title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=30 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Hidden microalgae diversity in reef systems: reanalysis of coral microbiomes reveals spatial patterns of coral-associated plastid communities in the Southwestern Atlantic Ocean (SWAO) link: https://peerj.com/articles/20116 last-modified: 2025-11-03 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 prevalent in coral plastidiomes may support corals nutritionally after coral bleaching, while other free-living and bloom-forming microalgae produce significantly more reactive oxygen species than Symbiodiniaceae, potentially driving oxidative stress. These results highlight microeukaryotic community variation across corals and its ecological relevance, offering a framework for using plastid-bearing communities as biomarkers of shifts in coral holobionts. creator: Clara P. Pires creator: Livia B. Villela creator: Rodrigo L. Moura creator: Paulo S. Salomon creator: Arthur W. Silva-Lima uri: https://doi.org/10.7717/peerj.20116 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Pires et al. title: Predation experiments with 3D-printed lizard models yield limited responses in pheasants link: https://peerj.com/articles/20103 last-modified: 2025-11-03 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. creator: Radovan Smolinský creator: Ivo Adam creator: Zuzana Hiadlovská creator: Shubhra Sau creator: Pavel Škrabánek creator: Natália Martínková uri: https://doi.org/10.7717/peerj.20103 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Smolinský et al. title: Plant morphological traits and ecological stoichiometry in disturbed vs. conserved forests link: https://peerj.com/articles/20301 last-modified: 2025-10-31 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. creator: Xiaoyin Guan creator: Haojun Xia creator: Shuming Li creator: Shuisheng Yu creator: Zihong Zheng creator: Julian Liu creator: Libin Liu uri: https://doi.org/10.7717/peerj.20301 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guan et al. title: Elevated SLC1A5 links to inflamed endothelial cells and proteinuria in membranous nephropathy patients link: https://peerj.com/articles/20271 last-modified: 2025-10-31 description: BackgroundMembranous 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.MethodsWe 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.ResultsTranscriptome 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.ConclusionThis study identified novel macrophage and endothelial cell subtypes and their interactions, positioning SLC1A5 as a potential biomarker for MN pathogenesis. 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 uri: https://doi.org/10.7717/peerj.20271 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tang et al. title: Gastric intestinal metaplasia subtypes and the effects of c-Myc expression on severity link: https://peerj.com/articles/20257 last-modified: 2025-10-31 description: BackgroundThe 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.MethodsA 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.ResultsGIM 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).ConclusionGIM incidence increases with age; however, the histological severity of GIM (as defined by the extent of mucosal gland involvement) within a single biopsy sample does not show a corresponding increase with age. The more severe the GIM is, the greater the proportion of type III GIM cases present. c-Myc expression did not correlate with GIM severity. Conversely, as the GIM subtype becomes more advanced (from type I to type III), c-Myc expression decreases. creator: Qinglu Yang creator: Lingzhi Lian creator: Jingying Shen creator: Qin Cao creator: Xuewei Wang creator: Pingping Hu uri: https://doi.org/10.7717/peerj.20257 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. 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 link: https://peerj.com/articles/20246 last-modified: 2025-10-31 description: BackgroundA 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.MethodsSamples 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.ResultsThe 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. creator: Ngoc-Son Tran creator: Thi-Phuong Pham creator: Minh Anh Dam creator: Chaichat Boonyanusith uri: https://doi.org/10.7717/peerj.20246 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tran et al. title: NAT10 inhibits ferroptosis and promotes the progression of renal clear cell carcinoma by regulating the NFE2L1-GPX4 signaling pathway link: https://peerj.com/articles/20224 last-modified: 2025-10-31 description: ObjectiveClear 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.MethodsIn 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.ResultsOur study demonstrated that NAT10 can enhance the malignant biological behavior of ccRCC, while simultaneously inhibiting markers associated with ferroptosis.ConclusionsTherefore, 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. creator: Chao Tan creator: Yang Wang creator: XinJie Zhang creator: ZiKang Li creator: Shubo Chen uri: https://doi.org/10.7717/peerj.20224 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tan et al. title: Detailed morphological characterization and improvement of keratinocyte outgrowth from plucked human hair follicle link: https://peerj.com/articles/20214 last-modified: 2025-10-31 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. creator: Stefanie Klingenstein creator: Judith Boenke creator: Lisa-Sophie Wüstner creator: Stefan Liebau creator: Moritz Klingenstein uri: https://doi.org/10.7717/peerj.20214 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Klingenstein et al. title: Impact of V-box