PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Distribution, ecological risk assessment and source identification of pollutants in soils of different land-use types in degraded wetlands
items: Land use and land cover dynamics and traditional agroforestry practices in Wonchi District, Ethiopia
items: Methodological approaches for estimating populations of the endangered dhole Cuon alpinus
items: SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.
items: Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study
items: Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition
items: Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish
items: Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans)
items: Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow
items: Functional network motifs defined through integration of protein-protein and genetic interactions

Distribution, ecological risk assessment and source identification of pollutants in soils of different land-use types in degraded wetlands
type: item
type: AcademicArticle
description: Background Urbanization and global warming are generating ecological degradation and land pattern alteration problems in natural wetlands. These changes are greatly affecting the ecological services of wetlands. Therefore, there is an urgent need to explore the relationship between pollutants and land-use type for wetland restoration purposes. Zaozhadian Lake is a freshwater wetland in the North China Plain, which is facing degradation and land-use types changes. An experiment for analyzing soil pollutants was conducted in three land-use types of farmland, lake, and ditch in the Zaozhadian Lake. The aims of this study were to identify the distribution, pollution degree, and sources of pollutants in different land-use types, and to explore the influence of land-use type changes on contamination. Methods In this study, surface sediments (0–10 cm) of three land types (farmland, lake, and ditch) in Zaozhadian Lake were collected, and heavy metals (Cu, Ni, Zn, Pb, Cd, Cr, Hg), As, total nitrogen (TN), total phosphorus (TP) and organic matter (OM) were determined. Kriging interpolation was used to visualize the pollutants distribution. The pollution degree of TN and TP was evaluated by the Nemerow pollution index. The pollution of heavy metals and As was evaluated by the geological accumulation index (Igeo) and the potential ecological risk index (RI). Then, dual hierarchical clustering analysis and the principal component analysis were performed to further analyze the impact of land type changes on pollutants. Results The heavy metal contents in the farmland were higher than other areas, while the TN (3.71 ± 1.03 g kg-1) and OM (57.17 ± 15.16 g kg−1) in lake sediments were higher than that in other regions. Farmland, lake, and ditches had low ecological risks, with RI values of 84.21, 71.34, and 50.78, respectively. The primary heavy metal pollutants are Pb, Cu, and Ni. Furthermore, Cu, As, Ni, Pb, and Zn were primarily derived from agriculture pollution, the source of C…
format: application/pdf
format: text/html
creator: Yangyang Han
creator: Hongjie Wang
creator: Guangming Zhang
creator: Shengqi Zhang
creator: Xingchun Liu
creator: Ling Liu
subject: Soil Science
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.12885
publisher: PeerJ Inc.
rights: © 2022 Han et al.
abstract: Background Urbanization and global warming are generating ecological degradation and land pattern alteration problems in natural wetlands. These changes are greatly affecting the ecological services of wetlands. Therefore, there is an urgent need to explore the relationship between pollutants and land-use type for wetland restoration purposes. Zaozhadian Lake is a freshwater wetland in the North China Plain, which is facing degradation and land-use types changes. An experiment for analyzing soil pollutants was conducted in three land-use types of farmland, lake, and ditch in the Zaozhadian Lake. The aims of this study were to identify the distribution, pollution degree, and sources of pollutants in different land-use types, and to explore the influence of land-use type changes on contamination. Methods In this study, surface sediments (0–10 cm) of three land types (farmland, lake, and ditch) in Zaozhadian Lake were collected, and heavy metals (Cu, Ni, Zn, Pb, Cd, Cr, Hg), As, total nitrogen (TN), total phosphorus (TP) and organic matter (OM) were determined. Kriging interpolation was used to visualize the pollutants distribution. The pollution degree of TN and TP was evaluated by the Nemerow pollution index. The pollution of heavy metals and As was evaluated by the geological accumulation index (Igeo) and the potential ecological risk index (RI). Then, dual hierarchical clustering analysis and the principal component analysis were performed to further analyze the impact of land type changes on pollutants. Results The heavy metal contents in the farmland were higher than other areas, while the TN (3.71 ± 1.03 g kg-1) and OM (57.17 ± 15.16 g kg−1) in lake sediments were higher than that in other regions. Farmland, lake, and ditches had low ecological risks, with RI values of 84.21, 71.34, and 50.78, respectively. The primary heavy metal pollutants are Pb, Cu, and Ni. Furthermore, Cu, As, Ni, Pb, and Zn were primarily derived from agriculture pollution, the source of C…
bibliographic citation: Han et al. (2022) Distribution, ecological risk assessment and source identification of pollutants in soils of different land-use types in degraded wetlands. PeerJ 10:e12885 https://doi.org/10.7717/peerj.12885
date submitted: 2021-09-16
date accepted: 2022-01-14
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Yangyang
author list: Agent
  family name: Wang
  given name: Hongjie
author list: Agent
  family name: Zhang
  given name: Guangming
author list: Agent
  family name: Zhang
  given name: Shengqi
author list: Agent
  family name: Liu
  given name: Xingchun
author list: Agent
  family name: Liu
  given name: Ling
doi: 10.7717/peerj.12885
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Han et al.
