PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Pyrrolizidine alkaloid variation in Senecio vulgaris populations from native and invasive ranges
items: MicroRNAs tend to synergistically control expression of genes encoding extensively-expressed proteins in humans
items: Presence of the tunicate Asterocarpa humilis on ship hulls and aquaculture facilities in the coast of the Biobío Region, south central Chile
items: Planting of neonicotinoid-coated corn raises honey bee mortality and sets back colony development
items: Exercise training with dietary restriction enhances circulating irisin level associated with increasing endothelial progenitor cell number in obese adults: an intervention study
items: The effects of captive versus wild rearing environments on long bone articular surfaces in common chimpanzees (Pan troglodytes)
items: The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes
items: Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton
items: Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model
items: Microbial communities in the reef water at Kham Island, lower Gulf of Thailand

Pyrrolizidine alkaloid variation in Senecio vulgaris populations from native and invasive ranges
type: item
type: AcademicArticle
description: Biological invasion is regarded as one of the greatest environmental problems facilitated by globalization. Some hypotheses about the invasive mechanisms of alien invasive plants consider the plant–herbivore interaction and the role of plant defense in this interaction. For example, the “Shift Defense Hypothesis” (SDH) argues that introduced plants evolve higher levels of qualitative defense chemicals and decreased levels of quantitative defense, as they are released of the selective pressures from specialist herbivores but still face attack from generalists. Common groundsel (Senecio vulgaris), originating from Europe, is a cosmopolitan invasive plant in temperate regions. As in other Senecio species, S. vulgaris contains pyrrolizidine alkaloids (PAs) as characteristic qualitative defense compounds. In this study, S. vulgaris plants originating from native and invasive ranges (Europe and China, respectively) were grown under identical conditions and harvested upon flowering. PA composition and concentration in shoot and root samples were determined using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). We investigated the differences between native and invasive S. vulgaris populations with regard to quantitative and qualitative variation of PAs. We identified 20 PAs, among which senecionine, senecionine N-oxide, integerrimine N-oxide and seneciphylline N-oxide were dominant in the roots. In the shoots, in addition to the 4 PAs dominant in roots, retrorsine N-oxide, spartioidine N-oxide and 2 non-identified PAs were also prevalent. The roots possessed a lower PA diversity but a higher total PA concentration than the shoots. Most individual PAs as well as the total PA concentration were strongly positively correlated between the roots and shoots. Both native and invasive S. vulgaris populations shared the pattern described above. However, there was a slight trend indicating lower PA diversity and lower total PA concentration in invasive S. vulgaris populati…
format: application/pdf
format: text/html
creator: Dandan Cheng
creator: Viet-Thang Nguyen
creator: Noel Ndihokubwayo
creator: Jiwen Ge
creator: Patrick P.J. Mulder
subject: Agricultural Science
subject: Biochemistry
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.3686
publisher: PeerJ Inc.
rights: © 2017 Cheng et al.
abstract: Biological invasion is regarded as one of the greatest environmental problems facilitated by globalization. Some hypotheses about the invasive mechanisms of alien invasive plants consider the plant–herbivore interaction and the role of plant defense in this interaction. For example, the “Shift Defense Hypothesis” (SDH) argues that introduced plants evolve higher levels of qualitative defense chemicals and decreased levels of quantitative defense, as they are released of the selective pressures from specialist herbivores but still face attack from generalists. Common groundsel (Senecio vulgaris), originating from Europe, is a cosmopolitan invasive plant in temperate regions. As in other Senecio species, S. vulgaris contains pyrrolizidine alkaloids (PAs) as characteristic qualitative defense compounds. In this study, S. vulgaris plants originating from native and invasive ranges (Europe and China, respectively) were grown under identical conditions and harvested upon flowering. PA composition and concentration in shoot and root samples were determined using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). We investigated the differences between native and invasive S. vulgaris populations with regard to quantitative and qualitative variation of PAs. We identified 20 PAs, among which senecionine, senecionine N-oxide, integerrimine N-oxide and seneciphylline N-oxide were dominant in the roots. In the shoots, in addition to the 4 PAs dominant in roots, retrorsine N-oxide, spartioidine N-oxide and 2 non-identified PAs were also prevalent. The roots possessed a lower PA diversity but a higher total PA concentration than the shoots. Most individual PAs as well as the total PA concentration were strongly positively correlated between the roots and shoots. Both native and invasive S. vulgaris populations shared the pattern described above. However, there was a slight trend indicating lower PA diversity and lower total PA concentration in invasive S. vulgaris populati…
bibliographic citation: Cheng et al. (2017) Pyrrolizidine alkaloid variation in Senecio vulgaris populations from native and invasive ranges. PeerJ 5:e3686 https://doi.org/10.7717/peerj.3686
date submitted: 2017-04-14
date accepted: 2017-07-24
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Dandan
author list: Agent
  family name: Nguyen
  given name: Viet-Thang
author list: Agent
  family name: Ndihokubwayo
  given name: Noel
author list: Agent
  family name: Ge
  given name: Jiwen
author list: Agent
  family name: Mulder
  given name: Patrick P.J.
doi: 10.7717/peerj.3686
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Cheng et al.
attribution name: Cheng et al.

