PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Development of a T-cell activation-related module with predictive value for the prognosis and immune checkpoint blockade therapy response in glioblastoma
items: The metabolism and role of free fatty acids in key physiological processes in insects of medical, veterinary and forensic importance
items: Wearable technology to inform the prediction and diagnosis of cardiorespiratory events: a scoping review
items: Effects of short-term nitrogen and phosphorus addition on leaf stoichiometry of a dominant alpine grass
items: Identification of HMMR as a prognostic biomarker for patients with lung adenocarcinoma via integrated bioinformatics analysis
items: 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
items: Small herbivores and abiotic heterogeneity promote trait variation of a saltmarsh plant in local communities
items: Ferric citrate is a safe and digestible source of iron in broilers and piglets
items: Impact of climatic conditions projected at the World Cup in Qatar 2022 on repeated maximal efforts in soccer players
items: A taxonomic outline of the Poecilimon affinis complex (Orthoptera) using the geometric morphometric approach

Development of a T-cell activation-related module with predictive value for the prognosis and immune checkpoint blockade therapy response in glioblastoma
type: item
type: AcademicArticle
description: Background Despite the rise in the use of immune checkpoint blockade drugs (ICBs) in recent years, there are no ICB drugs that are currently approved or under large-scale clinical trials for glioblastoma (GBM). T-cells, which mainly mediate adaptive immunity, are an important part of the tumor immune microenvironment. The activation of T-cells in tumors plays a key role in evaluating the sensitivity of patients to immunotherapy. Therefore, we applied bioinformatics approaches to construct a T-cell activation related risk score to study the effect of the activation of T-cells on the prognosis and ICB response of patients with GBM. Materials and Methods This study collected TCGA, CGGA, and GSE16011 glioma cohorts, as well as the IMvigor210 immunotherapy dataset, with complete mRNA expression profiles and clinical information. GraphPad Prism 8 and R 3.6.3 were used for bioinformatics analysis and plotting. Results The activation of T-cells in patients with GBM is characterized by obvious heterogeneity. We established a T-cell activation-related risk score based on five univariate Cox regression prognostic genes (CD276, IL15, SLC11A1, TNFSF4, and TREML2) in GBM. The risk score was an independent risk factor for poor prognosis. The overall survival time of patients in the high-risk group was significantly lower than in the low-risk group. Moreover, the high-risk score was accompanied by a stronger immune response and a more complex tumor immune microenvironment. “Hot tumors” were mainly enriched in the high-risk group, and high-risk group patients highly expressed inhibitory immune checkpoints (PD1, PD-L1, TIM3 etc.). By combining the risk and priming scores we obtained the immunotherapy score, which was shown to be a good evaluation index for sensitivity to GBM immunotherapy. Conclusions As an independent risk factor for poor prognosis, the T-cell activation-related risk score, combined with other clinical characteristics, could efficiently evaluate the survival of pati…
format: application/pdf
format: text/html
creator: Zihao Yan
creator: Siwen Chu
creator: Chen Zhu
creator: Yunhe Han
creator: Qingyu Liang
creator: Shuai Shen
creator: Wen Cheng
creator: Anhua Wu
subject: Bioinformatics
subject: Immunology
subject: Neurology
subject: Oncology
description: doi:10.7717/peerj.12547
publisher: PeerJ Inc.
rights: © 2021 Yan et al.
abstract: Background Despite the rise in the use of immune checkpoint blockade drugs (ICBs) in recent years, there are no ICB drugs that are currently approved or under large-scale clinical trials for glioblastoma (GBM). T-cells, which mainly mediate adaptive immunity, are an important part of the tumor immune microenvironment. The activation of T-cells in tumors plays a key role in evaluating the sensitivity of patients to immunotherapy. Therefore, we applied bioinformatics approaches to construct a T-cell activation related risk score to study the effect of the activation of T-cells on the prognosis and ICB response of patients with GBM. Materials and Methods This study collected TCGA, CGGA, and GSE16011 glioma cohorts, as well as the IMvigor210 immunotherapy dataset, with complete mRNA expression profiles and clinical information. GraphPad Prism 8 and R 3.6.3 were used for bioinformatics analysis and plotting. Results The activation of T-cells in patients with GBM is characterized by obvious heterogeneity. We established a T-cell activation-related risk score based on five univariate Cox regression prognostic genes (CD276, IL15, SLC11A1, TNFSF4, and TREML2) in GBM. The risk score was an independent risk factor for poor prognosis. The overall survival time of patients in the high-risk group was significantly lower than in the low-risk group. Moreover, the high-risk score was accompanied by a stronger immune response and a more complex tumor immune microenvironment. “Hot tumors” were mainly enriched in the high-risk group, and high-risk group patients highly expressed inhibitory immune checkpoints (PD1, PD-L1, TIM3 etc.). By combining the risk and priming scores we obtained the immunotherapy score, which was shown to be a good evaluation index for sensitivity to GBM immunotherapy. Conclusions As an independent risk factor for poor prognosis, the T-cell activation-related risk score, combined with other clinical characteristics, could efficiently evaluate the survival of pati…
bibliographic citation: Yan et al. (2021) Development of a T-cell activation-related module with predictive value for the prognosis and immune checkpoint blockade therapy response in glioblastoma. PeerJ 9:e12547 https://doi.org/10.7717/peerj.12547
date submitted: 2021-07-16
date accepted: 2021-11-04
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Zihao
author list: Agent
  family name: Chu
  given name: Siwen
author list: Agent
  family name: Zhu
  given name: Chen
author list: Agent
  family name: Han
  given name: Yunhe
author list: Agent
  family name: Liang
  given name: Qingyu
author list: Agent
  family name: Shen
  given name: Shuai
author list: Agent
  family name: Cheng
  given name: Wen
author list: Agent
  family name: Wu
  given name: Anhua
doi: 10.7717/peerj.12547
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: © 2021 Yan et al.
