PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Nicotine smoking is associated with impaired cognitive performance in Pakistani young people
items: Involvement of plasminogen activator inhibitor-1 and its related molecules in atrial fibrosis in patients with atrial fibrillation
items: The gut microbiome of the Sunda pangolin (Manis javanica) reveals its adaptation to specialized myrmecophagy
items: Reliability of hip muscle strength measured in principal and intermediate planes of movement
items: Effects of thiourea on the skull of Triturus newts during ontogeny
items: Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus
items: Alien plants of Europe: introduction pathways, gateways and time trends
items: A new pterosaur tracksite from the Lower Cretaceous of Wuerho, Junggar Basin, China: inferring the first putative pterosaur trackmaker
items: Early maternal separation is not associated with changes in telomere length in domestic kittens (Felis catus)
items: Guiclupea superstes, gen. et sp. nov., the youngest ellimmichthyiform (clupeomorph) fish to date from the Oligocene of South China

Nicotine smoking is associated with impaired cognitive performance in Pakistani young people
type: item
type: AcademicArticle
description: Nicotine smoking is the most common mode of tobacco smoking among young people. It affects the areas of the brain associated with memory, attention, and learning. This study has investigated the effect of nicotine smoking on cognitive performance. One hundred male volunteers (50 nicotine smokers and 50 nonsmokers) aged 18–30 years with similar socioeconomic backgrounds were recruited for this study. Clinical history of participants was obtained using a questionnaire. Their brain health and handedness were determined using the Mini Mental State Examination (MMSE) and the Edinburgh Handedness Inventory (EHI), respectively. The dependent variables examined in the study were attention-switching tasks (AST), pattern recognition memory (PRM), and choice reaction time (CRT). These parameters were assessed using the Cambridge Neuropsychological Automated Battery (CANTAB). The average ages of participating smokers and nonsmokers were 24.02 ± 3.41 years (mean ± standard deviation) and 22.68 ± 1.87 years, respectively. MMSE and EHI scores of smokers were 28.42 ± 1.09 and 99.75 ± 1.77, respectively; for nonsmokers, these scores were 28.54 ± 1.34 and 98 ± 1.91, respectively. The mean score for AST correct latency/delay was significantly higher (p = 0.050) in smokers (620.26 ± 142.03) than in nonsmokers (570.11 ± 108.39). The percentage of correct AST trials was significantly higher (p = 0.000) in nonsmokers (96.95 ± 2.18) than in smokers (83.75 ± 11.22). The PRM percent correct were significantly higher (p = 0.000) of nonsmokers (93.42 ± 8.34) than of smokers (79.75 ± 13.44). The mean correct latency for CRT was significantly higher (p = 0.009) in smokers (509.87 ± 129.83) than in nonsmokers (455.20 ± 65.73). From this data, it can be concluded that nicotine smoking is linked with impaired cognitive functions in smokers.
format: application/pdf
format: text/html
creator: Tuba Riaz
creator: Ghulam Murtaza
creator: Areej Arif
creator: Shahid Mahmood
creator: Razia Sultana
creator: Fawaz Al-Hussain
creator: Shahid Bashir
subject: Drugs and Devices
subject: Neurology
subject: Psychiatry and Psychology
subject: Public Health
subject: Respiratory Medicine
description: doi:10.7717/peerj.11470
publisher: PeerJ Inc.
rights: © 2021 Riaz et al.
abstract: Nicotine smoking is the most common mode of tobacco smoking among young people. It affects the areas of the brain associated with memory, attention, and learning. This study has investigated the effect of nicotine smoking on cognitive performance. One hundred male volunteers (50 nicotine smokers and 50 nonsmokers) aged 18–30 years with similar socioeconomic backgrounds were recruited for this study. Clinical history of participants was obtained using a questionnaire. Their brain health and handedness were determined using the Mini Mental State Examination (MMSE) and the Edinburgh Handedness Inventory (EHI), respectively. The dependent variables examined in the study were attention-switching tasks (AST), pattern recognition memory (PRM), and choice reaction time (CRT). These parameters were assessed using the Cambridge Neuropsychological Automated Battery (CANTAB). The average ages of participating smokers and nonsmokers were 24.02 ± 3.41 years (mean ± standard deviation) and 22.68 ± 1.87 years, respectively. MMSE and EHI scores of smokers were 28.42 ± 1.09 and 99.75 ± 1.77, respectively; for nonsmokers, these scores were 28.54 ± 1.34 and 98 ± 1.91, respectively. The mean score for AST correct latency/delay was significantly higher (p = 0.050) in smokers (620.26 ± 142.03) than in nonsmokers (570.11 ± 108.39). The percentage of correct AST trials was significantly higher (p = 0.000) in nonsmokers (96.95 ± 2.18) than in smokers (83.75 ± 11.22). The PRM percent correct were significantly higher (p = 0.000) of nonsmokers (93.42 ± 8.34) than of smokers (79.75 ± 13.44). The mean correct latency for CRT was significantly higher (p = 0.009) in smokers (509.87 ± 129.83) than in nonsmokers (455.20 ± 65.73). From this data, it can be concluded that nicotine smoking is linked with impaired cognitive functions in smokers.
