PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identifying multiple collagen gene family members as potential gastric cancer biomarkers using integrated bioinformatics analysis
items: Herbicide applications increase greenhouse gas emissions of alfalfa pasture in the inland arid region of northwest China
items: Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods
items: Agreement between the GAITRite® System and the Wearable Sensor BTS G-Walk® for measurement of gait parameters in healthy adults and Parkinson’s disease patients
items: Maternal trauma and fear history predict BDNF methylation and gene expression in newborns
items: A new insect trackway from the Upper Jurassic—Lower Cretaceous eolian sandstones of São Paulo State, Brazil: implications for reconstructing desert paleoecology
items: Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review
items: Plant-derived angiogenin fusion protein’s cytoprotective effect on trabecular meshwork damage induced by Benzalkonium chloride in mice
items: Oldest co-occurrence of Varanus and Python from Africa—first record of squamates from the early Miocene of Moghra Formation, Western Desert, Egypt
items: Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment

Identifying multiple collagen gene family members as potential gastric cancer biomarkers using integrated bioinformatics analysis
type: item
type: AcademicArticle
description: Background Gastric cancer is one of the most common malignant cancers worldwide. Despite substantial developments in therapeutic strategies, the five-year survival rate remains low. Therefore, novel biomarkers and therapeutic targets involved in the progression of gastric tumors need to be identified. Methods We obtained the mRNA microarray datasets GSE65801, GSE54129 and GSE79973 from the Gene Expression Omnibus database to acquire differentially expressed genes (DEGs). We used the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to analyze DEG pathways and functions, and the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape to obtain the protein–protein interaction (PPI) network. Next, we validated the hub gene expression levels using the Oncomine database and Gene Expression Profiling Interactive Analysis (GEPIA), and conducted stage expression and survival analysis. Results From the three microarray datasets, we identified nine major hub genes: COL1A1, COL1A2, COL3A1, COL5A2, COL4A1, FN1, COL5A1, COL4A2, and COL6A3. Conclusion Our study identified COL1A1 and COL1A2 as potential gastric cancer prognostic biomarkers.
format: application/pdf
format: text/html
creator: Zhaoxing Li
creator: Zhao Liu
creator: Zhiting Shao
creator: Chuang Li
creator: Yong Li
creator: Qingwei Liu
creator: Yifei Zhang
creator: Bibo Tan
creator: Yu Liu
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.9123
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background Gastric cancer is one of the most common malignant cancers worldwide. Despite substantial developments in therapeutic strategies, the five-year survival rate remains low. Therefore, novel biomarkers and therapeutic targets involved in the progression of gastric tumors need to be identified. Methods We obtained the mRNA microarray datasets GSE65801, GSE54129 and GSE79973 from the Gene Expression Omnibus database to acquire differentially expressed genes (DEGs). We used the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to analyze DEG pathways and functions, and the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape to obtain the protein–protein interaction (PPI) network. Next, we validated the hub gene expression levels using the Oncomine database and Gene Expression Profiling Interactive Analysis (GEPIA), and conducted stage expression and survival analysis. Results From the three microarray datasets, we identified nine major hub genes: COL1A1, COL1A2, COL3A1, COL5A2, COL4A1, FN1, COL5A1, COL4A2, and COL6A3. Conclusion Our study identified COL1A1 and COL1A2 as potential gastric cancer prognostic biomarkers.
bibliographic citation: Li et al. (2020) Identifying multiple collagen gene family members as potential gastric cancer biomarkers using integrated bioinformatics analysis. PeerJ 8:e9123 https://doi.org/10.7717/peerj.9123
date submitted: 2019-05-22
date accepted: 2020-04-13
issued: 2020-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhaoxing
author list: Agent
  family name: Liu
  given name: Zhao
author list: Agent
  family name: Shao
  given name: Zhiting
author list: Agent
  family name: Li
  given name: Chuang
author list: Agent
  family name: Li
  given name: Yong
author list: Agent
  family name: Liu
  given name: Qingwei
author list: Agent
  family name: Zhang
  given name: Yifei
author list: Agent
  family name: Tan
  given name: Bibo
author list: Agent
  family name: Liu
  given name: Yu
doi: 10.7717/peerj.9123
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-25
copyright: ©2020 Li et al.
attribution name: Li et al.

