PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Prevalence of risk factors associated with rupture of abdominal aortic aneurysm (AAA): a single center retrospective study
items: Three specific gut bacteria in the occurrence and development of colorectal cancer: a concerted effort
items: Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes
items: Vitamin D receptor-deficient keratinocytes-derived exosomal miR-4505 promotes the macrophage polarization towards the M1 phenotype
items: Resultant equations for training load monitoring during a standard microcycle in sub-elite youth football: a principal components approach
items: Submarine groundwater discharge interacts with creek geomorphology to affect eastern oyster Crassostrea virginica growth rates in a coastal Georgia creek
items: Microvertebrate faunal assemblages of the Favel Formation (late Cenomanian-middle Turonian) of Manitoba, Canada
items: GGA1 participates in spermatogenesis in mice under stress
items: Development, physicochemical characterization and in-vitro biocompatibility study of dromedary camel dentine derived hydroxyapatite for bone repair
items: Earthworms neutralize the influence of components of particulate pollutants on soil extracellular enzymatic functions in subtropical forests

Prevalence of risk factors associated with rupture of abdominal aortic aneurysm (AAA): a single center retrospective study
type: item
type: AcademicArticle
description: Background Abdominal aortic aneurysm (AAA) is a severe cardiovascular disease. The mortality rate for an AAA rupture is very high. Understanding the risk factors for AAA rupture would help AAA management, but little is known about these risk factors in the Chinese population. Methods This retrospective study included patients that were diagnosed with AAA during the last 5 years in a large national hospital in southern China. AAA patients were divided into a rupture and non-rupture group. Clinical data were extracted from the hospital medical record system. Clinical features were compared between the rupture and non-rupture groups. The associations between potential risk factors and rupture risk were evaluated using a multivariate logistic regression analysis. Results A total of 337 AAA patients were included for analysis in the present study. AAA diameter was significantly larger, and high-sensitivity C-reactive protein (hs-CRP) and serum creatinine levels were both significantly higher in AAA rupture patients. High-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and total cholesterol (TC) levels were significantly lower in AAA rupture patients. After adjustment, the multivariate logistic analysis found that AAA diameter and hs-CRP were independently positively associated with AAA rupture, and HDL-C level was adversely associated with AAA rupture. Conclusions Our data suggests that larger AAA diameter and higher hs-CRP level are associated with a higher risk of AAA rupture, and higher HDL-C level is associated with a lower risk of AAA rupture. The results of this study may be helpful for the management of AAA patients in southern China.
format: application/pdf
format: text/html
creator: Sudong Liu
creator: Caifu Long
creator: Yuanjia Hong
creator: Xiaodong Gu
creator: Ruiqiang Weng
creator: Zhixiong Zhong
subject: Cardiology
subject: Epidemiology
subject: Internal Medicine
description: doi:10.7717/peerj.15752
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Background Abdominal aortic aneurysm (AAA) is a severe cardiovascular disease. The mortality rate for an AAA rupture is very high. Understanding the risk factors for AAA rupture would help AAA management, but little is known about these risk factors in the Chinese population. Methods This retrospective study included patients that were diagnosed with AAA during the last 5 years in a large national hospital in southern China. AAA patients were divided into a rupture and non-rupture group. Clinical data were extracted from the hospital medical record system. Clinical features were compared between the rupture and non-rupture groups. The associations between potential risk factors and rupture risk were evaluated using a multivariate logistic regression analysis. Results A total of 337 AAA patients were included for analysis in the present study. AAA diameter was significantly larger, and high-sensitivity C-reactive protein (hs-CRP) and serum creatinine levels were both significantly higher in AAA rupture patients. High-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and total cholesterol (TC) levels were significantly lower in AAA rupture patients. After adjustment, the multivariate logistic analysis found that AAA diameter and hs-CRP were independently positively associated with AAA rupture, and HDL-C level was adversely associated with AAA rupture. Conclusions Our data suggests that larger AAA diameter and higher hs-CRP level are associated with a higher risk of AAA rupture, and higher HDL-C level is associated with a lower risk of AAA rupture. The results of this study may be helpful for the management of AAA patients in southern China.
bibliographic citation: Liu et al. (2023) Prevalence of risk factors associated with rupture of abdominal aortic aneurysm (AAA): a single center retrospective study. PeerJ 11:e15752 https://doi.org/10.7717/peerj.15752
date submitted: 2023-02-09
date accepted: 2023-06-23
issued: 2023-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Sudong
author list: Agent
  family name: Long
  given name: Caifu
author list: Agent
  family name: Hong
  given name: Yuanjia
author list: Agent
  family name: Gu
  given name: Xiaodong
author list: Agent
  family name: Weng
  given name: Ruiqiang
author list: Agent
  family name: Zhong
  given name: Zhixiong
doi: 10.7717/peerj.15752
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-04
copyright: © 2023 Liu et al.
attribution name: Liu et al.

