PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: In silico and in vitro identification of secoisolariciresinol as a re-sensitizer of P-glycoprotein-dependent doxorubicin-resistance NCI/ADR-RES cancer cells
items: Fire severity effects on resprouting of subtropical dune thicket of the Cape Floristic Region
items: Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis)
items: DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics
items: Succession of bacterial communities on carrion is independent of vertebrate scavengers
items: Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes
items: Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips
items: Non-linear responses of net ecosystem productivity to gradient warming in a paddy field in Northeast China
items: Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach
items: Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness

In silico and in vitro identification of secoisolariciresinol as a re-sensitizer of P-glycoprotein-dependent doxorubicin-resistance NCI/ADR-RES cancer cells
type: item
type: AcademicArticle
description: P-glycoprotein (P-gp) is one of the highly expressed cancer cell efflux transporters that cause the failure of chemotherapy. To reverse P-gp induced multidrug resistance, we employed a flaxseed-derived lignan; secoisolariciresinol (SECO) that acts as an inhibitor of breast cancer resistance protein; another efflux transporter that shares some substrate/inhibitor specificity with P-gp. Molecular dynamics (MD) simulation identified SECO as a possible P-gp inhibitor. Comparing root mean square deviation (RMSD) of P-gp bound with SECO with that bound to its standard inhibitor verapamil showed that fluctuations in RMSD were lower in P-gp bound to SECO demonstrating higher stability of the complex of P-gp with SECO. In addition, the superimposition of P-gp structures after MD simulation showed that the nucleotide-binding domains of P-gp bound to SECO undertook a more central closer position compared with that bound to verapamil. Using rhodamine efflux assay on NCI/ADR-RES cancer cells, SECO was confirmed as a P-gp inhibitor, where cells treated with 25 or 50 µM of SECO showed significantly higher fluorescence intensity compared to control. Using MTT assay, SECO alone showed dose-dependent cytotoxicity, where 25 or 50 µM of SECO caused significantly less NCI/ADR-RES cellular viability compared to control. Furthermore, when 50 µM of SECO was added to doxorubicin (DOX), an anticancer drug, SECO significantly enhanced DOX-induced cytotoxicity compared to DOX alone. The combination index calculated by CompuSyn software indicated synergism between DOX and SECO. Our results suggest SECO as a novel P-gp inhibitor that can re-sensitize cancer cells during DOX chemotherapy.
format: application/pdf
format: text/html
creator: Mohamed A. Morsy
creator: Azza A.K. El-Sheikh
creator: Ahmed R.N. Ibrahim
creator: Katharigatta N. Venugopala
creator: Mahmoud Kandeel
subject: Bioinformatics
subject: Pharmacology
description: doi:10.7717/peerj.9163
publisher: PeerJ Inc.
rights: © 2020 Morsy et al.
abstract: P-glycoprotein (P-gp) is one of the highly expressed cancer cell efflux transporters that cause the failure of chemotherapy. To reverse P-gp induced multidrug resistance, we employed a flaxseed-derived lignan; secoisolariciresinol (SECO) that acts as an inhibitor of breast cancer resistance protein; another efflux transporter that shares some substrate/inhibitor specificity with P-gp. Molecular dynamics (MD) simulation identified SECO as a possible P-gp inhibitor. Comparing root mean square deviation (RMSD) of P-gp bound with SECO with that bound to its standard inhibitor verapamil showed that fluctuations in RMSD were lower in P-gp bound to SECO demonstrating higher stability of the complex of P-gp with SECO. In addition, the superimposition of P-gp structures after MD simulation showed that the nucleotide-binding domains of P-gp bound to SECO undertook a more central closer position compared with that bound to verapamil. Using rhodamine efflux assay on NCI/ADR-RES cancer cells, SECO was confirmed as a P-gp inhibitor, where cells treated with 25 or 50 µM of SECO showed significantly higher fluorescence intensity compared to control. Using MTT assay, SECO alone showed dose-dependent cytotoxicity, where 25 or 50 µM of SECO caused significantly less NCI/ADR-RES cellular viability compared to control. Furthermore, when 50 µM of SECO was added to doxorubicin (DOX), an anticancer drug, SECO significantly enhanced DOX-induced cytotoxicity compared to DOX alone. The combination index calculated by CompuSyn software indicated synergism between DOX and SECO. Our results suggest SECO as a novel P-gp inhibitor that can re-sensitize cancer cells during DOX chemotherapy.
