PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of ZnO and CuO nanoparticles on the growth, nutrient absorption, and potential health risk of the seasonal vegetable Medicago polymorpha L.
items: Physiological and biochemical responses of hybrid maize (Zea mays L.) varieties grown under heat stress conditions
items: High metabolic load distance in professional soccer according to competitive level and playing positions
items: Context dependent prediction in DNA sequence using neural networks
items: Bioinformatics prediction and experimental verification of key biomarkers for diabetic kidney disease based on transcriptome sequencing in mice
items: Sexual dimorphism in the walrus mandible: comparative description and geometric morphometrics
items: Thermography in ergonomic assessment: a study of wood processing industry workers
items: Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of Plukenetia volubilis
items: Estuarine microbial networks and relationships vary between environmentally distinct communities
items: Hepatic metabolite responses to 4-day complete fasting and subsequent refeeding in rats

Effect of ZnO and CuO nanoparticles on the growth, nutrient absorption, and potential health risk of the seasonal vegetable Medicago polymorpha L.
type: item
type: AcademicArticle
description: Background Medicago polymorpha L., a seasonal vegetable, is commonly grown in China. The increasing use of nanoparticles (NPs) such as ZnO and CuO NPs in agriculture has raised concerns about their potential risks for plant growth and for human consumption. There is a lack of research on the effects of ZnO and CuO NPs on agronomic performance of Medicago polymorpha L. and their potential risks for human health. Methods In this study, different treatment concentrations of ZnO NPs (25, 50, 100, and 200 mg kg−1) and CuO NPs (10, 25, 50, and 100 mg kg−1) were used to determine their effects on the growth and nutrient absorption of Medicago polymorpha L., as well as their potential risk for human health. Results The results showed that ZnO and CuO NPs increased the fresh weight of Medicago polymorpha L. by 5.8–11.8 and 3.7–8.1%, respectively. The best performance for ZnO NPs occurred between 25–50 mg kg−1 and the best performance for CuO NPs occurred between 10–25 mg kg−1. Compared with the control, ZnO and CuO NPs improved the macronutrients phosphorus (P), potassium (K), magnesium (Mg), and calcium (Ca). The following micronutrients were also improved: iron (Fe), nickel (Ni), copper (Cu), zinc (Zn), and manganese (Mn), with the exception of nitrogen (N) accumulation. Low treatment concentrations exhibited more efficient nutrient uptake than high treatment concentrations. A comprehensive analysis showed that the optimum concentrations were 25 mg kg−1 for ZnO NPs and 10 mg kg−1 for CuO NPs. The potential non-carcinogenic health risk of Medicago polymorpha L. treated with ZnO and CuO NPs was analyzed according to the estimated daily intake (EDI), the hazard quotient (HQ), and the cumulative hazard quotient (CHQ). Compared with the oral reference dose, the EDI under different ZnO and CuO NPs treatments was lower. The HQ and CHQ under different ZnO and CuO NPs treatments were far below 1. This indicated that Medicago polymorpha L. treated with ZnO and CuO NPs did not pose a…
format: application/pdf
format: text/html
creator: Hongting Ji
creator: Zhi Guo
creator: Guodong Wang
creator: Xin Wang
creator: Hongjiang Liu
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.14038
publisher: PeerJ Inc.
rights: © 2022 Ji et al.
abstract: Background Medicago polymorpha L., a seasonal vegetable, is commonly grown in China. The increasing use of nanoparticles (NPs) such as ZnO and CuO NPs in agriculture has raised concerns about their potential risks for plant growth and for human consumption. There is a lack of research on the effects of ZnO and CuO NPs on agronomic performance of Medicago polymorpha L. and their potential risks for human health. Methods In this study, different treatment concentrations of ZnO NPs (25, 50, 100, and 200 mg kg−1) and CuO NPs (10, 25, 50, and 100 mg kg−1) were used to determine their effects on the growth and nutrient absorption of Medicago polymorpha L., as well as their potential risk for human health. Results The results showed that ZnO and CuO NPs increased the fresh weight of Medicago polymorpha L. by 5.8–11.8 and 3.7–8.1%, respectively. The best performance for ZnO NPs occurred between 25–50 mg kg−1 and the best performance for CuO NPs occurred between 10–25 mg kg−1. Compared with the control, ZnO and CuO NPs improved the macronutrients phosphorus (P), potassium (K), magnesium (Mg), and calcium (Ca). The following micronutrients were also improved: iron (Fe), nickel (Ni), copper (Cu), zinc (Zn), and manganese (Mn), with the exception of nitrogen (N) accumulation. Low treatment concentrations exhibited more efficient nutrient uptake than high treatment concentrations. A comprehensive analysis showed that the optimum concentrations were 25 mg kg−1 for ZnO NPs and 10 mg kg−1 for CuO NPs. The potential non-carcinogenic health risk of Medicago polymorpha L. treated with ZnO and CuO NPs was analyzed according to the estimated daily intake (EDI), the hazard quotient (HQ), and the cumulative hazard quotient (CHQ). Compared with the oral reference dose, the EDI under different ZnO and CuO NPs treatments was lower. The HQ and CHQ under different ZnO and CuO NPs treatments were far below 1. This indicated that Medicago polymorpha L. treated with ZnO and CuO NPs did not pose a…
bibliographic citation: Ji et al. (2022) Effect of ZnO and CuO nanoparticles on the growth, nutrient absorption, and potential health risk of the seasonal vegetable Medicago polymorpha L.. PeerJ 10:e14038 https://doi.org/10.7717/peerj.14038
date submitted: 2022-01-11
date accepted: 2022-08-18
issued: 2022-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Hongting
author list: Agent
  family name: Guo
  given name: Zhi
author list: Agent
  family name: Wang
  given name: Guodong
author list: Agent
  family name: Wang
  given name: Xin
author list: Agent
  family name: Liu
  given name: Hongjiang
doi: 10.7717/peerj.14038
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-21
copyright: ©2022 Ji et al.
attribution name: Ji et al.

