PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Depression and low physical activity are related to sarcopenia in hemodialysis: a single-center study
items: Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study
items: Identification of a three-gene-based prognostic model in multiple myeloma using bioinformatics analysis
items: Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum
items: Effects of biotransport and hydro-meteorological conditions on transport of trace elements in the Scott River (Bellsund, Spitsbergen)
items: Characterization of the microbiome of the invasive Asian toad in Madagascar across the expansion range and comparison with a native co-occurring species
items: Helicobacter pylori prevalence in healthy Mexican children: comparison between two non-invasive methods
items: Iron deficiency anemia among children aged 2–5 years in southern Ethiopia: a community-based cross-sectional study
items: Combination of ferulic acid, ligustrazine and tetrahydropalmatine inhibits invasion and metastasis through MMP/TIMP signaling in endometriosis
items: Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

Depression and low physical activity are related to sarcopenia in hemodialysis: a single-center study
type: item
type: AcademicArticle
description: Background The number of patients who suffer from chronic renal failure (CRF) has widely increased worldwide. Patients with advanced stages of CRF experience a gradual and progressive loss of muscle and fat mass leading to decreased physical activity and mental health problems. The loss of muscle mass in CRF might contribute to the development of sarcopenia. Therefore, this study aimed to explore the prevalence of sarcopenia and to determine the relationship of physical activity and mental state of depression with sarcopenia in hemodialysis patients. Methods A cross-sectional study was designed with a total of 104 male and female with a minimum age of 35 years. Based on the guidelines of the Asian Working Group for Sarcopenia in 2019, gait speed, muscle mass, and handgrip were used to define sarcopenia. In addition, participants were requested to perform a set of questionnaires to evaluate their physical activity and state of depression. Logistic regression analyses were used to explore the risk factors of sarcopenia. Results Thirty-four (32.69%) of 104 participants had sarcopenia. Compared to the 70 individuals without sarcopenia, they had a low physical activity and a high depression score (ps < .05). Furthermore, low physical activity and high depression scores in combination with sarcopenia were associated with an increased mortality risk. Low physical activity and high depression scores were also independently associated with sarcopenia in hemodialysis patients after controlling for age (odds ratio = 3.23, and 4.92, respectively).
format: application/pdf
format: text/html
creator: Kornanong Yuenyongchaiwat
creator: Sasikan Jongritthiporn
creator: Kasarn Somsamarn
creator: Oranat Sukkho
creator: Sasipim Pairojkittrakul
creator: Opas Traitanon
subject: Epidemiology
subject: Nephrology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11695
publisher: PeerJ Inc.
rights: © 2021 Yuenyongchaiwat et al.
abstract: Background The number of patients who suffer from chronic renal failure (CRF) has widely increased worldwide. Patients with advanced stages of CRF experience a gradual and progressive loss of muscle and fat mass leading to decreased physical activity and mental health problems. The loss of muscle mass in CRF might contribute to the development of sarcopenia. Therefore, this study aimed to explore the prevalence of sarcopenia and to determine the relationship of physical activity and mental state of depression with sarcopenia in hemodialysis patients. Methods A cross-sectional study was designed with a total of 104 male and female with a minimum age of 35 years. Based on the guidelines of the Asian Working Group for Sarcopenia in 2019, gait speed, muscle mass, and handgrip were used to define sarcopenia. In addition, participants were requested to perform a set of questionnaires to evaluate their physical activity and state of depression. Logistic regression analyses were used to explore the risk factors of sarcopenia. Results Thirty-four (32.69%) of 104 participants had sarcopenia. Compared to the 70 individuals without sarcopenia, they had a low physical activity and a high depression score (ps < .05). Furthermore, low physical activity and high depression scores in combination with sarcopenia were associated with an increased mortality risk. Low physical activity and high depression scores were also independently associated with sarcopenia in hemodialysis patients after controlling for age (odds ratio = 3.23, and 4.92, respectively).
bibliographic citation: Yuenyongchaiwat et al. (2021) Depression and low physical activity are related to sarcopenia in hemodialysis: a single-center study. PeerJ 9:e11695 https://doi.org/10.7717/peerj.11695
date submitted: 2021-02-12
date accepted: 2021-06-08
issued: 2021-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuenyongchaiwat
  given name: Kornanong
author list: Agent
  family name: Jongritthiporn
  given name: Sasikan
author list: Agent
  family name: Somsamarn
  given name: Kasarn
author list: Agent
  family name: Sukkho
  given name: Oranat
author list: Agent
  family name: Pairojkittrakul
  given name: Sasipim
author list: Agent
  family name: Traitanon
  given name: Opas
doi: 10.7717/peerj.11695
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-29
copyright: ©2021 Yuenyongchaiwat et al.
attribution name: Yuenyongchaiwat et al.

Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study
type: item
type: AcademicArticle
description: Background Early and accurate diagnosis of microorganism(s) is important to optimize antimicrobial therapy. Shotgun metagenomic sequencing technology, an unbiased and comprehensive method for pathogen identification, seems to potentially assist or even replace conventional microbiological methodology in the diagnosis of infectious diseases. However, evidence in clinical application of this platform is relatively limited. Methods To evaluate the capability of shotgun metagenomic sequencing technology in clinical practice, both shotgun metagenomic sequencing and conventional culture were performed in the PCR-positive body fluid specimens of 20 patients with suspected infection. The sequenced data were then analyzed for taxonomic identification of microbes and antibiotic resistance gene prediction using bioinformatics pipeline. Results Shotgun metagenomic sequencing results showed a concordance of 17/20 compared with culture results in bacterial detection, and a concordance of 20/20 compared with culture results in fungal detection. Besides, drug-resistant types annotated from antibiotic resistance genes showed much similarity with antibiotic classes identified by susceptibility tests, and more than half of the specimens had consistent drug types between shotgun metagenomic sequencing and culture results. Conclusions Pathogen identification and antibiotic resistance gene prediction by shotgun metagenomic sequencing identification had the potential to diagnose microorganisms in infectious diseases, and it was especially helpful for multiple microbial co-infections and for the cases where standard culture approached failed to identify microorganisms.
format: application/pdf
format: text/html
creator: Huan Chen
creator: Jun Li
creator: Shanshan Yan
creator: Hui Sun
creator: Chuyi Tan
creator: Meidong Liu
creator: Ke Liu
creator: Huali Zhang
creator: Mingxiang Zou
creator: Xianzhong Xiao
subject: Microbiology
subject: Molecular Biology
subject: Mycology
subject: Infectious Diseases
description: doi:10.7717/peerj.11699
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Background Early and accurate diagnosis of microorganism(s) is important to optimize antimicrobial therapy. Shotgun metagenomic sequencing technology, an unbiased and comprehensive method for pathogen identification, seems to potentially assist or even replace conventional microbiological methodology in the diagnosis of infectious diseases. However, evidence in clinical application of this platform is relatively limited. Methods To evaluate the capability of shotgun metagenomic sequencing technology in clinical practice, both shotgun metagenomic sequencing and conventional culture were performed in the PCR-positive body fluid specimens of 20 patients with suspected infection. The sequenced data were then analyzed for taxonomic identification of microbes and antibiotic resistance gene prediction using bioinformatics pipeline. Results Shotgun metagenomic sequencing results showed a concordance of 17/20 compared with culture results in bacterial detection, and a concordance of 20/20 compared with culture results in fungal detection. Besides, drug-resistant types annotated from antibiotic resistance genes showed much similarity with antibiotic classes identified by susceptibility tests, and more than half of the specimens had consistent drug types between shotgun metagenomic sequencing and culture results. Conclusions Pathogen identification and antibiotic resistance gene prediction by shotgun metagenomic sequencing identification had the potential to diagnose microorganisms in infectious diseases, and it was especially helpful for multiple microbial co-infections and for the cases where standard culture approached failed to identify microorganisms.
bibliographic citation: Chen et al. (2021) Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study. PeerJ 9:e11699 https://doi.org/10.7717/peerj.11699
date submitted: 2021-02-10
date accepted: 2021-06-08
issued: 2021-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Huan
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Yan
  given name: Shanshan
author list: Agent
  family name: Sun
  given name: Hui
author list: Agent
  family name: Tan
  given name: Chuyi
author list: Agent
  family name: Liu
  given name: Meidong
author list: Agent
  family name: Liu
  given name: Ke
author list: Agent
  family name: Zhang
  given name: Huali
author list: Agent
  family name: Zou
  given name: Mingxiang
author list: Agent
  family name: Xiao
  given name: Xianzhong
doi: 10.7717/peerj.11699
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-29
copyright: © 2021 Chen et al.
attribution name: Chen et al.

Identification of a three-gene-based prognostic model in multiple myeloma using bioinformatics analysis
type: item
type: AcademicArticle
description: Background Multiple myeloma (MM), the second most hematological malignancy, has high incidence and remains incurable till now. The pathogenesis of MM is poorly understood. This study aimed to identify novel prognostic model for MM on gene expression profiles. Methods Gene expression datas of MM (GSE6477, GSE136337) were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in GSE6477 between case samples and normal control samples were screened by the limma package. Meanwhile, enrichment analysis was conducted, and a protein-protein interaction (PPI) network of these DEGs was established by STRING and cytoscape software. Co-expression modules of genes were built by Weighted Correlation Network Analysis (WGCNA). Key genes were identified both from hub genes and the DEGs. Univariate and multivariate Cox congression were performed to screen independent prognostic genes to construct a predictive model. The predictive power of the model was evaluated by Kaplan–Meier curve and time-dependent receiver operating characteristic (ROC) curves. Finally, univariate and multivariate Cox regression analyse were used to investigate whether the prognostic model could be independent of other clinical parameters. Results GSE6477, including 101 case and 15 normal control, were screened as the datasets. A total of 178 DEGs were identified, including 59 up-regulated and 119 down-regulated genes. In WGCNA analysis, module black and module purple were the most relevant modules with cancer traits, and 92 hub genes in these two modules were selected for further analysis. Next, 47 genes were chosen both from the DEGs and hub genes as key genes. Three genes (LYVE1, RNASE1, and RNASE2) were finally screened by univariate and multivariate Cox regression analyses and used to construct a risk model. In addition, the three-gene prognostic model revealed independent and accurate prognostic capacity in relation to other clinical parameters for MM patients. …
format: application/pdf
format: text/html
creator: Ying Pan
creator: Ye Meng
creator: Zhimin Zhai
creator: Shudao Xiong
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Orthopedics
subject: Medical Genetics
description: doi:10.7717/peerj.11320
publisher: PeerJ Inc.