MicroRNAs tend to synergistically control expression of genes encoding extensively-expressed proteins in humans
type: item
type: AcademicArticle
description: Considering complicated microRNA (miRNA) biogenesis and action mechanisms, it was thought so high energy-consuming for a cell to afford simultaneous over-expression of many miRNAs. Thus it prompts that an alternative miRNA regulation pattern on protein-encoding genes must exist, which has characteristics of energy-saving and precise protein output. In this study, expression tendency of proteins encoded by miRNAs’ target genes was evaluated in human organ scale, followed by quantitative assessment of miRNA synergism. Expression tendency analysis suggests that universally expressed proteins (UEPs) tend to physically interact in clusters and participate in fundamental biological activities whereas disorderly expressed proteins (DEPs) are inclined to relatively independently execute organ-specific functions. Consistent with this, miRNAs that mainly target UEP-encoding mRNAs, such as miR-21, tend to collaboratively or even synergistically act with other miRNAs in fine-tuning protein output. Synergistic gene regulation may maximize miRNAs’ efficiency with less dependence on miRNAs’ abundance and overcome the deficiency that targeting plenty of genes by single miRNA makes miRNA-mediated regulation high-throughput but insufficient due to target gene dilution effect. Furthermore, our in vitro experiment verified that merely 25 nM transfection of miR-21 be sufficient to influence the overall state of various human cells. Thus miR-21 was identified as a hub in synergistic miRNA–miRNA interaction network. Our findings suggest that synergistic miRNA–miRNA interaction is an important endogenous miRNA regulation mode, which ensures adequate potency of miRNAs at low abundance, especially those implicated in fundamental biological regulation.
format: application/pdf
format: text/html
creator: Xue Chen
creator: Wei Zhao
creator: Ye Yuan
creator: Yan Bai
creator: Yong Sun
creator: Wenliang Zhu
creator: Zhimin Du
subject: Bioinformatics
subject: Cell Biology
subject: Computational Biology
description: doi:10.7717/peerj.3682
publisher: PeerJ Inc.
rights: © 2017 Chen et al.
abstract: Considering complicated microRNA (miRNA) biogenesis and action mechanisms, it was thought so high energy-consuming for a cell to afford simultaneous over-expression of many miRNAs. Thus it prompts that an alternative miRNA regulation pattern on protein-encoding genes must exist, which has characteristics of energy-saving and precise protein output. In this study, expression tendency of proteins encoded by miRNAs’ target genes was evaluated in human organ scale, followed by quantitative assessment of miRNA synergism. Expression tendency analysis suggests that universally expressed proteins (UEPs) tend to physically interact in clusters and participate in fundamental biological activities whereas disorderly expressed proteins (DEPs) are inclined to relatively independently execute organ-specific functions. Consistent with this, miRNAs that mainly target UEP-encoding mRNAs, such as miR-21, tend to collaboratively or even synergistically act with other miRNAs in fine-tuning protein output. Synergistic gene regulation may maximize miRNAs’ efficiency with less dependence on miRNAs’ abundance and overcome the deficiency that targeting plenty of genes by single miRNA makes miRNA-mediated regulation high-throughput but insufficient due to target gene dilution effect. Furthermore, our in vitro experiment verified that merely 25 nM transfection of miR-21 be sufficient to influence the overall state of various human cells. Thus miR-21 was identified as a hub in synergistic miRNA–miRNA interaction network. Our findings suggest that synergistic miRNA–miRNA interaction is an important endogenous miRNA regulation mode, which ensures adequate potency of miRNAs at low abundance, especially those implicated in fundamental biological regulation.
bibliographic citation: Chen et al. (2017) MicroRNAs tend to synergistically control expression of genes encoding extensively-expressed proteins in humans. PeerJ 5:e3682 https://doi.org/10.7717/peerj.3682
date submitted: 2017-03-04
date accepted: 2017-07-22
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xue
author list: Agent
  family name: Zhao
  given name: Wei
author list: Agent
  family name: Yuan
  given name: Ye
author list: Agent
  family name: Bai
  given name: Yan
author list: Agent
  family name: Sun
  given name: Yong
author list: Agent
  family name: Zhu
  given name: Wenliang
author list: Agent
  family name: Du
  given name: Zhimin
doi: 10.7717/peerj.3682
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Chen et al.
attribution name: Chen et al.

Presence of the tunicate Asterocarpa humilis on ship hulls and aquaculture facilities in the coast of the Biobío Region, south central Chile
type: item
type: AcademicArticle
description: Non-native ascidians are important members of the fouling community associated with artificial substrata and man-made structures. Being efficient fouling species, they are easily spread by human-mediated transports (e.g., with aquaculture trade and maritime transports). This is exemplified by the ascidian Asterocarpa humilis which displays a wide distribution in the Southern Hemisphere and has been recently reported in the Northern Hemisphere (NW Europe). In continental Chile, its first report dates back from 2000 for the locality of Antofagasta (23°S). Although there was no evidence about the vectors of introduction and spread, nor the source, some authors suggested maritime transport by ship hulls and aquaculture devices as putative introduction pathways and vectors. In the present study, we report for the first time the presence of A. humilis on the hull of an international ship in a commercial port in Concepción bay (36°S), south central Chile. We also found one individual associated to a seashell farm, 70 km far from Concepción bay. Further individuals were subsequently identified within Concepción bay: one juvenile settled upon international harbor pilings and a dozen individuals along aquaculture seashell longlines. For the first specimens sampled, species identification was ascertained using both morphological criteria and molecular barcoding, using the mitochondrial gene cytochrome c oxidase subunit I (COI) and a nuclear gene (ribosomal RNA 18S). The nuclear 18S gene and the mitochondrial gene COI clearly assigned the specimens to A. humilis, confirming our morphological identification. Two haplotypes were obtained with COI corresponding to haplotypes previously obtained with European and Northern Chilean specimens. The present study thus reports for the first time the presence of A. humilis in the Araucanian ecoregion, documenting the apparent expansion of this non-native tunicate in Chile over 2,000 km, spanning over three ecoregions. In addition we revea…
format: application/pdf
format: text/html
creator: Javier Pinochet
creator: Jean-Charles Leclerc
creator: Antonio Brante
creator: Claire Daguin-Thiébaut
creator: Christian Díaz
creator: Florence Tellier
creator: Frédérique Viard
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.3672
publisher: PeerJ Inc.
