PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new genus and species of frog from the Kem Kem (Morocco), the second neobatrachian from Cretaceous Africa
items: Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea
items: Tumor budding of cervical squamous cell carcinoma: epithelial-mesenchymal transition-like cancer stem cells?
items: Compensatory growth and understory soil stoichiometric features of Hippophae rhamnoides at different stubble heights
items: Effects of commercial beverages on the neurobehavioral motility of Caenorhabditis elegans
items: The oldest record of Saurosphargiformes (Diapsida) from South China could fill an ecological gap in the Early Triassic biotic recovery
items: Novel lncRNAs with diagnostic or prognostic value screened out from breast cancer via bioinformatics analyses
items: Low-level nutrient enrichment during thermal stress delays bleaching and ameliorates calcification in three Hawaiian reef coral species
items: ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17
items: Association between IL-1A and IL-1B gene polymorphisms with peri-implantitis in a Portuguese population—a pilot study

A new genus and species of frog from the Kem Kem (Morocco), the second neobatrachian from Cretaceous Africa
type: item
type: AcademicArticle
description: Neobatrachia, a clade representing the majority of extant anuran diversity, is thought to have emerged and diversified during the Cretaceous. Most of the early diversification of neobatrachians occurred in southern Gondwana, especially the regions that are today South America and Africa. Whereas five extinct neobatrachians have been described from the Cretaceous of South America in the last decade, only one is known from Africa. This difference in the known extinct diversity is linked to the lack of well-preserved specimens, understudy of fragmentary remains, and lack of known Cretaceous sites in Africa. Study of fragmentary anuran remains from Africa could allow for the identification of previously unknown neobatrachians, allowing for a better understanding of their early diversification. We reanalysed several previously described anuran specimens from the well-known Kem Kem beds, including using CT-scanning. Through our osteological study, we determined that several cranial bones and vertebrae represent a new hyperossified taxon for which we provide a formal description. Comparison to other hyperossified anurans revealed similarities and affinity of this new taxon with the neobatrachians Beelzebufo (extinct) and Ceratophrys (extant). Phylogenetic analyses supported this affinity, placing the new taxon within Neobatrachia in an unresolved clade of Ceratophryidae. This taxon is the oldest neobatrachian from Africa, and reveals that neobatrachians were already widespread throughout southern Gondwana during the earliest Late Cretaceous.
format: application/pdf
format: text/html
creator: Alfred Lemierre
creator: David C. Blackburn
subject: Biodiversity
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13699
publisher: PeerJ Inc.
rights: © 2022 Lemierre Lemierre and Blackburn
abstract: Neobatrachia, a clade representing the majority of extant anuran diversity, is thought to have emerged and diversified during the Cretaceous. Most of the early diversification of neobatrachians occurred in southern Gondwana, especially the regions that are today South America and Africa. Whereas five extinct neobatrachians have been described from the Cretaceous of South America in the last decade, only one is known from Africa. This difference in the known extinct diversity is linked to the lack of well-preserved specimens, understudy of fragmentary remains, and lack of known Cretaceous sites in Africa. Study of fragmentary anuran remains from Africa could allow for the identification of previously unknown neobatrachians, allowing for a better understanding of their early diversification. We reanalysed several previously described anuran specimens from the well-known Kem Kem beds, including using CT-scanning. Through our osteological study, we determined that several cranial bones and vertebrae represent a new hyperossified taxon for which we provide a formal description. Comparison to other hyperossified anurans revealed similarities and affinity of this new taxon with the neobatrachians Beelzebufo (extinct) and Ceratophrys (extant). Phylogenetic analyses supported this affinity, placing the new taxon within Neobatrachia in an unresolved clade of Ceratophryidae. This taxon is the oldest neobatrachian from Africa, and reveals that neobatrachians were already widespread throughout southern Gondwana during the earliest Late Cretaceous.
bibliographic citation: Lemierre et al. (2022) A new genus and species of frog from the Kem Kem (Morocco), the second neobatrachian from Cretaceous Africa. PeerJ 10:e13699 https://doi.org/10.7717/peerj.13699
date submitted: 2022-03-04
date accepted: 2022-06-17
issued: 2022-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lemierre
  given name: Alfred
author list: Agent
  family name: Blackburn
  given name: David C.
doi: 10.7717/peerj.13699
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-15
copyright: ©2022 Lemierre and Blackburn
attribution name: Lemierre Lemierre and Blackburn

Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea
type: item
type: AcademicArticle
description: The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91–1.00), and nucleotide diversity (π) was low (0.002–0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and FST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant FSTpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters.
format: application/pdf
format: text/html
creator: Noorul Azliana Jamaludin
creator: Jamsari Amirul Firdaus Jamaluddin
creator: Masazurah A. Rahim
creator: Noor Adelyna Mohammed Akib
creator: Sahat Ratmuangkhwang
creator: Wahidah Mohd Arshaad
creator: Siti Azizah Mohd Nor
subject: Genetics
subject: Marine Biology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.13706
publisher: PeerJ Inc.
rights: © 2022 Jamaludin et al.