bibliographic citation: Morsy et al. (2020) In silico and in vitro identification of secoisolariciresinol as a re-sensitizer of P-glycoprotein-dependent doxorubicin-resistance NCI/ADR-RES cancer cells. PeerJ 8:e9163 https://doi.org/10.7717/peerj.9163
date submitted: 2020-01-23
date accepted: 2020-04-18
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morsy
  given name: Mohamed A.
author list: Agent
  family name: El-Sheikh
  given name: Azza A.K.
author list: Agent
  family name: Ibrahim
  given name: Ahmed R.N.
author list: Agent
  family name: Venugopala
  given name: Katharigatta N.
author list: Agent
  family name: Kandeel
  given name: Mahmoud
doi: 10.7717/peerj.9163
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Morsy et al.
attribution name: Morsy et al.

Fire severity effects on resprouting of subtropical dune thicket of the Cape Floristic Region
type: item
type: AcademicArticle
description: It has been hypothesised that high-intensity fires prevent fire-dependent fynbos from being replaced by fire-avoiding subtropical thicket on dune landscapes of the Cape Floristic Region (CFR). Recent extensive fires provided an opportunity to test this hypothesis. We posit that (1) fire-related thicket shrub mortality would be size dependent, with smaller individuals suffering higher mortality than larger ones; and (2) that survival and resprouting vigour of thicket shrubs would be negatively correlated with fire severity. We assessed survival and resprouting vigour post-fire in relation to fire severity and pre-fire shrub size at two dune landscapes in the CFR. Fire severity was scored at the base of the shrub and categorised into four levels. Pre-fire size was quantified as an index of lignotuber diameter and stem count of each shrub. Resprouting vigour consisted of two variables; resprouting shoot count and resprouting canopy volume. A total of 29 species were surveyed. Post-fire survival of thicket was high (83–85%). We found that smaller shrubs did have a lower probability of post-fire survival than larger individuals but could detect no consistent relationship between shrub mortality and fire severity. Fire severity had a positive effect on resprouting shoot count but a variable effect on resprouting volume. Pre-fire size was positively related to survival and both measures of resprouting vigour. We conclude that thicket is resilient to high-severity fires but may be vulnerable to frequent fires. Prescribed high-intensity fires in dune landscapes are unlikely to reduce the extent of thicket and promote fynbos expansion.
format: application/pdf
format: text/html
creator: Tiaan Strydom
creator: Tineke Kraaij
creator: Mark Difford
creator: Richard M. Cowling
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Natural Resource Management
description: doi:10.7717/peerj.9240
publisher: PeerJ Inc.
rights: © 2020 Strydom et al.
abstract: It has been hypothesised that high-intensity fires prevent fire-dependent fynbos from being replaced by fire-avoiding subtropical thicket on dune landscapes of the Cape Floristic Region (CFR). Recent extensive fires provided an opportunity to test this hypothesis. We posit that (1) fire-related thicket shrub mortality would be size dependent, with smaller individuals suffering higher mortality than larger ones; and (2) that survival and resprouting vigour of thicket shrubs would be negatively correlated with fire severity. We assessed survival and resprouting vigour post-fire in relation to fire severity and pre-fire shrub size at two dune landscapes in the CFR. Fire severity was scored at the base of the shrub and categorised into four levels. Pre-fire size was quantified as an index of lignotuber diameter and stem count of each shrub. Resprouting vigour consisted of two variables; resprouting shoot count and resprouting canopy volume. A total of 29 species were surveyed. Post-fire survival of thicket was high (83–85%). We found that smaller shrubs did have a lower probability of post-fire survival than larger individuals but could detect no consistent relationship between shrub mortality and fire severity. Fire severity had a positive effect on resprouting shoot count but a variable effect on resprouting volume. Pre-fire size was positively related to survival and both measures of resprouting vigour. We conclude that thicket is resilient to high-severity fires but may be vulnerable to frequent fires. Prescribed high-intensity fires in dune landscapes are unlikely to reduce the extent of thicket and promote fynbos expansion.
bibliographic citation: Strydom et al. (2020) Fire severity effects on resprouting of subtropical dune thicket of the Cape Floristic Region. PeerJ 8:e9240 https://doi.org/10.7717/peerj.9240
date submitted: 2020-01-23
date accepted: 2020-05-05
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strydom
  given name: Tiaan
author list: Agent
  family name: Kraaij
  given name: Tineke
author list: Agent
  family name: Difford
  given name: Mark
author list: Agent
  family name: Cowling
  given name: Richard M.
doi: 10.7717/peerj.9240
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Strydom et al.
attribution name: Strydom et al.

Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis)
type: item
type: AcademicArticle
description: Background DNA-binding one zinc finger (Dof) proteins are plant-specific transcription factors important for seed development, hormone regulation, and defense against abiotic stress. Although drought stress is a key determinant of plant physiology and metabolic homeostasis, the role of Dof genes in different degrees of PEG6000-induced drought stress has received little attention. Methods Tea plants (Camellia sinensis) were exposed to mild, moderate and severe drought stress. The Tea Genome and Plant TFDB databases were used to identify Dof gene family members in the tea plant. Clustal W2.1, MEGA6.0, ScanProsite, SMART, ExPASy, GSDS, MEME and STRING were used to build a phylogenetic tree, predict the molecular masses and isoelectric points of the Dof proteins, and construct a predicted protein-protein interaction network between the CsDof TFs and proteins in the A. thaliana database. The expression patterns of Dof genes in different tissues were analyzed, and qRT-PCR was used to measure the expression of Dof genes under different degrees of drought stress in tea. Results We identified 16 Dof genes in tea (C. sinensis cv. Huangjinya) using whole-genome analysis. Through comparative analysis of tea and Arabidopsis thaliana, we divided the Dof genes into four families (A, B, C, and D). We identified 15 motifs in the amino acid sequences of the CsDof proteins. Gene sequences and motif structures were highly conserved among families, especially in the B1 and C2 subfamilies. The protein-protein interaction network indicated that multiple CsDof proteins may be involved in the response to drought stress. Real-time PCR was used to examine the tissue-specific expression patterns of the CsDof genes and to measure their responses to different levels of PEG6000-induced drought stress in mature leaves. Most CsDof genes responded to drought stress. These results provide information on the Dof gene family in tea, offer new insights into the function of CsDof genes in a perennial spe…
format: application/pdf
format: text/html
creator: Qian Yu
creator: Chen Li
creator: Jiucheng Zhang
creator: Yueyue Tian
creator: Hanyue Wang
creator: Yue Zhang
creator: Zhengqun Zhang
creator: Qinzeng Xiang
creator: Xiaoyang Han
creator: Lixia Zhang
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.9269
publisher: PeerJ Inc.
rights: © 2020 Yu et al.
abstract: Background DNA-binding one zinc finger (Dof) proteins are plant-specific transcription factors important for seed development, hormone regulation, and defense against abiotic stress. Although drought stress is a key determinant of plant physiology and metabolic homeostasis, the role of Dof genes in different degrees of PEG6000-induced drought stress has received little attention. Methods Tea plants (Camellia sinensis) were exposed to mild, moderate and severe drought stress. The Tea Genome and Plant TFDB databases were used to identify Dof gene family members in the tea plant. Clustal W2.1, MEGA6.0, ScanProsite, SMART, ExPASy, GSDS, MEME and STRING were used to build a phylogenetic tree, predict the molecular masses and isoelectric points of the Dof proteins, and construct a predicted protein-protein interaction network between the CsDof TFs and proteins in the A. thaliana database. The expression patterns of Dof genes in different tissues were analyzed, and qRT-PCR was used to measure the expression of Dof genes under different degrees of drought stress in tea. Results We identified 16 Dof genes in tea (C. sinensis cv. Huangjinya) using whole-genome analysis. Through comparative analysis of tea and Arabidopsis thaliana, we divided the Dof genes into four families (A, B, C, and D). We identified 15 motifs in the amino acid sequences of the CsDof proteins. Gene sequences and motif structures were highly conserved among families, especially in the B1 and C2 subfamilies. The protein-protein interaction network indicated that multiple CsDof proteins may be involved in the response to drought stress. Real-time PCR was used to examine the tissue-specific expression patterns of the CsDof genes and to measure their responses to different levels of PEG6000-induced drought stress in mature leaves. Most CsDof genes responded to drought stress. These results provide information on the Dof gene family in tea, offer new insights into the function of CsDof genes in a perennial spe…
bibliographic citation: Yu et al. (2020) Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis). PeerJ 8:e9269 https://doi.org/10.7717/peerj.9269
date submitted: 2020-01-08
date accepted: 2020-05-10
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Qian
author list: Agent
  family name: Li
  given name: Chen
author list: Agent
  family name: Zhang
  given name: Jiucheng
author list: Agent
  family name: Tian
  given name: Yueyue
author list: Agent
  family name: Wang
  given name: Hanyue
author list: Agent
  family name: Zhang
  given name: Yue
author list: Agent
  family name: Zhang
  given name: Zhengqun
author list: Agent
  family name: Xiang
  given name: Qinzeng
author list: Agent
  family name: Han
  given name: Xiaoyang
author list: Agent
  family name: Zhang
  given name: Lixia
doi: 10.7717/peerj.9269
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: ©2020 Yu et al.
attribution name: Yu et al.

DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics
type: item
type: AcademicArticle
description: Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.
format: application/pdf
format: text/html
creator: Jérémy Gauthier
creator: Charlotte Mouden
creator: Tomasz Suchan
creator: Nadir Alvarez
creator: Nils Arrigo
creator: Chloé Riou
creator: Claire Lemaitre
creator: Pierre Peterlongo
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.9291
publisher: PeerJ Inc.
rights: © 2020 Gauthier et al.
abstract: Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.
bibliographic citation: Gauthier et al. (2020) DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics. PeerJ 8:e9291 https://doi.org/10.7717/peerj.9291
date submitted: 2020-01-20
date accepted: 2020-05-13
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gauthier
  given name: Jérémy
author list: Agent
  family name: Mouden
  given name: Charlotte
author list: Agent
  family name: Suchan
  given name: Tomasz
author list: Agent
  family name: Alvarez
  given name: Nadir
author list: Agent
  family name: Arrigo
  given name: Nils
author list: Agent
  family name: Riou
  given name: Chloé
author list: Agent
  family name: Lemaitre
  given name: Claire
author list: Agent
  family name: Peterlongo
  given name: Pierre
doi: 10.7717/peerj.9291
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Gauthier et al.
attribution name: Gauthier et al.

Succession of bacterial communities on carrion is independent of vertebrate scavengers
type: item
type: AcademicArticle
description: The decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by vertebrate scavenging.
format: application/pdf
format: text/html
creator: Cody R. Dangerfield
creator: Ethan H. Frehner
creator: Evan R. Buechley
creator: Çağan H. Şekercioğlu
creator: William J. Brazelton
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.9307
publisher: PeerJ Inc.
rights: © 2020 Dangerfield et al.
abstract: The decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by vertebrate scavenging.
bibliographic citation: Dangerfield et al. (2020) Succession of bacterial communities on carrion is independent of vertebrate scavengers. PeerJ 8:e9307 https://doi.org/10.7717/peerj.9307
date submitted: 2019-08-28
date accepted: 2020-05-17
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dangerfield
  given name: Cody R.
author list: Agent
  family name: Frehner
  given name: Ethan H.
author list: Agent
  family name: Buechley
  given name: Evan R.
author list: Agent
  family name: Şekercioğlu
  given name: Çağan H.
author list: Agent
  family name: Brazelton
  given name: William J.
doi: 10.7717/peerj.9307
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: ©2020 Dangerfield et al.
attribution name: Dangerfield et al.

Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes
type: item
type: AcademicArticle
description: Background Dextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of Cinnamomum trees, e.g., C. burmannii and C. camphor, are the main sources from which D-borneol is extracted by steam distillation, yet with low yields. Insufficient supply of D-borneol has hampered its clinical use and production of patent remedies for a long time. Biological synthesis of D-borneol offers an additional approach; however, mechanisms of D-borneol biosynthesis remain mostly unresolved. Hence, it is important and necessary to elucidate the biosynthetic pathway of D-borneol. Results Comparative analysis on the gene expression patterns of different D-borneol production C. burmannii samples facilitates elucidation on the underlying biosynthetic pathway of D-borneol. Herein, we collected three different chemotypes of C. burmannii, which harbor different contents of D-borneol.A total of 100,218 unigenes with an N50 of 1,128 bp were assembled de novo using Trinity from a total of 21.21 Gb clean bases. We used BLASTx analysis against several public databases to annotate 45,485 unigenes (45.38%) to at least one database, among which 82 unigenes were assigned to terpenoid biosynthesis pathways by KEGG annotation. In addition, we defined 8,860 unigenes as differentially expressed genes (DEGs), among which 13 DEGs were associated with terpenoid biosynthesis pathways. One 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and two monoterpene synthase, designated as CbDXS9, CbTPS2 and CbTPS3, were up-regulated in the high-borneol group compared to the low-borneol and borneol-free groups, and might be vital to biosynthesis of D-borneol in C. burmannii. In addition, we identified one WRKY, two BHLH, one AP2/ERF and three MYB candidate genes, which exhibited the same expression patterns as CbTPS2 and CbTPS3, suggesting that these transcription factors might potentially regulate D-borneol biosynthesis. Fin…
format: application/pdf
format: text/html
creator: Zerui Yang
creator: Wenli An
creator: Shanshan Liu
creator: Yuying Huang
creator: Chunzhu Xie
creator: Song Huang
creator: Xiasheng Zheng
subject: Biochemistry
subject: Plant Science
subject: Synthetic Biology
description: doi:10.7717/peerj.9311
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Background Dextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of Cinnamomum trees, e.g., C. burmannii and C. camphor, are the main sources from which D-borneol is extracted by steam distillation, yet with low yields. Insufficient supply of D-borneol has hampered its clinical use and production of patent remedies for a long time. Biological synthesis of D-borneol offers an additional approach; however, mechanisms of D-borneol biosynthesis remain mostly unresolved. Hence, it is important and necessary to elucidate the biosynthetic pathway of D-borneol. Results Comparative analysis on the gene expression patterns of different D-borneol production C. burmannii samples facilitates elucidation on the underlying biosynthetic pathway of D-borneol. Herein, we collected three different chemotypes of C. burmannii, which harbor different contents of D-borneol.A total of 100,218 unigenes with an N50 of 1,128 bp were assembled de novo using Trinity from a total of 21.21 Gb clean bases. We used BLASTx analysis against several public databases to annotate 45,485 unigenes (45.38%) to at least one database, among which 82 unigenes were assigned to terpenoid biosynthesis pathways by KEGG annotation. In addition, we defined 8,860 unigenes as differentially expressed genes (DEGs), among which 13 DEGs were associated with terpenoid biosynthesis pathways. One 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and two monoterpene synthase, designated as CbDXS9, CbTPS2 and CbTPS3, were up-regulated in the high-borneol group compared to the low-borneol and borneol-free groups, and might be vital to biosynthesis of D-borneol in C. burmannii. In addition, we identified one WRKY, two BHLH, one AP2/ERF and three MYB candidate genes, which exhibited the same expression patterns as CbTPS2 and CbTPS3, suggesting that these transcription factors might potentially regulate D-borneol biosynthesis. Fin…
bibliographic citation: Yang et al. (2020) Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes. PeerJ 8:e9311 https://doi.org/10.7717/peerj.9311
date submitted: 2019-12-09
date accepted: 2020-05-17
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Zerui
author list: Agent
  family name: An
  given name: Wenli
author list: Agent
  family name: Liu
  given name: Shanshan
author list: Agent
  family name: Huang
  given name: Yuying
author list: Agent
  family name: Xie
  given name: Chunzhu
author list: Agent
  family name: Huang
  given name: Song
author list: Agent
  family name: Zheng
  given name: Xiasheng
doi: 10.7717/peerj.9311
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips
type: item
type: AcademicArticle
description: Aluminum (Al) toxicity in acid soil is a worldwide agricultural problem that inhibits crop growth and productivity. However, the signal pathways associated with Al tolerance in plants remain largely unclear. In this study, tandem mass tag (TMT)-based quantitative proteomic methods were used to identify the differentially expressed plasma membrane (PM) proteins in Tamba black soybean (TBS) root tips under Al stress. Data are available via ProteomeXchange with identifier PXD017160. In addition, parallel reaction monitoring (PRM) was used to verify the protein quantitative data. The results showed that 907 PM proteins were identified in Al-treated plants. Among them, compared to untreated plants, 90 proteins were differentially expressed (DEPs) with 46 up-regulated and 44 down-regulated (fold change > 1.3 or < 0.77, p < 0.05). Functional enrichment based on GO, KEGG and protein domain revealed that the DEPs were associated with membrane trafficking and transporters, modifying cell wall composition, defense response and signal transduction. In conclusion, our results highlight the involvement of GmMATE13, GmMATE75, GmMATE87 and H+-ATPase in Al-induced citrate secretion in PM of TBS roots, and ABC transporters and Ca2+ have been implicated in internal detoxification and signaling of Al, respectively. Importantly, our data provides six receptor-like protein kinases (RLKs) as candidate proteins for further investigating Al signal transmembrane mechanisms.
