PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Investigation of spatiotemporal evolution and driving mechanisms of carbon sources and sinks in dry-hot valleys under extreme climate events: a case study of the Nu River dry-hot valley
items: From trace to trace maker: Oligocene–Miocene coprolites of southern Poland and their potential producers
items: Hidden microalgae diversity in reef systems: reanalysis of coral microbiomes reveals spatial patterns of coral-associated plastid communities in the Southwestern Atlantic Ocean (SWAO)
items: Predation experiments with 3D-printed lizard models yield limited responses in pheasants
items: Plant morphological traits and ecological stoichiometry in disturbed vs. conserved forests
items: Elevated SLC1A5 links to inflamed endothelial cells and proteinuria in membranous nephropathy patients
items: Gastric intestinal metaplasia subtypes and the effects of c-Myc expression on severity
items: https://peerj.com/articles/20246
items: NAT10 inhibits ferroptosis and promotes the progression of renal clear cell carcinoma by regulating the NFE2L1-GPX4 signaling pathway
items: Detailed morphological characterization and improvement of keratinocyte outgrowth from plucked human hair follicle

Investigation of spatiotemporal evolution and driving mechanisms of carbon sources and sinks in dry-hot valleys under extreme climate events: a case study of the Nu River dry-hot valley
type: item
type: AcademicArticle
description: Under global climate change, the rising frequency of extreme weather events profoundly affects ecosystem carbon cycles. However, in the ecologically fragile dry-hot valleys of Southwest China, the response of carbon source-sink dynamics to these extremes remains unclear, which hinders effective regional carbon management. This study investigates the Nu River dry-hot valley, using the Google Earth Engine platform to process multi-source remote sensing and meteorological data from 2001–2024. We established a framework of 15 extreme climate indices and applied Sen-Mann-Kendall trend analysis, Pearson correlation, and threshold regression models to explore the spatiotemporal evolution of carbon dynamics and their non-linear response to extreme climate. Our results show that: (1) The region’s carbon sink capacity displayed a fluctuating but overall increasing trend with significant spatial heterogeneity; areas of substantial increase were concentrated in the southern, low-altitude zones. (2) Extreme climate events triggered non-linear carbon cycle responses by altering hydrothermal conditions. The synergy of high temperatures and intense, short-duration precipitation weakened the carbon sink, whereas dispersed rainfall alleviated drought stress and enhanced carbon fixation. (3) Both extreme temperature and precipitation indices showed clear regulatory thresholds, above which their effects were significantly amplified; this reveals that the carbon cycle in the dry-hot valley is highly sensitive to extreme events and exhibits distinct threshold-driven responses. This research provides a theoretical basis for the mechanisms regulating carbon flux in dry-hot ecosystems under a variable climate and offers crucial scientific support for optimising regional pathways to carbon neutrality and implementing climate-adaptive management.
format: application/pdf
format: text/html
creator: Haojun Sun
creator: Shaoyun Zhang
creator: Shanshan Liu
creator: Liping Zhang
subject: Soil Science
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20268
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Under global climate change, the rising frequency of extreme weather events profoundly affects ecosystem carbon cycles. However, in the ecologically fragile dry-hot valleys of Southwest China, the response of carbon source-sink dynamics to these extremes remains unclear, which hinders effective regional carbon management. This study investigates the Nu River dry-hot valley, using the Google Earth Engine platform to process multi-source remote sensing and meteorological data from 2001–2024. We established a framework of 15 extreme climate indices and applied Sen-Mann-Kendall trend analysis, Pearson correlation, and threshold regression models to explore the spatiotemporal evolution of carbon dynamics and their non-linear response to extreme climate. Our results show that: (1) The region’s carbon sink capacity displayed a fluctuating but overall increasing trend with significant spatial heterogeneity; areas of substantial increase were concentrated in the southern, low-altitude zones. (2) Extreme climate events triggered non-linear carbon cycle responses by altering hydrothermal conditions. The synergy of high temperatures and intense, short-duration precipitation weakened the carbon sink, whereas dispersed rainfall alleviated drought stress and enhanced carbon fixation. (3) Both extreme temperature and precipitation indices showed clear regulatory thresholds, above which their effects were significantly amplified; this reveals that the carbon cycle in the dry-hot valley is highly sensitive to extreme events and exhibits distinct threshold-driven responses. This research provides a theoretical basis for the mechanisms regulating carbon flux in dry-hot ecosystems under a variable climate and offers crucial scientific support for optimising regional pathways to carbon neutrality and implementing climate-adaptive management.
bibliographic citation: Sun et al. (2025) Investigation of spatiotemporal evolution and driving mechanisms of carbon sources and sinks in dry-hot valleys under extreme climate events: a case study of the Nu River dry-hot valley. PeerJ 13:e20268 https://doi.org/10.7717/peerj.20268
date submitted: 2025-05-23
date accepted: 2025-09-30
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Haojun
author list: Agent
  family name: Zhang
  given name: Shaoyun
author list: Agent
  family name: Liu
  given name: Shanshan
author list: Agent
  family name: Zhang
  given name: Liping
doi: 10.7717/peerj.20268
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: ©2025 Sun et al.
attribution name: Sun et al.

