PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Hypoxia and metabolic inhibitors alter the intracellular ATP:ADP ratio and membrane potential in human coronary artery smooth muscle cells
items: Exogenous Fe2+ alleviated the toxicity of CuO nanoparticles on Pseudomonas tolaasii Y-11 under different nitrogen sources
items: Effects of rhodioloside on the neurological functions of rats with total cerebral ischemia/reperfusion and cone neuron injury in the hippocampal CA1 region
items: The land flatworm Amaga expatria (Geoplanidae) in Guadeloupe and Martinique: new reports and molecular characterization including complete mitogenome
items: Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats
items: Loading history changes the morphology and compressive force-induced expression of receptor activator of nuclear factor kappa B ligand/osteoprotegerin in MLO-Y4 osteocytes
items: MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
items: Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans
items: The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species
items: Foraging efficiency, social status and body condition in group-living horses and ponies

Hypoxia and metabolic inhibitors alter the intracellular ATP:ADP ratio and membrane potential in human coronary artery smooth muscle cells
type: item
type: AcademicArticle
description: ATP-sensitive potassium (KATP) channels couple cellular metabolism to excitability, making them ideal candidate sensors for hypoxic vasodilation. However, it is still unknown whether cellular nucleotide levels are affected sufficiently to activate vascular KATP channels during hypoxia. To address this fundamental issue, we measured changes in the intracellular ATP:ADP ratio using the biosensors Perceval/PercevalHR, and membrane potential using the fluorescent probe DiBAC4(3) in human coronary artery smooth muscle cells (HCASMCs). ATP:ADP ratio was significantly reduced by exposure to hypoxia. Application of metabolic inhibitors for oxidative phosphorylation also reduced ATP:ADP ratio. Hyperpolarization caused by inhibiting oxidative phosphorylation was blocked by either 10 µM glibenclamide or 60 mM K+. Hyperpolarization caused by hypoxia was abolished by 60 mM K+ but not by individual K+ channel inhibitors. Taken together, these results suggest hypoxia causes hyperpolarization in part by modulating K+ channels in SMCs.
format: application/pdf
format: text/html
creator: Mingming Yang
creator: Caroline Dart
creator: Tomoko Kamishima
creator: John M. Quayle
subject: Cell Biology
subject: Molecular Biology
subject: Anatomy and Physiology
subject: Cardiology
description: doi:10.7717/peerj.10344
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: ATP-sensitive potassium (KATP) channels couple cellular metabolism to excitability, making them ideal candidate sensors for hypoxic vasodilation. However, it is still unknown whether cellular nucleotide levels are affected sufficiently to activate vascular KATP channels during hypoxia. To address this fundamental issue, we measured changes in the intracellular ATP:ADP ratio using the biosensors Perceval/PercevalHR, and membrane potential using the fluorescent probe DiBAC4(3) in human coronary artery smooth muscle cells (HCASMCs). ATP:ADP ratio was significantly reduced by exposure to hypoxia. Application of metabolic inhibitors for oxidative phosphorylation also reduced ATP:ADP ratio. Hyperpolarization caused by inhibiting oxidative phosphorylation was blocked by either 10 µM glibenclamide or 60 mM K+. Hyperpolarization caused by hypoxia was abolished by 60 mM K+ but not by individual K+ channel inhibitors. Taken together, these results suggest hypoxia causes hyperpolarization in part by modulating K+ channels in SMCs.
bibliographic citation: Yang et al. (2020) Hypoxia and metabolic inhibitors alter the intracellular ATP:ADP ratio and membrane potential in human coronary artery smooth muscle cells. PeerJ 8:e10344 https://doi.org/10.7717/peerj.10344
date submitted: 2020-06-05
date accepted: 2020-10-20
issued: 2020-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Mingming
author list: Agent
  family name: Dart
  given name: Caroline
author list: Agent
  family name: Kamishima
  given name: Tomoko
author list: Agent
  family name: Quayle
  given name: John M.
