PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exploring the influence of self-identification on perceptual judgments of physical and social causality
items: Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum
items: PTX3 mediates PI3K/AKT/mTOR signaling to downregulate apoptosis and autophagy to attenuate myocardial injury in sepsis
items: Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil
items: Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex
items: A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026
items: Identification of YUC genes associated with leaf wrinkling trait in Tacai variety of Chinese cabbage
items: Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis
items: Machine learning approaches to debris flow susceptibility analyses in the Yunnan section of the Nujiang River Basin
items: Terrestrial wildlife as indicators of microplastic pollution in western Thailand

Exploring the influence of self-identification on perceptual judgments of physical and social causality
type: item
type: AcademicArticle
description: People tend to overestimate the causal contribution of the self to the observed outcome in various situations, a cognitive bias known as the ‘illusion of control.’ This study delves into whether this cognitive bias impacts causality judgments in animations depicting physical and social causal interactions. In two experiments, participants were instructed to associate themselves and a hypothetical stranger identity with two geometrical shapes (a circle and a square). Subsequently, they viewed animations portraying these shapes assuming the roles of agent and patient in causal interactions. Within one block, the shape related to the self served as the agent, while the shape associated with the stranger played the role of the patient. Conversely, in the other block, the identity-role association was reversed. We posited that the perception of the self as a causal agent might influence explicit judgments of physical and social causality. Experiment 1 demonstrated that physical causality ratings were solely shaped by kinematic cues. In Experiment 2, emphasising social causality, the dominance of kinematic parameters was confirmed. Therefore, contrary to the hypothesis anticipating diminished causality ratings with specific identity-role associations, results indicated negligible impact of our manipulation. The study contributes to understanding the interplay between kinematic and non-kinematic cues in human causal reasoning. It suggests that explicit judgments of causality in simple animations primarily rely on low-level kinematic cues, with the cognitive bias of overestimating the self’s contribution playing a negligible role.
format: application/pdf
format: text/html
creator: Michele Vicovaro
creator: Francesca Squadrelli Saraceno
creator: Mario Dalmaso
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.17449
publisher: PeerJ Inc.
rights: © 2024 Vicovaro et al.
abstract: People tend to overestimate the causal contribution of the self to the observed outcome in various situations, a cognitive bias known as the ‘illusion of control.’ This study delves into whether this cognitive bias impacts causality judgments in animations depicting physical and social causal interactions. In two experiments, participants were instructed to associate themselves and a hypothetical stranger identity with two geometrical shapes (a circle and a square). Subsequently, they viewed animations portraying these shapes assuming the roles of agent and patient in causal interactions. Within one block, the shape related to the self served as the agent, while the shape associated with the stranger played the role of the patient. Conversely, in the other block, the identity-role association was reversed. We posited that the perception of the self as a causal agent might influence explicit judgments of physical and social causality. Experiment 1 demonstrated that physical causality ratings were solely shaped by kinematic cues. In Experiment 2, emphasising social causality, the dominance of kinematic parameters was confirmed. Therefore, contrary to the hypothesis anticipating diminished causality ratings with specific identity-role associations, results indicated negligible impact of our manipulation. The study contributes to understanding the interplay between kinematic and non-kinematic cues in human causal reasoning. It suggests that explicit judgments of causality in simple animations primarily rely on low-level kinematic cues, with the cognitive bias of overestimating the self’s contribution playing a negligible role.
bibliographic citation: Vicovaro et al. (2024) Exploring the influence of self-identification on perceptual judgments of physical and social causality. PeerJ 12:e17449 https://doi.org/10.7717/peerj.17449
date submitted: 2024-02-14
date accepted: 2024-05-02
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vicovaro
  given name: Michele
author list: Agent
  family name: Squadrelli Saraceno
  given name: Francesca
author list: Agent
  family name: Dalmaso
  given name: Mario
doi: 10.7717/peerj.17449
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: © 2024 Vicovaro et al.
attribution name: Vicovaro et al.

Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum
type: item
type: AcademicArticle
description: Background Condyloma acuminatum (CA) is caused by low-risk human papillomavirus, and is characterized by high recurrence after treatment. The RNA modification N6-methyladenosine (m6A) plays an important role during diverse viral infections, including high-risk HPV infection in cervical cancer. However, it is unclear whether low-risk HPV infection changes the RNA m6A methylation in CA. Methods High-throughputm6A-sequencing was performed to profile the transcriptome-wide mRNA modifications of CA tissues infected by LR-HPVs and the paired normal tissues from CA patients. We further investigated the regulation of alternative splicing by RNA binding proteins (RBPs) with altered m6A modification and constructed a regulatory network among these RBPs, regulated alternative splicing events (RASEs) and regulated alternative splicing genes (RASGs) in CA. Results The results show that the m6A level in CA tissues differed from that in the paired controls. Furthermore, cell cycle- and cell adhesion- associated genes with m6A modification were differentially expressed in CA tissues compared to the paired controls. In particular, seven RNA binding protein genes with specific m6A methylated sites, showed a higher or lower expression at the mRNA level in CA tissues than in the paired normal tissues. In addition, these differentially expressed RNA binding protein genes would regulate the alternative splicing pattern of apoptotic process genes in CA tissue. Conclusions Our study reveals a sophisticated m6A modification profile in CA tissue that affects the response of host cells to HPV infection, and provides cues for the further exploration of the roles of m6A and the development of a novel treatment strategy for CA.
format: application/pdf
format: text/html
creator: Xiaoyan Liu
creator: Bo Xie
creator: Su Wang
creator: Yinhua Wu
creator: Yu Zhang
creator: Liming Ruan
subject: Molecular Biology
subject: Dermatology
subject: Infectious Diseases
subject: Women’s Health
description: doi:10.7717/peerj.17376
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Background Condyloma acuminatum (CA) is caused by low-risk human papillomavirus, and is characterized by high recurrence after treatment. The RNA modification N6-methyladenosine (m6A) plays an important role during diverse viral infections, including high-risk HPV infection in cervical cancer. However, it is unclear whether low-risk HPV infection changes the RNA m6A methylation in CA. Methods High-throughputm6A-sequencing was performed to profile the transcriptome-wide mRNA modifications of CA tissues infected by LR-HPVs and the paired normal tissues from CA patients. We further investigated the regulation of alternative splicing by RNA binding proteins (RBPs) with altered m6A modification and constructed a regulatory network among these RBPs, regulated alternative splicing events (RASEs) and regulated alternative splicing genes (RASGs) in CA. Results The results show that the m6A level in CA tissues differed from that in the paired controls. Furthermore, cell cycle- and cell adhesion- associated genes with m6A modification were differentially expressed in CA tissues compared to the paired controls. In particular, seven RNA binding protein genes with specific m6A methylated sites, showed a higher or lower expression at the mRNA level in CA tissues than in the paired normal tissues. In addition, these differentially expressed RNA binding protein genes would regulate the alternative splicing pattern of apoptotic process genes in CA tissue. Conclusions Our study reveals a sophisticated m6A modification profile in CA tissue that affects the response of host cells to HPV infection, and provides cues for the further exploration of the roles of m6A and the development of a novel treatment strategy for CA.
bibliographic citation: Liu et al. (2024) Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum. PeerJ 12:e17376 https://doi.org/10.7717/peerj.17376
date submitted: 2023-12-26
date accepted: 2024-04-19
issued: 2024-05-20
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: Xie
  given name: Bo
author list: Agent
  family name: Wang
  given name: Su
author list: Agent
  family name: Wu
  given name: Yinhua
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Ruan
  given name: Liming
doi: 10.7717/peerj.17376
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: ©2024 Liu et al.
attribution name: Liu et al.

PTX3 mediates PI3K/AKT/mTOR signaling to downregulate apoptosis and autophagy to attenuate myocardial injury in sepsis
type: item
type: AcademicArticle
description: Background This study aimed to investigate the effect and mechanism of Pentraxin 3 (PTX3) on myocardial injury in sepsis. Methods Thirty male C57BL/6 mice were randomly assigned to Groups A, B, or C. Mice in Groups A and B were injected with unloaded lentivirus, while mice in Group C were injected with lentivirus encoding PTX3 overexpression. Seven days after injection, septic myocardial injury mouse models were constructed following intraperitoneal injection with LPS in Groups B and C, and mice in Group A were intraperitoneally injected with normal saline. Cardiac function was examined using echocardiography; pathological variation of myocardial cells was measured through HE staining, transmission electron microscopy, and TUNEL staining; and Western blot was used to measure the expression of PI3K/AKT/mTOR pathway-related, autophagy-related, and apoptosis-related proteins in mice myocardial cells. Results PTX3 significantly improved cardiac function and structure in sepsis-stricken mice, and PTX3 alleviated cardiac damage caused by sepsis. PTX3 reduced the relative protein expression of p-PI3K, p-AKT, mTOR, LC3I/II, Beclin, ATG5, Bax, Caspase-3, and Caspase-9 in septic mouse cardiomyocytes and increased the relative protein expression of Bcl-2. Conclusion PTX3 can attenuate myocardial injury in sepsis due to the down-regulation of apoptosis and autophagy induced by the PI3K/AKT/mTOR pathway.
