PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function
items: Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony
items: Native trees of Mexico: diversity, distribution, uses and conservation
items: Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness
items: Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China
items: Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies
items: Mesenchymal stem cell exosomes reverse acute lung injury through Nrf-2/ARE and NF-κB signaling pathways
items: Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs
items: Radiolarian assemblages in the shelf area of the East China Sea and Yellow Sea and their ecological indication of the Kuroshio Current derivative branches
items: Development of a noninvasive photograph-based method for the evaluation of body condition in free-ranging brown bears

Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function
type: item
type: AcademicArticle
description: Triceratops is one of the well-known Cretaceous ceratopsian dinosaurs. The ecology of Triceratops has been controversial because of its unique morphological features. However, arguments based on brain and inner ear structures have been scarce. In this study, two braincases (FPDM-V-9677 and FPDM-V-9775) were analyzed with computed tomography to generate three-dimensional virtual renderings of the endocasts of the cranial cavities and bony labyrinths. Quantitative analysis, including comparison of linear measurements of the degree of development of the olfactory bulb and inner ear, was performed on these virtual endocasts to acquire detailed neuroanatomical information. When compared with other dinosaurs, the olfactory bulb of Triceratops is relatively small, indicating that Triceratops had a reduced acuity in sense of smell. The lateral semicircular canal reveals that the basicranial axis of Triceratops is approximately 45° to the ground, which is an effective angle to display their horns as well as frill, and to graze. The semicircular canals of Triceratops are relatively smaller than those of primitive ceratopsians, such as Psittacosaurus and Protoceratops, suggesting that sensory input for the reflexive stabilization of gaze and posture of Triceratops was less developed than that of primitive ceratopsians. The cochlear length of Triceratops is relatively short when compared with other dinosaurs. Because cochlear length correlates with hearing frequency, Triceratops was likely adapted to hearing low frequencies.
format: application/pdf
format: text/html
creator: Rina Sakagami
creator: Soichiro Kawabe
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.9888
publisher: PeerJ Inc.
rights: © 2020 Sakagami and Kawabe
abstract: Triceratops is one of the well-known Cretaceous ceratopsian dinosaurs. The ecology of Triceratops has been controversial because of its unique morphological features. However, arguments based on brain and inner ear structures have been scarce. In this study, two braincases (FPDM-V-9677 and FPDM-V-9775) were analyzed with computed tomography to generate three-dimensional virtual renderings of the endocasts of the cranial cavities and bony labyrinths. Quantitative analysis, including comparison of linear measurements of the degree of development of the olfactory bulb and inner ear, was performed on these virtual endocasts to acquire detailed neuroanatomical information. When compared with other dinosaurs, the olfactory bulb of Triceratops is relatively small, indicating that Triceratops had a reduced acuity in sense of smell. The lateral semicircular canal reveals that the basicranial axis of Triceratops is approximately 45° to the ground, which is an effective angle to display their horns as well as frill, and to graze. The semicircular canals of Triceratops are relatively smaller than those of primitive ceratopsians, such as Psittacosaurus and Protoceratops, suggesting that sensory input for the reflexive stabilization of gaze and posture of Triceratops was less developed than that of primitive ceratopsians. The cochlear length of Triceratops is relatively short when compared with other dinosaurs. Because cochlear length correlates with hearing frequency, Triceratops was likely adapted to hearing low frequencies.
bibliographic citation: Sakagami et al. (2020) Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function. PeerJ 8:e9888 https://doi.org/10.7717/peerj.9888
date submitted: 2020-03-12
date accepted: 2020-08-17
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sakagami
  given name: Rina
author list: Agent
  family name: Kawabe
  given name: Soichiro
doi: 10.7717/peerj.9888
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Sakagami and Kawabe
attribution name: Sakagami and Kawabe

Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony
type: item
type: AcademicArticle
description: The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment.
format: application/pdf
format: text/html
creator: Chang Liu
creator: Hongmei Lei
creator: Xueqin Ran
creator: Jiafu Wang
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.9889
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment.
bibliographic citation: Liu et al. (2020) Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony. PeerJ 8:e9889 https://doi.org/10.7717/peerj.9889
date submitted: 2019-11-25
date accepted: 2020-08-17
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chang
author list: Agent
  family name: Lei
  given name: Hongmei
author list: Agent
  family name: Ran
  given name: Xueqin
author list: Agent
  family name: Wang
  given name: Jiafu
doi: 10.7717/peerj.9889
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Liu et al.
attribution name: Liu et al.

