PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The combined effects of light intensity, temperature, and water potential on wall deposition in regulating hypocotyl elongation of Brassica rapa
items: At the crossroads of botanical collections and molecular genetics laboratory: a preliminary study of obtaining amplifiable DNA from moss herbarium material
items: Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs (Sus scrofa ussuricus)
items: An improved similarity-based approach to predicting and mapping soil organic carbon and soil total nitrogen in a coastal region of northeastern China
items: The combined impacts of wheat spatial position and phenology on cereal aphid abundance
items: Isolation and functional analyses of PvFAD2 and PvFAD3 involved in the biosynthesis of polyunsaturated fatty acids from Sacha Inchi (Plukenetia volubilis)
items: Effects of mining on the molybdenum absorption and translocation of plants in the Luanchuan molybdenum mine
items: The high expression of MTH1 and NUDT5 predict a poor survival and are associated with malignancy of esophageal squamous cell carcinoma
items: Comprehensive analysis reveals a metabolic ten-gene signature in hepatocellular carcinoma
items: Estimating food resource availability in arid environments with Sentinel 2 satellite imagery

The combined effects of light intensity, temperature, and water potential on wall deposition in regulating hypocotyl elongation of Brassica rapa
type: item
type: AcademicArticle
description: Hypocotyl elongation is a critical sign of seed germination and seedling growth, and it is regulated by multi-environmental factors. Light, temperature, and water potential are the major environmental stimuli, and their regulatory mechanism on hypocotyl growth has been extensively studied at molecular level. However, the converged point in signaling process of light, temperature, and water potential on modulating hypocotyl elongation is still unclear. In the present study, we found cell wall was the co-target of the three environmental factors in regulating hypocotyl elongation by analyzing the extension kinetics of hypocotyl and the changes in hypocotyl cell wall of Brassica rapa under the combined effects of light intensity, temperature, and water potential. The three environmental factors regulated hypocotyl cell elongation both in isolation and in combination. Cell walls thickened, maintained, or thinned depending on growth conditions and developmental stages during hypocotyl elongation. Further analysis revealed that the imbalance in wall deposition and hypocotyl elongation led to dynamic changes in wall thickness. Low light repressed wall deposition by influencing the accumulation of cellulose, hemicellulose, and pectin; high temperature and high water potential had significant effects on pectin accumulation overall. It was concluded that wall deposition was tightly controlled during hypocotyl elongation, and low light, high temperature, and high water potential promoted hypocotyl elongation by repressing wall deposition, especially the deposition of pectin.
format: application/pdf
format: text/html
creator: Hongfei Wang
creator: Qingmao Shang
subject: Agricultural Science
subject: Developmental Biology
subject: Plant Science
description: doi:10.7717/peerj.9106
publisher: PeerJ Inc.
rights: © 2020 Wang and Shang
abstract: Hypocotyl elongation is a critical sign of seed germination and seedling growth, and it is regulated by multi-environmental factors. Light, temperature, and water potential are the major environmental stimuli, and their regulatory mechanism on hypocotyl growth has been extensively studied at molecular level. However, the converged point in signaling process of light, temperature, and water potential on modulating hypocotyl elongation is still unclear. In the present study, we found cell wall was the co-target of the three environmental factors in regulating hypocotyl elongation by analyzing the extension kinetics of hypocotyl and the changes in hypocotyl cell wall of Brassica rapa under the combined effects of light intensity, temperature, and water potential. The three environmental factors regulated hypocotyl cell elongation both in isolation and in combination. Cell walls thickened, maintained, or thinned depending on growth conditions and developmental stages during hypocotyl elongation. Further analysis revealed that the imbalance in wall deposition and hypocotyl elongation led to dynamic changes in wall thickness. Low light repressed wall deposition by influencing the accumulation of cellulose, hemicellulose, and pectin; high temperature and high water potential had significant effects on pectin accumulation overall. It was concluded that wall deposition was tightly controlled during hypocotyl elongation, and low light, high temperature, and high water potential promoted hypocotyl elongation by repressing wall deposition, especially the deposition of pectin.
bibliographic citation: Wang et al. (2020) The combined effects of light intensity, temperature, and water potential on wall deposition in regulating hypocotyl elongation of Brassica rapa. PeerJ 8:e9106 https://doi.org/10.7717/peerj.9106
date submitted: 2019-08-20
date accepted: 2020-04-10
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hongfei
author list: Agent
  family name: Shang
  given name: Qingmao
doi: 10.7717/peerj.9106
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Wang and Shang
attribution name: Wang and Shang

At the crossroads of botanical collections and molecular genetics laboratory: a preliminary study of obtaining amplifiable DNA from moss herbarium material
type: item
type: AcademicArticle
description: Background Research focused on extreme environments is often associated with difficulties in obtaining fresh plant material. Herbaria may provide great support as they house large collections of specimens from different parts of the world. Accordingly, there is also a growing interest in methods using herbarium specimens in molecular studies. Much of the literature on herbarium DNA is aimed to improve extraction and PCR amplification and is focused mostly on vascular plants. Here, I provide a brief study of DNA extraction efficiency from moss herbarium specimens, emphasizing the importance of herbaria as an invaluable source of material from hard-to-access geographical areas, such as the Antarctic region. Methods The presented study is based on herbarium collections of 25 moss species collected in the austral polar regions between 1979 and 2013. The majority of samples were obtained using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). The remaining, smaller part was extracted using an adapted CTAB-based approach. The performance of DNA extraction methods in terms of PCR amplification success was measured by testing several DNA fragments of various size. Furthermore, in order to estimate of DNA fragmentation level, an automated on-chip electrophoresis system was used. Results Results reveal that DNA purity and the length of the target genetic region are the fundamental agents which drive the successful PCR reaction. Conversely, the DNA yield and specimen age seem to be less relevant. With this study, I present also an optimized CTAB-based approach which may effectively suppress inhibitors in the herbarium DNA. This method can be considered a cheaper alternative to column-based technology, particularly useful for dealing with a large number of samples. Results of this study confirmed previous reports and contribute to filling the existing gap in molecular analyses which involve the use of herbarium collections of mosses.
