PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: A new species of Brachycephalus (Anura: Brachycephalidae) from Santa Catarina, southern Brazil
items: Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)
items: Synthetic lung surfactants containing SP-B and SP-C peptides plus novel phospholipase-resistant lipids or glycerophospholipids
items: Risk and clinical predictors of osteoporotic fracture in East Asian patients with chronic obstructive pulmonary disease: a population-based cohort study

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.
format: application/pdf
format: text/html
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 …
format: application/pdf
format: text/html
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…
format: application/pdf
format: text/html
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.

A new species of Brachycephalus (Anura: Brachycephalidae) from Santa Catarina, southern Brazil
type: item
type: AcademicArticle
description: A new species of Brachycephalus (Anura: Brachycephalidae) is described from the Atlantic Forest of northeastern state of Santa Catarina, southern Brazil. Nine specimens (eight adults and a juvenile) were collected from the leaf litter of montane forests 790–835 m above sea level (a.s.l.). The new species is a member of the pernix group by its bufoniform shape and the absence of dermal co-ossification and is distinguished from all its congeners by a combination of its general coloration (dorsal region of head, dorsum, legs, arms, and flanks light, brownish green to dark, olive green, with darker region in the middle of the dorsum and a white line along the vertebral column in most specimens) and by its smooth dorsum. The geographical distribution of the new species is highly reduced (extent of occurrence estimated as 25.04 ha, or possibly 34.37 ha). In addition, its habitat has experienced some level of degradation, raising concerns about the future conservation of the species. Preliminary density estimates suggest one calling individual every 3–4 m2 at 815–835 m a.s.l. and every 100 m2 at 790 m a.s.l. Together with the recently described B. boticario and B. fuscolineatus, the new species is among the southernmost species of Brachycephalus known to date.
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creator: Marcos R. Bornschein
creator: Luiz F. Ribeiro
creator: David C. Blackburn
creator: Edward L. Stanley
creator: Marcio R. Pie
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2629
publisher: PeerJ Inc.
rights: © 2016 Bornschein et al.
abstract: A new species of Brachycephalus (Anura: Brachycephalidae) is described from the Atlantic Forest of northeastern state of Santa Catarina, southern Brazil. Nine specimens (eight adults and a juvenile) were collected from the leaf litter of montane forests 790–835 m above sea level (a.s.l.). The new species is a member of the pernix group by its bufoniform shape and the absence of dermal co-ossification and is distinguished from all its congeners by a combination of its general coloration (dorsal region of head, dorsum, legs, arms, and flanks light, brownish green to dark, olive green, with darker region in the middle of the dorsum and a white line along the vertebral column in most specimens) and by its smooth dorsum. The geographical distribution of the new species is highly reduced (extent of occurrence estimated as 25.04 ha, or possibly 34.37 ha). In addition, its habitat has experienced some level of degradation, raising concerns about the future conservation of the species. Preliminary density estimates suggest one calling individual every 3–4 m2 at 815–835 m a.s.l. and every 100 m2 at 790 m a.s.l. Together with the recently described B. boticario and B. fuscolineatus, the new species is among the southernmost species of Brachycephalus known to date.
bibliographic citation: Bornschein et al. (2016) A new species of Brachycephalus (Anura: Brachycephalidae) from Santa Catarina, southern Brazil. PeerJ 4:e2629 https://doi.org/10.7717/peerj.2629
date submitted: 2016-05-24
date accepted: 2016-09-29
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bornschein
  given name: Marcos R.
author list: Agent
  family name: Ribeiro
  given name: Luiz F.
author list: Agent
  family name: Blackburn
  given name: David C.
author list: Agent
  family name: Stanley
  given name: Edward L.
author list: Agent
  family name: Pie
  given name: Marcio R.
doi: 10.7717/peerj.2629
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Bornschein et al.
attribution name: Bornschein et al.

Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)
type: item
type: AcademicArticle
description: Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues (testes, epididymis and vas deferens) of Peromyscus eremicus (Cactus mouse), a desert specialist. The transcriptome assembly process was optimized in order to produce a high quality and substantially complete annotated transcriptome. This composite transcriptome was generated to characterize the expressed transcripts in the male reproductive tract of P. eremicus, which will serve as a crucial resource for future research investigating our hypothesis that the male Cactus mouse possesses an adaptive reproductive phenotype to mitigate water-loss from ejaculate. This study reports genes under positive selection in the male Cactus mouse reproductive transcriptome relative to transcriptomes from Peromyscus maniculatus (deer mouse) and Mus musculus. Thus, this study expands upon existing genetic research in this species, and we provide a high quality transcriptome to enable further explorations of our proposed hypothesis for male Cactus mouse reproductive adaptations to minimize seminal fluid loss.
format: application/pdf
format: text/html
creator: Lauren L. Kordonowy
creator: Matthew D. MacManes
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.2617
publisher: PeerJ Inc.
rights: © 2016 Kordonowy and MacManes
abstract: Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues (testes, epididymis and vas deferens) of Peromyscus eremicus (Cactus mouse), a desert specialist. The transcriptome assembly process was optimized in order to produce a high quality and substantially complete annotated transcriptome. This composite transcriptome was generated to characterize the expressed transcripts in the male reproductive tract of P. eremicus, which will serve as a crucial resource for future research investigating our hypothesis that the male Cactus mouse possesses an adaptive reproductive phenotype to mitigate water-loss from ejaculate. This study reports genes under positive selection in the male Cactus mouse reproductive transcriptome relative to transcriptomes from Peromyscus maniculatus (deer mouse) and Mus musculus. Thus, this study expands upon existing genetic research in this species, and we provide a high quality transcriptome to enable further explorations of our proposed hypothesis for male Cactus mouse reproductive adaptations to minimize seminal fluid loss.
bibliographic citation: Kordonowy et al. (2016) Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse). PeerJ 4:e2617 https://doi.org/10.7717/peerj.2617
date submitted: 2016-04-20
date accepted: 2016-09-27
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kordonowy
  given name: Lauren L.
author list: Agent
  family name: MacManes
  given name: Matthew D.
doi: 10.7717/peerj.2617
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Kordonowy and MacManes
attribution name: Kordonowy and MacManes

Synthetic lung surfactants containing SP-B and SP-C peptides plus novel phospholipase-resistant lipids or glycerophospholipids
type: item
type: AcademicArticle
description: Background This study examines the biophysical and preclinical pulmonary activity of synthetic lung surfactants containing novel phospholipase-resistant phosphonolipids or synthetic glycerophospholipids combined with Super Mini-B (S-MB) DATK and/or SP-Css ion-lock 1 peptides that replicate the functional biophysics of surfactant proteins (SP)-B and SP-C. Phospholipase-resistant phosphonolipids used in synthetic surfactants are DEPN-8 and PG-1, molecular analogs of dipalmitoyl phosphatidylcholine (DPPC) and palmitoyl-oleoyl phosphatidylglycerol (POPG), while glycerophospholipids used are active lipid components of native surfactant (DPPC:POPC:POPG 5:3:2 by weight). The objective of the work is to test whether these novel lipid/peptide synthetic surfactants have favorable preclinical activity (biophysical, pulmonary) for therapeutic use in reversing surfactant deficiency or dysfunction in lung disease or injury. Methods Surface activity of synthetic lipid/peptide surfactants was assessed in vitro at 37 °C by measuring adsorption in a stirred subphase apparatus and dynamic surface tension lowering in pulsating and captive bubble surfactometers. Shear viscosity was measured as a function of shear rate on a Wells-Brookfield micro-viscometer. In vivo pulmonary activity was determined by measuring lung function (arterial oxygenation, dynamic lung compliance) in ventilated rats and rabbits with surfactant deficiency/dysfunction induced by saline lavage to lower arterial PO2 to <100 mmHg, consistent with clinical acute respiratory distress syndrome (ARDS). Results Synthetic surfactants containing 5:3:2 DPPC:POPC:POPG or 9:1 DEPN-8:PG-1 combined with 3% (by wt) of S-MB DATK, 3% SP-Css ion-lock 1, or 1.5% each of both peptides all adsorbed rapidly to low equilibrium surface tensions and also reduced surface tension to ≤1 mN/m under dynamic compression at 37 °C. However, dual-peptide surfactants containing 1.5% S-MB DATK + 1.5% SP-Css ion-lock 1 combined with 9:1 DEPN-8:PG-1 or…
format: application/pdf
format: text/html
creator: Robert H. Notter
creator: Rohun Gupta
creator: Adrian L. Schwan
creator: Zhengdong Wang
creator: Mohanad Gh Shkoor
creator: Frans J. Walther
subject: Bioengineering
subject: Biophysics
subject: Respiratory Medicine
subject: Synthetic Biology
description: doi:10.7717/peerj.2635
publisher: PeerJ Inc.