Native trees of Mexico: diversity, distribution, uses and conservation
type: item
type: AcademicArticle
description: Background Mexico is one of the most floristically rich countries in the world. Despite significant contributions made on the understanding of its unique flora, the knowledge on its diversity, geographic distribution and human uses, is still largely fragmented. Unfortunately, deforestation is heavily impacting this country and native tree species are under threat. The loss of trees has a direct impact on vital ecosystem services, affecting the natural capital of Mexico and people’s livelihoods. Given the importance of trees in Mexico for many aspects of human well-being, it is critical to have a more complete understanding of their diversity, distribution, traditional uses and conservation status. We aimed to produce the most comprehensive database and catalogue on native trees of Mexico by filling those gaps, to support their in situ and ex situ conservation, promote their sustainable use, and inform reforestation and livelihoods programmes. Methods A database with all the tree species reported for Mexico was prepared by compiling information from herbaria and reviewing the available floras. Species names were reconciled and various specialised sources were used to extract additional species information, i.e. endemic status, threat status, availability in seed collections, reports on plant uses and conservation actions currently in place. With this information, a comprehensive catalogue of native trees from Mexico was redacted. Available georeferenced records were used to map each species distribution and perform spatial analyses to identify gaps of information and priority areas for their conservation and exploration. Results Mexico has at least 2,885 native tree species, belonging to 612 genera and 128 families. Fabaceae is the most represented family and Quercus the most represented genus. Approximately 44% of tree species are endemic to the country. The southern part of the country showed the highest values of species richness. Six hundred and seventy-four spec…
format: application/pdf
format: text/html
creator: Oswaldo Tellez
creator: Efisio Mattana
creator: Mauricio Diazgranados
creator: Nicola Kühn
creator: Elena Castillo-Lorenzo
creator: Rafael Lira
creator: Leobardo Montes-Leyva
creator: Isela Rodriguez
creator: Cesar Mateo Flores Ortiz
creator: Michael Way
creator: Patricia Dávila
creator: Tiziana Ulian
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Plant Science
description: doi:10.7717/peerj.9898
publisher: PeerJ Inc.
rights: © 2020 Tellez et al.
abstract: Background Mexico is one of the most floristically rich countries in the world. Despite significant contributions made on the understanding of its unique flora, the knowledge on its diversity, geographic distribution and human uses, is still largely fragmented. Unfortunately, deforestation is heavily impacting this country and native tree species are under threat. The loss of trees has a direct impact on vital ecosystem services, affecting the natural capital of Mexico and people’s livelihoods. Given the importance of trees in Mexico for many aspects of human well-being, it is critical to have a more complete understanding of their diversity, distribution, traditional uses and conservation status. We aimed to produce the most comprehensive database and catalogue on native trees of Mexico by filling those gaps, to support their in situ and ex situ conservation, promote their sustainable use, and inform reforestation and livelihoods programmes. Methods A database with all the tree species reported for Mexico was prepared by compiling information from herbaria and reviewing the available floras. Species names were reconciled and various specialised sources were used to extract additional species information, i.e. endemic status, threat status, availability in seed collections, reports on plant uses and conservation actions currently in place. With this information, a comprehensive catalogue of native trees from Mexico was redacted. Available georeferenced records were used to map each species distribution and perform spatial analyses to identify gaps of information and priority areas for their conservation and exploration. Results Mexico has at least 2,885 native tree species, belonging to 612 genera and 128 families. Fabaceae is the most represented family and Quercus the most represented genus. Approximately 44% of tree species are endemic to the country. The southern part of the country showed the highest values of species richness. Six hundred and seventy-four spec…
bibliographic citation: Tellez et al. (2020) Native trees of Mexico: diversity, distribution, uses and conservation. PeerJ 8:e9898 https://doi.org/10.7717/peerj.9898
date submitted: 2020-05-04
date accepted: 2020-08-17
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tellez
  given name: Oswaldo
author list: Agent
  family name: Mattana
  given name: Efisio
author list: Agent
  family name: Diazgranados
  given name: Mauricio
author list: Agent
  family name: Kühn
  given name: Nicola
author list: Agent
  family name: Castillo-Lorenzo
  given name: Elena
author list: Agent
  family name: Lira
  given name: Rafael
author list: Agent
  family name: Montes-Leyva
  given name: Leobardo
author list: Agent
  family name: Rodriguez
  given name: Isela
author list: Agent
  family name: Flores Ortiz
  given name: Cesar Mateo
author list: Agent
  family name: Way
  given name: Michael
author list: Agent
  family name: Dávila
  given name: Patricia
author list: Agent
  family name: Ulian
  given name: Tiziana
doi: 10.7717/peerj.9898
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Tellez et al.
