PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum
items: Human papillomavirus infection and follow-up on positive results in 7222 female samples obtained from 2016 to 2019 in Hefei, China
items: What families really think about the quality of early intervention centers: a perspective from mixed methods
items: Construction and analysis of macrophage infiltration related circRNA-miRNA-mRNA regulatory networks in hepatocellular carcinoma
items: Soil organic matter dynamics in semiarid agroecosystems transitioning to dryland
items: Structure and expression analysis of seven salt-related ERF genes of Populus
items: Feroxichthys yunnanensis gen. et sp. nov. (Colobodontidae, Neopterygii), a large durophagous predator from the Middle Triassic (Anisian) Luoping Biota, eastern Yunnan, China
items: Spatial differentiation of gully clusters based on the regional scale: an example from northeastern China
items: Generation of human liver organoids from pluripotent stem cell-derived hepatic endoderms
items: Using trace elements to identify the geographic origin of migratory bats

Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum
type: item
type: AcademicArticle
description: Koalas (Phascolarctos cinereus) are highly specialized herbivorous marsupials that feed almost exclusively on Eucalyptus leaves, which are known to contain varying concentrations of many different toxic chemical compounds. The literature suggests that Lonepinella koalarum, a bacterium in the Pasteurellaceae family, can break down some of these toxic chemical compounds. Furthermore, in a previous study, we identified L. koalarum as the most predictive taxon of koala survival during antibiotic treatment. Therefore, we believe that this bacterium may be important for koala health. Here, we isolated a strain of L. koalarum from a healthy koala female and sequenced its genome using a combination of short-read and long-read sequencing. We placed the genome assembly into a phylogenetic tree based on 120 genome markers using the Genome Taxonomy Database (GTDB), which currently does not include any L. koalarum assemblies. Our genome assembly fell in the middle of a group of Haemophilus, Pasteurella and Basfia species. According to average nucleotide identity and a 16S rRNA gene tree, the closest relative of our isolate is L. koalarum strain Y17189. Then, we annotated the gene sequences and compared them to 55 closely related, publicly available genomes. Several genes that are known to be involved in carbohydrate metabolism could exclusively be found in L. koalarum relative to the other taxa in the pangenome, including glycoside hydrolase families GH2, GH31, GH32, GH43 and GH77. Among the predicted genes of L. koalarum were 79 candidates putatively involved in the degradation of plant secondary metabolites. Additionally, several genes coding for amino acid variants were found that had been shown to confer antibiotic resistance in other bacterial species against pulvomycin, beta-lactam antibiotics and the antibiotic efflux pump KpnH. In summary, this genetic characterization allows us to build hypotheses to explore the potentially beneficial role that L. koalarum might play in…
format: application/pdf
format: text/html
creator: Katherine E. Dahlhausen
creator: Guillaume Jospin
creator: David A. Coil
creator: Jonathan A. Eisen
creator: Laetitia G.E. Wilkins
subject: Bioinformatics
subject: Conservation Biology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.10177
publisher: PeerJ Inc.
rights: © 2020 Dahlhausen et al.
abstract: Koalas (Phascolarctos cinereus) are highly specialized herbivorous marsupials that feed almost exclusively on Eucalyptus leaves, which are known to contain varying concentrations of many different toxic chemical compounds. The literature suggests that Lonepinella koalarum, a bacterium in the Pasteurellaceae family, can break down some of these toxic chemical compounds. Furthermore, in a previous study, we identified L. koalarum as the most predictive taxon of koala survival during antibiotic treatment. Therefore, we believe that this bacterium may be important for koala health. Here, we isolated a strain of L. koalarum from a healthy koala female and sequenced its genome using a combination of short-read and long-read sequencing. We placed the genome assembly into a phylogenetic tree based on 120 genome markers using the Genome Taxonomy Database (GTDB), which currently does not include any L. koalarum assemblies. Our genome assembly fell in the middle of a group of Haemophilus, Pasteurella and Basfia species. According to average nucleotide identity and a 16S rRNA gene tree, the closest relative of our isolate is L. koalarum strain Y17189. Then, we annotated the gene sequences and compared them to 55 closely related, publicly available genomes. Several genes that are known to be involved in carbohydrate metabolism could exclusively be found in L. koalarum relative to the other taxa in the pangenome, including glycoside hydrolase families GH2, GH31, GH32, GH43 and GH77. Among the predicted genes of L. koalarum were 79 candidates putatively involved in the degradation of plant secondary metabolites. Additionally, several genes coding for amino acid variants were found that had been shown to confer antibiotic resistance in other bacterial species against pulvomycin, beta-lactam antibiotics and the antibiotic efflux pump KpnH. In summary, this genetic characterization allows us to build hypotheses to explore the potentially beneficial role that L. koalarum might play in…
bibliographic citation: Dahlhausen et al. (2020) Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum. PeerJ 8:e10177 https://doi.org/10.7717/peerj.10177
date submitted: 2020-03-27
date accepted: 2020-09-22
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dahlhausen
  given name: Katherine E.
author list: Agent
  family name: Jospin
  given name: Guillaume
author list: Agent
  family name: Coil
  given name: David A.
author list: Agent
  family name: Eisen
  given name: Jonathan A.
author list: Agent
  family name: Wilkins
  given name: Laetitia G.E.
doi: 10.7717/peerj.10177
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: © 2020 Dahlhausen et al.
attribution name: Dahlhausen et al.

