PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Prior experience of captivity affects behavioural responses to ‘novel’ environments
items: The relationship between the Functional Movement Screen and the Y Balance Test in youth footballers
items: Proteomic profile of serum from patients with schizophrenia spectrum disorders
items: Analysis of endophyte diversity of Gentiana officinalis among different tissue types and ages and their association with four medicinal secondary metabolites
items: Effects of melatonin on growth and antioxidant capacity of naked oat (Avena nuda L) seedlings under lead stress
items: Gender dimorphic M1 excitability during emotional processing: a transcranial magnetic stimulation study
items: Evolution of Helicobacter spp: variability of virulence factors and their relationship to pathogenicity
items: https://peerj.com/articles/13767
items: Genetic structure of the small yellow croaker (Larimichthys polyactis) across the Yellow Sea and the East China Sea by microsatellite DNA variation: implications for the division of management units
items: TRIM38 protects H9c2 cells from hypoxia/reoxygenation injury via the TRAF6/TAK1/NF-κB signalling pathway

Prior experience of captivity affects behavioural responses to ‘novel’ environments
type: item
type: AcademicArticle
description: Information ecology theory predicts that prior experience influences current behaviour, even if the information is acquired under a different context. However, when individuals are tested to quantify personality, cognition, or stress, we usually assume that the novelty of the test is consistent among individuals. Surprisingly, this ‘gambit of prior experience’ has rarely been explored. Therefore, here we make use of a wild population of great tits (Parus major) to test if prior experience of handling and captivity influences common measures of exploration (open field tests in two novel contexts: room and cage arenas), social response (simulated using a mirror), and behavioural stress (breathing rate). We found that birds with prior experience of captivity (caught previously for unrelated learning and foraging experiments) were more exploratory, but this depended on age: exploration and captivity experience (in terms of both absolute binary experience and the length of time spent in captivity) were associated more strongly in young (first-winter) birds than in adults. However, there was no association of prior experience of captivity with social response and breathing rate, and nor did the measures of exploration correlate. Together our results suggest that re-testing of individuals requires careful consideration, particularly for younger birds, and previous experiences can carry over and affect behaviours differently.
format: application/pdf
format: text/html
creator: Edward Kluen
creator: Katja Rönkä
creator: Rose Thorogood
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13905
publisher: PeerJ Inc.
rights: © 2022 Kluen et al.
abstract: Information ecology theory predicts that prior experience influences current behaviour, even if the information is acquired under a different context. However, when individuals are tested to quantify personality, cognition, or stress, we usually assume that the novelty of the test is consistent among individuals. Surprisingly, this ‘gambit of prior experience’ has rarely been explored. Therefore, here we make use of a wild population of great tits (Parus major) to test if prior experience of handling and captivity influences common measures of exploration (open field tests in two novel contexts: room and cage arenas), social response (simulated using a mirror), and behavioural stress (breathing rate). We found that birds with prior experience of captivity (caught previously for unrelated learning and foraging experiments) were more exploratory, but this depended on age: exploration and captivity experience (in terms of both absolute binary experience and the length of time spent in captivity) were associated more strongly in young (first-winter) birds than in adults. However, there was no association of prior experience of captivity with social response and breathing rate, and nor did the measures of exploration correlate. Together our results suggest that re-testing of individuals requires careful consideration, particularly for younger birds, and previous experiences can carry over and affect behaviours differently.
bibliographic citation: Kluen et al. (2022) Prior experience of captivity affects behavioural responses to ‘novel’ environments. PeerJ 10:e13905 https://doi.org/10.7717/peerj.13905
date submitted: 2022-02-15
date accepted: 2022-07-27
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kluen
  given name: Edward
author list: Agent
  family name: Rönkä
  given name: Katja
author list: Agent
  family name: Thorogood
  given name: Rose
doi: 10.7717/peerj.13905
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: ©2022 Kluen et al.
attribution name: Kluen et al.