attribution name: Yan et al.

The metabolism and role of free fatty acids in key physiological processes in insects of medical, veterinary and forensic importance
type: item
type: AcademicArticle
description: Insects are the most widespread group of organisms and more than one million species have been described. These animals have significant ecological functions, for example they are pollinators of many types of plants. However, they also have direct influence on human life in different manners. They have high medical and veterinary significance, stemming from their role as vectors of disease and infection of wounds and necrotic tissue; they are also plant pests, parasitoids and predators whose activities can influence agriculture. In addition, their use in medical treatments, such as maggot therapy of gangrene and wounds, has grown considerably. They also have many uses in forensic science to determine the minimum post-mortem interval and provide valuable information about the movement of the body, cause of the death, drug use, or poisoning. It has also been proposed that they may be used as model organisms to replace mammal systems in research. The present review describes the role of free fatty acids (FFAs) in key physiological processes in insects. By focusing on insects of medical, veterinary significance, we have limited our description of the physiological processes to those most important from the point of view of insect control; the study examines their effects on insect reproduction and resistance to the adverse effects of abiotic (low temperature) and biotic (pathogens) factors.
format: application/pdf
format: text/html
creator: Agata Kaczmarek
creator: Mieczysława Boguś
subject: Biochemistry
subject: Entomology
subject: Zoology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.12563
publisher: PeerJ Inc.
rights: © 2021 Kaczmarek and Boguś
abstract: Insects are the most widespread group of organisms and more than one million species have been described. These animals have significant ecological functions, for example they are pollinators of many types of plants. However, they also have direct influence on human life in different manners. They have high medical and veterinary significance, stemming from their role as vectors of disease and infection of wounds and necrotic tissue; they are also plant pests, parasitoids and predators whose activities can influence agriculture. In addition, their use in medical treatments, such as maggot therapy of gangrene and wounds, has grown considerably. They also have many uses in forensic science to determine the minimum post-mortem interval and provide valuable information about the movement of the body, cause of the death, drug use, or poisoning. It has also been proposed that they may be used as model organisms to replace mammal systems in research. The present review describes the role of free fatty acids (FFAs) in key physiological processes in insects. By focusing on insects of medical, veterinary significance, we have limited our description of the physiological processes to those most important from the point of view of insect control; the study examines their effects on insect reproduction and resistance to the adverse effects of abiotic (low temperature) and biotic (pathogens) factors.
bibliographic citation: Kaczmarek et al. (2021) The metabolism and role of free fatty acids in key physiological processes in insects of medical, veterinary and forensic importance. PeerJ 9:e12563 https://doi.org/10.7717/peerj.12563
date submitted: 2021-06-26
date accepted: 2021-11-07
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaczmarek
  given name: Agata
author list: Agent
  family name: Boguś
  given name: Mieczysława
doi: 10.7717/peerj.12563
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Kaczmarek and Boguś
attribution name: Kaczmarek and Boguś

Wearable technology to inform the prediction and diagnosis of cardiorespiratory events: a scoping review
type: item
type: AcademicArticle
description: Background The need for health systems that allow for continuous monitoring and early adverse event detection in individuals outside of the acute care setting has been highlighted by the global rise in chronic cardiorespiratory diseases and the recent COVID-19 pandemic. Currently, it is unclear what type of evidence exists concerning the use of physiological data collected from commercially available wrist and textile wearables to assist in clinical decision making. The aim of this review was therefore to systematically map and summarize the scientific literature surrounding the use of these wearables in clinical decision making as well as identify knowledge gaps to inform further research. Methodology Six electronic bibliographic databases were systematically searched (Ovid MEDLINE, EMBASE, CINAHL, PubMed, Scopus, and SportsDiscus). Publications from database inception to May 6, 2020 were reviewed for inclusion. Non-indexed literature relevant to this review was also searched systematically. Results were then collated, summarized and reported. Results A total of 107 citations were retrieved and assessed for eligibility with 31 citations included in the final analysis. A review of the 31 papers revealed three major study designs which included (1) observational studies (n = 19), (2) case control series and reports (n = 8), and (3) reviews (n = 2). All papers examined the use of wearable monitoring devices for clinical decisions in the cardiovascular domain, with cardiac arrhythmias being the most studied. When compared to electrocardiogram (ECG) the performance of the wearables in facilitating clinical decisions varied depending upon the type of wearable, user’s activity levels and setting in which they were employed. Observational studies collecting data in the inpatient and outpatient settings were equally represented. Eight case control series and reports were identified which reported on the use of wrist wearables in patients presenting to an emergency departmen…
format: application/pdf
format: text/html
creator: Hamzeh Khundaqji
creator: Wayne Hing
creator: James Furness
creator: Mike Climstein
subject: Cardiology
subject: Drugs and Devices
subject: Public Health
subject: Respiratory Medicine
description: doi:10.7717/peerj.12598
publisher: PeerJ Inc.