format: application/pdf
format: text/html
creator: Marta Saługa
subject: Biodiversity
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9109
publisher: PeerJ Inc.
rights: © 2020 Saługa
abstract: Background Research focused on extreme environments is often associated with difficulties in obtaining fresh plant material. Herbaria may provide great support as they house large collections of specimens from different parts of the world. Accordingly, there is also a growing interest in methods using herbarium specimens in molecular studies. Much of the literature on herbarium DNA is aimed to improve extraction and PCR amplification and is focused mostly on vascular plants. Here, I provide a brief study of DNA extraction efficiency from moss herbarium specimens, emphasizing the importance of herbaria as an invaluable source of material from hard-to-access geographical areas, such as the Antarctic region. Methods The presented study is based on herbarium collections of 25 moss species collected in the austral polar regions between 1979 and 2013. The majority of samples were obtained using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). The remaining, smaller part was extracted using an adapted CTAB-based approach. The performance of DNA extraction methods in terms of PCR amplification success was measured by testing several DNA fragments of various size. Furthermore, in order to estimate of DNA fragmentation level, an automated on-chip electrophoresis system was used. Results Results reveal that DNA purity and the length of the target genetic region are the fundamental agents which drive the successful PCR reaction. Conversely, the DNA yield and specimen age seem to be less relevant. With this study, I present also an optimized CTAB-based approach which may effectively suppress inhibitors in the herbarium DNA. This method can be considered a cheaper alternative to column-based technology, particularly useful for dealing with a large number of samples. Results of this study confirmed previous reports and contribute to filling the existing gap in molecular analyses which involve the use of herbarium collections of mosses.
bibliographic citation: Saługa (2020) At the crossroads of botanical collections and molecular genetics laboratory: a preliminary study of obtaining amplifiable DNA from moss herbarium material. PeerJ 8:e9109 https://doi.org/10.7717/peerj.9109
date submitted: 2019-08-14
date accepted: 2020-04-10
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saługa
  given name: Marta
doi: 10.7717/peerj.9109
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: © 2020 Saługa
attribution name: Saługa

Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs (Sus scrofa ussuricus)
type: item
type: AcademicArticle
description: Commensal microorganisms are essential to the normal development and function of many aspects of animal biology, including digestion, nutrient absorption, immunological development, behaviors, and evolution. The specific microbial composition and evolution of the intestinal tracts of wild pigs remain poorly characterized. This study therefore sought to assess the composition, distribution, and evolution of the intestinal microbiome of wild pigs. For these analyses, 16S rRNA V3-V4 regions from five gut sections prepared from each of three wild sows were sequenced to detect the microbiome composition. These analyses revealed the presence of 6,513 operational taxonomic units (OTUs) mostly distributed across 17 phyla and 163 genera in these samples, with Firmicutes and Actinobacteria being the most prevalent phyla of microbes present in cecum and jejunum samples, respectively. Moreover, the abundance of Actinobacteria in wild pigs was higher than that in domestic pigs. At the genus level the Bifidobacterium and Allobaculum species of microbes were most abundant in all tested gut sections, with higher relative abundance in wild pigs relative to domestic pigs, indicating that in the process of pig evolution, the intestinal microbes also evolved, and changes in the intestinal microbial diversity could have been one of the evolutionary forces of pigs. Intestinal microbial functional analyses also revealed the microbes present in the small intestine (duodenum, jejunum, and ileum) and large intestine (cecum and colon) of wild pigs to engage distinct metabolic spatial structures and pathways relative to one another. Overall, these results offer unique insights that would help to advance the current understanding of how the intestinal microbes interact with the host and affect the evolution of pigs.
format: application/pdf
format: text/html
creator: Guangli Yang
creator: Chuanxin Shi
creator: Shuhong Zhang
creator: Yan Liu
creator: Zhiqiang Li
creator: Fengyi Gao
creator: Yanyan Cui
creator: Yongfeng Yan
creator: Ming Li
subject: Evolutionary Studies
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.9124
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Commensal microorganisms are essential to the normal development and function of many aspects of animal biology, including digestion, nutrient absorption, immunological development, behaviors, and evolution. The specific microbial composition and evolution of the intestinal tracts of wild pigs remain poorly characterized. This study therefore sought to assess the composition, distribution, and evolution of the intestinal microbiome of wild pigs. For these analyses, 16S rRNA V3-V4 regions from five gut sections prepared from each of three wild sows were sequenced to detect the microbiome composition. These analyses revealed the presence of 6,513 operational taxonomic units (OTUs) mostly distributed across 17 phyla and 163 genera in these samples, with Firmicutes and Actinobacteria being the most prevalent phyla of microbes present in cecum and jejunum samples, respectively. Moreover, the abundance of Actinobacteria in wild pigs was higher than that in domestic pigs. At the genus level the Bifidobacterium and Allobaculum species of microbes were most abundant in all tested gut sections, with higher relative abundance in wild pigs relative to domestic pigs, indicating that in the process of pig evolution, the intestinal microbes also evolved, and changes in the intestinal microbial diversity could have been one of the evolutionary forces of pigs. Intestinal microbial functional analyses also revealed the microbes present in the small intestine (duodenum, jejunum, and ileum) and large intestine (cecum and colon) of wild pigs to engage distinct metabolic spatial structures and pathways relative to one another. Overall, these results offer unique insights that would help to advance the current understanding of how the intestinal microbes interact with the host and affect the evolution of pigs.
