PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effectiveness of seed dispersal by foxes in areas with different human disturbances in southern Chile
items: Efficacy and optimal dosage of various exercises for migraine: a multilevel network and dose-response meta-analysis
items: Genome-wide identification of calcium-dependent protein kinase (CDPK) family members in Phaseolus vulgaris L. and expression analysis during abiotic stresses
items: Role of necroptosis in pulpitis: integration of bacterial infection, immune imbalance, and oxidative stress
items: DNA metabarcoding of mites from small soil samples: limited agreement with morphological identifications but improved results from long-read sequencing
items: Alpha-centractin is a novel substrate of SETD3 methyltransferase in vitro
items: Mendelian randomization and nomogram-based prediction of hepatocellular carcinoma risk in patients with hepatitis B cirrhosis
items: Easier said than done: unexpected hurdles to preparing ∼1,000 cranial CT scans for data collection from an online digital repository
items: Effects of low-level electric current on the growth of Amphistegina lobifera and its photosynthetic diatom endosymbionts
items: Serum brain-derived neurotrophic factor, micronutrient status, and inflammatory cytokines in type 2 diabetes with nephropathy: a case–control analysis

Effectiveness of seed dispersal by foxes in areas with different human disturbances in southern Chile
type: item
type: AcademicArticle
description: Frugivorous mammals play a key role in forest regeneration by dispersing seeds yet their effectiveness can vary with landscape disturbance and the native or exotic status of the plant species. In the temperate forests of southern Chile, we evaluated the seed dispersal efficiency (SDE) of foxes (Lycalopex spp.) for native and exotic fleshy-fruited plants across 10 sites spanning a gradient from less to more disturbed landscapes. SDE was assessed though two components: quantity (frequency of feces containing seeds and number of seeds per plant species) and quality (proportion of viable seeds and their germination success under natural conditions). Between November 2022 and July 2023, we collected 199 fox fecal samples, of which 131 contained seeds. In total, we recovered of 23,012 seeds from three native species (Aristotelia chilensis, Gaultheria mucronata, Ugni molinae) and three exotic species (Prunus spp., Malus sylvestris, Rubus ulmifolius). Native seeds were more frequently found in feces from less disturbed landscapes, whereas exotic species exhibited more variable patterns. Seed viability was generally high and unaffected by landscape type, although germination rates were higher in less disturbed areas. Notably, G. mucronata failed to germinate in more disturbed landscapes despite high viability. Conversely, U. molinae showed significantly greater SDE in more disturbed areas due to higher seed quantity and germination. These findings demonstrate that foxes are effective seed dispersers of both native and exotic species, with their effectiveness shaped by landscape type and plant species. Our results highlight the dual ecological role of generalist frugivores in supporting native plant regeneration while potentially facilitating the spread of exotic species. We recommend that future conservation and restoration efforts consider these dynamics when managing fragmented temperate forests.
format: application/pdf
format: text/html
creator: Onaylis Triay-Limonta
creator: Rocío Paleo-López
creator: Camila J. Stuardo
creator: Carolina S. Ugarte
creator: Carlos E. Valdivia
creator: Constanza Napolitano
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.20150
publisher: PeerJ Inc.
rights: © 2025 Triay-Limonta et al.
abstract: Frugivorous mammals play a key role in forest regeneration by dispersing seeds yet their effectiveness can vary with landscape disturbance and the native or exotic status of the plant species. In the temperate forests of southern Chile, we evaluated the seed dispersal efficiency (SDE) of foxes (Lycalopex spp.) for native and exotic fleshy-fruited plants across 10 sites spanning a gradient from less to more disturbed landscapes. SDE was assessed though two components: quantity (frequency of feces containing seeds and number of seeds per plant species) and quality (proportion of viable seeds and their germination success under natural conditions). Between November 2022 and July 2023, we collected 199 fox fecal samples, of which 131 contained seeds. In total, we recovered of 23,012 seeds from three native species (Aristotelia chilensis, Gaultheria mucronata, Ugni molinae) and three exotic species (Prunus spp., Malus sylvestris, Rubus ulmifolius). Native seeds were more frequently found in feces from less disturbed landscapes, whereas exotic species exhibited more variable patterns. Seed viability was generally high and unaffected by landscape type, although germination rates were higher in less disturbed areas. Notably, G. mucronata failed to germinate in more disturbed landscapes despite high viability. Conversely, U. molinae showed significantly greater SDE in more disturbed areas due to higher seed quantity and germination. These findings demonstrate that foxes are effective seed dispersers of both native and exotic species, with their effectiveness shaped by landscape type and plant species. Our results highlight the dual ecological role of generalist frugivores in supporting native plant regeneration while potentially facilitating the spread of exotic species. We recommend that future conservation and restoration efforts consider these dynamics when managing fragmented temperate forests.
bibliographic citation: Triay-Limonta et al. (2025) Effectiveness of seed dispersal by foxes in areas with different human disturbances in southern Chile. PeerJ 13:e20150 https://doi.org/10.7717/peerj.20150
date submitted: 2025-02-21
date accepted: 2025-09-05
issued: 2025-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Triay-Limonta
  given name: Onaylis
author list: Agent
  family name: Paleo-López
  given name: Rocío
author list: Agent
  family name: Stuardo
  given name: Camila J.
author list: Agent
  family name: Ugarte
  given name: Carolina S.
author list: Agent
  family name: Valdivia
  given name: Carlos E.
author list: Agent
  family name: Napolitano
  given name: Constanza
doi: 10.7717/peerj.20150
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-21
copyright: ©2025 Triay-Limonta et al.
attribution name: Triay-Limonta et al.

