PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: An assessment of heavy metals in green sea turtle (Chelonia mydas) hatchlings from Saudi Arabia’s largest rookery, Ras Baridi
items: Synchrotron µ-XRF mapping analysis of trace elements in in-situ cultured Japanese red coral, Corallium japonicum
items: Fish habitat restoration on the basis of water morphology simulation
items: Estimating uncertainty in density surface models
items: The high diversity of gametogenic pathways in amphispermic water frog hybrids from Eastern Ukraine
items: Fine sand facilitates egg extrusion and improves reproductive output in female mud crab genus Scylla
items: Up-regulated IL-17 and Tnf signaling in bone marrow cells of young male osteogenesis imperfecta mice
items: Soil microbial community and physicochemical properties together drive soil organic carbon in Cunninghamia lanceolata plantations of different stand ages
items: C1orf74 positively regulates the EGFR/AKT/mTORC1 signaling in lung adenocarcinoma cells
items: A survey of researchers’ code sharing and code reuse practices, and assessment of interactive notebook prototypes

An assessment of heavy metals in green sea turtle (Chelonia mydas) hatchlings from Saudi Arabia’s largest rookery, Ras Baridi
type: item
type: AcademicArticle
description: Background Anthropogenic sources can lead to the accumulation of heavy metals in marine organisms through ingestion, absorption, or inhalation. For sea turtle embryos, heavy metals can be absorbed into the egg from the incubation environment or be maternally transferred to the offspring causing neurological, reproductive, and developmental problems. Here, we report heavy metal concentrations in green turtle hatchlings from the largest rookery on the Red Sea, Ras Baridi. Methods Deceased hatchlings were collected from two beaches near a cement factory at Ras Baridi, from which heavy metal concentrations (chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), selenium (Se), cadmium (Cd), and lead (Pb)) were measured from the liver, muscle, and residual yolk of the hatchlings. Results Although based on a small sample of hatchlings, the data presented here provides the first measurements of heavy metals from sea turtles in the Red Sea and highlights the link between human activity and its impact on the ecology of sea turtles. In general, the heavy metal concentrations of heavy metals were not significantly different between the beach next to the cement factory and the beach downwind from the factory. However, the concentrations of heavy metals were significantly different between sampled tissues (liver, muscle, and residual yolk). Discussion This study provides insight into current heavy metal levels in green turtle hatchlings, which can be used as bio-indicators for environmental contaminants as coastal development increases in the Red Sea. Moreover, we found a lack of standardized methodology to evaluate heavy metals in hatchling sea turtles. Future efforts should work toward creating comparable techniques for long-term heavy metal monitoring, as this is a useful determinant of anthropogenic pollution.
format: application/pdf
format: text/html
creator: Lyndsey K. Tanabe
creator: Kirsty Scott
creator: Vijayalaxmi Dasari
creator: Michael L. Berumen
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.13928
publisher: PeerJ Inc.
rights: © 2022 Tanabe et al.
abstract: Background Anthropogenic sources can lead to the accumulation of heavy metals in marine organisms through ingestion, absorption, or inhalation. For sea turtle embryos, heavy metals can be absorbed into the egg from the incubation environment or be maternally transferred to the offspring causing neurological, reproductive, and developmental problems. Here, we report heavy metal concentrations in green turtle hatchlings from the largest rookery on the Red Sea, Ras Baridi. Methods Deceased hatchlings were collected from two beaches near a cement factory at Ras Baridi, from which heavy metal concentrations (chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), selenium (Se), cadmium (Cd), and lead (Pb)) were measured from the liver, muscle, and residual yolk of the hatchlings. Results Although based on a small sample of hatchlings, the data presented here provides the first measurements of heavy metals from sea turtles in the Red Sea and highlights the link between human activity and its impact on the ecology of sea turtles. In general, the heavy metal concentrations of heavy metals were not significantly different between the beach next to the cement factory and the beach downwind from the factory. However, the concentrations of heavy metals were significantly different between sampled tissues (liver, muscle, and residual yolk). Discussion This study provides insight into current heavy metal levels in green turtle hatchlings, which can be used as bio-indicators for environmental contaminants as coastal development increases in the Red Sea. Moreover, we found a lack of standardized methodology to evaluate heavy metals in hatchling sea turtles. Future efforts should work toward creating comparable techniques for long-term heavy metal monitoring, as this is a useful determinant of anthropogenic pollution.
bibliographic citation: Tanabe et al. (2022) An assessment of heavy metals in green sea turtle (Chelonia mydas) hatchlings from Saudi Arabia’s largest rookery, Ras Baridi. PeerJ 10:e13928 https://doi.org/10.7717/peerj.13928
date submitted: 2022-05-02
date accepted: 2022-07-31
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tanabe
  given name: Lyndsey K.
author list: Agent
  family name: Scott
  given name: Kirsty
author list: Agent
  family name: Dasari
  given name: Vijayalaxmi
author list: Agent
  family name: Berumen
  given name: Michael L.
doi: 10.7717/peerj.13928
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Tanabe et al.
attribution name: Tanabe et al.