Human papillomavirus infection and follow-up on positive results in 7222 female samples obtained from 2016 to 2019 in Hefei, China
type: item
type: AcademicArticle
description: Background Human papillomavirus (HPV) infection rates in women vary regionally. This study analyzed HPV infection in women of different age groups in Hefei, China, performed follow-up on positive cases, and discussed infection prognoses. Methods Samples (7,222) of exfoliated cervical cells were collected in Hefei and tested with an HPV assay kit against 27 HPV genotypes. Statistical software was used to analyze the data. Results The total positive rate of infection was 17.13% (1,068 women), and the 51–60-year age group had the highest HPV infection rate (19.82%). There were statistically significant differences between rates in the 21–30 and 31–40 (P = 0.002), 21–30 and 41–50 (P = 0.0003), 21–30 and 51–60 (P = 0.00003), and 51–60 and >60 age groups (P = 0.046). High-risk infection (15.67%) and single infection (13.01%) were the main types of HPV infection. The dominant genotypes of high-risk infection were HPV 52 (2.42%), HPV 16 (2.01%), HPV 53 (1.43%), HPV 58 (1.32%) and HPV 66 (1.01%). We conducted follow-up on cases in 69 of 94 women who had a history of 1–4 years of positive infection, and in 18 (seven treated, 11 untreated) patients, infection status turned negative (26.09%). Seventeen of the fifty-one women whose infections did not turn negative received treatment. Persistent infection was predominantly observed in high-risk genotypes (56 of 69). Conclusions The results recommend that women in Hefei improve health awareness and receive a 9-valent vaccine. Additionally, women with persistent infections should consult a gynecologist to prevent cervical lesions.
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creator: Liduo Peng
creator: Liping Yin
creator: Yaqian Dai
creator: Yuanjing Peng
creator: Yuanhong Xu
creator: Huaqing Hu
creator: Jinping Qiao
subject: Virology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.10179
publisher: PeerJ Inc.
rights: © 2020 Peng et al.
abstract: Background Human papillomavirus (HPV) infection rates in women vary regionally. This study analyzed HPV infection in women of different age groups in Hefei, China, performed follow-up on positive cases, and discussed infection prognoses. Methods Samples (7,222) of exfoliated cervical cells were collected in Hefei and tested with an HPV assay kit against 27 HPV genotypes. Statistical software was used to analyze the data. Results The total positive rate of infection was 17.13% (1,068 women), and the 51–60-year age group had the highest HPV infection rate (19.82%). There were statistically significant differences between rates in the 21–30 and 31–40 (P = 0.002), 21–30 and 41–50 (P = 0.0003), 21–30 and 51–60 (P = 0.00003), and 51–60 and >60 age groups (P = 0.046). High-risk infection (15.67%) and single infection (13.01%) were the main types of HPV infection. The dominant genotypes of high-risk infection were HPV 52 (2.42%), HPV 16 (2.01%), HPV 53 (1.43%), HPV 58 (1.32%) and HPV 66 (1.01%). We conducted follow-up on cases in 69 of 94 women who had a history of 1–4 years of positive infection, and in 18 (seven treated, 11 untreated) patients, infection status turned negative (26.09%). Seventeen of the fifty-one women whose infections did not turn negative received treatment. Persistent infection was predominantly observed in high-risk genotypes (56 of 69). Conclusions The results recommend that women in Hefei improve health awareness and receive a 9-valent vaccine. Additionally, women with persistent infections should consult a gynecologist to prevent cervical lesions.
bibliographic citation: Peng et al. (2020) Human papillomavirus infection and follow-up on positive results in 7222 female samples obtained from 2016 to 2019 in Hefei, China. PeerJ 8:e10179 https://doi.org/10.7717/peerj.10179
date submitted: 2020-04-16
date accepted: 2020-09-23
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Liduo
author list: Agent
  family name: Yin
  given name: Liping
author list: Agent
  family name: Dai
  given name: Yaqian
author list: Agent
  family name: Peng
  given name: Yuanjing
author list: Agent
  family name: Xu
  given name: Yuanhong
author list: Agent
  family name: Hu
  given name: Huaqing
author list: Agent
  family name: Qiao
  given name: Jinping
doi: 10.7717/peerj.10179
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Peng et al.
attribution name: Peng et al.

What families really think about the quality of early intervention centers: a perspective from mixed methods
type: item
type: AcademicArticle
description: Background Families are a fundamental aspect in the current perspective of Early Intervention, and knowing their opinion with quantitative and qualitative research is necessary for its improvement. The objective of this research was to evaluate the quality of the service perceived in Early Intervention Centers and its relationship with satisfaction and future intention, as well as to identify factors that are associated with the perception of users. Methods A measurement model of 50 items and an open question to gather qualitative information was used in a sample of 233 participants. A confirmatory factor analysis and a regression analysis were conducted. Regarding the qualitative data, the information was subjected to a thematic content analysis in order to delve into the perception of the participants. Results The model showed a satisfactory fit and the regression analysis indicated that treatment rooms (β = − 0.28) and adaptation of activities (β = 0.27) have greater weight with respect to satisfaction, whereas for future intention, the factors of greater weight were adaptation of activities (β = 0.23) and location (β = 0.20). The qualitative analysis showed three themes: facilitators, barriers and suggestions for improvement. Within facilitators, the participants were satisfied with the Early Intervention professionals, and they made improvement suggestions for the detected barriers to improve the facilities and the follow-up of the child. Conclusions The study offers a wide perspective of the perception of the service with an active participation of families in the treatment within the Early Intervention service. This will allow professionals in Early Intervention, service providers and researchers to consider the families as intervention agents capable of providing their opinion and making decisions, and not only as passive elements.