attribution name: Han et al.

Land use and land cover dynamics and traditional agroforestry practices in Wonchi District, Ethiopia
type: item
type: AcademicArticle
description: Background Investigating the land use and land cover (LULC) dynamics and the status of traditional agroforestry practices provide important data for policymakers. The main objective of this study was to assess the LULC dynamics and traditional agroforestry practices among smallholder farmers across the two agro-ecological zones in Wonchi District of Ethiopia. Methods Landsat images were acquired from Earth Explorer, and changes in LULC were quantified with three Landsat sensors in the three time-series (1985, 2001, and 2019). Supervised classification with maximum likelihood technique was employed using ERDAS Imagine and ArcGIS. A ground survey was conducted with 100 key informants who were selected from 10 sites using a purposive sampling method. The collected data were subjected to direct matrix ranking, use-value analysis of most important multipurpose plant species, and semi-structured interviews were conducted for qualitative analysis. Results In total, 103 agroforestry plant species belonging to 44 families were identified in Wonchi District, of which 74 were indigenous including seven endemic and 29 exotic species. The highest species (13) were recorded in the Fabaceae family. About 61% of species were reported in the midland agro-ecological zone. A mixed farming system was the most frequently (56%) reported source of income. The results of LULC changes from 1985 to 2019 showed that the agroforestry cover increased from 31.1% to 34.9% and settlement including road construction increased from 12.5% to 31.6% of the total area with an annual rate change of 0.3% and 2.7%, respectively. These changes corresponded with a decreasing trend of the forest, cropland, water body, and shrub at a rate of 4.7%, 1.3%, 0.8%, and 0.5%, respectively. The LULC changes were more pronounced in the highlands than in the midlands of Wonchi District. Expansion of settlement and tenure policy change are the main drivers for these changes in the area. The authors recommended that prote…
format: application/pdf
format: text/html
creator: Misganaw Meragiaw
creator: Zerihun Woldu
creator: Bal Ram Singh
subject: Biodiversity
subject: Conservation Biology
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12898
publisher: PeerJ Inc.
rights: © 2022 Meragiaw et al.
abstract: Background Investigating the land use and land cover (LULC) dynamics and the status of traditional agroforestry practices provide important data for policymakers. The main objective of this study was to assess the LULC dynamics and traditional agroforestry practices among smallholder farmers across the two agro-ecological zones in Wonchi District of Ethiopia. Methods Landsat images were acquired from Earth Explorer, and changes in LULC were quantified with three Landsat sensors in the three time-series (1985, 2001, and 2019). Supervised classification with maximum likelihood technique was employed using ERDAS Imagine and ArcGIS. A ground survey was conducted with 100 key informants who were selected from 10 sites using a purposive sampling method. The collected data were subjected to direct matrix ranking, use-value analysis of most important multipurpose plant species, and semi-structured interviews were conducted for qualitative analysis. Results In total, 103 agroforestry plant species belonging to 44 families were identified in Wonchi District, of which 74 were indigenous including seven endemic and 29 exotic species. The highest species (13) were recorded in the Fabaceae family. About 61% of species were reported in the midland agro-ecological zone. A mixed farming system was the most frequently (56%) reported source of income. The results of LULC changes from 1985 to 2019 showed that the agroforestry cover increased from 31.1% to 34.9% and settlement including road construction increased from 12.5% to 31.6% of the total area with an annual rate change of 0.3% and 2.7%, respectively. These changes corresponded with a decreasing trend of the forest, cropland, water body, and shrub at a rate of 4.7%, 1.3%, 0.8%, and 0.5%, respectively. The LULC changes were more pronounced in the highlands than in the midlands of Wonchi District. Expansion of settlement and tenure policy change are the main drivers for these changes in the area. The authors recommended that prote…
bibliographic citation: Meragiaw et al. (2022) Land use and land cover dynamics and traditional agroforestry practices in Wonchi District, Ethiopia. PeerJ 10:e12898 https://doi.org/10.7717/peerj.12898
date submitted: 2021-10-29
date accepted: 2022-01-16
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meragiaw
  given name: Misganaw
author list: Agent
  family name: Woldu
  given name: Zerihun
author list: Agent
  family name: Singh
  given name: Bal Ram
doi: 10.7717/peerj.12898
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Meragiaw et al.
