PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exogenous hormones influence Brassica napus leaf cuticular wax deposition and cuticle function
items: Contributions of Latin American researchers in the understanding of the novel coronavirus outbreak: a literature review
items: Clonal diversity and genetic variation of the sedge Carex nigra in an alpine fen depend on soil nutrients
items: A new aggressive xenograft model of human colon cancer using cancer-associated fibroblasts
items: Culicidae-centric metabarcoding through targeted use of D2 ribosomal DNA primers
items: Simultaneous determination of phenolic metabolites in Chinese citrus and grape cultivars
items: Isolation, characterization, and cryopreservation of collared peccary skin-derived fibroblast cell lines
items: Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer
items: Incorporating reef fish avoidance behavior improves accuracy of species distribution models
items: Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis model

Exogenous hormones influence Brassica napus leaf cuticular wax deposition and cuticle function
type: item
type: AcademicArticle
description: Background Cuticular waxes cover plant surface and play important roles in protecting plants from abiotic and biotic stresses. The variations of wax deposition and chemical compositions under changing environments have been shown to be related to plant adaptations. However, it is still not clear whether the wax depositions could be adjusted to increase plant adaptations to stressed conditions. Methods In this study, exogenous methyl jasmonate (MeJA), the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) and salicylic acid (SA) were applied to test their effects on cuticular wax deposition in two Brassica napus cultivars, Zhongshuang 9 (ZS9, low wax coverage ) and Yuyou 19 (YY19, high wax coverage). Next, we measured the water loss rate and the transcriptional expression of genes involved in wax biosynthesis as well as genes related to disease defense. Results Seven wax compound classes, including fatty acids, aldehydes, alkanes, secondary alcohols, ketones, and unbranched as well as branched primary alcohols, were identified in B. napus leaf wax mixtures. MeJA, SA and ACC treatments had no significant effect on total wax amounts in YY19, whereas ACC reduced total wax amounts in ZS9. Overall, hormone treatments led to an increase in the amounts of aldehydes and ketones, and a decrease of secondary alcohol in ZS9, whereas they led to a decrease of alkane amounts and an increase of secondary alcohol amounts in YY19. Concomitantly, both cultivars also exhibited different changes in cuticle permeability, with leaf water loss rate per 15 min increased from 1.57% (averaged across treatments) at 1.57% (averaged across treatments) at 15 min to 3.12% at 30 min for ZS9 (except for ACC treated plant) and decreased for YY19. MeJA-treated plants of both cultivars relatively had higher water loss rate per 15 min when compared to other treatments. Conclusion. Our findings that B. napus leaf wax composition and cuticle permeability are altered by exogenous SA, MeJA and …
format: application/pdf
format: text/html
creator: Zheng Yuan
creator: Youwei Jiang
creator: Yuhua Liu
creator: Yi Xu
creator: Shuai Li
creator: Yanjun Guo
creator: Reinhard Jetter
creator: Yu Ni
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.9264
publisher: PeerJ Inc.
rights: © 2020 Yuan et al.
abstract: Background Cuticular waxes cover plant surface and play important roles in protecting plants from abiotic and biotic stresses. The variations of wax deposition and chemical compositions under changing environments have been shown to be related to plant adaptations. However, it is still not clear whether the wax depositions could be adjusted to increase plant adaptations to stressed conditions. Methods In this study, exogenous methyl jasmonate (MeJA), the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) and salicylic acid (SA) were applied to test their effects on cuticular wax deposition in two Brassica napus cultivars, Zhongshuang 9 (ZS9, low wax coverage ) and Yuyou 19 (YY19, high wax coverage). Next, we measured the water loss rate and the transcriptional expression of genes involved in wax biosynthesis as well as genes related to disease defense. Results Seven wax compound classes, including fatty acids, aldehydes, alkanes, secondary alcohols, ketones, and unbranched as well as branched primary alcohols, were identified in B. napus leaf wax mixtures. MeJA, SA and ACC treatments had no significant effect on total wax amounts in YY19, whereas ACC reduced total wax amounts in ZS9. Overall, hormone treatments led to an increase in the amounts of aldehydes and ketones, and a decrease of secondary alcohol in ZS9, whereas they led to a decrease of alkane amounts and an increase of secondary alcohol amounts in YY19. Concomitantly, both cultivars also exhibited different changes in cuticle permeability, with leaf water loss rate per 15 min increased from 1.57% (averaged across treatments) at 1.57% (averaged across treatments) at 15 min to 3.12% at 30 min for ZS9 (except for ACC treated plant) and decreased for YY19. MeJA-treated plants of both cultivars relatively had higher water loss rate per 15 min when compared to other treatments. Conclusion. Our findings that B. napus leaf wax composition and cuticle permeability are altered by exogenous SA, MeJA and …
bibliographic citation: Yuan et al. (2020) Exogenous hormones influence Brassica napus leaf cuticular wax deposition and cuticle function. PeerJ 8:e9264 https://doi.org/10.7717/peerj.9264
date submitted: 2019-12-30
date accepted: 2020-05-10
issued: 2020-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Zheng
author list: Agent
  family name: Jiang
  given name: Youwei
author list: Agent
  family name: Liu
  given name: Yuhua
author list: Agent
  family name: Xu
  given name: Yi
author list: Agent
  family name: Li
  given name: Shuai
author list: Agent
  family name: Guo
  given name: Yanjun
author list: Agent
  family name: Jetter
  given name: Reinhard
author list: Agent
  family name: Ni
  given name: Yu
doi: 10.7717/peerj.9264
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-04
copyright: ©2020 Yuan et al.
attribution name: Yuan et al.

