PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Pelagic larval duration, growth rate, and population genetic structure of the tidepool snake moray Uropterygius micropterus around the southern Ryukyu Islands, Taiwan, and the central Philippines
items: Primary producers may ameliorate impacts of daytime CO2 addition in a coastal marine ecosystem
items: Is high-intensity interval cycling feasible and more beneficial than continuous cycling for knee osteoarthritic patients? Results of a randomised control feasibility trial
items: Global opportunities for mariculture development to promote human nutrition
items: Differential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung cancer
items: The rice XA21 ectodomain fused to the Arabidopsis EFR cytoplasmic domain confers resistance to Xanthomonas oryzae pv. oryzae
items: Transcriptomic studies reveal a key metabolic pathway contributing to a well-maintained photosynthetic system under drought stress in foxtail millet (Setaria italica L.)
items: Biodiversity of the Great Barrier Reef—how adequately is it protected?
items: Nature-derived lignan compound VB-1 exerts hair growth-promoting effects by augmenting Wnt/β-catenin signaling in human dermal papilla cells
items: Asymmetries in mother-infant behaviour in Barbary macaques (Macaca sylvanus)

Pelagic larval duration, growth rate, and population genetic structure of the tidepool snake moray Uropterygius micropterus around the southern Ryukyu Islands, Taiwan, and the central Philippines
type: item
type: AcademicArticle
description: The relationships between pelagic larval duration (PLD) and geographic distribution patterns or population genetic structures of fishes remain obscure and highly variable among species. To further understand the early life history of the tidepool snake moray Uropterygius micropterus and the potential relationship between PLD and population genetic structure of this species, otolith microstructure and population genetics based on concatenated mtDNA sequence (cytochrome b and cytochrome oxidase subunit I, 1,336 bp) were analyzed for 195 specimens collected from eight locations around the southern Ryukyu Islands, Taiwan, and the central Philippines. Eels with longer PLD and lower otolith growth rates were observed at relatively higher latitudes with lower water temperatures (54.6 ± 7.7 days and 1.28 ± 0.16 µm day−1 on Ishigaki Island, Japan, vs. 43.9 ± 4.9 days and 1.60 ± 0.19 µm day−1 on Badian, the Philippines), suggesting that leptocephali grew faster and had shortened pelagic periods in warmer waters. Meanwhile, the eels along the southwest coast of Taiwan had relatively longer PLD (57.9 ± 10.5 days), which might be associated with the more complex ocean current systems compared to their counterparts collected along the east coast of Taiwan (52.6 ± 8.0 days). However, the southwestern and eastern Taiwan groups had similar otolith growth rates (1.33 ± 0.19 µm day−1 vs. 1.36 ± 0.16 µm day−1). Despite the intergroup variation in PLD, genetic analysis revealed fluent gene flow among the tidepool snake morays in the study regions, implying that intraspecies PLD variation had a weak effect on genetic structure. The leptocephalus stage might have ensured the widespread gene flow among the study areas and leptocephalus growth was likely influenced by regional water temperature.
format: application/pdf
format: text/html
creator: Wen-Chien Huang
creator: Jui-Tsung Chang
creator: Chun Liao
creator: Atsushi Tawa
creator: Yoshiyuki Iizuka
creator: Te-Yu Liao
creator: Jen-Chieh Shiao
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.4741
publisher: PeerJ Inc.
rights: © 2018 Huang et al.
abstract: The relationships between pelagic larval duration (PLD) and geographic distribution patterns or population genetic structures of fishes remain obscure and highly variable among species. To further understand the early life history of the tidepool snake moray Uropterygius micropterus and the potential relationship between PLD and population genetic structure of this species, otolith microstructure and population genetics based on concatenated mtDNA sequence (cytochrome b and cytochrome oxidase subunit I, 1,336 bp) were analyzed for 195 specimens collected from eight locations around the southern Ryukyu Islands, Taiwan, and the central Philippines. Eels with longer PLD and lower otolith growth rates were observed at relatively higher latitudes with lower water temperatures (54.6 ± 7.7 days and 1.28 ± 0.16 µm day−1 on Ishigaki Island, Japan, vs. 43.9 ± 4.9 days and 1.60 ± 0.19 µm day−1 on Badian, the Philippines), suggesting that leptocephali grew faster and had shortened pelagic periods in warmer waters. Meanwhile, the eels along the southwest coast of Taiwan had relatively longer PLD (57.9 ± 10.5 days), which might be associated with the more complex ocean current systems compared to their counterparts collected along the east coast of Taiwan (52.6 ± 8.0 days). However, the southwestern and eastern Taiwan groups had similar otolith growth rates (1.33 ± 0.19 µm day−1 vs. 1.36 ± 0.16 µm day−1). Despite the intergroup variation in PLD, genetic analysis revealed fluent gene flow among the tidepool snake morays in the study regions, implying that intraspecies PLD variation had a weak effect on genetic structure. The leptocephalus stage might have ensured the widespread gene flow among the study areas and leptocephalus growth was likely influenced by regional water temperature.
bibliographic citation: Huang et al. (2018) Pelagic larval duration, growth rate, and population genetic structure of the tidepool snake moray Uropterygius micropterus around the southern Ryukyu Islands, Taiwan, and the central Philippines. PeerJ 6:e4741 https://doi.org/10.7717/peerj.4741
date submitted: 2018-02-23
date accepted: 2018-04-19
issued: 2018-05-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Wen-Chien
author list: Agent
  family name: Chang
  given name: Jui-Tsung
author list: Agent
  family name: Liao
  given name: Chun
author list: Agent
  family name: Tawa
  given name: Atsushi
author list: Agent
  family name: Iizuka
  given name: Yoshiyuki
author list: Agent
  family name: Liao
  given name: Te-Yu
author list: Agent
  family name: Shiao
  given name: Jen-Chieh
doi: 10.7717/peerj.4741
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-09
copyright: ©2018 Huang et al.
attribution name: Huang et al.