abstract: The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91–1.00), and nucleotide diversity (π) was low (0.002–0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and FST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant FSTpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters.
bibliographic citation: Jamaludin et al. (2022) Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea. PeerJ 10:e13706 https://doi.org/10.7717/peerj.13706
date submitted: 2021-11-23
date accepted: 2022-06-19
issued: 2022-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jamaludin
  given name: Noorul Azliana
author list: Agent
  family name: Jamaluddin
  given name: Jamsari Amirul Firdaus
author list: Agent
  family name: Rahim
  given name: Masazurah A.
author list: Agent
  family name: Mohammed Akib
  given name: Noor Adelyna
author list: Agent
  family name: Ratmuangkhwang
  given name: Sahat
author list: Agent
  family name: Mohd Arshaad
  given name: Wahidah
author list: Agent
  family name: Mohd Nor
  given name: Siti Azizah
doi: 10.7717/peerj.13706
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-15
copyright: ©2022 Jamaludin et al.
attribution name: Jamaludin et al.

Tumor budding of cervical squamous cell carcinoma: epithelial-mesenchymal transition-like cancer stem cells?
type: item
type: AcademicArticle
description: Recent evidence indicates that cancer stem cells (CSCs) are the origin of cancers. Scientists have identified CSCs in various tumors and have suggested the existence of a variety of states of CSCs. The existence of epithelial–mesenchymal transition (EMT)-like CSCs has been confirmed in vitro, but they have not been identified in vivo. Tumor budding was defined as single cell or clusters of ≤ 5 cells at the invasive front of cancers. Such tumor budding is hypothesized to be closely related to EMT and linked to CSCs, especially to those migrating at the invasive front. Therefore, tumor budding has been proposed to represent EMT-like stem cells. However, this hypothesis has not yet been proven. Thus, we studied the expression of EMT markers, certain CSC markers of tumor budding, and the tumor center of cervical squamous cell carcinoma (CxSCC). We performed tissue chip analyses of 95 primary CxSCCs from patients. Expression of EMT and CSC markers (E-cadherin, β-catenin, vimentin, Ki67, CD44, SOX2 , and ALDH1A1) in a set of tumor samples on tissue chips (87 cases of tumor budding/the main tumor body) were evaluated by immunohistochemistry. We found that the cell-membranous expression of β-catenin was stronger in the main tumor body than in tumor buds. Compared with the main tumor body, tumor buds had reduced proliferative activity as measured by Ki67. Moreover, vimentin expression was high and E-cadherin expression was low in tumor buds. Expression of EMT-related markers suggested that tumor buds were correlated with EMT. We noted that CxSCC tumor buds had a CD44negative/low/SOX2high/ALDH1A1high staining pattern, indicating that tumor buds of CxSCC present CSC-like immunophenotypic features. Taken together, our data indicate that tumor buds in CxSCC may represent EMT-like CSCs in vivo.
format: application/pdf
format: text/html
creator: Shaoqiu Zheng
creator: Jing Luo
creator: Shoucheng Xie
creator: Shanming Lu
creator: Qinghua Liu
creator: Huanqin Xiao
creator: Wenjuan Luo
creator: Yanfang Huang
creator: Kun Liu
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.13745
publisher: PeerJ Inc.
rights: © 2022 Zheng et al.
abstract: Recent evidence indicates that cancer stem cells (CSCs) are the origin of cancers. Scientists have identified CSCs in various tumors and have suggested the existence of a variety of states of CSCs. The existence of epithelial–mesenchymal transition (EMT)-like CSCs has been confirmed in vitro, but they have not been identified in vivo. Tumor budding was defined as single cell or clusters of ≤ 5 cells at the invasive front of cancers. Such tumor budding is hypothesized to be closely related to EMT and linked to CSCs, especially to those migrating at the invasive front. Therefore, tumor budding has been proposed to represent EMT-like stem cells. However, this hypothesis has not yet been proven. Thus, we studied the expression of EMT markers, certain CSC markers of tumor budding, and the tumor center of cervical squamous cell carcinoma (CxSCC). We performed tissue chip analyses of 95 primary CxSCCs from patients. Expression of EMT and CSC markers (E-cadherin, β-catenin, vimentin, Ki67, CD44, SOX2 , and ALDH1A1) in a set of tumor samples on tissue chips (87 cases of tumor budding/the main tumor body) were evaluated by immunohistochemistry. We found that the cell-membranous expression of β-catenin was stronger in the main tumor body than in tumor buds. Compared with the main tumor body, tumor buds had reduced proliferative activity as measured by Ki67. Moreover, vimentin expression was high and E-cadherin expression was low in tumor buds. Expression of EMT-related markers suggested that tumor buds were correlated with EMT. We noted that CxSCC tumor buds had a CD44negative/low/SOX2high/ALDH1A1high staining pattern, indicating that tumor buds of CxSCC present CSC-like immunophenotypic features. Taken together, our data indicate that tumor buds in CxSCC may represent EMT-like CSCs in vivo.