Synchrotron µ-XRF mapping analysis of trace elements in in-situ cultured Japanese red coral, Corallium japonicum
type: item
type: AcademicArticle
description: Precious corals belong to the family Coralliidae (Cnidaria, Octocorallia), and their axis, which consists of high magnesian calcium carbonate, has long been used in jewelry. With its low growth rate and long lifespan, precious coral is a representative taxon of the vulnerable marine ecosystem. Due to years of overfishing, coral fishery has become a controversial issue. To estimate the growth rate and clarify the uptake process of trace elements in relation to the growth of the carbonate axis, Japanese red coral (Corallium japonicum) was cultured at a depth of 135 m off Takeshima Island, Kagoshima, Japan for 98 months and analyzed by microscopic X-ray fluorescence/soft X-ray photoabsorption (µ-XRF/XAS) speciation mapping. The growth rate was estimated to be 0.37 mm/year in diameter, and 10–11 growth rings were observed in a cross section of the axis. This estimated growth-rate value is the first ever to be obtained from the in-situ culture of Japanese precious coral. The fluctuation in water temperature near the in-situ-culture site was recorded for part of the culture period and then compared with the changes in the growth ring and the distribution of trace elements in a cross section of the coral axis during the same period. When the water temperature was increasing, the growth ring was light in color, sulfur and phosphorus concentrations were low, and magnesium was high. Conversely, a dark band in the growth ring, high sulfur and phosphorus, and low magnesium concentrations were observed when the water temperature was decreasing. In a cross section of the coral axis, the distribution of sulfur and magnesium from the center to the surface corresponded, respectively, to dark and light bands in the annual growth ring. Sulfur concentration was high in the dark band and low in the light band, while magnesium was negatively correlated with sulfur.
format: application/pdf
format: text/html
creator: Nozomu Iwasaki
creator: Hiroshi Hasegawa
creator: Yusuke Tamenori
creator: Mutsuro Kikunaga
creator: Toshihiro Yoshimura
creator: Hikaru Sawai
subject: Marine Biology
subject: Zoology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.13931
publisher: PeerJ Inc.
rights: © 2022 Iwasaki et al.
abstract: Precious corals belong to the family Coralliidae (Cnidaria, Octocorallia), and their axis, which consists of high magnesian calcium carbonate, has long been used in jewelry. With its low growth rate and long lifespan, precious coral is a representative taxon of the vulnerable marine ecosystem. Due to years of overfishing, coral fishery has become a controversial issue. To estimate the growth rate and clarify the uptake process of trace elements in relation to the growth of the carbonate axis, Japanese red coral (Corallium japonicum) was cultured at a depth of 135 m off Takeshima Island, Kagoshima, Japan for 98 months and analyzed by microscopic X-ray fluorescence/soft X-ray photoabsorption (µ-XRF/XAS) speciation mapping. The growth rate was estimated to be 0.37 mm/year in diameter, and 10–11 growth rings were observed in a cross section of the axis. This estimated growth-rate value is the first ever to be obtained from the in-situ culture of Japanese precious coral. The fluctuation in water temperature near the in-situ-culture site was recorded for part of the culture period and then compared with the changes in the growth ring and the distribution of trace elements in a cross section of the coral axis during the same period. When the water temperature was increasing, the growth ring was light in color, sulfur and phosphorus concentrations were low, and magnesium was high. Conversely, a dark band in the growth ring, high sulfur and phosphorus, and low magnesium concentrations were observed when the water temperature was decreasing. In a cross section of the coral axis, the distribution of sulfur and magnesium from the center to the surface corresponded, respectively, to dark and light bands in the annual growth ring. Sulfur concentration was high in the dark band and low in the light band, while magnesium was negatively correlated with sulfur.
bibliographic citation: Iwasaki et al. (2022) Synchrotron µ-XRF mapping analysis of trace elements in in-situ cultured Japanese red coral, Corallium japonicum. PeerJ 10:e13931 https://doi.org/10.7717/peerj.13931
date submitted: 2022-03-10
date accepted: 2022-07-31
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Iwasaki
  given name: Nozomu
author list: Agent
  family name: Hasegawa
  given name: Hiroshi
author list: Agent
  family name: Tamenori
  given name: Yusuke
author list: Agent
  family name: Kikunaga
  given name: Mutsuro
author list: Agent
  family name: Yoshimura
  given name: Toshihiro
author list: Agent
  family name: Sawai
  given name: Hikaru
doi: 10.7717/peerj.13931
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Iwasaki et al.
attribution name: Iwasaki et al.

