PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: An alternative peptone preparation using Hermetia illucens (Black soldier fly) hydrolysis: process optimization and performance evaluation
items: moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud
items: New records of immature aquatic Diptera from the Foulden Maar Fossil-Lagerstätte, New Zealand, and their biogeographic implications
items: Spatiotemporal variables comparison between drop jump and horizontal drop jump in elite jumpers and sprinters
items: Biodegradation of polyethylene in digestive gland homogenates of marine invertebrates
items: Novel diagnostic biomarkers related to necroptosis and immune infiltration landscape in acute myocardial infarction
items: First case of a reversed Parabothus taiwanensis Amaoka & Shen, 1993 from Taiwan (Pleuronectiformes: Bothidae), with first evidence of situs inversus viscerum in bothid
items: Transcriptomic and biochemical insights into fall armyworm (Spodoptera frugiperda) responses on silicon-treated maize
items: Non-invasive measurements to identify mungbean genotypes for waterlogging tolerance
items: Transcriptomic and targeted metabolome analyses revealed the regulatory mechanisms of the synthesis of bioactive compounds in Citrus grandis ‘tomentosa’

An alternative peptone preparation using Hermetia illucens (Black soldier fly) hydrolysis: process optimization and performance evaluation
type: item
type: AcademicArticle
description: Background Hermetia illucens (HI), commonly known as the black soldier fly, has been recognized for its prowess in resource utilization and environmental protection because of its ability to transform organic waste into animal feed for livestock, poultry, and aquaculture. However, the potential of the black soldier fly’s high protein content for more than cheap feedstock is still largely unexplored. Methods This study innovatively explores the potential of H. illucens larvae (HIL) protein as a peptone substitute for microbial culture media. Four commercial proteases (alkaline protease, trypsin, trypsase, and papain) were explored to hydrolyze the defatted HIL, and the experimental conditions were optimized via response surface methodology experimental design. The hydrolysate of the defatted HIL was subsequently vacuum freeze-dried and deployed as a growth medium for three bacterial strains (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli) to determine the growth kinetics between the HIL peptone and commercial peptone. Results The optimal conditions were 1.70% w/w complex enzyme (alkaline protease: trypsin at 1:1 ratio) at pH 7.0 and 54 °C for a duration of 4 h. Under these conditions, the hydrolysis of defatted HIL yielded 19.25% ±0.49%. A growth kinetic analysis showed no significant difference in growth parameters (μmax, Xmax, and λ) between the HIL peptone and commercial peptone, demonstrating that the HIL hydrolysate could serve as an effective, low-cost alternative to commercial peptone. This study introduces an innovative approach to HIL protein resource utilization, broadening its application beyond its current use in animal feed.
format: application/pdf
format: text/html
creator: Gaoqiang Liu
creator: Ming Foong Tiang
creator: Shixia Ma
creator: Zeyan Wei
creator: Xiaolin Liang
creator: Mohd Shaiful Sajab
creator: Peer Mohamed Abdul
creator: Xueyan Zhou
creator: Zhongren Ma
creator: Gongtao Ding
subject: Bioengineering
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.16995
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Background Hermetia illucens (HI), commonly known as the black soldier fly, has been recognized for its prowess in resource utilization and environmental protection because of its ability to transform organic waste into animal feed for livestock, poultry, and aquaculture. However, the potential of the black soldier fly’s high protein content for more than cheap feedstock is still largely unexplored. Methods This study innovatively explores the potential of H. illucens larvae (HIL) protein as a peptone substitute for microbial culture media. Four commercial proteases (alkaline protease, trypsin, trypsase, and papain) were explored to hydrolyze the defatted HIL, and the experimental conditions were optimized via response surface methodology experimental design. The hydrolysate of the defatted HIL was subsequently vacuum freeze-dried and deployed as a growth medium for three bacterial strains (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli) to determine the growth kinetics between the HIL peptone and commercial peptone. Results The optimal conditions were 1.70% w/w complex enzyme (alkaline protease: trypsin at 1:1 ratio) at pH 7.0 and 54 °C for a duration of 4 h. Under these conditions, the hydrolysis of defatted HIL yielded 19.25% ±0.49%. A growth kinetic analysis showed no significant difference in growth parameters (μmax, Xmax, and λ) between the HIL peptone and commercial peptone, demonstrating that the HIL hydrolysate could serve as an effective, low-cost alternative to commercial peptone. This study introduces an innovative approach to HIL protein resource utilization, broadening its application beyond its current use in animal feed.
bibliographic citation: Liu et al. (2024) An alternative peptone preparation using Hermetia illucens (Black soldier fly) hydrolysis: process optimization and performance evaluation. PeerJ 12:e16995 https://doi.org/10.7717/peerj.16995
date submitted: 2023-10-10
date accepted: 2024-02-01
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Gaoqiang
author list: Agent
  family name: Tiang
  given name: Ming Foong
author list: Agent
  family name: Ma
  given name: Shixia
author list: Agent
  family name: Wei
  given name: Zeyan
author list: Agent
  family name: Liang
  given name: Xiaolin
author list: Agent
  family name: Sajab
  given name: Mohd Shaiful
author list: Agent
  family name: Abdul
  given name: Peer Mohamed
author list: Agent
  family name: Zhou
  given name: Xueyan
author list: Agent
  family name: Ma
  given name: Zhongren
author list: Agent
  family name: Ding
  given name: Gongtao
doi: 10.7717/peerj.16995
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Liu et al.
attribution name: Liu et al.

moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud
type: item
type: AcademicArticle
description: Single-cell omics sequencing has rapidly advanced, enabling the quantification of diverse omics profiles at a single-cell resolution. To facilitate comprehensive biological insights, such as cellular differentiation trajectories, precise annotation of cell subtypes is essential. Conventional methods involve clustering cells and manually assigning subtypes based on canonical markers, a labor-intensive and expert-dependent process. Hence, an automated computational prediction framework is crucial. While several classification frameworks for predicting cell subtypes from single-cell RNA sequencing datasets exist, these methods solely rely on single-omics data, offering insights at a single molecular level. They often miss inter-omic correlations and a holistic understanding of cellular processes. To address this, the integration of multi-omics datasets from individual cells is essential for accurate subtype annotation. This article introduces moSCminer, a novel framework for classifying cell subtypes that harnesses the power of single-cell multi-omics sequencing datasets through an attention-based neural network operating at the omics level. By integrating three distinct omics datasets—gene expression, DNA methylation, and DNA accessibility—while accounting for their biological relationships, moSCminer excels at learning the relative significance of each omics feature. It then transforms this knowledge into a novel representation for cell subtype classification. Comparative evaluations against standard machine learning-based classifiers demonstrate moSCminer’s superior performance, consistently achieving the highest average performance on real datasets. The efficacy of multi-omics integration is further corroborated through an in-depth analysis of the omics-level attention module, which identifies potential markers for cell subtype annotation. To enhance accessibility and scalability, moSCminer is accessible as a user-friendly web-based platform seamlessly connected to…
format: application/pdf
format: text/html
creator: Joung Min Choi
creator: Chaelin Park
creator: Heejoon Chae
subject: Bioinformatics
subject: Computational Biology
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.17006
publisher: PeerJ Inc.
rights: © 2024 Choi et al.
abstract: Single-cell omics sequencing has rapidly advanced, enabling the quantification of diverse omics profiles at a single-cell resolution. To facilitate comprehensive biological insights, such as cellular differentiation trajectories, precise annotation of cell subtypes is essential. Conventional methods involve clustering cells and manually assigning subtypes based on canonical markers, a labor-intensive and expert-dependent process. Hence, an automated computational prediction framework is crucial. While several classification frameworks for predicting cell subtypes from single-cell RNA sequencing datasets exist, these methods solely rely on single-omics data, offering insights at a single molecular level. They often miss inter-omic correlations and a holistic understanding of cellular processes. To address this, the integration of multi-omics datasets from individual cells is essential for accurate subtype annotation. This article introduces moSCminer, a novel framework for classifying cell subtypes that harnesses the power of single-cell multi-omics sequencing datasets through an attention-based neural network operating at the omics level. By integrating three distinct omics datasets—gene expression, DNA methylation, and DNA accessibility—while accounting for their biological relationships, moSCminer excels at learning the relative significance of each omics feature. It then transforms this knowledge into a novel representation for cell subtype classification. Comparative evaluations against standard machine learning-based classifiers demonstrate moSCminer’s superior performance, consistently achieving the highest average performance on real datasets. The efficacy of multi-omics integration is further corroborated through an in-depth analysis of the omics-level attention module, which identifies potential markers for cell subtype annotation. To enhance accessibility and scalability, moSCminer is accessible as a user-friendly web-based platform seamlessly connected to…
bibliographic citation: Choi et al. (2024) moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud. PeerJ 12:e17006 https://doi.org/10.7717/peerj.17006
date submitted: 2023-11-22
date accepted: 2024-02-05
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Joung Min
author list: Agent
  family name: Park
  given name: Chaelin
author list: Agent
  family name: Chae
  given name: Heejoon
doi: 10.7717/peerj.17006
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Choi et al.
attribution name: Choi et al.

New records of immature aquatic Diptera from the Foulden Maar Fossil-Lagerstätte, New Zealand, and their biogeographic implications
type: item
type: AcademicArticle
description: Background The biogeographical and ecological history of true flies (Diptera) in New Zealand is little known due to a scarcity of fossil specimens. Here, we report a fauna of immature aquatic dipterans from freshwater diatomites of the early Miocene Foulden Maar Fossil-Lagerstätte in southern New Zealand. Methods We document 30 specimens of immature dipterans, mostly pupae, and compare their external morphology to extant aquatic Diptera. Based on the reconstructed paleoenvironment of Foulden Maar, we discuss taxonomic, ecological and taphonomic implications of this early Miocene fauna. Results Among Chironomidae, one pupal morphotype is attributed to Tanypodinae, one pupal morphotype and one larval morphotype are placed into Chironomus (Chironominae) and a further morphotype into Chironominae incertae sedis. Chaoboridae are represented by a pupal morphotype congeneric or very close to the extant Chaoborus, today globally distributed except for New Zealand. Additional immature specimens are likely larvae and puparia of brachyceran flies but cannot be identified to a narrower range. These finds document an aquatic dipteran fauna in New Zealand in the earliest Miocene and highlight Neogene extinction as a factor in shaping the extant Diptera fauna in New Zealand. Immature aquatic dipterans were a common and likely ecologically important component of the early Miocene Foulden Maar lake. Preservation of larvae and pupae may have been promoted by diatomaceous microbial mats and the light colour of the diatomite likely facilitated spotting of these minute fossils in the field.
