PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Decoupling species richness variation and spatial turnover in beta diversity across a fragmented landscape
items: The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA
items: Pituitary tissue-specific miR-7a-5p regulates FSH expression in rat anterior adenohypophyseal cells
items: Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure
items: Maturation trade-offs in octopus females and their progeny: energy, digestion and defence indicators
items: Evidence for an oncogenic role of HOXC6 in human non-small cell lung cancer
items: From climate zone to microhabitat—environmental factors affecting the coastal distribution of tiger beetles (Coleoptera: Cicindelidae) in the south-eastern European biodiversity hotspot
items: Aridity thresholds of soil microbial metabolic indices along a 3,200 km transect across arid and semi-arid regions in Northern China
items: Throwing light on dark diversity of vascular plants in China: predicting the distribution of dark and threatened species under global climate change
items: Salivary LDOC1 is a gender-difference biomarker of oral squamous cell carcinoma

Decoupling species richness variation and spatial turnover in beta diversity across a fragmented landscape
type: item
type: AcademicArticle
description: Background How habitat fragmentation affects the relationship between local richness and the variation in community composition across space is important to both ecology and conservation biology, but this effect remains poorly understood. Methods Here, we present an empirical study to address this topic in a fragmented landscape, the Thousand Island Lake (TIL), an artificial land-bridge island system with more than 1,000 islands, which provides an “experimental” fragmented landscape with a homogeneous matrix and similar successional history. We measured species composition and plant functional type (PFT) on 29 islands, and tested the effects of island area and isolation on the relationship between α- and β-diversity. General Linear Models were applied to test the impact of habitat fragmentation. In addition, variation partitioning was used to decouple α-diversity dependent and α-diversity independent spatial turnover in β-diversity of the plant community and across different PFTs. Results We found habitat fragmentation influences β-diversity of plants primarily by modifying local α-diversity, not spatial turnover in the TIL system. We also found area-dependent environmental filtering and differential plant responses across functional types were the most likely underlying driving mechanisms. Discussion These results highlight the importance of hierarchical linkages between components of biodiversity across scales in fragmented landscapes, and have practical conservation implications.
format: application/pdf
format: text/html
creator: Guang Hu
creator: Maxwell C. Wilson
creator: Jianguo Wu
creator: Jingjing Yu
creator: Mingjian Yu
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.6714
publisher: PeerJ Inc.
rights: © 2019 Hu et al.
abstract: Background How habitat fragmentation affects the relationship between local richness and the variation in community composition across space is important to both ecology and conservation biology, but this effect remains poorly understood. Methods Here, we present an empirical study to address this topic in a fragmented landscape, the Thousand Island Lake (TIL), an artificial land-bridge island system with more than 1,000 islands, which provides an “experimental” fragmented landscape with a homogeneous matrix and similar successional history. We measured species composition and plant functional type (PFT) on 29 islands, and tested the effects of island area and isolation on the relationship between α- and β-diversity. General Linear Models were applied to test the impact of habitat fragmentation. In addition, variation partitioning was used to decouple α-diversity dependent and α-diversity independent spatial turnover in β-diversity of the plant community and across different PFTs. Results We found habitat fragmentation influences β-diversity of plants primarily by modifying local α-diversity, not spatial turnover in the TIL system. We also found area-dependent environmental filtering and differential plant responses across functional types were the most likely underlying driving mechanisms. Discussion These results highlight the importance of hierarchical linkages between components of biodiversity across scales in fragmented landscapes, and have practical conservation implications.
bibliographic citation: Hu et al. (2019) Decoupling species richness variation and spatial turnover in beta diversity across a fragmented landscape. PeerJ 7:e6714 https://doi.org/10.7717/peerj.6714
date submitted: 2018-06-13
date accepted: 2019-03-05
issued: 2019-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Guang
author list: Agent
  family name: Wilson
  given name: Maxwell C.
author list: Agent
  family name: Wu
  given name: Jianguo
author list: Agent
  family name: Yu
  given name: Jingjing
author list: Agent
  family name: Yu
  given name: Mingjian
doi: 10.7717/peerj.6714
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-10
copyright: © 2019 Hu et al.
attribution name: Hu et al.

The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA
type: item
type: AcademicArticle
description: The ability of microorganisms to degrade xenobiotics can be exploited to develop cost-effective and eco-friendly bioremediation technologies. Microorganisms can degrade almost all organic pollutants, but this process might be very slow in some cases. A promising way to enhance removal of recalcitrant xenobiotics from the environment lies in the interactions between plant exudates such as plant secondary metabolites (PSMs) and microorganisms. Although there is a considerable body of evidence that PSMs can alter the microbial community composition and stimulate the microbial degradation of xenobiotics, their mechanisms of action remain poorly understood. With this in mind, our aim was to demonstrate that similarity between the chemical structures of PSMs and xenobiotics results in higher micropollutant degradation rates, and the occurrence of corresponding bacterial degradative genes. To verify this, the present study analyses the influence of syringic acid, a plant secondary metabolite, on the bacterial degradation of an herbicide, 4-chloro-2-methylphenoxyacetic acid (MCPA). In particular, the presence of appropriate MCPA degradative genes, MCPA removal efficiency and changes in samples phytotoxicity have been analyzed. Significant MCPA depletion was achieved in samples enriched with syringic acid. The results confirmed not only greater MCPA removal from the samples upon spiking with syringic acid, and thus decreased phytotoxicity, but also the presence of a greater number of genes responsible for MCPA biodegradation. 16S rRNA gene sequence analysis revealed ubiquitous enrichment of the β-proteobacteria Rhodoferax, Achromobacter, Burkholderia and Cupriavidus. The obtained results provide further confirmation that plant metabolites released into the rhizosphere can stimulate biodegradation of xenobiotics, including MCPA.
