PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)
items: Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress
items: Deletion of two-component system QseBC weakened virulence of Glaesserella parasuis in a murine acute infection model and adhesion to host cells
items: Pocillopora spp. growth analysis on restoration structures in an Eastern Tropical Pacific upwelling area
items: Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)
items: Intra- and interspecific competition resulting from spatial coexistence among larvae of closely-related caddisflies from the genus Hydropsyche
items: Selective effects of exercise on reactive and proactive inhibition in Parkinson’s disease
items: Inflammation and fibrosis in the coal dust-exposed lung described by confocal Raman spectroscopy
items: The role of the river in the functioning of marginal fen: a case study from the Biebrza Wetlands
items: Characterization of LC-MS based urine metabolomics in healthy children and adults

Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)
type: item
type: AcademicArticle
description: Background Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak’. Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. Methods Using 3D scans of species that span the disparity of shell morphology across the Class, multiple modes of scaling, translation, and rotation were applied to test for differences in shell shape. Point-based homologies were used to define body axes, which were then standardized to facilitate specimen alignment via rotation. Resulting alignments were compared using pairwise distances between specimen shapes as defined by surface semilandmarks. Results Analysis of 45 possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment corresponds to a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we suggest orientation via the hinge line for many analyses of shell shape across the Class, a formalization of the most common approach to morphometrics of shell form. This axis-based approach to aligning specimens facilitates the comparison of approximately continuous differences in shape among phylogenetically broad and morphologically disparate samples, not only within bivalv…
format: application/pdf
format: text/html
creator: Stewart M. Edie
creator: Katie S. Collins
creator: David Jablonski
subject: Evolutionary Studies
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.13617
publisher: PeerJ Inc.
rights: © 2022 Edie et al.
abstract: Background Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak’. Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. Methods Using 3D scans of species that span the disparity of shell morphology across the Class, multiple modes of scaling, translation, and rotation were applied to test for differences in shell shape. Point-based homologies were used to define body axes, which were then standardized to facilitate specimen alignment via rotation. Resulting alignments were compared using pairwise distances between specimen shapes as defined by surface semilandmarks. Results Analysis of 45 possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment corresponds to a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we suggest orientation via the hinge line for many analyses of shell shape across the Class, a formalization of the most common approach to morphometrics of shell form. This axis-based approach to aligning specimens facilitates the comparison of approximately continuous differences in shape among phylogenetically broad and morphologically disparate samples, not only within bivalv…
bibliographic citation: Edie et al. (2022) Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia). PeerJ 10:e13617 https://doi.org/10.7717/peerj.13617
date submitted: 2022-03-10
date accepted: 2022-06-01
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Edie
  given name: Stewart M.
author list: Agent
  family name: Collins
  given name: Katie S.
author list: Agent
  family name: Jablonski
  given name: David
doi: 10.7717/peerj.13617
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: © 2022 Edie et al.
attribution name: Edie et al.

Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress
type: item
type: AcademicArticle
description: Hydrangea (Hydrangea macrophylla (Thunb.) Ser.) is a famous ornamental plant species with high resistance to aluminum (Al). The aluminum-activated malate transporter (ALMT) family encodes anion channels, which participate in many physiological processes, such as Al tolerance, pH regulation, stomatal movement, and mineral nutrition. However, systematic studies on the gene family have not been reported in hydrangea. In this study, 11 candidate ALMT family members were identified from the transcriptome data for hydrangea, which could be divided into three clusters according to the phylogenetic tree. The protein physicochemical properties, phylogeny, conserved motifs and protein structure were analyzed. The distribution of base conservative motifs of HmALMTs was consistent with that of other species, with a highly conserved WEP motif. Furthermore, tissue-specific analysis showed that most of the HmALMTs were highly expressed in the stem under Al treatment. In addition, overexpression of HmALMT5, HmALMT9 and HmALMT11 in yeasts enhanced their tolerance to Al stress. Therefore, the above results reveal the functional role of HmALMTs underlying the Al tolerance of hydrangea. The present study provides a reference for further research to elucidate the functional mechanism and expression regulation of the ALMT gene family in hydrangea.