format: application/pdf
format: text/html
creator: Viktor O. Baranov
creator: Joachim T. Haug
creator: Uwe Kaulfuss
subject: Biodiversity
subject: Biogeography
subject: Entomology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17014
publisher: PeerJ Inc.
rights: © 2024 Baranov et al.
abstract: Background The biogeographical and ecological history of true flies (Diptera) in New Zealand is little known due to a scarcity of fossil specimens. Here, we report a fauna of immature aquatic dipterans from freshwater diatomites of the early Miocene Foulden Maar Fossil-Lagerstätte in southern New Zealand. Methods We document 30 specimens of immature dipterans, mostly pupae, and compare their external morphology to extant aquatic Diptera. Based on the reconstructed paleoenvironment of Foulden Maar, we discuss taxonomic, ecological and taphonomic implications of this early Miocene fauna. Results Among Chironomidae, one pupal morphotype is attributed to Tanypodinae, one pupal morphotype and one larval morphotype are placed into Chironomus (Chironominae) and a further morphotype into Chironominae incertae sedis. Chaoboridae are represented by a pupal morphotype congeneric or very close to the extant Chaoborus, today globally distributed except for New Zealand. Additional immature specimens are likely larvae and puparia of brachyceran flies but cannot be identified to a narrower range. These finds document an aquatic dipteran fauna in New Zealand in the earliest Miocene and highlight Neogene extinction as a factor in shaping the extant Diptera fauna in New Zealand. Immature aquatic dipterans were a common and likely ecologically important component of the early Miocene Foulden Maar lake. Preservation of larvae and pupae may have been promoted by diatomaceous microbial mats and the light colour of the diatomite likely facilitated spotting of these minute fossils in the field.
bibliographic citation: Baranov et al. (2024) New records of immature aquatic Diptera from the Foulden Maar Fossil-Lagerstätte, New Zealand, and their biogeographic implications. PeerJ 12:e17014 https://doi.org/10.7717/peerj.17014
date submitted: 2023-11-21
date accepted: 2024-02-05
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baranov
  given name: Viktor O.
author list: Agent
  family name: Haug
  given name: Joachim T.
author list: Agent
  family name: Kaulfuss
  given name: Uwe
doi: 10.7717/peerj.17014
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Baranov et al.
attribution name: Baranov et al.

Spatiotemporal variables comparison between drop jump and horizontal drop jump in elite jumpers and sprinters
type: item
type: AcademicArticle
description: Background General expectations speculated that there are differences between drop jump (DJ) and horizontal drop jump (HDJ) exercises. While these criteria may be valid, we have yet to find a report that explores these differences in competitive level athletes. Objective The study aimed to compare spatiotemporal variables in the drop jump (DJ) vs. the horizontal drop jump (HDJ) in elite jumpers and sprinters. Methods Sixteen international-level male athletes performed two DJ attempts at different fall heights 0.3, 0.4, and 0.5 m (DJ30, DJ40, and DJ50), and after 2 h, they performed two HDJ attempts (HDJ30, HDJ40, HDJ50). All jumps were performed on a Kistler force plate. The variables analyzed were ground contact time (GCT), flight time (FT), eccentric phase time, concentric phase time, and time to peak concentric force. Results The GCT was found to be significantly shorter in DJ vs. HDJ (Z = 4.980; p = 0.0001; ES = 3.11). FT was significantly lower in DJ30 versus HDJ30 (Z = 4.845; p = 0.0001, d = 3.79), but significantly higher in DJ40 vs. HDJ40 (Z = 4.437; p ≤ 0.0001, d = 3.70) and in DJ50 vs. HDJ50 (Z = 4.549; p ≤ 0.0001, d = 4.72). Conclusions It is concluded that the HDJ requires more time for force production, that the eccentric component requires more time than the concentric and that it is not recommended to use the HDJ over the DJ for reactive purposes. This is the first study that comprehensively compare the differences between DJ and HDJ, which will assist coaches and researchers in the design of future training strategies.
format: application/pdf
format: text/html
creator: Raynier Montoro-Bombú
creator: Paulo Miranda-Oliveira
creator: Maria João Valamatos
creator: Filipa João
creator: Tom JW Buurke
creator: Amândio Cupido Santos
creator: Luis Rama
subject: Sports Medicine
description: doi:10.7717/peerj.17026
publisher: PeerJ Inc.
rights: © 2024 Montoro-Bombú et al.
