PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats
items: Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks
items: Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ
items: Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy
items: Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene
items: Comparative morphology and trophic ecology in a population of the polymorphic lizard Sceloporus minor (Squamata: Phrynosomatidae) from central Mexico
items: The first North American Propterodon (Hyaenodonta: Hyaenodontidae), a new species from the late Uintan of Utah
items: Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community
items: TLR4 polymorphisms may increase susceptibility to periodontitis in Pg-positive individuals
items: Charcot-Marie-Tooth type 4B2 demyelinating neuropathy in miniature Schnauzer dogs caused by a novel splicing SBF2 (MTMR13) genetic variant: a new spontaneous clinical model

Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats
type: item
type: AcademicArticle
description: Background Arjunolic acid (AA) is a potent phytochemical with wider pharmacological activities. Despite potential medicinal properties on various in vitro and in vivo studies, there is still a dearth of scientific data related to its safety profile and toxicological parameters. The current study aimed to investigate acute toxicity of AA in normal female Sprague Dawley rats. Methods In this study, AA was administered orally at an individual dose of 300 and 2000 mg/kg body weight to group 1 and 2 respectively, while group 3 served as normal control. All the animals were observed for 2 weeks to determine any behavioral and physical changes. On day 15, blood was collected for hematological and biochemical investigation, later animals from all the three groups were euthanized to harvest and store essential organs for histopathological analysis. Four different staining techniques; hematoxylin and eosin, Masson trichrome, Periodic acid Schiff and Oil O Red were used to investigate any alterations in different tissues through microscopical observation. Results The results of the study showed no morbidity and mortality at two different dosage of AA treatment. Daily food & water intake, body weight, relative organ weight, hematological and biochemical parameters were detected to be normal with no severe alteration seen through microscopical investigation in the structure of harvested tissues. Our findings support the safety profile of AA, which was well tolerated at higher dose. Thus, an in-detail study on the subacute disease model is warranted.
format: application/pdf
format: text/html
creator: Khurram Aamir
creator: Hidayat Ullah Khan
creator: Chowdhury Faiz Hossain
creator: Mst. Rejina Afrin
creator: Imam Shaik
creator: Naguib Salleh
creator: Nelli Giribabu
creator: Aditya Arya
subject: Biochemistry
subject: Toxicology
subject: Hematology
subject: Histology
description: doi:10.7717/peerj.8045
publisher: PeerJ Inc.
rights: © 2019 Aamir et al.
abstract: Background Arjunolic acid (AA) is a potent phytochemical with wider pharmacological activities. Despite potential medicinal properties on various in vitro and in vivo studies, there is still a dearth of scientific data related to its safety profile and toxicological parameters. The current study aimed to investigate acute toxicity of AA in normal female Sprague Dawley rats. Methods In this study, AA was administered orally at an individual dose of 300 and 2000 mg/kg body weight to group 1 and 2 respectively, while group 3 served as normal control. All the animals were observed for 2 weeks to determine any behavioral and physical changes. On day 15, blood was collected for hematological and biochemical investigation, later animals from all the three groups were euthanized to harvest and store essential organs for histopathological analysis. Four different staining techniques; hematoxylin and eosin, Masson trichrome, Periodic acid Schiff and Oil O Red were used to investigate any alterations in different tissues through microscopical observation. Results The results of the study showed no morbidity and mortality at two different dosage of AA treatment. Daily food & water intake, body weight, relative organ weight, hematological and biochemical parameters were detected to be normal with no severe alteration seen through microscopical investigation in the structure of harvested tissues. Our findings support the safety profile of AA, which was well tolerated at higher dose. Thus, an in-detail study on the subacute disease model is warranted.
bibliographic citation: Aamir et al. (2019) Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats. PeerJ 7:e8045 https://doi.org/10.7717/peerj.8045
date submitted: 2019-07-29
date accepted: 2019-10-16
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aamir
  given name: Khurram
author list: Agent
  family name: Khan
  given name: Hidayat Ullah
author list: Agent
  family name: Hossain
  given name: Chowdhury Faiz
author list: Agent
  family name: Afrin
  given name: Mst. Rejina
author list: Agent
  family name: Shaik
  given name: Imam
author list: Agent
  family name: Salleh
  given name: Naguib
author list: Agent
  family name: Giribabu
  given name: Nelli
author list: Agent
  family name: Arya
  given name: Aditya
doi: 10.7717/peerj.8045
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: © 2019 Aamir et al.
attribution name: Aamir et al.

Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks
type: item
type: AcademicArticle
description: Purpose To investigate whether multi-view convolutional neural networks can improve a fully automated lymph node detection system for pelvic MR Lymphography (MRL) images of patients with prostate cancer. Methods A fully automated computer-aided detection (CAD) system had been previously developed to detect lymph nodes in MRL studies. The CAD system was extended with three types of 2D multi-view convolutional neural networks (CNN) aiming to reduce false positives (FP). A 2D multi-view CNN is an efficient approximation of a 3D CNN, and three types were evaluated: a 1-view, 3-view, and 9-view 2D CNN. The three deep learning CNN architectures were trained and configured on retrospective data of 240 prostate cancer patients that received MRL images as the standard of care between January 2008 and April 2010. The MRL used ferumoxtran-10 as a contrast agent and comprised at least two imaging sequences: a 3D T1-weighted and a 3D T2*-weighted sequence. A total of 5089 lymph nodes were annotated by two expert readers, reading in consensus. A first experiment compared the performance with and without CNNs and a second experiment compared the individual contribution of the 1-view, 3-view, or 9-view architecture to the performance. The performances were visually compared using free-receiver operating characteristic (FROC) analysis and statistically compared using partial area under the FROC curve analysis. Training and analysis were performed using bootstrapped FROC and 5-fold cross-validation. Results Adding multi-view CNNs significantly (p < 0.01) reduced false positive detections. The 3-view and 9-view CNN outperformed (p < 0.01) the 1-view CNN, reducing FP from 20.6 to 7.8/image at 80% sensitivity. Conclusion Multi-view convolutional neural networks significantly reduce false positives in a lymph node detection system for MRL images, and three orthogonal views are sufficient. At the achieved level of performance, CAD for MRL may help speed up finding lymph nodes and assessin…
format: application/pdf
format: text/html
creator: Oscar A. Debats
creator: Geert J.S. Litjens
creator: Henkjan J. Huisman
subject: Oncology
subject: Radiology and Medical Imaging
subject: Urology
description: doi:10.7717/peerj.8052
publisher: PeerJ Inc.
rights: © 2019 Debats et al.
abstract: Purpose To investigate whether multi-view convolutional neural networks can improve a fully automated lymph node detection system for pelvic MR Lymphography (MRL) images of patients with prostate cancer. Methods A fully automated computer-aided detection (CAD) system had been previously developed to detect lymph nodes in MRL studies. The CAD system was extended with three types of 2D multi-view convolutional neural networks (CNN) aiming to reduce false positives (FP). A 2D multi-view CNN is an efficient approximation of a 3D CNN, and three types were evaluated: a 1-view, 3-view, and 9-view 2D CNN. The three deep learning CNN architectures were trained and configured on retrospective data of 240 prostate cancer patients that received MRL images as the standard of care between January 2008 and April 2010. The MRL used ferumoxtran-10 as a contrast agent and comprised at least two imaging sequences: a 3D T1-weighted and a 3D T2*-weighted sequence. A total of 5089 lymph nodes were annotated by two expert readers, reading in consensus. A first experiment compared the performance with and without CNNs and a second experiment compared the individual contribution of the 1-view, 3-view, or 9-view architecture to the performance. The performances were visually compared using free-receiver operating characteristic (FROC) analysis and statistically compared using partial area under the FROC curve analysis. Training and analysis were performed using bootstrapped FROC and 5-fold cross-validation. Results Adding multi-view CNNs significantly (p < 0.01) reduced false positive detections. The 3-view and 9-view CNN outperformed (p < 0.01) the 1-view CNN, reducing FP from 20.6 to 7.8/image at 80% sensitivity. Conclusion Multi-view convolutional neural networks significantly reduce false positives in a lymph node detection system for MRL images, and three orthogonal views are sufficient. At the achieved level of performance, CAD for MRL may help speed up finding lymph nodes and assessin…
bibliographic citation: Debats et al. (2019) Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks. PeerJ 7:e8052 https://doi.org/10.7717/peerj.8052
date submitted: 2018-12-13
date accepted: 2019-10-17
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Debats
  given name: Oscar A.
author list: Agent
  family name: Litjens
  given name: Geert J.S.
author list: Agent
  family name: Huisman
  given name: Henkjan J.
doi: 10.7717/peerj.8052
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: ©2019 Debats et al.
attribution name: Debats et al.

Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ
type: item
type: AcademicArticle
description: Background In the predator–sea urchin–macrophyte trophic cascade, the ecological effect of sea urchins as grazers depends both on their density and the changes in foraging activity, which are influenced by various disturbing factors. However, the complete duration of the alarm reactions of echinoids has not been studied until now. Here, we tested a hypothesis that two cohabiting sea urchins, Mesocentrotus nudus and Strongylocentrotus intermedius, which differ morphologically, might display different behavioral responses to high hydrodynamic activity and predation. Methods We used continuous time-lapse video recording to clarify behavioral patterns of M. nudus and S. intermedius in presence of a large quantity of food (the kelp Saccharina japonica) but under different weather conditions and different types of predation threat: (1) calm weather conditions, (2) stormy weather conditions, (3) predation risk associated with the presence of several sea star species and (4) predation risk associated with an alarm stimulus (crushed conspecifics or heterospecifics). Three separate video recording experiments (134 days in total) were conducted under field conditions. Video recording analysis was performed to determine the number of specimens of each sea urchin species in the cameras’ field of view, size of sea urchins’ groups, movement patterns and the duration of the alarm responses of both sea urchin species. Results We showed that in the presence of kelp, M. nudus and S. intermedius exhibited both similar and different behavioral responses to hydrodynamics and predation threat. Under calm weather, movement patterns of both echinoids were similar but M. nudus exhibited the higher locomotion speed and distance traveled. Furthermore, S. intermedius but not M. nudus tended to group near the food substrate. The stormy weather caused a sharp decrease in movement activity followed by escape response in both echinoids. Six starfish species failed to predate on healthy sea urchins …
format: application/pdf
format: text/html
creator: Peter M. Zhadan
creator: Marina A. Vaschenko
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.8087
publisher: PeerJ Inc.