bibliographic citation: Yang et al. (2020) Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs (Sus scrofa ussuricus). PeerJ 8:e9124 https://doi.org/10.7717/peerj.9124
date submitted: 2019-10-09
date accepted: 2020-04-14
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Guangli
author list: Agent
  family name: Shi
  given name: Chuanxin
author list: Agent
  family name: Zhang
  given name: Shuhong
author list: Agent
  family name: Liu
  given name: Yan
author list: Agent
  family name: Li
  given name: Zhiqiang
author list: Agent
  family name: Gao
  given name: Fengyi
author list: Agent
  family name: Cui
  given name: Yanyan
author list: Agent
  family name: Yan
  given name: Yongfeng
author list: Agent
  family name: Li
  given name: Ming
doi: 10.7717/peerj.9124
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Yang et al.
attribution name: Yang et al.

An improved similarity-based approach to predicting and mapping soil organic carbon and soil total nitrogen in a coastal region of northeastern China
type: item
type: AcademicArticle
description: Soil organic carbon (SOC) and soil total nitrogen (STN) are major soil indicators for soil quality and fertility. Accurate mapping SOC and STN in soils would help both managed and natural soils and ecosystem management. This study developed an improved similarity-based approach (ISA) to predicting and mapping topsoil (0–20 cm soil depth) SOC and STN in a coastal region of northeastern China. Six environmental variables including elevation, slope gradient, topographic wetness index, the mean annual temperature, the mean annual temperature, and normalized difference vegetation index were used as predictors. Soil survey data in 2012 was designed based on the clustering of the study area into six climatic vegetation landscape units. In each landscape unit, 20–25 sampling points were determined at different landform positions considering local climate, soil type, elevation and other environmental factors, and finally 126 sampling points were obtained. Soil sampling from the depth of 0–20 cm were used for model prediction and validation. The ISA model performance was compared with the geographically weighted regression (GWR), regression kriging (RK), boosted regression trees (BRT) considering mean absolute prediction error (MAE), root mean square error (RMSE), coefficient of determination (R2), and maximum relative difference (RD) indices. We found that the ISA method performed best with the highest R2 and lowest MAE, RMSE compared to GWR, RK, and BRT methods. The ISA method could explain 76% and 83% of the total SOC and STN variability, respectively, 12–40% higher than other models in the study area. Elevation had the largest influence on SOC and STN distribution. We conclude that the developed ISA model is robust and effective in mapping SOC and STN, particularly in the areas with complex vegetation-landscape when limited samples are available. The method needs to be tested for other regions in our future research.
format: application/pdf
format: text/html
creator: Shuai Wang
creator: Kabindra Adhikari
creator: Qianlai Zhuang
creator: Zijiao Yang
creator: Xinxin Jin
creator: Qiubing Wang
creator: Zhenxing Bian
subject: Soil Science
subject: Biogeochemistry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9126
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Soil organic carbon (SOC) and soil total nitrogen (STN) are major soil indicators for soil quality and fertility. Accurate mapping SOC and STN in soils would help both managed and natural soils and ecosystem management. This study developed an improved similarity-based approach (ISA) to predicting and mapping topsoil (0–20 cm soil depth) SOC and STN in a coastal region of northeastern China. Six environmental variables including elevation, slope gradient, topographic wetness index, the mean annual temperature, the mean annual temperature, and normalized difference vegetation index were used as predictors. Soil survey data in 2012 was designed based on the clustering of the study area into six climatic vegetation landscape units. In each landscape unit, 20–25 sampling points were determined at different landform positions considering local climate, soil type, elevation and other environmental factors, and finally 126 sampling points were obtained. Soil sampling from the depth of 0–20 cm were used for model prediction and validation. The ISA model performance was compared with the geographically weighted regression (GWR), regression kriging (RK), boosted regression trees (BRT) considering mean absolute prediction error (MAE), root mean square error (RMSE), coefficient of determination (R2), and maximum relative difference (RD) indices. We found that the ISA method performed best with the highest R2 and lowest MAE, RMSE compared to GWR, RK, and BRT methods. The ISA method could explain 76% and 83% of the total SOC and STN variability, respectively, 12–40% higher than other models in the study area. Elevation had the largest influence on SOC and STN distribution. We conclude that the developed ISA model is robust and effective in mapping SOC and STN, particularly in the areas with complex vegetation-landscape when limited samples are available. The method needs to be tested for other regions in our future research.
bibliographic citation: Wang et al. (2020) An improved similarity-based approach to predicting and mapping soil organic carbon and soil total nitrogen in a coastal region of northeastern China. PeerJ 8:e9126 https://doi.org/10.7717/peerj.9126
date submitted: 2019-11-22
date accepted: 2020-04-14
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Shuai
author list: Agent
  family name: Adhikari
  given name: Kabindra
author list: Agent
  family name: Zhuang
  given name: Qianlai
author list: Agent
  family name: Yang
  given name: Zijiao
author list: Agent
  family name: Jin
  given name: Xinxin
author list: Agent
  family name: Wang
  given name: Qiubing
author list: Agent
  family name: Bian
  given name: Zhenxing
doi: 10.7717/peerj.9126
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Wang et al.
attribution name: Wang et al.