Fish habitat restoration on the basis of water morphology simulation
type: item
type: AcademicArticle
description: The hydrodynamic conditions of rivers affect fish habitats by influencing parameters such as river bottom topography. Ecological restoration projects change the water morphological characteristics of rivers. Here, water flow characteristics of the upper Yangtze River before and after the construction of a restoration project were analyzed using the computational fluid dynamics simulation method. The longitudinal diversion dam could divide the river into two flow velocity zones, and the outer flow is similar to the original river with a flow velocity of 0.75 m/s. However, flow velocity on the inner side of the river was about 0.25 m/s, forming a larger buffer area. The eddy became more diversified and stable, with a high eddy viscosity coefficient and less fluctuations, at 9 Pa·s; this was conducive to fish aggregation and spawning. At different depths, large gradient differences were observed between the inner and outer sides of the longitudinal diversion dam, and the turbulent current and upward flow of the inner side were obvious; this was more favorable to the aggregation of different fish species. The longitudinal dam body was under a pressure of about 200.2 Pa at the same flow rate; this was significantly lower than the pressure on the transverse dam body. The field flow test and fish survey data showed that the error rate of the simulation using the RNG turbulent model was less than 10% compared with actual mapping. After the restoration of fish habitats by the longitudinal diversion dam, the number of fish species in the area increased from 40 to 49; The density of fish in the water increased from 71.40 fish per 1,000 m2 before the project to 315.70 fish per 1,000 m2 after the project. These results can provide a reference for the rapid assessment of water morphology and fish habitat restoration in the future.
format: application/pdf
format: text/html
creator: Xiaolong Chen
creator: Xuan Che
creator: Xingguo Liu
creator: Lin Zhu
creator: Changfeng Tian
creator: Xinfeng Li
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Ecosystem Science
subject: Freshwater Biology
description: doi:10.7717/peerj.13943
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: The hydrodynamic conditions of rivers affect fish habitats by influencing parameters such as river bottom topography. Ecological restoration projects change the water morphological characteristics of rivers. Here, water flow characteristics of the upper Yangtze River before and after the construction of a restoration project were analyzed using the computational fluid dynamics simulation method. The longitudinal diversion dam could divide the river into two flow velocity zones, and the outer flow is similar to the original river with a flow velocity of 0.75 m/s. However, flow velocity on the inner side of the river was about 0.25 m/s, forming a larger buffer area. The eddy became more diversified and stable, with a high eddy viscosity coefficient and less fluctuations, at 9 Pa·s; this was conducive to fish aggregation and spawning. At different depths, large gradient differences were observed between the inner and outer sides of the longitudinal diversion dam, and the turbulent current and upward flow of the inner side were obvious; this was more favorable to the aggregation of different fish species. The longitudinal dam body was under a pressure of about 200.2 Pa at the same flow rate; this was significantly lower than the pressure on the transverse dam body. The field flow test and fish survey data showed that the error rate of the simulation using the RNG turbulent model was less than 10% compared with actual mapping. After the restoration of fish habitats by the longitudinal diversion dam, the number of fish species in the area increased from 40 to 49; The density of fish in the water increased from 71.40 fish per 1,000 m2 before the project to 315.70 fish per 1,000 m2 after the project. These results can provide a reference for the rapid assessment of water morphology and fish habitat restoration in the future.
bibliographic citation: Chen et al. (2022) Fish habitat restoration on the basis of water morphology simulation. PeerJ 10:e13943 https://doi.org/10.7717/peerj.13943
date submitted: 2022-03-28
date accepted: 2022-08-03
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xiaolong
author list: Agent
  family name: Che
  given name: Xuan
author list: Agent
  family name: Liu
  given name: Xingguo
author list: Agent
  family name: Zhu
  given name: Lin
author list: Agent
  family name: Tian
  given name: Changfeng
author list: Agent
  family name: Li
  given name: Xinfeng
doi: 10.7717/peerj.13943
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Chen et al.
attribution name: Chen et al.

Estimating uncertainty in density surface models
type: item
type: AcademicArticle
description: Providing uncertainty estimates for predictions derived from species distribution models is essential for management but there is little guidance on potential sources of uncertainty in predictions and how best to combine these. Here we show where uncertainty can arise in density surface models (a multi-stage spatial modelling approach for distance sampling data), focussing on cetacean density modelling. We propose an extensible, modular, hybrid analytical-simulation approach to encapsulate these sources. We provide example analyses of fin whales Balaenoptera physalus in the California Current Ecosystem.
format: application/pdf
format: text/html
creator: David L. Miller
creator: Elizabeth A. Becker
creator: Karin A. Forney
creator: Jason J. Roberts
creator: Ana Cañadas
creator: Robert S. Schick
subject: Conservation Biology
subject: Marine Biology
subject: Statistics
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13950
publisher: PeerJ Inc.
rights: © 2022 Miller et al.
abstract: Providing uncertainty estimates for predictions derived from species distribution models is essential for management but there is little guidance on potential sources of uncertainty in predictions and how best to combine these. Here we show where uncertainty can arise in density surface models (a multi-stage spatial modelling approach for distance sampling data), focussing on cetacean density modelling. We propose an extensible, modular, hybrid analytical-simulation approach to encapsulate these sources. We provide example analyses of fin whales Balaenoptera physalus in the California Current Ecosystem.
bibliographic citation: Miller et al. (2022) Estimating uncertainty in density surface models. PeerJ 10:e13950 https://doi.org/10.7717/peerj.13950
date submitted: 2022-06-30
date accepted: 2022-08-05
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Miller
  given name: David L.
author list: Agent
  family name: Becker
  given name: Elizabeth A.
author list: Agent
  family name: Forney
  given name: Karin A.
author list: Agent
  family name: Roberts
  given name: Jason J.
author list: Agent
  family name: Cañadas
  given name: Ana
author list: Agent
  family name: Schick
  given name: Robert S.
doi: 10.7717/peerj.13950
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
attribution name: Miller et al.