Three specific gut bacteria in the occurrence and development of colorectal cancer: a concerted effort
type: item
type: AcademicArticle
description: Colorectal cancer (CRC), which develops from the gradual evolution of tubular adenomas and serrated polyps in the colon and rectum, has a poor prognosis and a high mortality rate. In addition to genetics, lifestyle, and chronic diseases, intestinal integrity and microbiota (which facilitate digestion, metabolism, and immune regulation) could promote CRC development. For example, enterotoxigenic Bacteroides fragilis, genotoxic Escherichia coli (pks+ E. coli), and Fusobacterium nucleatum, members of the intestinal microbiota, are highly correlated in CRC. This review describes the roles and mechanisms of these three bacteria in CRC development. Their interaction during CRC initiation and progression has also been proposed. Our view is that in the precancerous stage of colorectal cancer, ETBF causes inflammation, leading to potential changes in intestinal ecology that may provide the basic conditions for pks+ E. coli colonization and induction of oncogenic mutations, when cancerous intestinal epithelial cells can further recruit F. nucleatum to colonise the lesion site and F. nucleatum may contribute to CRC advancement by primarily the development of cancer cells, stemization, and proliferation, which could create new and tailored preventive, screening and therapeutic interventions. However, there is the most dominant microbiota in each stage of CRC development, not neglecting the possibility that two or even all three bacteria could be engaged at any stage of the disease. The relationship between the associated gut microbiota and CRC development may provide important information for therapeutic strategies to assess the potential use of the associated gut microbiota in CRC studies, antibiotic therapy, and prevention strategies.
format: application/pdf
format: text/html
creator: Dengmei Gong
creator: Amma G Adomako-Bonsu
creator: Maijian Wang
creator: Jida Li
subject: Microbiology
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.15777
publisher: PeerJ Inc.
rights: © 2023 Gong et al.
abstract: Colorectal cancer (CRC), which develops from the gradual evolution of tubular adenomas and serrated polyps in the colon and rectum, has a poor prognosis and a high mortality rate. In addition to genetics, lifestyle, and chronic diseases, intestinal integrity and microbiota (which facilitate digestion, metabolism, and immune regulation) could promote CRC development. For example, enterotoxigenic Bacteroides fragilis, genotoxic Escherichia coli (pks+ E. coli), and Fusobacterium nucleatum, members of the intestinal microbiota, are highly correlated in CRC. This review describes the roles and mechanisms of these three bacteria in CRC development. Their interaction during CRC initiation and progression has also been proposed. Our view is that in the precancerous stage of colorectal cancer, ETBF causes inflammation, leading to potential changes in intestinal ecology that may provide the basic conditions for pks+ E. coli colonization and induction of oncogenic mutations, when cancerous intestinal epithelial cells can further recruit F. nucleatum to colonise the lesion site and F. nucleatum may contribute to CRC advancement by primarily the development of cancer cells, stemization, and proliferation, which could create new and tailored preventive, screening and therapeutic interventions. However, there is the most dominant microbiota in each stage of CRC development, not neglecting the possibility that two or even all three bacteria could be engaged at any stage of the disease. The relationship between the associated gut microbiota and CRC development may provide important information for therapeutic strategies to assess the potential use of the associated gut microbiota in CRC studies, antibiotic therapy, and prevention strategies.
bibliographic citation: Gong et al. (2023) Three specific gut bacteria in the occurrence and development of colorectal cancer: a concerted effort. PeerJ 11:e15777 https://doi.org/10.7717/peerj.15777
date submitted: 2023-02-22
date accepted: 2023-06-29
issued: 2023-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gong
  given name: Dengmei
author list: Agent
  family name: Adomako-Bonsu
  given name: Amma G
author list: Agent
  family name: Wang
  given name: Maijian
author list: Agent
  family name: Li
  given name: Jida
doi: 10.7717/peerj.15777
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-04
copyright: © 2023 Gong et al.
attribution name: Gong et al.

Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes
type: item
type: AcademicArticle
description: Background Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in the African plant genera Empogona and Tricalysia and, if present, to establish their identity. Methods Total DNA was extracted from the leaves of four species of the Coffeeae tribe (Empogona congesta, Tricalysia hensii, T. lasiodelphys, and T. semidecidua) and sequenced. Bacterial reads were filtered out and assembled. Phylogenetic analysis of the endophytes was used to reveal their identity and their relationship with known symbionts. Results All four species have non-nodulated leaf endophytes, which are identified as Caballeronia. The endophytes are distinct from each other but related to other nodulated and non-nodulated endophytes. An apparent phylogenetic or geographic pattern appears to be absent in endophytes or host plants. Caballeronia endophytes are present in the leaves of Empogona and Tricalysia, two genera not previously implicated in leaf symbiosis. This interaction is likely to be more widespread, and future discoveries are inevitable.
format: application/pdf
format: text/html
creator: Brecht Verstraete
creator: Steven Janssens
creator: Petra De Block
creator: Pieter Asselman
creator: Gabriela Méndez
creator: Serigne Ly
creator: Perla Hamon
creator: Romain Guyot
subject: Biodiversity
subject: Evolutionary Studies
subject: Molecular Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.15778
publisher: PeerJ Inc.
rights: © 2023 Verstraete et al.
abstract: Background Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in the African plant genera Empogona and Tricalysia and, if present, to establish their identity. Methods Total DNA was extracted from the leaves of four species of the Coffeeae tribe (Empogona congesta, Tricalysia hensii, T. lasiodelphys, and T. semidecidua) and sequenced. Bacterial reads were filtered out and assembled. Phylogenetic analysis of the endophytes was used to reveal their identity and their relationship with known symbionts. Results All four species have non-nodulated leaf endophytes, which are identified as Caballeronia. The endophytes are distinct from each other but related to other nodulated and non-nodulated endophytes. An apparent phylogenetic or geographic pattern appears to be absent in endophytes or host plants. Caballeronia endophytes are present in the leaves of Empogona and Tricalysia, two genera not previously implicated in leaf symbiosis. This interaction is likely to be more widespread, and future discoveries are inevitable.