doi: 10.7717/peerj.10344
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-10
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Exogenous Fe2+ alleviated the toxicity of CuO nanoparticles on Pseudomonas tolaasii Y-11 under different nitrogen sources
type: item
type: AcademicArticle
description: Extensive use of CuO nanoparticles (CuO-NPs ) inevitably leads to their accumulation in wastewater and toxicity to microorganisms that effectively treat nitrogen pollution. Due to the effects of different mediums, the sources of CuO-NPs-induced toxicity to microorganisms and methods to mitigating the toxicity are still unclear. In this study, CuO-NPs were found to impact the nitrate reduction of Pseudomonas tolaasii Y-11 mainly through the action of NPs themselves while inhibiting the ammonium transformation of strain Y-11 through releasing Cu2+. As the content of CuO-NPs increased from 0 to 20 mg/L, the removal efficiency of NO3− and NH4+ decreased from 42.29% and 29.83% to 2.05% and 2.33%, respectively. Exogenous Fe2+ significantly promoted the aggregation of CuO-NPs, reduced the possibility of contact with bacteria, and slowed down the damage of CuO-NPs to strain Y-11. When 0.01 mol/L Fe2+ was added to 0, 1, 5, 10 and 20 mg/L CuO-NPs treatment, the removal efficiencies of NO3- were 69.77%, 88.93%, 80.51%, 36.17% and 2.47%, respectively; the removal efficiencies of NH4+ were 55.95%, 96.71%, 38.11%, 20.71% and 7.43%, respectively. This study provides a method for mitigating the toxicity of CuO-NPs on functional microorganisms.
format: application/pdf
format: text/html
creator: Yuran Yang
creator: Can Zhang
creator: Xuejiao Huang
creator: Xuwei Gui
creator: Yifang Luo
creator: Zhenlun Li
subject: Microbiology
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.10351
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Extensive use of CuO nanoparticles (CuO-NPs ) inevitably leads to their accumulation in wastewater and toxicity to microorganisms that effectively treat nitrogen pollution. Due to the effects of different mediums, the sources of CuO-NPs-induced toxicity to microorganisms and methods to mitigating the toxicity are still unclear. In this study, CuO-NPs were found to impact the nitrate reduction of Pseudomonas tolaasii Y-11 mainly through the action of NPs themselves while inhibiting the ammonium transformation of strain Y-11 through releasing Cu2+. As the content of CuO-NPs increased from 0 to 20 mg/L, the removal efficiency of NO3− and NH4+ decreased from 42.29% and 29.83% to 2.05% and 2.33%, respectively. Exogenous Fe2+ significantly promoted the aggregation of CuO-NPs, reduced the possibility of contact with bacteria, and slowed down the damage of CuO-NPs to strain Y-11. When 0.01 mol/L Fe2+ was added to 0, 1, 5, 10 and 20 mg/L CuO-NPs treatment, the removal efficiencies of NO3- were 69.77%, 88.93%, 80.51%, 36.17% and 2.47%, respectively; the removal efficiencies of NH4+ were 55.95%, 96.71%, 38.11%, 20.71% and 7.43%, respectively. This study provides a method for mitigating the toxicity of CuO-NPs on functional microorganisms.
bibliographic citation: Yang et al. (2020) Exogenous Fe2+ alleviated the toxicity of CuO nanoparticles on Pseudomonas tolaasii Y-11 under different nitrogen sources. PeerJ 8:e10351 https://doi.org/10.7717/peerj.10351
date submitted: 2020-07-10
date accepted: 2020-10-21
issued: 2020-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yuran
author list: Agent
  family name: Zhang
  given name: Can
author list: Agent
  family name: Huang
  given name: Xuejiao
author list: Agent
  family name: Gui
  given name: Xuwei
author list: Agent
  family name: Luo
  given name: Yifang
author list: Agent
  family name: Li
  given name: Zhenlun
doi: 10.7717/peerj.10351
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-10
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Effects of rhodioloside on the neurological functions of rats with total cerebral ischemia/reperfusion and cone neuron injury in the hippocampal CA1 region
type: item
type: AcademicArticle
description: Rhodioloside, the main effective constituent of Rhodiola rosea, demonstrates antiaging and antioxidative stress functions and inhibits calcium overloading in cells. These functions imply that rhodioloside may exert protective effects on hippocampal neurons after total cerebral ischemia/reperfusion injury. In this study, male Wistar rat models of total cerebral ischemia were constructed and randomly divided into four groups: sham-operation, ischemia/reperfusion, low-dosage, and high-dosage groups. The result showed that rhodioloside treatment reduced the apoptosis rates of hippocampal neurons and the histological grades of cone cells in the hippocampal CA1 region, but neuronal density was significantly increased. Besides, the protein expressions of Bcl-2/Bax and p53 were measured and found Bcl-2/Bax was increased and p53 protein level was reduced. Therefore, rhodioloside might have protective effects on rats with ischemia/reperfusion brain injury.