attribution name: Meragiaw et al.

Methodological approaches for estimating populations of the endangered dhole Cuon alpinus
type: item
type: AcademicArticle
description: Large carnivores are important for maintaining ecosystem integrity and attract much research and conservation interest. For most carnivore species, estimating population density or abundance is challenging because they do not have unique markings for individual identification. This hinders status assessments for many threatened species, and calls for testing new methodological approaches. We examined past efforts to assess the population status of the endangered dhole (Cuon alpinus), and explored the application of a suite of recently developed models for estimating their populations using camera-trap data from India’s Western Ghats. We compared the performance of Site-Based Abundance (SBA), Space-to-Event (STE), and Time-to-Event (TTE) models against current knowledge of their population size in the area. We also applied two of these models (TTE and STE) to the co-occurring leopard (Panthera pardus), for which density estimates were available from Spatially Explicit Capture–Recapture (SECR) models, so as to simultaneously validate the accuracy of estimates for one marked and one unmarked species. Our review of literature (n = 38) showed that most assessments of dhole populations involved crude indices (relative abundance index; RAI) or estimates of occupancy and area of suitable habitat; very few studies attempted to estimate populations. Based on empirical data from our field surveys, the TTE and SBA models overestimated dhole population size beyond ecologically plausible limits, but the STE model produced reliable estimates for both the species. Our findings suggest that it is difficult to estimate population sizes of unmarked species when model assumptions are not fully met and data are sparse, which are commonplace for most ecological surveys in the tropics. Based on our assessment, we propose that practitioners who have access to photo-encounter data on dholes across Asia test old and new analytical approaches to increase the overall knowledge-base on the spec…
format: application/pdf
format: text/html
creator: Girish A. Punjabi
creator: Linnea Worsøe Havmøller
creator: Rasmus Worsøe Havmøller
creator: Dusit Ngoprasert
creator: Arjun Srivathsa
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.12905
publisher: PeerJ Inc.
rights: © 2022 Punjabi et al.
abstract: Large carnivores are important for maintaining ecosystem integrity and attract much research and conservation interest. For most carnivore species, estimating population density or abundance is challenging because they do not have unique markings for individual identification. This hinders status assessments for many threatened species, and calls for testing new methodological approaches. We examined past efforts to assess the population status of the endangered dhole (Cuon alpinus), and explored the application of a suite of recently developed models for estimating their populations using camera-trap data from India’s Western Ghats. We compared the performance of Site-Based Abundance (SBA), Space-to-Event (STE), and Time-to-Event (TTE) models against current knowledge of their population size in the area. We also applied two of these models (TTE and STE) to the co-occurring leopard (Panthera pardus), for which density estimates were available from Spatially Explicit Capture–Recapture (SECR) models, so as to simultaneously validate the accuracy of estimates for one marked and one unmarked species. Our review of literature (n = 38) showed that most assessments of dhole populations involved crude indices (relative abundance index; RAI) or estimates of occupancy and area of suitable habitat; very few studies attempted to estimate populations. Based on empirical data from our field surveys, the TTE and SBA models overestimated dhole population size beyond ecologically plausible limits, but the STE model produced reliable estimates for both the species. Our findings suggest that it is difficult to estimate population sizes of unmarked species when model assumptions are not fully met and data are sparse, which are commonplace for most ecological surveys in the tropics. Based on our assessment, we propose that practitioners who have access to photo-encounter data on dholes across Asia test old and new analytical approaches to increase the overall knowledge-base on the spec…
bibliographic citation: Punjabi et al. (2022) Methodological approaches for estimating populations of the endangered dhole Cuon alpinus. PeerJ 10:e12905 https://doi.org/10.7717/peerj.12905
date submitted: 2021-11-03
date accepted: 2022-01-17
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Punjabi
  given name: Girish A.
