PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Patient-reported fatigue in patients with rheumatoid arthritis who commence biologic therapy: a longitudinal study
items: Molecular characterization and phylogenetic analysis of a Squash leaf curl virus isolate from Baja California Sur, Mexico
items: Assessment on latitudinal tree species richness using environmental factors in the southeastern United States
items: The synergistic effect of concatenation in phylogenomics: the case in Pantoea
items: Cloning and characterization of a tyrosine decarboxylase involved in the biosynthesis of galanthamine in Lycoris aurea
items: Simulating the effects of climate change across the geographical distribution of two medicinal plants in the genus Nardostachys
items: Characterization of the iPSC-derived conditioned medium that promotes the growth of bovine corneal endothelial cells
items: Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium stress
items: Risk of acute exacerbation between acetaminophen and ibuprofen in children with asthma
items: Distribution of crabs along a habitat gradient on the Yellow Sea coast after Spartina alterniflora invasion

Patient-reported fatigue in patients with rheumatoid arthritis who commence biologic therapy: a longitudinal study
type: item
type: AcademicArticle
description: Aims and objectives To examine changes in patient-reported fatigue, over a twelve month period, in rheumatoid arthritis patients who commence biologic treatment, and to identify possible predictors for such changes. Background Fatigue is a burdensome symptom for patients with rheumatoid arthritis. Despite biologics being effective in reducing disease activity, patients still report fatigue. Design A longitudinal observational study. Methods A total of 48 patients were enrolled in the study. Fatigue was measured by the Fatigue Severity Scale. Independent samples T-tests were used to test gender differences, and paired samples T-tests were used to measure differences between repeated measures. Bivariate and multiple regression analyses were used to examine potential predictors for changes in fatigue, such as age, sex, Disease Activity Score 28, pain and physical and emotional well-being. Results Forty-seven patients completed the study. From baseline to 12-month follow-up, fatigue decreased significantly in both women and men. Analyses of predictors were performed step-wise, and the final model included sex and physical well-being. The results from this final step showed that female sex was the only significant predictor for changes in fatigue. Conclusion Patients commencing biologic therapy reported a significant reduction in fatigue. Female sex was a significant predictor of changes in fatigue. Relevance to clinical practice Despite improvements in pharmacological treatment, patients with rheumatoid arthritis still report fatigue. This is a multifaceted health problem encompassing personal and emotional factors in addition to the clinical factors directly connected to the disease.
format: application/pdf
format: text/html
creator: Hege Selheim Rinke
creator: Clara Beate Gram Gjesdal
creator: Heidi Markussen
creator: Jörg Assmus
creator: Gerd Karin Natvig
subject: Allergy and Clinical Immunology
subject: Nursing
subject: Rheumatology
description: doi:10.7717/peerj.6771
publisher: PeerJ Inc.
rights: © 2019 Rinke et al.
abstract: Aims and objectives To examine changes in patient-reported fatigue, over a twelve month period, in rheumatoid arthritis patients who commence biologic treatment, and to identify possible predictors for such changes. Background Fatigue is a burdensome symptom for patients with rheumatoid arthritis. Despite biologics being effective in reducing disease activity, patients still report fatigue. Design A longitudinal observational study. Methods A total of 48 patients were enrolled in the study. Fatigue was measured by the Fatigue Severity Scale. Independent samples T-tests were used to test gender differences, and paired samples T-tests were used to measure differences between repeated measures. Bivariate and multiple regression analyses were used to examine potential predictors for changes in fatigue, such as age, sex, Disease Activity Score 28, pain and physical and emotional well-being. Results Forty-seven patients completed the study. From baseline to 12-month follow-up, fatigue decreased significantly in both women and men. Analyses of predictors were performed step-wise, and the final model included sex and physical well-being. The results from this final step showed that female sex was the only significant predictor for changes in fatigue. Conclusion Patients commencing biologic therapy reported a significant reduction in fatigue. Female sex was a significant predictor of changes in fatigue. Relevance to clinical practice Despite improvements in pharmacological treatment, patients with rheumatoid arthritis still report fatigue. This is a multifaceted health problem encompassing personal and emotional factors in addition to the clinical factors directly connected to the disease.
bibliographic citation: Rinke et al. (2019) Patient-reported fatigue in patients with rheumatoid arthritis who commence biologic therapy: a longitudinal study. PeerJ 7:e6771 https://doi.org/10.7717/peerj.6771
date submitted: 2018-07-10
date accepted: 2019-03-12
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rinke
  given name: Hege Selheim
author list: Agent
  family name: Gjesdal
  given name: Clara Beate Gram
author list: Agent
  family name: Markussen
  given name: Heidi
author list: Agent
  family name: Assmus
  given name: Jörg
author list: Agent
  family name: Natvig
  given name: Gerd Karin
doi: 10.7717/peerj.6771
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Rinke et al.
attribution name: Rinke et al.