format: application/pdf
format: text/html
creator: Magdalena Urbaniak
creator: Elżbieta Mierzejewska
creator: Maciej Tankiewicz
subject: Agricultural Science
subject: Ecology
subject: Genetics
description: doi:10.7717/peerj.6745
publisher: PeerJ Inc.
rights: © 2019 Urbaniak et al.
abstract: The ability of microorganisms to degrade xenobiotics can be exploited to develop cost-effective and eco-friendly bioremediation technologies. Microorganisms can degrade almost all organic pollutants, but this process might be very slow in some cases. A promising way to enhance removal of recalcitrant xenobiotics from the environment lies in the interactions between plant exudates such as plant secondary metabolites (PSMs) and microorganisms. Although there is a considerable body of evidence that PSMs can alter the microbial community composition and stimulate the microbial degradation of xenobiotics, their mechanisms of action remain poorly understood. With this in mind, our aim was to demonstrate that similarity between the chemical structures of PSMs and xenobiotics results in higher micropollutant degradation rates, and the occurrence of corresponding bacterial degradative genes. To verify this, the present study analyses the influence of syringic acid, a plant secondary metabolite, on the bacterial degradation of an herbicide, 4-chloro-2-methylphenoxyacetic acid (MCPA). In particular, the presence of appropriate MCPA degradative genes, MCPA removal efficiency and changes in samples phytotoxicity have been analyzed. Significant MCPA depletion was achieved in samples enriched with syringic acid. The results confirmed not only greater MCPA removal from the samples upon spiking with syringic acid, and thus decreased phytotoxicity, but also the presence of a greater number of genes responsible for MCPA biodegradation. 16S rRNA gene sequence analysis revealed ubiquitous enrichment of the β-proteobacteria Rhodoferax, Achromobacter, Burkholderia and Cupriavidus. The obtained results provide further confirmation that plant metabolites released into the rhizosphere can stimulate biodegradation of xenobiotics, including MCPA.
bibliographic citation: Urbaniak et al. (2019) The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA. PeerJ 7:e6745 https://doi.org/10.7717/peerj.6745
date submitted: 2018-12-20
date accepted: 2019-02-27
issued: 2019-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Urbaniak
  given name: Magdalena
author list: Agent
  family name: Mierzejewska
  given name: Elżbieta
author list: Agent
  family name: Tankiewicz
  given name: Maciej
doi: 10.7717/peerj.6745
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-10
copyright: ©2019 Urbaniak et al.
attribution name: Urbaniak et al.

Pituitary tissue-specific miR-7a-5p regulates FSH expression in rat anterior adenohypophyseal cells
type: item
type: AcademicArticle
description: The follicle-stimulating hormone (FSH), which is synthesized and secreted by the anterior pituitary gland, plays an important role in regulating reproductive processes. In this study, using the TargetScan program, we predicted that microRNAs (miRNAs) regulate FSH secretion. Dual-luciferase reporter assays were performed and identified miR-7a-5p. MiR-7a-5p has been reported to regulate diverse cellular functions. However, it is unclear whether miR-7a-5p binds to mRNAs and regulates reproductive functions. Therefore, we constructed a suspension of rat anterior pituitary cells and cultured them under adaptive conditions, transfected miR-7a-5p mimics or inhibitor into the cell suspension and detected expression of the FSHb gene. The results demonstrated that miR-7a-5p downregulated FSHb expression levels, while treatment with miR-7a-5p inhibitors upregulated FSHb expression levels relative to those of negative control groups, as shown by quantitative PCR analysis. The results were confirmed with a subsequent experiment showing that FSH secretion was reduced after treatment with mimics and increased in the inhibitor groups, as shown by enzyme-linked immunosorbent assay. Our results indicated that miR-7a-5p downregulates FSHb expression levels, resulting in decreased FSH synthesis and secretion, which demonstrates the important role of miRNAs in the regulation of FSH and animal reproduction.
format: application/pdf
format: text/html
creator: Chang-Jiang Wang
creator: Hai-Xiang Guo
creator: Dong-Xu Han
creator: Ze-Wen Yu
creator: Yi Zheng
creator: Hao Jiang
creator: Yan Gao
creator: Bao Yuan
creator: Jia-Bao Zhang
subject: Cell Biology
subject: Molecular Biology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6458
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: The follicle-stimulating hormone (FSH), which is synthesized and secreted by the anterior pituitary gland, plays an important role in regulating reproductive processes. In this study, using the TargetScan program, we predicted that microRNAs (miRNAs) regulate FSH secretion. Dual-luciferase reporter assays were performed and identified miR-7a-5p. MiR-7a-5p has been reported to regulate diverse cellular functions. However, it is unclear whether miR-7a-5p binds to mRNAs and regulates reproductive functions. Therefore, we constructed a suspension of rat anterior pituitary cells and cultured them under adaptive conditions, transfected miR-7a-5p mimics or inhibitor into the cell suspension and detected expression of the FSHb gene. The results demonstrated that miR-7a-5p downregulated FSHb expression levels, while treatment with miR-7a-5p inhibitors upregulated FSHb expression levels relative to those of negative control groups, as shown by quantitative PCR analysis. The results were confirmed with a subsequent experiment showing that FSH secretion was reduced after treatment with mimics and increased in the inhibitor groups, as shown by enzyme-linked immunosorbent assay. Our results indicated that miR-7a-5p downregulates FSHb expression levels, resulting in decreased FSH synthesis and secretion, which demonstrates the important role of miRNAs in the regulation of FSH and animal reproduction.
