PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: RNA-sequencing analysis of the effect of luteolin on methamphetamine-induced hepatotoxicity in rats: a preliminary study
items: Genome-wide identification and characterization of the soybean SOD family during alkaline stress
items: Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.)
items: Isolation and characterization of vaginal Lactobacillus spp. in dromedary camels (Camelus dromedarius): in vitro evaluation of probiotic potential of selected isolates
items: Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing
items: Postharvest biochemical characteristics and ultrastructure of Coprinus comatus
items: Niche differentiation in the rhizosphere and endosphere fungal microbiome of wild Paris polyphylla Sm.
items: Association of the CACNA2D2 gene with schizophrenia in Chinese Han population
items: Prioritizing riparian corridors for ecosystem restoration in urbanizing watersheds
items: A novel transcript of MEF2D promotes myoblast differentiation and its variations associated with growth traits in chicken

RNA-sequencing analysis of the effect of luteolin on methamphetamine-induced hepatotoxicity in rats: a preliminary study
type: item
type: AcademicArticle
description: In this study, RNA-sequencing (RNA-seq) was utilized to investigate the effects of luteolin on hepatotoxicity caused by methamphetamine (METH). The rats in METH group were administrated with METH (15 mg/kg, two times per day) via intraperitoneal (i.p.) injections for four consecutive days. The rats in luteolin + METH group were firstly administrated with luteolin (100 mg/kg, once a day) by oral gavage for 3 days before METH treatment. Lueolin attenuated the hepatotoxicity induced by METH via histopathological and biochemical analysis. The results of RNA-seq showed that luteolin could regulate 497 differentially expressed genes (DEGs), and the selected DEGs were mainly enriched in eight pathways, according to KEGG analysis. Furthermore, qRT-PCR was utilized to verify the results of RNA-seq. Six genes were selected as follows: liver enriched antimicrobial peptide 2 (Leap2), fatty acid synthase (Fasn), fatty acid binding protein 5 (Fabp5), patatin like phospholipase domain containing 3 (Pnpla3), myelin basic protein (Mbp) and calmodulin 3 (Calm3). Though because of the design flaws, the luteolin group has not been included, this study demonstrated that luteolin might exert hepato-protective effects from METH via modulation of oxidative phosphorylation, cytochrome P450 and certain signaling pathways.
format: application/pdf
format: text/html
creator: Dong Qu
creator: Kaikai Zhang
creator: Lijian Chen
creator: Qi Wang
creator: Huijun Wang
subject: Drugs and Devices
subject: Gastroenterology and Hepatology
subject: Hematology
subject: Pharmacology
subject: Metabolic Sciences
description: doi:10.7717/peerj.8529
publisher: PeerJ Inc.
rights: © 2020 Qu et al.
abstract: In this study, RNA-sequencing (RNA-seq) was utilized to investigate the effects of luteolin on hepatotoxicity caused by methamphetamine (METH). The rats in METH group were administrated with METH (15 mg/kg, two times per day) via intraperitoneal (i.p.) injections for four consecutive days. The rats in luteolin + METH group were firstly administrated with luteolin (100 mg/kg, once a day) by oral gavage for 3 days before METH treatment. Lueolin attenuated the hepatotoxicity induced by METH via histopathological and biochemical analysis. The results of RNA-seq showed that luteolin could regulate 497 differentially expressed genes (DEGs), and the selected DEGs were mainly enriched in eight pathways, according to KEGG analysis. Furthermore, qRT-PCR was utilized to verify the results of RNA-seq. Six genes were selected as follows: liver enriched antimicrobial peptide 2 (Leap2), fatty acid synthase (Fasn), fatty acid binding protein 5 (Fabp5), patatin like phospholipase domain containing 3 (Pnpla3), myelin basic protein (Mbp) and calmodulin 3 (Calm3). Though because of the design flaws, the luteolin group has not been included, this study demonstrated that luteolin might exert hepato-protective effects from METH via modulation of oxidative phosphorylation, cytochrome P450 and certain signaling pathways.
bibliographic citation: Qu et al. (2020) RNA-sequencing analysis of the effect of luteolin on methamphetamine-induced hepatotoxicity in rats: a preliminary study. PeerJ 8:e8529 https://doi.org/10.7717/peerj.8529
date submitted: 2019-07-15
date accepted: 2020-01-07
issued: 2020-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qu
  given name: Dong
author list: Agent
  family name: Zhang
  given name: Kaikai
author list: Agent
  family name: Chen
  given name: Lijian
author list: Agent
  family name: Wang
  given name: Qi
author list: Agent
  family name: Wang
  given name: Huijun
doi: 10.7717/peerj.8529
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-06
copyright: © 2020 Qu et al.
attribution name: Qu et al.

