PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Influence of acute combined physical and cognitive exercise on cognitive function: an NIRS study
items: Spatiotemporal patterns of urban thermal environment and comfort across 180 cities in summer under China’s rapid urbanization
items: Physiological and immunological responses of sea cucumber Apostichopus japonicus during desiccation and subsequent resubmersion
items: Reconstruction of insect hormone pathways in an aquatic firefly, Sclerotia aquatilis (Coleoptera: Lampyridae), using RNA-seq
items: Age-associated changes of cytochrome P450 and related phase-2 gene/proteins in livers of rats
items: Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression
items: Histological evaluation of five suture materials in the telson ligament of the American horseshoe crab (Limulus polyphemus)
items: Taxonomic revision of black salamanders of the Aneides flavipunctatus complex (Caudata: Plethodontidae)
items: Fleas of black rats (Rattus rattus) as reservoir host of Bartonella spp. in Chile
items: Bioremediation of engine-oil contaminated soil using local residual organic matter

Influence of acute combined physical and cognitive exercise on cognitive function: an NIRS study
type: item
type: AcademicArticle
description: The purpose of this study is to investigate the effects of different types of acute exercise on cognitive function and cerebral oxygenation. A within-subject design was adopted. In total, 20 healthy older adults were enrolled in the study. They came to the laboratory individually on four separate days and completed four conditions of activity. Four conditions were sedentary reading control (RC), cognitive exercise (CE), physical exercise (PE) and cognitive + physical exercise (CE + PE). During these visits, participants completed the Stroop task before and immediately after the experimental condition, which consisted of 15 min of aerobic exercise, verbal fluency task (VFT), and dual task. The Stroop task included the following two conditions: a naming condition and an executive condition. The fNIRS is an optical method using near-infrared light to measure relative changes of oxygenated (O2Hb) and deoxygenated (HHb) hemoglobin in the cortex. The results indicate that acute exercise facilitates performance for executive tasks, not only combined cognition, but also the different results between combined exercise and single exercise. The fNIRS findings showed that acute single exercise influences oxygenation for executive tasks but not for naming tasks. Greater improvement was observed in the post-exercise session of combined exercise during the modified Stroop. These findings demonstrate that acute single exercise, single cognition exercise, and combined exercise enhanced the performance of the inhibition control task. Only acute combined exercise has a general facilitative effect on inhibition control. Combined exercise was shown to be superior to single exercise for task-efficient cerebral oxygenation and improved oxygen utilization during cortical activation in older individuals. Also, to maximize the performance of cognition it may be important for older adults to take part in more cognitive demand exercise or take more kinds of exercise.
format: application/pdf
format: text/html
creator: Zhiguang Ji
creator: Tian Feng
creator: Lingnan Mei
creator: Anmin Li
creator: Chunhua Zhang
subject: Neuroscience
subject: Geriatrics
subject: Neurology
subject: Ophthalmology
description: doi:10.7717/peerj.7418
publisher: PeerJ Inc.
rights: © 2019 Ji et al.
abstract: The purpose of this study is to investigate the effects of different types of acute exercise on cognitive function and cerebral oxygenation. A within-subject design was adopted. In total, 20 healthy older adults were enrolled in the study. They came to the laboratory individually on four separate days and completed four conditions of activity. Four conditions were sedentary reading control (RC), cognitive exercise (CE), physical exercise (PE) and cognitive + physical exercise (CE + PE). During these visits, participants completed the Stroop task before and immediately after the experimental condition, which consisted of 15 min of aerobic exercise, verbal fluency task (VFT), and dual task. The Stroop task included the following two conditions: a naming condition and an executive condition. The fNIRS is an optical method using near-infrared light to measure relative changes of oxygenated (O2Hb) and deoxygenated (HHb) hemoglobin in the cortex. The results indicate that acute exercise facilitates performance for executive tasks, not only combined cognition, but also the different results between combined exercise and single exercise. The fNIRS findings showed that acute single exercise influences oxygenation for executive tasks but not for naming tasks. Greater improvement was observed in the post-exercise session of combined exercise during the modified Stroop. These findings demonstrate that acute single exercise, single cognition exercise, and combined exercise enhanced the performance of the inhibition control task. Only acute combined exercise has a general facilitative effect on inhibition control. Combined exercise was shown to be superior to single exercise for task-efficient cerebral oxygenation and improved oxygen utilization during cortical activation in older individuals. Also, to maximize the performance of cognition it may be important for older adults to take part in more cognitive demand exercise or take more kinds of exercise.
bibliographic citation: Ji et al. (2019) Influence of acute combined physical and cognitive exercise on cognitive function: an NIRS study. PeerJ 7:e7418 https://doi.org/10.7717/peerj.7418
date submitted: 2018-09-19
date accepted: 2019-07-05
issued: 2019-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Zhiguang
author list: Agent
  family name: Feng
  given name: Tian
author list: Agent
  family name: Mei
  given name: Lingnan
author list: Agent
  family name: Li
  given name: Anmin
author list: Agent
  family name: Zhang
  given name: Chunhua
doi: 10.7717/peerj.7418
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-02
copyright: ©2019 Ji et al.
attribution name: Ji et al.

