alexander
author list: Agent
  family name: Gorzelak
  given name: Przemysław
author list: Agent
  family name: Salamon
  given name: Mariusz A.
doi: 10.7717/peerj.13652
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Brachaniec et al.
attribution name: Brachaniec et al.

Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation
type: item
type: AcademicArticle
description: Background Curcumin is an active compound derived from turmeric, Curcuma longa, and is known for its benefits to human health. The amoebicidal activity of curcumin against Acanthamoeba triangularis was recently discovered. However, a physiological change of intracellular pathways related to A. triangularis encystation mechanism, including autophagy in the surviving amoeba after curcumin treatment, has never been reported. This study aims to investigate the effect of curcumin on the survival of A. triangularis under nutrient starvation and nutrient-rich condition, as well as to evaluate the A. triangularis encystation and a physiological change of Acanthamoeba autophagy at the mRNA level. Methods In this study, A. triangularis amoebas were treated with a sublethal dose of curcumin under nutrient starvation and nutrient-rich condition and the surviving amoebas was investigated. Cysts formation and vacuolization were examined by microscopy and transcriptional expression of autophagy-related genes and other encystation-related genes were evaluated by real-time PCR. Results A. triangularis cysts were formed under nutrient starvation. However, in the presence of the autophagy inhibitor, 3-methyladenine (3-MA), the percentage of cysts was significantly reduced. Interestingly, in the presence of curcumin, most of the parasites remained in the trophozoite stage in both the starvation and nutrient-rich condition. In vacuolization analysis, the percentage of amoebas with enlarged vacuole was increased upon starvation. However, the percentage was significantly declined in the presence of curcumin and 3-MA. Molecular analysis of A. triangularis autophagy-related (ATG) genes showed that the mRNA expression of the ATG genes, ATG3, ATG8b, ATG12, ATG16, under the starvation with curcumin was at a basal level along the treatment. The results were similar to those of the curcumin-treated amoebas under a nutrient-rich condition, except AcATG16 which increased later. On the other hand, …
format: application/pdf
format: text/html
creator: Rachasak Boonhok
creator: Suthinee Sangkanu
creator: Suganya Phumjan
creator: Ramita Jongboonjua
creator: Nawarat Sangnopparat
creator: Pattamaporn Kwankaew
creator: Aman Tedasen
creator: Chooi Ling Lim
creator: Maria de Lourdes Pereira
creator: Mohammed Rahmatullah
creator: Polrat Wilairatana
creator: Christophe Wiart
creator: Karma G. Dolma
creator: Alok K. Paul
creator: Madhu Gupta
creator: Veeranoot Nissapatorn
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Parasitology
description: doi:10.7717/peerj.13657
publisher: PeerJ Inc.
rights: © 2022 Boonhok et al.
abstract: Background Curcumin is an active compound derived from turmeric, Curcuma longa, and is known for its benefits to human health. The amoebicidal activity of curcumin against Acanthamoeba triangularis was recently discovered. However, a physiological change of intracellular pathways related to A. triangularis encystation mechanism, including autophagy in the surviving amoeba after curcumin treatment, has never been reported. This study aims to investigate the effect of curcumin on the survival of A. triangularis under nutrient starvation and nutrient-rich condition, as well as to evaluate the A. triangularis encystation and a physiological change of Acanthamoeba autophagy at the mRNA level. Methods In this study, A. triangularis amoebas were treated with a sublethal dose of curcumin under nutrient starvation and nutrient-rich condition and the surviving amoebas was investigated. Cysts formation and vacuolization were examined by microscopy and transcriptional expression of autophagy-related genes and other encystation-related genes were evaluated by real-time PCR. Results A. triangularis cysts were formed under nutrient starvation. However, in the presence of the autophagy inhibitor, 3-methyladenine (3-MA), the percentage of cysts was significantly reduced. Interestingly, in the presence of curcumin, most of the parasites remained in the trophozoite stage in both the starvation and nutrient-rich condition. In vacuolization analysis, the percentage of amoebas with enlarged vacuole was increased upon starvation. However, the percentage was significantly declined in the presence of curcumin and 3-MA. Molecular analysis of A. triangularis autophagy-related (ATG) genes showed that the mRNA expression of the ATG genes, ATG3, ATG8b, ATG12, ATG16, under the starvation with curcumin was at a basal level along the treatment. The results were similar to those of the curcumin-treated amoebas under a nutrient-rich condition, except AcATG16 which increased later. On the other hand, …
bibliographic citation: Boonhok et al. (2022) Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation. PeerJ 10:e13657 https://doi.org/10.7717/peerj.13657
date submitted: 2022-03-25
date accepted: 2022-06-09
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boonhok
  given name: Rachasak
author list: Agent
  family name: Sangkanu
  given name: Suthinee
author list: Agent
  family name: Phumjan
  given name: Suganya
author list: Agent
  family name: Jongboonjua
  given name: Ramita
author list: Agent
  family name: Sangnopparat
  given name: Nawarat
author list: Agent
  family name: Kwankaew
  given name: Pattamaporn
author list: Agent
  family name: Tedasen
  given name: Aman
author list: Agent
  family name: Lim
  given name: Chooi Ling
author list: Agent
  family name: Pereira
  given name: Maria de Lourdes
author list: Agent
  family name: Rahmatullah
  given name: Mohammed
author list: Agent
  family name: Wilairatana
  given name: Polrat
author list: Agent
  family name: Wiart
  given name: Christophe
author list: Agent
  family name: Dolma
  given name: Karma G.