Genome-wide identification and characterization of the soybean SOD family during alkaline stress
type: item
type: AcademicArticle
description: Background Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported. Methods We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR. Results In this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1–2), FeSODs (GmFSD1–5) and Cu/ZnSODs (GmCSD1–6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future.
format: application/pdf
format: text/html
creator: Wenxiu Lu
creator: Huizi Duanmu
creator: Yanhua Qiao
creator: Xiaoxia Jin
creator: Yang Yu
creator: Lijie Yu
creator: Chao Chen
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.8457
publisher: PeerJ Inc.
rights: © 2020 Lu et al.
abstract: Background Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported. Methods We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR. Results In this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1–2), FeSODs (GmFSD1–5) and Cu/ZnSODs (GmCSD1–6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future.
bibliographic citation: Lu et al. (2020) Genome-wide identification and characterization of the soybean SOD family during alkaline stress. PeerJ 8:e8457 https://doi.org/10.7717/peerj.8457
date submitted: 2019-07-29
date accepted: 2019-12-24
issued: 2020-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Wenxiu
author list: Agent
  family name: Duanmu
  given name: Huizi
author list: Agent
  family name: Qiao
  given name: Yanhua
author list: Agent
  family name: Jin
  given name: Xiaoxia
author list: Agent
  family name: Yu
  given name: Yang
author list: Agent
  family name: Yu
  given name: Lijie
author list: Agent
  family name: Chen
  given name: Chao
doi: 10.7717/peerj.8457
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-05
copyright: © 2020 Lu et al.
attribution name: Lu et al.

Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.)
type: item
type: AcademicArticle
description: The heat shock transcription factor (Hsf) family, identified as one of the important gene families, participates in plant development process and some stress response. So far, there have been no reports on the research of the Hsf transcription factors in physic nut. In this study, seventeen putative Hsf genes identified from physic nut genome. Phylogenetic analysis manifested these genes classified into three groups: A, B and C. Chromosomal location showed that they distributed eight out of eleven linkage groups. Expression profiling indicated that fourteen JcHsf genes highly expressed in different tissues except JcHsf1, JcHsf6 and JcHsf13. In addition, induction of six and twelve JcHsf genes noted against salt stress and drought stress, respectively, which demonstrated that the JcHsf genes are involved in abiotic stress responses. Our results contribute to a better understanding of the JcHsf gene family and further study of its function.
format: application/pdf
format: text/html
creator: Lin Zhang
creator: Wei Chen
creator: Ben Shi
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8467
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: The heat shock transcription factor (Hsf) family, identified as one of the important gene families, participates in plant development process and some stress response. So far, there have been no reports on the research of the Hsf transcription factors in physic nut. In this study, seventeen putative Hsf genes identified from physic nut genome. Phylogenetic analysis manifested these genes classified into three groups: A, B and C. Chromosomal location showed that they distributed eight out of eleven linkage groups. Expression profiling indicated that fourteen JcHsf genes highly expressed in different tissues except JcHsf1, JcHsf6 and JcHsf13. In addition, induction of six and twelve JcHsf genes noted against salt stress and drought stress, respectively, which demonstrated that the JcHsf genes are involved in abiotic stress responses. Our results contribute to a better understanding of the JcHsf gene family and further study of its function.
bibliographic citation: Zhang et al. (2020) Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.). PeerJ 8:e8467 https://doi.org/10.7717/peerj.8467
date submitted: 2019-08-22
date accepted: 2019-12-27
issued: 2020-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Lin
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: Shi
  given name: Ben
doi: 10.7717/peerj.8467
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-05
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Isolation and characterization of vaginal Lactobacillus spp. in dromedary camels (Camelus dromedarius): in vitro evaluation of probiotic potential of selected isolates
type: item
type: AcademicArticle
description: Lactobacillus spp. is one of the beneficial lactic acid producing microbiota in the vagina, which is important for a healthy vaginal environment. However, little is known about vaginal Lactobacillus in dromedary camels (Camelus dromedarius). Therefore, this study aimed to isolate vaginal lactic acid bacteria (LAB) in dromedary camels and to study the probiotic potential of selected isolates. A total of 75 vaginal swabs were collected from pluriparous, non-pregnant, non-lactating dromedary camels. The LAB were isolated using deMan, Rogosa and Sharpe broth and agar media. Suspected LAB isolates were subjected to catalase testing and Gram staining and examined for indole production, nitrate reduction, hemolytic activity, cell surface hydrophobicity, auto- and coaggregation, antibacterial activity and characterized by 16S rRNA amplification and sequencing. Eighteen LABs were isolated from the 75 vaginal swabs. Among the 18 LAB isolates, six were Lactobacillus plantarum, eight were Lactobacillus fermentum, and four were Lactobacillus rhamnosus. None of the LAB isolates was hemolytic and only four LAB were H2O2 producing. The percentage of hydrophobicity ranged from 0% to 49.6%, 0% to 44.3% and 0% to 41.6% for hexadecane, xylene and toluene, respectively. All isolates showed higher (P < 0.05) autoaggregation after 24 h of incubation compared to 4 h. Furthermore, all LAB showed higher coaggregation (P < 0.05) and antimicrobial activity toward Staphylococcus aureus than to Escherichia coli. All LAB isolates were vancomycin resistant and sensitive to streptomycin, erythromycin, kanamycin and chloramphenicol. Only, three LAB isolates were resistant to tetracycline. The dromedary camel vaginal LAB isolates exhibited varying degrees of in vitro probiotic properties tested in this study and showed promising activity against the most common bacterial causes of endometritis in dromedary camels. Further investigation of the in vivo effect of these isolates is warranted.