Contributions of Latin American researchers in the understanding of the novel coronavirus outbreak: a literature review
type: item
type: AcademicArticle
description: This article aimed to give the visibility of Latin American researchers’ contributions to the comprehension of COVID-19; our method was a literature review. Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, in less than 4 months, researchers have published a significant number of articles related to this novel virus. For instance, a search focused on the Scopus database on 10 April 2020, showed 1,224 documents published by authors with 1,797 affiliations from 80 countries. A total of 25.4%, 24.0% and 12.6% of these national affiliations were from China, Europe and the USA, respectively, making these regions leaders in COVID-19 research. In the case of Latin America, on 10 April 2020, we searched different databases, such as Scopus, PubMed and Web of Science, finding that the contribution of this region was 2.7 ± 0.6% of the total publications found. In other words, we found 153 publications related to COVID-19 with at least one Latin American researcher. We summarized and processed the information from these 153 publications, finding active participation in topics like medical, social and environmental considerations, bioinformatics and epidemiology.
format: application/pdf
format: text/html
creator: Karen Y. Fiesco-Sepúlveda
creator: Luis Miguel Serrano-Bermúdez
subject: Bioinformatics
subject: Epidemiology
subject: Global Health
subject: Infectious Diseases
description: doi:10.7717/peerj.9332
publisher: PeerJ Inc.
rights: © 2020 Fiesco-Sepúlveda and Serrano-Bermúdez
abstract: This article aimed to give the visibility of Latin American researchers’ contributions to the comprehension of COVID-19; our method was a literature review. Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, in less than 4 months, researchers have published a significant number of articles related to this novel virus. For instance, a search focused on the Scopus database on 10 April 2020, showed 1,224 documents published by authors with 1,797 affiliations from 80 countries. A total of 25.4%, 24.0% and 12.6% of these national affiliations were from China, Europe and the USA, respectively, making these regions leaders in COVID-19 research. In the case of Latin America, on 10 April 2020, we searched different databases, such as Scopus, PubMed and Web of Science, finding that the contribution of this region was 2.7 ± 0.6% of the total publications found. In other words, we found 153 publications related to COVID-19 with at least one Latin American researcher. We summarized and processed the information from these 153 publications, finding active participation in topics like medical, social and environmental considerations, bioinformatics and epidemiology.
bibliographic citation: Fiesco-Sepúlveda et al. (2020) Contributions of Latin American researchers in the understanding of the novel coronavirus outbreak: a literature review. PeerJ 8:e9332 https://doi.org/10.7717/peerj.9332
date submitted: 2020-04-23
date accepted: 2020-05-19
issued: 2020-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fiesco-Sepúlveda
  given name: Karen Y.
author list: Agent
  family name: Serrano-Bermúdez
  given name: Luis Miguel
doi: 10.7717/peerj.9332
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-04
copyright: © 2020 Fiesco-Sepúlveda and Serrano-Bermúdez
attribution name: Fiesco-Sepúlveda and Serrano-Bermúdez

Clonal diversity and genetic variation of the sedge Carex nigra in an alpine fen depend on soil nutrients
type: item
type: AcademicArticle
description: In this study we analysed the impact of water regime and soil nutrients on the clonal diversity and genetic variation of the sedge Carex nigra in a central alpine fen. For our analysis, we established 16 study plots randomly distributed over the fen. We determined the exact elevation of each plot as an indicator for the water regime and measured the content of phosphorous and potassium in the soil of each plot. Clonal diversity and genetic variation of C. nigra were assessed with nuclear microsatellites using leaf material collected in 20 subplots along a diagonal cross within each study plot. The influence of water regime and soil mineral nutrients on clonal diversity and genetic variation was estimated by Bayesian multiple regression. Our study revealed a clear impact of soil nutrient conditions on clonal diversity and genetic variation of C. nigra, which increased with the concentration of phosphorous and decreased with the concentration of potassium. Key background to these findings seems to be the relative offspring success from generative as compared to clonal propagation. Phosphorous acquisition is essential during seedling establishment. Clonal diversity and genetic variation increase, therefore, at sites with higher phosphorous contents due to more successful recruitment. High levels of clonal diversity and genetic variation at sites of low potassium availability may in contrast be mainly caused by increased plant susceptibility to abiotic stress under conditions of potassium deficiency, which brings about more gaps in C. nigra stands and favors the ingrowth from other clones or recruitment from seeds.
format: application/pdf
format: text/html
creator: Christoph Reisch
creator: Stefanie Meier
creator: Christoph Schmid
creator: Maik Bartelheimer
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.8887
publisher: PeerJ Inc.
rights: © 2020 Reisch et al.
