PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland
items: Non-target effects of a glyphosate-based herbicide on Common toad larvae (Bufo bufo, Amphibia) and associated algae are altered by temperature
items: Whole-brain ex-vivo quantitative MRI of the cuprizone mouse model
items: Therapeutic role of human hepatocyte growth factor (HGF) in treating hair loss
items: Production of cytotoxic compounds in dedifferentiated cells of Jatropha curcas L. (Euphorbiaceae)
items: Ischemic postconditioning and pinacidil suppress calcium overload in anoxia-reoxygenation cardiomyocytes via down-regulation of the calcium-sensing receptor
items: Root bacterial endophytes alter plant phenotype, but not physiology
items: A potential third Manta Ray species near the Yucatán Peninsula? Evidence for a recently diverged and novel genetic Manta group from the Gulf of Mexico
items: Effects of CO2 laser irradiation on matrix-rich biofilm development formation–an in vitro study
items: Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics

The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland
type: item
type: AcademicArticle
description: Background Ferox Trout are large, long-lived piscivorous Brown Trout (Salmo trutta). Due to their exceptionally large size, Ferox Trout are highly sought after by anglers while their life-history strategy, which includes delayed maturation, multiphasic growth and extended longevity, is of interest to ecological and evolutionary modelers. However, despite their recreational and theoretical importance, little is known about the typical abundance of Ferox Trout. Methods To rectify this situation a 16 year angling-based mark-recapture study was conducted on Loch Rannoch, which at 19 km2 is one of the largest lakes in the United Kingdom. Results A hierarchical Bayesian Jolly-Seber analysis of the data suggest that if individual differences in catchability are negligible the population of Ferox Trout in Loch Rannoch in 2009 was approximately 71 fish. The results also suggest that a single, often unaccompanied, highly-experienced angler was able to catch roughly 8% of the available fish on an annual basis. Discussion It is recommended that anglers adopt a precautionary approach and release all trout with a fork length ≥400 mm caught by trolling in Loch Rannoch. There is an urgent need to assess the status of Ferox Trout in other lakes.
format: application/pdf
format: text/html
creator: Alastair Thorne
creator: Alisdair I. MacDonald
creator: Joseph L. Thorley
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Freshwater Biology
subject: Statistics
description: doi:10.7717/peerj.2646
publisher: PeerJ Inc.
rights: © 2016 Thorne et al.
abstract: Background Ferox Trout are large, long-lived piscivorous Brown Trout (Salmo trutta). Due to their exceptionally large size, Ferox Trout are highly sought after by anglers while their life-history strategy, which includes delayed maturation, multiphasic growth and extended longevity, is of interest to ecological and evolutionary modelers. However, despite their recreational and theoretical importance, little is known about the typical abundance of Ferox Trout. Methods To rectify this situation a 16 year angling-based mark-recapture study was conducted on Loch Rannoch, which at 19 km2 is one of the largest lakes in the United Kingdom. Results A hierarchical Bayesian Jolly-Seber analysis of the data suggest that if individual differences in catchability are negligible the population of Ferox Trout in Loch Rannoch in 2009 was approximately 71 fish. The results also suggest that a single, often unaccompanied, highly-experienced angler was able to catch roughly 8% of the available fish on an annual basis. Discussion It is recommended that anglers adopt a precautionary approach and release all trout with a fork length ≥400 mm caught by trolling in Loch Rannoch. There is an urgent need to assess the status of Ferox Trout in other lakes.
bibliographic citation: Thorne et al. (2016) The abundance of large, piscivorous Ferox Trout (Salmo trutta) in Loch Rannoch, Scotland. PeerJ 4:e2646 https://doi.org/10.7717/peerj.2646
date submitted: 2016-05-11
date accepted: 2016-10-03
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thorne
  given name: Alastair
author list: Agent
  family name: MacDonald
  given name: Alisdair I.
author list: Agent
  family name: Thorley
  given name: Joseph L.
doi: 10.7717/peerj.2646
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: ©2016 Thorne et al.
attribution name: Thorne et al.