The high diversity of gametogenic pathways in amphispermic water frog hybrids from Eastern Ukraine
type: item
type: AcademicArticle
description: Interspecific hybridization can disrupt canonical gametogenic pathways, leading to the emergence of clonal and hemiclonal organisms. Such gametogenic alterations usually include genome endoreplication and/or premeiotic elimination of one of the parental genomes. The hybrid frog Pelophylax esculentus exploits genome endoreplication and genome elimination to produce haploid gametes with chromosomes of only one parental species. To reproduce, hybrids coexist with one of the parental species and form specific population systems. Here, we investigated the mechanism of spermatogenesis in diploid P. esculentus from sympatric populations of P. ridibundus using fluorescent in situ hybridization. We found that the genome composition and ploidy of germ cells, meiotic cells, and spermatids vary among P. esculentus individuals. The spermatogenic patterns observed in various hybrid males suggest the occurrence of at least six diverse germ cell populations, each with a specific premeiotic genome elimination and endoreplication pathway. Besides co-occurring aberrant cells detected during meiosis and gamete aneuploidy, alterations in genome duplication and endoreplication have led to either haploid or diploid sperm production. Diploid P. esculentus males from mixed populations of P. ridibundus rarely follow classical hybridogenesis. Instead, hybrid males simultaneously produce gametes with different genome compositions and ploidy levels. The persistence of the studied mixed populations highly relies on gametes containing a genome of the other parental species, P. lessonae.
format: application/pdf
format: text/html
creator: Eleonora Pustovalova
creator: Lukaš Choleva
creator: Dmytro Shabanov
creator: Dmitrij Dedukh
subject: Aquaculture, Fisheries and Fish Science
subject: Genetics
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.13957
publisher: PeerJ Inc.
rights: © 2022 Pustovalova et al.
abstract: Interspecific hybridization can disrupt canonical gametogenic pathways, leading to the emergence of clonal and hemiclonal organisms. Such gametogenic alterations usually include genome endoreplication and/or premeiotic elimination of one of the parental genomes. The hybrid frog Pelophylax esculentus exploits genome endoreplication and genome elimination to produce haploid gametes with chromosomes of only one parental species. To reproduce, hybrids coexist with one of the parental species and form specific population systems. Here, we investigated the mechanism of spermatogenesis in diploid P. esculentus from sympatric populations of P. ridibundus using fluorescent in situ hybridization. We found that the genome composition and ploidy of germ cells, meiotic cells, and spermatids vary among P. esculentus individuals. The spermatogenic patterns observed in various hybrid males suggest the occurrence of at least six diverse germ cell populations, each with a specific premeiotic genome elimination and endoreplication pathway. Besides co-occurring aberrant cells detected during meiosis and gamete aneuploidy, alterations in genome duplication and endoreplication have led to either haploid or diploid sperm production. Diploid P. esculentus males from mixed populations of P. ridibundus rarely follow classical hybridogenesis. Instead, hybrid males simultaneously produce gametes with different genome compositions and ploidy levels. The persistence of the studied mixed populations highly relies on gametes containing a genome of the other parental species, P. lessonae.
bibliographic citation: Pustovalova et al. (2022) The high diversity of gametogenic pathways in amphispermic water frog hybrids from Eastern Ukraine. PeerJ 10:e13957 https://doi.org/10.7717/peerj.13957
date submitted: 2022-06-23
date accepted: 2022-08-06
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pustovalova
  given name: Eleonora
author list: Agent
  family name: Choleva
  given name: Lukaš
author list: Agent
  family name: Shabanov
  given name: Dmytro
author list: Agent
  family name: Dedukh
  given name: Dmitrij
doi: 10.7717/peerj.13957
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: ©2022 Pustovalova et al.
attribution name: Pustovalova et al.

Fine sand facilitates egg extrusion and improves reproductive output in female mud crab genus Scylla
type: item
type: AcademicArticle
description: Mud crabs (genus Scylla) are gaining attention as potential aquaculture species due to their lucrative market price and high demand. One of the essential components of mud crab culture is broodstock quality. The optimisation of mud crab broodstock culture currently focused on its nutritional aspects and common rearing parameters, including stocking density and temperature. The use of sandy substrate to induce egg extrusion in female Scylla broodstock is common; however, its optimisation has never been conducted. This study investigated (1) the substrate association of two Scylla species (S. olivacea, S. paramamosain) during broodstock conditioning until egg extrusion when the choices of fine (66.99 ± 14.48 μm) and coarse (656.17 ± 38.13 μm) sands were given; (2) the female reproductive output when S. olivacea females were individually exposed to either fine sand, coarse sand, or no sand treatments. Females, spawners and non-spawners, of S. olivacea and S. paramamosain were associated with fine sand and none was observed to bury in the coarse sand tray. The occurrence of egg extrusion was not significantly different between species but moderately associated with the duration of visits (stayed in sand for 1 d, 2 d, ≥3 d). The final incubation period in the sand tray was more than 2 days in all cases, except for one female S. paramamosain (buried in the sand for 1 day prior to egg extrusion). When no choice was available, the highest percentage (58.3%) of females extruded eggs in fine sand treatment, followed by coarse sand treatment (33.3%), and no sand treatment (8.3%). Sand type influenced the weight of egg clutch, total egg number, fecundity, and clutch size. These results suggest that fine sand (<70 μm) substrate should be incorporated into Scylla broodstock rearing to maximise female reproductive output.