bibliographic citation: Wang et al. (2019) Pituitary tissue-specific miR-7a-5p regulates FSH expression in rat anterior adenohypophyseal cells. PeerJ 7:e6458 https://doi.org/10.7717/peerj.6458
date submitted: 2018-09-18
date accepted: 2019-01-16
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Chang-Jiang
author list: Agent
  family name: Guo
  given name: Hai-Xiang
author list: Agent
  family name: Han
  given name: Dong-Xu
author list: Agent
  family name: Yu
  given name: Ze-Wen
author list: Agent
  family name: Zheng
  given name: Yi
author list: Agent
  family name: Jiang
  given name: Hao
author list: Agent
  family name: Gao
  given name: Yan
author list: Agent
  family name: Yuan
  given name: Bao
author list: Agent
  family name: Zhang
  given name: Jia-Bao
doi: 10.7717/peerj.6458
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure
type: item
type: AcademicArticle
description: Ascent to high altitude feels uncomfortable in part because of a decreased partial pressure of oxygen due to the decrease in barometric pressure. The molecular mechanisms causing injury in liver tissue after exposure to a hypoxic environment are widely unknown. The liver must physiologically and metabolically change to improve tolerance to altitude-induced hypoxia. Since the liver is the largest metabolic organ and regulates many physiological and metabolic processes, it plays an important part in high altitude adaptation. The cellular response to hypoxia results in changes in the gene expression profile. The present study explores these changes in a rat model. To comprehensively investigate the gene expression and physiological changes under hypobaric hypoxia, we used genome-wide transcription profiling. Little is known about the genome-wide transcriptional response to acute and chronic hypobaric hypoxia in the livers of rats. In this study, we carried out RNA-Sequencing (RNA-Seq) of liver tissue from rats in three groups, normal control rats (L), rats exposed to acute hypobaric hypoxia for 2 weeks (W2L) and rats chronically exposed to hypobaric hypoxia for 4 weeks (W4L), to explore the transcriptional profile of acute and chronic mountain sickness in a mammal under a controlled time-course. We identified 497 differentially expressed genes between the three groups. A principal component analysis revealed large differences between the acute and chronic hypobaric hypoxia groups compared with the control group. Several immune-related and metabolic pathways, such as cytokine-cytokine receptor interaction and galactose metabolism, were highly enriched in the KEGG pathway analysis. Similar results were found in the Gene Ontology analysis. Cogena analysis showed that the immune-related pathways were mainly upregulated and enriched in the acute hypobaric hypoxia group.
format: application/pdf
format: text/html
creator: Zhenguo Xu
creator: Zhilong Jia
creator: Jinlong Shi
creator: Zeyu Zhang
creator: Xiaojian Gao
creator: Qian Jia
creator: Bohan Liu
creator: Jixuan Liu
creator: Chunlei Liu
creator: Xiaojing Zhao
creator: Kunlun He
subject: Bioinformatics
subject: Genetics
subject: Anatomy and Physiology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.6499
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Ascent to high altitude feels uncomfortable in part because of a decreased partial pressure of oxygen due to the decrease in barometric pressure. The molecular mechanisms causing injury in liver tissue after exposure to a hypoxic environment are widely unknown. The liver must physiologically and metabolically change to improve tolerance to altitude-induced hypoxia. Since the liver is the largest metabolic organ and regulates many physiological and metabolic processes, it plays an important part in high altitude adaptation. The cellular response to hypoxia results in changes in the gene expression profile. The present study explores these changes in a rat model. To comprehensively investigate the gene expression and physiological changes under hypobaric hypoxia, we used genome-wide transcription profiling. Little is known about the genome-wide transcriptional response to acute and chronic hypobaric hypoxia in the livers of rats. In this study, we carried out RNA-Sequencing (RNA-Seq) of liver tissue from rats in three groups, normal control rats (L), rats exposed to acute hypobaric hypoxia for 2 weeks (W2L) and rats chronically exposed to hypobaric hypoxia for 4 weeks (W4L), to explore the transcriptional profile of acute and chronic mountain sickness in a mammal under a controlled time-course. We identified 497 differentially expressed genes between the three groups. A principal component analysis revealed large differences between the acute and chronic hypobaric hypoxia groups compared with the control group. Several immune-related and metabolic pathways, such as cytokine-cytokine receptor interaction and galactose metabolism, were highly enriched in the KEGG pathway analysis. Similar results were found in the Gene Ontology analysis. Cogena analysis showed that the immune-related pathways were mainly upregulated and enriched in the acute hypobaric hypoxia group.
bibliographic citation: Xu et al. (2019) Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure. PeerJ 7:e6499 https://doi.org/10.7717/peerj.6499
date submitted: 2018-10-26
date accepted: 2019-01-21
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Zhenguo
author list: Agent
  family name: Jia
  given name: Zhilong
author list: Agent
  family name: Shi
  given name: Jinlong
author list: Agent
  family name: Zhang
  given name: Zeyu
author list: Agent
  family name: Gao
  given name: Xiaojian
author list: Agent
  family name: Jia
  given name: Qian
author list: Agent
  family name: Liu
  given name: Bohan
author list: Agent
  family name: Liu
  given name: Jixuan
author list: Agent
  family name: Liu
  given name: Chunlei
author list: Agent
  family name: Zhao
  given name: Xiaojing
author list: Agent
  family name: He
  given name: Kunlun
doi: 10.7717/peerj.6499
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: ©2019 Xu et al.
attribution name: Xu et al.