rights: © 2019 Zhadan and Vaschenko
abstract: Background In the predator–sea urchin–macrophyte trophic cascade, the ecological effect of sea urchins as grazers depends both on their density and the changes in foraging activity, which are influenced by various disturbing factors. However, the complete duration of the alarm reactions of echinoids has not been studied until now. Here, we tested a hypothesis that two cohabiting sea urchins, Mesocentrotus nudus and Strongylocentrotus intermedius, which differ morphologically, might display different behavioral responses to high hydrodynamic activity and predation. Methods We used continuous time-lapse video recording to clarify behavioral patterns of M. nudus and S. intermedius in presence of a large quantity of food (the kelp Saccharina japonica) but under different weather conditions and different types of predation threat: (1) calm weather conditions, (2) stormy weather conditions, (3) predation risk associated with the presence of several sea star species and (4) predation risk associated with an alarm stimulus (crushed conspecifics or heterospecifics). Three separate video recording experiments (134 days in total) were conducted under field conditions. Video recording analysis was performed to determine the number of specimens of each sea urchin species in the cameras’ field of view, size of sea urchins’ groups, movement patterns and the duration of the alarm responses of both sea urchin species. Results We showed that in the presence of kelp, M. nudus and S. intermedius exhibited both similar and different behavioral responses to hydrodynamics and predation threat. Under calm weather, movement patterns of both echinoids were similar but M. nudus exhibited the higher locomotion speed and distance traveled. Furthermore, S. intermedius but not M. nudus tended to group near the food substrate. The stormy weather caused a sharp decrease in movement activity followed by escape response in both echinoids. Six starfish species failed to predate on healthy sea urchins …
bibliographic citation: Zhadan et al. (2019) Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ. PeerJ 7:e8087 https://doi.org/10.7717/peerj.8087
date submitted: 2019-06-05
date accepted: 2019-10-23
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhadan
  given name: Peter M.
author list: Agent
  family name: Vaschenko
  given name: Marina A.
doi: 10.7717/peerj.8087
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: © 2019 Zhadan and Vaschenko
attribution name: Zhadan and Vaschenko

Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy
type: item
type: AcademicArticle
description: Several squat lobster specimens of the genus Munidopsis were collected from an artificially placed carcass fall (cow bones) on Weijia Guyot in the western Pacific Ocean. Based on morphological comparisons and molecular analysis, three specimens were confirmed as juveniles of M. albatrossae Pequegnat & Pequegnat, 1973, which represents the first record of this species in the western Pacific. The other specimens collected are newly described as Munidopsis spinifrons sp. nov., which is distinguished from the closely related species in having a spinose rostrum and basal lateral eyespine on the eyestalk. The M. albatrossae from Weijia Guyot exhibited very low genetic distances when compared with a conspecific sample from Monterey Bay, USA, and the closely related species M. aries (A. Milne Edwards, 1880) from the northeastern Atlantic. A phylogenetic tree based on the mtCOI gene shows M. spinifrons sp. nov. as sister to M. vrijenhoeki Jones & Macpherson, 2007 and M. nitida (A. Milne Edwards, 1880), although M. vrijenhoeki presents a complex relationship with other species in the clade. The systematic status of the new species and the closely related species are discussed.
format: application/pdf
format: text/html
creator: Dong Dong
creator: Peng Xu
creator: Xin-Zheng Li
creator: Chunsheng Wang
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.8089
publisher: PeerJ Inc.
rights: © 2019 Dong et al.
abstract: Several squat lobster specimens of the genus Munidopsis were collected from an artificially placed carcass fall (cow bones) on Weijia Guyot in the western Pacific Ocean. Based on morphological comparisons and molecular analysis, three specimens were confirmed as juveniles of M. albatrossae Pequegnat & Pequegnat, 1973, which represents the first record of this species in the western Pacific. The other specimens collected are newly described as Munidopsis spinifrons sp. nov., which is distinguished from the closely related species in having a spinose rostrum and basal lateral eyespine on the eyestalk. The M. albatrossae from Weijia Guyot exhibited very low genetic distances when compared with a conspecific sample from Monterey Bay, USA, and the closely related species M. aries (A. Milne Edwards, 1880) from the northeastern Atlantic. A phylogenetic tree based on the mtCOI gene shows M. spinifrons sp. nov. as sister to M. vrijenhoeki Jones & Macpherson, 2007 and M. nitida (A. Milne Edwards, 1880), although M. vrijenhoeki presents a complex relationship with other species in the clade. The systematic status of the new species and the closely related species are discussed.
bibliographic citation: Dong et al. (2019) Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy. PeerJ 7:e8089 https://doi.org/10.7717/peerj.8089
date submitted: 2019-09-18
date accepted: 2019-10-23
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Dong
author list: Agent
  family name: Xu
  given name: Peng
author list: Agent
  family name: Li
  given name: Xin-Zheng
author list: Agent
  family name: Wang
  given name: Chunsheng
doi: 10.7717/peerj.8089
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: ©2019 Dong et al.
attribution name: Dong et al.

Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene
type: item
type: AcademicArticle
description: Delta bovine papillomaviruses (δBPVs) causes fibropapillomas or bladder cancer in cattle. E5 is the major oncogene of δBPVs; however, the influence that E5 oncogene has on host microRNA (miRNA) and mRNA expression profiles remains little elucidated. In the present study, small RNA sequencing and RNA sequencing were used to explore alterations in miRNAs and mRNAs in E5 over-expressing Madin-Darby bovine kidney (MDBK) cells compared with controls. In total, 77 miRNAs (including 30 bovine-derived miRNAs) and 223 genes were differentially expressed (DE) following E5 overexpression. The dysregulated genes were mainly involved in metabolic and biosynthetic processes. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, 22 DEGs and nine DE miRNAs were selected for RT-qPCR validation. Of these, downregulation of six miRNAs, bta-miR-34c, bta-miR-122, bta-miR-195, bta-miR-449b, bta-miR-2425-5p, and bta-miR-2428-3p were confirmed; In addition, upregulation of 16 genes, ACSS2, DDIT4, INHBE, INSIG1, PNRC1, PSAT1, PSPH, PYCR1, SC4MOL, SLC34A2, SCD, SPARC, IDI1, PCK2, HMGCS1, and SMIM14 and downregulation of two genes, BATF3 and WFDC2 were confirmed. Specially, bta-miR-34c and bta-miR-449b potentially regulated PYCR1 and DDIT4, which were involved in cancer progression and angiogenesis. Our study presented for the first time the comprehensive miRNA and mRNA alterations in MDBK cells expressing the BPV E5 oncogene, providing new insights into the tumorigenesis induced by BPV E5.
format: application/pdf
format: text/html
creator: Feng Pang
creator: Zhen Chen
creator: Chengqiang Wang
creator: Mengmeng Zhang
creator: Zhenxing Zhang
creator: Xiaohong Yang
creator: Yiying Zheng
creator: Ang Liu
creator: Yiwen Cheng
creator: Jie Chen
creator: Bin Li
creator: Li Du
creator: Fengyang Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.8098
publisher: PeerJ Inc.
rights: © 2019 Pang et al.
abstract: Delta bovine papillomaviruses (δBPVs) causes fibropapillomas or bladder cancer in cattle. E5 is the major oncogene of δBPVs; however, the influence that E5 oncogene has on host microRNA (miRNA) and mRNA expression profiles remains little elucidated. In the present study, small RNA sequencing and RNA sequencing were used to explore alterations in miRNAs and mRNAs in E5 over-expressing Madin-Darby bovine kidney (MDBK) cells compared with controls. In total, 77 miRNAs (including 30 bovine-derived miRNAs) and 223 genes were differentially expressed (DE) following E5 overexpression. The dysregulated genes were mainly involved in metabolic and biosynthetic processes. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, 22 DEGs and nine DE miRNAs were selected for RT-qPCR validation. Of these, downregulation of six miRNAs, bta-miR-34c, bta-miR-122, bta-miR-195, bta-miR-449b, bta-miR-2425-5p, and bta-miR-2428-3p were confirmed; In addition, upregulation of 16 genes, ACSS2, DDIT4, INHBE, INSIG1, PNRC1, PSAT1, PSPH, PYCR1, SC4MOL, SLC34A2, SCD, SPARC, IDI1, PCK2, HMGCS1, and SMIM14 and downregulation of two genes, BATF3 and WFDC2 were confirmed. Specially, bta-miR-34c and bta-miR-449b potentially regulated PYCR1 and DDIT4, which were involved in cancer progression and angiogenesis. Our study presented for the first time the comprehensive miRNA and mRNA alterations in MDBK cells expressing the BPV E5 oncogene, providing new insights into the tumorigenesis induced by BPV E5.
bibliographic citation: Pang et al. (2019) Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene. PeerJ 7:e8098 https://doi.org/10.7717/peerj.8098
date submitted: 2019-07-13
date accepted: 2019-10-24
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pang
  given name: Feng
author list: Agent
  family name: Chen
  given name: Zhen
author list: Agent
  family name: Wang
  given name: Chengqiang
author list: Agent
  family name: Zhang
  given name: Mengmeng
author list: Agent
  family name: Zhang
  given name: Zhenxing
author list: Agent
  family name: Yang
  given name: Xiaohong
author list: Agent
  family name: Zheng
  given name: Yiying
author list: Agent
  family name: Liu
  given name: Ang
author list: Agent
  family name: Cheng
  given name: Yiwen
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Li
  given name: Bin
author list: Agent
  family name: Du
  given name: Li
author list: Agent
  family name: Wang
  given name: Fengyang
doi: 10.7717/peerj.8098
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: © 2019 Pang et al.
attribution name: Pang et al.