format: application/pdf
format: text/html
creator: Ziyi Qin
creator: Shuangshuang Chen
creator: Jing Feng
creator: Huijie Chen
creator: Xiangyu Qi
creator: Huadi Wang
creator: Yanming Deng
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13620
publisher: PeerJ Inc.
rights: © 2022 Qin et al.
abstract: Hydrangea (Hydrangea macrophylla (Thunb.) Ser.) is a famous ornamental plant species with high resistance to aluminum (Al). The aluminum-activated malate transporter (ALMT) family encodes anion channels, which participate in many physiological processes, such as Al tolerance, pH regulation, stomatal movement, and mineral nutrition. However, systematic studies on the gene family have not been reported in hydrangea. In this study, 11 candidate ALMT family members were identified from the transcriptome data for hydrangea, which could be divided into three clusters according to the phylogenetic tree. The protein physicochemical properties, phylogeny, conserved motifs and protein structure were analyzed. The distribution of base conservative motifs of HmALMTs was consistent with that of other species, with a highly conserved WEP motif. Furthermore, tissue-specific analysis showed that most of the HmALMTs were highly expressed in the stem under Al treatment. In addition, overexpression of HmALMT5, HmALMT9 and HmALMT11 in yeasts enhanced their tolerance to Al stress. Therefore, the above results reveal the functional role of HmALMTs underlying the Al tolerance of hydrangea. The present study provides a reference for further research to elucidate the functional mechanism and expression regulation of the ALMT gene family in hydrangea.
bibliographic citation: Qin et al. (2022) Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress. PeerJ 10:e13620 https://doi.org/10.7717/peerj.13620
date submitted: 2022-02-22
date accepted: 2022-06-02
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Ziyi
author list: Agent
  family name: Chen
  given name: Shuangshuang
author list: Agent
  family name: Feng
  given name: Jing
author list: Agent
  family name: Chen
  given name: Huijie
author list: Agent
  family name: Qi
  given name: Xiangyu
author list: Agent
  family name: Wang
  given name: Huadi
author list: Agent
  family name: Deng
  given name: Yanming
doi: 10.7717/peerj.13620
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: © 2022 Qin et al.
attribution name: Qin et al.

Deletion of two-component system QseBC weakened virulence of Glaesserella parasuis in a murine acute infection model and adhesion to host cells
type: item
type: AcademicArticle
description: The widespread two-component system (TCS), QseBC, involves vital virulence regulators in Enterobacteriaceae and Pasteurellaceae. Here we studied the function of QseBC in Glaesserella parasuis. A ΔqseBC mutant was constructed using a Glaesserella parasuis serovar 11 clinical strain SC1401 by natural transformation. Immunofluorescence was used to evaluate cellular adhesion, the levels of inflammation and apoptosis. The ability of ΔqseBC and ΔqseC mutant strains to adhere to PAM and MLE-12 cells was significantly reduced. Additionally, by focusing on the clinical signs, H&E, and IFA for inflammation and apoptosis, we found that the ΔqseBC mutant weakened virulence in the murine models. Together, these findings suggest that QseBC plays an important role in the virulence of Glaesserella parasuis.
format: application/pdf
format: text/html
creator: Xuefeng Yan
creator: Ke Dai
creator: Congwei Gu
creator: Zehui Yu
creator: Manli He
creator: Wudian Xiao
creator: Mingde Zhao
creator: Lvqin He
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.13648
publisher: PeerJ Inc.
rights: © 2022 Yan et al.
abstract: The widespread two-component system (TCS), QseBC, involves vital virulence regulators in Enterobacteriaceae and Pasteurellaceae. Here we studied the function of QseBC in Glaesserella parasuis. A ΔqseBC mutant was constructed using a Glaesserella parasuis serovar 11 clinical strain SC1401 by natural transformation. Immunofluorescence was used to evaluate cellular adhesion, the levels of inflammation and apoptosis. The ability of ΔqseBC and ΔqseC mutant strains to adhere to PAM and MLE-12 cells was significantly reduced. Additionally, by focusing on the clinical signs, H&E, and IFA for inflammation and apoptosis, we found that the ΔqseBC mutant weakened virulence in the murine models. Together, these findings suggest that QseBC plays an important role in the virulence of Glaesserella parasuis.