Non-target effects of a glyphosate-based herbicide on Common toad larvae (Bufo bufo, Amphibia) and associated algae are altered by temperature
type: item
type: AcademicArticle
description: Background Glyphosate-based herbicides are the most widely used pesticides in agriculture, horticulture, municipalities and private gardens that can potentially contaminate nearby water bodies inhabited by amphibians and algae. Moreover, the development and diversity of these aquatic organisms could also be affected by human-induced climate change that might lead to more periods with extreme temperatures. However, to what extent non-target effects of these herbicides on amphibians or algae are altered by varying temperature is not well known. Methods We studied effects of five concentrations of the glyphosate-based herbicide formulation Roundup PowerFlex (0, 1.5, 3, 4 mg acid equivalent glyphosate L−1 as a one time addition and a pulse treatment of totally 4 mg a.e. glyphosate L−1) on larval development of Common toads (Bufo bufo, L.; Amphibia: Anura) and associated algae communities under two temperature regimes (15 vs. 20 °C). Results Herbicide contamination reduced tail growth (−8%), induced the occurrence of tail deformations (i.e. lacerated or crooked tails) and reduced algae diversity (−6%). Higher water temperature increased tadpole growth (tail and body length (tl/bl) +66%, length-to-width ratio +4%) and decreased algae diversity (−21%). No clear relation between herbicide concentrations and tadpole growth or algae density or diversity was observed. Interactive effects of herbicides and temperature affected growth parameters, tail deformation and tadpole mortality indicating that the herbicide effects are temperature-dependent. Remarkably, herbicide-temperature interactions resulted in deformed tails in 34% of all herbicide treated tadpoles at 15 °C whereas no tail deformations were observed for the herbicide-free control at 15 °C or any tadpole at 20 °C; herbicide-induced mortality was higher at 15 °C but lower at 20 °C. Discussion These herbicide- and temperature-induced changes may have decided effects on ecological interactions in freshwater ecosystems. …
format: application/pdf
format: text/html
creator: Fabian Baier
creator: Edith Gruber
creator: Thomas Hein
creator: Elisabeth Bondar-Kunze
creator: Marina Ivanković
creator: Axel Mentler
creator: Carsten A. Brühl
creator: Bernhard Spangl
creator: Johann G. Zaller
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Ecotoxicology
description: doi:10.7717/peerj.2641
publisher: PeerJ Inc.
rights: © 2016 Baier et al.
abstract: Background Glyphosate-based herbicides are the most widely used pesticides in agriculture, horticulture, municipalities and private gardens that can potentially contaminate nearby water bodies inhabited by amphibians and algae. Moreover, the development and diversity of these aquatic organisms could also be affected by human-induced climate change that might lead to more periods with extreme temperatures. However, to what extent non-target effects of these herbicides on amphibians or algae are altered by varying temperature is not well known. Methods We studied effects of five concentrations of the glyphosate-based herbicide formulation Roundup PowerFlex (0, 1.5, 3, 4 mg acid equivalent glyphosate L−1 as a one time addition and a pulse treatment of totally 4 mg a.e. glyphosate L−1) on larval development of Common toads (Bufo bufo, L.; Amphibia: Anura) and associated algae communities under two temperature regimes (15 vs. 20 °C). Results Herbicide contamination reduced tail growth (−8%), induced the occurrence of tail deformations (i.e. lacerated or crooked tails) and reduced algae diversity (−6%). Higher water temperature increased tadpole growth (tail and body length (tl/bl) +66%, length-to-width ratio +4%) and decreased algae diversity (−21%). No clear relation between herbicide concentrations and tadpole growth or algae density or diversity was observed. Interactive effects of herbicides and temperature affected growth parameters, tail deformation and tadpole mortality indicating that the herbicide effects are temperature-dependent. Remarkably, herbicide-temperature interactions resulted in deformed tails in 34% of all herbicide treated tadpoles at 15 °C whereas no tail deformations were observed for the herbicide-free control at 15 °C or any tadpole at 20 °C; herbicide-induced mortality was higher at 15 °C but lower at 20 °C. Discussion These herbicide- and temperature-induced changes may have decided effects on ecological interactions in freshwater ecosystems. …
bibliographic citation: Baier et al. (2016) Non-target effects of a glyphosate-based herbicide on Common toad larvae (Bufo bufo, Amphibia) and associated algae are altered by temperature. PeerJ 4:e2641 https://doi.org/10.7717/peerj.2641
date submitted: 2016-08-22
date accepted: 2016-09-30
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baier
  given name: Fabian
author list: Agent
  family name: Gruber
  given name: Edith
author list: Agent
  family name: Hein
  given name: Thomas
author list: Agent
  family name: Bondar-Kunze
  given name: Elisabeth
author list: Agent
  family name: Ivanković
  given name: Marina
author list: Agent
  family name: Mentler
  given name: Axel
author list: Agent
  family name: Brühl
  given name: Carsten A.