format: application/pdf
format: text/html
creator: Yue Zhang
creator: Xinqing Guo
creator: Guohua Wang
creator: Jidan Liu
creator: Peiyu Liang
creator: Huan Wang
creator: Chunyan Zhu
creator: Qiong Wu
subject: Neuroscience
subject: Neurology
subject: Public Health
description: doi:10.7717/peerj.10056
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Rhodioloside, the main effective constituent of Rhodiola rosea, demonstrates antiaging and antioxidative stress functions and inhibits calcium overloading in cells. These functions imply that rhodioloside may exert protective effects on hippocampal neurons after total cerebral ischemia/reperfusion injury. In this study, male Wistar rat models of total cerebral ischemia were constructed and randomly divided into four groups: sham-operation, ischemia/reperfusion, low-dosage, and high-dosage groups. The result showed that rhodioloside treatment reduced the apoptosis rates of hippocampal neurons and the histological grades of cone cells in the hippocampal CA1 region, but neuronal density was significantly increased. Besides, the protein expressions of Bcl-2/Bax and p53 were measured and found Bcl-2/Bax was increased and p53 protein level was reduced. Therefore, rhodioloside might have protective effects on rats with ischemia/reperfusion brain injury.
bibliographic citation: Zhang et al. (2020) Effects of rhodioloside on the neurological functions of rats with total cerebral ischemia/reperfusion and cone neuron injury in the hippocampal CA1 region. PeerJ 8:e10056 https://doi.org/10.7717/peerj.10056
date submitted: 2020-05-11
date accepted: 2020-09-07
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yue
author list: Agent
  family name: Guo
  given name: Xinqing
author list: Agent
  family name: Wang
  given name: Guohua
author list: Agent
  family name: Liu
  given name: Jidan
author list: Agent
  family name: Liang
  given name: Peiyu
author list: Agent
  family name: Wang
  given name: Huan
author list: Agent
  family name: Zhu
  given name: Chunyan
author list: Agent
  family name: Wu
  given name: Qiong
doi: 10.7717/peerj.10056
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

The land flatworm Amaga expatria (Geoplanidae) in Guadeloupe and Martinique: new reports and molecular characterization including complete mitogenome
type: item
type: AcademicArticle
description: Background The land flatworm Amaga expatria Jones & Sterrer, 2005 (Geoplanidae) was described from two specimens collected in Bermuda in 1963 and 1988 and not recorded since. Methods On the basis of a citizen science project, we received observations in the field, photographs and specimens from non-professionals and local scientists in Martinique and Guadeloupe. We barcoded (COI) specimens from both islands and studied the histology of the reproductive organs of one specimen. Based on Next Generation Sequencing, we obtained the complete mitogenome of A. expatria and some information on its prey from contaminating DNA. Results We add records from 2006 to 2019 in two French islands of the Caribbean arc, Guadeloupe (six records) and Martinique (14 records), based on photographs obtained from citizen science and specimens examined. A specimen from Martinique was studied for histology of the copulatory organs and barcoded for the COI gene; its anatomy was similar to the holotype, therefore confirming species identification. The COI gene was identical for several specimens from Martinique and Guadeloupe and differed from the closest species by more than 10%; molecular characterisation of the species is thus possible by standard molecular barcoding techniques. The mitogenome is 14,962 bp in length and contains 12 protein coding genes, two rRNA genes and 22 tRNA genes; for two protein genes it was not possible to determine the start codon. The mitogenome was compared with the few available mitogenomes from geoplanids and the most similar was Obama nungara, a species from South America. An analysis of contaminating DNA in the digestive system suggests that A. expatria preys on terrestrial molluscs, and citizen science observations in the field suggest that prey include molluscs and earthworms; the species thus could be a threat to biodiversity of soil animals in the Caribbean.