bibliographic citation: Yan et al. (2022) Deletion of two-component system QseBC weakened virulence of Glaesserella parasuis in a murine acute infection model and adhesion to host cells. PeerJ 10:e13648 https://doi.org/10.7717/peerj.13648
date submitted: 2022-01-14
date accepted: 2022-06-07
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Xuefeng
author list: Agent
  family name: Dai
  given name: Ke
author list: Agent
  family name: Gu
  given name: Congwei
author list: Agent
  family name: Yu
  given name: Zehui
author list: Agent
  family name: He
  given name: Manli
author list: Agent
  family name: Xiao
  given name: Wudian
author list: Agent
  family name: Zhao
  given name: Mingde
author list: Agent
  family name: He
  given name: Lvqin
doi: 10.7717/peerj.13648
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: ©2022 Yan et al.
attribution name: Yan et al.

Pocillopora spp. growth analysis on restoration structures in an Eastern Tropical Pacific upwelling area
type: item
type: AcademicArticle
description: Coral reefs in Culebra Bay (North Pacific of Costa Rica) are threatened by multiple anthropogenic disturbances including global warming, overfishing, eutrophication, and invasive species outbreaks. It is possible to assist their recovery by implementing ecological restoration techniques. This study used artificial hexagonal steel structures, called “spiders” to compare growth of Pocillopora spp. coral fragments of different sizes. Three initial fragment class sizes were used: 2, 5 and 8 cm, with each class size having 42 initial fragments. Changes in fragment length, width and area were measured monthly from January to December 2020. Results showed an overall survivorship of 70.21%, and no significant differences in survivorship and linear growth rate were detected between class sizes. The linear growth rates are 4.49 ± 1.19 cm year−1, 5.35 ± 1.48 cm year−1 and 3.25 ± 2.22 cm year−1 for the 2, 5 and 8 cm initial class sizes, respectively. Our results do not show significant differences in growth rates between the different initial fragment sizes. However, since small fragments (2 cm) present higher mortality during the first month, we recommend using larger fragments. In addition, coral fragments grew 48% more during the non-upwelling season, which may suggest that it might be more effective and safer to start the restoration efforts during this period.
format: application/pdf
format: text/html
creator: Lisa Combillet
creator: Sònia Fabregat-Malé
creator: Sebastián Mena
creator: José Andrés Marín-Moraga
creator: Monica Gutierrez
creator: Juan José Alvarado
subject: Conservation Biology
subject: Ecosystem Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.13248
publisher: PeerJ Inc.
rights: © 2022 Combillet et al.
abstract: Coral reefs in Culebra Bay (North Pacific of Costa Rica) are threatened by multiple anthropogenic disturbances including global warming, overfishing, eutrophication, and invasive species outbreaks. It is possible to assist their recovery by implementing ecological restoration techniques. This study used artificial hexagonal steel structures, called “spiders” to compare growth of Pocillopora spp. coral fragments of different sizes. Three initial fragment class sizes were used: 2, 5 and 8 cm, with each class size having 42 initial fragments. Changes in fragment length, width and area were measured monthly from January to December 2020. Results showed an overall survivorship of 70.21%, and no significant differences in survivorship and linear growth rate were detected between class sizes. The linear growth rates are 4.49 ± 1.19 cm year−1, 5.35 ± 1.48 cm year−1 and 3.25 ± 2.22 cm year−1 for the 2, 5 and 8 cm initial class sizes, respectively. Our results do not show significant differences in growth rates between the different initial fragment sizes. However, since small fragments (2 cm) present higher mortality during the first month, we recommend using larger fragments. In addition, coral fragments grew 48% more during the non-upwelling season, which may suggest that it might be more effective and safer to start the restoration efforts during this period.
