PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
items: Predicting population: development and validation of a new predictive nomogram for evaluating medication nonadherence risk in a type 2 diabetes
items: Biochemical analysis of collagens from the bone of lizardfish (Saurida tumbil Bloch, 1795) extracted with different acids
items: Spring diet and energy intake of tundra swan (Cygnus columbianus) at the Yellow River National Wetland in Baotou, China
items: Geomorphically controlled coral distribution in degraded shallow reefs of the Western Caribbean
items: Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics
items: PhosVarDeep: deep-learning based prediction of phospho-variants using sequence information
items: Textural quality, growth parameters and oxidative responses in Nile tilapia (Oreochromis niloticus) fed faba bean water extract diet
items: Full vaccination coverage and associated factors among children aged 12 to 23 months in remote rural area of Demba Gofa District, Southern Ethiopia
items: 3,4-dihydroxyphenylethyl alcohol glycoside reduces acetaminophen-induced acute liver failure in mice by inhibiting hepatocyte ferroptosis and pyroptosis

Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
type: item
type: AcademicArticle
description: Background The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature. Methods In this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction. Results We found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C.
format: application/pdf
format: text/html
creator: Hanna M. Bensch
creator: Conny Tolf
creator: Jonas Waldenström
creator: Daniel Lundin
creator: Markus Zöttl
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.13095
publisher: PeerJ Inc.
rights: © 2022 Bensch et al.
abstract: Background The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature. Methods In this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction. Results We found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C.
bibliographic citation: Bensch et al. (2022) Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples. PeerJ 10:e13095 https://doi.org/10.7717/peerj.13095
date submitted: 2021-11-30
date accepted: 2022-02-20
issued: 2022-03-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bensch
  given name: Hanna M.
author list: Agent
  family name: Tolf
  given name: Conny
author list: Agent
  family name: Waldenström
  given name: Jonas
author list: Agent
  family name: Lundin
  given name: Daniel
author list: Agent
  family name: Zöttl
  given name: Markus
doi: 10.7717/peerj.13095
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-15
copyright: ©2022 Bensch et al.
attribution name: Bensch et al.

Predicting population: development and validation of a new predictive nomogram for evaluating medication nonadherence risk in a type 2 diabetes
type: item
type: AcademicArticle
description: Background Diabetes mellitus is a growing global health challenge and affects patients of all ages. Treatment aims to keep blood glucose levels close to normal and to prevent or delay complications. However, adherence to antidiabetic medicines is often unsatisfactory. Purpose Here, we established and internally validated a medication nonadherence risk nomogram for use in Chinese type 2 diabetes mellitus (T2DM) patients. Methods This cross-sectional study was carried out from July–December 2020 on randomly selected T2DM patients visiting a diabetes clinic and included 753 participants. Adherence was analyzed based on an eight-item Morisky Medication Adherence Scale (MMAS-8). Other data, including patient demographics, treatment, complications, and comorbidities, were also collected on questionnaires. Optimization of feature selection to develop the medication nonadherence risk model was achieved using the least absolute shrinkage and selection operator regression model (LASSO). A prediction model comprising features selected from LASSO model was designed by applying multivariable logistic regression analysis. The decision curve analysis, calibration plot, and C-index were utilized to assess the performance of the model in terms of discrimination, calibration, and clinical usefulness. Bootstrapping validation was applied for internal validation. Results The prediction nomogram comprised several factors including sex, marital status, education level, employment, distance, self-monitoringofbloodglucose, disease duration, and dosing frequency of daily hypoglycemics (pills, insulin, or glucagon-like peptide-1). The model exhibited good calibration and good discrimination (C-index = 0.79, 95% CI [0.75–0.83]). In the validation samples, a high C-index (0.75) was achieved. Results of the decision curve analysis revealed that the nonadherence nomogram could be applied in clinical practice in cases where the intervention is decided at a nonadherence possibility threshold of 12…
format: application/pdf
format: text/html
creator: NaRen QiMuge
creator: Xu Fang
creator: Baocheng Chang
creator: Dong Mei Li
creator: Yuanyuan Li
subject: Diabetes and Endocrinology
subject: Drugs and Devices
subject: Public Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.13102
publisher: PeerJ Inc.
rights: © 2022 QiMuge et al.