format: application/pdf
format: text/html
creator: Yunmin Wei
creator: Caode Jiang
creator: Rongrong Han
creator: Yonghong Xie
creator: Lusheng Liu
creator: Yongxiong Yu
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.9312
publisher: PeerJ Inc.
rights: © 2020 Wei et al.
abstract: Aluminum (Al) toxicity in acid soil is a worldwide agricultural problem that inhibits crop growth and productivity. However, the signal pathways associated with Al tolerance in plants remain largely unclear. In this study, tandem mass tag (TMT)-based quantitative proteomic methods were used to identify the differentially expressed plasma membrane (PM) proteins in Tamba black soybean (TBS) root tips under Al stress. Data are available via ProteomeXchange with identifier PXD017160. In addition, parallel reaction monitoring (PRM) was used to verify the protein quantitative data. The results showed that 907 PM proteins were identified in Al-treated plants. Among them, compared to untreated plants, 90 proteins were differentially expressed (DEPs) with 46 up-regulated and 44 down-regulated (fold change > 1.3 or < 0.77, p < 0.05). Functional enrichment based on GO, KEGG and protein domain revealed that the DEPs were associated with membrane trafficking and transporters, modifying cell wall composition, defense response and signal transduction. In conclusion, our results highlight the involvement of GmMATE13, GmMATE75, GmMATE87 and H+-ATPase in Al-induced citrate secretion in PM of TBS roots, and ABC transporters and Ca2+ have been implicated in internal detoxification and signaling of Al, respectively. Importantly, our data provides six receptor-like protein kinases (RLKs) as candidate proteins for further investigating Al signal transmembrane mechanisms.
bibliographic citation: Wei et al. (2020) Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips. PeerJ 8:e9312 https://doi.org/10.7717/peerj.9312
date submitted: 2020-02-10
date accepted: 2020-05-17
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Yunmin
author list: Agent
  family name: Jiang
  given name: Caode
author list: Agent
  family name: Han
  given name: Rongrong
author list: Agent
  family name: Xie
  given name: Yonghong
author list: Agent
  family name: Liu
  given name: Lusheng
author list: Agent
  family name: Yu
  given name: Yongxiong
doi: 10.7717/peerj.9312
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Wei et al.
attribution name: Wei et al.

Non-linear responses of net ecosystem productivity to gradient warming in a paddy field in Northeast China
type: item
type: AcademicArticle
description: Global warming has a known impact on ecosystems but there is a lack of understanding about its impact on ecosystem processes. Net ecosystem productivity (NEP) and its components play a key part in the global carbon cycle. Analysing the impact of global warming on NEP will improve our understanding of how warming affects ecosystems. In our study, conducted in 2018, five warming treatments were manipulated (0 W, 500 W, 1000 W, 1500 W, and 3000 W) using three repetitions of far infrared open warming over a paddy field in Northeast China. NEP and its two related components, gross primary productivity (GPP) and ecosystem respiration (ER), were measured using the static chamber-infrared gas analyser method to explore the effects of different warming magnitudes on NEP. Results showed that measurement dates, warming treatments, and their interactions significantly affected NEP, ER, and GPP. Warming significantly increased NEP and its components but they showed a non-linear response to different warming magnitudes. The maximum increases in NEP and its components occurred at 1500 W warming. NEP is closely related to its components and the non-linear response of NEP may have primarily resulted from that of GPP. Gradient warming non-linearly increased GPP in the paddy field studied in Northeast China, resulting in the non-linear response of NEP. This study provides a basis for predicting the responses of carbon cycles in future climate events.
format: application/pdf
format: text/html
creator: Yulu Sun
creator: Fuyao Qu
creator: Xianjin Zhu
creator: Bei Sun
creator: Guojiao Wang
creator: Hong Yin
creator: Tao Wan
creator: Xiaowen Song
creator: Qian Chen
subject: Ecology
subject: Ecosystem Science
subject: Climate Change Biology
description: doi:10.7717/peerj.9327
publisher: PeerJ Inc.
rights: © 2020 Sun et al.