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creator: Rita Pilar Romero-Galisteo
creator: Pablo Gálvez Ruiz
creator: Angel Blanco Villaseñor
creator: Maria Rodríguez-Bailón
creator: Manuel González-Sánchez
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.10193
publisher: PeerJ Inc.
rights: © 2020 Romero-Galisteo et al.
abstract: Background Families are a fundamental aspect in the current perspective of Early Intervention, and knowing their opinion with quantitative and qualitative research is necessary for its improvement. The objective of this research was to evaluate the quality of the service perceived in Early Intervention Centers and its relationship with satisfaction and future intention, as well as to identify factors that are associated with the perception of users. Methods A measurement model of 50 items and an open question to gather qualitative information was used in a sample of 233 participants. A confirmatory factor analysis and a regression analysis were conducted. Regarding the qualitative data, the information was subjected to a thematic content analysis in order to delve into the perception of the participants. Results The model showed a satisfactory fit and the regression analysis indicated that treatment rooms (β = − 0.28) and adaptation of activities (β = 0.27) have greater weight with respect to satisfaction, whereas for future intention, the factors of greater weight were adaptation of activities (β = 0.23) and location (β = 0.20). The qualitative analysis showed three themes: facilitators, barriers and suggestions for improvement. Within facilitators, the participants were satisfied with the Early Intervention professionals, and they made improvement suggestions for the detected barriers to improve the facilities and the follow-up of the child. Conclusions The study offers a wide perspective of the perception of the service with an active participation of families in the treatment within the Early Intervention service. This will allow professionals in Early Intervention, service providers and researchers to consider the families as intervention agents capable of providing their opinion and making decisions, and not only as passive elements.
bibliographic citation: Romero-Galisteo et al. (2020) What families really think about the quality of early intervention centers: a perspective from mixed methods. PeerJ 8:e10193 https://doi.org/10.7717/peerj.10193
date submitted: 2019-10-21
date accepted: 2020-09-24
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Romero-Galisteo
  given name: Rita Pilar
author list: Agent
  family name: Gálvez Ruiz
  given name: Pablo
author list: Agent
  family name: Blanco Villaseñor
  given name: Angel
author list: Agent
  family name: Rodríguez-Bailón
  given name: Maria
author list: Agent
  family name: González-Sánchez
  given name: Manuel
doi: 10.7717/peerj.10193
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Romero-Galisteo et al.
attribution name: Romero-Galisteo et al.

Construction and analysis of macrophage infiltration related circRNA-miRNA-mRNA regulatory networks in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Macrophage play a crucial role in regulating tumor progression. This study intended to investigate the circular RNA (circRNA) regulatory network associated with macrophage infiltration in hepatocellular carcinoma (HCC). Methods The immune cell fractions of HCC from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium were calculated by Estimation of the Proportion of Immune and Cancer cells algorithm. The differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs) and circRNAs (DEcircRNAs) were identified from HCC and adjacent non-tumor cases of TCGA or Gene Expression Omnibus database. The DEmRNAs related to macrophage were selected by weighted gene co-expression network analysis and then utilized to generate the circRNA-miRNA-mRNA network. A hub circRNA regulatory network was established based on the co-expressed DEmiRNAs and DEmRNAs owning contrary correlation with the clinical characteristics, survival and macrophage infiltration level. A gene signature based on the DEmRNAs in hub network was also generated for further evaluation. The circRNA binding bite for miRNA was detected by luciferase assay. Results High macrophage fraction predicted good survival for HCC. A circRNA-miRNA-mRNA network was constructed by 27 macrophage related DEmRNAs, 21 DEmiRNAs, and 15 DEcircRNAs. Among this network, the expression of hsa-miR-139-5p was negatively correlated with CDCA8, KPNA2, PRC1 or TOP2A. Hsa-miR-139-5p low or targeted DEmRNA high expression was associated with low macrophage infiltration, high grade, advanced stage and poor prognosis of HCC. Additionally, the risk score generated by 4-DEmRNA signature could reflect the macrophage infiltration status and function as an independent prognostic factor for HCC. Finally, hsa_circ_0007456 acting on hsa-miR-139-5p related network was viewed as the hub circRNA regulatory network. Taken together, some circRNA regulatory networks may be associated with macrophage infiltration, which provides c…
format: application/pdf
format: text/html