format: application/pdf
format: text/html
creator: Hanafiah Fazhan
creator: Khor Waiho
creator: Alexander Chong Shu-Chien
creator: Youji Wang
creator: Mhd Ikhwanuddin
creator: Muyassar H. Abualreesh
creator: Nor Azman Kasan
creator: Qingyang Wu
creator: Sabri Muda
creator: Chin Siang Sor
creator: Mohamad Jalilah
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.13961
publisher: PeerJ Inc.
rights: © 2022 Fazhan et al.
abstract: Mud crabs (genus Scylla) are gaining attention as potential aquaculture species due to their lucrative market price and high demand. One of the essential components of mud crab culture is broodstock quality. The optimisation of mud crab broodstock culture currently focused on its nutritional aspects and common rearing parameters, including stocking density and temperature. The use of sandy substrate to induce egg extrusion in female Scylla broodstock is common; however, its optimisation has never been conducted. This study investigated (1) the substrate association of two Scylla species (S. olivacea, S. paramamosain) during broodstock conditioning until egg extrusion when the choices of fine (66.99 ± 14.48 μm) and coarse (656.17 ± 38.13 μm) sands were given; (2) the female reproductive output when S. olivacea females were individually exposed to either fine sand, coarse sand, or no sand treatments. Females, spawners and non-spawners, of S. olivacea and S. paramamosain were associated with fine sand and none was observed to bury in the coarse sand tray. The occurrence of egg extrusion was not significantly different between species but moderately associated with the duration of visits (stayed in sand for 1 d, 2 d, ≥3 d). The final incubation period in the sand tray was more than 2 days in all cases, except for one female S. paramamosain (buried in the sand for 1 day prior to egg extrusion). When no choice was available, the highest percentage (58.3%) of females extruded eggs in fine sand treatment, followed by coarse sand treatment (33.3%), and no sand treatment (8.3%). Sand type influenced the weight of egg clutch, total egg number, fecundity, and clutch size. These results suggest that fine sand (<70 μm) substrate should be incorporated into Scylla broodstock rearing to maximise female reproductive output.
bibliographic citation: Fazhan et al. (2022) Fine sand facilitates egg extrusion and improves reproductive output in female mud crab genus Scylla. PeerJ 10:e13961 https://doi.org/10.7717/peerj.13961
date submitted: 2022-05-18
date accepted: 2022-08-07
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fazhan
  given name: Hanafiah
author list: Agent
  family name: Waiho
  given name: Khor
author list: Agent
  family name: Shu-Chien
  given name: Alexander Chong
author list: Agent
  family name: Wang
  given name: Youji
author list: Agent
  family name: Ikhwanuddin
  given name: Mhd
author list: Agent
  family name: Abualreesh
  given name: Muyassar H.
author list: Agent
  family name: Kasan
  given name: Nor Azman
author list: Agent
  family name: Wu
  given name: Qingyang
author list: Agent
  family name: Muda
  given name: Sabri
author list: Agent
  family name: Sor
  given name: Chin Siang
author list: Agent
  family name: Jalilah
  given name: Mohamad
doi: 10.7717/peerj.13961
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Fazhan et al.
attribution name: Fazhan et al.

Up-regulated IL-17 and Tnf signaling in bone marrow cells of young male osteogenesis imperfecta mice
type: item
type: AcademicArticle
description: Osteogenesis imperfecta (OI) is a congenital bone dysplasia mainly caused by either defective production or assembly of type I collagen. The skeletal phenotypes especially fractures are often seen in OI adolescents. Studies have found that an increased number of osteoclasts and excessive bone resorption existed in collagen-related OI, which has not been well understood. Emerging evidence has suggested that inflammation may be associated with OI. We speculated that the bone marrow (BM) niche had similar inflammatory changes and performed RNA-sequencing (RNA-seq) in BM cells derived from young male mice to analyze the related differentially expressed genes (DEGs) and pathways. Data showed that there were 117 shared DEGs (Q ≤ 0.05, |log2FC| ≥ 1) in BM cells isolated from two types of OI murine models that respectively simulate different OI types. Gene Ontology (GO) (Q ≤ 0.05) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) (Q ≤ 0.05) analysis and real-time PCR validation indicated the dysregulated biology process of cellular response to interferon (Ifn) together with upregulated IL-17 signaling, tumor necrosis factor (Tnf) signaling and osteoclast differentiation in OI BM niche. Either defective collagen production or abnormal collagen assembly shared similar alterations in gene profiles and pathways involving inflammation and osteoclast activation. Data presented here not only contributed to understanding of the mechanism of the enhanced bone absorption in the bones of OI, but also provided more evidence to develop potential anti-inflammation therapies.