format: application/pdf
format: text/html
creator: Jean-Lou Justine
creator: Delphine Gey
creator: Jessica Thévenot
creator: Romain Gastineau
creator: Hugh D. Jones
subject: Agricultural Science
subject: Conservation Biology
subject: Molecular Biology
subject: Soil Science
subject: Zoology
description: doi:10.7717/peerj.10098
publisher: PeerJ Inc.
rights: © 2020 Justine et al.
abstract: Background The land flatworm Amaga expatria Jones & Sterrer, 2005 (Geoplanidae) was described from two specimens collected in Bermuda in 1963 and 1988 and not recorded since. Methods On the basis of a citizen science project, we received observations in the field, photographs and specimens from non-professionals and local scientists in Martinique and Guadeloupe. We barcoded (COI) specimens from both islands and studied the histology of the reproductive organs of one specimen. Based on Next Generation Sequencing, we obtained the complete mitogenome of A. expatria and some information on its prey from contaminating DNA. Results We add records from 2006 to 2019 in two French islands of the Caribbean arc, Guadeloupe (six records) and Martinique (14 records), based on photographs obtained from citizen science and specimens examined. A specimen from Martinique was studied for histology of the copulatory organs and barcoded for the COI gene; its anatomy was similar to the holotype, therefore confirming species identification. The COI gene was identical for several specimens from Martinique and Guadeloupe and differed from the closest species by more than 10%; molecular characterisation of the species is thus possible by standard molecular barcoding techniques. The mitogenome is 14,962 bp in length and contains 12 protein coding genes, two rRNA genes and 22 tRNA genes; for two protein genes it was not possible to determine the start codon. The mitogenome was compared with the few available mitogenomes from geoplanids and the most similar was Obama nungara, a species from South America. An analysis of contaminating DNA in the digestive system suggests that A. expatria preys on terrestrial molluscs, and citizen science observations in the field suggest that prey include molluscs and earthworms; the species thus could be a threat to biodiversity of soil animals in the Caribbean.
bibliographic citation: Justine et al. (2020) The land flatworm Amaga expatria (Geoplanidae) in Guadeloupe and Martinique: new reports and molecular characterization including complete mitogenome. PeerJ 8:e10098 https://doi.org/10.7717/peerj.10098
date submitted: 2020-06-18
date accepted: 2020-09-14
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Justine
  given name: Jean-Lou
author list: Agent
  family name: Gey
  given name: Delphine
author list: Agent
  family name: Thévenot
  given name: Jessica
author list: Agent
  family name: Gastineau
  given name: Romain
author list: Agent
  family name: Jones
  given name: Hugh D.
doi: 10.7717/peerj.10098
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Justine et al.
attribution name: Justine et al.

Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats
type: item
type: AcademicArticle
description: Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.
format: application/pdf
format: text/html
creator: Xuefeng Fu
creator: Bingru Zhao
creator: Kechuan Tian
creator: Yujiang Wu
creator: Langda Suo
creator: Gui Ba
creator: Deji Ciren
creator: Ji De
creator: Cuoji Awang
creator: Shuangbao Gun
creator: Bohui Yang
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10217
publisher: PeerJ Inc.
rights: © 2020 Fu et al.
abstract: Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.
bibliographic citation: Fu et al. (2020) Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats. PeerJ 8:e10217 https://doi.org/10.7717/peerj.10217
date submitted: 2020-07-16
date accepted: 2020-09-29
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Fu
  given name: Xuefeng
author list: Agent
  family name: Zhao
  given name: Bingru
author list: Agent
  family name: Tian
  given name: Kechuan
author list: Agent
  family name: Wu
  given name: Yujiang
author list: Agent
  family name: Suo
  given name: Langda
author list: Agent
  family name: Ba
  given name: Gui
author list: Agent
  family name: Ciren
  given name: Deji
author list: Agent
  family name: De
  given name: Ji
author list: Agent
  family name: Awang
  given name: Cuoji
author list: Agent
  family name: Gun
  given name: Shuangbao
author list: Agent
  family name: Yang
  given name: Bohui
doi: 10.7717/peerj.10217
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: ©2020 Fu et al.
attribution name: Fu et al.