author list: Agent
  family name: Paul
  given name: Alok K.
author list: Agent
  family name: Gupta
  given name: Madhu
author list: Agent
  family name: Nissapatorn
  given name: Veeranoot
doi: 10.7717/peerj.13657
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Boonhok et al.
attribution name: Boonhok et al.

Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.
type: item
type: AcademicArticle
description: Dioscorea cirrhosa is a plant that is used as a dye as well as in medicine. Many metabolites with pharmacological activity exist in the tubers of D. cirrhosa. However, little is known about the mechanism regulating biosynthesis in these metabolites. In this study, transcriptome and metabolome profiling were performed in four color tubers. A total of 531 metabolites, including 62 flavonoids, were identified. Epicatechin and proanthocyanin B2 were the key metabolites that exhibited high content levels in the four tubers. These metabolites were divided into nine classes with distinct change patterns. A total of 22,865 differentially expressed genes (DEGs) were identified by transcriptome analysis. Among these DEGs, we identified 67 candidate genes related to the flavonoid biosynthesis pathway and three genes that played pivotal roles in proanthocyanin (PA) synthesis. A weighted gene co-expression network analysis (WGCNA) revealed that the two modules, “MEblue” and “MEblack,” were two key gene sets strongly associated with phenylpropanoid and flavonoid biosynthesis. We also found that the plant hormone signal transduction biological process exhibited activity in the late stage of tuber color formation. Additionally, we identified 37 hub transcript factors related to flavonoid biosynthesis, of which 24 were found to be highly associated with flavonoid pathway genes. In addition to the MYB-bHLH-WD40 (MBW) genes, we found that the plant hormone gene families exhibited high expression levels. This study provides a reference for understanding the synthesis of D. cirrhosa tuber metabolites at the molecular level and provides a foundation for the further development of D. cirrhosa related plant pigments as well as its further use in the pharmaceutical industry.
format: application/pdf
format: text/html
creator: Lin Yan
creator: Haijun Yang
creator: Qiang Ye
creator: Zhihua Huang
creator: Hongying Zhou
creator: Dafang Cui
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13659
publisher: PeerJ Inc.
rights: © 2022 Yan et al.
abstract: Dioscorea cirrhosa is a plant that is used as a dye as well as in medicine. Many metabolites with pharmacological activity exist in the tubers of D. cirrhosa. However, little is known about the mechanism regulating biosynthesis in these metabolites. In this study, transcriptome and metabolome profiling were performed in four color tubers. A total of 531 metabolites, including 62 flavonoids, were identified. Epicatechin and proanthocyanin B2 were the key metabolites that exhibited high content levels in the four tubers. These metabolites were divided into nine classes with distinct change patterns. A total of 22,865 differentially expressed genes (DEGs) were identified by transcriptome analysis. Among these DEGs, we identified 67 candidate genes related to the flavonoid biosynthesis pathway and three genes that played pivotal roles in proanthocyanin (PA) synthesis. A weighted gene co-expression network analysis (WGCNA) revealed that the two modules, “MEblue” and “MEblack,” were two key gene sets strongly associated with phenylpropanoid and flavonoid biosynthesis. We also found that the plant hormone signal transduction biological process exhibited activity in the late stage of tuber color formation. Additionally, we identified 37 hub transcript factors related to flavonoid biosynthesis, of which 24 were found to be highly associated with flavonoid pathway genes. In addition to the MYB-bHLH-WD40 (MBW) genes, we found that the plant hormone gene families exhibited high expression levels. This study provides a reference for understanding the synthesis of D. cirrhosa tuber metabolites at the molecular level and provides a foundation for the further development of D. cirrhosa related plant pigments as well as its further use in the pharmaceutical industry.