attribution name: Tellez et al.

Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness
type: item
type: AcademicArticle
description: Cannibalism is considered one of the causes of intra-cohort size divergence in fish and is usually believed to result in increased fitness in terms of survival and reproduction, but direct evidence of this is lacking. Population demographics of the clearhead icefish (Protosalanx chinensis) from Lake Xingkai (Khanka) were investigated for one year. Size-frequencies exhibited a bimodal distribution from July through January, where the population diverged into an upper and a lower modal group based on size. Stomach content analysis confirmed the occurrence of cannibalism, where fish belonging to the larger, upper modal group preyed upon those of the smaller, lower modal group. We found P. chinensis does not spawn until all of the oocytes have reached maturity and then a single spawning event occurs although the oocytes may develope asynchronously in the ovary. Upper modal group females matured slightly earlier than those of the lower modal group, and reproductive investment was considerably greater in the upper modal group than the lower modal group. The lower modal males made up the majority of the population after the spawning period, which meant they may have few opportunities to participate in reproduction. Therefore, piscivory and cannibalism of P. chinensis appears to have increased fitness of the fish belonging to the upper modal group and greatly reduced the fitness of those belonging to the lower modal group.
format: application/pdf
format: text/html
creator: Fujiang Tang
creator: Wei Liu
creator: Jilong Wang
creator: James Henne
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.9900
publisher: PeerJ Inc.
rights: © 2020 Tang et al.
abstract: Cannibalism is considered one of the causes of intra-cohort size divergence in fish and is usually believed to result in increased fitness in terms of survival and reproduction, but direct evidence of this is lacking. Population demographics of the clearhead icefish (Protosalanx chinensis) from Lake Xingkai (Khanka) were investigated for one year. Size-frequencies exhibited a bimodal distribution from July through January, where the population diverged into an upper and a lower modal group based on size. Stomach content analysis confirmed the occurrence of cannibalism, where fish belonging to the larger, upper modal group preyed upon those of the smaller, lower modal group. We found P. chinensis does not spawn until all of the oocytes have reached maturity and then a single spawning event occurs although the oocytes may develope asynchronously in the ovary. Upper modal group females matured slightly earlier than those of the lower modal group, and reproductive investment was considerably greater in the upper modal group than the lower modal group. The lower modal males made up the majority of the population after the spawning period, which meant they may have few opportunities to participate in reproduction. Therefore, piscivory and cannibalism of P. chinensis appears to have increased fitness of the fish belonging to the upper modal group and greatly reduced the fitness of those belonging to the lower modal group.
bibliographic citation: Tang et al. (2020) Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness. PeerJ 8:e9900 https://doi.org/10.7717/peerj.9900
date submitted: 2020-02-27
date accepted: 2020-08-18
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Tang
  given name: Fujiang
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Wang
  given name: Jilong
author list: Agent
  family name: Henne
  given name: James
doi: 10.7717/peerj.9900
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Tang et al.
attribution name: Tang et al.

Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China
type: item
type: AcademicArticle
description: Nutrient resorption from senesced leaves is an important mechanism for nutrient conservation in plants. However, little is known about the effect of grazing on plant nutrient resorption from senesced leaves, especially in semiarid ecosystems. Here, we evaluated the effects of grazing on N and P resorption in the three most dominant grass species in a typical steppe in northern China. We identified the key pathways of grazing-induced effects on N and P resorption efficiency. Grazing increased N and P concentrations in the green leaves of Leymus chinensis and Stipa grandis but not in Cleistogenes squarossa. Both L. chinensis and S. grandis exhibited an increasing trend of leaf N resorption, whereas C. squarrosa recorded a decline in both leaf N and P resorption efficiency under grazing. Structural equation models showed that grazing is the primary driver of the changes in N resorption efficiency of the three dominant grass species. For L. chinensis, the P concentration in green and senesced leaves increased the P resorption efficiency, whereas the senesced leaf P concentration played an important role in the P resorption efficiency of C. squarrosa. Grazing directly drove the change in P resorption efficiency of S. grandis. Our results suggest that large variations in nutrient resorption patterns among plant species depend on leaf nutritional status and nutrient-use strategies under overgrazing, and indicate that overgrazing may have indirect effects on plant-mediated nutrient cycling via inducing shifts in the dominance of the three plant species.
format: application/pdf
format: text/html
creator: Zhen Wang
creator: Saheed Olaide Jimoh
creator: Xiliang Li
creator: Baoming Ji
creator: Paul C. Struik
creator: Shixian Sun
creator: Ji Lei
creator: Yong Ding
creator: Yong Zhang
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
description: doi:10.7717/peerj.9915
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Nutrient resorption from senesced leaves is an important mechanism for nutrient conservation in plants. However, little is known about the effect of grazing on plant nutrient resorption from senesced leaves, especially in semiarid ecosystems. Here, we evaluated the effects of grazing on N and P resorption in the three most dominant grass species in a typical steppe in northern China. We identified the key pathways of grazing-induced effects on N and P resorption efficiency. Grazing increased N and P concentrations in the green leaves of Leymus chinensis and Stipa grandis but not in Cleistogenes squarossa. Both L. chinensis and S. grandis exhibited an increasing trend of leaf N resorption, whereas C. squarrosa recorded a decline in both leaf N and P resorption efficiency under grazing. Structural equation models showed that grazing is the primary driver of the changes in N resorption efficiency of the three dominant grass species. For L. chinensis, the P concentration in green and senesced leaves increased the P resorption efficiency, whereas the senesced leaf P concentration played an important role in the P resorption efficiency of C. squarrosa. Grazing directly drove the change in P resorption efficiency of S. grandis. Our results suggest that large variations in nutrient resorption patterns among plant species depend on leaf nutritional status and nutrient-use strategies under overgrazing, and indicate that overgrazing may have indirect effects on plant-mediated nutrient cycling via inducing shifts in the dominance of the three plant species.
bibliographic citation: Wang et al. (2020) Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China. PeerJ 8:e9915 https://doi.org/10.7717/peerj.9915
date submitted: 2020-05-26
date accepted: 2020-08-19
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhen
author list: Agent
  family name: Jimoh
  given name: Saheed Olaide
author list: Agent
  family name: Li
  given name: Xiliang
author list: Agent
  family name: Ji
  given name: Baoming
author list: Agent
  family name: Struik
  given name: Paul C.
author list: Agent
  family name: Sun
  given name: Shixian
author list: Agent
  family name: Lei
  given name: Ji
author list: Agent
  family name: Ding
  given name: Yong
author list: Agent
  family name: Zhang
  given name: Yong
doi: 10.7717/peerj.9915
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies
type: item
type: AcademicArticle
description: Dietary habits in extinct species cannot be directly observed; thus, in the absence of extraordinary evidence, they must be reconstructed with a combination of morphological proxies. Such proxies often include information on dental organization and function such as tooth formation time and tooth replacement rate. In extinct organisms, tooth formation times and tooth replacement rate are calculated, in part via extrapolation of the space between incremental lines in dental tissues representing daily growth (von Ebner Line Increment Width; VEIW). However, to date, little work has been conducted testing assumptions about the primary data underpinning these calculations, specifically, the potential impact of differential sampling and data extrapolation protocols. To address this, we tested a variety of intradental, intramandibular, and ontogentic sampling effects on calculations of mean VEIW, tooth formation times, and replacement rates using histological sections and CT reconstructions of a growth series of three specimens of the extant archosaurian Alligator mississippiensis. We find transect position within the tooth and transect orientation with respect to von Ebner lines to have the greatest impact on calculations of mean VEIW—a maximum number of VEIW measurements should be made as near to the central axis (CA) as possible. Measuring in regions away from the central axis can reduce mean VEIW by up to 36%, causing inflated calculations of tooth formation time. We find little demonstrable impact to calculations of mean VEIW from the practice of subsampling along a transect, or from using mean VEIW derived from one portion of the dentition to extrapolate for other regions of the dentition. Subsampling along transects contributes only minor variations in mean VEIW (<12%) that are dwarfed by the standard deviation (SD). Moreover, variation in VEIW with distance from the pulp cavity likely reflects idiosyncratic patterns related to life history, which are difficult to co…
format: application/pdf
format: text/html
creator: Jens C.D. Kosch
creator: Lindsay E. Zanno
subject: Paleontology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.9918
publisher: PeerJ Inc.