Efficacy and optimal dosage of various exercises for migraine: a multilevel network and dose-response meta-analysis
type: item
type: AcademicArticle
description: Background To elucidate the relative efficacy of diverse exercise modalities for migraine and quantify the optimal therapeutic dosage. Method A systematic search was conducted across four electronic databases from their inception to May 2025. Two reviewers independently performed data extraction and risk of bias assessment. A multilevel network meta-analysis (ML-NMA) integrated with a dose-response analysis was employed to comprehensively compare these interventions. Results Twenty-seven randomized controlled trials (RCTs) (n = 1,611) were included. The most effective interventions were combined aerobic+resistance exercise (g = − 1.85, 95% credible interval (CrI): [−2.53 to −1.18]; surface under the cumulative ranking curve (SUCRA) = 0.91), followed by resistance exercise (g = − 1.45, 95% CrI [−1.79 to −1.10]; SUCRA = 0.81), yoga (g = − 0.35, 95% CrI [−0.63 to −0.06]; SUCRA = 0.49), and tai chi (g = − 0.48, 95% CrI [−0.91 to −0.05]; SUCRA = 0.46). The dose-response analysis identified an optimal therapeutic window of 300-600 metabolic equivalent of task (MET)-min/week, an intensity of 4.5–5.5 METs, and a duration of 8–10 weeks. The overall certainty of evidence was rated from very low to low. Conclusion Combined aerobic+resistance exercise, resistance exercise, tai chi, and yoga represent promising therapeutic options for migraine. The optimal dose was identified as approximately 70–135 minutes of moderate-intensity or 45–90 minutes of vigorous-intensity activity weekly, for 8–10 weeks. These findings, however, must be interpreted with caution due to the low quality of the underlying evidence.
format: application/pdf
format: text/html
creator: Jingyi Xie
creator: Yupeng Lin
creator: Bin Wang
subject: Evidence Based Medicine
subject: Neurology
subject: Sports Medicine
description: doi:10.7717/peerj.20254
publisher: PeerJ Inc.
rights: © 2025 Xie et al.
abstract: Background To elucidate the relative efficacy of diverse exercise modalities for migraine and quantify the optimal therapeutic dosage. Method A systematic search was conducted across four electronic databases from their inception to May 2025. Two reviewers independently performed data extraction and risk of bias assessment. A multilevel network meta-analysis (ML-NMA) integrated with a dose-response analysis was employed to comprehensively compare these interventions. Results Twenty-seven randomized controlled trials (RCTs) (n = 1,611) were included. The most effective interventions were combined aerobic+resistance exercise (g = − 1.85, 95% credible interval (CrI): [−2.53 to −1.18]; surface under the cumulative ranking curve (SUCRA) = 0.91), followed by resistance exercise (g = − 1.45, 95% CrI [−1.79 to −1.10]; SUCRA = 0.81), yoga (g = − 0.35, 95% CrI [−0.63 to −0.06]; SUCRA = 0.49), and tai chi (g = − 0.48, 95% CrI [−0.91 to −0.05]; SUCRA = 0.46). The dose-response analysis identified an optimal therapeutic window of 300-600 metabolic equivalent of task (MET)-min/week, an intensity of 4.5–5.5 METs, and a duration of 8–10 weeks. The overall certainty of evidence was rated from very low to low. Conclusion Combined aerobic+resistance exercise, resistance exercise, tai chi, and yoga represent promising therapeutic options for migraine. The optimal dose was identified as approximately 70–135 minutes of moderate-intensity or 45–90 minutes of vigorous-intensity activity weekly, for 8–10 weeks. These findings, however, must be interpreted with caution due to the low quality of the underlying evidence.
bibliographic citation: Xie et al. (2025) Efficacy and optimal dosage of various exercises for migraine: a multilevel network and dose-response meta-analysis. PeerJ 13:e20254 https://doi.org/10.7717/peerj.20254
date submitted: 2025-07-30
date accepted: 2025-09-26
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Jingyi
author list: Agent
  family name: Lin
  given name: Yupeng
author list: Agent
  family name: Wang
  given name: Bin
doi: 10.7717/peerj.20254
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Xie et al.
attribution name: Xie et al.

Genome-wide identification of calcium-dependent protein kinase (CDPK) family members in Phaseolus vulgaris L. and expression analysis during abiotic stresses
type: item
type: AcademicArticle
description: Background Calcium-dependent protein kinases (CDPKs) are a family of enzymes that are essential in plant signaling pathways. These kinases are activated in response to changes in calcium ion (Ca2+) concentration under stress conditions. Although CDPK gene families have been investigated in various plants, comprehensive genome-wide analyses and expression studies of CDPK genes in Phaseolus vulgaris L. under abiotic stress have not yet been performed. The objective of this research is to perform a genome-wide analysis of the CDPK gene family in common bean and evaluate the expression patterns of these genes under salt and drought stress conditions. Methods This study presents a comprehensive bioinformatics analysis focusing on the phylogenetic relationships, chromosomal distribution, gene structures, conserved motifs, promoter regulatory elements, and expression profiles under salt and drought stress conditions of the CDPK gene family in common bean. Results In this study, 25 PvCDPK genes were identified in the common bean genome. The lengths of proteins vary between 298 and 582 amino acids (aa), and their molecular weights (kDa) range from 33.43 kDa to 65.13 kDa. The majority of the PvCDPKs located on a total of eight chromosomes have six introns. Phylogenetic analysis revealed that PvCDPK proteins are grouped into three major clades along with Arabidopsis thaliana and Glycine max orthologs. The divergence times for six pairs of segmentally duplicated genes ranged from 48.94 million years ago (MYA) to 65.57 MYA, while tandem duplicates ranged from 32.09 to 84.95 MYA. Conclusions Comparative expression analysis of PvCDPK genes revealed varying expression levels depending on the two common bean cultivars. Furthermore, these observations suggest that PvCDPK genes could be essential for the growth and development of common beans in response to abiotic stresses such as drought and salt. This is the first study to investigate the CDPK gene family in common bean, and the id…
format: application/pdf
format: text/html
creator: Gülşen Güçlü
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.20217
publisher: PeerJ Inc.