Spatiotemporal patterns of urban thermal environment and comfort across 180 cities in summer under China’s rapid urbanization
type: item
type: AcademicArticle
description: Background China is considered as the largest and most rapidly urbanizing nation in the world. However, possible changes of urban thermal environment and comfort under the rapid urbanization in China still remain poorly understood at a national scale. Methods Based on the data collected from 180 cities in 1990, 2005, and 2015 in China, the spatiotemporal patterns of urban thermal environment and comfort in summer and their relationships with urbanization variables were investigated in this study. Results Our results indicate that urban thermal environment has changed greatly during the 25 years. Furthermore, the changes of urban climate in different regions are inconsistent. The Physiological Equivalent Temperature (PET) at most cities (81%) in China increased from 1990 to 2015, which suggested that urban thermal comfort in China was also deteriorating during the 25 years. However, while the PET of some cities in China began to decrease from 2005 to 2015, there were still 33% of cities that had positive trends,which mainly located in North region. Urbanization resulted in a significant influence on urban climate. Compared to southern cities, northern cities were more sensitive to urbanization impact. The most important contribution to increasing of PET for urbanization variables is gross domestic product, followed by urban population. The analysis results reveal changing patterns of urban thermal comfort in China during summer season. It can help urban government and managers improve urban thermal environment and comfort.
format: application/pdf
format: text/html
creator: Zhibin Ren
creator: Yao Fu
creator: Yunxia Du
creator: Hongbo Zhao
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.7424
publisher: PeerJ Inc.
rights: © 2019 Ren et al.
abstract: Background China is considered as the largest and most rapidly urbanizing nation in the world. However, possible changes of urban thermal environment and comfort under the rapid urbanization in China still remain poorly understood at a national scale. Methods Based on the data collected from 180 cities in 1990, 2005, and 2015 in China, the spatiotemporal patterns of urban thermal environment and comfort in summer and their relationships with urbanization variables were investigated in this study. Results Our results indicate that urban thermal environment has changed greatly during the 25 years. Furthermore, the changes of urban climate in different regions are inconsistent. The Physiological Equivalent Temperature (PET) at most cities (81%) in China increased from 1990 to 2015, which suggested that urban thermal comfort in China was also deteriorating during the 25 years. However, while the PET of some cities in China began to decrease from 2005 to 2015, there were still 33% of cities that had positive trends,which mainly located in North region. Urbanization resulted in a significant influence on urban climate. Compared to southern cities, northern cities were more sensitive to urbanization impact. The most important contribution to increasing of PET for urbanization variables is gross domestic product, followed by urban population. The analysis results reveal changing patterns of urban thermal comfort in China during summer season. It can help urban government and managers improve urban thermal environment and comfort.
bibliographic citation: Ren et al. (2019) Spatiotemporal patterns of urban thermal environment and comfort across 180 cities in summer under China’s rapid urbanization. PeerJ 7:e7424 https://doi.org/10.7717/peerj.7424
date submitted: 2019-04-27
date accepted: 2019-07-07
issued: 2019-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Zhibin
author list: Agent
  family name: Fu
  given name: Yao
author list: Agent
  family name: Du
  given name: Yunxia
author list: Agent
  family name: Zhao
  given name: Hongbo
doi: 10.7717/peerj.7424
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-02
copyright: ©2019 Ren et al.
attribution name: Ren et al.

Physiological and immunological responses of sea cucumber Apostichopus japonicus during desiccation and subsequent resubmersion
type: item
type: AcademicArticle
description: Desiccation is one of the extremely stressful situations experienced by aquatic animals, and sea cucumber usually suffers from desiccation stress during transportation without water. The present study was conducted to evaluate the effect of desiccation and subsequent resubmersion on physiological stress, oxidative damage, antioxidant status and non-specific immune response of Apostichopus japonicus, providing valuable information on the health management of sea cucumber culturing. Control and desiccation groups were set up, and each group has three replicates. After 1, 3 and 6 h of desiccation, individuals were resubmersed in aerated seawater for a 24 h recovery in three batches, which were represented as D1, D3 and D6, respectively. The results showed that glucose level in coelomic fluid of sea cucumber significantly decreased after desiccation, whereas lactate, cortisol and osmolality showed remarkable ascending trends. Thereafter, all stress parameters gently recovered towards normal levels as control group during 24 h resubmersion. The prolonged desiccation at D6 treatment induced the significant increases of malondialdehyde (MDA) and reactive oxygen species (ROS) contents, as well as relatively lower superoxide dismutase (SOD) and catalase (CAT) activities. During the period of desiccation and subsequent resubmersion, sea cucumber adjusted antioxidant defense to reduce the concentrations of MDA and ROS as a strategy for protecting against oxidative damage. Desiccation also had significant effects on non-specific immune parameters (total coelomocytes counts, TCC; complement C3; total nitric oxide synthase, T-NOS; lysozyme, LSZ; alkaline phosphatase, AKP) of A. japonicus, which could be recovered to some extent during resubmersion. In conclusion, less than 6 h of desiccation did not induce irreparable damage to sea cucumber, and was recommended for handling and shipping live sea cucumbers.
format: application/pdf
format: text/html
creator: Shiying Hou
creator: Zewei Jin
creator: Wenwen Jiang
creator: Liang Chi
creator: Bin Xia
creator: Jinghua Chen
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Immunology
subject: Metabolic Sciences
subject: Environmental Impacts
description: doi:10.7717/peerj.7427
publisher: PeerJ Inc.
rights: © 2019 Hou et al.