The relationship between the Functional Movement Screen and the Y Balance Test in youth footballers
type: item
type: AcademicArticle
description: Background The Functional Movement Screen (FMS) and the Y Balance Test (Y-BT) are screening tools to detect movement deficits and to identify footballers at high risk of injury. If these tools are able to identify athletes with high risk of injury, they should measure the same construct and also be highly correlated. Objectives The aim of the study was to determine the relationship between the FMS and Y-BT in youth footballers. The present study also aimed to assess the degree of association between the FMS and Y-BT considering high-injury-risk (FMS <= 14 points and Y-BT <= 89.6%) and low-injury-risk groups (FMS > 14 points and Y-BT > 89.6%). Method A sample of 226 healthy athletes (mean age: 14.0 ± 2.3 years) was selected from a football club. The FMS and Y-BT data were collected from all participants. The Y-BT raw data were normalised to the relative length of the lower limbs. Spearman’s correlation was used in the analysis. Results For the whole group, there was a moderate correlation (R = 0.41; p < 0.001) between the composite FMS score and composite Y-BT score. The strength of relationships varied from weak to moderate between the FMS subtests and most Y-BT results for each direction. In the high-injury-risk group, there was no correlation (R = 0.11; p = 0.61) between the composite FMS score and composite Y-BT score. For the low-injury-risk group, there was a weak significant correlation (R = 0.27; p < 0.007) between the composite FMS score and composite Y-BT score. Additionally, 56 and 53 athletes were classified to the high-injury-risk group based on the FMS and Y-BT, respectively. Only 23 athletes were classified to the high-risk group by both tests. Conclusions Youth footballers showed only weak to moderate correlations between the FMS and the Y-BT. Footballers classified in the high-injury-risk group based on the FMS and Y-BT presented a different relationship between the FMS and Y-BT tasks compared to the low-injury-risk group. The results confirmed that …
format: application/pdf
format: text/html
creator: Damian Sikora
creator: Pawel Linek
subject: Kinesiology
subject: Pediatrics
subject: Rehabilitation
description: doi:10.7717/peerj.13906
publisher: PeerJ Inc.
rights: © 2022 Sikora and Linek
abstract: Background The Functional Movement Screen (FMS) and the Y Balance Test (Y-BT) are screening tools to detect movement deficits and to identify footballers at high risk of injury. If these tools are able to identify athletes with high risk of injury, they should measure the same construct and also be highly correlated. Objectives The aim of the study was to determine the relationship between the FMS and Y-BT in youth footballers. The present study also aimed to assess the degree of association between the FMS and Y-BT considering high-injury-risk (FMS <= 14 points and Y-BT <= 89.6%) and low-injury-risk groups (FMS > 14 points and Y-BT > 89.6%). Method A sample of 226 healthy athletes (mean age: 14.0 ± 2.3 years) was selected from a football club. The FMS and Y-BT data were collected from all participants. The Y-BT raw data were normalised to the relative length of the lower limbs. Spearman’s correlation was used in the analysis. Results For the whole group, there was a moderate correlation (R = 0.41; p < 0.001) between the composite FMS score and composite Y-BT score. The strength of relationships varied from weak to moderate between the FMS subtests and most Y-BT results for each direction. In the high-injury-risk group, there was no correlation (R = 0.11; p = 0.61) between the composite FMS score and composite Y-BT score. For the low-injury-risk group, there was a weak significant correlation (R = 0.27; p < 0.007) between the composite FMS score and composite Y-BT score. Additionally, 56 and 53 athletes were classified to the high-injury-risk group based on the FMS and Y-BT, respectively. Only 23 athletes were classified to the high-risk group by both tests. Conclusions Youth footballers showed only weak to moderate correlations between the FMS and the Y-BT. Footballers classified in the high-injury-risk group based on the FMS and Y-BT presented a different relationship between the FMS and Y-BT tasks compared to the low-injury-risk group. The results confirmed that …
bibliographic citation: Sikora et al. (2022) The relationship between the Functional Movement Screen and the Y Balance Test in youth footballers. PeerJ 10:e13906 https://doi.org/10.7717/peerj.13906
date submitted: 2022-02-24
date accepted: 2022-07-27
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sikora
  given name: Damian
author list: Agent
  family name: Linek
  given name: Pawel
doi: 10.7717/peerj.13906
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: © 2022 Sikora and Linek
attribution name: Sikora and Linek

Proteomic profile of serum from patients with schizophrenia spectrum disorders
type: item
type: AcademicArticle
description: This article describes the most likely classes of proteins and molecular processes that specifically characterize schizophrenic spectrum disorders such as simple and paranoid schizophrenia, schizotypal disorder, and acute polymorphic psychotic disorder (APPD). The identification of patients’ serum proteins was carried out using mass spectrometry. For patients with paranoid schizophrenia, the proteins responsible for translation and transcription are characteristic. A significant part of the proteins of patients with simple schizophrenia regulate the cell’s main metabolic and transport processes. These are proteins of the receptor system, vesicular transport, and extracellular matrix, which mainly carry out catabolic processes. The proteins of patients with schizotypal disorder mostly coincided with the classes of other patients, apart from chaperone proteins, which were not found in other studied groups. These proteins are mainly involved in anabolic processes. The main classes of proteins found in patients with APPD are responsible for the metabolism of nucleic acids. Active apoptosis processes were also revealed in these patients. These results from our basic knowledge about the molecular mechanisms of the pathogenesis of these disorders.