rights: © 2021 Khundaqji et al.
abstract: Background The need for health systems that allow for continuous monitoring and early adverse event detection in individuals outside of the acute care setting has been highlighted by the global rise in chronic cardiorespiratory diseases and the recent COVID-19 pandemic. Currently, it is unclear what type of evidence exists concerning the use of physiological data collected from commercially available wrist and textile wearables to assist in clinical decision making. The aim of this review was therefore to systematically map and summarize the scientific literature surrounding the use of these wearables in clinical decision making as well as identify knowledge gaps to inform further research. Methodology Six electronic bibliographic databases were systematically searched (Ovid MEDLINE, EMBASE, CINAHL, PubMed, Scopus, and SportsDiscus). Publications from database inception to May 6, 2020 were reviewed for inclusion. Non-indexed literature relevant to this review was also searched systematically. Results were then collated, summarized and reported. Results A total of 107 citations were retrieved and assessed for eligibility with 31 citations included in the final analysis. A review of the 31 papers revealed three major study designs which included (1) observational studies (n = 19), (2) case control series and reports (n = 8), and (3) reviews (n = 2). All papers examined the use of wearable monitoring devices for clinical decisions in the cardiovascular domain, with cardiac arrhythmias being the most studied. When compared to electrocardiogram (ECG) the performance of the wearables in facilitating clinical decisions varied depending upon the type of wearable, user’s activity levels and setting in which they were employed. Observational studies collecting data in the inpatient and outpatient settings were equally represented. Eight case control series and reports were identified which reported on the use of wrist wearables in patients presenting to an emergency departmen…
bibliographic citation: Khundaqji et al. (2021) Wearable technology to inform the prediction and diagnosis of cardiorespiratory events: a scoping review. PeerJ 9:e12598 https://doi.org/10.7717/peerj.12598
date submitted: 2021-07-21
date accepted: 2021-11-15
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khundaqji
  given name: Hamzeh
author list: Agent
  family name: Hing
  given name: Wayne
author list: Agent
  family name: Furness
  given name: James
author list: Agent
  family name: Climstein
  given name: Mike
doi: 10.7717/peerj.12598
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Khundaqji et al.
attribution name: Khundaqji et al.

Effects of short-term nitrogen and phosphorus addition on leaf stoichiometry of a dominant alpine grass
type: item
type: AcademicArticle
description: The effects of increasing nitrogen (N) and phosphorus (P) deposition on the nutrient stoichiometry of soil and plant are gaining improving recognition. However, whether and how the responses of N cycle coupled with P of the soil–plant system to external N and P deposition in alpine grassland is still unclear. A short-term external N and P addition experiment was conducted in an alpine grazing grassland in the KunLun Mountain to explore the effects of short-term N and P addition on the nutrient stoichiometry in soil and plant. Different rates of N addition (ranging from 0.5 g N m−2 yr−1 to 24 g N m−2 yr−1) and P addition (ranging from 0.05 g N m−2 yr−1 to 3.2 g P m−2 yr−1) were supplied, and the soil available N, P, leaf N and P stoichiometry of Seriphidium rhodanthum which dominant in the alpine ecosystem were measured. Results showed that N addition increased soil inorganic N, leaf C, leaf N, and leaf N:P ratio but decreased soil available P and leaf C:P. Furthermore, P addition increased soil available P, leaf P, soil inorganic N, leaf N, and leaf C and reduced leaf C:N, C:P, and N:P ratios. Leaf N:P was positively related to N addition gradient. Leaf C:P and leaf N:P were significantly negatively related to P addition gradient. Although external N and P addition changed the value of leaf N:P, the ratio was always lower than 16 in all treatments. The influences of P addition on soil and plant mainly caused the increase in soil available P concentration. In addition, the N and P cycles in the soil–plant system were tightly coupled in P addition but decoupled in N addition condition. The nutrient stoichiometry of soil and leaf responded differently to continuous N and P addition gradients. These data suggested that the alpine grazing grassland was limited by P rather than N due to long-term N deposition and uniform fertilization. Moreover, increasing P addition alleviated P limitation. Therefore, the imbalanced N and P input could change the strategy of nutrient use…
format: application/pdf