The combined impacts of wheat spatial position and phenology on cereal aphid abundance
type: item
type: AcademicArticle
description: Background Wheat is a staple crop that suffers from massive yield losses caused by cereal aphids. Many factors can determine the abundance of cereal aphids and the damage they cause to plants; among them are the plant’s genetic background, as well as environmental conditions such as spatial position within the plot, the composition and the distance from neighboring vegetation. Although the effects of these factors have been under scrutiny for many years, the combined effect of both factors on aphid populations is not fully understood. The goal of this study was to examine the collective impact of genotype and environment on wheat phenology (developmental stages), chemical diversity (metabolites), and insect susceptibility, as manifested by cereal aphid abundance. Methods To determine the influence of plant genotype on the metrics mentioned above, we measured the phenology, chemical profile, and aphid abundance of four wheat genotypes, including the tetraploid wild emmer (Triticum turgidum ssp. dicoccoides cv. Zavitan), tetraploid durum (Triticum turgidum ssp. durum cv. Svevo), and two hexaploid spring bread (Triticum aestivum), ‘Rotem’ and ‘Chinese Spring’. These genotypes are referred to as “focal” plants. To evaluate the impact of the environment, we scored the distance of each focal plant (spatial position) from two neighboring vegetation types: (i) natural resource and (ii) monoculture wheat resource. Results The results demonstrated that the wild emmer wheat was the most aphid-resistant, while the bread wheat Rotem was most aphid-susceptible. Aphids were more abundant in plants that matured early. The spatial position analysis demonstrated that aphids were more abundant in focal plants located closer to the margin monoculture wheat resource rather than to the natural resource, suggesting a resource concentration effect. The analysis of metabolic diversity showed that the levels of three specialized metabolites from the flavonoid class, differed between the whea…
format: application/pdf
format: text/html
creator: Zhaniya S. Batyrshina
creator: Alon Cna’ani
creator: Tamir Rozenberg
creator: Merav Seifan
creator: Vered Tzin
subject: Agricultural Science
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.9142
publisher: PeerJ Inc.
rights: © 2020 Batyrshina et al.
abstract: Background Wheat is a staple crop that suffers from massive yield losses caused by cereal aphids. Many factors can determine the abundance of cereal aphids and the damage they cause to plants; among them are the plant’s genetic background, as well as environmental conditions such as spatial position within the plot, the composition and the distance from neighboring vegetation. Although the effects of these factors have been under scrutiny for many years, the combined effect of both factors on aphid populations is not fully understood. The goal of this study was to examine the collective impact of genotype and environment on wheat phenology (developmental stages), chemical diversity (metabolites), and insect susceptibility, as manifested by cereal aphid abundance. Methods To determine the influence of plant genotype on the metrics mentioned above, we measured the phenology, chemical profile, and aphid abundance of four wheat genotypes, including the tetraploid wild emmer (Triticum turgidum ssp. dicoccoides cv. Zavitan), tetraploid durum (Triticum turgidum ssp. durum cv. Svevo), and two hexaploid spring bread (Triticum aestivum), ‘Rotem’ and ‘Chinese Spring’. These genotypes are referred to as “focal” plants. To evaluate the impact of the environment, we scored the distance of each focal plant (spatial position) from two neighboring vegetation types: (i) natural resource and (ii) monoculture wheat resource. Results The results demonstrated that the wild emmer wheat was the most aphid-resistant, while the bread wheat Rotem was most aphid-susceptible. Aphids were more abundant in plants that matured early. The spatial position analysis demonstrated that aphids were more abundant in focal plants located closer to the margin monoculture wheat resource rather than to the natural resource, suggesting a resource concentration effect. The analysis of metabolic diversity showed that the levels of three specialized metabolites from the flavonoid class, differed between the whea…
bibliographic citation: Batyrshina et al. (2020) The combined impacts of wheat spatial position and phenology on cereal aphid abundance. PeerJ 8:e9142 https://doi.org/10.7717/peerj.9142
date submitted: 2019-11-29
date accepted: 2020-04-16
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Batyrshina
  given name: Zhaniya S.
author list: Agent
  family name: Cna’ani
  given name: Alon
author list: Agent
  family name: Rozenberg
  given name: Tamir
author list: Agent
  family name: Seifan
  given name: Merav
author list: Agent
  family name: Tzin
  given name: Vered
doi: 10.7717/peerj.9142
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: © 2020 Batyrshina et al.
attribution name: Batyrshina et al.