format: application/pdf
format: text/html
creator: Na Cui
creator: Zhi Chen
creator: Zhanbiao Yu
creator: Xiaowei Lv
creator: Zhenjie Hu
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.17263
publisher: PeerJ Inc.
rights: © 2024 Cui et al.
abstract: Background This study aimed to investigate the effect and mechanism of Pentraxin 3 (PTX3) on myocardial injury in sepsis. Methods Thirty male C57BL/6 mice were randomly assigned to Groups A, B, or C. Mice in Groups A and B were injected with unloaded lentivirus, while mice in Group C were injected with lentivirus encoding PTX3 overexpression. Seven days after injection, septic myocardial injury mouse models were constructed following intraperitoneal injection with LPS in Groups B and C, and mice in Group A were intraperitoneally injected with normal saline. Cardiac function was examined using echocardiography; pathological variation of myocardial cells was measured through HE staining, transmission electron microscopy, and TUNEL staining; and Western blot was used to measure the expression of PI3K/AKT/mTOR pathway-related, autophagy-related, and apoptosis-related proteins in mice myocardial cells. Results PTX3 significantly improved cardiac function and structure in sepsis-stricken mice, and PTX3 alleviated cardiac damage caused by sepsis. PTX3 reduced the relative protein expression of p-PI3K, p-AKT, mTOR, LC3I/II, Beclin, ATG5, Bax, Caspase-3, and Caspase-9 in septic mouse cardiomyocytes and increased the relative protein expression of Bcl-2. Conclusion PTX3 can attenuate myocardial injury in sepsis due to the down-regulation of apoptosis and autophagy induced by the PI3K/AKT/mTOR pathway.
bibliographic citation: Cui et al. (2024) PTX3 mediates PI3K/AKT/mTOR signaling to downregulate apoptosis and autophagy to attenuate myocardial injury in sepsis. PeerJ 12:e17263 https://doi.org/10.7717/peerj.17263
date submitted: 2023-10-13
date accepted: 2024-03-28
issued: 2024-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Na
author list: Agent
  family name: Chen
  given name: Zhi
author list: Agent
  family name: Yu
  given name: Zhanbiao
author list: Agent
  family name: Lv
  given name: Xiaowei
author list: Agent
  family name: Hu
  given name: Zhenjie
doi: 10.7717/peerj.17263
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: © 2024 Cui et al.
attribution name: Cui et al.

Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil
type: item
type: AcademicArticle
description: Background Salmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil’s relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses. Methods Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Results wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to bi…
format: application/pdf
format: text/html
creator: Felipe P. Vilela
creator: Andrei G. Felice
creator: Amanda A. Seribelli
creator: Dália P. Rodrigues
creator: Siomar C. Soares
creator: Marc W. Allard
creator: Juliana P. Falcão
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.17306
publisher: PeerJ Inc.
rights: © 2024 Vilela et al.
abstract: Background Salmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil’s relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses. Methods Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Results wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to bi…
bibliographic citation: Vilela et al. (2024) Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil. PeerJ 12:e17306 https://doi.org/10.7717/peerj.17306
date submitted: 2023-06-02
date accepted: 2024-04-04
issued: 2024-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vilela
  given name: Felipe P.
author list: Agent
  family name: Felice
  given name: Andrei G.
author list: Agent
  family name: Seribelli
  given name: Amanda A.
author list: Agent
  family name: Rodrigues
  given name: Dália P.
author list: Agent
  family name: Soares
  given name: Siomar C.
author list: Agent
  family name: Allard
  given name: Marc W.
author list: Agent
  family name: Falcão
  given name: Juliana P.
doi: 10.7717/peerj.17306
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: ©2024 Vilela et al.
attribution name: Vilela et al.

Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex
type: item
type: AcademicArticle
description: Anthropogenic climate change and the associated increase in sea temperatures are projected to greatly impact marine ecosystems. Temperature variation can influence the interactions between species, leading to cascading effects on the abundance, diversity and composition of communities. Such changes in community structure can have consequences on ecosystem stability, processes and the services it provides. Therefore, it is important to better understand the role of species interactions in the development of communities and how they are influenced by environmental factors like temperature. The coexistence of closely related cryptic species, with significant biological and ecological differences, makes this even more complex. This study investigated the effect of temperature on species growth and both intra- and interspecific interactions of three species within the free-living nematode Litoditis marina complex. To achieve this, closed microcosm experiments were conducted on the L. marina species Pm I, Pm III and Pm IV in monoculture and combined cultures at two temperature treatments of 15 °C and 20 °C. A population model was constructed to elucidate and quantify the effects of intra- and interspecific interactions on nematode populations. The relative competitive abilities of the investigated species were quantified using the Modern Coexistence Theory (MCT) framework. Temperature had strong and disparate effects on the population growth of the distinct L. marina species. This indicates temperature could play an important role in the distribution of these cryptic species. Both competitive and facilitative interactions were observed in the experiments. Temperature affected both the type and the strength of the species interactions, suggesting a change in temperature could impact the coexistence of these closely related species, alter community dynamics and consequently affect ecosystem processes and services.
format: application/pdf
format: text/html
creator: Anna-Maria Vafeiadou
creator: Kevin Geldhof
creator: Wissam Barhdadi
creator: Jan M. Baetens
creator: Bernard De Baets
creator: Tom Moens
creator: Aisling J. Daly
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Climate Change Biology
subject: Population Biology
description: doi:10.7717/peerj.17324
publisher: PeerJ Inc.
rights: © 2024 Vafeiadou et al.
abstract: Anthropogenic climate change and the associated increase in sea temperatures are projected to greatly impact marine ecosystems. Temperature variation can influence the interactions between species, leading to cascading effects on the abundance, diversity and composition of communities. Such changes in community structure can have consequences on ecosystem stability, processes and the services it provides. Therefore, it is important to better understand the role of species interactions in the development of communities and how they are influenced by environmental factors like temperature. The coexistence of closely related cryptic species, with significant biological and ecological differences, makes this even more complex. This study investigated the effect of temperature on species growth and both intra- and interspecific interactions of three species within the free-living nematode Litoditis marina complex. To achieve this, closed microcosm experiments were conducted on the L. marina species Pm I, Pm III and Pm IV in monoculture and combined cultures at two temperature treatments of 15 °C and 20 °C. A population model was constructed to elucidate and quantify the effects of intra- and interspecific interactions on nematode populations. The relative competitive abilities of the investigated species were quantified using the Modern Coexistence Theory (MCT) framework. Temperature had strong and disparate effects on the population growth of the distinct L. marina species. This indicates temperature could play an important role in the distribution of these cryptic species. Both competitive and facilitative interactions were observed in the experiments. Temperature affected both the type and the strength of the species interactions, suggesting a change in temperature could impact the coexistence of these closely related species, alter community dynamics and consequently affect ecosystem processes and services.
bibliographic citation: Vafeiadou et al. (2024) Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex. PeerJ 12:e17324 https://doi.org/10.7717/peerj.17324
date submitted: 2024-02-09
date accepted: 2024-04-10
issued: 2024-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vafeiadou
  given name: Anna-Maria
author list: Agent
  family name: Geldhof
  given name: Kevin
author list: Agent
  family name: Barhdadi
  given name: Wissam
author list: Agent
  family name: Baetens
  given name: Jan M.
author list: Agent
  family name: De Baets
  given name: Bernard
author list: Agent
  family name: Moens
  given name: Tom
author list: Agent
  family name: Daly
  given name: Aisling J.
doi: 10.7717/peerj.17324
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: ©2024 Vafeiadou et al.
attribution name: Vafeiadou et al.