abstract: In this study we analysed the impact of water regime and soil nutrients on the clonal diversity and genetic variation of the sedge Carex nigra in a central alpine fen. For our analysis, we established 16 study plots randomly distributed over the fen. We determined the exact elevation of each plot as an indicator for the water regime and measured the content of phosphorous and potassium in the soil of each plot. Clonal diversity and genetic variation of C. nigra were assessed with nuclear microsatellites using leaf material collected in 20 subplots along a diagonal cross within each study plot. The influence of water regime and soil mineral nutrients on clonal diversity and genetic variation was estimated by Bayesian multiple regression. Our study revealed a clear impact of soil nutrient conditions on clonal diversity and genetic variation of C. nigra, which increased with the concentration of phosphorous and decreased with the concentration of potassium. Key background to these findings seems to be the relative offspring success from generative as compared to clonal propagation. Phosphorous acquisition is essential during seedling establishment. Clonal diversity and genetic variation increase, therefore, at sites with higher phosphorous contents due to more successful recruitment. High levels of clonal diversity and genetic variation at sites of low potassium availability may in contrast be mainly caused by increased plant susceptibility to abiotic stress under conditions of potassium deficiency, which brings about more gaps in C. nigra stands and favors the ingrowth from other clones or recruitment from seeds.
bibliographic citation: Reisch et al. (2020) Clonal diversity and genetic variation of the sedge Carex nigra in an alpine fen depend on soil nutrients. PeerJ 8:e8887 https://doi.org/10.7717/peerj.8887
date submitted: 2019-11-28
date accepted: 2020-03-11
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reisch
  given name: Christoph
author list: Agent
  family name: Meier
  given name: Stefanie
author list: Agent
  family name: Schmid
  given name: Christoph
author list: Agent
  family name: Bartelheimer
  given name: Maik
doi: 10.7717/peerj.8887
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: ©2020 Reisch et al.
attribution name: Reisch et al.

A new aggressive xenograft model of human colon cancer using cancer-associated fibroblasts
type: item
type: AcademicArticle
description: Background Colorectal cancer is the second leading cause of cancer death. Almost half of the patients present recurrence within 5 years after the treatment of the primary tumor, the majority, with metastasis. On the other hand, in the search for new animal models that simulate metastatic cancer, it has been suggested that fibroblasts immersed in the peritumoral stroma (cancer-associated fibroblasts (CAFs)), play a relevant role in the development of cancer. The objective of this study was to identify an adequate animal model to study metastatic colon cancer and the application of new treatments. Methods Human CAFs and normal fibroblasts (NF) for transplant and culture were obtained from surgical fresh samples of patients with adenocarcinoma of sigmoid colon. Stromal cell purity was evaluated by morphology and immunostaining with vimentin (VIM) as a fibroblast marker and anti-proColXIα1 as a specific human CAF marker. Phenotypic characterization of cultured stromal cells was performed by co-staining with mesenchymal and epithelial cell markers. For identification in mice, human CAFs were labeled with the PKH26 red fluorescence dye. Cell line HT-29 was used as tumor cells. Transplant in the head of the pancreas of 34 SCID mice was performed in four different groups, as follows: I. 150,000 CAFS (n = 12), IIa. 1.5 million HT29 cells (n = 7), IIb. 150,000 NF+1.5 million HT29 cells (n = 5), III. 150,000 CAFS+1.5 million HT29 cells (n = 10). After euthanasia performed one month later, histological analysis was made using hematoxylin–eosin and anti-proColXIα1. A histopathological score system based on three features (tumor volume, desmoplasia and number of metastasized organs) was established to compare the tumor severity. Results The CAFs and NF cultured were proColXIα1+/VIM+, proColXIα1/alphaSMA+ and proColXIα1+/CK19+ in different proportions without differences among them, but the CAFs growth curve was significantly larger than that of the NF (p < 0.05). No tumor develop…
format: application/pdf
format: text/html
creator: Ester Fernando-Macías
creator: Maria Teresa Fernández-García
creator: Eva García-Pérez
creator: Belén Porrero Guerrero
creator: Camilo López-Arévalo
creator: Raquel Rodríguez-Uría
creator: Sandra Sanz-Navarro
creator: José Fernando Vázquez-Villa
creator: María Carmen Muñíz-Salgueiro
creator: Laura Suárez-Fernández
creator: José A. Galván
creator: Clara Barneo-Caragol
creator: Marcos García-Ocaña
creator: Juan R. de los Toyos
creator: Luis Barneo-Serra
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.9045
publisher: PeerJ Inc.
rights: © 2020 Fernando-Macías et al.