Maturation trade-offs in octopus females and their progeny: energy, digestion and defence indicators
type: item
type: AcademicArticle
description: Sexual maturation and reproduction influence the status of a number of physiological processes and consequently the ecology and behaviour of cephalopods. Using Octopus mimus as a study model, the present work was focused in the changes in biochemical compound and activity that take place during gonadal maturation of females and its consequences in embryo and hatchlings characteristics. To do that, a total of 31 adult females of O. mimus were sampled to follow metabolites (ovaries and digestive gland) and digestive enzyme activities (alkaline and acidic proteases) during physiological and functional maturation. Levels of protein (Prot), triacylglyceride (TG), cholesterol (Chol), glucose (Glu), and glycogen (Gly) were evaluated. Groups of eggs coming from mature females were also sampled along development and after hatching (paralarvae of 1 and 3 days old) to track metabolites (Prot, TG, Glu, Gly, TG, Chol), digestive enzymes activity (Lipase, alkaline proteases, and acidic proteases), and antioxidant/detoxification defence indicators with embryos development. Based on the data obtained, we hypothesized that immature females store Chol in their ovaries, probably from the food they ingested, but switch to TG reserves at the beginning of the maturation processes. At the same time, results suggest that these processes were energetically supported by Glu, obtained probably from Gly breakdown by gluconeogenic pathways. Also, was observed that embryos metabolites and enzyme activities (digestive and antioxidant/detoxification enzymes) where maintained without significant changes and in a low activity during the whole organogenesis, meaning that organogenesis is relatively not energetically costly. In contrast, after organogenesis, a mobilization of nutrients and activation of the metabolic and digestive enzymes was observed, together with increments in consumption of yolk and Gly, and reduction in lipid peroxidation. Derived from our results, we also have the hypothesis tha…
format: application/pdf
format: text/html
creator: Alberto Olivares
creator: Gabriela Rodríguez-Fuentes
creator: Maite Mascaró
creator: Ariadna Sanchez Arteaga
creator: Karen Ortega
creator: Claudia Caamal Monsreal
creator: Nelly Tremblay
creator: Carlos Rosas
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Marine Biology
description: doi:10.7717/peerj.6618
publisher: PeerJ Inc.
rights: © 2019 Olivares et al.
abstract: Sexual maturation and reproduction influence the status of a number of physiological processes and consequently the ecology and behaviour of cephalopods. Using Octopus mimus as a study model, the present work was focused in the changes in biochemical compound and activity that take place during gonadal maturation of females and its consequences in embryo and hatchlings characteristics. To do that, a total of 31 adult females of O. mimus were sampled to follow metabolites (ovaries and digestive gland) and digestive enzyme activities (alkaline and acidic proteases) during physiological and functional maturation. Levels of protein (Prot), triacylglyceride (TG), cholesterol (Chol), glucose (Glu), and glycogen (Gly) were evaluated. Groups of eggs coming from mature females were also sampled along development and after hatching (paralarvae of 1 and 3 days old) to track metabolites (Prot, TG, Glu, Gly, TG, Chol), digestive enzymes activity (Lipase, alkaline proteases, and acidic proteases), and antioxidant/detoxification defence indicators with embryos development. Based on the data obtained, we hypothesized that immature females store Chol in their ovaries, probably from the food they ingested, but switch to TG reserves at the beginning of the maturation processes. At the same time, results suggest that these processes were energetically supported by Glu, obtained probably from Gly breakdown by gluconeogenic pathways. Also, was observed that embryos metabolites and enzyme activities (digestive and antioxidant/detoxification enzymes) where maintained without significant changes and in a low activity during the whole organogenesis, meaning that organogenesis is relatively not energetically costly. In contrast, after organogenesis, a mobilization of nutrients and activation of the metabolic and digestive enzymes was observed, together with increments in consumption of yolk and Gly, and reduction in lipid peroxidation. Derived from our results, we also have the hypothesis tha…
bibliographic citation: Olivares et al. (2019) Maturation trade-offs in octopus females and their progeny: energy, digestion and defence indicators. PeerJ 7:e6618 https://doi.org/10.7717/peerj.6618
date submitted: 2018-06-04
date accepted: 2019-02-14
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olivares
  given name: Alberto
author list: Agent
  family name: Rodríguez-Fuentes
  given name: Gabriela
author list: Agent
  family name: Mascaró
  given name: Maite
author list: Agent
  family name: Sanchez Arteaga
  given name: Ariadna
author list: Agent
  family name: Ortega
  given name: Karen
author list: Agent
  family name: Caamal Monsreal
  given name: Claudia
author list: Agent
  family name: Tremblay
  given name: Nelly
author list: Agent
  family name: Rosas
  given name: Carlos
doi: 10.7717/peerj.6618
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: © 2019 Olivares et al.
attribution name: Olivares et al.