bibliographic citation: Riaz et al. (2021) Nicotine smoking is associated with impaired cognitive performance in Pakistani young people. PeerJ 9:e11470 https://doi.org/10.7717/peerj.11470
date submitted: 2020-10-07
date accepted: 2021-04-26
issued: 2021-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Riaz
  given name: Tuba
author list: Agent
  family name: Murtaza
  given name: Ghulam
author list: Agent
  family name: Arif
  given name: Areej
author list: Agent
  family name: Mahmood
  given name: Shahid
author list: Agent
  family name: Sultana
  given name: Razia
author list: Agent
  family name: Al-Hussain
  given name: Fawaz
author list: Agent
  family name: Bashir
  given name: Shahid
doi: 10.7717/peerj.11470
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-02
copyright: ©2021 Riaz et al.
attribution name: Riaz et al.

Involvement of plasminogen activator inhibitor-1 and its related molecules in atrial fibrosis in patients with atrial fibrillation
type: item
type: AcademicArticle
description: Atrial fibrillation is the most common form of cardiac arrhythmia. Atrial fibrosis is a significant feature of atrial fibrillation though its mechanism is not well understood. We searched the Gene Expression Omnibus database to compare mRNA expression patterns between atrial fibrillation and sinus rhythm samples; one hundred and forty eight differentially expressed genes were identified. Most of these genes were significantly enriched in the extracellular matrix organization process and collagen-activated tyrosine kinase receptor signaling pathway. To screen hub genes involved in atrial fibrosis, we constructed a protein-protein interaction network and found that three hub genes (SERPINE1/plasminogen activator inhibitor-1/PAI-1, TIMP Metallopeptidase Inhibitor 3/TIMP3 and decorin/DCN) play vital roles in atrial fibrosis, especially plasminogen activator inhibitor-1. Elevated plasminogen activator inhibitor-1 expression was positively correlated with the p53 signaling pathway. Plasminogen activator inhibitor-1 and p53 protein expression levels were verified in patients with sinus rhythm and atrial fibrillation by Western blot analysis. Compared with the sinus rhythm controls, p53 and plasminogen activator inhibitor-1 protein expressions were upregulated in the atrial tissues of patients with atrial fibrillation. p53 was also found to regulate plasminogen activator inhibitor-1 based on the results of cellular and molecular experiments. Thus, the p53/plasminogen activator inhibitor-1 signaling axis may participate in the pathophysiological processes of atrial fibrillation, and plasminogen activator inhibitor-1 may serve as a new therapeutic biomarker in atrial fibrillation.
format: application/pdf
format: text/html
creator: Qiaoqiao Li
creator: Yingyu Lai
creator: Xiaoyan Gao
creator: Xin Li
creator: Chun-Yu Deng
creator: Huiming Guo
creator: Junfei Zhao
creator: Hui Yang
creator: Yuwen Xu
creator: Shulin Wu
creator: Yumei Xue
creator: Fang Rao
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Cardiology
description: doi:10.7717/peerj.11488
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Atrial fibrillation is the most common form of cardiac arrhythmia. Atrial fibrosis is a significant feature of atrial fibrillation though its mechanism is not well understood. We searched the Gene Expression Omnibus database to compare mRNA expression patterns between atrial fibrillation and sinus rhythm samples; one hundred and forty eight differentially expressed genes were identified. Most of these genes were significantly enriched in the extracellular matrix organization process and collagen-activated tyrosine kinase receptor signaling pathway. To screen hub genes involved in atrial fibrosis, we constructed a protein-protein interaction network and found that three hub genes (SERPINE1/plasminogen activator inhibitor-1/PAI-1, TIMP Metallopeptidase Inhibitor 3/TIMP3 and decorin/DCN) play vital roles in atrial fibrosis, especially plasminogen activator inhibitor-1. Elevated plasminogen activator inhibitor-1 expression was positively correlated with the p53 signaling pathway. Plasminogen activator inhibitor-1 and p53 protein expression levels were verified in patients with sinus rhythm and atrial fibrillation by Western blot analysis. Compared with the sinus rhythm controls, p53 and plasminogen activator inhibitor-1 protein expressions were upregulated in the atrial tissues of patients with atrial fibrillation. p53 was also found to regulate plasminogen activator inhibitor-1 based on the results of cellular and molecular experiments. Thus, the p53/plasminogen activator inhibitor-1 signaling axis may participate in the pathophysiological processes of atrial fibrillation, and plasminogen activator inhibitor-1 may serve as a new therapeutic biomarker in atrial fibrillation.
bibliographic citation: Li et al. (2021) Involvement of plasminogen activator inhibitor-1 and its related molecules in atrial fibrosis in patients with atrial fibrillation. PeerJ 9:e11488 https://doi.org/10.7717/peerj.11488
date submitted: 2020-12-27
date accepted: 2021-04-27
issued: 2021-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Qiaoqiao
author list: Agent
  family name: Lai
  given name: Yingyu
author list: Agent
  family name: Gao
  given name: Xiaoyan
author list: Agent
  family name: Li
  given name: Xin
author list: Agent
  family name: Deng
  given name: Chun-Yu
author list: Agent
  family name: Guo
  given name: Huiming
author list: Agent
  family name: Zhao
  given name: Junfei
author list: Agent
  family name: Yang
  given name: Hui
author list: Agent
  family name: Xu
  given name: Yuwen
author list: Agent
  family name: Wu
  given name: Shulin
author list: Agent
  family name: Xue
  given name: Yumei
author list: Agent
  family name: Rao
  given name: Fang
doi: 10.7717/peerj.11488
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-02
copyright: ©2021 Li et al.
attribution name: Li et al.