rights: © 2020 Kosch and Zanno
abstract: Dietary habits in extinct species cannot be directly observed; thus, in the absence of extraordinary evidence, they must be reconstructed with a combination of morphological proxies. Such proxies often include information on dental organization and function such as tooth formation time and tooth replacement rate. In extinct organisms, tooth formation times and tooth replacement rate are calculated, in part via extrapolation of the space between incremental lines in dental tissues representing daily growth (von Ebner Line Increment Width; VEIW). However, to date, little work has been conducted testing assumptions about the primary data underpinning these calculations, specifically, the potential impact of differential sampling and data extrapolation protocols. To address this, we tested a variety of intradental, intramandibular, and ontogentic sampling effects on calculations of mean VEIW, tooth formation times, and replacement rates using histological sections and CT reconstructions of a growth series of three specimens of the extant archosaurian Alligator mississippiensis. We find transect position within the tooth and transect orientation with respect to von Ebner lines to have the greatest impact on calculations of mean VEIW—a maximum number of VEIW measurements should be made as near to the central axis (CA) as possible. Measuring in regions away from the central axis can reduce mean VEIW by up to 36%, causing inflated calculations of tooth formation time. We find little demonstrable impact to calculations of mean VEIW from the practice of subsampling along a transect, or from using mean VEIW derived from one portion of the dentition to extrapolate for other regions of the dentition. Subsampling along transects contributes only minor variations in mean VEIW (<12%) that are dwarfed by the standard deviation (SD). Moreover, variation in VEIW with distance from the pulp cavity likely reflects idiosyncratic patterns related to life history, which are difficult to co…
bibliographic citation: Kosch et al. (2020) Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies. PeerJ 8:e9918 https://doi.org/10.7717/peerj.9918
date submitted: 2020-04-03
date accepted: 2020-08-20
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kosch
  given name: Jens C.D.
author list: Agent
  family name: Zanno
  given name: Lindsay E.
doi: 10.7717/peerj.9918
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: © 2020 Kosch and Zanno
attribution name: Kosch and Zanno

Mesenchymal stem cell exosomes reverse acute lung injury through Nrf-2/ARE and NF-κB signaling pathways
type: item
type: AcademicArticle
description: Acute lung injury (ALI) is associated with histopathological diffuse alveolar damage. The potential role of mesenchymal stem cells (MSCs) in the treatment of various clinical disorders have been widely documented, such as those for ALI. Recent evidence has demonstrated that exosomes from endothelial progenitor cells can improve outcomes of the lipopolysaccharide (LPS)-induced ALI. However, there has been no research on the potential role of MSC-exosomes in the treatment of sepsis-induced ALI, which is worth further exploration. Thus, the objective of our study was to identify whether the MSC-exosomes could reverse ALI. The ALI model induced by LPS was established in this study. MTT assay was performed to test cell proliferation. Expression of inflammatory factors (TNF-α, IL-6, and IL-10) in the LPS-treated type II alveolar epithelial cells (AECs) (MLE-12) was detected by ELISA. After co-culture of MSC-exosomes with LPS-treated MLE-12 cells, we found that the cell proliferation of MLE-12 cells gradually increased. Furthermore, we selected five of the Nrf-2/ARE- and NF-κB signaling pathway-related genes to explore if MSC-exosomes could reverse LPS-induced ALI through Nrf-2/ARE and NF-κB signaling pathways. QRT-PCR and western blot experiment results showed that the expression of these five genes were significantly regulated after stimulation with high-concentration LPS and exosome intervention. Taken together, these findings highlighted the fact that MSC-exosomes could reverse ALI through the Nrf-2/ARE and NF-κB signaling pathways. The MSC-exosome may be the potential future therapeutic strategy for the treatment of ALI.