Evidence for an oncogenic role of HOXC6 in human non-small cell lung cancer
type: item
type: AcademicArticle
description: Background Identification of specific biomarkers is important for the diagnosis and treatment of non-small cell lung cancer (NSCLC). HOXC6 is a homeodomain-containing transcription factor that is highly expressed in several human cancers; however, its role in NSCLC remains unknown. Methods The expression and protein levels of HOXC6 were assessed in NSCLC tissue samples by Quantitative real-time PCR (qRT-PCR) and immunohistochemistry, respectively. HOXC6 was transfected into the NSCLC cell lines A549 and PC9, and used to investigate its effect on proliferation, migration, and invasion using CFSE, wound healing, and Matrigel invasion assays. Next-generation sequencing was also used to identify downstream targets of HOXC6 and to gain insights into the molecular mechanisms underlying its biological function. Results HOXC6 expression was significantly increased in 66.6% (20/30) of NSCLC tumor samples in comparison to normal controls. HOXC6 promoted proliferation, migration, and invasion of NSCLC cells in vitro. RNA-seq analysis demonstrated the upregulation of 310 and 112 genes in A549-HOXC6 and PC9-HOXC6 cells, respectively, and the downregulation of 665 and 385 genes in A549-HOXC6 and PC9-HOXC6 cells, respectively. HOXC6 was also found to regulate the expression of genes such as CEACAM6, SPARC, WNT6, CST1, MMP2, and KRT13, which have documented pro-tumorigenic functions. Discussion HOXC6 is highly expressed in NSCLC, and it may enhance lung cancer progression by regulating the expression of pro-tumorigenic genes involved in proliferation, migration, and invasion. Our study highlighted the oncogenic potential of HOXC6, and suggests that it may be a novel biomarker for the diagnosis and treatment of NSCLC.
format: application/pdf
format: text/html
creator: Yingcheng Yang
creator: Xiaoping Tang
creator: Xueqin Song
creator: Li Tang
creator: Yong Cao
creator: Xu Liu
creator: Xiaoyan Wang
creator: Yan Li
creator: Minglan Yu
creator: Haisu Wan
creator: Feng Chen
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.6629
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Background Identification of specific biomarkers is important for the diagnosis and treatment of non-small cell lung cancer (NSCLC). HOXC6 is a homeodomain-containing transcription factor that is highly expressed in several human cancers; however, its role in NSCLC remains unknown. Methods The expression and protein levels of HOXC6 were assessed in NSCLC tissue samples by Quantitative real-time PCR (qRT-PCR) and immunohistochemistry, respectively. HOXC6 was transfected into the NSCLC cell lines A549 and PC9, and used to investigate its effect on proliferation, migration, and invasion using CFSE, wound healing, and Matrigel invasion assays. Next-generation sequencing was also used to identify downstream targets of HOXC6 and to gain insights into the molecular mechanisms underlying its biological function. Results HOXC6 expression was significantly increased in 66.6% (20/30) of NSCLC tumor samples in comparison to normal controls. HOXC6 promoted proliferation, migration, and invasion of NSCLC cells in vitro. RNA-seq analysis demonstrated the upregulation of 310 and 112 genes in A549-HOXC6 and PC9-HOXC6 cells, respectively, and the downregulation of 665 and 385 genes in A549-HOXC6 and PC9-HOXC6 cells, respectively. HOXC6 was also found to regulate the expression of genes such as CEACAM6, SPARC, WNT6, CST1, MMP2, and KRT13, which have documented pro-tumorigenic functions. Discussion HOXC6 is highly expressed in NSCLC, and it may enhance lung cancer progression by regulating the expression of pro-tumorigenic genes involved in proliferation, migration, and invasion. Our study highlighted the oncogenic potential of HOXC6, and suggests that it may be a novel biomarker for the diagnosis and treatment of NSCLC.
bibliographic citation: Yang et al. (2019) Evidence for an oncogenic role of HOXC6 in human non-small cell lung cancer. PeerJ 7:e6629 https://doi.org/10.7717/peerj.6629
date submitted: 2018-11-01
date accepted: 2019-02-15
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yingcheng
author list: Agent
  family name: Tang
  given name: Xiaoping
author list: Agent
  family name: Song
  given name: Xueqin
author list: Agent
  family name: Tang
  given name: Li
author list: Agent
  family name: Cao
  given name: Yong
author list: Agent
  family name: Liu
  given name: Xu
author list: Agent
  family name: Wang
  given name: Xiaoyan
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Yu
  given name: Minglan
author list: Agent
  family name: Wan
  given name: Haisu
author list: Agent
  family name: Chen
  given name: Feng
doi: 10.7717/peerj.6629
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: ©2019 Yang et al.
attribution name: Yang et al.