Physiological and biochemical responses of hybrid maize (Zea mays L.) varieties grown under heat stress conditions
type: item
type: AcademicArticle
description: Maize (Zea mays L.) is the second most commonly produced and consumed crop after wheat globally and is adversely affected by high heat, which is a significant abiotic stress factor. This study was carried out to determine the physiological and biochemical responses of hybrid corn varieties under heat stress (‘HS’) compared to control (‘C’) conditions during the 2020 and 2021 growing seasons. The experiment was conducted under natural conditions in the Southeastern region of Turkey, where the most intense temperatures are experienced. This experiment used split plots in randomized blocks with three replications, with ‘HS’ and ‘C’ growing conditions applied to the main plots and the different hybrid corn varieties (FAO 650) planted on the sub plots. Mean values of days to 50% tasseling (DT, day), grain yield (GY, kg ha−1), leaf water potential (LWP, %), chlorophyll-a (Chl-a, mg g−1), cell membrane damage (CMD, %), and total phenol content (TPC, μg g−1) were significantly different between years, growing conditions, and hybrid corn varieties. Changes in the climate played a significant role in the differences between the years and growing conditions (GC), while the genetic characteristics of the different corn varieties explained the differences in outcomes between them. The values of DT, GY, LWP, Chl-a, CMD, and TPC ranged from 49.06–53.15 days, 9,173.0–10,807.2 kg ha−1, 78.62–83.57%, 6.47–8.62 mg g−1, 9.61–13.54%, and 232.36–247.01 μg g−1, respectively. Significant correlations were recorded between all the parameters. Positive correlations were observed between all the variables except for CMD. The increased damage to cell membranes under ‘HS’ caused a decrease in the other measured variables, especially GY. In contrast, the GY increased with decreased CMD. CMD was important in determining the stress and tolerance level of corn varieties under ‘HS’ conditions. The GY and other physiological parameters of ADA 17.4 and SYM-307 candidate corn varieties surpassed the co…
format: application/pdf
format: text/html
creator: Timucin Tas
subject: Agricultural Science
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.14141
publisher: PeerJ Inc.
rights: © 2022 Tas
abstract: Maize (Zea mays L.) is the second most commonly produced and consumed crop after wheat globally and is adversely affected by high heat, which is a significant abiotic stress factor. This study was carried out to determine the physiological and biochemical responses of hybrid corn varieties under heat stress (‘HS’) compared to control (‘C’) conditions during the 2020 and 2021 growing seasons. The experiment was conducted under natural conditions in the Southeastern region of Turkey, where the most intense temperatures are experienced. This experiment used split plots in randomized blocks with three replications, with ‘HS’ and ‘C’ growing conditions applied to the main plots and the different hybrid corn varieties (FAO 650) planted on the sub plots. Mean values of days to 50% tasseling (DT, day), grain yield (GY, kg ha−1), leaf water potential (LWP, %), chlorophyll-a (Chl-a, mg g−1), cell membrane damage (CMD, %), and total phenol content (TPC, μg g−1) were significantly different between years, growing conditions, and hybrid corn varieties. Changes in the climate played a significant role in the differences between the years and growing conditions (GC), while the genetic characteristics of the different corn varieties explained the differences in outcomes between them. The values of DT, GY, LWP, Chl-a, CMD, and TPC ranged from 49.06–53.15 days, 9,173.0–10,807.2 kg ha−1, 78.62–83.57%, 6.47–8.62 mg g−1, 9.61–13.54%, and 232.36–247.01 μg g−1, respectively. Significant correlations were recorded between all the parameters. Positive correlations were observed between all the variables except for CMD. The increased damage to cell membranes under ‘HS’ caused a decrease in the other measured variables, especially GY. In contrast, the GY increased with decreased CMD. CMD was important in determining the stress and tolerance level of corn varieties under ‘HS’ conditions. The GY and other physiological parameters of ADA 17.4 and SYM-307 candidate corn varieties surpassed the co…
bibliographic citation: Tas (2022) Physiological and biochemical responses of hybrid maize (Zea mays L.) varieties grown under heat stress conditions. PeerJ 10:e14141 https://doi.org/10.7717/peerj.14141
date submitted: 2022-05-02
date accepted: 2022-09-07
issued: 2022-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tas
  given name: Timucin
doi: 10.7717/peerj.14141
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-21
copyright: © 2022 Tas
attribution name: Tas

High metabolic load distance in professional soccer according to competitive level and playing positions
type: item
type: AcademicArticle
description: Background High metabolic load distance provides global information about the soccer players’ total high-intensity activities. Thus, this study aimed to examine the Spanish professional soccer players’ high metabolic load distance profile, comparing competitive level and playing positions. Methods A total of 18,131 individual match observations were collected from outfield players competing during the 2018/2019 and 2019/20 seasons in the First and Second Spanish Professional Soccer Leagues (LaLiga™). High Metabolic Load Distance (HMLD; distance covered with a power consumption above 25.5 W·kg−1 and accelerations or decelerations (e.g., accelerating from 2 to 4 m·s−2 for 1 s) were included), and HMLD per minute (HMLDmin) were analyzed by the ChryonHego® video-tracking system. Players were classified according to their playing position as follows: Central Backs (CB), Full Backs (FB), Center Midfields (CM), Wide Midfields (WM), and Forwards (FW). Results No differences between competitive levels were found in any variable when all players were analyzed conjointly except for HMLDmin overall and during the second half. However, when playing positions were considered, differences between competitive levels were observed in all positions, mainly in HMLD and HMLD during the first-half variables. In addition, several differences between playing positions were observed, with CB presenting the lowest values in all variables compared to their counterparts in both competitive levels, whereas CM in First Division and WM in Second Division showed the highest values in the HMLD variables. Discussion The findings are of interest to analyze the HMLD in professional soccer players, enabling the adaptation and individualization of training in this population according to the competitive level and specific playing position of each player.