bibliographic citation: Yan et al. (2022) Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.. PeerJ 10:e13659 https://doi.org/10.7717/peerj.13659
date submitted: 2021-09-22
date accepted: 2022-06-09
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Lin
author list: Agent
  family name: Yang
  given name: Haijun
author list: Agent
  family name: Ye
  given name: Qiang
author list: Agent
  family name: Huang
  given name: Zhihua
author list: Agent
  family name: Zhou
  given name: Hongying
author list: Agent
  family name: Cui
  given name: Dafang
doi: 10.7717/peerj.13659
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: ©2022 Yan et al.
attribution name: Yan et al.

What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors
type: item
type: AcademicArticle
description: Artificial refuges provided by householders and/or conservation practitioners potentially represent one mechanism for mitigating declines in the availability of natural nest sites used for resting, breeding and hibernating in urban areas. The effectiveness of such refuges for different species is, however, not always known. In this study, we conducted a questionnaire survey of UK householders to identify factors associated with the use of ground-level nest boxes for West European hedgehogs (Erinaceus europaeus), a species of conservation concern. Overall, the percentage of boxes used at least once varied with season and type of use: summer day nesting (35.5–81.3%), breeding (7.2–28.2%), winter day nesting (20.1–66.5%) and hibernation (21.7–58.6%). The length of time the box had been deployed, the availability of artificial food and front garden to back garden access significantly increased the likelihood that a nest box had been used for all four nesting types, whereas other factors related to placement within the garden (e.g., in a sheltered location, on hardstanding such as paving, distance from the house) and resource provisioning (bedding) affected only some nesting behaviours. The factors most strongly associated with nest box use were the provisioning of food and bedding. These data suggest, therefore, that householders can adopt simple practices to increase the likelihood of their nest box being used. However, one significant limitation evident within these data is that, for welfare reasons, householders do not routinely monitor whether their box has been used. Consequently, future studies need to adopt strategies which enable householders to monitor their boxes continuously. Ultimately, such studies should compare the survival rates and reproductive success of hedgehogs within artificial refuges versus more natural nest sites, and whether these are affected by, for example, the impact of nest box design and placement on predation risk and internal microclima…
format: application/pdf
format: text/html
creator: Abigail Gazzard
creator: Philip J. Baker
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13662
publisher: PeerJ Inc.
rights: © 2022 Gazzard and Baker
abstract: Artificial refuges provided by householders and/or conservation practitioners potentially represent one mechanism for mitigating declines in the availability of natural nest sites used for resting, breeding and hibernating in urban areas. The effectiveness of such refuges for different species is, however, not always known. In this study, we conducted a questionnaire survey of UK householders to identify factors associated with the use of ground-level nest boxes for West European hedgehogs (Erinaceus europaeus), a species of conservation concern. Overall, the percentage of boxes used at least once varied with season and type of use: summer day nesting (35.5–81.3%), breeding (7.2–28.2%), winter day nesting (20.1–66.5%) and hibernation (21.7–58.6%). The length of time the box had been deployed, the availability of artificial food and front garden to back garden access significantly increased the likelihood that a nest box had been used for all four nesting types, whereas other factors related to placement within the garden (e.g., in a sheltered location, on hardstanding such as paving, distance from the house) and resource provisioning (bedding) affected only some nesting behaviours. The factors most strongly associated with nest box use were the provisioning of food and bedding. These data suggest, therefore, that householders can adopt simple practices to increase the likelihood of their nest box being used. However, one significant limitation evident within these data is that, for welfare reasons, householders do not routinely monitor whether their box has been used. Consequently, future studies need to adopt strategies which enable householders to monitor their boxes continuously. Ultimately, such studies should compare the survival rates and reproductive success of hedgehogs within artificial refuges versus more natural nest sites, and whether these are affected by, for example, the impact of nest box design and placement on predation risk and internal microclima…
bibliographic citation: Gazzard et al. (2022) What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors. PeerJ 10:e13662 https://doi.org/10.7717/peerj.13662
date submitted: 2022-03-09
date accepted: 2022-06-10
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gazzard
  given name: Abigail
author list: Agent
  family name: Baker
  given name: Philip J.