A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026
type: item
type: AcademicArticle
description: Background Urinary tract infections (UTIs) are very common worldwide. According to their symptomatology, these infections are classified as pyelonephritis, cystitis, or asymptomatic bacteriuria (AB). Approximately 75–95% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which is an extraintestinal bacterium that possesses virulence factors for bacterial adherence and invasion in the urinary tract. In addition, UPEC possesses type 6 secretion systems (T6SS) as virulence mechanisms that can participate in bacterial competition and in bacterial pathogenicity. UPEC UMN026 carries three genes, namely, ECUMN_0231, ECUMN_0232, and ECUMN_0233, which encode three uncharacterized proteins related to the T6SS that are conserved in strains from phylogroups B2 and D and have been proposed as biomarkers of UTIs. Aim To analyze the frequency of the ECUMN_0231, ECUMN_0232, ECUMN_0233, and vgrG genes in UTI isolates, as well as their expression in Luria Bertani (LB) medium and urine; to determine whether these genes are related to UTI symptoms or bacterial competence and to identify functional domains on the putative proteins. Methods The frequency of the ECUMN and vgrG genes in 99 clinical isolates from UPEC was determined by endpoint PCR. The relationship between gene presence and UTI symptomatology was determined using the chi2 test, with p < 0.05 considered to indicate statistical significance. The expression of the three ECUMN genes and vgrG was analyzed by RT-PCR. The antibacterial activity of strain UMN026 was determined by bacterial competence assays. The identification of functional domains and the docking were performed using bioinformatic tools. Results The ECUMN genes are conserved in 33.3% of clinical isolates from patients with symptomatic and asymptomatic UTIs and have no relationship with UTI symptomatology. Of the ECUMN+ isolates, only five (15.15%, 5/33) had the three ECUMN and vgrG genes. These genes were expressed in LB broth and urine in UPEC UMN026 b…
format: application/pdf
format: text/html
creator: América Casiano González
creator: Arantxa Pacheco Villanueva
creator: Natividad Castro-Alarcón
creator: Julio Méndez
creator: Ricardo Oropeza
creator: Verónica I. Martínez-Santos
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.17336
publisher: PeerJ Inc.
rights: © 2024 Casiano González et al.
abstract: Background Urinary tract infections (UTIs) are very common worldwide. According to their symptomatology, these infections are classified as pyelonephritis, cystitis, or asymptomatic bacteriuria (AB). Approximately 75–95% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which is an extraintestinal bacterium that possesses virulence factors for bacterial adherence and invasion in the urinary tract. In addition, UPEC possesses type 6 secretion systems (T6SS) as virulence mechanisms that can participate in bacterial competition and in bacterial pathogenicity. UPEC UMN026 carries three genes, namely, ECUMN_0231, ECUMN_0232, and ECUMN_0233, which encode three uncharacterized proteins related to the T6SS that are conserved in strains from phylogroups B2 and D and have been proposed as biomarkers of UTIs. Aim To analyze the frequency of the ECUMN_0231, ECUMN_0232, ECUMN_0233, and vgrG genes in UTI isolates, as well as their expression in Luria Bertani (LB) medium and urine; to determine whether these genes are related to UTI symptoms or bacterial competence and to identify functional domains on the putative proteins. Methods The frequency of the ECUMN and vgrG genes in 99 clinical isolates from UPEC was determined by endpoint PCR. The relationship between gene presence and UTI symptomatology was determined using the chi2 test, with p < 0.05 considered to indicate statistical significance. The expression of the three ECUMN genes and vgrG was analyzed by RT-PCR. The antibacterial activity of strain UMN026 was determined by bacterial competence assays. The identification of functional domains and the docking were performed using bioinformatic tools. Results The ECUMN genes are conserved in 33.3% of clinical isolates from patients with symptomatic and asymptomatic UTIs and have no relationship with UTI symptomatology. Of the ECUMN+ isolates, only five (15.15%, 5/33) had the three ECUMN and vgrG genes. These genes were expressed in LB broth and urine in UPEC UMN026 b…
bibliographic citation: Casiano González et al. (2024) A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026. PeerJ 12:e17336 https://doi.org/10.7717/peerj.17336
date submitted: 2023-12-18
date accepted: 2024-04-15
issued: 2024-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Casiano González
  given name: América
author list: Agent
  family name: Pacheco Villanueva
  given name: Arantxa
author list: Agent
  family name: Castro-Alarcón
  given name: Natividad
author list: Agent
  family name: Méndez
  given name: Julio
author list: Agent
  family name: Oropeza
  given name: Ricardo
author list: Agent
  family name: Martínez-Santos
  given name: Verónica I.
doi: 10.7717/peerj.17336
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: © 2024 Casiano González et al.
attribution name: Casiano González et al.