Herbicide applications increase greenhouse gas emissions of alfalfa pasture in the inland arid region of northwest China
type: item
type: AcademicArticle
description: Herbicides are used to control weeds in agricultural crops such as alfalfa (Medicago sativa L.), which is a forage crop. It is unclear what, if any, effect herbicides have on greenhouse gas (GHG) emissions when used on alfalfa. Our study was conducted in 2017 and 2018 to investigate the effects of two herbicides (Quizalofop-p-ethyl, QE and Bentazone, BT) on methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) emissions from soil planted with alfalfa. QE is used to control grasses and BT is used for broadleaf weed control. Soil CO2 emissions and soil uptake of CH4 increased significantly in both years following the QE and BT treatments, although CO2 emissions differed significantly between the trial years. N2O emissions decreased relative to the control and showed no significant differences between the trial years. The application of QE and BT on alfalfa resulted in a significant increase in CO2 emissions which contributed to a significant increase in GHG emissions. The application of QE influenced GHG emissions more than BT. We demonstrated the potential effect that herbicide applications have on GHG fluxes, which are important when considering the effect of agricultural practices on GHG emissions and the potential for global warming over the next 100 years.
format: application/pdf
format: text/html
creator: Lina Shi
creator: Yarong Guo
creator: Jiao Ning
creator: Shanning Lou
creator: Fujiang Hou
subject: Agricultural Science
subject: Soil Science
subject: Environmental Impacts
description: doi:10.7717/peerj.9231
publisher: PeerJ Inc.
rights: © 2020 Shi et al.
abstract: Herbicides are used to control weeds in agricultural crops such as alfalfa (Medicago sativa L.), which is a forage crop. It is unclear what, if any, effect herbicides have on greenhouse gas (GHG) emissions when used on alfalfa. Our study was conducted in 2017 and 2018 to investigate the effects of two herbicides (Quizalofop-p-ethyl, QE and Bentazone, BT) on methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) emissions from soil planted with alfalfa. QE is used to control grasses and BT is used for broadleaf weed control. Soil CO2 emissions and soil uptake of CH4 increased significantly in both years following the QE and BT treatments, although CO2 emissions differed significantly between the trial years. N2O emissions decreased relative to the control and showed no significant differences between the trial years. The application of QE and BT on alfalfa resulted in a significant increase in CO2 emissions which contributed to a significant increase in GHG emissions. The application of QE influenced GHG emissions more than BT. We demonstrated the potential effect that herbicide applications have on GHG fluxes, which are important when considering the effect of agricultural practices on GHG emissions and the potential for global warming over the next 100 years.
bibliographic citation: Shi et al. (2020) Herbicide applications increase greenhouse gas emissions of alfalfa pasture in the inland arid region of northwest China. PeerJ 8:e9231 https://doi.org/10.7717/peerj.9231
date submitted: 2020-01-17
date accepted: 2020-05-01
issued: 2020-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Lina
author list: Agent
  family name: Guo
  given name: Yarong
author list: Agent
  family name: Ning
  given name: Jiao
author list: Agent
  family name: Lou
  given name: Shanning
author list: Agent
  family name: Hou
  given name: Fujiang
doi: 10.7717/peerj.9231
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-25
copyright: © 2020 Shi et al.
attribution name: Shi et al.

Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods
type: item
type: AcademicArticle
description: Background Research has shown that Poly-ADP-ribose polymerases 1 (PARP-1) is a potential therapeutic target in the clinical treatment of breast cancer. An increasing number of studies have focused on the development of highly selective inhibitors that target PARP-1 over PARP-2, its closest isoform, to mitigate potential side effects. However, due to the highly conserved and similar binding sites of PARP-1 and PARP-2, there is a huge challenge for the discovery and design of PARP-1 inhibitors. Recently, it was reported that a potent PARP-1 inhibitor named NMS-P118 exhibited greater selectivity to PARP-1 over PARP-2 compared with a previously reported drug (Niraparib). However, the mechanisms underlying the effect of this inhibitor remains unclear. Methods In the present study, classical molecular dynamics (MD) simulations and accelerated molecular dynamics (aMD) simulations combined with structural and energetic analysis were used to investigate the structural dynamics and selective mechanisms of PARP-1 and PARP-2 that are bound to NMS-P118 and Niraparib with distinct selectivity. Results The results from classical MD simulations indicated that the selectivity of inhibitors may be controlled by electrostatic interactions, which were mainly due to the residues of Gln-322, Ser-328, Glu-335, and Tyr-455 in helix αF. The energetic differences were corroborated by the results from aMD simulations. Conclusion This study provides new insights about how inhibitors specifically bind to PARP-1 over PARP-2, which may help facilitate the design of highly selective PARP-1 inhibitors in the future.