doi: 10.7717/peerj.13662
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: ©2022 Gazzard and Baker
attribution name: Gazzard and Baker

A complete season with attendance restrictions confirms the relevant contribution of spectators to home advantage and referee bias in association football
type: item
type: AcademicArticle
description: Background Due to the unfortunate pandemic situation, the phenomena of home advantage and referee bias in sports have recently received a particular research attention, especially in association football. In this regard, several studies were conducted on the last portion of the 2019–20 season: the majority of them suggests a reduction—but not the elimination—of the two phenomena, with some exceptions in which no reduction was found or, at the other extreme, the phenomena were not observed at all. Methods The continuation of the pandemic made it possible to replicate the previous studies considering the complete 2020–21 season, thus with the important added value of having a fully balanced home/away schedule—and a higher number of matches—in the various leagues. In particular, the sample of the present study consisted of 3,898 matches from the first and second divisions of the UEFA top five ranked countries, that is, England, Spain, Italy, Germany, and France. For the home advantage, the following variables were examined: distribution of matches outcomes and home advantage for points (also for previous seasons from the 2014–15 one); ball possession; total shots; shots on goal; and corner kicks. Instead, for he referee bias, the following variables were examined: fouls; yellow cards; red cards; penalty kicks; and extra time. Chi-square tests were used to compare the distribution of matches outcomes, and t-tests to compare home vs. away data for the other variables in the 2020–21 season; Bayesian and equivalence analyses were also conducted. Results The main results are as follows: (a) the distribution of matches outcomes in the 2020–21 season was significantly different from that of the last five complete seasons with spectators (Chi-square = 37.42, df = 2, p < 0.001), with fewer home victories and more away victories; the resulting values of the home advantage for points were 54.95% for the 2020–21 season, and 59.36% for the previous seasons; (b) for the other home a…
format: application/pdf
format: text/html
creator: Fabrizio Sors
creator: Michele Grassi
creator: Tiziano Agostini
creator: Mauro Murgia
subject: Psychiatry and Psychology
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.13681
publisher: PeerJ Inc.
rights: © 2022 Sors et al.
abstract: Background Due to the unfortunate pandemic situation, the phenomena of home advantage and referee bias in sports have recently received a particular research attention, especially in association football. In this regard, several studies were conducted on the last portion of the 2019–20 season: the majority of them suggests a reduction—but not the elimination—of the two phenomena, with some exceptions in which no reduction was found or, at the other extreme, the phenomena were not observed at all. Methods The continuation of the pandemic made it possible to replicate the previous studies considering the complete 2020–21 season, thus with the important added value of having a fully balanced home/away schedule—and a higher number of matches—in the various leagues. In particular, the sample of the present study consisted of 3,898 matches from the first and second divisions of the UEFA top five ranked countries, that is, England, Spain, Italy, Germany, and France. For the home advantage, the following variables were examined: distribution of matches outcomes and home advantage for points (also for previous seasons from the 2014–15 one); ball possession; total shots; shots on goal; and corner kicks. Instead, for he referee bias, the following variables were examined: fouls; yellow cards; red cards; penalty kicks; and extra time. Chi-square tests were used to compare the distribution of matches outcomes, and t-tests to compare home vs. away data for the other variables in the 2020–21 season; Bayesian and equivalence analyses were also conducted. Results The main results are as follows: (a) the distribution of matches outcomes in the 2020–21 season was significantly different from that of the last five complete seasons with spectators (Chi-square = 37.42, df = 2, p < 0.001), with fewer home victories and more away victories; the resulting values of the home advantage for points were 54.95% for the 2020–21 season, and 59.36% for the previous seasons; (b) for the other home a…
bibliographic citation: Sors et al. (2022) A complete season with attendance restrictions confirms the relevant contribution of spectators to home advantage and referee bias in association football. PeerJ 10:e13681 https://doi.org/10.7717/peerj.13681
date submitted: 2021-11-26
date accepted: 2022-06-14
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sors
  given name: Fabrizio
author list: Agent
  family name: Grassi
  given name: Michele
author list: Agent
  family name: Agostini
  given name: Tiziano
author list: Agent
  family name: Murgia
  given name: Mauro
doi: 10.7717/peerj.13681
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Sors et al.
attribution name: Sors et al.