format: application/pdf
format: text/html
creator: Tomás García-Calvo
creator: José Carlos Ponce-Bordón
creator: Eduard Pons
creator: Roberto López del Campo
creator: Ricardo Resta
creator: Javier Raya-González
subject: Anatomy and Physiology
subject: Kinesiology
subject: Metabolic Sciences
subject: Sports Medicine
description: doi:10.7717/peerj.13318
publisher: PeerJ Inc.
rights: © 2022 García-Calvo et al.
abstract: Background High metabolic load distance provides global information about the soccer players’ total high-intensity activities. Thus, this study aimed to examine the Spanish professional soccer players’ high metabolic load distance profile, comparing competitive level and playing positions. Methods A total of 18,131 individual match observations were collected from outfield players competing during the 2018/2019 and 2019/20 seasons in the First and Second Spanish Professional Soccer Leagues (LaLiga™). High Metabolic Load Distance (HMLD; distance covered with a power consumption above 25.5 W·kg−1 and accelerations or decelerations (e.g., accelerating from 2 to 4 m·s−2 for 1 s) were included), and HMLD per minute (HMLDmin) were analyzed by the ChryonHego® video-tracking system. Players were classified according to their playing position as follows: Central Backs (CB), Full Backs (FB), Center Midfields (CM), Wide Midfields (WM), and Forwards (FW). Results No differences between competitive levels were found in any variable when all players were analyzed conjointly except for HMLDmin overall and during the second half. However, when playing positions were considered, differences between competitive levels were observed in all positions, mainly in HMLD and HMLD during the first-half variables. In addition, several differences between playing positions were observed, with CB presenting the lowest values in all variables compared to their counterparts in both competitive levels, whereas CM in First Division and WM in Second Division showed the highest values in the HMLD variables. Discussion The findings are of interest to analyze the HMLD in professional soccer players, enabling the adaptation and individualization of training in this population according to the competitive level and specific playing position of each player.
bibliographic citation: García-Calvo et al. (2022) High metabolic load distance in professional soccer according to competitive level and playing positions. PeerJ 10:e13318 https://doi.org/10.7717/peerj.13318
date submitted: 2022-02-18
date accepted: 2022-04-01
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Calvo
  given name: Tomás
author list: Agent
  family name: Ponce-Bordón
  given name: José Carlos
author list: Agent
  family name: Pons
  given name: Eduard
author list: Agent
  family name: López del Campo
  given name: Roberto
author list: Agent
  family name: Resta
  given name: Ricardo
author list: Agent
  family name: Raya-González
  given name: Javier
doi: 10.7717/peerj.13318
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: © 2022 García-Calvo et al.
attribution name: García-Calvo et al.

Context dependent prediction in DNA sequence using neural networks
type: item
type: AcademicArticle
description: One way to better understand the structure in DNA is by learning to predict the sequence. Here, we trained a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model was a neural network that obtained an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, the neural network performed significantly better than any of the alternative models by a large margin. We report on where the accuracy was obtained, first observing that the performance appeared to be uniform over the chromosomes. The models performed best in repetitive sequences, as expected, although their performance far from random in the more difficult coding sections, the proportions being ~70:40%. We further explored the sources of the accuracy, Fourier transforming the predictions revealed weak but clear periodic signals. In the human genome the characteristic periods hinted at connections to nucleosome positioning. We found similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before. On other large genomes similarly high accuracy was found, while lower predictive accuracy was observed on smaller genomes. Only in the mouse genome did we see periodic signals in the same range as in the human genome, though weaker and of a different type. This indicates that the sources of these signals are other or more than nucleosome arrangement. Interestingly, applying a model trained on the mouse genome to the human genome resulted in a performance far below that of the human model, except in the difficult coding regions. Despite the clear outcomes of the likelihood-ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures.