format: application/pdf
format: text/html
creator: Jun Li
creator: Xingqi Deng
creator: Xiangling Ji
creator: Xiaojun Shi
creator: Zhiying Ying
creator: Kan Shen
creator: Dongwei Xu
creator: Zhihui Cheng
subject: Biochemistry
subject: Cell Biology
subject: Respiratory Medicine
description: doi:10.7717/peerj.9928
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Acute lung injury (ALI) is associated with histopathological diffuse alveolar damage. The potential role of mesenchymal stem cells (MSCs) in the treatment of various clinical disorders have been widely documented, such as those for ALI. Recent evidence has demonstrated that exosomes from endothelial progenitor cells can improve outcomes of the lipopolysaccharide (LPS)-induced ALI. However, there has been no research on the potential role of MSC-exosomes in the treatment of sepsis-induced ALI, which is worth further exploration. Thus, the objective of our study was to identify whether the MSC-exosomes could reverse ALI. The ALI model induced by LPS was established in this study. MTT assay was performed to test cell proliferation. Expression of inflammatory factors (TNF-α, IL-6, and IL-10) in the LPS-treated type II alveolar epithelial cells (AECs) (MLE-12) was detected by ELISA. After co-culture of MSC-exosomes with LPS-treated MLE-12 cells, we found that the cell proliferation of MLE-12 cells gradually increased. Furthermore, we selected five of the Nrf-2/ARE- and NF-κB signaling pathway-related genes to explore if MSC-exosomes could reverse LPS-induced ALI through Nrf-2/ARE and NF-κB signaling pathways. QRT-PCR and western blot experiment results showed that the expression of these five genes were significantly regulated after stimulation with high-concentration LPS and exosome intervention. Taken together, these findings highlighted the fact that MSC-exosomes could reverse ALI through the Nrf-2/ARE and NF-κB signaling pathways. The MSC-exosome may be the potential future therapeutic strategy for the treatment of ALI.
bibliographic citation: Li et al. (2020) Mesenchymal stem cell exosomes reverse acute lung injury through Nrf-2/ARE and NF-κB signaling pathways. PeerJ 8:e9928 https://doi.org/10.7717/peerj.9928
date submitted: 2020-01-23
date accepted: 2020-08-21
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Deng
  given name: Xingqi
author list: Agent
  family name: Ji
  given name: Xiangling
author list: Agent
  family name: Shi
  given name: Xiaojun
author list: Agent
  family name: Ying
  given name: Zhiying
author list: Agent
  family name: Shen
  given name: Kan
author list: Agent
  family name: Xu
  given name: Dongwei
author list: Agent
  family name: Cheng
  given name: Zhihui
doi: 10.7717/peerj.9928
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Li et al.
attribution name: Li et al.

Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs
type: item
type: AcademicArticle
description: Using the crystal structure of SARS-CoV-2 papain-like protease (PLpro) as a template, we developed a pharmacophore model of functional centers of the PLpro inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PLpro. The conformations of these compounds underwent 3D fingerprint similarity clusterization, followed by docking of possible conformers to the binding pocket of PLpro. Docking of random compounds to the binding pocket of protease was also done for comparison. Free energies of the docking interaction for the selected compounds were lower than for random compounds. The drug list obtained includes inhibitors of HIV, hepatitis C, and cytomegalovirus (CMV), as well as a set of drugs that have demonstrated some activity in MERS, SARS-CoV, and SARS-CoV-2 therapy. We recommend testing of the selected compounds for treatment of COVID-19
format: application/pdf
format: text/html
creator: Valentina L. Kouznetsova
creator: Aidan Zhang
creator: Mahidhar Tatineni
creator: Mark A. Miller
creator: Igor F. Tsigelny
subject: Bioinformatics
subject: Biophysics
subject: Computational Biology
subject: Drugs and Devices
subject: Infectious Diseases
description: doi:10.7717/peerj.9965
publisher: PeerJ Inc.
rights: © 2020 Kouznetsova et al.