Comparative morphology and trophic ecology in a population of the polymorphic lizard Sceloporus minor (Squamata: Phrynosomatidae) from central Mexico
type: item
type: AcademicArticle
description: Polymorphism among individuals of the same population has generally been linked to alternative reproductive tactics, where different morphs can exhibit differences in their morphological, ecological, and behavioral attributes. These differences may result in a divergence in diet between morphs due to differential exploitation of habitat, morphological differences that influence prey selection, or differential energy expenditure that results in different nutritional needs. The present study analyzes the morphology (morphometry and body mass) and diet of red and yellow male morphs in a population (El Enzuelado) of the lizard Sceloporus minor from central Mexico. No differences between morphs were found for any of the morphometric variables analyzed (snout-vent length, tail length, jaw length, jaw width, head length, head width, head height, tibia length, femur length, forearm length and ventral patch length). In both morphs, allometric growth was observed in all body features analyzed, as well as in morphometric features of the head across seasons. Analysis of stomach contents showed that the diet of red males was composed of 12 categories of prey, while that of yellow males was composed of 10 categories; those categories of diet not shared between morphs (e.g., Isoptera, Psocoptera) were consumed by their respective morph in very low proportions. Categories of diet with the highest values of food importance for both groups were Coleoptera, Orthoptera, and leaves; a similar pattern was seen across seasons. This, in turn, is reflected in low niche breadth values for each morph and a very high niche overlap. There were no significant differences between morphs overall, or between morphs per season, in the weight and volume of stomach contents or in the number of prey items found in stomachs; however, differences in these variables across all males (independent of morph) were recorded between seasons. Likewise, no significant correlations were found between body size (sn…
format: application/pdf
format: text/html
creator: Aaron García-Rosales
creator: Aurelio Ramírez-Bautista
creator: Barry P. Stephenson
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.8099
publisher: PeerJ Inc.
rights: © 2019 García-Rosales et al.
abstract: Polymorphism among individuals of the same population has generally been linked to alternative reproductive tactics, where different morphs can exhibit differences in their morphological, ecological, and behavioral attributes. These differences may result in a divergence in diet between morphs due to differential exploitation of habitat, morphological differences that influence prey selection, or differential energy expenditure that results in different nutritional needs. The present study analyzes the morphology (morphometry and body mass) and diet of red and yellow male morphs in a population (El Enzuelado) of the lizard Sceloporus minor from central Mexico. No differences between morphs were found for any of the morphometric variables analyzed (snout-vent length, tail length, jaw length, jaw width, head length, head width, head height, tibia length, femur length, forearm length and ventral patch length). In both morphs, allometric growth was observed in all body features analyzed, as well as in morphometric features of the head across seasons. Analysis of stomach contents showed that the diet of red males was composed of 12 categories of prey, while that of yellow males was composed of 10 categories; those categories of diet not shared between morphs (e.g., Isoptera, Psocoptera) were consumed by their respective morph in very low proportions. Categories of diet with the highest values of food importance for both groups were Coleoptera, Orthoptera, and leaves; a similar pattern was seen across seasons. This, in turn, is reflected in low niche breadth values for each morph and a very high niche overlap. There were no significant differences between morphs overall, or between morphs per season, in the weight and volume of stomach contents or in the number of prey items found in stomachs; however, differences in these variables across all males (independent of morph) were recorded between seasons. Likewise, no significant correlations were found between body size (sn…
bibliographic citation: García-Rosales et al. (2019) Comparative morphology and trophic ecology in a population of the polymorphic lizard Sceloporus minor (Squamata: Phrynosomatidae) from central Mexico. PeerJ 7:e8099 https://doi.org/10.7717/peerj.8099
date submitted: 2019-01-29
date accepted: 2019-10-24
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Rosales
  given name: Aaron
author list: Agent
  family name: Ramírez-Bautista
  given name: Aurelio
author list: Agent
  family name: Stephenson
  given name: Barry P.
doi: 10.7717/peerj.8099
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: ©2019 García-Rosales et al.
attribution name: García-Rosales et al.

The first North American Propterodon (Hyaenodonta: Hyaenodontidae), a new species from the late Uintan of Utah
type: item
type: AcademicArticle
description: The carnivorous mammalian fauna from the Uintan (late middle Eocene) of North America remains relatively poorly documented. This is unfortunate, as this is a critical interval in the transition from “creodont” to carnivoran dominated carnivore guilds. This study reports a new species from the Uinta Formation of the Uinta Basin, Utah, the first North American species of the otherwise Asian hyaenodont genus Propterodon. The new species, Propterodon witteri, represented by a dentary with M2-3 from the late Uintan Leota Quarry, is larger than the well-known P. morrisi and P. tongi and has a larger M3 talonid, but is otherwise very similar. A phylogenetic analysis of hyaenodont interrelationships recovers P. witteri as a hyaenodontine but is generally poorly resolved. A relationship between Hyaenodontinae and Oxyaenoides, recovered by many recent analyses, is not supported. Among the Asian species of Propterodon, P. pishigouensis is reidentified as a machaeroidine oxyaenid and recombined as Apataelurus pishigouensis new combination. Isphanatherium ferganensis may also represent an Asian machaeroidine. Identification of a North American species of Propterodon and an Asian Apataelurus increases the similarity of North American Uintan and Asian Irdinmanhan faunas and suggests that there was substantial exchange of carnivorous fauna during the late middle Eocene.