From trace to trace maker: Oligocene–Miocene coprolites of southern Poland and their potential producers
type: item
type: AcademicArticle
description: In this paper we describe coprolites from deep-marine Oligocene sediments, shallow- and deep-marine Miocene deposits, as well as Miocene continental environments in southern and central Poland. The Oligocene and Miocene coprolites from marine environments (hereinafter referred to as M) are classified into six morphotypes: (M1) sinusoidal, (M2) elongated and straight, (M3) curved, (M4) irregular, (M5) S-shaped, and (M6) oval. Sinusoidal coprolites, previously interpreted as originating from predatory fish (e.g., Palimphyes, Oligophus, and indeterminate taxa), are reinterpreted here, based on actualistic observations, as crustacean (crab) faeces. Morphotypes (M2)–(M5) are attributed to fish, while the oval type (M6) is tentatively linked to columbid-like birds, although alternative producers cannot be excluded. Miocene deep-sea coprolites are represented by relatively long, complex fecal masses composed of constricted strings, suggesting holothurians or cephalopods as potential producers. Elongated Miocene coprolites from shallow-water environments are likely to have been produced by teleost fish - most likely Sparidae - or by sharks. However, other vertebrates, including toothed and toothless cetaceans and porpoises, cannot be ruled out. The terrestrial Miocene specimens include five morphotypes (hereinafter referred to as T-terrestrial, T1–T7): (T1) oval, (T2) sinusoidal, (T3) elongated with two submorphotypes (T3/1–siderite individuals and T3/2–apatite individuals), (T4) S-shaped, and (T5) irregular. They are interpreted as coprolites likely produced by snakes (T1–T3/1, T4, T5), and small mammals such as Sciuridae and/or Chiropteridae (T3/2). Overall, these data provide new insights into the diversity of post-Mesozoic coprolites and refine our understanding of their producers and associated ecosystems in Central Europe.
format: application/pdf
format: text/html
creator: Tomasz Brachaniec
creator: Dorota Środek
creator: Mateusz Salamon
creator: Michał Bugajski
creator: Piotr Duda
creator: Adam Danielak
creator: Magdalena Janiszewska
creator: Grzegorz Sadlok
creator: Wojciech Kuśnierczyk
subject: Ecology
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.20242
publisher: PeerJ Inc.
rights: © 2025 Brachaniec et al.
abstract: In this paper we describe coprolites from deep-marine Oligocene sediments, shallow- and deep-marine Miocene deposits, as well as Miocene continental environments in southern and central Poland. The Oligocene and Miocene coprolites from marine environments (hereinafter referred to as M) are classified into six morphotypes: (M1) sinusoidal, (M2) elongated and straight, (M3) curved, (M4) irregular, (M5) S-shaped, and (M6) oval. Sinusoidal coprolites, previously interpreted as originating from predatory fish (e.g., Palimphyes, Oligophus, and indeterminate taxa), are reinterpreted here, based on actualistic observations, as crustacean (crab) faeces. Morphotypes (M2)–(M5) are attributed to fish, while the oval type (M6) is tentatively linked to columbid-like birds, although alternative producers cannot be excluded. Miocene deep-sea coprolites are represented by relatively long, complex fecal masses composed of constricted strings, suggesting holothurians or cephalopods as potential producers. Elongated Miocene coprolites from shallow-water environments are likely to have been produced by teleost fish - most likely Sparidae - or by sharks. However, other vertebrates, including toothed and toothless cetaceans and porpoises, cannot be ruled out. The terrestrial Miocene specimens include five morphotypes (hereinafter referred to as T-terrestrial, T1–T7): (T1) oval, (T2) sinusoidal, (T3) elongated with two submorphotypes (T3/1–siderite individuals and T3/2–apatite individuals), (T4) S-shaped, and (T5) irregular. They are interpreted as coprolites likely produced by snakes (T1–T3/1, T4, T5), and small mammals such as Sciuridae and/or Chiropteridae (T3/2). Overall, these data provide new insights into the diversity of post-Mesozoic coprolites and refine our understanding of their producers and associated ecosystems in Central Europe.
bibliographic citation: Brachaniec et al. (2025) From trace to trace maker: Oligocene–Miocene coprolites of southern Poland and their potential producers. PeerJ 13:e20242 https://doi.org/10.7717/peerj.20242
date submitted: 2025-05-14
date accepted: 2025-09-24
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brachaniec
  given name: Tomasz
author list: Agent
  family name: Środek
  given name: Dorota
author list: Agent
  family name: Salamon
  given name: Mateusz
author list: Agent
  family name: Bugajski
  given name: Michał
author list: Agent
  family name: Duda
  given name: Piotr
author list: Agent
  family name: Danielak
  given name: Adam
author list: Agent
  family name: Janiszewska
  given name: Magdalena
author list: Agent
  family name: Sadlok
  given name: Grzegorz
author list: Agent
  family name: Kuśnierczyk
  given name: Wojciech
doi: 10.7717/peerj.20242
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: ©2025 Brachaniec et al.
attribution name: Brachaniec et al.