abstract: Using the crystal structure of SARS-CoV-2 papain-like protease (PLpro) as a template, we developed a pharmacophore model of functional centers of the PLpro inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PLpro. The conformations of these compounds underwent 3D fingerprint similarity clusterization, followed by docking of possible conformers to the binding pocket of PLpro. Docking of random compounds to the binding pocket of protease was also done for comparison. Free energies of the docking interaction for the selected compounds were lower than for random compounds. The drug list obtained includes inhibitors of HIV, hepatitis C, and cytomegalovirus (CMV), as well as a set of drugs that have demonstrated some activity in MERS, SARS-CoV, and SARS-CoV-2 therapy. We recommend testing of the selected compounds for treatment of COVID-19
bibliographic citation: Kouznetsova et al. (2020) Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs. PeerJ 8:e9965 https://doi.org/10.7717/peerj.9965
date submitted: 2020-07-01
date accepted: 2020-08-26
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kouznetsova
  given name: Valentina L.
author list: Agent
  family name: Zhang
  given name: Aidan
author list: Agent
  family name: Tatineni
  given name: Mahidhar
author list: Agent
  family name: Miller
  given name: Mark A.
author list: Agent
  family name: Tsigelny
  given name: Igor F.
doi: 10.7717/peerj.9965
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: © 2020 Kouznetsova et al.
attribution name: Kouznetsova et al.

Radiolarian assemblages in the shelf area of the East China Sea and Yellow Sea and their ecological indication of the Kuroshio Current derivative branches
type: item
type: AcademicArticle
description: We analyzed the radiolarian assemblages of 59 surface sediment samples collected from the Yellow Sea and East China Sea of the northwestern Pacific. In the study region, the Kuroshio Current and its derivative branches exerted a crucial impact on radiolarian composition and distribution. Radiolarians in the Yellow Sea shelf showed a quite low abundance as no tests were found in 15 of 25 Yellow Sea samples. Radiolarians in the East China Sea shelf could be divided into three regional groups: the East China Sea north region group, the East China Sea middle region group, and the East China Sea south region group. The results of the redundancy analysis suggested that the Sea Surface Temperature and Sea Surface Salinity were primary environmental variables explaining species-environment relationship. The gradients of temperature, salinity, and species diversity reflect the powerful influence of the Kuroshio Current in the study area.
format: application/pdf
format: text/html
creator: Hanxue Qu
creator: Yong Xu
creator: Jinbao Wang
creator: Xin-Zheng Li
subject: Biodiversity
subject: Marine Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.9976
publisher: PeerJ Inc.
rights: © 2020 Qu et al.
abstract: We analyzed the radiolarian assemblages of 59 surface sediment samples collected from the Yellow Sea and East China Sea of the northwestern Pacific. In the study region, the Kuroshio Current and its derivative branches exerted a crucial impact on radiolarian composition and distribution. Radiolarians in the Yellow Sea shelf showed a quite low abundance as no tests were found in 15 of 25 Yellow Sea samples. Radiolarians in the East China Sea shelf could be divided into three regional groups: the East China Sea north region group, the East China Sea middle region group, and the East China Sea south region group. The results of the redundancy analysis suggested that the Sea Surface Temperature and Sea Surface Salinity were primary environmental variables explaining species-environment relationship. The gradients of temperature, salinity, and species diversity reflect the powerful influence of the Kuroshio Current in the study area.
bibliographic citation: Qu et al. (2020) Radiolarian assemblages in the shelf area of the East China Sea and Yellow Sea and their ecological indication of the Kuroshio Current derivative branches. PeerJ 8:e9976 https://doi.org/10.7717/peerj.9976
date submitted: 2019-12-23
date accepted: 2020-08-26
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qu
  given name: Hanxue
author list: Agent
  family name: Xu
  given name: Yong
author list: Agent
  family name: Wang
  given name: Jinbao
author list: Agent
  family name: Li
  given name: Xin-Zheng
doi: 10.7717/peerj.9976
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Qu et al.
attribution name: Qu et al.