bibliographic citation: Zheng et al. (2022) Tumor budding of cervical squamous cell carcinoma: epithelial-mesenchymal transition-like cancer stem cells?. PeerJ 10:e13745 https://doi.org/10.7717/peerj.13745
date submitted: 2022-04-07
date accepted: 2022-06-27
issued: 2022-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Shaoqiu
author list: Agent
  family name: Luo
  given name: Jing
author list: Agent
  family name: Xie
  given name: Shoucheng
author list: Agent
  family name: Lu
  given name: Shanming
author list: Agent
  family name: Liu
  given name: Qinghua
author list: Agent
  family name: Xiao
  given name: Huanqin
author list: Agent
  family name: Luo
  given name: Wenjuan
author list: Agent
  family name: Huang
  given name: Yanfang
author list: Agent
  family name: Liu
  given name: Kun
doi: 10.7717/peerj.13745
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-15
copyright: ©2022 Zheng et al.
attribution name: Zheng et al.

Compensatory growth and understory soil stoichiometric features of Hippophae rhamnoides at different stubble heights
type: item
type: AcademicArticle
description: Background This study was aimed to explore the compensatory growth ability and influence mechanism of Hippophae rhamnoides at the decaying phase in feldspathic sandstone areas of Ordos, and clarify the stubble height when the compensatory growth ability of H. rhamnoides was the strongest. Methods The H. rhamnoides forests in the decaying phase from an exposed feldspathic sandstone zone of Ordos were chosen. The compensatory growth ability of H. rhamnoides at stubble height of 0 cm (S1), 10 cm (S2), 15 cm (S3), 20 cm (S4) and control (CK) was investigated with H. rhamnoides forests at the decaying stage in the exposed feldspathic sandstone areas of Ordos. Relationships of compensatory growth ability of H. rhamnoides and understory soil properties with understory soil stoichiometric features as well as the response mechanism to stubble height were explored. Results (1) Overcompensatory growth of H. rhamnoides in feldspathic sandstone areas occurred at all stubble heights. Especially, the plant height compensation index (1.45) and biomass compensation index (1.25) at the stubble height of 15 cm were both larger compared with other stubbling treatments. These results indicate the stubble height of 15 cm can well promote the growth of the ground part of H. rhamnoides. (2) All stubble heights significantly affected the contents and eco-stoichiometric ratios of soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP) in understory soils, but the influence rules differed. SOC, TN, and TP contents at all stubble heights were larger than those of the control, and maximized at the stubble height of 15 cm. The carbon(C): phosphorus(P) ratio, and nitrogen (N):(P) ratio after stubbling treatments were all lower compared with the control, and minimized to 19.52 and 1.84 respectively at the stubble height of 15 cm. (3) The understory C:N:P stoichiometric ratio of H. rhamnoides in feldspathic sandstone areas is jointly affected by compensatory growth, stubble height, an…
format: application/pdf
format: text/html
creator: Xin Wang
creator: Yuefeng Guo
creator: Wei Qi
creator: Li Zhen
creator: Yunfeng Yao
creator: Fucang Qin
subject: Agricultural Science
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.13363
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background This study was aimed to explore the compensatory growth ability and influence mechanism of Hippophae rhamnoides at the decaying phase in feldspathic sandstone areas of Ordos, and clarify the stubble height when the compensatory growth ability of H. rhamnoides was the strongest. Methods The H. rhamnoides forests in the decaying phase from an exposed feldspathic sandstone zone of Ordos were chosen. The compensatory growth ability of H. rhamnoides at stubble height of 0 cm (S1), 10 cm (S2), 15 cm (S3), 20 cm (S4) and control (CK) was investigated with H. rhamnoides forests at the decaying stage in the exposed feldspathic sandstone areas of Ordos. Relationships of compensatory growth ability of H. rhamnoides and understory soil properties with understory soil stoichiometric features as well as the response mechanism to stubble height were explored. Results (1) Overcompensatory growth of H. rhamnoides in feldspathic sandstone areas occurred at all stubble heights. Especially, the plant height compensation index (1.45) and biomass compensation index (1.25) at the stubble height of 15 cm were both larger compared with other stubbling treatments. These results indicate the stubble height of 15 cm can well promote the growth of the ground part of H. rhamnoides. (2) All stubble heights significantly affected the contents and eco-stoichiometric ratios of soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP) in understory soils, but the influence rules differed. SOC, TN, and TP contents at all stubble heights were larger than those of the control, and maximized at the stubble height of 15 cm. The carbon(C): phosphorus(P) ratio, and nitrogen (N):(P) ratio after stubbling treatments were all lower compared with the control, and minimized to 19.52 and 1.84 respectively at the stubble height of 15 cm. (3) The understory C:N:P stoichiometric ratio of H. rhamnoides in feldspathic sandstone areas is jointly affected by compensatory growth, stubble height, an…
bibliographic citation: Wang et al. (2022) Compensatory growth and understory soil stoichiometric features of Hippophae rhamnoides at different stubble heights. PeerJ 10:e13363 https://doi.org/10.7717/peerj.13363
date submitted: 2021-11-23
date accepted: 2022-04-09
issued: 2022-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xin
author list: Agent
  family name: Guo
  given name: Yuefeng
author list: Agent
  family name: Qi
  given name: Wei
author list: Agent
  family name: Zhen
  given name: Li
author list: Agent
  family name: Yao
  given name: Yunfeng
author list: Agent
  family name: Qin
  given name: Fucang
doi: 10.7717/peerj.13363
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-14
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Effects of commercial beverages on the neurobehavioral motility of Caenorhabditis elegans
type: item
type: AcademicArticle