The gut microbiome of the Sunda pangolin (Manis javanica) reveals its adaptation to specialized myrmecophagy
type: item
type: AcademicArticle
description: Background The gut microbiomes of mammals are closely related to the diets of their hosts. The Sunda pangolin (Manis javanica) is a specialized myrmecophage, but its gut microbiome has rarely been studied. Methods Using high-throughput Illumina barcoded 16S rRNA amplicons of nine fecal samples from nine captive Sunda pangolins, we investigated their gut microbiomes. Results The detected bacteria were classified into 14 phyla, 24 classes, 48 orders, 97 families, and 271 genera. The main bacterial phyla were Firmicutes (73.71%), Proteobacteria (18.42%), Actinobacteria (3.44%), and Bacteroidetes (0.51%). In the PCoA and neighbor-net network (PERMANOVA: pangolins vs. other diets, weighted UniFrac distance p < 0.01, unweighted UniFrac distance p < 0.001), the gut microbiomes of the Sunda pangolins were distinct from those of mammals with different diets, but were much closer to other myrmecophages, and to carnivores, while distant from herbivores. We identified some gut microbiomes related to the digestion of chitin, including Lactococcus, Bacteroides, Bacillus, and Staphylococcus species, which confirms that the gut microbiome of pangolins may help them to digest chitin. Significance The results will aid studies of extreme dietary adaption and the mechanisms of diet differentiation in mammals, as well as metagenomic studies, captive breeding, and ex situ conservation of pangolins.
format: application/pdf
format: text/html
creator: Fuhua Zhang
creator: Na Xu
creator: Wenhua Wang
creator: Yishuang Yu
creator: Shibao Wu
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.11490
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Background The gut microbiomes of mammals are closely related to the diets of their hosts. The Sunda pangolin (Manis javanica) is a specialized myrmecophage, but its gut microbiome has rarely been studied. Methods Using high-throughput Illumina barcoded 16S rRNA amplicons of nine fecal samples from nine captive Sunda pangolins, we investigated their gut microbiomes. Results The detected bacteria were classified into 14 phyla, 24 classes, 48 orders, 97 families, and 271 genera. The main bacterial phyla were Firmicutes (73.71%), Proteobacteria (18.42%), Actinobacteria (3.44%), and Bacteroidetes (0.51%). In the PCoA and neighbor-net network (PERMANOVA: pangolins vs. other diets, weighted UniFrac distance p < 0.01, unweighted UniFrac distance p < 0.001), the gut microbiomes of the Sunda pangolins were distinct from those of mammals with different diets, but were much closer to other myrmecophages, and to carnivores, while distant from herbivores. We identified some gut microbiomes related to the digestion of chitin, including Lactococcus, Bacteroides, Bacillus, and Staphylococcus species, which confirms that the gut microbiome of pangolins may help them to digest chitin. Significance The results will aid studies of extreme dietary adaption and the mechanisms of diet differentiation in mammals, as well as metagenomic studies, captive breeding, and ex situ conservation of pangolins.
bibliographic citation: Zhang et al. (2021) The gut microbiome of the Sunda pangolin (Manis javanica) reveals its adaptation to specialized myrmecophagy. PeerJ 9:e11490 https://doi.org/10.7717/peerj.11490
date submitted: 2021-01-26
date accepted: 2021-04-28
issued: 2021-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhang
  given name: Fuhua
author list: Agent
  family name: Xu
  given name: Na
author list: Agent
  family name: Wang
  given name: Wenhua
author list: Agent
  family name: Yu
  given name: Yishuang
author list: Agent
  family name: Wu
  given name: Shibao
doi: 10.7717/peerj.11490
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-02
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Reliability of hip muscle strength measured in principal and intermediate planes of movement
type: item
type: AcademicArticle
description: Background Muscle strength testing is widely used in clinical and athletic populations. Commercially available dynamometers are designed to assess strength in three principal planes (sagittal, transverse, frontal). However, the anatomy of the hip suggests muscles may only be recruited submaximally during tasks performed in these principal planes. Objective To evaluate the inter-session reliability of maximal isometric hip strength in the principal planes and three intermediate planes. Methods Twenty participants (26.1 ± 2.7 years, 50% female) attended two testing sessions 6.2 ± 1.8 days apart. Participants completed 3-5 maximal voluntary isometric contractions for hip abduction, adduction, flexion, extension, and internal and external rotation measured using a fixed uniaxial load cell (custom rig) and commercial dynamometer (Biodex). Three intermediate hip actions were also tested using the custom rig: extension with abduction, extension with external rotation, and extension with both abduction and external rotation. Results Moderate-to-excellent intraclass correlation coefficients were observed for all principal and intermediate muscle actions using the custom rig (0.72–0.95) and the Biodex (0.85–0.95). The minimum detectable change was also similar between devices (custom rig = 11–31%; Biodex = 9–20%). Bland-Altman analysis revealed poor agreement between devices (range between upper and lower limits of agreement = 77–131%). Conclusions Although the custom rig and Biodex showed similar reliability, both devices may lack the sensitivity to detect small changes in hip strength commonly observed following intervention.