Effect of icaritin on autophagy-related protein expression in TDP-43-transfected SH-SY5Y cells
type: item
type: AcademicArticle
description: Objective To study the protective effect and mechanism of icaritin (ICT) in a SH-SY5Y cells with virus-loaded TAR DNA-binding domain protein 43(TDP-43) by examining the effect of ICT on the expression of autophagy-related proteins in TDP-43-infected SH-SY5Y cells. Methods A TDP-43-induced neuronal cell injury model was established by transfecting well-growing SH-SY5Y cells with virus loaded with the TDP-43 gene. The changes in cell viability were detected by the CCK-8 method. After successful transfection, the establishment of the model was verified by real-time quantitative PCR (qPCR) and Western blot methods. After the cells were subjected to drug intervention with ICT, the changes in the expression levels of TDP-43, cleaved Caspase-3, LC3 II/I, Beclin-1 and p62 were detected by Western blotting. Results After ICT intervention, it was found that compared with that of the TDP-43 group, the cell viability of the TDP-43+ICT group increased, the expression level of TDP-43 decreased, and the expression levels of the apoptotic protein cleaved Caspase-3, autophagy protein Beclin-1, and LC3-II/I decreased, while the expression level of the autophagy protein p62 increased. Conclusion ICT has a protective effect on the SH-SY5Y cell injury model transfected with TDP-43. This protective effect may be related to reducing the protein expression of TDP-43 and inhibiting autophagy.
format: application/pdf
format: text/html
creator: Yanjun Zhou
creator: Nanqu Huang
creator: Yuanyuan Li
creator: Zhisheng Ba
creator: Yong Luo
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.13703
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Objective To study the protective effect and mechanism of icaritin (ICT) in a SH-SY5Y cells with virus-loaded TAR DNA-binding domain protein 43(TDP-43) by examining the effect of ICT on the expression of autophagy-related proteins in TDP-43-infected SH-SY5Y cells. Methods A TDP-43-induced neuronal cell injury model was established by transfecting well-growing SH-SY5Y cells with virus loaded with the TDP-43 gene. The changes in cell viability were detected by the CCK-8 method. After successful transfection, the establishment of the model was verified by real-time quantitative PCR (qPCR) and Western blot methods. After the cells were subjected to drug intervention with ICT, the changes in the expression levels of TDP-43, cleaved Caspase-3, LC3 II/I, Beclin-1 and p62 were detected by Western blotting. Results After ICT intervention, it was found that compared with that of the TDP-43 group, the cell viability of the TDP-43+ICT group increased, the expression level of TDP-43 decreased, and the expression levels of the apoptotic protein cleaved Caspase-3, autophagy protein Beclin-1, and LC3-II/I decreased, while the expression level of the autophagy protein p62 increased. Conclusion ICT has a protective effect on the SH-SY5Y cell injury model transfected with TDP-43. This protective effect may be related to reducing the protein expression of TDP-43 and inhibiting autophagy.
bibliographic citation: Zhou et al. (2022) Effect of icaritin on autophagy-related protein expression in TDP-43-transfected SH-SY5Y cells. PeerJ 10:e13703 https://doi.org/10.7717/peerj.13703
date submitted: 2021-12-27
date accepted: 2022-06-19
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Yanjun
author list: Agent
  family name: Huang
  given name: Nanqu
author list: Agent
  family name: Li
  given name: Yuanyuan
author list: Agent
  family name: Ba
  given name: Zhisheng
author list: Agent
  family name: Luo
  given name: Yong
doi: 10.7717/peerj.13703
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: ©2022 Zhou et al.
attribution name: Zhou et al.