abstract: Background Diabetes mellitus is a growing global health challenge and affects patients of all ages. Treatment aims to keep blood glucose levels close to normal and to prevent or delay complications. However, adherence to antidiabetic medicines is often unsatisfactory. Purpose Here, we established and internally validated a medication nonadherence risk nomogram for use in Chinese type 2 diabetes mellitus (T2DM) patients. Methods This cross-sectional study was carried out from July–December 2020 on randomly selected T2DM patients visiting a diabetes clinic and included 753 participants. Adherence was analyzed based on an eight-item Morisky Medication Adherence Scale (MMAS-8). Other data, including patient demographics, treatment, complications, and comorbidities, were also collected on questionnaires. Optimization of feature selection to develop the medication nonadherence risk model was achieved using the least absolute shrinkage and selection operator regression model (LASSO). A prediction model comprising features selected from LASSO model was designed by applying multivariable logistic regression analysis. The decision curve analysis, calibration plot, and C-index were utilized to assess the performance of the model in terms of discrimination, calibration, and clinical usefulness. Bootstrapping validation was applied for internal validation. Results The prediction nomogram comprised several factors including sex, marital status, education level, employment, distance, self-monitoringofbloodglucose, disease duration, and dosing frequency of daily hypoglycemics (pills, insulin, or glucagon-like peptide-1). The model exhibited good calibration and good discrimination (C-index = 0.79, 95% CI [0.75–0.83]). In the validation samples, a high C-index (0.75) was achieved. Results of the decision curve analysis revealed that the nonadherence nomogram could be applied in clinical practice in cases where the intervention is decided at a nonadherence possibility threshold of 12…
bibliographic citation: QiMuge et al. (2022) Predicting population: development and validation of a new predictive nomogram for evaluating medication nonadherence risk in a type 2 diabetes. PeerJ 10:e13102 https://doi.org/10.7717/peerj.13102
date submitted: 2021-09-20
date accepted: 2022-02-21
issued: 2022-03-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: QiMuge
  given name: NaRen
author list: Agent
  family name: Fang
  given name: Xu
author list: Agent
  family name: Chang
  given name: Baocheng
author list: Agent
  family name: Li
  given name: Dong Mei
author list: Agent
  family name: Li
  given name: Yuanyuan
doi: 10.7717/peerj.13102
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-15
copyright: © 2022 QiMuge et al.
attribution name: QiMuge et al.

Biochemical analysis of collagens from the bone of lizardfish (Saurida tumbil Bloch, 1795) extracted with different acids
type: item
type: AcademicArticle
description: Background Lizardfish (Saurida tumbil Bloch, 1795) bone is a fish by-product generated during industrial surimi processing. This by-product is an important source of collagen production since the use of terrestrial animal-based collagens no longer sought due to concern regarding the transfer of infectious diseases and religious issues. Hence, this study was carried out to determine the biochemical analysis of collagens from the bone of lizardfish extracted with different acids. Methods Lizardfish bone collagens were extracted with various acids (i.e., acetic, lactic and citric acids). All extraction processes were conducted in a chiller room (4 °C). The extracted collagens were biochemically characterized, such as hydroxyproline content, Ultraviolet (UV) absorption, X-ray diffraction (XRD), Fourier transform infrared spectroscopy spectra (FTIR), Differential scanning calorimetry (DSC) and solubility in different pH values and NaCl concentrations. Results The yield of extracted collagens ranged between 1.73% and 2.59%, with the highest (p < 0.05) observed in citric acid-extracted collagen (CaEC). Protein patterns confirmed that all-collagen samples had two identical subunits, α1 and α2, representing type I collagen. The highest whiteness value was found in acetic acid-extracted collagen (AaEC), but there was no significant difference (p ≥ 0.05) compared to lactic acid-extracted collagen (LaEC). UV absorption and XRD analysis reflected the characteristics of the collagen, as reported in the literature. For the FTIR, all acid-extracted collagen samples presented a triple helical structure. The thermal transition temperature (Tmax = 77.92–89.04 °C) was in accordance with collagen extracted from other fish species. All extracted collagens were highly soluble in acidic pH and low concentrations of NaCl (0–20 g/L). In conclusion, collagens extracted from lizardfish bone may be used as alternative sources of collagen in industrial settings, and AaEC would be considered supe…
format: application/pdf
format: text/html
creator: Abdul Aziz Jaziri
creator: Rossita Shapawi
creator: Ruzaidi Azli Mohd Mokhtar
creator: Wan Norhana Md. Noordin
creator: Nurul Huda
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.13103
publisher: PeerJ Inc.
rights: © 2022 Jaziri et al.