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creator: Wael M. El-Deeb
creator: Mahmoud Fayez
creator: Ibrahim Elsohaby
creator: Ibrahim Ghoneim
creator: Theeb Al-Marri
creator: Mahmoud Kandeel
creator: Magdy ElGioushy
subject: Agricultural Science
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.8500
publisher: PeerJ Inc.
rights: © 2020 El-Deeb et al.
abstract: Lactobacillus spp. is one of the beneficial lactic acid producing microbiota in the vagina, which is important for a healthy vaginal environment. However, little is known about vaginal Lactobacillus in dromedary camels (Camelus dromedarius). Therefore, this study aimed to isolate vaginal lactic acid bacteria (LAB) in dromedary camels and to study the probiotic potential of selected isolates. A total of 75 vaginal swabs were collected from pluriparous, non-pregnant, non-lactating dromedary camels. The LAB were isolated using deMan, Rogosa and Sharpe broth and agar media. Suspected LAB isolates were subjected to catalase testing and Gram staining and examined for indole production, nitrate reduction, hemolytic activity, cell surface hydrophobicity, auto- and coaggregation, antibacterial activity and characterized by 16S rRNA amplification and sequencing. Eighteen LABs were isolated from the 75 vaginal swabs. Among the 18 LAB isolates, six were Lactobacillus plantarum, eight were Lactobacillus fermentum, and four were Lactobacillus rhamnosus. None of the LAB isolates was hemolytic and only four LAB were H2O2 producing. The percentage of hydrophobicity ranged from 0% to 49.6%, 0% to 44.3% and 0% to 41.6% for hexadecane, xylene and toluene, respectively. All isolates showed higher (P < 0.05) autoaggregation after 24 h of incubation compared to 4 h. Furthermore, all LAB showed higher coaggregation (P < 0.05) and antimicrobial activity toward Staphylococcus aureus than to Escherichia coli. All LAB isolates were vancomycin resistant and sensitive to streptomycin, erythromycin, kanamycin and chloramphenicol. Only, three LAB isolates were resistant to tetracycline. The dromedary camel vaginal LAB isolates exhibited varying degrees of in vitro probiotic properties tested in this study and showed promising activity against the most common bacterial causes of endometritis in dromedary camels. Further investigation of the in vivo effect of these isolates is warranted.
bibliographic citation: El-Deeb et al. (2020) Isolation and characterization of vaginal Lactobacillus spp. in dromedary camels (Camelus dromedarius): in vitro evaluation of probiotic potential of selected isolates. PeerJ 8:e8500 https://doi.org/10.7717/peerj.8500
date submitted: 2019-11-15
date accepted: 2020-01-01
issued: 2020-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: El-Deeb
  given name: Wael M.
author list: Agent
  family name: Fayez
  given name: Mahmoud
author list: Agent
  family name: Elsohaby
  given name: Ibrahim
author list: Agent
  family name: Ghoneim
  given name: Ibrahim
author list: Agent
  family name: Al-Marri
  given name: Theeb
author list: Agent
  family name: Kandeel
  given name: Mahmoud
author list: Agent
  family name: ElGioushy
  given name: Magdy
doi: 10.7717/peerj.8500
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-05
copyright: © 2020 El-Deeb et al.
attribution name: El-Deeb et al.

Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing
type: item
type: AcademicArticle
description: During the early-life period, the hatchlings of red-eared slider turtles (Trachemys scripta elegans) rely on their own post-hatching internal yolk for several days before beginning to feed. The gut microbiome is critical for the adaptation of organisms to new environments, but, to date, how the microbiome taxa are assembled during early life of the turtle is unknown. In this study, the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) was systematically analyzed at four different growth stages (0 d, 10 d, 20 d, 30 d) by a high-throughput sequencing approach. Results showed that the dominant phyla were Firmicutes (58.23%) and Proteobacteria (41.42%) at 0-day, Firmicutes (92.94%) at 10-day, Firmicutes (67.08%) and Bacteroidetes (27.17%) at 20-day, and Firmicutes (56.46%), Bacteroidetes (22.55%) and Proteobacteria (20.66%) at 30-day post-hatching. Members of the Bacteroidaceae family were absent in 0-day and 10-day turtles, but dominated in 20-day and 30-day turtles. The abundance of Clostridium also showed the highest value in 10-day turtles. The richness of the intestinal microbiomes was lower at 0-day and 30-day than that at 10-day and 20-day, while the diversity was higher at 10-day and 30-day than that at 0-day and 20-day. The results endowed the turtles with an ability to enhance their tolerance to the environment.
format: application/pdf
format: text/html
creator: Qin Peng
creator: Yahui Chen
creator: Li Ding
creator: Zimiao Zhao
creator: Peiyu Yan
creator: Kenneth B. Storey
creator: Haitao Shi
creator: Meiling Hong
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.8501
publisher: PeerJ Inc.
rights: © 2020 Peng et al.
abstract: During the early-life period, the hatchlings of red-eared slider turtles (Trachemys scripta elegans) rely on their own post-hatching internal yolk for several days before beginning to feed. The gut microbiome is critical for the adaptation of organisms to new environments, but, to date, how the microbiome taxa are assembled during early life of the turtle is unknown. In this study, the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) was systematically analyzed at four different growth stages (0 d, 10 d, 20 d, 30 d) by a high-throughput sequencing approach. Results showed that the dominant phyla were Firmicutes (58.23%) and Proteobacteria (41.42%) at 0-day, Firmicutes (92.94%) at 10-day, Firmicutes (67.08%) and Bacteroidetes (27.17%) at 20-day, and Firmicutes (56.46%), Bacteroidetes (22.55%) and Proteobacteria (20.66%) at 30-day post-hatching. Members of the Bacteroidaceae family were absent in 0-day and 10-day turtles, but dominated in 20-day and 30-day turtles. The abundance of Clostridium also showed the highest value in 10-day turtles. The richness of the intestinal microbiomes was lower at 0-day and 30-day than that at 10-day and 20-day, while the diversity was higher at 10-day and 30-day than that at 0-day and 20-day. The results endowed the turtles with an ability to enhance their tolerance to the environment.
bibliographic citation: Peng et al. (2020) Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing. PeerJ 8:e8501 https://doi.org/10.7717/peerj.8501
date submitted: 2019-08-02
date accepted: 2020-01-01
issued: 2020-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Qin
author list: Agent
  family name: Chen
  given name: Yahui
author list: Agent
  family name: Ding
  given name: Li
author list: Agent
  family name: Zhao
  given name: Zimiao
author list: Agent
  family name: Yan
  given name: Peiyu
author list: Agent
  family name: Storey
  given name: Kenneth B.
author list: Agent
  family name: Shi
  given name: Haitao
author list: Agent
  family name: Hong
  given name: Meiling
doi: 10.7717/peerj.8501
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-05
copyright: ©2020 Peng et al.
attribution name: Peng et al.

Postharvest biochemical characteristics and ultrastructure of Coprinus comatus
type: item
type: AcademicArticle
description: Background Coprinus comatus is a novel cultivated edible fungus, hailed as a new preeminent breed of mushroom. However, C. comatus is difficult to keep fresh at room temperature after harvest due to high respiration, browning, self-dissolve and lack of physical protection. Methods In order to extend the shelf life of C. comatus and reduce its loss in storage, changes in quality, biochemical content, cell wall metabolism and ultrastructure of C. comatus (C.c77) under 4 °C and 90% RH storage regimes were investigated in this study. Results The results showed that: (1) After 10 days of storage, mushrooms appeared acutely browning, cap opening and flowing black juice, rendering the mushrooms commercially unacceptable. (2) The activity of SOD, CAT, POD gradually increased, peaked at the day 10, up to 31.62 U g−1 FW, 16.51 U g−1 FW, 0.33 U g−1 FW, respectively. High SOD, CAT, POD activity could be beneficial in protecting cells from ROS-induced injuries, alleviating lipid peroxidation and stabilizing membrane integrity. (3) The activities of chitinase, β-1,3-glucanase were significantly increased. Higher degrees of cell wall degradation observed during storage might be due to those enzymes’ high activities. (4) The fresh C. comatus had dense tissue and every single cell had the number of intracellular organelles which structure can be observed clearly. After 10 d storage, the number of intracellular organelles was declined and the structure was fuzzy, the nucleus disappeared. After 20 d storage, C. comatus’s organization was completely lost, many cells were stacked together and the cell wall was badly damaged.