rights: © 2016 Notter et al.
abstract: Background This study examines the biophysical and preclinical pulmonary activity of synthetic lung surfactants containing novel phospholipase-resistant phosphonolipids or synthetic glycerophospholipids combined with Super Mini-B (S-MB) DATK and/or SP-Css ion-lock 1 peptides that replicate the functional biophysics of surfactant proteins (SP)-B and SP-C. Phospholipase-resistant phosphonolipids used in synthetic surfactants are DEPN-8 and PG-1, molecular analogs of dipalmitoyl phosphatidylcholine (DPPC) and palmitoyl-oleoyl phosphatidylglycerol (POPG), while glycerophospholipids used are active lipid components of native surfactant (DPPC:POPC:POPG 5:3:2 by weight). The objective of the work is to test whether these novel lipid/peptide synthetic surfactants have favorable preclinical activity (biophysical, pulmonary) for therapeutic use in reversing surfactant deficiency or dysfunction in lung disease or injury. Methods Surface activity of synthetic lipid/peptide surfactants was assessed in vitro at 37 °C by measuring adsorption in a stirred subphase apparatus and dynamic surface tension lowering in pulsating and captive bubble surfactometers. Shear viscosity was measured as a function of shear rate on a Wells-Brookfield micro-viscometer. In vivo pulmonary activity was determined by measuring lung function (arterial oxygenation, dynamic lung compliance) in ventilated rats and rabbits with surfactant deficiency/dysfunction induced by saline lavage to lower arterial PO2 to <100 mmHg, consistent with clinical acute respiratory distress syndrome (ARDS). Results Synthetic surfactants containing 5:3:2 DPPC:POPC:POPG or 9:1 DEPN-8:PG-1 combined with 3% (by wt) of S-MB DATK, 3% SP-Css ion-lock 1, or 1.5% each of both peptides all adsorbed rapidly to low equilibrium surface tensions and also reduced surface tension to ≤1 mN/m under dynamic compression at 37 °C. However, dual-peptide surfactants containing 1.5% S-MB DATK + 1.5% SP-Css ion-lock 1 combined with 9:1 DEPN-8:PG-1 or…
bibliographic citation: Notter et al. (2016) Synthetic lung surfactants containing SP-B and SP-C peptides plus novel phospholipase-resistant lipids or glycerophospholipids. PeerJ 4:e2635 https://doi.org/10.7717/peerj.2635
date submitted: 2016-08-15
date accepted: 2016-09-30
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Notter
  given name: Robert H.
author list: Agent
  family name: Gupta
  given name: Rohun
author list: Agent
  family name: Schwan
  given name: Adrian L.
author list: Agent
  family name: Wang
  given name: Zhengdong
author list: Agent
  family name: Shkoor
  given name: Mohanad Gh
author list: Agent
  family name: Walther
  given name: Frans J.
doi: 10.7717/peerj.2635
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Notter et al.
attribution name: Notter et al.