Hidden microalgae diversity in reef systems: reanalysis of coral microbiomes reveals spatial patterns of coral-associated plastid communities in the Southwestern Atlantic Ocean (SWAO)
type: item
type: AcademicArticle
description: The microbial community associated with corals plays a critical role in reef ecosystems, yet studies mainly focus on prokaryotes and Symbiodiniaceae, overlooking other oxygen-evolving photosynthetic eukaryotes. This leaves a knowledge gap regarding potentially important microbiome members. Here, we revisited coral microbiome datasets to investigate the diversity of plastid-bearing eukaryotes associated with Southwestern Atlantic Ocean (SWAO) corals. We compiled an inventory of plastid-bearing communities, uncovering their diversity and exploring ecological patterns. We further applied this approach to analyze the plastidiomes (plastid-bearing communities) of corals from the Abrolhos Bank, the largest reef system in the region, as a case study. A systematic literature review of 16S rDNA-based coral microbiome was conducted, excluding studies lacking plastid 16S sequences. The search made in PubMed resulted in 19 studies reporting corals sampled from 2009 to 2022, which were compiled and reanalyzed. Sequences of chloroplast origin (Silva 132) were further taxonomically classified by consensus-BLASTn search with the PR2 plastid 16S database. The dataset encompassed reef water and coral microbiomes from eight coral species, emphasizing the genus Mussismilia. A total of 272 amplicon libraries yielded 707,949 plastid sequences, identifying 196 algal genera across 41 classes. Reef water and coral plastid communities differed markedly. Ostreobium (81%) and Calliarthron (49%) were the most prevalent genera in coral samples. Diatoms were common (>40% of samples) in the water and in corals, whereas corallicolids were exclusive to corals (31.8%). The Abrolhos case study revealed geographic variation in Mussismilia harttii plastidiomes, which were less diverse than those in the water column. Coral indicator taxa included Ostreobium, corallicolids, Navicula, and Amphora. Our findings identify plastidiome variations and their implications for the coral host. Lipid-rich diatoms pre…
format: application/pdf
format: text/html
creator: Clara P. Pires
creator: Livia B. Villela
creator: Rodrigo L. Moura
creator: Paulo S. Salomon
creator: Arthur W. Silva-Lima
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.20116
publisher: PeerJ Inc.
rights: © 2025 Pires et al.
abstract: The microbial community associated with corals plays a critical role in reef ecosystems, yet studies mainly focus on prokaryotes and Symbiodiniaceae, overlooking other oxygen-evolving photosynthetic eukaryotes. This leaves a knowledge gap regarding potentially important microbiome members. Here, we revisited coral microbiome datasets to investigate the diversity of plastid-bearing eukaryotes associated with Southwestern Atlantic Ocean (SWAO) corals. We compiled an inventory of plastid-bearing communities, uncovering their diversity and exploring ecological patterns. We further applied this approach to analyze the plastidiomes (plastid-bearing communities) of corals from the Abrolhos Bank, the largest reef system in the region, as a case study. A systematic literature review of 16S rDNA-based coral microbiome was conducted, excluding studies lacking plastid 16S sequences. The search made in PubMed resulted in 19 studies reporting corals sampled from 2009 to 2022, which were compiled and reanalyzed. Sequences of chloroplast origin (Silva 132) were further taxonomically classified by consensus-BLASTn search with the PR2 plastid 16S database. The dataset encompassed reef water and coral microbiomes from eight coral species, emphasizing the genus Mussismilia. A total of 272 amplicon libraries yielded 707,949 plastid sequences, identifying 196 algal genera across 41 classes. Reef water and coral plastid communities differed markedly. Ostreobium (81%) and Calliarthron (49%) were the most prevalent genera in coral samples. Diatoms were common (>40% of samples) in the water and in corals, whereas corallicolids were exclusive to corals (31.8%). The Abrolhos case study revealed geographic variation in Mussismilia harttii plastidiomes, which were less diverse than those in the water column. Coral indicator taxa included Ostreobium, corallicolids, Navicula, and Amphora. Our findings identify plastidiome variations and their implications for the coral host. Lipid-rich diatoms pre…
bibliographic citation: Pires et al. (2025) Hidden microalgae diversity in reef systems: reanalysis of coral microbiomes reveals spatial patterns of coral-associated plastid communities in the Southwestern Atlantic Ocean (SWAO). PeerJ 13:e20116 https://doi.org/10.7717/peerj.20116
date submitted: 2024-07-18
date accepted: 2025-09-01
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pires
  given name: Clara P.
author list: Agent
  family name: Villela
  given name: Livia B.
author list: Agent
  family name: Moura
  given name: Rodrigo L.
author list: Agent
  family name: Salomon
  given name: Paulo S.
author list: Agent
  family name: Silva-Lima
  given name: Arthur W.
doi: 10.7717/peerj.20116
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: © 2025 Pires et al.
attribution name: Pires et al.

Predation experiments with 3D-printed lizard models yield limited responses in pheasants
type: item
type: AcademicArticle
description: Animal colouration has been viewed as an adaptation shaped by both abiotic and biotic factors, balancing sexual attractiveness against predation risk. In studying predator-prey dynamics, using 3D models as prey surrogates is common, but material constraints can affect outcomes in both natural and seminatural settings. Here, we utilized 3D-printed models representing three colour morphs of sand lizards (Lacerta agilis) to investigate interactions with captive-bred pheasants (Phasianus colchicus) utilizing forced exploration experiments in an outdoor arena fitted with a grass carpet. The models adequately represented the lizard colouration across a reflectance spectral range of 330–800 nm. Our findings indicate that the pheasants generally exhibited a minimal response to static models, with significant differences observed only in younger birds (7–12 weeks old), demonstrating a higher alert response than adults. No effects were found relating to the colour morph or sex of the lizard models. These results suggest that immobile 3D-printed prey models may be insufficient to trigger natural predator responses in this predator-prey system, highlighting potential limitations of static models in eliciting predator reaction.