Molecular characterization and phylogenetic analysis of a Squash leaf curl virus isolate from Baja California Sur, Mexico
type: item
type: AcademicArticle
description: Background The begomovirus, squash leaf curl virus (SLCuV) is one of the causal agents of squash leaf curl (SLC) disease, which is among the most destructive diseases of cucurbit crops in tropical, subtropical, and semiarid regions worldwide. This disease was originally reported in the American continent with subsequent spread to the Mediterranean basin. Up to now, SLCuV has only been detected by PCR in Mexico. This study provides the first complete sequence of a Mexican SLCuV isolate from Baja California Sur (BCS). In addition, the genome of the virus was characterized, establishing its phylogenetic relationship with other SLCuV isolates. Methods The full genome (DNA-A and DNA-B) was amplified by rolling circle amplification, cloned and sequenced and the open reading frames (ORF) were annotated. Virus identification was performed according to the International Committee on Taxonomy of Viruses (ICTV) criteria for begomovirus species demarcation. To infer evolutionary relationship with other SLCuV isolates, phylogenetic and recombination analyses were performed. Results The SLCuV-[MX-BCS-La Paz-16] genome (DNA-A and DNA-B) had 99% identity with SLCuV reference genomes. The phylogenetic analysis showed that SLCuV-[MX-BCS-La Paz-16] is closely related to SLCuV isolates from the Middle East (Egypt, Israel, Palestine and Lebanon). No evidence of interspecific recombination was determined and iterons were 100% identical in all isolates in the SLCuV clade. Conclusions SLCuV-[MX-BCS-La Paz-16] showed low genetic variability in its genome, which could be due to a local adaptation process (isolate environment), suggesting that SLCuV isolates from the Middle East could have derived from the southwestern United States of America (USA) and northwestern Mexico.
format: application/pdf
format: text/html
creator: Diana Medina-Hernández
creator: M. Goretty Caamal-Chan
creator: Mayela Vargas-Salinas
creator: Abraham Loera-Muro
creator: Aarón Barraza
creator: Ramón Jaime Holguín-Peña
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
subject: Virology
description: doi:10.7717/peerj.6774
publisher: PeerJ Inc.
rights: © 2019 Medina-Hernández et al.
abstract: Background The begomovirus, squash leaf curl virus (SLCuV) is one of the causal agents of squash leaf curl (SLC) disease, which is among the most destructive diseases of cucurbit crops in tropical, subtropical, and semiarid regions worldwide. This disease was originally reported in the American continent with subsequent spread to the Mediterranean basin. Up to now, SLCuV has only been detected by PCR in Mexico. This study provides the first complete sequence of a Mexican SLCuV isolate from Baja California Sur (BCS). In addition, the genome of the virus was characterized, establishing its phylogenetic relationship with other SLCuV isolates. Methods The full genome (DNA-A and DNA-B) was amplified by rolling circle amplification, cloned and sequenced and the open reading frames (ORF) were annotated. Virus identification was performed according to the International Committee on Taxonomy of Viruses (ICTV) criteria for begomovirus species demarcation. To infer evolutionary relationship with other SLCuV isolates, phylogenetic and recombination analyses were performed. Results The SLCuV-[MX-BCS-La Paz-16] genome (DNA-A and DNA-B) had 99% identity with SLCuV reference genomes. The phylogenetic analysis showed that SLCuV-[MX-BCS-La Paz-16] is closely related to SLCuV isolates from the Middle East (Egypt, Israel, Palestine and Lebanon). No evidence of interspecific recombination was determined and iterons were 100% identical in all isolates in the SLCuV clade. Conclusions SLCuV-[MX-BCS-La Paz-16] showed low genetic variability in its genome, which could be due to a local adaptation process (isolate environment), suggesting that SLCuV isolates from the Middle East could have derived from the southwestern United States of America (USA) and northwestern Mexico.
bibliographic citation: Medina-Hernández et al. (2019) Molecular characterization and phylogenetic analysis of a Squash leaf curl virus isolate from Baja California Sur, Mexico. PeerJ 7:e6774 https://doi.org/10.7717/peerj.6774
date submitted: 2018-10-30
date accepted: 2019-03-12
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Medina-Hernández
  given name: Diana
author list: Agent
  family name: Caamal-Chan
  given name: M. Goretty
author list: Agent
  family name: Vargas-Salinas
  given name: Mayela
author list: Agent
  family name: Loera-Muro
  given name: Abraham
author list: Agent
  family name: Barraza
  given name: Aarón
author list: Agent
  family name: Holguín-Peña
  given name: Ramón Jaime
doi: 10.7717/peerj.6774
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Medina-Hernández et al.
attribution name: Medina-Hernández et al.