bibliographic citation: Combillet et al. (2022) Pocillopora spp. growth analysis on restoration structures in an Eastern Tropical Pacific upwelling area. PeerJ 10:e13248 https://doi.org/10.7717/peerj.13248
date submitted: 2021-10-01
date accepted: 2022-03-20
issued: 2022-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Combillet
  given name: Lisa
author list: Agent
  family name: Fabregat-Malé
  given name: Sònia
author list: Agent
  family name: Mena
  given name: Sebastián
author list: Agent
  family name: Marín-Moraga
  given name: José Andrés
author list: Agent
  family name: Gutierrez
  given name: Monica
author list: Agent
  family name: Alvarado
  given name: Juan José
doi: 10.7717/peerj.13248
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-23
copyright: © 2022 Combillet et al.
attribution name: Combillet et al.

Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)
type: item
type: AcademicArticle
description: The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called ‘variants of concern’ (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC s…
format: application/pdf
format: text/html
creator: Neetu Tyagi
creator: Rahila Sardar
creator: Dinesh Gupta
subject: Bioinformatics
subject: Virology
subject: COVID-19
description: doi:10.7717/peerj.13562
publisher: PeerJ Inc.
rights: © 2022 Tyagi et al.
abstract: The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called ‘variants of concern’ (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC s…
bibliographic citation: Tyagi et al. (2022) Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC). PeerJ 10:e13562 https://doi.org/10.7717/peerj.13562
date submitted: 2022-02-11
date accepted: 2022-05-19
issued: 2022-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tyagi
  given name: Neetu
author list: Agent
  family name: Sardar
  given name: Rahila
author list: Agent
  family name: Gupta
  given name: Dinesh
doi: 10.7717/peerj.13562
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-23
copyright: © 2022 Tyagi et al.
attribution name: Tyagi et al.

Intra- and interspecific competition resulting from spatial coexistence among larvae of closely-related caddisflies from the genus Hydropsyche
type: item
type: AcademicArticle
description: Caddisfly larvae commonly inhabit freshwater ecosystems, where they often create multi-species aggregations. However, while several strategies have been developed to avoid or reduce inter- and intraspecific interactions, most species choose the same time to seek a suitable place for pupation, which can increase competition. The current study assesses the competitive interactions among larvae (5th instar) of three co-existing Hydropsyche species, viz. H. contubernalis, H. pellucidula, and H. modesta, analysing their direct one-on-one interaction and various morphological features, such as size, weight, and mandibles. More than half of the interspecific conflicts ended with a draw, and 80% of intraspecific interactions with a decisive outcome. In fights between species, H. pellucidula was the most successful, and H. modesta the weakest. Our results confirm that among the larvae, competitive interactions were usually decided by body size, especially that of the head capsule. Although wider head capsule and higher weight were advantageous for ~60% of winning larvae, there were no distinct winning species. The chewing mouthpart turned out to be supportive in the fight: regardless of the species, longer and wider mandibles were significant for winning specimens, but not the distance between mandibles. Hence, acquiring a suitable place for pupation is determined by the possession of certain features enhancing the fighting potential of individual larvae, which does not exclude any species from the possibility of closing the life cycle. Future studies on interactions among caddisfly larvae could include experience in fights, volitional features and stridulation (not tested).
format: application/pdf
format: text/html
creator: Mariusz Tszydel
creator: Dagmara Błońska
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.13576
publisher: PeerJ Inc.
rights: © 2022 Tszydel and Błońska
abstract: Caddisfly larvae commonly inhabit freshwater ecosystems, where they often create multi-species aggregations. However, while several strategies have been developed to avoid or reduce inter- and intraspecific interactions, most species choose the same time to seek a suitable place for pupation, which can increase competition. The current study assesses the competitive interactions among larvae (5th instar) of three co-existing Hydropsyche species, viz. H. contubernalis, H. pellucidula, and H. modesta, analysing their direct one-on-one interaction and various morphological features, such as size, weight, and mandibles. More than half of the interspecific conflicts ended with a draw, and 80% of intraspecific interactions with a decisive outcome. In fights between species, H. pellucidula was the most successful, and H. modesta the weakest. Our results confirm that among the larvae, competitive interactions were usually decided by body size, especially that of the head capsule. Although wider head capsule and higher weight were advantageous for ~60% of winning larvae, there were no distinct winning species. The chewing mouthpart turned out to be supportive in the fight: regardless of the species, longer and wider mandibles were significant for winning specimens, but not the distance between mandibles. Hence, acquiring a suitable place for pupation is determined by the possession of certain features enhancing the fighting potential of individual larvae, which does not exclude any species from the possibility of closing the life cycle. Future studies on interactions among caddisfly larvae could include experience in fights, volitional features and stridulation (not tested).