rights: © 2021 Pan et al.
abstract: Background Multiple myeloma (MM), the second most hematological malignancy, has high incidence and remains incurable till now. The pathogenesis of MM is poorly understood. This study aimed to identify novel prognostic model for MM on gene expression profiles. Methods Gene expression datas of MM (GSE6477, GSE136337) were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in GSE6477 between case samples and normal control samples were screened by the limma package. Meanwhile, enrichment analysis was conducted, and a protein-protein interaction (PPI) network of these DEGs was established by STRING and cytoscape software. Co-expression modules of genes were built by Weighted Correlation Network Analysis (WGCNA). Key genes were identified both from hub genes and the DEGs. Univariate and multivariate Cox congression were performed to screen independent prognostic genes to construct a predictive model. The predictive power of the model was evaluated by Kaplan–Meier curve and time-dependent receiver operating characteristic (ROC) curves. Finally, univariate and multivariate Cox regression analyse were used to investigate whether the prognostic model could be independent of other clinical parameters. Results GSE6477, including 101 case and 15 normal control, were screened as the datasets. A total of 178 DEGs were identified, including 59 up-regulated and 119 down-regulated genes. In WGCNA analysis, module black and module purple were the most relevant modules with cancer traits, and 92 hub genes in these two modules were selected for further analysis. Next, 47 genes were chosen both from the DEGs and hub genes as key genes. Three genes (LYVE1, RNASE1, and RNASE2) were finally screened by univariate and multivariate Cox regression analyses and used to construct a risk model. In addition, the three-gene prognostic model revealed independent and accurate prognostic capacity in relation to other clinical parameters for MM patients. …
bibliographic citation: Pan et al. (2021) Identification of a three-gene-based prognostic model in multiple myeloma using bioinformatics analysis. PeerJ 9:e11320 https://doi.org/10.7717/peerj.11320
date submitted: 2020-11-12
date accepted: 2021-03-31
issued: 2021-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Ying
author list: Agent
  family name: Meng
  given name: Ye
author list: Agent
  family name: Zhai
  given name: Zhimin
author list: Agent
  family name: Xiong
  given name: Shudao
doi: 10.7717/peerj.11320
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-28
copyright: © 2021 Pan et al.
attribution name: Pan et al.

Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum
type: item
type: AcademicArticle
description: Background Sugarcane is a crop of global importance and has been expanding to areas with soils containing high levels of exchangeable aluminum (Al), which is a limiting factor for crop development in acidic soils. The study of the sugarcane physiological and nutritional behavior together with patterns of gene expression in response to Al stress may provide a basis for effective strategies to increase crop productivity in acidic soils. Methods Sugarcane cultivars were evaluated for physiological parameters (photosynthesis, stomatal conductance, and transpiration), nutrient (N, P, K, Ca, Mg, and S) and Al contents in leaves and roots and gene expression, of the genes MDH, SDH by qPCR, both related to the production of organic acids, and SOD, related to oxidative stress. Results Brazilian sugarcane RB867515, RB928064, and RB935744 cultivars exhibited very different responses to induced stress by Al. Exposure to Al caused up-regulation (SOD and MDH) or down-regulation (SDH, MDH, and SOD), depending on the cultivar, Al level, and plant tissue. The RB867515 cultivar was the most Al-tolerant, showing no decline of nutrient content in plant tissue, photosynthesis, transpiration, and stomatal conductance after exposure to Al; it exhibited the highest Al content in the roots, and showed important MDH and SOD gene expression in the roots. RB928064 only showed low expression of SOD in roots and leaves, while RB935744 showed important expression of the SOD gene only in the leaves. Sugarcane cultivars were classified in the following descending Al-tolerance order: RB867515 > RB928064 = RB935744. These results may contribute to the obtention of Al-tolerant cultivars that can play their genetic potential in soils of low fertility and with low demand for agricultural inputs; the selection of potential plants for breeding programs; the elucidation of Al detoxification mechanisms employed by sugarcane cultivars.
format: application/pdf
format: text/html
creator: Mariane de Souza Oliveira
creator: Sâmara Vieira Rocha
creator: Vanessa Karine Schneider
creator: Flavio Henrique-Silva
creator: Marcio Roberto Soares
creator: Andrea Soares-Costa
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11461
publisher: PeerJ Inc.
rights: © 2021 Oliveira et al.
abstract: Background Sugarcane is a crop of global importance and has been expanding to areas with soils containing high levels of exchangeable aluminum (Al), which is a limiting factor for crop development in acidic soils. The study of the sugarcane physiological and nutritional behavior together with patterns of gene expression in response to Al stress may provide a basis for effective strategies to increase crop productivity in acidic soils. Methods Sugarcane cultivars were evaluated for physiological parameters (photosynthesis, stomatal conductance, and transpiration), nutrient (N, P, K, Ca, Mg, and S) and Al contents in leaves and roots and gene expression, of the genes MDH, SDH by qPCR, both related to the production of organic acids, and SOD, related to oxidative stress. Results Brazilian sugarcane RB867515, RB928064, and RB935744 cultivars exhibited very different responses to induced stress by Al. Exposure to Al caused up-regulation (SOD and MDH) or down-regulation (SDH, MDH, and SOD), depending on the cultivar, Al level, and plant tissue. The RB867515 cultivar was the most Al-tolerant, showing no decline of nutrient content in plant tissue, photosynthesis, transpiration, and stomatal conductance after exposure to Al; it exhibited the highest Al content in the roots, and showed important MDH and SOD gene expression in the roots. RB928064 only showed low expression of SOD in roots and leaves, while RB935744 showed important expression of the SOD gene only in the leaves. Sugarcane cultivars were classified in the following descending Al-tolerance order: RB867515 > RB928064 = RB935744. These results may contribute to the obtention of Al-tolerant cultivars that can play their genetic potential in soils of low fertility and with low demand for agricultural inputs; the selection of potential plants for breeding programs; the elucidation of Al detoxification mechanisms employed by sugarcane cultivars.