format: application/pdf
format: text/html
creator: Yi Peng
creator: Tongling Li
creator: Huaming Jiang
creator: Yunfu Gu
creator: Qiang Chen
creator: Cairong Yang
creator: Wei liang Qi
creator: Song-qing Liu
creator: Xiaoping Zhang
subject: Agricultural Science
subject: Biochemistry
subject: Cell Biology
subject: Microbiology
description: doi:10.7717/peerj.8508
publisher: PeerJ Inc.
rights: © 2020 Peng et al.
abstract: Background Coprinus comatus is a novel cultivated edible fungus, hailed as a new preeminent breed of mushroom. However, C. comatus is difficult to keep fresh at room temperature after harvest due to high respiration, browning, self-dissolve and lack of physical protection. Methods In order to extend the shelf life of C. comatus and reduce its loss in storage, changes in quality, biochemical content, cell wall metabolism and ultrastructure of C. comatus (C.c77) under 4 °C and 90% RH storage regimes were investigated in this study. Results The results showed that: (1) After 10 days of storage, mushrooms appeared acutely browning, cap opening and flowing black juice, rendering the mushrooms commercially unacceptable. (2) The activity of SOD, CAT, POD gradually increased, peaked at the day 10, up to 31.62 U g−1 FW, 16.51 U g−1 FW, 0.33 U g−1 FW, respectively. High SOD, CAT, POD activity could be beneficial in protecting cells from ROS-induced injuries, alleviating lipid peroxidation and stabilizing membrane integrity. (3) The activities of chitinase, β-1,3-glucanase were significantly increased. Higher degrees of cell wall degradation observed during storage might be due to those enzymes’ high activities. (4) The fresh C. comatus had dense tissue and every single cell had the number of intracellular organelles which structure can be observed clearly. After 10 d storage, the number of intracellular organelles was declined and the structure was fuzzy, the nucleus disappeared. After 20 d storage, C. comatus’s organization was completely lost, many cells were stacked together and the cell wall was badly damaged.
bibliographic citation: Peng et al. (2020) Postharvest biochemical characteristics and ultrastructure of Coprinus comatus. PeerJ 8:e8508 https://doi.org/10.7717/peerj.8508
date submitted: 2019-10-06
date accepted: 2020-01-03
issued: 2020-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Yi
author list: Agent
  family name: Li
  given name: Tongling
author list: Agent
  family name: Jiang
  given name: Huaming
author list: Agent
  family name: Gu
  given name: Yunfu
author list: Agent
  family name: Chen
  given name: Qiang
author list: Agent
  family name: Yang
  given name: Cairong
author list: Agent
  family name: Qi
  given name: Wei liang
author list: Agent
  family name: Liu
  given name: Song-qing
author list: Agent
  family name: Zhang
  given name: Xiaoping
doi: 10.7717/peerj.8508
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-05
copyright: ©2020 Peng et al.
attribution name: Peng et al.

Niche differentiation in the rhizosphere and endosphere fungal microbiome of wild Paris polyphylla Sm.
type: item
type: AcademicArticle
description: Background The plant microbiome is one of the key determinants of plant health and metabolite production. The plant microbiome affects the plant’s absorption of nutrient elements, improves plant tolerance to negative environmental factors, increases the accumulation of active components, and alters tissue texture. The microbial community is also important for the accumulation of secondary metabolites by plants. However, there are few studies on the niche differentiation of endophytic microorganisms of plants, especially at different elevations. Methods We investigated the effects of altitude on the community composition of endophytic fungal communities and the differentiation of endophytic microorganisms among different niches in Paris polyphylla Sm. The rhizosphere soil, roots, rhizomes and leaves of wild-type P. polyphylla Sm. at different altitudes were sampled, and the fungal communities of all samples were analyzed by internal transcribed spacer one amplification sequencing. Results The results showed that in rhizosphere soil, the number of operational taxonomic units (OTUs) that could be classified or identified decreased significantly with increasing altitude, whereas in the endosphere of plants, the total number of OTUs was higher at intermediate altitudes than other altitudes. Furthermore, the structural variability in the rhizosphere fungal community was significantly lower than that in the endophytic communities. In addition, our results confirmed the presence of niche differentiation among members of the endophytic microbial community. Finally, we also determined that the predominant genus of mycobiota in the rhizome was Cadophora. This study provides insight into the relationships between the endosphere microbiome and plants and can guide the artificial cultivation of this plant.
