PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Postural control in girls with adolescent idiopathic scoliosis while wearing a Chêneau brace or performing active self-correction: a pilot study
items: Effects of shading on the growth and leaf photosynthetic characteristics of three forages in an apple orchard on the Loess Plateau of eastern Gansu, China
items: Comparative transcriptome analysis of panicle development under heat stress in two rice (Oryza sativa L.) cultivars differing in heat tolerance
items: Mapping research trends of retinal vein occlusion from 2009 to 2018: a bibliometric analysis
items: Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza
items: Tribe reassessment of the subhimalayan leafhopper genus Pseudosubhimalus (Homoptera: Cicadellidae) based on molecular phylogeny
items: Cyclodipeptides from Pseudomonas aeruginosa modulate the maize (Zea mays L.) root system and promote S6 ribosomal protein kinase activation
items: Early Agenian rhinocerotids from Wischberg (Canton Bern, Switzerland) and clarification of the systematics of the genus Diaceratherium
items: Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents
items: The effect of modulating the quantity of enzymes in a model ethanol pathway on metabolic flux in Synechocystis sp. PCC 6803

Postural control in girls with adolescent idiopathic scoliosis while wearing a Chêneau brace or performing active self-correction: a pilot study
type: item
type: AcademicArticle
description: Background It is known that adolescent idiopathic scoliosis (AIS) is often accompanied by balance deficits. This reciprocal relationship must be taken into account when prescribing new therapeutic modalities because these may differently affect postural control, interacting with therapy and influencing its results. Objective The purpose was to compare postural control in girls with AIS while wearing the Chêneau brace (BRA) or performing active self-correction (ASC) with their postural control in a quiet comfortable stance. Methods Nine subjects were evaluated on a force plate in three series of two 20-s quiet standing trials with eyes open or closed; three blocks were randomly arranged: normal quiet stance (QST), quiet stance with BRA, and quiet stance with ASC. On the basis of centre-of-pressure (COP) recordings, the spatial and temporal COP parameters were computed. Results and Discussion Performing ASC was associated with a significant backward excursion of the COP mean position with eyes open and closed (ES = 0.56 and 0.65, respectively; p < 0.05). This excursion was accompanied by an increase in the COP fractal dimension (ES = 1.05 and 0.98; p < 0.05) and frequency (ES = 0.78; p = 0.10 and ES = 1.14; p < 0.05) in the mediolateral (ML) plane. Finally, both therapeutic modalities decreased COP sample entropy with eyes closed in the anteroposterior (AP) plane. Wearing BRA resulted in ES = 1.45 (p < 0.05) while performing ASC in ES = 0.76 (p = 0.13). Conclusion The observed changes in the fractal dimension (complexity) and frequency caused by ASC account for better adaptability of patients to environmental demands and for their adequate resources of available postural strategies in the ML plane. These changes in sway structure were accompanied by a significant (around 25 mm) backward excursion of the mean COP position. However, this improvement was achieved at the cost of lower automaticity, i.e. higher attentional involvement in postural control in the AP plane. W…
format: application/pdf
format: text/html
creator: Elżbieta Piątek
creator: Michał Kuczyński
creator: Bożena Ostrowska
subject: Bioengineering
subject: Kinesiology
subject: Pediatrics
description: doi:10.7717/peerj.7513
publisher: PeerJ Inc.
rights: © 2019 Piątek et al.