abstract: Background Lizardfish (Saurida tumbil Bloch, 1795) bone is a fish by-product generated during industrial surimi processing. This by-product is an important source of collagen production since the use of terrestrial animal-based collagens no longer sought due to concern regarding the transfer of infectious diseases and religious issues. Hence, this study was carried out to determine the biochemical analysis of collagens from the bone of lizardfish extracted with different acids. Methods Lizardfish bone collagens were extracted with various acids (i.e., acetic, lactic and citric acids). All extraction processes were conducted in a chiller room (4 °C). The extracted collagens were biochemically characterized, such as hydroxyproline content, Ultraviolet (UV) absorption, X-ray diffraction (XRD), Fourier transform infrared spectroscopy spectra (FTIR), Differential scanning calorimetry (DSC) and solubility in different pH values and NaCl concentrations. Results The yield of extracted collagens ranged between 1.73% and 2.59%, with the highest (p < 0.05) observed in citric acid-extracted collagen (CaEC). Protein patterns confirmed that all-collagen samples had two identical subunits, α1 and α2, representing type I collagen. The highest whiteness value was found in acetic acid-extracted collagen (AaEC), but there was no significant difference (p ≥ 0.05) compared to lactic acid-extracted collagen (LaEC). UV absorption and XRD analysis reflected the characteristics of the collagen, as reported in the literature. For the FTIR, all acid-extracted collagen samples presented a triple helical structure. The thermal transition temperature (Tmax = 77.92–89.04 °C) was in accordance with collagen extracted from other fish species. All extracted collagens were highly soluble in acidic pH and low concentrations of NaCl (0–20 g/L). In conclusion, collagens extracted from lizardfish bone may be used as alternative sources of collagen in industrial settings, and AaEC would be considered supe…
bibliographic citation: Jaziri et al. (2022) Biochemical analysis of collagens from the bone of lizardfish (Saurida tumbil Bloch, 1795) extracted with different acids. PeerJ 10:e13103 https://doi.org/10.7717/peerj.13103
date submitted: 2021-11-01
date accepted: 2022-02-21
issued: 2022-03-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jaziri
  given name: Abdul Aziz
author list: Agent
  family name: Shapawi
  given name: Rossita
author list: Agent
  family name: Mohd Mokhtar
  given name: Ruzaidi Azli
author list: Agent
  family name: Md. Noordin
  given name: Wan Norhana
author list: Agent
  family name: Huda
  given name: Nurul
doi: 10.7717/peerj.13103
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-15
copyright: ©2022 Jaziri et al.
attribution name: Jaziri et al.

Spring diet and energy intake of tundra swan (Cygnus columbianus) at the Yellow River National Wetland in Baotou, China
type: item
type: AcademicArticle
description: The Yellow River National Wetland in Baotou, China is an important resting and energy replenishment place for many migratory birds, such as tundra swan (Cygnus columbianus). The energy supply of food available at stopover sites plays an important role in the life cycle of migratory birds. In order to understand diet composition and energy supply of tundra swans for further protection of them, in this study, fecal of tundra swans (C. columbianus) were collected and fecal microhistological analysis was conducted to analyze the feeding habits and the energy supply. Results showed that: (1) tundra swans (C. columbianus) mainly fed on twelve species of plants from five families, including corn (Zea mays), quinoa (Chenopodium album) and rice (Oryza sativa), this is related to local crops and abundant plants. (2) The energy provided by crops to tundra swans (C. columbianus) was significantly higher than other abundant plants in wetlands (P < 0.05), corn and rice were the most consumed food, and other abundant wetland plants play complementary roles. (3) The daily energy intake of tundra swans (C. columbianus) was much higher than their daily energy consumption, the daily net energy intake of tundra swans (C. columbianus) was 855.51 ± 182.88 kJ (mean ± standard deviations). This suggested that the wetland provides energy for continue migrating to the tundra swan (C. columbianus). For further protection of tundra swans (C. columbianus) and other migratory birds, the Baotou Yellow River National Wetland environment and the surrounding farmland habitat should be protected.
format: application/pdf
format: text/html
creator: Li Liu
creator: Chao Du
creator: Yan Sun
creator: Wenjing Li
creator: Jiyun Zhang
creator: Litong Cao
creator: Li Gao
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13113
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: The Yellow River National Wetland in Baotou, China is an important resting and energy replenishment place for many migratory birds, such as tundra swan (Cygnus columbianus). The energy supply of food available at stopover sites plays an important role in the life cycle of migratory birds. In order to understand diet composition and energy supply of tundra swans for further protection of them, in this study, fecal of tundra swans (C. columbianus) were collected and fecal microhistological analysis was conducted to analyze the feeding habits and the energy supply. Results showed that: (1) tundra swans (C. columbianus) mainly fed on twelve species of plants from five families, including corn (Zea mays), quinoa (Chenopodium album) and rice (Oryza sativa), this is related to local crops and abundant plants. (2) The energy provided by crops to tundra swans (C. columbianus) was significantly higher than other abundant plants in wetlands (P < 0.05), corn and rice were the most consumed food, and other abundant wetland plants play complementary roles. (3) The daily energy intake of tundra swans (C. columbianus) was much higher than their daily energy consumption, the daily net energy intake of tundra swans (C. columbianus) was 855.51 ± 182.88 kJ (mean ± standard deviations). This suggested that the wetland provides energy for continue migrating to the tundra swan (C. columbianus). For further protection of tundra swans (C. columbianus) and other migratory birds, the Baotou Yellow River National Wetland environment and the surrounding farmland habitat should be protected.