Assessment on latitudinal tree species richness using environmental factors in the southeastern United States
type: item
type: AcademicArticle
description: The southeastern region of the United States exhibits an unusual trend of decreasing tree species richness (TSR) from higher to lower latitudes over the Florida peninsula. This trend contradicts the widely marked latitudinal diversity gradient where species richness is highest in tropical zones and decreases towards extratropical regions. This study aims to assess the environmental factors that prompt this atypical inverse latitudinal gradient seen in TSR using the USDA Forest Service’s Forest Inventory and Analysis (FIA) database. Fifteen variables under four categories of forested area, groundwater, soil properties, and climate groups were examined to model TSR in the region. Generalized linear models (GLMs) with Poisson distributions first assessed individual variables to test explanatory power then the LASSO regularization method was utilized to extract two subsets of the most influential variables to predict TSR. Forest area and four climate variables (mean annual temperature, precipitation seasonality, mean temperature of coldest quarter, and mean precipitation of driest quarter) were the top five variables during the initial GLM assessment implying their potential individual influence in regulating TSR. Two subsets of LASSO models contained seven and three predictor variables, respectively. Frist subset includes seven predictors, presented in highest to low standardized coefficient, mean temperature of coldest quarter, forested area, precipitation seasonality, mean precipitation of driest quarter, water table depth, spodosol, and available water storage. The other subset further excluded four lowest influential variables from the first set, leaving the top three variables from the first subset. The first subset of the LASSO model predicted TSR with 63.4% explained deviance while the second subset reproduced 60.2% of deviance explained. With only three variables used, the second model outperformed the first model evaluated by the AIC value. We conclude that fo…
format: application/pdf
format: text/html
creator: Youngsang Kwon
creator: Taesoo Lee
creator: Alison Lang
creator: Dorian Burnette
subject: Biogeography
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6781
publisher: PeerJ Inc.
rights: © 2019 Kwon et al.
abstract: The southeastern region of the United States exhibits an unusual trend of decreasing tree species richness (TSR) from higher to lower latitudes over the Florida peninsula. This trend contradicts the widely marked latitudinal diversity gradient where species richness is highest in tropical zones and decreases towards extratropical regions. This study aims to assess the environmental factors that prompt this atypical inverse latitudinal gradient seen in TSR using the USDA Forest Service’s Forest Inventory and Analysis (FIA) database. Fifteen variables under four categories of forested area, groundwater, soil properties, and climate groups were examined to model TSR in the region. Generalized linear models (GLMs) with Poisson distributions first assessed individual variables to test explanatory power then the LASSO regularization method was utilized to extract two subsets of the most influential variables to predict TSR. Forest area and four climate variables (mean annual temperature, precipitation seasonality, mean temperature of coldest quarter, and mean precipitation of driest quarter) were the top five variables during the initial GLM assessment implying their potential individual influence in regulating TSR. Two subsets of LASSO models contained seven and three predictor variables, respectively. Frist subset includes seven predictors, presented in highest to low standardized coefficient, mean temperature of coldest quarter, forested area, precipitation seasonality, mean precipitation of driest quarter, water table depth, spodosol, and available water storage. The other subset further excluded four lowest influential variables from the first set, leaving the top three variables from the first subset. The first subset of the LASSO model predicted TSR with 63.4% explained deviance while the second subset reproduced 60.2% of deviance explained. With only three variables used, the second model outperformed the first model evaluated by the AIC value. We conclude that fo…
bibliographic citation: Kwon et al. (2019) Assessment on latitudinal tree species richness using environmental factors in the southeastern United States. PeerJ 7:e6781 https://doi.org/10.7717/peerj.6781
date submitted: 2018-11-08
date accepted: 2019-03-13
issued: 2019-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kwon
  given name: Youngsang
author list: Agent
  family name: Lee
  given name: Taesoo
author list: Agent
  family name: Lang
  given name: Alison
author list: Agent
  family name: Burnette
  given name: Dorian
doi: 10.7717/peerj.6781
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-17
copyright: ©2019 Kwon et al.
attribution name: Kwon et al.

The synergistic effect of concatenation in phylogenomics: the case in Pantoea
type: item
type: AcademicArticle
description: With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of si…
format: application/pdf
format: text/html
creator: Marike Palmer
creator: Stephanus N. Venter
creator: Alistair R. McTaggart
creator: Martin P.A. Coetzee
creator: Stephanie Van Wyk
creator: Juanita R. Avontuur
creator: Chrizelle W. Beukes
creator: Gerda Fourie
creator: Quentin C. Santana
creator: Magriet A. Van Der Nest
creator: Jochen Blom
creator: Emma T. Steenkamp
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.6698
publisher: PeerJ Inc.
rights: © 2019 Palmer et al.
abstract: With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of si…
bibliographic citation: Palmer et al. (2019) The synergistic effect of concatenation in phylogenomics: the case in Pantoea. PeerJ 7:e6698 https://doi.org/10.7717/peerj.6698
date submitted: 2018-10-23
date accepted: 2019-02-26
issued: 2019-04-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palmer
  given name: Marike
author list: Agent
  family name: Venter
  given name: Stephanus N.
author list: Agent
  family name: McTaggart
  given name: Alistair R.
author list: Agent
  family name: Coetzee
  given name: Martin P.A.
author list: Agent
  family name: Van Wyk
  given name: Stephanie
author list: Agent
  family name: Avontuur
  given name: Juanita R.
author list: Agent
  family name: Beukes
  given name: Chrizelle W.
author list: Agent
  family name: Fourie
  given name: Gerda
author list: Agent
  family name: Santana
  given name: Quentin C.
author list: Agent
  family name: Van Der Nest
  given name: Magriet A.
author list: Agent
  family name: Blom
  given name: Jochen
author list: Agent
  family name: Steenkamp
  given name: Emma T.
doi: 10.7717/peerj.6698
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-16
copyright: ©2019 Palmer et al.
attribution name: Palmer et al.