format: application/pdf
format: text/html
creator: Elena Dmitrieva
creator: Liudmila Smirnova
creator: Alexander Seregin
creator: Victor Zgoda
creator: Arkadij Semke
creator: Svetlana Ivanova
subject: Biochemistry
subject: Computational Biology
subject: Molecular Biology
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13907
publisher: PeerJ Inc.
rights: © 2022 Dmitrieva et al.
abstract: This article describes the most likely classes of proteins and molecular processes that specifically characterize schizophrenic spectrum disorders such as simple and paranoid schizophrenia, schizotypal disorder, and acute polymorphic psychotic disorder (APPD). The identification of patients’ serum proteins was carried out using mass spectrometry. For patients with paranoid schizophrenia, the proteins responsible for translation and transcription are characteristic. A significant part of the proteins of patients with simple schizophrenia regulate the cell’s main metabolic and transport processes. These are proteins of the receptor system, vesicular transport, and extracellular matrix, which mainly carry out catabolic processes. The proteins of patients with schizotypal disorder mostly coincided with the classes of other patients, apart from chaperone proteins, which were not found in other studied groups. These proteins are mainly involved in anabolic processes. The main classes of proteins found in patients with APPD are responsible for the metabolism of nucleic acids. Active apoptosis processes were also revealed in these patients. These results from our basic knowledge about the molecular mechanisms of the pathogenesis of these disorders.
bibliographic citation: Dmitrieva et al. (2022) Proteomic profile of serum from patients with schizophrenia spectrum disorders. PeerJ 10:e13907 https://doi.org/10.7717/peerj.13907
date submitted: 2022-05-19
date accepted: 2022-07-27
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dmitrieva
  given name: Elena
author list: Agent
  family name: Smirnova
  given name: Liudmila
author list: Agent
  family name: Seregin
  given name: Alexander
author list: Agent
  family name: Zgoda
  given name: Victor
author list: Agent
  family name: Semke
  given name: Arkadij
author list: Agent
  family name: Ivanova
  given name: Svetlana
doi: 10.7717/peerj.13907
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: ©2022 Dmitrieva et al.
attribution name: Dmitrieva et al.

Analysis of endophyte diversity of Gentiana officinalis among different tissue types and ages and their association with four medicinal secondary metabolites
type: item
type: AcademicArticle
description: Background The difference of metabolites in medicinal plants has always been concerned to be influenced by external environmental factors. However, the relationship between endophytes and host metabolites remains unclear. Methods In this study, we used 16S and ITS amplicon sequencing to compare endophyte diversity among different tissue types and ages of Gentiana officinalis. Endophyte diversity and abundance was also analyzed in relation to the abundance of four secondary metabolites (Gentiopicroside, Loganic acid, Swertiamarine and Sweroside). Results The diversity and richness of G. officinalis endophyte differed as a function of tissue types and ages. Four metabolites of G. officinalis were significantly correlated with the abundance of dominant endophyte genera. The predictive function analysis showed that metabolism was main function of endophytic bacteria in different tissue and year root samples, while saprotroph was dominant trophic modes of endophytic fungi in the different year root samples. The dominant trophic modes of endophytic fungi was saprotroph and pathotroph, and relative abundances differed in the different tissue samples. The results of this study will help to elucidate the plant-microbial interactions and provide key information on the role of endophytes in the production of G.officinalis and its important metabolites.
format: application/pdf
format: text/html
creator: QinZheng Hou
creator: DaWei Chen
creator: Yu-pei Wang
creator: Nurbiye Ehmet
creator: Jing Ma
creator: Kun Sun
subject: Agricultural Science
subject: Food Science and Technology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.13949
publisher: PeerJ Inc.
rights: © 2022 Hou et al.