Loading history changes the morphology and compressive force-induced expression of receptor activator of nuclear factor kappa B ligand/osteoprotegerin in MLO-Y4 osteocytes
type: item
type: AcademicArticle
description: Background In this study, we investigated the effect of the mechanical loading history on the expression of receptor activator of nuclear factor kappa B ligand (RANKL) and osteoprotegerin (OPG) in MLO-Y4 osteocyte-like cells. Methods Three hours after MLO-Y4 osteocytes were seeded, a continuous compressive force (CCF) of 31 dynes/cm2 with or without additional CCF (32 dynes/cm2) was loaded onto the osteocytes. After 36 h, the additional CCF (loading history) was removed for a recovery period of 10 h. The expression of RANKL, OPG, RANKL/OPG ratio, cell numbers, viability and morphology were time-dependently examined at 0, 3, 6 and 10 h. Then, the same additional CCF was applied again for 1 h to all osteocytes with or without the gap junction inhibitor to examine the expression of RANKL, OPG, the RANKL/OPG ratio and other genes that essential to characterize the phenotype of MLO-Y4 cells. Fluorescence recovery after photobleaching technique was also applied to test the differences of gap-junctional intercellular communications (GJIC) among MLO-Y4 cells. Results The expression of RANKL and OPG by MLO-Y4 osteocytes without a loading history was dramatically decreased and increased, respectively, in response to the 1-h loading of additional weight. However, the expression of RANKL, OPG and the RANKL/OPG ratio were maintained at the same level as in the control group in the MLO-Y4 osteocytes with a loading history but without gap junction inhibitor treatment. Treatment of loading history significantly changed the capacity of GJIC and protein expression of connexin 43 (Cx43) but not the mRNA expression of Cx43. No significant difference was observed in the cell number or viability between the MLO-Y4 osteocyte-like cells with and without a loading history or among different time checkpoints during the recovery period. The cell morphology showed significant changes and was correlated with the expression of OPG, Gja1 and Dmp1 during the recovery period. Conclusion Our finding…
format: application/pdf
format: text/html
creator: Ziyi Wang
creator: Yao Weng
creator: Yoshihito Ishihara
creator: Naoya Odagaki
creator: Ei Ei Hsu Hlaing
creator: Takashi Izawa
creator: Hirohiko Okamura
creator: Hiroshi Kamioka
subject: Biophysics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.10244
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background In this study, we investigated the effect of the mechanical loading history on the expression of receptor activator of nuclear factor kappa B ligand (RANKL) and osteoprotegerin (OPG) in MLO-Y4 osteocyte-like cells. Methods Three hours after MLO-Y4 osteocytes were seeded, a continuous compressive force (CCF) of 31 dynes/cm2 with or without additional CCF (32 dynes/cm2) was loaded onto the osteocytes. After 36 h, the additional CCF (loading history) was removed for a recovery period of 10 h. The expression of RANKL, OPG, RANKL/OPG ratio, cell numbers, viability and morphology were time-dependently examined at 0, 3, 6 and 10 h. Then, the same additional CCF was applied again for 1 h to all osteocytes with or without the gap junction inhibitor to examine the expression of RANKL, OPG, the RANKL/OPG ratio and other genes that essential to characterize the phenotype of MLO-Y4 cells. Fluorescence recovery after photobleaching technique was also applied to test the differences of gap-junctional intercellular communications (GJIC) among MLO-Y4 cells. Results The expression of RANKL and OPG by MLO-Y4 osteocytes without a loading history was dramatically decreased and increased, respectively, in response to the 1-h loading of additional weight. However, the expression of RANKL, OPG and the RANKL/OPG ratio were maintained at the same level as in the control group in the MLO-Y4 osteocytes with a loading history but without gap junction inhibitor treatment. Treatment of loading history significantly changed the capacity of GJIC and protein expression of connexin 43 (Cx43) but not the mRNA expression of Cx43. No significant difference was observed in the cell number or viability between the MLO-Y4 osteocyte-like cells with and without a loading history or among different time checkpoints during the recovery period. The cell morphology showed significant changes and was correlated with the expression of OPG, Gja1 and Dmp1 during the recovery period. Conclusion Our finding…
bibliographic citation: Wang et al. (2020) Loading history changes the morphology and compressive force-induced expression of receptor activator of nuclear factor kappa B ligand/osteoprotegerin in MLO-Y4 osteocytes. PeerJ 8:e10244 https://doi.org/10.7717/peerj.10244
date submitted: 2020-05-12
date accepted: 2020-10-05
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ziyi
author list: Agent
  family name: Weng
  given name: Yao
author list: Agent
  family name: Ishihara
  given name: Yoshihito
author list: Agent
  family name: Odagaki
  given name: Naoya
author list: Agent
  family name: Ei Hsu Hlaing
  given name: Ei
author list: Agent
  family name: Izawa
  given name: Takashi
author list: Agent
  family name: Okamura
  given name: Hirohiko
author list: Agent
  family name: Kamioka
  given name: Hiroshi
doi: 10.7717/peerj.10244
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Wang et al.