rights: © 2025 Güçlü
abstract: Background Calcium-dependent protein kinases (CDPKs) are a family of enzymes that are essential in plant signaling pathways. These kinases are activated in response to changes in calcium ion (Ca2+) concentration under stress conditions. Although CDPK gene families have been investigated in various plants, comprehensive genome-wide analyses and expression studies of CDPK genes in Phaseolus vulgaris L. under abiotic stress have not yet been performed. The objective of this research is to perform a genome-wide analysis of the CDPK gene family in common bean and evaluate the expression patterns of these genes under salt and drought stress conditions. Methods This study presents a comprehensive bioinformatics analysis focusing on the phylogenetic relationships, chromosomal distribution, gene structures, conserved motifs, promoter regulatory elements, and expression profiles under salt and drought stress conditions of the CDPK gene family in common bean. Results In this study, 25 PvCDPK genes were identified in the common bean genome. The lengths of proteins vary between 298 and 582 amino acids (aa), and their molecular weights (kDa) range from 33.43 kDa to 65.13 kDa. The majority of the PvCDPKs located on a total of eight chromosomes have six introns. Phylogenetic analysis revealed that PvCDPK proteins are grouped into three major clades along with Arabidopsis thaliana and Glycine max orthologs. The divergence times for six pairs of segmentally duplicated genes ranged from 48.94 million years ago (MYA) to 65.57 MYA, while tandem duplicates ranged from 32.09 to 84.95 MYA. Conclusions Comparative expression analysis of PvCDPK genes revealed varying expression levels depending on the two common bean cultivars. Furthermore, these observations suggest that PvCDPK genes could be essential for the growth and development of common beans in response to abiotic stresses such as drought and salt. This is the first study to investigate the CDPK gene family in common bean, and the id…
bibliographic citation: Güçlü (2025) Genome-wide identification of calcium-dependent protein kinase (CDPK) family members in Phaseolus vulgaris L. and expression analysis during abiotic stresses. PeerJ 13:e20217 https://doi.org/10.7717/peerj.20217
date submitted: 2025-05-26
date accepted: 2025-09-19
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Güçlü
  given name: Gülşen
doi: 10.7717/peerj.20217
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Güçlü
attribution name: Güçlü

Role of necroptosis in pulpitis: integration of bacterial infection, immune imbalance, and oxidative stress
type: item
type: AcademicArticle
description: Background Pulpitis is a common oral inflammatory condition driven by bacterial infection, immune imbalance, and oxidative stress, often involving pro-inflammatory cell death within the dental pulp. Necroptosis—a regulated, caspase-independent form of cell death mediated by the receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed-lineage kinase domain-like protein (MLKL)—has garnered growing interest in various infectious and inflammatory diseases. However, its specific role in pulpitis remains underexplored. Aim of the study This review aims to explore how bacterial infection, immune imbalance, and oxidative stress synergistically activate necroptosis, and proposes for the first time that excessive activation of necroptosis may contribute to the progression of pulpitis. Methodology A narrative review was conducted using PubMed, Web of Science, and Google Scholar. Searches employed the keywords “pulpitis”, “necroptosis”, and related MeSH terms, combined with Boolean operators. Results Based on a comprehensive review of the existing literature, this review is the first to propose that the integration of bacterial infection, immune imbalance, and oxidative stress may contribute to the progression of pulpitis from reversible inflammation to irreversible necrosis. Conclusion Bacterial infection in pulpitis may activate necroptosis through the Toll-Like Receptor 4 (TLR4)-RIPK3 pathway, leading to the release of damage-associated molecular patterns (DAMPs) that disrupt immune homeostasis, while mitochondrial dysfunction-induced ROS further aggravates oxidative stress. These interacting mechanisms may collectively exacerbate pulpal inflammation and tissue damage, ultimately resulting in irreversible pulpitis. Accordingly, targeting necroptosis pathways may offer a promising therapeutic approach for pulpitis.
format: application/pdf
format: text/html
creator: Xuefei Wang
creator: Yaying Wang
creator: Zhenyu Pang
creator: Peiyao Gong
creator: Xuyi Ma
creator: Yuhao Qiu
creator: Jianzhen Li
creator: Lianjie Peng
creator: Zhichao Liu
subject: Cell Biology
subject: Dentistry
subject: Immunology
description: doi:10.7717/peerj.20209
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Background Pulpitis is a common oral inflammatory condition driven by bacterial infection, immune imbalance, and oxidative stress, often involving pro-inflammatory cell death within the dental pulp. Necroptosis—a regulated, caspase-independent form of cell death mediated by the receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed-lineage kinase domain-like protein (MLKL)—has garnered growing interest in various infectious and inflammatory diseases. However, its specific role in pulpitis remains underexplored. Aim of the study This review aims to explore how bacterial infection, immune imbalance, and oxidative stress synergistically activate necroptosis, and proposes for the first time that excessive activation of necroptosis may contribute to the progression of pulpitis. Methodology A narrative review was conducted using PubMed, Web of Science, and Google Scholar. Searches employed the keywords “pulpitis”, “necroptosis”, and related MeSH terms, combined with Boolean operators. Results Based on a comprehensive review of the existing literature, this review is the first to propose that the integration of bacterial infection, immune imbalance, and oxidative stress may contribute to the progression of pulpitis from reversible inflammation to irreversible necrosis. Conclusion Bacterial infection in pulpitis may activate necroptosis through the Toll-Like Receptor 4 (TLR4)-RIPK3 pathway, leading to the release of damage-associated molecular patterns (DAMPs) that disrupt immune homeostasis, while mitochondrial dysfunction-induced ROS further aggravates oxidative stress. These interacting mechanisms may collectively exacerbate pulpal inflammation and tissue damage, ultimately resulting in irreversible pulpitis. Accordingly, targeting necroptosis pathways may offer a promising therapeutic approach for pulpitis.