format: application/pdf
format: text/html
creator: Radovan Smolinský
creator: Ivo Adam
creator: Zuzana Hiadlovská
creator: Shubhra Sau
creator: Pavel Škrabánek
creator: Natália Martínková
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.20103
publisher: PeerJ Inc.
rights: © 2025 Smolinský et al.
abstract: Animal colouration has been viewed as an adaptation shaped by both abiotic and biotic factors, balancing sexual attractiveness against predation risk. In studying predator-prey dynamics, using 3D models as prey surrogates is common, but material constraints can affect outcomes in both natural and seminatural settings. Here, we utilized 3D-printed models representing three colour morphs of sand lizards (Lacerta agilis) to investigate interactions with captive-bred pheasants (Phasianus colchicus) utilizing forced exploration experiments in an outdoor arena fitted with a grass carpet. The models adequately represented the lizard colouration across a reflectance spectral range of 330–800 nm. Our findings indicate that the pheasants generally exhibited a minimal response to static models, with significant differences observed only in younger birds (7–12 weeks old), demonstrating a higher alert response than adults. No effects were found relating to the colour morph or sex of the lizard models. These results suggest that immobile 3D-printed prey models may be insufficient to trigger natural predator responses in this predator-prey system, highlighting potential limitations of static models in eliciting predator reaction.
bibliographic citation: Smolinský et al. (2025) Predation experiments with 3D-printed lizard models yield limited responses in pheasants. PeerJ 13:e20103 https://doi.org/10.7717/peerj.20103
date submitted: 2025-06-20
date accepted: 2025-08-27
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smolinský
  given name: Radovan
author list: Agent
  family name: Adam
  given name: Ivo
author list: Agent
  family name: Hiadlovská
  given name: Zuzana
author list: Agent
  family name: Sau
  given name: Shubhra
author list: Agent
  family name: Škrabánek
  given name: Pavel
author list: Agent
  family name: Martínková
  given name: Natália
doi: 10.7717/peerj.20103
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: ©2025 Smolinský et al.
attribution name: Smolinský et al.

Plant morphological traits and ecological stoichiometry in disturbed vs. conserved forests
type: item
type: AcademicArticle
description: Global forests are currently facing significant anthropogenic disturbances. Previous research on plant functional traits has predominantly focused on relatively intact forests, often overlooking those that have experienced such disturbances. This oversight has lead to a scarcity of relevant data regarding disturbed forests in the global and Chinese plant functional trait databases, thereby limiting our understanding of the life history strategies employed by plants inhabiting these altered environments. This study presents data on 12 morphological traits and 24 ecological stoichiometry traits for 62 common species in disturbed forests and 43 species in conserved forests in East China. We analyzed the variability characteristics of these functional traits, explored functional trait differences between disturbed and conserved forests, and examined relationships among various functional traits to investigate disparities in life history strategies between the two forest types. The results indicated that the variability of plant functional traits was generally lower in disturbed forests compared to conserved ones. Most functional traits exhibited significant differences between the two forest types (P < 0.05). Additionally, stronger correlations among functional traits were noted in disturbed forests. From a functional trait perspective, plants in disturbed forests displayed high trait correlations and formed trait combinations indicative of a resource conservative strategy characterized by low specific leaf area, high dry matter content and tissue density across leaves, twigs, barks and stems; alongside heightened carbon investment but reduced al locations for nitrogen and phosphorus. A comprehensive investigation of plant functional traits in both disturbed and conserved forests will enrich the global and Chinese trait databases, providing insights into how forest plants adapt to disturbances and informing ecological restoration in degraded areas.
format: application/pdf
format: text/html
creator: Xiaoyin Guan
creator: Haojun Xia
creator: Shuming Li
creator: Shuisheng Yu
creator: Zihong Zheng
creator: Julian Liu
creator: Libin Liu
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.20301
publisher: PeerJ Inc.
rights: © 2025 Guan et al.
abstract: Global forests are currently facing significant anthropogenic disturbances. Previous research on plant functional traits has predominantly focused on relatively intact forests, often overlooking those that have experienced such disturbances. This oversight has lead to a scarcity of relevant data regarding disturbed forests in the global and Chinese plant functional trait databases, thereby limiting our understanding of the life history strategies employed by plants inhabiting these altered environments. This study presents data on 12 morphological traits and 24 ecological stoichiometry traits for 62 common species in disturbed forests and 43 species in conserved forests in East China. We analyzed the variability characteristics of these functional traits, explored functional trait differences between disturbed and conserved forests, and examined relationships among various functional traits to investigate disparities in life history strategies between the two forest types. The results indicated that the variability of plant functional traits was generally lower in disturbed forests compared to conserved ones. Most functional traits exhibited significant differences between the two forest types (P < 0.05). Additionally, stronger correlations among functional traits were noted in disturbed forests. From a functional trait perspective, plants in disturbed forests displayed high trait correlations and formed trait combinations indicative of a resource conservative strategy characterized by low specific leaf area, high dry matter content and tissue density across leaves, twigs, barks and stems; alongside heightened carbon investment but reduced al locations for nitrogen and phosphorus. A comprehensive investigation of plant functional traits in both disturbed and conserved forests will enrich the global and Chinese trait databases, providing insights into how forest plants adapt to disturbances and informing ecological restoration in degraded areas.
bibliographic citation: Guan et al. (2025) Plant morphological traits and ecological stoichiometry in disturbed vs. conserved forests. PeerJ 13:e20301 https://doi.org/10.7717/peerj.20301
date submitted: 2025-06-03
date accepted: 2025-10-06
issued: 2025-10-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guan
  given name: Xiaoyin
author list: Agent
  family name: Xia
  given name: Haojun
author list: Agent
  family name: Li
  given name: Shuming
author list: Agent
  family name: Yu
  given name: Shuisheng
author list: Agent
  family name: Zheng
  given name: Zihong
author list: Agent
  family name: Liu
  given name: Julian
author list: Agent
  family name: Liu
  given name: Libin
doi: 10.7717/peerj.20301
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-31
copyright: © 2025 Guan et al.
attribution name: Guan et al.