bibliographic citation: Oliveira et al. (2021) Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum. PeerJ 9:e11461 https://doi.org/10.7717/peerj.11461
date submitted: 2020-10-23
date accepted: 2021-04-26
issued: 2021-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira
  given name: Mariane de Souza
author list: Agent
  family name: Rocha
  given name: Sâmara Vieira
author list: Agent
  family name: Schneider
  given name: Vanessa Karine
author list: Agent
  family name: Henrique-Silva
  given name: Flavio
author list: Agent
  family name: Soares
  given name: Marcio Roberto
author list: Agent
  family name: Soares-Costa
  given name: Andrea
doi: 10.7717/peerj.11461
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-28
copyright: © 2021 Oliveira et al.
attribution name: Oliveira et al.

Effects of biotransport and hydro-meteorological conditions on transport of trace elements in the Scott River (Bellsund, Spitsbergen)
type: item
type: AcademicArticle
description: The shaping of surface water chemistry in the Svalbard Archipelago is strongly dependent on the geology of the catchment and the process of long-range transport of atmospheric pollutants (LRATP). It was found that the dissolved trace elements in the Scott River, which catchment is characterized by a decreasing degree of glaciation, were of the natural origin (i.a. weathering and dissolution of local geological substratum). The exception was Zn originated from LRATP. The paper describe the influence changes in hydro-meteorological conditions and the presence of a seabird colony on the variability in the transport of trace elements within the Scott River catchment. The work assesses long-time fluctuations in the concentration of twenty five trace elements (i.a. Al, Cr, Cu, Pb, Sr, and Zn) from eighty-four surface water samples and their relation to changes in water discharge (Q), precipitation (P), pH, and dissolved organic carbon (DOC) at two river sites (with one being under the influence of the biotransport factor). Based on the results of matrix correlation and cluster analysis it was found that the additional load of DOC from the nesting site of Larus Argentatus in the mouth section of the river drastically changed the hydro-geochemical cycle of Co, Ni, Zn, Ga, Sr, Rb, Ba and U (0.30 < r < 0.51). Furthermore, the results of cluster analysis confirmed that the bird colony’s nesting site was strongly responsible for the presence of U, Rb, Zn, Ni and marine-derived nutrients (e.g. Se and Li). The discharge of glacier meltwater and the alkaline character of water have a negative effect on the dissolution of Li and Mn (−0.31 < r < −0.51), but positively affect the level of Rb and U (r = 0.31 and 0.35, respectively) due to it being washing out a seabird nesting colony in the mouth section of the Scott River. It was observed that the event of rises in air temperature and rain, which results in increased water discharge, caused an intense transport of the trace elements …
format: application/pdf
format: text/html
creator: Sara Lehmann-Konera
creator: Waldemar Kociuba
creator: Stanisław Chmiel
creator: Łukasz Franczak
creator: Żaneta Polkowska
subject: Ecosystem Science
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.11477
publisher: PeerJ Inc.
rights: © 2021 Lehmann-Konera et al.
abstract: The shaping of surface water chemistry in the Svalbard Archipelago is strongly dependent on the geology of the catchment and the process of long-range transport of atmospheric pollutants (LRATP). It was found that the dissolved trace elements in the Scott River, which catchment is characterized by a decreasing degree of glaciation, were of the natural origin (i.a. weathering and dissolution of local geological substratum). The exception was Zn originated from LRATP. The paper describe the influence changes in hydro-meteorological conditions and the presence of a seabird colony on the variability in the transport of trace elements within the Scott River catchment. The work assesses long-time fluctuations in the concentration of twenty five trace elements (i.a. Al, Cr, Cu, Pb, Sr, and Zn) from eighty-four surface water samples and their relation to changes in water discharge (Q), precipitation (P), pH, and dissolved organic carbon (DOC) at two river sites (with one being under the influence of the biotransport factor). Based on the results of matrix correlation and cluster analysis it was found that the additional load of DOC from the nesting site of Larus Argentatus in the mouth section of the river drastically changed the hydro-geochemical cycle of Co, Ni, Zn, Ga, Sr, Rb, Ba and U (0.30 < r < 0.51). Furthermore, the results of cluster analysis confirmed that the bird colony’s nesting site was strongly responsible for the presence of U, Rb, Zn, Ni and marine-derived nutrients (e.g. Se and Li). The discharge of glacier meltwater and the alkaline character of water have a negative effect on the dissolution of Li and Mn (−0.31 < r < −0.51), but positively affect the level of Rb and U (r = 0.31 and 0.35, respectively) due to it being washing out a seabird nesting colony in the mouth section of the Scott River. It was observed that the event of rises in air temperature and rain, which results in increased water discharge, caused an intense transport of the trace elements …
bibliographic citation: Lehmann-Konera et al. (2021) Effects of biotransport and hydro-meteorological conditions on transport of trace elements in the Scott River (Bellsund, Spitsbergen). PeerJ 9:e11477 https://doi.org/10.7717/peerj.11477
date submitted: 2020-10-27
date accepted: 2021-04-27
issued: 2021-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lehmann-Konera
  given name: Sara
author list: Agent
  family name: Kociuba
  given name: Waldemar
author list: Agent
  family name: Chmiel
  given name: Stanisław
author list: Agent
  family name: Franczak
  given name: Łukasz
author list: Agent
  family name: Polkowska
  given name: Żaneta
doi: 10.7717/peerj.11477
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-28
copyright: © 2021 Lehmann-Konera et al.