bibliographic citation: Liu et al. (2022) Spring diet and energy intake of tundra swan (Cygnus columbianus) at the Yellow River National Wetland in Baotou, China. PeerJ 10:e13113 https://doi.org/10.7717/peerj.13113
date submitted: 2021-12-07
date accepted: 2022-02-23
issued: 2022-03-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Li
author list: Agent
  family name: Du
  given name: Chao
author list: Agent
  family name: Sun
  given name: Yan
author list: Agent
  family name: Li
  given name: Wenjing
author list: Agent
  family name: Zhang
  given name: Jiyun
author list: Agent
  family name: Cao
  given name: Litong
author list: Agent
  family name: Gao
  given name: Li
doi: 10.7717/peerj.13113
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-15
copyright: © 2022 Liu et al.
attribution name: Liu et al.

Geomorphically controlled coral distribution in degraded shallow reefs of the Western Caribbean
type: item
type: AcademicArticle
description: The development of coral reefs results from the interaction between ecological and geological processes in space and time. Their difference in scale, however, makes it difficult to detect the impact of ecological changes on geological reef development. The decline of coral cover over the last 50 years, for example, has dramatically impaired the function of ecological processes on reefs. Yet given the limited-resolution of their Holocene record, it is uncertain how this will impact accretion and structural integrity over longer timescales. In addition, reports of this ecological decline have focused on intrinsic parameters such as coral cover and colony size at the expense of extrinsic ones such as geomorphic and environmental variables. Despite these problems, several attempts have been made to predict the long-term accretion status of reefs based entirely on the contemporary health status of benthic communities. Here we explore how this ecological decline is represented within the reef geomorphic structure, which represents the long-term expression of reef development. Using a detailed geomorphic zonation scheme, we analyze the distribution and biodiversity of reef-building corals in fringing-reef systems of the Mesoamerican Reef tract. We find a depth-related pattern in community structure which shows that the relative species distribution between geomorphic zones is statistically different. Despite these differences, contemporary coral assemblages in all zones are dominated by the same group of pioneer generalist species. These findings imply that first, coral species distribution is still controlled by extrinsic processes that generate the geomorphic zonation; second, that coral biodiversity still reflects species zonation patterns reported by early studies; and third that dominance of pioneer species implies that modern coral assemblages are in a prolonged post-disturbance adjustment stage. In conclusion, any accurate assessment of the future viability of reefs…
format: application/pdf
format: text/html
creator: Alexis Enrique Medina-Valmaseda
creator: Paul Blanchon
creator: Lorenzo Alvarez-Filip
creator: Esmeralda Pérez-Cervantes
subject: Biogeography
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12590
publisher: PeerJ Inc.
rights: © 2022 Medina-Valmaseda et al.
abstract: The development of coral reefs results from the interaction between ecological and geological processes in space and time. Their difference in scale, however, makes it difficult to detect the impact of ecological changes on geological reef development. The decline of coral cover over the last 50 years, for example, has dramatically impaired the function of ecological processes on reefs. Yet given the limited-resolution of their Holocene record, it is uncertain how this will impact accretion and structural integrity over longer timescales. In addition, reports of this ecological decline have focused on intrinsic parameters such as coral cover and colony size at the expense of extrinsic ones such as geomorphic and environmental variables. Despite these problems, several attempts have been made to predict the long-term accretion status of reefs based entirely on the contemporary health status of benthic communities. Here we explore how this ecological decline is represented within the reef geomorphic structure, which represents the long-term expression of reef development. Using a detailed geomorphic zonation scheme, we analyze the distribution and biodiversity of reef-building corals in fringing-reef systems of the Mesoamerican Reef tract. We find a depth-related pattern in community structure which shows that the relative species distribution between geomorphic zones is statistically different. Despite these differences, contemporary coral assemblages in all zones are dominated by the same group of pioneer generalist species. These findings imply that first, coral species distribution is still controlled by extrinsic processes that generate the geomorphic zonation; second, that coral biodiversity still reflects species zonation patterns reported by early studies; and third that dominance of pioneer species implies that modern coral assemblages are in a prolonged post-disturbance adjustment stage. In conclusion, any accurate assessment of the future viability of reefs…
bibliographic citation: Medina-Valmaseda et al. (2022) Geomorphically controlled coral distribution in degraded shallow reefs of the Western Caribbean. PeerJ 10:e12590 https://doi.org/10.7717/peerj.12590
date submitted: 2021-04-15
date accepted: 2021-11-12
issued: 2022-03-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Medina-Valmaseda
  given name: Alexis Enrique
author list: Agent
  family name: Blanchon
  given name: Paul
author list: Agent
  family name: Alvarez-Filip
  given name: Lorenzo
author list: Agent
  family name: Pérez-Cervantes
  given name: Esmeralda
doi: 10.7717/peerj.12590
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-14
copyright: © 2022 Medina-Valmaseda et al.