Newly described nesting sites of the green sea turtle (Chelonia mydas) and the hawksbill sea turtle (Eretmochelys imbricata) in the central Red Sea
type: item
type: AcademicArticle
description: Background There is relatively little published information about sea turtle nesting distribution and seasonality in the Saudi Arabian Red Sea. Upcoming large-scale developments occurring along the Saudi Arabian Red Sea coast could negatively affect many sea turtle nesting beaches with potential impacts on the survival of local populations. Methods In 2019, two coastal beaches and three near-shore islands were surveyed for turtle nesting in the central Red Sea. We recorded all emergences, examined beach morphology, and collected sand samples to determine grain size, moisture content and colour. Results Sea turtle nesting was found at all surveyed sites, though emergence counts were often low. The limited occurrence of nesting at several previously undocumented sites suggests that nesting activity may be widespread, but sparsely distributed, in the central Red Sea region. In addition, nesting at novel sites appeared to favour the seaward side of islands, a pattern that was not observed in previously documented areas. The substrate of most surveyed sites was composed of calcium carbonate with Ras Baridi as the only exception; it was composed of dark quartz-rich sediment. This study highlights several important sea turtle rookeries while also demonstrating that low levels of nesting occur throughout the region, although inter-annual nesting patterns still need to be determined. Future developments should be steered away from key nesting areas and the seaward bias in marginal rookeries should be taken into account where possible.
format: application/pdf
format: text/html
creator: Kirsty Scott
creator: Lyndsey K. Tanabe
creator: Jeffrey D. Miller
creator: Michael L. Berumen
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.13408
publisher: PeerJ Inc.
rights: © 2022 Scott et al.
abstract: Background There is relatively little published information about sea turtle nesting distribution and seasonality in the Saudi Arabian Red Sea. Upcoming large-scale developments occurring along the Saudi Arabian Red Sea coast could negatively affect many sea turtle nesting beaches with potential impacts on the survival of local populations. Methods In 2019, two coastal beaches and three near-shore islands were surveyed for turtle nesting in the central Red Sea. We recorded all emergences, examined beach morphology, and collected sand samples to determine grain size, moisture content and colour. Results Sea turtle nesting was found at all surveyed sites, though emergence counts were often low. The limited occurrence of nesting at several previously undocumented sites suggests that nesting activity may be widespread, but sparsely distributed, in the central Red Sea region. In addition, nesting at novel sites appeared to favour the seaward side of islands, a pattern that was not observed in previously documented areas. The substrate of most surveyed sites was composed of calcium carbonate with Ras Baridi as the only exception; it was composed of dark quartz-rich sediment. This study highlights several important sea turtle rookeries while also demonstrating that low levels of nesting occur throughout the region, although inter-annual nesting patterns still need to be determined. Future developments should be steered away from key nesting areas and the seaward bias in marginal rookeries should be taken into account where possible.
bibliographic citation: Scott et al. (2022) Newly described nesting sites of the green sea turtle (Chelonia mydas) and the hawksbill sea turtle (Eretmochelys imbricata) in the central Red Sea. PeerJ 10:e13408 https://doi.org/10.7717/peerj.13408
date submitted: 2021-04-20
date accepted: 2022-04-19
issued: 2022-07-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scott
  given name: Kirsty
author list: Agent
  family name: Tanabe
  given name: Lyndsey K.
author list: Agent
  family name: Miller
  given name: Jeffrey D.
author list: Agent
  family name: Berumen
  given name: Michael L.
doi: 10.7717/peerj.13408
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-01
copyright: ©2022 Scott et al.
attribution name: Scott et al.