attribution name: Lehmann-Konera et al.

Characterization of the microbiome of the invasive Asian toad in Madagascar across the expansion range and comparison with a native co-occurring species
type: item
type: AcademicArticle
description: Biological invasions are on the rise, with each invader carrying a plethora of associated microbes. These microbes play important, yet poorly understood, ecological roles that can include assisting the hosts in colonization and adaptation processes or as possible pathogens. Understanding how these communities differ in an invasion scenario may help to understand the host’s resilience and adaptability. The Asian common toad, Duttaphrynus melanostictus is an invasive amphibian, which has recently established in Madagascar and is expected to pose numerous threats to the native ecosystems. We characterized the skin and gut bacterial communities of D. melanostictus in Toamasina (Eastern Madagascar), and compared them to those of a co-occurring native frog species, Ptychadena mascareniensis, at three sites where the toad arrived in different years. Microbial composition did not vary among sites, showing that D. melanostictus keeps a stable community across its expansion but significant differences were observed between these two amphibians. Moreover, D. melanostictus had richer and more diverse communities and also harboured a high percentage of total unique taxa (skin: 80%; gut: 52%). These differences may reflect the combination of multiple host-associated factors including microhabitat selection, skin features and dietary preferences.
format: application/pdf
format: text/html
creator: Bárbara Santos
creator: Molly C. Bletz
creator: Joana Sabino-Pinto
creator: Walter Cocca
creator: Jean Francois Solofoniaina Fidy
creator: Karen LM Freeman
creator: Sven Kuenzel
creator: Serge Ndriantsoa
creator: Jean Noel
creator: Tsanta Rakotonanahary
creator: Miguel Vences
creator: Angelica Crottini
subject: Biodiversity
subject: Genetics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.11532
publisher: PeerJ Inc.
rights: © 2021 Santos et al.
abstract: Biological invasions are on the rise, with each invader carrying a plethora of associated microbes. These microbes play important, yet poorly understood, ecological roles that can include assisting the hosts in colonization and adaptation processes or as possible pathogens. Understanding how these communities differ in an invasion scenario may help to understand the host’s resilience and adaptability. The Asian common toad, Duttaphrynus melanostictus is an invasive amphibian, which has recently established in Madagascar and is expected to pose numerous threats to the native ecosystems. We characterized the skin and gut bacterial communities of D. melanostictus in Toamasina (Eastern Madagascar), and compared them to those of a co-occurring native frog species, Ptychadena mascareniensis, at three sites where the toad arrived in different years. Microbial composition did not vary among sites, showing that D. melanostictus keeps a stable community across its expansion but significant differences were observed between these two amphibians. Moreover, D. melanostictus had richer and more diverse communities and also harboured a high percentage of total unique taxa (skin: 80%; gut: 52%). These differences may reflect the combination of multiple host-associated factors including microhabitat selection, skin features and dietary preferences.
bibliographic citation: Santos et al. (2021) Characterization of the microbiome of the invasive Asian toad in Madagascar across the expansion range and comparison with a native co-occurring species. PeerJ 9:e11532 https://doi.org/10.7717/peerj.11532
date submitted: 2020-10-07
date accepted: 2021-05-07
issued: 2021-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos
  given name: Bárbara
author list: Agent
  family name: Bletz
  given name: Molly C.
author list: Agent
  family name: Sabino-Pinto
  given name: Joana
author list: Agent
  family name: Cocca
  given name: Walter
author list: Agent
  family name: Fidy
  given name: Jean Francois Solofoniaina
author list: Agent
  family name: Freeman
  given name: Karen LM
author list: Agent
  family name: Kuenzel
  given name: Sven
author list: Agent
  family name: Ndriantsoa
  given name: Serge
author list: Agent
  family name: Noel
  given name: Jean
author list: Agent
  family name: Rakotonanahary
  given name: Tsanta
author list: Agent
  family name: Vences
  given name: Miguel
author list: Agent
  family name: Crottini
  given name: Angelica
doi: 10.7717/peerj.11532
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-28
copyright: ©2021 Santos et al.
attribution name: Santos et al.