author list: Agent
  family name: Spangl
  given name: Bernhard
author list: Agent
  family name: Zaller
  given name: Johann G.
doi: 10.7717/peerj.2641
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: © 2016 Baier et al.
attribution name: Baier et al.

Whole-brain ex-vivo quantitative MRI of the cuprizone mouse model
type: item
type: AcademicArticle
description: Myelin is a critical component of the nervous system and a major contributor to contrast in Magnetic Resonance (MR) images. However, the precise contribution of myelination to multiple MR modalities is still under debate. The cuprizone mouse is a well-established model of demyelination that has been used in several MR studies, but these have often imaged only a single slice and analysed a small region of interest in the corpus callosum. We imaged and analyzed the whole brain of the cuprizone mouse ex-vivo using high-resolution quantitative MR methods (multi-component relaxometry, Diffusion Tensor Imaging (DTI) and morphometry) and found changes in multiple regions, including the corpus callosum, cerebellum, thalamus and hippocampus. The presence of inflammation, confirmed with histology, presents difficulties in isolating the sensitivity and specificity of these MR methods to demyelination using this model.
format: application/pdf
format: text/html
creator: Tobias C. Wood
creator: Camilla Simmons
creator: Samuel A. Hurley
creator: Anthony C. Vernon
creator: Joel Torres
creator: Flavio Dell’Acqua
creator: Steve C.R. Williams
creator: Diana Cash
subject: Neuroscience
subject: Radiology and Medical Imaging
subject: Histology
description: doi:10.7717/peerj.2632
publisher: PeerJ Inc.
rights: © 2016 Wood et al.
abstract: Myelin is a critical component of the nervous system and a major contributor to contrast in Magnetic Resonance (MR) images. However, the precise contribution of myelination to multiple MR modalities is still under debate. The cuprizone mouse is a well-established model of demyelination that has been used in several MR studies, but these have often imaged only a single slice and analysed a small region of interest in the corpus callosum. We imaged and analyzed the whole brain of the cuprizone mouse ex-vivo using high-resolution quantitative MR methods (multi-component relaxometry, Diffusion Tensor Imaging (DTI) and morphometry) and found changes in multiple regions, including the corpus callosum, cerebellum, thalamus and hippocampus. The presence of inflammation, confirmed with histology, presents difficulties in isolating the sensitivity and specificity of these MR methods to demyelination using this model.
bibliographic citation: Wood et al. (2016) Whole-brain ex-vivo quantitative MRI of the cuprizone mouse model. PeerJ 4:e2632 https://doi.org/10.7717/peerj.2632
date submitted: 2016-07-28
date accepted: 2016-09-29
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wood
  given name: Tobias C.
author list: Agent
  family name: Simmons
  given name: Camilla
author list: Agent
  family name: Hurley
  given name: Samuel A.
author list: Agent
  family name: Vernon
  given name: Anthony C.
author list: Agent
  family name: Torres
  given name: Joel
author list: Agent
  family name: Dell’Acqua
  given name: Flavio
author list: Agent
  family name: Williams
  given name: Steve C.R.
author list: Agent
  family name: Cash
  given name: Diana
doi: 10.7717/peerj.2632
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: © 2016 Wood et al.
attribution name: Wood et al.