bibliographic citation: Tszydel et al. (2022) Intra- and interspecific competition resulting from spatial coexistence among larvae of closely-related caddisflies from the genus Hydropsyche. PeerJ 10:e13576 https://doi.org/10.7717/peerj.13576
date submitted: 2022-02-09
date accepted: 2022-05-22
issued: 2022-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tszydel
  given name: Mariusz
author list: Agent
  family name: Błońska
  given name: Dagmara
doi: 10.7717/peerj.13576
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-23
copyright: © 2022 Tszydel and Błońska
attribution name: Tszydel and Błońska

Selective effects of exercise on reactive and proactive inhibition in Parkinson’s disease
type: item
type: AcademicArticle
description: Objective Patients with Parkinson’s disease (PD) have an obvious motor inhibition disorder, which is closely related to their motor symptoms. Although previous studies have shown that exercise can improve their inhibition deficits, the effect of exercise on different types of inhibition (proactive and reactive inhibition) has not been addressed. Methods We used a behavioral paradigm combined with a series of questionnaires to explore the effect of long-term exercise on different types of motor inhibition in 59 patients with PD aged 55–75 years. According to the intensity and frequency of exercise, the participants were divided into regular-exercise and no-exercise groups. To obtain the average reference value for inhibition ability at the same age, we also recruited 30 healthy elderly people as controls. Results The main defect in the motor inhibition of PD is reactive inhibition, while proactive inhibition has no obvious differences compared with healthy controls. Additionally, compared with the non-exercise group, PD in the exercise group showed significantly better reaction speeds and reactive control ability, fewer motor symptoms and negative emotions. Conclusions Taken together, the motor inhibition defects of patients with PD affect only reactive inhibition. In addition, PD with exercise reported fewer negative emotions than that of the non-exercise group, indicating that exercise can relieve negative emotions and improve behavioral symptoms and quality of life in PD to a certain extent. We demonstrate for the first time that exercise has and can improve reactive inhibition in PD patients and has no effect on proactive inhibition.
format: application/pdf
format: text/html
creator: Zhen Wang
creator: Yan-Ling Pi
creator: Yin Wu
creator: Jianing Wei
creator: Yuting Li
creator: Jian Zhang
subject: Cognitive Disorders
subject: Psychiatry and Psychology
subject: Rehabilitation
description: doi:10.7717/peerj.13628
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Objective Patients with Parkinson’s disease (PD) have an obvious motor inhibition disorder, which is closely related to their motor symptoms. Although previous studies have shown that exercise can improve their inhibition deficits, the effect of exercise on different types of inhibition (proactive and reactive inhibition) has not been addressed. Methods We used a behavioral paradigm combined with a series of questionnaires to explore the effect of long-term exercise on different types of motor inhibition in 59 patients with PD aged 55–75 years. According to the intensity and frequency of exercise, the participants were divided into regular-exercise and no-exercise groups. To obtain the average reference value for inhibition ability at the same age, we also recruited 30 healthy elderly people as controls. Results The main defect in the motor inhibition of PD is reactive inhibition, while proactive inhibition has no obvious differences compared with healthy controls. Additionally, compared with the non-exercise group, PD in the exercise group showed significantly better reaction speeds and reactive control ability, fewer motor symptoms and negative emotions. Conclusions Taken together, the motor inhibition defects of patients with PD affect only reactive inhibition. In addition, PD with exercise reported fewer negative emotions than that of the non-exercise group, indicating that exercise can relieve negative emotions and improve behavioral symptoms and quality of life in PD to a certain extent. We demonstrate for the first time that exercise has and can improve reactive inhibition in PD patients and has no effect on proactive inhibition.