rights: © 2017 Pinochet et al.
abstract: Non-native ascidians are important members of the fouling community associated with artificial substrata and man-made structures. Being efficient fouling species, they are easily spread by human-mediated transports (e.g., with aquaculture trade and maritime transports). This is exemplified by the ascidian Asterocarpa humilis which displays a wide distribution in the Southern Hemisphere and has been recently reported in the Northern Hemisphere (NW Europe). In continental Chile, its first report dates back from 2000 for the locality of Antofagasta (23°S). Although there was no evidence about the vectors of introduction and spread, nor the source, some authors suggested maritime transport by ship hulls and aquaculture devices as putative introduction pathways and vectors. In the present study, we report for the first time the presence of A. humilis on the hull of an international ship in a commercial port in Concepción bay (36°S), south central Chile. We also found one individual associated to a seashell farm, 70 km far from Concepción bay. Further individuals were subsequently identified within Concepción bay: one juvenile settled upon international harbor pilings and a dozen individuals along aquaculture seashell longlines. For the first specimens sampled, species identification was ascertained using both morphological criteria and molecular barcoding, using the mitochondrial gene cytochrome c oxidase subunit I (COI) and a nuclear gene (ribosomal RNA 18S). The nuclear 18S gene and the mitochondrial gene COI clearly assigned the specimens to A. humilis, confirming our morphological identification. Two haplotypes were obtained with COI corresponding to haplotypes previously obtained with European and Northern Chilean specimens. The present study thus reports for the first time the presence of A. humilis in the Araucanian ecoregion, documenting the apparent expansion of this non-native tunicate in Chile over 2,000 km, spanning over three ecoregions. In addition we revea…
bibliographic citation: Pinochet et al. (2017) Presence of the tunicate Asterocarpa humilis on ship hulls and aquaculture facilities in the coast of the Biobío Region, south central Chile. PeerJ 5:e3672 https://doi.org/10.7717/peerj.3672
date submitted: 2017-04-11
date accepted: 2017-07-21
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pinochet
  given name: Javier
author list: Agent
  family name: Leclerc
  given name: Jean-Charles
author list: Agent
  family name: Brante
  given name: Antonio
author list: Agent
  family name: Daguin-Thiébaut
  given name: Claire
author list: Agent
  family name: Díaz
  given name: Christian
author list: Agent
  family name: Tellier
  given name: Florence
author list: Agent
  family name: Viard
  given name: Frédérique
doi: 10.7717/peerj.3672
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Pinochet et al.
attribution name: Pinochet et al.

Planting of neonicotinoid-coated corn raises honey bee mortality and sets back colony development
type: item
type: AcademicArticle
description: Worldwide occurrences of honey bee colony losses have raised concerns about bee health and the sustainability of pollination-dependent crops. While multiple causal factors have been identified, seed coating with insecticides of the neonicotinoid family has been the focus of much discussion and research. Nonetheless, few studies have investigated the impacts of these insecticides under field conditions or in commercial beekeeping operations. Given that corn-seed coating constitutes the largest single use of neonicotinoid, our study compared honey bee mortality from commercial apiaries located in two different agricultural settings, i.e. corn-dominated areas and corn-free environments, during the corn planting season. Data was collected in 2012 and 2013 from 26 bee yards. Dead honey bees from five hives in each apiary were counted and collected, and samples were analyzed using a multi-residue LC-MS/MS method. Long-term effects on colony development were simulated based on a honey bee population dynamic model. Mortality survey showed that colonies located in a corn-dominated area had daily mortality counts 3.51 times those of colonies from corn crop-free sites. Chemical analyses revealed that honey bees were exposed to various agricultural pesticides during the corn planting season, but were primarily subjected to neonicotinoid compounds (54% of analysed samples contained clothianidin, and 31% contained both clothianidin and thiamethoxam). Performance development simulations performed on hive populations’ show that increased mortality during the corn planting season sets back colony development and bears contributions to collapse risk but, most of all, reduces the effectiveness and value of colonies for pollination services. Our results also have implications for the numerous large-scale and worldwide-cultivated crops that currently rely on pre-emptive use of neonicotinoid seed treatments.
format: application/pdf
format: text/html
creator: Olivier Samson-Robert
creator: Geneviève Labrie
creator: Madeleine Chagnon
creator: Valérie Fournier
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.3670
publisher: PeerJ Inc.
rights: © 2017 Samson-Robert et al.