Isolation and functional analyses of PvFAD2 and PvFAD3 involved in the biosynthesis of polyunsaturated fatty acids from Sacha Inchi (Plukenetia volubilis)
type: item
type: AcademicArticle
description: The development of ω-3 fatty acid-rich vegetable oils is essential to enrich the production of functional foods. Sacha Inchi (Plukenetia volubilis L.) is a unique oilseed crop with much potential. Its seeds contain rich polyunsaturated fatty acids (PUFAs), especially linoleic acid (LA, C18:2) and α-linolenic acid (ALA, C18:3). Endoplasmic reticulum -located ω-6 and ω-3 fatty acid desaturases (FAD) are responsible for the biosynthesis of LA and ALA, respectively, in plant seeds. Here, we isolated two full-length FAD genes from Sacha Inchi, named PvFAD2 and PvFAD3, which encoded predicted amino acid residues of 384 and 379 in protein, respectively. Protein sequence and subcellular localization analysis revealed that they were located in the endoplasmic reticulum (ER). Heterologous expression in Saccharomyces cerevisiae confirmed that PvFAD2 and PvFAD3 could catalyze LA and ALA synthesis, respectively. The stability and catalytic efficiency of the PvFAD3 protein may be closely related to temperature. In transgenic tobacco, using seed-specific expression promoters, PvFAD2 and PvFAD3 significantly promotes the production of LA (from 68% to 70.5%) and ALA (from 0.7% to 3.1%) in seed oil. These results show that PvFAD2 and PvFAD3 do, indeed, function as crucial enzymes for PUFAs biosynthesis, and provide a key gene source for the sustainable production of lipids with tailored fatty acid compositions via genetic engineering in other oil crops.
format: application/pdf
format: text/html
creator: Tianquan Yang
creator: Xiaojuan Wang
creator: Tingnan Dong
creator: Wei Xu
creator: Aizhong Liu
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9169
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: The development of ω-3 fatty acid-rich vegetable oils is essential to enrich the production of functional foods. Sacha Inchi (Plukenetia volubilis L.) is a unique oilseed crop with much potential. Its seeds contain rich polyunsaturated fatty acids (PUFAs), especially linoleic acid (LA, C18:2) and α-linolenic acid (ALA, C18:3). Endoplasmic reticulum -located ω-6 and ω-3 fatty acid desaturases (FAD) are responsible for the biosynthesis of LA and ALA, respectively, in plant seeds. Here, we isolated two full-length FAD genes from Sacha Inchi, named PvFAD2 and PvFAD3, which encoded predicted amino acid residues of 384 and 379 in protein, respectively. Protein sequence and subcellular localization analysis revealed that they were located in the endoplasmic reticulum (ER). Heterologous expression in Saccharomyces cerevisiae confirmed that PvFAD2 and PvFAD3 could catalyze LA and ALA synthesis, respectively. The stability and catalytic efficiency of the PvFAD3 protein may be closely related to temperature. In transgenic tobacco, using seed-specific expression promoters, PvFAD2 and PvFAD3 significantly promotes the production of LA (from 68% to 70.5%) and ALA (from 0.7% to 3.1%) in seed oil. These results show that PvFAD2 and PvFAD3 do, indeed, function as crucial enzymes for PUFAs biosynthesis, and provide a key gene source for the sustainable production of lipids with tailored fatty acid compositions via genetic engineering in other oil crops.
bibliographic citation: Yang et al. (2020) Isolation and functional analyses of PvFAD2 and PvFAD3 involved in the biosynthesis of polyunsaturated fatty acids from Sacha Inchi (Plukenetia volubilis). PeerJ 8:e9169 https://doi.org/10.7717/peerj.9169
date submitted: 2019-12-19
date accepted: 2020-04-20
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Tianquan
author list: Agent
  family name: Wang
  given name: Xiaojuan
author list: Agent
  family name: Dong
  given name: Tingnan
author list: Agent
  family name: Xu
  given name: Wei
author list: Agent
  family name: Liu
  given name: Aizhong
doi: 10.7717/peerj.9169
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Effects of mining on the molybdenum absorption and translocation of plants in the Luanchuan molybdenum mine
type: item
type: AcademicArticle
description: Background There is a critical need to examine whether mining of molybdenum (Mo) ore will affect Mo absorption and translocation by plants at a community level. Methods Indigenous plants and their rhizospheric soil (0–20 cm) growing in two different areas including the mining and the unexploited areas were collected from the Luanchuan Mo mine—one of the largest Mo mines in Asia. The concentrations of Mo and other heavy metals of plants or soil were measured by ICP-AES. Mo absorption and translocation in plants growing in two areas were investigated and compared. Heavy metal pollution in soil was also evaluated by the potential ecological hazard index method. Results Mo concentration in mining soils was higher with the changes from 108.13 to 268.13 mg kg−1 compared to unexploited area. Mo concentrations in shoots and roots of plants growing in the mining area were also significant higher than those growing in the unexploited area with 2.59 and 2.99 times, respectively. The Mo translocation factor of plants growing in the unexploited area was 1.61, which reached 1.69 times that of plants growing in the mining area. Mo was the main heavy metal pollutant in the soil of both the mining and the unexploited areas. Conclusion Mining of Mo had changed not only the Mo concentration in soil but also Mo absorption and translocation in plants. Plants growing in the mining area absorbed more Mo from the soil but translocated relatively less to shoots than plants of the unexploited area. However, the mechanisms of Mo absorption and translocation of plants in mining area should be further studied in the future.