format: text/html
creator: YaLan Liu
creator: Bo Liu
creator: Zewei Yue
creator: Fanjiang Zeng
creator: Xiangyi Li
creator: Lei Li
subject: Agricultural Science
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.12611
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: The effects of increasing nitrogen (N) and phosphorus (P) deposition on the nutrient stoichiometry of soil and plant are gaining improving recognition. However, whether and how the responses of N cycle coupled with P of the soil–plant system to external N and P deposition in alpine grassland is still unclear. A short-term external N and P addition experiment was conducted in an alpine grazing grassland in the KunLun Mountain to explore the effects of short-term N and P addition on the nutrient stoichiometry in soil and plant. Different rates of N addition (ranging from 0.5 g N m−2 yr−1 to 24 g N m−2 yr−1) and P addition (ranging from 0.05 g N m−2 yr−1 to 3.2 g P m−2 yr−1) were supplied, and the soil available N, P, leaf N and P stoichiometry of Seriphidium rhodanthum which dominant in the alpine ecosystem were measured. Results showed that N addition increased soil inorganic N, leaf C, leaf N, and leaf N:P ratio but decreased soil available P and leaf C:P. Furthermore, P addition increased soil available P, leaf P, soil inorganic N, leaf N, and leaf C and reduced leaf C:N, C:P, and N:P ratios. Leaf N:P was positively related to N addition gradient. Leaf C:P and leaf N:P were significantly negatively related to P addition gradient. Although external N and P addition changed the value of leaf N:P, the ratio was always lower than 16 in all treatments. The influences of P addition on soil and plant mainly caused the increase in soil available P concentration. In addition, the N and P cycles in the soil–plant system were tightly coupled in P addition but decoupled in N addition condition. The nutrient stoichiometry of soil and leaf responded differently to continuous N and P addition gradients. These data suggested that the alpine grazing grassland was limited by P rather than N due to long-term N deposition and uniform fertilization. Moreover, increasing P addition alleviated P limitation. Therefore, the imbalanced N and P input could change the strategy of nutrient use…
bibliographic citation: Liu et al. (2021) Effects of short-term nitrogen and phosphorus addition on leaf stoichiometry of a dominant alpine grass. PeerJ 9:e12611 https://doi.org/10.7717/peerj.12611
date submitted: 2021-08-09
date accepted: 2021-11-18
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: YaLan
author list: Agent
  family name: Liu
  given name: Bo
author list: Agent
  family name: Yue
  given name: Zewei
author list: Agent
  family name: Zeng
  given name: Fanjiang
author list: Agent
  family name: Li
  given name: Xiangyi
author list: Agent
  family name: Li
  given name: Lei
doi: 10.7717/peerj.12611
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: © 2021 Liu et al.
attribution name: Liu et al.

Identification of HMMR as a prognostic biomarker for patients with lung adenocarcinoma via integrated bioinformatics analysis
type: item
type: AcademicArticle
description: Background Lung adenocarcinoma (LUAD) is the most prevalent tumor in lung carcinoma cases and threatens human life seriously worldwide. Here we attempt to identify a prognostic biomarker and potential therapeutic target for LUAD patients. Methods Differentially expressed genes (DEGs) shared by GSE18842, GSE75037, GSE101929 and GSE19188 profiles were determined and used for protein-protein interaction analysis, enrichment analysis and clinical correlation analysis to search for the core gene, whose expression was further validated in multiple databases and LUAD cells (A549 and PC-9) by quantitative real-time PCR (qRT-PCR) and western blot analyses. Its prognostic value was estimated using the Kaplan-Meier method, meta-analysis and Cox regression analysis based on the Cancer Genome Atlas (TCGA) dataset and co-expression analysis was conducted using the Oncomine database. Gene Set Enrichment Analysis (GSEA) was performed to illuminate the potential functions of the core gene. Results A total of 115 shared DEGs were found, of which 24 DEGs were identified as candidate hub genes with potential functions associated with cell cycle and FOXM1 transcription factor network. Among these candidates, HMMR was identified as the core gene, which was highly expressed in LUAD as verified by multiple datasets and cell samples. Besides, high HMMR expression was found to independently predict poor survival in patients with LUAD. Co-expression analysis showed that HMMR was closely related to FOXM1 and was mainly involved in cell cycle as suggested by GSEA. Conclusion HMMR might be served as an independent prognostic biomarker for LUAD patients, which needs further validation in subsequent studies.