bibliographic citation: Verstraete et al. (2023) Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes. PeerJ 11:e15778 https://doi.org/10.7717/peerj.15778
date submitted: 2022-12-16
date accepted: 2023-06-29
issued: 2023-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Verstraete
  given name: Brecht
author list: Agent
  family name: Janssens
  given name: Steven
author list: Agent
  family name: De Block
  given name: Petra
author list: Agent
  family name: Asselman
  given name: Pieter
author list: Agent
  family name: Méndez
  given name: Gabriela
author list: Agent
  family name: Ly
  given name: Serigne
author list: Agent
  family name: Hamon
  given name: Perla
author list: Agent
  family name: Guyot
  given name: Romain
doi: 10.7717/peerj.15778
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-04
copyright: ©2023 Verstraete et al.
attribution name: Verstraete et al.

Vitamin D receptor-deficient keratinocytes-derived exosomal miR-4505 promotes the macrophage polarization towards the M1 phenotype
type: item
type: AcademicArticle
description: Background The vitamin D receptor (VDR) has a low level of expression in the keratinocytes of patients with psoriasis and plays a role in the development of the disease. Furthermore, the crosstalk between macrophages and psoriatic keratinocytes-derived exosomes is critical for psoriasis progression. However, the effects of VDR-deficient keratinocytes-derived exosomes (Exos-shVDR) on macrophages and their underlying mechanisms remain largely unknown. Methods VDR-deficient keratinocytes were constructed by infecting HaCaT cells with a VDR-targeting lentivirus, mimicking the VDR-deficient state observed in psoriatic keratinocytes. Exosomes were characterized using transmission electron microscopy, nanoparticle tracking analysis, and Western blot. The effect of Exos-shVDR on macrophage proliferation, apoptosis, and M1/M2 polarization was assessed using cell counting kit-8 assay (CCK-8), flow cytometer, real-time quantitative polymerasechain reaction (RT-qPCR), and enzyme-linked immunosorbent assay (ELISA). The mechanism underlying the effect of Exos-shVDR on macrophage function was elucidated through data mining, bioinformatics, RT-qPCR, and rescue experiments. Results Our results revealed that both Exos-shVDR and Exos-shNC exhibited typical exosome characteristics, including a hemispheroid shape with a concave side and particle size ranging from 50 to 100 nm. The levels of expression of VDR were significantly lower in Exos-shVDR than in Exos-shNC. Functional experiments demonstrated that Exos-shVDR significantly promoted macrophage proliferation and polarization towards the M1 phenotype while inhibiting macrophage apoptosis. Moreover, miR-4505 was highly expressed in the skin tissue of patients with psoriasis. Its overexpression significantly increased macrophage proliferation and polarization towards M1 and inhibited apoptosis. Furthermore, the effects of Exos-shVDR on macrophage function occur through miR-4505. Conclusions Exos-shVDR exacerbates macrophage proliferat…
format: application/pdf
format: text/html
creator: Wen Sun
creator: Jianqin Chen
creator: Jingting Li
creator: Xiaoguang She
creator: Hu Ma
creator: Shali Wang
creator: Jing Liu
creator: Yuan Yuan
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15798
publisher: PeerJ Inc.
rights: © 2023 Sun et al.
abstract: Background The vitamin D receptor (VDR) has a low level of expression in the keratinocytes of patients with psoriasis and plays a role in the development of the disease. Furthermore, the crosstalk between macrophages and psoriatic keratinocytes-derived exosomes is critical for psoriasis progression. However, the effects of VDR-deficient keratinocytes-derived exosomes (Exos-shVDR) on macrophages and their underlying mechanisms remain largely unknown. Methods VDR-deficient keratinocytes were constructed by infecting HaCaT cells with a VDR-targeting lentivirus, mimicking the VDR-deficient state observed in psoriatic keratinocytes. Exosomes were characterized using transmission electron microscopy, nanoparticle tracking analysis, and Western blot. The effect of Exos-shVDR on macrophage proliferation, apoptosis, and M1/M2 polarization was assessed using cell counting kit-8 assay (CCK-8), flow cytometer, real-time quantitative polymerasechain reaction (RT-qPCR), and enzyme-linked immunosorbent assay (ELISA). The mechanism underlying the effect of Exos-shVDR on macrophage function was elucidated through data mining, bioinformatics, RT-qPCR, and rescue experiments. Results Our results revealed that both Exos-shVDR and Exos-shNC exhibited typical exosome characteristics, including a hemispheroid shape with a concave side and particle size ranging from 50 to 100 nm. The levels of expression of VDR were significantly lower in Exos-shVDR than in Exos-shNC. Functional experiments demonstrated that Exos-shVDR significantly promoted macrophage proliferation and polarization towards the M1 phenotype while inhibiting macrophage apoptosis. Moreover, miR-4505 was highly expressed in the skin tissue of patients with psoriasis. Its overexpression significantly increased macrophage proliferation and polarization towards M1 and inhibited apoptosis. Furthermore, the effects of Exos-shVDR on macrophage function occur through miR-4505. Conclusions Exos-shVDR exacerbates macrophage proliferat…
bibliographic citation: Sun et al. (2023) Vitamin D receptor-deficient keratinocytes-derived exosomal miR-4505 promotes the macrophage polarization towards the M1 phenotype. PeerJ 11:e15798 https://doi.org/10.7717/peerj.15798
date submitted: 2023-05-09
date accepted: 2023-07-05
issued: 2023-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Wen
author list: Agent
  family name: Chen
  given name: Jianqin
author list: Agent
  family name: Li
  given name: Jingting
author list: Agent
  family name: She
  given name: Xiaoguang
author list: Agent
  family name: Ma
  given name: Hu
author list: Agent
  family name: Wang
  given name: Shali
author list: Agent
  family name: Liu
  given name: Jing
author list: Agent
  family name: Yuan
  given name: Yuan
doi: 10.7717/peerj.15798
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-04
copyright: © 2023 Sun et al.