bibliographic citation: Wang et al. (2025) Role of necroptosis in pulpitis: integration of bacterial infection, immune imbalance, and oxidative stress. PeerJ 13:e20209 https://doi.org/10.7717/peerj.20209
date submitted: 2025-03-11
date accepted: 2025-09-18
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xuefei
author list: Agent
  family name: Wang
  given name: Yaying
author list: Agent
  family name: Pang
  given name: Zhenyu
author list: Agent
  family name: Gong
  given name: Peiyao
author list: Agent
  family name: Ma
  given name: Xuyi
author list: Agent
  family name: Qiu
  given name: Yuhao
author list: Agent
  family name: Li
  given name: Jianzhen
author list: Agent
  family name: Peng
  given name: Lianjie
author list: Agent
  family name: Liu
  given name: Zhichao
doi: 10.7717/peerj.20209
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Wang et al.
attribution name: Wang et al.

DNA metabarcoding of mites from small soil samples: limited agreement with morphological identifications but improved results from long-read sequencing
type: item
type: AcademicArticle
description: The characterization of soil mite (Acari) communities traditionally follows morphological identifications of specimens extracted from soil, which is a highly laborious and time-consuming process. Metabarcoding has become an increasingly utilized approach for species identification from environmental DNA (eDNA) samples, but whether the metabarcoding approaches align with the morphological identification data on soil mites has rarely been addressed. Here, we examine the congruence of soil mite communities between morphological and metabarcoding datasets. The morphological dataset was generated by extracting mite specimens from the soil samples, whereas molecular datasets represent two types of cytochrome c oxidase subunit I (COI) amplicons produced directly from soil eDNA (from 0.2 g and 2 g soil samples) and sequenced with Illumina (313 base pairs amplicons) and PacBio (658 base pairs amplicons) platforms. We found that specimen extraction from soil samples, followed by morphological identification, yielded the highest number of mite species. Despite significantly lower mite richness in the metabarcoding datasets, PacBio datasets provided more reliable community profiles that aligned strongly with the morphological data. This indicates that soil sample quantities generally used for microbial analyses are also informative in studying soil faunal communities. Furthermore, our results indicate that methodological choices (herein PacBio vs. Illumina) have a greater influence on mite community detection than the amount of input soil used for DNA extraction. Interestingly, the patterns of the entire metazoan community in the metabarcoding datasets strongly mirrored those of the morphologically identified mite communities alone, indicating that soil mites serve as a powerful ecological indicator group.
format: application/pdf
format: text/html
creator: Sirle Varusk
creator: Kaarel Sammet
creator: Manikandan Ariyan
creator: Khairiah Mubarak Alwutayd
creator: Sten Anslan
subject: Biodiversity
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.20205
publisher: PeerJ Inc.
rights: © 2025 Varusk et al.
abstract: The characterization of soil mite (Acari) communities traditionally follows morphological identifications of specimens extracted from soil, which is a highly laborious and time-consuming process. Metabarcoding has become an increasingly utilized approach for species identification from environmental DNA (eDNA) samples, but whether the metabarcoding approaches align with the morphological identification data on soil mites has rarely been addressed. Here, we examine the congruence of soil mite communities between morphological and metabarcoding datasets. The morphological dataset was generated by extracting mite specimens from the soil samples, whereas molecular datasets represent two types of cytochrome c oxidase subunit I (COI) amplicons produced directly from soil eDNA (from 0.2 g and 2 g soil samples) and sequenced with Illumina (313 base pairs amplicons) and PacBio (658 base pairs amplicons) platforms. We found that specimen extraction from soil samples, followed by morphological identification, yielded the highest number of mite species. Despite significantly lower mite richness in the metabarcoding datasets, PacBio datasets provided more reliable community profiles that aligned strongly with the morphological data. This indicates that soil sample quantities generally used for microbial analyses are also informative in studying soil faunal communities. Furthermore, our results indicate that methodological choices (herein PacBio vs. Illumina) have a greater influence on mite community detection than the amount of input soil used for DNA extraction. Interestingly, the patterns of the entire metazoan community in the metabarcoding datasets strongly mirrored those of the morphologically identified mite communities alone, indicating that soil mites serve as a powerful ecological indicator group.
bibliographic citation: Varusk et al. (2025) DNA metabarcoding of mites from small soil samples: limited agreement with morphological identifications but improved results from long-read sequencing. PeerJ 13:e20205 https://doi.org/10.7717/peerj.20205
date submitted: 2025-07-08
date accepted: 2025-09-17
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Varusk
  given name: Sirle
author list: Agent
  family name: Sammet
  given name: Kaarel
author list: Agent
  family name: Ariyan
  given name: Manikandan
author list: Agent
  family name: Mubarak Alwutayd
  given name: Khairiah
author list: Agent
  family name: Anslan
  given name: Sten
doi: 10.7717/peerj.20205
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Varusk et al.
attribution name: Varusk et al.