abstract: Background The difference of metabolites in medicinal plants has always been concerned to be influenced by external environmental factors. However, the relationship between endophytes and host metabolites remains unclear. Methods In this study, we used 16S and ITS amplicon sequencing to compare endophyte diversity among different tissue types and ages of Gentiana officinalis. Endophyte diversity and abundance was also analyzed in relation to the abundance of four secondary metabolites (Gentiopicroside, Loganic acid, Swertiamarine and Sweroside). Results The diversity and richness of G. officinalis endophyte differed as a function of tissue types and ages. Four metabolites of G. officinalis were significantly correlated with the abundance of dominant endophyte genera. The predictive function analysis showed that metabolism was main function of endophytic bacteria in different tissue and year root samples, while saprotroph was dominant trophic modes of endophytic fungi in the different year root samples. The dominant trophic modes of endophytic fungi was saprotroph and pathotroph, and relative abundances differed in the different tissue samples. The results of this study will help to elucidate the plant-microbial interactions and provide key information on the role of endophytes in the production of G.officinalis and its important metabolites.
bibliographic citation: Hou et al. (2022) Analysis of endophyte diversity of Gentiana officinalis among different tissue types and ages and their association with four medicinal secondary metabolites. PeerJ 10:e13949 https://doi.org/10.7717/peerj.13949
date submitted: 2021-12-01
date accepted: 2022-08-04
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: QinZheng
author list: Agent
  family name: Chen
  given name: DaWei
author list: Agent
  family name: Wang
  given name: Yu-pei
author list: Agent
  family name: Ehmet
  given name: Nurbiye
author list: Agent
  family name: Ma
  given name: Jing
author list: Agent
  family name: Sun
  given name: Kun
doi: 10.7717/peerj.13949
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: © 2022 Hou et al.
attribution name: Hou et al.

Effects of melatonin on growth and antioxidant capacity of naked oat (Avena nuda L) seedlings under lead stress
type: item
type: AcademicArticle
description: Melatonin (MT) plays an important role in plant response to abiotic stress. In recent years, lead (Pb) pollution has seriously affected the living environment of plants. In this study, we applied two different concentrations of MT to naked oat seedlings under Pb stress to explore the effect of MT on naked oat seedlings under Pb pollution. The results showed that Pb stress seriously inhibited the growth and development of naked oat seedlings, which was alleviated by MT. MT could increase the soluble protein content and decrease the proline content of naked oat seedlings to maintain the osmotic balance of naked oat seedlings. The application of MT could accelerate the removal of reactive oxygen species (ROS) and improve the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), so as to maintain the redox balance in naked oat seedlings. Exogenous melatonin could significantly increase the chlorophyll content of naked oat seedlings under Pb treatment, so as to improve the photosynthesis efficiency of naked oat seedlings. MT could also remarkably up regulate the expression of the genes of LOX, POX and Asmap1, and affect the expression of transcription factors NAC and WRKY1. It might regulate the expression of downstream genes through MAPKs pathways and TFs to improve the Pb tolerance of naked oat seedlings. These results proved that MT could significantly promote the growth and development of naked oats seedlings under Pb stress, which is expected to be applied in agricultural production practice.
format: application/pdf
format: text/html
creator: Kai Wang
creator: Jinjin He
creator: Ningbo Zhao
creator: Yajing Zhao
creator: Fangbing Qi
creator: Fenggui Fan
creator: Yingjuan Wang
subject: Agricultural Science
subject: Biotechnology
subject: Plant Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.13978
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Melatonin (MT) plays an important role in plant response to abiotic stress. In recent years, lead (Pb) pollution has seriously affected the living environment of plants. In this study, we applied two different concentrations of MT to naked oat seedlings under Pb stress to explore the effect of MT on naked oat seedlings under Pb pollution. The results showed that Pb stress seriously inhibited the growth and development of naked oat seedlings, which was alleviated by MT. MT could increase the soluble protein content and decrease the proline content of naked oat seedlings to maintain the osmotic balance of naked oat seedlings. The application of MT could accelerate the removal of reactive oxygen species (ROS) and improve the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), so as to maintain the redox balance in naked oat seedlings. Exogenous melatonin could significantly increase the chlorophyll content of naked oat seedlings under Pb treatment, so as to improve the photosynthesis efficiency of naked oat seedlings. MT could also remarkably up regulate the expression of the genes of LOX, POX and Asmap1, and affect the expression of transcription factors NAC and WRKY1. It might regulate the expression of downstream genes through MAPKs pathways and TFs to improve the Pb tolerance of naked oat seedlings. These results proved that MT could significantly promote the growth and development of naked oats seedlings under Pb stress, which is expected to be applied in agricultural production practice.