author list: Agent
  family name: Havmøller
  given name: Linnea Worsøe
author list: Agent
  family name: Havmøller
  given name: Rasmus Worsøe
author list: Agent
  family name: Ngoprasert
  given name: Dusit
author list: Agent
  family name: Srivathsa
  given name: Arjun
doi: 10.7717/peerj.12905
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Punjabi et al.
attribution name: Punjabi et al.

SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.
type: item
type: AcademicArticle
description: Background Pogostemon cablin (Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, P. cablin is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil. Methods To better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed de novo transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads. Results In this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of P. cablin. We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were “terpenoid backbone biosynthesis”, “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “sesquiterpenoid and triterpenoid biosynthesis”, “ubiquinone and other terpenoid-quinone biosynthesis”, “flavonoid biosynthesis”, and “flavone and flavonol biosynthesis”. However, the main pathways of the patchouliol-type also included “diterpene biosynthesis” …
format: application/pdf
format: text/html
creator: Hongyi Zhang
creator: Wenjing Deng
creator: Changhua Lu
creator: Mengling He
creator: Hanjing Yan
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12940
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Pogostemon cablin (Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, P. cablin is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil. Methods To better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed de novo transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads. Results In this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of P. cablin. We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were “terpenoid backbone biosynthesis”, “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “sesquiterpenoid and triterpenoid biosynthesis”, “ubiquinone and other terpenoid-quinone biosynthesis”, “flavonoid biosynthesis”, and “flavone and flavonol biosynthesis”. However, the main pathways of the patchouliol-type also included “diterpene biosynthesis” …
bibliographic citation: Zhang et al. (2022) SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.. PeerJ 10:e12940 https://doi.org/10.7717/peerj.12940
date submitted: 2021-06-04
date accepted: 2022-01-24
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Hongyi
author list: Agent
  family name: Deng
  given name: Wenjing
author list: Agent
  family name: Lu
  given name: Changhua
author list: Agent
  family name: He
  given name: Mengling
author list: Agent
  family name: Yan
  given name: Hanjing
doi: 10.7717/peerj.12940
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study
type: item
type: AcademicArticle
description: Background In the United States, state-level policies requiring vaccination of school-going children constitute a critical strategy for improving vaccination coverage. However, policies allowing vaccination exemptions have also been implemented and contribute to reductions in vaccination coverage and potential increases in the burden of vaccine-preventable diseases. Understanding the geographic disparities in the distribution of vaccination exemptions and identifying high risk areas is necessary for guiding resource allocation and public health control strategies. This study investigated geographic disparities in vaccination exemptions as well as socioeconomic and demographic predictors of vaccination exemptions in Florida. Methods Vaccination exemption data were obtained from the Florida Department of Health’s Florida HealthCHARTS web interface. Spatial patterns in geographic distribution of total and non-medical vaccination exemptions were assessed using county-level choropleth maps. Negative binomial models were used to identify significant predictors of county-level risks of both total and non-medical vaccination exemptions. Results Total exemptions varied from 0 to 30.2 per 10,000 people. Nine counties had exemption risks in the top two classes (10.4–15.9 and 15.9–30.2 exemptions per 10,000 people). These counties were distributed in five distinct areas: Western Panhandle, central northern area, central, South-eastern coastal area, and the southern coastal border of the state. Non-medical exemptions varied from 0 to 10.4 per 10,000 people. Fifteen counties had exemption risks in the top two classes (3.7–5.6 and 5.6–10.4 exemptions per 10,000 people), and were located in six distinct areas: Western and Central Panhandle, Northeastern, Central-eastern coastal area, Central-western coastal area, and the South-western coastal border of the state. Predictors of high risk of total vaccination exemptions were high density of primary care providers (p < 0.001), high me…
format: application/pdf
format: text/html
creator: Corinne B. Tandy
creator: Agricola Odoi
subject: Epidemiology
subject: Immunology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.12973
publisher: PeerJ Inc.