format: application/pdf
format: text/html
creator: Kejing Yin
creator: Zhaoyong Shi
creator: Mengge Zhang
creator: Yajuan Li
subject: Plant Science
subject: Soil Science
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.9183
publisher: PeerJ Inc.
rights: © 2020 Yin et al.
abstract: Background There is a critical need to examine whether mining of molybdenum (Mo) ore will affect Mo absorption and translocation by plants at a community level. Methods Indigenous plants and their rhizospheric soil (0–20 cm) growing in two different areas including the mining and the unexploited areas were collected from the Luanchuan Mo mine—one of the largest Mo mines in Asia. The concentrations of Mo and other heavy metals of plants or soil were measured by ICP-AES. Mo absorption and translocation in plants growing in two areas were investigated and compared. Heavy metal pollution in soil was also evaluated by the potential ecological hazard index method. Results Mo concentration in mining soils was higher with the changes from 108.13 to 268.13 mg kg−1 compared to unexploited area. Mo concentrations in shoots and roots of plants growing in the mining area were also significant higher than those growing in the unexploited area with 2.59 and 2.99 times, respectively. The Mo translocation factor of plants growing in the unexploited area was 1.61, which reached 1.69 times that of plants growing in the mining area. Mo was the main heavy metal pollutant in the soil of both the mining and the unexploited areas. Conclusion Mining of Mo had changed not only the Mo concentration in soil but also Mo absorption and translocation in plants. Plants growing in the mining area absorbed more Mo from the soil but translocated relatively less to shoots than plants of the unexploited area. However, the mechanisms of Mo absorption and translocation of plants in mining area should be further studied in the future.
bibliographic citation: Yin et al. (2020) Effects of mining on the molybdenum absorption and translocation of plants in the Luanchuan molybdenum mine. PeerJ 8:e9183 https://doi.org/10.7717/peerj.9183
date submitted: 2020-02-06
date accepted: 2020-04-22
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Kejing
author list: Agent
  family name: Shi
  given name: Zhaoyong
author list: Agent
  family name: Zhang
  given name: Mengge
author list: Agent
  family name: Li
  given name: Yajuan
doi: 10.7717/peerj.9183
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Yin et al.
attribution name: Yin et al.

The high expression of MTH1 and NUDT5 predict a poor survival and are associated with malignancy of esophageal squamous cell carcinoma
type: item
type: AcademicArticle
description: Background MTH1 and NUDT5 effectively degrade nucleotides containing 8-oxoguanine. MTH1 and NUDT5 have been linked to the malignancy of multiple cancers. However, their functions in tumor growth and metastasis in esophageal squamous carcinoma (ESCC) remain obscure. Our present study aims to explore their prognostic value in ESCC and investigate their function in MTH1 or NUDT5-knockout tumor cells. Methods MTH1 and NUDT5 protein expression in ESCC adjacent normal tissues and tumor tissues was examined by immunohistochemistry staining. Kaplan–Meier curves were used to assess the association between their expression and overall survival (OS) in ESCC patients. Univariate and Multivariate Cox regression analyses were generated to determine the correlation between these protein expression and OS of ESCC patients. Protein expression in ESCC cell lines were measured by Western blotting. To explore the potential effects of the MTH1 and NUDT5 protein in ESCC, cell models with MTH1 or NUDT5 depletion were established. CCK-8, cell cycle, Western blotting, migration and invasion assays were performed. Results Our present study demonstrated that the levels of MTH1 and NUDT5 were upregulated in ESCC cell lines and ESCC tissues, the expression of MTH1 and NUDT5 in ESCC tissues was significantly higher than in adjacent non-tumorous, and higher levels of MTH1 and NUDT5 predicted a worse prognosis in patients with ESCC. MTH1 and NUDT5 are novel biomarkers of the progression of ESCC and a poor prognosis. We also found for the first time that the high expression of NUDT5 independently predicted lower OS in patients with ESCC (hazard ratio (HR) 1.751; 95% confidence interval (CI) [1.056–2.903]; p = 0.030). In addition, the depletion of MTH1 and NUDT5 strongly suppressed the proliferation of ESCC cells and significantly delayed the G1 phase of the cell cycle. Furthermore, we found that MTH1 and NUDT5 silencing inhibited epithelial–mesenchymal transition mainly by the MAPK/MEK/ERK dependen…
format: application/pdf
format: text/html
creator: Jing-Jing Wang
creator: Teng-Hui Liu
creator: Jin Li
creator: Dan-Ni Li
creator: Xin-Yuan Tian
creator: Qiu-Geng Ouyang
creator: Jian-Ping Cai
subject: Bioinformatics
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.9195
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background MTH1 and NUDT5 effectively degrade nucleotides containing 8-oxoguanine. MTH1 and NUDT5 have been linked to the malignancy of multiple cancers. However, their functions in tumor growth and metastasis in esophageal squamous carcinoma (ESCC) remain obscure. Our present study aims to explore their prognostic value in ESCC and investigate their function in MTH1 or NUDT5-knockout tumor cells. Methods MTH1 and NUDT5 protein expression in ESCC adjacent normal tissues and tumor tissues was examined by immunohistochemistry staining. Kaplan–Meier curves were used to assess the association between their expression and overall survival (OS) in ESCC patients. Univariate and Multivariate Cox regression analyses were generated to determine the correlation between these protein expression and OS of ESCC patients. Protein expression in ESCC cell lines were measured by Western blotting. To explore the potential effects of the MTH1 and NUDT5 protein in ESCC, cell models with MTH1 or NUDT5 depletion were established. CCK-8, cell cycle, Western blotting, migration and invasion assays were performed. Results Our present study demonstrated that the levels of MTH1 and NUDT5 were upregulated in ESCC cell lines and ESCC tissues, the expression of MTH1 and NUDT5 in ESCC tissues was significantly higher than in adjacent non-tumorous, and higher levels of MTH1 and NUDT5 predicted a worse prognosis in patients with ESCC. MTH1 and NUDT5 are novel biomarkers of the progression of ESCC and a poor prognosis. We also found for the first time that the high expression of NUDT5 independently predicted lower OS in patients with ESCC (hazard ratio (HR) 1.751; 95% confidence interval (CI) [1.056–2.903]; p = 0.030). In addition, the depletion of MTH1 and NUDT5 strongly suppressed the proliferation of ESCC cells and significantly delayed the G1 phase of the cell cycle. Furthermore, we found that MTH1 and NUDT5 silencing inhibited epithelial–mesenchymal transition mainly by the MAPK/MEK/ERK dependen…