Elevated SLC1A5 links to inflamed endothelial cells and proteinuria in membranous nephropathy patients
type: item
type: AcademicArticle
description: Background Membranous nephropathy (MN) is an autoimmune glomerular disorder characterized by persistent proteinuria. Elucidating its pathophysiological mechanisms and signaling pathways is crucial for improving diagnostic and therapeutic strategies. Methods We performed differential analysis on the MN glomerular transcriptome and assessed immune infiltration. Single-cell analysis identified key genes’ subcellular localization, while pseudotime and cell communication analyses determined subpopulations linked to MN progression. Genes causally related to MN onset were screened using Mendelian randomization, and serum core genes were correlated with proteinuria via ELISA. Results Transcriptome analysis revealed 95 differentially expressed genes, predominantly enriched in immune and metabolic pathways. Macrophage polarization played a pivotal role in MN, with monocytes/macrophages and endothelial cells identified as key contributors. Pseudotemporal analysis showed elevated pro-inflammatory macrophages and inflammatory endothelial cells in high-proteinuria patients. Macrophage-endothelial cell communication involved key signaling molecules. hdWGCNA analysis identified three molecular sets linked to inflammatory cells, with Mendelian randomization confirming their causal relationship to MN. SLC1A5 was identified as a key gene, and serum sample validation confirmed its strong correlation with proteinuria. Conclusion This study identified novel macrophage and endothelial cell subtypes and their interactions, positioning SLC1A5 as a potential biomarker for MN pathogenesis.
format: application/pdf
format: text/html
creator: Qingqin Tang
creator: Yi Ling
creator: Jianzhong Li
creator: Bin Feng
creator: Sheng Zhang
creator: Deyu Xu
creator: Ling Zhou
creator: Lei Shen
creator: Guoyuan Lu
creator: Mingyu Chen
creator: Longwei Qiao
creator: Yuting Liang
subject: Molecular Biology
subject: Immunology
subject: Nephrology
subject: Statistics
description: doi:10.7717/peerj.20271
publisher: PeerJ Inc.
rights: © 2025 Tang et al.
abstract: Background Membranous nephropathy (MN) is an autoimmune glomerular disorder characterized by persistent proteinuria. Elucidating its pathophysiological mechanisms and signaling pathways is crucial for improving diagnostic and therapeutic strategies. Methods We performed differential analysis on the MN glomerular transcriptome and assessed immune infiltration. Single-cell analysis identified key genes’ subcellular localization, while pseudotime and cell communication analyses determined subpopulations linked to MN progression. Genes causally related to MN onset were screened using Mendelian randomization, and serum core genes were correlated with proteinuria via ELISA. Results Transcriptome analysis revealed 95 differentially expressed genes, predominantly enriched in immune and metabolic pathways. Macrophage polarization played a pivotal role in MN, with monocytes/macrophages and endothelial cells identified as key contributors. Pseudotemporal analysis showed elevated pro-inflammatory macrophages and inflammatory endothelial cells in high-proteinuria patients. Macrophage-endothelial cell communication involved key signaling molecules. hdWGCNA analysis identified three molecular sets linked to inflammatory cells, with Mendelian randomization confirming their causal relationship to MN. SLC1A5 was identified as a key gene, and serum sample validation confirmed its strong correlation with proteinuria. Conclusion This study identified novel macrophage and endothelial cell subtypes and their interactions, positioning SLC1A5 as a potential biomarker for MN pathogenesis.
bibliographic citation: Tang et al. (2025) Elevated SLC1A5 links to inflamed endothelial cells and proteinuria in membranous nephropathy patients. PeerJ 13:e20271 https://doi.org/10.7717/peerj.20271
date submitted: 2024-12-02
date accepted: 2025-09-30
issued: 2025-10-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Qingqin
author list: Agent
  family name: Ling
  given name: Yi
author list: Agent
  family name: Li
  given name: Jianzhong
author list: Agent
  family name: Feng
  given name: Bin
author list: Agent
  family name: Zhang
  given name: Sheng
author list: Agent
  family name: Xu
  given name: Deyu
author list: Agent
  family name: Zhou
  given name: Ling
author list: Agent
  family name: Shen
  given name: Lei
author list: Agent
  family name: Lu
  given name: Guoyuan
author list: Agent
  family name: Chen
  given name: Mingyu
author list: Agent
  family name: Qiao
  given name: Longwei
author list: Agent
  family name: Liang
  given name: Yuting
doi: 10.7717/peerj.20271
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-31
copyright: ©2025 Tang et al.
attribution name: Tang et al.