rights: © 2022 Tandy and Odoi
abstract: Background In the United States, state-level policies requiring vaccination of school-going children constitute a critical strategy for improving vaccination coverage. However, policies allowing vaccination exemptions have also been implemented and contribute to reductions in vaccination coverage and potential increases in the burden of vaccine-preventable diseases. Understanding the geographic disparities in the distribution of vaccination exemptions and identifying high risk areas is necessary for guiding resource allocation and public health control strategies. This study investigated geographic disparities in vaccination exemptions as well as socioeconomic and demographic predictors of vaccination exemptions in Florida. Methods Vaccination exemption data were obtained from the Florida Department of Health’s Florida HealthCHARTS web interface. Spatial patterns in geographic distribution of total and non-medical vaccination exemptions were assessed using county-level choropleth maps. Negative binomial models were used to identify significant predictors of county-level risks of both total and non-medical vaccination exemptions. Results Total exemptions varied from 0 to 30.2 per 10,000 people. Nine counties had exemption risks in the top two classes (10.4–15.9 and 15.9–30.2 exemptions per 10,000 people). These counties were distributed in five distinct areas: Western Panhandle, central northern area, central, South-eastern coastal area, and the southern coastal border of the state. Non-medical exemptions varied from 0 to 10.4 per 10,000 people. Fifteen counties had exemption risks in the top two classes (3.7–5.6 and 5.6–10.4 exemptions per 10,000 people), and were located in six distinct areas: Western and Central Panhandle, Northeastern, Central-eastern coastal area, Central-western coastal area, and the South-western coastal border of the state. Predictors of high risk of total vaccination exemptions were high density of primary care providers (p < 0.001), high me…
bibliographic citation: Tandy et al. (2022) Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study. PeerJ 10:e12973 https://doi.org/10.7717/peerj.12973
date submitted: 2021-09-07
date accepted: 2022-01-31
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tandy
  given name: Corinne B.
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.12973
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Tandy and Odoi
attribution name: Tandy and Odoi

Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition
type: item
type: AcademicArticle
description: Background Oral squamous cell carcinoma (OSCC), the most common type of primary malignant tumor in the oral cavity, is a lethal disease with high recurrence and mortality rates. Butyrate, a metabolite produced by periodontal pathogens, has been linked to oral diseases. The purpose of this study was to evaluate the effect of sodium butyrate (NaB) on the proliferation, migration, and invasion of OSCC cells in vitro and to explore the potential mechanism. Methods Two OSCC cell lines (HSC-4 and SCC-9) were treated with NaB at different concentrations. The cell proliferation was assayed by CCK-8, ethylene deoxyuridine (EdU), and flow cytometry. Wound healing and transwell assay were performed to detect cell migration and invasion. Changes in epithelial-mesenchymal transition (EMT) markers, including E-cadherin, Vimentin, and SNAI1, were evaluated by quantitative real-time PCR (qRT-PCR), western blot, and immunofluorescent staining. The expression levels of matrix metalloproteinases (MMPs) were analyzed by qRT-PCR and gelatin zymography. Results Our results showed that NaB inhibited the proliferation of OSCC cells and induced cell cycle arrest at G1 phase, but NaB significantly enhanced cell migration and invasion compared with the control group. Further mechanistic investigation demonstrated that NaB induced EMT by increasing the expression of Vimentin and SNAI1, decreasing the expression of membrane-bound E-cadherin, and correspondingly promoting E-cadherin translocation from the membrane to the cytoplasm. In addition, the overexpression of MMP1/2/9/13 was closely related to NaB treatment. Conclusions Our study conclude that butyrate may promote the migration and invasion of OSCC cells by inducing EMT. These findings indicate that butyrate may contribute to OSCC metastasis.
format: application/pdf
format: text/html
creator: Wenli Zang
creator: Junchao Liu
creator: Fengxue Geng
creator: Dongjuan Liu
creator: Shuwei Zhang
creator: Yuchao Li
creator: Yaping Pan
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Oncology
subject: Otorhinolaryngology
description: doi:10.7717/peerj.12991
publisher: PeerJ Inc.
rights: © 2022 Zang et al.