creator: Yuhan Chen
creator: Yalin Li
creator: Guanglei Zheng
creator: Peitao Zhou
subject: Bioinformatics
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.10198
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Background Macrophage play a crucial role in regulating tumor progression. This study intended to investigate the circular RNA (circRNA) regulatory network associated with macrophage infiltration in hepatocellular carcinoma (HCC). Methods The immune cell fractions of HCC from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium were calculated by Estimation of the Proportion of Immune and Cancer cells algorithm. The differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs) and circRNAs (DEcircRNAs) were identified from HCC and adjacent non-tumor cases of TCGA or Gene Expression Omnibus database. The DEmRNAs related to macrophage were selected by weighted gene co-expression network analysis and then utilized to generate the circRNA-miRNA-mRNA network. A hub circRNA regulatory network was established based on the co-expressed DEmiRNAs and DEmRNAs owning contrary correlation with the clinical characteristics, survival and macrophage infiltration level. A gene signature based on the DEmRNAs in hub network was also generated for further evaluation. The circRNA binding bite for miRNA was detected by luciferase assay. Results High macrophage fraction predicted good survival for HCC. A circRNA-miRNA-mRNA network was constructed by 27 macrophage related DEmRNAs, 21 DEmiRNAs, and 15 DEcircRNAs. Among this network, the expression of hsa-miR-139-5p was negatively correlated with CDCA8, KPNA2, PRC1 or TOP2A. Hsa-miR-139-5p low or targeted DEmRNA high expression was associated with low macrophage infiltration, high grade, advanced stage and poor prognosis of HCC. Additionally, the risk score generated by 4-DEmRNA signature could reflect the macrophage infiltration status and function as an independent prognostic factor for HCC. Finally, hsa_circ_0007456 acting on hsa-miR-139-5p related network was viewed as the hub circRNA regulatory network. Taken together, some circRNA regulatory networks may be associated with macrophage infiltration, which provides c…
bibliographic citation: Chen et al. (2020) Construction and analysis of macrophage infiltration related circRNA-miRNA-mRNA regulatory networks in hepatocellular carcinoma. PeerJ 8:e10198 https://doi.org/10.7717/peerj.10198
date submitted: 2020-08-20
date accepted: 2020-09-26
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yuhan
author list: Agent
  family name: Li
  given name: Yalin
author list: Agent
  family name: Zheng
  given name: Guanglei
author list: Agent
  family name: Zhou
  given name: Peitao
doi: 10.7717/peerj.10198
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Chen et al.
attribution name: Chen et al.

Soil organic matter dynamics in semiarid agroecosystems transitioning to dryland
type: item
type: AcademicArticle
description: Recent interest in improving soil health and agricultural sustainability recognizes the value of soil organic carbon (SOC) sequestration and nutrient cycling. The main goal of this study was to evaluate the response of various SOC and nitrogen (N) components in semiarid cropping systems transitioning from limited-irrigation to dryland and a restored grassland in the Southern High Plains of USA. Cropping systems evaluated include dryland winter wheat (Triticum aestivum L.)–sorghum (Sorghum bicolor L.)–fallow with conventional tillage (DLCTF) and no-tillage (DLNTF), limited-irrigation winter wheat–sorghum–fallow with no-tillage and cover cropping (LINTC) and no-tillage fallow (LINTF), and an undisturbed grassland (NG). Soil samples were collected from 0–15 cm and 15–30 cm depths and analyzed for SOC, total N, inorganic N, and soil microbial biomass carbon (SMBC) contents. The CO2 and N2O release during a eight-weeks long laboratory incubation were also analyzed. Results show 14% and 13% reduction in SOC and total N from 0–30 cm depth with the transition from limited-irrigation to dryland cropping systems while 51% more SOC and 41% more total N with the transition to grassland. The SMBC was 42% less in dryland cropping systems and 100% more in NG than the limited-irrigation cropping systems. However, the grassland was N limited, with 93% less inorganic N in NG compared to only 11% less in dryland cropping systems than in limited-irrigation cropping systems. The microbial respiration measured as CO2-C was highest in NG, followed by limited-irrigation and dryland cropping systems. The N2O-N release showed the lowest rate of N loss from dryland cropping systems, followed by NG and limited-irrigation cropping systems. This study demonstrated loss of SOC and N in agroecosystems transitioned to dryland crop-fallow systems, with greater magnitude of change observed in the biologically active fraction of soil organic matter. Grassland restoration could be an important strategy…
format: application/pdf
format: text/html
creator: Rajan Ghimire
creator: Babu Ram Khanal
subject: Agricultural Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.10199
publisher: PeerJ Inc.