abstract: Background Colorectal cancer is the second leading cause of cancer death. Almost half of the patients present recurrence within 5 years after the treatment of the primary tumor, the majority, with metastasis. On the other hand, in the search for new animal models that simulate metastatic cancer, it has been suggested that fibroblasts immersed in the peritumoral stroma (cancer-associated fibroblasts (CAFs)), play a relevant role in the development of cancer. The objective of this study was to identify an adequate animal model to study metastatic colon cancer and the application of new treatments. Methods Human CAFs and normal fibroblasts (NF) for transplant and culture were obtained from surgical fresh samples of patients with adenocarcinoma of sigmoid colon. Stromal cell purity was evaluated by morphology and immunostaining with vimentin (VIM) as a fibroblast marker and anti-proColXIα1 as a specific human CAF marker. Phenotypic characterization of cultured stromal cells was performed by co-staining with mesenchymal and epithelial cell markers. For identification in mice, human CAFs were labeled with the PKH26 red fluorescence dye. Cell line HT-29 was used as tumor cells. Transplant in the head of the pancreas of 34 SCID mice was performed in four different groups, as follows: I. 150,000 CAFS (n = 12), IIa. 1.5 million HT29 cells (n = 7), IIb. 150,000 NF+1.5 million HT29 cells (n = 5), III. 150,000 CAFS+1.5 million HT29 cells (n = 10). After euthanasia performed one month later, histological analysis was made using hematoxylin–eosin and anti-proColXIα1. A histopathological score system based on three features (tumor volume, desmoplasia and number of metastasized organs) was established to compare the tumor severity. Results The CAFs and NF cultured were proColXIα1+/VIM+, proColXIα1/alphaSMA+ and proColXIα1+/CK19+ in different proportions without differences among them, but the CAFs growth curve was significantly larger than that of the NF (p < 0.05). No tumor develop…
bibliographic citation: Fernando-Macías et al. (2020) A new aggressive xenograft model of human colon cancer using cancer-associated fibroblasts. PeerJ 8:e9045 https://doi.org/10.7717/peerj.9045
date submitted: 2019-11-18
date accepted: 2020-04-02
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fernando-Macías
  given name: Ester
author list: Agent
  family name: Fernández-García
  given name: Maria Teresa
author list: Agent
  family name: García-Pérez
  given name: Eva
author list: Agent
  family name: Porrero Guerrero
  given name: Belén
author list: Agent
  family name: López-Arévalo
  given name: Camilo
author list: Agent
  family name: Rodríguez-Uría
  given name: Raquel
author list: Agent
  family name: Sanz-Navarro
  given name: Sandra
author list: Agent
  family name: Vázquez-Villa
  given name: José Fernando
author list: Agent
  family name: Muñíz-Salgueiro
  given name: María Carmen
author list: Agent
  family name: Suárez-Fernández
  given name: Laura
author list: Agent
  family name: Galván
  given name: José A.
author list: Agent
  family name: Barneo-Caragol
  given name: Clara
author list: Agent
  family name: García-Ocaña
  given name: Marcos
author list: Agent
  family name: de los Toyos
  given name: Juan R.
author list: Agent
  family name: Barneo-Serra
  given name: Luis
doi: 10.7717/peerj.9045
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 Fernando-Macías et al.
attribution name: Fernando-Macías et al.

Culicidae-centric metabarcoding through targeted use of D2 ribosomal DNA primers
type: item
type: AcademicArticle
description: A practical limitation to many metabarcoding initiatives is that sampling methods tend to collect many non-target taxa, which become “amplicon noise” that can saturate Next Generation Sequencing results and lead to both financial and resource inefficiencies. An available molecular tool that can significantly decrease these non-target amplicons and decrease the need for pre-DNA-extraction sorting of bycatch is the design of PCR primers tailored to the taxa under investigation. We assessed whether the D2 extension segment of the 28S ribosomal operon can limit this shortcoming within the context of mosquito (Culicidae) monitoring. We designed PCR primers that are fully conserved across mosquitos and exclude from amplification most other taxa likely to be collected with current sampling apparatuses. We show that, given enough sequencing depth, D2 is an effective marker for the detection of mosquito sequences within mock genomic DNA pools. As few as 3,050 quality-filtered Illumina reads were able to recover all 17 species in a bulk pool containing as little as 0.2% of constituent DNA from single taxa. We also mixed these mosquito DNA pools with high concentrations of non-Culicidae bycatch DNA and show that the component mosquito species are generally still recoverable and faithful to their original relative frequencies. Finally, we show that there is little loss of fidelity in abundance parameters when pools from degraded DNA samples were sequenced using the D2 primers.
format: application/pdf
format: text/html
creator: Pedro M. Pedro
creator: Jandui Amorim
creator: Martha V.R. Rojas
creator: Ivy Luizi Sá
creator: Allan Kardec Ribeiro Galardo
creator: Noel Fernandes Santos Neto
creator: Dario Pires de Carvalho
creator: Kaio Augusto Nabas Ribeiro
creator: Maria Tereza Pepe Razzolini
creator: Maria Anice Mureb Sallum
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Molecular Biology
subject: Epidemiology
description: doi:10.7717/peerj.9057
publisher: PeerJ Inc.
rights: © 2020 Pedro et al.
abstract: A practical limitation to many metabarcoding initiatives is that sampling methods tend to collect many non-target taxa, which become “amplicon noise” that can saturate Next Generation Sequencing results and lead to both financial and resource inefficiencies. An available molecular tool that can significantly decrease these non-target amplicons and decrease the need for pre-DNA-extraction sorting of bycatch is the design of PCR primers tailored to the taxa under investigation. We assessed whether the D2 extension segment of the 28S ribosomal operon can limit this shortcoming within the context of mosquito (Culicidae) monitoring. We designed PCR primers that are fully conserved across mosquitos and exclude from amplification most other taxa likely to be collected with current sampling apparatuses. We show that, given enough sequencing depth, D2 is an effective marker for the detection of mosquito sequences within mock genomic DNA pools. As few as 3,050 quality-filtered Illumina reads were able to recover all 17 species in a bulk pool containing as little as 0.2% of constituent DNA from single taxa. We also mixed these mosquito DNA pools with high concentrations of non-Culicidae bycatch DNA and show that the component mosquito species are generally still recoverable and faithful to their original relative frequencies. Finally, we show that there is little loss of fidelity in abundance parameters when pools from degraded DNA samples were sequenced using the D2 primers.