attribution name: Wang et al.

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
type: item
type: AcademicArticle
description: The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpressed transcripts, it is possible to efficiently narrow candidate genes encoding pathway enzymes and more easily predict both functions and functional associations. Mutual Rank (MR)-based coexpression analyses in plants accurately demonstrate functional associations for many specialized metabolic pathways; however, despite the clear predictive value of MR analyses, the application is uncommonly used to drive new pathway discoveries. Moreover, many coexpression databases aid in the prediction of both functional associations and gene functions, but lack customizability for refined hypothesis testing. To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses. MutRank provides an intuitive graphical user interface with multiple customizable features that integrates user-provided data and supporting information suitable for personal computers. Tabular and graphical outputs facilitate the rapid analyses of both unbiased and user-defined coexpression results that accelerate gene function predictions. We highlight the recent utility of MR analyses for functional predictions and discoveries in defining two maize terpenoid antibiotic pathways. Beyond applications in biosynthetic pathway discovery, MutRank provides a simple, customizable and user-friendly interface to enable coexpression analyses relating to a brea…
format: application/pdf
format: text/html
creator: Elly Poretsky
creator: Alisa Huffaker
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10264
publisher: PeerJ Inc.
rights: © 2020 Poretsky and Huffaker
abstract: The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpressed transcripts, it is possible to efficiently narrow candidate genes encoding pathway enzymes and more easily predict both functions and functional associations. Mutual Rank (MR)-based coexpression analyses in plants accurately demonstrate functional associations for many specialized metabolic pathways; however, despite the clear predictive value of MR analyses, the application is uncommonly used to drive new pathway discoveries. Moreover, many coexpression databases aid in the prediction of both functional associations and gene functions, but lack customizability for refined hypothesis testing. To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses. MutRank provides an intuitive graphical user interface with multiple customizable features that integrates user-provided data and supporting information suitable for personal computers. Tabular and graphical outputs facilitate the rapid analyses of both unbiased and user-defined coexpression results that accelerate gene function predictions. We highlight the recent utility of MR analyses for functional predictions and discoveries in defining two maize terpenoid antibiotic pathways. Beyond applications in biosynthetic pathway discovery, MutRank provides a simple, customizable and user-friendly interface to enable coexpression analyses relating to a brea…
bibliographic citation: Poretsky et al. (2020) MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. PeerJ 8:e10264 https://doi.org/10.7717/peerj.10264
date submitted: 2020-08-25
date accepted: 2020-10-07
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Poretsky
  given name: Elly
author list: Agent
  family name: Huffaker
  given name: Alisa
doi: 10.7717/peerj.10264
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Poretsky and Huffaker
attribution name: Poretsky and Huffaker

Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans
type: item
type: AcademicArticle
description: Effects of substrate and water depth on the physiological status of a submerged macrophyte, Vallisneria natans (Lour.) H. Hara, were determined by measuring biomarkers in leaves and roots, to understand factors limiting the re-establishment of V. natans in urban eutrophic ponds. Ramets of V. natans were grown in the laboratory using aquaria containing water and bottom mud from a eutrophic pond and maintained under sufficient light in an incubator. The growth and chlorophyll-a (Chl-a) content of leaves were greater in aquaria with mud than in those with sand, which was used as the reference substrate. The contents of a peroxidation product (malondialdehyde (MDA)) and three antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD)) in leaves and roots, used as stress biomarkers, changed during the experiment, although differences in these contents between mud and sand were not consistent across the experimental days. To control water depth in the field, ramets of V. natans were grown in cages with different substrates (mud and sand) installed at different depths (0.5, 1.2, and 2.0 m) in the pond. The mean light quantum during the experiment decreased with increasing depth, from 79.3 μmol/m2 s at 0.5 m to 7.9 μmol/m2 s at 2.0 m. The Chl-a content in leaves decreased, whereas the MDA content in both leaves and roots increased with increasing water depth. All enzyme activities increased at the beginning and then decreased to the end of the experiment at 2.0 m depth, suggesting deterioration of enzyme activities due to depth-related stress. The MDA content and CAT activity were higher for sand than for mud, whereas the difference in the growth and the leaf Chl-a content between substrates remained unclear in the pond. On comparing the laboratory and field experiments, the leaf Chl-a content was found to be lower and the MDA content and enzyme activities exhibited sharp increase for ramets grown in the pond, even at 0.5 m depth, when compared wi…
format: application/pdf
format: text/html
creator: Aimin Hao
creator: Sohei Kobayashi
creator: Huilin Huang
creator: Qi Mi
creator: Yasushi Iseri
subject: Ecosystem Science
subject: Plant Science
subject: Freshwater Biology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.10273
publisher: PeerJ Inc.