format: application/pdf
format: text/html
creator: Yan Wang
creator: Hanping Wang
creator: HuYin Cheng
creator: Fan Chang
creator: Yi Wan
creator: Xiaoping She
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.8510
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background The plant microbiome is one of the key determinants of plant health and metabolite production. The plant microbiome affects the plant’s absorption of nutrient elements, improves plant tolerance to negative environmental factors, increases the accumulation of active components, and alters tissue texture. The microbial community is also important for the accumulation of secondary metabolites by plants. However, there are few studies on the niche differentiation of endophytic microorganisms of plants, especially at different elevations. Methods We investigated the effects of altitude on the community composition of endophytic fungal communities and the differentiation of endophytic microorganisms among different niches in Paris polyphylla Sm. The rhizosphere soil, roots, rhizomes and leaves of wild-type P. polyphylla Sm. at different altitudes were sampled, and the fungal communities of all samples were analyzed by internal transcribed spacer one amplification sequencing. Results The results showed that in rhizosphere soil, the number of operational taxonomic units (OTUs) that could be classified or identified decreased significantly with increasing altitude, whereas in the endosphere of plants, the total number of OTUs was higher at intermediate altitudes than other altitudes. Furthermore, the structural variability in the rhizosphere fungal community was significantly lower than that in the endophytic communities. In addition, our results confirmed the presence of niche differentiation among members of the endophytic microbial community. Finally, we also determined that the predominant genus of mycobiota in the rhizome was Cadophora. This study provides insight into the relationships between the endosphere microbiome and plants and can guide the artificial cultivation of this plant.
bibliographic citation: Wang et al. (2020) Niche differentiation in the rhizosphere and endosphere fungal microbiome of wild Paris polyphylla Sm.. PeerJ 8:e8510 https://doi.org/10.7717/peerj.8510
date submitted: 2019-07-16
date accepted: 2020-01-03
issued: 2020-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Wang
  given name: Hanping
author list: Agent
  family name: Cheng
  given name: HuYin
author list: Agent
  family name: Chang
  given name: Fan
author list: Agent
  family name: Wan
  given name: Yi
author list: Agent
  family name: She
  given name: Xiaoping
doi: 10.7717/peerj.8510
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-05
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Association of the CACNA2D2 gene with schizophrenia in Chinese Han population
type: item
type: AcademicArticle
description: Background Schizophrenia (SCZ) is a severely complex psychiatric disorder in which ~80% can be explained by genetic factors. Single nucleotide polymorphisms (SNPs) in calcium channel genes are potential genetic risk factors for a spectrum of psychiatric disorders including SCZ. This study evaluated the association between SNPs in the voltage-gated calcium channel auxiliary subunit alpha2delta 2 gene (CACNA2D2) and SCZ in the Han Chinese population of Northeast China. Methods A total of 761 SCZ patients and 775 healthy controls were involved in this case-control study. Three SNPs (rs3806706, rs45536634 and rs12496815) of CACNA2D2 were genotyped by the MALDI-TOF-MS technology. Genotype distribution and allele frequency differences between cases and controls were tested by Chi-square (χ2) in males and females respectively using SPSS 24.0 software. Linkage disequilibrium and haplotype analyses were conducted using Haploview4.2. The false discovery rate correction was utilized to control for Type I error by R3.2.3. Results There was a significant difference in allele frequencies (χ2 = 9.545, Padj = 0.006) and genotype distributions (χ2 = 9.275, Padj = 0.006) of rs45536634 between female SCZ patients and female healthy controls after adjusting for multiple comparisons. Minor allele A (OR = 1.871, 95% CI [1.251–2.798]) and genotype GA + AA (OR = 1.931, 95% CI [1.259–2.963]) were associated with an increased risk of SCZ. Subjects with haplotype AG consisting of rs45536634 and rs12496815 alleles had a higher risk of SCZ (OR = 1.91, 95% CI [1.26–2.90]) compared those with other haplotypes. Conclusions This study provides evidence that CACNA2D2 polymorphisms may influence the susceptibility to SCZ in Han Chinese women.
format: application/pdf
format: text/html
creator: Yingli Fu
creator: Na Zhou
creator: Wei Bai
creator: Yaoyao Sun
creator: Xin Chen
creator: Yueying Wang
creator: Mingyuan Zhang
creator: Changgui Kou
creator: Yaqin Yu
creator: Qiong Yu
subject: Genetics
subject: Epidemiology
description: doi:10.7717/peerj.8521
publisher: PeerJ Inc.
rights: © 2020 Fu et al.