bibliographic citation: Pedro et al. (2020) Culicidae-centric metabarcoding through targeted use of D2 ribosomal DNA primers. PeerJ 8:e9057 https://doi.org/10.7717/peerj.9057
date submitted: 2019-12-02
date accepted: 2020-04-03
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pedro
  given name: Pedro M.
author list: Agent
  family name: Amorim
  given name: Jandui
author list: Agent
  family name: Rojas
  given name: Martha V.R.
author list: Agent
  family name: Sá
  given name: Ivy Luizi
author list: Agent
  family name: Galardo
  given name: Allan Kardec Ribeiro
author list: Agent
  family name: Santos Neto
  given name: Noel Fernandes
author list: Agent
  family name: Pires de Carvalho
  given name: Dario
author list: Agent
  family name: Nabas Ribeiro
  given name: Kaio Augusto
author list: Agent
  family name: Razzolini
  given name: Maria Tereza Pepe
author list: Agent
  family name: Sallum
  given name: Maria Anice Mureb
doi: 10.7717/peerj.9057
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: ©2020 Pedro et al.
attribution name: Pedro et al.

Simultaneous determination of phenolic metabolites in Chinese citrus and grape cultivars
type: item
type: AcademicArticle
description: Background As the major bioactive compounds in citrus and grape, it is significant to use the contents of flavonoids and phenolic acids as quality evaluation criteria to provide a better view of classifying the quality and understanding the potential health benefits of each fruit variety. Methods A total of 15 varieties of citrus and 12 varieties of grapes were collected from Fujian, China. High-performance liquid chromatography method was used for the simultaneous determination of 17 phenolic compounds, including gallic acid, chlorogenic acid, caffeic acid, syringic acid, ρ-coumaric acid, ferulic acid, benzoic acid, salicylic acid, catechin, epicatechin, resveratrol, rutin, naringin, hesperidin, quercetin, nobiletin and tangeritin in the peels of citrus and grape cultivars. Further, the cultivars of citrus and grape were classified using principal component analysis (PCA) and hierarchical cluster analysis (HCA). Results A thorough separation of the 17 compounds was achieved within 100 min. The tested method exhibited good linearity (the limits of detection and limits of quantification were in the range of 0.03–1.83 µg/mL and 0.09–5.55 µg/mL, respectively), precision (the relative standard deviations of repeatability were 1.02–1.97%), and recovery (92.2–102.82%) for all the compounds, which could be used for the simultaneous determination of phenolic compounds in citrus and grape. Hesperidin (12.93–26,160.98 µg/g DW) and salicylic acid (5.35–751.02 µg/g DW) were the main flavonoids and phenolic acids in 15 citrus varieties, respectively. Besides, the hesperidin (ND to 605.48 µg/g DW) and salicylic acid (ND to 1,461.79 µg/g DW) were found as the highest flavonoid and the most abundant phenolic acid in grapes, respectively. A total of 15 citrus and 12 grape samples were classified into two main groups by PCA and HCA with strong consistency.
format: application/pdf
format: text/html
creator: Yuan Chen
creator: Yanyun Hong
creator: Daofu Yang
creator: Zhigang He
creator: Xiaozi Lin
creator: Guojun Wang
creator: Wenquan Yu
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.9083
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Background As the major bioactive compounds in citrus and grape, it is significant to use the contents of flavonoids and phenolic acids as quality evaluation criteria to provide a better view of classifying the quality and understanding the potential health benefits of each fruit variety. Methods A total of 15 varieties of citrus and 12 varieties of grapes were collected from Fujian, China. High-performance liquid chromatography method was used for the simultaneous determination of 17 phenolic compounds, including gallic acid, chlorogenic acid, caffeic acid, syringic acid, ρ-coumaric acid, ferulic acid, benzoic acid, salicylic acid, catechin, epicatechin, resveratrol, rutin, naringin, hesperidin, quercetin, nobiletin and tangeritin in the peels of citrus and grape cultivars. Further, the cultivars of citrus and grape were classified using principal component analysis (PCA) and hierarchical cluster analysis (HCA). Results A thorough separation of the 17 compounds was achieved within 100 min. The tested method exhibited good linearity (the limits of detection and limits of quantification were in the range of 0.03–1.83 µg/mL and 0.09–5.55 µg/mL, respectively), precision (the relative standard deviations of repeatability were 1.02–1.97%), and recovery (92.2–102.82%) for all the compounds, which could be used for the simultaneous determination of phenolic compounds in citrus and grape. Hesperidin (12.93–26,160.98 µg/g DW) and salicylic acid (5.35–751.02 µg/g DW) were the main flavonoids and phenolic acids in 15 citrus varieties, respectively. Besides, the hesperidin (ND to 605.48 µg/g DW) and salicylic acid (ND to 1,461.79 µg/g DW) were found as the highest flavonoid and the most abundant phenolic acid in grapes, respectively. A total of 15 citrus and 12 grape samples were classified into two main groups by PCA and HCA with strong consistency.