Can high-intensity interval training and small-sided games be effective for improving physical fitness after detraining? A parallel study design in youth male soccer players
type: item
type: AcademicArticle
description: Background The aim of this study was two-fold: (i) analyze the within-group physical fitness adaptations promoted by a detraining period (4 weeks) followed by an intervention period (4 weeks) using small-sided games (SSGs) or running-based high intensity interval training (HIIT); and (ii) analyze the between-group differences aiming to identify the effectiveness of each training intervention on the physical fitness of youth male soccer players. Methods This study followed a randomized parallel study design. Forty male soccer players (age: 16.4 ± 0.5 years old) were assessed three times: (i) baseline; (ii) after 4 weeks of detraining; and (iii) after a retraining period of 4 weeks. After returning from detraining, players were randomized to an SSG-based training intervention (n = 20) or running-based HIIT (n = 20). Interventions lasted 4 weeks, with a training frequency of three sessions per week. At all timepoints, players were assessed by: (i) anthropometry (height, body mass, fat mass (FM)), countermovement jump (CMJ), standing broad jump (SBJ), triple hop jump (THJ), linear sprint test (5-, 10-, and 20-m), zig-zag test with (ZZwB) and without (ZZwoB) ball, three corner run test (3CRT), Y-balance test and the Yo-Yo intermittent recovery test level 1 (YYIRT). Mixed ANOVA (time * group) was conducted for testing interactions between the three timepoints of repeated measures and the two groups. Effect size (ES) for pairwise comparisons was calculated using Cohen’s. Results Between-group analysis revealed significantly smaller SBJ (t = −2.424, p = 0.020, d = −0.767 small ES) and THT (t = −4.353, p < 0.001, d = −1.376 large ES) in the SSG group after the retraining period. At the same time, SSG presented significantly greater FM after retraining compared to HIIT (t = 3.736, p < 0.001, d = 1.181 large ES). Additionally, SSG had significantly smaller values than HIIT in the ZZwB (t = −3.645, p < 0.001, d = −1.153 large ES), but greater times in the ZZwoB (t = 2.679, p = …
format: application/pdf
format: text/html
creator: Filipe Manuel Clemente
creator: Yusuf Soylu
creator: Ersan Arslan
creator: Bulent Kilit
creator: Joel Garrett
creator: Daniel van den Hoek
creator: Georgian Badicu
creator: Ana Filipa Silva
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.13514
publisher: PeerJ Inc.
rights: © 2022 Clemente et al.
abstract: Background The aim of this study was two-fold: (i) analyze the within-group physical fitness adaptations promoted by a detraining period (4 weeks) followed by an intervention period (4 weeks) using small-sided games (SSGs) or running-based high intensity interval training (HIIT); and (ii) analyze the between-group differences aiming to identify the effectiveness of each training intervention on the physical fitness of youth male soccer players. Methods This study followed a randomized parallel study design. Forty male soccer players (age: 16.4 ± 0.5 years old) were assessed three times: (i) baseline; (ii) after 4 weeks of detraining; and (iii) after a retraining period of 4 weeks. After returning from detraining, players were randomized to an SSG-based training intervention (n = 20) or running-based HIIT (n = 20). Interventions lasted 4 weeks, with a training frequency of three sessions per week. At all timepoints, players were assessed by: (i) anthropometry (height, body mass, fat mass (FM)), countermovement jump (CMJ), standing broad jump (SBJ), triple hop jump (THJ), linear sprint test (5-, 10-, and 20-m), zig-zag test with (ZZwB) and without (ZZwoB) ball, three corner run test (3CRT), Y-balance test and the Yo-Yo intermittent recovery test level 1 (YYIRT). Mixed ANOVA (time * group) was conducted for testing interactions between the three timepoints of repeated measures and the two groups. Effect size (ES) for pairwise comparisons was calculated using Cohen’s. Results Between-group analysis revealed significantly smaller SBJ (t = −2.424, p = 0.020, d = −0.767 small ES) and THT (t = −4.353, p < 0.001, d = −1.376 large ES) in the SSG group after the retraining period. At the same time, SSG presented significantly greater FM after retraining compared to HIIT (t = 3.736, p < 0.001, d = 1.181 large ES). Additionally, SSG had significantly smaller values than HIIT in the ZZwB (t = −3.645, p < 0.001, d = −1.153 large ES), but greater times in the ZZwoB (t = 2.679, p = …
bibliographic citation: Clemente et al. (2022) Can high-intensity interval training and small-sided games be effective for improving physical fitness after detraining? A parallel study design in youth male soccer players. PeerJ 10:e13514 https://doi.org/10.7717/peerj.13514
date submitted: 2022-02-28
date accepted: 2022-05-09
issued: 2022-07-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clemente
  given name: Filipe Manuel
author list: Agent
  family name: Soylu
  given name: Yusuf
author list: Agent
  family name: Arslan
  given name: Ersan
author list: Agent
  family name: Kilit
  given name: Bulent
author list: Agent
  family name: Garrett
  given name: Joel
author list: Agent
  family name: van den Hoek
  given name: Daniel
author list: Agent
  family name: Badicu
  given name: Georgian
author list: Agent
  family name: Filipa Silva
  given name: Ana
doi: 10.7717/peerj.13514
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-01
copyright: © 2022 Clemente et al.
attribution name: Clemente et al.