Identification of YUC genes associated with leaf wrinkling trait in Tacai variety of Chinese cabbage
type: item
type: AcademicArticle
description: Chinese cabbage (Brassica campestris L. ssp. chinensis (L.) Makino) stands as a widely cultivated leafy vegetable in China, with its leaf morphology significantly influencing both quality and yield. Despite its agricultural importance, the precise mechanisms governing leaf wrinkling development remain elusive. This investigation focuses on ‘Wutacai’, a representative cultivar of the Tacai variety (Brassica campestris L. ssp. chinensis var. rosularis Tsen et Lee), renowned for its distinct leaf wrinkling characteristics. Within the genome of ‘Wutacai’, we identified a total of 18 YUCs, designated as BraWTC_YUCs, revealing their conservation within the Brassica genus, and their close homology to YUCs in Arabidopsis. Expression profiling unveiled that BraWTC_YUCs in Chinese Cabbage exhibited organ-specific and leaf position-dependent variation. Additionally, transcriptome sequencing data from the flat leaf cultivar ‘Suzhouqing’ and the wrinkled leaf cultivar ‘Wutacai’ revealed differentially expressed genes (DEGs) related to auxin during the early phases of leaf development, particularly the YUC gene. In summary, this study successfully identified the YUC gene family in ‘Wutacai’ and elucidated its potential function in leaf wrinkling trait, to provide valuable insights into the prospective molecular mechanisms that regulate leaf wrinkling in Chinese cabbage.
format: application/pdf
format: text/html
creator: Xuelian Ye
creator: Ji Sun
creator: Yuan Tian
creator: Jingwen Chen
creator: Xiangtan Yao
creator: Xinhua Quan
creator: Li Huang
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.17337
publisher: PeerJ Inc.
rights: © 2024 Ye et al.
abstract: Chinese cabbage (Brassica campestris L. ssp. chinensis (L.) Makino) stands as a widely cultivated leafy vegetable in China, with its leaf morphology significantly influencing both quality and yield. Despite its agricultural importance, the precise mechanisms governing leaf wrinkling development remain elusive. This investigation focuses on ‘Wutacai’, a representative cultivar of the Tacai variety (Brassica campestris L. ssp. chinensis var. rosularis Tsen et Lee), renowned for its distinct leaf wrinkling characteristics. Within the genome of ‘Wutacai’, we identified a total of 18 YUCs, designated as BraWTC_YUCs, revealing their conservation within the Brassica genus, and their close homology to YUCs in Arabidopsis. Expression profiling unveiled that BraWTC_YUCs in Chinese Cabbage exhibited organ-specific and leaf position-dependent variation. Additionally, transcriptome sequencing data from the flat leaf cultivar ‘Suzhouqing’ and the wrinkled leaf cultivar ‘Wutacai’ revealed differentially expressed genes (DEGs) related to auxin during the early phases of leaf development, particularly the YUC gene. In summary, this study successfully identified the YUC gene family in ‘Wutacai’ and elucidated its potential function in leaf wrinkling trait, to provide valuable insights into the prospective molecular mechanisms that regulate leaf wrinkling in Chinese cabbage.
bibliographic citation: Ye et al. (2024) Identification of YUC genes associated with leaf wrinkling trait in Tacai variety of Chinese cabbage. PeerJ 12:e17337 https://doi.org/10.7717/peerj.17337
date submitted: 2023-12-19
date accepted: 2024-04-15
issued: 2024-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Xuelian
author list: Agent
  family name: Sun
  given name: Ji
author list: Agent
  family name: Tian
  given name: Yuan
author list: Agent
  family name: Chen
  given name: Jingwen
author list: Agent
  family name: Yao
  given name: Xiangtan
author list: Agent
  family name: Quan
  given name: Xinhua
author list: Agent
  family name: Huang
  given name: Li
doi: 10.7717/peerj.17337
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: © 2024 Ye et al.
attribution name: Ye et al.

Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis
type: item
type: AcademicArticle
description: Background Antibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, Nematostella vectensis. Methods Ampicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL−1, and in combination at 50 µg mL−1 each, to assess their impact on N. vectensis. First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones. Results Under most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as Microbacterium and Vibrio. The acute antibiotic exposure resulted in differe…
format: application/pdf
format: text/html
creator: Quinton Krueger
creator: Britney Phippen
creator: Adam Reitzel
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.17349
publisher: PeerJ Inc.
rights: © 2024 Krueger et al.
abstract: Background Antibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, Nematostella vectensis. Methods Ampicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL−1, and in combination at 50 µg mL−1 each, to assess their impact on N. vectensis. First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones. Results Under most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as Microbacterium and Vibrio. The acute antibiotic exposure resulted in differe…
bibliographic citation: Krueger et al. (2024) Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis. PeerJ 12:e17349 https://doi.org/10.7717/peerj.17349
date submitted: 2023-10-06
date accepted: 2024-04-17
issued: 2024-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krueger
  given name: Quinton
author list: Agent
  family name: Phippen
  given name: Britney
author list: Agent
  family name: Reitzel
  given name: Adam
doi: 10.7717/peerj.17349
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: ©2024 Krueger et al.
attribution name: Krueger et al.

Machine learning approaches to debris flow susceptibility analyses in the Yunnan section of the Nujiang River Basin
type: item
type: AcademicArticle
description: Background The Yunnan section of the Nujiang River (YNR) Basin in the alpine-valley area is one of the most critical areas of debris flow in China. Methods We analyzed the applicability of three machine learning algorithms to model of susceptibility to debris flow—Random Forest (RF), the linear kernel support vector machine (Linear SVM), and the radial basis function support vector machine (RBFSVM)—and compared 20 factors to determine the dominant controlling in debris flow occurrence in the region. Results We found that (1) RF outperformed RBFSVM and Linear SVM in terms of accuracy, (2) topographic conditions were prerequisites, and geology, precipitation, vegetation, and anthropogenic influence were critical to forming debris flows. Also, the relative elevation difference was the most prominent evaluation factor of debris flow susceptibility, and (3) susceptibility maps based on RF’s debris flow susceptibility (DFS) showed that zones with very high susceptibility were distributed along the mainstream of the Nujiang River. These findings provide methodological guidance and reference for improvement of DFS assessment. It enriches the content of DFS studies in the alpine-valley areas.
format: application/pdf
format: text/html
creator: Jingyi Zhou
creator: Jiangcheng Huang
creator: Zhengbao Sun
creator: Qi Yi
creator: Aoyang He
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.17352
publisher: PeerJ Inc.
rights: © 2024 Zhou et al.
abstract: Background The Yunnan section of the Nujiang River (YNR) Basin in the alpine-valley area is one of the most critical areas of debris flow in China. Methods We analyzed the applicability of three machine learning algorithms to model of susceptibility to debris flow—Random Forest (RF), the linear kernel support vector machine (Linear SVM), and the radial basis function support vector machine (RBFSVM)—and compared 20 factors to determine the dominant controlling in debris flow occurrence in the region. Results We found that (1) RF outperformed RBFSVM and Linear SVM in terms of accuracy, (2) topographic conditions were prerequisites, and geology, precipitation, vegetation, and anthropogenic influence were critical to forming debris flows. Also, the relative elevation difference was the most prominent evaluation factor of debris flow susceptibility, and (3) susceptibility maps based on RF’s debris flow susceptibility (DFS) showed that zones with very high susceptibility were distributed along the mainstream of the Nujiang River. These findings provide methodological guidance and reference for improvement of DFS assessment. It enriches the content of DFS studies in the alpine-valley areas.
bibliographic citation: Zhou et al. (2024) Machine learning approaches to debris flow susceptibility analyses in the Yunnan section of the Nujiang River Basin. PeerJ 12:e17352 https://doi.org/10.7717/peerj.17352
date submitted: 2023-10-06
date accepted: 2024-04-17
issued: 2024-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Jingyi
author list: Agent
  family name: Huang
  given name: Jiangcheng
author list: Agent
  family name: Sun
  given name: Zhengbao
author list: Agent
  family name: Yi
  given name: Qi
author list: Agent
  family name: He
  given name: Aoyang
doi: 10.7717/peerj.17352
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: © 2024 Zhou et al.
attribution name: Zhou et al.