abstract: Global warming has a known impact on ecosystems but there is a lack of understanding about its impact on ecosystem processes. Net ecosystem productivity (NEP) and its components play a key part in the global carbon cycle. Analysing the impact of global warming on NEP will improve our understanding of how warming affects ecosystems. In our study, conducted in 2018, five warming treatments were manipulated (0 W, 500 W, 1000 W, 1500 W, and 3000 W) using three repetitions of far infrared open warming over a paddy field in Northeast China. NEP and its two related components, gross primary productivity (GPP) and ecosystem respiration (ER), were measured using the static chamber-infrared gas analyser method to explore the effects of different warming magnitudes on NEP. Results showed that measurement dates, warming treatments, and their interactions significantly affected NEP, ER, and GPP. Warming significantly increased NEP and its components but they showed a non-linear response to different warming magnitudes. The maximum increases in NEP and its components occurred at 1500 W warming. NEP is closely related to its components and the non-linear response of NEP may have primarily resulted from that of GPP. Gradient warming non-linearly increased GPP in the paddy field studied in Northeast China, resulting in the non-linear response of NEP. This study provides a basis for predicting the responses of carbon cycles in future climate events.
bibliographic citation: Sun et al. (2020) Non-linear responses of net ecosystem productivity to gradient warming in a paddy field in Northeast China. PeerJ 8:e9327 https://doi.org/10.7717/peerj.9327
date submitted: 2019-11-18
date accepted: 2020-05-18
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Yulu
author list: Agent
  family name: Qu
  given name: Fuyao
author list: Agent
  family name: Zhu
  given name: Xianjin
author list: Agent
  family name: Sun
  given name: Bei
author list: Agent
  family name: Wang
  given name: Guojiao
author list: Agent
  family name: Yin
  given name: Hong
author list: Agent
  family name: Wan
  given name: Tao
author list: Agent
  family name: Song
  given name: Xiaowen
author list: Agent
  family name: Chen
  given name: Qian
doi: 10.7717/peerj.9327
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: ©2020 Sun et al.
attribution name: Sun et al.

Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach
type: item
type: AcademicArticle
description: Background Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization, and the identification of effective therapeutic strategy is a need of the hour to combat SARS-CoV-2 infection. In this scenario, the drug repurposing approach is widely used for the rapid identification of potential drugs against SARS-CoV-2, considering viral and host factors. Methods We adopted a host transcriptome-based drug repurposing strategy utilizing the publicly available high throughput gene expression data on SARS-CoV-2 and other respiratory infection viruses. Based on the consistency in expression status of host factors in different cell types and previous evidence reported in the literature, pro-viral factors of SARS-CoV-2 identified and subject to drug repurposing analysis based on DrugBank and Connectivity Map (CMap) using the web tool, CLUE. Results The upregulated pro-viral factors such as TYMP, PTGS2, C1S, CFB, IFI44, XAF1, CXCL2, and CXCL3 were identified in early infection models of SARS-CoV-2. By further analysis of the drug-perturbed expression profiles in the connectivity map, 27 drugs that can reverse the expression of pro-viral factors were identified, and importantly, twelve of them reported to have anti-viral activity. The direct inhibition of the PTGS2 gene product can be considered as another therapeutic strategy for SARS-CoV-2 infection and could suggest six approved PTGS2 inhibitor drugs for the treatment of COVID-19. The computational study could propose candidate repurposable drugs against COVID-19, and further experimental studies are required for validation.
format: application/pdf
format: text/html
creator: Tamizhini Loganathan
creator: Srimathy Ramachandran
creator: Prakash Shankaran
creator: Devipriya Nagarajan
creator: Suma Mohan S
subject: Bioinformatics
subject: Virology
description: doi:10.7717/peerj.9357
publisher: PeerJ Inc.
rights: © 2020 Loganathan et al.
abstract: Background Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization, and the identification of effective therapeutic strategy is a need of the hour to combat SARS-CoV-2 infection. In this scenario, the drug repurposing approach is widely used for the rapid identification of potential drugs against SARS-CoV-2, considering viral and host factors. Methods We adopted a host transcriptome-based drug repurposing strategy utilizing the publicly available high throughput gene expression data on SARS-CoV-2 and other respiratory infection viruses. Based on the consistency in expression status of host factors in different cell types and previous evidence reported in the literature, pro-viral factors of SARS-CoV-2 identified and subject to drug repurposing analysis based on DrugBank and Connectivity Map (CMap) using the web tool, CLUE. Results The upregulated pro-viral factors such as TYMP, PTGS2, C1S, CFB, IFI44, XAF1, CXCL2, and CXCL3 were identified in early infection models of SARS-CoV-2. By further analysis of the drug-perturbed expression profiles in the connectivity map, 27 drugs that can reverse the expression of pro-viral factors were identified, and importantly, twelve of them reported to have anti-viral activity. The direct inhibition of the PTGS2 gene product can be considered as another therapeutic strategy for SARS-CoV-2 infection and could suggest six approved PTGS2 inhibitor drugs for the treatment of COVID-19. The computational study could propose candidate repurposable drugs against COVID-19, and further experimental studies are required for validation.