rights: © 2020 Ghimire and Khanal
abstract: Recent interest in improving soil health and agricultural sustainability recognizes the value of soil organic carbon (SOC) sequestration and nutrient cycling. The main goal of this study was to evaluate the response of various SOC and nitrogen (N) components in semiarid cropping systems transitioning from limited-irrigation to dryland and a restored grassland in the Southern High Plains of USA. Cropping systems evaluated include dryland winter wheat (Triticum aestivum L.)–sorghum (Sorghum bicolor L.)–fallow with conventional tillage (DLCTF) and no-tillage (DLNTF), limited-irrigation winter wheat–sorghum–fallow with no-tillage and cover cropping (LINTC) and no-tillage fallow (LINTF), and an undisturbed grassland (NG). Soil samples were collected from 0–15 cm and 15–30 cm depths and analyzed for SOC, total N, inorganic N, and soil microbial biomass carbon (SMBC) contents. The CO2 and N2O release during a eight-weeks long laboratory incubation were also analyzed. Results show 14% and 13% reduction in SOC and total N from 0–30 cm depth with the transition from limited-irrigation to dryland cropping systems while 51% more SOC and 41% more total N with the transition to grassland. The SMBC was 42% less in dryland cropping systems and 100% more in NG than the limited-irrigation cropping systems. However, the grassland was N limited, with 93% less inorganic N in NG compared to only 11% less in dryland cropping systems than in limited-irrigation cropping systems. The microbial respiration measured as CO2-C was highest in NG, followed by limited-irrigation and dryland cropping systems. The N2O-N release showed the lowest rate of N loss from dryland cropping systems, followed by NG and limited-irrigation cropping systems. This study demonstrated loss of SOC and N in agroecosystems transitioned to dryland crop-fallow systems, with greater magnitude of change observed in the biologically active fraction of soil organic matter. Grassland restoration could be an important strategy…
bibliographic citation: Ghimire et al. (2020) Soil organic matter dynamics in semiarid agroecosystems transitioning to dryland. PeerJ 8:e10199 https://doi.org/10.7717/peerj.10199
date submitted: 2020-07-17
date accepted: 2020-09-26
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ghimire
  given name: Rajan
author list: Agent
  family name: Khanal
  given name: Babu Ram
doi: 10.7717/peerj.10199
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Ghimire and Khanal
attribution name: Ghimire and Khanal

Structure and expression analysis of seven salt-related ERF genes of Populus
type: item
type: AcademicArticle
description: Ethylene response factors (ERFs) are plant-specific transcription factors (TFs) that play important roles in plant growth and stress defense and have received a great amount of attention in recent years. In this study, seven ERF genes related to abiotic stress tolerance and response were identified in plants of the Populus genus. Systematic bioinformatics, including sequence phylogeny, genome organisation, gene structure, gene ontology (GO) annotation, etc. were detected. Expression-pattern of these seven ERF genes were analyzed using RT-qPCR and cross validated using RNA-Seq. Data from a phylogenetic tree and multiple alignment of protein sequences indicated that these seven ERF TFs belong to three subfamilies and contain AP2, YRG, and RAYD conserved domains, which may interact with downstream target genes to regulate the plant stress response. An analysis of the structure and promoter region of these seven ERF genes showed that they have multiple stress-related motifs and cis-elements, which may play roles in the plant stress-tolerance process through a transcriptional regulation mechanism; moreover, the cellular_component and molecular_function terms associated with these ERFs determined by GO annotation supported this hypothesis. In addition, the spatio-temporal expression pattern of these seven ERFs, as detected using RT-qPCR and RNA-seq, suggested that they play a critical role in mediating the salt response and tolerance in a dynamic and tissue-specific manner. The results of this study provide a solid basis to explore the functions of the stress-related ERF TFs in Populus abiotic stress tolerance and development process.
format: application/pdf
format: text/html
creator: Juanjuan Huang
creator: Shengji Wang
creator: Xingdou Wang
creator: Yan Fan
creator: Youzhi Han
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.10206
publisher: PeerJ Inc.
rights: © 2020 Huang et al.
abstract: Ethylene response factors (ERFs) are plant-specific transcription factors (TFs) that play important roles in plant growth and stress defense and have received a great amount of attention in recent years. In this study, seven ERF genes related to abiotic stress tolerance and response were identified in plants of the Populus genus. Systematic bioinformatics, including sequence phylogeny, genome organisation, gene structure, gene ontology (GO) annotation, etc. were detected. Expression-pattern of these seven ERF genes were analyzed using RT-qPCR and cross validated using RNA-Seq. Data from a phylogenetic tree and multiple alignment of protein sequences indicated that these seven ERF TFs belong to three subfamilies and contain AP2, YRG, and RAYD conserved domains, which may interact with downstream target genes to regulate the plant stress response. An analysis of the structure and promoter region of these seven ERF genes showed that they have multiple stress-related motifs and cis-elements, which may play roles in the plant stress-tolerance process through a transcriptional regulation mechanism; moreover, the cellular_component and molecular_function terms associated with these ERFs determined by GO annotation supported this hypothesis. In addition, the spatio-temporal expression pattern of these seven ERFs, as detected using RT-qPCR and RNA-seq, suggested that they play a critical role in mediating the salt response and tolerance in a dynamic and tissue-specific manner. The results of this study provide a solid basis to explore the functions of the stress-related ERF TFs in Populus abiotic stress tolerance and development process.
bibliographic citation: Huang et al. (2020) Structure and expression analysis of seven salt-related ERF genes of Populus. PeerJ 8:e10206 https://doi.org/10.7717/peerj.10206
date submitted: 2020-07-03
date accepted: 2020-09-28
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Juanjuan
author list: Agent
  family name: Wang
  given name: Shengji
author list: Agent
  family name: Wang
  given name: Xingdou
author list: Agent
  family name: Fan
  given name: Yan
author list: Agent
  family name: Han
  given name: Youzhi
doi: 10.7717/peerj.10206
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Huang et al.
attribution name: Huang et al.