abstract: Background General expectations speculated that there are differences between drop jump (DJ) and horizontal drop jump (HDJ) exercises. While these criteria may be valid, we have yet to find a report that explores these differences in competitive level athletes. Objective The study aimed to compare spatiotemporal variables in the drop jump (DJ) vs. the horizontal drop jump (HDJ) in elite jumpers and sprinters. Methods Sixteen international-level male athletes performed two DJ attempts at different fall heights 0.3, 0.4, and 0.5 m (DJ30, DJ40, and DJ50), and after 2 h, they performed two HDJ attempts (HDJ30, HDJ40, HDJ50). All jumps were performed on a Kistler force plate. The variables analyzed were ground contact time (GCT), flight time (FT), eccentric phase time, concentric phase time, and time to peak concentric force. Results The GCT was found to be significantly shorter in DJ vs. HDJ (Z = 4.980; p = 0.0001; ES = 3.11). FT was significantly lower in DJ30 versus HDJ30 (Z = 4.845; p = 0.0001, d = 3.79), but significantly higher in DJ40 vs. HDJ40 (Z = 4.437; p ≤ 0.0001, d = 3.70) and in DJ50 vs. HDJ50 (Z = 4.549; p ≤ 0.0001, d = 4.72). Conclusions It is concluded that the HDJ requires more time for force production, that the eccentric component requires more time than the concentric and that it is not recommended to use the HDJ over the DJ for reactive purposes. This is the first study that comprehensively compare the differences between DJ and HDJ, which will assist coaches and researchers in the design of future training strategies.
bibliographic citation: Montoro-Bombú et al. (2024) Spatiotemporal variables comparison between drop jump and horizontal drop jump in elite jumpers and sprinters. PeerJ 12:e17026 https://doi.org/10.7717/peerj.17026
date submitted: 2023-11-06
date accepted: 2024-02-07
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montoro-Bombú
  given name: Raynier
author list: Agent
  family name: Miranda-Oliveira
  given name: Paulo
author list: Agent
  family name: Valamatos
  given name: Maria João
author list: Agent
  family name: João
  given name: Filipa
author list: Agent
  family name: Buurke
  given name: Tom JW
author list: Agent
  family name: Cupido Santos
  given name: Amândio
author list: Agent
  family name: Rama
  given name: Luis
doi: 10.7717/peerj.17026
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Montoro-Bombú et al.
attribution name: Montoro-Bombú et al.

Biodegradation of polyethylene in digestive gland homogenates of marine invertebrates
type: item
type: AcademicArticle
description: Вiotic factors may be the driving force of plastic fragmentation along with abiotic factors. Since understanding the processes of biodegradation and biological depolymerization of plastic is important, a new methodological approach was proposed in this study to investigate the role of marine invertebrate digestive enzymes in plastic biodegradation. The aim of this study is to evaluate the possibility of enzymatic biodegradation of polyethylene fragments in the digestive gland homogenate of marine invertebrates differing in their feeding type (Strongylocentrotus nudus, Patiria pectinifera, Mizuhopecten yessoensis). Significant changes are found in the functional groups of the polymer after 3 days of incubation in the digestive gland homogenates of the studied marine invertebrates. A significant increase in the calculated CI (carbonyl index) and COI (сarbon-oxygen index) indices compared to the control sample was observed. The results suggest that digestive enzymes of studied organisms may play an important role in the biogeochemical cycling of plastic.
format: application/pdf
format: text/html
creator: Aleksandra Istomina
creator: Victor Chelomin
creator: Andrey Mazur
creator: Avianna Zhukovskaya
creator: Alexander Karpenko
creator: Marina Mazur
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.17041
publisher: PeerJ Inc.
rights: © 2024 Istomina et al.
abstract: Вiotic factors may be the driving force of plastic fragmentation along with abiotic factors. Since understanding the processes of biodegradation and biological depolymerization of plastic is important, a new methodological approach was proposed in this study to investigate the role of marine invertebrate digestive enzymes in plastic biodegradation. The aim of this study is to evaluate the possibility of enzymatic biodegradation of polyethylene fragments in the digestive gland homogenate of marine invertebrates differing in their feeding type (Strongylocentrotus nudus, Patiria pectinifera, Mizuhopecten yessoensis). Significant changes are found in the functional groups of the polymer after 3 days of incubation in the digestive gland homogenates of the studied marine invertebrates. A significant increase in the calculated CI (carbonyl index) and COI (сarbon-oxygen index) indices compared to the control sample was observed. The results suggest that digestive enzymes of studied organisms may play an important role in the biogeochemical cycling of plastic.
bibliographic citation: Istomina et al. (2024) Biodegradation of polyethylene in digestive gland homogenates of marine invertebrates. PeerJ 12:e17041 https://doi.org/10.7717/peerj.17041
date submitted: 2023-11-20
date accepted: 2024-02-12
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Istomina
  given name: Aleksandra
author list: Agent
  family name: Chelomin
  given name: Victor
author list: Agent
  family name: Mazur
  given name: Andrey
author list: Agent
  family name: Zhukovskaya
  given name: Avianna
author list: Agent
  family name: Karpenko
  given name: Alexander
author list: Agent
  family name: Mazur
  given name: Marina
doi: 10.7717/peerj.17041
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Istomina et al.
attribution name: Istomina et al.