bibliographic citation: Wang et al. (2020) The high expression of MTH1 and NUDT5 predict a poor survival and are associated with malignancy of esophageal squamous cell carcinoma. PeerJ 8:e9195 https://doi.org/10.7717/peerj.9195
date submitted: 2020-02-19
date accepted: 2020-04-24
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jing-Jing
author list: Agent
  family name: Liu
  given name: Teng-Hui
author list: Agent
  family name: Li
  given name: Jin
author list: Agent
  family name: Li
  given name: Dan-Ni
author list: Agent
  family name: Tian
  given name: Xin-Yuan
author list: Agent
  family name: Ouyang
  given name: Qiu-Geng
author list: Agent
  family name: Cai
  given name: Jian-Ping
doi: 10.7717/peerj.9195
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Comprehensive analysis reveals a metabolic ten-gene signature in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Due to the complicated molecular and cellular heterogeneity in hepatocellular carcinoma (HCC), the morbidity and mortality still remains high level in the world. However, the number of novel metabolic biomarkers and prognostic models could be applied to predict the survival of HCC patients is still small. In this study, we constructed a metabolic gene signature by systematically analyzing the data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and International Cancer Genome Consortium (ICGC). Methods Differentially expressed genes (DEGs) between tumors and paired non-tumor samples of 50 patients from TCGA dataset were calculated for subsequent analysis. Univariate cox proportional hazard regression and LASSO analysis were performed to construct a gene signature. The Kaplan–Meier analysis, time-dependent receiver operating characteristic (ROC), Univariate and Multivariate Cox regression analysis, stratification analysis were used to assess the prognostic value of the gene signature. Furthermore, the reliability and validity were validated in four types of testing cohorts. Moreover, the diagnostic capability of the gene signature was investigated to further explore the clinical significance. Finally, Go enrichment analysis and Gene Set Enrichment Analysis (GSEA) have been performed to reveal the different biological processes and signaling pathways which were active in high risk or low risk group. Results Ten prognostic genes were identified and a gene signature were constructed to predict overall survival (OS). The gene signature has demonstrated an excellent ability for predicting survival prognosis. Univariate and Multivariate analysis revealed the gene signature was an independent prognostic factor. Furthermore, stratification analysis indicated the model was a clinically and statistically significant for all subgroups. Moreover, the gene signature demonstrated a high diagnostic capability in differentiating normal tissue and HCC. F…
format: application/pdf
format: text/html
creator: Zhipeng Zhu
creator: Lulu Li
creator: Jiuhua Xu
creator: Weipeng Ye
creator: Borong Chen
creator: Junjie Zeng
creator: Zhengjie Huang
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.9201
publisher: PeerJ Inc.
rights: © 2020 Zhu et al.
abstract: Background Due to the complicated molecular and cellular heterogeneity in hepatocellular carcinoma (HCC), the morbidity and mortality still remains high level in the world. However, the number of novel metabolic biomarkers and prognostic models could be applied to predict the survival of HCC patients is still small. In this study, we constructed a metabolic gene signature by systematically analyzing the data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and International Cancer Genome Consortium (ICGC). Methods Differentially expressed genes (DEGs) between tumors and paired non-tumor samples of 50 patients from TCGA dataset were calculated for subsequent analysis. Univariate cox proportional hazard regression and LASSO analysis were performed to construct a gene signature. The Kaplan–Meier analysis, time-dependent receiver operating characteristic (ROC), Univariate and Multivariate Cox regression analysis, stratification analysis were used to assess the prognostic value of the gene signature. Furthermore, the reliability and validity were validated in four types of testing cohorts. Moreover, the diagnostic capability of the gene signature was investigated to further explore the clinical significance. Finally, Go enrichment analysis and Gene Set Enrichment Analysis (GSEA) have been performed to reveal the different biological processes and signaling pathways which were active in high risk or low risk group. Results Ten prognostic genes were identified and a gene signature were constructed to predict overall survival (OS). The gene signature has demonstrated an excellent ability for predicting survival prognosis. Univariate and Multivariate analysis revealed the gene signature was an independent prognostic factor. Furthermore, stratification analysis indicated the model was a clinically and statistically significant for all subgroups. Moreover, the gene signature demonstrated a high diagnostic capability in differentiating normal tissue and HCC. F…
bibliographic citation: Zhu et al. (2020) Comprehensive analysis reveals a metabolic ten-gene signature in hepatocellular carcinoma. PeerJ 8:e9201 https://doi.org/10.7717/peerj.9201
date submitted: 2020-02-06
date accepted: 2020-04-24
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Zhipeng
author list: Agent
  family name: Li
  given name: Lulu
author list: Agent
  family name: Xu
  given name: Jiuhua
author list: Agent
  family name: Ye
  given name: Weipeng
author list: Agent
  family name: Chen
  given name: Borong
author list: Agent
  family name: Zeng
  given name: Junjie
author list: Agent
  family name: Huang
  given name: Zhengjie
doi: 10.7717/peerj.9201
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: © 2020 Zhu et al.