Alpha-centractin is a novel substrate of SETD3 methyltransferase in vitro
type: item
type: AcademicArticle
description: Background The SETD3 enzyme, a protein histidine methyltransferase, catalyzes the Nτ-methylation of the histidine 73 residue in β-actin. This post-translational modification is important for maintaining cytoskeleton integrity, and actin remains the only known substrate of this methyltransferase to date. However, SETD3 was also postulated to play a role in the regulation of processes that are not directly related to actin homeostasis, such as cell cycle control and response to hypoxic conditions. These findings suggest that actin may not be the sole substrate of SETD3 methyltransferase. Here, we demonstrate that SETD3 methylates additional proteins in human cells, and α-centractin (ACTR1A) may be one of them. Methods Three different human SETD3 knockout cell lines (HAP1, HeLa, HEK293T) were generated with the CRISPR/Cas9 method and used as a source of SETD3 substrates. Fluorography was used to detect the SETD3-dependent methylation of proteins present in cell lysates, while the TurboID biotin ligase proximity labeling technique was used to isolate proteins that interact with SETD3. The molecular identity of the proteins was determined by mass spectrometry and the activity of recombinant SETD3 towards potential substrates was tested using a radiochemical assay. Results Fluorography revealed that SETD3 methylates at least five novel proteins besides β-actin in HAP1 cells. TurboID proximity labeling identified α-centractin, a key dynactin subunit, as an SETD3 interactor and an in vitro methylation target, suggesting that SETD3 potentially regulates not only actin cytoskeleton dynamics but also dynein-mediated intracellular transport.
format: application/pdf
format: text/html
creator: Apolonia Witecka
creator: Paulina Emmel
creator: Klaudia Ślusarczyk
creator: Julia Z. Kamińska
creator: Michał Zaród
creator: Takao Ishikawa
creator: Jakub Drożak
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.20195
publisher: PeerJ Inc.
rights: © 2025 Witecka et al.
abstract: Background The SETD3 enzyme, a protein histidine methyltransferase, catalyzes the Nτ-methylation of the histidine 73 residue in β-actin. This post-translational modification is important for maintaining cytoskeleton integrity, and actin remains the only known substrate of this methyltransferase to date. However, SETD3 was also postulated to play a role in the regulation of processes that are not directly related to actin homeostasis, such as cell cycle control and response to hypoxic conditions. These findings suggest that actin may not be the sole substrate of SETD3 methyltransferase. Here, we demonstrate that SETD3 methylates additional proteins in human cells, and α-centractin (ACTR1A) may be one of them. Methods Three different human SETD3 knockout cell lines (HAP1, HeLa, HEK293T) were generated with the CRISPR/Cas9 method and used as a source of SETD3 substrates. Fluorography was used to detect the SETD3-dependent methylation of proteins present in cell lysates, while the TurboID biotin ligase proximity labeling technique was used to isolate proteins that interact with SETD3. The molecular identity of the proteins was determined by mass spectrometry and the activity of recombinant SETD3 towards potential substrates was tested using a radiochemical assay. Results Fluorography revealed that SETD3 methylates at least five novel proteins besides β-actin in HAP1 cells. TurboID proximity labeling identified α-centractin, a key dynactin subunit, as an SETD3 interactor and an in vitro methylation target, suggesting that SETD3 potentially regulates not only actin cytoskeleton dynamics but also dynein-mediated intracellular transport.
bibliographic citation: Witecka et al. (2025) Alpha-centractin is a novel substrate of SETD3 methyltransferase in vitro. PeerJ 13:e20195 https://doi.org/10.7717/peerj.20195
date submitted: 2024-07-04
date accepted: 2025-09-15
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Witecka
  given name: Apolonia
author list: Agent
  family name: Emmel
  given name: Paulina
author list: Agent
  family name: Ślusarczyk
  given name: Klaudia
author list: Agent
  family name: Kamińska
  given name: Julia Z.
author list: Agent
  family name: Zaród
  given name: Michał
author list: Agent
  family name: Ishikawa
  given name: Takao
author list: Agent
  family name: Drożak
  given name: Jakub
doi: 10.7717/peerj.20195
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Witecka et al.
attribution name: Witecka et al.

Mendelian randomization and nomogram-based prediction of hepatocellular carcinoma risk in patients with hepatitis B cirrhosis
type: item
type: AcademicArticle
description: Background To innovatively integrate genetic causality and multidimensional clinical indicators, we aimed to investigate causal relationships between metabolic-inflammatory biomarkers and hepatocellular carcinoma (HCC) risk in hepatitis B-related cirrhosis (HBV-C) using Mendelian randomization (MR), and develop a precision prediction model combining genetic evidence with nonlinear biochemical dynamics. Methods Leveraging bidirectional approaches, we first performed two-sample MR analysis on GWAS datasets (UK Biobank, n = 456,348) to establish causality between low-density lipoprotein (LDL) and HCC. In a retrospective cohort of patients with HBV-related cirrhosis from our institution (n = 147; 2022–2024), we identified nonlinear LDL-HCC thresholds via restricted cubic splines (RCS) and engineered a novel “A-index” (a composite score derived from principal component analysis (PCA) integrating alpha-fetoprotein (AFP), aspartate aminotransferase (AST), and alanine aminotransferase (ALT)). Machine learning-driven logistic regression synthesized LDL, A-index, and clinical predictors into a nomogram, rigorously validated by area under the curve-receiver operating characteristic (AUC-ROC), calibration curves, and decision curve analysis (DCA). Results MR analysis revealed a robust causal link between reduced LDL levels and elevated HCC risk (OR = 0.472, 95% CI [0.259–0.860]; P = 0.014), with RCS identifying a critical LDL threshold at 2.28 mmol/L—below which HCC risk escalated exponentially. The PCA-synthesized A-index outperformed individual biomarkers (AUC = 0.652 vs. AFP = 0.579). The final nomogram integrating LDL dynamics, A-index, age, sex, prothrombin time, and antiviral therapy achieved exceptional discrimination (AUC = 0.938) and clinical net benefit across risk thresholds. Conclusion This study introduces a novel causal inference-guided prediction model, addressing the long-standing debate on LDL’s dual role in hepatocarcinogenesis. By integrating MR-validated gen…
format: application/pdf
format: text/html
creator: Xiaolong Zheng
creator: Yiping Hong
creator: Wei Wei
subject: Genetics
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.20179
publisher: PeerJ Inc.