attribution name: Sun et al.

Resultant equations for training load monitoring during a standard microcycle in sub-elite youth football: a principal components approach
type: item
type: AcademicArticle
description: Applying data-reduction techniques to extract meaningful information from electronic performance and tracking systems (EPTS) has become a hot topic in football training load (TL) monitoring. The aim of this study was to reduce the dimensionality of the internal and external load measures, by a principal component approach, to describe and explain the resultant equations for TL monitoring during a standard in-season microcycle in sub-elite youth football. Additionally, it is intended to identify the most representative measure for each principal component. A principal component analysis (PCA) was conducted with a Monte Carlo parallel analysis and VariMax rotation to extract baseline characteristics, external TL, heart rate (HR)-based measures and perceived exertion. Training data were collected from sixty sub-elite young football players during a 6-week training period using 18 Hz global positioning system (GPS) with inertial sensors, 1 Hz short-range telemetry system, total quality recovery (TQR) and rating of perceived exertion (RPE). Five principal components accounted for 68.7% of the total variance explained in the training data. Resultant equations from PCA was subdivided into: (1) explosiveness, accelerations and impacts (27.4%); (2) high-speed running (16.2%); (3) HR-based measures (10.0%); (4) baseline characteristics (8.3%); and (5) average running velocity (6.7%). Considering the highest factor in each principal component, decelerations (PCA 1), sprint distance (PCA 2), average HR (PCA 3), chronological age (PCA 4) and maximal speed (PCA 5) are the conditional dimension to be considered in TL monitoring during a standard microcycle in sub-elite youth football players. Current research provides the first composite equations to extract the most representative components during a standard in-season microcycle in sub-elite youth football players. Futures research should expand the resultant equations within training days, by considering other well-being measur…
format: application/pdf
format: text/html
creator: José Eduardo Teixeira
creator: Pedro Forte
creator: Ricardo Ferraz
creator: Luís Branquinho
creator: Ryland Morgans
creator: António José Silva
creator: António Miguel Monteiro
creator: Tiago M. Barbosa
subject: Kinesiology
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.15806
publisher: PeerJ Inc.
rights: © 2023 Teixeira et al.
abstract: Applying data-reduction techniques to extract meaningful information from electronic performance and tracking systems (EPTS) has become a hot topic in football training load (TL) monitoring. The aim of this study was to reduce the dimensionality of the internal and external load measures, by a principal component approach, to describe and explain the resultant equations for TL monitoring during a standard in-season microcycle in sub-elite youth football. Additionally, it is intended to identify the most representative measure for each principal component. A principal component analysis (PCA) was conducted with a Monte Carlo parallel analysis and VariMax rotation to extract baseline characteristics, external TL, heart rate (HR)-based measures and perceived exertion. Training data were collected from sixty sub-elite young football players during a 6-week training period using 18 Hz global positioning system (GPS) with inertial sensors, 1 Hz short-range telemetry system, total quality recovery (TQR) and rating of perceived exertion (RPE). Five principal components accounted for 68.7% of the total variance explained in the training data. Resultant equations from PCA was subdivided into: (1) explosiveness, accelerations and impacts (27.4%); (2) high-speed running (16.2%); (3) HR-based measures (10.0%); (4) baseline characteristics (8.3%); and (5) average running velocity (6.7%). Considering the highest factor in each principal component, decelerations (PCA 1), sprint distance (PCA 2), average HR (PCA 3), chronological age (PCA 4) and maximal speed (PCA 5) are the conditional dimension to be considered in TL monitoring during a standard microcycle in sub-elite youth football players. Current research provides the first composite equations to extract the most representative components during a standard in-season microcycle in sub-elite youth football players. Futures research should expand the resultant equations within training days, by considering other well-being measur…
bibliographic citation: Teixeira et al. (2023) Resultant equations for training load monitoring during a standard microcycle in sub-elite youth football: a principal components approach. PeerJ 11:e15806 https://doi.org/10.7717/peerj.15806
date submitted: 2023-01-26
date accepted: 2023-07-07
issued: 2023-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Teixeira
  given name: José Eduardo
author list: Agent
  family name: Forte
  given name: Pedro
author list: Agent
  family name: Ferraz
  given name: Ricardo
author list: Agent
  family name: Branquinho
  given name: Luís
author list: Agent
  family name: Morgans
  given name: Ryland
author list: Agent
  family name: Silva
  given name: António José
author list: Agent
  family name: Monteiro
  given name: António Miguel
author list: Agent
  family name: Barbosa
  given name: Tiago M.
doi: 10.7717/peerj.15806
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-04
copyright: © 2023 Teixeira et al.
attribution name: Teixeira et al.