format: application/pdf
format: text/html
creator: Hongye Hu
creator: Buran Chen
creator: Danni Zheng
creator: Guanli Huang
subject: Molecular Biology
subject: Oncology
subject: Pharmacology
subject: Computational Science
description: doi:10.7717/peerj.9241
publisher: PeerJ Inc.
rights: © 2020 Hu et al.
abstract: Background Research has shown that Poly-ADP-ribose polymerases 1 (PARP-1) is a potential therapeutic target in the clinical treatment of breast cancer. An increasing number of studies have focused on the development of highly selective inhibitors that target PARP-1 over PARP-2, its closest isoform, to mitigate potential side effects. However, due to the highly conserved and similar binding sites of PARP-1 and PARP-2, there is a huge challenge for the discovery and design of PARP-1 inhibitors. Recently, it was reported that a potent PARP-1 inhibitor named NMS-P118 exhibited greater selectivity to PARP-1 over PARP-2 compared with a previously reported drug (Niraparib). However, the mechanisms underlying the effect of this inhibitor remains unclear. Methods In the present study, classical molecular dynamics (MD) simulations and accelerated molecular dynamics (aMD) simulations combined with structural and energetic analysis were used to investigate the structural dynamics and selective mechanisms of PARP-1 and PARP-2 that are bound to NMS-P118 and Niraparib with distinct selectivity. Results The results from classical MD simulations indicated that the selectivity of inhibitors may be controlled by electrostatic interactions, which were mainly due to the residues of Gln-322, Ser-328, Glu-335, and Tyr-455 in helix αF. The energetic differences were corroborated by the results from aMD simulations. Conclusion This study provides new insights about how inhibitors specifically bind to PARP-1 over PARP-2, which may help facilitate the design of highly selective PARP-1 inhibitors in the future.
bibliographic citation: Hu et al. (2020) Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods. PeerJ 8:e9241 https://doi.org/10.7717/peerj.9241
date submitted: 2020-03-27
date accepted: 2020-05-05
issued: 2020-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Hongye
author list: Agent
  family name: Chen
  given name: Buran
author list: Agent
  family name: Zheng
  given name: Danni
author list: Agent
  family name: Huang
  given name: Guanli
doi: 10.7717/peerj.9241
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-25
copyright: ©2020 Hu et al.
attribution name: Hu et al.

Agreement between the GAITRite® System and the Wearable Sensor BTS G-Walk® for measurement of gait parameters in healthy adults and Parkinson’s disease patients
type: item
type: AcademicArticle
description: Background Nowadays, the most widely used types of wearable sensors in gait analysis are inertial sensors. The aim of the study was to assess the agreement between two different systems for measuring gait parameters (inertial sensor vs. electronic walkway) on healthy control subjects (HC) and patients with Parkinson’s disease (PD). Methods Forty healthy volunteers (26 men, 14 women, mean age 58.7 ± 7.7 years) participated in the study and 24 PD patients (19 men, five women, mean age 62.7 ± 9.8 years). Each participant walked across an electronic walkway, GAITRite, with embedded pressure sensors at their preferred walking speed. Concurrently a G-Walk sensor was attached with a semi-elastic belt to the L5 spinal segment of the subject. Walking speed, cadence, stride duration, stride length, stance, swing, single support and double support phase values were compared between both systems. Results The Passing-Bablock regression slope line manifested the values closest to 1.00 for cadence and stride duration (0.99 ≤ 1.00) in both groups. The slope of other parameters varied between 0.26 (double support duration in PD) and 1.74 (duration of single support for HC). The mean square error confirmed the best fit of the regression line for speed, stride duration and stride length. The y-intercepts showed higher systematic error in PD than HC for speed, stance, swing, and single support phases. Conclusions The final results of this study indicate that the G-Walk system can be used for evaluating the gait characteristics of the healthy subjects as well as the PD patients. However, the duration of the gait cycle phases should be used with caution due to the presence of a systematic error.
format: application/pdf
format: text/html
creator: Slávka Vítečková
creator: Hana Horáková
creator: Kamila Poláková
creator: Radim Krupička
creator: Evžen Růžička
creator: Hana Brožová
subject: Bioengineering
subject: Kinesiology
description: doi:10.7717/peerj.8835
publisher: PeerJ Inc.
rights: © 2020 Vítečková et al.