Novel diagnostic biomarkers related to necroptosis and immune infiltration landscape in acute myocardial infarction
type: item
type: AcademicArticle
description: Background Acute myocardial infarction (AMI) can occur suddenly, which may induce deadly outcomes, and the population suffering from AMI presents a younger trend. Necroptosis, the new cell necrosis type, is associated with the pathogenic mechanisms of diverse cardiovascular diseases (CVDs). Its diagnostic value and molecular mechanisms in AMI are still unclear. Objective: This study focused on determining key necroptosis-related genes as well as immune infiltration in AMI. Methods We first examined the GSE66360 dataset for identifying necroptosis-related differentially expressed genes (NRDEGs). Thereafter, GO and functional annotation were performed, then a PPI network was built. In addition, “CIBERSORT” in R was applied in comparing different immune infiltration degrees in AMI compared with control groups. The receiver operating characteristic (ROC) curve was plotted to evaluate whether hub NRDEGs could be used in AMI diagnosis. Associations of immune cells with candidate NRDEGs biomarkers were examined by Spearman analysis. Finally, hub NRDEGs were validated by cell qPCR assays and another two datasets. Results A total of 15 NRDEGs were identified and multiple enrichment terms associated with necroptosis were discovered through GO and KEGG analysis. Upon module analysis, 10 hub NRDEGs were filtered out, and the top six hub NRDEGs were identified after ROC analysis. These top six NRDEGs might have a certain effect on modulating immune infiltrating cells, especially for mast cells activated, NK cells activated and neutrophils. Finally, two AMI datasets and qPCR assay came to identical findings. Conclusion Our results offer the reliable molecular biomarkers and new perspectives for necroptosis in AMI, which lay a certain foundation for developing novel anti-AMI therapeutic targets.
format: application/pdf
format: text/html
creator: Wenfa Wu
creator: Hongxing Fan
creator: Junlin Cen
creator: Pei Huang
creator: Guidong Li
creator: Yanping Tan
creator: Gen Liu
creator: Baoshan Hong
subject: Bioinformatics
subject: Molecular Biology
subject: Cardiology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17044
publisher: PeerJ Inc.
rights: © 2024 Wu et al.
abstract: Background Acute myocardial infarction (AMI) can occur suddenly, which may induce deadly outcomes, and the population suffering from AMI presents a younger trend. Necroptosis, the new cell necrosis type, is associated with the pathogenic mechanisms of diverse cardiovascular diseases (CVDs). Its diagnostic value and molecular mechanisms in AMI are still unclear. Objective: This study focused on determining key necroptosis-related genes as well as immune infiltration in AMI. Methods We first examined the GSE66360 dataset for identifying necroptosis-related differentially expressed genes (NRDEGs). Thereafter, GO and functional annotation were performed, then a PPI network was built. In addition, “CIBERSORT” in R was applied in comparing different immune infiltration degrees in AMI compared with control groups. The receiver operating characteristic (ROC) curve was plotted to evaluate whether hub NRDEGs could be used in AMI diagnosis. Associations of immune cells with candidate NRDEGs biomarkers were examined by Spearman analysis. Finally, hub NRDEGs were validated by cell qPCR assays and another two datasets. Results A total of 15 NRDEGs were identified and multiple enrichment terms associated with necroptosis were discovered through GO and KEGG analysis. Upon module analysis, 10 hub NRDEGs were filtered out, and the top six hub NRDEGs were identified after ROC analysis. These top six NRDEGs might have a certain effect on modulating immune infiltrating cells, especially for mast cells activated, NK cells activated and neutrophils. Finally, two AMI datasets and qPCR assay came to identical findings. Conclusion Our results offer the reliable molecular biomarkers and new perspectives for necroptosis in AMI, which lay a certain foundation for developing novel anti-AMI therapeutic targets.
bibliographic citation: Wu et al. (2024) Novel diagnostic biomarkers related to necroptosis and immune infiltration landscape in acute myocardial infarction. PeerJ 12:e17044 https://doi.org/10.7717/peerj.17044
date submitted: 2023-06-29
date accepted: 2024-02-13
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wu
  given name: Wenfa
author list: Agent
  family name: Fan
  given name: Hongxing
author list: Agent
  family name: Cen
  given name: Junlin
author list: Agent
  family name: Huang
  given name: Pei
author list: Agent
  family name: Li
  given name: Guidong
author list: Agent
  family name: Tan
  given name: Yanping
author list: Agent
  family name: Liu
  given name: Gen
author list: Agent
  family name: Hong
  given name: Baoshan
doi: 10.7717/peerj.17044
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Wu et al.
attribution name: Wu et al.

First case of a reversed Parabothus taiwanensis Amaoka & Shen, 1993 from Taiwan (Pleuronectiformes: Bothidae), with first evidence of situs inversus viscerum in bothid
type: item
type: AcademicArticle
description: Background Reversed condition is rarely found in most flatfishes in natural environment, except for some certain species. The mechanism controlling the reversals in flatfishes has been studied in some cultivated species, whereas some have only few cases for the entire family and remain unclear. Here, we report the first record of a dextral (reversed) specimen of Parabothus taiwanensis Amaoka & Shen, 1993 collected off southwestern Taiwan recently. It represents the second reversed case ever recorded in Bothidae. We aim to provide a detailed description of this dextral specimen and compared to the sinistral (normal) specimens collected from the vicinity. Methods Specimens were fixed in 4% formaldehyde and transferred to 70% ethanol for preservation. Meristic and morphometric characters were examined for both dextral and sinistral specimens. Dissections were made on specimens to confirm the position of internal organs. Lastly, X-radiographs were taken to elucidate the osteological features. Results As a result, no differences of both meristic and morphometric characters were observed between the dextral and sinistral specimens. Nevertheless, situs inversus viscerum is discovered in the dextral specimen for the first time in Bothidae and the sixth record within flatfishes.