abstract: Worldwide occurrences of honey bee colony losses have raised concerns about bee health and the sustainability of pollination-dependent crops. While multiple causal factors have been identified, seed coating with insecticides of the neonicotinoid family has been the focus of much discussion and research. Nonetheless, few studies have investigated the impacts of these insecticides under field conditions or in commercial beekeeping operations. Given that corn-seed coating constitutes the largest single use of neonicotinoid, our study compared honey bee mortality from commercial apiaries located in two different agricultural settings, i.e. corn-dominated areas and corn-free environments, during the corn planting season. Data was collected in 2012 and 2013 from 26 bee yards. Dead honey bees from five hives in each apiary were counted and collected, and samples were analyzed using a multi-residue LC-MS/MS method. Long-term effects on colony development were simulated based on a honey bee population dynamic model. Mortality survey showed that colonies located in a corn-dominated area had daily mortality counts 3.51 times those of colonies from corn crop-free sites. Chemical analyses revealed that honey bees were exposed to various agricultural pesticides during the corn planting season, but were primarily subjected to neonicotinoid compounds (54% of analysed samples contained clothianidin, and 31% contained both clothianidin and thiamethoxam). Performance development simulations performed on hive populations’ show that increased mortality during the corn planting season sets back colony development and bears contributions to collapse risk but, most of all, reduces the effectiveness and value of colonies for pollination services. Our results also have implications for the numerous large-scale and worldwide-cultivated crops that currently rely on pre-emptive use of neonicotinoid seed treatments.
bibliographic citation: Samson-Robert et al. (2017) Planting of neonicotinoid-coated corn raises honey bee mortality and sets back colony development. PeerJ 5:e3670 https://doi.org/10.7717/peerj.3670
date submitted: 2017-05-16
date accepted: 2017-07-20
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Samson-Robert
  given name: Olivier
author list: Agent
  family name: Labrie
  given name: Geneviève
author list: Agent
  family name: Chagnon
  given name: Madeleine
author list: Agent
  family name: Fournier
  given name: Valérie
doi: 10.7717/peerj.3670
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Samson-Robert et al.
attribution name: Samson-Robert et al.

Exercise training with dietary restriction enhances circulating irisin level associated with increasing endothelial progenitor cell number in obese adults: an intervention study
type: item
type: AcademicArticle
description: Objective Circulating endothelial progenitor cells (EPCs) correlate negatively with obesity. Previous studies have shown that exercise significantly restores circulating EPC levels in obese people; however, the underlying mechanisms have not been elucidated. Recently, irisin has been reported to have a critical role in the regulation of EPCs. This exercise-induced myokine has been demonstrated to play a therapeutic role in obesity. In this study, we hypothesized that the increase in circulating irisin may form a link with increasing EPC levels in obese people after exercise. Methods Seventeen obese adults completed an 8-week program of combined exercise and dietary intervention. Clinical characteristics, blood biochemistry, and circulating irisin levels of subjects were measured before and after eight weeks of training. EPC levels were evaluated via flow cytometry, and EPC migratory and adhesive functions were also determined. Results Circulating irisin levels significantly increased following the 8-week training program (P < 0.05). We furthermore observed an improvement in EPC numbers (P < 0.05), and EPC migratory and adhesive functions (P < 0.001 and P < 0.05, respectively) after the intervention. Additionally, we detected a positive correlation between changes in irisin and changes in EPC number (r = 0.52, P < 0.05). Discussion For the first time, a positive correlation between increasing irisin levels and increasing EPC levels has been reported after an 8-week program, consisting of exercise and dietary intervention. This result suggests a novel effect of irisin on the regulation of EPC mobilization, which might contribute to improvement of endothelial function in obese people.
format: application/pdf
format: text/html
creator: Junhao Huang
creator: Shen Wang
creator: Fengpeng Xu
creator: Dan Wang
creator: Honggang Yin
creator: Qinhao Lai
creator: Jingwen Liao
creator: Xiaohui Hou
creator: Min Hu
subject: Neuroscience
subject: Cardiology
subject: Clinical Trials
subject: Nutrition
description: doi:10.7717/peerj.3669
publisher: PeerJ Inc.
rights: © 2017 Huang et al.
abstract: Objective Circulating endothelial progenitor cells (EPCs) correlate negatively with obesity. Previous studies have shown that exercise significantly restores circulating EPC levels in obese people; however, the underlying mechanisms have not been elucidated. Recently, irisin has been reported to have a critical role in the regulation of EPCs. This exercise-induced myokine has been demonstrated to play a therapeutic role in obesity. In this study, we hypothesized that the increase in circulating irisin may form a link with increasing EPC levels in obese people after exercise. Methods Seventeen obese adults completed an 8-week program of combined exercise and dietary intervention. Clinical characteristics, blood biochemistry, and circulating irisin levels of subjects were measured before and after eight weeks of training. EPC levels were evaluated via flow cytometry, and EPC migratory and adhesive functions were also determined. Results Circulating irisin levels significantly increased following the 8-week training program (P < 0.05). We furthermore observed an improvement in EPC numbers (P < 0.05), and EPC migratory and adhesive functions (P < 0.001 and P < 0.05, respectively) after the intervention. Additionally, we detected a positive correlation between changes in irisin and changes in EPC number (r = 0.52, P < 0.05). Discussion For the first time, a positive correlation between increasing irisin levels and increasing EPC levels has been reported after an 8-week program, consisting of exercise and dietary intervention. This result suggests a novel effect of irisin on the regulation of EPC mobilization, which might contribute to improvement of endothelial function in obese people.
bibliographic citation: Huang et al. (2017) Exercise training with dietary restriction enhances circulating irisin level associated with increasing endothelial progenitor cell number in obese adults: an intervention study. PeerJ 5:e3669 https://doi.org/10.7717/peerj.3669
date submitted: 2017-05-23
date accepted: 2017-07-20
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Junhao
author list: Agent
  family name: Wang
  given name: Shen
author list: Agent
  family name: Xu
  given name: Fengpeng
author list: Agent
  family name: Wang
  given name: Dan
author list: Agent
  family name: Yin
  given name: Honggang
author list: Agent
  family name: Lai
  given name: Qinhao
author list: Agent
  family name: Liao
  given name: Jingwen
author list: Agent
  family name: Hou
  given name: Xiaohui
author list: Agent
  family name: Hu
  given name: Min
doi: 10.7717/peerj.3669
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Huang et al.
attribution name: Huang et al.