Therapeutic role of human hepatocyte growth factor (HGF) in treating hair loss
type: item
type: AcademicArticle
description: Hepatocyte growth factor (HGF) is a paracrine hormone that plays an important role in epithelial-mesenchymal transition. HGF secreted by mesenchymal cells affects many properties of epithelial cells, such as proliferation, motility, and morphology. HGF has been reported to promote follicular growth. The purpose of the present study is to investigate the therapeutic role of HGF in hair loss treatment. A recombinant vector containing the human HGF (hHGF) gene (pTARGET-hHGF) was constructed, and the expression of hHGF in vitro was quantitatively and qualitatively evaluated. The effect of hHGF on hair growth was tested in mice, and results demonstrated that pTARGET-hHGF was successfully delivered into fibroblasts in vitro leading to a high expression of hHGF. Local injections of the pTARGET-hHGF recombinant vector into mice resulted in multiple beneficial effects compared to placebo, including faster hair regeneration, improved follicle development, and significantly increased HGF receptor (HGF-R). In conclusion, we have established a nonviral vector of hHGF which could be utilized to manipulate the sheath fibroblasts surrounding hair follicles (HF), thereby stimulating hair regeneration.
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creator: Yonghao Qi
creator: Miao Li
creator: Lian Xu
creator: Zhijing Chang
creator: Xiong Shu
creator: Lijun Zhou
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.2624
publisher: PeerJ Inc.
rights: © 2016 Qi et al.
abstract: Hepatocyte growth factor (HGF) is a paracrine hormone that plays an important role in epithelial-mesenchymal transition. HGF secreted by mesenchymal cells affects many properties of epithelial cells, such as proliferation, motility, and morphology. HGF has been reported to promote follicular growth. The purpose of the present study is to investigate the therapeutic role of HGF in hair loss treatment. A recombinant vector containing the human HGF (hHGF) gene (pTARGET-hHGF) was constructed, and the expression of hHGF in vitro was quantitatively and qualitatively evaluated. The effect of hHGF on hair growth was tested in mice, and results demonstrated that pTARGET-hHGF was successfully delivered into fibroblasts in vitro leading to a high expression of hHGF. Local injections of the pTARGET-hHGF recombinant vector into mice resulted in multiple beneficial effects compared to placebo, including faster hair regeneration, improved follicle development, and significantly increased HGF receptor (HGF-R). In conclusion, we have established a nonviral vector of hHGF which could be utilized to manipulate the sheath fibroblasts surrounding hair follicles (HF), thereby stimulating hair regeneration.
bibliographic citation: Qi et al. (2016) Therapeutic role of human hepatocyte growth factor (HGF) in treating hair loss. PeerJ 4:e2624 https://doi.org/10.7717/peerj.2624
date submitted: 2016-06-04
date accepted: 2016-09-27
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Yonghao
author list: Agent
  family name: Li
  given name: Miao
author list: Agent
  family name: Xu
  given name: Lian
author list: Agent
  family name: Chang
  given name: Zhijing
author list: Agent
  family name: Shu
  given name: Xiong
author list: Agent
  family name: Zhou
  given name: Lijun
doi: 10.7717/peerj.2624
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: © 2016 Qi et al.
attribution name: Qi et al.

Production of cytotoxic compounds in dedifferentiated cells of Jatropha curcas L. (Euphorbiaceae)
type: item
type: AcademicArticle
description: This study addresses the in vitro culture as an alternative to obtain compounds with cytotoxic activity from the medicinal plant Jatropha curcas (Euphorbiaceae). We determined the presence of cytotoxic compounds in both whole plants and dedifferentiated cells. We evaluated the effect of auxin, cytokinins and light on callus induction in cotyledon explants. We found that the most effective combination to induce callus was the auxin 2,4-D (5 mM) with the cytokinin 6-BAP (2.5 mM), on Murashige-Skoog medium in darkness. We compared the callogenic potential among accessions from different geographic origins, finding that ARR-251107-MFG7 is most prone to form callus. The roots of J. curcas grown in field produced a compound chromatographically similar to the cytotoxic diterpene jatrophone. The profile of compounds extracted from the dedifferentiated cells was similar to that of the whole plant, including a relatively abundant stilbene-like compound. This study contributes to the future establishment of protocols to produce anti-cancer compounds from J. curcas cultivated in vitro.