insertion on promoter activity and virus-inducibility in transgenic Arabidopsis thaliana link: https://peerj.com/articles/20178 last-modified: 2025-10-31 description: Synthetic pathogen-inducible promoters (SPIPs) are essential for precise gene regulation in plant genetic engineering. However, natural promoters often exhibit limitations in expression strength and specificity. In this study, we modified the WGFS promoter by incorporating V-box dimers, elements known for their virus-inducible activities, at different positions within its sequence. We thus created three new SPIPs: VWGFS, WGVFS, and WGFSV. These modified promoters were then used in transgenic Arabidopsis thaliana to evaluate their transcriptional properties through β-glucuronidase gene (GUS) staining and Quantitative real-time PCR (qPCR) analysis. Results showed that the insertion of V-box elements at different positions significantly affected the basal transcriptional activity and virus-inducibility. Notably, WGVFS and WGFSV exhibited higher basal activity than VWGFS, with WGFSV showing the highest response to tobacco mosaic virus (TMV) induction. qPCR analysis further revealed that WGFSV had enhanced inducibility by various inducers such as TMV, abscisic acid (ABA), salicylic acid (SA), and ethylene (Eth). This suggests that V-box insertion can alter promoter activity and inducibility, with the midstream position yielding the most desirable characteristics. The transcriptional activities of WGVFS in response to TMV, ABA, SA, and Eth were 1.473, 1.109, 2.030, and 1.088, respectively. Additionally, a typical binary function relationship was observed between the V-box insertion position and transcriptional expression level. The maximum model-predicted value was 1.096 when the V-box was inserted at the 99 bp downstream position. These findings help optimize promoters for plant disease resistance gene control, which may have uses beyond viral induction. This study contributes to the development of synthetic promoters with specific activity for plant genetic engineering. creator: Zhenchi Huang creator: Peiyi Cai creator: Meishi Huang creator: Jiating Chen creator: Weixin Gan creator: Limin Wu creator: Xiaoming Li creator: Zhihua Wu uri: https://doi.org/10.7717/peerj.20178 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Physiochemical screening of road avenue plants in better landscape management of highly polluted urbanized city (Lahore), Pakistan link: https://peerj.com/articles/20121 last-modified: 2025-10-31 description: Lahore has been consistently ranked as the world’s most polluted city. Because of combative ideas to construct highways, underpasses and flyovers, Lahore had lost a remarkable percentage of its tree cover over the past 15 years. The present study focuses on the outcomes of rapidly increasing air pollution on roadside vegetation. In current study, species such as Alstonia scholaris L., Bougainvillea spectabilis Willd., Dalbergia sissoo Roxb. Eucalyptus globulus Labill., Ficus virens Aiton, Ficus benjamina L., Ficus religiosa Linn., Morus alba L., Murraya paniculata L., Putranjiva roxburghii Wall., Polyalthia longifolia Sonn., Rubia tinctorum L. found on the seven busiest roads of Lahore were selected (on the basis of traffic densities) for biomonitoring. These plants were selected due to their prevalence and commonly occurrence on these selected roads. Variation on biochemical parameters like chlorophyll a, b, total chlorophyll content & carotenoids and physiological parameters like stomatal conductance, transpiration rate and photosynthetic rate were found in triplicate. By analyzing these parameters quality of air and health of plants can also be assessed. In this study the dust load was maximum on the leaves of Alstonia scholaris L. (0.02 ± 0.005), Ficus religiosa Linn. (0.02 ± 0.003), and Morus alba L. (0.02 ± 0.003) Reduction in chlorophyll was noticed in Alstonia scholaris L. (0.44 ± 0.22) and Polyalthia longiflia Sonn. (0.41 ± 0.22) while the chlorophyll concentration of Eucalyptus globulus Labill. (0.71 ± 0.16), followed by Ficus benjamina L. (0.80 ± 0.25), Ficus religiosa Linn. (0.81 ± 0.30), Ficus virens Aiton. (0.64 ± 0.22), Morus alba L. (1.80 ± 0.27) and Putranjiva roxburghii Wall. (2.55 ± 0.43), was higher at polluted sites. The reduction in carotenoid content was found in Murraya paniculata L. (4.12 ± 2.18) while it was highest in Eucalyptus globulus Labill. (9.12 ± 0.71) Due to the pollution stress the changes in photosynthetic rate of Alstonia scholaris L. (25.36 ± 13.10), Bougainvillea spectabilis Willd. (34.37 ± 19.92), Dalbergia sissoo Roxb. (28.23 ± 11.25), Murraya paniculata L. (26.80 ± 7.75), Polyalthia longifolia Sonn. (42.27 ± 22.87), and Rubia tinctorum L. (30.60 ± 4.07) was observed. The current research distinctly signifies Eucalyptus globulus Labill., Ficus benjamina L., Ficus religiosa Linn., Ficus virens Aiton., Morus alba L. and Putranjiva roxburghii Wall., have capability to hold on the stress triggered by roadside pollutants. The findings are useful to urban green space landscapers in harsh climates as they choose appropriate species that can offer a variety of ecosystem services, such as resistance to air pollution and lowering of temperature without compromising plant survival. creator: Bushra Munam creator: Sohaib Muhammad creator: Muhammad Tayyab creator: Hafiza Komal Hanif creator: Mahrukh Majeed creator: Hassan Nawaz creator: Muhammad Jawad Tariq Khan creator: Summiya Faisal creator: Muhammad Hasnain creator: Sarah Maryam Malik creator: Muhammad Bilal creator: Muhammad Zahid uri: https://doi.org/10.7717/peerj.20121 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Munam et al.