abstract: Background Nowadays, the most widely used types of wearable sensors in gait analysis are inertial sensors. The aim of the study was to assess the agreement between two different systems for measuring gait parameters (inertial sensor vs. electronic walkway) on healthy control subjects (HC) and patients with Parkinson’s disease (PD). Methods Forty healthy volunteers (26 men, 14 women, mean age 58.7 ± 7.7 years) participated in the study and 24 PD patients (19 men, five women, mean age 62.7 ± 9.8 years). Each participant walked across an electronic walkway, GAITRite, with embedded pressure sensors at their preferred walking speed. Concurrently a G-Walk sensor was attached with a semi-elastic belt to the L5 spinal segment of the subject. Walking speed, cadence, stride duration, stride length, stance, swing, single support and double support phase values were compared between both systems. Results The Passing-Bablock regression slope line manifested the values closest to 1.00 for cadence and stride duration (0.99 ≤ 1.00) in both groups. The slope of other parameters varied between 0.26 (double support duration in PD) and 1.74 (duration of single support for HC). The mean square error confirmed the best fit of the regression line for speed, stride duration and stride length. The y-intercepts showed higher systematic error in PD than HC for speed, stance, swing, and single support phases. Conclusions The final results of this study indicate that the G-Walk system can be used for evaluating the gait characteristics of the healthy subjects as well as the PD patients. However, the duration of the gait cycle phases should be used with caution due to the presence of a systematic error.
bibliographic citation: Vítečková et al. (2020) Agreement between the GAITRite® System and the Wearable Sensor BTS G-Walk® for measurement of gait parameters in healthy adults and Parkinson’s disease patients. PeerJ 8:e8835 https://doi.org/10.7717/peerj.8835
date submitted: 2019-05-14
date accepted: 2020-03-02
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vítečková
  given name: Slávka
author list: Agent
  family name: Horáková
  given name: Hana
author list: Agent
  family name: Poláková
  given name: Kamila
author list: Agent
  family name: Krupička
  given name: Radim
author list: Agent
  family name: Růžička
  given name: Evžen
author list: Agent
  family name: Brožová
  given name: Hana
doi: 10.7717/peerj.8835
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Vítečková et al.
attribution name: Vítečková et al.

Maternal trauma and fear history predict BDNF methylation and gene expression in newborns
type: item
type: AcademicArticle
description: Trauma and related fear exert significant influence on mental and physical health throughout the lifespan and are associated with intergenerational patterns of development, health, and behavior. DNA methylation and gene expression are involved in our developmental adaptations to our experiences and can be influenced by social interventions. Patterns of DNA methylation and expression of a gene involved in neurodevelopment and psychiatric risk (BDNF) have been linked with childhood trauma. Given the intergenerational patterns of health and behavior, and previous links between childhood trauma and BDNF methylation and expression, this study investigated the potential for maternal history of traumatic experiences to influence development in her newborn, via changes in her newborn’s BDNF methylation and expression. We found that mothers’ trauma history was associated with epigenetic regulation of BDNF in their newborns. Moreover, the association between maternal trauma and BDNF methylation and expression patterns were moderated by newborn sex. Male newborns showed increased BDNF expression with maternal exposure to child abuse (p = .001), and increased BDNF methylation with greater maternal fear (p = .001). Female newborns showed reduced BDNF expression with greater maternal fear (p = .004). Practitioners strive to identify prevention and intervention avenues that will reduce the harmful effects of trauma. Future research should consider the potential for maternal historical trauma experiences to influence offspring DNA methylation and gene expression in a manner that could alter development and inform novel prevention strategies.
format: application/pdf
format: text/html
creator: Stefanie R. Pilkay
creator: Terri Combs-Orme
creator: Frances Tylavsky
creator: Nicole Bush
creator: Alicia K. Smith
subject: Genetics
subject: Neuroscience
description: doi:10.7717/peerj.8858
publisher: PeerJ Inc.
rights: © 2020 Pilkay et al.