bibliographic citation: Chen et al. (2020) Simultaneous determination of phenolic metabolites in Chinese citrus and grape cultivars. PeerJ 8:e9083 https://doi.org/10.7717/peerj.9083
date submitted: 2020-01-15
date accepted: 2020-04-08
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yuan
author list: Agent
  family name: Hong
  given name: Yanyun
author list: Agent
  family name: Yang
  given name: Daofu
author list: Agent
  family name: He
  given name: Zhigang
author list: Agent
  family name: Lin
  given name: Xiaozi
author list: Agent
  family name: Wang
  given name: Guojun
author list: Agent
  family name: Yu
  given name: Wenquan
doi: 10.7717/peerj.9083
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 Chen et al.
attribution name: Chen et al.

Isolation, characterization, and cryopreservation of collared peccary skin-derived fibroblast cell lines
type: item
type: AcademicArticle
description: Background Biobanking of cell lines is a promising tool of support for wildlife conservation. In particular, the ability to preserve fibroblast cell lines derived from collared peccaries is of significance as these wild mammals are unique to the Americas and play a large role in maintaining the ecosystem. We identified collared peccary fibroblasts by immunofluorescence and evaluated their morphology, growth and adherence capacity. Further, we monitored the viability and metabolic activity of the fibroblasts to determine the effects of passage number and cryopreservation on establishment of cell lines. Methods Skin biopsies were collected from the peripheral ear region from five adult animals in captivity. Initially, cells were isolated from fragments and cultured in the Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 2% antibiotic–antimycotic solution under a controlled atmosphere (38.5 °C, 5% CO2). We evaluated the maintenance of primary cells for morphology, adherence capacity of explants, explants in subconfluence, cell growth and absence of contamination. Moreover, we identified the fibroblast cells by immunofluorescence. Additionally, to evaluate the influence of the number of passages (first, third and tenth passage) and cryopreservation on establishment of cell lines, fibroblasts were analysed for the viability, metabolic activity, population doubling time (PDT), levels of reactive oxygen species (ROS), and mitochondrial membrane potential (ΔΨm). Results All explants (20/20) adhered to the dish in 2.4 days ± 0.5 with growth around the explants in 4.6 days ± 0.7, and subconfluence was observed within 7.8 days ± 1.0. Moreover, by morphology and immunocytochemistry analyses, cells were identified as fibroblasts which presented oval nuclei, a fusiform shape and positive vimentin staining. No contamination was observed after culture without antibiotics and antifungals for 30 days. While there was no difference observed for cell viabil…
format: application/pdf
format: text/html
creator: Alana Azevedo Borges
creator: Gabriela Pereira De Oliveira Lira
creator: Lucas Emanuel Nascimento
creator: Maria Valéria De Oliveira Santos
creator: Moacir Franco De Oliveira
creator: Alexandre Rodrigues Silva
creator: Alexsandra Fernandes Pereira
subject: Cell Biology
subject: Conservation Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.9136
publisher: PeerJ Inc.
rights: © 2020 Borges et al.
abstract: Background Biobanking of cell lines is a promising tool of support for wildlife conservation. In particular, the ability to preserve fibroblast cell lines derived from collared peccaries is of significance as these wild mammals are unique to the Americas and play a large role in maintaining the ecosystem. We identified collared peccary fibroblasts by immunofluorescence and evaluated their morphology, growth and adherence capacity. Further, we monitored the viability and metabolic activity of the fibroblasts to determine the effects of passage number and cryopreservation on establishment of cell lines. Methods Skin biopsies were collected from the peripheral ear region from five adult animals in captivity. Initially, cells were isolated from fragments and cultured in the Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 2% antibiotic–antimycotic solution under a controlled atmosphere (38.5 °C, 5% CO2). We evaluated the maintenance of primary cells for morphology, adherence capacity of explants, explants in subconfluence, cell growth and absence of contamination. Moreover, we identified the fibroblast cells by immunofluorescence. Additionally, to evaluate the influence of the number of passages (first, third and tenth passage) and cryopreservation on establishment of cell lines, fibroblasts were analysed for the viability, metabolic activity, population doubling time (PDT), levels of reactive oxygen species (ROS), and mitochondrial membrane potential (ΔΨm). Results All explants (20/20) adhered to the dish in 2.4 days ± 0.5 with growth around the explants in 4.6 days ± 0.7, and subconfluence was observed within 7.8 days ± 1.0. Moreover, by morphology and immunocytochemistry analyses, cells were identified as fibroblasts which presented oval nuclei, a fusiform shape and positive vimentin staining. No contamination was observed after culture without antibiotics and antifungals for 30 days. While there was no difference observed for cell viabil…
bibliographic citation: Borges et al. (2020) Isolation, characterization, and cryopreservation of collared peccary skin-derived fibroblast cell lines. PeerJ 8:e9136 https://doi.org/10.7717/peerj.9136
date submitted: 2019-11-20
date accepted: 2020-04-15
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borges
  given name: Alana Azevedo
author list: Agent
  family name: Lira
  given name: Gabriela Pereira De Oliveira
author list: Agent
  family name: Nascimento
  given name: Lucas Emanuel
author list: Agent
  family name: Santos
  given name: Maria Valéria De Oliveira
author list: Agent
  family name: Oliveira
  given name: Moacir Franco De
author list: Agent
  family name: Silva
  given name: Alexandre Rodrigues
author list: Agent
  family name: Pereira
  given name: Alexsandra Fernandes
doi: 10.7717/peerj.9136
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 Borges et al.
attribution name: Borges et al.

Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer
type: item
type: AcademicArticle
description: Background Previous studies have indicated that chronic inflammation linked to H. pylori infection is the leading causes for gastric cancer (GC). However, the exact mechanism is not entirely clear until now. Purpose To identify the key molecules and TFs involved in H. pylori infection and to provide new insights into H. pylori-associated carcinogenesis and lay the groundwork for the prevention of GC. Results GO and KEGG analysis revealed that the DEGs of Hp+-NAG were mainly associated with the immune response, chemokine activity, extracellular region and rheumatoid arthritis pathway. The DEGs of Hp+-AG-IM were related to the apical plasma membrane, intestinal cholesterol absorption, transporter activity and fat digestion and absorption pathway. In Hp+-NAG network, the expression of TNF, CXCL8, MMP9, CXCL9, CXCL1, CCL20, CTLA4, CXCL2, C3, SAA1 and FOXP3, JUN had statistical significance between normal and cancer in TCGA database. In Hp+-AG-IM network the expression of APOA4, GCG, CYP3A4, XPNPEP2 and FOXP3, JUN were statistically different in the comparison of normal and cancer in TCGA database. FOXP3 were negatively associated with overall survival, and the association for JUN was positive. Conclusion The current study identified key DEGs and their transcriptional regulatory networks involved in H. pylori-associated NAG, AG-IM and GC and found that patients with higher expressed FOXP3 or lower expressed JUN had shorter overall survival time. Our study provided new directions for inflammation-associated oncogenic transformation involved in H. pylori infection.
format: application/pdf
format: text/html
creator: Honghao Yin
creator: Aining Chu
creator: Songyi Liu
creator: Yuan Yuan
creator: Yuehua Gong
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
subject: Oncology
description: doi:10.7717/peerj.9223
publisher: PeerJ Inc.
rights: © 2020 Yin et al.
abstract: Background Previous studies have indicated that chronic inflammation linked to H. pylori infection is the leading causes for gastric cancer (GC). However, the exact mechanism is not entirely clear until now. Purpose To identify the key molecules and TFs involved in H. pylori infection and to provide new insights into H. pylori-associated carcinogenesis and lay the groundwork for the prevention of GC. Results GO and KEGG analysis revealed that the DEGs of Hp+-NAG were mainly associated with the immune response, chemokine activity, extracellular region and rheumatoid arthritis pathway. The DEGs of Hp+-AG-IM were related to the apical plasma membrane, intestinal cholesterol absorption, transporter activity and fat digestion and absorption pathway. In Hp+-NAG network, the expression of TNF, CXCL8, MMP9, CXCL9, CXCL1, CCL20, CTLA4, CXCL2, C3, SAA1 and FOXP3, JUN had statistical significance between normal and cancer in TCGA database. In Hp+-AG-IM network the expression of APOA4, GCG, CYP3A4, XPNPEP2 and FOXP3, JUN were statistically different in the comparison of normal and cancer in TCGA database. FOXP3 were negatively associated with overall survival, and the association for JUN was positive. Conclusion The current study identified key DEGs and their transcriptional regulatory networks involved in H. pylori-associated NAG, AG-IM and GC and found that patients with higher expressed FOXP3 or lower expressed JUN had shorter overall survival time. Our study provided new directions for inflammation-associated oncogenic transformation involved in H. pylori infection.
bibliographic citation: Yin et al. (2020) Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer. PeerJ 8:e9223 https://doi.org/10.7717/peerj.9223
date submitted: 2019-12-11
date accepted: 2020-04-29
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Honghao
author list: Agent
  family name: Chu
  given name: Aining
author list: Agent
  family name: Liu
  given name: Songyi
author list: Agent
  family name: Yuan
  given name: Yuan
author list: Agent
  family name: Gong
  given name: Yuehua
doi: 10.7717/peerj.9223
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: ©2020 Yin et al.
attribution name: Yin et al.