Primary producers may ameliorate impacts of daytime CO2 addition in a coastal marine ecosystem
type: item
type: AcademicArticle
description: Predicting the impacts of ocean acidification in coastal habitats is complicated by bio-physical feedbacks between organisms and carbonate chemistry. Daily changes in pH and other carbonate parameters in coastal ecosystems, associated with processes such as photosynthesis and respiration, often greatly exceed global mean predicted changes over the next century. We assessed the strength of these feedbacks under projected elevated CO2 levels by conducting a field experiment in 10 macrophyte-dominated tide pools on the coast of California, USA. We evaluated changes in carbonate parameters over time and found that under ambient conditions, daytime changes in pH, pCO2, net ecosystem calcification (NEC), and O2 concentrations were strongly related to rates of net community production (NCP). CO2 was added to pools during daytime low tides, which should have reduced pH and enhanced pCO2. However, photosynthesis rapidly reduced pCO2 and increased pH, so effects of CO2 addition were not apparent unless we accounted for seaweed and surfgrass abundances. In the absence of macrophytes, CO2 addition caused pH to decline by ∼0.6 units and pCO2 to increase by ∼487 µatm over 6 hr during the daytime low tide. As macrophyte abundances increased, the impacts of CO2 addition declined because more CO2 was absorbed due to photosynthesis. Effects of CO2addition were, therefore, modified by feedbacks between NCP, pH, pCO2, and NEC. Our results underscore the potential importance of coastal macrophytes in ameliorating impacts of ocean acidification.
format: application/pdf
format: text/html
creator: Matthew E.S. Bracken
creator: Nyssa J. Silbiger
creator: Genevieve Bernatchez
creator: Cascade J.B. Sorte
subject: Ecology
subject: Marine Biology
subject: Climate Change Biology
subject: Biogeochemistry
description: doi:10.7717/peerj.4739
publisher: PeerJ Inc.
rights: © 2018 Bracken et al.
abstract: Predicting the impacts of ocean acidification in coastal habitats is complicated by bio-physical feedbacks between organisms and carbonate chemistry. Daily changes in pH and other carbonate parameters in coastal ecosystems, associated with processes such as photosynthesis and respiration, often greatly exceed global mean predicted changes over the next century. We assessed the strength of these feedbacks under projected elevated CO2 levels by conducting a field experiment in 10 macrophyte-dominated tide pools on the coast of California, USA. We evaluated changes in carbonate parameters over time and found that under ambient conditions, daytime changes in pH, pCO2, net ecosystem calcification (NEC), and O2 concentrations were strongly related to rates of net community production (NCP). CO2 was added to pools during daytime low tides, which should have reduced pH and enhanced pCO2. However, photosynthesis rapidly reduced pCO2 and increased pH, so effects of CO2 addition were not apparent unless we accounted for seaweed and surfgrass abundances. In the absence of macrophytes, CO2 addition caused pH to decline by ∼0.6 units and pCO2 to increase by ∼487 µatm over 6 hr during the daytime low tide. As macrophyte abundances increased, the impacts of CO2 addition declined because more CO2 was absorbed due to photosynthesis. Effects of CO2addition were, therefore, modified by feedbacks between NCP, pH, pCO2, and NEC. Our results underscore the potential importance of coastal macrophytes in ameliorating impacts of ocean acidification.
bibliographic citation: Bracken et al. (2018) Primary producers may ameliorate impacts of daytime CO2 addition in a coastal marine ecosystem. PeerJ 6:e4739 https://doi.org/10.7717/peerj.4739
date submitted: 2018-03-10
date accepted: 2018-04-19
issued: 2018-05-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bracken
  given name: Matthew E.S.
author list: Agent
  family name: Silbiger
  given name: Nyssa J.
author list: Agent
  family name: Bernatchez
  given name: Genevieve
author list: Agent
  family name: Sorte
  given name: Cascade J.B.
doi: 10.7717/peerj.4739
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-09
copyright: ©2018 Bracken et al.
attribution name: Bracken et al.