abstract: Trauma and related fear exert significant influence on mental and physical health throughout the lifespan and are associated with intergenerational patterns of development, health, and behavior. DNA methylation and gene expression are involved in our developmental adaptations to our experiences and can be influenced by social interventions. Patterns of DNA methylation and expression of a gene involved in neurodevelopment and psychiatric risk (BDNF) have been linked with childhood trauma. Given the intergenerational patterns of health and behavior, and previous links between childhood trauma and BDNF methylation and expression, this study investigated the potential for maternal history of traumatic experiences to influence development in her newborn, via changes in her newborn’s BDNF methylation and expression. We found that mothers’ trauma history was associated with epigenetic regulation of BDNF in their newborns. Moreover, the association between maternal trauma and BDNF methylation and expression patterns were moderated by newborn sex. Male newborns showed increased BDNF expression with maternal exposure to child abuse (p = .001), and increased BDNF methylation with greater maternal fear (p = .001). Female newborns showed reduced BDNF expression with greater maternal fear (p = .004). Practitioners strive to identify prevention and intervention avenues that will reduce the harmful effects of trauma. Future research should consider the potential for maternal historical trauma experiences to influence offspring DNA methylation and gene expression in a manner that could alter development and inform novel prevention strategies.
bibliographic citation: Pilkay et al. (2020) Maternal trauma and fear history predict BDNF methylation and gene expression in newborns. PeerJ 8:e8858 https://doi.org/10.7717/peerj.8858
date submitted: 2019-11-21
date accepted: 2020-03-05
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pilkay
  given name: Stefanie R.
author list: Agent
  family name: Combs-Orme
  given name: Terri
author list: Agent
  family name: Tylavsky
  given name: Frances
author list: Agent
  family name: Bush
  given name: Nicole
author list: Agent
  family name: Smith
  given name: Alicia K.
doi: 10.7717/peerj.8858
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Pilkay et al.
attribution name: Pilkay et al.

A new insect trackway from the Upper Jurassic—Lower Cretaceous eolian sandstones of São Paulo State, Brazil: implications for reconstructing desert paleoecology
type: item
type: AcademicArticle
description: The new ichnospecies Paleohelcura araraquarensis isp. nov. is described from the Upper Jurassic-Lower Cretaceous Botucatu Formation of Brazil. This formation records a gigantic eolian sand sea (erg), formed under an arid climate in the south-central part of Gondwana. This trackway is composed of two track rows, whose internal width is less than one-quarter of the external width, with alternating to staggered series, consisting of three elliptical tracks that can vary from slightly elongated to tapered or circular. The trackways were found in yellowish/reddish sandstone in a quarry in the Araraquara municipality, São Paulo State. Comparisons with neoichnological studies and morphological inferences indicate that the producer of Paleohelcura araraquarensis isp. nov. was most likely a pterygote insect, and so could have fulfilled one of the ecological roles that different species of this group are capable of performing in dune deserts. The producer could have had a herbivorous or carnivorous diet or been part of the fauna of omnivores, being able to adopt herbivorous, carnivorous, and saprophagous diets when necessary. In modern dune deserts, some species of pterygote insects are detritivores (like Tenebrionidae), relying on organic matter that accumulated among the sand grains of the dunes during dry periods with no plant growth. The presence of additional burrows suggests that the Botucatu paleodesert would have had a detritivorous fauna like this. Based on the interpretation of the ichnofossil producers, it was possible to reconstruct the food web of this paleodesert. All the omnivorous and herbivorous invertebrates and the herbivorous ornithopod dinosaurs made up the primary consumers. These animals were, in turn, the food source for bigger carnivorous or omnivorous animals unable to feed on detritus, like arachnids, possible predatory insects, mammaliaforms, and theropod dinosaurs. The highest trophic level was occupied by larger theropod dinosaurs and mammaliafor…
format: application/pdf
format: text/html
creator: Bernardo de C.P. e M. Peixoto
creator: M. Gabriela Mángano
creator: Nicholas J. Minter
creator: Luciana Bueno dos Reis Fernandes
creator: Marcelo Adorna Fernandes
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Entomology
subject: Paleontology
description: doi:10.7717/peerj.8880
publisher: PeerJ Inc.
rights: © 2020 Peixoto et al.