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creator: Isidro Ovando-Medina
creator: Leny P. Pérez-Díaz
creator: Sonia Ruiz-González
creator: Miguel Salvador-Figueroa
creator: Marcos E. Urbina-Reyes
creator: Lourdes Adriano-Anaya
subject: Biodiversity
subject: Biotechnology
subject: Plant Science
subject: Drugs and Devices
description: doi:10.7717/peerj.2616
publisher: PeerJ Inc.
rights: © 2016 Ovando-Medina et al.
abstract: This study addresses the in vitro culture as an alternative to obtain compounds with cytotoxic activity from the medicinal plant Jatropha curcas (Euphorbiaceae). We determined the presence of cytotoxic compounds in both whole plants and dedifferentiated cells. We evaluated the effect of auxin, cytokinins and light on callus induction in cotyledon explants. We found that the most effective combination to induce callus was the auxin 2,4-D (5 mM) with the cytokinin 6-BAP (2.5 mM), on Murashige-Skoog medium in darkness. We compared the callogenic potential among accessions from different geographic origins, finding that ARR-251107-MFG7 is most prone to form callus. The roots of J. curcas grown in field produced a compound chromatographically similar to the cytotoxic diterpene jatrophone. The profile of compounds extracted from the dedifferentiated cells was similar to that of the whole plant, including a relatively abundant stilbene-like compound. This study contributes to the future establishment of protocols to produce anti-cancer compounds from J. curcas cultivated in vitro.
bibliographic citation: Ovando-Medina et al. (2016) Production of cytotoxic compounds in dedifferentiated cells of Jatropha curcas L. (Euphorbiaceae). PeerJ 4:e2616 https://doi.org/10.7717/peerj.2616
date submitted: 2016-04-29
date accepted: 2016-09-27
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ovando-Medina
  given name: Isidro
author list: Agent
  family name: Pérez-Díaz
  given name: Leny P.
author list: Agent
  family name: Ruiz-González
  given name: Sonia
author list: Agent
  family name: Salvador-Figueroa
  given name: Miguel
author list: Agent
  family name: Urbina-Reyes
  given name: Marcos E.
author list: Agent
  family name: Adriano-Anaya
  given name: Lourdes
doi: 10.7717/peerj.2616
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: ©2016 Ovando-Medina et al.
attribution name: Ovando-Medina et al.

Ischemic postconditioning and pinacidil suppress calcium overload in anoxia-reoxygenation cardiomyocytes via down-regulation of the calcium-sensing receptor
type: item
type: AcademicArticle
description: Ischemic postconditioning (IPC) and ATP sensitive potassium channel (KATP) agonists (e.g. pinacidil and diazoxide) postconditioning are effective methods to defeat myocardial ischemia-reperfusion (I/R) injury, but their specific mechanisms of reducing I/R injury are not fully understood. We observed an intracellular free calcium ([Ca2+]i) overload in Anoxia/reoxygenation (A/R) cardiomyocytes, which can be reversed by KATP agonists diazoxide or pinacidil. The calcium-sensing receptor (CaSR) regulates intracellular calcium homeostasis. CaSR was reported to be involved in the I/R-induced apoptosis in rat cardiomyocytes. We therefore hypothesize that IPC and pinacidil postconditioning (PPC) reduce calcium overload in I/R cardiomyocytes by the down-regulation of CaSR. A/R model was established with adult rat caridomyocyte. mRNA and protein expression of CaSR were detected, IPC, PPC and KATP’s effects on [Ca2+]i concentration was assayed too. IPC and PPC ameliorated A/R insult induced [Ca2+]i overload in cardiomyocytes. In addition, they down-regulated the mRNA and protein level of CaSR as we expected. CaSR agonist spermine and KATP blocker glibenclamide offset IPC’s effects on CaSR expression and [Ca2+]i modulation. Our data indicate that CaSR down-regulation contributes to the mitigation of calcium overload in A/R cardiomyocytes, which may partially represents IPC and KATP’s myocardial protective mechanism under I/R circumstances.
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creator: Lin Zhang
creator: Song Cao
creator: Shengli Deng
creator: Gang Yao
creator: Tian Yu
subject: Anesthesiology and Pain Management
subject: Cardiology
subject: Cell Biology
description: doi:10.7717/peerj.2612
publisher: PeerJ Inc.
rights: © 2016 Zhang et al.