description: To study the effects of different types of commercially available drinks/beverages on neurobehavior using the model organism C. elegans, and critically review their potential health hazards. Eighteen kinds of beverages from the supermarket were randomly selected and grouped into seven categories namely functional beverage, tea beverage, plant protein beverage, fruit juice beverage, dairy beverage, carbonated beverage and coffee beverage. The pH value, specific gravity and osmotic pressure were also examined. The L4 stage N2 worms were exposed to different concentration of tested beverages (0, 62.5, 125, 250 and 500 µL/mL) for 24 h to measure the survival rate and locomotory behavior such as head thrashing, body bending as well as pharyngeal pumping. All the 18 beverages tested did not induce any visible lethal effects in the nematodes. However, exposure to different types of tested beverages exhibited different effects on the behavioral ability of C. elegans: (1) sports functional beverage and herbal tea drink accelerated the head thrashing and body bending of nematodes when compared to the control group (P < 0.05). (2) The vibration frequency of the pharyngeal pump of nematodes was significantly accelerated after treated with three plant protein beverages (almond milk, coconut milk and milk tea) and dairy products A and B (P < 0.05), and decelerated after treatment with other tested beverages. (3) Carbonated beverage significantly inhibits the head thrashing, body bending and pharyngeal pumping vibration (P < 0.05). Our results indicate that 18 kinds of popular beverages in the market have different influence on the neurobehavior in C. elegans, which may be related to their different components or properties. Further research would be required to conduct a systematic analysis of the effect of beverages by appropriate kinds, taking into consideration other endpoints such as reproduction, lifespan and molecular stress response, etc., and to elucidate the mechanism fo…
format: application/pdf
format: text/html
creator: Wenjing Zhang
creator: Nan Zhang
creator: Shan Zheng
creator: Wei Zhang
creator: Jingjing Liu
creator: Liwei He
creator: Anastasia Ngozi Ezemaduka
creator: Guojun Li
creator: Junyu Ning
creator: Bo Xian
creator: Shan Gao
subject: Animal Behavior
subject: Biochemistry
subject: Neuroscience
subject: Toxicology
description: doi:10.7717/peerj.13563
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: To study the effects of different types of commercially available drinks/beverages on neurobehavior using the model organism C. elegans, and critically review their potential health hazards. Eighteen kinds of beverages from the supermarket were randomly selected and grouped into seven categories namely functional beverage, tea beverage, plant protein beverage, fruit juice beverage, dairy beverage, carbonated beverage and coffee beverage. The pH value, specific gravity and osmotic pressure were also examined. The L4 stage N2 worms were exposed to different concentration of tested beverages (0, 62.5, 125, 250 and 500 µL/mL) for 24 h to measure the survival rate and locomotory behavior such as head thrashing, body bending as well as pharyngeal pumping. All the 18 beverages tested did not induce any visible lethal effects in the nematodes. However, exposure to different types of tested beverages exhibited different effects on the behavioral ability of C. elegans: (1) sports functional beverage and herbal tea drink accelerated the head thrashing and body bending of nematodes when compared to the control group (P < 0.05). (2) The vibration frequency of the pharyngeal pump of nematodes was significantly accelerated after treated with three plant protein beverages (almond milk, coconut milk and milk tea) and dairy products A and B (P < 0.05), and decelerated after treatment with other tested beverages. (3) Carbonated beverage significantly inhibits the head thrashing, body bending and pharyngeal pumping vibration (P < 0.05). Our results indicate that 18 kinds of popular beverages in the market have different influence on the neurobehavior in C. elegans, which may be related to their different components or properties. Further research would be required to conduct a systematic analysis of the effect of beverages by appropriate kinds, taking into consideration other endpoints such as reproduction, lifespan and molecular stress response, etc., and to elucidate the mechanism fo…
bibliographic citation: Zhang et al. (2022) Effects of commercial beverages on the neurobehavioral motility of Caenorhabditis elegans. PeerJ 10:e13563 https://doi.org/10.7717/peerj.13563
date submitted: 2022-02-14
date accepted: 2022-05-19
issued: 2022-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Wenjing
author list: Agent
  family name: Zhang
  given name: Nan
author list: Agent
  family name: Zheng
  given name: Shan
author list: Agent
  family name: Zhang
  given name: Wei
author list: Agent
  family name: Liu
  given name: Jingjing
author list: Agent
  family name: He
  given name: Liwei
author list: Agent
  family name: Ezemaduka
  given name: Anastasia Ngozi
author list: Agent
  family name: Li
  given name: Guojun
author list: Agent
  family name: Ning
  given name: Junyu
author list: Agent
  family name: Xian
  given name: Bo
author list: Agent
  family name: Gao
  given name: Shan
doi: 10.7717/peerj.13563
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-14
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

The oldest record of Saurosphargiformes (Diapsida) from South China could fill an ecological gap in the Early Triassic biotic recovery
type: item
type: AcademicArticle
description: Diversification following the end-Permian mass extinction marks the initiation of Mesozoic reptile dominance and of modern marine ecosystems, yet major clades are best known from the Middle Triassic suggesting delayed recovery, while Early Triassic localities produce poorly preserved specimens or have restricted diversity. Here we describe Pomolispondylus biani gen. et sp. nov. from the Early Triassic Nanzhang-Yuan’an Fauna of China assigned to Saurosphargiformes tax. nov., a clade known only from the Middle Triassic or later, which includes Saurosphargidae, and likely is the sister taxon to Sauropterygia. Pomolispondylus biani is allied to Saurosphargidae by the extended transverse processes of dorsal vertebrae and a low, table-like dorsal surface on the neural spine; however, it does not have the typical extensive osteoderms. Rather an unusual tuberous texture on the dorsal neural spine and rudimentary ossifications lateral to the gastralia are observed. Discovery of Pomolispondylus biani extends the known range of Saurosphargiformes and increases the taxic and ecological diversity of the Nanzhang-Yuan’an Fauna. Its small size fills a different ecological niche with respect to previously found species, but the overall food web remains notably different in structure to Middle Triassic and later ecosystems, suggesting this fauna represents a transitional stage during recovery rather than its endpoint.