attribution name: Zhu et al.

Estimating food resource availability in arid environments with Sentinel 2 satellite imagery
type: item
type: AcademicArticle
description: Background In arid environments, plant primary productivity is generally low and highly variable both spatially and temporally. Resources are not evenly distributed in space and time (e.g., soil nutrients, water), and depend on global (El Niño/ Southern Oscillation) and local climate parameters. The launch of the Sentinel2-satellite, part of the European Copernicus program, has led to the provision of freely available data with a high spatial resolution (10 m per pixel). Here, we aimed to test whether Sentinel2-imagery can be used to quantify the spatial variability of a minor tussock grass (Enneapogon spp.) in an Australian arid area and whether we can identify different vegetation cover (e.g., grass from shrubs) along different temporal scenarios. Although short-lasting, the Enneapogon grassland has been identified as a key primary food source to animals in the arid environment. If we are able to identify and monitor the productivity of this species remotely, it will provide an important new tool for examining food resource dynamics and subsequent animal responses to them in arid habitat. Methods We combined field vegetation surveys and Sentinel2-imagery to test if satellite spectral data can predict the spatial variability of Enneapogon over time, through GLMMs. Additionally, a cluster analysis (‘gower’ distance, ‘complete’ method), based on Enneapogon seed-productivity, and total vegetation cover in October 2016, identified three clusters: bare ground, grass dominated and shrub dominated. We compared the vegetation indices between these different clusters from October 2016 to January 2017. Results We found that MSAVI2 and NDVI correlated with the proportion of Enneapogon with seeds across the landscape and this relationship changed over time. Both vegetation indices (MSAVI2 and NDVI) were higher in patches with high seed-productivity of Enneapogon than in bare soil, but only in October, a climatically-favorable period during which this dominant grass reached pea…
format: application/pdf
format: text/html
creator: Caterina Funghi
creator: René H.J. Heim
creator: Wiebke Schuett
creator: Simon C. Griffith
creator: Jens Oldeland
subject: Animal Behavior
subject: Ecology
subject: Ecosystem Science
description: doi:10.7717/peerj.9209
publisher: PeerJ Inc.
rights: © 2020 Funghi et al.
abstract: Background In arid environments, plant primary productivity is generally low and highly variable both spatially and temporally. Resources are not evenly distributed in space and time (e.g., soil nutrients, water), and depend on global (El Niño/ Southern Oscillation) and local climate parameters. The launch of the Sentinel2-satellite, part of the European Copernicus program, has led to the provision of freely available data with a high spatial resolution (10 m per pixel). Here, we aimed to test whether Sentinel2-imagery can be used to quantify the spatial variability of a minor tussock grass (Enneapogon spp.) in an Australian arid area and whether we can identify different vegetation cover (e.g., grass from shrubs) along different temporal scenarios. Although short-lasting, the Enneapogon grassland has been identified as a key primary food source to animals in the arid environment. If we are able to identify and monitor the productivity of this species remotely, it will provide an important new tool for examining food resource dynamics and subsequent animal responses to them in arid habitat. Methods We combined field vegetation surveys and Sentinel2-imagery to test if satellite spectral data can predict the spatial variability of Enneapogon over time, through GLMMs. Additionally, a cluster analysis (‘gower’ distance, ‘complete’ method), based on Enneapogon seed-productivity, and total vegetation cover in October 2016, identified three clusters: bare ground, grass dominated and shrub dominated. We compared the vegetation indices between these different clusters from October 2016 to January 2017. Results We found that MSAVI2 and NDVI correlated with the proportion of Enneapogon with seeds across the landscape and this relationship changed over time. Both vegetation indices (MSAVI2 and NDVI) were higher in patches with high seed-productivity of Enneapogon than in bare soil, but only in October, a climatically-favorable period during which this dominant grass reached pea…
bibliographic citation: Funghi et al. (2020) Estimating food resource availability in arid environments with Sentinel 2 satellite imagery. PeerJ 8:e9209 https://doi.org/10.7717/peerj.9209
date submitted: 2019-09-03
date accepted: 2020-04-27
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Funghi
  given name: Caterina
author list: Agent
  family name: Heim
  given name: René H.J.
author list: Agent
  family name: Schuett
  given name: Wiebke
author list: Agent
  family name: Griffith
  given name: Simon C.
author list: Agent
  family name: Oldeland
  given name: Jens
doi: 10.7717/peerj.9209
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Funghi et al.
attribution name: Funghi et al.

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