abstract: Desiccation is one of the extremely stressful situations experienced by aquatic animals, and sea cucumber usually suffers from desiccation stress during transportation without water. The present study was conducted to evaluate the effect of desiccation and subsequent resubmersion on physiological stress, oxidative damage, antioxidant status and non-specific immune response of Apostichopus japonicus, providing valuable information on the health management of sea cucumber culturing. Control and desiccation groups were set up, and each group has three replicates. After 1, 3 and 6 h of desiccation, individuals were resubmersed in aerated seawater for a 24 h recovery in three batches, which were represented as D1, D3 and D6, respectively. The results showed that glucose level in coelomic fluid of sea cucumber significantly decreased after desiccation, whereas lactate, cortisol and osmolality showed remarkable ascending trends. Thereafter, all stress parameters gently recovered towards normal levels as control group during 24 h resubmersion. The prolonged desiccation at D6 treatment induced the significant increases of malondialdehyde (MDA) and reactive oxygen species (ROS) contents, as well as relatively lower superoxide dismutase (SOD) and catalase (CAT) activities. During the period of desiccation and subsequent resubmersion, sea cucumber adjusted antioxidant defense to reduce the concentrations of MDA and ROS as a strategy for protecting against oxidative damage. Desiccation also had significant effects on non-specific immune parameters (total coelomocytes counts, TCC; complement C3; total nitric oxide synthase, T-NOS; lysozyme, LSZ; alkaline phosphatase, AKP) of A. japonicus, which could be recovered to some extent during resubmersion. In conclusion, less than 6 h of desiccation did not induce irreparable damage to sea cucumber, and was recommended for handling and shipping live sea cucumbers.
bibliographic citation: Hou et al. (2019) Physiological and immunological responses of sea cucumber Apostichopus japonicus during desiccation and subsequent resubmersion. PeerJ 7:e7427 https://doi.org/10.7717/peerj.7427
date submitted: 2019-04-28
date accepted: 2019-07-07
issued: 2019-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Shiying
author list: Agent
  family name: Jin
  given name: Zewei
author list: Agent
  family name: Jiang
  given name: Wenwen
author list: Agent
  family name: Chi
  given name: Liang
author list: Agent
  family name: Xia
  given name: Bin
author list: Agent
  family name: Chen
  given name: Jinghua
doi: 10.7717/peerj.7427
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-02
copyright: ©2019 Hou et al.
attribution name: Hou et al.

Reconstruction of insect hormone pathways in an aquatic firefly, Sclerotia aquatilis (Coleoptera: Lampyridae), using RNA-seq
type: item
type: AcademicArticle
description: Insect hormones: ecdysteroids and juvenile hormones have crucial functions during the regulation of different developmental pathways in insects. Insect metamorphosis is one of the primary pathways regulated by these hormones. The insect hormone biosynthetic pathway is conserved among arthropods, including insects, with some variations in the form of hormones used among each group of insects. In this study, the candidate genes involved in the insect hormone pathways and their functional roles were assessed in an aquatic firefly, Sclerotia aquatilis using a high-throughput RNA sequencing technique. Illumina next-generation sequencing (NGS) was used to generate transcriptome data for the different developmental stages (i.e., larva, pupa, and adult) of S. aquatilis. A total of 82,022 unigenes were generated across all different developmental stages. Functional annotation was performed for each gene, based on multiple biological databases, generating 46,230 unigenes. These unigenes were subsequently mapped using KEGG pathways. Accordingly, 221 protein-encoding genes involved in the insect hormone pathways were identified, including, JHAMT, CYP15A1, JHE, and Halloween family genes. Twenty potential gene candidates associated with the biosynthetic and degradation pathways for insect hormones were subjected to real-time PCR, reverse transcriptase PCR (RT-PCR) and sequencing analyses. The real-time PCR results showed similar expression patterns as those observed for transcriptome expression profiles for most of the examined genes. RT-PCR and Sanger sequencing confirmed the expressed coding sequences of these gene candidates. This study is the first to examine firefly insect hormone pathways, facilitating a better understanding of firefly growth and development.
format: application/pdf
format: text/html
creator: Pornchanan Chanchay
creator: Wanwipa Vongsangnak
creator: Anchana Thancharoen
creator: Ajaraporn Sriboonlert
subject: Bioinformatics
subject: Developmental Biology
subject: Entomology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.7428
publisher: PeerJ Inc.
rights: © 2019 Chanchay et al.
abstract: Insect hormones: ecdysteroids and juvenile hormones have crucial functions during the regulation of different developmental pathways in insects. Insect metamorphosis is one of the primary pathways regulated by these hormones. The insect hormone biosynthetic pathway is conserved among arthropods, including insects, with some variations in the form of hormones used among each group of insects. In this study, the candidate genes involved in the insect hormone pathways and their functional roles were assessed in an aquatic firefly, Sclerotia aquatilis using a high-throughput RNA sequencing technique. Illumina next-generation sequencing (NGS) was used to generate transcriptome data for the different developmental stages (i.e., larva, pupa, and adult) of S. aquatilis. A total of 82,022 unigenes were generated across all different developmental stages. Functional annotation was performed for each gene, based on multiple biological databases, generating 46,230 unigenes. These unigenes were subsequently mapped using KEGG pathways. Accordingly, 221 protein-encoding genes involved in the insect hormone pathways were identified, including, JHAMT, CYP15A1, JHE, and Halloween family genes. Twenty potential gene candidates associated with the biosynthetic and degradation pathways for insect hormones were subjected to real-time PCR, reverse transcriptase PCR (RT-PCR) and sequencing analyses. The real-time PCR results showed similar expression patterns as those observed for transcriptome expression profiles for most of the examined genes. RT-PCR and Sanger sequencing confirmed the expressed coding sequences of these gene candidates. This study is the first to examine firefly insect hormone pathways, facilitating a better understanding of firefly growth and development.