Terrestrial wildlife as indicators of microplastic pollution in western Thailand
type: item
type: AcademicArticle
description: Plastic pollution in terrestrial wildlife represents a new conservation challenge, with research in this area, especially within protected areas (PAs), being scant. This study documents the accumulation of microplastics (MPs) in terrestrial wildlife both inside and outside PAs in western Thailand. Carcasses of road-killed vertebrates in good condition, as well as live tadpoles, were collected to examine their exposure to plastic pollution. The digestive tracts of the vertebrate carcasses and the entire bodies of tadpoles were analyzed for MPs, which were identified if they measured over 50 µm. A total of 136 individuals from 48 vertebrate species were examined. The sample comprised snakes (44.12%), birds (11.03%), lizards (5.15%), tadpoles (32.25%), amphibians (5.88%), and mammals (1.47%). In total, 387 MPs were found in 44 species (91.67%), with an average occurrence of 3.25 ± 3.63 MPs per individual or 0.05 ± 0.08 MPs per gram of body weight. The quantities of MPs significantly varied among the animal groups, both in terms of number per individual (p < 0.05) and number per gram of body weight (p < 0.01). Furthermore, a significant difference in MP quantities was observed between specimens collected inside and outside PAs on an individual basis (p < 0.05), but not on a body weight basis (p = 0.07). Most MPs were fibers (77%), followed by fragments (22.22%), with only a minimal presence of film (0.52%) and foam (0.26%). Of all the MPs identified, 36.84% were confirmed as plastics or fibers made from natural materials, and 31.58% were plastics, including Polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), Polyvinylidene chloride (PVDC), and polyester (PES). Additionally, fibers made of cotton, and those containing polyurethane (PU), rayon, PES, and combinations of rayon and PU, were identified. The quantities of MPs were significantly influenced by animal body weight, factors associated with human settlement/activity, and land use types. Our find…
format: application/pdf
format: text/html
creator: Jiraporn Teampanpong
creator: Prateep Duengkae
subject: Biodiversity
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.17384
publisher: PeerJ Inc.
rights: © 2024 Teampanpong and Duengkae
abstract: Plastic pollution in terrestrial wildlife represents a new conservation challenge, with research in this area, especially within protected areas (PAs), being scant. This study documents the accumulation of microplastics (MPs) in terrestrial wildlife both inside and outside PAs in western Thailand. Carcasses of road-killed vertebrates in good condition, as well as live tadpoles, were collected to examine their exposure to plastic pollution. The digestive tracts of the vertebrate carcasses and the entire bodies of tadpoles were analyzed for MPs, which were identified if they measured over 50 µm. A total of 136 individuals from 48 vertebrate species were examined. The sample comprised snakes (44.12%), birds (11.03%), lizards (5.15%), tadpoles (32.25%), amphibians (5.88%), and mammals (1.47%). In total, 387 MPs were found in 44 species (91.67%), with an average occurrence of 3.25 ± 3.63 MPs per individual or 0.05 ± 0.08 MPs per gram of body weight. The quantities of MPs significantly varied among the animal groups, both in terms of number per individual (p < 0.05) and number per gram of body weight (p < 0.01). Furthermore, a significant difference in MP quantities was observed between specimens collected inside and outside PAs on an individual basis (p < 0.05), but not on a body weight basis (p = 0.07). Most MPs were fibers (77%), followed by fragments (22.22%), with only a minimal presence of film (0.52%) and foam (0.26%). Of all the MPs identified, 36.84% were confirmed as plastics or fibers made from natural materials, and 31.58% were plastics, including Polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), Polyvinylidene chloride (PVDC), and polyester (PES). Additionally, fibers made of cotton, and those containing polyurethane (PU), rayon, PES, and combinations of rayon and PU, were identified. The quantities of MPs were significantly influenced by animal body weight, factors associated with human settlement/activity, and land use types. Our find…
bibliographic citation: Teampanpong et al. (2024) Terrestrial wildlife as indicators of microplastic pollution in western Thailand. PeerJ 12:e17384 https://doi.org/10.7717/peerj.17384
date submitted: 2024-01-03
date accepted: 2024-04-22
issued: 2024-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Teampanpong
  given name: Jiraporn
author list: Agent
  family name: Duengkae
  given name: Prateep
doi: 10.7717/peerj.17384
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: © 2024 Teampanpong and Duengkae
attribution name: Teampanpong and Duengkae

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