rights: © 2025 Zheng et al.
abstract: Background To innovatively integrate genetic causality and multidimensional clinical indicators, we aimed to investigate causal relationships between metabolic-inflammatory biomarkers and hepatocellular carcinoma (HCC) risk in hepatitis B-related cirrhosis (HBV-C) using Mendelian randomization (MR), and develop a precision prediction model combining genetic evidence with nonlinear biochemical dynamics. Methods Leveraging bidirectional approaches, we first performed two-sample MR analysis on GWAS datasets (UK Biobank, n = 456,348) to establish causality between low-density lipoprotein (LDL) and HCC. In a retrospective cohort of patients with HBV-related cirrhosis from our institution (n = 147; 2022–2024), we identified nonlinear LDL-HCC thresholds via restricted cubic splines (RCS) and engineered a novel “A-index” (a composite score derived from principal component analysis (PCA) integrating alpha-fetoprotein (AFP), aspartate aminotransferase (AST), and alanine aminotransferase (ALT)). Machine learning-driven logistic regression synthesized LDL, A-index, and clinical predictors into a nomogram, rigorously validated by area under the curve-receiver operating characteristic (AUC-ROC), calibration curves, and decision curve analysis (DCA). Results MR analysis revealed a robust causal link between reduced LDL levels and elevated HCC risk (OR = 0.472, 95% CI [0.259–0.860]; P = 0.014), with RCS identifying a critical LDL threshold at 2.28 mmol/L—below which HCC risk escalated exponentially. The PCA-synthesized A-index outperformed individual biomarkers (AUC = 0.652 vs. AFP = 0.579). The final nomogram integrating LDL dynamics, A-index, age, sex, prothrombin time, and antiviral therapy achieved exceptional discrimination (AUC = 0.938) and clinical net benefit across risk thresholds. Conclusion This study introduces a novel causal inference-guided prediction model, addressing the long-standing debate on LDL’s dual role in hepatocarcinogenesis. By integrating MR-validated gen…
bibliographic citation: Zheng et al. (2025) Mendelian randomization and nomogram-based prediction of hepatocellular carcinoma risk in patients with hepatitis B cirrhosis. PeerJ 13:e20179 https://doi.org/10.7717/peerj.20179
date submitted: 2025-03-18
date accepted: 2025-09-12
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Xiaolong
author list: Agent
  family name: Hong
  given name: Yiping
author list: Agent
  family name: Wei
  given name: Wei
doi: 10.7717/peerj.20179
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Zheng et al.
attribution name: Zheng et al.

Easier said than done: unexpected hurdles to preparing ∼1,000 cranial CT scans for data collection from an online digital repository
type: item
type: AcademicArticle
description: Background As science becomes more open and accessible, researchers are increasingly encouraged—and sometimes required—to share their digital data on public repositories. While this promotes transparency and reusability, it can also introduce challenges. We highlight one such challenge by detailing our experience processing computerized tomography (CT) scans of 985 baboon skulls downloaded from MorphoSource, part of a quantitative genetic study of craniodental variation in the pedigreed baboon colony from the Southwest National Primate Research Center. When importing DICOM files into 3D Slicer, 182 of the 985 scans (18.5%) generated an “inconsistent slice spacing” error. When prompted, 3D Slicer “corrected” this by regularizing the slice spacing. However, this led to a mismatch between the slice spacing reported on MorphoSource and the spacing adjusted by 3D Slicer. Methods To determine which slice spacing was accurate, we compared Prosthion-Basion (PR-BA) distances measured directly from physical skulls (using calipers and a Microscribe) with those derived from the CT models. We ran paired t-tests to determine whether there were differences between them. Our comparison sample included five randomly selected skulls from the error group and fifteen ramdon skulls from the error-free group (which exhibited various slice spacings when scanned). Results For scans without the slice spacing error, there was strong agreement between physical and digital measurements, indicating metadata accuracy. For error-generating scans, measurements based on 3D Slicer’s corrected spacing and Amira-Avizo both aligned well with the physical data. In contrast, manually overriding the spacing to match the MorphoSource metadata led to overestimations of the PR-BA distance. Conclusion Although the discrepancy was straightforward to describe, resolving it required over 250 person-hours across 8 months. Accessing physical specimens, conducting repeated measurements, and cross-validating with mu…
format: application/pdf
format: text/html
creator: Mario Modesto-Mata
creator: Arthur Thiebaut
creator: Kristin L. Krueger
creator: A. Murat Maga
creator: Jessica L. Joganic
creator: Timothy M. Ryan
creator: Joan T. Richtsmeier
creator: James M. Cheverud
creator: Leslea J. Hlusko
subject: Anthropology
subject: Bioinformatics
subject: Paleontology
subject: Human-Computer Interaction
description: doi:10.7717/peerj.20172
publisher: PeerJ Inc.
rights: © 2025 Modesto-Mata et al.