bibliographic citation: Wang et al. (2022) Effects of melatonin on growth and antioxidant capacity of naked oat (Avena nuda L) seedlings under lead stress. PeerJ 10:e13978 https://doi.org/10.7717/peerj.13978
date submitted: 2022-05-11
date accepted: 2022-08-10
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Kai
author list: Agent
  family name: He
  given name: Jinjin
author list: Agent
  family name: Zhao
  given name: Ningbo
author list: Agent
  family name: Zhao
  given name: Yajing
author list: Agent
  family name: Qi
  given name: Fangbing
author list: Agent
  family name: Fan
  given name: Fenggui
author list: Agent
  family name: Wang
  given name: Yingjuan
doi: 10.7717/peerj.13978
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Gender dimorphic M1 excitability during emotional processing: a transcranial magnetic stimulation study
type: item
type: AcademicArticle
description: Background It is widely held that emotions prime the body for action. However, the influence of gender on primary motor cortex (M1) excitability during emotional processing is not well explored. Methods Using single-pulse transcranial magnetic stimulation (TMS), we stimulated the right or left M1 at 150 ms and 300 ms after emotional stimulation onset (presentation of negative, neutral, and positive pictures to male and female subjects). Motor-evoked potentials (MEPs) ratio induced by single-pulse TMS was used to assess changes in corticospinal excitability. Results In response to right M1 stimulation, males demonstrated higher MEP ratios following presentation of negative pictures at 150 ms while MEP ratios in response to presentation of positive pictures were greater at 300 ms. Furthermore, male subjects showed larger MEP ratios in right M1 versus left M1 at 300 ms after initiation of positive pictures, indicating lateralization of motor excitability in male subjects. Conclusions The current study thus provides neurophysiological evidence to support gender differences and functional lateralization of motor excitability in response to emotional stimuli.
format: application/pdf
format: text/html
creator: Fanghui Qiu
creator: Yu Zhou
creator: Lanlan Zhang
creator: Jian Zhang
creator: Hui Liu
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13987
publisher: PeerJ Inc.
rights: © 2022 Qiu et al.
abstract: Background It is widely held that emotions prime the body for action. However, the influence of gender on primary motor cortex (M1) excitability during emotional processing is not well explored. Methods Using single-pulse transcranial magnetic stimulation (TMS), we stimulated the right or left M1 at 150 ms and 300 ms after emotional stimulation onset (presentation of negative, neutral, and positive pictures to male and female subjects). Motor-evoked potentials (MEPs) ratio induced by single-pulse TMS was used to assess changes in corticospinal excitability. Results In response to right M1 stimulation, males demonstrated higher MEP ratios following presentation of negative pictures at 150 ms while MEP ratios in response to presentation of positive pictures were greater at 300 ms. Furthermore, male subjects showed larger MEP ratios in right M1 versus left M1 at 300 ms after initiation of positive pictures, indicating lateralization of motor excitability in male subjects. Conclusions The current study thus provides neurophysiological evidence to support gender differences and functional lateralization of motor excitability in response to emotional stimuli.
bibliographic citation: Qiu et al. (2022) Gender dimorphic M1 excitability during emotional processing: a transcranial magnetic stimulation study. PeerJ 10:e13987 https://doi.org/10.7717/peerj.13987
date submitted: 2022-04-29
date accepted: 2022-08-11
issued: 2022-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiu
  given name: Fanghui
author list: Agent
  family name: Zhou
  given name: Yu
author list: Agent
  family name: Zhang
  given name: Lanlan
author list: Agent
  family name: Zhang
  given name: Jian
author list: Agent
  family name: Liu
  given name: Hui
doi: 10.7717/peerj.13987
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-30
copyright: ©2022 Qiu et al.
attribution name: Qiu et al.

Evolution of Helicobacter spp: variability of virulence factors and their relationship to pathogenicity
type: item
type: AcademicArticle
description: Background Virulence factors (VF) are bacteria-associated molecules that assist to colonize the host at the cellular level. Bacterial virulence is highly dynamic and specific pathogens have a broad array of VFs. The genus Helicobacter is gram-negative, microaerobic, flagellated, and mucus-inhabiting bacteria associated with gastrointestinal inflammation. To investigate about their pathogenicity, several Helicobacter species have been characterized and sequenced. Since the variability and possible origin of VF in the genus are not clear, our goal was to perform a comparative analysis of Helicobacter species in order to investigate VF variability and their evolutionary origin. Methods The complete genomes of 22 Helicobacter species available in NCBI were analyzed, using computational tools. We identifyed gain and loss events in VF genes, which were categorized in seven functional groups to determine their most parsimonious evolutionary origin. After verifying the annotation of all VF genes, a phylogeny from conserved VF organized by Helicobacter species according to gastric Helicobacter species (GHS) or enterohepatic (EHS) classification was obtained. Results Gain and loss analysis of VF orthologous in Helicobacter ssp revealed the most possible evolutionary origin for each gene set. Microevolutionary events in urease and flagella genes were detected during the evolution of the genus. Our results pointed that acquisition of ureases and adherence genes and deletion of cytotoxins in some lineages, as well as variation in VF genes copy number, would be related to host adaptation during evolution of the Helicobacter genus. Our findings provided new insights about the genetic differences between GHS and EHS and their relationship with pathogenicity.