abstract: Background It is known that adolescent idiopathic scoliosis (AIS) is often accompanied by balance deficits. This reciprocal relationship must be taken into account when prescribing new therapeutic modalities because these may differently affect postural control, interacting with therapy and influencing its results. Objective The purpose was to compare postural control in girls with AIS while wearing the Chêneau brace (BRA) or performing active self-correction (ASC) with their postural control in a quiet comfortable stance. Methods Nine subjects were evaluated on a force plate in three series of two 20-s quiet standing trials with eyes open or closed; three blocks were randomly arranged: normal quiet stance (QST), quiet stance with BRA, and quiet stance with ASC. On the basis of centre-of-pressure (COP) recordings, the spatial and temporal COP parameters were computed. Results and Discussion Performing ASC was associated with a significant backward excursion of the COP mean position with eyes open and closed (ES = 0.56 and 0.65, respectively; p < 0.05). This excursion was accompanied by an increase in the COP fractal dimension (ES = 1.05 and 0.98; p < 0.05) and frequency (ES = 0.78; p = 0.10 and ES = 1.14; p < 0.05) in the mediolateral (ML) plane. Finally, both therapeutic modalities decreased COP sample entropy with eyes closed in the anteroposterior (AP) plane. Wearing BRA resulted in ES = 1.45 (p < 0.05) while performing ASC in ES = 0.76 (p = 0.13). Conclusion The observed changes in the fractal dimension (complexity) and frequency caused by ASC account for better adaptability of patients to environmental demands and for their adequate resources of available postural strategies in the ML plane. These changes in sway structure were accompanied by a significant (around 25 mm) backward excursion of the mean COP position. However, this improvement was achieved at the cost of lower automaticity, i.e. higher attentional involvement in postural control in the AP plane. W…
bibliographic citation: Piątek et al. (2019) Postural control in girls with adolescent idiopathic scoliosis while wearing a Chêneau brace or performing active self-correction: a pilot study. PeerJ 7:e7513 https://doi.org/10.7717/peerj.7513
date submitted: 2019-03-27
date accepted: 2019-07-18
issued: 2019-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Piątek
  given name: Elżbieta
author list: Agent
  family name: Kuczyński
  given name: Michał
author list: Agent
  family name: Ostrowska
  given name: Bożena
doi: 10.7717/peerj.7513
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-29
copyright: ©2019 Piątek et al.
attribution name: Piątek et al.

Effects of shading on the growth and leaf photosynthetic characteristics of three forages in an apple orchard on the Loess Plateau of eastern Gansu, China
type: item
type: AcademicArticle
description: Background Inclusion of forage into the orchard is of great help in promoting the use efficiency of resources, while shading from trees restricts forage growth and production in the Loess Plateau of China. This study was aimed to investigate how tree shading affected leaf trait, photosynthetic gas exchange and chlorophyll feature of forages under the tree in the orchard-forage system. Methods The shading treatments were set as partially cutting branches (reduced shading), normal fruit tree shading (normal shading) and normal tree shading plus sun-shading net (enhanced shading) in an apple orchard. Leaf trait, photosynthesis, chlorophyll component and fluorescence related parameters were measured with lucerne (Medicago sativa), white clover (Trifolium repens) and cocksfoot (Dactylis glomerata) which were sown under apple trees. Results Shading imposed significant impacts on the growth and leaf photosynthetic characteristics, while there were differences among species. Enhanced shading decreased leaf thickness, leaf dry matter content (LDMC) and leaf mass per unit area (LMA). Biomass accumulation decreased with enhanced shading in cocksfoot, but did not change in white clover and lucerne which had much lower biomass accumulation than cocksfoot. Enhanced shading reduced net photosynthetic rate (Pn) of white clover and lucerne, but rarely affected cocksfoot, while it decreased instantaneous water use efficiency (WUEi) of cocksfoot but had few effects on the other forages. Enhanced shading reduced leaf dark respiration rate (Rd), light compensation point (LCP) and maximum assimilation rate. The Rd and LCP of cocksfoot were much lower than those of white clover and lucerne. Chlorophyll contents and chlorophyll a/b changed little with shading. Cocksfoot had the highest contents but lowest ratio. Maximum photochemical rate of photosystem II increased and non-photochemical quenching decreased with enhanced shading in cocksfoot, while did not change in the other forages. Disc…
format: application/pdf
format: text/html
creator: Mei Yang
creator: Minguo Liu
creator: Jiaoyun Lu
creator: Huimin Yang
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.7594
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Background Inclusion of forage into the orchard is of great help in promoting the use efficiency of resources, while shading from trees restricts forage growth and production in the Loess Plateau of China. This study was aimed to investigate how tree shading affected leaf trait, photosynthetic gas exchange and chlorophyll feature of forages under the tree in the orchard-forage system. Methods The shading treatments were set as partially cutting branches (reduced shading), normal fruit tree shading (normal shading) and normal tree shading plus sun-shading net (enhanced shading) in an apple orchard. Leaf trait, photosynthesis, chlorophyll component and fluorescence related parameters were measured with lucerne (Medicago sativa), white clover (Trifolium repens) and cocksfoot (Dactylis glomerata) which were sown under apple trees. Results Shading imposed significant impacts on the growth and leaf photosynthetic characteristics, while there were differences among species. Enhanced shading decreased leaf thickness, leaf dry matter content (LDMC) and leaf mass per unit area (LMA). Biomass accumulation decreased with enhanced shading in cocksfoot, but did not change in white clover and lucerne which had much lower biomass accumulation than cocksfoot. Enhanced shading reduced net photosynthetic rate (Pn) of white clover and lucerne, but rarely affected cocksfoot, while it decreased instantaneous water use efficiency (WUEi) of cocksfoot but had few effects on the other forages. Enhanced shading reduced leaf dark respiration rate (Rd), light compensation point (LCP) and maximum assimilation rate. The Rd and LCP of cocksfoot were much lower than those of white clover and lucerne. Chlorophyll contents and chlorophyll a/b changed little with shading. Cocksfoot had the highest contents but lowest ratio. Maximum photochemical rate of photosystem II increased and non-photochemical quenching decreased with enhanced shading in cocksfoot, while did not change in the other forages. Disc…
bibliographic citation: Yang et al. (2019) Effects of shading on the growth and leaf photosynthetic characteristics of three forages in an apple orchard on the Loess Plateau of eastern Gansu, China. PeerJ 7:e7594 https://doi.org/10.7717/peerj.7594
date submitted: 2019-05-16
date accepted: 2019-07-31
issued: 2019-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Mei
author list: Agent
  family name: Liu
  given name: Minguo
author list: Agent
  family name: Lu
  given name: Jiaoyun
author list: Agent
  family name: Yang
  given name: Huimin
doi: 10.7717/peerj.7594
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-29
copyright: ©2019 Yang et al.