Is high-intensity interval cycling feasible and more beneficial than continuous cycling for knee osteoarthritic patients? Results of a randomised control feasibility trial
type: item
type: AcademicArticle
description: Background Knee osteoarthritis (OA) patients often suffer joint pain and stiffness, which contributes to negative changes in body composition, strength, physical performance (function), physical activity and health-related quality of life. To reduce these symptoms and side effects of knee OA, moderate-intensity continuous training (MICT) cycling is often recommended. While resistance training is considered the optimal form of training to improve sarcopenic outcomes, it imposes higher joint loads and requires supervision, either initially or continuously by trained exercise professionals. Therefore, this pilot study sought to gain some insight into the feasibility and potential benefits of high-intensity interval training (HIIT) cycling as an alternative exercise option to MICT cycling for individuals with knee OA. Methods Twenty-seven middle-aged and older adults with knee OA were randomly allocated to either MICT or HIIT, with both programs involving four unsupervised home-based cycling sessions (∼25 min per session) each week for eight weeks. Feasibility was assessed by enrolment rate, withdrawal rate, exercise adherence and number of adverse effects. Efficacy was assessed by health-related quality of life (Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and Lequesne index), physical function (Timed Up and Go (TUG), Sit to Stand (STS) and preferred gait speed) and body composition (body mass, BMI, body fat percentage and muscle mass). Results Twenty-seven of the interested 50 potential participants (54%) enrolled in the study, with 17 of the 27 participants completing the trial (withdrawal rate of 37%); with the primary withdrawal reasons being unrelated injuries or illness or family related issues. Of the 17 participants who completed the trial, exercise adherence was very high (HIIT 94%; MICT 88%). While only three individuals (one in the MICT and two in the HIIT group) reported adverse events, a total of 28 adverse events were reported, w…
format: application/pdf
format: text/html
creator: Justin W. Keogh
creator: Josephine Grigg
creator: Christopher J. Vertullo
subject: Kinesiology
description: doi:10.7717/peerj.4738
publisher: PeerJ Inc.
rights: © 2018 Keogh et al.
abstract: Background Knee osteoarthritis (OA) patients often suffer joint pain and stiffness, which contributes to negative changes in body composition, strength, physical performance (function), physical activity and health-related quality of life. To reduce these symptoms and side effects of knee OA, moderate-intensity continuous training (MICT) cycling is often recommended. While resistance training is considered the optimal form of training to improve sarcopenic outcomes, it imposes higher joint loads and requires supervision, either initially or continuously by trained exercise professionals. Therefore, this pilot study sought to gain some insight into the feasibility and potential benefits of high-intensity interval training (HIIT) cycling as an alternative exercise option to MICT cycling for individuals with knee OA. Methods Twenty-seven middle-aged and older adults with knee OA were randomly allocated to either MICT or HIIT, with both programs involving four unsupervised home-based cycling sessions (∼25 min per session) each week for eight weeks. Feasibility was assessed by enrolment rate, withdrawal rate, exercise adherence and number of adverse effects. Efficacy was assessed by health-related quality of life (Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and Lequesne index), physical function (Timed Up and Go (TUG), Sit to Stand (STS) and preferred gait speed) and body composition (body mass, BMI, body fat percentage and muscle mass). Results Twenty-seven of the interested 50 potential participants (54%) enrolled in the study, with 17 of the 27 participants completing the trial (withdrawal rate of 37%); with the primary withdrawal reasons being unrelated injuries or illness or family related issues. Of the 17 participants who completed the trial, exercise adherence was very high (HIIT 94%; MICT 88%). While only three individuals (one in the MICT and two in the HIIT group) reported adverse events, a total of 28 adverse events were reported, w…
bibliographic citation: Keogh et al. (2018) Is high-intensity interval cycling feasible and more beneficial than continuous cycling for knee osteoarthritic patients? Results of a randomised control feasibility trial. PeerJ 6:e4738 https://doi.org/10.7717/peerj.4738
date submitted: 2018-02-24
date accepted: 2018-04-19
issued: 2018-05-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Keogh
  given name: Justin W.
author list: Agent
  family name: Grigg
  given name: Josephine
author list: Agent
  family name: Vertullo
  given name: Christopher J.
doi: 10.7717/peerj.4738
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-09
copyright: © 2018 Keogh et al.
attribution name: Keogh et al.

Global opportunities for mariculture development to promote human nutrition
type: item
type: AcademicArticle
description: An estimated two billion people worldwide currently suffer from micronutrient malnutrition, and almost one billion are calorie deficient. Providing adequate nutrition is a growing global challenge. Seafood is one of the most important sources of both protein and micronutrients for many, yet production from wild capture fisheries has stagnated. In contrast, aquaculture is the world’s fastest-growing food production sector and now supplies over half of all seafood consumed globally. Mariculture, or the farming of brackish and marine species, accounts for roughly one-third of all aquaculture production and has received increasing attention as a potential supplement for wild-caught marine fisheries. By analyzing global patterns in seafood reliance, malnutrition levels, and economic opportunity, this study identifies where mariculture has the greatest potential to improve human nutrition. We calculate a mariculture opportunity index for 117 coastal nations by drawing on a diverse set of seafood production, trade, consumption, and nutrition data. Seventeen primary variables are combined into country-level scores for reliance on seafood, opportunity for nutritional improvement, and opportunity for economic development of mariculture. The final mariculture opportunity score identifies countries with high seafood reliance combined with high nutritional and economic opportunity scores. We find that island nations in Southeast Asia and the Caribbean are consistently identified as countries with high mariculture opportunity. In other regions, nutritional and economic opportunity scores are not significantly correlated, and we discuss the implications of this finding for crafting appropriate development policy. Finally, we identify key challenges to ameliorating malnutrition through mariculture development, including insufficient policy infrastructure, government instability, and ensuring local consumption of farmed fish. Our analysis is an important step towards prioritizing na…
format: application/pdf
format: text/html
creator: Owen R. Liu
creator: Renato Molina
creator: Margaret Wilson
creator: Benjamin S. Halpern
subject: Aquaculture, Fisheries and Fish Science
subject: Global Health
subject: Nutrition
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.4733
publisher: PeerJ Inc.