format: application/pdf
format: text/html
creator: Zhaodong Li
creator: Hongtian Fei
creator: Siyu Lei
creator: Fengtong Hao
creator: Lijie Yang
creator: Wanze Li
creator: Laney Zhang
creator: Rui Fei
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.12624
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background Lung adenocarcinoma (LUAD) is the most prevalent tumor in lung carcinoma cases and threatens human life seriously worldwide. Here we attempt to identify a prognostic biomarker and potential therapeutic target for LUAD patients. Methods Differentially expressed genes (DEGs) shared by GSE18842, GSE75037, GSE101929 and GSE19188 profiles were determined and used for protein-protein interaction analysis, enrichment analysis and clinical correlation analysis to search for the core gene, whose expression was further validated in multiple databases and LUAD cells (A549 and PC-9) by quantitative real-time PCR (qRT-PCR) and western blot analyses. Its prognostic value was estimated using the Kaplan-Meier method, meta-analysis and Cox regression analysis based on the Cancer Genome Atlas (TCGA) dataset and co-expression analysis was conducted using the Oncomine database. Gene Set Enrichment Analysis (GSEA) was performed to illuminate the potential functions of the core gene. Results A total of 115 shared DEGs were found, of which 24 DEGs were identified as candidate hub genes with potential functions associated with cell cycle and FOXM1 transcription factor network. Among these candidates, HMMR was identified as the core gene, which was highly expressed in LUAD as verified by multiple datasets and cell samples. Besides, high HMMR expression was found to independently predict poor survival in patients with LUAD. Co-expression analysis showed that HMMR was closely related to FOXM1 and was mainly involved in cell cycle as suggested by GSEA. Conclusion HMMR might be served as an independent prognostic biomarker for LUAD patients, which needs further validation in subsequent studies.
bibliographic citation: Li et al. (2021) Identification of HMMR as a prognostic biomarker for patients with lung adenocarcinoma via integrated bioinformatics analysis. PeerJ 9:e12624 https://doi.org/10.7717/peerj.12624
date submitted: 2021-05-17
date accepted: 2021-11-19
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhaodong
author list: Agent
  family name: Fei
  given name: Hongtian
author list: Agent
  family name: Lei
  given name: Siyu
author list: Agent
  family name: Hao
  given name: Fengtong
author list: Agent
  family name: Yang
  given name: Lijie
author list: Agent
  family name: Li
  given name: Wanze
author list: Agent
  family name: Zhang
  given name: Laney
author list: Agent
  family name: Fei
  given name: Rui
doi: 10.7717/peerj.12624
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: © 2021 Li et al.
attribution name: Li et al.

3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
type: item
type: AcademicArticle
description: Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.
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format: text/html
creator: Michael C. Tross
creator: Mathieu Gaillard
creator: Mackenzie Zwiener
creator: Chenyong Miao
creator: Ryleigh J. Grove
creator: Bosheng Li
creator: Bedrich Benes
creator: James C. Schnable
subject: Agricultural Science
subject: Computational Biology
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12628
publisher: PeerJ Inc.
rights: © 2021 Tross et al.
abstract: Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.
bibliographic citation: Tross et al. (2021) 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves. PeerJ 9:e12628 https://doi.org/10.7717/peerj.12628
date submitted: 2021-09-22
date accepted: 2021-11-21
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tross
  given name: Michael C.
author list: Agent
  family name: Gaillard
  given name: Mathieu
author list: Agent
  family name: Zwiener
  given name: Mackenzie
author list: Agent
  family name: Miao
  given name: Chenyong
author list: Agent
  family name: Grove
  given name: Ryleigh J.
author list: Agent
  family name: Li
  given name: Bosheng
author list: Agent
  family name: Benes
  given name: Bedrich
author list: Agent
  family name: Schnable
  given name: James C.
doi: 10.7717/peerj.12628
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Tross et al.
attribution name: Tross et al.

Small herbivores and abiotic heterogeneity promote trait variation of a saltmarsh plant in local communities
type: item
type: AcademicArticle
description: Intraspecific trait variation (ITV) enables plants to respond to global changes. However, causes for ITV, especially from biotic components such as herbivory, are not well understood. We explored whether small vertebrate herbivores (hares and geese) impact ITV of a dominant clonal plant (Elytrigia atherica) in local communities. Moreover, we looked at the relative importance of their direct (e.g., selective grazing) and indirect effects (altering genotypic richness/diversity and abiotic environment) on ITV. We used exclosures at two successional stages in a Dutch saltmarsh, where grazing pressure at the early successional stage was ca. 1.5 times higher than that of the intermediate successional stage. We measured key functional traits of E. atherica including height, aboveground biomass, flowering (flower or not), specific leaf area, and leaf dry matter content in local communities (1 m × 1 m plots) inside and outside the exclosures. We determined genotypic richness and diversity of each plant using molecular markers. We further measured abiotic variations in topography and clay thickness (a proxy for soil total nitrogen). Structural equation models revealed that small herbivores significantly promoted ITV in height and flowering at the early successional stage, while they marginally promoted ITV in height at the intermediate successional stage. Moreover, the direct effects of herbivores played a major role in promoting ITV. Small herbivores decreased genotypic diversity at the intermediate successional stage, but genotypic richness and diversity did not impact ITV. Small herbivores did not alter topographic variation and variation in clay thickness, but these variations increased ITV in all traits at the early successional stage. Small herbivores may not only impact trait means in plants as studies have shown but also their ITV.