attribution name: Yang et al.

Comparative transcriptome analysis of panicle development under heat stress in two rice (Oryza sativa L.) cultivars differing in heat tolerance
type: item
type: AcademicArticle
description: Heat stress inhibits rice panicle development and reduces the spikelet number per panicle. This study investigated the mechanism involved in heat-induced damage to panicle development and spikelet formation in rice cultivars that differ in heat tolerance. Transcriptome data from developing panicles grown at 40 °C or 32 °C were compared for two rice cultivars: heat-tolerant Huanghuazhan and heat-susceptible IR36. Of the differentially expressed genes (DEGs), 4,070 heat stress-responsive genes were identified, including 1,688 heat-resistant-cultivar-related genes (RHR), 707 heat-susceptible-cultivar-related genes (SHR), and 1,675 common heat stress-responsive genes (CHR). A Gene Ontology (GO) analysis showed that the DEGs in the RHR category were significantly enriched in 54 gene ontology terms, some of which improved heat tolerance, including those in the WRKY, HD-ZIP, ERF, and MADS transcription factor families. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs in the RHR and SHR categories were enriched in 15 and 11 significant metabolic pathways, respectively. Improved signal transduction capabilities of endogenous hormones under high temperature seemed to promote heat tolerance, while impaired starch and sucrose metabolism under high temperature might have inhibited young panicle development. Our transcriptome analysis provides insights into the different molecular mechanisms of heat stress tolerance in developing rice.
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creator: Yaliang Wang
creator: Yikai Zhang
creator: Qiang Zhang
creator: Yongtao Cui
creator: Jing Xiang
creator: Huizhe Chen
creator: Guohui Hu
creator: Yanhua Chen
creator: Xiaodan Wang
creator: Defeng Zhu
creator: Yuping Zhang
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.7595
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Heat stress inhibits rice panicle development and reduces the spikelet number per panicle. This study investigated the mechanism involved in heat-induced damage to panicle development and spikelet formation in rice cultivars that differ in heat tolerance. Transcriptome data from developing panicles grown at 40 °C or 32 °C were compared for two rice cultivars: heat-tolerant Huanghuazhan and heat-susceptible IR36. Of the differentially expressed genes (DEGs), 4,070 heat stress-responsive genes were identified, including 1,688 heat-resistant-cultivar-related genes (RHR), 707 heat-susceptible-cultivar-related genes (SHR), and 1,675 common heat stress-responsive genes (CHR). A Gene Ontology (GO) analysis showed that the DEGs in the RHR category were significantly enriched in 54 gene ontology terms, some of which improved heat tolerance, including those in the WRKY, HD-ZIP, ERF, and MADS transcription factor families. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs in the RHR and SHR categories were enriched in 15 and 11 significant metabolic pathways, respectively. Improved signal transduction capabilities of endogenous hormones under high temperature seemed to promote heat tolerance, while impaired starch and sucrose metabolism under high temperature might have inhibited young panicle development. Our transcriptome analysis provides insights into the different molecular mechanisms of heat stress tolerance in developing rice.