format: application/pdf
format: text/html
creator: Christian Grønbæk
creator: Yuhu Liang
creator: Desmond Elliott
creator: Anders Krogh
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Mathematical Biology
subject: Data Science
description: doi:10.7717/peerj.13666
publisher: PeerJ Inc.
rights: © 2022 Grønbæk et al.
abstract: One way to better understand the structure in DNA is by learning to predict the sequence. Here, we trained a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model was a neural network that obtained an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, the neural network performed significantly better than any of the alternative models by a large margin. We report on where the accuracy was obtained, first observing that the performance appeared to be uniform over the chromosomes. The models performed best in repetitive sequences, as expected, although their performance far from random in the more difficult coding sections, the proportions being ~70:40%. We further explored the sources of the accuracy, Fourier transforming the predictions revealed weak but clear periodic signals. In the human genome the characteristic periods hinted at connections to nucleosome positioning. We found similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before. On other large genomes similarly high accuracy was found, while lower predictive accuracy was observed on smaller genomes. Only in the mouse genome did we see periodic signals in the same range as in the human genome, though weaker and of a different type. This indicates that the sources of these signals are other or more than nucleosome arrangement. Interestingly, applying a model trained on the mouse genome to the human genome resulted in a performance far below that of the human model, except in the difficult coding regions. Despite the clear outcomes of the likelihood-ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures.
bibliographic citation: Grønbæk et al. (2022) Context dependent prediction in DNA sequence using neural networks. PeerJ 10:e13666 https://doi.org/10.7717/peerj.13666
date submitted: 2022-01-04
date accepted: 2022-06-10
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grønbæk
  given name: Christian
author list: Agent
  family name: Liang
  given name: Yuhu
author list: Agent
  family name: Elliott
  given name: Desmond
author list: Agent
  family name: Krogh
  given name: Anders
doi: 10.7717/peerj.13666
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: © 2022 Grønbæk et al.
attribution name: Grønbæk et al.

Bioinformatics prediction and experimental verification of key biomarkers for diabetic kidney disease based on transcriptome sequencing in mice
type: item
type: AcademicArticle
description: Background Diabetic kidney disease (DKD) is the leading cause of death in people with type 2 diabetes mellitus (T2DM). The main objective of this study is to find the potential biomarkers for DKD. Materials and Methods Two datasets (GSE86300 and GSE184836) retrieved from Gene Expression Omnibus (GEO) database were used, combined with our RNA sequencing (RNA-seq) results of DKD mice (C57 BLKS-32w db/db) and non-diabetic (db/m) mice for further analysis. After processing the expression matrix of the three sets of data using R software “Limma”, differential expression analysis was performed. The significantly differentially expressed genes (DEGs) (—logFC— > 1, p-value < 0.05) were visualized by heatmaps and volcano plots respectively. Next, the co-expression genes expressed in the three groups of DEGs were obtained by constructing a Venn diagram. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were further analyzed the related functions and enrichment pathways of these co-expression genes. Then, qRT-PCR was used to verify the expression levels of co-expression genes in the kidney of DKD and control mice. Finally, protein-protein interaction network (PPI), GO, KEGG analysis and Pearson correlation test were performed on the experimentally validated genes, in order to clarify the possible mechanism of them in DKD. Results Our RNA-seq results identified a total of 125 DEGs, including 59 up-regulated and 66 down-regulated DEGs. At the same time, 183 up-regulated and 153 down-regulated DEGs were obtained in GEO database GSE86300, and 76 up-regulated and 117 down-regulated DEGs were obtained in GSE184836. Venn diagram showed that 13 co-expression DEGs among the three groups of DEGs. GO analysis showed that biological processes (BP) were mainly enriched inresponse to stilbenoid, response to fatty acid, response to nutrient, positive regulation of macrophage derived foam cell differentiation, triglyceride metabolic…
format: application/pdf
format: text/html
creator: Jing Zhao
creator: Kaiying He
creator: Hongxuan Du
creator: Guohua Wei
creator: Yuejia Wen
creator: Jiaqi Wang
creator: Xiaochun Zhou
creator: Jianqin Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Diabetes and Endocrinology
subject: Nephrology
subject: Medical Genetics
description: doi:10.7717/peerj.13932
publisher: PeerJ Inc.
rights: © 2022 Zhao et al.