Gastric intestinal metaplasia subtypes and the effects of c-Myc expression on severity
type: item
type: AcademicArticle
description: Background The association between gastric intestinal metaplasia severity grades, histological subtypes, and oncogenic potential remains unclear. This study explored gastric intestinal metaplasia (GIM) subtypes and c-Myc protein expression across mild, moderate, and severe GIM cases. Methods A total of 180 paraffin-embedded gastroscopy biopsy samples from patients diagnosed with atrophic gastritis were selected, with 60 cases each of mild, moderate, and severe GIM. Alcian blue-Periodic acid-Schiff (AB-PAS) and high iron diamine (HID) staining were used to classify GIM into types I-III. Immunohistochemistry was performed to assess c-Myc expression, with low, moderate, and high expression defined as the percentage of c-Myc-positive cells in the GIM area of <15%, 15–40%, and ≥ 40%, respectively. Spearman and Kruskal–Wallis tests were used to analyze the correlation between GIM severity, GIM subtype, and c-Myc expression. Results GIM was predominantly diagnosed in middle-aged and elderly individuals. Regarding the subtype, 53.89% were type II, 25.56% were type III, and 20.56% were type I. Low c-Myc expression was present in 47.78% of cases, moderate expression in 36.67%, and high expression in 15.56%. Neither the severity of GIM nor its subtype or c-Myc expression level was correlated with age or sex. Type III GIM accounted for approximately 10% of mild-to-moderate cases, whereas > 50% of severe GIM cases were type III. A positive correlation was found between GIM severity and subtype (rs = 0.376, P < 0.05). There was no significant correlation in c-Myc expression across different GIM severities. From type I to type III GIM, the proportion of low c-Myc expression increased and that of high expression decreased, whereas that of moderate expression remained almost unchanged. A negative correlation was observed between the GIM subtype and c-Myc expression (rs = −0.148, P < 0.05). Conclusion GIM incidence increases with age; however, the histological severity of GIM (as def…
format: application/pdf
format: text/html
creator: Qinglu Yang
creator: Lingzhi Lian
creator: Jingying Shen
creator: Qin Cao
creator: Xuewei Wang
creator: Pingping Hu
subject: Gastroenterology and Hepatology
subject: Pathology
description: doi:10.7717/peerj.20257
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: Background The association between gastric intestinal metaplasia severity grades, histological subtypes, and oncogenic potential remains unclear. This study explored gastric intestinal metaplasia (GIM) subtypes and c-Myc protein expression across mild, moderate, and severe GIM cases. Methods A total of 180 paraffin-embedded gastroscopy biopsy samples from patients diagnosed with atrophic gastritis were selected, with 60 cases each of mild, moderate, and severe GIM. Alcian blue-Periodic acid-Schiff (AB-PAS) and high iron diamine (HID) staining were used to classify GIM into types I-III. Immunohistochemistry was performed to assess c-Myc expression, with low, moderate, and high expression defined as the percentage of c-Myc-positive cells in the GIM area of <15%, 15–40%, and ≥ 40%, respectively. Spearman and Kruskal–Wallis tests were used to analyze the correlation between GIM severity, GIM subtype, and c-Myc expression. Results GIM was predominantly diagnosed in middle-aged and elderly individuals. Regarding the subtype, 53.89% were type II, 25.56% were type III, and 20.56% were type I. Low c-Myc expression was present in 47.78% of cases, moderate expression in 36.67%, and high expression in 15.56%. Neither the severity of GIM nor its subtype or c-Myc expression level was correlated with age or sex. Type III GIM accounted for approximately 10% of mild-to-moderate cases, whereas > 50% of severe GIM cases were type III. A positive correlation was found between GIM severity and subtype (rs = 0.376, P < 0.05). There was no significant correlation in c-Myc expression across different GIM severities. From type I to type III GIM, the proportion of low c-Myc expression increased and that of high expression decreased, whereas that of moderate expression remained almost unchanged. A negative correlation was observed between the GIM subtype and c-Myc expression (rs = −0.148, P < 0.05). Conclusion GIM incidence increases with age; however, the histological severity of GIM (as def…
bibliographic citation: Yang et al. (2025) Gastric intestinal metaplasia subtypes and the effects of c-Myc expression on severity. PeerJ 13:e20257 https://doi.org/10.7717/peerj.20257
date submitted: 2025-05-05
date accepted: 2025-09-26
issued: 2025-10-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Qinglu
author list: Agent
  family name: Lian
  given name: Lingzhi
author list: Agent
  family name: Shen
  given name: Jingying
author list: Agent
  family name: Cao
  given name: Qin
author list: Agent
  family name: Wang
  given name: Xuewei
author list: Agent
  family name: Hu
  given name: Pingping
doi: 10.7717/peerj.20257
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-31
copyright: ©2025 Yang et al.
attribution name: Yang et al.