Helicobacter pylori prevalence in healthy Mexican children: comparison between two non-invasive methods
type: item
type: AcademicArticle
description: Background Helicobacter pylori detection in asymptomatic children with suspected infection or with symptoms that suggest gastric pathology is problematic, since most of the methods depend on the endoscopic study, an invasive and expensive method. Non-invasive methods can be a feasible alternative but must be validated. The purpose of this study was to evaluate the concordance between H. pylori DNA detection in saliva and dental plaque by PCR, with antigen detection in stool by immunochromatography, among asymptomatic children in the state of Guerrero, Mexico. Methods Dental plaque, saliva, and stool samples were obtained from 171 children between 6 and 12 years old. H. pylori detection in saliva and dental plaque was performed by PCR using specific primers for the 16S rRNA gene, while the detection in stool samples was performed by immunochromatography using the CerTest kit. Results We found an overall H. pylori prevalence of 59.6% (102/171). Of the H. pylori positive children 18% (20/111) were positive in saliva samples, 28.1% (34/121) in dental plaque samples, and 50.4% (71/141) in stool samples. A higher prevalence was found in girls (64.7%, p = 0.002). Although some of the children declared some dyspeptic symptoms, these were no related to H. pylori. In conclusion, we found a high prevalence of H. pylori in asymptomatic children and the highest proportion was detected by stool antigen test, which was the most feasible method to detect H. pylori infection.
format: application/pdf
format: text/html
creator: Verónica I. Martínez-Santos
creator: Manuel Hernández Catalán
creator: Luis Octavio Ojeda Salazar
creator: Octavio Andrei Orozco Gómez
creator: Sandra Ines Lorenzo
creator: Rayver Santos Gómez
creator: Norma S. Romero-Castro
creator: Roxana Reyes Ríos
creator: Dinorah Nashely Martinez Carrillo
creator: Gloria Fernández-Tilapa
subject: Microbiology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
subject: Pediatrics
description: doi:10.7717/peerj.11546
publisher: PeerJ Inc.
rights: © 2021 Martínez-Santos et al.
abstract: Background Helicobacter pylori detection in asymptomatic children with suspected infection or with symptoms that suggest gastric pathology is problematic, since most of the methods depend on the endoscopic study, an invasive and expensive method. Non-invasive methods can be a feasible alternative but must be validated. The purpose of this study was to evaluate the concordance between H. pylori DNA detection in saliva and dental plaque by PCR, with antigen detection in stool by immunochromatography, among asymptomatic children in the state of Guerrero, Mexico. Methods Dental plaque, saliva, and stool samples were obtained from 171 children between 6 and 12 years old. H. pylori detection in saliva and dental plaque was performed by PCR using specific primers for the 16S rRNA gene, while the detection in stool samples was performed by immunochromatography using the CerTest kit. Results We found an overall H. pylori prevalence of 59.6% (102/171). Of the H. pylori positive children 18% (20/111) were positive in saliva samples, 28.1% (34/121) in dental plaque samples, and 50.4% (71/141) in stool samples. A higher prevalence was found in girls (64.7%, p = 0.002). Although some of the children declared some dyspeptic symptoms, these were no related to H. pylori. In conclusion, we found a high prevalence of H. pylori in asymptomatic children and the highest proportion was detected by stool antigen test, which was the most feasible method to detect H. pylori infection.
bibliographic citation: Martínez-Santos et al. (2021) Helicobacter pylori prevalence in healthy Mexican children: comparison between two non-invasive methods. PeerJ 9:e11546 https://doi.org/10.7717/peerj.11546
date submitted: 2020-12-21
date accepted: 2021-05-11
issued: 2021-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Santos
  given name: Verónica I.
author list: Agent
  family name: Hernández Catalán
  given name: Manuel
author list: Agent
  family name: Ojeda Salazar
  given name: Luis Octavio
author list: Agent
  family name: Orozco Gómez
  given name: Octavio Andrei
author list: Agent
  family name: Lorenzo
  given name: Sandra Ines
author list: Agent
  family name: Santos Gómez
  given name: Rayver
author list: Agent
  family name: Romero-Castro
  given name: Norma S.
author list: Agent
  family name: Reyes Ríos
  given name: Roxana
author list: Agent
  family name: Martinez Carrillo
  given name: Dinorah Nashely
author list: Agent
  family name: Fernández-Tilapa
  given name: Gloria
doi: 10.7717/peerj.11546
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-28
copyright: © 2021 Martínez-Santos et al.
attribution name: Martínez-Santos et al.