format: application/pdf
format: text/html
creator: Qingqing Chen
creator: Christian Smit
creator: Ido Pen
creator: Han Olff
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Plant Science
subject: Zoology
description: doi:10.7717/peerj.12633
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Intraspecific trait variation (ITV) enables plants to respond to global changes. However, causes for ITV, especially from biotic components such as herbivory, are not well understood. We explored whether small vertebrate herbivores (hares and geese) impact ITV of a dominant clonal plant (Elytrigia atherica) in local communities. Moreover, we looked at the relative importance of their direct (e.g., selective grazing) and indirect effects (altering genotypic richness/diversity and abiotic environment) on ITV. We used exclosures at two successional stages in a Dutch saltmarsh, where grazing pressure at the early successional stage was ca. 1.5 times higher than that of the intermediate successional stage. We measured key functional traits of E. atherica including height, aboveground biomass, flowering (flower or not), specific leaf area, and leaf dry matter content in local communities (1 m × 1 m plots) inside and outside the exclosures. We determined genotypic richness and diversity of each plant using molecular markers. We further measured abiotic variations in topography and clay thickness (a proxy for soil total nitrogen). Structural equation models revealed that small herbivores significantly promoted ITV in height and flowering at the early successional stage, while they marginally promoted ITV in height at the intermediate successional stage. Moreover, the direct effects of herbivores played a major role in promoting ITV. Small herbivores decreased genotypic diversity at the intermediate successional stage, but genotypic richness and diversity did not impact ITV. Small herbivores did not alter topographic variation and variation in clay thickness, but these variations increased ITV in all traits at the early successional stage. Small herbivores may not only impact trait means in plants as studies have shown but also their ITV.
bibliographic citation: Chen et al. (2021) Small herbivores and abiotic heterogeneity promote trait variation of a saltmarsh plant in local communities. PeerJ 9:e12633 https://doi.org/10.7717/peerj.12633
date submitted: 2021-06-09
date accepted: 2021-11-22
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Qingqing
author list: Agent
  family name: Smit
  given name: Christian
author list: Agent
  family name: Pen
  given name: Ido
author list: Agent
  family name: Olff
  given name: Han
doi: 10.7717/peerj.12633
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Chen et al.
attribution name: Chen et al.

Ferric citrate is a safe and digestible source of iron in broilers and piglets
type: item
type: AcademicArticle
description: Background Iron (Fe) is traditionally supplemented in poultry and swine diets using inorganic forms (e.g. sulfates, oxides). However, research suggests that organic sources are more beneficial due to greater bioavailability. In this paper, we present results from four studies aimed at assessing ferric citrate (CI-FER™, Akeso Biomedical Inc., Burlington, MA, USA) as a safe and effective source of Fe for broilers and piglets. Methods A total of four studies were performed in Germany following standard farming practices for each species. One study in day-old broiler chicks and one study in weaned piglets were designed as target animal safety studies where animals were randomly allocated to one of three treatment groups: a negative control group, the proposed dose group and a multifold dose group. Broilers and pigs were fed the experimental diets for 35 and 42 days, respectively. In each study, average daily feed intake, average daily weight gain and feed conversion ratio were measured, and blood samples were taken at study end for routine biochemistry and haematology. The other two studies were designed to evaluate different sources of dietary Fe for weaned piglets bred and managed under standard farm conditions. All piglets received routine Fe injections (200 mg Fe dextran, intramuscular) on day 3 of age, as well as the experimental diets for 42 days. In both studies, performance parameters were measured. In one study, Fe digestibility and serum Fe, superoxide dismutase and haptoglobin were also measured. In all studies, the general health status of the animals was monitored daily and all culls and mortality recorded. Each study followed a complete randomised block design. Results In broilers, ferric citrate was well tolerated up to 2,000 mg/kg feed (×10 the recommended inclusion rate) and no adverse effects on growth, blood parameters or mortality were observed. In piglets, ferric citrate was well tolerated up to 5,000 mg/kg feed (×10 the recommended inclusion rate) …
format: application/pdf
format: text/html
creator: Klaus Männer
creator: Hannah Lester
creator: Eliana Henriquez-Rodriguez
subject: Agricultural Science
subject: Biochemistry
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.12636
publisher: PeerJ Inc.
rights: © 2021 Männer et al.