https://peerj.com/articles/20246
type: item
type: AcademicArticle
title: Schizopera vietnamica sp. nov. (Copepoda, Harpacticoida, Miraciidae), a new species from a mangrove zone in Vietnam, with description of a new species, and a key to the species from the Oriental region, Sulawesi, and East Asia
description: Background A new species of harpacticoid copepod of the genus Schizopera, S. vietnamica sp. nov., was found. This is the first record of the genus for the country. Methods Samples were collected in July 2023, using a plankton net with a mesh size of 50 µm. The body parts of the specimens were dissected and mounted on glass slides. Morphological examination was carried out at 1,000× magnification. Habitus and appendages were then drawn using a drawing tube attached to a compound microscope. Results The new species differed from all its congeners in the relative length and chaetotaxy of the caudal rami, length of the proximal endopodal segment of the female first swimming leg relative to the exopod, armature of the middle and the distal endopodal segments of the second to the fourth swimming leg, segmentation and chaetotaxy of the fifth swimming leg. The new species resembles most S. neglecta in the loss of the inner seta on the proximal endopodal segment of the second to the fourth swimming legs, as well as in the shape and setular ornamentation of the inner margin of the caudal rami. A key to the species of the genus known from the Oriental region, Sulawesi and East Asia is provided.
format: application/pdf
format: text/html
creator: Ngoc-Son Tran
creator: Thi-Phuong Pham
creator: Minh Anh Dam
creator: Chaichat Boonyanusith
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.20246
publisher: PeerJ Inc.
rights: © 2025 Tran et al.
abstract: Background A new species of harpacticoid copepod of the genus Schizopera, S. vietnamica sp. nov., was found. This is the first record of the genus for the country. Methods Samples were collected in July 2023, using a plankton net with a mesh size of 50 µm. The body parts of the specimens were dissected and mounted on glass slides. Morphological examination was carried out at 1,000× magnification. Habitus and appendages were then drawn using a drawing tube attached to a compound microscope. Results The new species differed from all its congeners in the relative length and chaetotaxy of the caudal rami, length of the proximal endopodal segment of the female first swimming leg relative to the exopod, armature of the middle and the distal endopodal segments of the second to the fourth swimming leg, segmentation and chaetotaxy of the fifth swimming leg. The new species resembles most S. neglecta in the loss of the inner seta on the proximal endopodal segment of the second to the fourth swimming legs, as well as in the shape and setular ornamentation of the inner margin of the caudal rami. A key to the species of the genus known from the Oriental region, Sulawesi and East Asia is provided.
bibliographic citation: Tran et al. (2025) Schizopera vietnamica sp. nov. (Copepoda, Harpacticoida, Miraciidae), a new species from a mangrove zone in Vietnam, with description of a new species, and a key to the species from the Oriental region, Sulawesi, and East Asia. PeerJ 13:e20246 https://doi.org/10.7717/peerj.20246
date submitted: 2025-06-28
date accepted: 2025-09-25
issued: 2025-10-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tran
  given name: Ngoc-Son
author list: Agent
  family name: Pham
  given name: Thi-Phuong
author list: Agent
  family name: Dam
  given name: Minh Anh
author list: Agent
  family name: Boonyanusith
  given name: Chaichat
doi: 10.7717/peerj.20246
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-31
copyright: ©2025 Tran et al.
attribution name: Tran et al.

NAT10 inhibits ferroptosis and promotes the progression of renal clear cell carcinoma by regulating the NFE2L1-GPX4 signaling pathway
type: item
type: AcademicArticle
description: Objective Clear cell renal cell carcinoma (ccRCC) is a prevalent pathological subtype of renal cell carcinoma that arises from renal tubular epithelial cells. ccRCC has long been characterized by high mortality, and at present, surgical resection is the only curative treatment, but its effectiveness is low and survival rates are low. N-acetyltransferase 10 (NAT10) is a protein that acts as an acetyltransferase, has distinct catalytic and regulatory functions, and is involved in the progression of various cancers such as bladder cancer, hepatocellular carcinoma, and multiple myeloma. Ferroptosis is a novel form of programmed cell death that is iron-dependent and distinct from apoptosis, necrosis, and autophagy. Therefore, this study aimed to investigate the potential functions of NAT10 in this context, with a particular focus on its interactions and mechanisms involving ferroptosis. Methods In this study, immunohistochemistry, immunofluorescence, and Western blotting were utilized to evaluate the changes of NAT10 and ferroptosis-related marker proteins. Plasmid vectors were utilized to establish stable ccRCC cell lines with NAT10 overexpression and knockdown. Cell proliferation, scratch, and invasion assays were conducted to assess the impact of NAT10 modification on cell proliferation and migration capabilities. Meanwhile, remodelin hydrobromide (HBr) treatment was given to ccRCC cells to observe the variations in cell proliferation ability and ferroptosis marker proteins. Results Our study demonstrated that NAT10 can enhance the malignant biological behavior of ccRCC, while simultaneously inhibiting markers associated with ferroptosis. Conclusions Therefore, this study suggests that NAT10 may exert a pro-cancer effect by modulating the nuclear factor erythroid-2, like-1(NFE2L1)-glutathione peroxidase-4(GPX4)signaling pathway in ccRCC, indicating its potential as a new therapeutic target for this malignancy.
format: application/pdf
format: text/html
creator: Chao Tan
creator: Yang Wang
creator: XinJie Zhang
creator: ZiKang Li
creator: Shubo Chen
subject: Biochemistry
subject: Cell Biology
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.20224
publisher: PeerJ Inc.
rights: © 2025 Tan et al.