abstract: Ischemic postconditioning (IPC) and ATP sensitive potassium channel (KATP) agonists (e.g. pinacidil and diazoxide) postconditioning are effective methods to defeat myocardial ischemia-reperfusion (I/R) injury, but their specific mechanisms of reducing I/R injury are not fully understood. We observed an intracellular free calcium ([Ca2+]i) overload in Anoxia/reoxygenation (A/R) cardiomyocytes, which can be reversed by KATP agonists diazoxide or pinacidil. The calcium-sensing receptor (CaSR) regulates intracellular calcium homeostasis. CaSR was reported to be involved in the I/R-induced apoptosis in rat cardiomyocytes. We therefore hypothesize that IPC and pinacidil postconditioning (PPC) reduce calcium overload in I/R cardiomyocytes by the down-regulation of CaSR. A/R model was established with adult rat caridomyocyte. mRNA and protein expression of CaSR were detected, IPC, PPC and KATP’s effects on [Ca2+]i concentration was assayed too. IPC and PPC ameliorated A/R insult induced [Ca2+]i overload in cardiomyocytes. In addition, they down-regulated the mRNA and protein level of CaSR as we expected. CaSR agonist spermine and KATP blocker glibenclamide offset IPC’s effects on CaSR expression and [Ca2+]i modulation. Our data indicate that CaSR down-regulation contributes to the mitigation of calcium overload in A/R cardiomyocytes, which may partially represents IPC and KATP’s myocardial protective mechanism under I/R circumstances.
bibliographic citation: Zhang et al. (2016) Ischemic postconditioning and pinacidil suppress calcium overload in anoxia-reoxygenation cardiomyocytes via down-regulation of the calcium-sensing receptor. PeerJ 4:e2612 https://doi.org/10.7717/peerj.2612
date submitted: 2016-04-05
date accepted: 2016-09-26
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Lin
author list: Agent
  family name: Cao
  given name: Song
author list: Agent
  family name: Deng
  given name: Shengli
author list: Agent
  family name: Yao
  given name: Gang
author list: Agent
  family name: Yu
  given name: Tian
doi: 10.7717/peerj.2612
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: © 2016 Zhang et al.
attribution name: Zhang et al.

Root bacterial endophytes alter plant phenotype, but not physiology
type: item
type: AcademicArticle
description: Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light–Asat, and saturating CO2–Amax). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.
format: application/pdf
format: text/html
creator: Jeremiah A. Henning
creator: David J. Weston
creator: Dale A. Pelletier
creator: Collin M. Timm
creator: Sara S. Jawdy
creator: Aimée T. Classen
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.2606
publisher: PeerJ Inc.
rights: © 2016 Henning et al.
abstract: Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light–Asat, and saturating CO2–Amax). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.
bibliographic citation: Henning et al. (2016) Root bacterial endophytes alter plant phenotype, but not physiology. PeerJ 4:e2606 https://doi.org/10.7717/peerj.2606
date submitted: 2016-06-27
date accepted: 2016-09-24
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Henning
  given name: Jeremiah A.
author list: Agent
  family name: Weston
  given name: David J.
author list: Agent
  family name: Pelletier
  given name: Dale A.
author list: Agent
  family name: Timm
  given name: Collin M.
author list: Agent
  family name: Jawdy
  given name: Sara S.
author list: Agent
  family name: Classen
  given name: Aimée T.
doi: 10.7717/peerj.2606
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: © 2016 Henning et al.
attribution name: Henning et al.

A potential third Manta Ray species near the Yucatán Peninsula? Evidence for a recently diverged and novel genetic Manta group from the Gulf of Mexico
type: item
type: AcademicArticle
description: We present genetic and morphometric support for a third, distinct, and recently diverged group of Manta ray that appears resident to the Yucatán coastal waters of the Gulf of Mexico. Individuals of the genus Manta from Isla Holbox are markedly different from the other described manta rays in their morphology, habitat preference, and genetic makeup. Herein referred to as the Yucatán Manta Ray, these individuals form two genetically distinct groups: (1) a group of mtDNA haplotypes divergent (0.78%) from the currently recognized Manta birostris and M. alfredi species, and (2) a group possessing mtDNA haplotypes of M. birostris and highly similar haplotypes. The latter suggests the potential for either introgressive hybridization between Yucatán Manta Rays and M. birostris, or the retention of ancestral M. birostris signatures among Yucatán Manta Rays. Divergence of the genetically distinct Yucatán Manta Ray from M. birostris appears quite recent (<100,000 YBP) following fit to an Isolation-with-Migration model, with additional support for asymmetrical gene flow from M. birostris into the Yucatán Manta Ray. Formal naming of the Yucatán Manta Ray cannot yet be assigned until an in-depth taxonomic study and further confirmation of the genetic identity of existing type specimens has been performed.