Cloning and characterization of a tyrosine decarboxylase involved in the biosynthesis of galanthamine in Lycoris aurea
type: item
type: AcademicArticle
description: Background Galanthamine, one kind of Amaryllidaceae alkaloid extracted from the Lycoris species, is used in the treatment of Alzheimer’s disease. In regards to medical and economic importance, the biosynthesis and regulatory mechanism of the secondary metabolites in Lycoris remain uninvestigated. Methods BLAST was used to identify the sequence of tyrosine decarboxylase in the transcriptome of Lycoris aurea (L’Hér) Herb. The enzyme activity of this TYDC was determined by using heterologous expressed protein in the Escherichia coli cells. The related productive contents of tyramine were detected using High Performance Liquid Chromatography (HPLC). According to the available micro RNA sequencing profiles and degradome database of L. aurea, microRNA396 were isolated, which targets to LaTYDC1 and RNA Ligase-Mediated-Rapid Amplification of cDNA Ends (RLM-RACE) were used to confirm the cleavage. The expression levels of miR396 and LaTYDC1 were measured using a quantitative real-time polymerase chain reaction (qRT-PCR). Results LaTYDC1 was mainly expressed in root, bulb, leaf and flower fitting the models for galanthamine accumulation. This decarboxylase efficiently catalyzes tyrosine to tyramine conversion. Under methyl jasmonate (MeJA) treatment, the expression of LaTYDC1 and the content of tyramine sharply increase. The use of RLM-RACE confirms that miR396 promotes the degradation of LaTYDC1 mRNA. Under MeJA treatment, the expression of miR396 was suppressed while the expression level of LaTYDC1 sharply increased. Following the increase of the miR396 transcriptional level, LaTYDC1 was significantly repressed. Conclusion LaTYDC1 participates in the biosynthesis of galanthamine, and is regulated by miR396. This finding also provides genetic strategy for improving the yield of galanthamine in the future.
format: application/pdf
format: text/html
creator: Rong Wang
creator: Xiaokang Han
creator: Sheng Xu
creator: Bing Xia
creator: Yumei Jiang
creator: Yong Xue
creator: Ren Wang
subject: Molecular Biology
subject: Plant Science
subject: Synthetic Biology
description: doi:10.7717/peerj.6729
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Galanthamine, one kind of Amaryllidaceae alkaloid extracted from the Lycoris species, is used in the treatment of Alzheimer’s disease. In regards to medical and economic importance, the biosynthesis and regulatory mechanism of the secondary metabolites in Lycoris remain uninvestigated. Methods BLAST was used to identify the sequence of tyrosine decarboxylase in the transcriptome of Lycoris aurea (L’Hér) Herb. The enzyme activity of this TYDC was determined by using heterologous expressed protein in the Escherichia coli cells. The related productive contents of tyramine were detected using High Performance Liquid Chromatography (HPLC). According to the available micro RNA sequencing profiles and degradome database of L. aurea, microRNA396 were isolated, which targets to LaTYDC1 and RNA Ligase-Mediated-Rapid Amplification of cDNA Ends (RLM-RACE) were used to confirm the cleavage. The expression levels of miR396 and LaTYDC1 were measured using a quantitative real-time polymerase chain reaction (qRT-PCR). Results LaTYDC1 was mainly expressed in root, bulb, leaf and flower fitting the models for galanthamine accumulation. This decarboxylase efficiently catalyzes tyrosine to tyramine conversion. Under methyl jasmonate (MeJA) treatment, the expression of LaTYDC1 and the content of tyramine sharply increase. The use of RLM-RACE confirms that miR396 promotes the degradation of LaTYDC1 mRNA. Under MeJA treatment, the expression of miR396 was suppressed while the expression level of LaTYDC1 sharply increased. Following the increase of the miR396 transcriptional level, LaTYDC1 was significantly repressed. Conclusion LaTYDC1 participates in the biosynthesis of galanthamine, and is regulated by miR396. This finding also provides genetic strategy for improving the yield of galanthamine in the future.
bibliographic citation: Wang et al. (2019) Cloning and characterization of a tyrosine decarboxylase involved in the biosynthesis of galanthamine in Lycoris aurea. PeerJ 7:e6729 https://doi.org/10.7717/peerj.6729
date submitted: 2018-11-22
date accepted: 2019-03-06
issued: 2019-04-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Rong
author list: Agent
  family name: Han
  given name: Xiaokang
author list: Agent
  family name: Xu
  given name: Sheng
author list: Agent
  family name: Xia
  given name: Bing
author list: Agent
  family name: Jiang
  given name: Yumei
author list: Agent
  family name: Xue
  given name: Yong
author list: Agent
  family name: Wang
  given name: Ren
doi: 10.7717/peerj.6729
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-16
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Simulating the effects of climate change across the geographical distribution of two medicinal plants in the genus Nardostachys
type: item
type: AcademicArticle
description: Background The medicinal plants of Radix et Rhizoma Nardostachyos include Nardostachys jatamansi and N. chinensis. Traditionally, the two plants have been used to treat many diseases. Because of their special aroma, they are also commonly used in the food and cosmetics industry. Recently, N. jatamansi and N. chinensis have been overexploited due to their economic importance, resulting in a sharp decline in their wild resources. Predicting potential distributions of the genus Nardostachys under different climate scenarios and understanding its preferred habitat are of great significance for their conservation, artificial cultivation, and assessment of their value. Methods The Maxent model was used to predict the potential geographical distributions of the genus Nardostachys under current and future climatic conditions based on two representative concentration pathways (RCP2.6 and RCP8.5) for the 2050s and 2070s. These data were used to study the effects of climate variables. Results The results show that the potential distribution of the two species will increase, thus more suitable habitats will be present in China. The suitable habitat for N. chinensis presents a relatively stable growth compared to N. jatamansi. In addition, precipitation plays a crucial role in modeling the effects of climate change on the genus Nardostachys. This study provides theoretical guidance for the cultivation of N. chinensis.