attribution name: Medina-Valmaseda et al.

Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics
type: item
type: AcademicArticle
description: Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.
format: application/pdf
format: text/html
creator: Jose M. Irazoqui
creator: Maria F. Eberhardt
creator: Maria M. Adjad
creator: Ariel F. Amadio
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.12772
publisher: PeerJ Inc.
rights: © 2022 Irazoqui et al.
abstract: Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.
bibliographic citation: Irazoqui et al. (2022) Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics. PeerJ 10:e12772 https://doi.org/10.7717/peerj.12772
date submitted: 2021-07-13
date accepted: 2021-12-19
issued: 2022-03-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Irazoqui
  given name: Jose M.
author list: Agent
  family name: Eberhardt
  given name: Maria F.
author list: Agent
  family name: Adjad
  given name: Maria M.
author list: Agent
  family name: Amadio
  given name: Ariel F.
doi: 10.7717/peerj.12772
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-14
copyright: © 2022 Irazoqui et al.
attribution name: Irazoqui et al.

PhosVarDeep: deep-learning based prediction of phospho-variants using sequence information
type: item
type: AcademicArticle
description: Human DNA sequencing has revealed numerous single nucleotide variants associated with complex diseases. Researchers have shown that these variants have potential effects on protein function, one of which is to disrupt protein phosphorylation. Based on conventional machine learning algorithms, several computational methods for predicting phospho-variants have been developed, but their performance still leaves considerable room for improvement. In recent years, deep learning has been successfully applied in biological sequence analysis with its efficient sequence pattern learning ability, which provides a powerful tool for improving phospho-variant prediction based on protein sequence information. In the study, we present PhosVarDeep, a novel unified deep-learning framework for phospho-variant prediction. PhosVarDeep takes reference and variant sequences as inputs and adopts a Siamese-like CNN architecture containing two identical subnetworks and a prediction module. In each subnetwork, general phosphorylation sequence features are extracted by a pre-trained sequence feature encoding network and then fed into a CNN module for capturing variant-aware phosphorylation sequence features. After that, a prediction module is introduced to integrate the outputs of the two subnetworks and generate the prediction results of phospho-variants. Comprehensive experimental results on phospho-variant data demonstrates that our method significantly improves the prediction performance of phospho-variants and compares favorably with existing conventional machine learning methods.
format: application/pdf
format: text/html
creator: Xia Liu
creator: Minghui Wang
creator: Ao Li
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.12847
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Human DNA sequencing has revealed numerous single nucleotide variants associated with complex diseases. Researchers have shown that these variants have potential effects on protein function, one of which is to disrupt protein phosphorylation. Based on conventional machine learning algorithms, several computational methods for predicting phospho-variants have been developed, but their performance still leaves considerable room for improvement. In recent years, deep learning has been successfully applied in biological sequence analysis with its efficient sequence pattern learning ability, which provides a powerful tool for improving phospho-variant prediction based on protein sequence information. In the study, we present PhosVarDeep, a novel unified deep-learning framework for phospho-variant prediction. PhosVarDeep takes reference and variant sequences as inputs and adopts a Siamese-like CNN architecture containing two identical subnetworks and a prediction module. In each subnetwork, general phosphorylation sequence features are extracted by a pre-trained sequence feature encoding network and then fed into a CNN module for capturing variant-aware phosphorylation sequence features. After that, a prediction module is introduced to integrate the outputs of the two subnetworks and generate the prediction results of phospho-variants. Comprehensive experimental results on phospho-variant data demonstrates that our method significantly improves the prediction performance of phospho-variants and compares favorably with existing conventional machine learning methods.