Submarine groundwater discharge interacts with creek geomorphology to affect eastern oyster Crassostrea virginica growth rates in a coastal Georgia creek
type: item
type: AcademicArticle
description: Eastern oysters, Crassostrea virginica, are commercially important coastal species that provide many ecosystem services for coastal communities. Unfortunately, 85% of oyster reefs have been lost globally, prompting investments in restoration efforts to rebuild populations. Managers often consider several well-studied environmental and water quality parameters when making restoration site decisions. However, recent research suggests that submarine groundwater discharge (SGD) may play a role in driving the distribution of oysters in some estuaries. Specifically, SGD may result in localized areas of low dissolved oxygen and low pH that could inhibit oyster recruitment and survival. However, SGD may interact with other potential oyster stressors, including creek geomorphology. On point bars, sediment accumulation could alter growth rates of oysters and physiology, and it is possible that the two factors, SGD and creek geomorphology, could interact to impact oyster growth. We conducted a field experiment to examine the effects of SGD and creek geomorphology on oyster growth rates in a marsh-lined tidal creek in Georgia, USA. High and low SGD sites were paired within point bars and cut banks. Oysters were deployed in cages for 72 days and growth rates were determined. We found a significant interaction between SGD and creek geomorphology on oyster growth rates. Oysters grew at significantly faster rates at locations on accretionary point bars regardless of SGD flux, whereas, on erosional cut banks, high SGD flux significantly reduced oyster growth rate relative to low SGD flux. It appears that SGD may negatively influence oyster growth at specific creek locations, likely due to the presence of other stressors. Therefore, it is important to consider potential interacting and confounding stressors when managing oyster populations. As SGD is still a relatively understudied potential stressor for oysters, it is critical to continue to examine how groundwater might influence o…
format: application/pdf
format: text/html
creator: John M. Carroll
creator: Walker de la Torre
creator: Jacque L. Kelly
subject: Ecology
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.15837
publisher: PeerJ Inc.
rights: © 2023 Carroll et al.
abstract: Eastern oysters, Crassostrea virginica, are commercially important coastal species that provide many ecosystem services for coastal communities. Unfortunately, 85% of oyster reefs have been lost globally, prompting investments in restoration efforts to rebuild populations. Managers often consider several well-studied environmental and water quality parameters when making restoration site decisions. However, recent research suggests that submarine groundwater discharge (SGD) may play a role in driving the distribution of oysters in some estuaries. Specifically, SGD may result in localized areas of low dissolved oxygen and low pH that could inhibit oyster recruitment and survival. However, SGD may interact with other potential oyster stressors, including creek geomorphology. On point bars, sediment accumulation could alter growth rates of oysters and physiology, and it is possible that the two factors, SGD and creek geomorphology, could interact to impact oyster growth. We conducted a field experiment to examine the effects of SGD and creek geomorphology on oyster growth rates in a marsh-lined tidal creek in Georgia, USA. High and low SGD sites were paired within point bars and cut banks. Oysters were deployed in cages for 72 days and growth rates were determined. We found a significant interaction between SGD and creek geomorphology on oyster growth rates. Oysters grew at significantly faster rates at locations on accretionary point bars regardless of SGD flux, whereas, on erosional cut banks, high SGD flux significantly reduced oyster growth rate relative to low SGD flux. It appears that SGD may negatively influence oyster growth at specific creek locations, likely due to the presence of other stressors. Therefore, it is important to consider potential interacting and confounding stressors when managing oyster populations. As SGD is still a relatively understudied potential stressor for oysters, it is critical to continue to examine how groundwater might influence o…
bibliographic citation: Carroll et al. (2023) Submarine groundwater discharge interacts with creek geomorphology to affect eastern oyster Crassostrea virginica growth rates in a coastal Georgia creek. PeerJ 11:e15837 https://doi.org/10.7717/peerj.15837
date submitted: 2023-01-17
date accepted: 2023-07-11
issued: 2023-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carroll
  given name: John M.
author list: Agent
  family name: de la Torre
  given name: Walker
author list: Agent
  family name: Kelly
  given name: Jacque L.
doi: 10.7717/peerj.15837
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-04
copyright: © 2023 Carroll et al.
attribution name: Carroll et al.

Microvertebrate faunal assemblages of the Favel Formation (late Cenomanian-middle Turonian) of Manitoba, Canada
type: item
type: AcademicArticle
description: Microvertebrate assemblages of the Upper Cretaceous (late Cenomanian to mid-Turonian) Favel Formation of Manitoba are formally described for the first time. New vertebrate occurrences from the Favel Formation include the actinopterygians Caturidae indet., cf. Albulidae incertae sedis, Micropycnodon kansasensis, Pachyrhizodus minimus, Protosphyraena sp., Thryptodus loomisi, chondrichthyans Ischyrhiza cf. mira, I. texana, Ptychodus marginalis, P. occidentalis, and P. rhombodus, the avian cf. Ichthyornis sp., the reptile Testudines indet., and an unknown taxon referred to as Vertebrate A. Changes in faunal occurrences throughout the formation suggest an offshore open marine environment for the lower and middle horizons and nearshore marine for the upper horizon, represent ing mid- and late stages of the Greenhorn third-order marine cycle. This newly described diversity increases biogeographic affinities of the late Cenomanian to mid-Turonian vertebrate assemblages of Manitoba with central WIS localities in South Dakota and Kansas, providing additional support for a central vertebrate biogeographic subprovince during late Cenomanian to early Turonian times, as well as WIS localities further south in Texas decreasing the gradient of the north-south or central-south community boundary during early and mid-Turonian times.