bibliographic citation: Wang et al. (2019) Comparative transcriptome analysis of panicle development under heat stress in two rice (Oryza sativa L.) cultivars differing in heat tolerance. PeerJ 7:e7595 https://doi.org/10.7717/peerj.7595
date submitted: 2018-12-19
date accepted: 2019-07-31
issued: 2019-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yaliang
author list: Agent
  family name: Zhang
  given name: Yikai
author list: Agent
  family name: Zhang
  given name: Qiang
author list: Agent
  family name: Cui
  given name: Yongtao
author list: Agent
  family name: Xiang
  given name: Jing
author list: Agent
  family name: Chen
  given name: Huizhe
author list: Agent
  family name: Hu
  given name: Guohui
author list: Agent
  family name: Chen
  given name: Yanhua
author list: Agent
  family name: Wang
  given name: Xiaodan
author list: Agent
  family name: Zhu
  given name: Defeng
author list: Agent
  family name: Zhang
  given name: Yuping
doi: 10.7717/peerj.7595
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-29
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Mapping research trends of retinal vein occlusion from 2009 to 2018: a bibliometric analysis
type: item
type: AcademicArticle
description: Objectives To map publication trends and explore research hotspots of retinal vein occlusion (RVO) study. Methods Based on Web of Science Core Collection (WoSCC), a bibliometric analysis was carried out. The knowledge map was constructed by VOSviewer v.1.6.10 to visualize the annual publication number, the distribution of countries, international collaborations, author productivity, source journals, cited reference and keywords in this field. Results A total of 2,135 peer-reviewed papers were retrieved on RVO from 2009 to 2018. The United States ranks highest among countries with the most publications and the most active institution was Kyoto University. Noma H contributed the most publications in this field. Retina—The Journal of Retinal and Vitreous Disease was the most prolific journal in RVO research. The top cited references mainly presented anti-VEGF medications on the management of RVO. The keywords formed six clusters: (1) Risk factors and pathogenesis of RVO; (2) Metabolismof RVO; (3) Therapeutic use of corticosteroids on RVO; (4) Diagnostic methodsof RVO; (5) Management of macular edema secondary to RVO (6) Anti-VEGFtreatment of RVO. Conclusions The six major research hotspots could provide an insight into RVO research and valuable information for researchers to identify potential collaborators and partner institutions.
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format: text/html
creator: Fangkun Zhao
creator: Fengkun Du
creator: Dong Shi
creator: Wenkai Zhou
creator: Youhong Jiang
creator: Liwei Ma
subject: Bioinformatics
subject: Epidemiology
subject: Ophthalmology
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.7603
publisher: PeerJ Inc.
rights: © 2019 Zhao et al.
abstract: Objectives To map publication trends and explore research hotspots of retinal vein occlusion (RVO) study. Methods Based on Web of Science Core Collection (WoSCC), a bibliometric analysis was carried out. The knowledge map was constructed by VOSviewer v.1.6.10 to visualize the annual publication number, the distribution of countries, international collaborations, author productivity, source journals, cited reference and keywords in this field. Results A total of 2,135 peer-reviewed papers were retrieved on RVO from 2009 to 2018. The United States ranks highest among countries with the most publications and the most active institution was Kyoto University. Noma H contributed the most publications in this field. Retina—The Journal of Retinal and Vitreous Disease was the most prolific journal in RVO research. The top cited references mainly presented anti-VEGF medications on the management of RVO. The keywords formed six clusters: (1) Risk factors and pathogenesis of RVO; (2) Metabolismof RVO; (3) Therapeutic use of corticosteroids on RVO; (4) Diagnostic methodsof RVO; (5) Management of macular edema secondary to RVO (6) Anti-VEGFtreatment of RVO. Conclusions The six major research hotspots could provide an insight into RVO research and valuable information for researchers to identify potential collaborators and partner institutions.
bibliographic citation: Zhao et al. (2019) Mapping research trends of retinal vein occlusion from 2009 to 2018: a bibliometric analysis. PeerJ 7:e7603 https://doi.org/10.7717/peerj.7603
date submitted: 2019-03-16
date accepted: 2019-08-01
issued: 2019-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Fangkun
author list: Agent
  family name: Du
  given name: Fengkun
author list: Agent
  family name: Shi
  given name: Dong
author list: Agent
  family name: Zhou
  given name: Wenkai
author list: Agent
  family name: Jiang
  given name: Youhong
author list: Agent
  family name: Ma
  given name: Liwei
doi: 10.7717/peerj.7603
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-29
copyright: ©2019 Zhao et al.
attribution name: Zhao et al.

Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza
type: item
type: AcademicArticle
description: Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1–SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1–C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5′ RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza.
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format: text/html
creator: Caili Li
creator: Dongqiao Li
creator: Hong Zhou
creator: Jiang Li
creator: Shanfa Lu
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.7605
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1–SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1–C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5′ RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza.
bibliographic citation: Li et al. (2019) Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza. PeerJ 7:e7605 https://doi.org/10.7717/peerj.7605
date submitted: 2019-02-19
date accepted: 2019-08-02
issued: 2019-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Caili
author list: Agent
  family name: Li
  given name: Dongqiao
author list: Agent
  family name: Zhou
  given name: Hong
author list: Agent
  family name: Li
  given name: Jiang
author list: Agent
  family name: Lu
  given name: Shanfa
doi: 10.7717/peerj.7605
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-29
copyright: © 2019 Li et al.
attribution name: Li et al.

Tribe reassessment of the subhimalayan leafhopper genus Pseudosubhimalus (Homoptera: Cicadellidae) based on molecular phylogeny
type: item
type: AcademicArticle
description: The phylogeny of the Pseudosubhimalus were investigated using of two different data sets, including 91 taxa and 3853 aligned nucleotide positions from the histone H3, 28S rDNA (D2 & D9–10 region). The results suggest the placement of genus in the tribe Ciacadulini, as it was clustered with Cicadulini genera. Relationships between genera of the Cicadulini were strongly supported and leads placement to tribe Cicadulini from Athysanini. Along with this, genus Pseudosubhimalus Ghauri is revised, and P. trilobatus sp. nov. (Himachal Pradesh: Katrain) is added, described from Indian subcontinent and deposited to National Pusa Collection, IARI, New Delhi, with repository number RRS1.
format: application/pdf
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creator: GN Niranjana
creator: Naresh M. Meshram
creator: Pathour R. Shashank
creator: Stuti
creator: Tahseen Raza Hashmi
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.7162
publisher: PeerJ Inc.
rights: © 2019 Niranjana et al.
abstract: The phylogeny of the Pseudosubhimalus were investigated using of two different data sets, including 91 taxa and 3853 aligned nucleotide positions from the histone H3, 28S rDNA (D2 & D9–10 region). The results suggest the placement of genus in the tribe Ciacadulini, as it was clustered with Cicadulini genera. Relationships between genera of the Cicadulini were strongly supported and leads placement to tribe Cicadulini from Athysanini. Along with this, genus Pseudosubhimalus Ghauri is revised, and P. trilobatus sp. nov. (Himachal Pradesh: Katrain) is added, described from Indian subcontinent and deposited to National Pusa Collection, IARI, New Delhi, with repository number RRS1.
bibliographic citation: Niranjana et al. (2019) Tribe reassessment of the subhimalayan leafhopper genus Pseudosubhimalus (Homoptera: Cicadellidae) based on molecular phylogeny. PeerJ 7:e7162 https://doi.org/10.7717/peerj.7162
date submitted: 2019-01-24
date accepted: 2019-05-22
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niranjana
  given name: GN
author list: Agent
  family name: Meshram
  given name: Naresh M.
author list: Agent
  family name: Shashank
  given name: Pathour R.
author list: Agent
  family name: Stuti
author list: Agent
  family name: Hashmi
  given name: Tahseen Raza
doi: 10.7717/peerj.7162
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Niranjana et al.
attribution name: Niranjana et al.