bibliographic citation: Chanchay et al. (2019) Reconstruction of insect hormone pathways in an aquatic firefly, Sclerotia aquatilis (Coleoptera: Lampyridae), using RNA-seq. PeerJ 7:e7428 https://doi.org/10.7717/peerj.7428
date submitted: 2019-03-16
date accepted: 2019-07-07
issued: 2019-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chanchay
  given name: Pornchanan
author list: Agent
  family name: Vongsangnak
  given name: Wanwipa
author list: Agent
  family name: Thancharoen
  given name: Anchana
author list: Agent
  family name: Sriboonlert
  given name: Ajaraporn
doi: 10.7717/peerj.7428
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-02
copyright: ©2019 Chanchay et al.
attribution name: Chanchay et al.

Age-associated changes of cytochrome P450 and related phase-2 gene/proteins in livers of rats
type: item
type: AcademicArticle
description: Cytochrome P450s (CYPs) are phase-I metabolic enzymes playing important roles in drug metabolism, dietary chemicals and endogenous molecules. Age is a key factor influencing P450s expression. Thus, age-related changes of CYP 1–4 families and bile acid homeostasis-related CYPs, the corresponding nuclear receptors and a few phase-II genes were examined. Livers from male Sprague-Dawley rats at fetus (−2 d), neonates (1, 7, and 14 d), weanling (21 d), puberty (28 and 35 d), adulthood (60 and 180 d), and aging (540 and 800 d) were collected and subjected to qPCR analysis. Liver proteins from 14, 28, 60, 180, 540 and 800 days of age were also extracted for selected protein analysis by western blot. In general, there were three patterns of their expression: Some of the drug-metabolizing enzymes and related nuclear receptors were low in fetal and neonatal stage, increased with liver maturation and decreased quickly at aging (AhR, Cyp1a1, Cyp2b1, Cyp2b2, Cyp3a1, Cyp3a2, Ugt1a2); the majority of P450s (Cyp1a2, Cyp2c6, Cyp2c11, Cyp2d2, Cyp2e1, CAR, PXR, FXR, Cyp7a1, Cyp7b1. Cyp8b1, Cyp27a1, Ugt1a1, Sult1a1, Sult1a2) maintained relatively high levels throughout the adulthood, and decreased at 800 days of age; and some had an early peak between 7 and 14 days (CAR, PXR, PPARα, Cyp4a1, Ugt1a2). The protein expression of CYP1A2, CYP2B1, CYP2E1, CYP3A1, CYP4A1, and CYP7A1 corresponded the trend of mRNA changes. In summary, this study characterized three expression patterns of 16 CYPs, five nuclear receptors, and four phase-II genes during development and aging in rat liver, adding to our understanding of age-related CYP expression changes and age-related disorders.
format: application/pdf
format: text/html
creator: Shang-Fu Xu
creator: An-Ling Hu
creator: Lu Xie
creator: Jia-Jia Liu
creator: Qin Wu
creator: Jie Liu
subject: Biochemistry
subject: Toxicology
subject: Pharmacology
subject: Metabolic Sciences
description: doi:10.7717/peerj.7429
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Cytochrome P450s (CYPs) are phase-I metabolic enzymes playing important roles in drug metabolism, dietary chemicals and endogenous molecules. Age is a key factor influencing P450s expression. Thus, age-related changes of CYP 1–4 families and bile acid homeostasis-related CYPs, the corresponding nuclear receptors and a few phase-II genes were examined. Livers from male Sprague-Dawley rats at fetus (−2 d), neonates (1, 7, and 14 d), weanling (21 d), puberty (28 and 35 d), adulthood (60 and 180 d), and aging (540 and 800 d) were collected and subjected to qPCR analysis. Liver proteins from 14, 28, 60, 180, 540 and 800 days of age were also extracted for selected protein analysis by western blot. In general, there were three patterns of their expression: Some of the drug-metabolizing enzymes and related nuclear receptors were low in fetal and neonatal stage, increased with liver maturation and decreased quickly at aging (AhR, Cyp1a1, Cyp2b1, Cyp2b2, Cyp3a1, Cyp3a2, Ugt1a2); the majority of P450s (Cyp1a2, Cyp2c6, Cyp2c11, Cyp2d2, Cyp2e1, CAR, PXR, FXR, Cyp7a1, Cyp7b1. Cyp8b1, Cyp27a1, Ugt1a1, Sult1a1, Sult1a2) maintained relatively high levels throughout the adulthood, and decreased at 800 days of age; and some had an early peak between 7 and 14 days (CAR, PXR, PPARα, Cyp4a1, Ugt1a2). The protein expression of CYP1A2, CYP2B1, CYP2E1, CYP3A1, CYP4A1, and CYP7A1 corresponded the trend of mRNA changes. In summary, this study characterized three expression patterns of 16 CYPs, five nuclear receptors, and four phase-II genes during development and aging in rat liver, adding to our understanding of age-related CYP expression changes and age-related disorders.
bibliographic citation: Xu et al. (2019) Age-associated changes of cytochrome P450 and related phase-2 gene/proteins in livers of rats. PeerJ 7:e7429 https://doi.org/10.7717/peerj.7429
date submitted: 2019-04-10
date accepted: 2019-07-07
issued: 2019-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Shang-Fu
author list: Agent
  family name: Hu
  given name: An-Ling
author list: Agent
  family name: Xie
  given name: Lu
author list: Agent
  family name: Liu
  given name: Jia-Jia
author list: Agent
  family name: Wu
  given name: Qin
author list: Agent
  family name: Liu
  given name: Jie
doi: 10.7717/peerj.7429
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-02
copyright: ©2019 Xu et al.
attribution name: Xu et al.

Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression
type: item
type: AcademicArticle
description: Delta bovine papillomaviruses (δBPVs) mainly infect cattle and cause fibropapillomas. δBPVs encode three oncogenes, E5, E6 and E7. The effect of E6 on microRNA (miRNA) and mRNA expression profiles is not well characterized. In this study, RNA sequencing and small RNA sequencing were used to explore alterations in mRNAs and miRNAs in E6 over-expressing NIH/3T3 cells (NH-E6) compared with control cells (NH-GFP). We found that 350 genes (181 upregulated and 169 downregulated) and 54 miRNAs (26 upregulated and 28 downregulated) were differentially expressed (DE) following E6 expression. The top 20 significantly enriched GO terms in “biological process” included inflammatory response, innate immune response, immune response, immune system process, positive regulation of apoptotic process, cell adhesion, and angiogenesis. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, we selected 19 immune-response related DEGs and 11 DE miRNAs for qPCR validation. Of these, upregulation of 12 genes, Ccl2, Ccl7, Cxcl1, Cxcl5, Tlr2, Nfkbia, Fas, Il1rl1, Ltbp1, Rab32, and Zc3h12a, Dclk1 and downregulation of four genes, Agtr2, Ptx3, Sfrp1, and Thbs1 were confirmed. Ccl2, Ccl7, Cxcl1 and Cxcl5 were upregulated more than ten-fold in NH-E6 compared with NH-GFP. Also, upregulation of three miRNAs, mmu-miR-129-2-3p, mmu-miR-149-5p-R-2 and mmu-miR-222-3p, and downregulation of five miRNAs, mmu-miR-582-3p-R+1, mmu-miR-582-5p, mmu-miR-708-3p, mmu-miR-708-5p and mmu-miR-1197-3p, were confirmed. Our study describes changes in both mRNA and miRNA profiles in response to BPV E6 expression, providing new insights into BPV E6 oncogene functions.
format: application/pdf
format: text/html
creator: Feng Pang
creator: Mengmeng Zhang
creator: Guohua Li
creator: Zhenxing Zhang
creator: Haifeng Huang
creator: Baobao Li
creator: Chengqiang Wang
creator: Xiaohong Yang
creator: Yiying Zheng
creator: Qi An
creator: Luyin Zhang
creator: Li Du
creator: Fengyang Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.7442
publisher: PeerJ Inc.
rights: © 2019 Pang et al.
abstract: Delta bovine papillomaviruses (δBPVs) mainly infect cattle and cause fibropapillomas. δBPVs encode three oncogenes, E5, E6 and E7. The effect of E6 on microRNA (miRNA) and mRNA expression profiles is not well characterized. In this study, RNA sequencing and small RNA sequencing were used to explore alterations in mRNAs and miRNAs in E6 over-expressing NIH/3T3 cells (NH-E6) compared with control cells (NH-GFP). We found that 350 genes (181 upregulated and 169 downregulated) and 54 miRNAs (26 upregulated and 28 downregulated) were differentially expressed (DE) following E6 expression. The top 20 significantly enriched GO terms in “biological process” included inflammatory response, innate immune response, immune response, immune system process, positive regulation of apoptotic process, cell adhesion, and angiogenesis. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, we selected 19 immune-response related DEGs and 11 DE miRNAs for qPCR validation. Of these, upregulation of 12 genes, Ccl2, Ccl7, Cxcl1, Cxcl5, Tlr2, Nfkbia, Fas, Il1rl1, Ltbp1, Rab32, and Zc3h12a, Dclk1 and downregulation of four genes, Agtr2, Ptx3, Sfrp1, and Thbs1 were confirmed. Ccl2, Ccl7, Cxcl1 and Cxcl5 were upregulated more than ten-fold in NH-E6 compared with NH-GFP. Also, upregulation of three miRNAs, mmu-miR-129-2-3p, mmu-miR-149-5p-R-2 and mmu-miR-222-3p, and downregulation of five miRNAs, mmu-miR-582-3p-R+1, mmu-miR-582-5p, mmu-miR-708-3p, mmu-miR-708-5p and mmu-miR-1197-3p, were confirmed. Our study describes changes in both mRNA and miRNA profiles in response to BPV E6 expression, providing new insights into BPV E6 oncogene functions.
bibliographic citation: Pang et al. (2019) Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression. PeerJ 7:e7442 https://doi.org/10.7717/peerj.7442
date submitted: 2019-04-18
date accepted: 2019-07-09
issued: 2019-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pang
  given name: Feng
author list: Agent
  family name: Zhang
  given name: Mengmeng
author list: Agent
  family name: Li
  given name: Guohua
author list: Agent
  family name: Zhang
  given name: Zhenxing
author list: Agent
  family name: Huang
  given name: Haifeng
author list: Agent
  family name: Li
  given name: Baobao
author list: Agent
  family name: Wang
  given name: Chengqiang
author list: Agent
  family name: Yang
  given name: Xiaohong
author list: Agent
  family name: Zheng
  given name: Yiying
author list: Agent
  family name: An
  given name: Qi
author list: Agent
  family name: Zhang
  given name: Luyin
author list: Agent
  family name: Du
  given name: Li
author list: Agent
  family name: Wang
  given name: Fengyang
doi: 10.7717/peerj.7442
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-02
copyright: ©2019 Pang et al.
attribution name: Pang et al.