abstract: Background Diabetic kidney disease (DKD) is the leading cause of death in people with type 2 diabetes mellitus (T2DM). The main objective of this study is to find the potential biomarkers for DKD. Materials and Methods Two datasets (GSE86300 and GSE184836) retrieved from Gene Expression Omnibus (GEO) database were used, combined with our RNA sequencing (RNA-seq) results of DKD mice (C57 BLKS-32w db/db) and non-diabetic (db/m) mice for further analysis. After processing the expression matrix of the three sets of data using R software “Limma”, differential expression analysis was performed. The significantly differentially expressed genes (DEGs) (—logFC— > 1, p-value < 0.05) were visualized by heatmaps and volcano plots respectively. Next, the co-expression genes expressed in the three groups of DEGs were obtained by constructing a Venn diagram. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were further analyzed the related functions and enrichment pathways of these co-expression genes. Then, qRT-PCR was used to verify the expression levels of co-expression genes in the kidney of DKD and control mice. Finally, protein-protein interaction network (PPI), GO, KEGG analysis and Pearson correlation test were performed on the experimentally validated genes, in order to clarify the possible mechanism of them in DKD. Results Our RNA-seq results identified a total of 125 DEGs, including 59 up-regulated and 66 down-regulated DEGs. At the same time, 183 up-regulated and 153 down-regulated DEGs were obtained in GEO database GSE86300, and 76 up-regulated and 117 down-regulated DEGs were obtained in GSE184836. Venn diagram showed that 13 co-expression DEGs among the three groups of DEGs. GO analysis showed that biological processes (BP) were mainly enriched inresponse to stilbenoid, response to fatty acid, response to nutrient, positive regulation of macrophage derived foam cell differentiation, triglyceride metabolic…
bibliographic citation: Zhao et al. (2022) Bioinformatics prediction and experimental verification of key biomarkers for diabetic kidney disease based on transcriptome sequencing in mice. PeerJ 10:e13932 https://doi.org/10.7717/peerj.13932
date submitted: 2022-05-24
date accepted: 2022-07-31
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Jing
author list: Agent
  family name: He
  given name: Kaiying
author list: Agent
  family name: Du
  given name: Hongxuan
author list: Agent
  family name: Wei
  given name: Guohua
author list: Agent
  family name: Wen
  given name: Yuejia
author list: Agent
  family name: Wang
  given name: Jiaqi
author list: Agent
  family name: Zhou
  given name: Xiaochun
author list: Agent
  family name: Wang
  given name: Jianqin
doi: 10.7717/peerj.13932
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: ©2022 Zhao et al.
attribution name: Zhao et al.

Sexual dimorphism in the walrus mandible: comparative description and geometric morphometrics
type: item
type: AcademicArticle
description: The modern walrus Odobenus rosmarus is characterized by marked sexual dimorphism, related to its polygynous behavior and the aggressive competition between males during the breeding season. Previous studies treated skeletal sexual dimorphism in walruses either qualitatively or with basic quantitative measurements. The present study combines a detailed qualitative comparison of male and female walrus mandibles with quantitative two-dimensional geometric morphometrics analysis (principal component analysis, Procrustes ANOVA and a linear discriminant analysis). In addition to identifying previously recognized sexually dimorphic features (e.g., convexity of the anterior margin of the mandible in adult males), our study finds new morphological differences between males and females, such as a relative dorsal expansion of the anterior part of the mandible and an accentuated concavity between the dorsal margin and the coronoid process in adult males. Both our qualitative comparisons and quantitative analyses demonstrate that sexual dimorphism as expressed in the mandible of extant walruses is statistically significant and that (variation in) mandibular morphology can be used as tool to attribute sex with a good degree of accuracy to isolated mandibles or skeletons lacking the cranium. Sexual dimorphism in walruses is directly related to their sexual behavior, characterized as aggressive in males and linked to a polygynous reproduction system. Indeed, the difference in size of the tusks between males and females but also the use of these during intraspecific fights, can reasonably account for this great mandibular morphological disparity between adult males and females, but also among different ontogenetic stages. Finally, the results obtained in the present study may serve as a starting point for assessing sexual dimorphism more in-depth and studying inter- and intraspecific variation in the mandibles of fossil walruses by identifying quantified size and shape mandibular fe…
format: application/pdf
format: text/html
creator: Mathieu Boisville
creator: Narimane Chatar
creator: Olivier Lambert
creator: Leonard Dewaele
subject: Marine Biology
subject: Taxonomy
subject: Zoology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.13940
publisher: PeerJ Inc.
rights: © 2022 Boisville et al.
abstract: The modern walrus Odobenus rosmarus is characterized by marked sexual dimorphism, related to its polygynous behavior and the aggressive competition between males during the breeding season. Previous studies treated skeletal sexual dimorphism in walruses either qualitatively or with basic quantitative measurements. The present study combines a detailed qualitative comparison of male and female walrus mandibles with quantitative two-dimensional geometric morphometrics analysis (principal component analysis, Procrustes ANOVA and a linear discriminant analysis). In addition to identifying previously recognized sexually dimorphic features (e.g., convexity of the anterior margin of the mandible in adult males), our study finds new morphological differences between males and females, such as a relative dorsal expansion of the anterior part of the mandible and an accentuated concavity between the dorsal margin and the coronoid process in adult males. Both our qualitative comparisons and quantitative analyses demonstrate that sexual dimorphism as expressed in the mandible of extant walruses is statistically significant and that (variation in) mandibular morphology can be used as tool to attribute sex with a good degree of accuracy to isolated mandibles or skeletons lacking the cranium. Sexual dimorphism in walruses is directly related to their sexual behavior, characterized as aggressive in males and linked to a polygynous reproduction system. Indeed, the difference in size of the tusks between males and females but also the use of these during intraspecific fights, can reasonably account for this great mandibular morphological disparity between adult males and females, but also among different ontogenetic stages. Finally, the results obtained in the present study may serve as a starting point for assessing sexual dimorphism more in-depth and studying inter- and intraspecific variation in the mandibles of fossil walruses by identifying quantified size and shape mandibular fe…
bibliographic citation: Boisville et al. (2022) Sexual dimorphism in the walrus mandible: comparative description and geometric morphometrics. PeerJ 10:e13940 https://doi.org/10.7717/peerj.13940
date submitted: 2022-04-28
date accepted: 2022-08-02
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boisville
  given name: Mathieu
author list: Agent
  family name: Chatar
  given name: Narimane
author list: Agent
  family name: Lambert
  given name: Olivier
author list: Agent
  family name: Dewaele
  given name: Leonard
doi: 10.7717/peerj.13940
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: ©2022 Boisville et al.
attribution name: Boisville et al.