From climate zone to microhabitat—environmental factors affecting the coastal distribution of tiger beetles (Coleoptera: Cicindelidae) in the south-eastern European biodiversity hotspot
type: item
type: AcademicArticle
description: Background Tiger beetles (Coleoptera: Cicindelidae) are predatory insects usually occurring in various sandy habitats. In south-eastern Europe, especially in lowland areas located close to the sea coast, the diversity of Cicindelidae is one of the highest in the Palaearctic realm. Although previous studies conducted in different areas of the world show that many species are habitat specialists, unfortunately little is known about environmental factors affecting the diversity and distribution of tiger beetles in this region. Material and Methods Habitat preferences for 12 tiger beetles taxa were analysed. Over 100 samples collected in eight countries located in coastal areas of the Black and Mediterranean Seas were studied, for which climate data, macrohabitat types, and soil parameters (soil humidity, salinity, pH, and structure) were investigated. Results Most studied Cicindelidae were characterised by narrow or very narrow habitat specialisation and did not co-occur with other ones, including 11 taxa found as habitat specialists occurring only in one or two types of macrohabitat. The most eurythopic species was Calomera littoralis nemoralis which occupied four macrohabitat types. The climatic zone, altitude, and humidity were found as the most important factors in the distribution of the studied tiger beetle species. Salt marshes and sandy sea beaches were noted as the most diverse macrohabitat types. Discussion Tiger beetle fauna of south-eastern Europe consists mainly of habitat specialists sensitive to environmental changes, which makes these beetles perfect bioindicators. Moreover, as a great number of studied Cicindelidae taxa occur in habitats which are under a significant human impact, we suggest that in the studied area the group can be successfully used as a flagship taxon for insect and nature conservation.
format: application/pdf
format: text/html
creator: Radomir Jaskuła
creator: Mateusz Płóciennik
creator: Axel Schwerk
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.6676
publisher: PeerJ Inc.
rights: © 2019 Jaskuła et al.
abstract: Background Tiger beetles (Coleoptera: Cicindelidae) are predatory insects usually occurring in various sandy habitats. In south-eastern Europe, especially in lowland areas located close to the sea coast, the diversity of Cicindelidae is one of the highest in the Palaearctic realm. Although previous studies conducted in different areas of the world show that many species are habitat specialists, unfortunately little is known about environmental factors affecting the diversity and distribution of tiger beetles in this region. Material and Methods Habitat preferences for 12 tiger beetles taxa were analysed. Over 100 samples collected in eight countries located in coastal areas of the Black and Mediterranean Seas were studied, for which climate data, macrohabitat types, and soil parameters (soil humidity, salinity, pH, and structure) were investigated. Results Most studied Cicindelidae were characterised by narrow or very narrow habitat specialisation and did not co-occur with other ones, including 11 taxa found as habitat specialists occurring only in one or two types of macrohabitat. The most eurythopic species was Calomera littoralis nemoralis which occupied four macrohabitat types. The climatic zone, altitude, and humidity were found as the most important factors in the distribution of the studied tiger beetle species. Salt marshes and sandy sea beaches were noted as the most diverse macrohabitat types. Discussion Tiger beetle fauna of south-eastern Europe consists mainly of habitat specialists sensitive to environmental changes, which makes these beetles perfect bioindicators. Moreover, as a great number of studied Cicindelidae taxa occur in habitats which are under a significant human impact, we suggest that in the studied area the group can be successfully used as a flagship taxon for insect and nature conservation.
bibliographic citation: Jaskuła et al. (2019) From climate zone to microhabitat—environmental factors affecting the coastal distribution of tiger beetles (Coleoptera: Cicindelidae) in the south-eastern European biodiversity hotspot. PeerJ 7:e6676 https://doi.org/10.7717/peerj.6676
date submitted: 2019-01-18
date accepted: 2019-02-25
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jaskuła
  given name: Radomir
author list: Agent
  family name: Płóciennik
  given name: Mateusz
author list: Agent
  family name: Schwerk
  given name: Axel
doi: 10.7717/peerj.6676
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: © 2019 Jaskuła et al.
attribution name: Jaskuła et al.

Aridity thresholds of soil microbial metabolic indices along a 3,200 km transect across arid and semi-arid regions in Northern China
type: item
type: AcademicArticle
description: Soil microbial processes are crucial for understanding the ecological functions of arid and semi-arid lands which occupy approximately 40% of the global terrestrial ecosystems. However, how soil microbial metabolic activities may change across a wide aridity gradient in drylands remains unclear. Here, we investigated three soil microbial metabolic indices (soil organic carbon (SOC)-based microbial respiration, metabolic quotient, and microbial biomass as a proportion of total SOC) and the degree of carbon limitation for microbial respiration along a 3,200 km transect with a wide aridity gradient. The aridity gradient was customarily expressed using the aridity index (AI) which was calculated as the ratio of mean annual precipitation to mean annual evaporation, therefore, a lower AI value indicated a higher degree of aridity. Our results showed non-linear relationships between AI values and the metabolic indices with a clear aridity threshold for each of the three metabolic indices along the aridity gradient, respectively (AI = 0.13 for basal respiration, AI = 0.17 for metabolic quotient, and AI = 0.17 for MBC:SOC ratio). These metabolic indices linearly declined when AI was above the thresholds, but did not show any clear patterns when AI was below the thresholds. We also found that soil microbial respiration was highly limited by available carbon substrates at locations with higher primary production and relatively lower level of water limitation when AI was above the threshold, a counter-intuitive pattern that microbes were more starved in ecosystems with more substrate input. However, the increasing level of carbon limitation did correspond to the declining trend of the three metabolic indices along the AI gradient, which indicates that the carbon limitation influences microbial metabolism. We also found that the ratio of microbial biomass carbon to SOC in arid regions (AI < 0.2) with extremely low precipitation and primary production were not quantitatively rela…
format: application/pdf
format: text/html
creator: Jianfeng Hou
creator: Feike A. Dijkstra
creator: Xiuwei Zhang
creator: Chao Wang
creator: Xiaotao Lü
creator: Peng Wang
creator: Xingguo Han
creator: Weixin Cheng
subject: Ecology
subject: Soil Science
description: doi:10.7717/peerj.6712
publisher: PeerJ Inc.