Histological evaluation of five suture materials in the telson ligament of the American horseshoe crab (Limulus polyphemus)
type: item
type: AcademicArticle
description: An ideal suture material supports healing, minimizes inflammation, and decreases the likelihood of secondary infection. While there are published recommendations for suture materials in some invertebrates, there are no published recommendations for Limulus polyphemus or any chelicerate. This study evaluates the histological reaction of horseshoe crabs to five commonly used suture materials: monofilament nylon, silk, poliglecaprone, polydioxanone, and polyglycolic acid. None of the materials were superior with regards to holding nor was there any dehiscence. Nylon evoked the least amount of tissue reaction. This work also provides a histopathological description of the soft membrane at the hinge area between the opisthosoma and telson (telson ligament) and comments on euthanasia with intracardiac eugenol.
format: application/pdf
format: text/html
creator: Ami E. Krasner
creator: Amy Hancock-Ronemus
creator: Larry S. Christian
creator: Emily H. Griffith
creator: Gregory A. Lewbart
creator: Jerry M. Law
subject: Marine Biology
subject: Veterinary Medicine
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.7061
publisher: PeerJ Inc.
rights: © 2019 Krasner et al.
abstract: An ideal suture material supports healing, minimizes inflammation, and decreases the likelihood of secondary infection. While there are published recommendations for suture materials in some invertebrates, there are no published recommendations for Limulus polyphemus or any chelicerate. This study evaluates the histological reaction of horseshoe crabs to five commonly used suture materials: monofilament nylon, silk, poliglecaprone, polydioxanone, and polyglycolic acid. None of the materials were superior with regards to holding nor was there any dehiscence. Nylon evoked the least amount of tissue reaction. This work also provides a histopathological description of the soft membrane at the hinge area between the opisthosoma and telson (telson ligament) and comments on euthanasia with intracardiac eugenol.
bibliographic citation: Krasner et al. (2019) Histological evaluation of five suture materials in the telson ligament of the American horseshoe crab (Limulus polyphemus). PeerJ 7:e7061 https://doi.org/10.7717/peerj.7061
date submitted: 2018-11-12
date accepted: 2019-05-03
issued: 2019-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krasner
  given name: Ami E.
author list: Agent
  family name: Hancock-Ronemus
  given name: Amy
author list: Agent
  family name: Christian
  given name: Larry S.
author list: Agent
  family name: Griffith
  given name: Emily H.
author list: Agent
  family name: Lewbart
  given name: Gregory A.
author list: Agent
  family name: Law
  given name: Jerry M.
doi: 10.7717/peerj.7061
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-01
copyright: ©2019 Krasner et al.
attribution name: Krasner et al.

Taxonomic revision of black salamanders of the Aneides flavipunctatus complex (Caudata: Plethodontidae)
type: item
type: AcademicArticle
description: We present a taxonomic revision of the black salamander (Aneides flavipunctatus) complex of northwestern California and extreme southeastern Oregon. The revision is based on a number of published works as well as new molecular and morphological data presented herein. The subspecies Aneides flavipunctatus niger Myers & Maslin 1948 is raised in rank to a full species. It is isolated far to the south of the main range on the San Francisco Peninsula, south and west of San Francisco Bay. Another geographically isolated set of populations occurs well inland in Shasta County, northern CA, mainly in the vicinity of Shasta Lake. It is raised from synonymy and recognized as Aneides iecanus (Cope 1883). The remaining taxa occur mainly along and inland from the coast from the vicinity of the Russian River and Lake Berryessa/Putah Creek, north to the vicinity of the Smith River near the Oregon border and more inland along the Klamath and Trinity Rivers and tributaries into Oregon. The northern segment of this nearly continuous range is named Aneides klamathensis Reilly and Wake 2019. We use molecular data to provide a detailed examination of a narrow contact zone between the northern A. klamathensis and the more southern A. flavipunctatus in southern Humboldt County in the vicinity of the Van Duzen and main fork of the Eel rivers. To the south is the remnant of the former species and it takes the name Aneides flavipunctatus (Strauch 1870). It is highly diversified morphologically and genetically and requires additional study.
format: application/pdf
format: text/html
creator: Sean B. Reilly
creator: David B. Wake
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7370
publisher: PeerJ Inc.