abstract: Background As science becomes more open and accessible, researchers are increasingly encouraged—and sometimes required—to share their digital data on public repositories. While this promotes transparency and reusability, it can also introduce challenges. We highlight one such challenge by detailing our experience processing computerized tomography (CT) scans of 985 baboon skulls downloaded from MorphoSource, part of a quantitative genetic study of craniodental variation in the pedigreed baboon colony from the Southwest National Primate Research Center. When importing DICOM files into 3D Slicer, 182 of the 985 scans (18.5%) generated an “inconsistent slice spacing” error. When prompted, 3D Slicer “corrected” this by regularizing the slice spacing. However, this led to a mismatch between the slice spacing reported on MorphoSource and the spacing adjusted by 3D Slicer. Methods To determine which slice spacing was accurate, we compared Prosthion-Basion (PR-BA) distances measured directly from physical skulls (using calipers and a Microscribe) with those derived from the CT models. We ran paired t-tests to determine whether there were differences between them. Our comparison sample included five randomly selected skulls from the error group and fifteen ramdon skulls from the error-free group (which exhibited various slice spacings when scanned). Results For scans without the slice spacing error, there was strong agreement between physical and digital measurements, indicating metadata accuracy. For error-generating scans, measurements based on 3D Slicer’s corrected spacing and Amira-Avizo both aligned well with the physical data. In contrast, manually overriding the spacing to match the MorphoSource metadata led to overestimations of the PR-BA distance. Conclusion Although the discrepancy was straightforward to describe, resolving it required over 250 person-hours across 8 months. Accessing physical specimens, conducting repeated measurements, and cross-validating with mu…
bibliographic citation: Modesto-Mata et al. (2025) Easier said than done: unexpected hurdles to preparing ∼1,000 cranial CT scans for data collection from an online digital repository. PeerJ 13:e20172 https://doi.org/10.7717/peerj.20172
date submitted: 2025-05-15
date accepted: 2025-09-11
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Modesto-Mata
  given name: Mario
author list: Agent
  family name: Thiebaut
  given name: Arthur
author list: Agent
  family name: Krueger
  given name: Kristin L.
author list: Agent
  family name: Maga
  given name: A. Murat
author list: Agent
  family name: Joganic
  given name: Jessica L.
author list: Agent
  family name: Ryan
  given name: Timothy M.
author list: Agent
  family name: Richtsmeier
  given name: Joan T.
author list: Agent
  family name: Cheverud
  given name: James M.
author list: Agent
  family name: Hlusko
  given name: Leslea J.
doi: 10.7717/peerj.20172
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Modesto-Mata et al.
attribution name: Modesto-Mata et al.

Effects of low-level electric current on the growth of Amphistegina lobifera and its photosynthetic diatom endosymbionts
type: item
type: AcademicArticle
description: Larger benthic foraminifera (LBF) are key carbonate producers and significantly contribute to carbonate reef sediments. As the ongoing climate change threatens the calcification capacity of many marine organisms, novel approaches are being explored to support reef resilience. Among these, low-voltage electric stimulation has shown promise in enhancing calcification in corals and other marine calcifiers by stimulating electrodeposition of calcium carbonate. However, the potential of this technique to support calcification in LBF has not yet been assessed. To close this gap, the present study investigates the effects of low electric current densities on the LBF species Amphistegina lobifera. To avoid inducing mortality, the current densities were carefully selected based on previous findings and were applied in two 30-day experiments. Pulse-Amplitude Modulation (PAM) fluorometry (Fv:Fm) was used to measure the photosynthetic efficiency of the diatom endosymbionts, and total pigment content (Chl a) was analysed via a plate reader to assess pigment changes due to the electric stimulation. Growth was analysed by measuring the maximum diameter and counting the formation of new chambers labelled with the fluorogenic dye calcein. The results of both experiments show that electric stimulation did not affect the maximum quantum yield (Fv:Fm) and Chl a content. Furthermore, all treatments exhibited positive growth, but no significant growth enhancement was observed compared to the controls. The highest growth and chamber formation rate were found at current densities of 1 and 1.43 µA/cm2, which represent the highest growth rates obtained in the experiments, as an additional increase in current density to 2.86 µA/cm2 did not seem to further enhance growth. These results suggest that low electric current can influence foraminiferal growth, and the conditions necessary for a significant enhancement remain to be investigated.
format: application/pdf
format: text/html
creator: Federica Rebecchi
creator: Davide Lattanzi
creator: Sigal Abramovich
creator: Patrizia Ambrogini
creator: Fabrizio Frontalini
creator: Christiane Schmidt
subject: Biotechnology
subject: Marine Biology
description: doi:10.7717/peerj.20160
publisher: PeerJ Inc.
rights: © 2025 Rebecchi et al.
abstract: Larger benthic foraminifera (LBF) are key carbonate producers and significantly contribute to carbonate reef sediments. As the ongoing climate change threatens the calcification capacity of many marine organisms, novel approaches are being explored to support reef resilience. Among these, low-voltage electric stimulation has shown promise in enhancing calcification in corals and other marine calcifiers by stimulating electrodeposition of calcium carbonate. However, the potential of this technique to support calcification in LBF has not yet been assessed. To close this gap, the present study investigates the effects of low electric current densities on the LBF species Amphistegina lobifera. To avoid inducing mortality, the current densities were carefully selected based on previous findings and were applied in two 30-day experiments. Pulse-Amplitude Modulation (PAM) fluorometry (Fv:Fm) was used to measure the photosynthetic efficiency of the diatom endosymbionts, and total pigment content (Chl a) was analysed via a plate reader to assess pigment changes due to the electric stimulation. Growth was analysed by measuring the maximum diameter and counting the formation of new chambers labelled with the fluorogenic dye calcein. The results of both experiments show that electric stimulation did not affect the maximum quantum yield (Fv:Fm) and Chl a content. Furthermore, all treatments exhibited positive growth, but no significant growth enhancement was observed compared to the controls. The highest growth and chamber formation rate were found at current densities of 1 and 1.43 µA/cm2, which represent the highest growth rates obtained in the experiments, as an additional increase in current density to 2.86 µA/cm2 did not seem to further enhance growth. These results suggest that low electric current can influence foraminiferal growth, and the conditions necessary for a significant enhancement remain to be investigated.