Feroxichthys yunnanensis gen. et sp. nov. (Colobodontidae, Neopterygii), a large durophagous predator from the Middle Triassic (Anisian) Luoping Biota, eastern Yunnan, China
type: item
type: AcademicArticle
description: Neopterygii is a large group of ray-finned fishes which underwent a rapid radiation in the Middle Triassic. Until recently, 11 stem neopterygians have been recovered from the early Middle Triassic Luoping Biota in eastern Yunnan, China, and they are small to medium-sized fishes. Here, I report the discovery of a new stem neopterygian, Feroxichthys yunnanensis gen. et sp. nov. from the Luoping Biota, which represents the first evidence of large-sized stem neopteygians in this biota with a total length of ~340 mm (290 mm in standard length). The skull of the new taxon is exceptionally well-preserved, showing some peculiar features rarely known in other stem neopterygians, for example fusion of paired premaxillae, fusion of lacrimal with maxilla, and a fused parieto-dermopterotic with a strong posterior process. Phylogenetic studies recover Feroxichthys as a basal colobodontid, and a revised diagnosis of this family is presented. The feeding apparatus indicates that Feroxichthys might have been predominantly durophagous, resembling other colobodontids. However, the anterior peg-like teeth in the jaws of Feroxichthys are much longer and stronger than other colobodontids, enabling a more powerful initial prey capture before food was passed posteriorly to molariform teeth for crushing in the oral cavity. As a mysterious large durophagous predator previously unknown from the Luoping Biota, the new finding is important not only for understanding the early diversification of neopterygians during this age but also for investigating the trophic structure in this marine ecosystem.
format: application/pdf
format: text/html
creator: Guang-Hui Xu
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10229
publisher: PeerJ Inc.
rights: © 2020 Xu
abstract: Neopterygii is a large group of ray-finned fishes which underwent a rapid radiation in the Middle Triassic. Until recently, 11 stem neopterygians have been recovered from the early Middle Triassic Luoping Biota in eastern Yunnan, China, and they are small to medium-sized fishes. Here, I report the discovery of a new stem neopterygian, Feroxichthys yunnanensis gen. et sp. nov. from the Luoping Biota, which represents the first evidence of large-sized stem neopteygians in this biota with a total length of ~340 mm (290 mm in standard length). The skull of the new taxon is exceptionally well-preserved, showing some peculiar features rarely known in other stem neopterygians, for example fusion of paired premaxillae, fusion of lacrimal with maxilla, and a fused parieto-dermopterotic with a strong posterior process. Phylogenetic studies recover Feroxichthys as a basal colobodontid, and a revised diagnosis of this family is presented. The feeding apparatus indicates that Feroxichthys might have been predominantly durophagous, resembling other colobodontids. However, the anterior peg-like teeth in the jaws of Feroxichthys are much longer and stronger than other colobodontids, enabling a more powerful initial prey capture before food was passed posteriorly to molariform teeth for crushing in the oral cavity. As a mysterious large durophagous predator previously unknown from the Luoping Biota, the new finding is important not only for understanding the early diversification of neopterygians during this age but also for investigating the trophic structure in this marine ecosystem.
bibliographic citation: Xu (2020) Feroxichthys yunnanensis gen. et sp. nov. (Colobodontidae, Neopterygii), a large durophagous predator from the Middle Triassic (Anisian) Luoping Biota, eastern Yunnan, China. PeerJ 8:e10229 https://doi.org/10.7717/peerj.10229
date submitted: 2020-05-04
date accepted: 2020-10-02
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Guang-Hui
doi: 10.7717/peerj.10229
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: © 2020 Xu
attribution name: Xu

Spatial differentiation of gully clusters based on the regional scale: an example from northeastern China
type: item
type: AcademicArticle
description: Gully erosion represents a serious environmental threat around the world, but their spatial distribution law are unclear at the regional scale. To quantitatively characterize the spatial distribution model of gullies and determine the regularity of regional differentiation, this paper used spatial analyst and statistics method to study the spatial distribution of gullies in 34 sample areas of northeastern China based on interpretations of high-resolution remote sensing images. The results showed that the kernel density could quantitatively describe the continuous spatial clustering of gullies. Gullies in northeastern China had the characteristics of a spatially unbalanced distribution at the scale of the sample area. The average kernel density of the 34 sample areas (Moran’s I was 0.43, P¡0.01P < 0.01) also indicated clustering distribution at the regional scale. The horizontal clustering characteristics of gullies exhibited an azonal distribution of being low values in the middle plain and high values on the three mountainous areas. The average kernel density in the southeastern part of the study area was highest (maximum value of 2.38). In the vertical direction, gullies were relatively undeveloped in low- and high-altitude areas, while middle-altitude areas were beneficial to the development of gullies. The effect of height differences on gully development was more significant than altitude. As the height difference increased, gullies tended to be more clustered, which can be expressed by a power function. The results of this study will not only help to understand the regional differentiation characteristics of gullies but will also provide a scientific reference for the study of spatial distribution of gullies in future.
format: application/pdf
format: text/html
creator: Ying Zhao
creator: Bin Zhang
creator: Wei Qin
creator: Jun Luo
creator: Hui Liu
creator: Qingchun Deng
creator: Wei Lv
creator: Yuli He
creator: Houling Wang
subject: Soil Science
subject: Ecohydrology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9907
publisher: PeerJ Inc.
rights: © 2020 Zhao et al.