Development of a noninvasive photograph-based method for the evaluation of body condition in free-ranging brown bears
type: item
type: AcademicArticle
description: Body condition is an important determinant of health, and its evaluation has practical applications for the conservation and management of mammals. We developed a noninvasive method that uses photographs to assess the body condition of free-ranging brown bears (Ursus arctos) in the Shiretoko Peninsula, Hokkaido, Japan. First, we weighed and measured 476 bears captured during 1998–2017 and calculated their body condition index (BCI) based on residuals from the regression of body mass against body length. BCI showed seasonal changes and was lower in spring and summer than in autumn. The torso height:body length ratio was strongly correlated with BCI, which suggests that it can be used as an indicator of body condition. Second, we examined the precision of photograph-based measurements using an identifiable bear in the Rusha area, a special wildlife protection area on the peninsula. A total of 220 lateral photographs of this bear were taken September 24–26, 2017, and classified according to bear posture. The torso height:body/torso length ratio was calculated with four measurement methods and compared among bear postures in the photographs. The results showed torso height:horizontal torso length (TH:HTL) to be the indicator that could be applied to photographs of the most diverse postures, and its coefficient of variation for measurements was <5%. In addition, when analyzing photographs of this bear taken from June to October during 2016–2018, TH:HTL was significantly higher in autumn than in spring/summer, which indicates that this ratio reflects seasonal changes in body condition in wild bears. Third, we calculated BCI from actual measurements of seven females captured in the Rusha area and TH:HTL from photographs of the same individuals. We found a significant positive relationship between TH:HTL and BCI, which suggests that the body condition of brown bears can be estimated with high accuracy based on photographs. Our simple and accurate method is useful for monito…
format: application/pdf
format: text/html
creator: Yuri Shirane
creator: Fumihiko Mori
creator: Masami Yamanaka
creator: Masanao Nakanishi
creator: Tsuyoshi Ishinazaka
creator: Tsutomu Mano
creator: Mina Jimbo
creator: Mariko Sashika
creator: Toshio Tsubota
creator: Michito Shimozuru
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.9982
publisher: PeerJ Inc.
rights: © 2020 Shirane et al.
abstract: Body condition is an important determinant of health, and its evaluation has practical applications for the conservation and management of mammals. We developed a noninvasive method that uses photographs to assess the body condition of free-ranging brown bears (Ursus arctos) in the Shiretoko Peninsula, Hokkaido, Japan. First, we weighed and measured 476 bears captured during 1998–2017 and calculated their body condition index (BCI) based on residuals from the regression of body mass against body length. BCI showed seasonal changes and was lower in spring and summer than in autumn. The torso height:body length ratio was strongly correlated with BCI, which suggests that it can be used as an indicator of body condition. Second, we examined the precision of photograph-based measurements using an identifiable bear in the Rusha area, a special wildlife protection area on the peninsula. A total of 220 lateral photographs of this bear were taken September 24–26, 2017, and classified according to bear posture. The torso height:body/torso length ratio was calculated with four measurement methods and compared among bear postures in the photographs. The results showed torso height:horizontal torso length (TH:HTL) to be the indicator that could be applied to photographs of the most diverse postures, and its coefficient of variation for measurements was <5%. In addition, when analyzing photographs of this bear taken from June to October during 2016–2018, TH:HTL was significantly higher in autumn than in spring/summer, which indicates that this ratio reflects seasonal changes in body condition in wild bears. Third, we calculated BCI from actual measurements of seven females captured in the Rusha area and TH:HTL from photographs of the same individuals. We found a significant positive relationship between TH:HTL and BCI, which suggests that the body condition of brown bears can be estimated with high accuracy based on photographs. Our simple and accurate method is useful for monito…
bibliographic citation: Shirane et al. (2020) Development of a noninvasive photograph-based method for the evaluation of body condition in free-ranging brown bears. PeerJ 8:e9982 https://doi.org/10.7717/peerj.9982
date submitted: 2020-06-10
date accepted: 2020-08-27
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shirane
  given name: Yuri
author list: Agent
  family name: Mori
  given name: Fumihiko
author list: Agent
  family name: Yamanaka
  given name: Masami
author list: Agent
  family name: Nakanishi
  given name: Masanao
author list: Agent
  family name: Ishinazaka
  given name: Tsuyoshi
author list: Agent
  family name: Mano
  given name: Tsutomu
author list: Agent
  family name: Jimbo
  given name: Mina
author list: Agent
  family name: Sashika
  given name: Mariko
author list: Agent
  family name: Tsubota
  given name: Toshio
author list: Agent
  family name: Shimozuru
  given name: Michito
doi: 10.7717/peerj.9982
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Shirane et al.
attribution name: Shirane et al.

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