bibliographic citation: Liu et al. (2022) PhosVarDeep: deep-learning based prediction of phospho-variants using sequence information. PeerJ 10:e12847 https://doi.org/10.7717/peerj.12847
date submitted: 2021-10-22
date accepted: 2022-01-07
issued: 2022-03-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xia
author list: Agent
  family name: Wang
  given name: Minghui
author list: Agent
  family name: Li
  given name: Ao
doi: 10.7717/peerj.12847
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-14
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Textural quality, growth parameters and oxidative responses in Nile tilapia (Oreochromis niloticus) fed faba bean water extract diet
type: item
type: AcademicArticle
description: Texture is one of the key quality attributes used in the fresh and processed fish industry to assess product quality and consumer acceptability. To improve the textural quality of tilapia, we formulated the expanded pellet diet (EPD) and pellet diet (PD), both containing faba bean (Vicia faba, FB) water extract, a previously reported potential aquafeed additive to increase flesh texture. The common diet was used as a control. After Nile tilapia (Oreochromis niloticus) were fed three kinds of experimental diet for 120 days, muscle textural quality, growth parameters, oxidative response and immune parameters were analyzed. The results showed that there was no significant difference in the growth parameters between the three groups (P > 0.05). The highest measure of textural quality (hardness and chewiness) was found for the PD group, followed by the EPD and the control (P < 0.05). Less oxidative damage to the hepatopancreas and intestine was found in the EPD compared with the PD group, as demonstrated by the decreased levels of reactive oxygen species and increased levels of nicotinamide adenine dinucleotide and intestinal digestive enzyme activity (amylase and lipase). Taken together, this study highlights the potential usefulness in commercial settings of FB water extract for improving the textural quality of tilapia, and EPD containing faba bean water extract could be more advanced substitute for faba bean in tilapia culture in term of both effectiveness in textural quality improvement and health status enhancement compared with PD.
format: application/pdf
format: text/html
creator: Yichao Li
creator: Junming Zhang
creator: Bing Fu
creator: Jun Xie
creator: Guangjun Wang
creator: Jingjing Tian
creator: Yun Xia
creator: Ermeng Yu
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Food Science and Technology
description: doi:10.7717/peerj.13048
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Texture is one of the key quality attributes used in the fresh and processed fish industry to assess product quality and consumer acceptability. To improve the textural quality of tilapia, we formulated the expanded pellet diet (EPD) and pellet diet (PD), both containing faba bean (Vicia faba, FB) water extract, a previously reported potential aquafeed additive to increase flesh texture. The common diet was used as a control. After Nile tilapia (Oreochromis niloticus) were fed three kinds of experimental diet for 120 days, muscle textural quality, growth parameters, oxidative response and immune parameters were analyzed. The results showed that there was no significant difference in the growth parameters between the three groups (P > 0.05). The highest measure of textural quality (hardness and chewiness) was found for the PD group, followed by the EPD and the control (P < 0.05). Less oxidative damage to the hepatopancreas and intestine was found in the EPD compared with the PD group, as demonstrated by the decreased levels of reactive oxygen species and increased levels of nicotinamide adenine dinucleotide and intestinal digestive enzyme activity (amylase and lipase). Taken together, this study highlights the potential usefulness in commercial settings of FB water extract for improving the textural quality of tilapia, and EPD containing faba bean water extract could be more advanced substitute for faba bean in tilapia culture in term of both effectiveness in textural quality improvement and health status enhancement compared with PD.
bibliographic citation: Li et al. (2022) Textural quality, growth parameters and oxidative responses in Nile tilapia (Oreochromis niloticus) fed faba bean water extract diet. PeerJ 10:e13048 https://doi.org/10.7717/peerj.13048
date submitted: 2021-11-22
date accepted: 2022-02-11
issued: 2022-03-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yichao
author list: Agent
  family name: Zhang
  given name: Junming
author list: Agent
  family name: Fu
  given name: Bing
author list: Agent
  family name: Xie
  given name: Jun
author list: Agent
  family name: Wang
  given name: Guangjun
author list: Agent
  family name: Tian
  given name: Jingjing
author list: Agent
  family name: Xia
  given name: Yun
author list: Agent
  family name: Yu
  given name: Ermeng
doi: 10.7717/peerj.13048
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-14
copyright: ©2022 Li et al.
attribution name: Li et al.