bibliographic citation: Wang et al. (2022) Selective effects of exercise on reactive and proactive inhibition in Parkinson’s disease. PeerJ 10:e13628 https://doi.org/10.7717/peerj.13628
date submitted: 2022-03-02
date accepted: 2022-06-02
issued: 2022-06-23
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: Pi
  given name: Yan-Ling
author list: Agent
  family name: Wu
  given name: Yin
author list: Agent
  family name: Wei
  given name: Jianing
author list: Agent
  family name: Li
  given name: Yuting
author list: Agent
  family name: Zhang
  given name: Jian
author list: Agent
  family name: Wang
  given name: Zhen
doi: 10.7717/peerj.13628
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-23
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Inflammation and fibrosis in the coal dust-exposed lung described by confocal Raman spectroscopy
type: item
type: AcademicArticle
description: Background Coal workers’ pneumoconiosis (CWP) is an occupational disease that severely damages the life and health of miners. However, little is known about the molecular and cellular mechanisms changes associated with lung inflammation and fibrosis induced by coal dust. As a non-destructive technique for measuring biological tissue, confocal Raman spectroscopy provides accurate molecular fingerprints of label-free tissues and cells. Here, the progression of lung inflammation and fibrosis in a murine model of CWP was evaluated using confocal Raman spectroscopy. Methods A mouse model of CWP was constructed and biochemical analysis in lungs exposed to coal dust after 1 month (CWP-1M) and 3 months (CWP-3M) vs control tissues (NS) were used by confocal Raman spectroscopy. H&E, immunohistochemical and collagen staining were used to evaluate the histopathology alterations in the lung tissues. Results The CWP murine model was successfully constructed, and the mouse lung tissues showed progression of inflammation and fibrosis, accompanied by changes in NF-κB, p53, Bax, and Ki67. Meanwhile, significant differences in Raman bands were observed among the different groups, particularly changes at 1,248, 1,448, 1,572, and 746 cm−1. These changes were consistent with collagen, Ki67, and Bax levels in the CWP and NS groups. Conclusion Confocal Raman spectroscopy represented a novel approach to the identification of the biochemical changes in CWP lungs and provides potential biomarkers of inflammation and fibrosis.
format: application/pdf
format: text/html
creator: Wenyang Wang
creator: Min Mu
creator: Yuanjie Zou
creator: Bing Li
creator: Hangbing Cao
creator: Dong Hu
creator: Xinrong Tao
subject: Biochemistry
subject: Cell Biology
subject: Toxicology
subject: Public Health
subject: Histology
description: doi:10.7717/peerj.13632
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Coal workers’ pneumoconiosis (CWP) is an occupational disease that severely damages the life and health of miners. However, little is known about the molecular and cellular mechanisms changes associated with lung inflammation and fibrosis induced by coal dust. As a non-destructive technique for measuring biological tissue, confocal Raman spectroscopy provides accurate molecular fingerprints of label-free tissues and cells. Here, the progression of lung inflammation and fibrosis in a murine model of CWP was evaluated using confocal Raman spectroscopy. Methods A mouse model of CWP was constructed and biochemical analysis in lungs exposed to coal dust after 1 month (CWP-1M) and 3 months (CWP-3M) vs control tissues (NS) were used by confocal Raman spectroscopy. H&E, immunohistochemical and collagen staining were used to evaluate the histopathology alterations in the lung tissues. Results The CWP murine model was successfully constructed, and the mouse lung tissues showed progression of inflammation and fibrosis, accompanied by changes in NF-κB, p53, Bax, and Ki67. Meanwhile, significant differences in Raman bands were observed among the different groups, particularly changes at 1,248, 1,448, 1,572, and 746 cm−1. These changes were consistent with collagen, Ki67, and Bax levels in the CWP and NS groups. Conclusion Confocal Raman spectroscopy represented a novel approach to the identification of the biochemical changes in CWP lungs and provides potential biomarkers of inflammation and fibrosis.