Thermography in ergonomic assessment: a study of wood processing industry workers
type: item
type: AcademicArticle
description: Background Workers in the wood processing industry perform activities that demand great physical and ergonomic demands, which favors the emergence of inflammatory processes and in turn the occurrence of heat regions in the body, thus making it possible to assess the inflammatory level by means of temperature gradients. This study aimed to evaluate the use of thermography as an ergonomic analysis tool to identify regions with musculoskeletal overload in workers in a wood processing industry. Methods The study was conducted with nine workers in the central-west region of Brazil. The evaluations to obtain the thermographic images were carried out before the beginning of the workday, on Monday (day I) and on Friday (day II), in order to verify the overload regions in the accumulation of days worked. The thermal images were collected in an acclimatized room with controlled conditions where the participants remained with the upper part of their bodies bare for acclimatization, and then the lumbar and scapular regions were evaluated. The images were obtained using the FLUKE TI 400 Thermal Imager, with analysis using the SmartView software program to demarcate the body regions of interest. Results The mean temperature values obtained on day I did not significantly differ from the mean values obtained on day II. Qualitative analysis showed thermal patterns with high temperature at the same points on both evaluated days. Although the thermographic analysis performed in this study cannot provide definitive results, they generally helped to provide evidence for a more accurate diagnosis in the evaluated workers.
format: application/pdf
format: text/html
creator: Denise Ransolin Soranso
creator: Luciano José Minette
creator: Marcio Marçal
creator: João Carlos Bouzas Marins
creator: Stanley Schettino
creator: Roldão Carlos A. Lima
creator: Michel Oliveira
subject: Global Health
subject: Kinesiology
subject: Radiology and Medical Imaging
subject: Environmental Health
subject: Biomechanics
description: doi:10.7717/peerj.13973
publisher: PeerJ Inc.
rights: © 2022 Soranso et al.
abstract: Background Workers in the wood processing industry perform activities that demand great physical and ergonomic demands, which favors the emergence of inflammatory processes and in turn the occurrence of heat regions in the body, thus making it possible to assess the inflammatory level by means of temperature gradients. This study aimed to evaluate the use of thermography as an ergonomic analysis tool to identify regions with musculoskeletal overload in workers in a wood processing industry. Methods The study was conducted with nine workers in the central-west region of Brazil. The evaluations to obtain the thermographic images were carried out before the beginning of the workday, on Monday (day I) and on Friday (day II), in order to verify the overload regions in the accumulation of days worked. The thermal images were collected in an acclimatized room with controlled conditions where the participants remained with the upper part of their bodies bare for acclimatization, and then the lumbar and scapular regions were evaluated. The images were obtained using the FLUKE TI 400 Thermal Imager, with analysis using the SmartView software program to demarcate the body regions of interest. Results The mean temperature values obtained on day I did not significantly differ from the mean values obtained on day II. Qualitative analysis showed thermal patterns with high temperature at the same points on both evaluated days. Although the thermographic analysis performed in this study cannot provide definitive results, they generally helped to provide evidence for a more accurate diagnosis in the evaluated workers.
bibliographic citation: Soranso et al. (2022) Thermography in ergonomic assessment: a study of wood processing industry workers. PeerJ 10:e13973 https://doi.org/10.7717/peerj.13973
date submitted: 2022-05-16
date accepted: 2022-08-09
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soranso
  given name: Denise Ransolin
author list: Agent
  family name: Minette
  given name: Luciano José
author list: Agent
  family name: Marçal
  given name: Marcio
author list: Agent
  family name: Marins
  given name: João Carlos Bouzas
author list: Agent
  family name: Schettino
  given name: Stanley
author list: Agent
  family name: Lima
  given name: Roldão Carlos A.
author list: Agent
  family name: Oliveira
  given name: Michel
doi: 10.7717/peerj.13973
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: ©2022 Soranso et al.
attribution name: Soranso et al.

Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of Plukenetia volubilis
type: item
type: AcademicArticle
description: Background Plukenetia volubilis is cultivated as a valuable oilseed crop, and its mature seeds are rich in polyunsaturated fatty acids (FAs), which are widely used in food and pharmaceutical industries. Recently, next-generation sequencing (NGS) transcriptome studies in P. volubilis indicated that some candidate genes were involved in oil biosynthesis. The NGS were inaccuracies in assembly of some candidate genes, leading to unknown errors in date analyses. However, single molecular real-time (SMRT) sequencing can overcome these assembled errors. Unfortunately, this technique has not been reported in P. volubilis. Methods The total oil content of P. volubilis seed (PVS) was determined using Soxhlet extraction system. The FA composition were analyzed by gas chromatography. Combining PacBio SMRT and Illumina technologies, the transcriptome analysis of developing PVS was performed. Functional annotation and differential expression were performed by BLAST software (version 2.2.26) and RSEM software (version 1.2.31), respectively. The lncRNA-targeted transcripts were predicted in developing PVS using LncTar tool. Results By Soxhlet extraction system, the oil content of superior plant-type (SPT) was 13.47% higher than that of inferior plant-type (IPT) at mature PVS. The most abundant FAs were C18:2 and C18:3, among which C18:3 content of SPT was 1.11-fold higher than that of IPT. Combined with PacBio and Illumina platform, 68,971 non-redundant genes were obtained, among which 7,823 long non-coding RNAs (lncRNAs) and 7,798 lncRNA-targeted genes were predicted. In developing seed, the expressions of 57 TFs showed a significantly positive correlation with oil contents, including WRI1-like1, LEC1-like1, and MYB44-like. Comparative analysis of expression profiles between SPT and IPT implied that orthologs of FAD3, PDCT, PDAT, and DAGT2 were possibly important for the accumulation of polyunsaturated FAs. Together, these results provide a reference for oil biosynthesis of P. vol…
format: application/pdf
format: text/html
creator: Yijun Fu
creator: Kaisen Huo
creator: Xingjie Pei
creator: Chongjun Liang
creator: Xinya Meng
creator: Xiqiang Song
creator: Jia Wang
creator: Jun Niu
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13998
publisher: PeerJ Inc.
rights: © 2022 Fu et al.
abstract: Background Plukenetia volubilis is cultivated as a valuable oilseed crop, and its mature seeds are rich in polyunsaturated fatty acids (FAs), which are widely used in food and pharmaceutical industries. Recently, next-generation sequencing (NGS) transcriptome studies in P. volubilis indicated that some candidate genes were involved in oil biosynthesis. The NGS were inaccuracies in assembly of some candidate genes, leading to unknown errors in date analyses. However, single molecular real-time (SMRT) sequencing can overcome these assembled errors. Unfortunately, this technique has not been reported in P. volubilis. Methods The total oil content of P. volubilis seed (PVS) was determined using Soxhlet extraction system. The FA composition were analyzed by gas chromatography. Combining PacBio SMRT and Illumina technologies, the transcriptome analysis of developing PVS was performed. Functional annotation and differential expression were performed by BLAST software (version 2.2.26) and RSEM software (version 1.2.31), respectively. The lncRNA-targeted transcripts were predicted in developing PVS using LncTar tool. Results By Soxhlet extraction system, the oil content of superior plant-type (SPT) was 13.47% higher than that of inferior plant-type (IPT) at mature PVS. The most abundant FAs were C18:2 and C18:3, among which C18:3 content of SPT was 1.11-fold higher than that of IPT. Combined with PacBio and Illumina platform, 68,971 non-redundant genes were obtained, among which 7,823 long non-coding RNAs (lncRNAs) and 7,798 lncRNA-targeted genes were predicted. In developing seed, the expressions of 57 TFs showed a significantly positive correlation with oil contents, including WRI1-like1, LEC1-like1, and MYB44-like. Comparative analysis of expression profiles between SPT and IPT implied that orthologs of FAD3, PDCT, PDAT, and DAGT2 were possibly important for the accumulation of polyunsaturated FAs. Together, these results provide a reference for oil biosynthesis of P. vol…
bibliographic citation: Fu et al. (2022) Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of Plukenetia volubilis. PeerJ 10:e13998 https://doi.org/10.7717/peerj.13998
date submitted: 2022-03-29
date accepted: 2022-08-12
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Yijun
author list: Agent
  family name: Huo
  given name: Kaisen
author list: Agent
  family name: Pei
  given name: Xingjie
author list: Agent
  family name: Liang
  given name: Chongjun
author list: Agent
  family name: Meng
  given name: Xinya
author list: Agent
  family name: Song
  given name: Xiqiang
author list: Agent
  family name: Wang
  given name: Jia
author list: Agent
  family name: Niu
  given name: Jun
doi: 10.7717/peerj.13998
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: ©2022 Fu et al.
attribution name: Fu et al.

Estuarine microbial networks and relationships vary between environmentally distinct communities
type: item
type: AcademicArticle
description: Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO3, and SiO4; only NH4 was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. …
format: application/pdf
format: text/html
creator: Sean R. Anderson
creator: Elizabeth L. Harvey
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.14005
publisher: PeerJ Inc.
rights: © 2022 Anderson and Harvey
abstract: Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO3, and SiO4; only NH4 was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. …
bibliographic citation: Anderson et al. (2022) Estuarine microbial networks and relationships vary between environmentally distinct communities. PeerJ 10:e14005 https://doi.org/10.7717/peerj.14005
date submitted: 2022-01-07
date accepted: 2022-08-14
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Anderson
  given name: Sean R.
author list: Agent
  family name: Harvey
  given name: Elizabeth L.