format: application/pdf
format: text/html
creator: Aaron A. Kilmury
creator: Aaron Anderson
creator: Dhuranka S. Wijesinghe
creator: Ashley F. Verstraete
creator: William Ezeana
creator: Ashley E. Anderson
creator: Kirstin S. Brink
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.15493
publisher: PeerJ Inc.
rights: © 2023 Kilmury et al.
abstract: Microvertebrate assemblages of the Upper Cretaceous (late Cenomanian to mid-Turonian) Favel Formation of Manitoba are formally described for the first time. New vertebrate occurrences from the Favel Formation include the actinopterygians Caturidae indet., cf. Albulidae incertae sedis, Micropycnodon kansasensis, Pachyrhizodus minimus, Protosphyraena sp., Thryptodus loomisi, chondrichthyans Ischyrhiza cf. mira, I. texana, Ptychodus marginalis, P. occidentalis, and P. rhombodus, the avian cf. Ichthyornis sp., the reptile Testudines indet., and an unknown taxon referred to as Vertebrate A. Changes in faunal occurrences throughout the formation suggest an offshore open marine environment for the lower and middle horizons and nearshore marine for the upper horizon, represent ing mid- and late stages of the Greenhorn third-order marine cycle. This newly described diversity increases biogeographic affinities of the late Cenomanian to mid-Turonian vertebrate assemblages of Manitoba with central WIS localities in South Dakota and Kansas, providing additional support for a central vertebrate biogeographic subprovince during late Cenomanian to early Turonian times, as well as WIS localities further south in Texas decreasing the gradient of the north-south or central-south community boundary during early and mid-Turonian times.
bibliographic citation: Kilmury et al. (2023) Microvertebrate faunal assemblages of the Favel Formation (late Cenomanian-middle Turonian) of Manitoba, Canada. PeerJ 11:e15493 https://doi.org/10.7717/peerj.15493
date submitted: 2023-01-03
date accepted: 2023-05-11
issued: 2023-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kilmury
  given name: Aaron A.
author list: Agent
  family name: Anderson
  given name: Aaron
author list: Agent
  family name: Wijesinghe
  given name: Dhuranka S.
author list: Agent
  family name: Verstraete
  given name: Ashley F.
author list: Agent
  family name: Ezeana
  given name: William
author list: Agent
  family name: Anderson
  given name: Ashley E.
author list: Agent
  family name: Brink
  given name: Kirstin S.
doi: 10.7717/peerj.15493
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-03
copyright: © 2023 Kilmury et al.
attribution name: Kilmury et al.

GGA1 participates in spermatogenesis in mice under stress
type: item
type: AcademicArticle
description: Background Infertility is recognized as a common and worrisome problem of human reproduction worldwide. Based on previous studies, male factors account for about half of all infertility cases. Exposure to environmental toxicants is an important contributor to male infertility. Bisphenol A (BPA) is the most prominent toxic environmental contaminant worldwide affecting the male reproductive system. BPA can impair the function of the Golgi apparatus which is important in spermatogenesis. GGA1 is known as Golgi-localized, gamma adaptin ear-containing, ARF-binding protein 1. Previously, it has been shown that GGA1 is associated with spermatogenesis in Drosophila, however, its function in mammalian spermatogenesis remains unclear. Methods Gga1 knockout mice were generated using the CRISPR/Cas9 system. Gga1-/- male mice and wild-type littermates received intraperitoneal (i.p.) injections of BPA (40 µg/kg) once daily for 2 weeks. Histological and immunofluorescence staining were performed to analyze the phenotypes of these mice. Results Male mice lacking Gga1 had normal fertility without any obvious defects in spermatogenesis, sperm count and sperm morphology. Gga1 ablation led to infertility in male mice exposed to BPA, along with a significant reduction in sperm count, sperm motility and the percentage of normal sperm. Histological analysis of the seminiferous epithelium showed that spermatogenesis was severely disorganized, while apoptotic germ cells were significantly increased in the Gga1 null mice exposed to BPA. Our findings suggest that Gga1 protects spermatogenesis against damage induced by environmental pollutants.
format: application/pdf
format: text/html
creator: Haoyun Jiao
creator: Yinghong Chen
creator: Tingting Han
creator: Qiyu Pan
creator: Fei Gao
creator: Guoping Li
subject: Biochemistry
subject: Developmental Biology
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.15673
publisher: PeerJ Inc.
rights: © 2023 Jiao et al.