abstract: Gully erosion represents a serious environmental threat around the world, but their spatial distribution law are unclear at the regional scale. To quantitatively characterize the spatial distribution model of gullies and determine the regularity of regional differentiation, this paper used spatial analyst and statistics method to study the spatial distribution of gullies in 34 sample areas of northeastern China based on interpretations of high-resolution remote sensing images. The results showed that the kernel density could quantitatively describe the continuous spatial clustering of gullies. Gullies in northeastern China had the characteristics of a spatially unbalanced distribution at the scale of the sample area. The average kernel density of the 34 sample areas (Moran’s I was 0.43, P¡0.01P < 0.01) also indicated clustering distribution at the regional scale. The horizontal clustering characteristics of gullies exhibited an azonal distribution of being low values in the middle plain and high values on the three mountainous areas. The average kernel density in the southeastern part of the study area was highest (maximum value of 2.38). In the vertical direction, gullies were relatively undeveloped in low- and high-altitude areas, while middle-altitude areas were beneficial to the development of gullies. The effect of height differences on gully development was more significant than altitude. As the height difference increased, gullies tended to be more clustered, which can be expressed by a power function. The results of this study will not only help to understand the regional differentiation characteristics of gullies but will also provide a scientific reference for the study of spatial distribution of gullies in future.
bibliographic citation: Zhao et al. (2020) Spatial differentiation of gully clusters based on the regional scale: an example from northeastern China. PeerJ 8:e9907 https://doi.org/10.7717/peerj.9907
date submitted: 2020-05-06
date accepted: 2020-08-18
issued: 2020-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Bin
author list: Agent
  family name: Qin
  given name: Wei
author list: Agent
  family name: Luo
  given name: Jun
author list: Agent
  family name: Liu
  given name: Hui
author list: Agent
  family name: Deng
  given name: Qingchun
author list: Agent
  family name: Lv
  given name: Wei
author list: Agent
  family name: He
  given name: Yuli
author list: Agent
  family name: Wang
  given name: Houling
doi: 10.7717/peerj.9907
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-19
copyright: ©2020 Zhao et al.
attribution name: Zhao et al.

Generation of human liver organoids from pluripotent stem cell-derived hepatic endoderms
type: item
type: AcademicArticle
description: Background The use of a personalized liver organoid derived from human-induced pluripotent stem cells (HuiPSCs) is advancing the use of in vitro disease models for the design of specific, effective therapies for individuals. Collecting patient peripheral blood cells for HuiPSC generation is preferable because it is less invasive; however, the capability of blood cell-derived HuiPSCs for hepatic differentiation and liver organoid formation remains uncertain. Moreover, the currently available methods for liver organoid formation require a multistep process of cell differentiation or a combination of hepatic endodermal, endothelial and mesenchymal cells, which is a major hurdle for the application of personalized liver organoids in high-throughput testing of drug toxicity and safety. To demonstrate the capability of blood cell-derived HuiPSCs for liver organoid formation without support from endothelial and mesenchymal cells. Methods The peripheral blood-derived HuiPSCs first differentiated into hepatic endoderm (HE) in two-dimensional (2D) culture on Matrigel-coated plates under hypoxia for 10 days. The HE was then collected and cultured in 3D culture using 50% Matrigel under ambient oxygen. The maturation of hepatocytes was further induced by adding hepatocyte growth medium containing HGF and oncostatin M on top of the 3D culture and incubating the culture for an additional 12–17 days. The function of the liver organoids was assessed using expression analysis of hepatocyte-specific gene and proteins. Albumin (ALB) synthesis, glycogen and lipid storage, and metabolism of indocyanine were evaluated. The spatial distribution of albumin was examined using immunofluorescence and confocal microscopy. Results CD34+ hematopoietic cell-derived HuiPSCs were capable of differentiating into definitive endoderm expressing SOX17 and FOXA2, hepatic endoderm expressing FOXA2, hepatoblasts expressing AFP and hepatocytes expressing ALB. On day 25 of the 2D culture, cells expressed SOX…
format: application/pdf
format: text/html
creator: Kasem Kulkeaw
creator: Alisa Tubsuwan
creator: Nongnat Tongkrajang
creator: Narisara Whangviboonkij
subject: Cell Biology
subject: Molecular Biology
subject: Anatomy and Physiology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.9968
publisher: PeerJ Inc.
rights: © 2020 Kulkeaw et al.