abstract: Background Iron (Fe) is traditionally supplemented in poultry and swine diets using inorganic forms (e.g. sulfates, oxides). However, research suggests that organic sources are more beneficial due to greater bioavailability. In this paper, we present results from four studies aimed at assessing ferric citrate (CI-FER™, Akeso Biomedical Inc., Burlington, MA, USA) as a safe and effective source of Fe for broilers and piglets. Methods A total of four studies were performed in Germany following standard farming practices for each species. One study in day-old broiler chicks and one study in weaned piglets were designed as target animal safety studies where animals were randomly allocated to one of three treatment groups: a negative control group, the proposed dose group and a multifold dose group. Broilers and pigs were fed the experimental diets for 35 and 42 days, respectively. In each study, average daily feed intake, average daily weight gain and feed conversion ratio were measured, and blood samples were taken at study end for routine biochemistry and haematology. The other two studies were designed to evaluate different sources of dietary Fe for weaned piglets bred and managed under standard farm conditions. All piglets received routine Fe injections (200 mg Fe dextran, intramuscular) on day 3 of age, as well as the experimental diets for 42 days. In both studies, performance parameters were measured. In one study, Fe digestibility and serum Fe, superoxide dismutase and haptoglobin were also measured. In all studies, the general health status of the animals was monitored daily and all culls and mortality recorded. Each study followed a complete randomised block design. Results In broilers, ferric citrate was well tolerated up to 2,000 mg/kg feed (×10 the recommended inclusion rate) and no adverse effects on growth, blood parameters or mortality were observed. In piglets, ferric citrate was well tolerated up to 5,000 mg/kg feed (×10 the recommended inclusion rate) …
bibliographic citation: Männer et al. (2021) Ferric citrate is a safe and digestible source of iron in broilers and piglets. PeerJ 9:e12636 https://doi.org/10.7717/peerj.12636
date submitted: 2021-07-30
date accepted: 2021-11-23
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Männer
  given name: Klaus
author list: Agent
  family name: Lester
  given name: Hannah
author list: Agent
  family name: Henriquez-Rodriguez
  given name: Eliana
doi: 10.7717/peerj.12636
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: © 2021 Männer et al.
attribution name: Männer et al.

Impact of climatic conditions projected at the World Cup in Qatar 2022 on repeated maximal efforts in soccer players
type: item
type: AcademicArticle
description: This study aimed to investigate the relationship between the climatic conditions predicted for the 2022 FIFA World Cup in Qatar and the capacity for repeated maximum effort (RSA), of soccer players. Twenty-four semi-professional soccer players participated in the study. The exercise test consisted of ten 6-second maximal efforts on a cycloergometer. A 90-second passive rest interval was used. Mechanical parameters were recorded in each repetition, and biochemical parameters at rest and even repetitions. The test was performed in a Weiss Technik WK-26 climate chamber under two different conditions: (1) thermoneutral (TNC - 20.5 °C; 58.7% humidity); (2) predicted for the 2022 World Cup in Qatar (QSC - 28.5 ± 1.92 °C; 58.7 ± 8.64% humidity). Significantly higher mean maximum power values were recorded in the second repetition under QSC conditions (1731,8 ± 214,4 W) (p = 0.025). A significantly longer time to reach maximum power was also recorded under TNC conditions compared to QSC conditions in repetition 2 (1,32 ± 0,33 s), (1,05 ± 0,29 s) (p = 0.016) and 6 (1,41 ± 0,48 s), (1,17 ± 0,25) (p = 0.036). There was a significantly higher rate of power loss, between repetition 2 (p = 0.023) and 4 (p = 0.043) under QSC conditions, compared to TNC. Considering the biochemical parameters, a significantly higher pO2 concentration was registered under QSC conditions in the 10th repetition (p = 0.006). The ambient temperature during exercise should be taken into account to determine the anaerobic exercise capacity of the athletes. At higher temperatures, there is a greater capacity for maximal effort, in terms of maximal power achieved, but with a greater decrease in performance.
format: application/pdf
format: text/html
creator: Wiktor Chodor
creator: Paweł Chmura
creator: Jan Chmura
creator: Marcin Andrzejewski
creator: Ewa Jówko
creator: Tomasz Buraczewski
creator: Adrian Drożdżowski
creator: Andrzej Rokita
creator: Marek Konefał
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.12658
publisher: PeerJ Inc.
rights: © 2021 Chodor et al.
abstract: This study aimed to investigate the relationship between the climatic conditions predicted for the 2022 FIFA World Cup in Qatar and the capacity for repeated maximum effort (RSA), of soccer players. Twenty-four semi-professional soccer players participated in the study. The exercise test consisted of ten 6-second maximal efforts on a cycloergometer. A 90-second passive rest interval was used. Mechanical parameters were recorded in each repetition, and biochemical parameters at rest and even repetitions. The test was performed in a Weiss Technik WK-26 climate chamber under two different conditions: (1) thermoneutral (TNC - 20.5 °C; 58.7% humidity); (2) predicted for the 2022 World Cup in Qatar (QSC - 28.5 ± 1.92 °C; 58.7 ± 8.64% humidity). Significantly higher mean maximum power values were recorded in the second repetition under QSC conditions (1731,8 ± 214,4 W) (p = 0.025). A significantly longer time to reach maximum power was also recorded under TNC conditions compared to QSC conditions in repetition 2 (1,32 ± 0,33 s), (1,05 ± 0,29 s) (p = 0.016) and 6 (1,41 ± 0,48 s), (1,17 ± 0,25) (p = 0.036). There was a significantly higher rate of power loss, between repetition 2 (p = 0.023) and 4 (p = 0.043) under QSC conditions, compared to TNC. Considering the biochemical parameters, a significantly higher pO2 concentration was registered under QSC conditions in the 10th repetition (p = 0.006). The ambient temperature during exercise should be taken into account to determine the anaerobic exercise capacity of the athletes. At higher temperatures, there is a greater capacity for maximal effort, in terms of maximal power achieved, but with a greater decrease in performance.