format: application/pdf
format: text/html
creator: Carlos F. Prada
creator: Maria A. Casadiego
creator: Caio CM Freire
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.13120
publisher: PeerJ Inc.
rights: © 2022 Prada et al.
abstract: Background Virulence factors (VF) are bacteria-associated molecules that assist to colonize the host at the cellular level. Bacterial virulence is highly dynamic and specific pathogens have a broad array of VFs. The genus Helicobacter is gram-negative, microaerobic, flagellated, and mucus-inhabiting bacteria associated with gastrointestinal inflammation. To investigate about their pathogenicity, several Helicobacter species have been characterized and sequenced. Since the variability and possible origin of VF in the genus are not clear, our goal was to perform a comparative analysis of Helicobacter species in order to investigate VF variability and their evolutionary origin. Methods The complete genomes of 22 Helicobacter species available in NCBI were analyzed, using computational tools. We identifyed gain and loss events in VF genes, which were categorized in seven functional groups to determine their most parsimonious evolutionary origin. After verifying the annotation of all VF genes, a phylogeny from conserved VF organized by Helicobacter species according to gastric Helicobacter species (GHS) or enterohepatic (EHS) classification was obtained. Results Gain and loss analysis of VF orthologous in Helicobacter ssp revealed the most possible evolutionary origin for each gene set. Microevolutionary events in urease and flagella genes were detected during the evolution of the genus. Our results pointed that acquisition of ureases and adherence genes and deletion of cytotoxins in some lineages, as well as variation in VF genes copy number, would be related to host adaptation during evolution of the Helicobacter genus. Our findings provided new insights about the genetic differences between GHS and EHS and their relationship with pathogenicity.
bibliographic citation: Prada et al. (2022) Evolution of Helicobacter spp: variability of virulence factors and their relationship to pathogenicity. PeerJ 10:e13120 https://doi.org/10.7717/peerj.13120
date submitted: 2021-09-16
date accepted: 2022-02-24
issued: 2022-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prada
  given name: Carlos F.
author list: Agent
  family name: Casadiego
  given name: Maria A.
author list: Agent
  family name: Freire
  given name: Caio CM
doi: 10.7717/peerj.13120
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-29
copyright: © 2022 Prada et al.
attribution name: Prada et al.

https://peerj.com/articles/13767
type: item
type: AcademicArticle
title: Accelerating the discovery of rare tree species in Amazonian forests: integrating long monitoring tree plot data with metabolomics and phylogenetics for the description of a new species in the hyperdiverse genus Inga Mill
description: In species-rich regions and highly speciose genera, the need for species identification and taxonomic recognition has led to the development of emergent technologies. Here, we combine long-term plot data with untargated metabolomics, and morphological and phylogenetic data to describe a new rare species in the hyperdiverse genus of trees Inga Mill. Our combined data show that Inga coleyana is a new lineage splitting from their closest relatives I. coruscans and I. cylindrica. Moreover, analyses of the chemical defensive profile demonstrate that I. coleyana has a very distinctive chemistry from their closest relatives, with I. coleyana having a chemistry based on saponins and I. cylindrica and I. coruscans producing a series of dihydroflavonols in addition to saponins. Finally, data from our network of plots suggest that I. coleyana is a rare and probably endemic taxon in the hyper-diverse genus Inga. Thus, the synergy produced by different approaches, such as long-term plot data and metabolomics, could accelerate taxonomic recognition in challenging tropical biomes.
format: application/pdf
format: text/html
creator: Juan Ernesto Guevara Andino
creator: Consuelo Hernández
creator: Renato Valencia
creator: Dale Forrister
creator: María-José Endara
subject: Biodiversity
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.13767
publisher: PeerJ Inc.
rights: © 2022 Guevara Andino et al.