bibliographic citation: Wang et al. (2022) Inflammation and fibrosis in the coal dust-exposed lung described by confocal Raman spectroscopy. PeerJ 10:e13632 https://doi.org/10.7717/peerj.13632
date submitted: 2022-03-28
date accepted: 2022-06-03
issued: 2022-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Wenyang
author list: Agent
  family name: Mu
  given name: Min
author list: Agent
  family name: Zou
  given name: Yuanjie
author list: Agent
  family name: Li
  given name: Bing
author list: Agent
  family name: Cao
  given name: Hangbing
author list: Agent
  family name: Hu
  given name: Dong
author list: Agent
  family name: Tao
  given name: Xinrong
doi: 10.7717/peerj.13632
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-23
copyright: © 2022 Wang et al.
attribution name: Wang et al.

The role of the river in the functioning of marginal fen: a case study from the Biebrza Wetlands
type: item
type: AcademicArticle
description: Study region The area of interest is the Upper Biebrza Valley, located in NE Poland. Study focus We examined water exchange at the river-fen interface in a near-natural wetland system using the combined field research-modeling approach. The authors chose the Biebrza River as the research object: it is a specific case of fen marginal valley rivers, and it flows in the peat layer without direct connection to the mineral soil layer. Our case study introduces two new aspects not yet considered in the scientific literature: (1) the riparian aquifer is fen and (2) the river has no direct contact with the mineral layer. The following research questions were investigated: What is the role of the river in feeding and draining a fen? Which drainage paths are important for water exchange in a near-natural river-fen system? How important are the morphological settings for the river-fen relations? We applied a systematic hydrological research approach based on field measurements and observations of the river and surrounding fen hydrological characteristics, as well as on the modelling results. New hydrological insights for the region We demonstrated that morphological settings have a significant influence on river-fen relations. We also demonstrated that due to the undeniable need to introduce increased protection and restoration of marginal fens, we may focus on river status in narrow valleys; however, in the wide valleys, the limitation of the drainage layer by decreasing the intensity of evapotranspiration is more promising. We propose to distinguish zones in the fen river valley to include them when proposing protection or conservation plans.
format: application/pdf
format: text/html
creator: Maria Grodzka-Łukaszewska
creator: Grzegorz Sinicyn
creator: Mateusz Grygoruk
creator: Dorota Mirosław-Świątek
creator: Ignacy Kardel
creator: Tomasz Okruszko
subject: Ecosystem Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.13418
publisher: PeerJ Inc.
rights: © 2022 Grodzka-Łukaszewska et al.
abstract: Study region The area of interest is the Upper Biebrza Valley, located in NE Poland. Study focus We examined water exchange at the river-fen interface in a near-natural wetland system using the combined field research-modeling approach. The authors chose the Biebrza River as the research object: it is a specific case of fen marginal valley rivers, and it flows in the peat layer without direct connection to the mineral soil layer. Our case study introduces two new aspects not yet considered in the scientific literature: (1) the riparian aquifer is fen and (2) the river has no direct contact with the mineral layer. The following research questions were investigated: What is the role of the river in feeding and draining a fen? Which drainage paths are important for water exchange in a near-natural river-fen system? How important are the morphological settings for the river-fen relations? We applied a systematic hydrological research approach based on field measurements and observations of the river and surrounding fen hydrological characteristics, as well as on the modelling results. New hydrological insights for the region We demonstrated that morphological settings have a significant influence on river-fen relations. We also demonstrated that due to the undeniable need to introduce increased protection and restoration of marginal fens, we may focus on river status in narrow valleys; however, in the wide valleys, the limitation of the drainage layer by decreasing the intensity of evapotranspiration is more promising. We propose to distinguish zones in the fen river valley to include them when proposing protection or conservation plans.
bibliographic citation: Grodzka-Łukaszewska et al. (2022) The role of the river in the functioning of marginal fen: a case study from the Biebrza Wetlands. PeerJ 10:e13418 https://doi.org/10.7717/peerj.13418
date submitted: 2021-12-07
date accepted: 2022-04-20
issued: 2022-06-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grodzka-Łukaszewska
  given name: Maria
author list: Agent
  family name: Sinicyn
  given name: Grzegorz
author list: Agent
  family name: Grygoruk
  given name: Mateusz
author list: Agent
  family name: Mirosław-Świątek
  given name: Dorota
author list: Agent
  family name: Kardel
  given name: Ignacy
author list: Agent
  family name: Okruszko
  given name: Tomasz
doi: 10.7717/peerj.13418
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-22
copyright: ©2022 Grodzka-Łukaszewska et al.
attribution name: Grodzka-Łukaszewska et al.