format: application/pdf
format: text/html
creator: Shawn P. Zack
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.8136
publisher: PeerJ Inc.
rights: © 2019 Zack
abstract: The carnivorous mammalian fauna from the Uintan (late middle Eocene) of North America remains relatively poorly documented. This is unfortunate, as this is a critical interval in the transition from “creodont” to carnivoran dominated carnivore guilds. This study reports a new species from the Uinta Formation of the Uinta Basin, Utah, the first North American species of the otherwise Asian hyaenodont genus Propterodon. The new species, Propterodon witteri, represented by a dentary with M2-3 from the late Uintan Leota Quarry, is larger than the well-known P. morrisi and P. tongi and has a larger M3 talonid, but is otherwise very similar. A phylogenetic analysis of hyaenodont interrelationships recovers P. witteri as a hyaenodontine but is generally poorly resolved. A relationship between Hyaenodontinae and Oxyaenoides, recovered by many recent analyses, is not supported. Among the Asian species of Propterodon, P. pishigouensis is reidentified as a machaeroidine oxyaenid and recombined as Apataelurus pishigouensis new combination. Isphanatherium ferganensis may also represent an Asian machaeroidine. Identification of a North American species of Propterodon and an Asian Apataelurus increases the similarity of North American Uintan and Asian Irdinmanhan faunas and suggests that there was substantial exchange of carnivorous fauna during the late middle Eocene.
bibliographic citation: Zack (2019) The first North American Propterodon (Hyaenodonta: Hyaenodontidae), a new species from the late Uintan of Utah. PeerJ 7:e8136 https://doi.org/10.7717/peerj.8136
date submitted: 2019-07-01
date accepted: 2019-11-01
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zack
  given name: Shawn P.
doi: 10.7717/peerj.8136
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: ©2019 Zack
attribution name: Zack

Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community
type: item
type: AcademicArticle
description: Di-2-ethylhexyl phthalate (DEHP) is a plasticizer used in consumer products and building materials, including polyvinyl chloride flooring material. DEHP adsorbs from material and leaches into soil, water, or dust and presents an exposure risk to building occupants by inhalation, ingestion, or absorption. A number of bacterial isolates are demonstrated to degrade DEHP in culture, but bacteria may be susceptible to it as well, thus this study examined the relation of DEHP to bacterial communities in dust. Polyvinyl chloride flooring was seeded with homogenized house dust and incubated for up to 14 days, and bacterial communities in dust were identified at days 1, 7, and 14 using the V3–V4 regions of the bacterial 16S rRNA gene. DEHP concentration in dust increased over time, as expected, and bacterial richness and Shannon diversity were negatively correlated with DEHP concentration. Some sequence variants of Bacillus, Corynebacterium jeddahense, Streptococcus, and Peptoniphilus were relatively more abundant at low concentrations of DEHP, while some Sphingomonas, Chryseobacterium, and a member of the Enterobacteriaceae family were relatively more abundant at higher concentrations. The built environment is known to host lower microbial diversity and biomass than natural environments, and DEHP or other chemicals indoors may contribute to this paucity.
format: application/pdf
format: text/html
creator: Samantha Velazquez
creator: Chenyang Bi
creator: Jeff Kline
creator: Susie Nunez
creator: Rich Corsi
creator: Ying Xu
creator: Suzanne L. Ishaq
subject: Genomics
subject: Microbiology
subject: Coupled Natural and Human Systems
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.8147
publisher: PeerJ Inc.
rights: © 2019 Velazquez et al.
abstract: Di-2-ethylhexyl phthalate (DEHP) is a plasticizer used in consumer products and building materials, including polyvinyl chloride flooring material. DEHP adsorbs from material and leaches into soil, water, or dust and presents an exposure risk to building occupants by inhalation, ingestion, or absorption. A number of bacterial isolates are demonstrated to degrade DEHP in culture, but bacteria may be susceptible to it as well, thus this study examined the relation of DEHP to bacterial communities in dust. Polyvinyl chloride flooring was seeded with homogenized house dust and incubated for up to 14 days, and bacterial communities in dust were identified at days 1, 7, and 14 using the V3–V4 regions of the bacterial 16S rRNA gene. DEHP concentration in dust increased over time, as expected, and bacterial richness and Shannon diversity were negatively correlated with DEHP concentration. Some sequence variants of Bacillus, Corynebacterium jeddahense, Streptococcus, and Peptoniphilus were relatively more abundant at low concentrations of DEHP, while some Sphingomonas, Chryseobacterium, and a member of the Enterobacteriaceae family were relatively more abundant at higher concentrations. The built environment is known to host lower microbial diversity and biomass than natural environments, and DEHP or other chemicals indoors may contribute to this paucity.
bibliographic citation: Velazquez et al. (2019) Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community. PeerJ 7:e8147 https://doi.org/10.7717/peerj.8147
date submitted: 2019-09-24
date accepted: 2019-11-03
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Velazquez
  given name: Samantha
author list: Agent
  family name: Bi
  given name: Chenyang
author list: Agent
  family name: Kline
  given name: Jeff
author list: Agent
  family name: Nunez
  given name: Susie
author list: Agent
  family name: Corsi
  given name: Rich
author list: Agent
  family name: Xu
  given name: Ying
author list: Agent
  family name: Ishaq
  given name: Suzanne L.
doi: 10.7717/peerj.8147
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: © 2019 Velazquez et al.
attribution name: Velazquez et al.