format: application/pdf
format: text/html
creator: Junjun Li
creator: Jie Wu
creator: Kezhong Peng
creator: Gang Fan
creator: Haiqing Yu
creator: Wenguo Wang
creator: Yang He
subject: Biogeography
subject: Ecology
subject: Climate Change Biology
description: doi:10.7717/peerj.6730
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background The medicinal plants of Radix et Rhizoma Nardostachyos include Nardostachys jatamansi and N. chinensis. Traditionally, the two plants have been used to treat many diseases. Because of their special aroma, they are also commonly used in the food and cosmetics industry. Recently, N. jatamansi and N. chinensis have been overexploited due to their economic importance, resulting in a sharp decline in their wild resources. Predicting potential distributions of the genus Nardostachys under different climate scenarios and understanding its preferred habitat are of great significance for their conservation, artificial cultivation, and assessment of their value. Methods The Maxent model was used to predict the potential geographical distributions of the genus Nardostachys under current and future climatic conditions based on two representative concentration pathways (RCP2.6 and RCP8.5) for the 2050s and 2070s. These data were used to study the effects of climate variables. Results The results show that the potential distribution of the two species will increase, thus more suitable habitats will be present in China. The suitable habitat for N. chinensis presents a relatively stable growth compared to N. jatamansi. In addition, precipitation plays a crucial role in modeling the effects of climate change on the genus Nardostachys. This study provides theoretical guidance for the cultivation of N. chinensis.
bibliographic citation: Li et al. (2019) Simulating the effects of climate change across the geographical distribution of two medicinal plants in the genus Nardostachys. PeerJ 7:e6730 https://doi.org/10.7717/peerj.6730
date submitted: 2018-11-23
date accepted: 2019-03-06
issued: 2019-04-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Junjun
author list: Agent
  family name: Wu
  given name: Jie
author list: Agent
  family name: Peng
  given name: Kezhong
author list: Agent
  family name: Fan
  given name: Gang
author list: Agent
  family name: Yu
  given name: Haiqing
author list: Agent
  family name: Wang
  given name: Wenguo
author list: Agent
  family name: He
  given name: Yang
doi: 10.7717/peerj.6730
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-16
copyright: © 2019 Li et al.
attribution name: Li et al.

Characterization of the iPSC-derived conditioned medium that promotes the growth of bovine corneal endothelial cells
type: item
type: AcademicArticle
description: Corneal endothelial cells (CECs) maintain corneal transparency and visual acuity. However, the limited proliferative capability of these cells in vitro has prompted researchers to find efficient culturing techniques for them. The aim of our study was to evaluate the use of conditioned medium (CM) obtained from induced pluripotent stem cells (iPSCs) as a source for the effective proliferation of bovine CECs (B-CECs). In our study, the proliferative ability of B-CECs was moderately enhanced when the cells were grown in 25% iPSC conditioned medium (iPSC-CM). Additionally, hexagonal cell morphology was maintained until passage 4, as opposed to the irregular and enlarged shape observed in control corneal endothelial medium (CEM). B-CECs in both the 25% iPSC-CM and CEM groups expressed and Na+-K+-ATPase. The gene expression levels of NIFK, Na+-K+-ATPase, Col4A and Col8A and the percentage of cells entering S and G2 phases were higher in the iPSC-CM group. The number of apoptotic cells also decreased in the iPSC-CM group. In comparison to the control cultures, iPSC-CM facilitated cell migration, and these cells showed better barrier functions after several passages. The mechanism of cell proliferation mediated by iPSC-CM was also investigated, and phosphorylation of Akt was observed in B-CECs after exposure to iPSC-CM and showed sustained phosphorylation induced for up to 180 min in iPSC-CM. Our findings indicate that iPSC-CM may employ PI3-kinase signaling in regulating cell cycle progression, which can lead to enhanced cellular proliferation. Effective component analysis of the CM showed that in the iPSC-CM group, the expression of activin-A was significantly increased. If activin-A is added as a supplement, it could help to maintain the morphology of the cells, similar to that of CM. Hence, we conclude that activin-A is one of the effective components of CM in promoting cell proliferation and maintaining cell morphology.