The effects of captive versus wild rearing environments on long bone articular surfaces in common chimpanzees (Pan troglodytes)
type: item
type: AcademicArticle
description: The physical environments of captive and wild animals frequently differ in substrate types and compliance. As a result, there is an assumption that differences in rearing environments between captive and wild individuals produce differences in skeletal morphology. Here, this hypothesis is tested using a sample of 42 captive and wild common chimpanzees (Pan troglodytes). Articular surface areas of the humerus, radius, ulna, femur, and tibia were calculated from linear breadth measurements, adjusted for size differences using Mosimann shape variables, and compared across sex and environmental groups using two-way ANOVA. Results indicate that the articular surfaces of the wrist and knee differ between captive and wild chimpanzees; captive individuals have significantly larger distal ulna and tibial plateau articular surfaces. In both captive and wild chimpanzees, males have significantly larger femoral condyles and distal radius surfaces than females. Finally, there is an interaction effect between sex and rearing in the articular surfaces of the femoral condyles and distal radius in which captive males have significantly larger surface areas than all other sex-rearing groups. These data suggest that long bone articular surfaces may be sensitive to differences experienced by captive and wild individuals, such as differences in diet, body mass, positional behaviors, and presumed loading environments. Importantly, these results only find differences due to rearing environment in some long bone articular surfaces. Thus, future work on skeletal morphology could cautiously incorporate data from captive individuals, but should first investigate potential intraspecific differences between captive and wild individuals.
format: application/pdf
format: text/html
creator: Kristi L. Lewton
subject: Anthropology
subject: Zoology
description: doi:10.7717/peerj.3668
publisher: PeerJ Inc.
rights: © 2017 Lewton
abstract: The physical environments of captive and wild animals frequently differ in substrate types and compliance. As a result, there is an assumption that differences in rearing environments between captive and wild individuals produce differences in skeletal morphology. Here, this hypothesis is tested using a sample of 42 captive and wild common chimpanzees (Pan troglodytes). Articular surface areas of the humerus, radius, ulna, femur, and tibia were calculated from linear breadth measurements, adjusted for size differences using Mosimann shape variables, and compared across sex and environmental groups using two-way ANOVA. Results indicate that the articular surfaces of the wrist and knee differ between captive and wild chimpanzees; captive individuals have significantly larger distal ulna and tibial plateau articular surfaces. In both captive and wild chimpanzees, males have significantly larger femoral condyles and distal radius surfaces than females. Finally, there is an interaction effect between sex and rearing in the articular surfaces of the femoral condyles and distal radius in which captive males have significantly larger surface areas than all other sex-rearing groups. These data suggest that long bone articular surfaces may be sensitive to differences experienced by captive and wild individuals, such as differences in diet, body mass, positional behaviors, and presumed loading environments. Importantly, these results only find differences due to rearing environment in some long bone articular surfaces. Thus, future work on skeletal morphology could cautiously incorporate data from captive individuals, but should first investigate potential intraspecific differences between captive and wild individuals.
bibliographic citation: Lewton (2017) The effects of captive versus wild rearing environments on long bone articular surfaces in common chimpanzees (Pan troglodytes). PeerJ 5:e3668 https://doi.org/10.7717/peerj.3668
date submitted: 2017-07-04
date accepted: 2017-07-19
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lewton
  given name: Kristi L.
doi: 10.7717/peerj.3668
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Lewton
attribution name: Lewton

The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes
type: item
type: AcademicArticle
description: Background Hypoxia-inducible factor (HIF)-1 is involved in the regulation of hypoxic preconditioning in cardiomyocytes. Under hypoxic conditions, HIF-1α accumulates and is translocated to the nucleus, where it forms an active complex with HIF-1β and activates transcription of approximately 60 kinds of hypoxia-adaptive genes. Microtubules are hollow tubular structures in the cell that maintain cellular morphology and that transport substances. This study attempted to clarify the role of microtubule structure in the endonuclear aggregation of HIF-1α following hypoxic preconditioning of cardiomyocytes. Methods Primary rat cardiomyocytes were isolated and cultured. The cardiomyocyte culture system was used to establish a hypoxia model and a hypoxic preconditioning model. Interventions were performed on primary cardiomyocytes using a microtubule-depolymerizing agent and different concentrations of a microtubule stabilizer. The microtubule structure and the degree of HIF-1α nuclear aggregation were observed by confocal laser scanning microscopy. The expression of HIF-1α in the cytoplasm and nucleus was detected using Western blotting. Cardiomyocyte energy content, reflected by adenosine triphosphate/adenosine diphosphate (ATP/ADP), and key glycolytic enzymes were monitored by colorimetry and high-performance liquid chromatography (HPLC). Reactive oxygen species (ROS) production was also used to comprehensively assess whether microtubule stabilization can enhance the myocardial protective effect of hypoxic preconditioning. Results During prolonged hypoxia, it was found that the destruction of the microtubule network structure of cardiomyocytes was gradually aggravated. After this preconditioning, an abundance of HIF-1α was clustered in the nucleus. When the microtubules were depolymerized and hypoxia pretreatment was performed, HIF-1α clustering occurred around the nucleus, and HIF-1α nuclear expression was low. The levels of key glycolytic enzymes were significantly highe…
format: application/pdf
format: text/html
creator: Hai Guo
creator: Hong Zheng
creator: Jianjiang Wu
creator: Hai-ping Ma
creator: Jin Yu
creator: Maimaitili Yiliyaer
subject: Anesthesiology and Pain Management
subject: Cardiology
subject: Cell Biology
description: doi:10.7717/peerj.3662
publisher: PeerJ Inc.