abstract: Background Oral squamous cell carcinoma (OSCC), the most common type of primary malignant tumor in the oral cavity, is a lethal disease with high recurrence and mortality rates. Butyrate, a metabolite produced by periodontal pathogens, has been linked to oral diseases. The purpose of this study was to evaluate the effect of sodium butyrate (NaB) on the proliferation, migration, and invasion of OSCC cells in vitro and to explore the potential mechanism. Methods Two OSCC cell lines (HSC-4 and SCC-9) were treated with NaB at different concentrations. The cell proliferation was assayed by CCK-8, ethylene deoxyuridine (EdU), and flow cytometry. Wound healing and transwell assay were performed to detect cell migration and invasion. Changes in epithelial-mesenchymal transition (EMT) markers, including E-cadherin, Vimentin, and SNAI1, were evaluated by quantitative real-time PCR (qRT-PCR), western blot, and immunofluorescent staining. The expression levels of matrix metalloproteinases (MMPs) were analyzed by qRT-PCR and gelatin zymography. Results Our results showed that NaB inhibited the proliferation of OSCC cells and induced cell cycle arrest at G1 phase, but NaB significantly enhanced cell migration and invasion compared with the control group. Further mechanistic investigation demonstrated that NaB induced EMT by increasing the expression of Vimentin and SNAI1, decreasing the expression of membrane-bound E-cadherin, and correspondingly promoting E-cadherin translocation from the membrane to the cytoplasm. In addition, the overexpression of MMP1/2/9/13 was closely related to NaB treatment. Conclusions Our study conclude that butyrate may promote the migration and invasion of OSCC cells by inducing EMT. These findings indicate that butyrate may contribute to OSCC metastasis.
bibliographic citation: Zang et al. (2022) Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition. PeerJ 10:e12991 https://doi.org/10.7717/peerj.12991
date submitted: 2021-08-19
date accepted: 2022-02-02
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zang
  given name: Wenli
author list: Agent
  family name: Liu
  given name: Junchao
author list: Agent
  family name: Geng
  given name: Fengxue
author list: Agent
  family name: Liu
  given name: Dongjuan
author list: Agent
  family name: Zhang
  given name: Shuwei
author list: Agent
  family name: Li
  given name: Yuchao
author list: Agent
  family name: Pan
  given name: Yaping
doi: 10.7717/peerj.12991
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Zang et al.
attribution name: Zang et al.

Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish
type: item
type: AcademicArticle
description: The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.
format: application/pdf
format: text/html
creator: Lasse Nyholm
creator: Iñaki Odriozola
creator: Garazi Martin Bideguren
creator: Ostaizka Aizpurua
creator: Antton Alberdi
subject: Aquaculture, Fisheries and Fish Science
subject: Mathematical Biology
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.12992
publisher: PeerJ Inc.
rights: © 2022 Nyholm et al.
abstract: The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.
bibliographic citation: Nyholm et al. (2022) Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish. PeerJ 10:e12992 https://doi.org/10.7717/peerj.12992
date submitted: 2021-11-11
date accepted: 2022-02-02
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nyholm
  given name: Lasse
author list: Agent
  family name: Odriozola
  given name: Iñaki
author list: Agent
  family name: Martin Bideguren
  given name: Garazi
author list: Agent
  family name: Aizpurua
  given name: Ostaizka
author list: Agent
  family name: Alberdi
  given name: Antton
doi: 10.7717/peerj.12992
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Nyholm et al.
attribution name: Nyholm et al.

Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans)
type: item
type: AcademicArticle
description: Toads release toxic dry secretions from glands in their skin. Toxin possesses a wide range of biological effects, but little is known about its specific gene expression pattern and regulatory mechanisms. The Asiatic toad (Bufo gargarizans) is widely used to produce toxin. Here, we explored the gene expression of 30 tissue samples from three different skin sites (parotoid gland, dorsal skin, and abdomen skin) of B. gargarizans. After de novo assembly, 783,130 unigenes with an average length of 489 bp (N50 = 556 bp) were obtained. A total of 9,248 significant differentially expressed genes (DEGs) were detected. There were 8,819 DEGs between the parotoid gland and abdomen skin and 1,299 DEGs between the dorsal skin and abdomen skin, while only 1,283 DEGs were obtained between the parotoid gland and dorsal skin. Through enrichment analysis, it was found that the detected differential gene expressions corresponded to the different functions of different skin sites. Our key findings were the genetic expression of toxin secretion, the protection function of skin, and the related genes such as HSD3B, Cyp2c, and CAT, LGALS9. In conclusion, we provide useful transcript resources to study the gene expression and gene function of B. gargarizans and other amphibians. The detected DEGs between different sites of the skin provided better insights into the genetic mechanisms of toxin secretion and the protection function of skin for amphibians.