Iron deficiency anemia among children aged 2–5 years in southern Ethiopia: a community-based cross-sectional study
type: item
type: AcademicArticle
description: Background Iron-deficiency anemia (IDA) is a common type of nutritional anemia in low-income countries, including Ethiopia. However, there is limited data on iron deficiency anemia prevalence and associated factors in Ethiopia, particularly for children aged 2 to 5 years. Objectives To establish the prevalence of iron deficiency anemia and associated risk factors, focusing on iron-rich food consumption among children aged 2 to 5 years in southern Ethiopia. Methods A community-based cross-sectional study was conducted in southern Ethiopia in 2017, involving 331 randomly selected children aged 2 to 5 years old. A structured questionnaire was used to collect information about the children and the households. Venous blood was collected from each child in a test tube to measure hemoglobin, ferritin, and C-reactive protein (CRP). Hemoglobin levels were determined using Hemocue®301 and adjusted for altitude. Anemia was defined as hemoglobin levels <11 g/dl. Ferritin was adjusted for inflammation based on CRP concentration and low ferritin concentration defined as adjusted ferritin concentration <12 µg/L. IDA was considered when a child had both hemoglobin level <11g/dl and low ferritin concentration. Bi-variable and multivariable logistic regression models were performed to identify factors associated with IDA and iron-rich food consumption. Results The prevalence of iron deficiency anemia was 25%, and the total anemia prevalence was 32%. Only 15% of children consumed iron-rich foods in the preceding 24 h, and 30% of children consumed iron-rich foods at least once in the preceding week. IDA decreased as the height for age z-score increased (Adjusted Odds Ratio 0.7; 95% CI [0.5–0.9]). Mothers with increased educational level (AOR 1.1; 1.0–1.2) and households with increased dietary diversity (AOR 1.4; 1.2–1.6) consumed more iron-rich foods. Conclusions Iron deficiency anaemia was a moderate public health problem in southern Ethiopia, and the iron-rich food consumption was lo…
format: application/pdf
format: text/html
creator: Alemselam Zebdewos Orsango
creator: Wossene Habtu
creator: Tadesse Lejisa
creator: Eskindir Loha
creator: Bernt Lindtjørn
creator: Ingunn Marie S. Engebretsen
subject: Epidemiology
subject: Hematology
subject: Nutrition
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.11649
publisher: PeerJ Inc.
rights: © 2021 Orsango et al.
abstract: Background Iron-deficiency anemia (IDA) is a common type of nutritional anemia in low-income countries, including Ethiopia. However, there is limited data on iron deficiency anemia prevalence and associated factors in Ethiopia, particularly for children aged 2 to 5 years. Objectives To establish the prevalence of iron deficiency anemia and associated risk factors, focusing on iron-rich food consumption among children aged 2 to 5 years in southern Ethiopia. Methods A community-based cross-sectional study was conducted in southern Ethiopia in 2017, involving 331 randomly selected children aged 2 to 5 years old. A structured questionnaire was used to collect information about the children and the households. Venous blood was collected from each child in a test tube to measure hemoglobin, ferritin, and C-reactive protein (CRP). Hemoglobin levels were determined using Hemocue®301 and adjusted for altitude. Anemia was defined as hemoglobin levels <11 g/dl. Ferritin was adjusted for inflammation based on CRP concentration and low ferritin concentration defined as adjusted ferritin concentration <12 µg/L. IDA was considered when a child had both hemoglobin level <11g/dl and low ferritin concentration. Bi-variable and multivariable logistic regression models were performed to identify factors associated with IDA and iron-rich food consumption. Results The prevalence of iron deficiency anemia was 25%, and the total anemia prevalence was 32%. Only 15% of children consumed iron-rich foods in the preceding 24 h, and 30% of children consumed iron-rich foods at least once in the preceding week. IDA decreased as the height for age z-score increased (Adjusted Odds Ratio 0.7; 95% CI [0.5–0.9]). Mothers with increased educational level (AOR 1.1; 1.0–1.2) and households with increased dietary diversity (AOR 1.4; 1.2–1.6) consumed more iron-rich foods. Conclusions Iron deficiency anaemia was a moderate public health problem in southern Ethiopia, and the iron-rich food consumption was lo…
bibliographic citation: Orsango et al. (2021) Iron deficiency anemia among children aged 2–5 years in southern Ethiopia: a community-based cross-sectional study. PeerJ 9:e11649 https://doi.org/10.7717/peerj.11649
date submitted: 2020-12-16
date accepted: 2021-05-29
issued: 2021-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Orsango
  given name: Alemselam Zebdewos
author list: Agent
  family name: Habtu
  given name: Wossene
author list: Agent
  family name: Lejisa
  given name: Tadesse
author list: Agent
  family name: Loha
  given name: Eskindir
author list: Agent
  family name: Lindtjørn
  given name: Bernt
author list: Agent
  family name: Engebretsen
  given name: Ingunn Marie S.
doi: 10.7717/peerj.11649
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-28
copyright: © 2021 Orsango et al.
attribution name: Orsango et al.

Combination of ferulic acid, ligustrazine and tetrahydropalmatine inhibits invasion and metastasis through MMP/TIMP signaling in endometriosis
type: item
type: AcademicArticle
description: Background The design of the combination of ferulic acid, ligustrazine and tetrahydropalmatine (FLT) is inspired by the Chinese herbal prescription Foshou San. Previous work has shown that FLT inhibited endometriosis growth in rat autograft models. However, the mechanism behind this is unclear. MMP/TIMP signaling is considered as the vital pathway of metastasis and invasion in endometriosis. In this study, we aim to disclose effects of FLT on MMP/TIMP signaling in invasion and metastasis during endometrial cells and xenograft endometriosis. Methods In vivo, effect of FLT on endometriosis was evaluated in a xenogeneic mice model. In vitro, cell viability assay was performed with an IC50 measurement of FLT in hEM15A and HEC1-B cells. The effect of FLT on invasion and metastasis was analyzed in scratch wound and transwell assay. Gene and protein expression of MMP/TIMP signaling were detected by qPCR and Western blotting. Results In xenograft endometriosis, FLT reduced ectopic volume without effect on weight. FLT inhibitory effects on cell growth exhibited a dose-dependent manner in hEM15A and HEC1-B cells. IC50s of FLT in hEM15A cells were 839.30 ± 121.11 or 483.53 ±156.91 μg·ml−1 after the treatment for 24 or 48 h, respectively. In HEC1-B cells, IC50 values of 24 or 48 h were 625.20 ± 59.52 or 250.30 ± 68.12 μg·ml−1. In addition, FLT significantly inhibited invasion and metastasis in scratch wound and transwell assay. Furthermore, FLT inactivated MMP/TIMP signaling with decreasing expression of MMP-2/9, and an enhancing expression of TIMP-1. Conclusions MMP/TIMP inactivation is a reasonable explanation for the inhibition of FLT on invasion and metastasis in endometriosis. This result reveals a potential mechanism on the role of FLT in endometriosis and may benefit for its further application.