rights: © 2019 Reilly and Wake
abstract: We present a taxonomic revision of the black salamander (Aneides flavipunctatus) complex of northwestern California and extreme southeastern Oregon. The revision is based on a number of published works as well as new molecular and morphological data presented herein. The subspecies Aneides flavipunctatus niger Myers & Maslin 1948 is raised in rank to a full species. It is isolated far to the south of the main range on the San Francisco Peninsula, south and west of San Francisco Bay. Another geographically isolated set of populations occurs well inland in Shasta County, northern CA, mainly in the vicinity of Shasta Lake. It is raised from synonymy and recognized as Aneides iecanus (Cope 1883). The remaining taxa occur mainly along and inland from the coast from the vicinity of the Russian River and Lake Berryessa/Putah Creek, north to the vicinity of the Smith River near the Oregon border and more inland along the Klamath and Trinity Rivers and tributaries into Oregon. The northern segment of this nearly continuous range is named Aneides klamathensis Reilly and Wake 2019. We use molecular data to provide a detailed examination of a narrow contact zone between the northern A. klamathensis and the more southern A. flavipunctatus in southern Humboldt County in the vicinity of the Van Duzen and main fork of the Eel rivers. To the south is the remnant of the former species and it takes the name Aneides flavipunctatus (Strauch 1870). It is highly diversified morphologically and genetically and requires additional study.
bibliographic citation: Reilly et al. (2019) Taxonomic revision of black salamanders of the Aneides flavipunctatus complex (Caudata: Plethodontidae). PeerJ 7:e7370 https://doi.org/10.7717/peerj.7370
date submitted: 2019-04-09
date accepted: 2019-06-27
issued: 2019-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reilly
  given name: Sean B.
author list: Agent
  family name: Wake
  given name: David B.
doi: 10.7717/peerj.7370
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-01
copyright: ©2019 Reilly and Wake
attribution name: Reilly and Wake

Fleas of black rats (Rattus rattus) as reservoir host of Bartonella spp. in Chile
type: item
type: AcademicArticle
description: Background Rattus rattus is a widely distributed, invasive species that presents an important role in disease transmission, either directly or through vector arthropods such as fleas. These black rats can transmit a wide variety of pathogens, including bacteria of the genus Bartonella, which can cause diseases in humans and animals. In Chile, no data are available identifying fleas from synanthropic rodents as Bartonella vectors. The aim of this study was to investigate the prevalence of Bartonella spp. in the fleas of R. rattus in areas with different climate conditions and featuring different human population densities. Methods In all, 174 fleas collected from 261 R. rattus captured from 30 localities with different human densities (cities, villages, and wild areas) across five hydrographic zones of Chile (hyper-arid, arid, semi-arid, sub-humid, and hyper-humid) were examined. Bartonella spp. presence was determined through polymerase chain reaction, using gltA and rpoB genes, which were concatenated to perform a similarity analysis with BLAST and phylogenetic analysis. Results Overall, 15 fleas species were identified; Bartonella gltA and rpoB fragments were detected in 21.2% (37/174) and 19.5% (34/174) of fleas, respectively. A total of 10 of the 15 fleas species found were positive for Bartonella DNA. Leptopsylla segnis was the most commonly collected flea species (n = 55), and it also presented a high prevalence of Bartonella DNA (P% = 34.5%). The highest numbers of fleas of this species were collected in villages of the arid zone. There were no seasonal differences in the prevalence of Bartonella DNA. The presence of Bartonella DNA in fleas was recorded in all hydrographic areas, and the arid zone presented the highest prevalence of this species. Regarding areas with different human densities, the highest prevalence was noted in the villages (34.8% gltA and 31.8% rpoB), followed by cities (14.8% gltA and 11.1% rpoB) and wild areas (7.4% gltA and 14.8% rpoB). …
format: application/pdf
format: text/html
creator: Lucila Moreno Salas
creator: Mario Espinoza-Carniglia
creator: Nicol Lizama Schmeisser
creator: L. Gonzalo Torres
creator: María Carolina Silva-de la Fuente
creator: Marcela Lareschi
creator: Daniel González-Acuña
subject: Parasitology
subject: Veterinary Medicine
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.7371
publisher: PeerJ Inc.
rights: © 2019 Moreno Salas et al.
abstract: Background Rattus rattus is a widely distributed, invasive species that presents an important role in disease transmission, either directly or through vector arthropods such as fleas. These black rats can transmit a wide variety of pathogens, including bacteria of the genus Bartonella, which can cause diseases in humans and animals. In Chile, no data are available identifying fleas from synanthropic rodents as Bartonella vectors. The aim of this study was to investigate the prevalence of Bartonella spp. in the fleas of R. rattus in areas with different climate conditions and featuring different human population densities. Methods In all, 174 fleas collected from 261 R. rattus captured from 30 localities with different human densities (cities, villages, and wild areas) across five hydrographic zones of Chile (hyper-arid, arid, semi-arid, sub-humid, and hyper-humid) were examined. Bartonella spp. presence was determined through polymerase chain reaction, using gltA and rpoB genes, which were concatenated to perform a similarity analysis with BLAST and phylogenetic analysis. Results Overall, 15 fleas species were identified; Bartonella gltA and rpoB fragments were detected in 21.2% (37/174) and 19.5% (34/174) of fleas, respectively. A total of 10 of the 15 fleas species found were positive for Bartonella DNA. Leptopsylla segnis was the most commonly collected flea species (n = 55), and it also presented a high prevalence of Bartonella DNA (P% = 34.5%). The highest numbers of fleas of this species were collected in villages of the arid zone. There were no seasonal differences in the prevalence of Bartonella DNA. The presence of Bartonella DNA in fleas was recorded in all hydrographic areas, and the arid zone presented the highest prevalence of this species. Regarding areas with different human densities, the highest prevalence was noted in the villages (34.8% gltA and 31.8% rpoB), followed by cities (14.8% gltA and 11.1% rpoB) and wild areas (7.4% gltA and 14.8% rpoB). …
bibliographic citation: Moreno Salas et al. (2019) Fleas of black rats (Rattus rattus) as reservoir host of Bartonella spp. in Chile. PeerJ 7:e7371 https://doi.org/10.7717/peerj.7371
date submitted: 2019-04-26
date accepted: 2019-06-27
issued: 2019-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreno Salas
  given name: Lucila
author list: Agent
  family name: Espinoza-Carniglia
  given name: Mario
author list: Agent
  family name: Lizama Schmeisser
  given name: Nicol
author list: Agent
  family name: Torres
  given name: L. Gonzalo
author list: Agent
  family name: Silva-de la Fuente
  given name: María Carolina
author list: Agent
  family name: Lareschi
  given name: Marcela
author list: Agent
  family name: González-Acuña
  given name: Daniel
doi: 10.7717/peerj.7371
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-01
copyright: © 2019 Moreno Salas et al.