rights: © 2020 Hao et al.
abstract: Effects of substrate and water depth on the physiological status of a submerged macrophyte, Vallisneria natans (Lour.) H. Hara, were determined by measuring biomarkers in leaves and roots, to understand factors limiting the re-establishment of V. natans in urban eutrophic ponds. Ramets of V. natans were grown in the laboratory using aquaria containing water and bottom mud from a eutrophic pond and maintained under sufficient light in an incubator. The growth and chlorophyll-a (Chl-a) content of leaves were greater in aquaria with mud than in those with sand, which was used as the reference substrate. The contents of a peroxidation product (malondialdehyde (MDA)) and three antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD)) in leaves and roots, used as stress biomarkers, changed during the experiment, although differences in these contents between mud and sand were not consistent across the experimental days. To control water depth in the field, ramets of V. natans were grown in cages with different substrates (mud and sand) installed at different depths (0.5, 1.2, and 2.0 m) in the pond. The mean light quantum during the experiment decreased with increasing depth, from 79.3 μmol/m2 s at 0.5 m to 7.9 μmol/m2 s at 2.0 m. The Chl-a content in leaves decreased, whereas the MDA content in both leaves and roots increased with increasing water depth. All enzyme activities increased at the beginning and then decreased to the end of the experiment at 2.0 m depth, suggesting deterioration of enzyme activities due to depth-related stress. The MDA content and CAT activity were higher for sand than for mud, whereas the difference in the growth and the leaf Chl-a content between substrates remained unclear in the pond. On comparing the laboratory and field experiments, the leaf Chl-a content was found to be lower and the MDA content and enzyme activities exhibited sharp increase for ramets grown in the pond, even at 0.5 m depth, when compared wi…
bibliographic citation: Hao et al. (2020) Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans. PeerJ 8:e10273 https://doi.org/10.7717/peerj.10273
date submitted: 2020-05-06
date accepted: 2020-10-08
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Aimin
author list: Agent
  family name: Kobayashi
  given name: Sohei
author list: Agent
  family name: Huang
  given name: Huilin
author list: Agent
  family name: Mi
  given name: Qi
author list: Agent
  family name: Iseri
  given name: Yasushi
doi: 10.7717/peerj.10273
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Hao et al.
attribution name: Hao et al.

The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species
type: item
type: AcademicArticle
description: Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.
format: application/pdf
format: text/html
creator: Mirella Pupo Santos
creator: João V.S. Rabelo Araujo
creator: Arthur V. Sant’anna Lopes
creator: Julio Cesar Fiorio Vettorazzi
creator: Marcela Santana Bastos Boechat
creator: Fernanda AbreuSantana Arêdes
creator: Naiara Viana Campos
creator: Emiliano Nicolas Calderon
creator: Fernando M. Gomes Santos
creator: Tais Nogueira Fernandes
creator: Rodrigo Nunes da Fonseca
creator: Messias Gonzaga Pereira
creator: Guilherme Oliveira
creator: Daniel Basilio Zandonadi
creator: RodrigoLemes Martins
creator: Francisco de Assis Esteves
subject: Conservation Biology
subject: Genetics
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.10274
publisher: PeerJ Inc.