rights: © 2019 Hou et al.
abstract: Soil microbial processes are crucial for understanding the ecological functions of arid and semi-arid lands which occupy approximately 40% of the global terrestrial ecosystems. However, how soil microbial metabolic activities may change across a wide aridity gradient in drylands remains unclear. Here, we investigated three soil microbial metabolic indices (soil organic carbon (SOC)-based microbial respiration, metabolic quotient, and microbial biomass as a proportion of total SOC) and the degree of carbon limitation for microbial respiration along a 3,200 km transect with a wide aridity gradient. The aridity gradient was customarily expressed using the aridity index (AI) which was calculated as the ratio of mean annual precipitation to mean annual evaporation, therefore, a lower AI value indicated a higher degree of aridity. Our results showed non-linear relationships between AI values and the metabolic indices with a clear aridity threshold for each of the three metabolic indices along the aridity gradient, respectively (AI = 0.13 for basal respiration, AI = 0.17 for metabolic quotient, and AI = 0.17 for MBC:SOC ratio). These metabolic indices linearly declined when AI was above the thresholds, but did not show any clear patterns when AI was below the thresholds. We also found that soil microbial respiration was highly limited by available carbon substrates at locations with higher primary production and relatively lower level of water limitation when AI was above the threshold, a counter-intuitive pattern that microbes were more starved in ecosystems with more substrate input. However, the increasing level of carbon limitation did correspond to the declining trend of the three metabolic indices along the AI gradient, which indicates that the carbon limitation influences microbial metabolism. We also found that the ratio of microbial biomass carbon to SOC in arid regions (AI < 0.2) with extremely low precipitation and primary production were not quantitatively rela…
bibliographic citation: Hou et al. (2019) Aridity thresholds of soil microbial metabolic indices along a 3,200 km transect across arid and semi-arid regions in Northern China. PeerJ 7:e6712 https://doi.org/10.7717/peerj.6712
date submitted: 2018-10-05
date accepted: 2019-03-05
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Jianfeng
author list: Agent
  family name: Dijkstra
  given name: Feike A.
author list: Agent
  family name: Zhang
  given name: Xiuwei
author list: Agent
  family name: Wang
  given name: Chao
author list: Agent
  family name: Lü
  given name: Xiaotao
author list: Agent
  family name: Wang
  given name: Peng
author list: Agent
  family name: Han
  given name: Xingguo
author list: Agent
  family name: Cheng
  given name: Weixin
doi: 10.7717/peerj.6712
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: © 2019 Hou et al.
attribution name: Hou et al.

Throwing light on dark diversity of vascular plants in China: predicting the distribution of dark and threatened species under global climate change
type: item
type: AcademicArticle
description: Background As global climate change accelerates, ecologists and conservationists are increasingly investigating changes in biodiversity and predicting species distribution based on species observed at sites, but rarely consider those plant species that could potentially inhabit but are absent from these areas (i.e., the dark diversity and its distribution). Here, we estimated the dark diversity of vascular plants in China and picked up threatened dark species from the result, and applied maximum entropy (MaxEnt) model to project current and future distributions of those dark species in their potential regions (those regions that have these dark species). Methods We used the Beals probability index to estimate dark diversity in China based on available species distribution information and explored which environmental variables had significant impacts on dark diversity by incorporating bioclimatic data into the random forest (RF) model. We collected occurrence data of threatened dark species (Eucommia ulmoides, Liriodendron chinense, Phoebe bournei, Fagus longipetiolata, Amentotaxus argotaenia, and Cathaya argyrophylla) and related bioclimatic information that can be used to predict their distributions. In addition, we used MaxEnt modeling to project their distributions in suitable areas under future (2050 and 2070) climate change scenarios. Results We found that every study region’s dark diversity was lower than its observed species richness. In these areas, their numbers of dark species are ranging from 0 to 215, with a generally increasing trend from western regions to the east. RF results showed that temperature variables had a more significant effect on dark diversity than those associated with precipitation. The results of MaxEnt modeling showed that most threatened dark species were climatically suitable in their potential regions from current to 2070. Discussions The results of this study provide the first ever dark diversity patterns concentrated in China, ev…
format: application/pdf
format: text/html
creator: Lili Tang
creator: Runxi Wang
creator: Kate S. He
creator: Cong Shi
creator: Tong Yang
creator: Yaping Huang
creator: Pufan Zheng
creator: Fuchen Shi
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Climate Change Biology
description: doi:10.7717/peerj.6731
publisher: PeerJ Inc.
rights: © 2019 Tang et al.