rights: © 2017 Guo et al.
abstract: Background Hypoxia-inducible factor (HIF)-1 is involved in the regulation of hypoxic preconditioning in cardiomyocytes. Under hypoxic conditions, HIF-1α accumulates and is translocated to the nucleus, where it forms an active complex with HIF-1β and activates transcription of approximately 60 kinds of hypoxia-adaptive genes. Microtubules are hollow tubular structures in the cell that maintain cellular morphology and that transport substances. This study attempted to clarify the role of microtubule structure in the endonuclear aggregation of HIF-1α following hypoxic preconditioning of cardiomyocytes. Methods Primary rat cardiomyocytes were isolated and cultured. The cardiomyocyte culture system was used to establish a hypoxia model and a hypoxic preconditioning model. Interventions were performed on primary cardiomyocytes using a microtubule-depolymerizing agent and different concentrations of a microtubule stabilizer. The microtubule structure and the degree of HIF-1α nuclear aggregation were observed by confocal laser scanning microscopy. The expression of HIF-1α in the cytoplasm and nucleus was detected using Western blotting. Cardiomyocyte energy content, reflected by adenosine triphosphate/adenosine diphosphate (ATP/ADP), and key glycolytic enzymes were monitored by colorimetry and high-performance liquid chromatography (HPLC). Reactive oxygen species (ROS) production was also used to comprehensively assess whether microtubule stabilization can enhance the myocardial protective effect of hypoxic preconditioning. Results During prolonged hypoxia, it was found that the destruction of the microtubule network structure of cardiomyocytes was gradually aggravated. After this preconditioning, an abundance of HIF-1α was clustered in the nucleus. When the microtubules were depolymerized and hypoxia pretreatment was performed, HIF-1α clustering occurred around the nucleus, and HIF-1α nuclear expression was low. The levels of key glycolytic enzymes were significantly highe…
bibliographic citation: Guo et al. (2017) The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes. PeerJ 5:e3662 https://doi.org/10.7717/peerj.3662
date submitted: 2017-01-19
date accepted: 2017-07-18
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Hai
author list: Agent
  family name: Zheng
  given name: Hong
author list: Agent
  family name: Wu
  given name: Jianjiang
author list: Agent
  family name: Ma
  given name: Hai-ping
author list: Agent
  family name: Yu
  given name: Jin
author list: Agent
  family name: Yiliyaer
  given name: Maimaitili
doi: 10.7717/peerj.3662
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Guo et al.
attribution name: Guo et al.

Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton
type: item
type: AcademicArticle
description: Calcineurin B-like (CBL) proteins, as calcium sensors, play pivotal roles in plant responses to diverse abiotic stresses and in growth and development through interaction with CBL-interacting protein kinases (CIPKs). However, knowledge about functions and evolution of CBLs in Gossypium plants is scarce. Here, we conducted a genome-wide survey and identified 13, 13 and 22 CBL genes in the progenitor diploid Gossypium arboreum and Gossypium raimondii, and the cultivated allotetraploid Gossypium hirsutum, respectively. Analysis of physical properties, chromosomal locations, conserved domains and phylogeny indicated rather conserved nature of CBLs among the three Gossypium species. Moreover, these CBLs have closer genetic evolutionary relationship with the CBLs from cocoa than with those from other plants. Most CBL genes underwent evolution under purifying selection in the three Gossypium plants. Additionally, nearly all G. hirsutum CBL (GhCBL) genes were expressed in the root, stem, leaf, flower and fiber. Many GhCBLs were preferentially expressed in the flower while several GhCBLs were mainly expressed in roots. Expression patterns of GhCBL genes in response to potassium deficiency were also studied. The expression of most GhCBLs were moderately induced in roots after treatments with low-potassium stress. Yeast two-hybrid experiments indicated that GhCBL1-2, GhCBL1-3, GhCBL4-4, GhCBL8, GhCBL9 and GhCBL10-3 interacted with GhCIPK23, respectively. Our results provided a comprehensive view of the CBLs and valuable information for researchers to further investigate the roles and functional mechanisms of the CBLs in Gossypium.
format: application/pdf
format: text/html
creator: Tingting Lu
creator: Gaofeng Zhang
creator: Lirong Sun
creator: Ji Wang
creator: Fushun Hao
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3653
publisher: PeerJ Inc.
rights: © 2017 Lu et al.