format: application/pdf
format: text/html
creator: Yo Su
creator: Hsuan-Ching Ho
creator: Tah-Wei Chu
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.16829
publisher: PeerJ Inc.
rights: © 2024 Su et al.
abstract: Background Reversed condition is rarely found in most flatfishes in natural environment, except for some certain species. The mechanism controlling the reversals in flatfishes has been studied in some cultivated species, whereas some have only few cases for the entire family and remain unclear. Here, we report the first record of a dextral (reversed) specimen of Parabothus taiwanensis Amaoka & Shen, 1993 collected off southwestern Taiwan recently. It represents the second reversed case ever recorded in Bothidae. We aim to provide a detailed description of this dextral specimen and compared to the sinistral (normal) specimens collected from the vicinity. Methods Specimens were fixed in 4% formaldehyde and transferred to 70% ethanol for preservation. Meristic and morphometric characters were examined for both dextral and sinistral specimens. Dissections were made on specimens to confirm the position of internal organs. Lastly, X-radiographs were taken to elucidate the osteological features. Results As a result, no differences of both meristic and morphometric characters were observed between the dextral and sinistral specimens. Nevertheless, situs inversus viscerum is discovered in the dextral specimen for the first time in Bothidae and the sixth record within flatfishes.
bibliographic citation: Su et al. (2024) First case of a reversed Parabothus taiwanensis Amaoka & Shen, 1993 from Taiwan (Pleuronectiformes: Bothidae), with first evidence of situs inversus viscerum in bothid. PeerJ 12:e16829 https://doi.org/10.7717/peerj.16829
date submitted: 2023-10-06
date accepted: 2024-01-04
issued: 2024-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Yo
author list: Agent
  family name: Ho
  given name: Hsuan-Ching
author list: Agent
  family name: Chu
  given name: Tah-Wei
doi: 10.7717/peerj.16829
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-23
copyright: ©2024 Su et al.
attribution name: Su et al.

Transcriptomic and biochemical insights into fall armyworm (Spodoptera frugiperda) responses on silicon-treated maize
type: item
type: AcademicArticle
description: Background The fall armyworm, Spodoptera frugiperda, is an agricultural pest of significant economic concern globally, known for its adaptability, pesticide resistance, and damage to key crops such as maize. Conventional chemical pesticides pose challenges, including the development of resistance and environmental pollution. The study aims to investigate an alternative solution: the application of soluble silicon (Si) sources to enhance plant resistance against the fall armyworm. Methods Silicon dioxide (SiO2) and potassium silicate (K2SiO3) were applied to maize plants via foliar spray. Transcriptomic and biochemical analyses were performed to study the gene expression changes in the fall armyworm feeding on Si-treated maize. Results Results indicated a significant impact on gene expression, with a large number of differentially expressed genes (DEGs) identified in both SiO2 and K2SiO3 treatments. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified critical DEGs involved in specific pathways, including amino acid, carbohydrate, lipid, energy, xenobiotics metabolisms, signal transduction, and posttranslational modification, significantly altered at both Si sources. Biochemical analyses further revealed that Si treatments inhibited several enzyme activities (glutamate dehydrogenase, trehalase, glucose-6-phosphate dehydrogenase, chitinase, juvenile hormone esterase, and cyclooxygenase while simultaneously inducing others (total protein, lipopolysaccharide, fatty acid synthase, ATPase, and cytochrome P450), thus suggesting a toxic effect on the fall armyworm. In conclusion, Si applications on maize influence the gene expression and biochemical activities of the fall armyworm, potentially offering a sustainable pest management strategy.
format: application/pdf
format: text/html
creator: Inzamam Ul Haq
creator: Ke-Xin Zhang
creator: Yuping Gou
creator: Dina Hajjar
creator: Arwa A. Makki
creator: Wafa A.H. Alkherb
creator: Habib Ali
creator: Changzhong Liu
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Plant Science
subject: Toxicology
description: doi:10.7717/peerj.16859
publisher: PeerJ Inc.
rights: © 2024 Ul Haq et al.
abstract: Background The fall armyworm, Spodoptera frugiperda, is an agricultural pest of significant economic concern globally, known for its adaptability, pesticide resistance, and damage to key crops such as maize. Conventional chemical pesticides pose challenges, including the development of resistance and environmental pollution. The study aims to investigate an alternative solution: the application of soluble silicon (Si) sources to enhance plant resistance against the fall armyworm. Methods Silicon dioxide (SiO2) and potassium silicate (K2SiO3) were applied to maize plants via foliar spray. Transcriptomic and biochemical analyses were performed to study the gene expression changes in the fall armyworm feeding on Si-treated maize. Results Results indicated a significant impact on gene expression, with a large number of differentially expressed genes (DEGs) identified in both SiO2 and K2SiO3 treatments. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified critical DEGs involved in specific pathways, including amino acid, carbohydrate, lipid, energy, xenobiotics metabolisms, signal transduction, and posttranslational modification, significantly altered at both Si sources. Biochemical analyses further revealed that Si treatments inhibited several enzyme activities (glutamate dehydrogenase, trehalase, glucose-6-phosphate dehydrogenase, chitinase, juvenile hormone esterase, and cyclooxygenase while simultaneously inducing others (total protein, lipopolysaccharide, fatty acid synthase, ATPase, and cytochrome P450), thus suggesting a toxic effect on the fall armyworm. In conclusion, Si applications on maize influence the gene expression and biochemical activities of the fall armyworm, potentially offering a sustainable pest management strategy.