Incorporating reef fish avoidance behavior improves accuracy of species distribution models
type: item
type: AcademicArticle
description: Species distribution models (SDMs) are used to interpret and map fish distributions based on habitat variables and other drivers. Reef fish avoidance behavior has been shown to vary in the presence of divers and is primarily driven by spearfishing pressure. Diver avoidance behavior or fish wariness may spatially influence counts and other descriptive measures of fish assemblages. Because fish assemblage metrics are response variables for SDMs, measures of fish wariness may be useful as predictors in SDMs of fishes targeted by spearfishing. We used a diver operated stereo-video system to conduct fish surveys and record minimum approach distance (MAD) of targeted reef fishes inside and outside of two marine reserves on the island of Oʻahu in the main Hawaiian Islands. By comparing MAD between sites and management types we tested the assumption that it provides a proxy for fish wariness related to spearfishing pressure. We then compared the accuracy of SDMs which included MAD as a predictor with SDMs that did not. Individual measures of MAD differed between sites though not management types. When included as a predictor, MAD averaged at the transect level greatly improved the accuracy of SDMs of targeted fish biomass.
format: application/pdf
format: text/html
creator: Kostantinos A. Stamoulis
creator: Jade M.S. Delevaux
creator: Ivor D. Williams
creator: Alan M. Friedlander
creator: Jake Reichard
creator: Keith Kamikawa
creator: Euan S. Harvey
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9246
publisher: PeerJ Inc.
rights: © 2020 Stamoulis et al.
abstract: Species distribution models (SDMs) are used to interpret and map fish distributions based on habitat variables and other drivers. Reef fish avoidance behavior has been shown to vary in the presence of divers and is primarily driven by spearfishing pressure. Diver avoidance behavior or fish wariness may spatially influence counts and other descriptive measures of fish assemblages. Because fish assemblage metrics are response variables for SDMs, measures of fish wariness may be useful as predictors in SDMs of fishes targeted by spearfishing. We used a diver operated stereo-video system to conduct fish surveys and record minimum approach distance (MAD) of targeted reef fishes inside and outside of two marine reserves on the island of Oʻahu in the main Hawaiian Islands. By comparing MAD between sites and management types we tested the assumption that it provides a proxy for fish wariness related to spearfishing pressure. We then compared the accuracy of SDMs which included MAD as a predictor with SDMs that did not. Individual measures of MAD differed between sites though not management types. When included as a predictor, MAD averaged at the transect level greatly improved the accuracy of SDMs of targeted fish biomass.
bibliographic citation: Stamoulis et al. (2020) Incorporating reef fish avoidance behavior improves accuracy of species distribution models. PeerJ 8:e9246 https://doi.org/10.7717/peerj.9246
date submitted: 2020-01-14
date accepted: 2020-05-07
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stamoulis
  given name: Kostantinos A.
author list: Agent
  family name: Delevaux
  given name: Jade M.S.
author list: Agent
  family name: Williams
  given name: Ivor D.
author list: Agent
  family name: Friedlander
  given name: Alan M.
author list: Agent
  family name: Reichard
  given name: Jake
author list: Agent
  family name: Kamikawa
  given name: Keith
author list: Agent
  family name: Harvey
  given name: Euan S.
doi: 10.7717/peerj.9246
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: ©2020 Stamoulis et al.
attribution name: Stamoulis et al.

Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis model
type: item
type: AcademicArticle
description: Ecosystem models require the specification of initial conditions, and these initial conditions have some level of uncertainty. It is important to allow for uncertainty when presenting model results, because it reduces the risk of errant or non-representative results. It is crucial that model results are presented as an envelope of what is likely, rather than presenting only one instance. We perturbed the initial conditions of the Chatham Rise Atlantis model and analysed the effect of this uncertainty on the model’s dynamics by comparing the model outputs resulting from many initial condition perturbations. At the species group level, we found some species groups were more sensitive than others, with lower trophic level species groups generally more sensitive to perturbations of the initial conditions. We recommend testing for robust system dynamics by assessing the consistency of ecosystem indicators in response to fishing pressure under perturbed initial conditions. In any set of scenarios explored using complex end-to-end ecosystem models, we recommend that associated uncertainty analysis be included with perturbations of the initial conditions.
format: application/pdf
format: text/html
creator: Vidette L. McGregor
creator: Elizabeth A. Fulton
creator: Matthew R. Dunn
subject: Aquaculture, Fisheries and Fish Science
subject: Ecosystem Science
subject: Mathematical Biology
subject: Statistics
subject: Population Biology
description: doi:10.7717/peerj.9254
publisher: PeerJ Inc.
rights: © 2020 McGregor et al.
abstract: Ecosystem models require the specification of initial conditions, and these initial conditions have some level of uncertainty. It is important to allow for uncertainty when presenting model results, because it reduces the risk of errant or non-representative results. It is crucial that model results are presented as an envelope of what is likely, rather than presenting only one instance. We perturbed the initial conditions of the Chatham Rise Atlantis model and analysed the effect of this uncertainty on the model’s dynamics by comparing the model outputs resulting from many initial condition perturbations. At the species group level, we found some species groups were more sensitive than others, with lower trophic level species groups generally more sensitive to perturbations of the initial conditions. We recommend testing for robust system dynamics by assessing the consistency of ecosystem indicators in response to fishing pressure under perturbed initial conditions. In any set of scenarios explored using complex end-to-end ecosystem models, we recommend that associated uncertainty analysis be included with perturbations of the initial conditions.
bibliographic citation: McGregor et al. (2020) Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis model. PeerJ 8:e9254 https://doi.org/10.7717/peerj.9254
date submitted: 2019-09-18
date accepted: 2020-05-08
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McGregor
  given name: Vidette L.
author list: Agent
  family name: Fulton
  given name: Elizabeth A.
author list: Agent
  family name: Dunn
  given name: Matthew R.
doi: 10.7717/peerj.9254
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 McGregor et al.
attribution name: McGregor et al.

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