abstract: Background Schizophrenia (SCZ) is a severely complex psychiatric disorder in which ~80% can be explained by genetic factors. Single nucleotide polymorphisms (SNPs) in calcium channel genes are potential genetic risk factors for a spectrum of psychiatric disorders including SCZ. This study evaluated the association between SNPs in the voltage-gated calcium channel auxiliary subunit alpha2delta 2 gene (CACNA2D2) and SCZ in the Han Chinese population of Northeast China. Methods A total of 761 SCZ patients and 775 healthy controls were involved in this case-control study. Three SNPs (rs3806706, rs45536634 and rs12496815) of CACNA2D2 were genotyped by the MALDI-TOF-MS technology. Genotype distribution and allele frequency differences between cases and controls were tested by Chi-square (χ2) in males and females respectively using SPSS 24.0 software. Linkage disequilibrium and haplotype analyses were conducted using Haploview4.2. The false discovery rate correction was utilized to control for Type I error by R3.2.3. Results There was a significant difference in allele frequencies (χ2 = 9.545, Padj = 0.006) and genotype distributions (χ2 = 9.275, Padj = 0.006) of rs45536634 between female SCZ patients and female healthy controls after adjusting for multiple comparisons. Minor allele A (OR = 1.871, 95% CI [1.251–2.798]) and genotype GA + AA (OR = 1.931, 95% CI [1.259–2.963]) were associated with an increased risk of SCZ. Subjects with haplotype AG consisting of rs45536634 and rs12496815 alleles had a higher risk of SCZ (OR = 1.91, 95% CI [1.26–2.90]) compared those with other haplotypes. Conclusions This study provides evidence that CACNA2D2 polymorphisms may influence the susceptibility to SCZ in Han Chinese women.
bibliographic citation: Fu et al. (2020) Association of the CACNA2D2 gene with schizophrenia in Chinese Han population. PeerJ 8:e8521 https://doi.org/10.7717/peerj.8521
date submitted: 2019-07-24
date accepted: 2020-01-07
issued: 2020-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Yingli
author list: Agent
  family name: Zhou
  given name: Na
author list: Agent
  family name: Bai
  given name: Wei
author list: Agent
  family name: Sun
  given name: Yaoyao
author list: Agent
  family name: Chen
  given name: Xin
author list: Agent
  family name: Wang
  given name: Yueying
author list: Agent
  family name: Zhang
  given name: Mingyuan
author list: Agent
  family name: Kou
  given name: Changgui
author list: Agent
  family name: Yu
  given name: Yaqin
author list: Agent
  family name: Yu
  given name: Qiong
doi: 10.7717/peerj.8521
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-05
copyright: © 2020 Fu et al.
attribution name: Fu et al.

Prioritizing riparian corridors for ecosystem restoration in urbanizing watersheds
type: item
type: AcademicArticle
description: Background Riparian corridors can affect nutrient, organic matter, and sediment transport, all of which shape water quality in streams and connected downstream waters. When functioning riparian corridors remain intact, they provide highly valued water quality ecosystem services. However, in rapidly urbanizing watersheds, riparian corridors are susceptible to development modifications that adversely affect those ecosystem services. Protecting high quality riparian corridors or restoring low quality corridors are widely advocated as watershed level water quality management options for protecting those ecosystem services. The two approaches, protection or restoration, should be viewed as complementary by watershed managers and provide a foundation for targeting highly functioning riparian corridors for protection or for identifying poorly functioning corridors for restoration. Ascertaining which strategy to use is often motivated by a specific ecosystem service, for example water quality, upon which watershed management is focused. We have previously reported on a spatially explicit model that focused on identifying riparian corridors that have specific characteristics that make them well suited for purposes of preservation and protection focused on water quality. Here we hypothesize that focusing on restoration, rather than protection, can be the basis for developing a watershed level strategy for improving water quality in urbanizing watersheds. Methods The model described here represents a geographic information system (GIS) based approach that utilizes riparian characteristics extracted from 40-meter wide corridors centered on streams and rivers. The model focuses on drinking water reservoir watersheds that can be analyzed at the sub-watershed level. Sub-watershed riparian data (vegetation, soil erodibility and surface slope) are scaled and weighted based on watershed management theories for water quality, and riparian restoration scores are assigned. Those scores …
format: application/pdf
format: text/html
creator: Samuel F. Atkinson
creator: Matthew C. Lake
subject: Conservation Biology
subject: Ecosystem Science
subject: Natural Resource Management
description: doi:10.7717/peerj.8174
publisher: PeerJ Inc.