format: application/pdf
format: text/html
creator: Chenyi Shao
creator: Yi Liu
creator: Jiaci Li
creator: Ziyun Liu
creator: Yuxia Zhao
creator: Yaqing Jing
creator: Zhe Lv
creator: Ting Fu
creator: Zihan Wang
creator: Guang Li
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13963
publisher: PeerJ Inc.
rights: © 2022 Shao et al.
abstract: Osteogenesis imperfecta (OI) is a congenital bone dysplasia mainly caused by either defective production or assembly of type I collagen. The skeletal phenotypes especially fractures are often seen in OI adolescents. Studies have found that an increased number of osteoclasts and excessive bone resorption existed in collagen-related OI, which has not been well understood. Emerging evidence has suggested that inflammation may be associated with OI. We speculated that the bone marrow (BM) niche had similar inflammatory changes and performed RNA-sequencing (RNA-seq) in BM cells derived from young male mice to analyze the related differentially expressed genes (DEGs) and pathways. Data showed that there were 117 shared DEGs (Q ≤ 0.05, |log2FC| ≥ 1) in BM cells isolated from two types of OI murine models that respectively simulate different OI types. Gene Ontology (GO) (Q ≤ 0.05) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) (Q ≤ 0.05) analysis and real-time PCR validation indicated the dysregulated biology process of cellular response to interferon (Ifn) together with upregulated IL-17 signaling, tumor necrosis factor (Tnf) signaling and osteoclast differentiation in OI BM niche. Either defective collagen production or abnormal collagen assembly shared similar alterations in gene profiles and pathways involving inflammation and osteoclast activation. Data presented here not only contributed to understanding of the mechanism of the enhanced bone absorption in the bones of OI, but also provided more evidence to develop potential anti-inflammation therapies.
bibliographic citation: Shao et al. (2022) Up-regulated IL-17 and Tnf signaling in bone marrow cells of young male osteogenesis imperfecta mice. PeerJ 10:e13963 https://doi.org/10.7717/peerj.13963
date submitted: 2022-05-24
date accepted: 2022-08-08
issued: 2022-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shao
  given name: Chenyi
author list: Agent
  family name: Liu
  given name: Yi
author list: Agent
  family name: Li
  given name: Jiaci
author list: Agent
  family name: Liu
  given name: Ziyun
author list: Agent
  family name: Zhao
  given name: Yuxia
author list: Agent
  family name: Jing
  given name: Yaqing
author list: Agent
  family name: Lv
  given name: Zhe
author list: Agent
  family name: Fu
  given name: Ting
author list: Agent
  family name: Wang
  given name: Zihan
author list: Agent
  family name: Li
  given name: Guang
doi: 10.7717/peerj.13963
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-23
copyright: © 2022 Shao et al.
attribution name: Shao et al.

Soil microbial community and physicochemical properties together drive soil organic carbon in Cunninghamia lanceolata plantations of different stand ages
type: item
type: AcademicArticle
description: Carbon sequestration in forest soil is critical for reducing atmospheric greenhouse gas concentrations and slowing down global warming. However, little is known about the difference in soil organic carbon (SOC) among different stand ages and the relative importance of biotic and abiotic variations such as soil microbial community and soil physicochemical properties in the regulation of SOC in forests. In the present study, we measured the SOC of the topsoil (0-10 cm) in Chinese subtropical Cunninghamia lanceolata plantations of three different stand ages (young plantation of 6 years, middle-aged plantation of 12 years, and mature plantation of 25 years). We further measured microbial community composition by phospholipid fatty acid (PLFA) analysis and soil organic carbon physical fractions by wet sieving and density floating as well as other physicochemical properties. The effects of the main impact factors on SOC were investigated. The results showed that: the middle-aged plantation had significantly higher SOC (10.63 g kg−1) than the young plantation (5.33 g kg−1), and that of the mature plantation (7.83 g kg−1) was in between. Besides, the soil total PLFAs and all the functional groups (i.e., bacteria, fungi, actinomycetes, Gram-positive bacteria, and Gram-negative bacteria) of PLFAs were significantly higher in the middle-aged plantation than in the young plantation and the mature plantation. Soil physicochemical properties, including physical fractions, differed among plantations of the three stand ages. Notably, the proportion of organic carbon protected within microaggregates was significantly higher in the middle-aged plantation (40.4%) than those in the young plantation (29.2%) and the mature plantation (27.8%), indicating that the middle-aged Cunninghamia lanceolata plantation had stronger soil organic carbon stability. Both soil microbial community and physicochemical properties exerted dominant effects on SOC and jointly explained 82.7% of the variance o…
format: application/pdf
format: text/html
creator: Ye Yuan
creator: Juan Li
creator: Liang Yao
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.13873
publisher: PeerJ Inc.
rights: © 2022 Yuan et al.