format: application/pdf
format: text/html
creator: Basilio A.M. Goncalves
creator: David J. Saxby
creator: Adam Kositsky
creator: Rod S. Barrett
creator: Laura E. Diamond
subject: Biophysics
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.11521
publisher: PeerJ Inc.
rights: © 2021 Goncalves et al.
abstract: Background Muscle strength testing is widely used in clinical and athletic populations. Commercially available dynamometers are designed to assess strength in three principal planes (sagittal, transverse, frontal). However, the anatomy of the hip suggests muscles may only be recruited submaximally during tasks performed in these principal planes. Objective To evaluate the inter-session reliability of maximal isometric hip strength in the principal planes and three intermediate planes. Methods Twenty participants (26.1 ± 2.7 years, 50% female) attended two testing sessions 6.2 ± 1.8 days apart. Participants completed 3-5 maximal voluntary isometric contractions for hip abduction, adduction, flexion, extension, and internal and external rotation measured using a fixed uniaxial load cell (custom rig) and commercial dynamometer (Biodex). Three intermediate hip actions were also tested using the custom rig: extension with abduction, extension with external rotation, and extension with both abduction and external rotation. Results Moderate-to-excellent intraclass correlation coefficients were observed for all principal and intermediate muscle actions using the custom rig (0.72–0.95) and the Biodex (0.85–0.95). The minimum detectable change was also similar between devices (custom rig = 11–31%; Biodex = 9–20%). Bland-Altman analysis revealed poor agreement between devices (range between upper and lower limits of agreement = 77–131%). Conclusions Although the custom rig and Biodex showed similar reliability, both devices may lack the sensitivity to detect small changes in hip strength commonly observed following intervention.
bibliographic citation: Goncalves et al. (2021) Reliability of hip muscle strength measured in principal and intermediate planes of movement. PeerJ 9:e11521 https://doi.org/10.7717/peerj.11521
date submitted: 2020-10-29
date accepted: 2021-05-05
issued: 2021-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Goncalves
  given name: Basilio A.M.
author list: Agent
  family name: Saxby
  given name: David J.
author list: Agent
  family name: Kositsky
  given name: Adam
author list: Agent
  family name: Barrett
  given name: Rod S.
author list: Agent
  family name: Diamond
  given name: Laura E.
doi: 10.7717/peerj.11521
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-02
copyright: ©2021 Goncalves et al.
attribution name: Goncalves et al.

Effects of thiourea on the skull of Triturus newts during ontogeny
type: item
type: AcademicArticle
description: Background In amphibians, thyroid hormone (TH) has a profound role in cranial development, especially in ossification of the late-appearing bones and remodeling of the skull. In the present study, we explored the influence of TH deficiency on bone ossification and resulting skull shape during the ontogeny of Triturus newt hybrid larvae obtained from interspecific crosses between T. ivanbureschi and T. macedonicus. Methods Larvae were treated with two concentrations of thiourea (an endocrine disruptor that chemically inhibits synthesis of TH) during the midlarval and late larval periods. Morphological differences of the cranium were assessed at the end of the midlarval period (ontogenetic stage 62) and the metamorphic stage after treatment during the late larval period. Results There was no difference in the ossification level and shape of the skull between the experimental groups (control and two treatment concentrations) at stage 62. During the late larval period and metamorphosis, TH deficit had a significant impact on the level of bone ossification and skull shape with no differences between the two treatment concentrations of thiourea. The most pronounced differences in bone development were: the palatopterygoid failed to disintegrate into the palatal and pterygoid portions, retardation was observed in development of the maxilla, nasal and prefrontal bones and larval organization of the vomer was retained in thiourea-treated larvae. Conclusions This implies that deficiency of TH caused retardation in development and arrested metamorphic cranium skeletal reorganization, which resulted in divergent cranial shape compared to the control group. Our results confirmed that skull remodeling and ossification of late-appearing bones is TH–dependent, as in other studied Urodela species. Also, our results indicate that TH plays an important role in the establishment of skull shape during the ontogeny of Triturus newts, especially during the late larval period and metamorph…
format: application/pdf
format: text/html
creator: Maja Ajduković
creator: Tijana Vučić
creator: Milena Cvijanović
subject: Developmental Biology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.11535
publisher: PeerJ Inc.
rights: © 2021 Ajduković et al.