abstract: Calcineurin B-like (CBL) proteins, as calcium sensors, play pivotal roles in plant responses to diverse abiotic stresses and in growth and development through interaction with CBL-interacting protein kinases (CIPKs). However, knowledge about functions and evolution of CBLs in Gossypium plants is scarce. Here, we conducted a genome-wide survey and identified 13, 13 and 22 CBL genes in the progenitor diploid Gossypium arboreum and Gossypium raimondii, and the cultivated allotetraploid Gossypium hirsutum, respectively. Analysis of physical properties, chromosomal locations, conserved domains and phylogeny indicated rather conserved nature of CBLs among the three Gossypium species. Moreover, these CBLs have closer genetic evolutionary relationship with the CBLs from cocoa than with those from other plants. Most CBL genes underwent evolution under purifying selection in the three Gossypium plants. Additionally, nearly all G. hirsutum CBL (GhCBL) genes were expressed in the root, stem, leaf, flower and fiber. Many GhCBLs were preferentially expressed in the flower while several GhCBLs were mainly expressed in roots. Expression patterns of GhCBL genes in response to potassium deficiency were also studied. The expression of most GhCBLs were moderately induced in roots after treatments with low-potassium stress. Yeast two-hybrid experiments indicated that GhCBL1-2, GhCBL1-3, GhCBL4-4, GhCBL8, GhCBL9 and GhCBL10-3 interacted with GhCIPK23, respectively. Our results provided a comprehensive view of the CBLs and valuable information for researchers to further investigate the roles and functional mechanisms of the CBLs in Gossypium.
bibliographic citation: Lu et al. (2017) Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton. PeerJ 5:e3653 https://doi.org/10.7717/peerj.3653
date submitted: 2017-04-25
date accepted: 2017-07-14
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Tingting
author list: Agent
  family name: Zhang
  given name: Gaofeng
author list: Agent
  family name: Sun
  given name: Lirong
author list: Agent
  family name: Wang
  given name: Ji
author list: Agent
  family name: Hao
  given name: Fushun
doi: 10.7717/peerj.3653
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Lu et al.
attribution name: Lu et al.

Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model
type: item
type: AcademicArticle
description: Objective The trabecular meshwork (TM) is the primary substrate of outflow resistance in glaucomatous eyes. Repopulating diseased TM with fresh, functional TM cells might be a viable therapeutic approach. Decellularized TM scaffolds have previously been produced by ablating cells with suicide gene therapy or saponin, which risks incomplete cell removal or dissolution of the extracellular matrix, respectively. We hypothesized that improved trabecular meshwork cell ablation would result from freeze-thaw cycles compared to chemical treatment. Materials and Methods We obtained 24 porcine eyes from a local abattoir, dissected and mounted them in an anterior segment perfusion within two hours of sacrifice. Intraocular pressure (IOP) was recorded continuously by a pressure transducer system. After 72 h of IOP stabilization, eight eyes were assigned to freeze-thaw (F) ablation (−80 °C × 2), to 0.02% saponin (S) treatment, or the control group (C), respectively. The TM was transduced with an eGFP expressing feline immunodeficiency viral (FIV) vector and tracked via fluorescent microscopy to confirm ablation. Following treatment, the eyes were perfused with standard tissue culture media for 180 h. TM histology was assessed by hematoxylin and eosin staining. TM viability was evaluated by a calcein AM/propidium iodide (PI) assay. The TM extracellular matrix was stained with Picro Sirius Red. We measured IOP and modeled it with a linear mixed effects model using a B-spline function of time with five degrees of freedom. Results F and S experienced a similar IOP reduction of 30% from baseline (P = 0.64). IOP reduction of about 30% occurred in F within 24 h and in S within 48 h. Live visualization of eGFP demonstrated that F conferred a complete ablation of all TM cells and only a partial ablation in S. Histological analysis and Picro Sirius staining confirmed that no TM cells survived in F while the extracellular matrix remained. The viability assay showed very low PI and no calce…
format: application/pdf
format: text/html
creator: Yalong Dang
creator: Susannah Waxman
creator: Chao Wang
creator: Adrianna Jensen
creator: Ralitsa T. Loewen
creator: Richard A. Bilonick
creator: Nils A. Loewen
subject: Bioengineering
subject: Biotechnology
subject: Ophthalmology
description: doi:10.7717/peerj.3629
publisher: PeerJ Inc.
rights: © 2017 Dang et al.
abstract: Objective The trabecular meshwork (TM) is the primary substrate of outflow resistance in glaucomatous eyes. Repopulating diseased TM with fresh, functional TM cells might be a viable therapeutic approach. Decellularized TM scaffolds have previously been produced by ablating cells with suicide gene therapy or saponin, which risks incomplete cell removal or dissolution of the extracellular matrix, respectively. We hypothesized that improved trabecular meshwork cell ablation would result from freeze-thaw cycles compared to chemical treatment. Materials and Methods We obtained 24 porcine eyes from a local abattoir, dissected and mounted them in an anterior segment perfusion within two hours of sacrifice. Intraocular pressure (IOP) was recorded continuously by a pressure transducer system. After 72 h of IOP stabilization, eight eyes were assigned to freeze-thaw (F) ablation (−80 °C × 2), to 0.02% saponin (S) treatment, or the control group (C), respectively. The TM was transduced with an eGFP expressing feline immunodeficiency viral (FIV) vector and tracked via fluorescent microscopy to confirm ablation. Following treatment, the eyes were perfused with standard tissue culture media for 180 h. TM histology was assessed by hematoxylin and eosin staining. TM viability was evaluated by a calcein AM/propidium iodide (PI) assay. The TM extracellular matrix was stained with Picro Sirius Red. We measured IOP and modeled it with a linear mixed effects model using a B-spline function of time with five degrees of freedom. Results F and S experienced a similar IOP reduction of 30% from baseline (P = 0.64). IOP reduction of about 30% occurred in F within 24 h and in S within 48 h. Live visualization of eGFP demonstrated that F conferred a complete ablation of all TM cells and only a partial ablation in S. Histological analysis and Picro Sirius staining confirmed that no TM cells survived in F while the extracellular matrix remained. The viability assay showed very low PI and no calce…
bibliographic citation: Dang et al. (2017) Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model. PeerJ 5:e3629 https://doi.org/10.7717/peerj.3629
date submitted: 2017-02-07
date accepted: 2017-07-10
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dang
  given name: Yalong
author list: Agent
  family name: Waxman
  given name: Susannah
author list: Agent
  family name: Wang
  given name: Chao
author list: Agent
  family name: Jensen
  given name: Adrianna
author list: Agent
  family name: Loewen
  given name: Ralitsa T.
author list: Agent
  family name: Bilonick
  given name: Richard A.
author list: Agent
  family name: Loewen
  given name: Nils A.
doi: 10.7717/peerj.3629
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Dang et al.
attribution name: Dang et al.