abstract: Carbon sequestration in forest soil is critical for reducing atmospheric greenhouse gas concentrations and slowing down global warming. However, little is known about the difference in soil organic carbon (SOC) among different stand ages and the relative importance of biotic and abiotic variations such as soil microbial community and soil physicochemical properties in the regulation of SOC in forests. In the present study, we measured the SOC of the topsoil (0-10 cm) in Chinese subtropical Cunninghamia lanceolata plantations of three different stand ages (young plantation of 6 years, middle-aged plantation of 12 years, and mature plantation of 25 years). We further measured microbial community composition by phospholipid fatty acid (PLFA) analysis and soil organic carbon physical fractions by wet sieving and density floating as well as other physicochemical properties. The effects of the main impact factors on SOC were investigated. The results showed that: the middle-aged plantation had significantly higher SOC (10.63 g kg−1) than the young plantation (5.33 g kg−1), and that of the mature plantation (7.83 g kg−1) was in between. Besides, the soil total PLFAs and all the functional groups (i.e., bacteria, fungi, actinomycetes, Gram-positive bacteria, and Gram-negative bacteria) of PLFAs were significantly higher in the middle-aged plantation than in the young plantation and the mature plantation. Soil physicochemical properties, including physical fractions, differed among plantations of the three stand ages. Notably, the proportion of organic carbon protected within microaggregates was significantly higher in the middle-aged plantation (40.4%) than those in the young plantation (29.2%) and the mature plantation (27.8%), indicating that the middle-aged Cunninghamia lanceolata plantation had stronger soil organic carbon stability. Both soil microbial community and physicochemical properties exerted dominant effects on SOC and jointly explained 82.7% of the variance o…
bibliographic citation: Yuan et al. (2022) Soil microbial community and physicochemical properties together drive soil organic carbon in Cunninghamia lanceolata plantations of different stand ages. PeerJ 10:e13873 https://doi.org/10.7717/peerj.13873
date submitted: 2022-06-13
date accepted: 2022-07-19
issued: 2022-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Ye
author list: Agent
  family name: Li
  given name: Juan
author list: Agent
  family name: Yao
  given name: Liang
doi: 10.7717/peerj.13873
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-22
copyright: ©2022 Yuan et al.
attribution name: Yuan et al.

C1orf74 positively regulates the EGFR/AKT/mTORC1 signaling in lung adenocarcinoma cells
type: item
type: AcademicArticle
description: Background Lung adenocarcinoma (LUAD) is a major type of lung cancer with poor prognosis and low 5-year survival rate, which urgently needs further investigation in order to elucidate its mechanisms completely and discover novel therapeutic targets. C1orf74 is a novel protein with unknown function either in normal cells or cancer cells. The aim of this study is to investigate the expression and function of C1orf74 in LUAD cells. Methods The expression of C1orf74 in LUAD was analyzed using the LUAD datasets from public databases. The prognostic value of C1orf74 in LUAD was analyzed using Kaplan-Meier Plotter. C1orf74 expression in LUAD cell line A549, H1993 and HCC827 was silenced using small interfering RNA, and then the effects of C1orf74 knockdown on proliferation, migration and invasion of LUAD cells were detected by colony formation assay and Transwell assay, the role of C1orf74 in EGFR/AKT/mTORC1 signaling pathway was examined by Western blot, and the function of C1orf74 in cell cycle was detected by flow cytometry. Results The results of LUAD clinical data showed that C1orf74 was upregulated in LUAD tissues, and its high expression was associated with poor prognosis. The results from cultured LUAD cells demonstrated that C1orf74 knockdown inhibited cell proliferation, migration and invasion, but induced cell cycle arrest and autophagy. Moreover, C1orf74 knockdown suppressed EGFR/AKT/mTORC1 signaling in LUAD cells. In conclusion, the present study revealed that C1orf74 is upregulated in LUAD tissues and plays an oncogenic role in LUAD, and that C1orf74 positively regulates cell proliferation and mobility through the EGFR/AKT/mTORC1 signaling pathway in LUAD cells.
format: application/pdf
format: text/html
creator: Jinyong Guo
creator: Aili Li
creator: Ruolin Guo
creator: Qiufeng He
creator: Youru Wu
creator: Yi Gou
creator: Junfei Jin
creator: Guojin Huang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13908
publisher: PeerJ Inc.
rights: © 2022 Guo et al.