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creator: Silvia Hinojosa-Alvarez
creator: Ryan P. Walter
creator: Pindaro Diaz-Jaimes
creator: Felipe Galván-Magaña
creator: E. Misty Paig-Tran
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.2586
publisher: PeerJ Inc.
rights: © 2016 Hinojosa-Alvarez et al.
abstract: We present genetic and morphometric support for a third, distinct, and recently diverged group of Manta ray that appears resident to the Yucatán coastal waters of the Gulf of Mexico. Individuals of the genus Manta from Isla Holbox are markedly different from the other described manta rays in their morphology, habitat preference, and genetic makeup. Herein referred to as the Yucatán Manta Ray, these individuals form two genetically distinct groups: (1) a group of mtDNA haplotypes divergent (0.78%) from the currently recognized Manta birostris and M. alfredi species, and (2) a group possessing mtDNA haplotypes of M. birostris and highly similar haplotypes. The latter suggests the potential for either introgressive hybridization between Yucatán Manta Rays and M. birostris, or the retention of ancestral M. birostris signatures among Yucatán Manta Rays. Divergence of the genetically distinct Yucatán Manta Ray from M. birostris appears quite recent (<100,000 YBP) following fit to an Isolation-with-Migration model, with additional support for asymmetrical gene flow from M. birostris into the Yucatán Manta Ray. Formal naming of the Yucatán Manta Ray cannot yet be assigned until an in-depth taxonomic study and further confirmation of the genetic identity of existing type specimens has been performed.
bibliographic citation: Hinojosa-Alvarez et al. (2016) A potential third Manta Ray species near the Yucatán Peninsula? Evidence for a recently diverged and novel genetic Manta group from the Gulf of Mexico. PeerJ 4:e2586 https://doi.org/10.7717/peerj.2586
date submitted: 2016-03-09
date accepted: 2016-09-20
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hinojosa-Alvarez
  given name: Silvia
author list: Agent
  family name: Walter
  given name: Ryan P.
author list: Agent
  family name: Diaz-Jaimes
  given name: Pindaro
author list: Agent
  family name: Galván-Magaña
  given name: Felipe
author list: Agent
  family name: Paig-Tran
  given name: E. Misty
doi: 10.7717/peerj.2586
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: ©2016 Hinojosa-Alvarez et al.
attribution name: Hinojosa-Alvarez et al.

Effects of CO2 laser irradiation on matrix-rich biofilm development formation–an in vitro study
type: item
type: AcademicArticle
description: Background A carbon dioxide (CO2) laser has been used to morphologically and chemically modify the dental enamel surface as well as to make it more resistant to demineralization. Despite a variety of experiments demonstrating the inhibitory effect of a CO2 laser in reduce enamel demineralization, little is known about the effect of surface irradiated on bacterial growth. Thus, this in vitro study was preformed to evaluate the biofilm formation on enamel previously irradiated with a CO2 laser (λ = 10.6 µM). Methods For this in vitro study, 96 specimens of bovine enamel were employed, which were divided into two groups (n = 48): 1) Control-non-irradiated surface and 2) Irradiated enamel surface. Biofilms were grown on the enamel specimens by one, three and five days under intermittent cariogenic condition in the irradiated and non-irradiated surface. In each assessment time, the biofilm were evaluated by dry weigh, counting the number of viable colonies and, in fifth day, were evaluated by polysaccharides analysis, quantitative real time Polymerase Chain Reaction (PCR) as well as by contact angle. In addition, the morphology of biofilms was characterized by fluorescence microscopy and field emission scanning electron microscopy (FESEM). Initially, the assumptions of equal variances and normal distribution of errors were conferred and the results are analyzed statistically by t-test and Mann Whitney test. Results The mean of log CFU/mL obtained for the one-day biofilm evaluation showed that there is statistical difference between the experimental groups. When biofilms were exposed to the CO2 laser, CFU/mL and CFU/dry weight in three day was reduced significantly compared with control group. The difference in the genes expression (Glucosyltransferases (gtfB) and Glucan-binding protein (gbpB)) and polysaccharides was not statically significant. Contact angle was increased relative to control when the surface was irradiated with the CO2 laser. Similar morphology was also …
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creator: Bruna Raquel Zancopé
creator: Vanessa B. Dainezi
creator: Marinês Nobre-dos-Santos
creator: Sillas Duarte
creator: Vanessa Pardi
creator: Ramiro M. Murata
subject: Biochemistry
subject: Dentistry
description: doi:10.7717/peerj.2458
publisher: PeerJ Inc.