Cyclodipeptides from Pseudomonas aeruginosa modulate the maize (Zea mays L.) root system and promote S6 ribosomal protein kinase activation
type: item
type: AcademicArticle
description: Background Pseudomonas aeruginosa is an opportunistic and pathogenic bacterium with the ability to produce cyclodipeptides (CDPs), which belong to a large family of molecules with important biological activities. Excessive amounts of CDPs produced by Pseudomonas strains can activate an auxin response in Arabidopsis thaliana and promote plant growth. Target of rapamycin (TOR) is an evolutionarily conserved eukaryotic protein kinase that coordinates cell growth and metabolic processes in response to environmental and nutritional signals. Target of rapamycin kinase phosphorylates various substrates, of which S6 ribosomal protein kinase (S6K) is particularly well known. The PI3K/Akt/mTOR/S6K signaling pathway has been studied extensively in mammals because of its association with fundamental biological processes including cell differentiation. However, evidences suggest that this pathway also has specific and conserved functions in plants and may thus be conserved, as are several of its components like TOR complex 1 and S6K proteins. In plants, TOR-S6K signaling has been shown to be modulated in response to plant growth promoters or stressors. Methods In this study, we evaluated the effects of P. aeruginosa CDPs on the growth and root development of maize plants (Zea mays L.) by adding different CDPs concentrations on culture plant media, as well as the effect on the phosphorylation of the maize S6K protein (ZmS6K) by protein electrophoresis and western blot. Results Our results showed that P. aeruginosa CDPs promoted maize growth and development, including modifications in the root system architecture, correlating with the increased ZmS6K phosphorylation and changes induced in electrophoretic mobility, suggesting post-translational modifications on ZmS6K. These findings suggest that the plant growth-promoting effect of the Pseudomonas genus, associated with the CDPs production, involves the TOR/S6K signaling pathway as a mechanism of plant growth and root development i…
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format: text/html
creator: Iván Corona-Sánchez
creator: Cesar Arturo Peña-Uribe
creator: Omar González-López
creator: Javier Villegas
creator: Jesus Campos-Garcia
creator: Homero Reyes de la Cruz
subject: Agricultural Science
subject: Biochemistry
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.7494
publisher: PeerJ Inc.
rights: © 2019 Corona-Sánchez et al.
abstract: Background Pseudomonas aeruginosa is an opportunistic and pathogenic bacterium with the ability to produce cyclodipeptides (CDPs), which belong to a large family of molecules with important biological activities. Excessive amounts of CDPs produced by Pseudomonas strains can activate an auxin response in Arabidopsis thaliana and promote plant growth. Target of rapamycin (TOR) is an evolutionarily conserved eukaryotic protein kinase that coordinates cell growth and metabolic processes in response to environmental and nutritional signals. Target of rapamycin kinase phosphorylates various substrates, of which S6 ribosomal protein kinase (S6K) is particularly well known. The PI3K/Akt/mTOR/S6K signaling pathway has been studied extensively in mammals because of its association with fundamental biological processes including cell differentiation. However, evidences suggest that this pathway also has specific and conserved functions in plants and may thus be conserved, as are several of its components like TOR complex 1 and S6K proteins. In plants, TOR-S6K signaling has been shown to be modulated in response to plant growth promoters or stressors. Methods In this study, we evaluated the effects of P. aeruginosa CDPs on the growth and root development of maize plants (Zea mays L.) by adding different CDPs concentrations on culture plant media, as well as the effect on the phosphorylation of the maize S6K protein (ZmS6K) by protein electrophoresis and western blot. Results Our results showed that P. aeruginosa CDPs promoted maize growth and development, including modifications in the root system architecture, correlating with the increased ZmS6K phosphorylation and changes induced in electrophoretic mobility, suggesting post-translational modifications on ZmS6K. These findings suggest that the plant growth-promoting effect of the Pseudomonas genus, associated with the CDPs production, involves the TOR/S6K signaling pathway as a mechanism of plant growth and root development i…
bibliographic citation: Corona-Sánchez et al. (2019) Cyclodipeptides from Pseudomonas aeruginosa modulate the maize (Zea mays L.) root system and promote S6 ribosomal protein kinase activation. PeerJ 7:e7494 https://doi.org/10.7717/peerj.7494
date submitted: 2019-04-10
date accepted: 2019-07-16
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Corona-Sánchez
  given name: Iván
author list: Agent
  family name: Peña-Uribe
  given name: Cesar Arturo
author list: Agent
  family name: González-López
  given name: Omar
author list: Agent
  family name: Villegas
  given name: Javier
author list: Agent
  family name: Campos-Garcia
  given name: Jesus
author list: Agent
  family name: Reyes de la Cruz
  given name: Homero
doi: 10.7717/peerj.7494
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: © 2019 Corona-Sánchez et al.
attribution name: Corona-Sánchez et al.