rights: © 2020 Atkinson and Lake
abstract: Background Riparian corridors can affect nutrient, organic matter, and sediment transport, all of which shape water quality in streams and connected downstream waters. When functioning riparian corridors remain intact, they provide highly valued water quality ecosystem services. However, in rapidly urbanizing watersheds, riparian corridors are susceptible to development modifications that adversely affect those ecosystem services. Protecting high quality riparian corridors or restoring low quality corridors are widely advocated as watershed level water quality management options for protecting those ecosystem services. The two approaches, protection or restoration, should be viewed as complementary by watershed managers and provide a foundation for targeting highly functioning riparian corridors for protection or for identifying poorly functioning corridors for restoration. Ascertaining which strategy to use is often motivated by a specific ecosystem service, for example water quality, upon which watershed management is focused. We have previously reported on a spatially explicit model that focused on identifying riparian corridors that have specific characteristics that make them well suited for purposes of preservation and protection focused on water quality. Here we hypothesize that focusing on restoration, rather than protection, can be the basis for developing a watershed level strategy for improving water quality in urbanizing watersheds. Methods The model described here represents a geographic information system (GIS) based approach that utilizes riparian characteristics extracted from 40-meter wide corridors centered on streams and rivers. The model focuses on drinking water reservoir watersheds that can be analyzed at the sub-watershed level. Sub-watershed riparian data (vegetation, soil erodibility and surface slope) are scaled and weighted based on watershed management theories for water quality, and riparian restoration scores are assigned. Those scores …
bibliographic citation: Atkinson et al. (2020) Prioritizing riparian corridors for ecosystem restoration in urbanizing watersheds. PeerJ 8:e8174 https://doi.org/10.7717/peerj.8174
date submitted: 2019-06-19
date accepted: 2019-11-06
issued: 2020-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Atkinson
  given name: Samuel F.
author list: Agent
  family name: Lake
  given name: Matthew C.
doi: 10.7717/peerj.8174
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-04
copyright: ©2020 Atkinson and Lake
attribution name: Atkinson and Lake

A novel transcript of MEF2D promotes myoblast differentiation and its variations associated with growth traits in chicken
type: item
type: AcademicArticle
description: Background Development of skeletal muscle is closely related to broiler production traits. The myocyte-specific enhancer binding factor (MEF) 2D gene (MEF2D) and its variant transcripts play important parts in myogenesis. Methods To identify the transcript variants of chicken MEF2D gene and their function, this study cloned chicken MEF2D gene and identified its transcript variants from different tissue samples. The expression levels of different transcripts of MEF2D gene in different tissues and different periods were measured, and their effects on myoblast proliferation and differentiation were investigated. Variations in MEF2D were identified and association analysis with chicken production traits carried out. Results Four novel transcript variants of MEF2D were obtained, all of which contained highly conserved sequences, including MADS-Box and MEF2-Domain functional regions. Transcript MEF2D-V4 was expressed specifically in muscle, and its expression was increased during embryonic muscle development. The MEF2D-V4 could promote differentiation of chicken myoblasts and its expression was regulated by RBFOX2. The single nucleotide polymorphism g.36186C > T generated a TAG stop codon, caused MEF2D-V4 to terminate translation early, and was associated with several growth traits, especially on early body weight. Conclusion We cloned the muscle-specific transcript of MEF2D and preliminarily revealed its role in embryonic muscle development.
format: application/pdf
format: text/html
creator: Hongjia Ouyang
creator: Jiao Yu
creator: Xiaolan Chen
creator: Zhijun Wang
creator: Qinghua Nie
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.8351
publisher: PeerJ Inc.
rights: © 2020 Ouyang et al.
abstract: Background Development of skeletal muscle is closely related to broiler production traits. The myocyte-specific enhancer binding factor (MEF) 2D gene (MEF2D) and its variant transcripts play important parts in myogenesis. Methods To identify the transcript variants of chicken MEF2D gene and their function, this study cloned chicken MEF2D gene and identified its transcript variants from different tissue samples. The expression levels of different transcripts of MEF2D gene in different tissues and different periods were measured, and their effects on myoblast proliferation and differentiation were investigated. Variations in MEF2D were identified and association analysis with chicken production traits carried out. Results Four novel transcript variants of MEF2D were obtained, all of which contained highly conserved sequences, including MADS-Box and MEF2-Domain functional regions. Transcript MEF2D-V4 was expressed specifically in muscle, and its expression was increased during embryonic muscle development. The MEF2D-V4 could promote differentiation of chicken myoblasts and its expression was regulated by RBFOX2. The single nucleotide polymorphism g.36186C > T generated a TAG stop codon, caused MEF2D-V4 to terminate translation early, and was associated with several growth traits, especially on early body weight. Conclusion We cloned the muscle-specific transcript of MEF2D and preliminarily revealed its role in embryonic muscle development.
bibliographic citation: Ouyang et al. (2020) A novel transcript of MEF2D promotes myoblast differentiation and its variations associated with growth traits in chicken. PeerJ 8:e8351 https://doi.org/10.7717/peerj.8351
date submitted: 2019-06-17
date accepted: 2019-12-04
issued: 2020-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ouyang
  given name: Hongjia
author list: Agent
  family name: Yu
  given name: Jiao
author list: Agent
  family name: Chen
  given name: Xiaolan
author list: Agent
  family name: Wang
  given name: Zhijun
author list: Agent
  family name: Nie
  given name: Qinghua
doi: 10.7717/peerj.8351
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-04
copyright: © 2020 Ouyang et al.
attribution name: Ouyang et al.

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