format: application/pdf
format: text/html
creator: Qing Liu
creator: Yonglong Guo
creator: Shiwei Liu
creator: Peiyuan Wang
creator: Yunxia Xue
creator: Zekai Cui
creator: Jiansu Chen
subject: Cell Biology
subject: Ophthalmology
description: doi:10.7717/peerj.6734
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Corneal endothelial cells (CECs) maintain corneal transparency and visual acuity. However, the limited proliferative capability of these cells in vitro has prompted researchers to find efficient culturing techniques for them. The aim of our study was to evaluate the use of conditioned medium (CM) obtained from induced pluripotent stem cells (iPSCs) as a source for the effective proliferation of bovine CECs (B-CECs). In our study, the proliferative ability of B-CECs was moderately enhanced when the cells were grown in 25% iPSC conditioned medium (iPSC-CM). Additionally, hexagonal cell morphology was maintained until passage 4, as opposed to the irregular and enlarged shape observed in control corneal endothelial medium (CEM). B-CECs in both the 25% iPSC-CM and CEM groups expressed and Na+-K+-ATPase. The gene expression levels of NIFK, Na+-K+-ATPase, Col4A and Col8A and the percentage of cells entering S and G2 phases were higher in the iPSC-CM group. The number of apoptotic cells also decreased in the iPSC-CM group. In comparison to the control cultures, iPSC-CM facilitated cell migration, and these cells showed better barrier functions after several passages. The mechanism of cell proliferation mediated by iPSC-CM was also investigated, and phosphorylation of Akt was observed in B-CECs after exposure to iPSC-CM and showed sustained phosphorylation induced for up to 180 min in iPSC-CM. Our findings indicate that iPSC-CM may employ PI3-kinase signaling in regulating cell cycle progression, which can lead to enhanced cellular proliferation. Effective component analysis of the CM showed that in the iPSC-CM group, the expression of activin-A was significantly increased. If activin-A is added as a supplement, it could help to maintain the morphology of the cells, similar to that of CM. Hence, we conclude that activin-A is one of the effective components of CM in promoting cell proliferation and maintaining cell morphology.
bibliographic citation: Liu et al. (2019) Characterization of the iPSC-derived conditioned medium that promotes the growth of bovine corneal endothelial cells. PeerJ 7:e6734 https://doi.org/10.7717/peerj.6734
date submitted: 2018-11-26
date accepted: 2019-03-07
issued: 2019-04-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Qing
author list: Agent
  family name: Guo
  given name: Yonglong
author list: Agent
  family name: Liu
  given name: Shiwei
author list: Agent
  family name: Wang
  given name: Peiyuan
author list: Agent
  family name: Xue
  given name: Yunxia
author list: Agent
  family name: Cui
  given name: Zekai
author list: Agent
  family name: Chen
  given name: Jiansu
doi: 10.7717/peerj.6734
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-16
copyright: © 2019 Liu et al.
attribution name: Liu et al.

Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium stress
type: item
type: AcademicArticle
description: Background The herb Sedum alfredii (S. alfredii) Hance is a hyperaccumulator of heavy metals (cadmium (Cd), zinc (Zn) and lead (Pb)); therefore, it could be a candidate plant for efficient phytoremediation. The GDSL esterase/lipase protein (GELP) family plays important roles in plant defense and growth. Although the GELP family members in a variety of plants have been cloned and analyzed, there are limited studies on the family’s responses to heavy metal-stress conditions. Methods Multiple sequence alignments and phylogenetic analyses were performed according to the criteria described. A WGCNA was used to construct co-expression regulatory networks. The roots of S. alfredii seedlings were treated with 100 µM CdCl2 for qRT-PCR to analyze expression levels in different tissues. SaGLIP8 was transformed into the Cd sensitive mutant strain yeast Δycf1 to investigate its role in resistance and accumulation to Cd. Results We analyzed GELP family members from genomic data of S. alfredii. A phylogenetic tree divided the 80 identified family members into three clades. The promoters of the 80 genes contained certain elements related to abiotic stress, such as TC-rich repeats (defense and stress responsiveness), heat shock elements (heat stress) and MYB-binding sites (drought-inducibility). In addition, 66 members had tissue-specific expression patterns and significant responses to Cd stress. In total, 13 hub genes were obtained, based on an existing S. alfredii transcriptome database, that control 459 edge genes, which were classified into five classes of functions in a co-expression subnetwork: cell wall and defense function, lipid and esterase, stress and tolerance, transport and transcription factor activity. Among the hub genes, Sa13F.102 (SaGLIP8), with a high expression level in all tissues, could increase Cd tolerance and accumulation in yeast when overexpressed. Conclusion Based on genomic data of S. alfredii, we conducted phylogenetic analyses, as well as conserved do…
format: application/pdf
format: text/html
creator: He Li
creator: Xiaojiao Han
creator: Wenmin Qiu
creator: Dong Xu
creator: Ying Wang
creator: Miao Yu
creator: Xianqi Hu
creator: Renying Zhuo
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6741