bibliographic citation: Loganathan et al. (2020) Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach. PeerJ 8:e9357 https://doi.org/10.7717/peerj.9357
date submitted: 2020-04-20
date accepted: 2020-05-24
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Loganathan
  given name: Tamizhini
author list: Agent
  family name: Ramachandran
  given name: Srimathy
author list: Agent
  family name: Shankaran
  given name: Prakash
author list: Agent
  family name: Nagarajan
  given name: Devipriya
author list: Agent
  family name: Mohan S
  given name: Suma
doi: 10.7717/peerj.9357
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Loganathan et al.
attribution name: Loganathan et al.

Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness
type: item
type: AcademicArticle
description: Active commuting to and from school (ACS) has been recognized as a potential tool to improve physical fitness. Thus, this study aims to test the relationships between the average slope in the ACS and physical fitness, as well as to verify the mediator role of fatness in the relationship between average slope and physical fitness. A total of 257 participants, 137 boys and 120 girls, from 22 schools belonged to first and second High School grades participated in this study. Based on self-reported measure and Google Earth, participants were grouped into the active commuter (number of trips was ≥5, and the time of the trip was ≥15 min), mixed commuter (number of weekly trips was <5, and the time spent on the trip was <15 min) and passive commuter groups (those who reported traveling regularly by car, motorcycle, or bus). Specifically, in the active commuter group, a positive association between the average slope in the ACS with fatness was found, which in turn was positively related to strength lower limbs and cardiorrespiratory fitness. The average slope was not significantly associated with physical fitness indicators. Furtheremore, fatness did not mediate the relathionship between average slope and physical fitness. This research concluded positive associations between average slope and the body fat in the ACS. The tendency of findings signal that the average slope should be taken into account along with the distance, time and frequency of the active commuting.
format: application/pdf
format: text/html
creator: Pedro Antonio Sánchez Miguel
creator: David Sánchez Oliva
creator: Mikel Vaquero Solís
creator: J. J. Pulido
creator: Miguel Angel Tapia Serrano
subject: Evidence Based Medicine
subject: Global Health
subject: Kinesiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.8824
publisher: PeerJ Inc.
rights: © 2020 Sánchez Miguel et al.
abstract: Active commuting to and from school (ACS) has been recognized as a potential tool to improve physical fitness. Thus, this study aims to test the relationships between the average slope in the ACS and physical fitness, as well as to verify the mediator role of fatness in the relationship between average slope and physical fitness. A total of 257 participants, 137 boys and 120 girls, from 22 schools belonged to first and second High School grades participated in this study. Based on self-reported measure and Google Earth, participants were grouped into the active commuter (number of trips was ≥5, and the time of the trip was ≥15 min), mixed commuter (number of weekly trips was <5, and the time spent on the trip was <15 min) and passive commuter groups (those who reported traveling regularly by car, motorcycle, or bus). Specifically, in the active commuter group, a positive association between the average slope in the ACS with fatness was found, which in turn was positively related to strength lower limbs and cardiorrespiratory fitness. The average slope was not significantly associated with physical fitness indicators. Furtheremore, fatness did not mediate the relathionship between average slope and physical fitness. This research concluded positive associations between average slope and the body fat in the ACS. The tendency of findings signal that the average slope should be taken into account along with the distance, time and frequency of the active commuting.
bibliographic citation: Sánchez Miguel et al. (2020) Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness. PeerJ 8:e8824 https://doi.org/10.7717/peerj.8824
date submitted: 2019-09-12
date accepted: 2020-02-28
issued: 2020-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sánchez Miguel
  given name: Pedro Antonio
author list: Agent
  family name: Sánchez Oliva
  given name: David
author list: Agent
  family name: Vaquero Solís
  given name: Mikel
author list: Agent
  family name: Pulido
  given name: J. J.
author list: Agent
  family name: Tapia Serrano
  given name: Miguel Angel
doi: 10.7717/peerj.8824
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-09
copyright: © 2020 Sánchez Miguel et al.
attribution name: Sánchez Miguel et al.

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