Dopamine receptor activation elicits a possible stress-related coping behavior in a wild-caught songbird
type: item
type: AcademicArticle
description: Animals experience stress throughout their lives and exhibit both physiological and behavioral responses to cope with it. The stress response can become harmful when prolonged and increasing evidence suggests that dopamine plays a critical role in extinguishing the stress response. In particular, activation of the D2 dopamine receptor reduces glucocorticoids and increases coping behavior, i.e., behavioral responses to adverse stimuli that reduce the harmful effects of stress. However, few studies have examined the effects of dopamine on the stress responses of wild species. We therefore tested the hypothesis that activation of the D2 dopamine receptor influences coping-like behavior in a wild-caught species. We recorded behavior of house sparrows (Passer domesticus) before and after they received injections of D2 dopamine agonists, D2 dopamine antagonists, or saline. House sparrows are common in urban environments and understanding how they cope with stress may help us better understand how animals cope with urban stressors. We found that the birds significantly increased biting of inanimate objects after the agonist but there was no change following the antagonist or saline. The biting of inanimate objects may be a mechanism of behavioral coping. This change in biting behavior was not correlated with general movement. This study supports the hypothesis that D2 dopamine receptor activation is involved in the regulation of the stress response in a wild bird.
format: application/pdf
format: text/html
creator: Melanie R. Florkowski
creator: Jessica L. Yorzinski
subject: Animal Behavior
subject: Neuroscience
description: doi:10.7717/peerj.13520
publisher: PeerJ Inc.
rights: © 2022 Florkowski and Yorzinski
abstract: Animals experience stress throughout their lives and exhibit both physiological and behavioral responses to cope with it. The stress response can become harmful when prolonged and increasing evidence suggests that dopamine plays a critical role in extinguishing the stress response. In particular, activation of the D2 dopamine receptor reduces glucocorticoids and increases coping behavior, i.e., behavioral responses to adverse stimuli that reduce the harmful effects of stress. However, few studies have examined the effects of dopamine on the stress responses of wild species. We therefore tested the hypothesis that activation of the D2 dopamine receptor influences coping-like behavior in a wild-caught species. We recorded behavior of house sparrows (Passer domesticus) before and after they received injections of D2 dopamine agonists, D2 dopamine antagonists, or saline. House sparrows are common in urban environments and understanding how they cope with stress may help us better understand how animals cope with urban stressors. We found that the birds significantly increased biting of inanimate objects after the agonist but there was no change following the antagonist or saline. The biting of inanimate objects may be a mechanism of behavioral coping. This change in biting behavior was not correlated with general movement. This study supports the hypothesis that D2 dopamine receptor activation is involved in the regulation of the stress response in a wild bird.
bibliographic citation: Florkowski et al. (2022) Dopamine receptor activation elicits a possible stress-related coping behavior in a wild-caught songbird. PeerJ 10:e13520 https://doi.org/10.7717/peerj.13520
date submitted: 2022-01-21
date accepted: 2022-05-09
issued: 2022-07-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Florkowski
  given name: Melanie R.
author list: Agent
  family name: Yorzinski
  given name: Jessica L.
doi: 10.7717/peerj.13520
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-01
copyright: © 2022 Florkowski and Yorzinski
attribution name: Florkowski and Yorzinski

Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae)
type: item
type: AcademicArticle
description: Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. M…
format: application/pdf
format: text/html
creator: Changhong Li
creator: Yu Liu
creator: Furong Lin
creator: Yongqi Zheng
creator: Ping Huang
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13570
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. M…
bibliographic citation: Li et al. (2022) Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae). PeerJ 10:e13570 https://doi.org/10.7717/peerj.13570
date submitted: 2021-11-19
date accepted: 2022-05-20
issued: 2022-07-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Changhong
author list: Agent
  family name: Liu
  given name: Yu
author list: Agent
  family name: Lin
  given name: Furong
author list: Agent
  family name: Zheng
  given name: Yongqi
author list: Agent
  family name: Huang
  given name: Ping
doi: 10.7717/peerj.13570
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-01
copyright: ©2022 Li et al.
attribution name: Li et al.

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