format: application/pdf
format: text/html
creator: Long Cheng
creator: Benjamin C. Moon
creator: Chunbo Yan
creator: Ryosuke Motani
creator: Dayong Jiang
creator: Zhihui An
creator: Zichen Fang
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.13569
publisher: PeerJ Inc.
rights: © 2022 Cheng et al.
abstract: Diversification following the end-Permian mass extinction marks the initiation of Mesozoic reptile dominance and of modern marine ecosystems, yet major clades are best known from the Middle Triassic suggesting delayed recovery, while Early Triassic localities produce poorly preserved specimens or have restricted diversity. Here we describe Pomolispondylus biani gen. et sp. nov. from the Early Triassic Nanzhang-Yuan’an Fauna of China assigned to Saurosphargiformes tax. nov., a clade known only from the Middle Triassic or later, which includes Saurosphargidae, and likely is the sister taxon to Sauropterygia. Pomolispondylus biani is allied to Saurosphargidae by the extended transverse processes of dorsal vertebrae and a low, table-like dorsal surface on the neural spine; however, it does not have the typical extensive osteoderms. Rather an unusual tuberous texture on the dorsal neural spine and rudimentary ossifications lateral to the gastralia are observed. Discovery of Pomolispondylus biani extends the known range of Saurosphargiformes and increases the taxic and ecological diversity of the Nanzhang-Yuan’an Fauna. Its small size fills a different ecological niche with respect to previously found species, but the overall food web remains notably different in structure to Middle Triassic and later ecosystems, suggesting this fauna represents a transitional stage during recovery rather than its endpoint.
bibliographic citation: Cheng et al. (2022) The oldest record of Saurosphargiformes (Diapsida) from South China could fill an ecological gap in the Early Triassic biotic recovery. PeerJ 10:e13569 https://doi.org/10.7717/peerj.13569
date submitted: 2021-11-05
date accepted: 2022-05-20
issued: 2022-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Long
author list: Agent
  family name: C. Moon
  given name: Benjamin
author list: Agent
  family name: Yan
  given name: Chunbo
author list: Agent
  family name: Motani
  given name: Ryosuke
author list: Agent
  family name: Jiang
  given name: Dayong
author list: Agent
  family name: An
  given name: Zhihui
author list: Agent
  family name: Fang
  given name: Zichen
doi: 10.7717/peerj.13569
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-14
copyright: © 2022 Cheng et al.
attribution name: Cheng et al.