bibliographic citation: Ul Haq et al. (2024) Transcriptomic and biochemical insights into fall armyworm (Spodoptera frugiperda) responses on silicon-treated maize. PeerJ 12:e16859 https://doi.org/10.7717/peerj.16859
date submitted: 2023-10-30
date accepted: 2024-01-09
issued: 2024-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ul Haq
  given name: Inzamam
author list: Agent
  family name: Zhang
  given name: Ke-Xin
author list: Agent
  family name: Gou
  given name: Yuping
author list: Agent
  family name: Hajjar
  given name: Dina
author list: Agent
  family name: Makki
  given name: Arwa A.
author list: Agent
  family name: Alkherb
  given name: Wafa A.H.
author list: Agent
  family name: Ali
  given name: Habib
author list: Agent
  family name: Liu
  given name: Changzhong
doi: 10.7717/peerj.16859
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-23
copyright: ©2024 Ul Haq et al.
attribution name: Ul Haq et al.

Non-invasive measurements to identify mungbean genotypes for waterlogging tolerance
type: item
type: AcademicArticle
description: As the best-fit leguminous crop for intercropping across time and space, mungbean promises to sustain soil health, carbon sequestration, and nutritional security across the globe. However, it is susceptible to waterlogging, a significant constraint that persists during heavy rains. Since the predicted climate change scenario features fewer but more intense rainy days. Hence, waterlogging tolerance in mungbean has been one of the major breeding objectives. The present experiment aimed to employ non-destructive tools to phenotype stress tolerance traits in mungbean genotypes exposed to waterlogging and estimate the association among the traits. A total of 12 mungbean genotypes were used in the present study to assess waterlogging tolerance at the seedling stage. Plant responses to stress were determined non-destructively using normalized difference vegetation index (NDVI) and chlorophyll fluorescence parameters at different time intervals. NDVI and grain yield were positively associated with control (r = 0.64) and stress (r = 0.59). Similarly, chlorophyll fluorescence (quantum yield of PS-II) also had a significant positive association with grain yield under both control (r = 0.52) and stress (r = 0.66) conditions. Hence, it is suggested that NDVI and chlorophyll fluorescence promise to serve as traits for non-destructive phenotyping waterlogging tolerance in mungbean genotypes. With the methods proposed in our study, it is possible to phenotype hundreds of plants for waterlogging tolerance efficiently.
format: application/pdf
format: text/html
creator: PS Basavaraj
creator: Krishna Kumar Jangid
creator: Rohit Babar
creator: Jagadish Rane
creator: KM Boraiah
creator: CB Harisha
creator: Hanamanth Halli
creator: Aliza Pradhan
creator: Kuldeep Tripathi
creator: K Sammi Reddy
creator: M Prabhakar
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.16872
publisher: PeerJ Inc.
rights: © 2024 Basavaraj et al.
abstract: As the best-fit leguminous crop for intercropping across time and space, mungbean promises to sustain soil health, carbon sequestration, and nutritional security across the globe. However, it is susceptible to waterlogging, a significant constraint that persists during heavy rains. Since the predicted climate change scenario features fewer but more intense rainy days. Hence, waterlogging tolerance in mungbean has been one of the major breeding objectives. The present experiment aimed to employ non-destructive tools to phenotype stress tolerance traits in mungbean genotypes exposed to waterlogging and estimate the association among the traits. A total of 12 mungbean genotypes were used in the present study to assess waterlogging tolerance at the seedling stage. Plant responses to stress were determined non-destructively using normalized difference vegetation index (NDVI) and chlorophyll fluorescence parameters at different time intervals. NDVI and grain yield were positively associated with control (r = 0.64) and stress (r = 0.59). Similarly, chlorophyll fluorescence (quantum yield of PS-II) also had a significant positive association with grain yield under both control (r = 0.52) and stress (r = 0.66) conditions. Hence, it is suggested that NDVI and chlorophyll fluorescence promise to serve as traits for non-destructive phenotyping waterlogging tolerance in mungbean genotypes. With the methods proposed in our study, it is possible to phenotype hundreds of plants for waterlogging tolerance efficiently.
bibliographic citation: Basavaraj et al. (2024) Non-invasive measurements to identify mungbean genotypes for waterlogging tolerance. PeerJ 12:e16872 https://doi.org/10.7717/peerj.16872
date submitted: 2023-09-06
date accepted: 2024-01-10
issued: 2024-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Basavaraj
  given name: PS
author list: Agent
  family name: Jangid
  given name: Krishna Kumar
author list: Agent
  family name: Babar
  given name: Rohit
author list: Agent
  family name: Rane
  given name: Jagadish
author list: Agent
  family name: Boraiah
  given name: KM
author list: Agent
  family name: Harisha
  given name: CB
author list: Agent
  family name: Halli
  given name: Hanamanth
author list: Agent
  family name: Pradhan
  given name: Aliza
author list: Agent
  family name: Tripathi
  given name: Kuldeep
author list: Agent
  family name: Sammi Reddy
  given name: K
author list: Agent
  family name: Prabhakar
  given name: M
doi: 10.7717/peerj.16872
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-23
copyright: ©2024 Basavaraj et al.
attribution name: Basavaraj et al.