abstract: Background In amphibians, thyroid hormone (TH) has a profound role in cranial development, especially in ossification of the late-appearing bones and remodeling of the skull. In the present study, we explored the influence of TH deficiency on bone ossification and resulting skull shape during the ontogeny of Triturus newt hybrid larvae obtained from interspecific crosses between T. ivanbureschi and T. macedonicus. Methods Larvae were treated with two concentrations of thiourea (an endocrine disruptor that chemically inhibits synthesis of TH) during the midlarval and late larval periods. Morphological differences of the cranium were assessed at the end of the midlarval period (ontogenetic stage 62) and the metamorphic stage after treatment during the late larval period. Results There was no difference in the ossification level and shape of the skull between the experimental groups (control and two treatment concentrations) at stage 62. During the late larval period and metamorphosis, TH deficit had a significant impact on the level of bone ossification and skull shape with no differences between the two treatment concentrations of thiourea. The most pronounced differences in bone development were: the palatopterygoid failed to disintegrate into the palatal and pterygoid portions, retardation was observed in development of the maxilla, nasal and prefrontal bones and larval organization of the vomer was retained in thiourea-treated larvae. Conclusions This implies that deficiency of TH caused retardation in development and arrested metamorphic cranium skeletal reorganization, which resulted in divergent cranial shape compared to the control group. Our results confirmed that skull remodeling and ossification of late-appearing bones is TH–dependent, as in other studied Urodela species. Also, our results indicate that TH plays an important role in the establishment of skull shape during the ontogeny of Triturus newts, especially during the late larval period and metamorph…
bibliographic citation: Ajduković et al. (2021) Effects of thiourea on the skull of Triturus newts during ontogeny. PeerJ 9:e11535 https://doi.org/10.7717/peerj.11535
date submitted: 2020-12-04
date accepted: 2021-05-07
issued: 2021-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ajduković
  given name: Maja
author list: Agent
  family name: Vučić
  given name: Tijana
author list: Agent
  family name: Cvijanović
  given name: Milena
doi: 10.7717/peerj.11535
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-02
copyright: ©2021 Ajduković et al.
attribution name: Ajduković et al.

Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus
type: item
type: AcademicArticle
description: Background Oseltamivir (OTV)-resistant influenza virus exhibits His-to-Tyr mutation at residue 274 (H274Y) in N1 neuraminidase (NA). However, the molecular mechanisms by which the H274Y mutation in NA reduces its binding affinity to OTV have not been fully elucidated. Methods In this study, we used dynamic residue interaction network (dRIN) analysis based on molecular dynamics simulation to investigate the correlation between the OTV binding site of NA and its H274Y mutation site. Results dRIN analysis revealed that the OTV binding site and H274Y mutation site of NA interact via the three interface residues connecting them. H274Y mutation significantly enhanced the interaction between residue 274 and the three interface residues in NA, thereby significantly decreasing the interaction between OTV and its surrounding loop 150 residues. Thus, we concluded that such changes in residue interactions could reduce the binding affinity of OTV to NA, resulting in drug resistant influenza viruses. Using dRIN analysis, we succeeded in understanding the characteristic changes in residue interactions due to H274Y mutation, which can elucidate the molecular mechanism of reduction in OTV binding affinity to influenza NA. Finally, the dRIN analysis used in this study can be widely applied to various systems such as individual proteins, protein-ligand complexes, and protein-protein complexes, to characterize the dynamic aspects of the interactions.
format: application/pdf
format: text/html
creator: Mohini Yadav
creator: Manabu Igarashi
creator: Norifumi Yamamoto
subject: Biophysics
subject: Molecular Biology
subject: Drugs and Devices
subject: Infectious Diseases
subject: Computational Science
description: doi:10.7717/peerj.11552
publisher: PeerJ Inc.
rights: © 2021 Yadav et al.
abstract: Background Oseltamivir (OTV)-resistant influenza virus exhibits His-to-Tyr mutation at residue 274 (H274Y) in N1 neuraminidase (NA). However, the molecular mechanisms by which the H274Y mutation in NA reduces its binding affinity to OTV have not been fully elucidated. Methods In this study, we used dynamic residue interaction network (dRIN) analysis based on molecular dynamics simulation to investigate the correlation between the OTV binding site of NA and its H274Y mutation site. Results dRIN analysis revealed that the OTV binding site and H274Y mutation site of NA interact via the three interface residues connecting them. H274Y mutation significantly enhanced the interaction between residue 274 and the three interface residues in NA, thereby significantly decreasing the interaction between OTV and its surrounding loop 150 residues. Thus, we concluded that such changes in residue interactions could reduce the binding affinity of OTV to NA, resulting in drug resistant influenza viruses. Using dRIN analysis, we succeeded in understanding the characteristic changes in residue interactions due to H274Y mutation, which can elucidate the molecular mechanism of reduction in OTV binding affinity to influenza NA. Finally, the dRIN analysis used in this study can be widely applied to various systems such as individual proteins, protein-ligand complexes, and protein-protein complexes, to characterize the dynamic aspects of the interactions.
bibliographic citation: Yadav et al. (2021) Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. PeerJ 9:e11552 https://doi.org/10.7717/peerj.11552
date submitted: 2021-02-26
date accepted: 2021-05-11
issued: 2021-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yadav
  given name: Mohini
author list: Agent
  family name: Igarashi
  given name: Manabu
author list: Agent
  family name: Yamamoto
  given name: Norifumi
doi: 10.7717/peerj.11552
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-02
copyright: ©2021 Yadav et al.
attribution name: Yadav et al.