abstract: Objective Clear cell renal cell carcinoma (ccRCC) is a prevalent pathological subtype of renal cell carcinoma that arises from renal tubular epithelial cells. ccRCC has long been characterized by high mortality, and at present, surgical resection is the only curative treatment, but its effectiveness is low and survival rates are low. N-acetyltransferase 10 (NAT10) is a protein that acts as an acetyltransferase, has distinct catalytic and regulatory functions, and is involved in the progression of various cancers such as bladder cancer, hepatocellular carcinoma, and multiple myeloma. Ferroptosis is a novel form of programmed cell death that is iron-dependent and distinct from apoptosis, necrosis, and autophagy. Therefore, this study aimed to investigate the potential functions of NAT10 in this context, with a particular focus on its interactions and mechanisms involving ferroptosis. Methods In this study, immunohistochemistry, immunofluorescence, and Western blotting were utilized to evaluate the changes of NAT10 and ferroptosis-related marker proteins. Plasmid vectors were utilized to establish stable ccRCC cell lines with NAT10 overexpression and knockdown. Cell proliferation, scratch, and invasion assays were conducted to assess the impact of NAT10 modification on cell proliferation and migration capabilities. Meanwhile, remodelin hydrobromide (HBr) treatment was given to ccRCC cells to observe the variations in cell proliferation ability and ferroptosis marker proteins. Results Our study demonstrated that NAT10 can enhance the malignant biological behavior of ccRCC, while simultaneously inhibiting markers associated with ferroptosis. Conclusions Therefore, this study suggests that NAT10 may exert a pro-cancer effect by modulating the nuclear factor erythroid-2, like-1(NFE2L1)-glutathione peroxidase-4(GPX4)signaling pathway in ccRCC, indicating its potential as a new therapeutic target for this malignancy.
bibliographic citation: Tan et al. (2025) NAT10 inhibits ferroptosis and promotes the progression of renal clear cell carcinoma by regulating the NFE2L1-GPX4 signaling pathway. PeerJ 13:e20224 https://doi.org/10.7717/peerj.20224
date submitted: 2025-05-07
date accepted: 2025-09-22
issued: 2025-10-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Chao
author list: Agent
  family name: Wang
  given name: Yang
author list: Agent
  family name: Zhang
  given name: XinJie
author list: Agent
  family name: Li
  given name: ZiKang
author list: Agent
  family name: Chen
  given name: Shubo
doi: 10.7717/peerj.20224
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-31
copyright: ©2025 Tan et al.
attribution name: Tan et al.

Detailed morphological characterization and improvement of keratinocyte outgrowth from plucked human hair follicle
type: item
type: AcademicArticle
description: In this study, a detailed analysis of the outgrowth of primary keratinocytes from plucked human hair follicles was conducted. Plucked hair follicles offer an easily accessible and non-invasive method as a primary cell source for adult somatic keratinocytes, providing a simple starting material for induced pluripotent stem cell (iPSC) reprogramming. In this study, we laid our focus on the precise examination of timing and location of the first keratinocyte outgrowth after plucking, as well as the morphological changes that occur during cultivation. Our results show that the region of the hair follicle, from which the initial outgrowth occurs, is crucial for successful cultivation. Additionally, first appearing protrusions and first visible cells show the same specific marker expression as the intact outer root sheath. We therefore conclude that initially appearing keratinocytes arise from the basal layer of the outer root sheath. To improve the whole process, the protocol was adjusted to reduce the time until successful outgrowth. These optimizations are particularly relevant for developing a standardized protocol that works efficiently across all individuals, including patients with difficult-to-culture hair follicles. The accelerated cell harvesting could prove valuable in future applications in regenerative medicine, especially for patients where culture times have previously been too long.
format: application/pdf
format: text/html
creator: Stefanie Klingenstein
creator: Judith Boenke
creator: Lisa-Sophie Wüstner
creator: Stefan Liebau
creator: Moritz Klingenstein
subject: Cell Biology
subject: Anatomy and Physiology
subject: Dermatology
subject: Histology
description: doi:10.7717/peerj.20214
publisher: PeerJ Inc.
rights: © 2025 Klingenstein et al.
abstract: In this study, a detailed analysis of the outgrowth of primary keratinocytes from plucked human hair follicles was conducted. Plucked hair follicles offer an easily accessible and non-invasive method as a primary cell source for adult somatic keratinocytes, providing a simple starting material for induced pluripotent stem cell (iPSC) reprogramming. In this study, we laid our focus on the precise examination of timing and location of the first keratinocyte outgrowth after plucking, as well as the morphological changes that occur during cultivation. Our results show that the region of the hair follicle, from which the initial outgrowth occurs, is crucial for successful cultivation. Additionally, first appearing protrusions and first visible cells show the same specific marker expression as the intact outer root sheath. We therefore conclude that initially appearing keratinocytes arise from the basal layer of the outer root sheath. To improve the whole process, the protocol was adjusted to reduce the time until successful outgrowth. These optimizations are particularly relevant for developing a standardized protocol that works efficiently across all individuals, including patients with difficult-to-culture hair follicles. The accelerated cell harvesting could prove valuable in future applications in regenerative medicine, especially for patients where culture times have previously been too long.
bibliographic citation: Klingenstein et al. (2025) Detailed morphological characterization and improvement of keratinocyte outgrowth from plucked human hair follicle. PeerJ 13:e20214 https://doi.org/10.7717/peerj.20214
date submitted: 2025-06-05
date accepted: 2025-09-19
issued: 2025-10-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klingenstein
  given name: Stefanie
author list: Agent
  family name: Boenke
  given name: Judith
author list: Agent
  family name: Wüstner
  given name: Lisa-Sophie
author list: Agent
  family name: Liebau
  given name: Stefan
author list: Agent
  family name: Klingenstein
  given name: Moritz
doi: 10.7717/peerj.20214
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-31
copyright: © 2025 Klingenstein et al.
attribution name: Klingenstein et al.

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