Early Agenian rhinocerotids from Wischberg (Canton Bern, Switzerland) and clarification of the systematics of the genus Diaceratherium
type: item
type: AcademicArticle
description: Background Wischberg is a Swiss locality in Bern Canton which has yielded numerous vertebrates remains from the earliest Miocene (= MN1). It has a very rich faunal diversity, one of the richest in Switzerland for this age. Among all the mammals reported in the original faunal list 70 years ago, three rhinocerotid species were identified. The material consists of two fragmentary skulls, cranial fragments, several mandibles, teeth and postcranial bones, in a rather good state of preservation. Results After reexamination of the material from this locality (curated in three different Swiss museums) and comparison with holotype specimens, we show that all rhinocerotid specimens from Wischberg can be referred to two species only. Most of the material can be attributed to the large-sized teleoceratine Diaceratherium lemanense, while only a few specimens, including a skull and mandible, belong to the much smaller sized Pleuroceros pleuroceros. We describe and illustrate for the first time most of these fossil remains. However, the systematics of the genus Diaceratherium is currently controversial, and based on our new observations we consider seven species as valid, though a large-scale phylogenetic study should be done in the future to resolve it. The rhinocerotid association found in Wischberg is nonetheless typical of the MN1 biozone, which results from a faunal renewal occurring just before the end of the Oligocene.
format: application/pdf
format: text/html
creator: Claire Jame
creator: Jérémy Tissier
creator: Olivier Maridet
creator: Damien Becker
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.7517
publisher: PeerJ Inc.
rights: © 2019 Jame et al.
abstract: Background Wischberg is a Swiss locality in Bern Canton which has yielded numerous vertebrates remains from the earliest Miocene (= MN1). It has a very rich faunal diversity, one of the richest in Switzerland for this age. Among all the mammals reported in the original faunal list 70 years ago, three rhinocerotid species were identified. The material consists of two fragmentary skulls, cranial fragments, several mandibles, teeth and postcranial bones, in a rather good state of preservation. Results After reexamination of the material from this locality (curated in three different Swiss museums) and comparison with holotype specimens, we show that all rhinocerotid specimens from Wischberg can be referred to two species only. Most of the material can be attributed to the large-sized teleoceratine Diaceratherium lemanense, while only a few specimens, including a skull and mandible, belong to the much smaller sized Pleuroceros pleuroceros. We describe and illustrate for the first time most of these fossil remains. However, the systematics of the genus Diaceratherium is currently controversial, and based on our new observations we consider seven species as valid, though a large-scale phylogenetic study should be done in the future to resolve it. The rhinocerotid association found in Wischberg is nonetheless typical of the MN1 biozone, which results from a faunal renewal occurring just before the end of the Oligocene.
bibliographic citation: Jame et al. (2019) Early Agenian rhinocerotids from Wischberg (Canton Bern, Switzerland) and clarification of the systematics of the genus Diaceratherium. PeerJ 7:e7517 https://doi.org/10.7717/peerj.7517
date submitted: 2019-05-16
date accepted: 2019-07-19
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jame
  given name: Claire
author list: Agent
  family name: Tissier
  given name: Jérémy
author list: Agent
  family name: Maridet
  given name: Olivier
author list: Agent
  family name: Becker
  given name: Damien
doi: 10.7717/peerj.7517
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: © 2019 Jame et al.
attribution name: Jame et al.

Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents
type: item
type: AcademicArticle
description: In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ∼70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents.
format: application/pdf
format: text/html
creator: Jianzhou Qu
creator: Shutu Xu
creator: Xiaokang Tian
creator: Ting Li
creator: Licheng Wang
creator: Yuyue Zhong
creator: Jiquan Xue
creator: Dongwei Guo
subject: Developmental Biology
subject: Plant Science
description: doi:10.7717/peerj.7528
publisher: PeerJ Inc.
rights: © 2019 Qu et al.
abstract: In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ∼70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents.
bibliographic citation: Qu et al. (2019) Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents. PeerJ 7:e7528 https://doi.org/10.7717/peerj.7528
date submitted: 2019-03-08
date accepted: 2019-07-22
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qu
  given name: Jianzhou
author list: Agent
  family name: Xu
  given name: Shutu
author list: Agent
  family name: Tian
  given name: Xiaokang
author list: Agent
  family name: Li
  given name: Ting
author list: Agent
  family name: Wang
  given name: Licheng
author list: Agent
  family name: Zhong
  given name: Yuyue
author list: Agent
  family name: Xue
  given name: Jiquan
author list: Agent
  family name: Guo
  given name: Dongwei
doi: 10.7717/peerj.7528
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Qu et al.
attribution name: Qu et al.