doi: 10.7717/peerj.14005
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: ©2022 Anderson and Harvey
attribution name: Anderson and Harvey

Hepatic metabolite responses to 4-day complete fasting and subsequent refeeding in rats
type: item
type: AcademicArticle
description: Background Fasting has been widely used to improve various metabolic diseases in humans. Adaptive fasting is necessary for metabolic adaptation during prolonged fasting, which could overcome the great advantages of short-term fasting. The liver is the main organ responsible for energy metabolism and metabolic homeostasis. To date, we lack literature that describes the physiologically relevant adaptations of the liver during prolonged fasting and refeeding. For that reason, this study aims to evaluate the response of the liver of Sprague-Dawley (SD) rats to prolonged fasting and refeeding. Methods Sixty-six male SD rats were divided into the fasting groups, which were fasted for 0, 4, 8, 12, 24, 48, 72, or 96 h, and the refeeding groups, which were refed for 1, 3, or 6 days after 96 h of fasting. Serum glucose, TG, FFA, β-hydroxybutyrate, insulin, glucagon, leptin, adiponectin and FGF21 levels were assessed. The glucose content, PEPCK activity, TG concentration and FFA content were measured in liver tissue, and the expression of genes involved in gluconeogenesis (PEPCK and G6Pase), ketogenesis (PPARα, CPT-1a and HMGCS2) and the protein expression of nutrient-sensing signaling molecules (AMPK, mTOR and SIRT1) were determined by RT-qPCR and western blotting, respectively. Results Fasting significantly decreased the body weight, which was totally recovered to baseline after 3 days of refeeding. A 4-day fast triggered an energy metabolic substrate shift from glucose to ketones and caused serum hormone changes and changes in the protein expression levels of nutrient-sensing signaling molecules. Glycogenolysis served as the primary fuel source during the first 24 h of fasting, while gluconeogenesis supplied the most glucose thereafter. Serum FFA concentrations increased significantly with 48 h of fasting. Serum FFAs partly caused high serum β-hydroxybutyrate levels, which became an important energy source with the prolongation of the fasting duration. One day of refeeding …
format: application/pdf
format: text/html
creator: Xiukun Sui
creator: Hailong Wang
creator: Feng Wu
creator: Chao Yang
creator: Hongyu Zhang
creator: Zihan Xu
creator: Yaxiu Guo
creator: ZhiFeng Guo
creator: Bingmu Xin
creator: Ting Ma
creator: Yinghui Li
creator: Zhongquan Dai
subject: Biochemistry
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Nutrition
subject: Metabolic Sciences
description: doi:10.7717/peerj.14009
publisher: PeerJ Inc.
rights: © 2022 Sui et al.
abstract: Background Fasting has been widely used to improve various metabolic diseases in humans. Adaptive fasting is necessary for metabolic adaptation during prolonged fasting, which could overcome the great advantages of short-term fasting. The liver is the main organ responsible for energy metabolism and metabolic homeostasis. To date, we lack literature that describes the physiologically relevant adaptations of the liver during prolonged fasting and refeeding. For that reason, this study aims to evaluate the response of the liver of Sprague-Dawley (SD) rats to prolonged fasting and refeeding. Methods Sixty-six male SD rats were divided into the fasting groups, which were fasted for 0, 4, 8, 12, 24, 48, 72, or 96 h, and the refeeding groups, which were refed for 1, 3, or 6 days after 96 h of fasting. Serum glucose, TG, FFA, β-hydroxybutyrate, insulin, glucagon, leptin, adiponectin and FGF21 levels were assessed. The glucose content, PEPCK activity, TG concentration and FFA content were measured in liver tissue, and the expression of genes involved in gluconeogenesis (PEPCK and G6Pase), ketogenesis (PPARα, CPT-1a and HMGCS2) and the protein expression of nutrient-sensing signaling molecules (AMPK, mTOR and SIRT1) were determined by RT-qPCR and western blotting, respectively. Results Fasting significantly decreased the body weight, which was totally recovered to baseline after 3 days of refeeding. A 4-day fast triggered an energy metabolic substrate shift from glucose to ketones and caused serum hormone changes and changes in the protein expression levels of nutrient-sensing signaling molecules. Glycogenolysis served as the primary fuel source during the first 24 h of fasting, while gluconeogenesis supplied the most glucose thereafter. Serum FFA concentrations increased significantly with 48 h of fasting. Serum FFAs partly caused high serum β-hydroxybutyrate levels, which became an important energy source with the prolongation of the fasting duration. One day of refeeding …
bibliographic citation: Sui et al. (2022) Hepatic metabolite responses to 4-day complete fasting and subsequent refeeding in rats. PeerJ 10:e14009 https://doi.org/10.7717/peerj.14009
date submitted: 2022-02-08
date accepted: 2022-08-15
issued: 2022-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sui
  given name: Xiukun
author list: Agent
  family name: Wang
  given name: Hailong
author list: Agent
  family name: Wu
  given name: Feng
author list: Agent
  family name: Yang
  given name: Chao
author list: Agent
  family name: Zhang
  given name: Hongyu
author list: Agent
  family name: Xu
  given name: Zihan
author list: Agent
  family name: Guo
  given name: Yaxiu
author list: Agent
  family name: Guo
  given name: ZhiFeng
author list: Agent
  family name: Xin
  given name: Bingmu
author list: Agent
  family name: Ma
  given name: Ting
author list: Agent
  family name: Li
  given name: Yinghui
author list: Agent
  family name: Dai
  given name: Zhongquan
doi: 10.7717/peerj.14009
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-20
copyright: ©2022 Sui et al.
attribution name: Sui et al.

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