Microbial communities in the reef water at Kham Island, lower Gulf of Thailand
type: item
type: AcademicArticle
description: Coral reefs are among the most biodiverse habitats on Earth, but knowledge of their associated marinemicrobiome remains limited. To increase the understanding of the coral reef ecosystem in the lower Gulf of Thailand, this study utilized 16S and 18S rRNA gene-based pyrosequencing to identify the prokaryotic and eukaryotic microbiota present in the reef water at Kham Island, Trat province, Thailand (N6.97 E100.86). The obtained result was then compared with the published microbiota from different coral reef water and marine sites. The coral reefs at Kham Island are of the fringe type. The reefs remain preserved and abundant. The community similarity indices (i.e., Lennon similarity index, Yue & Clayton similarity index) indicated that the prokaryotic composition of Kham was closely related to that of Kra, another fringing reef site in the lower Gulf of Thailand, followed by coral reef water microbiota at GS048b (Cooks Bay, Fr. Polynesia), Palmyra (Northern Line Islands, United States) and GS108b (Coccos Keeling, Australia), respectively. Additionally, the microbial eukaryotic populations at Kham was analyzed and compared with the available database at Kra. Both eukaryotic microbiota, in summer and winter seasons, were correlated. An abundance of Dinophysis acuminata was noted in the summer season, in accordance with its reported cause of diarrhoeatic shellfish outbreak in the summer season elsewhere. The slightly lower biodiversity in Kham than at Kra might reflect the partly habitat difference due to coastal anthropogenic activities and minor water circulation, as Kham locates close to the mainland and is surrounded by islands (e.g., Chang and Kut islands). The global marine microbiota comparison suggested relatively similar microbial structures among coral sites irrespective of geographical location, supporting the importance of coral-associated marine microbiomes, and Spearman’s correlation analysis between community membership and factors of shore distance and se…
format: application/pdf
format: text/html
creator: Naraporn Somboonna
creator: Alisa Wilantho
creator: Somchai Monanunsap
creator: Suchana Chavanich
creator: Sithichoke Tangphatsornruang
creator: Sissades Tongsima
subject: Biodiversity
subject: Marine Biology
subject: Microbiology
subject: Natural Resource Management
description: doi:10.7717/peerj.3625
publisher: PeerJ Inc.
rights: © 2017 Somboonna et al.
abstract: Coral reefs are among the most biodiverse habitats on Earth, but knowledge of their associated marinemicrobiome remains limited. To increase the understanding of the coral reef ecosystem in the lower Gulf of Thailand, this study utilized 16S and 18S rRNA gene-based pyrosequencing to identify the prokaryotic and eukaryotic microbiota present in the reef water at Kham Island, Trat province, Thailand (N6.97 E100.86). The obtained result was then compared with the published microbiota from different coral reef water and marine sites. The coral reefs at Kham Island are of the fringe type. The reefs remain preserved and abundant. The community similarity indices (i.e., Lennon similarity index, Yue & Clayton similarity index) indicated that the prokaryotic composition of Kham was closely related to that of Kra, another fringing reef site in the lower Gulf of Thailand, followed by coral reef water microbiota at GS048b (Cooks Bay, Fr. Polynesia), Palmyra (Northern Line Islands, United States) and GS108b (Coccos Keeling, Australia), respectively. Additionally, the microbial eukaryotic populations at Kham was analyzed and compared with the available database at Kra. Both eukaryotic microbiota, in summer and winter seasons, were correlated. An abundance of Dinophysis acuminata was noted in the summer season, in accordance with its reported cause of diarrhoeatic shellfish outbreak in the summer season elsewhere. The slightly lower biodiversity in Kham than at Kra might reflect the partly habitat difference due to coastal anthropogenic activities and minor water circulation, as Kham locates close to the mainland and is surrounded by islands (e.g., Chang and Kut islands). The global marine microbiota comparison suggested relatively similar microbial structures among coral sites irrespective of geographical location, supporting the importance of coral-associated marine microbiomes, and Spearman’s correlation analysis between community membership and factors of shore distance and se…
bibliographic citation: Somboonna et al. (2017) Microbial communities in the reef water at Kham Island, lower Gulf of Thailand. PeerJ 5:e3625 https://doi.org/10.7717/peerj.3625
date submitted: 2017-03-09
date accepted: 2017-07-08
issued: 2017-08-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Somboonna
  given name: Naraporn
author list: Agent
  family name: Wilantho
  given name: Alisa
author list: Agent
  family name: Monanunsap
  given name: Somchai
author list: Agent
  family name: Chavanich
  given name: Suchana
author list: Agent
  family name: Tangphatsornruang
  given name: Sithichoke
author list: Agent
  family name: Tongsima
  given name: Sissades
doi: 10.7717/peerj.3625
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-14
copyright: ©2017 Somboonna et al.
attribution name: Somboonna et al.

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