rights: © 2018 Liu et al.
abstract: An estimated two billion people worldwide currently suffer from micronutrient malnutrition, and almost one billion are calorie deficient. Providing adequate nutrition is a growing global challenge. Seafood is one of the most important sources of both protein and micronutrients for many, yet production from wild capture fisheries has stagnated. In contrast, aquaculture is the world’s fastest-growing food production sector and now supplies over half of all seafood consumed globally. Mariculture, or the farming of brackish and marine species, accounts for roughly one-third of all aquaculture production and has received increasing attention as a potential supplement for wild-caught marine fisheries. By analyzing global patterns in seafood reliance, malnutrition levels, and economic opportunity, this study identifies where mariculture has the greatest potential to improve human nutrition. We calculate a mariculture opportunity index for 117 coastal nations by drawing on a diverse set of seafood production, trade, consumption, and nutrition data. Seventeen primary variables are combined into country-level scores for reliance on seafood, opportunity for nutritional improvement, and opportunity for economic development of mariculture. The final mariculture opportunity score identifies countries with high seafood reliance combined with high nutritional and economic opportunity scores. We find that island nations in Southeast Asia and the Caribbean are consistently identified as countries with high mariculture opportunity. In other regions, nutritional and economic opportunity scores are not significantly correlated, and we discuss the implications of this finding for crafting appropriate development policy. Finally, we identify key challenges to ameliorating malnutrition through mariculture development, including insufficient policy infrastructure, government instability, and ensuring local consumption of farmed fish. Our analysis is an important step towards prioritizing na…
bibliographic citation: Liu et al. (2018) Global opportunities for mariculture development to promote human nutrition. PeerJ 6:e4733 https://doi.org/10.7717/peerj.4733
date submitted: 2018-01-12
date accepted: 2018-04-18
issued: 2018-05-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Owen R.
author list: Agent
  family name: Molina
  given name: Renato
author list: Agent
  family name: Wilson
  given name: Margaret
author list: Agent
  family name: Halpern
  given name: Benjamin S.
doi: 10.7717/peerj.4733
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-09
copyright: ©2018 Liu et al.
attribution name: Liu et al.

Differential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung cancer
type: item
type: AcademicArticle
description: Background Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these “housekeeping genes” (HKGs) could separate one normal human tissue type from another. Current focus on identifying “specific disease markers” is problematic as single gene expression in a given sample represents the specific cellular states of the sample at the time of collection. In this study, we examine the diagnostic and prognostic potential of the variable expressions of HKGs in lung cancers. Methods Microarray and RNA-seq data for normal lungs, lung adenocarcinomas (AD), squamous cell carcinomas of the lung (SQCLC), and small cell carcinomas of the lung (SCLC) were collected from online databases. Using 374 of 451 HKGs, differentially expressed genes between pairs of sample types were determined via two-sided, homoscedastic t-test. Principal component analysis and hierarchical clustering classified normal lung and lung cancers subtypes according to relative gene expression variations. We used uni- and multi-variate cox-regressions to identify significant predictors of overall survival in AD patients. Classifying genes were selected using a set of training samples and then validated using an independent test set. Gene Ontology was examined by PANTHER. Results This study showed that the differential expression patterns of 242, 245, and 99 HKGs were able to distinguish normal lung from AD, SCLC, and SQCLC, respectively. From these, 70 HKGs were common across the three lung cancer subtypes. These HKGs have low expression variation compared to current lung cancer markers (e.g., EGFR, KRAS) and were involved in the most common biological processes (e.g., metabolism, stress response). In addition, the expression pattern of 106 HKGs alone was a significant classifier of AD versus SQCLC. We further highlighted that a panel of 13 HKGs was an independent predictor of overall survival and c…
format: application/pdf
format: text/html
creator: Yu-Chun Chang
creator: Yan Ding
creator: Lingsheng Dong
creator: Lang-Jing Zhu
creator: Roderick V. Jensen
creator: Li-Li Hsiao
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.4719
publisher: PeerJ Inc.
rights: © 2018 Chang et al.
abstract: Background Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these “housekeeping genes” (HKGs) could separate one normal human tissue type from another. Current focus on identifying “specific disease markers” is problematic as single gene expression in a given sample represents the specific cellular states of the sample at the time of collection. In this study, we examine the diagnostic and prognostic potential of the variable expressions of HKGs in lung cancers. Methods Microarray and RNA-seq data for normal lungs, lung adenocarcinomas (AD), squamous cell carcinomas of the lung (SQCLC), and small cell carcinomas of the lung (SCLC) were collected from online databases. Using 374 of 451 HKGs, differentially expressed genes between pairs of sample types were determined via two-sided, homoscedastic t-test. Principal component analysis and hierarchical clustering classified normal lung and lung cancers subtypes according to relative gene expression variations. We used uni- and multi-variate cox-regressions to identify significant predictors of overall survival in AD patients. Classifying genes were selected using a set of training samples and then validated using an independent test set. Gene Ontology was examined by PANTHER. Results This study showed that the differential expression patterns of 242, 245, and 99 HKGs were able to distinguish normal lung from AD, SCLC, and SQCLC, respectively. From these, 70 HKGs were common across the three lung cancer subtypes. These HKGs have low expression variation compared to current lung cancer markers (e.g., EGFR, KRAS) and were involved in the most common biological processes (e.g., metabolism, stress response). In addition, the expression pattern of 106 HKGs alone was a significant classifier of AD versus SQCLC. We further highlighted that a panel of 13 HKGs was an independent predictor of overall survival and c…
bibliographic citation: Chang et al. (2018) Differential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung cancer. PeerJ 6:e4719 https://doi.org/10.7717/peerj.4719
date submitted: 2018-01-08
date accepted: 2018-04-16
issued: 2018-05-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Yu-Chun
author list: Agent
  family name: Ding
  given name: Yan
author list: Agent
  family name: Dong
  given name: Lingsheng
author list: Agent
  family name: Zhu
  given name: Lang-Jing
author list: Agent
  family name: Jensen
  given name: Roderick V.