abstract: Background Lung adenocarcinoma (LUAD) is a major type of lung cancer with poor prognosis and low 5-year survival rate, which urgently needs further investigation in order to elucidate its mechanisms completely and discover novel therapeutic targets. C1orf74 is a novel protein with unknown function either in normal cells or cancer cells. The aim of this study is to investigate the expression and function of C1orf74 in LUAD cells. Methods The expression of C1orf74 in LUAD was analyzed using the LUAD datasets from public databases. The prognostic value of C1orf74 in LUAD was analyzed using Kaplan-Meier Plotter. C1orf74 expression in LUAD cell line A549, H1993 and HCC827 was silenced using small interfering RNA, and then the effects of C1orf74 knockdown on proliferation, migration and invasion of LUAD cells were detected by colony formation assay and Transwell assay, the role of C1orf74 in EGFR/AKT/mTORC1 signaling pathway was examined by Western blot, and the function of C1orf74 in cell cycle was detected by flow cytometry. Results The results of LUAD clinical data showed that C1orf74 was upregulated in LUAD tissues, and its high expression was associated with poor prognosis. The results from cultured LUAD cells demonstrated that C1orf74 knockdown inhibited cell proliferation, migration and invasion, but induced cell cycle arrest and autophagy. Moreover, C1orf74 knockdown suppressed EGFR/AKT/mTORC1 signaling in LUAD cells. In conclusion, the present study revealed that C1orf74 is upregulated in LUAD tissues and plays an oncogenic role in LUAD, and that C1orf74 positively regulates cell proliferation and mobility through the EGFR/AKT/mTORC1 signaling pathway in LUAD cells.
bibliographic citation: Guo et al. (2022) C1orf74 positively regulates the EGFR/AKT/mTORC1 signaling in lung adenocarcinoma cells. PeerJ 10:e13908 https://doi.org/10.7717/peerj.13908
date submitted: 2022-04-20
date accepted: 2022-07-27
issued: 2022-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Jinyong
author list: Agent
  family name: Li
  given name: Aili
author list: Agent
  family name: Guo
  given name: Ruolin
author list: Agent
  family name: He
  given name: Qiufeng
author list: Agent
  family name: Wu
  given name: Youru
author list: Agent
  family name: Gou
  given name: Yi
author list: Agent
  family name: Jin
  given name: Junfei
author list: Agent
  family name: Huang
  given name: Guojin
doi: 10.7717/peerj.13908
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-22
copyright: © 2022 Guo et al.
attribution name: Guo et al.

A survey of researchers’ code sharing and code reuse practices, and assessment of interactive notebook prototypes
type: item
type: AcademicArticle
description: This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code sharing. We surveyed 188 researchers in computational biology. Respondents were asked about how often and why they look at code, which methods of accessing code they find useful and why, what aspects of code sharing are important to them, and how satisfied they are with their ability to complete these tasks. Respondents were asked to look at a prototype code notebook and give feedback on its features. Respondents were also asked how much time they spent preparing code and if they would be willing to increase this to use a code sharing tool, such as a notebook. As a reader of research articles the most common reason (70%) for looking at code was to gain a better understanding of the article. The most commonly encountered method for code sharing–linking articles to a code repository–was also the most useful method of accessing code from the reader’s perspective. As authors, the respondents were largely satisfied with their ability to carry out tasks related to code sharing. The most important of these tasks were ensuring that the code was running in the correct environment, and sharing code with good documentation. The average researcher, according to our results, is unwilling to incur additional costs (in time, effort or expenditure) that are currently needed to use code sharing tools alongside a publication. We infer this means we need different models for funding and producing interactive or executable research outputs if they are to reach a large number of researchers. For the purpose of increasing the amount of code shared by authors, PLOS Computational Biology is, as a result, focusing on policy rather than tools.
format: application/pdf
format: text/html
creator: Lauren Cadwallader
creator: Iain Hrynaszkiewicz
subject: Bioinformatics
subject: Computational Biology
subject: Science Policy
subject: Computational Science
description: doi:10.7717/peerj.13933
publisher: PeerJ Inc.
rights: © 2022 Cadwallader and Hrynaszkiewicz
abstract: This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code sharing. We surveyed 188 researchers in computational biology. Respondents were asked about how often and why they look at code, which methods of accessing code they find useful and why, what aspects of code sharing are important to them, and how satisfied they are with their ability to complete these tasks. Respondents were asked to look at a prototype code notebook and give feedback on its features. Respondents were also asked how much time they spent preparing code and if they would be willing to increase this to use a code sharing tool, such as a notebook. As a reader of research articles the most common reason (70%) for looking at code was to gain a better understanding of the article. The most commonly encountered method for code sharing–linking articles to a code repository–was also the most useful method of accessing code from the reader’s perspective. As authors, the respondents were largely satisfied with their ability to carry out tasks related to code sharing. The most important of these tasks were ensuring that the code was running in the correct environment, and sharing code with good documentation. The average researcher, according to our results, is unwilling to incur additional costs (in time, effort or expenditure) that are currently needed to use code sharing tools alongside a publication. We infer this means we need different models for funding and producing interactive or executable research outputs if they are to reach a large number of researchers. For the purpose of increasing the amount of code shared by authors, PLOS Computational Biology is, as a result, focusing on policy rather than tools.
bibliographic citation: Cadwallader et al. (2022) A survey of researchers’ code sharing and code reuse practices, and assessment of interactive notebook prototypes. PeerJ 10:e13933 https://doi.org/10.7717/peerj.13933
date submitted: 2022-06-07
date accepted: 2022-08-01
issued: 2022-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cadwallader
  given name: Lauren
author list: Agent
  family name: Hrynaszkiewicz
  given name: Iain
doi: 10.7717/peerj.13933
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-22
copyright: ©2022 Cadwallader and Hrynaszkiewicz
attribution name: Cadwallader and Hrynaszkiewicz

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