attribution name: Moreno Salas et al.

Bioremediation of engine-oil contaminated soil using local residual organic matter
type: item
type: AcademicArticle
description: Soil remediation industries continue to seek technologies to speed-up treatment and reduce operating costs. Some processes are energy intensive and, in some cases, transport can be the main source of carbon emissions. Residual fertilizing materials (RFM), such as organic residues, have the potential to be beneficial bioremediation agents. Following a circular economy framework, we investigated the feasibility of sourcing RFMs locally to reduce transport and assess possible bioremediation efficiency gains. RFMs were recruited within 100 km of the treatment site: ramial chipped wood (RCW), horse manure (MANR) and brewer spent grain (BSG). They were added to the land treatment unit’s baseline fertilizer treatment (FERT, “F”) to measure if they improved the remediation efficiency of an engine oil-contaminated soil (7,500 ± 100 mg kg−1). Results indicate that MANR-F was the only amendment more effective than FERT for petroleum hydrocarbons (PHC) reduction, while emitting the least CO2 overall. RCW-F was equivalent to FERT but retained more moisture. Although BSG contributed the most nitrogen to the soil, BSG-F retained excessive moisture, emitted more volatile organic compounds, contained less soil O2, and was less effective than the baseline treatment. Significantly more of the C16–C22 fraction was removed (63% ± 22%) than all other fractions (C22–C28, C28–C34, C34–C40), which were equally removed. Microbial community-level physiological profiling was conducted with Biolog Ecoplates™, and catabolic diversity differed between treatments (utilization rates of 31 carbon sources). MANR-F has the potential to increase PHC-remediation speed and efficiency compared to inorganic fertilizer alone. Other RFM promote moisture retention and diverse microbial catabolic activity. A variety of RFM are present across the globe and some can offer low-cost amendments to boost remediation efficiency, while reducing treatment time compared to traditional fertilizer-only methods.
format: application/pdf
format: text/html
creator: Kawina Robichaud
creator: Miriam Lebeau
creator: Sylvain Martineau
creator: Marc Amyot
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.7389
publisher: PeerJ Inc.
rights: © 2019 Robichaud et al.
abstract: Soil remediation industries continue to seek technologies to speed-up treatment and reduce operating costs. Some processes are energy intensive and, in some cases, transport can be the main source of carbon emissions. Residual fertilizing materials (RFM), such as organic residues, have the potential to be beneficial bioremediation agents. Following a circular economy framework, we investigated the feasibility of sourcing RFMs locally to reduce transport and assess possible bioremediation efficiency gains. RFMs were recruited within 100 km of the treatment site: ramial chipped wood (RCW), horse manure (MANR) and brewer spent grain (BSG). They were added to the land treatment unit’s baseline fertilizer treatment (FERT, “F”) to measure if they improved the remediation efficiency of an engine oil-contaminated soil (7,500 ± 100 mg kg−1). Results indicate that MANR-F was the only amendment more effective than FERT for petroleum hydrocarbons (PHC) reduction, while emitting the least CO2 overall. RCW-F was equivalent to FERT but retained more moisture. Although BSG contributed the most nitrogen to the soil, BSG-F retained excessive moisture, emitted more volatile organic compounds, contained less soil O2, and was less effective than the baseline treatment. Significantly more of the C16–C22 fraction was removed (63% ± 22%) than all other fractions (C22–C28, C28–C34, C34–C40), which were equally removed. Microbial community-level physiological profiling was conducted with Biolog Ecoplates™, and catabolic diversity differed between treatments (utilization rates of 31 carbon sources). MANR-F has the potential to increase PHC-remediation speed and efficiency compared to inorganic fertilizer alone. Other RFM promote moisture retention and diverse microbial catabolic activity. A variety of RFM are present across the globe and some can offer low-cost amendments to boost remediation efficiency, while reducing treatment time compared to traditional fertilizer-only methods.
bibliographic citation: Robichaud et al. (2019) Bioremediation of engine-oil contaminated soil using local residual organic matter. PeerJ 7:e7389 https://doi.org/10.7717/peerj.7389
date submitted: 2019-02-19
date accepted: 2019-07-01
issued: 2019-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robichaud
  given name: Kawina
author list: Agent
  family name: Lebeau
  given name: Miriam
author list: Agent
  family name: Martineau
  given name: Sylvain
author list: Agent
  family name: Amyot
  given name: Marc
doi: 10.7717/peerj.7389
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-01
copyright: © 2019 Robichaud et al.
attribution name: Robichaud et al.

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