author list: Agent
  family name: Hsiao
  given name: Li-Li
doi: 10.7717/peerj.4719
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-09
copyright: ©2018 Chang et al.
attribution name: Chang et al.

The rice XA21 ectodomain fused to the Arabidopsis EFR cytoplasmic domain confers resistance to Xanthomonas oryzae pv. oryzae
type: item
type: AcademicArticle
description: Rice (Oryza sativa) plants expressing the XA21 cell-surface receptor kinase are resistant to Xanthomonas oryzae pv. oryzae (Xoo) infection. We previously demonstrated that expressing a chimeric protein containing the ELONGATION FACTOR Tu RECEPTOR (EFR) ectodomain and the XA21 endodomain (EFR:XA21) in rice does not confer robust resistance to Xoo. To test if the XA21 ectodomain is required for Xoo resistance, we produced transgenic rice lines expressing a chimeric protein consisting of the XA21 ectodomain and EFR endodomain (XA21:EFR) and inoculated these lines with Xoo. We also tested if the XA21:EFR rice plants respond to a synthetic sulfated 21 amino acid derivative (RaxX21-sY) of the activator of XA21-mediated immunity, RaxX. We found that five independently transformed XA21:EFR rice lines displayed resistance to Xoo as measured by lesion length analysis, and showed that five lines share characteristic markers of the XA21 defense response (generation of reactive oxygen species and defense response gene expression) after treatment with RaxX21-sY. Our results indicate that expression of the XA21:EFR chimeric receptor in rice confers resistance to Xoo. These results suggest that the endodomain of the EFR and XA21 immune receptors are interchangeable and the XA21 ectodomain is the key determinant conferring robust resistance to Xoo.
format: application/pdf
format: text/html
creator: Nicholas C. Thomas
creator: Nir Oksenberg
creator: Furong Liu
creator: Daniel Caddell
creator: Alina Nalyvayko
creator: Yen Nguyen
creator: Benjamin Schwessinger
creator: Pamela C. Ronald
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.4456
publisher: PeerJ Inc.
rights: © 2018 Thomas et al.
abstract: Rice (Oryza sativa) plants expressing the XA21 cell-surface receptor kinase are resistant to Xanthomonas oryzae pv. oryzae (Xoo) infection. We previously demonstrated that expressing a chimeric protein containing the ELONGATION FACTOR Tu RECEPTOR (EFR) ectodomain and the XA21 endodomain (EFR:XA21) in rice does not confer robust resistance to Xoo. To test if the XA21 ectodomain is required for Xoo resistance, we produced transgenic rice lines expressing a chimeric protein consisting of the XA21 ectodomain and EFR endodomain (XA21:EFR) and inoculated these lines with Xoo. We also tested if the XA21:EFR rice plants respond to a synthetic sulfated 21 amino acid derivative (RaxX21-sY) of the activator of XA21-mediated immunity, RaxX. We found that five independently transformed XA21:EFR rice lines displayed resistance to Xoo as measured by lesion length analysis, and showed that five lines share characteristic markers of the XA21 defense response (generation of reactive oxygen species and defense response gene expression) after treatment with RaxX21-sY. Our results indicate that expression of the XA21:EFR chimeric receptor in rice confers resistance to Xoo. These results suggest that the endodomain of the EFR and XA21 immune receptors are interchangeable and the XA21 ectodomain is the key determinant conferring robust resistance to Xoo.
bibliographic citation: Thomas et al. (2018) The rice XA21 ectodomain fused to the Arabidopsis EFR cytoplasmic domain confers resistance to Xanthomonas oryzae pv. oryzae. PeerJ 6:e4456 https://doi.org/10.7717/peerj.4456
date submitted: 2017-04-19
date accepted: 2018-02-15
issued: 2018-05-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomas
  given name: Nicholas C.
author list: Agent
  family name: Oksenberg
  given name: Nir
author list: Agent
  family name: Liu
  given name: Furong
author list: Agent
  family name: Caddell
  given name: Daniel
author list: Agent
  family name: Nalyvayko
  given name: Alina
author list: Agent
  family name: Nguyen
  given name: Yen
author list: Agent
  family name: Schwessinger
  given name: Benjamin
author list: Agent
  family name: Ronald
  given name: Pamela C.
doi: 10.7717/peerj.4456
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-09
copyright: © 2018 Thomas et al.
attribution name: Thomas et al.