abstract: In species-rich regions and highly speciose genera, the need for species identification and taxonomic recognition has led to the development of emergent technologies. Here, we combine long-term plot data with untargated metabolomics, and morphological and phylogenetic data to describe a new rare species in the hyperdiverse genus of trees Inga Mill. Our combined data show that Inga coleyana is a new lineage splitting from their closest relatives I. coruscans and I. cylindrica. Moreover, analyses of the chemical defensive profile demonstrate that I. coleyana has a very distinctive chemistry from their closest relatives, with I. coleyana having a chemistry based on saponins and I. cylindrica and I. coruscans producing a series of dihydroflavonols in addition to saponins. Finally, data from our network of plots suggest that I. coleyana is a rare and probably endemic taxon in the hyper-diverse genus Inga. Thus, the synergy produced by different approaches, such as long-term plot data and metabolomics, could accelerate taxonomic recognition in challenging tropical biomes.
bibliographic citation: Guevara Andino et al. (2022) Accelerating the discovery of rare tree species in Amazonian forests: integrating long monitoring tree plot data with metabolomics and phylogenetics for the description of a new species in the hyperdiverse genus Inga Mill. PeerJ 10:e13767 https://doi.org/10.7717/peerj.13767
date submitted: 2022-03-24
date accepted: 2022-06-30
issued: 2022-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guevara Andino
  given name: Juan Ernesto
author list: Agent
  family name: Hernández
  given name: Consuelo
author list: Agent
  family name: Valencia
  given name: Renato
author list: Agent
  family name: Forrister
  given name: Dale
author list: Agent
  family name: Endara
  given name: María-José
doi: 10.7717/peerj.13767
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-29
copyright: ©2022 Guevara Andino et al.
attribution name: Guevara Andino et al.

Genetic structure of the small yellow croaker (Larimichthys polyactis) across the Yellow Sea and the East China Sea by microsatellite DNA variation: implications for the division of management units
type: item
type: AcademicArticle
description: The small yellow croaker, Larimichthys polyactis, is a commercial fish of the order Perciformes that mainly inhabit estuaries and coastal waters.In recent years, the resources and catch of L. polyactis have undergone huge fluctuations. To detect genetic variations caused by the fluctuation of resources, genetic diversity of L. polyactis in the coastal waters of China were analyzed in this study using microsatellite DNA marker. The results revealed high genetic diversity of this species. The STRUCTURE, DAPC and FST results all indicated that there was no genetic structure consistent with the distribution pattern. Overall, our main findings are in agreement with previous studies, indicating that L. polyactis showed high genetic diversity and low genetic differentiation. Our results for high genetic connectivity among L. polyactis localities provide insights into the development of management strategies, that is, to manage this species as a single management unit.
format: application/pdf
format: text/html
creator: Jian Zheng
creator: Yunrong Yan
creator: Zhonglu Li
creator: Na Song
subject: Biogeography
subject: Conservation Biology
subject: Genetics
description: doi:10.7717/peerj.13789
publisher: PeerJ Inc.
rights: © 2022 Zheng et al.
abstract: The small yellow croaker, Larimichthys polyactis, is a commercial fish of the order Perciformes that mainly inhabit estuaries and coastal waters.In recent years, the resources and catch of L. polyactis have undergone huge fluctuations. To detect genetic variations caused by the fluctuation of resources, genetic diversity of L. polyactis in the coastal waters of China were analyzed in this study using microsatellite DNA marker. The results revealed high genetic diversity of this species. The STRUCTURE, DAPC and FST results all indicated that there was no genetic structure consistent with the distribution pattern. Overall, our main findings are in agreement with previous studies, indicating that L. polyactis showed high genetic diversity and low genetic differentiation. Our results for high genetic connectivity among L. polyactis localities provide insights into the development of management strategies, that is, to manage this species as a single management unit.
bibliographic citation: Zheng et al. (2022) Genetic structure of the small yellow croaker (Larimichthys polyactis) across the Yellow Sea and the East China Sea by microsatellite DNA variation: implications for the division of management units. PeerJ 10:e13789 https://doi.org/10.7717/peerj.13789
date submitted: 2021-10-13
date accepted: 2022-07-05
issued: 2022-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Jian
author list: Agent
  family name: Yan
  given name: Yunrong
author list: Agent
  family name: Li
  given name: Zhonglu
author list: Agent
  family name: Song
  given name: Na
doi: 10.7717/peerj.13789
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-29
copyright: ©2022 Zheng et al.
attribution name: Zheng et al.