Alien plants of Europe: introduction pathways, gateways and time trends
type: item
type: AcademicArticle
description: The Convention on Biological Diversity (CBD) pathways classification framework used in the implementation of the European Union’s (EU) Regulation 1143/2014 on invasive alien species (IAS Regulation) has recently been adopted by the European Alien Species Information Network (EASIN), the official information system supporting the implementation of the IAS Regulation. In the current paper, the result of an alignment of the primary introduction pathways of all alien plants in Europe included in the EASIN catalogue is presented, based on the CBD framework. In total, 6,250 alien plant taxa (marine plants excluded), both alien to Europe (native range outside Europe) and alien in Europe (native range partially in Europe) are reported. Altogether 5,175 plant taxa had their primary introduction pathway aligned based on the CBD framework, while for the rest the pathway remains unknown. In addition, the taxonomy, year and country of its first record in the wild are provided for each taxon. Our analyses reveal that the main primary introduction pathways of alien plants into Europe are linked to accidental escapes from ornamental and horticultural activities. Northwestern European countries seem to act as the main gateway areas of alien plants into Europe. Recent first observations of new alien taxa growing spontaneously exhibit a contemporary accelerating trend for plants alien to Europe, particularly linked to ornamental and horticultural activities. On the other hand, the number of new plants alien in Europe seems to have stabilized over the last few decades. The present work can assist in the prioritization of introduction pathways control, with the target of slowing down the rate of alien plants introductions into Europe, following also the requirements of the IAS Regulation.
format: application/pdf
format: text/html
creator: Margarita Arianoutsou
creator: Ioannis Bazos
creator: Anastasia Christopoulou
creator: Yannis Kokkoris
creator: Andreas Zikos
creator: Sevasti Zervou
creator: Pinelopi Delipetrou
creator: Ana Cristina Cardoso
creator: Ivan Deriu
creator: Eugenio Gervasini
creator: Konstantinos Tsiamis
subject: Agricultural Science
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.11270
publisher: PeerJ Inc.
rights: © 2021 Arianoutsou et al.
abstract: The Convention on Biological Diversity (CBD) pathways classification framework used in the implementation of the European Union’s (EU) Regulation 1143/2014 on invasive alien species (IAS Regulation) has recently been adopted by the European Alien Species Information Network (EASIN), the official information system supporting the implementation of the IAS Regulation. In the current paper, the result of an alignment of the primary introduction pathways of all alien plants in Europe included in the EASIN catalogue is presented, based on the CBD framework. In total, 6,250 alien plant taxa (marine plants excluded), both alien to Europe (native range outside Europe) and alien in Europe (native range partially in Europe) are reported. Altogether 5,175 plant taxa had their primary introduction pathway aligned based on the CBD framework, while for the rest the pathway remains unknown. In addition, the taxonomy, year and country of its first record in the wild are provided for each taxon. Our analyses reveal that the main primary introduction pathways of alien plants into Europe are linked to accidental escapes from ornamental and horticultural activities. Northwestern European countries seem to act as the main gateway areas of alien plants into Europe. Recent first observations of new alien taxa growing spontaneously exhibit a contemporary accelerating trend for plants alien to Europe, particularly linked to ornamental and horticultural activities. On the other hand, the number of new plants alien in Europe seems to have stabilized over the last few decades. The present work can assist in the prioritization of introduction pathways control, with the target of slowing down the rate of alien plants introductions into Europe, following also the requirements of the IAS Regulation.
bibliographic citation: Arianoutsou et al. (2021) Alien plants of Europe: introduction pathways, gateways and time trends. PeerJ 9:e11270 https://doi.org/10.7717/peerj.11270
date submitted: 2020-07-31
date accepted: 2021-03-23
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arianoutsou
  given name: Margarita
author list: Agent
  family name: Bazos
  given name: Ioannis
author list: Agent
  family name: Christopoulou
  given name: Anastasia
author list: Agent
  family name: Kokkoris
  given name: Yannis
author list: Agent
  family name: Zikos
  given name: Andreas
author list: Agent
  family name: Zervou
  given name: Sevasti
author list: Agent
  family name: Delipetrou
  given name: Pinelopi
author list: Agent
  family name: Cardoso
  given name: Ana Cristina
author list: Agent
  family name: Deriu
  given name: Ivan
author list: Agent
  family name: Gervasini
  given name: Eugenio
author list: Agent
  family name: Tsiamis
  given name: Konstantinos
doi: 10.7717/peerj.11270
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: ©2021 Arianoutsou et al.
attribution name: Arianoutsou et al.