Transcriptomic studies reveal a key metabolic pathway contributing to a well-maintained photosynthetic system under drought stress in foxtail millet (Setaria italica L.)
type: item
type: AcademicArticle
description: Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet (Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F1 hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents. A transcriptomic study using leaves collected six days after drought treatment, when the soil water content was about ∼20%, identified 3066, 1895, and 2148 differentially expressed genes (DEGs) in M79, E1 and H1 compared to the respective untreated controls, respectively. Further analysis revealed 17 Gene Ontology (GO) enrichments and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in M79, including photosystem II (PSII) oxygen-evolving complex, peroxidase (POD) activity, plant hormone signal transduction, and chlorophyll biosynthesis. Co-regulation analysis suggested that these DEGs in M79 contributed to the formation of a regulatory network involving multiple biological processes and pathways including photosynthesis, signal transduction, transcriptional regulation, redox regulation, hormonal signaling, and osmotic regulation. RNA-seq analysis also showed that some photosynthesis-related DEGs were highly expressed in M79 compared to its parental lines under drought stress. These results indicate that various molecular pathways, including photosynthesis, respond to drought stress in M79, and provide abundant molecular information for further analysis of the underlying mechanism responding to this stress.
format: application/pdf
format: text/html
creator: Weiping Shi
creator: Jingye Cheng
creator: Xiaojie Wen
creator: Jixiang Wang
creator: Guanyan Shi
creator: Jiayan Yao
creator: Liyuan Hou
creator: Qian Sun
creator: Peng Xiang
creator: Xiangyang Yuan
creator: Shuqi Dong
creator: Pingyi Guo
creator: Jie Guo
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.4752
publisher: PeerJ Inc.
rights: © 2018 Shi et al.
abstract: Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet (Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F1 hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents. A transcriptomic study using leaves collected six days after drought treatment, when the soil water content was about ∼20%, identified 3066, 1895, and 2148 differentially expressed genes (DEGs) in M79, E1 and H1 compared to the respective untreated controls, respectively. Further analysis revealed 17 Gene Ontology (GO) enrichments and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in M79, including photosystem II (PSII) oxygen-evolving complex, peroxidase (POD) activity, plant hormone signal transduction, and chlorophyll biosynthesis. Co-regulation analysis suggested that these DEGs in M79 contributed to the formation of a regulatory network involving multiple biological processes and pathways including photosynthesis, signal transduction, transcriptional regulation, redox regulation, hormonal signaling, and osmotic regulation. RNA-seq analysis also showed that some photosynthesis-related DEGs were highly expressed in M79 compared to its parental lines under drought stress. These results indicate that various molecular pathways, including photosynthesis, respond to drought stress in M79, and provide abundant molecular information for further analysis of the underlying mechanism responding to this stress.
bibliographic citation: Shi et al. (2018) Transcriptomic studies reveal a key metabolic pathway contributing to a well-maintained photosynthetic system under drought stress in foxtail millet (Setaria italica L.). PeerJ 6:e4752 https://doi.org/10.7717/peerj.4752
date submitted: 2018-02-27
date accepted: 2018-04-22
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Weiping
author list: Agent
  family name: Cheng
  given name: Jingye
author list: Agent
  family name: Wen
  given name: Xiaojie
author list: Agent
  family name: Wang
  given name: Jixiang
author list: Agent
  family name: Shi
  given name: Guanyan
author list: Agent
  family name: Yao
  given name: Jiayan
author list: Agent
  family name: Hou
  given name: Liyuan
author list: Agent
  family name: Sun
  given name: Qian
author list: Agent
  family name: Xiang
  given name: Peng
author list: Agent
  family name: Yuan
  given name: Xiangyang
author list: Agent
  family name: Dong
  given name: Shuqi
author list: Agent
  family name: Guo
  given name: Pingyi
author list: Agent
  family name: Guo
  given name: Jie
doi: 10.7717/peerj.4752
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: ©2018 Shi et al.
attribution name: Shi et al.

Biodiversity of the Great Barrier Reef—how adequately is it protected?
type: item
type: AcademicArticle
description: Background The Great Barrier Reef (GBR) is the world’s most iconic coral reef ecosystem, recognised internationally as a World Heritage Area of outstanding significance. Safeguarding the biodiversity of this universally important reef is a core legislative objective; however, ongoing cumulative impacts including widespread coral bleaching and other detrimental impacts have heightened conservation concerns for the future of the GBR. Methods Here we review the literature to report on processes threatening species on the GBR, the status of marine biodiversity, and evaluate the extent of species-level monitoring and reporting. We assess how many species are listed as threatened at a global scale and explore whether these same species are protected under national threatened species legislation. We conclude this review by providing future directions for protecting potentially endangered elements of biodiversity within the GBR. Results Most of the threats identified to be harming the diversity of marine life on the GBR over the last two–three decades remain to be effectively addressed and many are worsening. The inherent resilience of this globally significant coral reef ecosystem has been seriously compromised and various elements of the biological diversity for which it is renowned may be at risk of silent extinction. We show at least 136 of the 12,000+ animal species known to occur on the GBR (approximately 20% of the 700 species assessed by the IUCN) occur in elevated categories of threat (Critically Endangered, Endangered or Vulnerable) at a global scale. Despite the wider background level of threat for these 136 species, only 23 of them are listed as threatened under regional or national legislation. Discussion To adequately protect the biodiversity values of the GBR, it may be necessary to conduct further targeted species-level monitoring and reporting to complement ecosystem management approaches. Conducting a vigorous value of information analysis would provide th…
format: application/pdf
format: text/html
creator: Zoe T. Richards
creator: Jon C. Day
subject: Biodiversity
subject: Marine Biology
subject: Climate Change Biology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.4747
publisher: PeerJ Inc.