rights: © 2016 Zancope et al.
abstract: Background A carbon dioxide (CO2) laser has been used to morphologically and chemically modify the dental enamel surface as well as to make it more resistant to demineralization. Despite a variety of experiments demonstrating the inhibitory effect of a CO2 laser in reduce enamel demineralization, little is known about the effect of surface irradiated on bacterial growth. Thus, this in vitro study was preformed to evaluate the biofilm formation on enamel previously irradiated with a CO2 laser (λ = 10.6 µM). Methods For this in vitro study, 96 specimens of bovine enamel were employed, which were divided into two groups (n = 48): 1) Control-non-irradiated surface and 2) Irradiated enamel surface. Biofilms were grown on the enamel specimens by one, three and five days under intermittent cariogenic condition in the irradiated and non-irradiated surface. In each assessment time, the biofilm were evaluated by dry weigh, counting the number of viable colonies and, in fifth day, were evaluated by polysaccharides analysis, quantitative real time Polymerase Chain Reaction (PCR) as well as by contact angle. In addition, the morphology of biofilms was characterized by fluorescence microscopy and field emission scanning electron microscopy (FESEM). Initially, the assumptions of equal variances and normal distribution of errors were conferred and the results are analyzed statistically by t-test and Mann Whitney test. Results The mean of log CFU/mL obtained for the one-day biofilm evaluation showed that there is statistical difference between the experimental groups. When biofilms were exposed to the CO2 laser, CFU/mL and CFU/dry weight in three day was reduced significantly compared with control group. The difference in the genes expression (Glucosyltransferases (gtfB) and Glucan-binding protein (gbpB)) and polysaccharides was not statically significant. Contact angle was increased relative to control when the surface was irradiated with the CO2 laser. Similar morphology was also …
bibliographic citation: Zancopé et al. (2016) Effects of CO2 laser irradiation on matrix-rich biofilm development formation–an in vitro study. PeerJ 4:e2458 https://doi.org/10.7717/peerj.2458
date submitted: 2016-03-05
date accepted: 2016-08-17
issued: 2016-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zancopé
  given name: Bruna Raquel
author list: Agent
  family name: Dainezi
  given name: Vanessa B.
author list: Agent
  family name: Nobre-dos-Santos
  given name: Marinês
author list: Agent
  family name: Duarte
  given name: Sillas
author list: Agent
  family name: Pardi
  given name: Vanessa
author list: Agent
  family name: Murata
  given name: Ramiro M.
doi: 10.7717/peerj.2458
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-01
copyright: © 2016 Zancope et al.
attribution name: Zancope et al.

Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics
type: item
type: AcademicArticle
description: Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these da…
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creator: Elena R. Schroeter
creator: Caroline J. DeHart
creator: Mary H. Schweitzer
creator: Paul M. Thomas
creator: Neil L. Kelleher
subject: Bioinformatics
subject: Molecular Biology
subject: Paleontology
description: doi:10.7717/peerj.2603
publisher: PeerJ Inc.
rights: © 2016 Schroeter et al.
abstract: Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these da…
bibliographic citation: Schroeter et al. (2016) Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics. PeerJ 4:e2603 https://doi.org/10.7717/peerj.2603
date submitted: 2016-06-21
date accepted: 2016-09-20
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schroeter
  given name: Elena R.
author list: Agent
  family name: DeHart
  given name: Caroline J.
author list: Agent
  family name: Schweitzer
  given name: Mary H.
author list: Agent
  family name: Thomas
  given name: Paul M.
author list: Agent
  family name: Kelleher
  given name: Neil L.
doi: 10.7717/peerj.2603
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Schroeter et al.
attribution name: Schroeter et al.

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