abstract: Background As global climate change accelerates, ecologists and conservationists are increasingly investigating changes in biodiversity and predicting species distribution based on species observed at sites, but rarely consider those plant species that could potentially inhabit but are absent from these areas (i.e., the dark diversity and its distribution). Here, we estimated the dark diversity of vascular plants in China and picked up threatened dark species from the result, and applied maximum entropy (MaxEnt) model to project current and future distributions of those dark species in their potential regions (those regions that have these dark species). Methods We used the Beals probability index to estimate dark diversity in China based on available species distribution information and explored which environmental variables had significant impacts on dark diversity by incorporating bioclimatic data into the random forest (RF) model. We collected occurrence data of threatened dark species (Eucommia ulmoides, Liriodendron chinense, Phoebe bournei, Fagus longipetiolata, Amentotaxus argotaenia, and Cathaya argyrophylla) and related bioclimatic information that can be used to predict their distributions. In addition, we used MaxEnt modeling to project their distributions in suitable areas under future (2050 and 2070) climate change scenarios. Results We found that every study region’s dark diversity was lower than its observed species richness. In these areas, their numbers of dark species are ranging from 0 to 215, with a generally increasing trend from western regions to the east. RF results showed that temperature variables had a more significant effect on dark diversity than those associated with precipitation. The results of MaxEnt modeling showed that most threatened dark species were climatically suitable in their potential regions from current to 2070. Discussions The results of this study provide the first ever dark diversity patterns concentrated in China, ev…
bibliographic citation: Tang et al. (2019) Throwing light on dark diversity of vascular plants in China: predicting the distribution of dark and threatened species under global climate change. PeerJ 7:e6731 https://doi.org/10.7717/peerj.6731
date submitted: 2018-08-28
date accepted: 2019-03-06
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Lili
author list: Agent
  family name: Wang
  given name: Runxi
author list: Agent
  family name: He
  given name: Kate S.
author list: Agent
  family name: Shi
  given name: Cong
author list: Agent
  family name: Yang
  given name: Tong
author list: Agent
  family name: Huang
  given name: Yaping
author list: Agent
  family name: Zheng
  given name: Pufan
author list: Agent
  family name: Shi
  given name: Fuchen
doi: 10.7717/peerj.6731
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: © 2019 Tang et al.
attribution name: Tang et al.

Salivary LDOC1 is a gender-difference biomarker of oral squamous cell carcinoma
type: item
type: AcademicArticle
description: Background The X-linked tumor suppressor gene LDOC1 is reported to be involved in oral cancer. The detection of biomarkers in salivary RNA is a non-invasive strategy for diagnosing many diseases. The aim of the present study was to investigate the potential of salivary LDOC1 as a biomarker of oral cancer. Methods We determined the expression levels of LDOC1 in the saliva of oral squamous cell carcinoma (OSCC) subjects, and investigated its correlation with various clinicopathological characteristics. The expression levels of salivary LDOC1 were detected in 53 OSCC subjects and 43 healthy controls using quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis. We used Fisher’s exact test to analyze the correlations between expression levels and clinicopathological characteristics. Results Salivary LDOC1 was significantly upregulated in females with OSCC (p = 0.0072), and significantly downregulated in males with OSCC (p = 0.0206). Eighty-nine percent of male OSCC subjects who smoked expressed low levels of LDOC1. OSCC cell lines derived from male OSCC subjects expressed low levels of LDOC1. Conclusions A high level of salivary LDOC1 expression is a biomarker of OSCC in females. A high percentage of male OSCC subjects who smoke express low levels of salivary LDOC1. A low level of salivary LDOC1 expression is a biomarker of OSCC in males.
format: application/pdf
format: text/html
creator: Chung-Ji Liu
creator: Jen-Hao Chen
creator: Shih-Min Hsia
creator: Chiu-Chu Liao
creator: Hui-Wen Chang
creator: Tzong-Ming Shieh
creator: Yin-Hwa Shih
subject: Bioinformatics
subject: Dentistry
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.6732
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Background The X-linked tumor suppressor gene LDOC1 is reported to be involved in oral cancer. The detection of biomarkers in salivary RNA is a non-invasive strategy for diagnosing many diseases. The aim of the present study was to investigate the potential of salivary LDOC1 as a biomarker of oral cancer. Methods We determined the expression levels of LDOC1 in the saliva of oral squamous cell carcinoma (OSCC) subjects, and investigated its correlation with various clinicopathological characteristics. The expression levels of salivary LDOC1 were detected in 53 OSCC subjects and 43 healthy controls using quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis. We used Fisher’s exact test to analyze the correlations between expression levels and clinicopathological characteristics. Results Salivary LDOC1 was significantly upregulated in females with OSCC (p = 0.0072), and significantly downregulated in males with OSCC (p = 0.0206). Eighty-nine percent of male OSCC subjects who smoked expressed low levels of LDOC1. OSCC cell lines derived from male OSCC subjects expressed low levels of LDOC1. Conclusions A high level of salivary LDOC1 expression is a biomarker of OSCC in females. A high percentage of male OSCC subjects who smoke express low levels of salivary LDOC1. A low level of salivary LDOC1 expression is a biomarker of OSCC in males.
bibliographic citation: Liu et al. (2019) Salivary LDOC1 is a gender-difference biomarker of oral squamous cell carcinoma. PeerJ 7:e6732 https://doi.org/10.7717/peerj.6732
date submitted: 2019-01-31
date accepted: 2019-03-05
issued: 2019-04-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chung-Ji
author list: Agent
  family name: Chen
  given name: Jen-Hao
author list: Agent
  family name: Hsia
  given name: Shih-Min
author list: Agent
  family name: Liao
  given name: Chiu-Chu
author list: Agent
  family name: Chang
  given name: Hui-Wen
author list: Agent
  family name: Shieh
  given name: Tzong-Ming
author list: Agent
  family name: Shih
  given name: Yin-Hwa
doi: 10.7717/peerj.6732
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-09
copyright: ©2019 Liu et al.
attribution name: Liu et al.

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