rights: © 2018 Richards et al.
abstract: Background The Great Barrier Reef (GBR) is the world’s most iconic coral reef ecosystem, recognised internationally as a World Heritage Area of outstanding significance. Safeguarding the biodiversity of this universally important reef is a core legislative objective; however, ongoing cumulative impacts including widespread coral bleaching and other detrimental impacts have heightened conservation concerns for the future of the GBR. Methods Here we review the literature to report on processes threatening species on the GBR, the status of marine biodiversity, and evaluate the extent of species-level monitoring and reporting. We assess how many species are listed as threatened at a global scale and explore whether these same species are protected under national threatened species legislation. We conclude this review by providing future directions for protecting potentially endangered elements of biodiversity within the GBR. Results Most of the threats identified to be harming the diversity of marine life on the GBR over the last two–three decades remain to be effectively addressed and many are worsening. The inherent resilience of this globally significant coral reef ecosystem has been seriously compromised and various elements of the biological diversity for which it is renowned may be at risk of silent extinction. We show at least 136 of the 12,000+ animal species known to occur on the GBR (approximately 20% of the 700 species assessed by the IUCN) occur in elevated categories of threat (Critically Endangered, Endangered or Vulnerable) at a global scale. Despite the wider background level of threat for these 136 species, only 23 of them are listed as threatened under regional or national legislation. Discussion To adequately protect the biodiversity values of the GBR, it may be necessary to conduct further targeted species-level monitoring and reporting to complement ecosystem management approaches. Conducting a vigorous value of information analysis would provide th…
bibliographic citation: Richards et al. (2018) Biodiversity of the Great Barrier Reef—how adequately is it protected?. PeerJ 6:e4747 https://doi.org/10.7717/peerj.4747
date submitted: 2017-10-27
date accepted: 2018-04-21
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Richards
  given name: Zoe T.
author list: Agent
  family name: Day
  given name: Jon C.
doi: 10.7717/peerj.4747
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: © 2018 Richards and Day
attribution name: Richards et al.

Nature-derived lignan compound VB-1 exerts hair growth-promoting effects by augmenting Wnt/β-catenin signaling in human dermal papilla cells
type: item
type: AcademicArticle
description: Background Vitexin is a kind of lignan compound which has been shown to possess a variety of pharmacological effects, such as anti-inflammatory, anti-oxidative and anti-cancer activities. However the effect of vitexin on hair regeneration has not been elaborated. Methods The proliferation of human dermal papilla cells (hDPCs) was examined by cell counting and continuous cell culture after vitexin compound 1 (VB-1) was treated. The expression of lef1, wnt5a, bmp2, bmp4, alpl and vcan was examined by RT-PCR. The expression of dkk1, tgf-β1, active-β-Catenin, and AXIN2 was examined by RT-PCR or immunoblotting. Hair shaft growth was measured in the absence or presence of VB-1. Results We demonstrated that VB-1 significantly promotes the proliferation of hDPCs in a concentration-dependent manner within a certain concentration range. Among the hair growth-related genes investigated, dkk1 was clearly down-regulated in hDPCs treated with VB-1. The increased active β-Catenin and decreased AXIN2 protein levels suggest that VB-1 facilitates Wnt/β-catenin signaling in hDPCs in vitro. The expression of DP signature genes was also upregulated after VB-1 treatment. Our study further indicated that VB-1 promotes human hair follicle (HF) growth by HF organ culture assay. Discussion VB-1 may exert hair growth-promoting effects via augmenting Wnt/β-catenin signaling in hDPCs.
format: application/pdf
format: text/html
creator: Jieshu Luo
creator: Mengting Chen
creator: Yingzi Liu
creator: Hongfu Xie
creator: Jian Yuan
creator: Yingjun Zhou
creator: Jinsong Ding
creator: Zhili Deng
creator: Ji Li
subject: Cell Biology
subject: Molecular Biology
subject: Dermatology
subject: Pharmacology
description: doi:10.7717/peerj.4737
publisher: PeerJ Inc.
rights: © 2018 Luo et al.
abstract: Background Vitexin is a kind of lignan compound which has been shown to possess a variety of pharmacological effects, such as anti-inflammatory, anti-oxidative and anti-cancer activities. However the effect of vitexin on hair regeneration has not been elaborated. Methods The proliferation of human dermal papilla cells (hDPCs) was examined by cell counting and continuous cell culture after vitexin compound 1 (VB-1) was treated. The expression of lef1, wnt5a, bmp2, bmp4, alpl and vcan was examined by RT-PCR. The expression of dkk1, tgf-β1, active-β-Catenin, and AXIN2 was examined by RT-PCR or immunoblotting. Hair shaft growth was measured in the absence or presence of VB-1. Results We demonstrated that VB-1 significantly promotes the proliferation of hDPCs in a concentration-dependent manner within a certain concentration range. Among the hair growth-related genes investigated, dkk1 was clearly down-regulated in hDPCs treated with VB-1. The increased active β-Catenin and decreased AXIN2 protein levels suggest that VB-1 facilitates Wnt/β-catenin signaling in hDPCs in vitro. The expression of DP signature genes was also upregulated after VB-1 treatment. Our study further indicated that VB-1 promotes human hair follicle (HF) growth by HF organ culture assay. Discussion VB-1 may exert hair growth-promoting effects via augmenting Wnt/β-catenin signaling in hDPCs.