format: application/pdf
format: text/html
creator: Yue Lan
creator: Lewei He
creator: Xue Dong
creator: Ruixiang Tang
creator: Wanyu Li
creator: Jiao Wang
creator: Lei Wang
creator: Bisong Yue
creator: Megan Price
creator: Tao Guo
creator: Zhenxin Fan
subject: Bioinformatics
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12993
publisher: PeerJ Inc.
rights: © 2022 Lan et al.
abstract: Toads release toxic dry secretions from glands in their skin. Toxin possesses a wide range of biological effects, but little is known about its specific gene expression pattern and regulatory mechanisms. The Asiatic toad (Bufo gargarizans) is widely used to produce toxin. Here, we explored the gene expression of 30 tissue samples from three different skin sites (parotoid gland, dorsal skin, and abdomen skin) of B. gargarizans. After de novo assembly, 783,130 unigenes with an average length of 489 bp (N50 = 556 bp) were obtained. A total of 9,248 significant differentially expressed genes (DEGs) were detected. There were 8,819 DEGs between the parotoid gland and abdomen skin and 1,299 DEGs between the dorsal skin and abdomen skin, while only 1,283 DEGs were obtained between the parotoid gland and dorsal skin. Through enrichment analysis, it was found that the detected differential gene expressions corresponded to the different functions of different skin sites. Our key findings were the genetic expression of toxin secretion, the protection function of skin, and the related genes such as HSD3B, Cyp2c, and CAT, LGALS9. In conclusion, we provide useful transcript resources to study the gene expression and gene function of B. gargarizans and other amphibians. The detected DEGs between different sites of the skin provided better insights into the genetic mechanisms of toxin secretion and the protection function of skin for amphibians.
bibliographic citation: Lan et al. (2022) Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans). PeerJ 10:e12993 https://doi.org/10.7717/peerj.12993
date submitted: 2021-07-27
date accepted: 2022-02-02
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lan
  given name: Yue
author list: Agent
  family name: He
  given name: Lewei
author list: Agent
  family name: Dong
  given name: Xue
author list: Agent
  family name: Tang
  given name: Ruixiang
author list: Agent
  family name: Li
  given name: Wanyu
author list: Agent
  family name: Wang
  given name: Jiao
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Yue
  given name: Bisong
author list: Agent
  family name: Price
  given name: Megan
author list: Agent
  family name: Guo
  given name: Tao
author list: Agent
  family name: Fan
  given name: Zhenxin
doi: 10.7717/peerj.12993
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Lan et al.
attribution name: Lan et al.

Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow
type: item
type: AcademicArticle
description: Objective The purpose of the present study was to determine the effects of starch sugar by-product (SSB) feeding on the rumen in-vitro digestibility, in situ disappearance rate, and lactating dairy cow. Methods To determine the rumen in vitro digestibility, 50 mL of the buffer-rumen fluid mixture was dispensed into a 125 mL serum bottle containing 0.5 g of dry matter (DM) of substrates. Nitrogen gas (N2, 99.9% pure) was flushed into the serum bottles and three replications were incubated at 0, 2, 4, 8, 16, 24, and 48 h. To determine the in-situ disappearance rate, SSB was incubated for 0, 2, 4, 8, 16, 24, and 48 hours in nylon bags (5 × 10 cm, 45*m pore size) placed within the ventral sac of two cannulated Holstein cows.. A total of sixteen Holstein Friesian cows (60.5 ± 20.4 months old, 706.8 ± 3.4 kg initial body wieght) fed experimental diets during the experimental periods. The treatments were basal diet (control) and 3.0% DM of SSB, with the diet formulated according to national research council (NRC) nutrient requirements of dairy cattle guideline. An experiment was conducted with a randomized block design for six weeks based on body weight. Results Soluble fraction (fraction a) of DM and crude protein (CP) was 28.99 and 11.92%DM, fraction b of DM and CP was 44.63 and 31.61% DM, and c value of DM and CP was 26.38 and 56.47%DM. As an increase SSB level in total mixed ration (TMR), there was a decrease in gas production at 0, 16, and 48 h (p < 0.05). As an increase SSB level in TMR, there was a decrease in acetate to propionate ratio at 8, 16, 24, and 48 h (p < 0.05). Dry matter intake, milk production, and milk composition did not differ between the treatments. All blood profile contents did not differ between treatments. Conclusion A diet containing 3.0% SSB could be fed to ruminants without adverse effects on rumen fermentation.