TLR4 polymorphisms may increase susceptibility to periodontitis in Pg-positive individuals
type: item
type: AcademicArticle
description: Objective To investigate the correlation between the single nucleotide polymorphisms (SNPs) in the toll-like receptor 4 (TLR4) gene and the susceptibility to chronic periodontitis. Design 241 Chinese subjects from the cohort of Beijing Shijingshan Community were recruited. Buccal swab samples, the whole unstimulated saliva and periodontal clinical parameters were collected. Human DNA extracted from buccal swab samples were used for genotyping eight SNPs of the TLR4 gene (rs11536889, rs1927906, rs1927911, rs2149356, rs4986790, rs4986791, rs2737190, rs787384) by the Sequenom MassARRAY system. Porphyromonas gingivalis (P. gingivalis) was detected from the deposition of the whole unstimulated saliva through polymerase chain reaction (PCR) method based on 16S rRNA. The correlation between SNPs of TLR4 and chronic periodontitis susceptibility in the whole subjects and the patients detected with P. gingivalis was investigated. Results The variants of rs4986790 and rs4986791 were not found in 241 Chinese subjects. Moreover, there was no significant difference in the distribution of theother6 SNPs of TLR4 between groups of none/mild -periodontitis and moderate/severe-periodontitis subjects. When combined with P. gingivalis infection, rs1927911 (TT/CC+CT), rs2149356 (TT/GG+GT) and rs2737190 (GG/AA+AG) were independent risk factors of chronic periodontitis. Conclusion Three SNPs of TLR4, i.e., rs1927911 (TT/CC+CT), rs2149356 (TT/GG+GT) and rs2737190 (GG/AA+AG), were associated with moderate/severe chronic periodontitis in Chinese population infected with P. gingivalis. P. gingivalis, which interacted with TLR4 gene plays an important role in the pathogenesis of periodontitis.
format: application/pdf
format: text/html
creator: Wenjing Li
creator: Xiaojing Cao
creator: Lu He
creator: Huanxin Meng
creator: Bingtao Yang
creator: Yanting Liao
subject: Genetics
subject: Microbiology
subject: Dentistry
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.7828
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Objective To investigate the correlation between the single nucleotide polymorphisms (SNPs) in the toll-like receptor 4 (TLR4) gene and the susceptibility to chronic periodontitis. Design 241 Chinese subjects from the cohort of Beijing Shijingshan Community were recruited. Buccal swab samples, the whole unstimulated saliva and periodontal clinical parameters were collected. Human DNA extracted from buccal swab samples were used for genotyping eight SNPs of the TLR4 gene (rs11536889, rs1927906, rs1927911, rs2149356, rs4986790, rs4986791, rs2737190, rs787384) by the Sequenom MassARRAY system. Porphyromonas gingivalis (P. gingivalis) was detected from the deposition of the whole unstimulated saliva through polymerase chain reaction (PCR) method based on 16S rRNA. The correlation between SNPs of TLR4 and chronic periodontitis susceptibility in the whole subjects and the patients detected with P. gingivalis was investigated. Results The variants of rs4986790 and rs4986791 were not found in 241 Chinese subjects. Moreover, there was no significant difference in the distribution of theother6 SNPs of TLR4 between groups of none/mild -periodontitis and moderate/severe-periodontitis subjects. When combined with P. gingivalis infection, rs1927911 (TT/CC+CT), rs2149356 (TT/GG+GT) and rs2737190 (GG/AA+AG) were independent risk factors of chronic periodontitis. Conclusion Three SNPs of TLR4, i.e., rs1927911 (TT/CC+CT), rs2149356 (TT/GG+GT) and rs2737190 (GG/AA+AG), were associated with moderate/severe chronic periodontitis in Chinese population infected with P. gingivalis. P. gingivalis, which interacted with TLR4 gene plays an important role in the pathogenesis of periodontitis.
bibliographic citation: Li et al. (2019) TLR4 polymorphisms may increase susceptibility to periodontitis in Pg-positive individuals. PeerJ 7:e7828 https://doi.org/10.7717/peerj.7828
date submitted: 2019-07-05
date accepted: 2019-09-03
issued: 2019-11-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Wenjing
author list: Agent
  family name: Cao
  given name: Xiaojing
author list: Agent
  family name: He
  given name: Lu
author list: Agent
  family name: Meng
  given name: Huanxin
author list: Agent
  family name: Yang
  given name: Bingtao
author list: Agent
  family name: Liao
  given name: Yanting
doi: 10.7717/peerj.7828
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-21
copyright: ©2019 Li et al.
attribution name: Li et al.