Novel lncRNAs with diagnostic or prognostic value screened out from breast cancer via bioinformatics analyses
type: item
type: AcademicArticle
description: Background Recent studies have shown that long non-coding RNAs (lncRNAs) may play key regulatory roles in many malignant tumors. This study investigated the use of novel lncRNA biomarkers in the diagnosis and prognosis of breast cancer. Materials and Methods The database subsets of The Cancer Genome Atlas (TCGA) by RNA-seq for comparing analysis of tissue samples between breast cancer and normal control groups were downloaded. Additionally, anticoagulant peripheral blood samples were collected and used in this cohort study. The extracellular vesicles (EVs) from the plasma were extracted and sequenced, then analyzed to determine the expressive profiles of the lncRNAs, and the cancer-related differentially expressed lncRNAs were screened out. The expressive profiles and associated downstream-mRNAs were assessed using bioinformatics (such as weighted correlation network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichments, Receiver-Operating Characteristic (ROC) curve and survival analysis, etc.) to investigate the diagnostic and prognostic values of these EV lncRNAs and their effectors. Results In this study, 41 breast cancer-related lncRNAs were screen out from two datasets of tissue and fresh collected plasma samples of breast cancer via the transcriptomic and bioinformatics techniques. A total of 19 gene modules were identified with WGCNA analysis, of which five modules were significantly correlated with the clinical stage of breast cancer, including 28 lncRNA candidates. The ROC curves of these lncRNAs revealed that the area under the curve (AUC) of all candidates were great than 70%. However, eight lncRNAs had an AUC >70%, indicating that the combined one has a good diagnostic value. In addition, the results of survival analysis suggested that two lncRNAs with low expressive levels may indicate the poor prognosis of breast cancer. By tissue sample verification, C15orf54, AL157935.1, LINC01117, and SNHG3 were determine…
format: application/pdf
format: text/html
creator: Hongxian Wang
creator: Lirong Shu
creator: Nan Niu
creator: Chenyang Zhao
creator: Shuqi Lu
creator: Yanhua Li
creator: Huanyu Wang
creator: Yao Liu
creator: Tianhui Zou
creator: Jiawei Zou
creator: Xiaoqin Wu
creator: Yun Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.13641
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Recent studies have shown that long non-coding RNAs (lncRNAs) may play key regulatory roles in many malignant tumors. This study investigated the use of novel lncRNA biomarkers in the diagnosis and prognosis of breast cancer. Materials and Methods The database subsets of The Cancer Genome Atlas (TCGA) by RNA-seq for comparing analysis of tissue samples between breast cancer and normal control groups were downloaded. Additionally, anticoagulant peripheral blood samples were collected and used in this cohort study. The extracellular vesicles (EVs) from the plasma were extracted and sequenced, then analyzed to determine the expressive profiles of the lncRNAs, and the cancer-related differentially expressed lncRNAs were screened out. The expressive profiles and associated downstream-mRNAs were assessed using bioinformatics (such as weighted correlation network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichments, Receiver-Operating Characteristic (ROC) curve and survival analysis, etc.) to investigate the diagnostic and prognostic values of these EV lncRNAs and their effectors. Results In this study, 41 breast cancer-related lncRNAs were screen out from two datasets of tissue and fresh collected plasma samples of breast cancer via the transcriptomic and bioinformatics techniques. A total of 19 gene modules were identified with WGCNA analysis, of which five modules were significantly correlated with the clinical stage of breast cancer, including 28 lncRNA candidates. The ROC curves of these lncRNAs revealed that the area under the curve (AUC) of all candidates were great than 70%. However, eight lncRNAs had an AUC >70%, indicating that the combined one has a good diagnostic value. In addition, the results of survival analysis suggested that two lncRNAs with low expressive levels may indicate the poor prognosis of breast cancer. By tissue sample verification, C15orf54, AL157935.1, LINC01117, and SNHG3 were determine…
bibliographic citation: Wang et al. (2022) Novel lncRNAs with diagnostic or prognostic value screened out from breast cancer via bioinformatics analyses. PeerJ 10:e13641 https://doi.org/10.7717/peerj.13641
date submitted: 2021-07-19
date accepted: 2022-06-07
issued: 2022-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hongxian
author list: Agent
  family name: Shu
  given name: Lirong
author list: Agent
  family name: Niu
  given name: Nan
author list: Agent
  family name: Zhao
  given name: Chenyang
author list: Agent
  family name: Lu
  given name: Shuqi
author list: Agent
  family name: Li
  given name: Yanhua
author list: Agent
  family name: Wang
  given name: Huanyu
author list: Agent
  family name: Liu
  given name: Yao
author list: Agent
  family name: Zou
  given name: Tianhui
author list: Agent
  family name: Zou
  given name: Jiawei
author list: Agent
  family name: Wu
  given name: Xiaoqin
author list: Agent
  family name: Wang
  given name: Yun
doi: 10.7717/peerj.13641
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-14
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Low-level nutrient enrichment during thermal stress delays bleaching and ameliorates calcification in three Hawaiian reef coral species
type: item
type: AcademicArticle
description: Terrestrial-based nutrient pollution has emerged as one of the most detrimental factors to coral health in many reef habitats. Recent studies have shown that excessive dissolved inorganic nutrients can reduce coral thermal tolerance thresholds and even exacerbate bleaching during thermal stress, yet the effects of minor nutrient enrichment under heat stress have not been extensively studied. In this study, Lobactis scutaria, Montipora capitata, and Pocillopora acuta colonies under heated conditions (~30.5 °C) were exposed to low and balanced nitrogen and phosphorous concentrations over a 31-day heating period. Coral colonies were collected from Kāne‘ohe Bay, O‘ahu, which has a unique history of nutrient pollution, and held in mesocosms that allowed for environmental manipulation yet are also influenced by local field conditions. Principal findings included delays in the bleaching of nutrient-enriched heated colonies as compared to heated-only colonies, in addition to relatively greater calcification rates and lower proportions of early-stage paling. Species-specific outcomes were prevalent, with L. scutaria demonstrating no difference in calcification with enrichment under heat stress. By the end of the heating stage, however, many heated colonies were at least partially impacted by bleaching or mortality. Despite this, our findings suggest that low levels of balanced nutrient enrichment may serve as a mitigative force during thermal events. Further field-based studies will be required to assess these results in different reef habitats.