abstract: The new ichnospecies Paleohelcura araraquarensis isp. nov. is described from the Upper Jurassic-Lower Cretaceous Botucatu Formation of Brazil. This formation records a gigantic eolian sand sea (erg), formed under an arid climate in the south-central part of Gondwana. This trackway is composed of two track rows, whose internal width is less than one-quarter of the external width, with alternating to staggered series, consisting of three elliptical tracks that can vary from slightly elongated to tapered or circular. The trackways were found in yellowish/reddish sandstone in a quarry in the Araraquara municipality, São Paulo State. Comparisons with neoichnological studies and morphological inferences indicate that the producer of Paleohelcura araraquarensis isp. nov. was most likely a pterygote insect, and so could have fulfilled one of the ecological roles that different species of this group are capable of performing in dune deserts. The producer could have had a herbivorous or carnivorous diet or been part of the fauna of omnivores, being able to adopt herbivorous, carnivorous, and saprophagous diets when necessary. In modern dune deserts, some species of pterygote insects are detritivores (like Tenebrionidae), relying on organic matter that accumulated among the sand grains of the dunes during dry periods with no plant growth. The presence of additional burrows suggests that the Botucatu paleodesert would have had a detritivorous fauna like this. Based on the interpretation of the ichnofossil producers, it was possible to reconstruct the food web of this paleodesert. All the omnivorous and herbivorous invertebrates and the herbivorous ornithopod dinosaurs made up the primary consumers. These animals were, in turn, the food source for bigger carnivorous or omnivorous animals unable to feed on detritus, like arachnids, possible predatory insects, mammaliaforms, and theropod dinosaurs. The highest trophic level was occupied by larger theropod dinosaurs and mammaliafor…
bibliographic citation: Peixoto et al. (2020) A new insect trackway from the Upper Jurassic—Lower Cretaceous eolian sandstones of São Paulo State, Brazil: implications for reconstructing desert paleoecology. PeerJ 8:e8880 https://doi.org/10.7717/peerj.8880
date submitted: 2019-11-06
date accepted: 2020-03-10
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peixoto
  given name: Bernardo de C.P. e M.
author list: Agent
  family name: Mángano
  given name: M. Gabriela
author list: Agent
  family name: Minter
  given name: Nicholas J.
author list: Agent
  family name: dos Reis Fernandes
  given name: Luciana Bueno
author list: Agent
  family name: Fernandes
  given name: Marcelo Adorna
doi: 10.7717/peerj.8880
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Peixoto et al.
attribution name: Peixoto et al.

Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review
type: item
type: AcademicArticle
description: The animal’s blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular markers are in progress. The standard and modern biochemical tests are commonly used for general screening and, finally, complete diagnosis of animal health. Interpretation of major biochemical parameters is similar across animal species, but there are a few peculiarities in each case, especially well-known for cattle. The following directions are discussed here: hematological indicators; “total protein” and its fractions; some enzymes; major low-molecular metabolites (glucose, lipids, bilirubin, etc.); cations and anions. As example, the numerous correlations between DT data and biochemical parameters of cattle serum have been obtained and discussed. Changes in the cell-free nucleic acids (cfDNA) circulating in the blood have been studied and analyzed in a variety of conditions; for example, pregnancy, infectious and chronic diseases, and cancer. CfDNA can easily be detected using standard molecular biological techniques like DNA amplification and next-generation sequencing. The application of digital PCR even allows exact quantification of copy number variations which are for example important in prenatal diagnosis of chromosomal aberrations.
format: application/pdf
format: text/html
creator: Sergei Yu. Zaitsev
creator: Nadezhda V. Bogolyubova
creator: Xuying Zhang
creator: Bertram Brenig
subject: Biochemistry
subject: Veterinary Medicine
description: doi:10.7717/peerj.8997
publisher: PeerJ Inc.
rights: © 2020 Zaitsev et al.
abstract: The animal’s blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular markers are in progress. The standard and modern biochemical tests are commonly used for general screening and, finally, complete diagnosis of animal health. Interpretation of major biochemical parameters is similar across animal species, but there are a few peculiarities in each case, especially well-known for cattle. The following directions are discussed here: hematological indicators; “total protein” and its fractions; some enzymes; major low-molecular metabolites (glucose, lipids, bilirubin, etc.); cations and anions. As example, the numerous correlations between DT data and biochemical parameters of cattle serum have been obtained and discussed. Changes in the cell-free nucleic acids (cfDNA) circulating in the blood have been studied and analyzed in a variety of conditions; for example, pregnancy, infectious and chronic diseases, and cancer. CfDNA can easily be detected using standard molecular biological techniques like DNA amplification and next-generation sequencing. The application of digital PCR even allows exact quantification of copy number variations which are for example important in prenatal diagnosis of chromosomal aberrations.
bibliographic citation: Zaitsev et al. (2020) Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review. PeerJ 8:e8997 https://doi.org/10.7717/peerj.8997
date submitted: 2019-06-20
date accepted: 2020-03-26
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zaitsev
  given name: Sergei Yu.
author list: Agent
  family name: Bogolyubova
  given name: Nadezhda V.
author list: Agent
  family name: Zhang
  given name: Xuying
author list: Agent
  family name: Brenig
  given name: Bertram
doi: 10.7717/peerj.8997
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: © 2020 Zaitsev et al.
attribution name: Zaitsev et al.