format: application/pdf
format: text/html
creator: Yi Tan
creator: Chengling Zhang
creator: Ying Zhang
creator: Xueshan Dai
creator: Qinghua Wei
creator: Jiahui Wei
creator: Pingli Xu
creator: Yi Chen
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.11664
publisher: PeerJ Inc.
rights: © 2021 Tan et al.
abstract: Background The design of the combination of ferulic acid, ligustrazine and tetrahydropalmatine (FLT) is inspired by the Chinese herbal prescription Foshou San. Previous work has shown that FLT inhibited endometriosis growth in rat autograft models. However, the mechanism behind this is unclear. MMP/TIMP signaling is considered as the vital pathway of metastasis and invasion in endometriosis. In this study, we aim to disclose effects of FLT on MMP/TIMP signaling in invasion and metastasis during endometrial cells and xenograft endometriosis. Methods In vivo, effect of FLT on endometriosis was evaluated in a xenogeneic mice model. In vitro, cell viability assay was performed with an IC50 measurement of FLT in hEM15A and HEC1-B cells. The effect of FLT on invasion and metastasis was analyzed in scratch wound and transwell assay. Gene and protein expression of MMP/TIMP signaling were detected by qPCR and Western blotting. Results In xenograft endometriosis, FLT reduced ectopic volume without effect on weight. FLT inhibitory effects on cell growth exhibited a dose-dependent manner in hEM15A and HEC1-B cells. IC50s of FLT in hEM15A cells were 839.30 ± 121.11 or 483.53 ±156.91 μg·ml−1 after the treatment for 24 or 48 h, respectively. In HEC1-B cells, IC50 values of 24 or 48 h were 625.20 ± 59.52 or 250.30 ± 68.12 μg·ml−1. In addition, FLT significantly inhibited invasion and metastasis in scratch wound and transwell assay. Furthermore, FLT inactivated MMP/TIMP signaling with decreasing expression of MMP-2/9, and an enhancing expression of TIMP-1. Conclusions MMP/TIMP inactivation is a reasonable explanation for the inhibition of FLT on invasion and metastasis in endometriosis. This result reveals a potential mechanism on the role of FLT in endometriosis and may benefit for its further application.
bibliographic citation: Tan et al. (2021) Combination of ferulic acid, ligustrazine and tetrahydropalmatine inhibits invasion and metastasis through MMP/TIMP signaling in endometriosis. PeerJ 9:e11664 https://doi.org/10.7717/peerj.11664
date submitted: 2020-12-31
date accepted: 2021-06-02
issued: 2021-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Yi
author list: Agent
  family name: Zhang
  given name: Chengling
author list: Agent
  family name: Zhang
  given name: Ying
author list: Agent
  family name: Dai
  given name: Xueshan
author list: Agent
  family name: Wei
  given name: Qinghua
author list: Agent
  family name: Wei
  given name: Jiahui
author list: Agent
  family name: Xu
  given name: Pingli
author list: Agent
  family name: Chen
  given name: Yi
doi: 10.7717/peerj.11664
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-28
copyright: © 2021 Tan et al.
attribution name: Tan et al.

Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize
type: item
type: AcademicArticle
description: As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P < 2.03 × 10-6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.
format: application/pdf
format: text/html
creator: Yinchao Zhang
creator: Peng Liu
creator: Chen Wang
creator: Na Zhang
creator: Yuxiao Zhu
creator: Chaoying Zou
creator: Guangsheng Yuan
creator: Cong Yang
creator: Shibin Gao
creator: Guangtang Pan
creator: Langlang Ma
creator: Yaou Shen
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11707
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P < 2.03 × 10-6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.
bibliographic citation: Zhang et al. (2021) Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize. PeerJ 9:e11707 https://doi.org/10.7717/peerj.11707
date submitted: 2021-03-04
date accepted: 2021-06-08
issued: 2021-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yinchao
author list: Agent
  family name: Liu
  given name: Peng
author list: Agent
  family name: Wang
  given name: Chen
author list: Agent
  family name: Zhang
  given name: Na
author list: Agent
  family name: Zhu
  given name: Yuxiao
author list: Agent
  family name: Zou
  given name: Chaoying
author list: Agent
  family name: Yuan
  given name: Guangsheng
author list: Agent
  family name: Yang
  given name: Cong
author list: Agent
  family name: Gao
  given name: Shibin
author list: Agent
  family name: Pan
  given name: Guangtang
author list: Agent
  family name: Ma
  given name: Langlang
author list: Agent
  family name: Shen
  given name: Yaou
doi: 10.7717/peerj.11707
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-28
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

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