TRIM38 protects H9c2 cells from hypoxia/reoxygenation injury via the TRAF6/TAK1/NF-κB signalling pathway
type: item
type: AcademicArticle
description: Tripartite motif (TRIM) 38 is a ubiquitin E3 protein ligase that is involved in various intracellular physiological processes. However, the role of TRIM38 in myocardial ischaemia/reperfusion (I/R) injury remains to be elucidated. We aimed to establish an in vitro cellular hypoxia/reperfusion (H/R) model to explore the role and potential mechanisms of TRIM38 in H9c2, a rat cardiomyoblast cell line. Recombinant adenoviruses for silencing or overexpressing TRIM38 were constructed and transfected into H9c2 cells. Western blotanalysisshowed that TRIM38 expression was significantly decreased after H/R injury. Functionally, TRIM38 expression relieved inflammatory responses and oxidative stress, and inhibited H/R-induced apoptosis in H9c2 cells. Mechanistically, TRIM38 overexpression inhibited H/R-induced transforming growth factor beta-activated kinase 1 (TAK1)/nuclear factor-kappa B (NF-κB) pathway activity in H9c2 cells. The opposite results were observed after TRIM38 knockdown. Furthermore, H/R-induced injury aggravated by TRIM38 deficiency in H9c2 cells was reversed upon treatment with 5Z-7-oxozeaenol, a TAK1 inhibitor. Therefore, TRIM38 reduction attenuated the anti-apoptotic capacity and anti-inflammatory potential of H/R-stimulated H9c2 cells by activating the TAK1/NF-κB signalling pathway. Specifically, TRIM38 alleviated H/R-induced H9c2 cell injury by promoting TNF receptor-associated factor 6 degradation, which led to the inactivation of the TAK1/NF-κB signalling pathway. Thus, our study provides new insights into the molecular mechanisms underlying H/R-induced myocardial injuries.
format: application/pdf
format: text/html
creator: Zhengri Lu
creator: Mengen Deng
creator: Genshan Ma
creator: Lijuan Chen
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13815
publisher: PeerJ Inc.
rights: © 2022 Lu et al.
abstract: Tripartite motif (TRIM) 38 is a ubiquitin E3 protein ligase that is involved in various intracellular physiological processes. However, the role of TRIM38 in myocardial ischaemia/reperfusion (I/R) injury remains to be elucidated. We aimed to establish an in vitro cellular hypoxia/reperfusion (H/R) model to explore the role and potential mechanisms of TRIM38 in H9c2, a rat cardiomyoblast cell line. Recombinant adenoviruses for silencing or overexpressing TRIM38 were constructed and transfected into H9c2 cells. Western blotanalysisshowed that TRIM38 expression was significantly decreased after H/R injury. Functionally, TRIM38 expression relieved inflammatory responses and oxidative stress, and inhibited H/R-induced apoptosis in H9c2 cells. Mechanistically, TRIM38 overexpression inhibited H/R-induced transforming growth factor beta-activated kinase 1 (TAK1)/nuclear factor-kappa B (NF-κB) pathway activity in H9c2 cells. The opposite results were observed after TRIM38 knockdown. Furthermore, H/R-induced injury aggravated by TRIM38 deficiency in H9c2 cells was reversed upon treatment with 5Z-7-oxozeaenol, a TAK1 inhibitor. Therefore, TRIM38 reduction attenuated the anti-apoptotic capacity and anti-inflammatory potential of H/R-stimulated H9c2 cells by activating the TAK1/NF-κB signalling pathway. Specifically, TRIM38 alleviated H/R-induced H9c2 cell injury by promoting TNF receptor-associated factor 6 degradation, which led to the inactivation of the TAK1/NF-κB signalling pathway. Thus, our study provides new insights into the molecular mechanisms underlying H/R-induced myocardial injuries.
bibliographic citation: Lu et al. (2022) TRIM38 protects H9c2 cells from hypoxia/reoxygenation injury via the TRAF6/TAK1/NF-κB signalling pathway. PeerJ 10:e13815 https://doi.org/10.7717/peerj.13815
date submitted: 2022-03-14
date accepted: 2022-07-08
issued: 2022-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Zhengri
author list: Agent
  family name: Deng
  given name: Mengen
author list: Agent
  family name: Ma
  given name: Genshan
author list: Agent
  family name: Chen
  given name: Lijuan
doi: 10.7717/peerj.13815
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-29
copyright: ©2022 Lu et al.
attribution name: Lu et al.

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