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background The herb Sedum alfredii (S. alfredii) Hance is a hyperaccumulator of heavy metals (cadmium (Cd), zinc (Zn) and lead (Pb)); therefore, it could be a candidate plant for efficient phytoremediation. The GDSL esterase/lipase protein (GELP) family plays important roles in plant defense and growth. Although the GELP family members in a variety of plants have been cloned and analyzed, there are limited studies on the family’s responses to heavy metal-stress conditions. Methods Multiple sequence alignments and phylogenetic analyses were performed according to the criteria described. A WGCNA was used to construct co-expression regulatory networks. The roots of S. alfredii seedlings were treated with 100 µM CdCl2 for qRT-PCR to analyze expression levels in different tissues. SaGLIP8 was transformed into the Cd sensitive mutant strain yeast Δycf1 to investigate its role in resistance and accumulation to Cd. Results We analyzed GELP family members from genomic data of S. alfredii. A phylogenetic tree divided the 80 identified family members into three clades. The promoters of the 80 genes contained certain elements related to abiotic stress, such as TC-rich repeats (defense and stress responsiveness), heat shock elements (heat stress) and MYB-binding sites (drought-inducibility). In addition, 66 members had tissue-specific expression patterns and significant responses to Cd stress. In total, 13 hub genes were obtained, based on an existing S. alfredii transcriptome database, that control 459 edge genes, which were classified into five classes of functions in a co-expression subnetwork: cell wall and defense function, lipid and esterase, stress and tolerance, transport and transcription factor activity. Among the hub genes, Sa13F.102 (SaGLIP8), with a high expression level in all tissues, could increase Cd tolerance and accumulation in yeast when overexpressed. Conclusion Based on genomic data of S. alfredii, we conducted phylogenetic analyses, as well as conserved do…
bibliographic citation: Li et al. (2019) Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium stress. PeerJ 7:e6741 https://doi.org/10.7717/peerj.6741
date submitted: 2019-01-25
date accepted: 2019-03-07
issued: 2019-04-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: He
author list: Agent
  family name: Han
  given name: Xiaojiao
author list: Agent
  family name: Qiu
  given name: Wenmin
author list: Agent
  family name: Xu
  given name: Dong
author list: Agent
  family name: Wang
  given name: Ying
author list: Agent
  family name: Yu
  given name: Miao
author list: Agent
  family name: Hu
  given name: Xianqi
author list: Agent
  family name: Zhuo
  given name: Renying
doi: 10.7717/peerj.6741
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-16
copyright: ©2019 Li et al.
attribution name: Li et al.

Risk of acute exacerbation between acetaminophen and ibuprofen in children with asthma
type: item
type: AcademicArticle
description: Background Antipyretics are widely prescribed in pediatric practice. Some reports have mentioned that acetaminophen and non-steroid anti-inflammatory drugs may negatively affect asthma control by causing asthma exacerbation (AE). However, many confounding factors can also influence the risks. We assessed the impact of using acetaminophen or ibuprofen on AE in asthmatic children, especially those with strong risk factors. Methods We used the 2010 Taiwan National Health Insurance Research Database and identified 983 children with persistent asthma aged 1–5 years old; among them, 591 used acetaminophen alone and 392 used ibuprofen alone in 2010. Then, we analyzed the risk of AE over 52 weeks in the patients with and without severe AE in the previous year. Results The ibuprofen group had a higher risk of an emergency room (ER) visit or hospitalization for AE (odds ratio (OR) = 2.10, 95% confidence interval (CI) [1.17–3.76], P = 0.01). Among asthmatic children who had severe AE in the previous year, the risk of AE was higher in the ibuprofen group than in the acetaminophen group (OR = 3.28, 95% CI [1.30–8.29], P = 0.01), where as among those who did not, the risks of AE were similar between the acetaminophen and ibuprofen groups (OR = 1.52, 95% CI [0.71–3.25], P = 0.28). Conclusions Among young asthmatic children, use of ibuprofen was associated with a higher risk of AE than acetaminophen, if they had severe AE with ER visit or hospitalization in the previous year. Pediatricians should use antipyretics among children with asthma after a full evaluation of the risk.
format: application/pdf
format: text/html
creator: Lin-Shien Fu
creator: Che-Chen Lin
creator: Chia-Yi Wei
creator: Ching-Heng Lin
creator: Yung-Chieh Huang
subject: Allergy and Clinical Immunology
subject: Immunology
subject: Pediatrics
subject: Respiratory Medicine
description: doi:10.7717/peerj.6760
publisher: PeerJ Inc.
rights: © 2019 Fu et al.
abstract: Background Antipyretics are widely prescribed in pediatric practice. Some reports have mentioned that acetaminophen and non-steroid anti-inflammatory drugs may negatively affect asthma control by causing asthma exacerbation (AE). However, many confounding factors can also influence the risks. We assessed the impact of using acetaminophen or ibuprofen on AE in asthmatic children, especially those with strong risk factors. Methods We used the 2010 Taiwan National Health Insurance Research Database and identified 983 children with persistent asthma aged 1–5 years old; among them, 591 used acetaminophen alone and 392 used ibuprofen alone in 2010. Then, we analyzed the risk of AE over 52 weeks in the patients with and without severe AE in the previous year. Results The ibuprofen group had a higher risk of an emergency room (ER) visit or hospitalization for AE (odds ratio (OR) = 2.10, 95% confidence interval (CI) [1.17–3.76], P = 0.01). Among asthmatic children who had severe AE in the previous year, the risk of AE was higher in the ibuprofen group than in the acetaminophen group (OR = 3.28, 95% CI [1.30–8.29], P = 0.01), where as among those who did not, the risks of AE were similar between the acetaminophen and ibuprofen groups (OR = 1.52, 95% CI [0.71–3.25], P = 0.28). Conclusions Among young asthmatic children, use of ibuprofen was associated with a higher risk of AE than acetaminophen, if they had severe AE with ER visit or hospitalization in the previous year. Pediatricians should use antipyretics among children with asthma after a full evaluation of the risk.