format: application/pdf
format: text/html
creator: Ji Hoon J. Han
creator: Matthew P. Stefanak
creator: Ku‘ulei S. Rodgers
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Environmental Contamination and Remediation
subject: Biological Oceanography
description: doi:10.7717/peerj.13707
publisher: PeerJ Inc.
rights: © 2022 Han et al.
abstract: Terrestrial-based nutrient pollution has emerged as one of the most detrimental factors to coral health in many reef habitats. Recent studies have shown that excessive dissolved inorganic nutrients can reduce coral thermal tolerance thresholds and even exacerbate bleaching during thermal stress, yet the effects of minor nutrient enrichment under heat stress have not been extensively studied. In this study, Lobactis scutaria, Montipora capitata, and Pocillopora acuta colonies under heated conditions (~30.5 °C) were exposed to low and balanced nitrogen and phosphorous concentrations over a 31-day heating period. Coral colonies were collected from Kāne‘ohe Bay, O‘ahu, which has a unique history of nutrient pollution, and held in mesocosms that allowed for environmental manipulation yet are also influenced by local field conditions. Principal findings included delays in the bleaching of nutrient-enriched heated colonies as compared to heated-only colonies, in addition to relatively greater calcification rates and lower proportions of early-stage paling. Species-specific outcomes were prevalent, with L. scutaria demonstrating no difference in calcification with enrichment under heat stress. By the end of the heating stage, however, many heated colonies were at least partially impacted by bleaching or mortality. Despite this, our findings suggest that low levels of balanced nutrient enrichment may serve as a mitigative force during thermal events. Further field-based studies will be required to assess these results in different reef habitats.
bibliographic citation: Han et al. (2022) Low-level nutrient enrichment during thermal stress delays bleaching and ameliorates calcification in three Hawaiian reef coral species. PeerJ 10:e13707 https://doi.org/10.7717/peerj.13707
date submitted: 2022-01-31
date accepted: 2022-06-19
issued: 2022-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Ji Hoon J.
author list: Agent
  family name: Stefanak
  given name: Matthew P.
author list: Agent
  family name: Rodgers
  given name: Ku‘ulei S.
doi: 10.7717/peerj.13707
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-14
copyright: © 2022 Han et al.
attribution name: Han et al.

ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17
type: item
type: AcademicArticle
description: Background The auxin indole-3-acetic acid (IAA) is a type of endogenous plant hormone with a low concentration in plants, but it plays an important role in their growth and development. The AUX/IAA gene family was found to be an early sensitive auxin gene with a complicated way of regulating growth and development in plants. The regulation of root growth and development by AUX/IAA family genes has been reported in Arabidopsis, rice and maize. Results In this study, subcellular localization indicated that ZmIAA1-ZmIAA6 primarily played a role in the nucleus. A thermogram analysis showed that AUX/IAA genes were highly expressed in the roots, which was also confirmed by the maize tissue expression patterns. In maize overexpressing ZmIAA5, the length of the main root, the number of lateral roots, and the stalk height at the seedling stage were significantly increased compared with those of the wild type, while the EMS mutant zmiaa5 was significantly reduced. The total number of roots and the dry weight of maize overexpressing ZmIAA5 at the mature stage were also significantly increased compared with those of the wild type, while those of the mutant zmiaa5 was significantly reduced. Yeast one-hybrid experiments showed that ZmTCP15/16/17 could specifically bind to the ZmIAA5 promoter region. Bimolecular fluorescence complementation and yeast two-hybridization indicated an interaction between ZmIAA5 and ZmARF5. Conclusions Taken together, the results of this study indicate that ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17.
format: application/pdf
format: text/html
creator: Feiyang Yang
creator: Yutian Shi
creator: Manli Zhao
creator: Beijiu Cheng
creator: Xiaoyu Li
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13710
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Background The auxin indole-3-acetic acid (IAA) is a type of endogenous plant hormone with a low concentration in plants, but it plays an important role in their growth and development. The AUX/IAA gene family was found to be an early sensitive auxin gene with a complicated way of regulating growth and development in plants. The regulation of root growth and development by AUX/IAA family genes has been reported in Arabidopsis, rice and maize. Results In this study, subcellular localization indicated that ZmIAA1-ZmIAA6 primarily played a role in the nucleus. A thermogram analysis showed that AUX/IAA genes were highly expressed in the roots, which was also confirmed by the maize tissue expression patterns. In maize overexpressing ZmIAA5, the length of the main root, the number of lateral roots, and the stalk height at the seedling stage were significantly increased compared with those of the wild type, while the EMS mutant zmiaa5 was significantly reduced. The total number of roots and the dry weight of maize overexpressing ZmIAA5 at the mature stage were also significantly increased compared with those of the wild type, while those of the mutant zmiaa5 was significantly reduced. Yeast one-hybrid experiments showed that ZmTCP15/16/17 could specifically bind to the ZmIAA5 promoter region. Bimolecular fluorescence complementation and yeast two-hybridization indicated an interaction between ZmIAA5 and ZmARF5. Conclusions Taken together, the results of this study indicate that ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17.
bibliographic citation: Yang et al. (2022) ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17. PeerJ 10:e13710 https://doi.org/10.7717/peerj.13710
date submitted: 2022-05-05
date accepted: 2022-06-19
issued: 2022-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Feiyang
author list: Agent
  family name: Shi
  given name: Yutian
author list: Agent
  family name: Zhao
  given name: Manli
author list: Agent
  family name: Cheng
  given name: Beijiu
author list: Agent
  family name: Li
  given name: Xiaoyu
doi: 10.7717/peerj.13710
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-14
copyright: ©2022 Yang et al.
attribution name: Yang et al.