format: application/pdf
format: text/html
creator: Yongjun Choi
creator: Suhun Kim
creator: Sangrak Lee
creator: Youngjun Na
subject: Agricultural Science
subject: Biochemistry
subject: Veterinary Medicine
description: doi:10.7717/peerj.12998
publisher: PeerJ Inc.
rights: © 2022 Choi et al.
abstract: Objective The purpose of the present study was to determine the effects of starch sugar by-product (SSB) feeding on the rumen in-vitro digestibility, in situ disappearance rate, and lactating dairy cow. Methods To determine the rumen in vitro digestibility, 50 mL of the buffer-rumen fluid mixture was dispensed into a 125 mL serum bottle containing 0.5 g of dry matter (DM) of substrates. Nitrogen gas (N2, 99.9% pure) was flushed into the serum bottles and three replications were incubated at 0, 2, 4, 8, 16, 24, and 48 h. To determine the in-situ disappearance rate, SSB was incubated for 0, 2, 4, 8, 16, 24, and 48 hours in nylon bags (5 × 10 cm, 45*m pore size) placed within the ventral sac of two cannulated Holstein cows.. A total of sixteen Holstein Friesian cows (60.5 ± 20.4 months old, 706.8 ± 3.4 kg initial body wieght) fed experimental diets during the experimental periods. The treatments were basal diet (control) and 3.0% DM of SSB, with the diet formulated according to national research council (NRC) nutrient requirements of dairy cattle guideline. An experiment was conducted with a randomized block design for six weeks based on body weight. Results Soluble fraction (fraction a) of DM and crude protein (CP) was 28.99 and 11.92%DM, fraction b of DM and CP was 44.63 and 31.61% DM, and c value of DM and CP was 26.38 and 56.47%DM. As an increase SSB level in total mixed ration (TMR), there was a decrease in gas production at 0, 16, and 48 h (p < 0.05). As an increase SSB level in TMR, there was a decrease in acetate to propionate ratio at 8, 16, 24, and 48 h (p < 0.05). Dry matter intake, milk production, and milk composition did not differ between the treatments. All blood profile contents did not differ between treatments. Conclusion A diet containing 3.0% SSB could be fed to ruminants without adverse effects on rumen fermentation.
bibliographic citation: Choi et al. (2022) Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow. PeerJ 10:e12998 https://doi.org/10.7717/peerj.12998
date submitted: 2021-10-20
date accepted: 2022-02-02
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Yongjun
author list: Agent
  family name: Kim
  given name: Suhun
author list: Agent
  family name: Lee
  given name: Sangrak
author list: Agent
  family name: Na
  given name: Youngjun
doi: 10.7717/peerj.12998
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Choi et al.
attribution name: Choi et al.

Functional network motifs defined through integration of protein-protein and genetic interactions
type: item
type: AcademicArticle
description: Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.
format: application/pdf
format: text/html
creator: Amruta Sahoo
creator: Sebastian Pechmann
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Data Science
description: doi:10.7717/peerj.13016
publisher: PeerJ Inc.
rights: © 2022 Sahoo and Pechmann
abstract: Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.
bibliographic citation: Sahoo et al. (2022) Functional network motifs defined through integration of protein-protein and genetic interactions. PeerJ 10:e13016 https://doi.org/10.7717/peerj.13016
date submitted: 2021-11-11
date accepted: 2022-02-06
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sahoo
  given name: Amruta
author list: Agent
  family name: Pechmann
  given name: Sebastian
doi: 10.7717/peerj.13016
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Sahoo and Pechmann
attribution name: Sahoo and Pechmann

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