bibliographic citation: Rebecchi et al. (2025) Effects of low-level electric current on the growth of Amphistegina lobifera and its photosynthetic diatom endosymbionts. PeerJ 13:e20160 https://doi.org/10.7717/peerj.20160
date submitted: 2025-03-20
date accepted: 2025-09-10
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rebecchi
  given name: Federica
author list: Agent
  family name: Lattanzi
  given name: Davide
author list: Agent
  family name: Abramovich
  given name: Sigal
author list: Agent
  family name: Ambrogini
  given name: Patrizia
author list: Agent
  family name: Frontalini
  given name: Fabrizio
author list: Agent
  family name: Schmidt
  given name: Christiane
doi: 10.7717/peerj.20160
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Rebecchi et al.
attribution name: Rebecchi et al.

Serum brain-derived neurotrophic factor, micronutrient status, and inflammatory cytokines in type 2 diabetes with nephropathy: a case–control analysis
type: item
type: AcademicArticle
description: Background Brain-derived neurotrophic factor (BDNF) levels are lower in diabetic patients compared to healthy individuals, and may be further affected by nephropathy. This study aimed to evaluate serum BDNF levels in diabetic patients with nephropathy without complications and compare them to levels in healthy control subjects. Methods A case–control study was conducted involving three groups: healthy individuals (controls), diabetic patients without complications (DM), and diabetic nephropathy patients (DN). Serum BDNF levels were measured using the sandwich Enzyme-Linked Immunosorbent Assay (ELISA) technique, alongside serum levels of interleukin (IL)-12, IL-16, folic acid, vitamin B12, vitamin D3, total cholesterol, triglycerides, high density lipoprotein (HDL), hemoglobin A1c (HbA1c), urea, creatinine, total calcium, and zinc. Results Serum BDNF levels were significantly lower in the DN group compared to the DM and control groups (42.1, 34.1, and 27.23 ng/mL, respectively). In the DM group, BDNF showed a direct correlation with HbA1c and urea (r = 0.26 and r = 0.35, respectively), and an inverse correlation with fasting plasma glucose (FPG) (r = − 0.30). In the DN group, BDNF was directly correlated with FPG (r = 0.31) and serum creatinine (r = 0.27). The area under the curve (AUC) for BDNF in distinguishing DN from controls was 0.938, and 0.738 for DN versus DM. Conclusion Serum BDNF levels are markedly reduced in type 2 diabetic patients with nephropathy and correlate with deficiencies in vitamins D, B12, folate, and zinc, as well as elevated IL-6 and IL-12. BDNF may serve as a biomarker for diabetic kidney disease, highlighting the importance of nutritional status, inflammation control, and neurotrophic support.
format: application/pdf
format: text/html
creator: Huda Jaber Waheed
creator: Nawfal A. Numan
subject: Diabetes and Endocrinology
subject: Nephrology
subject: Pathology
subject: Medical Genetics
subject: Mental Health
description: doi:10.7717/peerj.20086
publisher: PeerJ Inc.
rights: © 2025 Waheed and Numan
abstract: Background Brain-derived neurotrophic factor (BDNF) levels are lower in diabetic patients compared to healthy individuals, and may be further affected by nephropathy. This study aimed to evaluate serum BDNF levels in diabetic patients with nephropathy without complications and compare them to levels in healthy control subjects. Methods A case–control study was conducted involving three groups: healthy individuals (controls), diabetic patients without complications (DM), and diabetic nephropathy patients (DN). Serum BDNF levels were measured using the sandwich Enzyme-Linked Immunosorbent Assay (ELISA) technique, alongside serum levels of interleukin (IL)-12, IL-16, folic acid, vitamin B12, vitamin D3, total cholesterol, triglycerides, high density lipoprotein (HDL), hemoglobin A1c (HbA1c), urea, creatinine, total calcium, and zinc. Results Serum BDNF levels were significantly lower in the DN group compared to the DM and control groups (42.1, 34.1, and 27.23 ng/mL, respectively). In the DM group, BDNF showed a direct correlation with HbA1c and urea (r = 0.26 and r = 0.35, respectively), and an inverse correlation with fasting plasma glucose (FPG) (r = − 0.30). In the DN group, BDNF was directly correlated with FPG (r = 0.31) and serum creatinine (r = 0.27). The area under the curve (AUC) for BDNF in distinguishing DN from controls was 0.938, and 0.738 for DN versus DM. Conclusion Serum BDNF levels are markedly reduced in type 2 diabetic patients with nephropathy and correlate with deficiencies in vitamins D, B12, folate, and zinc, as well as elevated IL-6 and IL-12. BDNF may serve as a biomarker for diabetic kidney disease, highlighting the importance of nutritional status, inflammation control, and neurotrophic support.
bibliographic citation: Waheed et al. (2025) Serum brain-derived neurotrophic factor, micronutrient status, and inflammatory cytokines in type 2 diabetes with nephropathy: a case–control analysis. PeerJ 13:e20086 https://doi.org/10.7717/peerj.20086
date submitted: 2025-04-28
date accepted: 2025-08-26
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Waheed
  given name: Huda Jaber
author list: Agent
  family name: Numan
  given name: Nawfal A.
doi: 10.7717/peerj.20086
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Waheed and Numan
attribution name: Waheed and Numan

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