bibliographic citation: Chodor et al. (2021) Impact of climatic conditions projected at the World Cup in Qatar 2022 on repeated maximal efforts in soccer players. PeerJ 9:e12658 https://doi.org/10.7717/peerj.12658
date submitted: 2021-08-30
date accepted: 2021-11-30
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chodor
  given name: Wiktor
author list: Agent
  family name: Chmura
  given name: Paweł
author list: Agent
  family name: Chmura
  given name: Jan
author list: Agent
  family name: Andrzejewski
  given name: Marcin
author list: Agent
  family name: Jówko
  given name: Ewa
author list: Agent
  family name: Buraczewski
  given name: Tomasz
author list: Agent
  family name: Drożdżowski
  given name: Adrian
author list: Agent
  family name: Rokita
  given name: Andrzej
author list: Agent
  family name: Konefał
  given name: Marek
doi: 10.7717/peerj.12658
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Chodor et al.
attribution name: Chodor et al.

A taxonomic outline of the Poecilimon affinis complex (Orthoptera) using the geometric morphometric approach
type: item
type: AcademicArticle
description: The genus Poecilimon contains 145 species, widely distributed in the Palaearctic, among which the Poecilimon ornatus group has the greatest diversity in the Balkans. Despite several revisions of the genus, the systematics of the species group, and in particular, of the taxa associated with the species Poecilimon affinis, is still unsolved. Due to morphological similarity, P. affinis with its subspecies, P. nonveilleri and P. pseudornatus form the Poecilimon affinis complex. The aim of this study is to test the hypotheses of an outlined species complex, namely the P. affinis complex, within the P. ornatus group using morphological data. Geometric analysis was conducted to explore variation in the structure of the male tegmen, ovipositor, male cercus, and male pronotum. The number of teeth and stridulatory file measurements provided additional information on morphological variation within the complex. A phylogenetic tree based on the cytochrome c oxidase subunit I gene (COI) was used for comparison with the morphological data. Canonical variate analysis showed that male tegmen and male cercus are good morphostructures to distinguish the taxa belonging to the P. affinis complex from other species in the P. ornatus group. This may confirm our assumption for the designation of the P. affinis complex. The results of the principal component analysis of stridulatory file measurements, molecular data, and CVA of the ovipositor suggest adding two additional species to the complex: P. ornatus and P. hoelzeli.
format: application/pdf
format: text/html
creator: Maciej Kociński
creator: Beata Grzywacz
creator: Georgi Hristov
creator: Dragan Chobanov
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12668
publisher: PeerJ Inc.
rights: © 2021 Kociński et al.
abstract: The genus Poecilimon contains 145 species, widely distributed in the Palaearctic, among which the Poecilimon ornatus group has the greatest diversity in the Balkans. Despite several revisions of the genus, the systematics of the species group, and in particular, of the taxa associated with the species Poecilimon affinis, is still unsolved. Due to morphological similarity, P. affinis with its subspecies, P. nonveilleri and P. pseudornatus form the Poecilimon affinis complex. The aim of this study is to test the hypotheses of an outlined species complex, namely the P. affinis complex, within the P. ornatus group using morphological data. Geometric analysis was conducted to explore variation in the structure of the male tegmen, ovipositor, male cercus, and male pronotum. The number of teeth and stridulatory file measurements provided additional information on morphological variation within the complex. A phylogenetic tree based on the cytochrome c oxidase subunit I gene (COI) was used for comparison with the morphological data. Canonical variate analysis showed that male tegmen and male cercus are good morphostructures to distinguish the taxa belonging to the P. affinis complex from other species in the P. ornatus group. This may confirm our assumption for the designation of the P. affinis complex. The results of the principal component analysis of stridulatory file measurements, molecular data, and CVA of the ovipositor suggest adding two additional species to the complex: P. ornatus and P. hoelzeli.
bibliographic citation: Kociński et al. (2021) A taxonomic outline of the Poecilimon affinis complex (Orthoptera) using the geometric morphometric approach. PeerJ 9:e12668 https://doi.org/10.7717/peerj.12668
date submitted: 2021-09-17
date accepted: 2021-12-01
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kociński
  given name: Maciej
author list: Agent
  family name: Grzywacz
  given name: Beata
author list: Agent
  family name: Hristov
  given name: Georgi
author list: Agent
  family name: Chobanov
  given name: Dragan
doi: 10.7717/peerj.12668
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Kociński et al.
attribution name: Kociński et al.

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