abstract: Background The use of a personalized liver organoid derived from human-induced pluripotent stem cells (HuiPSCs) is advancing the use of in vitro disease models for the design of specific, effective therapies for individuals. Collecting patient peripheral blood cells for HuiPSC generation is preferable because it is less invasive; however, the capability of blood cell-derived HuiPSCs for hepatic differentiation and liver organoid formation remains uncertain. Moreover, the currently available methods for liver organoid formation require a multistep process of cell differentiation or a combination of hepatic endodermal, endothelial and mesenchymal cells, which is a major hurdle for the application of personalized liver organoids in high-throughput testing of drug toxicity and safety. To demonstrate the capability of blood cell-derived HuiPSCs for liver organoid formation without support from endothelial and mesenchymal cells. Methods The peripheral blood-derived HuiPSCs first differentiated into hepatic endoderm (HE) in two-dimensional (2D) culture on Matrigel-coated plates under hypoxia for 10 days. The HE was then collected and cultured in 3D culture using 50% Matrigel under ambient oxygen. The maturation of hepatocytes was further induced by adding hepatocyte growth medium containing HGF and oncostatin M on top of the 3D culture and incubating the culture for an additional 12–17 days. The function of the liver organoids was assessed using expression analysis of hepatocyte-specific gene and proteins. Albumin (ALB) synthesis, glycogen and lipid storage, and metabolism of indocyanine were evaluated. The spatial distribution of albumin was examined using immunofluorescence and confocal microscopy. Results CD34+ hematopoietic cell-derived HuiPSCs were capable of differentiating into definitive endoderm expressing SOX17 and FOXA2, hepatic endoderm expressing FOXA2, hepatoblasts expressing AFP and hepatocytes expressing ALB. On day 25 of the 2D culture, cells expressed SOX…
bibliographic citation: Kulkeaw et al. (2020) Generation of human liver organoids from pluripotent stem cell-derived hepatic endoderms. PeerJ 8:e9968 https://doi.org/10.7717/peerj.9968
date submitted: 2020-02-05
date accepted: 2020-08-26
issued: 2020-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kulkeaw
  given name: Kasem
author list: Agent
  family name: Tubsuwan
  given name: Alisa
author list: Agent
  family name: Tongkrajang
  given name: Nongnat
author list: Agent
  family name: Whangviboonkij
  given name: Narisara
doi: 10.7717/peerj.9968
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-19
copyright: ©2020 Kulkeaw et al.
attribution name: Kulkeaw et al.

Using trace elements to identify the geographic origin of migratory bats
type: item
type: AcademicArticle
description: The expansion of the wind energy industry has had benefits in terms of increased renewable energy production but has also led to increased mortality of migratory bats due to interactions with wind turbines. A key question that could guide bat-related management activities is identifying the geographic origin of bats killed at wind-energy facilities. Generating this information requires developing new methods for identifying the geographic sources of individual bats. Here we explore the viability of assigning geographic origin using trace element analyses of fur to infer the summer molting location of eastern red bats (Lasiurus borealis). Our approach is based on the idea that the concentration of trace elements in bat fur is related through the food chain to the amount of trace elements present in the soil, which varies across large geographic scales. Specifically, we used inductively coupled plasma–mass spectrometry to determine the concentration of fourteen trace elements in fur of 126 known-origin eastern red bats to generate a basemap for assignment throughout the range of this species in eastern North America. We then compared this map to publicly available soil trace element concentrations for the U.S. and Canada, used a probabilistic framework to generate likelihood-of-origin maps for each bat, and assessed how well trace element profiles predicted the origins of these individuals. Overall, our results suggest that trace elements allow successful assignment of individual bats 80% of the time while reducing probable locations in half. Our study supports the use of trace elements to identify the geographic origin of eastern red and perhaps other migratory bats, particularly when combined with data from other biomarkers such as genetic and stable isotope data.
format: application/pdf
format: text/html
creator: Jamin G. Wieringa
creator: Juliet Nagel
creator: David M. Nelson
creator: Bryan C. Carstens
creator: H. Lisle Gibbs
subject: Biochemistry
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.10082
publisher: PeerJ Inc.
rights: © 2020 Wieringa et al.
abstract: The expansion of the wind energy industry has had benefits in terms of increased renewable energy production but has also led to increased mortality of migratory bats due to interactions with wind turbines. A key question that could guide bat-related management activities is identifying the geographic origin of bats killed at wind-energy facilities. Generating this information requires developing new methods for identifying the geographic sources of individual bats. Here we explore the viability of assigning geographic origin using trace element analyses of fur to infer the summer molting location of eastern red bats (Lasiurus borealis). Our approach is based on the idea that the concentration of trace elements in bat fur is related through the food chain to the amount of trace elements present in the soil, which varies across large geographic scales. Specifically, we used inductively coupled plasma–mass spectrometry to determine the concentration of fourteen trace elements in fur of 126 known-origin eastern red bats to generate a basemap for assignment throughout the range of this species in eastern North America. We then compared this map to publicly available soil trace element concentrations for the U.S. and Canada, used a probabilistic framework to generate likelihood-of-origin maps for each bat, and assessed how well trace element profiles predicted the origins of these individuals. Overall, our results suggest that trace elements allow successful assignment of individual bats 80% of the time while reducing probable locations in half. Our study supports the use of trace elements to identify the geographic origin of eastern red and perhaps other migratory bats, particularly when combined with data from other biomarkers such as genetic and stable isotope data.
bibliographic citation: Wieringa et al. (2020) Using trace elements to identify the geographic origin of migratory bats. PeerJ 8:e10082 https://doi.org/10.7717/peerj.10082
date submitted: 2020-03-30
date accepted: 2020-09-11
issued: 2020-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wieringa
  given name: Jamin G.
author list: Agent
  family name: Nagel
  given name: Juliet
author list: Agent
  family name: Nelson
  given name: David M.
author list: Agent
  family name: Carstens
  given name: Bryan C.
author list: Agent
  family name: Gibbs
  given name: H. Lisle
doi: 10.7717/peerj.10082
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-19
copyright: ©2020 Wieringa et al.
attribution name: Wieringa et al.

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