Risk and clinical predictors of osteoporotic fracture in East Asian patients with chronic obstructive pulmonary disease: a population-based cohort study
type: item
type: AcademicArticle
description: Introduction Osteoporosis is becoming an impending epidemic in the Asia-Pacific region. The association between risk of osteoporotic fracture (OTPF) and chronic obstructive pulmonary disease (COPD) in East Asian patients is yet to be fully examined. We conducted a nationwide population-based retrospective cohort study of 98,700 patients aged ≥50 years with or without COPD using a national administrative claims dataset. Materials and Methods The patients were divided into COPD and comparison groups comprising 19,740 and 78,960 patients, respectively. The groups were 1 to 4 matched for age, gender, index date, diabetes mellitus, pre-existing osteoporosis and chronic kidney disease. Information such as the geographic area where southern part represented more sunshine exposure, smoking-related diagnoses, alcohol use disorder, whether there was regular use of inhaled corticosteroids and oral corticosteroids, vitamin D prescriptions, Charlson-Deyo comorbidity index score, and other relevant medical comorbidities were extracted for analysis. They were followed up until OTPF or the end of the year 2013. The outcome measure was an osteoporotic vertebral fracture and other long-bone fractures. A multivariate Cox model was constructed to derive adjusted hazard ratios (aHR) for OTPF with corresponding 95% confidence intervals (CI) after controlling for age, sex, insurance premium category, vitamin D prescription, osteoporosis, and coronary heart disease (CHD). Kaplan–Meier curves of the probability of OTPF-free survival for each cohort were compared using the log-rank test. Patients with OTPF during the first follow-up year were excluded from the overall risk calculation. Contributing factors to the increased risk of OTPF in COPD patients were examined in a sensitivity analysis. Results After a total follow-up of 68,743 patient-years for the COPD group and 278,051 patient-years for the matched comparison group, the HR for OTPF was 1.24 (95% CI [1.02–1.51]; P = 0.0322) in COPD p…
format: application/pdf
format: text/html
creator: Ping-Hsueh Lee
creator: Victor C. Kok
creator: Po-Liang Chou
creator: Ming-Chang Ku
creator: Yu-Ching Chen
creator: Jorng-Tzong Horng
subject: Epidemiology
subject: Geriatrics
subject: Global Health
subject: Orthopedics
subject: Respiratory Medicine
description: doi:10.7717/peerj.2634
publisher: PeerJ Inc.
rights: © 2016 Lee et al.
abstract: Introduction Osteoporosis is becoming an impending epidemic in the Asia-Pacific region. The association between risk of osteoporotic fracture (OTPF) and chronic obstructive pulmonary disease (COPD) in East Asian patients is yet to be fully examined. We conducted a nationwide population-based retrospective cohort study of 98,700 patients aged ≥50 years with or without COPD using a national administrative claims dataset. Materials and Methods The patients were divided into COPD and comparison groups comprising 19,740 and 78,960 patients, respectively. The groups were 1 to 4 matched for age, gender, index date, diabetes mellitus, pre-existing osteoporosis and chronic kidney disease. Information such as the geographic area where southern part represented more sunshine exposure, smoking-related diagnoses, alcohol use disorder, whether there was regular use of inhaled corticosteroids and oral corticosteroids, vitamin D prescriptions, Charlson-Deyo comorbidity index score, and other relevant medical comorbidities were extracted for analysis. They were followed up until OTPF or the end of the year 2013. The outcome measure was an osteoporotic vertebral fracture and other long-bone fractures. A multivariate Cox model was constructed to derive adjusted hazard ratios (aHR) for OTPF with corresponding 95% confidence intervals (CI) after controlling for age, sex, insurance premium category, vitamin D prescription, osteoporosis, and coronary heart disease (CHD). Kaplan–Meier curves of the probability of OTPF-free survival for each cohort were compared using the log-rank test. Patients with OTPF during the first follow-up year were excluded from the overall risk calculation. Contributing factors to the increased risk of OTPF in COPD patients were examined in a sensitivity analysis. Results After a total follow-up of 68,743 patient-years for the COPD group and 278,051 patient-years for the matched comparison group, the HR for OTPF was 1.24 (95% CI [1.02–1.51]; P = 0.0322) in COPD p…
bibliographic citation: Lee et al. (2016) Risk and clinical predictors of osteoporotic fracture in East Asian patients with chronic obstructive pulmonary disease: a population-based cohort study. PeerJ 4:e2634 https://doi.org/10.7717/peerj.2634
date submitted: 2016-07-04
date accepted: 2016-09-30
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Ping-Hsueh
author list: Agent
  family name: Kok
  given name: Victor C.
author list: Agent
  family name: Chou
  given name: Po-Liang
author list: Agent
  family name: Ku
  given name: Ming-Chang
author list: Agent
  family name: Chen
  given name: Yu-Ching
author list: Agent
  family name: Horng
  given name: Jorng-Tzong
doi: 10.7717/peerj.2634
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Lee et al.
attribution name: Lee et al.

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