Plant-derived angiogenin fusion protein’s cytoprotective effect on trabecular meshwork damage induced by Benzalkonium chloride in mice
type: item
type: AcademicArticle
description: Background Benzalkonium chloride (BAK), commonly used in glaucoma treatment, is an eye drop preservative with dose-dependent toxicity. Previous studies have observed the multi-functional benefits of angiogenin (ANG) against glaucoma. In our study, we evaluated ANG’s cytoprotective effect on the trabecular meshwork (TM) damage induced by BAK. Additionally, we developed a plant-derived ANG fusion protein and evaluated its effect on TM structure and function. Methods We synthesized plant-derived ANG (ANG-FcK) by fuzing immunoglobulin G’s Fc region and KDEL to conventional recombinant human ANG (Rh-ANG) purified from transgenic tobacco plants. We established a mouse model using BAK to look for degenerative changes in the TM, and to evaluate the protective effects of ANG-FcK and Rh-ANG. Intraocular pressure (IOP) was measured for 4 weeks and ultrastructural changes, deposition of fluorescent microbeads, type I and IV collagen, fibronectin, laminin and α-SMA expression were analyzed after the mice were euthanized. Results TM structural and functional degeneration were induced by 0.1% BAK instillation in mice. ANG co-treatment preserved TM outflow function, which we measured using IOP and a microbead tracer. ANG prevented phenotypic and ultrastructure changes, and that protective effect might be related to the anti-fibrosis mechanism. We observed a similar cytoprotective effect in the BAK-induced degenerative TM mouse model, suggesting that plant-derived ANG-FcK could be a promising glaucoma treatment.
format: application/pdf
format: text/html
creator: Jae Hoon Jeong
creator: Soo Jin Lee
creator: Kisung Ko
creator: Jeong Hwan Lee
creator: Jungmook Lyu
creator: Moon Hyang Park
creator: Jaeku Kang
creator: Jae Chan Kim
subject: Bioengineering
subject: Drugs and Devices
subject: Ophthalmology
subject: Pharmacology
description: doi:10.7717/peerj.9084
publisher: PeerJ Inc.
rights: © 2020 Jeong et al.
abstract: Background Benzalkonium chloride (BAK), commonly used in glaucoma treatment, is an eye drop preservative with dose-dependent toxicity. Previous studies have observed the multi-functional benefits of angiogenin (ANG) against glaucoma. In our study, we evaluated ANG’s cytoprotective effect on the trabecular meshwork (TM) damage induced by BAK. Additionally, we developed a plant-derived ANG fusion protein and evaluated its effect on TM structure and function. Methods We synthesized plant-derived ANG (ANG-FcK) by fuzing immunoglobulin G’s Fc region and KDEL to conventional recombinant human ANG (Rh-ANG) purified from transgenic tobacco plants. We established a mouse model using BAK to look for degenerative changes in the TM, and to evaluate the protective effects of ANG-FcK and Rh-ANG. Intraocular pressure (IOP) was measured for 4 weeks and ultrastructural changes, deposition of fluorescent microbeads, type I and IV collagen, fibronectin, laminin and α-SMA expression were analyzed after the mice were euthanized. Results TM structural and functional degeneration were induced by 0.1% BAK instillation in mice. ANG co-treatment preserved TM outflow function, which we measured using IOP and a microbead tracer. ANG prevented phenotypic and ultrastructure changes, and that protective effect might be related to the anti-fibrosis mechanism. We observed a similar cytoprotective effect in the BAK-induced degenerative TM mouse model, suggesting that plant-derived ANG-FcK could be a promising glaucoma treatment.
bibliographic citation: Jeong et al. (2020) Plant-derived angiogenin fusion protein’s cytoprotective effect on trabecular meshwork damage induced by Benzalkonium chloride in mice. PeerJ 8:e9084 https://doi.org/10.7717/peerj.9084
date submitted: 2019-11-04
date accepted: 2020-04-08
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jeong
  given name: Jae Hoon
author list: Agent
  family name: Lee
  given name: Soo Jin
author list: Agent
  family name: Ko
  given name: Kisung
author list: Agent
  family name: Lee
  given name: Jeong Hwan
author list: Agent
  family name: Lyu
  given name: Jungmook
author list: Agent
  family name: Park
  given name: Moon Hyang
author list: Agent
  family name: Kang
  given name: Jaeku
author list: Agent
  family name: Kim
  given name: Jae Chan
doi: 10.7717/peerj.9084
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: © 2020 Jeong et al.
attribution name: Jeong et al.