Full vaccination coverage and associated factors among children aged 12 to 23 months in remote rural area of Demba Gofa District, Southern Ethiopia
type: item
type: AcademicArticle
description: Background Full vaccination refers to the administration of vaccines/antigens recommended for children in the first year of life. However, little is known about full vaccination in remote, rural Ethiopia. This study aimed to measure full vaccination coverage and associated factors among children aged 12 to 23 months in Demba Gofa District, Southern Ethiopia. Methods A community-based cross-sectional study was conducted in April and May 2019 using a multistage sampling technique to select 677 mothers with children 12–23 months of age. Data was collected using a pre-tested structured questionnaire, and data were edited, coded, entered, and cleaned using Epi Info v3.1 and analyzed using SPSS v20. Bivariate and multivariable logistic regression was used to understand associations between dependent and independent variables. Results Three-hundred and nine children (47.0%) were fully vaccinated, 274 (41.7%) were partially vaccinated, and 74 (11.3%) were not vaccinated at all. Children were more likely to be vaccinated if decisions were made jointly with husbands (AOR = 1.88, 95% CI [1.06–3.34]), were made by mothers (AOR = 4.03, 95% CI [1.66–9.78]), followed postnatal care (AOR = 5.02, 95% CI [2.28–11.05]), if the child’s age for completing vaccination was known (AOR = 2.54, 95% CI [1.04–6.23]), and if vaccinations did not make the child sick (AOR = 0.32, 95% CI [0.16–0.64]). Conclusion Full vaccination coverage was less than average in the study district and far below the governmental target (90%) necessary for sustained control of vaccine-preventable diseases. Interventions targeted towards maternal healthcare decision-making, postnatal care, knowledge on vaccination timing, and importance should be prioritized to improve full vaccination coverage. A continuous supply of vaccination cards needs to be ensured to improve vaccination conditions.
format: application/pdf
format: text/html
creator: Tadele Dana Darebo
creator: Bahru Belachew Oshe
creator: Chala Wegi Diro
subject: Immunology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.13081
publisher: PeerJ Inc.
rights: © 2022 Darebo et al.
abstract: Background Full vaccination refers to the administration of vaccines/antigens recommended for children in the first year of life. However, little is known about full vaccination in remote, rural Ethiopia. This study aimed to measure full vaccination coverage and associated factors among children aged 12 to 23 months in Demba Gofa District, Southern Ethiopia. Methods A community-based cross-sectional study was conducted in April and May 2019 using a multistage sampling technique to select 677 mothers with children 12–23 months of age. Data was collected using a pre-tested structured questionnaire, and data were edited, coded, entered, and cleaned using Epi Info v3.1 and analyzed using SPSS v20. Bivariate and multivariable logistic regression was used to understand associations between dependent and independent variables. Results Three-hundred and nine children (47.0%) were fully vaccinated, 274 (41.7%) were partially vaccinated, and 74 (11.3%) were not vaccinated at all. Children were more likely to be vaccinated if decisions were made jointly with husbands (AOR = 1.88, 95% CI [1.06–3.34]), were made by mothers (AOR = 4.03, 95% CI [1.66–9.78]), followed postnatal care (AOR = 5.02, 95% CI [2.28–11.05]), if the child’s age for completing vaccination was known (AOR = 2.54, 95% CI [1.04–6.23]), and if vaccinations did not make the child sick (AOR = 0.32, 95% CI [0.16–0.64]). Conclusion Full vaccination coverage was less than average in the study district and far below the governmental target (90%) necessary for sustained control of vaccine-preventable diseases. Interventions targeted towards maternal healthcare decision-making, postnatal care, knowledge on vaccination timing, and importance should be prioritized to improve full vaccination coverage. A continuous supply of vaccination cards needs to be ensured to improve vaccination conditions.
bibliographic citation: Darebo et al. (2022) Full vaccination coverage and associated factors among children aged 12 to 23 months in remote rural area of Demba Gofa District, Southern Ethiopia. PeerJ 10:e13081 https://doi.org/10.7717/peerj.13081
date submitted: 2021-06-26
date accepted: 2022-02-16
issued: 2022-03-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Darebo
  given name: Tadele Dana
author list: Agent
  family name: Oshe
  given name: Bahru Belachew
author list: Agent
  family name: Diro
  given name: Chala Wegi
doi: 10.7717/peerj.13081
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-14
copyright: © 2022 Darebo et al.
attribution name: Darebo et al.