Charcot-Marie-Tooth type 4B2 demyelinating neuropathy in miniature Schnauzer dogs caused by a novel splicing SBF2 (MTMR13) genetic variant: a new spontaneous clinical model
type: item
type: AcademicArticle
description: Background Charcot-Marie-Tooth (CMT) disease is the most common neuromuscular disorder in humans affecting 40 out of 100,000 individuals. In 2008, we described the clinical, electrophysiological and pathological findings of a demyelinating motor and sensory neuropathy in Miniature Schnauzer dogs, with a suspected autosomal recessive mode of inheritance based on pedigree analysis. The discovery of additional cases has followed this work and led to a genome-wide association mapping approach to search for the underlying genetic cause of the disease. Methods For genome wide association screening, genomic DNA samples from affected and unaffected dogs were genotyped using the Illumina CanineHD SNP genotyping array. SBF2 and its variant were sequenced using primers and PCRs. RNA was extracted from muscle of an unaffected and an affected dog and RT-PCR performed. Immunohistochemistry for myelin basic protein was performed on peripheral nerve section specimens. Results The genome-wide association study gave an indicative signal on canine chromosome 21. Although the signal was not of genome-wide significance due to the small number of cases, the SBF2 (also known as MTMR13) gene within the region of shared case homozygosity was a strong positional candidate, as 22 genetic variants in the gene have been associated with demyelinating forms of Charcot-Marie-Tooth disease in humans. Sequencing of SBF2 in cases revealed a splice donor site genetic variant, resulting in cryptic splicing and predicted early termination of the protein based on RNA sequencing results. Conclusions This study reports the first genetic variant in Miniature Schnauzer dogs responsible for the occurrence of a demyelinating peripheral neuropathy with abnormally folded myelin. This discovery establishes a genotype/phenotype correlation in affected Miniature Schnauzers that can be used for the diagnosis of these dogs. It further supports the dog as a natural model of a human disease; in this instance, Charcot-M…
format: application/pdf
format: text/html
creator: Nicolas Granger
creator: Alejandro Luján Feliu-Pascual
creator: Charlotte Spicer
creator: Sally Ricketts
creator: Rebekkah Hitti
creator: Oliver Forman
creator: Joshua Hersheson
creator: Henry Houlden
subject: Genetics
subject: Veterinary Medicine
subject: Neurology
description: doi:10.7717/peerj.7983
publisher: PeerJ Inc.
rights: © 2019 Granger et al.
abstract: Background Charcot-Marie-Tooth (CMT) disease is the most common neuromuscular disorder in humans affecting 40 out of 100,000 individuals. In 2008, we described the clinical, electrophysiological and pathological findings of a demyelinating motor and sensory neuropathy in Miniature Schnauzer dogs, with a suspected autosomal recessive mode of inheritance based on pedigree analysis. The discovery of additional cases has followed this work and led to a genome-wide association mapping approach to search for the underlying genetic cause of the disease. Methods For genome wide association screening, genomic DNA samples from affected and unaffected dogs were genotyped using the Illumina CanineHD SNP genotyping array. SBF2 and its variant were sequenced using primers and PCRs. RNA was extracted from muscle of an unaffected and an affected dog and RT-PCR performed. Immunohistochemistry for myelin basic protein was performed on peripheral nerve section specimens. Results The genome-wide association study gave an indicative signal on canine chromosome 21. Although the signal was not of genome-wide significance due to the small number of cases, the SBF2 (also known as MTMR13) gene within the region of shared case homozygosity was a strong positional candidate, as 22 genetic variants in the gene have been associated with demyelinating forms of Charcot-Marie-Tooth disease in humans. Sequencing of SBF2 in cases revealed a splice donor site genetic variant, resulting in cryptic splicing and predicted early termination of the protein based on RNA sequencing results. Conclusions This study reports the first genetic variant in Miniature Schnauzer dogs responsible for the occurrence of a demyelinating peripheral neuropathy with abnormally folded myelin. This discovery establishes a genotype/phenotype correlation in affected Miniature Schnauzers that can be used for the diagnosis of these dogs. It further supports the dog as a natural model of a human disease; in this instance, Charcot-M…
bibliographic citation: Granger et al. (2019) Charcot-Marie-Tooth type 4B2 demyelinating neuropathy in miniature Schnauzer dogs caused by a novel splicing SBF2 (MTMR13) genetic variant: a new spontaneous clinical model. PeerJ 7:e7983 https://doi.org/10.7717/peerj.7983
date submitted: 2019-06-10
date accepted: 2019-10-02
issued: 2019-11-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Granger
  given name: Nicolas
author list: Agent
  family name: Luján Feliu-Pascual
  given name: Alejandro
author list: Agent
  family name: Spicer
  given name: Charlotte
author list: Agent
  family name: Ricketts
  given name: Sally
author list: Agent
  family name: Hitti
  given name: Rebekkah
author list: Agent
  family name: Forman
  given name: Oliver
author list: Agent
  family name: Hersheson
  given name: Joshua
author list: Agent
  family name: Houlden
  given name: Henry
doi: 10.7717/peerj.7983
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-21
copyright: ©2019 Granger et al.
attribution name: Granger et al.

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