abstract: Background Infertility is recognized as a common and worrisome problem of human reproduction worldwide. Based on previous studies, male factors account for about half of all infertility cases. Exposure to environmental toxicants is an important contributor to male infertility. Bisphenol A (BPA) is the most prominent toxic environmental contaminant worldwide affecting the male reproductive system. BPA can impair the function of the Golgi apparatus which is important in spermatogenesis. GGA1 is known as Golgi-localized, gamma adaptin ear-containing, ARF-binding protein 1. Previously, it has been shown that GGA1 is associated with spermatogenesis in Drosophila, however, its function in mammalian spermatogenesis remains unclear. Methods Gga1 knockout mice were generated using the CRISPR/Cas9 system. Gga1-/- male mice and wild-type littermates received intraperitoneal (i.p.) injections of BPA (40 µg/kg) once daily for 2 weeks. Histological and immunofluorescence staining were performed to analyze the phenotypes of these mice. Results Male mice lacking Gga1 had normal fertility without any obvious defects in spermatogenesis, sperm count and sperm morphology. Gga1 ablation led to infertility in male mice exposed to BPA, along with a significant reduction in sperm count, sperm motility and the percentage of normal sperm. Histological analysis of the seminiferous epithelium showed that spermatogenesis was severely disorganized, while apoptotic germ cells were significantly increased in the Gga1 null mice exposed to BPA. Our findings suggest that Gga1 protects spermatogenesis against damage induced by environmental pollutants.
bibliographic citation: Jiao et al. (2023) GGA1 participates in spermatogenesis in mice under stress. PeerJ 11:e15673 https://doi.org/10.7717/peerj.15673
date submitted: 2023-03-09
date accepted: 2023-06-11
issued: 2023-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiao
  given name: Haoyun
author list: Agent
  family name: Chen
  given name: Yinghong
author list: Agent
  family name: Han
  given name: Tingting
author list: Agent
  family name: Pan
  given name: Qiyu
author list: Agent
  family name: Gao
  given name: Fei
author list: Agent
  family name: Li
  given name: Guoping
doi: 10.7717/peerj.15673
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-03
copyright: ©2023 Jiao et al.
attribution name: Jiao et al.

Development, physicochemical characterization and in-vitro biocompatibility study of dromedary camel dentine derived hydroxyapatite for bone repair
type: item
type: AcademicArticle
description: This study aimed to produce hydroxyapatite from the dentine portion of camel teeth using a defatting and deproteinizing procedure and characterize its physicochemical and biocompatibility properties. Biowaste such as waste camel teeth is a valuable source of hydroxyapatite, the main inorganic constituent of human bone and teeth which is frequently used as bone grafts in the biomedical field. Fourier Transform infrared (FTIR), and micro-Raman spectroscopy confirmed the functional groups as-sociated with hydroxyapatite. X-ray diffraction (XRD) studies showed camel dentine-derived hydroxyapatite (CDHA) corresponded with hydroxyapatite spectra. Scanning electron micros-copy (SEM) demonstrated the presence of dentinal tubules measuring from 1.69–2.91 µm. The inorganic phases of CDHA were primarily constituted of calcium and phosphorus, with trace levels of sodium, magnesium, potassium, and strontium, according to energy dispersive X-ray analysis (EDX) and inductively coupled plasma mass spectrometry (ICP-MS). After 28 days of incubation in simulated body fluid (SBF), the pH of the CDHA scaffold elevated to 9.2. in-vitro biocompatibility studies showed that the CDHA enabled Saos-2 cells to proliferate and express the bone marker osteonectin after 14 days of culture. For applications such as bone augmentation and filling bone gaps, CDHA offers a promising material. However, to evaluate the clinical feasibility of the CDHA, further in-vivo studies are required.
format: application/pdf
format: text/html
creator: Zohaib Khurshid
creator: Mohammed Farhan A. Alfarhan
creator: Yasmin Bayan
creator: Javed Mazher
creator: Necdet Adanir
creator: George J. Dias
creator: Paul R. Cooper
creator: Jithendra Ratnayake
subject: Biochemistry
subject: Bioengineering
subject: Zoology
description: doi:10.7717/peerj.15711
publisher: PeerJ Inc.
rights: © 2023 Khurshid et al.
abstract: This study aimed to produce hydroxyapatite from the dentine portion of camel teeth using a defatting and deproteinizing procedure and characterize its physicochemical and biocompatibility properties. Biowaste such as waste camel teeth is a valuable source of hydroxyapatite, the main inorganic constituent of human bone and teeth which is frequently used as bone grafts in the biomedical field. Fourier Transform infrared (FTIR), and micro-Raman spectroscopy confirmed the functional groups as-sociated with hydroxyapatite. X-ray diffraction (XRD) studies showed camel dentine-derived hydroxyapatite (CDHA) corresponded with hydroxyapatite spectra. Scanning electron micros-copy (SEM) demonstrated the presence of dentinal tubules measuring from 1.69–2.91 µm. The inorganic phases of CDHA were primarily constituted of calcium and phosphorus, with trace levels of sodium, magnesium, potassium, and strontium, according to energy dispersive X-ray analysis (EDX) and inductively coupled plasma mass spectrometry (ICP-MS). After 28 days of incubation in simulated body fluid (SBF), the pH of the CDHA scaffold elevated to 9.2. in-vitro biocompatibility studies showed that the CDHA enabled Saos-2 cells to proliferate and express the bone marker osteonectin after 14 days of culture. For applications such as bone augmentation and filling bone gaps, CDHA offers a promising material. However, to evaluate the clinical feasibility of the CDHA, further in-vivo studies are required.
bibliographic citation: Khurshid et al. (2023) Development, physicochemical characterization and in-vitro biocompatibility study of dromedary camel dentine derived hydroxyapatite for bone repair. PeerJ 11:e15711 https://doi.org/10.7717/peerj.15711
date submitted: 2023-04-28
date accepted: 2023-06-15
issued: 2023-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khurshid
  given name: Zohaib
author list: Agent
  family name: Alfarhan
  given name: Mohammed Farhan A.
author list: Agent
  family name: Bayan
  given name: Yasmin
author list: Agent
  family name: Mazher
  given name: Javed
author list: Agent
  family name: Adanir
  given name: Necdet
author list: Agent
  family name: Dias
  given name: George J.
author list: Agent
  family name: Cooper
  given name: Paul R.
author list: Agent
  family name: Ratnayake
  given name: Jithendra
doi: 10.7717/peerj.15711
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-03
copyright: ©2023 Khurshid et al.
attribution name: Khurshid et al.