3,4-dihydroxyphenylethyl alcohol glycoside reduces acetaminophen-induced acute liver failure in mice by inhibiting hepatocyte ferroptosis and pyroptosis
type: item
type: AcademicArticle
description: APAP is one of the most commonly used antipyretic and pain medications, but excessive use can cause liver toxicity and damage. 3,4-dihydroxyphenylethyl alcohol glycoside (DAG) is a component isolated from Sargentodoxa cuneata known to have anti-apoptotic, anti-oxidation and anti-inflammatory effects. However, the effects of DAG on acute liver failure (ALF) are largely unknown. The purpose of this study is to study the protective effects and mechanism of DAG on APAP-induced ALF in mice. We established an ALF model in adult male pathogen-free C57BL/6 mice treated with APAP (300 mg/kg) by intraperitoneal injection and resolved by 24 h. Hematoxylin and eosin (HE) staining was used to evaluate the pathological changes in mouse liver tissue. The infiltration of neutrophils in liver tissue and reactive oxygen species (ROS) in AML12 cells were analyzed by flow cytometry. The levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), glutathione (GSH), malondialdehyde (MDA), catalase (CAT), and superoxide dismutase (SOD) were analyzed using relevant kits. Our results show that DAG reduced APAP-induced serum ALT and AST levels, histopathological changes, liver neutrophil infiltration and proinflammatory cytokines production, also attenuated the accumulation of MDA and the exhaustion of GSH, CAT and SOD. In vitro experiment indicated that DAG dose-dependently inhibited APAP-induced the levels of pro-inflammatory factors (IL-1β and IL18), and reactive oxygen species (ROS) and preventing GSH depletion in mouse AML12 hepatocytes. More interestingly, DAG inhibited the expression of ERK, HO-1, NLRP3, Caspase1 (p20) and Gasdermin-D and upregulated the expression of GPX4 in liver tissues and AML12hepatocytes. Therefore, our results indicate that DAG may act as a potential agent to treat ALF induced by APAP by inhibiting hepatocyte ferroptosis and pyroptosis.
format: application/pdf
format: text/html
creator: Tianyu Liu
creator: Lei Yang
creator: Hejun Gao
creator: Yuzhen Zhuo
creator: Zhengwei Tu
creator: Yongqin Wang
creator: Jing Xun
creator: Qi Zhang
creator: Lanqiu Zhang
creator: Ximo Wang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.13082
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: APAP is one of the most commonly used antipyretic and pain medications, but excessive use can cause liver toxicity and damage. 3,4-dihydroxyphenylethyl alcohol glycoside (DAG) is a component isolated from Sargentodoxa cuneata known to have anti-apoptotic, anti-oxidation and anti-inflammatory effects. However, the effects of DAG on acute liver failure (ALF) are largely unknown. The purpose of this study is to study the protective effects and mechanism of DAG on APAP-induced ALF in mice. We established an ALF model in adult male pathogen-free C57BL/6 mice treated with APAP (300 mg/kg) by intraperitoneal injection and resolved by 24 h. Hematoxylin and eosin (HE) staining was used to evaluate the pathological changes in mouse liver tissue. The infiltration of neutrophils in liver tissue and reactive oxygen species (ROS) in AML12 cells were analyzed by flow cytometry. The levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), glutathione (GSH), malondialdehyde (MDA), catalase (CAT), and superoxide dismutase (SOD) were analyzed using relevant kits. Our results show that DAG reduced APAP-induced serum ALT and AST levels, histopathological changes, liver neutrophil infiltration and proinflammatory cytokines production, also attenuated the accumulation of MDA and the exhaustion of GSH, CAT and SOD. In vitro experiment indicated that DAG dose-dependently inhibited APAP-induced the levels of pro-inflammatory factors (IL-1β and IL18), and reactive oxygen species (ROS) and preventing GSH depletion in mouse AML12 hepatocytes. More interestingly, DAG inhibited the expression of ERK, HO-1, NLRP3, Caspase1 (p20) and Gasdermin-D and upregulated the expression of GPX4 in liver tissues and AML12hepatocytes. Therefore, our results indicate that DAG may act as a potential agent to treat ALF induced by APAP by inhibiting hepatocyte ferroptosis and pyroptosis.
bibliographic citation: Liu et al. (2022) 3,4-dihydroxyphenylethyl alcohol glycoside reduces acetaminophen-induced acute liver failure in mice by inhibiting hepatocyte ferroptosis and pyroptosis. PeerJ 10:e13082 https://doi.org/10.7717/peerj.13082
date submitted: 2021-09-07
date accepted: 2022-02-16
issued: 2022-03-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Tianyu
author list: Agent
  family name: Yang
  given name: Lei
author list: Agent
  family name: Gao
  given name: Hejun
author list: Agent
  family name: Zhuo
  given name: Yuzhen
author list: Agent
  family name: Tu
  given name: Zhengwei
author list: Agent
  family name: Wang
  given name: Yongqin
author list: Agent
  family name: Xun
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Qi
author list: Agent
  family name: Zhang
  given name: Lanqiu
author list: Agent
  family name: Wang
  given name: Ximo
doi: 10.7717/peerj.13082
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-14
copyright: ©2022 Liu et al.
attribution name: Liu et al.

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