Characterization of LC-MS based urine metabolomics in healthy children and adults
type: item
type: AcademicArticle
description: Previous studies reported that sex and age could influence urine metabolomics, which should be considered in biomarker discovery. As a consequence, for the baseline of urine metabolomics characteristics, it becomes critical to avoid confounding effects in clinical cohort studies. In this study, we provided a comprehensive lifespan characterization of urine metabolomics in a cohort of 348 healthy children and 315 adults, aged 1 to 78 years, using liquid chromatography coupled with high resolution mass spectrometry. Our results suggest that sex-dependent urine metabolites are much greater in adults than in children. The pantothenate and CoA biosynthesis and alanine metabolism pathways were enriched in early life. Androgen and estrogen metabolism showed high activity during adolescence and youth stages. Pyrimidine metabolism was enriched in the geriatric stage. Based on the above analysis, metabolomic characteristics of each age stage were provided. This work could help us understand the baseline of urine metabolism characteristics and contribute to further studies of clinical disease biomarker discovery.
format: application/pdf
format: text/html
creator: Xiaoyan Liu
creator: Xiaoyi Tian
creator: Shi Qinghong
creator: Haidan Sun
creator: Li Jing
creator: Xiaoyue Tang
creator: Zhengguang Guo
creator: Ying Liu
creator: Yan Wang
creator: Jie Ma
creator: Ren Na
creator: Chengyan He
creator: Wenqi Song
creator: Wei Sun
subject: Biochemistry
subject: Molecular Biology
subject: Health Policy
subject: Pediatrics
subject: Metabolic Sciences
description: doi:10.7717/peerj.13545
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Previous studies reported that sex and age could influence urine metabolomics, which should be considered in biomarker discovery. As a consequence, for the baseline of urine metabolomics characteristics, it becomes critical to avoid confounding effects in clinical cohort studies. In this study, we provided a comprehensive lifespan characterization of urine metabolomics in a cohort of 348 healthy children and 315 adults, aged 1 to 78 years, using liquid chromatography coupled with high resolution mass spectrometry. Our results suggest that sex-dependent urine metabolites are much greater in adults than in children. The pantothenate and CoA biosynthesis and alanine metabolism pathways were enriched in early life. Androgen and estrogen metabolism showed high activity during adolescence and youth stages. Pyrimidine metabolism was enriched in the geriatric stage. Based on the above analysis, metabolomic characteristics of each age stage were provided. This work could help us understand the baseline of urine metabolism characteristics and contribute to further studies of clinical disease biomarker discovery.
bibliographic citation: Liu et al. (2022) Characterization of LC-MS based urine metabolomics in healthy children and adults. PeerJ 10:e13545 https://doi.org/10.7717/peerj.13545
date submitted: 2021-11-25
date accepted: 2022-05-16
issued: 2022-06-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiaoyan
author list: Agent
  family name: Tian
  given name: Xiaoyi
author list: Agent
  family name: Qinghong
  given name: Shi
author list: Agent
  family name: Sun
  given name: Haidan
author list: Agent
  family name: Jing
  given name: Li
author list: Agent
  family name: Tang
  given name: Xiaoyue
author list: Agent
  family name: Guo
  given name: Zhengguang
author list: Agent
  family name: Liu
  given name: Ying
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Ma
  given name: Jie
author list: Agent
  family name: Na
  given name: Ren
author list: Agent
  family name: He
  given name: Chengyan
author list: Agent
  family name: Song
  given name: Wenqi
author list: Agent
  family name: Sun
  given name: Wei
doi: 10.7717/peerj.13545
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-22
copyright: ©2022 Liu et al.
attribution name: Liu et al.

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