Oldest co-occurrence of Varanus and Python from Africa—first record of squamates from the early Miocene of Moghra Formation, Western Desert, Egypt
type: item
type: AcademicArticle
description: Lizard and snake remains from the early Miocene (Burdigalian) of the Moghra Formation, Egypt, are described herein. This material comprises the first fossil remains of squamates recovered from the otherwise rich and well known vertebrate assemblage of Moghra. The material pertains to two different genera, the varanid lizard Varanus and the pythonid snake Python and adds to the so far rather poorly known squamate fossil record from Africa. On the basis of the new remains, Moghra marks the oldest so far described co-occurrence of Varanus and Python in the African continent. The close sympatry of these two genera in the African fossil record is thoroughly analyzed and discussed, a co-existence, which is still widespread in the extant herpetofauna of the continent. Situated rather close to the so called “Levantine Corridor” and dated at the Burdigalian, practically when Afro-Arabia collided with Eurasia, the Moghra squamate assemblage offers the potential of important insights in the biogeography and dispersal events of vertebrate groups during the early Miocene.
format: application/pdf
format: text/html
creator: Georgios L. Georgalis
creator: Mohamed K. Abdel Gawad
creator: Safiya M. Hassan
creator: Ahmed N. El-Barkooky
creator: Mohamed A. Hamdan
subject: Biodiversity
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9092
publisher: PeerJ Inc.
rights: © 2020 Georgalis et al.
abstract: Lizard and snake remains from the early Miocene (Burdigalian) of the Moghra Formation, Egypt, are described herein. This material comprises the first fossil remains of squamates recovered from the otherwise rich and well known vertebrate assemblage of Moghra. The material pertains to two different genera, the varanid lizard Varanus and the pythonid snake Python and adds to the so far rather poorly known squamate fossil record from Africa. On the basis of the new remains, Moghra marks the oldest so far described co-occurrence of Varanus and Python in the African continent. The close sympatry of these two genera in the African fossil record is thoroughly analyzed and discussed, a co-existence, which is still widespread in the extant herpetofauna of the continent. Situated rather close to the so called “Levantine Corridor” and dated at the Burdigalian, practically when Afro-Arabia collided with Eurasia, the Moghra squamate assemblage offers the potential of important insights in the biogeography and dispersal events of vertebrate groups during the early Miocene.
bibliographic citation: Georgalis et al. (2020) Oldest co-occurrence of Varanus and Python from Africa—first record of squamates from the early Miocene of Moghra Formation, Western Desert, Egypt. PeerJ 8:e9092 https://doi.org/10.7717/peerj.9092
date submitted: 2020-01-14
date accepted: 2020-04-09
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Georgalis
  given name: Georgios L.
author list: Agent
  family name: Abdel Gawad
  given name: Mohamed K.
author list: Agent
  family name: Hassan
  given name: Safiya M.
author list: Agent
  family name: El-Barkooky
  given name: Ahmed N.
author list: Agent
  family name: Hamdan
  given name: Mohamed A.
doi: 10.7717/peerj.9092
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Georgalis et al.
attribution name: Georgalis et al.

Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment
type: item
type: AcademicArticle
description: The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.
format: application/pdf
format: text/html
creator: Shuilian He
creator: Yang Yang
creator: Ziwei Li
creator: Xuejiao Wang
creator: Yanbing Guo
creator: Hongzhi Wu
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9132
publisher: PeerJ Inc.
rights: © 2020 He et al.
abstract: The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.
bibliographic citation: He et al. (2020) Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment. PeerJ 8:e9132 https://doi.org/10.7717/peerj.9132
date submitted: 2019-12-05
date accepted: 2020-04-14
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Shuilian
author list: Agent
  family name: Yang
  given name: Yang
author list: Agent
  family name: Li
  given name: Ziwei
author list: Agent
  family name: Wang
  given name: Xuejiao
author list: Agent
  family name: Guo
  given name: Yanbing
author list: Agent
  family name: Wu
  given name: Hongzhi
doi: 10.7717/peerj.9132
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 He et al.
attribution name: He et al.

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