A new pterosaur tracksite from the Lower Cretaceous of Wuerho, Junggar Basin, China: inferring the first putative pterosaur trackmaker
type: item
type: AcademicArticle
description: We report the discovery of 114 small pterosaur footprints preserved in a greyish-green fine sandstone slab comprising 57 manus imprints and 57 pes imprints. Due to the chaotic distribution of footprints, the trackways are difficult to recognize. The pes imprints are sub-triangular and enlongate, the metatarsal part is roughly subequal to the digital part. The manus imprints are asymmetrical, longer than wide, and the lengths of digits I–III gradually increase. According to the diagnostic features of the Wuerho small pterosaur tracks, the present set was classified as Pteraichnus and is different from the nine reported valid ichnospecies of Pteraichnus. We therefore propose a new ichnospecies, Pteraichnus wuerhoensis isp. nov. The description is based on the anatomical characteristics (lengths of digits I–IV, length of digital part, length of metatarsal part) extracted from the pes imprints and comparisons with the pes bone fossils of Noripterus complicidens. We infer that the footprints were probably left by N. complicidens and the total width of the wings was presumably 2–2.3 m. In addition, the high density (365 per square meter) and varied sizes of the Wuerho small pterosaur tracks suggest that many pterosaurs of different ages lived in Huangyangquan Reservoir tracksite 1 area. Thus the trackmakers may have had gregarious behavior.
format: application/pdf
format: text/html
creator: Yang Li
creator: Xiaolin Wang
creator: Shunxing Jiang
subject: Animal Behavior
subject: Biodiversity
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.11361
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: We report the discovery of 114 small pterosaur footprints preserved in a greyish-green fine sandstone slab comprising 57 manus imprints and 57 pes imprints. Due to the chaotic distribution of footprints, the trackways are difficult to recognize. The pes imprints are sub-triangular and enlongate, the metatarsal part is roughly subequal to the digital part. The manus imprints are asymmetrical, longer than wide, and the lengths of digits I–III gradually increase. According to the diagnostic features of the Wuerho small pterosaur tracks, the present set was classified as Pteraichnus and is different from the nine reported valid ichnospecies of Pteraichnus. We therefore propose a new ichnospecies, Pteraichnus wuerhoensis isp. nov. The description is based on the anatomical characteristics (lengths of digits I–IV, length of digital part, length of metatarsal part) extracted from the pes imprints and comparisons with the pes bone fossils of Noripterus complicidens. We infer that the footprints were probably left by N. complicidens and the total width of the wings was presumably 2–2.3 m. In addition, the high density (365 per square meter) and varied sizes of the Wuerho small pterosaur tracks suggest that many pterosaurs of different ages lived in Huangyangquan Reservoir tracksite 1 area. Thus the trackmakers may have had gregarious behavior.
bibliographic citation: Li et al. (2021) A new pterosaur tracksite from the Lower Cretaceous of Wuerho, Junggar Basin, China: inferring the first putative pterosaur trackmaker. PeerJ 9:e11361 https://doi.org/10.7717/peerj.11361
date submitted: 2020-10-21
date accepted: 2021-04-06
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yang
author list: Agent
  family name: Wang
  given name: Xiaolin
author list: Agent
  family name: Jiang
  given name: Shunxing
doi: 10.7717/peerj.11361
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: © 2021 Li et al.
attribution name: Li et al.

Early maternal separation is not associated with changes in telomere length in domestic kittens (Felis catus)
type: item
type: AcademicArticle
description: Objective Studies of multiple species have found that adverse early life experiences, including childhood trauma and maternal separation, can result in accelerated telomere shortening. The objective of this study was to determine if premature separation from the mother affected telomere length in domestic kittens (Felis catus). Subjects were 42 orphaned kittens and 10 mother-reared kittens from local animal rescue groups and shelters. DNA was extracted from whole blood collected from kittens at approximately 1 week and 2 months of age. Telomere length was assessed by qPCR (quantitative polymerase chain reaction) from a total of 86 samples and expressed as a ratio of telomere PCR relative to a single copy gene PCR (T/S). Results A generalized linear mixed model found there were no detectable differences in telomere length based on survival (F1, 76.2 = 3.35, p = 0.07), orphan status (F1, 56.5 = 0.44, p = 0.51), time point (F1, 43.5 = 0.19, p = 0.67), or the interaction between orphan status and time (F1, 43.5 = 0.86, p = 0.36). Although in other species telomere shortening is commonly associated with aging, even early in life, we did not find evidence for telomere shortening by two months of age. Our results suggest that the experience of early maternal separation in domestic cats who are subsequently hand-reared by humans does not accelerate telomere shortening compared to mother-reared kittens, at least in the first few months of life.
format: application/pdf
format: text/html
creator: Mikel Delgado
creator: C.A. Tony Buffington
creator: Melissa Bain
creator: Dana L. Smith
creator: Karen Vernau
subject: Developmental Biology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.11394
publisher: PeerJ Inc.
rights: © 2021 Delgado et al.