bibliographic citation: Fu et al. (2019) Risk of acute exacerbation between acetaminophen and ibuprofen in children with asthma. PeerJ 7:e6760 https://doi.org/10.7717/peerj.6760
date submitted: 2018-10-24
date accepted: 2019-03-09
issued: 2019-04-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Lin-Shien
author list: Agent
  family name: Lin
  given name: Che-Chen
author list: Agent
  family name: Wei
  given name: Chia-Yi
author list: Agent
  family name: Lin
  given name: Ching-Heng
author list: Agent
  family name: Huang
  given name: Yung-Chieh
doi: 10.7717/peerj.6760
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-16
copyright: © 2019 Fu et al.
attribution name: Fu et al.

Distribution of crabs along a habitat gradient on the Yellow Sea coast after Spartina alterniflora invasion
type: item
type: AcademicArticle
description: The effects of Spartina alterniflora invasion on macrobenthos have long been of concern; however, there is currently no unified conclusion regarding these effects. Most studies on crabs focus on one species or limited habitat types, and assessments of the community-level effects of S. alterniflora invasion considering multiple species and habitat types have rarely been conducted. In this study, we sampled crabs along a habitat gradient from the shoreline to inland areas on the Yellow Sea coast, including the mudflat, S. alterniflora marsh, Suaeda salsa marsh and Phragmites australis marsh. A total of 10 crab species were found among all habitats, with five species in the mudflat, six species in S. alterniflora marsh, seven species in S. salsa marsh and four species in P. australis marsh. The Shannon index values for the crab communities were similar between S. alterniflora marsh and S. salsa marsh, and these values were significantly higher than those for the mudflat and P. australis marsh. However, the total biomass of crabs was highest in the mudflat, and Metaplax longipes, Philyra pisum and Macrophthalmus dilatatus exclusively preferred the mudflat. The analysis of principal components and similarities showed that the crab community structure in S. alterniflora marsh was most similar to that in S. salsa marsh, while the crab community structure in the mudflat was most different from that in the other habitat types. Our results demonstrate that the distribution of crabs varies across a habitat gradient after S. alterniflora invasion and that the crab community in S. alterniflora marsh is slightly different from that associated with the local vegetation but shows a large difference from that in the mudflat. This study indicates that some crab species may have adapted to habitat containing alien S. alterniflora, while other crab species reject this new marsh type. The effects of the distribution of crabs after S. alterniflora invasion on the regional ecosystem need …
format: application/pdf
format: text/html
creator: Pan Chen
creator: Yan Zhang
creator: Xiaojing Zhu
creator: Changhu Lu
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Population Biology
description: doi:10.7717/peerj.6775
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: The effects of Spartina alterniflora invasion on macrobenthos have long been of concern; however, there is currently no unified conclusion regarding these effects. Most studies on crabs focus on one species or limited habitat types, and assessments of the community-level effects of S. alterniflora invasion considering multiple species and habitat types have rarely been conducted. In this study, we sampled crabs along a habitat gradient from the shoreline to inland areas on the Yellow Sea coast, including the mudflat, S. alterniflora marsh, Suaeda salsa marsh and Phragmites australis marsh. A total of 10 crab species were found among all habitats, with five species in the mudflat, six species in S. alterniflora marsh, seven species in S. salsa marsh and four species in P. australis marsh. The Shannon index values for the crab communities were similar between S. alterniflora marsh and S. salsa marsh, and these values were significantly higher than those for the mudflat and P. australis marsh. However, the total biomass of crabs was highest in the mudflat, and Metaplax longipes, Philyra pisum and Macrophthalmus dilatatus exclusively preferred the mudflat. The analysis of principal components and similarities showed that the crab community structure in S. alterniflora marsh was most similar to that in S. salsa marsh, while the crab community structure in the mudflat was most different from that in the other habitat types. Our results demonstrate that the distribution of crabs varies across a habitat gradient after S. alterniflora invasion and that the crab community in S. alterniflora marsh is slightly different from that associated with the local vegetation but shows a large difference from that in the mudflat. This study indicates that some crab species may have adapted to habitat containing alien S. alterniflora, while other crab species reject this new marsh type. The effects of the distribution of crabs after S. alterniflora invasion on the regional ecosystem need …
bibliographic citation: Chen et al. (2019) Distribution of crabs along a habitat gradient on the Yellow Sea coast after Spartina alterniflora invasion. PeerJ 7:e6775 https://doi.org/10.7717/peerj.6775
date submitted: 2018-12-12
date accepted: 2019-03-12
issued: 2019-04-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Pan
author list: Agent
  family name: Zhang
  given name: Yan
author list: Agent
  family name: Zhu
  given name: Xiaojing
author list: Agent
  family name: Lu
  given name: Changhu
doi: 10.7717/peerj.6775
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-16
copyright: © 2019 Chen et al.
attribution name: Chen et al.

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