Association between IL-1A and IL-1B gene polymorphisms with peri-implantitis in a Portuguese population—a pilot study
type: item
type: AcademicArticle
description: Background Scientific evidence indicates that biological complications in dental implants tend to be concentrated in a subset of individuals, which seems to imply that the host response may play a determining role in implant success. Over the last few decades, several polymorphisms have been studied. Polymorphisms in the interleukin (IL) 1 gene cluster have been associated with periodontitis. There are some similar features in the sequence of immunopathological events in peri-implant and periodontal infections. We aimed to investigate if individuals carrying the genetic single nucleotide polymorphism (SNP) in the IL-1A (rs1800587) and IL-1B (rs1143634) genes are more susceptible to develop peri-implantitis. Methods A cross-sectional analytic pilot study was conducted in 20 Caucasian Portuguese subjects divided into two groups: 10 subjects with peri-implantitis and 10 subjects with peri-implant health (control group). Samples containing cells from the buccal mucosa were stored at −20 °C and later submitted to the DNA extraction process. Genetic analysis was performed using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Data were analyzed by using descriptive and inferential statistical methodologies. Results For the IL-1A (−889) gene polymorphism, it was observed that the mutated allele was present in a higher percentage in the peri-implantitis group compared to the control group (30% vs 15% respectively, Fisher’s exact test, p = 0.45). For the IL-1B (+3954) gene polymorphism, it was also observed that the altered allele was present in a higher percentage in the disease group compared to the control group (35% vs 10% respectively, Fisher’s exact test, p = 0.13). The positive genotype (at least one allele with nucleotide sequence changed in both genes) was detected in six patients, five belonging to the disease group and one to the health group. Conclusions Regarding IL-1 gene polymorphisms, there was no statistically…
format: application/pdf
format: text/html
creator: José Maria Cardoso
creator: Ana Clara Ribeiro
creator: Constança Palos
creator: Luis Proença
creator: Susana Noronha
creator: Ricardo Castro Alves
subject: Molecular Biology
subject: Dentistry
subject: Otorhinolaryngology
subject: Medical Genetics
description: doi:10.7717/peerj.13729
publisher: PeerJ Inc.
rights: © 2022 Cardoso et al.
abstract: Background Scientific evidence indicates that biological complications in dental implants tend to be concentrated in a subset of individuals, which seems to imply that the host response may play a determining role in implant success. Over the last few decades, several polymorphisms have been studied. Polymorphisms in the interleukin (IL) 1 gene cluster have been associated with periodontitis. There are some similar features in the sequence of immunopathological events in peri-implant and periodontal infections. We aimed to investigate if individuals carrying the genetic single nucleotide polymorphism (SNP) in the IL-1A (rs1800587) and IL-1B (rs1143634) genes are more susceptible to develop peri-implantitis. Methods A cross-sectional analytic pilot study was conducted in 20 Caucasian Portuguese subjects divided into two groups: 10 subjects with peri-implantitis and 10 subjects with peri-implant health (control group). Samples containing cells from the buccal mucosa were stored at −20 °C and later submitted to the DNA extraction process. Genetic analysis was performed using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Data were analyzed by using descriptive and inferential statistical methodologies. Results For the IL-1A (−889) gene polymorphism, it was observed that the mutated allele was present in a higher percentage in the peri-implantitis group compared to the control group (30% vs 15% respectively, Fisher’s exact test, p = 0.45). For the IL-1B (+3954) gene polymorphism, it was also observed that the altered allele was present in a higher percentage in the disease group compared to the control group (35% vs 10% respectively, Fisher’s exact test, p = 0.13). The positive genotype (at least one allele with nucleotide sequence changed in both genes) was detected in six patients, five belonging to the disease group and one to the health group. Conclusions Regarding IL-1 gene polymorphisms, there was no statistically…
bibliographic citation: Cardoso et al. (2022) Association between IL-1A and IL-1B gene polymorphisms with peri-implantitis in a Portuguese population—a pilot study. PeerJ 10:e13729 https://doi.org/10.7717/peerj.13729
date submitted: 2022-01-21
date accepted: 2022-06-23
issued: 2022-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cardoso
  given name: José Maria
author list: Agent
  family name: Ribeiro
  given name: Ana Clara
author list: Agent
  family name: Palos
  given name: Constança
author list: Agent
  family name: Proença
  given name: Luis
author list: Agent
  family name: Noronha
  given name: Susana
author list: Agent
  family name: Alves
  given name: Ricardo Castro
doi: 10.7717/peerj.13729
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-14
copyright: ©2022 Cardoso et al.
attribution name: Cardoso et al.

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