The effect of modulating the quantity of enzymes in a model ethanol pathway on metabolic flux in Synechocystis sp. PCC 6803
type: item
type: AcademicArticle
description: Synthetic metabolism allows new metabolic capabilities to be introduced into strains for biotechnology applications. Such engineered metabolic pathways are unlikely to function optimally as initially designed and native metabolism may not efficiently support the introduced pathway without further intervention. To develop our understanding of optimal metabolic engineering strategies, a two-enzyme ethanol pathway consisting of pyruvate decarboxylase and acetaldehyde reductase was introduced into Synechocystis sp. PCC 6803. We characteriseda new set of ribosome binding site sequences in Synechocystis sp. PCC 6803 providing a range of translation strengths for different genes under test. The effect of ribosome-bindingsite sequence, operon design and modifications to native metabolism on pathway flux was analysed by HPLC. The accumulation of all introduced proteins was also quantified using selected reaction monitoring mass spectrometry. Pathway productivity was more strongly dependent on the accumulation of pyruvate decarboxylase than acetaldehyde reductase. In fact, abolishment of reductase over-expression resulted in the greatest ethanol productivity, most likely because strains harbouringsingle-gene constructs accumulated more pyruvate decarboxylase than strains carrying any of the multi-gene constructs. Overall, several lessons were learned. Firstly, the expression level of the first gene in anyoperon influenced the expression level of subsequent genes, demonstrating that translational coupling can also occur in cyanobacteria. Longer operons resulted in lower protein abundance for proximally-encoded cistrons. And, implementation of metabolic engineering strategies that have previously been shown to enhance the growth or yield of pyruvate dependent products, through co-expression with pyruvate kinase and/or fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase, indicated that other factors had greater control over growth and metabolic flux under the tested con…
format: application/pdf
format: text/html
creator: Paulina Bartasun
creator: Nicole Prandi
creator: Marko Storch
creator: Yarin Aknin
creator: Mark Bennett
creator: Arianna Palma
creator: Geoff Baldwin
creator: Yumiko Sakuragi
creator: Patrik R. Jones
creator: John Rowland
subject: Biotechnology
subject: Synthetic Biology
description: doi:10.7717/peerj.7529
publisher: PeerJ Inc.
rights: © 2019 Bartasun et al.
abstract: Synthetic metabolism allows new metabolic capabilities to be introduced into strains for biotechnology applications. Such engineered metabolic pathways are unlikely to function optimally as initially designed and native metabolism may not efficiently support the introduced pathway without further intervention. To develop our understanding of optimal metabolic engineering strategies, a two-enzyme ethanol pathway consisting of pyruvate decarboxylase and acetaldehyde reductase was introduced into Synechocystis sp. PCC 6803. We characteriseda new set of ribosome binding site sequences in Synechocystis sp. PCC 6803 providing a range of translation strengths for different genes under test. The effect of ribosome-bindingsite sequence, operon design and modifications to native metabolism on pathway flux was analysed by HPLC. The accumulation of all introduced proteins was also quantified using selected reaction monitoring mass spectrometry. Pathway productivity was more strongly dependent on the accumulation of pyruvate decarboxylase than acetaldehyde reductase. In fact, abolishment of reductase over-expression resulted in the greatest ethanol productivity, most likely because strains harbouringsingle-gene constructs accumulated more pyruvate decarboxylase than strains carrying any of the multi-gene constructs. Overall, several lessons were learned. Firstly, the expression level of the first gene in anyoperon influenced the expression level of subsequent genes, demonstrating that translational coupling can also occur in cyanobacteria. Longer operons resulted in lower protein abundance for proximally-encoded cistrons. And, implementation of metabolic engineering strategies that have previously been shown to enhance the growth or yield of pyruvate dependent products, through co-expression with pyruvate kinase and/or fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase, indicated that other factors had greater control over growth and metabolic flux under the tested con…
bibliographic citation: Bartasun et al. (2019) The effect of modulating the quantity of enzymes in a model ethanol pathway on metabolic flux in Synechocystis sp. PCC 6803. PeerJ 7:e7529 https://doi.org/10.7717/peerj.7529
date submitted: 2019-04-10
date accepted: 2019-07-22
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bartasun
  given name: Paulina
author list: Agent
  family name: Prandi
  given name: Nicole
author list: Agent
  family name: Storch
  given name: Marko
author list: Agent
  family name: Aknin
  given name: Yarin
author list: Agent
  family name: Bennett
  given name: Mark
author list: Agent
  family name: Palma
  given name: Arianna
author list: Agent
  family name: Baldwin
  given name: Geoff
author list: Agent
  family name: Sakuragi
  given name: Yumiko
author list: Agent
  family name: Jones
  given name: Patrik R.
author list: Agent
  family name: Rowland
  given name: John
doi: 10.7717/peerj.7529
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Bartasun et al.
attribution name: Bartasun et al.

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