Transcriptomic and targeted metabolome analyses revealed the regulatory mechanisms of the synthesis of bioactive compounds in Citrus grandis ‘tomentosa’
type: item
type: AcademicArticle
description: Exocarpium Citri Grandis is a popular Chinese herbal medicine prepared from Citrus grandis ‘tomentosa’, and it is rich in several bioactive compounds, including flavonoids, coumarins, and volatile oils. However, studies are yet to elucidate the mechanisms of synthesis and regulation of these active components. Therefore, the present study examined the profiles of flavonoids and volatile oil bioactive compounds in plant petals, fruits, and tender leaves, and then performed RNA sequencing on different tissues to identify putative genes involved in the synthesis of bioactive compounds. The results show that the naringin, naringenin, and coumarin contents of the fruitlets were significantly higher than those of the tender leaves and petals, whereas the tender leaves had significantly higher levels of rhoifolin and apigenin. A total of 49 volatile oils, of which 10 were mainly found in flowers, 15 were mainly found in fruits, and 18 were mainly found in leaves, were identified. RNA sequencing identified 9,942 genes that were differentially expressed in different tissues. Further analysis showed that 20, 15, and 74 differentially expressed genes were involved in regulating flavonoid synthesis, regulating coumarin synthesis, and synthesis and regulation of terpenoids, respectively. CHI1 (Cg7g005600) and 1,2Rhat gene (Cg1g023820) may be involved in the regulation of naringin synthesis in C. grandis fruits. The HDR (Cg8g006150) gene, HMGS gene (Cg5g009630) and GGPS (Cg1g003650) may be involved in the regulation and synthesis of volatile oils in C. grandis petals. Overall, the findings of the present study enhance our understanding of the regulatory mechanisms of secondary metabolites in C. grandis, which could promote the breeding of C. grandis with desired characteristics.
format: application/pdf
format: text/html
creator: Xinmin Huang
creator: Xiaoli Liu
creator: Qi Wang
creator: Yanqing Zhou
creator: Shiting Deng
creator: Qinqin He
creator: Hanbing Han
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.16881
publisher: PeerJ Inc.
rights: © 2024 Huang et al.
abstract: Exocarpium Citri Grandis is a popular Chinese herbal medicine prepared from Citrus grandis ‘tomentosa’, and it is rich in several bioactive compounds, including flavonoids, coumarins, and volatile oils. However, studies are yet to elucidate the mechanisms of synthesis and regulation of these active components. Therefore, the present study examined the profiles of flavonoids and volatile oil bioactive compounds in plant petals, fruits, and tender leaves, and then performed RNA sequencing on different tissues to identify putative genes involved in the synthesis of bioactive compounds. The results show that the naringin, naringenin, and coumarin contents of the fruitlets were significantly higher than those of the tender leaves and petals, whereas the tender leaves had significantly higher levels of rhoifolin and apigenin. A total of 49 volatile oils, of which 10 were mainly found in flowers, 15 were mainly found in fruits, and 18 were mainly found in leaves, were identified. RNA sequencing identified 9,942 genes that were differentially expressed in different tissues. Further analysis showed that 20, 15, and 74 differentially expressed genes were involved in regulating flavonoid synthesis, regulating coumarin synthesis, and synthesis and regulation of terpenoids, respectively. CHI1 (Cg7g005600) and 1,2Rhat gene (Cg1g023820) may be involved in the regulation of naringin synthesis in C. grandis fruits. The HDR (Cg8g006150) gene, HMGS gene (Cg5g009630) and GGPS (Cg1g003650) may be involved in the regulation and synthesis of volatile oils in C. grandis petals. Overall, the findings of the present study enhance our understanding of the regulatory mechanisms of secondary metabolites in C. grandis, which could promote the breeding of C. grandis with desired characteristics.
bibliographic citation: Huang et al. (2024) Transcriptomic and targeted metabolome analyses revealed the regulatory mechanisms of the synthesis of bioactive compounds in Citrus grandis ‘tomentosa’. PeerJ 12:e16881 https://doi.org/10.7717/peerj.16881
date submitted: 2022-06-21
date accepted: 2024-01-12
issued: 2024-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Xinmin
author list: Agent
  family name: Liu
  given name: Xiaoli
author list: Agent
  family name: Wang
  given name: Qi
author list: Agent
  family name: Zhou
  given name: Yanqing
author list: Agent
  family name: Deng
  given name: Shiting
author list: Agent
  family name: He
  given name: Qinqin
author list: Agent
  family name: Han
  given name: Hanbing
doi: 10.7717/peerj.16881
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-23
copyright: ©2024 Huang et al.
attribution name: Huang et al.

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