rights: © 2020 Santos et al.
abstract: Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.
bibliographic citation: Santos et al. (2020) The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species. PeerJ 8:e10274 https://doi.org/10.7717/peerj.10274
date submitted: 2020-05-13
date accepted: 2020-10-08
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos
  given name: Mirella Pupo
author list: Agent
  family name: Araujo
  given name: João V.S. Rabelo
author list: Agent
  family name: Lopes
  given name: Arthur V. Sant’anna
author list: Agent
  family name: Vettorazzi
  given name: Julio Cesar Fiorio
author list: Agent
  family name: Boechat
  given name: Marcela Santana Bastos
author list: Agent
  family name: Arêdes
  given name: Fernanda AbreuSantana
author list: Agent
  family name: Campos
  given name: Naiara Viana
author list: Agent
  family name: Calderon
  given name: Emiliano Nicolas
author list: Agent
  family name: Santos
  given name: Fernando M. Gomes
author list: Agent
  family name: Fernandes
  given name: Tais Nogueira
author list: Agent
  family name: da Fonseca
  given name: Rodrigo Nunes
author list: Agent
  family name: Pereira
  given name: Messias Gonzaga
author list: Agent
  family name: Oliveira
  given name: Guilherme
author list: Agent
  family name: Zandonadi
  given name: Daniel Basilio
author list: Agent
  family name: Martins
  given name: RodrigoLemes
author list: Agent
  family name: Esteves
  given name: Francisco de Assis
doi: 10.7717/peerj.10274
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: ©2020 Santos et al.
attribution name: Santos et al.

Foraging efficiency, social status and body condition in group-living horses and ponies
type: item
type: AcademicArticle
description: Individual animals experience different costs and benefits associated with group living, which may impact on their foraging efficiency in ways not yet well specified. This study investigated associations between social dominance, body condition and interruptions to foraging behaviour in a cross-sectional study of 116 domestic horses and ponies, kept in 20 discrete herds. Social dominance was measured for each individual alongside observations of winter foraging behaviour. During bouts of foraging, the duration, frequency and category (vigilance, movement, social displacements given and received, scratching and startle responses) of interruptions were recorded, with total interruption time taken as a proxy measure of foraging efficiency. Total foraging time was not influenced by body condition or social dominance. Body condition was associated with social dominance, but more strongly associated with foraging efficiency. Specifically, lower body condition was associated with greater vigilance. This demonstrates that factors other than social dominance can result in stable differences in winter body condition.
format: application/pdf
format: text/html
creator: Sarah L. Giles
creator: Pat Harris
creator: Sean A. Rands
creator: Christine J. Nicol
subject: Animal Behavior
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.10305
publisher: PeerJ Inc.
rights: © 2020 Giles et al.
abstract: Individual animals experience different costs and benefits associated with group living, which may impact on their foraging efficiency in ways not yet well specified. This study investigated associations between social dominance, body condition and interruptions to foraging behaviour in a cross-sectional study of 116 domestic horses and ponies, kept in 20 discrete herds. Social dominance was measured for each individual alongside observations of winter foraging behaviour. During bouts of foraging, the duration, frequency and category (vigilance, movement, social displacements given and received, scratching and startle responses) of interruptions were recorded, with total interruption time taken as a proxy measure of foraging efficiency. Total foraging time was not influenced by body condition or social dominance. Body condition was associated with social dominance, but more strongly associated with foraging efficiency. Specifically, lower body condition was associated with greater vigilance. This demonstrates that factors other than social dominance can result in stable differences in winter body condition.
bibliographic citation: Giles et al. (2020) Foraging efficiency, social status and body condition in group-living horses and ponies. PeerJ 8:e10305 https://doi.org/10.7717/peerj.10305
date submitted: 2020-02-25
date accepted: 2020-10-15
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giles
  given name: Sarah L.
author list: Agent
  family name: Harris
  given name: Pat
author list: Agent
  family name: Rands
  given name: Sean A.
author list: Agent
  family name: Nicol
  given name: Christine J.
doi: 10.7717/peerj.10305
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Giles et al.
attribution name: Giles et al.

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