bibliographic citation: Luo et al. (2018) Nature-derived lignan compound VB-1 exerts hair growth-promoting effects by augmenting Wnt/β-catenin signaling in human dermal papilla cells. PeerJ 6:e4737 https://doi.org/10.7717/peerj.4737
date submitted: 2018-02-27
date accepted: 2018-04-20
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Jieshu
author list: Agent
  family name: Chen
  given name: Mengting
author list: Agent
  family name: Liu
  given name: Yingzi
author list: Agent
  family name: Xie
  given name: Hongfu
author list: Agent
  family name: Yuan
  given name: Jian
author list: Agent
  family name: Zhou
  given name: Yingjun
author list: Agent
  family name: Ding
  given name: Jinsong
author list: Agent
  family name: Deng
  given name: Zhili
author list: Agent
  family name: Li
  given name: Ji
doi: 10.7717/peerj.4737
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: ©2018 Luo et al.
attribution name: Luo et al.

Asymmetries in mother-infant behaviour in Barbary macaques (Macaca sylvanus)
type: item
type: AcademicArticle
description: Asymmetries in the maternal behaviour and anatomy might play an important role in the development of primate manual lateralization. In particular, early life asymmetries in mother’s and infant’s behaviour have been suggested to be associated with the development of the hand preference of the offspring. The aim of this study was to investigate the presence of behavioural asymmetries in different behavioural categories of mother-infant dyads of zoo-living Barbary macaques (Macaca sylvanus). The study subjects were 14 Barbary macaques involved in seven mother-infant dyads housed in Parco Natura Viva, Italy. For the mothers, bouts of hand preference for maternal cradling and infant retrieval were collected. For the infants, we focused on nipple preference and hand preference for clinging on mother ventrum. Moreover, we collected bouts of hand preference for food reaching in both groups. No significant group-level bias was found for any of the behavioural categories in either mothers or infants. However, at the individual level, six out of seven mothers showed a significant cradling bias, three toward the right hand and three toward the left hand. Moreover, all infants showed a significant nipple preference, six toward the mother’s right nipple, one toward the left nipple. Furthermore, a significant correlation was found between the infant nipple preference and their hand preference for food reaching, suggesting that maternal environment rather than behaviour might affect the development of hand preference in Old World monkeys. Our findings seem partially to add to previous literature on perceptual lateralization in different species of non-primate mammals, reporting a lateral bias in mother-infant interactions. Given the incongruences between our study and previous research in great apes and humans, our results seem to suggest possible phylogenetic differences in the lateralization of mothers and infants within the Primates order.
format: application/pdf
format: text/html
creator: Barbara Regaiolli
creator: Caterina Spiezio
creator: William Donald Hopkins
subject: Animal Behavior
subject: Developmental Biology
subject: Ecology
subject: Evolutionary Studies
subject: Neuroscience
description: doi:10.7717/peerj.4736
publisher: PeerJ Inc.
rights: © 2018 Regaiolli et al.
abstract: Asymmetries in the maternal behaviour and anatomy might play an important role in the development of primate manual lateralization. In particular, early life asymmetries in mother’s and infant’s behaviour have been suggested to be associated with the development of the hand preference of the offspring. The aim of this study was to investigate the presence of behavioural asymmetries in different behavioural categories of mother-infant dyads of zoo-living Barbary macaques (Macaca sylvanus). The study subjects were 14 Barbary macaques involved in seven mother-infant dyads housed in Parco Natura Viva, Italy. For the mothers, bouts of hand preference for maternal cradling and infant retrieval were collected. For the infants, we focused on nipple preference and hand preference for clinging on mother ventrum. Moreover, we collected bouts of hand preference for food reaching in both groups. No significant group-level bias was found for any of the behavioural categories in either mothers or infants. However, at the individual level, six out of seven mothers showed a significant cradling bias, three toward the right hand and three toward the left hand. Moreover, all infants showed a significant nipple preference, six toward the mother’s right nipple, one toward the left nipple. Furthermore, a significant correlation was found between the infant nipple preference and their hand preference for food reaching, suggesting that maternal environment rather than behaviour might affect the development of hand preference in Old World monkeys. Our findings seem partially to add to previous literature on perceptual lateralization in different species of non-primate mammals, reporting a lateral bias in mother-infant interactions. Given the incongruences between our study and previous research in great apes and humans, our results seem to suggest possible phylogenetic differences in the lateralization of mothers and infants within the Primates order.
bibliographic citation: Regaiolli et al. (2018) Asymmetries in mother-infant behaviour in Barbary macaques (Macaca sylvanus). PeerJ 6:e4736 https://doi.org/10.7717/peerj.4736
date submitted: 2018-02-23
date accepted: 2018-04-19
issued: 2018-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Regaiolli
  given name: Barbara
author list: Agent
  family name: Spiezio
  given name: Caterina
author list: Agent
  family name: Hopkins
  given name: William Donald
doi: 10.7717/peerj.4736
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-08
copyright: ©2018 Regaiolli et al.
attribution name: Regaiolli et al.

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