Earthworms neutralize the influence of components of particulate pollutants on soil extracellular enzymatic functions in subtropical forests
type: item
type: AcademicArticle
description: Human activities are increasing the input of atmospheric particulate pollutants to forests. The components of particulate pollutants include inorganic anions, base cations and hydrocarbons. Continuous input of particulate pollutants may affect soil functioning in forests, but their effects may be modified by soil fauna. However, studies investigating how soil fauna affects the effects of particulate pollutants on soil functioning are lacking. Here, we investigated how earthworms and the particulate components interact in affecting soil enzymatic functions in a deciduous (Quercus variabilis) and a coniferous (Pinus massoniana) forest in southeast China. We manipulated the addition of nitrogen (N, ammonium nitrate), sodium (Na, sodium chloride) and polycyclic aromatic hydrocarbons (PAHs, five mixed PAHs) in field mesocosms with and without Eisenia fetida, an earthworm species colonizing forests in eastern China. After one year, N and Na addition increased, whereas PAHs decreased soil enzymatic functions, based on average Z scores of extracellular enzyme activities. Earthworms generally stabilized soil enzymatic functions via neutralizing the effects of N, Na and PAHs addition in the deciduous but not in the coniferous forest. Specifically, earthworms neutralized the effects of N and Na addition on soil pH and the effects of the addition of PAHs on soil microbial biomass. Further, both particulate components and earthworms changed the correlations among soil enzymatic and other ecosystem functions in the deciduous forest, but the effects depended on the type of particulate components. Generally, the effects of particulate components and earthworms on soil enzymatic functions were weaker in the coniferous than the deciduous forest. Overall, the results indicate that earthworms stabilize soil enzymatic functions in the deciduous but not the coniferous forest irrespective of the type of particulate components. This suggests that earthworms may neutralize the influence of …
format: application/pdf
format: text/html
creator: Junbo Yang
creator: Jingzhong Lu
creator: Yinghui Yang
creator: Kai Tian
creator: Xiangshi Kong
creator: Xingjun Tian
creator: Stefan Scheu
subject: Ecology
subject: Soil Science
subject: Zoology
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.15720
publisher: PeerJ Inc.
rights: © 2023 Yang et al.
abstract: Human activities are increasing the input of atmospheric particulate pollutants to forests. The components of particulate pollutants include inorganic anions, base cations and hydrocarbons. Continuous input of particulate pollutants may affect soil functioning in forests, but their effects may be modified by soil fauna. However, studies investigating how soil fauna affects the effects of particulate pollutants on soil functioning are lacking. Here, we investigated how earthworms and the particulate components interact in affecting soil enzymatic functions in a deciduous (Quercus variabilis) and a coniferous (Pinus massoniana) forest in southeast China. We manipulated the addition of nitrogen (N, ammonium nitrate), sodium (Na, sodium chloride) and polycyclic aromatic hydrocarbons (PAHs, five mixed PAHs) in field mesocosms with and without Eisenia fetida, an earthworm species colonizing forests in eastern China. After one year, N and Na addition increased, whereas PAHs decreased soil enzymatic functions, based on average Z scores of extracellular enzyme activities. Earthworms generally stabilized soil enzymatic functions via neutralizing the effects of N, Na and PAHs addition in the deciduous but not in the coniferous forest. Specifically, earthworms neutralized the effects of N and Na addition on soil pH and the effects of the addition of PAHs on soil microbial biomass. Further, both particulate components and earthworms changed the correlations among soil enzymatic and other ecosystem functions in the deciduous forest, but the effects depended on the type of particulate components. Generally, the effects of particulate components and earthworms on soil enzymatic functions were weaker in the coniferous than the deciduous forest. Overall, the results indicate that earthworms stabilize soil enzymatic functions in the deciduous but not the coniferous forest irrespective of the type of particulate components. This suggests that earthworms may neutralize the influence of …
bibliographic citation: Yang et al. (2023) Earthworms neutralize the influence of components of particulate pollutants on soil extracellular enzymatic functions in subtropical forests. PeerJ 11:e15720 https://doi.org/10.7717/peerj.15720
date submitted: 2022-12-23
date accepted: 2023-06-16
issued: 2023-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Junbo
author list: Agent
  family name: Lu
  given name: Jingzhong
author list: Agent
  family name: Yang
  given name: Yinghui
author list: Agent
  family name: Tian
  given name: Kai
author list: Agent
  family name: Kong
  given name: Xiangshi
author list: Agent
  family name: Tian
  given name: Xingjun
author list: Agent
  family name: Scheu
  given name: Stefan
doi: 10.7717/peerj.15720
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-03
copyright: ©2023 Yang et al.
attribution name: Yang et al.

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