abstract: Objective Studies of multiple species have found that adverse early life experiences, including childhood trauma and maternal separation, can result in accelerated telomere shortening. The objective of this study was to determine if premature separation from the mother affected telomere length in domestic kittens (Felis catus). Subjects were 42 orphaned kittens and 10 mother-reared kittens from local animal rescue groups and shelters. DNA was extracted from whole blood collected from kittens at approximately 1 week and 2 months of age. Telomere length was assessed by qPCR (quantitative polymerase chain reaction) from a total of 86 samples and expressed as a ratio of telomere PCR relative to a single copy gene PCR (T/S). Results A generalized linear mixed model found there were no detectable differences in telomere length based on survival (F1, 76.2 = 3.35, p = 0.07), orphan status (F1, 56.5 = 0.44, p = 0.51), time point (F1, 43.5 = 0.19, p = 0.67), or the interaction between orphan status and time (F1, 43.5 = 0.86, p = 0.36). Although in other species telomere shortening is commonly associated with aging, even early in life, we did not find evidence for telomere shortening by two months of age. Our results suggest that the experience of early maternal separation in domestic cats who are subsequently hand-reared by humans does not accelerate telomere shortening compared to mother-reared kittens, at least in the first few months of life.
bibliographic citation: Delgado et al. (2021) Early maternal separation is not associated with changes in telomere length in domestic kittens (Felis catus). PeerJ 9:e11394 https://doi.org/10.7717/peerj.11394
date submitted: 2020-08-28
date accepted: 2021-04-12
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Delgado
  given name: Mikel
author list: Agent
  family name: Buffington
  given name: C.A. Tony
author list: Agent
  family name: Bain
  given name: Melissa
author list: Agent
  family name: Smith
  given name: Dana L.
author list: Agent
  family name: Vernau
  given name: Karen
doi: 10.7717/peerj.11394
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: ©2021 Delgado et al.
attribution name: Delgado et al.

Guiclupea superstes, gen. et sp. nov., the youngest ellimmichthyiform (clupeomorph) fish to date from the Oligocene of South China
type: item
type: AcademicArticle
description: A new ellimmichthyiform, Guiclupea superstes, gen. et sp. nov., from the Oligocene Ningming Formation of Ningming Basin, Guangxi Zhuang Autonomous Region, South China is described herein. With relatively large body size, parietals meeting at the midline, anterior ceratohyal with a beryciform foramen in the center, a complete predorsal scutes series of very high number and about equally-size scutes with radiating ridges on dorsal surface, first preural centrum unfused with first uroneural but fused with the parhypural, and first ural centrum of roughly the same size as the preural centrum, Guiclupea superstes cannot be assigned to the order Clupeiformes. The phylogenetic analyses using parsimony and Bayesian inference methods with Chanos/Elops as outgroup respectively suggests that the new form is closer to ellimmichthyiform genus Diplomystus than to any other fishes, although there are some discrepancies between the two criteria and different outgroups used. It shares with Diplomystus the high supraoccipital crest, pelvic-fin insertion in advance of dorsal fin origin, and the number of predorsal scutes more than 20. The new form represents the youngest ellimmichthyiform fish record in the world. Its discovery indicates that the members of the Ellimmichthyiformes had a wider distribution range and a longer evolutional history than previously known.
format: application/pdf
format: text/html
creator: Gengjiao Chen
creator: Mee-mann Chang
creator: Feixiang Wu
creator: Xiaowen Liao
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.11418
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: A new ellimmichthyiform, Guiclupea superstes, gen. et sp. nov., from the Oligocene Ningming Formation of Ningming Basin, Guangxi Zhuang Autonomous Region, South China is described herein. With relatively large body size, parietals meeting at the midline, anterior ceratohyal with a beryciform foramen in the center, a complete predorsal scutes series of very high number and about equally-size scutes with radiating ridges on dorsal surface, first preural centrum unfused with first uroneural but fused with the parhypural, and first ural centrum of roughly the same size as the preural centrum, Guiclupea superstes cannot be assigned to the order Clupeiformes. The phylogenetic analyses using parsimony and Bayesian inference methods with Chanos/Elops as outgroup respectively suggests that the new form is closer to ellimmichthyiform genus Diplomystus than to any other fishes, although there are some discrepancies between the two criteria and different outgroups used. It shares with Diplomystus the high supraoccipital crest, pelvic-fin insertion in advance of dorsal fin origin, and the number of predorsal scutes more than 20. The new form represents the youngest ellimmichthyiform fish record in the world. Its discovery indicates that the members of the Ellimmichthyiformes had a wider distribution range and a longer evolutional history than previously known.
bibliographic citation: Chen et al. (2021) Guiclupea superstes, gen. et sp. nov., the youngest ellimmichthyiform (clupeomorph) fish to date from the Oligocene of South China. PeerJ 9:e11418 https://doi.org/10.7717/peerj.11418
date submitted: 2020-12-17
date accepted: 2021-04-16
issued: 2021-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Gengjiao
author list: Agent
  family name: Chang
  given name: Mee-mann
author list: Agent
  family name: Wu
  given name: Feixiang
author list: Agent
  family name: Liao
  given name: Xiaowen
doi: 10.7717/peerj.11418
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-01
copyright: ©2021 Chen et al.
attribution name: Chen et al.

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